http://2009.igem.org/wiki/index.php?title=Special:Contributions/DRTarjan&feed=atom&limit=50&target=DRTarjan&year=&month=2009.igem.org - User contributions [en]2024-03-28T20:53:54ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/IGEM_PublicityIGEM Publicity2009-11-10T05:35:09Z<p>DRTarjan: /* team specific */</p>
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[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 />
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<div style="color:#aaa; padding-bottom:20px;">(Members of the press, please see the [[Press_Kit | iGEM Press Kit]])</div><br />
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<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 />
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====<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 />
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====<font size=5><font color=dodgerblue>'''news articles</font><font color=mediumseagreen> about iGEM 2009'''</font></font>====<br />
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<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 />
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Post the name of your team, the title of your article, where it was featured, and provide a link to it. <br />
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''Example'':<br> <br />
'''Team Example''': ''Title of article'', Nature, [link]<br />
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====<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 />
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====<font size=4><font color=dodgerblue>'''team specific'''</font></font>====<br />
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*'''[[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 />
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*'''[[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 />
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*'''[[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 />
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*'''[[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 />
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*'''[[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 />
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*'''[[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 />
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*'''[[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>DRTarjanhttp://2009.igem.org/Team:Virginia/PartsTeam:Virginia/Parts2009-10-22T03:58:50Z<p>DRTarjan: </p>
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==Natural==<br />
PCS: [http://partsregistry.org/Part:BBa_K231001 BBa_K231001]<br />
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==Synthetic==<br />
ABP: [http://partsregistry.org/Part:BBa_K231001 BBa_K231000]</div>DRTarjanhttp://2009.igem.org/Team:Virginia/EthicsTeam:Virginia/Ethics2009-10-22T03:57:26Z<p>DRTarjan: </p>
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==The Synthetic Biologist's Guide to Talking to the Media==<br />
[http://people.virginia.edu/~drt5p/VGEM/Virginia-Media_Guidelines_for_Synbiologists.pdf Download PDF pamphlet]</div>DRTarjanhttp://2009.igem.org/Team:Virginia/EthicsTeam:Virginia/Ethics2009-10-22T03:55:27Z<p>DRTarjan: New page: <html> <link rel="stylesheet" href="http://people.virginia.edu/~drt5p/VGEM/2009wiki/c-pop.css" type="text/css" /> <style type="text/css"> </style> <a href="https://2009.igem.org/wiki/index....</p>
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==The Synthetic Biologist's Guide to Talking to the Media==<br />
[http://people.virginia.edu/~drt5p/VGEM/Virginia-Media_Guidelines_for_Synbiologists.pdf Download PDF pamphlet]</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ApproachTeam:Virginia/Approach2009-10-22T03:51:49Z<p>DRTarjan: </p>
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__NOTOC__<br />
[[Image:Approach.png|200px]]<br />
[[Image:Ecol_nat.png|thumb|400px|The endogenuos ''E. coli'' arsenic detoxification pathway]]<br />
<div style="font-size: 150%">We had two goals: <br />
#Remove the arsenite efflux mechanism in ''E. coli'' <br />
#Create an arsenic sequestration mechanism</div><br />
<br />
<br />
=ArsB Knock-out=<br />
[[Image:Ecol_nat-ArsBKO.PNG|thumb|400px|Knocking out the arsB transmembrane ion transporter largely prevents efflux]]<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a [http://ecoli.naist.jp/GB6/info.jsp?id=JW3469 single gene knock-out for arsB] from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection]. This KO strain (JW3469) performed was verified in control growth curves in the presence of arsenic. (See [[Team:Virginia/Data|Results]]).<br />
<br />
<br />
=Sequestration Mechanism=<br />
