http://2010.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=500&target=Kris2010.igem.org - User contributions [en]2024-03-29T02:27:08ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:UTDallas/Project_ProjectOverviewTeam:UTDallas/Project ProjectOverview2010-10-28T03:33:03Z<p>Kris: /* Project Overview */</p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Project_ProjectOverview Project Overview]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Introduction Introduction]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
== Project Overview ==<br />
<br />
Millions of gallons of toxic petroleum are released into the ocean each year as a result of accidents such as oil spills or natural geological seepage.<br />
<br />
Crude oil is a complex mixture of hydrocarbons consisting largely of n-alkane and aromatic hydrocarbons. Saturated hydrocarbons with linear or branched chains comprise the alkane series, which includes paraffinic hydrocarbons. Unsaturated hydrocarbons with benzene rings comprise the aromatic series, which includes the BTEX compounds.<br />
<br />
The World Water Assessment Program, the UN’s flagship water protection initiative, describes a host of health risks associated with these chemicals, some of which are enumerated in the table below (adapted from WWAP brochure)<br />
<br />
[[Image:WWAP_table.JPG]]<br />
<br />
While petroleum constituents are generally found around industry, nitrates are a common ingredient in fertilizers, whose use is widespread in agricultural practice. Nutrient-rich runoff enriches water sources such as lakes, rivers and aquifers with nitrates in a process called eutrophication. This facilitates the onset of algal blooms that deprive the native organisms of oxygen and essential nutrients. Afflicted water sources are difficult and expensive to restore and the process could further harm the wildlife.<br />
<br />
Due to stable, unreactive chemical structures, many of the aforementioned chemicals are persistent contaminants that circulate through the environment, thus polluting usable water supplies and marine ecosystems for extended periods of time. In fact, crude residues from the 2002 Prestige spill are still, 8 years later, encountered along Glacian shores. The need to control and mitigate the circulation of such chemicals is therefore both eminent and urgent. To that end, the UT Dallas iGEM team is developing novel, modular biosensors that enable cheap, on-site detection of aromatics, nitrates/nitrites and alkanes in low concentrations using an Escherichia coli chassis. <br />
<br />
The aromatics sensor builds on the previous work of the Michigan 2009 and Glasgow 2007 teams. Team Glasgow produced a successfully characterized fusion of the pR constitutive promoter and XylR transcription factor of the pu promoter. Team Michigan produced a fusion of the pu promoter and GFP, but failed to characterize the construct. The XylR protein forms a dimer with aromatic compounds, which positively regulates the pu promoter. In this way, E. coli co-transformed with these constructs can express GFP and demonstrate sensing capabilities in the presence of aromatics. We successfully characterized the function of the Michigan 2009 construct and demonstrated that it works as expected. <br />
<br />
[[Image:Xylene.png|600px]]]<br />
<br />
<br />
The nitrate/nitrite sensor builds on parts submitted by the Edinburgh 2009 team. This includes a fusion of the nitrate/nitrite-inducible pYeaR promoter and GFP. The pYeaR promoter is positively regulated by the presence of nitrates/nitrites, thus driving the transcription of GFP. This work improves the characterization of these parts by expanding on sensing capabilities using GFP and RFP reporter systems and induction by a variety of nitrate/nitrite compounds.<br />
<br />
[[Image:Nitrate.png|400px]]]<br />
<br />
<br />
The alkane sensor includes components of the alkane metabolic pathway of Pseudomonas putida OCT. The promoter region pAlkB drives the transcription of the alk gene cluster. AlkS, its transcription factor, is encoded by the alkS gene. We ordered oligonucleotides from Sigma-Aldrich containing the appropriate sticky ends for the fusion of pAlkB to a fluorescent protein part to form a reporter construct. A plasmid containing alkS was kindly provided by Dr. Jan Roelof van der Meer of the University of Lausanne in Switzerland, who helped pioneer luminescent whole-cell biosensors. AlkS binds to n-alkanes to form a dimer that positively regulates the pAlkB promoter to drive the expression of fluorescent protein. The two plasmids containing the promoter/fluorescent protein fusion and the AlkS transcription factor were to be co-transformed into DH5a to characterize sensing capabilities. Unfortunately, we were unable to realize the alkane sensor component due to issues with the ligation of the ordered oligonucleotides to the iGEM backbone. We tried various other approaches including ligation after dephosphorylation of the vector and phosphorylation of the insert as well as blunt-end ligations. After a number of trials, pAlkB failed to properly ligate onto the iGEM backbone. We assess that this was due to compatible sticky ends that caused it to repeatedly self-ligate.<br />
