http://2009.igem.org/wiki/index.php?title=Special:Contributions/Vmullin&feed=atom&limit=50&target=Vmullin&year=&month=2009.igem.org - User contributions [en]2024-03-29T13:56:18ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-12T20:15:08Z<p>Vmullin: /* general */</p>
<hr />
<div>__NOTOC__<br />
[https://2008.igem.org/IGEM_Publicity iGEM 2008 Publicity] | [http://parts.mit.edu/igem07/index.php/Media iGEM 2007 Publicity] | [http://parts.mit.edu/wiki/index.php/IGEM_News iGEM 2006 Publicity]<br />
<br />
<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
<br />
<html><br />
<iframe frameborder="0" width="728" height="90" marginwidth="0" marginheight="0" style="margin:0px 0px 25px 100px;"<br />
src="http://www.google.com/uds/modules/elements/newsshow/iframe.html?q=iGEM&rsz=large&format=728x90"><br />
</iframe><br />
</html><br />
<br />
<br />
<span style="color:#1e90ff; font-size:175%">'''blogs </span><span style="color:#3cb371; font-size:175%">covering iGEM 2009'''</span><br />
* The [http://igem.sdu.dk/ <span style="color:#453221; font-size: 130%">'''SDU-Denmark'''</span>] team blog about their iGEM experience.<br />
* A blog about the iGEM project of the [http://aboutgmos.org/iGEM <span style="color:#453221; font-size: 130%">'''Uppsala-Sweden'''</span>] team.<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''video/radio</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
*'''Slovenia, Heidelberg, SDU-Denmark''': [http://www.dradio.de/dlf/sendungen/forschak/1062608/ Die Biobastler von Boston], Nov 2, 2009, Deutschlandfunk radio (in German).<br />
*'''Cambridge, Imperial''': [http://www.sciencefriday.com/program/archives/200911063 Synthetic Biology Competition], Nov 6, 2009, NPR Science Friday (in English).<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
<br />
<br />
If you would like to share an article that was written about iGEM or your iGEM team, please link to it on this page. If you have multiple articles featuring your team, link to them all individually!<br />
<br />
Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
<br />
''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
<br />
====<font size=4><font color=dodgerblue>'''general'''</font></font>====<br />
*'''The Economist''': ''Biohacking: Hacking goes squishy'' Sep 3, 2009 [http://www.economist.com/search/displaystory.cfm?story_id=14299634 The Economist]<br />
*'''The Scientist''': ''Brick by Brick'' Feb 1, 2009. [http://www.the-scientist.com/article/display/55378/ The Scientist]<br />
*'''Technology Review''': ''A Genetically Engineered Rainbow of Bacteria'' Nov 03, 2009. [http://www.technologyreview.com/blog/editors/24351/ Technology Review]<br />
*'''Discovery News''': '' Bright Bacteria Wins Synthetic Biology Competition'' Nov 6, 2009. [http://blogs.discoverychannel.co.uk/discovery-news/2009/11/bright-bacteria-wins-synthetic-biology-competition.html Discovery News]<br />
*'''Wired''': '' Building new life forms at the iGEM Jamboree'' Nov 9, 2009. [http://www.wired.co.uk/news/archive/2009-11/09/building-new-life-forms-at-the-igem-jamboree.aspx Wired]<br />
<br />
====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
<br />
*'''[[Team:IBB_Pune]]''': "<i>Bio-champs in the making</i>" (English), [http://www.punemirror.in/index.aspx?Page=article&sectname=News%20-%20City&sectid=2&contentid=200909142009091423331646a131eacc#ftr2 (Monday, September 14, 2009 at 11:33:25 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Ganiti Prakriyanmadhe Jeevanuncha Vaapar! (Use of Bacteria in mathematical devices)</i>" (Marathi), [http://beta.esakal.com/2009/09/09220618/pune-use-of-bacterias-in-maths.html(Wednesday, September 09th, 2009 AT 10:09 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Synthetic Biologiteel Bharari ("Advances in Synthetic Biology")</i>" (Marathi), [https://2009.igem.org/Team:IBB_Pune/press (Wednesday 7 October 2009)]<br />
<br />
*'''[[Team:Groningen]]''': "<i>Synthetic biology students from Groningen in the race for best bacterium</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/groningse-studenten-synthetische-biologie-maken-bacterie City of Talent (August 20, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>Talent of the Purest Water</i>" (Dutch, advertisement) [http://www.volkskrant.nl/vk-online/VK/20091024___/1_003/ad6.html Volkskrant, (October 24 2009)]<br />
*'''[[Team:Groningen]]''': "<i>RUG-team in finals synthetic biology</i>" (Dutch), [http://www.uk.rug.nl/cms-basis/nieuws.php?subaction=showfull&id=1257343172&archive=&start_from=&ucat=1 UK (Paper of the Groningen University) (November 4, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>Team iGEM Groningen wins golden medal</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/team-igem-groningen-wint-gouden-medaille City of Talent (November 10, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>Gold and a place in the finals for Groningen contestants iGEM 2009</i>" (Dutch), [http://www.rug.nl/Corporate/nieuws/archief/archief2009/persberichten/174_09 Press release University Groningen (November 11, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>Performance of world class RUG in Boston</i>" (Dutch), [http://www.groningergezinsbode.nl/profile/redactiegroningergezinsbode/article73205.ece/wereldprestatie_rug_in_boston Groninger Gezinsbode (November 11, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>Groningen students finalists gentech-competition</i>" (Dutch), [http://www.studned.nl/1084/wetenschap/groningse-studenten-finalisten-gentech-wedstrijd StudNed.nl (November 11, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>International price for Groningen students</i>" (Dutch), [http://www.rtvnoord.nl/nieuws/indexwm.asp?actie=totaalbericht&pid=86497 RTV-Noord (November 11, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>Gold and a place in the finals for Groningen contestants iGEM 2009</i>" (Dutch), [http://www.noorderlink.nl/nieuws/goud-en-een-finale-plaats-voor-groningse-deelnemers-igem-2009 NoorderLink (November 11, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>Gold and a place in the finals for Groningen contestants iGEM 2009</i>" (Dutch), [http://www.headlinez.nl/?nr=2295334 HeadLinez.nl (November 11, 2009)]<br />
*'''[[Team:Groningen]]''': "<i>With a pacmanbacterium in de finals</i>" (Dutch), [http://www.uk.rug.nl/archief/jaargang39/11/12e.php UK (Paper of the Groningen University) (November 12, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Un concours organisé par le M.I.T : en route pour Boston ! </i>" (French), [http://www.supbiotech.fr/2009/09/boston-supbiotech-igem.html (September 08, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Les étudiants de la biotech interpellent la biologie synthétique</i>" (French), [http://www.vivagora.org/spip.php?breve210 (October 09, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>Un equipo de la UAB, en el concurso de biología sintética del MIT</i>" (Spanish), [http://www.uab.es/servlet/Satellite?cid=1096481466568&pagename=UABDivulga%2FPage%2FTemplatePageDetallArticleInvestigar&param1=1253860327385 (September 23, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>UAB to participate in the synthetic biology competition at MIT</i>" (English), [http://www.uab.es/servlet/Satellite/latest-news/news-detail/uab-to-participate-in-the-synthetic-biology-competition-at-mit-1096476786473.html?noticiaid=1253657853358 (September 23, 2009)]<br />
<br />
*'''[[Team:Valencia]]''': "<i>TheValencia team is awarded the Synthetic Standard Prize</i>" (Spanish), [http://www.elpais.com/articulo/sociedad/Levaduras/funcionan/pixeles/elpepuespval/20091103elpepusoc_9/Tes]<br />
<br />
*'''[[Team:Cambridge]]''': "<i>University of Cambridge team wins iGEM synthetic biology competition </i>" (English), [http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.html (November 5 2009)]<br />
<br />
*'''[[Team:Virginia]]''': ''[http://www.washingtonpost.com/wp-dyn/content/article/2009/10/22/AR2009102204628.html New works of science nonfiction]'', The Washington Post (October 23, 2009)</div>Vmullinhttp://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-09T15:08:32Z<p>Vmullin: /* video/radio about iGEM 2009 */</p>
<hr />
<div>__NOTOC__<br />
[https://2008.igem.org/IGEM_Publicity iGEM 2008 Publicity] | [http://parts.mit.edu/igem07/index.php/Media iGEM 2007 Publicity] | [http://parts.mit.edu/wiki/index.php/IGEM_News iGEM 2006 Publicity]<br />
<br />
<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
<br />
<html><br />
<iframe frameborder="0" width="728" height="90" marginwidth="0" marginheight="0" style="margin:0px 0px 25px 100px;"<br />
src="http://www.google.com/uds/modules/elements/newsshow/iframe.html?q=iGEM&rsz=large&format=728x90"><br />
</iframe><br />
</html><br />
<br />
<br />
<span style="color:#1e90ff; font-size:175%">'''blogs </span><span style="color:#3cb371; font-size:175%">covering iGEM 2009'''</span><br />
* The [http://igem.sdu.dk/ <span style="color:#453221; font-size: 130%">'''SDU-Denmark'''</span>] team blog about their iGEM experience.<br />
* A blog about the iGEM project of the [http://aboutgmos.org/iGEM <span style="color:#453221; font-size: 130%">'''Uppsala-Sweden'''</span>] team.<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''video/radio</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
*'''Slovenia, Heidelberg, SDU-Denmark''': [http://www.dradio.de/dlf/sendungen/forschak/1062608/ Die Biobastler von Boston], Nov 2, 2009, Deutschlandfunk radio (in German).<br />
*'''Cambridge, Imperial''': [http://www.sciencefriday.com/program/archives/200911063 Synthetic Biology Competition], Nov 6, 2009, NPR Science Friday (in English).<br />
<br />
====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
<br />
<br />
If you would like to share an article that was written about iGEM or your iGEM team, please link to it on this page. If you have multiple articles featuring your team, link to them all individually!<br />
<br />
Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
<br />
''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
<br />
====<font size=4><font color=dodgerblue>'''general'''</font></font>====<br />
*'''The Economist''': ''Biohacking: Hacking goes squishy'' Sep 3, 2009 [http://www.economist.com/search/displaystory.cfm?story_id=14299634 The Economist]<br />
*'''The Scientist''': ''Brick by Brick'' Feb 1, 2009. [http://www.the-scientist.com/article/display/55378/ The Scientist]<br />
*'''Technology Review''': ''A Genetically Engineered Rainbow of Bacteria'' November 03, 2009. [http://www.technologyreview.com/blog/editors/24351/ Technology Review]<br />
<br />
====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
<br />
*'''[[Team:IBB_Pune]]''': "<i>Bio-champs in the making</i>" (English), [http://www.punemirror.in/index.aspx?Page=article&sectname=News%20-%20City&sectid=2&contentid=200909142009091423331646a131eacc#ftr2 (Monday, September 14, 2009 at 11:33:25 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Ganiti Prakriyanmadhe Jeevanuncha Vaapar! (Use of Bacteria in mathematical devices)</i>" (Marathi), [http://beta.esakal.com/2009/09/09220618/pune-use-of-bacterias-in-maths.html(Wednesday, September 09th, 2009 AT 10:09 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Synthetic Biologiteel Bharari ("Advances in Synthetic Biology")</i>" (Marathi), [https://2009.igem.org/Team:IBB_Pune/press (Wednesday 7 October 2009)]<br />
<br />
*'''[[Team:Groningen]]''': "<i>Synthetic biology students from Groningen in the race for best bacterium</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/groningse-studenten-synthetische-biologie-maken-bacterie City of Talent (August 20, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Un concours organisé par le M.I.T : en route pour Boston ! </i>" (French), [http://www.supbiotech.fr/2009/09/boston-supbiotech-igem.html (September 08, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Les étudiants de la biotech interpellent la biologie synthétique</i>" (French), [http://www.vivagora.org/spip.php?breve210 (October 09, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>Un equipo de la UAB, en el concurso de biología sintética del MIT</i>" (Spanish), [http://www.uab.es/servlet/Satellite?cid=1096481466568&pagename=UABDivulga%2FPage%2FTemplatePageDetallArticleInvestigar&param1=1253860327385 (September 23, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>UAB to participate in the synthetic biology competition at MIT</i>" (English), [http://www.uab.es/servlet/Satellite/latest-news/news-detail/uab-to-participate-in-the-synthetic-biology-competition-at-mit-1096476786473.html?noticiaid=1253657853358 (September 23, 2009)]<br />
<br />
*'''[[Team:Valencia]]''': "<i>TheValencia team is awarded the Synthetic Standard Prize</i>" (Spanish), [http://www.elpais.com/articulo/sociedad/Levaduras/funcionan/pixeles/elpepuespval/20091103elpepusoc_9/Tes]<br />
<br />
*'''[[Team:Cambridge]]''': "<i>University of Cambridge team wins iGEM synthetic biology competition </i>" (English), [http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.html (November 5 2009)]</div>Vmullinhttp://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-09T15:08:02Z<p>Vmullin: /* video/radio about iGEM 2009 */</p>
<hr />
<div>__NOTOC__<br />
[https://2008.igem.org/IGEM_Publicity iGEM 2008 Publicity] | [http://parts.mit.edu/igem07/index.php/Media iGEM 2007 Publicity] | [http://parts.mit.edu/wiki/index.php/IGEM_News iGEM 2006 Publicity]<br />
<br />
<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
<br />
<html><br />
<iframe frameborder="0" width="728" height="90" marginwidth="0" marginheight="0" style="margin:0px 0px 25px 100px;"<br />
src="http://www.google.com/uds/modules/elements/newsshow/iframe.html?q=iGEM&rsz=large&format=728x90"><br />
</iframe><br />
</html><br />
<br />
<br />
<span style="color:#1e90ff; font-size:175%">'''blogs </span><span style="color:#3cb371; font-size:175%">covering iGEM 2009'''</span><br />
* The [http://igem.sdu.dk/ <span style="color:#453221; font-size: 130%">'''SDU-Denmark'''</span>] team blog about their iGEM experience.<br />
* A blog about the iGEM project of the [http://aboutgmos.org/iGEM <span style="color:#453221; font-size: 130%">'''Uppsala-Sweden'''</span>] team.<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''video/radio</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
*'''Slovenia, Heidelberg, SDU-Denmark''': [http://www.dradio.de/dlf/sendungen/forschak/1062608/ Die Biobastler von Boston], Nov 2, 2009, Deutschlandfunk radio (in German).<br />
*'''Cambridge, Imperial''': [http://www.sciencefriday.com/program/archives/200911063], Nov 6, 2009, NPR Science Friday (in English).<br />
<br />
====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
<br />
<br />
If you would like to share an article that was written about iGEM or your iGEM team, please link to it on this page. If you have multiple articles featuring your team, link to them all individually!<br />
<br />
Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
<br />
''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
<br />
====<font size=4><font color=dodgerblue>'''general'''</font></font>====<br />
*'''The Economist''': ''Biohacking: Hacking goes squishy'' Sep 3, 2009 [http://www.economist.com/search/displaystory.cfm?story_id=14299634 The Economist]<br />
*'''The Scientist''': ''Brick by Brick'' Feb 1, 2009. [http://www.the-scientist.com/article/display/55378/ The Scientist]<br />
*'''Technology Review''': ''A Genetically Engineered Rainbow of Bacteria'' November 03, 2009. [http://www.technologyreview.com/blog/editors/24351/ Technology Review]<br />
<br />
====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
<br />
*'''[[Team:IBB_Pune]]''': "<i>Bio-champs in the making</i>" (English), [http://www.punemirror.in/index.aspx?Page=article&sectname=News%20-%20City&sectid=2&contentid=200909142009091423331646a131eacc#ftr2 (Monday, September 14, 2009 at 11:33:25 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Ganiti Prakriyanmadhe Jeevanuncha Vaapar! (Use of Bacteria in mathematical devices)</i>" (Marathi), [http://beta.esakal.com/2009/09/09220618/pune-use-of-bacterias-in-maths.html(Wednesday, September 09th, 2009 AT 10:09 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Synthetic Biologiteel Bharari ("Advances in Synthetic Biology")</i>" (Marathi), [https://2009.igem.org/Team:IBB_Pune/press (Wednesday 7 October 2009)]<br />
<br />
*'''[[Team:Groningen]]''': "<i>Synthetic biology students from Groningen in the race for best bacterium</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/groningse-studenten-synthetische-biologie-maken-bacterie City of Talent (August 20, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Un concours organisé par le M.I.T : en route pour Boston ! </i>" (French), [http://www.supbiotech.fr/2009/09/boston-supbiotech-igem.html (September 08, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Les étudiants de la biotech interpellent la biologie synthétique</i>" (French), [http://www.vivagora.org/spip.php?breve210 (October 09, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>Un equipo de la UAB, en el concurso de biología sintética del MIT</i>" (Spanish), [http://www.uab.es/servlet/Satellite?cid=1096481466568&pagename=UABDivulga%2FPage%2FTemplatePageDetallArticleInvestigar&param1=1253860327385 (September 23, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>UAB to participate in the synthetic biology competition at MIT</i>" (English), [http://www.uab.es/servlet/Satellite/latest-news/news-detail/uab-to-participate-in-the-synthetic-biology-competition-at-mit-1096476786473.html?noticiaid=1253657853358 (September 23, 2009)]<br />
<br />
*'''[[Team:Valencia]]''': "<i>TheValencia team is awarded the Synthetic Standard Prize</i>" (Spanish), [http://www.elpais.com/articulo/sociedad/Levaduras/funcionan/pixeles/elpepuespval/20091103elpepusoc_9/Tes]<br />
<br />
*'''[[Team:Cambridge]]''': "<i>University of Cambridge team wins iGEM synthetic biology competition </i>" (English), [http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.html (November 5 2009)]</div>Vmullinhttp://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-09T15:07:40Z<p>Vmullin: /* video/radio about iGEM 2009 */</p>
<hr />
<div>__NOTOC__<br />
[https://2008.igem.org/IGEM_Publicity iGEM 2008 Publicity] | [http://parts.mit.edu/igem07/index.php/Media iGEM 2007 Publicity] | [http://parts.mit.edu/wiki/index.php/IGEM_News iGEM 2006 Publicity]<br />
<br />
<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
<br />
<html><br />
<iframe frameborder="0" width="728" height="90" marginwidth="0" marginheight="0" style="margin:0px 0px 25px 100px;"<br />
src="http://www.google.com/uds/modules/elements/newsshow/iframe.html?q=iGEM&rsz=large&format=728x90"><br />
</iframe><br />
</html><br />
<br />
<br />
<span style="color:#1e90ff; font-size:175%">'''blogs </span><span style="color:#3cb371; font-size:175%">covering iGEM 2009'''</span><br />
* The [http://igem.sdu.dk/ <span style="color:#453221; font-size: 130%">'''SDU-Denmark'''</span>] team blog about their iGEM experience.<br />
* A blog about the iGEM project of the [http://aboutgmos.org/iGEM <span style="color:#453221; font-size: 130%">'''Uppsala-Sweden'''</span>] team.<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''video/radio</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
*'''Slovenia, Heidelberg, SDU-Denmark''': [http://www.dradio.de/dlf/sendungen/forschak/1062608/ Die Biobastler von Boston], Nov 2, 2009, Deutschlandfunk radio (in German).<br />
*'''Cambridge, Imperial''': [hhttp://www.sciencefriday.com/program/archives/200911063], Nov 6, 2009, NPR Science Friday (in English).<br />
<br />
====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
<br />
<br />
If you would like to share an article that was written about iGEM or your iGEM team, please link to it on this page. If you have multiple articles featuring your team, link to them all individually!<br />
<br />
Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
<br />
''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
<br />
====<font size=4><font color=dodgerblue>'''general'''</font></font>====<br />
*'''The Economist''': ''Biohacking: Hacking goes squishy'' Sep 3, 2009 [http://www.economist.com/search/displaystory.cfm?story_id=14299634 The Economist]<br />
*'''The Scientist''': ''Brick by Brick'' Feb 1, 2009. [http://www.the-scientist.com/article/display/55378/ The Scientist]<br />
*'''Technology Review''': ''A Genetically Engineered Rainbow of Bacteria'' November 03, 2009. [http://www.technologyreview.com/blog/editors/24351/ Technology Review]<br />
<br />
====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
<br />
*'''[[Team:IBB_Pune]]''': "<i>Bio-champs in the making</i>" (English), [http://www.punemirror.in/index.aspx?Page=article&sectname=News%20-%20City&sectid=2&contentid=200909142009091423331646a131eacc#ftr2 (Monday, September 14, 2009 at 11:33:25 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Ganiti Prakriyanmadhe Jeevanuncha Vaapar! (Use of Bacteria in mathematical devices)</i>" (Marathi), [http://beta.esakal.com/2009/09/09220618/pune-use-of-bacterias-in-maths.html(Wednesday, September 09th, 2009 AT 10:09 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Synthetic Biologiteel Bharari ("Advances in Synthetic Biology")</i>" (Marathi), [https://2009.igem.org/Team:IBB_Pune/press (Wednesday 7 October 2009)]<br />
<br />
*'''[[Team:Groningen]]''': "<i>Synthetic biology students from Groningen in the race for best bacterium</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/groningse-studenten-synthetische-biologie-maken-bacterie City of Talent (August 20, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Un concours organisé par le M.I.T : en route pour Boston ! </i>" (French), [http://www.supbiotech.fr/2009/09/boston-supbiotech-igem.html (September 08, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Les étudiants de la biotech interpellent la biologie synthétique</i>" (French), [http://www.vivagora.org/spip.php?breve210 (October 09, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>Un equipo de la UAB, en el concurso de biología sintética del MIT</i>" (Spanish), [http://www.uab.es/servlet/Satellite?cid=1096481466568&pagename=UABDivulga%2FPage%2FTemplatePageDetallArticleInvestigar&param1=1253860327385 (September 23, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>UAB to participate in the synthetic biology competition at MIT</i>" (English), [http://www.uab.es/servlet/Satellite/latest-news/news-detail/uab-to-participate-in-the-synthetic-biology-competition-at-mit-1096476786473.html?noticiaid=1253657853358 (September 23, 2009)]<br />
<br />
*'''[[Team:Valencia]]''': "<i>TheValencia team is awarded the Synthetic Standard Prize</i>" (Spanish), [http://www.elpais.com/articulo/sociedad/Levaduras/funcionan/pixeles/elpepuespval/20091103elpepusoc_9/Tes]<br />
<br />
*'''[[Team:Cambridge]]''': "<i>University of Cambridge team wins iGEM synthetic biology competition </i>" (English), [http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.html (November 5 2009)]</div>Vmullinhttp://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-05T23:48:58Z<p>Vmullin: /* team specific */</p>
<hr />
<div>__NOTOC__<br />
[https://2008.igem.org/IGEM_Publicity iGEM 2008 Publicity] | [http://parts.mit.edu/igem07/index.php/Media iGEM 2007 Publicity] | [http://parts.mit.edu/wiki/index.php/IGEM_News iGEM 2006 Publicity]<br />
<br />
<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