Most microbial detoxification/resistance strategies involve efflux of heavy metals. In plants such as ''Arabidopsis'' such functions have not been observed. They may be explained by plants' inability to simply pump toxins into a surrounding solute. Instead they have evolved the ability to synthesize metallothioneins. ''Arabidopsis'' specifically synthesizes phytochelatins, a type of metallothionein. These cysteine rich peptides provide alternative binding sites for arsenic and other heavy metals. <br />
<br />
<br />
==Phytochelatin synthase==<br />
[[Image:Ecoli_mod2.png|thumb|400px|PCS synthesizes PC which binds and sequesters arsenic]]<br />
Part: [http://partsregistry.org/Part:BBa_K231001 BBa_K231001]<br />
This enzyme catalyzes the conversion of glutathione (GSH) to phytochelatin (PC). Its precursor GSH exists endogenously in ''E. coli'' making integration of PCS function relatively simple. The gene was codon and synthesized in an IPTG inducable pJexpress vector from DNA2.0. This construct was then expressed in JW3469. Induced samples displayed significantly faster growth in the presence of arsenic compared to uninduced samples. (See [[Team:Virginia/Data|Results]]).<br />
<br />
==Arsenic binding peptide==<br />
[[Image:Ecoli_mod1.png|thumb|400px|The synthetic metallothionein ABP binds As(III) much like PC]]<br />
Part: [http://partsregistry.org/Part:BBa_K231000 BBa_K231000]<br />
This synthetic peptide has the same properties as the natural PC which give it arsenic binding function. However we eliminated the need for the metabolically stressful synthesis and operation of an additional protein. The end product is relatively simple therefore it can be directly synthesized from amino acid precursors. ABP takes advantage of rational peptide engineering to optimize its binding properties.<br />
<br />
ABP was synthesized in an inducible expression vector much like PCS and expressed in KO cells. (See [[Team:Virginia/Data|Results]]).<br />
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<br />
<br />
<br />
<br />
=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
#*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
#*See above.<br />
# What does your local biosafety group think about your project?<br />
#*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
#*Hopefully they will make the world safer rather than raise safety issues! (No)</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ApproachTeam:Virginia/Approach2009-10-22T03:45:22Z<p>DRTarjan: /* Sequestration Mechanism */</p>
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__NOTOC__<br />
[[Image:Approach.png|200px]]<br />
[[Image:Ecol_nat.png|thumb|400px|The endogenuos ''E. coli'' arsenic detoxification pathway]]<br />
<div style="font-size: 150%">We had two goals: <br />
#Remove the arsenite efflux mechanism in ''E. coli'' <br />
#Create an arsenic sequestration mechanism</div><br />
<br />
<br />
=ArsB Knock-out=<br />
[[Image:Ecol_nat-ArsBKO.PNG|thumb|400px|Knocking out the arsB transmembrane ion transporter largely prevents efflux]]<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a [http://ecoli.naist.jp/GB6/info.jsp?id=JW3469 single gene knock-out for arsB] from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection]. This KO strain (JW3469) performed was verified in control growth curves in the presence of arsenic. (See [[Team:Virginia/Data|Results]]).<br />
<br />
<br />
=Sequestration Mechanism=<br />
Most microbial detoxification/resistance strategies involve efflux of heavy metals. In plants such as ''Arabidopsis'' such functions have not been observed. They may be explained by plants' inability to simply pump toxins into a surrounding solute. Instead they have evolved the ability to synthesize metallothioneins. ''Arabidopsis'' specifically synthesizes phytochelatins, a type of metallothionein. These cysteine rich peptides provide alternative binding sites for arsenic and other heavy metals. <br />
<br />
<br />
==Phytochelatin synthase==<br />
[[Image:Ecoli_mod2.png|thumb|400px|PCS synthesizes PC which binds and sequesters arsenic]]<br />
Part: [http://partsregistry.org/Part:BBa_K231001 BBa_K231001]<br />
This enzyme catalyzes the conversion of glutathione (GSH) to phytochelatin (PC). Its precursor GSH exists endogenously in ''E. coli'' making integration of PCS function relatively simple. The gene was codon and synthesized in an IPTG inducable pJexpress vector from DNA2.0. This construct was then expressed in JW3469. Induced samples displayed significantly faster growth in the presence of arsenic compared to uninduced samples. (See [[Team:Virginia/Data|Results]]).<br />
<br />
==Arsenic binding peptide==<br />
[[Image:Ecoli_mod1.png|thumb|400px|The synthetic metallothionein ABP binds As(III) much like PC]]<br />
Part: [http://partsregistry.org/Part:BBa_K231000 BBa_K231000]<br />