<br />
[[Image:Alkane.png|600px]]]</div>Krishttp://2010.igem.org/Team:UTDallas/Project_ProjectOverviewTeam:UTDallas/Project ProjectOverview2010-10-28T03:29:37Z<p>Kris: /* Project Overview */</p>
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{| style="color:gold;background-color:#666666;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="100%" align="center"<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_ProjectOverview Project Overview]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Introduction Introduction]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
== Project Overview ==<br />
<br />
Millions of gallons of toxic petroleum are released into the ocean each year as a result of accidents such as oil spills or natural geological seepage.<br />
<br />
Crude oil is a complex mixture of hydrocarbons consisting largely of n-alkane and aromatic hydrocarbons. Saturated hydrocarbons with linear or branched chains comprise the alkane series, which includes paraffinic hydrocarbons. Unsaturated hydrocarbons with benzene rings comprise the aromatic series, which includes the BTEX compounds.<br />
<br />
The World Water Assessment Program, the UN’s flagship water protection initiative, describes a host of health risks associated with these chemicals, some of which are enumerated in the table below (adapted from WWAP brochure)<br />
<br />
[[Image:WWAP_table.JPG]]<br />
<br />
While petroleum constituents are generally found around industry, nitrates are a common ingredient in fertilizers, whose use is widespread in agricultural practice. Nutrient-rich runoff enriches water sources such as lakes, rivers and aquifers with nitrates in a process called eutrophication. This facilitates the onset of algal blooms that deprive the native organisms of oxygen and essential nutrients. Afflicted water sources are difficult and expensive to restore and the process could further harm the wildlife.<br />
<br />
Due to stable, unreactive chemical structures, many of the aforementioned chemicals are persistent contaminants that circulate through the environment, thus polluting usable water supplies and marine ecosystems for extended periods of time. In fact, crude residues from the 2002 Prestige spill are still, 8 years later, encountered along Glacian shores. The need to control and mitigate the circulation of such chemicals is therefore both eminent and urgent. To that end, the UT Dallas iGEM team is developing novel, modular biosensors that enable cheap, on-site detection of aromatics, nitrates/nitrites and alkanes in low concentrations using an Escherichia coli chassis. <br />
<br />
The aromatics sensor builds on the previous work of the Michigan 2009 and Glasgow 2007 teams. Team Glasgow produced a successfully characterized fusion of the pR constitutive promoter and XylR transcription factor of the pu promoter. Team Michigan produced a fusion of the pu promoter and GFP, but failed to characterize the construct. The XylR protein forms a dimer with aromatic compounds, which positively regulates the pu promoter. In this way, E. coli co-transformed with these constructs can express GFP and demonstrate sensing capabilities in the presence of aromatics. We successfully characterized the function of the Michigan 2009 construct and demonstrated that it works as expected. <br />
<br />
[[Image:Xylene.png|250px]]]<br />
<br />
<br />
The nitrate/nitrite sensor builds on parts submitted by the Edinburgh 2009 team. This includes a fusion of the nitrate/nitrite-inducible pYeaR promoter and GFP. The pYeaR promoter is positively regulated by the presence of nitrates/nitrites, thus driving the transcription of GFP. This work improves the characterization of these parts by expanding on sensing capabilities using GFP and RFP reporter systems and induction by a variety of nitrate/nitrite compounds.<br />
<br />
[[Image:Nitrate.png|150px]]]<br />
<br />
<br />