<br />
<html><br />
<iframe frameborder="0" width="728" height="90" marginwidth="0" marginheight="0" style="margin:0px 0px 25px 100px;"<br />
src="http://www.google.com/uds/modules/elements/newsshow/iframe.html?q=iGEM&rsz=large&format=728x90"><br />
</iframe><br />
</html><br />
<br />
<br />
<span style="color:#1e90ff; font-size:175%">'''blogs </span><span style="color:#3cb371; font-size:175%">covering iGEM 2009'''</span><br />
* The [http://igem.sdu.dk/ <span style="color:#453221; font-size: 130%">'''SDU-Denmark'''</span>] team blog about their iGEM experience.<br />
* A blog about the iGEM project of the [http://aboutgmos.org/iGEM <span style="color:#453221; font-size: 130%">'''Uppsala-Sweden'''</span>] team.<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''video/radio</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
*'''Slovenia, Heidelberg, SDU-Denmark''': [http://www.dradio.de/dlf/sendungen/forschak/1062608/ Die Biobastler von Boston], Nov 2, 2009, Deutschlandfunk radio (in German).<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
<br />
<br />
If you would like to share an article that was written about iGEM or your iGEM team, please link to it on this page. If you have multiple articles featuring your team, link to them all individually!<br />
<br />
Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
<br />
''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
<br />
====<font size=4><font color=dodgerblue>'''general'''</font></font>====<br />
*'''The Economist''': ''Biohacking: Hacking goes squishy'' Sep 3, 2009 [http://www.economist.com/search/displaystory.cfm?story_id=14299634 The Economist]<br />
*'''The Scientist''': ''Brick by Brick'' Feb 1, 2009. [http://www.the-scientist.com/article/display/55378/ The Scientist]<br />
*'''Technology Review''': ''A Genetically Engineered Rainbow of Bacteria'' November 03, 2009. [http://www.technologyreview.com/blog/editors/24351/ Technology Review]<br />
<br />
====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
<br />
*'''[[Team:IBB_Pune]]''': "<i>Bio-champs in the making</i>" (English), [http://www.punemirror.in/index.aspx?Page=article&sectname=News%20-%20City&sectid=2&contentid=200909142009091423331646a131eacc#ftr2 (Monday, September 14, 2009 at 11:33:25 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Ganiti Prakriyanmadhe Jeevanuncha Vaapar! (Use of Bacteria in mathematical devices)</i>" (Marathi), [http://beta.esakal.com/2009/09/09220618/pune-use-of-bacterias-in-maths.html(Wednesday, September 09th, 2009 AT 10:09 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Synthetic Biologiteel Bharari ("Advances in Synthetic Biology")</i>" (Marathi), [https://2009.igem.org/Team:IBB_Pune/press (Wednesday 7 October 2009)]<br />
<br />
*'''[[Team:Groningen]]''': "<i>Synthetic biology students from Groningen in the race for best bacterium</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/groningse-studenten-synthetische-biologie-maken-bacterie City of Talent (August 20, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Un concours organisé par le M.I.T : en route pour Boston ! </i>" (French), [http://www.supbiotech.fr/2009/09/boston-supbiotech-igem.html (September 08, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Les étudiants de la biotech interpellent la biologie synthétique</i>" (French), [http://www.vivagora.org/spip.php?breve210 (October 09, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>Un equipo de la UAB, en el concurso de biología sintética del MIT</i>" (Spanish), [http://www.uab.es/servlet/Satellite?cid=1096481466568&pagename=UABDivulga%2FPage%2FTemplatePageDetallArticleInvestigar&param1=1253860327385 (September 23, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>UAB to participate in the synthetic biology competition at MIT</i>" (English), [http://www.uab.es/servlet/Satellite/latest-news/news-detail/uab-to-participate-in-the-synthetic-biology-competition-at-mit-1096476786473.html?noticiaid=1253657853358 (September 23, 2009)]<br />
<br />
*'''[[Team:Valencia]]''': "<i>TheValencia team is awarded the Synthetic Standard Prize</i>" (Spanish), [http://www.elpais.com/articulo/sociedad/Levaduras/funcionan/pixeles/elpepuespval/20091103elpepusoc_9/Tes]<br />
<br />
*'''[[Team:Cambridge]]''': "<i>University of Cambridge team wins iGEM synthetic biology competition </i>" (English), [http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.html (November 5 2009)]</div>Vmullinhttp://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-05T21:29:31Z<p>Vmullin: </p>
<hr />
<div>__NOTOC__<br />
[https://2008.igem.org/IGEM_Publicity iGEM 2008 Publicity] | [http://parts.mit.edu/igem07/index.php/Media iGEM 2007 Publicity] | [http://parts.mit.edu/wiki/index.php/IGEM_News iGEM 2006 Publicity]<br />
<br />
<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
<br />
<html><br />
<iframe frameborder="0" width="728" height="90" marginwidth="0" marginheight="0" style="margin:0px 0px 25px 100px;"<br />
src="http://www.google.com/uds/modules/elements/newsshow/iframe.html?q=iGEM&rsz=large&format=728x90"><br />
</iframe><br />
</html><br />
<br />
<br />
<span style="color:#1e90ff; font-size:175%">'''blogs </span><span style="color:#3cb371; font-size:175%">covering iGEM 2009'''</span><br />
* The [http://igem.sdu.dk/ <span style="color:#453221; font-size: 130%">'''SDU-Denmark'''</span>] team blog about their iGEM experience.<br />
* A blog about the iGEM project of the [http://aboutgmos.org/iGEM <span style="color:#453221; font-size: 130%">'''Uppsala-Sweden'''</span>] team.<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''video/radio</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
*'''Slovenia, Heidelberg, SDU-Denmark''': [http://www.dradio.de/dlf/sendungen/forschak/1062608/ Die Biobastler von Boston], Nov 2, 2009, Deutschlandfunk radio (in German).<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
<br />
<br />
If you would like to share an article that was written about iGEM or your iGEM team, please link to it on this page. If you have multiple articles featuring your team, link to them all individually!<br />
<br />
Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
<br />
''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
<br />
====<font size=4><font color=dodgerblue>'''general'''</font></font>====<br />
*'''The Economist''': ''Biohacking: Hacking goes squishy'' Sep 3, 2009 [http://www.economist.com/search/displaystory.cfm?story_id=14299634 The Economist]<br />
*'''The Scientist''': ''Brick by Brick'' Feb 1, 2009. [http://www.the-scientist.com/article/display/55378/ The Scientist]<br />
*'''Technology Review''': ''A Genetically Engineered Rainbow of Bacteria'' November 03, 2009. [http://www.technologyreview.com/blog/editors/24351/ Technology Review]<br />
<br />
====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
<br />
*'''[[Team:IBB_Pune]]''': "<i>Bio-champs in the making</i>" (English), [http://www.punemirror.in/index.aspx?Page=article&sectname=News%20-%20City&sectid=2&contentid=200909142009091423331646a131eacc#ftr2 (Monday, September 14, 2009 at 11:33:25 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Ganiti Prakriyanmadhe Jeevanuncha Vaapar! (Use of Bacteria in mathematical devices)</i>" (Marathi), [http://beta.esakal.com/2009/09/09220618/pune-use-of-bacterias-in-maths.html(Wednesday, September 09th, 2009 AT 10:09 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Synthetic Biologiteel Bharari ("Advances in Synthetic Biology")</i>" (Marathi), [https://2009.igem.org/Team:IBB_Pune/press (Wednesday 7 October 2009)]<br />
<br />
*'''[[Team:Groningen]]''': "<i>Synthetic biology students from Groningen in the race for best bacterium</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/groningse-studenten-synthetische-biologie-maken-bacterie City of Talent (August 20, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Un concours organisé par le M.I.T : en route pour Boston ! </i>" (French), [http://www.supbiotech.fr/2009/09/boston-supbiotech-igem.html (September 08, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Les étudiants de la biotech interpellent la biologie synthétique</i>" (French), [http://www.vivagora.org/spip.php?breve210 (October 09, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>Un equipo de la UAB, en el concurso de biología sintética del MIT</i>" (Spanish), [http://www.uab.es/servlet/Satellite?cid=1096481466568&pagename=UABDivulga%2FPage%2FTemplatePageDetallArticleInvestigar&param1=1253860327385 (September 23, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>UAB to participate in the synthetic biology competition at MIT</i>" (English), [http://www.uab.es/servlet/Satellite/latest-news/news-detail/uab-to-participate-in-the-synthetic-biology-competition-at-mit-1096476786473.html?noticiaid=1253657853358 (September 23, 2009)]<br />
<br />
*'''[[Team:Valencia]]''': "<i>TheValencia team is awarded the Synthetic Standard Prize</i>" (Spanish), [http://www.elpais.com/articulo/sociedad/Levaduras/funcionan/pixeles/elpepuespval/20091103elpepusoc_9/Tes]<br />
<br />
*'''[[Team:Cambridge]]''': "<i>University of Cambridge team wins iGEM synthetic biology competition </i>" (English), [http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.htm (November 5 2009)]</div>Vmullinhttp://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-05T21:28:23Z<p>Vmullin: </p>
<hr />
<div>__NOTOC__<br />
[https://2008.igem.org/IGEM_Publicity iGEM 2008 Publicity] | [http://parts.mit.edu/igem07/index.php/Media iGEM 2007 Publicity] | [http://parts.mit.edu/wiki/index.php/IGEM_News iGEM 2006 Publicity]<br />
<br />
<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
<br />
<html><br />
<iframe frameborder="0" width="728" height="90" marginwidth="0" marginheight="0" style="margin:0px 0px 25px 100px;"<br />
src="http://www.google.com/uds/modules/elements/newsshow/iframe.html?q=iGEM&rsz=large&format=728x90"><br />
</iframe><br />
</html><br />
<br />
<br />
<span style="color:#1e90ff; font-size:175%">'''blogs </span><span style="color:#3cb371; font-size:175%">covering iGEM 2009'''</span><br />
* The [http://igem.sdu.dk/ <span style="color:#453221; font-size: 130%">'''SDU-Denmark'''</span>] team blog about their iGEM experience.<br />
* A blog about the iGEM project of the [http://aboutgmos.org/iGEM <span style="color:#453221; font-size: 130%">'''Uppsala-Sweden'''</span>] team.<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''video/radio</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
*'''Slovenia, Heidelberg, SDU-Denmark''': [http://www.dradio.de/dlf/sendungen/forschak/1062608/ Die Biobastler von Boston], Nov 2, 2009, Deutschlandfunk radio (in German).<br />
<br />
<br />
<br />
<br />
====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
<br />
<br />
If you would like to share an article that was written about iGEM or your iGEM team, please link to it on this page. If you have multiple articles featuring your team, link to them all individually!<br />
<br />
Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
<br />
''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
<br />
====<font size=4><font color=dodgerblue>'''general'''</font></font>====<br />
*'''The Economist''': ''Biohacking: Hacking goes squishy'' Sep 3, 2009 [http://www.economist.com/search/displaystory.cfm?story_id=14299634 The Economist]<br />
*'''The Scientist''': ''Brick by Brick'' Feb 1, 2009. [http://www.the-scientist.com/article/display/55378/ The Scientist]<br />
*'''Technology Review''': ''A Genetically Engineered Rainbow of Bacteria'' November 03, 2009. [http://www.technologyreview.com/blog/editors/24351/ Technology Review]<br />
<br />
====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
<br />
*'''[[Team:IBB_Pune]]''': "<i>Bio-champs in the making</i>" (English), [http://www.punemirror.in/index.aspx?Page=article&sectname=News%20-%20City&sectid=2&contentid=200909142009091423331646a131eacc#ftr2 (Monday, September 14, 2009 at 11:33:25 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Ganiti Prakriyanmadhe Jeevanuncha Vaapar! (Use of Bacteria in mathematical devices)</i>" (Marathi), [http://beta.esakal.com/2009/09/09220618/pune-use-of-bacterias-in-maths.html(Wednesday, September 09th, 2009 AT 10:09 PM)]<br />
*'''[[Team:IBB_Pune]]''': "<i>Synthetic Biologiteel Bharari ("Advances in Synthetic Biology")</i>" (Marathi), [https://2009.igem.org/Team:IBB_Pune/press (Wednesday 7 October 2009)]<br />
<br />
*'''[[Team:Groningen]]''': "<i>Synthetic biology students from Groningen in the race for best bacterium</i>" (Dutch), [http://www.cityoftalent.nl/nl/content/nieuws/nieuws/groningse-studenten-synthetische-biologie-maken-bacterie City of Talent (August 20, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Un concours organisé par le M.I.T : en route pour Boston ! </i>" (French), [http://www.supbiotech.fr/2009/09/boston-supbiotech-igem.html (September 08, 2009)]<br />
<br />
*'''[[Team:SupBiotech-Paris]]''': "<i>Les étudiants de la biotech interpellent la biologie synthétique</i>" (French), [http://www.vivagora.org/spip.php?breve210 (October 09, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>Un equipo de la UAB, en el concurso de biología sintética del MIT</i>" (Spanish), [http://www.uab.es/servlet/Satellite?cid=1096481466568&pagename=UABDivulga%2FPage%2FTemplatePageDetallArticleInvestigar&param1=1253860327385 (September 23, 2009)]<br />
<br />
*'''[[Team:UAB-Barcelona]]''': "<i>UAB to participate in the synthetic biology competition at MIT</i>" (English), [http://www.uab.es/servlet/Satellite/latest-news/news-detail/uab-to-participate-in-the-synthetic-biology-competition-at-mit-1096476786473.html?noticiaid=1253657853358 (September 23, 2009)]<br />
<br />
*'''[[Team:Valencia]]''': "<i>TheValencia team is awarded the Synthetic Standard Prize</i>" (Spanish), [http://www.elpais.com/articulo/sociedad/Levaduras/funcionan/pixeles/elpepuespval/20091103elpepusoc_9/Tes]<br />
<br />
*'''[[Team:Cambridge]]''': "<i>University of Cambridge team wins iGEM synthetic biology competition </i>" (English), [http://www.biotechniques.com/news/University-of-Cambridge-team-wins-iGEM-synthetic-biology-competition/biotechniques-180278.htm]</div>Vmullinhttp://2009.igem.org/File:Cambridgeplates.jpgFile:Cambridgeplates.jpg2009-10-21T23:56:55Z<p>Vmullin: </p>
<hr />
<div></div>Vmullinhttp://2009.igem.org/Team:Cambridge/ProjectTeam:Cambridge/Project2009-10-21T23:56:27Z<p>Vmullin: /* Project Details */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Project =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Abstract | Introduction ]]<br />
[[#Project Details | Project Details]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The E. Chromi project strived to facilitate biosensor design and construction. We designed and characterised two types of parts - Sensitivity Tuners and Colour Generators. The availability of these parts on the registry could revolutionize biosensor design in the future - when new promoters that sense novel inputs are characterized and submitted to the registry, Sensitivity Tuners and Colour Generators can be implemented to tune the sensitivity of the promoter to detect a concentration appropriate to the biosensor's desired application, and to report the presence of an inducer in a cheap, user-friendly fashion.<br />
<br />
===Improving Biosensors===<br />
<br />
The Parts Registry's repertoire of input-sensitive devices is incredibly varied. Teams have engineered ''E. coli'' to be sensitive to a wide range of environmentally significant compounds, including arsenic, mercury, lead, cyanide, etc., to genetically engineer biosensors as an alternative to other technologies. The Cambridge 2009 iGEM team identified two stumbling blocks to biosensor design. <br />
<br />
*'''Output''': Previous iGEM biosensor projects have used pH, electrical conductance, and fluorescence as output. However, these reporter mechanisms require further steps to read the output. While this is acceptable for First World applications, for biosensors to have true Third World applications, a simpler output is necessary.<br />
<br />
*'''Response to Input''': By utilizing an input-sensitive promoter, the biosensor is limited by the sensitivity of the promoter. For example, the promoter might be sensitive to input concentrations which have no real world meaning. The promoter's sensitivity could be too high, so it reports concentrations below levels of real-world interest. Alternately, the promoter's sensitivity could be too low, so it reports concentrations above those which mark the boundary between "safe" and "dangerous." A second limitation is the the behavior of the PoPS output from the promoter; for example, output may vary linearly with input. This type of response is incompatible with a digital "safe" or "dangerous" output.<br />
<br />
===Our Solutions===<br />
<br />
*'''A Sensitivity Tuner''': To avoid being limited to the sensitivity of the promoter and in order to be able to detect distinct concentrations of an inducer using just one promoter, we see the need for a set of sensitivity tuners. These devices allow you to "tune" your biosensor, such that it reports meaningful concentrations of the inducer appropriate to the biosensor's application. The sensitivity tuner also modifies the PoPS output from the promoter's native behavior to a sigmoidal "on" or "off" response pattern.<br />
*'''Colour Output''': What if we could "see" the concentration of an inducer in a sample by a change in colour of the biosensor? Many prey species are brightly coloured, showing off clearly the fact that they are poisonous or otherwise harmful to potential predators, a phenomenon known as aposematism or warning colouration. Humans use colour as a means of conveying information as well - we can "see" if a child has a fever using a thermometer strip and we can "see" the pH of a solution using a pH indicator. Colour can be a meaningful but simple output solution for biosensors, adapting nature's idea of warning colouration.<br />
<br />
== Project Details==<br />
<br />
===Design===<br />
<br />
<br />
====The Product====<br />
<br />
<br />
We envisioned a marketable product that reports the concentration of an inducer by colour. Imagine a dipstick with wells, each of which contain pigment-expressing bacteria in response to an inducer. However, each strain is sensitive to a different concentration of the inducer. The concentration of the inducer in the test solution can be determined by reading the pattern of pigmentation.<br />
<br />
[[Image:Cambridge_prototype5.jpg|300px]]<br />
<br />
<br />
<br />
====The Genetically Engineered Machine====<br />
<br />
Each bacterial strain is a machine built from a three part system. <br />
<br />
<br />
[[Image:Cambridge_newGenericdevicE2.jpg|400px]]<br />
<br />
<br />
*'''Sensor''': The sensor system is sensitive to different concentrations of an inducer.<br />
<br />
*'''Sensitivity Tuner''': This device is responsible for the setting the sensitivity to the inducer, and acts as an "on" switch to activate pigment production once the inducer has reached a threshold.<br />
<br />
*'''Colour Generator''': Responsible for pigment production.<br />
<br />
===Components===<br />
<br />
The three part system can be abstracted by the diagram below:<br />
<br />
[[Image:abstraction6.jpg | 500 px]]<br />
<br />
The components of each of the black boxes is as follows:<br />
<br />
[[Image:Cambridge_systemdiagram7.jpg | 500 px]]<br />
<br />
The sensor, sensitivity tuner, and colour should be viewed as separate parts that are pieced together to build a tunable biosensor that utilizes colour as output. The Parts Registry already has an impressive selection of parts that can be used as sensors. The Cambridge 2009 iGEM team focused on developing a selection of different sensitivity tuner parts and a selection of different pigment producing parts. <br />
<br />
*'''Sensitivity Tuner''': These constructs are based on Cambridge 2007's amplifiers. The general construct is composed of a gene coding for a phage activator protein and a phage activator-sensitive promoter. With PoPS input, the phage activator gene is transcribed. After translation to produce the phage activator protein, the protein binds to the phage activator-sensitive promoter to activate transcription. Thus it is a device that generates a distinct PoPS out given a PoPS in. With an input-sensitive promoter alone, output generally varies linearly with input--this, at least, is the case with the arabinose-sensitive promoter pBad/Arac (BBa_I0500). However, when a sensitivity tuner is placed downstream of the input-sensitive promoter, the output versus input behavior is altered such that output increases dramatically at a certain input, resulting in sigmoidal behavior with a distinctive threshold. <br />
<br />
*'''Colour Generator''': Though ''E. coli'' does not naturally produce pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most promising candidates into ''E. coli''.<br />
<br />
===Kits of Parts===<br />
<br />
The culmination of our project was to generate and characterize two kits of of parts - one of Sensitivity Tuners and one of Colour Generators.<br />
<br />
'''Sensitivity Tuners''': There are 3 different activator genes and 5 different activator-sensitive promoters in the registry. 15 combinations are possible, and each has a distinct threshold and peak rate of output. The table below summarizes the parts we designed and characterised:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
'''Colour Generators''': We have devoted our summer to 3 different pigment systems: <br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce violet and two shades of green<br />
<br />
We designed and characterised the following biobricks:<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
[[Image:cambridgeplates.jpg]]<br />
<br />
Potential exists to expand both of these kits of parts further using more phage activators and phage promoters that are not yet in the registry <br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/ProjectTeam:Cambridge/Project2009-10-21T23:55:02Z<p>Vmullin: /* Project Details */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Project =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Abstract | Introduction ]]<br />
[[#Project Details | Project Details]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The E. Chromi project strived to facilitate biosensor design and construction. We designed and characterised two types of parts - Sensitivity Tuners and Colour Generators. The availability of these parts on the registry could revolutionize biosensor design in the future - when new promoters that sense novel inputs are characterized and submitted to the registry, Sensitivity Tuners and Colour Generators can be implemented to tune the sensitivity of the promoter to detect a concentration appropriate to the biosensor's desired application, and to report the presence of an inducer in a cheap, user-friendly fashion.<br />
<br />
===Improving Biosensors===<br />
<br />
The Parts Registry's repertoire of input-sensitive devices is incredibly varied. Teams have engineered ''E. coli'' to be sensitive to a wide range of environmentally significant compounds, including arsenic, mercury, lead, cyanide, etc., to genetically engineer biosensors as an alternative to other technologies. The Cambridge 2009 iGEM team identified two stumbling blocks to biosensor design. <br />
<br />