This synthetic peptide has the same properties as the natural PC which give it arsenic binding function. However we eliminated the need for the metabolically stressful synthesis and operation of an additional protein. The end product is relatively simple therefore it can be directly synthesized from amino acid precursors.<br />
ABP takes advantage of rational peptide engineering to optimize its binding properties.<br />
<br />
=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
#*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
#*See above.<br />
# What does your local biosafety group think about your project?<br />
#*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
#*Hopefully they will make the world safer rather than raise safety issues! (No)</div>DRTarjanhttp://2009.igem.org/File:Ecoli_mod1.pngFile:Ecoli mod1.png2009-10-22T03:41:18Z<p>DRTarjan: </p>
<hr />
<div></div>DRTarjanhttp://2009.igem.org/Team:Virginia/ApproachTeam:Virginia/Approach2009-10-22T03:39:02Z<p>DRTarjan: </p>
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__NOTOC__<br />
[[Image:Approach.png|200px]]<br />
[[Image:Ecol_nat.png|thumb|400px|The endogenuos ''E. coli'' arsenic detoxification pathway]]<br />
<div style="font-size: 150%">We had two goals: <br />
#Remove the arsenite efflux mechanism in ''E. coli'' <br />
#Create an arsenic sequestration mechanism</div><br />
<br />
<br />
=ArsB Knock-out=<br />
[[Image:Ecol_nat-ArsBKO.PNG|thumb|400px|Knocking out the arsB transmembrane ion transporter largely prevents efflux]]<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a [http://ecoli.naist.jp/GB6/info.jsp?id=JW3469 single gene knock-out for arsB] from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection]. This KO strain (JW3469) performed was verified in control growth curves in the presence of arsenic. (See [[Team:Virginia/Data|Results]]).<br />
<br />
<br />
=Sequestration Mechanism=<br />
Most microbial detoxification/resistance strategies involve efflux of heavy metals. In plants such as ''Arabidopsis'' such functions have not been observed. They may be explained by plants' inability to simply pump toxins into a surrounding solute. Instead they have evolved the ability to synthesize metallothioneins. ''Arabidopsis'' specifically synthesizes phytochelatins, a type of metallothionein. These cysteine rich peptides provide alternative binding sites for arsenic and other heavy metals. <br />
<br />
<br />
==Phytochelatin synthase==<br />
[[Image:Ecoli_mod2.png|thumb|400px|PCS synthesizes PC which binds and sequesters arsenic]]<br />
Part: [http://partsregistry.org/Part:BBa_K231001 BBa_K231001]<br />
This enzyme catalyzes the conversion of glutathione (GSH) to phytochelatin (PC). Its precursor GSH exists endogenously in ''E. coli'' making integration of PCS function relatively simple. The gene was codon and synthesized in an IPTG inducable pJexpress vector from DNA2.0. This construct was then expressed in JW3469. Induced samples displayed significantly faster growth in the presence of arsenic compared to uninduced samples. (See [[Team:Virginia/Data|Results]]).<br />
<br />
<br />
<br />
=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
#*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
#*See above.<br />
# What does your local biosafety group think about your project?<br />
#*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
#*Hopefully they will make the world safer rather than raise safety issues! (No)</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ApproachTeam:Virginia/Approach2009-10-22T03:28:33Z<p>DRTarjan: </p>
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<a href="https://2009.igem.org/wiki/index.php?title=Team:Virginia/Approach&action=edit">edit</a><br />
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__NOTOC__<br />
[[Image:Approach.png|200px]]<br />
[[Image:Ecol_nat.png|thumb|400px|The endogenuos ''E. coli'' arsenic detoxification pathway]]<br />
<div style="font-size: 150%">We had two goals: <br />
#Remove the arsenite efflux mechanism in ''E. coli'' <br />
#Create a sequestration mechanism</div><br />
<br />
<br />
=ArsB Knock-out=<br />
[[Image:Ecol_nat-ArsBKO.PNG|thumb|400px|Knocking out the arsB transmembrane ion transporter largely prevents efflux]]<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a [http://ecoli.naist.jp/GB6/info.jsp?id=JW3469 single gene knock-out for arsB] from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection].<br />
<br />
<br />
=Sequestration Mechanism=<br />
Most microbial detoxification/resistance strategies involve efflux of heavy metals. In plants such as ''Arabidopsis'' such functions have not been observed. They may be explained by plants' inability to simply pump toxins into a surrounding solute. Instead they have evolved the ability to synthesize metallothioneins. ''Arabidopsis'' specifically synthesizes phytochelatins, a type of metallothionein. These cysteine rich peptides provide alternative binding sites for arsenic and other heavy metals. <br />