The alkane sensor includes components of the alkane metabolic pathway of Pseudomonas putida OCT. The promoter region pAlkB drives the transcription of the alk gene cluster. AlkS, its transcription factor, is encoded by the alkS gene. We ordered oligonucleotides from Sigma-Aldrich containing the appropriate sticky ends for the fusion of pAlkB to a fluorescent protein part to form a reporter construct. A plasmid containing alkS was kindly provided by Dr. Jan Roelof van der Meer of the University of Lausanne in Switzerland, who helped pioneer luminescent whole-cell biosensors. AlkS binds to n-alkanes to form a dimer that positively regulates the pAlkB promoter to drive the expression of fluorescent protein. The two plasmids containing the promoter/fluorescent protein fusion and the AlkS transcription factor were to be co-transformed into DH5a to characterize sensing capabilities. Unfortunately, we were unable to realize the alkane sensor component due to issues with the ligation of the ordered oligonucleotides to the iGEM backbone. We tried various other approaches including ligation after dephosphorylation of the vector and phosphorylation of the insert as well as blunt-end ligations. After a number of trials, pAlkB failed to properly ligate onto the iGEM backbone. We assess that this was due to compatible sticky ends that caused it to repeatedly self-ligate.<br />
<br />
[[Image:Alkane.png|250px]]]</div>Krishttp://2010.igem.org/Team:UTDallas/Project_ProjectOverviewTeam:UTDallas/Project ProjectOverview2010-10-28T03:20:39Z<p>Kris: /* Project Overview */</p>
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{| style="color:gold;background-color:#666666;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="100%" align="center"<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_ProjectOverview Project Overview]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Introduction Introduction]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
== Project Overview ==<br />
<br />
Millions of gallons of toxic petroleum are released into the ocean each year as a result of accidents such as oil spills or natural geological seepage.<br />
<br />
Crude oil is a complex mixture of hydrocarbons consisting largely of n-alkane and aromatic hydrocarbons. Saturated hydrocarbons with linear or branched chains comprise the alkane series, which includes paraffinic hydrocarbons. Unsaturated hydrocarbons with benzene rings comprise the aromatic series, which includes the BTEX compounds.<br />
<br />
The World Water Assessment Program, the UN’s flagship water protection initiative, describes a host of health risks associated with these chemicals, some of which are enumerated in the table below (adapted from WWAP brochure)<br />
<br />
[[Image:WWAP_table.JPG]]<br />
<br />
While petroleum constituents are generally found around industry, nitrates are a common ingredient in fertilizers, whose use is widespread in agricultural practice. Nutrient-rich runoff enriches water sources such as lakes, rivers and aquifers with nitrates in a process called eutrophication. This facilitates the onset of algal blooms that deprive the native organisms of oxygen and essential nutrients. Afflicted water sources are difficult and expensive to restore and the process could further harm the wildlife.<br />
<br />
Due to stable, unreactive chemical structures, many of the aforementioned chemicals are persistent contaminants that circulate through the environment, thus polluting usable water supplies and marine ecosystems for extended periods of time. In fact, crude residues from the 2002 Prestige spill are still, 8 years later, encountered along Glacian shores. The need to control and mitigate the circulation of such chemicals is therefore both eminent and urgent. To that end, the UT Dallas iGEM team is developing novel, modular biosensors that enable cheap, on-site detection of aromatics, nitrates/nitrites and alkanes in low concentrations using an Escherichia coli chassis. <br />
<br />
The aromatics sensor builds on the previous work of the Michigan 2009 and Glasgow 2007 teams. Team Glasgow produced a successfully characterized fusion of the pR constitutive promoter and XylR transcription factor of the pu promoter. Team Michigan produced a fusion of the pu promoter and GFP, but failed to characterize the construct. The XylR protein forms a dimer with aromatic compounds, which positively regulates the pu promoter. In this way, E. coli co-transformed with these constructs can express GFP and demonstrate sensing capabilities in the presence of aromatics. We successfully characterized the function of the Michigan 2009 construct and demonstrated that it works as expected. <br />
<br />
[[Image:Xylene.png|600px]]]<br />
<br />
<br />