*'''Output''': Previous iGEM biosensor projects have used pH, electrical conductance, and fluorescence as output. However, these reporter mechanisms require further steps to read the output. While this is acceptable for First World applications, for biosensors to have true Third World applications, a simpler output is necessary.<br />
<br />
*'''Response to Input''': By utilizing an input-sensitive promoter, the biosensor is limited by the sensitivity of the promoter. For example, the promoter might be sensitive to input concentrations which have no real world meaning. The promoter's sensitivity could be too high, so it reports concentrations below levels of real-world interest. Alternately, the promoter's sensitivity could be too low, so it reports concentrations above those which mark the boundary between "safe" and "dangerous." A second limitation is the the behavior of the PoPS output from the promoter; for example, output may vary linearly with input. This type of response is incompatible with a digital "safe" or "dangerous" output.<br />
<br />
===Our Solutions===<br />
<br />
*'''A Sensitivity Tuner''': To avoid being limited to the sensitivity of the promoter and in order to be able to detect distinct concentrations of an inducer using just one promoter, we see the need for a set of sensitivity tuners. These devices allow you to "tune" your biosensor, such that it reports meaningful concentrations of the inducer appropriate to the biosensor's application. The sensitivity tuner also modifies the PoPS output from the promoter's native behavior to a sigmoidal "on" or "off" response pattern.<br />
*'''Colour Output''': What if we could "see" the concentration of an inducer in a sample by a change in colour of the biosensor? Many prey species are brightly coloured, showing off clearly the fact that they are poisonous or otherwise harmful to potential predators, a phenomenon known as aposematism or warning colouration. Humans use colour as a means of conveying information as well - we can "see" if a child has a fever using a thermometer strip and we can "see" the pH of a solution using a pH indicator. Colour can be a meaningful but simple output solution for biosensors, adapting nature's idea of warning colouration.<br />
<br />
== Project Details==<br />
<br />
===Design===<br />
<br />
<br />
====The Product====<br />
<br />
<br />
We envisioned a marketable product that reports the concentration of an inducer by colour. Imagine a dipstick with wells, each of which contain pigment-expressing bacteria in response to an inducer. However, each strain is sensitive to a different concentration of the inducer. The concentration of the inducer in the test solution can be determined by reading the pattern of pigmentation.<br />
<br />
[[Image:Cambridge_prototype5.jpg|300px]]<br />
<br />
<br />
<br />
====The Genetically Engineered Machine====<br />
<br />
Each bacterial strain is a machine built from a three part system. <br />
<br />
<br />
[[Image:Cambridge_newGenericdevicE2.jpg|400px]]<br />
<br />
<br />
*'''Sensor''': The sensor system is sensitive to different concentrations of an inducer.<br />
<br />
*'''Sensitivity Tuner''': This device is responsible for the setting the sensitivity to the inducer, and acts as an "on" switch to activate pigment production once the inducer has reached a threshold.<br />
<br />
*'''Colour Generator''': Responsible for pigment production.<br />
<br />
===Components===<br />
<br />
The three part system can be abstracted by the diagram below:<br />
<br />
[[Image:abstraction6.jpg | 500 px]]<br />
<br />
The components of each of the black boxes is as follows:<br />
<br />
[[Image:Cambridge_systemdiagram7.jpg | 500 px]]<br />
<br />
The sensor, sensitivity tuner, and colour should be viewed as separate parts that are pieced together to build a tunable biosensor that utilizes colour as output. The Parts Registry already has an impressive selection of parts that can be used as sensors. The Cambridge 2009 iGEM team focused on developing a selection of different sensitivity tuner parts and a selection of different pigment producing parts. <br />
<br />
*'''Sensitivity Tuner''': These constructs are based on Cambridge 2007's amplifiers. The general construct is composed of a gene coding for a phage activator protein and a phage activator-sensitive promoter. With PoPS input, the phage activator gene is transcribed. After translation to produce the phage activator protein, the protein binds to the phage activator-sensitive promoter to activate transcription. Thus it is a device that generates a distinct PoPS out given a PoPS in. With an input-sensitive promoter alone, output generally varies linearly with input--this, at least, is the case with the arabinose-sensitive promoter pBad/Arac (BBa_I0500). However, when a sensitivity tuner is placed downstream of the input-sensitive promoter, the output versus input behavior is altered such that output increases dramatically at a certain input, resulting in sigmoidal behavior with a distinctive threshold. <br />
<br />
*'''Colour Generator''': Though ''E. coli'' does not naturally produce pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most promising candidates into ''E. coli''.<br />
<br />
===Kits of Parts===<br />
<br />
The culmination of our project was to generate and characterize two kits of of parts - one of Sensitivity Tuners and one of Colour Generators.<br />
<br />
'''Sensitivity Tuners''': There are 3 different activator genes and 5 different activator-sensitive promoters in the registry. 15 combinations are possible, and each has a distinct threshold and peak rate of output. The table below summarizes the parts we designed and characterised:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
'''Colour Generators''': We have devoted our summer to 3 different pigment systems: <br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce violet and two shades of green<br />
<br />
We designed and characterised the following biobricks:<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
[[Image:plates.jpg]]<br />
<br />
Potential exists to expand both of these kits of parts further using more phage activators and phage promoters that are not yet in the registry <br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/ProjectTeam:Cambridge/Project2009-10-21T23:50:49Z<p>Vmullin: /* Project Details */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Project =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Abstract | Introduction ]]<br />
[[#Project Details | Project Details]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The E. Chromi project strived to facilitate biosensor design and construction. We designed and characterised two types of parts - Sensitivity Tuners and Colour Generators. The availability of these parts on the registry could revolutionize biosensor design in the future - when new promoters that sense novel inputs are characterized and submitted to the registry, Sensitivity Tuners and Colour Generators can be implemented to tune the sensitivity of the promoter to detect a concentration appropriate to the biosensor's desired application, and to report the presence of an inducer in a cheap, user-friendly fashion.<br />
<br />
===Improving Biosensors===<br />
<br />
The Parts Registry's repertoire of input-sensitive devices is incredibly varied. Teams have engineered ''E. coli'' to be sensitive to a wide range of environmentally significant compounds, including arsenic, mercury, lead, cyanide, etc., to genetically engineer biosensors as an alternative to other technologies. The Cambridge 2009 iGEM team identified two stumbling blocks to biosensor design. <br />
<br />
*'''Output''': Previous iGEM biosensor projects have used pH, electrical conductance, and fluorescence as output. However, these reporter mechanisms require further steps to read the output. While this is acceptable for First World applications, for biosensors to have true Third World applications, a simpler output is necessary.<br />
<br />
*'''Response to Input''': By utilizing an input-sensitive promoter, the biosensor is limited by the sensitivity of the promoter. For example, the promoter might be sensitive to input concentrations which have no real world meaning. The promoter's sensitivity could be too high, so it reports concentrations below levels of real-world interest. Alternately, the promoter's sensitivity could be too low, so it reports concentrations above those which mark the boundary between "safe" and "dangerous." A second limitation is the the behavior of the PoPS output from the promoter; for example, output may vary linearly with input. This type of response is incompatible with a digital "safe" or "dangerous" output.<br />
<br />
===Our Solutions===<br />
<br />
*'''A Sensitivity Tuner''': To avoid being limited to the sensitivity of the promoter and in order to be able to detect distinct concentrations of an inducer using just one promoter, we see the need for a set of sensitivity tuners. These devices allow you to "tune" your biosensor, such that it reports meaningful concentrations of the inducer appropriate to the biosensor's application. The sensitivity tuner also modifies the PoPS output from the promoter's native behavior to a sigmoidal "on" or "off" response pattern.<br />
*'''Colour Output''': What if we could "see" the concentration of an inducer in a sample by a change in colour of the biosensor? Many prey species are brightly coloured, showing off clearly the fact that they are poisonous or otherwise harmful to potential predators, a phenomenon known as aposematism or warning colouration. Humans use colour as a means of conveying information as well - we can "see" if a child has a fever using a thermometer strip and we can "see" the pH of a solution using a pH indicator. Colour can be a meaningful but simple output solution for biosensors, adapting nature's idea of warning colouration.<br />
<br />
== Project Details==<br />
<br />
===Design===<br />
<br />
<br />
====The Product====<br />
<br />
<br />
We envisioned a marketable product that reports the concentration of an inducer by colour. Imagine a dipstick with wells, each of which contain pigment-expressing bacteria in response to an inducer. However, each strain is sensitive to a different concentration of the inducer. The concentration of the inducer in the test solution can be determined by reading the pattern of pigmentation.<br />
<br />
[[Image:Cambridge_prototype5.jpg|300px]]<br />
<br />
<br />
<br />
====The Genetically Engineered Machine====<br />
<br />
Each bacterial strain is a machine built from a three part system. <br />
<br />
<br />
[[Image:Cambridge_newGenericdevicE2.jpg|400px]]<br />
<br />
<br />
*'''Sensor''': The sensor system is sensitive to different concentrations of an inducer.<br />
<br />
*'''Sensitivity Tuner''': This device is responsible for the setting the sensitivity to the inducer, and acts as an "on" switch to activate pigment production once the inducer has reached a threshold.<br />
<br />
*'''Colour Generator''': Responsible for pigment production.<br />
<br />
===Components===<br />
<br />
The three part system can be abstracted by the diagram below:<br />
<br />
[[Image:abstraction6.jpg | 500 px]]<br />
<br />
The components of each of the black boxes is as follows:<br />
<br />
[[Image:Cambridge_systemdiagram7.jpg | 500 px]]<br />
<br />
The sensor, sensitivity tuner, and colour should be viewed as separate parts that are pieced together to build a tunable biosensor that utilizes colour as output. The Parts Registry already has an impressive selection of parts that can be used as sensors. The Cambridge 2009 iGEM team focused on developing a selection of different sensitivity tuner parts and a selection of different pigment producing parts. <br />
<br />
*'''Sensitivity Tuner''': These constructs are based on Cambridge 2007's amplifiers. The general construct is composed of a gene coding for a phage activator protein and a phage activator-sensitive promoter. With PoPS input, the phage activator gene is transcribed. After translation to produce the phage activator protein, the protein binds to the phage activator-sensitive promoter to activate transcription. Thus it is a device that generates a distinct PoPS out given a PoPS in. With an input-sensitive promoter alone, output generally varies linearly with input--this, at least, is the case with the arabinose-sensitive promoter pBad/Arac (BBa_I0500). However, when a sensitivity tuner is placed downstream of the input-sensitive promoter, the output versus input behavior is altered such that output increases dramatically at a certain input, resulting in sigmoidal behavior with a distinctive threshold. <br />
<br />
*'''Colour Generator''': Though ''E. coli'' does not naturally produce pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most promising candidates into ''E. coli''.<br />
<br />
===Kits of Parts===<br />
<br />
The culmination of our project was to generate and characterize two kits of of parts - one of Sensitivity Tuners and one of Colour Generators.<br />
<br />
'''Sensitivity Tuners''': There are 3 different activator genes and 5 different activator-sensitive promoters in the registry. 15 combinations are possible, and each has a distinct threshold and peak rate of output. The table below summarizes the parts we designed and characterised:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
'''Colour Generators''': We have devoted our summer to 3 different pigment systems: <br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce violet and two shades of green<br />
<br />
We designed and characterised the following biobricks:<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
[[Image:plates]]<br />
<br />
Potential exists to expand both of these kits of parts further using more phage activators and phage promoters that are not yet in the registry <br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/ProjectTeam:Cambridge/Project2009-10-21T23:47:40Z<p>Vmullin: /* Design */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Project =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Abstract | Introduction ]]<br />
[[#Project Details | Project Details]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The E. Chromi project strived to facilitate biosensor design and construction. We designed and characterised two types of parts - Sensitivity Tuners and Colour Generators. The availability of these parts on the registry could revolutionize biosensor design in the future - when new promoters that sense novel inputs are characterized and submitted to the registry, Sensitivity Tuners and Colour Generators can be implemented to tune the sensitivity of the promoter to detect a concentration appropriate to the biosensor's desired application, and to report the presence of an inducer in a cheap, user-friendly fashion.<br />
<br />
===Improving Biosensors===<br />
<br />
The Parts Registry's repertoire of input-sensitive devices is incredibly varied. Teams have engineered ''E. coli'' to be sensitive to a wide range of environmentally significant compounds, including arsenic, mercury, lead, cyanide, etc., to genetically engineer biosensors as an alternative to other technologies. The Cambridge 2009 iGEM team identified two stumbling blocks to biosensor design. <br />
<br />
*'''Output''': Previous iGEM biosensor projects have used pH, electrical conductance, and fluorescence as output. However, these reporter mechanisms require further steps to read the output. While this is acceptable for First World applications, for biosensors to have true Third World applications, a simpler output is necessary.<br />
<br />
*'''Response to Input''': By utilizing an input-sensitive promoter, the biosensor is limited by the sensitivity of the promoter. For example, the promoter might be sensitive to input concentrations which have no real world meaning. The promoter's sensitivity could be too high, so it reports concentrations below levels of real-world interest. Alternately, the promoter's sensitivity could be too low, so it reports concentrations above those which mark the boundary between "safe" and "dangerous." A second limitation is the the behavior of the PoPS output from the promoter; for example, output may vary linearly with input. This type of response is incompatible with a digital "safe" or "dangerous" output.<br />
<br />
===Our Solutions===<br />
<br />
*'''A Sensitivity Tuner''': To avoid being limited to the sensitivity of the promoter and in order to be able to detect distinct concentrations of an inducer using just one promoter, we see the need for a set of sensitivity tuners. These devices allow you to "tune" your biosensor, such that it reports meaningful concentrations of the inducer appropriate to the biosensor's application. The sensitivity tuner also modifies the PoPS output from the promoter's native behavior to a sigmoidal "on" or "off" response pattern.<br />
*'''Colour Output''': What if we could "see" the concentration of an inducer in a sample by a change in colour of the biosensor? Many prey species are brightly coloured, showing off clearly the fact that they are poisonous or otherwise harmful to potential predators, a phenomenon known as aposematism or warning colouration. Humans use colour as a means of conveying information as well - we can "see" if a child has a fever using a thermometer strip and we can "see" the pH of a solution using a pH indicator. Colour can be a meaningful but simple output solution for biosensors, adapting nature's idea of warning colouration.<br />
<br />
== Project Details==<br />
<br />
===Design===<br />
<br />
<br />
====The Product====<br />
<br />
<br />
We envisioned a marketable product that reports the concentration of an inducer by colour. Imagine a dipstick with wells, each of which contain pigment-expressing bacteria in response to an inducer. However, each strain is sensitive to a different concentration of the inducer. The concentration of the inducer in the test solution can be determined by reading the pattern of pigmentation.<br />
<br />
[[Image:Cambridge_prototype5.jpg|300px]]<br />
<br />
<br />
<br />
====The Genetically Engineered Machine====<br />
<br />
Each bacterial strain is a machine built from a three part system. <br />
<br />
<br />
[[Image:Cambridge_newGenericdevicE2.jpg|400px]]<br />
<br />
<br />
*'''Sensor''': The sensor system is sensitive to different concentrations of an inducer.<br />
<br />
*'''Sensitivity Tuner''': This device is responsible for the setting the sensitivity to the inducer, and acts as an "on" switch to activate pigment production once the inducer has reached a threshold.<br />
<br />
*'''Colour Generator''': Responsible for pigment production.<br />
<br />
===Components===<br />
<br />
The three part system can be abstracted by the diagram below:<br />
<br />
[[Image:abstraction6.jpg | 500 px]]<br />
<br />
The components of each of the black boxes is as follows:<br />
<br />
[[Image:Cambridge_systemdiagram7.jpg | 500 px]]<br />
<br />
The sensor, sensitivity tuner, and colour should be viewed as separate parts that are pieced together to build a tunable biosensor that utilizes colour as output. The Parts Registry already has an impressive selection of parts that can be used as sensors. The Cambridge 2009 iGEM team focused on developing a selection of different sensitivity tuner parts and a selection of different pigment producing parts. <br />
<br />
*'''Sensitivity Tuner''': These constructs are based on Cambridge 2007's amplifiers. The general construct is composed of a gene coding for a phage activator protein and a phage activator-sensitive promoter. With PoPS input, the phage activator gene is transcribed. After translation to produce the phage activator protein, the protein binds to the phage activator-sensitive promoter to activate transcription. Thus it is a device that generates a distinct PoPS out given a PoPS in. With an input-sensitive promoter alone, output generally varies linearly with input--this, at least, is the case with the arabinose-sensitive promoter pBad/Arac (BBa_I0500). However, when a sensitivity tuner is placed downstream of the input-sensitive promoter, the output versus input behavior is altered such that output increases dramatically at a certain input, resulting in sigmoidal behavior with a distinctive threshold. <br />
<br />
*'''Colour Generator''': Though ''E. coli'' does not naturally produce pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most promising candidates into ''E. coli''.<br />
<br />
===Kits of Parts===<br />
<br />
The culmination of our project was to generate and characterize two kits of of parts - one of Sensitivity Tuners and one of Colour Generators.<br />
<br />
'''Sensitivity Tuners''': There are 3 different activator genes and 5 different activator-sensitive promoters in the registry. 15 combinations are possible, and each has a distinct threshold and peak rate of output. The table below summarizes the parts we designed and characterised:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
'''Colour Generators''': We have devoted our summer to 3 different pigment systems: <br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce violet and two shades of green<br />
<br />
We designed and characterised the following biobricks:<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
<br />
Potential exists to expand both of these kits of parts further using more phage activators and phage promoters that are not yet in the registry <br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/ProjectTeam:Cambridge/Project2009-10-21T23:44:55Z<p>Vmullin: /* Design */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Project =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Abstract | Introduction ]]<br />
[[#Project Details | Project Details]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The E. Chromi project strived to facilitate biosensor design and construction. We designed and characterised two types of parts - Sensitivity Tuners and Colour Generators. The availability of these parts on the registry could revolutionize biosensor design in the future - when new promoters that sense novel inputs are characterized and submitted to the registry, Sensitivity Tuners and Colour Generators can be implemented to tune the sensitivity of the promoter to detect a concentration appropriate to the biosensor's desired application, and to report the presence of an inducer in a cheap, user-friendly fashion.<br />
<br />
===Improving Biosensors===<br />
<br />
The Parts Registry's repertoire of input-sensitive devices is incredibly varied. Teams have engineered ''E. coli'' to be sensitive to a wide range of environmentally significant compounds, including arsenic, mercury, lead, cyanide, etc., to genetically engineer biosensors as an alternative to other technologies. The Cambridge 2009 iGEM team identified two stumbling blocks to biosensor design. <br />
<br />
*'''Output''': Previous iGEM biosensor projects have used pH, electrical conductance, and fluorescence as output. However, these reporter mechanisms require further steps to read the output. While this is acceptable for First World applications, for biosensors to have true Third World applications, a simpler output is necessary.<br />
<br />