==Phytochelatin synthase==<br />
<br />
=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
#*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
#*See above.<br />
# What does your local biosafety group think about your project?<br />
#*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
#*Hopefully they will make the world safer rather than raise safety issues! (No)</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ApproachTeam:Virginia/Approach2009-10-22T03:11:29Z<p>DRTarjan: </p>
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<br />
[[Image:Approach.png|200px]]<br />
[[Image:Ecol_nat.png|thumb|400px|The endogenuos ''E. coli'' arsenic detoxification pathway]]<br />
We had two goals: <br />
#Remove the arsenite efflux mechanism in ''E. coli'' <br />
#Create a sequestration mechanism<br />
<br />
<br />
<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a single gene knock-out from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection] for arsB.<br />
<br />
<br />
=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
#*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
#*See above.<br />
# What does your local biosafety group think about your project?<br />
#*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
#*Hopefully they will make the world safer rather than raise safety issues! (No)</div>DRTarjanhttp://2009.igem.org/File:Ecol_nat-ArsBKO.PNGFile:Ecol nat-ArsBKO.PNG2009-10-22T03:11:05Z<p>DRTarjan: </p>
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[[Image:Approach.png|200px]]<br />
<br />
We had two goals: <br />
#Remove the arsenite efflux mechanism in ''E. coli'' <br />
#Create a sequestration mechanism<br />
<br />
[[Image:Ecol_nat.png|thumb|400px|The endogenuos ''E. coli'' arsenic detoxification pathway]]<br />
<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a single gene knock-out from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection] for arsB.<br />
<br />
<br />
=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
#*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
#*See above.<br />
# What does your local biosafety group think about your project?<br />
#*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
#*Hopefully they will make the world safer rather than raise safety issues! (No)</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ApproachTeam:Virginia/Approach2009-10-22T02:57:04Z<p>DRTarjan: /* Safety */</p>
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=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
#*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
#*See above.<br />
# What does your local biosafety group think about your project?<br />
#*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
#*Hopefully they will make the world safer rather than raise safety issues! (No)</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ApproachTeam:Virginia/Approach2009-10-22T02:55:45Z<p>DRTarjan: </p>
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=Safety=<br />
# Would any of your project ideas raise safety issues in terms of: (researcher safety, public safety, or environmental safety?)<br />
*The University's Environmental Health and Safety department was involved in our project from the beginning. Team members absolved training to handle arsenic and proper precautions were taken in the lab for storage.<br />
# Is there a local biosafety group, committee, or review board at your institution?<br />
*See above.<br />
# What does your local biosafety group think about your project?<br />
*See above.<br />
# Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
*Hopefully they will make the world safer rather than raise safety issues!</div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-22T02:43:30Z<p>DRTarjan: /* Arsenic Sponge */</p>
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[[Image:Idea.png|200px]] [[Image:Spongeman.PNG]]<br />
=Biosequestration=<br />
The use of microbial species for environmental remediation of heavy metals has been extensively studied. They can be used to sequester, precipitate or modify heavy metals to detoxify them. Two major inorganic cations of arsenic are both toxic to varying degrees. (See [[Team:Virginia/Problem#Toxicity|''Toxicity'']]). <br />
<br />
<br />
=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. A successful biosequestration strategy needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
<br />
<br />
=Arsenic Sponge=<br />
This engineered strain of ''E. coli'' will absorb arsenic and sequester it, safely removing it from the surrounding environment. This will be accomplished by making it both deficient for the arsenic efflux pump gene and also incorporating an arsenic binding mechanism using metallothioneins. This class of cysteine rich peptides can bind arsenic, as well as other heavy metals, preventing it from interfering with cellular function.</div>DRTarjanhttp://2009.igem.org/Team:VirginiaTeam:Virginia2009-10-22T02:42:39Z<p>DRTarjan: </p>