The nitrate/nitrite sensor builds on parts submitted by the Edinburgh 2009 team. This includes a fusion of the nitrate/nitrite-inducible pYeaR promoter and GFP. The pYeaR promoter is positively regulated by the presence of nitrates/nitrites, thus driving the transcription of GFP. This work improves the characterization of these parts by expanding on sensing capabilities using GFP and RFP reporter systems and induction by a variety of nitrate/nitrite compounds.<br />
<br />
[[Image:Nitrate.png|300px]]]<br />
<br />
<br />
The alkane sensor includes components of the alkane metabolic pathway of Pseudomonas putida OCT. The promoter region pAlkB drives the transcription of the alk gene cluster. AlkS, its transcription factor, is encoded by the alkS gene. We ordered oligonucleotides from Sigma-Aldrich containing the appropriate sticky ends for the fusion of pAlkB to a fluorescent protein part to form a reporter construct. A plasmid containing alkS was kindly provided by Dr. Jan Roelof van der Meer of the University of Lausanne in Switzerland, who helped pioneer luminescent whole-cell biosensors. AlkS binds to n-alkanes to form a dimer that positively regulates the pAlkB promoter to drive the expression of fluorescent protein. The two plasmids containing the promoter/fluorescent protein fusion and the AlkS transcription factor were to be co-transformed into DH5a to characterize sensing capabilities. Unfortunately, we were unable to realize the alkane sensor component due to issues with the ligation of the ordered oligonucleotides to the iGEM backbone. We tried various other approaches including ligation after dephosphorylation of the vector and phosphorylation of the insert as well as blunt-end ligations. After a number of trials, pAlkB failed to properly ligate onto the iGEM backbone. We assess that this was due to compatible sticky ends that caused it to repeatedly self-ligate.<br />
<br />
[[Image:Alkane.png|500px]]]</div>Krishttp://2010.igem.org/Team:UTDallas/Project_ProjectOverviewTeam:UTDallas/Project ProjectOverview2010-10-28T03:18:33Z<p>Kris: /* Project Overview */</p>
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{| style="color:gold;background-color:#666666;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="100%" align="center"<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_ProjectOverview Project Overview]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Introduction Introduction]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
== Project Overview ==<br />
<br />
Millions of gallons of toxic petroleum are released into the ocean each year as a result of accidents such as oil spills or natural geological seepage.<br />
<br />
Crude oil is a complex mixture of hydrocarbons consisting largely of n-alkane and aromatic hydrocarbons. Saturated hydrocarbons with linear or branched chains comprise the alkane series, which includes paraffinic hydrocarbons. Unsaturated hydrocarbons with benzene rings comprise the aromatic series, which includes the BTEX compounds.<br />
<br />
The World Water Assessment Program, the UN’s flagship water protection initiative, describes a host of health risks associated with these chemicals, some of which are enumerated in the table below (adapted from WWAP brochure)<br />
<br />
[[Image:WWAP_table.JPG]]<br />
<br />
While petroleum constituents are generally found around industry, nitrates are a common ingredient in fertilizers, whose use is widespread in agricultural practice. Nutrient-rich runoff enriches water sources such as lakes, rivers and aquifers with nitrates in a process called eutrophication. This facilitates the onset of algal blooms that deprive the native organisms of oxygen and essential nutrients. Afflicted water sources are difficult and expensive to restore and the process could further harm the wildlife.<br />
<br />
Due to stable, unreactive chemical structures, many of the aforementioned chemicals are persistent contaminants that circulate through the environment, thus polluting usable water supplies and marine ecosystems for extended periods of time. In fact, crude residues from the 2002 Prestige spill are still, 8 years later, encountered along Glacian shores. The need to control and mitigate the circulation of such chemicals is therefore both eminent and urgent. To that end, the UT Dallas iGEM team is developing novel, modular biosensors that enable cheap, on-site detection of aromatics, nitrates/nitrites and alkanes in low concentrations using an Escherichia coli chassis. <br />
<br />