*'''Response to Input''': By utilizing an input-sensitive promoter, the biosensor is limited by the sensitivity of the promoter. For example, the promoter might be sensitive to input concentrations which have no real world meaning. The promoter's sensitivity could be too high, so it reports concentrations below levels of real-world interest. Alternately, the promoter's sensitivity could be too low, so it reports concentrations above those which mark the boundary between "safe" and "dangerous." A second limitation is the the behavior of the PoPS output from the promoter; for example, output may vary linearly with input. This type of response is incompatible with a digital "safe" or "dangerous" output.<br />
<br />
===Our Solutions===<br />
<br />
*'''A Sensitivity Tuner''': To avoid being limited to the sensitivity of the promoter and in order to be able to detect distinct concentrations of an inducer using just one promoter, we see the need for a set of sensitivity tuners. These devices allow you to "tune" your biosensor, such that it reports meaningful concentrations of the inducer appropriate to the biosensor's application. The sensitivity tuner also modifies the PoPS output from the promoter's native behavior to a sigmoidal "on" or "off" response pattern.<br />
*'''Colour Output''': What if we could "see" the concentration of an inducer in a sample by a change in colour of the biosensor? Many prey species are brightly coloured, showing off clearly the fact that they are poisonous or otherwise harmful to potential predators, a phenomenon known as aposematism or warning colouration. Humans use colour as a means of conveying information as well - we can "see" if a child has a fever using a thermometer strip and we can "see" the pH of a solution using a pH indicator. Colour can be a meaningful but simple output solution for biosensors, adapting nature's idea of warning colouration.<br />
<br />
== Project Details==<br />
<br />
===Design===<br />
[[Image:Cambridge_prototype5.jpg|300px |thumb| The Product]]<br />
<br />
====The Product====<br />
<br />
<br />
<br />
We envisioned a marketable product that reports the concentration of an inducer by colour. Imagine a dipstick with wells, each of which contain pigment-expressing bacteria in response to an inducer. However, each strain is sensitive to a different concentration of the inducer. The concentration of the inducer in the test solution can be determined by reading the pattern of pigmentation.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Image:Cambridge_newGenericdevicE2.jpg|400px |thumb| The Genetically Engineered Machine]]<br />
====The Genetically Engineered Machine====<br />
<br />
Each bacterial strain is a machine built from a three part system. <br />
<br />
*'''Sensor''': The sensor system is sensitive to different concentrations of an inducer.<br />
<br />
*'''Sensitivity Tuner''': This device is responsible for the setting the sensitivity to the inducer, and acts as an "on" switch to activate pigment production once the inducer has reached a threshold.<br />
<br />
*'''Colour Generator''': Responsible for pigment production.<br />
<br />
===Components===<br />
<br />
The three part system can be abstracted by the diagram below:<br />
<br />
[[Image:abstraction6.jpg | 500 px]]<br />
<br />
The components of each of the black boxes is as follows:<br />
<br />
[[Image:Cambridge_systemdiagram7.jpg | 500 px]]<br />
<br />
The sensor, sensitivity tuner, and colour should be viewed as separate parts that are pieced together to build a tunable biosensor that utilizes colour as output. The Parts Registry already has an impressive selection of parts that can be used as sensors. The Cambridge 2009 iGEM team focused on developing a selection of different sensitivity tuner parts and a selection of different pigment producing parts. <br />
<br />
*'''Sensitivity Tuner''': These constructs are based on Cambridge 2007's amplifiers. The general construct is composed of a gene coding for a phage activator protein and a phage activator-sensitive promoter. With PoPS input, the phage activator gene is transcribed. After translation to produce the phage activator protein, the protein binds to the phage activator-sensitive promoter to activate transcription. Thus it is a device that generates a distinct PoPS out given a PoPS in. With an input-sensitive promoter alone, output generally varies linearly with input--this, at least, is the case with the arabinose-sensitive promoter pBad/Arac (BBa_I0500). However, when a sensitivity tuner is placed downstream of the input-sensitive promoter, the output versus input behavior is altered such that output increases dramatically at a certain input, resulting in sigmoidal behavior with a distinctive threshold. <br />
<br />
*'''Colour Generator''': Though ''E. coli'' does not naturally produce pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most promising candidates into ''E. coli''.<br />
<br />
===Kits of Parts===<br />
<br />
The culmination of our project was to generate and characterize two kits of of parts - one of Sensitivity Tuners and one of Colour Generators.<br />
<br />
'''Sensitivity Tuners''': There are 3 different activator genes and 5 different activator-sensitive promoters in the registry. 15 combinations are possible, and each has a distinct threshold and peak rate of output. The table below summarizes the parts we designed and characterised:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
'''Colour Generators''': We have devoted our summer to 3 different pigment systems: <br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce violet and two shades of green<br />
<br />
We designed and characterised the following biobricks:<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
<br />
Potential exists to expand both of these kits of parts further using more phage activators and phage promoters that are not yet in the registry <br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/ProjectTeam:Cambridge/Project2009-10-21T23:43:30Z<p>Vmullin: /* Design */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Project =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Abstract | Introduction ]]<br />
[[#Project Details | Project Details]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The E. Chromi project strived to facilitate biosensor design and construction. We designed and characterised two types of parts - Sensitivity Tuners and Colour Generators. The availability of these parts on the registry could revolutionize biosensor design in the future - when new promoters that sense novel inputs are characterized and submitted to the registry, Sensitivity Tuners and Colour Generators can be implemented to tune the sensitivity of the promoter to detect a concentration appropriate to the biosensor's desired application, and to report the presence of an inducer in a cheap, user-friendly fashion.<br />
<br />
===Improving Biosensors===<br />
<br />
The Parts Registry's repertoire of input-sensitive devices is incredibly varied. Teams have engineered ''E. coli'' to be sensitive to a wide range of environmentally significant compounds, including arsenic, mercury, lead, cyanide, etc., to genetically engineer biosensors as an alternative to other technologies. The Cambridge 2009 iGEM team identified two stumbling blocks to biosensor design. <br />
<br />
*'''Output''': Previous iGEM biosensor projects have used pH, electrical conductance, and fluorescence as output. However, these reporter mechanisms require further steps to read the output. While this is acceptable for First World applications, for biosensors to have true Third World applications, a simpler output is necessary.<br />
<br />
*'''Response to Input''': By utilizing an input-sensitive promoter, the biosensor is limited by the sensitivity of the promoter. For example, the promoter might be sensitive to input concentrations which have no real world meaning. The promoter's sensitivity could be too high, so it reports concentrations below levels of real-world interest. Alternately, the promoter's sensitivity could be too low, so it reports concentrations above those which mark the boundary between "safe" and "dangerous." A second limitation is the the behavior of the PoPS output from the promoter; for example, output may vary linearly with input. This type of response is incompatible with a digital "safe" or "dangerous" output.<br />
<br />
===Our Solutions===<br />
<br />
*'''A Sensitivity Tuner''': To avoid being limited to the sensitivity of the promoter and in order to be able to detect distinct concentrations of an inducer using just one promoter, we see the need for a set of sensitivity tuners. These devices allow you to "tune" your biosensor, such that it reports meaningful concentrations of the inducer appropriate to the biosensor's application. The sensitivity tuner also modifies the PoPS output from the promoter's native behavior to a sigmoidal "on" or "off" response pattern.<br />
*'''Colour Output''': What if we could "see" the concentration of an inducer in a sample by a change in colour of the biosensor? Many prey species are brightly coloured, showing off clearly the fact that they are poisonous or otherwise harmful to potential predators, a phenomenon known as aposematism or warning colouration. Humans use colour as a means of conveying information as well - we can "see" if a child has a fever using a thermometer strip and we can "see" the pH of a solution using a pH indicator. Colour can be a meaningful but simple output solution for biosensors, adapting nature's idea of warning colouration.<br />
<br />
== Project Details==<br />
<br />
===Design===<br />
[[Image:Cambridge_prototype5.jpg|400px |thumb| right| The Product]]<br />
<br />
====The Product====<br />
<br />
<br />
<br />
We envisioned a marketable product that reports the concentration of an inducer by colour. Imagine a dipstick with wells, each of which contain pigment-expressing bacteria in response to an inducer. However, each strain is sensitive to a different concentration of the inducer. The concentration of the inducer in the test solution can be determined by reading the pattern of pigmentation.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Image:Cambridge_newGenericdevicE2.jpg|400px |thumb| right| The Genetically Engineered Machine]]<br />
====The Genetically Engineered Machine====<br />
<br />
Each bacterial strain is a machine built from a three part system. <br />
<br />
*'''Sensor''': The sensor system is sensitive to different concentrations of an inducer.<br />
<br />
*'''Sensitivity Tuner''': This device is responsible for the setting the sensitivity to the inducer, and acts as an "on" switch to activate pigment production once the inducer has reached a threshold.<br />
<br />
*'''Colour Generator''': Responsible for pigment production.<br />
<br />
===Components===<br />
<br />
The three part system can be abstracted by the diagram below:<br />
<br />
[[Image:abstraction6.jpg | 500 px]]<br />
<br />
The components of each of the black boxes is as follows:<br />
<br />
[[Image:Cambridge_systemdiagram7.jpg | 500 px]]<br />
<br />
The sensor, sensitivity tuner, and colour should be viewed as separate parts that are pieced together to build a tunable biosensor that utilizes colour as output. The Parts Registry already has an impressive selection of parts that can be used as sensors. The Cambridge 2009 iGEM team focused on developing a selection of different sensitivity tuner parts and a selection of different pigment producing parts. <br />
<br />
*'''Sensitivity Tuner''': These constructs are based on Cambridge 2007's amplifiers. The general construct is composed of a gene coding for a phage activator protein and a phage activator-sensitive promoter. With PoPS input, the phage activator gene is transcribed. After translation to produce the phage activator protein, the protein binds to the phage activator-sensitive promoter to activate transcription. Thus it is a device that generates a distinct PoPS out given a PoPS in. With an input-sensitive promoter alone, output generally varies linearly with input--this, at least, is the case with the arabinose-sensitive promoter pBad/Arac (BBa_I0500). However, when a sensitivity tuner is placed downstream of the input-sensitive promoter, the output versus input behavior is altered such that output increases dramatically at a certain input, resulting in sigmoidal behavior with a distinctive threshold. <br />
<br />
*'''Colour Generator''': Though ''E. coli'' does not naturally produce pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most promising candidates into ''E. coli''.<br />
<br />
===Kits of Parts===<br />
<br />
The culmination of our project was to generate and characterize two kits of of parts - one of Sensitivity Tuners and one of Colour Generators.<br />
<br />
'''Sensitivity Tuners''': There are 3 different activator genes and 5 different activator-sensitive promoters in the registry. 15 combinations are possible, and each has a distinct threshold and peak rate of output. The table below summarizes the parts we designed and characterised:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
'''Colour Generators''': We have devoted our summer to 3 different pigment systems: <br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce violet and two shades of green<br />
<br />
We designed and characterised the following biobricks:<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
<br />
Potential exists to expand both of these kits of parts further using more phage activators and phage promoters that are not yet in the registry <br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME02Team:Cambridge/Project/ME022009-10-21T23:35:41Z<p>Vmullin: /* Constructing the BioBrick */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design==<br />
<br />
<br />
<br />
===Constructing the BioBrick===<br />
<br />
'''Biobrick'''<br />
<br />
Our aim is to make the MelA gene into a biobrick as follows:<br />
<br />
[[Image:MelAbiobrick.jpg]]<br />
<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274001</partinfo><br />
|Reporter<br />
|''''MelA'''. The gene (melA) codes for a tyrosinase which produces a dark brown pigment from L-tyrosine. Production of the pigment requires the addition of copper and L-tyrosine supplements (the copper acts as a cofactor for the gene product) but no other precursors. The BioBrick sequence includes the native ribosome binding site. <br />
| 1844bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
In order to do so, we had to remove forbidden restriction sites within the gene using primers and the in-fusion PCR technique. Primers were ordered as shown by the image below, to add the prefix and suffix and change the PstI restriction site from CTGCAG to CTGCAA:<br />
<br />
[[Image:MelA primer map.JPG]]<br />
<br />
The PCR's will be done in the following steps, in order to remove both sites and prepare the gene as a biobrick:<br />
<br />
[[Image:MelA.png]]<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME02Team:Cambridge/Project/ME022009-10-21T23:35:22Z<p>Vmullin: /* Biobrick Parts */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design==<br />
<br />
<br />
<br />
===Constructing the BioBrick===<br />
<br />
'''Biobrick'''<br />
<br />
Our aim is to make the MelA gene into a biobrick as follows:<br />
<br />
[[Image:MelAbiobrick.jpg]]<br />
<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274001</partinfo><br />
|Reporter<br />
|''''MelA'''. The gene (melA) codes for a tyrosinase which produces a dark brown pigment from L-tyrosine. Production of the pigment requires the addition of copper and L-tyrosine supplements (the copper acts as a cofactor for the gene product) but no other precursors. The BioBrick sequence includes the native ribosome binding site. <br />
| 1844bpbp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
In order to do so, we had to remove forbidden restriction sites within the gene using primers and the in-fusion PCR technique. Primers were ordered as shown by the image below, to add the prefix and suffix and change the PstI restriction site from CTGCAG to CTGCAA:<br />
<br />
[[Image:MelA primer map.JPG]]<br />
<br />
The PCR's will be done in the following steps, in order to remove both sites and prepare the gene as a biobrick:<br />
<br />
[[Image:MelA.png]]<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME02Team:Cambridge/Project/ME022009-10-21T23:35:07Z<p>Vmullin: /* Constructing the BioBrick */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design==<br />
<br />
<br />
<br />
===Constructing the BioBrick===<br />
<br />
'''Biobrick'''<br />
<br />
Our aim is to make the MelA gene into a biobrick as follows:<br />
<br />
[[Image:MelAbiobrick.jpg]]<br />
<br />
===Biobrick Parts===<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274001</partinfo><br />
|Reporter<br />
|''''MelA'''. The gene (melA) codes for a tyrosinase which produces a dark brown pigment from L-tyrosine. Production of the pigment requires the addition of copper and L-tyrosine supplements (the copper acts as a cofactor for the gene product) but no other precursors. The BioBrick sequence includes the native ribosome binding site. <br />
| 1844bpbp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
In order to do so, we had to remove forbidden restriction sites within the gene using primers and the in-fusion PCR technique. Primers were ordered as shown by the image below, to add the prefix and suffix and change the PstI restriction site from CTGCAG to CTGCAA:<br />
<br />
[[Image:MelA primer map.JPG]]<br />
<br />
The PCR's will be done in the following steps, in order to remove both sites and prepare the gene as a biobrick:<br />
<br />
[[Image:MelA.png]]<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/PigmentsTeam:Cambridge/Project/Pigments2009-10-21T23:26:49Z<p>Vmullin: /* Choosing Pigments */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Colour Generators =<br />
<br />
==The Kit of Parts==<br />
<br />
The Cambridge 2009 iGEM team searched far and wide to find suitable pigments that could be used as outputs. Though ''E. coli'' does not naturally produce any pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most prominent candidates into ''E. coli''. In particular, we have devoted our summer to 3 different pigment systems:<br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
[[Image:Cam09_ca1.jpg|300px]][[Image:Cam09_ca2.jpg|300px]]<br />
<br />
<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
[[Image:SDC105451.JPG|400px]]<br />
<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce voilet, green, and blue.<br />
[[Image:Cam09_vio.jpg|300px]][[Image:Cam09_gre.jpg|300px]]<br />
<br />
As as a result of our efforts, this summer, we have submitted the following biobricks to the Registry. We hope that in the future this this kit of parts will be expanded in the future.<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
==Choosing Pigments==<br />
<br />
We chose to pursue these 3 pigment systems for two main reasons.<br />
'''Visual Diversity''': Not only do these devices come from different bacterial species, but between these systems we've almost made -- as cheesey as it sounds -- all the colours of the rainbow.<br />
<br />
[[Image:RAINBOW.png|700px]]<br />
<br />
'''Design''': We were able to use a variety of different techniques to build and design these pigment systems as biobricks. The carotenoid parts were already in the Registry, and were used standard assembly protocols to build pigment producing devices. The melanin system is a single gene which we endeavoured to turn into a biobrick by PCR. Finally, we designed the violacein operon for synthesis, codon optimizing it for both E. coli and B. subtilis and designing it so it is easy to manipulate to generate different pigments.<br />
<br />
'''Potential for Gene Manipulation''': The melanin system is particularly elegant in that a single gene is able to generate pigment as long as the bacteria are supplemented with copper and tyrosine. On the flip side, the carotenoid and violacein systems are multi-gene operons that make more than one pigment each. Further, they generate pigments without any supplements to the media.<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/PigmentsTeam:Cambridge/Project/Pigments2009-10-21T23:26:25Z<p>Vmullin: /* Choosing Pigments */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Colour Generators =<br />
<br />
==The Kit of Parts==<br />
<br />
The Cambridge 2009 iGEM team searched far and wide to find suitable pigments that could be used as outputs. Though ''E. coli'' does not naturally produce any pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most prominent candidates into ''E. coli''. In particular, we have devoted our summer to 3 different pigment systems:<br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
[[Image:Cam09_ca1.jpg|300px]][[Image:Cam09_ca2.jpg|300px]]<br />
<br />
<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
[[Image:SDC105451.JPG|400px]]<br />
<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce voilet, green, and blue.<br />
[[Image:Cam09_vio.jpg|300px]][[Image:Cam09_gre.jpg|300px]]<br />
<br />
As as a result of our efforts, this summer, we have submitted the following biobricks to the Registry. We hope that in the future this this kit of parts will be expanded in the future.<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
==Choosing Pigments==<br />
<br />
We chose to pursue these 3 pigment systems for two main reasons.<br />
'''Visual Diversity''': Not only do these devices come from different bacterial species, but between these systems we've almost made -- as cheesey as it sounds -- all the colours of the rainbow.<br />
[[Image:RAINBOW.png|700px]]<br />
<br />
'''Design''': We were able to use a variety of different techniques to build and design these pigment systems as biobricks. The carotenoid parts were already in the Registry, and were used standard assembly protocols to build pigment producing devices. The melanin system is a single gene which we endeavoured to turn into a biobrick by PCR. Finally, we designed the violacein operon for synthesis, codon optimizing it for both E. coli and B. subtilis and designing it so it is easy to manipulate to generate different pigments.<br />
<br />
'''Potential for Gene Manipulation''': The melanin system is particularly elegant in that a single gene is able to generate pigment as long as the bacteria are supplemented with copper and tyrosine. On the flip side, the carotenoid and violacein systems are multi-gene operons that make more than one pigment each. Further, they generate pigments without any supplements to the media.<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/PigmentsTeam:Cambridge/Project/Pigments2009-10-21T23:24:47Z<p>Vmullin: /* Colour Generators */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Colour Generators =<br />
<br />
==The Kit of Parts==<br />
<br />
The Cambridge 2009 iGEM team searched far and wide to find suitable pigments that could be used as outputs. Though ''E. coli'' does not naturally produce any pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most prominent candidates into ''E. coli''. In particular, we have devoted our summer to 3 different pigment systems:<br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
[[Image:Cam09_ca1.jpg|300px]][[Image:Cam09_ca2.jpg|300px]]<br />
<br />
<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
[[Image:SDC105451.JPG|400px]]<br />
<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce voilet, green, and blue.<br />