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=Testing=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/Sandbox_popTeam:Virginia/Sandbox pop2009-10-22T02:31:17Z<p>DRTarjan: </p>
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=Testing=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/Sandbox_popTeam:Virginia/Sandbox pop2009-10-22T02:28:24Z<p>DRTarjan: </p>
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=Testing=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/Sandbox_popTeam:Virginia/Sandbox pop2009-10-22T02:25:08Z<p>DRTarjan: </p>
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=Testing=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/Sandbox_popTeam:Virginia/Sandbox pop2009-10-22T02:19:54Z<p>DRTarjan: </p>
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=Testing=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/Sandbox_popTeam:Virginia/Sandbox pop2009-10-22T02:19:10Z<p>DRTarjan: </p>
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=Testing=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/Sandbox_popTeam:Virginia/Sandbox pop2009-10-22T02:18:38Z<p>DRTarjan: </p>
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=Testing=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-22T02:04:59Z<p>DRTarjan: /* Arsenic Sponge */</p>
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[[Image:Idea.png|200px]] [[Image:Spongeman.PNG]]<br />
=Biosequestration=<br />
The use of microbial species for environmental remediation of heavy metals has been extensively studied. They can be used to sequester, precipitate or modify heavy metals to detoxify them. Two major inorganic cations of arsenic are both toxic to varying degrees. (See [[Team:Virginia/Problem#Toxicity|''Toxicity'']]). <br />
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=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. A successful biosequestration strategy needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
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=Arsenic Sponge=<br />
This engineered strain of ''E. coli'' will absorb arsenic and sequester it, safely removing it from the surrounding environment. This will be accomplished by making it both deficient for the arsenic efflux pump gene and also incorporating an arsenic binding mechanism using metallothioneins. This class of cysteine rich peptides can bind arsenic as well as other heavy metals, preventing it from interfering with cellular function.</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ProblemTeam:Virginia/Problem2009-10-22T01:58:33Z<p>DRTarjan: </p>
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=Arsenic Contamination=<br />
Ground-water contaminated with arsenic affects an estimated 137 million people worldwide. Existing water treatment methods are expensive and/or difficult to implement in a rural setting. This year we're exploring the possibility of using a ''bioremediation'' approach to tackle this issue. Can we harness the power of synthetic biology to help create an inexpensive arsenic sequestration mechanism? Here we present the work of the 2009 Virginia Team to create a prototype '''Arsenic Sponge'''.<br />
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(Cost analysis of other methods sidebar)<br />
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=Toxicity=</div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-22T01:57:16Z<p>DRTarjan: </p>
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[[Image:Idea.png|200px]] [[Image:Spongeman.PNG]]<br />
=Biosequestration=<br />
The use of microbial species for environmental remediation of heavy metals has been extensively studied. They can be used to sequester, precipitate or modify heavy metals to detoxify them. Two major inorganic cations of arsenic are both toxic to varying degrees. (See [[Team:Virginia/Problem#Toxicity|''Toxicity'']]). <br />
<br />
<br />
=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. A successful biosequestration strategy needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
<br />
<br />
=Arsenic Sponge=<br />
This engineered strain of ''E. coli'' is both deficient for the arsenic efflux pump gene and it also incorporates an arsenic binding mechanism using metallothioneins. This class of cysteine rich peptides can bind arsenic as well as other heavy metals, preventing it from interfering with cellular function. (Solubility?)<br />
<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a single gene knock-out from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection] for arsB.</div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-22T01:40:37Z<p>DRTarjan: </p>
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=Biosequestration=<br />