The aromatics sensor builds on the previous work of the Michigan 2009 and Glasgow 2007 teams. Team Glasgow produced a successfully characterized fusion of the pR constitutive promoter and XylR transcription factor of the pu promoter. Team Michigan produced a fusion of the pu promoter and GFP, but failed to characterize the construct. The XylR protein forms a dimer with aromatic compounds, which positively regulates the pu promoter. In this way, E. coli co-transformed with these constructs can express GFP and demonstrate sensing capabilities in the presence of aromatics. We successfully characterized the function of the Michigan 2009 construct and demonstrated that it works as expected. <br />
[[Image:Xylene.png]]<br />
<br />
<br />
The nitrate/nitrite sensor builds on parts submitted by the Edinburgh 2009 team. This includes a fusion of the nitrate/nitrite-inducible pYeaR promoter and GFP. The pYeaR promoter is positively regulated by the presence of nitrates/nitrites, thus driving the transcription of GFP. This work improves the characterization of these parts by expanding on sensing capabilities using GFP and RFP reporter systems and induction by a variety of nitrate/nitrite compounds.<br />
[[Image:Nitrate.png]]<br />
<br />
<br />
The alkane sensor includes components of the alkane metabolic pathway of Pseudomonas putida OCT. The promoter region pAlkB drives the transcription of the alk gene cluster. AlkS, its transcription factor, is encoded by the alkS gene. We ordered oligonucleotides from Sigma-Aldrich containing the appropriate sticky ends for the fusion of pAlkB to a fluorescent protein part to form a reporter construct. A plasmid containing alkS was kindly provided by Dr. Jan Roelof van der Meer of the University of Lausanne in Switzerland, who helped pioneer luminescent whole-cell biosensors. AlkS binds to n-alkanes to form a dimer that positively regulates the pAlkB promoter to drive the expression of fluorescent protein. The two plasmids containing the promoter/fluorescent protein fusion and the AlkS transcription factor were to be co-transformed into DH5a to characterize sensing capabilities. Unfortunately, we were unable to realize the alkane sensor component due to issues with the ligation of the ordered oligonucleotides to the iGEM backbone. We tried various other approaches including ligation after dephosphorylation of the vector and phosphorylation of the insert as well as blunt-end ligations. After a number of trials, pAlkB failed to properly ligate onto the iGEM backbone. We assess that this was due to compatible sticky ends that caused it to repeatedly self-ligate.<br />
[[Image:Alkane.png]]</div>Krishttp://2010.igem.org/File:Xylene.pngFile:Xylene.png2010-10-28T03:15:19Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/File:Nitrate.pngFile:Nitrate.png2010-10-28T03:14:06Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/File:Alkane.pngFile:Alkane.png2010-10-28T03:12:25Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/Team:UTDallas/Project_ProjectOverviewTeam:UTDallas/Project ProjectOverview2010-10-28T03:08:15Z<p>Kris: /* Project Overview */</p>
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{| style="color:gold;background-color:#666666;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="100%" align="center"<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_ProjectOverview Project Overview]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Introduction Introduction]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
== Project Overview ==<br />
<br />
Millions of gallons of toxic petroleum are released into the ocean each year as a result of accidents such as oil spills or natural geological seepage.<br />
<br />
Crude oil is a complex mixture of hydrocarbons consisting largely of n-alkane and aromatic hydrocarbons. Saturated hydrocarbons with linear or branched chains comprise the alkane series, which includes paraffinic hydrocarbons. Unsaturated hydrocarbons with benzene rings comprise the aromatic series, which includes the BTEX compounds.<br />
<br />
The World Water Assessment Program, the UN’s flagship water protection initiative, describes a host of health risks associated with these chemicals, some of which are enumerated in the table below (adapted from WWAP brochure)<br />
<br />
[[Image:WWAP_table.JPG]]<br />
<br />
While petroleum constituents are generally found around industry, nitrates are a common ingredient in fertilizers, whose use is widespread in agricultural practice. Nutrient-rich runoff enriches water sources such as lakes, rivers and aquifers with nitrates in a process called eutrophication. This facilitates the onset of algal blooms that deprive the native organisms of oxygen and essential nutrients. Afflicted water sources are difficult and expensive to restore and the process could further harm the wildlife.<br />
<br />