[[Image:Cam09_vio.jpg|300px]][[Image:Cam09_gre.jpg|300px]]<br />
<br />
As as a result of our efforts, this summer, we have submitted the following biobricks to the Registry. We hope that in the future this this kit of parts will be expanded in the future.<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
==Choosing Pigments==<br />
<br />
We chose to pursue these 3 pigment systems for two main reasons.<br />
'''Visual Diversity''': Not only do these devices come from different bacterial species, but between these systems we've almost made -- as cheesey as it sounds -- all the colours of the rainbow.<br />
<br />
[[Image:RAINBOW.png|700px]]<br />
<br />
'''Design''': We were able to use a variety of different techniques to build and design these pigment systems as biobricks. The carotenoid parts were already in the Registry, and were used standard assembly protocols to build pigment producing devices. The melanin system is a single gene which we endeavoured to turn into a biobrick by PCR. Finally, we designed the violacein operon for synthesis, codon optimizing it for both E. coli and B. subtilis and designing it so it is easy to manipulate to generate different pigments.<br />
<br />
'''Potential for Gene Manipulation''': The melanin system is particularly elegant in that a single gene is able to generate pigment as long as the bacteria are supplemented with copper and tyrosine. On the flip side, the carotenoid and violacein systems are multi-gene operons that make more than one pigment each. Further, they generate pigments without any supplements to the media.<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/File:SDC105451.JPGFile:SDC105451.JPG2009-10-21T23:23:53Z<p>Vmullin: </p>
<hr />
<div></div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/PigmentsTeam:Cambridge/Project/Pigments2009-10-21T23:23:35Z<p>Vmullin: /* The Kit of Parts */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Colour Generators =<br />
<br />
==The Kit of Parts==<br />
<br />
The Cambridge 2009 iGEM team searched far and wide to find suitable pigments that could be used as outputs. Though ''E. coli'' does not naturally produce any pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most prominent candidates into ''E. coli''. In particular, we have devoted our summer to 3 different pigment systems:<br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
[[Image:Cam09_ca1.jpg|300px]][[Image:Cam09_ca2.jpg|300px]]<br />
<br />
<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
[[Image:SDC105451.JPG|600px]]<br />
<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce voilet, green, and blue.<br />
[[Image:Cam09_vio.jpg|300px]][[Image:Cam09_gre.jpg|300px]]<br />
<br />
As as a result of our efforts, this summer, we have submitted the following biobricks to the Registry. We hope that in the future this this kit of parts will be expanded in the future.<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
==Choosing Pigments==<br />
<br />
We chose to pursue these 3 pigment systems for two main reasons.<br />
'''Visual Diversity''': Not only do these devices come from different bacterial species, but between these systems we've almost made -- as cheesey as it sounds -- all the colours of the rainbow.<br />
<br />
[[Image:RAINBOW.png|700px]]<br />
<br />
'''Design''': We were able to use a variety of different techniques to build and design these pigment systems as biobricks. The carotenoid parts were already in the Registry, and were used standard assembly protocols to build pigment producing devices. The melanin system is a single gene which we endeavoured to turn into a biobrick by PCR. Finally, we designed the violacein operon for synthesis, codon optimizing it for both E. coli and B. subtilis and designing it so it is easy to manipulate to generate different pigments.<br />
<br />
'''Potential for Gene Manipulation''': The melanin system is particularly elegant in that a single gene is able to generate pigment as long as the bacteria are supplemented with copper and tyrosine. On the flip side, the carotenoid and violacein systems are multi-gene operons that make more than one pigment each. Further, they generate pigments without any supplements to the media.<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI03Team:Cambridge/Project/VI032009-10-21T23:19:26Z<p>Vmullin: /* Characterisation */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Characterisation ==<br />
<br />
=== Proof of pigment production===<br />
'''Successful Pigment Production'''<br />
<br />
We transformed Top10 with pPSX-Vio+. After three colour eventually appeared, as shown below. Interestingly, the pigment appears to remain within the bacteria, with little or no bleeding into the media. We took the violacein pigment bacteria (right plate in photo) out of the fridge to find that the purple colour had started to develop. They were therefore left at room temperature overnight. The colour appears to be within the bacteria, with little or no bleeding into the media. The control plate (left plate) is the untransformed TOP10 ''E. coli''.<br />
<br />
[[Image:Cambridge Violacein Pigment.jpg | 300px]]<br />
<br />
Left: control plate - untransformed TOP10 E. coli, Right: Top10 transformed with pPSX-Vio+.<br />
<br />
'''Multiple Pigment Production from the Violacein operon'''<br />
<br />
Top10 transformed with the DNA we received from DNA2.0 showed vibrant pigment production.<br />
<br />
[[Image:Cam09_vio.jpg|300px]][[Image:Cam09_vio1.jpg|300px]]<br />
<br />
Left: Violacein growth on agar plate (overnight). Right: Single colonies.<br />
<br />
Further, we were able to remove VioC or VioD from the operon to produce a green pigment.<br />
<br />
<br />
[[Image:Cam09_gre.jpg|300px]][[Image:Cam09_gre1.jpg|300px]]<br />
<br />
Left: Lawn of green bacteria on agar plate (overnight), derived by removing one gene from the violacein cassette. Right: Green colonies on agar plate.<br />
<br />
=== Characterisation of colour output ===<br />
<br />
We characterised the violacein pigment by carrying out the acetone extraction protocol used for carotene. The results were normalised for OD and then plotted as a graph of absorption units against wavelength:<br />
<br />
[[Image:Vio wavelength graph.JPG]]<br />
<br />
We also looked at absorbance at 584nm (the maximum absorbance for violacein):<br />
<br />
[[Image:Vio absorbance.JPG]]<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/PigmentsTeam:Cambridge/Project/Pigments2009-10-21T23:10:43Z<p>Vmullin: /* Choosing Pigments */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Colour Generators =<br />
<br />
==The Kit of Parts==<br />
<br />
The Cambridge 2009 iGEM team searched far and wide to find suitable pigments that could be used as outputs. Though ''E. coli'' does not naturally produce any pigment, several other bacterial species secrete pigmented antibiotics. We mined bacterial genomes for pigment-producing operons, and transformed the most prominent candidates into ''E. coli''. In particular, we have devoted our summer to 3 different pigment systems:<br />
:*'''[[Team:Cambridge/Project/CA01 |Carotenoids]]''': The enzymes required for carotenoid production originally come from ''Pantoea ananatis,'' and were available in the registry. We used them to produce orange and red.<br />
:*'''[[Team:Cambridge/Project/ME01 |Melanin]]''': The tyrosinase required for melanin production originally comes from ''Rhizobium etli'' and produces brown.<br />
:*'''[[Team:Cambridge/Project/VI01 |Violacein]]''': The enzymes required for voilacein production originally come from ''Chromobacterium violacein.'' The operon can be manipulated to produce voilet, green, and blue.<br />
<br />
As as a result of our efforts, this summer, we have submitted the following biobricks to the Registry. We hope that in the future this this kit of parts will be expanded in the future.<br />
<br />
{|border="1" cellpadding="5"<br />
|-<br />
!Biobrick<br />
!Colour<br />
<br />
|-<br />
|<partinfo>BBa_K274100</partinfo><br />
|Red<br />
<br />
|-<br />
|<partinfo>BBa_K274200</partinfo><br />
|Orange<br />
<br />
|-<br />
|<partinfo>BBa_K274001</partinfo><br />
|Brown<br />
<br />
|-<br />
|<partinfo>BBa_K274002</partinfo><br />
|Violet<br />
<br />
|-<br />
|<partinfo>BBa_K274003</partinfo><br />
|Dark Green<br />
<br />
|-<br />
|<partinfo>BBa_K274004</partinfo><br />
|Light Green<br />
<br />
|}<br />
<br />
==Choosing Pigments==<br />
<br />
We chose to pursue these 3 pigment systems for two main reasons.<br />
'''Visual Diversity''': Not only do these devices come from different bacterial species, but between these systems we've almost made -- as cheesey as it sounds -- all the colours of the rainbow.<br />
<br />
[[Image:RAINBOW.png|700px]]<br />
<br />
'''Design''': We were able to use a variety of different techniques to build and design these pigment systems as biobricks. The carotenoid parts were already in the Registry, and were used standard assembly protocols to build pigment producing devices. The melanin system is a single gene which we endeavoured to turn into a biobrick by PCR. Finally, we designed the violacein operon for synthesis, codon optimizing it for both E. coli and B. subtilis and designing it so it is easy to manipulate to generate different pigments.<br />
<br />
'''Potential for Gene Manipulation''': The melanin system is particularly elegant in that a single gene is able to generate pigment as long as the bacteria are supplemented with copper and tyrosine. On the flip side, the carotenoid and violacein systems are multi-gene operons that make more than one pigment each. Further, they generate pigments without any supplements to the media.<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/ImageGallery/TEAMTeam:Cambridge/ImageGallery/TEAM2009-10-21T23:09:17Z<p>Vmullin: /* Images / Team */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
=Images / Team=<br />
<br />
During our summer doing iGEM we had several workshops designed to hone our presentation skills, catch everyone up on the details of Synthetic biology, and encourage us to think outside the box to consider the far-reaching implications of project, especially for pigments. <br />
<br />
== Preparing the Presentation ==<br />
<br />
October 2009: The team gathers at the house of Jim Haseloff to give a preliminary run of our presentation. We then have a brainstorming session with James King on artistic uses of our pigment producing bacteria.<br />
<br />
<html><object width='720' height='700'><param name='movie' value='http://www.slideflickr.com/slide/UkIo82fp'></param><param name='wmode' value='transparent'></param><embed src='http://www.slideflickr.com/slide/UkIo82fp' type='application/x-shockwave-flash' wmode='transparent' width='720' height='700'></embed></object></html><br />
<br />
== Colour Futures Workshop ==<br />
<br />
August 2009: In the Colours Future workshop (organised by Daisy Ginsburg and James King from the Royal College of Art) we concentrated on our various pigments, considering how the ability to exploit pigments from the natural world--not just from bacteria, but from plants and animals--might affect the world we live in. What if pigments are used as reporters for applications beyond bacterial biosensors? What if we harnessed natural pigments and used them to artificially colour the world, even ourselves? What ramifications might these leaps and bounds have? <br />
<br />
<br />
== Part of 2 week course - Dragon's Den Challenge ==<br />
<br />
Mid-July 2009 - At the end of the 2 week intro course, particpants tried their hand at designing a real world application for a synthetic biology project, then tried to market it to a panel of judges reluctant to give out money. The idea is based on a [http://www.bbc.co.uk/dragonsden/ TV show by the BBC] if you are not familiar with it.<br />
<br />
<html><object width='720' height='700'><param name='movie' value='http://www.slideflickr.com/slide/THKHn3HP'></param><param name='wmode' value='transparent'></param><embed src='http://www.slideflickr.com/slide/THKHn3HP' type='application/x-shockwave-flash' wmode='transparent' width='720' height='700'></embed></object></html><br />
<br />
== Our 2 week crash course in Synthetic Biology ==<br />
<br />
Beginning of July 2009 - The 7 iGEM team members and other students from the Royal College of Art, London School of Economics, and Cambridge gather at the Haseloff Lab, Cambridge for a 2 week introduction to Synthetic Biology and iGEM.<br />
<br />
<html><object width='720' height='700'><param name='movie' value='http://www.slideflickr.com/slide/8rpZTcoD'></param><param name='wmode' value='transparent'></param><embed src='http://www.slideflickr.com/slide/8rpZTcoD' type='application/x-shockwave-flash' wmode='transparent' width='720' height='700'></embed></object></html><br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/Amplification/CharacterisationTeam:Cambridge/Project/Amplification/Characterisation2009-10-21T23:00:58Z<p>Vmullin: /* The Sensitivity Tuner */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= The Sensitivity Tuner =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Introduction | Introduction ]]<br />
[[#Characterisation | Characterisation]]<br />
[[# Data| Data]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The Cambridge 2007 iGEM team build 15 "amplifiers," constructs with RFP and GFP reporters that amplified the PoPS output of the promoter pBad/AraC (<partinfo>BBa_I0500</partinfo>), as described below:<br />
<br />
[[Image:amplifier07.jpg]]<br />
<br />
We re-designed these constructs to be PoPS converters as follows...<br />
<br />
[[Image:thresholddevice3.jpg]] <br />
<br />
...and generated our own set of Sensitivity Tuners:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
<br />
In order to characterize these phage activator/promoter constructs, we used the corresponding Cambridge 2007 amplifier as an illustration of how our Sensitivity Tuners alter the behaviour of pBad/AraC. These parts are very useful for characterisation as they contain fluorescent reporters; the parts we designed, which lack an input promoter and fluorescent reporters, are more useful parts for other iGEM teams to incorporate into their own projects. <br />
<br />
== Characterisation ==<br />
<br />
For characterisation, we moved the Cambridge 2007 amplifiers onto a low copy plasmid in order to make meaningful comparisons with <partinfo>BBa_J69591</partinfo>, the standard promoter. We looked at a few major characteristics relating input (arabinose) to output (GFP) and how they are modified compared to pBad/AraC on its own.<br />
<br />
[[Image:characterization3.jpg]]<br />
<br />
For our characterization assay, we transformed the ''E. coli'' strain BW27783 with the Cambridge 2007 amplifiers (biobricks summarised in the table below):<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_I746370</partinfo> || <partinfo>BBa_I746380</partinfo>||<partinfo>BBa_I746390</partinfo><br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_I746371</partinfo><br />
|<partinfo>BBa_I746381</partinfo><br />
|<partinfo>BBa_I746391</partinfo><br />
|-<br />
! PP promoter<br />
|<partinfo>BBa_I746372</partinfo><br />
|<partinfo>BBa_I746382</partinfo><br />
|<partinfo>BBa_I746392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_I746374</partinfo><br />
|<partinfo>BBa_I746384</partinfo><br />
|<partinfo>BBa_I746394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_I746375</partinfo><br />
|<partinfo>BBa_I746385</partinfo><br />
|<partinfo>BBa_I746395</partinfo><br />
|}<br />
<br />
The BW27783 strain is ideal for assays using arabinose as it expresses arabinose transporters in the membrane constitutively (rather than in response to the detection of arabinose) and is unable to metabolise arabinose. We used a standard assay for each construct. We characterised cultures transformed with the amplifier constructs in exponential phase at the following arabinose concentrations: 0, 0.1, 0.5, 1, 10, 50, 100, and 500 uM. The controls that we ran for each assay included LB, untransformed BW27783, and J59691, the standard promoter. With the data we gathered, we were able to update the Registry pages of the Cambridge 2007 amplifiers, and also illustrated the ability of our Sensitivity Tuners to modulate the transcriptional system downstream of pBad/AraC.<br />
<br />
==Data==<br />
<br />
=== Maximum Rates against Arabinose Concentrations ===<br />
<br />
==== 80 ====<br />
[[Image:Cambridge_maxrates1.jpg | 600px]]<br />
<br />
==== 81 ====<br />
[[Image:Cambridge_maxrates2.jpg | 600px]]<br />
<br />
==== 82 ====<br />
[[Image:Cambridge_maxrates3.jpg | 600px]]<br />
<br />
==== 84 ====<br />
[[Image:Cambridge_maxrates4.jpg | 600px]]<br />
<br />
==== 85 ====<br />
[[Image:Cambridge_maxrates5.jpg | 600px]]<br />
<br />
==== 90 ====<br />
[[Image:Cambridge_maxrates6.jpg | 600px]]<br />
<br />
==== 92 ====<br />
[[Image:Cambridge_maxrates7.jpg | 600px]]<br />
<br />
==== 94 ====<br />
[[Image:Cambridge_maxrates8.jpg | 600px]]<br />
<br />
==== 95 ====<br />
[[Image:Cambridge_maxrates9.jpg | 600px]]<br />
<br />
<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/AmplificationTeam:Cambridge/Project/Amplification2009-10-21T22:45:13Z<p>Vmullin: /* Sensitivity Tuners */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Sensitivity Tuners =<br />
<br />
==Previous Work==<br />
<br />
Part of the iGEM mission is to build on previous projects. The Cambridge 2007 iGEM team developed a PoPS amplifier system using phage activators and promoters. The system works by using a PoPS input to make an activator protein, as shown in the diagram from their wiki below, which then binds to a promoter and generates a PoPS output. <br />
<br />
[[Image:amplifier07.jpg]]<br />
<br />
<br />
In order to quantify the ratio between PoPS in and PoPS out, the team built the following construction on the high copy plasmid pSB1A2, with mRFP and GFP as PoPS reporter. They genenerated 15 total combinations of different activators and promoters.<br />
<br />
In addition to analysing the characteristics of the Cambridge 2007 constructs, we looked at [https://2009.igem.org/Team:Cambridge/Modelling models] of alternatives ways to alter the sensitivity of a promoter<br />
<br />
[[Image:construction07.jpg]]<br />
<br />
<br />
They successfully quantified the PoPS amplification factors for each activator/promoter combination after arabinose induction.<br />
<br />
==Kit of Parts==<br />
<br />
The Cambridge 2009 team analyzed the properties of these constructs, paying particular attention to how adding phage activator and promoter combinations downstream of pBad altered the behaviour of pBad. In particular, it caught our attention that the phage activator and promoter combinations changed the sensitivity of pBad. We sought to thoroughly characterise each combination to generate a useful description of each so that future iGEM teams seeking to build biosensors can easily identify which combination is appropriate, depending on how they desire to manipulate their chosen promoter. Further, we redesigned the 2007 team's constructs, removing the fluorescent reporter genes used for characterisation, as follows:<br />
<br />
[[Image:thresholddevice3.jpg]] = [[Image:converter.jpg]] <br />
<br />
The table summarizes the Sensitivity Tuners we designed and characterised: <br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/AmplificationTeam:Cambridge/Project/Amplification2009-10-21T22:32:01Z<p>Vmullin: /* Previous Work */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= Sensitivity Tuners =<br />
<br />
==Previous Work==<br />
<br />
Part of the iGEM mission is to build on previous projects. The Cambridge 2007 iGEM team developed a PoPS amplifier system using phage activators and promoters. The system works by using a PoPS input to make an activator protein, as shown in the diagram from their wiki below, which then binds to a promoter and generates a PoPS output. <br />
<br />
[[Image:amplifier07.jpg]]<br />
<br />
<br />
In order to quantify the ratio between PoPS in and PoPS out, the team built the following construction on the high copy plasmid pSB1A2, with mRFP and GFP as PoPS reporter. They genenerated 15 total combinations of different activators and promoters.<br />
<br />
In addition to analysing the characteristics of the Cambridge 2007 constructs, we looked at [https://2009.igem.org/Team:Cambridge/Modelling | models] of alternatives ways to alter the sensitivity of a promoter<br />
<br />
[[Image:construction07.jpg]]<br />
<br />
<br />
They successfully quantified the PoPS amplification factors for each activator/promoter combination after arabinose induction.<br />
<br />
==Kit of Parts==<br />
<br />
The Cambridge 2009 team analyzed the properties of these constructs, paying particular attention to how adding phage activator and promoter combinations downstream of pBad altered the behaviour of pBad. In particular, it caught our attention that the phage activator and promoter combinations changed the sensitivity of pBad. We sought to thoroughly characterise each combination to generate a useful description of each so that future iGEM teams seeking to build biosensors can easily identify which combination is appropriate, depending on how they desire to manipulate their chosen promoter. Further, we redesigned the 2007 team's constructs, removing the fluorescent reporter genes used for characterisation, as follows:<br />
<br />
[[Image:thresholddevice3.jpg]] = [[Image:converter.jpg]] <br />
<br />
The table summarizes the Sensitivity Tuners we designed and characterised: <br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/ModellingTeam:Cambridge/Modelling2009-10-21T22:27:05Z<p>Vmullin: /* Modelling */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
=Modelling=<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Introduction | Introduction ]]<br />
[[#Basic Phage Activators | Basic Phage Activators ]]<br />
[[#Extended Systems | Extended Systems ]]<br />
[[#Modelling Basics | Modelling Basics ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
This project focuses on novel outputs, for example, for environmental sensors. However, there is a need for an 'adaptor'; a middle section to the machine that takes an input and processes it. Our initial work was based around the development of an amplifier that permits a large output that is clearly visible. The next planned stage was the creation of a system that allows switching on of output at different calibrated input signal levels. Creating a model allows the feasibility of the proposed systems to be tested. A basic model of the original amplifier system was put forward, building on both our data and the Cambridge 2007 data. <br />
<br />
===Modelling the phage activator system===<br />
<br />
This is the basic 'amplifier' system that consists of an input sensitive promoter system,a protein activator and sensitive promoter. It can therefore be divided into two boxes, the approach taken in putting forward an initial model.<br />
<br />
====The pBAD promoter====<br />
An arabinose input acts as an inducer, permitting transcription, by binding the AraC transcription factor. This is a dual transcription factor; when unbound to arabinose a dimer restricts access of polymersase to reduce basal levels of transcription, upon binding arabinose the conformation changes and the dimer permits binding of polymerase. [[#References | [1]]]<br />
<br />