The use of microbial species for environmental remediation of heavy metals has been extensively studied. They can be used to sequester, precipitate or modify heavy metals to detoxify them. Two major inorganic cations of arsenic are both toxic to varying degrees. (See [[Team:Virginia/Problem#Toxicity|''Toxicity'']]). Precipitation would not be compatible with the requirement for this system to be simple to implement ...<br />
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=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. A successful biosequestration strategy needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
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=Arsenic Sponge=<br />
This engineered strain of ''E. coli'' is both deficient for the arsenic efflux pump gene and it also incorporates an arsenic binding mechanism using metallothioneins. This class of cysteine rich peptides can bind arsenic as well as other heavy metals, preventing it from interfering with cellular function. (Solubility?)<br />
<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a single gene knock-out from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection] for arsB.</div>DRTarjanhttp://2009.igem.org/File:Spongeman.PNGFile:Spongeman.PNG2009-10-22T01:34:07Z<p>DRTarjan: </p>
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<div></div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-22T01:31:22Z<p>DRTarjan: </p>
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=Biosequestration=<br />
The use of microbial species for environmental remediation of heavy metals has been extensively studied. They can be used to sequester, precipitate or modify heavy metals to detoxify them. Two major inorganic cations of arsenic are both toxic to varying degrees. (See [[Team:Virginia/Problem#Toxicity|''Toxicity'']]). Pre<br />
<br />
=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. A successful biosequestration strategy needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
<br />
=Arsenic Sponge=<br />
This engineered strain of ''E. coli'' is both deficient for the arsenic efflux pump gene and it also incorporates an arsenic binding mechanism using metallothioneins. This class of cysteine rich peptides can bind arsenic as well as other heavy metals, preventing it from interfering with cellular function. (Solubility?)<br />
<br />
''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a single gene knock-out from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection] for arsB.</div>DRTarjanhttp://2009.igem.org/File:Ecoli_mod2.pngFile:Ecoli mod2.png2009-10-22T01:18:05Z<p>DRTarjan: </p>
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<div></div>DRTarjanhttp://2009.igem.org/File:Ecol_nat.pngFile:Ecol nat.png2009-10-22T01:00:54Z<p>DRTarjan: uploaded a new version of "Image:Ecol nat.png"</p>
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<div></div>DRTarjanhttp://2009.igem.org/File:Ecol_nat.pngFile:Ecol nat.png2009-10-22T00:30:20Z<p>DRTarjan: </p>
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<div></div>DRTarjanhttp://2009.igem.org/File:Background3.gifFile:Background3.gif2009-10-21T22:48:30Z<p>DRTarjan: uploaded a new version of "Image:Background3.gif"</p>
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<div></div>DRTarjanhttp://2009.igem.org/Team:Virginia/TeamTeam:Virginia/Team2009-10-21T17:17:39Z<p>DRTarjan: /* Helping other Teams */</p>
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[[Image:V_Team.png|200px]]<br />
*Joe Bozzay (BME '10)<br />
*Maria Fini (BME '10)<br />
*Brandon Freshcorn (BME '10)<br />
*Rohini Manaktala (BME '11)<br />
*Dan Tarjan (Biology '10)<br />
*Thaddeus Webb (Biology '10)<br />
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==Advisors==<br />
*Erik Fernandez, Chemical Engineering<br />
*Inchan Kwon, Chemical Engineering<br />
*Jason Papin, Biomedical Engineering<br />
*Keith Kozminski, Biology<br />
*Michael Timko, Biology<br />
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==Special Thanks==<br />
*Kay Christopher<br />
*Kim Yasutis<br />
*Matt Oberhardt<br />
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=Helping other Teams=<br />
*We helped the Brown University team by supplying them with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K156010 BBa_K156010] as the version supplied by the registry did not seem functional.<br />
*The VCU team visited us here in Charlottesville, Va. on Oct 18, 2009 for a joint practice presentation session. Both teams received invaluable feedback on their projects and improved inter-university relations!<br />
[[Image:VGEM_VCU_meetup.jpg|500px|thumb|center|The VCU team visits for practice presentations]]</div>DRTarjanhttp://2009.igem.org/Team:Virginia/TeamTeam:Virginia/Team2009-10-21T17:17:18Z<p>DRTarjan: /* Helping other Teams */</p>
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[[Image:V_Team.png|200px]]<br />