Due to stable, unreactive chemical structures, many of the aforementioned chemicals are persistent contaminants that circulate through the environment, thus polluting usable water supplies and marine ecosystems for extended periods of time. In fact, crude residues from the 2002 Prestige spill are still, 8 years later, encountered along Glacian shores. The need to control and mitigate the circulation of such chemicals is therefore both eminent and urgent. To that end, the UT Dallas iGEM team is developing novel, modular biosensors that enable cheap, on-site detection of aromatics, nitrates/nitrites and alkanes in low concentrations using an Escherichia coli chassis. <br />
<br />
The aromatics sensor builds on the previous work of the Michigan 2009 and Glasgow 2007 teams. Team Glasgow produced a successfully characterized fusion of the pR constitutive promoter and XylR transcription factor of the pu promoter. Team Michigan produced a fusion of the pu promoter and GFP, but failed to characterize the construct. The XylR protein forms a dimer with aromatic compounds, which positively regulates the pu promoter. In this way, E. coli co-transformed with these constructs can express GFP and demonstrate sensing capabilities in the presence of aromatics. We successfully characterized the function of the Michigan 2009 construct and demonstrated that it works as expected. <br />
<br />
The nitrate/nitrite sensor builds on parts submitted by the Edinburgh 2009 team. This includes a fusion of the nitrate/nitrite-inducible pYeaR promoter and GFP. The pYeaR promoter is positively regulated by the presence of nitrates/nitrites, thus driving the transcription of GFP. This work improves the characterization of these parts by expanding on sensing capabilities using a GFP reporter system and induction by a variety of nitrate/nitrite compounds.<br />
<br />
The alkane sensor includes components of the alkane metabolic pathway of Pseudomonas putida OCT. The promoter region pAlkB drives the transcription of the alk gene cluster. AlkS, its transcription factor, is encoded by the alkS gene. We ordered oligonucleotides from Sigma-Aldrich containing the appropriate sticky ends for the fusion of pAlkB to a fluorescent protein part to form a reporter construct. A plasmid containing alkS was kindly provided by Dr. Jan Roelof van der Meer of the University of Lausanne in Switzerland, who helped pioneer luminescent whole-cell biosensors. AlkS binds to n-alkanes to form a dimer that positively regulates the pAlkB promoter to drive the expression of fluorescent protein. The two plasmids containing the promoter/fluorescent protein fusion and the AlkS transcription factor were to be co-transformed into DH5a to characterize sensing capabilities. Unfortunately, we were unable to realize the alkane sensor component due to issues with the ligation of the ordered oligonucleotides to the iGEM backbone. We tried various other approaches including ligation after dephosphorylation of the vector and phosphorylation of the insert as well as blunt-end ligations. After a number of trials, pAlkB failed to properly ligate onto the iGEM backbone. We assess that this was due to compatible sticky ends that caused it to repeatedly self-ligate.</div>Krishttp://2010.igem.org/Team:UTDallas/TeamTeam:UTDallas/Team2010-10-28T03:06:41Z<p>Kris: /* Pictures */</p>
<hr />
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{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
=Advisors=<br />
====Dr. Leonidas Bleris====<br />
I am an Assistant Professor with the Electrical Engineering Department of the University of Texas at Dallas.<br />
<br />
====Dr. Hyun-Joo Nam====<br />
I am an Assistant Professor with the Bioengineering Department of the University of Texas at Dallas.<br />
<br />
=Students=<br />
====Jacob White====<br />
<div style="clear:both;"></div><br />
I am a PhD student in Biomedical Engineering at UTD. I have a BS in Electrical Engineering and a BS in Biochemistry.<br />
<br />
====Sameer Sant====<br />
I am an sophomore molecular biology major at UT Dallas.<br />
<div style="clear:both;"></div><br />
<br />
====Kristina Ehrhardt====<br />
<br />
<div style="clear:both;"></div><br />
I am a senior Biochemistry undergraduate student at UTD.<br />
<br />
====Mitu Bhattatiry====<br />
<!--[[Image:NSERL_windows.PNG|left|100x200px]]--><br />
I am a high school student and a rising senior at Coppell High School. I am researching at UTD through the Nanoexplorers program at the Nanotech Institute. I think iGEM is a truly unique experience and I am looking forward to the iGEM Jamboree in November!<br />
<div style="clear:both;"></div><br />
<br />
====Lagnajeet Pradhan====<br />