To model this situation, araC is first assumed to take the role of a repressor that reversibly binds and unbinds a site on the DNA. If it binds arabinose, it is sequestered and cannot bind the DNA. Here, an input function is created, after Alon [[#References | [2]]]. This gives the rate of transcription from the promoter dependent on the concentration of arabinose. Since mRNA is then translated at a roughly constant rate, it is related with a multiplicative constant to the rate of protein production, in this case activator and RFP.<br />
<br />
[[Image:Cambridge Eq1.gif | center]]<br />
<br />
This gives the rate of transcription as a function of X* which represents the concentration of active repressor, unbound to arabinose. B is the maximum rate of transcription, here this rate is when induced by arabinose at highest concentration. K_d is the dissociation constant (see modelling derivations). Parameters must be found by a parameter scan for sensible values or by comparing to already gathered data.<br />
<br />
The concentration of 'active' repressor is given as a function of arabinose concentration by:<br />
<br />
[[Image:Cambridge Eq2.gif | center]]<br />
<br />
where X^T is the total amount of araC available, bound or unbound. A is arabinose concentration. n is the number of arabinose molecules binding to each molecule of the repressor, and K is a binding constant. n was taken to be two by assuming that each araC dimer needs two molecules to be bound before it can permit transcription.<br />
<br />
<br />
Combining these two gives the overall input function, which has leaky transcription included at A = 0, seen in the actual results.<br />
<br />
====The Activator and its Promoter====<br />
<br />
This is based on a similar idea. Activator is made by transcription from pBAD, the mRNA is then translated (the potential time delays will be taken into account). The activity of the phage promoter is dependent on activator concentration according to:<br />
<br />
[[Image:Cambridge Eq3.gif | center ]]<br />
<br />
Assuming that translation rates remain constant, the rate of GFP and RFP production would be expected to be multiples of the above promoter activities/ input functions (which represent rate of transcription)<br />
<br />
The aim of this area of work is to fit the activator plate reader to curves in an attempt to better charactertise them in terms of hill function parameters after Canton [[#References | [3]]].<br />
<br />
===Making a Latch===<br />
<br />
A switch that remains on once stimulated would be useful if it was only necessary, say, to see if a hazardous contaminant had ever been present in a sample (it could still be there in low levels etc.). A method proposed is positive feedback; an activator placed downstream of its own promoter (as well as the reporter/ pigment) will, in theory, keep pigment production going. The rate of activator production from its own promoter is given in equation 3 above, which is dependent on activator concentration itself.<br />
<br />
===Modelling the proposed switching levels system===<br />
This idea was summarised in the diagram and discussion included in week 4 dry work:[[Image:Cambridge_thresholds.png ]]<br />
<br />
Most of these model systems will rely on the very basic equations outlined above, with extensions to add levels of complexity, such as the transport of arabinose into a cell. <br />
<br />
==Basic Phage Activators==<br />
<br />
The first step is to take a look at the preliminary data to try to find appropriate parameters. An overall aim for the modelling of this system is to refine the model to each component and attempt to predict how different combinations of components will behave. The data collection separates the promoter and activator by use of both RFP and GFP reporters.<br />
<br />
The basic model for the relationship between input concentration and GFP output rate of production is a Hill Function. The aim is to characterise each activator-promoter system and fit it to this basic model:<br />
<br />
[[Image:Cambridge_Eq3.gif | center]]<br />
<br />
The three parameters we require are the maximum output rate, the dissociation or binding constant and the hill coefficient.<br />
<br />
Having studied the behaviour of the actual phage activator systems we discovered that each construct 'switched on' at different input levels; they have different effective binding constants. This gives us the behaviour required for a threshold system without much further development.<br />
<br />
===Investigating the Model===<br />
<br />
Before data was available we changed parameters to investigate the effects and to check that our programs were working as expected. Week 6, in particular Tuesday, summarises this work.<br />
<br />
==Extended Systems==<br />
<br />
Despite the ability of the activator systems to switch on at different levels, before this was apparent an exercise in modelling different methods of achieving such a system was carried out. There were three proposed mechanisms for such a system. All are based on the presence of both a repressor and an activator of some form. <br />
* 1. Repressor and Activator bind at different sites, but transcription only occurs if the activator is bound alone.<br />
*2. The repressor and activator bind at different sites but the binding of one prevents binding of the other (by blocking the site for example). <br />
<br />
These assume that the repressor and activator are both transcription factors. In effect, these are bistable switches. <br />
<br />
*3. The activator (input of some form) prevents the production of a repressor that is otherwise continually expressed in the cell.<br />
<br />
Looking at the effects of changing parameters was carried out during weeks 6 and 7.<br />
<br />
==Modelling Basics==<br />
<br />
In order to model the kinetics of gene transcription and translation, the approach taken is similar to that in enzyme kinetics. The transcription factors bind reversibly to the relevant site on the DNA and depending upon the particular case, transcription is promoted or repressed. <br />
<br />
The steps of working out the input function (which describes the rate of transcription as a function of the inducer concentration) of a gene are finding the concentration of active repressor (that unbound to the inducer, in this case, arabinose) and then finding the effect of that repressor on transcription.<br />
<br />
We have taken araC to act as a repressor in these models, although as mentioned, it has dual activity, remaining on the DNA after arabinose binding to promote transcription. <br />
<br />
====Binding of repressor to site on DNA====<br />
<br />
First, working out the probability of the DNA site being occupied or free in the presence of a concentration of transcription factor. The equation describing the reversible DNA-Factor complex [DnX] formation is given below. Note that more than one molecule of repressor, the number here is given by n.<br />
<br />
[[Image:Cambridge_modbasics1.gif | center | 140px]]<br />
<br />
k_1 is the forward rate constant, k_2 is for the reverse reaction.<br />
<br />
The probability of the DNA site being free of the repressor is given by [D]/[D_t] where D_t is the total amount of free DNA binding site available. Assuming a pseudo steady state where [Dnx] is stable, so that d[DnX]/dt = 0, and including the constraint that<br />
<br />
[[Image:Cambridge_modbasics2.gif |center| 140px]]<br />
<br />
allows the probability of finding a DNA site free of the repressor to be found by simple substitution and rearrangement of the rate equation below.<br />
<br />
[[Image:Cambridge_modbasics3.gif |center| 260px]]<br />
<br />
This gives the repressor dependent input function of the gene:<br />
<br />
[[Image:Cambridge Eq1.gif | center]]<br />
<br />
The constant K_d is effectively the nth root of k_2/k_1, as can be found by following through the derivations.<br />
<br />
====Sequestering of the repressor AraC by binding to arabinose====<br />
<br />
Again, a similar approach is taken as in enzyme kinetics. Effectively, all of the above derivation is followed but this time the amount of active repressor, X*, is found. This assumes that the amount of AraC repressor bound to arabinose is in pseudo steady state. The total effect of the two repressing systems becomes that of an activator and in effect the detail could be hidden to have a simple activated transcription model. This approach would be the best to pursue in characterising the activator systems. <br />
<br />
====The Phage Activator Systems====<br />
<br />
Including the pBAD promoter as described above, an additional level of complication needs to be taken account of with the phage activator systems. Here the activator promotes transcription, so the input function for the gene under the activator controlled promoter is found from the probability that the DNA binding site is occupied. This is [DnX]/[D_t] where [DnX] here represents the amount of activator-DNA binding site complex (note this is not the amount of free DNA sites this time). Otherwise, the derivation is as above, with the assumption again that [DnX] is in pseudo steady state.<br />
<br />
==References==<br />
<br />
1. [http://www.ncbi.nlm.nih.gov/pubmed/9600836 Apo-AraC actively seeks to loop. Schleif J.Mol. Biol (1988) 278, 529-538]<br />
<br />
2. AN INTRODUCTION TO SYSTEMS BIOLOGY Design Principles Of Biological Circuits. Uri Alon<br />
<br />
3. [http://partsregistry.org/Part:BBa_F2620 BBa_F2620 Parts Registry entry with characterisation.]<br />
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<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:CambridgeTeam:Cambridge2009-10-21T22:18:04Z<p>Vmullin: /* E. Chromi */</p>
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<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
=E. Chromi=<br />
[[Image:Cambridge_Frontpage2.png|400px|right]]<br />
<br />
'''The Cambridge [https://2009.igem.org/Main_Page 2009 iGEM] team has created two kits of parts that will facilitate the design and construction of biosensors in the the future. <br />
<br />
Previous iGEM teams have focused on genetically engineering bacterial biosensors by enabling bacteria to respond to novel inputs, especially biologically significant compounds. There is an unmistakable need to also develop devices that can 1) manipulate input by changing the behaviour of the response of the input-sensitive promoter, and that can 2) report a response using clear, user-friendly outputs. The most popular output is the expression of a fluorescent protein, detectable using fluorescence microscopy. But, what if we could simply see the output with our own eyes? <br />
<br />
We successfully characterised a set of transcriptional systems for calibrated output - [https://2009.igem.org/Team:Cambridge/Project/Amplification |Sensitivity Tuners]. We also successfully expressed a spectrum of pigments in ''E. coli,'' designing a set of [https://2009.igem.org/Team:Cambridge/Project/Pigments | Colour Generators].<br />
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<div class="imagelink_1">[https://2009.igem.org/Team:Cambridge/Project]</div><div class="imagelink_2">[https://2009.igem.org/Team:Cambridge/Project/Amplification]</div><div class="imagelink_3">[https://2009.igem.org/Team:Cambridge/Project/Pigments]</div><div class="imagelink_4">[https://2009.igem.org/Team:Cambridge/ImageGallery/TEAM]</div><div class="imagelink_5">[https://2009.igem.org/Team:Cambridge/Team]</div><div class="imagelink_6">[https://2009.igem.org/Team:Cambridge/ImageGallery]</div><br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:CambridgeTeam:Cambridge2009-10-21T22:17:42Z<p>Vmullin: /* E. Chromi */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
=E. Chromi=<br />
[[Image:Cambridge_Frontpage2.png|400px|right]]<br />
<br />
'''The Cambridge [https://2009.igem.org/Main_Page 2009 iGEM] team has created two kits of parts that will facilitate the design and construction of biosensors in the the future. <br />
<br />
Previous iGEM teams have focused on genetically engineering bacterial biosensors by enabling bacteria to respond to novel inputs, especially biologically significant compounds. There is an unmistakable need to also develop devices that can 1) manipulate input by changing the behaviour of the response of the input-sensitive promoter, and that can 2) report a response using clear, user-friendly outputs. The most popular output is the expression of a fluorescent protein, detectable using fluorescence microscopy. But, what if we could simply see the output with our own eyes? <br />
<br />
We successfully characterised a set of transcriptional systems for calibrated output - [[https://2009.igem.org/Team:Cambridge/Project/Amplification |Sensitivity Tuners]]. We also successfully expressed a spectrum of pigments in ''E. coli,'' designing a set of [[https://2009.igem.org/Team:Cambridge/Project/Pigments | Colour Generators]] <br />
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<div class="imagelink_1">[https://2009.igem.org/Team:Cambridge/Project]</div><div class="imagelink_2">[https://2009.igem.org/Team:Cambridge/Project/Amplification]</div><div class="imagelink_3">[https://2009.igem.org/Team:Cambridge/Project/Pigments]</div><div class="imagelink_4">[https://2009.igem.org/Team:Cambridge/ImageGallery/TEAM]</div><div class="imagelink_5">[https://2009.igem.org/Team:Cambridge/Team]</div><div class="imagelink_6">[https://2009.igem.org/Team:Cambridge/ImageGallery]</div><br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME02Team:Cambridge/Project/ME022009-10-21T22:12:12Z<p>Vmullin: /* Constructing the BioBrick */</p>
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<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
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= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
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<br />
== Design==<br />
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<br />
===Constructing the BioBrick===<br />
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'''Biobrick'''<br />
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Our aim is to make the MelA gene into a biobrick as follows:<br />
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[[Image:MelAbiobrick.jpg]]<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
| <partinfo>BBa_K274001</partinfo><br />
| Reporter<br />
| '''MelA'''. The gene (melA) codes for a tyrosinase which produces a dark brown pigment from L-tyrosine. Production of the pigment requires the addition of copper and L-tyrosine supplements (the copper acts as a cofactor for the gene product) but no other precursors. The BioBrick sequence includes the native ribosome binding site. <br />
| 1844bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
In order to do so, we had to remove forbidden restriction sites within the gene using primers and the in-fusion PCR technique. Primers were ordered as shown by the image below, to add the prefix and suffix and change the PstI restriction site from CTGCAG to CTGCAA:<br />
<br />
[[Image:MelA primer map.JPG]]<br />
<br />
The PCR's will be done in the following steps, in order to remove both sites and prepare the gene as a biobrick:<br />
<br />
[[Image:MelA.png]]<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME03Team:Cambridge/Project/ME032009-10-21T22:11:38Z<p>Vmullin: /* Characterisation */</p>
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<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
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<br />
== Characterisation ==<br />
<br />
'''Successful Pigment Production'''<br />
<br />
In order to produce pigment, bacteria transformed with pTRCmelA must be plated on media supplemented with copper and tyrosine. Supplementation with copper is necessary as copper is a cofactor for the tyrosinase, and tyrosine is a precursor to melanin biosynthesis. (Cabrera-Valladares et al, (2006).<br />
<br />
We transformed Top10 E. coli with pTRCmelA and plated them, using LA supplemented with 15ug/ml copper, 0.2ug/ul tyrosine. Below is a plate that was incubated at 37 degrees for 24 hours and then left on the bench at room temperature over the weekend. Pigment was clearly produced, and it appears to have diffused out of the colonies. <br />
<br />
[[Image:SDC10545.JPG|500px]]<br />
<br />
Left: Top10 transformed with plasmid containing the MelA gene. Right: untransformed Top10. <br />
<br />
'''Control Experiments'''<br />
<br />
To show that the brown colour was a result of the MelA gene and not natural oxidation of the LA supplements, a control plate without any bacteria was incubated for the same amount of time and showed no change in colour (data not shown).<br />
<br />
'''Optimization'''<br />
<br />
On pTRCmelA, the MelA gene is under the control of the lac repressor. The photo above shows leaky expression of the promoter, as no IPTG was not added. We then experimented with the addition of IPTG and varying tyrosine concentrations to see the effect on pigment production. As the photo below shows, the greatest pigment production was achieved with IPTG induction and the highest concentration of tyrosine.<br />
<br />
[[Image:Cambridge SDC12335.JPG | 300px]]<br />
<br />
From left to right, top row: 1mM IPTG with 0.075 mg/mL tyrosine, 1mM IPTG and 0.3 mg/mL tyrosine, and then 1mM IPTG and 0.6 mg/mL tyrosine<br />
From left to right, bottom row: 0.075 mg/mL tyrosine, 0.3 mg/mL tyrosine, and then 0.6 mg/mL tyrosine.<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME04Team:Cambridge/Project/ME042009-10-21T22:11:00Z<p>Vmullin: /* Reference */</p>
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<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Reference ==<br />
<br />
Harald Claus, Heinz Decker, Bacterial tyrosinases, Systematic and Applied Microbiology, Volume 29, Issue 1, 24 January 2006, Pages 3-14, ISSN 0723-2020, DOI: 10.1016/j.syapm.2005.07.012. [http://www.sciencedirect.com/science/article/B7GVX-4H21K91-1/2/01b208fb507ed1fecacbacb867720104]<br />
<br />
<br />
Santos, C. N., and G. Stephanopoulos. 2008. Melanin-based high-throughput screen for L-tyrosine production in Escherichia coli. Appl. Environ. Microbiol. 74:1190-1197 [http://aem.asm.org/cgi/content/abstract/74/4/1190]<br />
<br />
N. Cabrera-Valladares, A. Martínez, S. Piñero, V.H. Lagunas-Muñoz, R. Tinoco and R. de Anda et al., Expression of the melA gene from Rhizobium etli CFN42 in Escherichia coli and characterization of the encoded tyrosinase, Enzyme Microb Technol 38 (6) (2006), pp. 772–779 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TG1-4H21NC4-4&_user=1495569&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&]<br />
<br />
<br />
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{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI03Team:Cambridge/Project/VI032009-10-21T22:08:15Z<p>Vmullin: /* Proof of pigment production */</p>
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<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Characterisation ==<br />
<br />
=== Proof of pigment production===<br />
'''Successful Pigment Production'''<br />
<br />
We transformed Top10 with pPSX-Vio+. After three colour eventually appeared, as shown below. Interestingly, the pigment appears to remain within the bacteria, with little or no bleeding into the media. We took the violacein pigment bacteria (right plate in photo) out of the fridge to find that the purple colour had started to develop. They were therefore left at room temperature overnight. The colour appears to be within the bacteria, with little or no bleeding into the media. The control plate (left plate) is the untransformed TOP10 ''E. coli''.<br />
<br />
[[Image:Cambridge Violacein Pigment.jpg | 300px]]<br />
<br />
Left: control plate - untransformed TOP10 E. coli, Right: Top10 transformed with pPSX-Vio+.<br />
<br />
'''Pigment production efficienty'''<br />
<br />
The Vio operon is currently on a very low copy number plasmid; moving it onto a higher copy number plasmid may accelerate pigment production.<br />
<br />
=== Characterisation of colour output ===<br />
<br />
We characterised the violacein pigment by carrying out the acetone extraction protocol used for carotene. The results were normalised for OD and then plotted as a graph of absorption units against wavelength:<br />
<br />
[[Image:Vio wavelength graph.JPG]]<br />
<br />
We also looked at absorbance at 584nm (the maximum absorbance for violacein):<br />
<br />
[[Image:Vio absorbance.JPG]]<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI02Team:Cambridge/Project/VI022009-10-21T22:07:23Z<p>Vmullin: /* Creating colours */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design ==<br />
<br />
The Vio operon had numerous forbidden restriction sites, far too many to remove by PCR. We thus decided to synthesize it. This allowes us too remove these restriction sites and optimize codon usage for E. coli, to create the following biobrick:<br />
<br />
[[Image:violaceinoperon.jpg]]<br />
<br />
As DNA2.0 very generously agreed to synthesize the entire operon for us, we designed it to include all the five genes, each preceded by a ribosome binding site, and flanked by the prefix and suffix. The final plan for the inserted operon is shown below:<br />
<br />
[[Image:Design sent to DNA 2.0.PNG]]<br />
<br />
This will be held under a repressible promoter on the pJexpress cloning cassette from DNA2.0. We codon optimised the operon for both ''E. coli'' and ''B. subtilis'', and designed it to include restriction sites with complementary sticky ends around vioD and vioC. This allowed us to remove both genes easily to create more colours from the vio operon.<br />
<br />
===Creating colours===<br />
<br />
Once the violacein biobrick arrived we expressed in in TOP10 ''E. coli'' to create the purple pigment. We then carried out two more digests to see if we could create further colours:<br />
:*BamHI and BglII = removed vioC and produced a dark green pigment<br />
:*BglII and BclI = removed vioD and produced a light green pigment<br />
<br />
With more time, we would have been able to use this system to create colour logic gates; where different inputs would create a mix of different coloured outputs. This is discussed further on the [https://2009.igem.org/Team:Cambridge/Future | Future] page, where we explore the different potentials and implications of our project.<br />
<br />
Both of these new pigments were entered into the registry, along with the whole violacein operon for the purple pigment.<br />
<br />
===Biobrick Parts===<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274002</partinfo><br />
|Reporter<br />
|'''Violacein'''. Produces a purple pigment (violacein) from L-tyrosine. The operon contains five genes (VioA-E) each with their own ribosome binding sites.<br />
| 7346bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274003</partinfo><br />
|Reporter<br />
|'''Vio operon ABDE'''. Produces a dark green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioC gene removed by restriction digest with BamHI and BglII. This sequence contains four genes, vioA, vioB vioD and vioE, each preceded by their own ribosome binding site.<br />
| 6032bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274004</partinfo><br />
|Reporter<br />
|'''Vio operon ABCE'''. Produces a light green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioD gene removed by restriction digest with BglII and BclI. This sequence contains four genes, vioA, vioB vioC and vioE, each preceded by their own ribosome binding site.<br />