*Joe Bozzay (BME '10)<br />
*Maria Fini (BME '10)<br />
*Brandon Freshcorn (BME '10)<br />
*Rohini Manaktala (BME '11)<br />
*Dan Tarjan (Biology '10)<br />
*Thaddeus Webb (Biology '10)<br />
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==Advisors==<br />
*Erik Fernandez, Chemical Engineering<br />
*Inchan Kwon, Chemical Engineering<br />
*Jason Papin, Biomedical Engineering<br />
*Keith Kozminski, Biology<br />
*Michael Timko, Biology<br />
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==Special Thanks==<br />
*Kay Christopher<br />
*Kim Yasutis<br />
*Matt Oberhardt<br />
<br />
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=Helping other Teams=<br />
*We helped the Brown University team by supplying them with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K156010 BBa_K156010] as the version supplied by the registry did not seem functional.<br />
*The VCU team visited us here in Charlottesville, Va. on Oct 18, 2009 for a joint practice presentation session. Both teams received invaluable feedback on their projects and improved inter-university relations!<br />
[[Image:VGEM_VCU_meetup.jpg|500px|thumb|center|The VCU team visits the Virginia for practice presentations]]</div>DRTarjanhttp://2009.igem.org/Team:Virginia/TeamTeam:Virginia/Team2009-10-21T17:15:59Z<p>DRTarjan: </p>
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[[Image:V_Team.png|200px]]<br />
*Joe Bozzay (BME '10)<br />
*Maria Fini (BME '10)<br />
*Brandon Freshcorn (BME '10)<br />
*Rohini Manaktala (BME '11)<br />
*Dan Tarjan (Biology '10)<br />
*Thaddeus Webb (Biology '10)<br />
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==Advisors==<br />
*Erik Fernandez, Chemical Engineering<br />
*Inchan Kwon, Chemical Engineering<br />
*Jason Papin, Biomedical Engineering<br />
*Keith Kozminski, Biology<br />
*Michael Timko, Biology<br />
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==Special Thanks==<br />
*Kay Christopher<br />
*Kim Yasutis<br />
*Matt Oberhardt<br />
<br />
<br />
=Helping other Teams=<br />
*We helped the Brown University team by supplying them with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K156010 BBa_K156010].<br />
*The VCU team visited us here in Charlottesville, Va. on Oct 18, 2009 for a joint practice presentation session. Both teams received invaluable feedback on their projects and improved inter-university relations!<br />
[[Image:VGEM_VCU_meetup.jpg|500px|thumb|center|The VCU team visits the Virginia for practice presentations]]</div>DRTarjanhttp://2009.igem.org/Team:Virginia/TeamTeam:Virginia/Team2009-10-21T17:15:43Z<p>DRTarjan: </p>
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[[Image:V_Team.png|200px]]<br />
*Joe Bozzay (BME '10)<br />
*Maria Fini (BME '10)<br />
*Brandon Freshcorn (BME '10)<br />
*Rohini Manaktala (BME '11)<br />
*Dan Tarjan (Biology '10)<br />
*Thaddeus Webb (Biology '10)<br />
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==Advisors==<br />
*Erik Fernandez, Chemical Engineering<br />
*Inchan Kwon, Chemical Engineering<br />
*Jason Papin, Biomedical Engineering<br />
*Keith Kozminski, Biology<br />
*Michael Timko, Biology<br />
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==Special Thanks==<br />
*Kay Christopher<br />
*Kim Yasutis<br />
*Matt Oberhardt<br />
<br />
=Helping other Teams=<br />
*We helped the Brown University team by supplying them with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K156010 BBa_K156010].<br />
*The VCU team visited us here in Charlottesville, Va. on Oct 18, 2009 for a joint practice presentation session. Both teams received invaluable feedback on their projects and improved inter-university relations!<br />
[[Image:VGEM_VCU_meetup.jpg|500px|thumb|center|The VCU team visits the Virginia for practice presentations]]</div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-21T17:01:35Z<p>DRTarjan: </p>
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=Biosequestration=<br />
(Intro about biosequestration)<br />
=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. A successful biosequestration strategy needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
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=Arsenic Sponge=<br />
This engineered strain of ''E. coli'' is both deficient for the arsenic efflux pump gene and it also incorporates an arsenic binding mechanism using metallothioneins. This class of cysteine rich peptides can bind arsenic as well as other heavy metals, preventing it from interfering with cellular function. (Solubility?)<br />
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''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB arsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a single gene knock-out from the [http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html Keio Collection] for arsB.</div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-21T17:00:41Z<p>DRTarjan: </p>