I am doing my Masters in Biomedical engineering at UTD. <br />
<div style="clear:both;"></div><br />
</span><br />
<br />
=Acknowledgements=<br />
<br />
UT Dallas iGEM would like to acknowledge Dr. Jan Roelof van der Meer of the University of Lausanne for kindly providing us with a plasmid containing the alkS gene.<br />
<br />
=Pictures=<br />
[[Image:Kristina.JPG|250px]]<br />
*Kristina working with the fluorescence microscope<br />
[[Image:OurLab2.JPG|250px]]<br />
*Sameer, Mitu, and LP in the lab<br />
[[Image:LP.JPG|250px]]<br />
*LP at work in the lab<br />
[[Image:Schedule.JPG|250px]]<br />
*Sameer and Kristina working on our schedule<br />
[[Image:Sameer.JPG|250px]]<br />
*Sameer playing tic tac toe<br />
[[Image:Everyone.JPG|250px]]<br />
*Our team hard at work</div>Krishttp://2010.igem.org/File:Sameer.JPGFile:Sameer.JPG2010-10-28T03:05:38Z<p>Kris: uploaded a new version of "Image:Sameer.JPG"</p>
<hr />
<div></div>Krishttp://2010.igem.org/File:Schedule.JPGFile:Schedule.JPG2010-10-28T03:04:12Z<p>Kris: uploaded a new version of "Image:Schedule.JPG"</p>
<hr />
<div></div>Krishttp://2010.igem.org/File:LP.JPGFile:LP.JPG2010-10-28T03:03:07Z<p>Kris: uploaded a new version of "Image:LP.JPG"</p>
<hr />
<div></div>Krishttp://2010.igem.org/File:OurLab2.JPGFile:OurLab2.JPG2010-10-28T03:00:25Z<p>Kris: uploaded a new version of "Image:OurLab2.JPG"</p>
<hr />
<div></div>Krishttp://2010.igem.org/Team:UTDallas/SafetyTeam:UTDallas/Safety2010-10-28T02:58:25Z<p>Kris: /* Safety */</p>
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<span style="color:#EDE8E8"><br />
==Safety==<br />
<br />
Please use this page to answer the safety questions posed on the [[Safety | safety page]].<br />
<br />
Safety Questions: <br><br />
'''1. Would any of your project ideas raise safety issues in terms of researcher, public, or environmental safety?''' <br><br />
*Materials that pose a safety risk (i.e. cell cultures, ethidium bromide, UV transilluminator, etc) are handled according to standard lab safety protocol and Materials Safety Data Sheets. Materials containing safety hazards are disposed in separate containers with “biohazard” designations. Appropriate protective gear, such as gloves, is worn at all times. Our bacterial chassis, E. coli DH5α, is disabled to where it is nonpathogenic and cannot survive outside of lab conditions. In addition, all exposed counters are disinfected using 70% ethanol after each use of the lab. All lab equipment is thoroughly cleaned and autoclaved after use and access to the lab is limited by cardkey. <br />
'''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?''' <br><br />
*We worked with genes encoding known properties and utilized safety measures to ensure that biohazardous materials including antibiotic-resistant cells are contained within the lab and are appropriately disposed. Therefore, we assess that none of our submitted parts raise safety issues.<br />
'''3. Is there a local biosafety group, committee, or review board at your institution?''' <br><br />
*UT Dallas has an Institutional Biosafety Committee that manages all safety responsibilities under NIH “Guidelines for Research Involving Recombinant DNA Molecules”. Throughout the course of this work, we ensured that all lab activity respected safety measures. <br />
'''4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?''' <br><br />
*The iGEM plasmid backbone could be programmed to include an "inactivation mechanism" whose induction can be used to regulate the activity of cells endowed with BioBrick parts. Disseminating pertinent safety information through the Registry is a practical alternative to engineering biosafety measures into parts, devices and systems.<br />
<br />
</span></div>Krishttp://2010.igem.org/Team:UTDallas/SafetyTeam:UTDallas/Safety2010-10-28T02:57:39Z<p>Kris: /* Safety */</p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
==Safety==<br />
<br />
Please use this page to answer the safety questions posed on the [[Safety | safety page]].<br />
<br />
Safety Questions: <br><br />
'''1. Would any of your project ideas raise safety issues in terms of researcher, public, or environmental safety?''' <br><br />
*Materials that pose a safety risk (i.e. cell cultures, ethidium bromide, UV transilluminator, etc) are handled according to standard lab safety protocol and Materials Safety Data Sheets. Materials containing safety hazards are disposed in separate containers with “biohazard” designations. Appropriate protective gear, such as gloves, is worn at all times. Our bacterial chassis, E. coli DH5α, is disabled to where it is nonpathogenic and cannot survive outside of lab conditions. In addition, all exposed counters are disinfected using 70% ethanol after each use of the lab. All lab equipment is thoroughly cleaned and autoclaved after use and access to the lab is limited by cardkey. <br />