| 6200bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI02Team:Cambridge/Project/VI022009-10-21T22:07:07Z<p>Vmullin: /* Creating colours */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design ==<br />
<br />
The Vio operon had numerous forbidden restriction sites, far too many to remove by PCR. We thus decided to synthesize it. This allowes us too remove these restriction sites and optimize codon usage for E. coli, to create the following biobrick:<br />
<br />
[[Image:violaceinoperon.jpg]]<br />
<br />
As DNA2.0 very generously agreed to synthesize the entire operon for us, we designed it to include all the five genes, each preceded by a ribosome binding site, and flanked by the prefix and suffix. The final plan for the inserted operon is shown below:<br />
<br />
[[Image:Design sent to DNA 2.0.PNG]]<br />
<br />
This will be held under a repressible promoter on the pJexpress cloning cassette from DNA2.0. We codon optimised the operon for both ''E. coli'' and ''B. subtilis'', and designed it to include restriction sites with complementary sticky ends around vioD and vioC. This allowed us to remove both genes easily to create more colours from the vio operon.<br />
<br />
===Creating colours===<br />
<br />
Once the violacein biobrick arrived we expressed in in TOP10 ''E. coli'' to create the purple pigment. We then carried out two more digests to see if we could create further colours:<br />
:*BamHI and BglII = removed vioC and produced a dark green pigment<br />
:*BglII and BclI = removed vioD and produced a light green pigment<br />
<br />
With more time, we would have been able to use this system to create colour logic gates; where different inputs would create a mix of different coloured outputs. This is discussed further on the '[[https://2009.igem.org/Team:Cambridge/Future | Future]] page, where we explore the different potentials and implications of our project.<br />
<br />
Both of these new pigments were entered into the registry, along with the whole violacein operon for the purple pigment.<br />
<br />
===Biobrick Parts===<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274002</partinfo><br />
|Reporter<br />
|'''Violacein'''. Produces a purple pigment (violacein) from L-tyrosine. The operon contains five genes (VioA-E) each with their own ribosome binding sites.<br />
| 7346bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274003</partinfo><br />
|Reporter<br />
|'''Vio operon ABDE'''. Produces a dark green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioC gene removed by restriction digest with BamHI and BglII. This sequence contains four genes, vioA, vioB vioD and vioE, each preceded by their own ribosome binding site.<br />
| 6032bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274004</partinfo><br />
|Reporter<br />
|'''Vio operon ABCE'''. Produces a light green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioD gene removed by restriction digest with BglII and BclI. This sequence contains four genes, vioA, vioB vioC and vioE, each preceded by their own ribosome binding site.<br />
| 6200bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI02Team:Cambridge/Project/VI022009-10-21T22:06:52Z<p>Vmullin: /* Design */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design ==<br />
<br />
The Vio operon had numerous forbidden restriction sites, far too many to remove by PCR. We thus decided to synthesize it. This allowes us too remove these restriction sites and optimize codon usage for E. coli, to create the following biobrick:<br />
<br />
[[Image:violaceinoperon.jpg]]<br />
<br />
As DNA2.0 very generously agreed to synthesize the entire operon for us, we designed it to include all the five genes, each preceded by a ribosome binding site, and flanked by the prefix and suffix. The final plan for the inserted operon is shown below:<br />
<br />
[[Image:Design sent to DNA 2.0.PNG]]<br />
<br />
This will be held under a repressible promoter on the pJexpress cloning cassette from DNA2.0. We codon optimised the operon for both ''E. coli'' and ''B. subtilis'', and designed it to include restriction sites with complementary sticky ends around vioD and vioC. This allowed us to remove both genes easily to create more colours from the vio operon.<br />
<br />
===Creating colours===<br />
<br />
Once the violacein biobrick arrived we expressed in in TOP10 ''E. coli'' to create the purple pigment. We then carried out two more digests to see if we could create further colours:<br />
:*BamHI and BglII = removed vioC and produced a dark green pigment<br />
:*BglII and BclI = removed vioD and produced a light green pigment<br />
<br />
With more time, we would have been able to use this system to create colour logic gates; where different inputs would create a mix of different coloured outputs. This is discussed further on the '[[https://2009.igem.org/Team:Cambridge/Future |Future]] page, where we explore the different potentials and implications of our project.<br />
<br />
Both of these new pigments were entered into the registry, along with the whole violacein operon for the purple pigment.<br />
<br />
===Biobrick Parts===<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274002</partinfo><br />
|Reporter<br />
|'''Violacein'''. Produces a purple pigment (violacein) from L-tyrosine. The operon contains five genes (VioA-E) each with their own ribosome binding sites.<br />
| 7346bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274003</partinfo><br />
|Reporter<br />
|'''Vio operon ABDE'''. Produces a dark green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioC gene removed by restriction digest with BamHI and BglII. This sequence contains four genes, vioA, vioB vioD and vioE, each preceded by their own ribosome binding site.<br />
| 6032bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274004</partinfo><br />
|Reporter<br />
|'''Vio operon ABCE'''. Produces a light green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioD gene removed by restriction digest with BglII and BclI. This sequence contains four genes, vioA, vioB vioC and vioE, each preceded by their own ribosome binding site.<br />
| 6200bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI01Team:Cambridge/Project/VI012009-10-21T22:06:02Z<p>Vmullin: /* Background */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Background ==<br />
'''Violacein Biosynthesis'''<br />
<br />
The Violacein pigment is produced from L-tryptophan via a pathway involving five enzymes, VioA-E. This forms a purple colour which remains within the individual cell colonies. This synthesis pathway is shown below:<br />
<br />
[[Image:Violacein pigment production.jpg]]<br />
<br />
From August et al (2000). <br />
<br />
The vioE is used in the step just after the vioB for the 1-2 shift of the indole ring. Sánchez et. al (2006) <br />
<br />
Further, as module 5 is Aqua, expressing the genes under different promoters will allow us to produce at least two different colours. Sanchez suggests that removing vioD can produce a dark blue, while removing vio C produces a dark green. Our actual results showed that the ABDE construct produced a dark green pigment while the ABCE produced light green.<br />
<br />
'''Vio Operon'''<br />
<br />
Our VioA-E genes are from ''Chromobacterium voilaceum ATCC 12472'' in the pPSX vio+ plasmid. This was kindly provided by John Pemberton; Department of Microbiology and parasitology, University of Queensland, Brisbane, Australia. (Sarovich & Pemberton (2007) Plasmid 57:306-313) <br />
<br />
*pPSX sequence ID FJ422118<br />
*vio gene cluster complete cds AB032799 and AF172851.<br />
<br />
We aim to successfully express violacein in ''E. coli,'' to synthesize the violacein operon as a biobrick, and to manipulate the operon to produce the other two pigments.<br />
<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI04Team:Cambridge/Project/VI042009-10-21T22:02:49Z<p>Vmullin: /* Reference */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Reference ==<br />
<br />
Welch M, Govindarajan S, Ness JE, Villalobos A, Gurney A, et al. 2009 Design Parameters to Control Synthetic Gene Expression in Escherichia coli. [http://www.horizonpress.com/jmmb/v2/v2n4/26.pdf]<br />
<br />
P.R. August, T.H. Grossman, C. Minor, M.P. Draper, I.A. MacNeil, J.M. Pemberton, K.M. Call, d. Holt, and M. S. Osbourne, Sequence Analysis and Functional Characterization of the Violacein Biosynthetic Pathway from Chromobacterium violaceum, J. Mol. Microbiol. Biotechnol. (2000) 2(4): 513-519.[http://www3.interscience.wiley.com/cgi-bin/fulltext/112732008/HTMLSTART?CRETRY=1&SRETRY=0]<br />
<br />
César Sánchez, Dr., Alfredo F. Braña, Prof. Dr., Carmen Méndez, Prof. Dr., José A. Salas, Prof. Dr. Reevaluation of the Violacein Biosynthetic Pathway and its Relationship to Indolocarbazole Biosynthesis [http://www3.interscience.wiley.com/journal/112732008/abstract]<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI04Team:Cambridge/Project/VI042009-10-21T22:02:09Z<p>Vmullin: /* Reference */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Reference ==<br />
<br />
Welch M, Govindarajan S, Ness JE, Villalobos A, Gurney A, et al. 2009 Design Parameters to Control Synthetic Gene Expression in Escherichia coli. [http://www.horizonpress.com/jmmb/v2/v2n4/26.pdf]<br />
<br />
P.R. August, T.H. Grossman, C. Minor, M.P. Draper, I.A. MacNeil, J.M. Pemberton, K.M. Call, d. Holt, and M. S. Osbourne, Sequence Analysis and Functional Characterization of the Violacein Biosynthetic Pathway from Chromobacterium violaceum, J. Mol. Microbiol. Biotechnol. (2000) 2(4): 513-519.[http://www3.interscience.wiley.com/cgi-bin/fulltext/112732008/HTMLSTART?CRETRY=1&SRETRY=0]<br />
<br />
César Sánchez, Dr., Alfredo F. Braña, Prof. Dr., Carmen Méndez, Prof. Dr., José A. Salas, Prof. Dr. Reevaluation of the Violacein Biosynthetic Pathway and its Relationship to Indolocarbazole Biosynthesi<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI02Team:Cambridge/Project/VI022009-10-21T22:00:56Z<p>Vmullin: /* Creating colours */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design ==<br />
<br />
The Vio operon had numerous forbidden restriction sites, far too many to remove by PCR. We thus decided to synthesize it. This allowes us too remove these restriction sites and optimize codon usage for E. coli, to create the following biobrick:<br />
<br />
[[Image:violaceinoperon.jpg]]<br />
<br />
As DNA2.0 very generously agreed to synthesize the entire operon for us, we designed it to include all the five genes, each preceded by a ribosome binding site, and flanked by the prefix and suffix. The final plan for the inserted operon is shown below:<br />
<br />
[[Image:Design sent to DNA 2.0.PNG]]<br />
<br />
This will be held under a repressible promoter on the pJexpress cloning cassette from DNA2.0. We designed it to include restriction sites with complementary sticky ends around vioD and vioC. This allowed us to remove both genes easily to create more colours from the vio operon.<br />
<br />
===Creating colours===<br />
<br />
Once the violacein biobrick arrived we expressed in in TOP10 ''E. coli'' to create the purple pigment. We then carried out two more digests to see if we could create further colours:<br />
:*BamHI and BglII = removed vioC and produced a dark green pigment<br />
:*BglII and BclI = removed vioD and produced a light green pigment<br />
<br />
With more time, we would have been able to use this system to create colour logic gates; where different inputs would create a mix of different coloured outputs. This is discussed further on the '[[https://2009.igem.org/Team:Cambridge/Future |Future]] page, where we explore the different potentials and implications of our project.<br />
<br />
Both of these new pigments were entered into the registry, along with the whole violacein operon for the purple pigment.<br />
<br />
===Biobrick Parts===<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274002</partinfo><br />
|Reporter<br />
|'''Violacein'''. Produces a purple pigment (violacein) from L-tyrosine. The operon contains five genes (VioA-E) each with their own ribosome binding sites.<br />
| 7346bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274003</partinfo><br />
|Reporter<br />
|'''Vio operon ABDE'''. Produces a dark green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioC gene removed by restriction digest with BamHI and BglII. This sequence contains four genes, vioA, vioB vioD and vioE, each preceded by their own ribosome binding site.<br />
| 6032bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274004</partinfo><br />
|Reporter<br />
|'''Vio operon ABCE'''. Produces a light green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioD gene removed by restriction digest with BglII and BclI. This sequence contains four genes, vioA, vioB vioC and vioE, each preceded by their own ribosome binding site.<br />
| 6200bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/VI02Team:Cambridge/Project/VI022009-10-21T21:59:48Z<p>Vmullin: /* Creating colours */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Violacein Pigments =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/VI01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/VI04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
<br />
== Design ==<br />
<br />
The Vio operon had numerous forbidden restriction sites, far too many to remove by PCR. We thus decided to synthesize it. This allowes us too remove these restriction sites and optimize codon usage for E. coli, to create the following biobrick:<br />
<br />
[[Image:violaceinoperon.jpg]]<br />
<br />
As DNA2.0 very generously agreed to synthesize the entire operon for us, we designed it to include all the five genes, each preceded by a ribosome binding site, and flanked by the prefix and suffix. The final plan for the inserted operon is shown below:<br />
<br />
[[Image:Design sent to DNA 2.0.PNG]]<br />
<br />
This will be held under a repressible promoter on the pJexpress cloning cassette from DNA2.0. We designed it to include restriction sites with complementary sticky ends around vioD and vioC. This allowed us to remove both genes easily to create more colours from the vio operon.<br />
<br />
===Creating colours===<br />
<br />
Once the violacein biobrick arrived we expressed in in TOP10 ''E. coli'' to create the purple pigment. We then carried out two more digests to see if we could create further colours:<br />
:*BamHI and BglII = removed vioC and produced a dark green pigment<br />
:*BglII and BclI = removed vioD and produced a light green pigment<br />
<br />
With more time, we would have been able to use this system to create colour logic gates; where different inputs would create a mix of different coloured outputs. This is discussed further on the 'Future' page, where we explore the different potentials and implications of our project. [[https://2009.igem.org/Team:Cambridge/Future]]<br />
<br />
Both of these new pigments were entered into the registry, along with the whole violacein operon for the purple pigment.<br />
<br />
===Biobrick Parts===<br />
<br />
<!--DONT EDIT THIS BIT:----------------------------------------------------------------------------><br />
{| style="color:#CCC; background-color:#3D5089;" cellpadding="6" cellspacing="0" border="1"<br />
! Registry Code<br />
! Type<br />
! Sequence Description / Notes<br />
! Length<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<!----------------------------------------EDIT HERE ONWARDS----------------------------------------><br />
<br />
| <partinfo>BBa_K274002</partinfo><br />
|Reporter<br />
|'''Violacein'''. Produces a purple pigment (violacein) from L-tyrosine. The operon contains five genes (VioA-E) each with their own ribosome binding sites.<br />
| 7346bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274003</partinfo><br />
|Reporter<br />
|'''Vio operon ABDE'''. Produces a dark green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioC gene removed by restriction digest with BamHI and BglII. This sequence contains four genes, vioA, vioB vioD and vioE, each preceded by their own ribosome binding site.<br />
| 6032bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
<br />
|<partinfo>BBa_K274004</partinfo><br />
|Reporter<br />
|'''Vio operon ABCE'''. Produces a light green pigment from L-tyrosine. Formed from the vio operon biobrick (BBa_K274002) with the vioD gene removed by restriction digest with BglII and BclI. This sequence contains four genes, vioA, vioB vioC and vioE, each preceded by their own ribosome binding site.<br />
| 6200bp<br />
|- style="color:#333; background-color:#A3C3FF;" cellpadding="6" cellspacing="0" border="1"<br />
|}<br />
<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME01Team:Cambridge/Project/ME012009-10-21T21:58:50Z<p>Vmullin: /* Melanin Pigment */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Background ==<br />
<br />
'''Melanin Production'''<br />
<br />
The MelA gene codes for a tyrosinase. Tyrosinases catalyze two reactions, as described in the figure below. Melanin is a macromolecular compound produced by the polymerization of the quinone product of the second reaction, and has a characteristic brown colour.<br />
<br />
[[Image:Tyrosinase action.jpg]] <br />
<br />
From Claus and Decker, 2006<br />
<br />
'''MelA'''<br />
<br />
Our MelA gene is from ''Rhizobium etli.'' Further, it is a mutant; it has a C to T substitution at the 1,000th nucleotide, which creates a Proline to Serine mutation that reduces the amount of time before melanin production is visible. (Santos et al. 2008) The plasmid pTRCmelA was provided by Christine Sanntos from the lab of G. Stephanopoulos to Duncan Rowe under the materials transfers agreement.<br />
<br />
Using pTRCmelA as a template, we aim to show melanin expression in ''E. coli'' and isolate the MelA gene in biobrick form.<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME01Team:Cambridge/Project/ME012009-10-21T21:56:42Z<p>Vmullin: /* Background */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Background ==<br />
<br />
'''Melanin Production'''<br />
<br />
The MelA gene codes for a tyrosinase. Tyrosinases catalyze two reactions, as described in the figure below. Melanin is a macromolecular compound produced by the polymerization of the quinone product of the second reaction, and has a characteristic brown colour.<br />
<br />
[[Image:Tyrosinase action.jpg]] <br />
<br />
From Claus and Decker, 2006<br />
<br />
'''MelA'''<br />
<br />
Our MelA gene is from ''Rhizobium etli.'' Further, it is a mutant; it has a C to T substitution at the 1,000th nucleotide, which creates a Proline to Serine mutation that reduces the amount of time before melanin production is visible. (Santos et al. 2008) The plasmid was provided by Christine Sanntos from the lab of G. Stephanopoulos to Duncan Rowe under the materials transfers agreement.<br />
<br />
=== Action plan of our team ===<br />
<br />
Our action plan is as follows:<br />
<br />
:1. Test for melanin production<br />
:2. Isolate MelA gene in biobrick form<br />
:3. Integrate Mel biobrick into system (e.g amplification of logic gate system)<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/ME01Team:Cambridge/Project/ME012009-10-21T21:55:55Z<p>Vmullin: /* Background */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= Melanin Pigment =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[https://2009.igem.org/Team:Cambridge/Project/ME01 Background]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME02 Design]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME03 Characterisation]<br />
[https://2009.igem.org/Team:Cambridge/Project/ME04 Reference]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Background ==<br />
<br />
'''Melanin Production'''<br />
<br />
The MelA gene codes for a tyrosinase. Tyrosinases catalyze two reactions, as described in the figure below. Melanin is a macromolecular compound produced by the polymerization of the quinone product of the second reaction, and has a characteristic brown colour.<br />
<br />
[[Image:Tyrosinase action.jpg]] <br />
<br />
From Claus and Decker, 2006<br />
<br />
'''MelA'''<br />
<br />
Our MelA gene is from ''Rhizobium etli.'' Further, it is a mutant; it has a C to T substitution at the 1,000th nucleotide, which creates a Proline to Serine mutation that reduces the amount of time before melanin production is visible. (Santos, C. N., and G. Stephanopoulos. 2008. Melanin-based high-throughput screen for L-tyrosine production in Escherichia coli. Appl. Environ. Microbiol. 74:1190-1197 [http://aem.asm.org/cgi/reprint/74/4/1190]) The plasmid was provided by Christine Sanntos from the lab of G. Stephanopoulos to Duncan Rowe under the materials transfers agreement.<br />
<br />
=== Action plan of our team ===<br />
<br />
Our action plan is as follows:<br />
<br />
:1. Test for melanin production<br />
:2. Isolate MelA gene in biobrick form<br />
:3. Integrate Mel biobrick into system (e.g amplification of logic gate system)<br />
<br />
{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/FutureTeam:Cambridge/Future2009-10-21T21:53:53Z<p>Vmullin: /* The Distant Future - potential for colour */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= The Future =<br />
<br />
Synthetic biology is an exciting new area of science, and continues to rapidly develop and change. It has the potential for use in a wide variety of areas, and new technologies. We considered these issues throughout the summer, and took part in workshops which explored the potential for our devices in the future.<br />
<br />
===The Near Future===<br />
<br />
====Applications of the sensitivity tuner and colour output====<br />
<br />
We believe that our kits of sensitivity tuners and colour-generating devices can be applied directly to environmental sensing. For proof of concept, we attached our sensitivity tuners to the arabinose sensor. However there are so many different sensors in the registry (and in the natural world!) which could benefit from this device. The registry already contains promoters for lead, arsenic and other pollutants, and we would like to undertake more work to show that the sensitivity tuners are compatible with these promoters. The use of the sensitivity tuner would confer on these promoters the ability to distinguish more accurately distinct pollutant levels, and the pigment output would allow them to be used without expensive equpient, in places where this may be impractical or too costly. We looked at the potential for this system in helping countries such as Bangladesh, which has severe problems with arsenic pollution, in areas where expensive sensor devices are unavailable.<br />
<br />
====Expanding our selection of sensitivity tuners and pigment-producing operons====<br />
<br />
The 2009 Cambridge iGEM team has generated two kits of parts - a kit of Sensitivity Tuners, and a kit of Colour Generators. Each could be expanded - more phage activators and phage promoters could be added to the Registry, and other pigments of bacterial origin could be made into biobricks. We hope that we have illustrated a standard method to characterize Sensitivity Tuners and to design and describe new pigments that future iGEM teams can reproduce.<br />
<br />
====Manipulation of Pigment operons====<br />
<br />