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=Biosequestration=<br />
(Intro about biosequestration)<br />
=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. A successful biosequestration strategy needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
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=Arsenic Sponge=<br />
This engineered strain of ''E. coli'' is both deficient for the arsenic efflux pump gene and it also incorporates an arsenic binding mechanism using metallothioneins. This class of cysteine rich peptides can bind arsenic as well as other heavy metals, preventing it from interfering with cellular function. (Solubility?)<br />
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''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB ArsB] ion transporter to specifically transport arsenite (As(III)) ions out of the cytoplasm. We obtained a single knock-out strain from the Keio Collection for arsB.</div>DRTarjanhttp://2009.igem.org/File:VGEM_VCU_meetup.jpgFile:VGEM VCU meetup.jpg2009-10-21T16:27:27Z<p>DRTarjan: </p>
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<div></div>DRTarjanhttp://2009.igem.org/Team:Virginia/PartsTeam:Virginia/Parts2009-10-21T16:18:01Z<p>DRTarjan: </p>
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{{ #calendar: title=Team:Virginia |year=2009 | month=05 | query=preload=Template:VirginiaNotebook2}}<br />
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{{ #calendar: title=Team:Virginia |year=2009 | month=08 | query=preload=Template:VirginiaNotebook2}}</div>DRTarjanhttp://2009.igem.org/Team:Virginia/TeamTeam:Virginia/Team2009-10-21T16:06:14Z<p>DRTarjan: </p>
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[[Image:Team.png|right|frame|Caption]]<br />
*Joe Bozzay (BME '10)<br />
*Maria Fini (BME '10)<br />
*Brandon Freshcorn (BME '10)<br />
*Rohini Manaktala (BME '11)<br />
*Dan Tarjan (Biology '10)<br />
*Thaddeus Webb (Biology '10)<br />
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==Advisors==<br />
*Erik Fernandez, Chemical Engineering<br />
*Inchan Kwon, Chemical Engineering<br />
*Jason Papin, Biomedical Engineering<br />
*Keith Kozminski, Biology<br />
*Michael Timko, Biology<br />
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==Special Thanks==<br />
*Kay Christopher<br />
*Kim Yasutis<br />
*Matt Oberhardt</div>DRTarjanhttp://2009.igem.org/Team:Virginia/IdeaTeam:Virginia/Idea2009-10-21T16:03:57Z<p>DRTarjan: </p>
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=Biosequestration=<br />
(Intro about biosequestration)<br />
=Storage and binding=<br />
Surveying evolved strategies for arsenic detoxification in bacteria shows that the most common mechanisms involve the efflux of arsenic ions. Our goal is to sequester arsenic, therefore to use a microbial chassis we must inhibit its efflux mechanism. However, storage of free arsenic ions in a cell will be toxic. Therefore a successful arsenic sponge needs to also incorporate a binding mechanism that allows the cell to accumulate significant amounts of arsenic. <br />
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''Escherichia coli'' uses the [http://ecoliwiki.net/colipedia/index.php/arsB ArsB] ion transporter</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ProblemTeam:Virginia/Problem2009-10-21T15:57:50Z<p>DRTarjan: </p>
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=Arsenic Contamination=<br />
Ground-water contaminated with arsenic affects an estimated 137 million people worldwide. Existing water treatment methods are expensive and/or difficult to implement in a rural setting. This year we're exploring the possibility of using a ''bioremediation'' approach to tackle this issue. Can we harness the power of synthetic biology to help create an inexpensive arsenic sequestration mechanism? Here we present the work of the 2009 Virginia Team to create a prototype '''Arsenic Sponge'''.<br />
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(Cost analysis of other methods sidebar)</div>DRTarjanhttp://2009.igem.org/Team:Virginia/ProblemTeam:Virginia/Problem2009-10-21T15:57:07Z<p>DRTarjan: </p>
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Ground-water contaminated with arsenic affects an estimated 137 million people worldwide. Existing water treatment methods are expensive and/or difficult to implement in a rural setting. This year we're exploring the possibility of using a ''bioremediation'' approach to tackle this issue. Can we harness the power of synthetic biology to help create an inexpensive arsenic sequestration mechanism? Here we present the work of the 2009 Virginia Team to create a prototype '''Arsenic Sponge'''.<br />
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(Cost analysis of other methods sidebar)</div>DRTarjan