The carotenoid and violacein operons are able to produce more than one pigment each. This gives future iGEM teams the opportunity to manipulate these operons. For example, with the carotenoid system, there is the potential to change red to orange. Inducible colour change has particular application to our dipstick prototype. If the bacteria in each well constitutively expressed orange pigment, this would be an indication that the bacteria were alive. The change from red to orange would be induced by the pollutant. As for violacein, colour logic could be used to detect combinations of pollutants:<br />
<br />
[[Image:colourlogic.jpg]]<br />
<br />
===The Distant Future - potential for colour===<br />
<br />
In the Colours Future workshop (organised by Daisy Ginsburg and James King from the Royal College of Art) we concentrated on our various pigments, considering how the ability to exploit pigments from the natural world--not just from bacteria, but from plants and animals--might affect the world we live in. What if pigments are used as reporters for applications beyond bacterial biosensors? What if we harnessed natural pigments and used them to artificially colour the world, even ourselves? What ramifications might these leaps and bounds have? We divided these considerations into four main groups:<br />
<br />
'''Products'''<br />
<br />
Both bacterial pigments and synthetic biology in general has the potential to be used to create many different products and technologies. Crispian, Alan and Caitlin explored the use of synthetic biology in a range of products from childrens toys to commencial food-colouring. This would create issues of property and patents; if the biobrick for colour is in an open source registry, would this create problems for people hopeing to patent a certain colour, or a gene for a colour? Megan and Mike took this to an extreme with a sketch from a world where the colour orange was patented, and it's use under strict control.<br />
<br />
'''Services'''<br />
<br />
Along with new technologies, comes the creation of new services, providing jobs that previously did not exist. Working with synthetic biology tools and products could become an industry in itself, with a unique skill-set. As the design of devices reaches higher levels of abstraction, the concept becomes more available for different industries to use, and provides new ways to consider the workings in biological cells. In view of our colours, we imagined a future where pigments from the natural world were in high demand, creating the job of 'colour-hunter', people looking for the brightest and best colours, from the smallest and most easily reproducible genetic systems.<br />
<br />
'''Groups'''<br />
<br />
New technologies and ways of thinking also have a social effect. Products create gaps between the have and have-nots, while changes in employment patterns and sectors can create a need for new skill-sets. The field of synthetic biology is becoming more widely recognised as a group (and a degree title!) that more and more people are becoming part of. Shuna, Siming and Viv looked at how colours could effect social groupings and cultures, especially given that different cultures will have very different associations for each colour. <br />
<br />
'''Laws'''<br />
<br />
Synthetic biology, and the parts registry is open source, and yet the world of products and services relies heavily on ownership and property rights. This creates issues of property and patents; which may require new laws. Megan, Mike, and Tom took this to an extreme with a sketch from a world where the colour orange was patented, and it's use under strict control (much to the anger of coutries whose national flags contain the colour, as well as a certain well known mobile phone provider!)<br />
<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/FutureTeam:Cambridge/Future2009-10-21T21:53:19Z<p>Vmullin: /* The Future */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= The Future =<br />
<br />
Synthetic biology is an exciting new area of science, and continues to rapidly develop and change. It has the potential for use in a wide variety of areas, and new technologies. We considered these issues throughout the summer, and took part in workshops which explored the potential for our devices in the future.<br />
<br />
===The Near Future===<br />
<br />
====Applications of the sensitivity tuner and colour output====<br />
<br />
We believe that our kits of sensitivity tuners and colour-generating devices can be applied directly to environmental sensing. For proof of concept, we attached our sensitivity tuners to the arabinose sensor. However there are so many different sensors in the registry (and in the natural world!) which could benefit from this device. The registry already contains promoters for lead, arsenic and other pollutants, and we would like to undertake more work to show that the sensitivity tuners are compatible with these promoters. The use of the sensitivity tuner would confer on these promoters the ability to distinguish more accurately distinct pollutant levels, and the pigment output would allow them to be used without expensive equpient, in places where this may be impractical or too costly. We looked at the potential for this system in helping countries such as Bangladesh, which has severe problems with arsenic pollution, in areas where expensive sensor devices are unavailable.<br />
<br />
====Expanding our selection of sensitivity tuners and pigment-producing operons====<br />
<br />
The 2009 Cambridge iGEM team has generated two kits of parts - a kit of Sensitivity Tuners, and a kit of Colour Generators. Each could be expanded - more phage activators and phage promoters could be added to the Registry, and other pigments of bacterial origin could be made into biobricks. We hope that we have illustrated a standard method to characterize Sensitivity Tuners and to design and describe new pigments that future iGEM teams can reproduce.<br />
<br />
====Manipulation of Pigment operons====<br />
<br />
The carotenoid and violacein operons are able to produce more than one pigment each. This gives future iGEM teams the opportunity to manipulate these operons. For example, with the carotenoid system, there is the potential to change red to orange. Inducible colour change has particular application to our dipstick prototype. If the bacteria in each well constitutively expressed orange pigment, this would be an indication that the bacteria were alive. The change from red to orange would be induced by the pollutant. As for violacein, colour logic could be used to detect combinations of pollutants:<br />
<br />
[[Image:colourlogic.jpg]]<br />
<br />
===The Distant Future - potential for colour===<br />
<br />
In the Colours Future workshop (organised by Daisy Ginsburg and James King from the Royal College of Art) we concentrated on our various pigments, considering how the ability to exploit pigments from the natural world--not just from bacteria, but from plants and animals--might affect the world we live in. What if pigments are used as reporters for applications beyond bacteria biosensors? What if we harnessed natural pigments and used them to artificially colour the world, even ourselves? What ramifications might these leaps and bounds have? We divided these considerations into four main groups:<br />
<br />
'''Products'''<br />
<br />
Both bacterial pigments and synthetic biology in general has the potential to be used to create many different products and technologies. Crispian, Alan and Caitlin explored the use of synthetic biology in a range of products from childrens toys to commencial food-colouring. This would create issues of property and patents; if the biobrick for colour is in an open source registry, would this create problems for people hopeing to patent a certain colour, or a gene for a colour? Megan and Mike took this to an extreme with a sketch from a world where the colour orange was patented, and it's use under strict control.<br />
<br />
'''Services'''<br />
<br />
Along with new technologies, comes the creation of new services, providing jobs that previously did not exist. Working with synthetic biology tools and products could become an industry in itself, with a unique skill-set. As the design of devices reaches higher levels of abstraction, the concept becomes more available for different industries to use, and provides new ways to consider the workings in biological cells. In view of our colours, we imagined a future where pigments from the natural world were in high demand, creating the job of 'colour-hunter', people looking for the brightest and best colours, from the smallest and most easily reproducible genetic systems.<br />
<br />
'''Groups'''<br />
<br />
New technologies and ways of thinking also have a social effect. Products create gaps between the have and have-nots, while changes in employment patterns and sectors can create a need for new skill-sets. The field of synthetic biology is becoming more widely recognised as a group (and a degree title!) that more and more people are becoming part of. Shuna, Siming and Viv looked at how colours could effect social groupings and cultures, especially given that different cultures will have very different associations for each colour. <br />
<br />
'''Laws'''<br />
<br />
Synthetic biology, and the parts registry is open source, and yet the world of products and services relies heavily on ownership and property rights. This creates issues of property and patents; which may require new laws. Megan, Mike, and Tom took this to an extreme with a sketch from a world where the colour orange was patented, and it's use under strict control (much to the anger of coutries whose national flags contain the colour, as well as a certain well known mobile phone provider!)<br />
<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/FutureTeam:Cambridge/Future2009-10-21T21:45:26Z<p>Vmullin: /* Expanding our selection of sensitivity tuners and pigment-producing operons */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
<br />
= The Future =<br />
<br />
Synthetic biology is an exciting new area of science, that is rapidly developing and changing. It has the potential for use in a wide variety of areas, and new technologies. We considered these issues throughout the summer, and took part in workshops which explored the potential for our devices in the future.<br />
<br />
===The Near Future===<br />
<br />
====Applications of the sensitivity tuner and colour output====<br />
<br />
We believe that our kits of sensitivity tuners and colour-generating devices can be applied directly to environmental sensing. For proof of concept, we attached our sensitivity tuners to the arabinose sensor. However there are so many different sensors in the registry (and in the natural world!) which could benefit from this device. The registry already contains promoters for lead, arsenic and other pollutants, and we would like to undertake more work to show that the sensitivity tuners are compatible with these promoters. The use of the sensitivity tuner would confer on these promoters the ability to distinguish more accurately distinct pollutant levels, and the pigment output would allow them to be used without expensive equpient, in places where this may be impractical or too costly. We looked at the potential for this system in helping countries such as Bangladesh, which has severe problems with arsenic pollution, in areas where expensive sensor devices are unavailable.<br />
<br />
====Expanding our selection of sensitivity tuners and pigment-producing operons====<br />
<br />
The 2009 Cambridge iGEM team has generated two kits of parts - a kit of Sensitivity Tuners, and a kit of Colour Generators. Each could be expanded - more phage activators and phage promoters could be added to the Registry, and other pigments of bacterial origin could be made into biobricks. We hope that we have illustrated a standard method to characterize Sensitivity Tuners and to design and describe new pigments that future iGEM teams can reproduce.<br />
<br />
====Manipulation of Pigment operons====<br />
<br />
The carotenoid and violacein operons are able to produce more than one pigment each. This gives future iGEM teams the opportunity to manipulate these operons. For example, with the carotenoid system, there is the potential to change red to orange. Inducible colour change has particular application to our dipstick prototype. If the bacteria in each well constitutively expressed orange pigment, this would be an indication that the bacteria were alive. The change from red to orange would be induced by the pollutant. As for violacein, colour logic could be used to detect combinations of pollutants:<br />
<br />
[[Image:colourlogic.jpg]]<br />
<br />
===The Distant Future - potential for colour===<br />
<br />
In the Colours Future workshop (organised by Daisy Ginsburg and James King from the Royal College of Art) we concentrated on our various pigments, considering how the ability to exploit pigments from the natural world--not just from bacteria, but from plants and animals--might affect the world we live in. We divided these considerations into four main groups:<br />
<br />
'''Products'''<br />
<br />
Both bacterial pigments and synthetic biology in general has the potential to be used to create many different products and technologies. Crispian, Alan and Caitlin explored the use of synthetic biology in a range of products from childrens toys to commencial food-colouring. This would create issues of property and patents; if the biobrick for colour is in an open source registry, would this create problems for people hopeing to patent a certain colour, or a gene for a colour? Megan and Mike took this to an extreme with a sketch from a world where the colour orange was patented, and it's use under strict control.<br />
<br />
'''Services'''<br />
<br />
Along with new technologies, comes the creation of new services, providing jobs that previously did not exist. Working with synthetic biology tools and products could become an industry in itself, with a unique skill-set. As the design of devices reaches higher levels of abstraction, the concept becomes more available for different industries to use, and provides new ways to consider the workings in biological cells. In view of our colours, we imagined a future where pigments from the natural world were in high demand, creating the job of 'colour-hunter', people looking for the brightest and best colours, from the smallest and most easily reproducible genetic systems.<br />
<br />
'''Groups'''<br />
<br />
New technologies and ways of thinking also have a social effect. Products created gaps between the have and have-nots, while changes in employment patterns and sectors can create a need for new skill-sets. The field of synthetic biology is becoming more widely recognised as a group (and a degree title!) that more and more people are becoming part of. Shuna, Siming and Viv looked at how colours could effect social groupings and cultures, especially given that different cultures will have very different associations for each colour. <br />
<br />
'''Laws'''<br />
<br />
Synthetic biology, and the parts registry is open source, and yet the world of products and services relies heavily on ownership and property rights. This creates issues of property and patents; which may require new laws. Megan and Mike took this to an extreme with a sketch from a world where the colour orange was patented, and it's use under strict control (much to the anger of coutries whose national flags contain the colour, as well as a certain well known mobile phone provider!)<br />
<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/Amplification/CharacterisationTeam:Cambridge/Project/Amplification/Characterisation2009-10-21T21:42:31Z<p>Vmullin: /* Characterisation */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= The Sensitivity Tuner =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Introduction | Introduction ]]<br />
[[#Characterisation | Characterisation ]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The Cambridge 2007 iGEM team build 15 "amplifiers," constructs with RFP and GFP reporters that amplified the PoPS output of the promoter pBad/AraC (<partinfo>BBa_I0500</partinfo>), as described below:<br />
<br />
[[Image:amplifier07.jpg]]<br />
<br />
We re-designed these constructs to be PoPS converters as follows...<br />
<br />
[[Image:thresholddevice3.jpg]] <br />
<br />
...and generated our own set of Sensitivity Tuners:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
<br />
In order to characterize these phage activator/promoter constructs, we used the corresponding Cambridge 2007 amplifier as an illustration of how our Sensitivity Tuners alter the behaviour of pBad/AraC. These parts are very useful for characterisation as they contain fluorescent reporters; the parts we designed, which lack an input promoter and fluorescent reporters, are more useful parts for other iGEM teams to incorporate into their own projects. For characterisation, we moved the Cambridge 2007 amplifiers onto a low copy plasmid in order to make meaningful comparisons with <partinfo>BBa_J69591</partinfo>, the standard promoter. We looked at a few major characteristics relating input (arabinose) to output (GFP) and how they are modified compared to pBad/AraC on its own.<br />
<br />
[[Image:characterization3.jpg]]<br />
<br />
== Characterisation ==<br />
<br />
We were able to update the Registry pages of the Cambridge 2007 amplifiers, as summarised below.<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_I746370</partinfo> || <partinfo>BBa_I746380</partinfo>||<partinfo>BBa_I746390</partinfo><br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_I746371</partinfo><br />
|<partinfo>BBa_I746381</partinfo><br />
|<partinfo>BBa_I746391</partinfo><br />
|-<br />
! PP promoter<br />
|<partinfo>BBa_I746372</partinfo><br />
|<partinfo>BBa_I746382</partinfo><br />
|<partinfo>BBa_I746392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_I746374</partinfo><br />
|<partinfo>BBa_I746384</partinfo><br />
|<partinfo>BBa_I746394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_I746375</partinfo><br />
|<partinfo>BBa_I746385</partinfo><br />
|<partinfo>BBa_I746395</partinfo><br />
|}<br />
<br />
=== Maximum Rates against Arabinose Concentrations ===<br />
<br />
==== 80 ====<br />
[[Image:Cambridge_maxrates1.jpg | 600px]]<br />
<br />
==== 81 ====<br />
[[Image:Cambridge_maxrates2.jpg | 600px]]<br />
<br />
==== 82 ====<br />
[[Image:Cambridge_maxrates3.jpg | 600px]]<br />
<br />
==== 84 ====<br />
[[Image:Cambridge_maxrates4.jpg | 600px]]<br />
<br />
==== 85 ====<br />
[[Image:Cambridge_maxrates5.jpg | 600px]]<br />
<br />
==== 90 ====<br />
[[Image:Cambridge_maxrates6.jpg | 600px]]<br />
<br />
==== 92 ====<br />
[[Image:Cambridge_maxrates7.jpg | 600px]]<br />
<br />
==== 94 ====<br />
[[Image:Cambridge_maxrates8.jpg | 600px]]<br />
<br />
==== 95 ====<br />
[[Image:Cambridge_maxrates9.jpg | 600px]]<br />
<br />
<br />
<br />
<!--Do not remove the first and last lines in this page!-->{{Template:CambridgeBottom}}</div>Vmullinhttp://2009.igem.org/Team:Cambridge/Project/Amplification/CharacterisationTeam:Cambridge/Project/Amplification/Characterisation2009-10-21T21:41:40Z<p>Vmullin: /* Characterisation */</p>
<hr />
<div>{{Template:Cambridge2}}<!--Do not remove the first and last lines in this page!--><br />
= The Sensitivity Tuner =<br />
<br />
<!-- This is for the top grey / blue links bar !--><br />
{{Template:Cambridgetemplatetop}}<br />
[[#Introduction | Introduction ]]<br />
[[#Characterisation | Characterisation ]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
[[# | ]]<br />
{{Template:Cambridgetemplatebottom}}<br />
<br />
== Introduction ==<br />
<br />
The Cambridge 2007 iGEM team build 15 "amplifiers," constructs with RFP and GFP reporters that amplified the PoPS output of the promoter pBad/AraC (<partinfo>BBa_I0500</partinfo>), as described below:<br />
<br />
[[Image:amplifier07.jpg]]<br />
<br />
We re-designed these constructs to be PoPS converters as follows...<br />
<br />
[[Image:thresholddevice3.jpg]] <br />
<br />
...and generated our own set of Sensitivity Tuners:<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_K274370</partinfo> || <partinfo>BBa_K274380</partinfo>||<br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_K274371</partinfo><br />
|<partinfo>BBa_K274381</partinfo><br />
|<partinfo>BBa_K274391</partinfo><br />
|-<br />
! PP promoter<br />
|<br />
|<partinfo>BBa_K274382</partinfo><br />
|<partinfo>BBa_K274392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_K274374</partinfo><br />
|<partinfo>BBa_K274384</partinfo><br />
|<partinfo>BBa_K274394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_K274375</partinfo><br />
|<br />
|<partinfo>BBa_K274395</partinfo><br />
|}<br />
<br />
In order to characterize these phage activator/promoter constructs, we used the corresponding Cambridge 2007 amplifier as an illustration of how our Sensitivity Tuners alter the behaviour of pBad/AraC. These parts are very useful for characterisation as they contain fluorescent reporters; the parts we designed, which lack an input promoter and fluorescent reporters, are more useful parts for other iGEM teams to incorporate into their own projects. For characterisation, we moved the Cambridge 2007 amplifiers onto a low copy plasmid in order to make meaningful comparisons with <partinfo>BBa_J69591</partinfo>, the standard promoter. We looked at a few major characteristics relating input (arabinose) to output (GFP) and how they are modified compared to pBad/AraC on its own.<br />
<br />
[[Image:characterization3.jpg]]<br />
<br />
== Characterisation ==<br />
<br />
We were able to update the Registry pages of the Cambridge 2007 amplifiers, as summarised below.<br />
<br />
<br />
{| border="1"<br />
|+ <br />
! !! P2 ogr activator !! PSP3 pag activator !! phiR73 delta activator<br />
|-<br />
! PF promoter<br />
| <partinfo>BBa_I746370</partinfo> || <partinfo>BBa_I746380</partinfo>||<partinfo>BBa_I746390</partinfo><br />
|-<br />
! PO promoter<br />
|<partinfo>BBa_I746371</partinfo><br />
|<partinfo>BBa_I746381</partinfo><br />
|<partinfo>BBa_I746391</partinfo><br />
|-<br />
! PP promoter<br />
|<partinfo>BBa_I746372</partinfo><br />
|<partinfo>BBa_I746382</partinfo><br />
|<partinfo>BBa_I746392</partinfo><br />
|-<br />
! Psid promoter<br />
|<partinfo>BBa_I746374</partinfo><br />
|<partinfo>BBa_I746384</partinfo><br />
|<partinfo>BBa_I746394</partinfo><br />
|-<br />
! PLL promoter<br />
|<partinfo>BBa_I746375</partinfo><br />
|<partinfo>BBa_I746385</partinfo><br />
|<partinfo>BBa_I746395</partinfo><br />
|}<br />
<br />
=== Maximum Rates against Arabinose Concentrations ===<br />
<br />
==== 80 ====<br />
[[Image:Cambridge_maxrates1.jpg | 600px]]<br />
<br />
==== 81 ====<br />
[[Image:Cambridge_maxrates2.jpg | 600px]]<br />
<br />
==== 82 ====<br />
[[Image:Cambridge_maxrates3.jpg | 600px]]<br />
<br />
==== 84 ====<br />
[[Image:Cambridge_maxrates4.jpg | 600px]]<br />
<br />
==== 85 ====<br />
[[Image:Cambridge_maxrates5.jpg | 600px]]<br />
<br />
==== 90 ====<br />
[[Image:Cambridge_maxrates6.jpg | 600px]]<br />
<br />
==== 92 ====<br />
[[Image:Cambridge_maxrates7.jpg | 600px]]<br />
<br />
==== 94 ====<br />
[[Image:Cambridge_maxrates8.jpg | 600px]]<br />
<br />
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