'''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?''' <br><br />
*We worked with genes encoding known properties and utilized safety measures to ensure that biohazardous materials including antibiotic-resistant cells are contained within the lab and are appropriately disposed. Therefore, we assess that none of our submitted parts raise safety issues.<br />
'''3. Is there a local biosafety group, committee, or review board at your institution?''' <br><br />
*UT Dallas has an Institutional Biosafety Committee (http://provost.utdallas.edu/policy/utdpp1016) that manages all safety responsibilities under NIH “Guidelines for Research Involving Recombinant DNA Molecules”. Throughout the course of this work, we ensured that all lab activity respected safety measures. <br />
'''4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?''' <br><br />
*The iGEM plasmid backbone could be programmed to include an "inactivation mechanism" whose induction can be used to regulate the activity of cells endowed with BioBrick parts. Disseminating pertinent safety information through the Registry is a practical alternative to engineering biosafety measures into parts, devices and systems.<br />
<br />
</span></div>Krishttp://2010.igem.org/Team:UTDallas/TeamTeam:UTDallas/Team2010-10-28T02:54:05Z<p>Kris: /* Pictures */</p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
=Advisors=<br />
====Dr. Leonidas Bleris====<br />
I am an Assistant Professor with the Electrical Engineering Department of the University of Texas at Dallas.<br />
<br />
====Dr. Hyun-Joo Nam====<br />
I am an Assistant Professor with the Bioengineering Department of the University of Texas at Dallas.<br />
<br />
=Students=<br />
====Jacob White====<br />
<div style="clear:both;"></div><br />
I am a PhD student in Biomedical Engineering at UTD. I have a BS in Electrical Engineering and a BS in Biochemistry.<br />
<br />
====Sameer Sant====<br />
I am an sophomore molecular biology major at UT Dallas.<br />
<div style="clear:both;"></div><br />
<br />
====Kristina Ehrhardt====<br />
<br />
<div style="clear:both;"></div><br />
I am a senior Biochemistry undergraduate student at UTD.<br />
<br />
====Mitu Bhattatiry====<br />
<!--[[Image:NSERL_windows.PNG|left|100x200px]]--><br />
I am a high school student and a rising senior at Coppell High School. I am researching at UTD through the Nanoexplorers program at the Nanotech Institute. I think iGEM is a truly unique experience and I am looking forward to the iGEM Jamboree in November!<br />
<div style="clear:both;"></div><br />
<br />
====Lagnajeet Pradhan====<br />
I am doing my Masters in Biomedical engineering at UTD. <br />
<div style="clear:both;"></div><br />
</span><br />
<br />
=Pictures=<br />
[[Image:Kristina.JPG|250px]]<br />
*Kristina working with the fluorescence microscope<br />
[[Image:OurLab2.JPG|250px]]<br />
*Sameer, Mitu, and LP in the lab<br />
[[Image:LP.JPG|250px]]<br />
*LP at work in the lab<br />
[[Image:Schedule.JPG|250px]]<br />
*Sameer and Kristina working on our schedule<br />
[[Image:Sameer.JPG|250px]]<br />
*Sameer playing tic tac toe<br />
[[Image:Everyone.JPG|250px]]<br />
*Our lab hard at work</div>Krishttp://2010.igem.org/File:OurLab2.JPGFile:OurLab2.JPG2010-10-28T02:52:23Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/File:Everyone.JPGFile:Everyone.JPG2010-10-28T02:49:50Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T02:48:14Z<p>Kris: /* Results */</p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
<br />
===Results===<br />
*All images were taken with Olympus IX81 automated inverted microscope specially equipped for live cell imaging. All experiments were performed with DH5α E.coli cells. The filter sets we used are: 545/30x (excitation) and 620/60m (emission) filters for DsRed, 470/40x (excitation) and 525/50m (emission) for GFP. Data collection and processing was performed by the SlideBook software.<br />
*The data was taken using cells that were grown overnight in 2mL of LB broth that had 50ug/mL of the appropriate antibiotic at 37C and 220rpm. This was used in a 1:50 dilution. Each sample had 40uL from the broth grown overnight and 2mL of the LB broth with the appropriate antibiotic. These were allowed to grow until a predetermined OD. Then the contaminants were added and the cells were allowed to grow for another 2 hours, before the images were taken.<br />
<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
*The images shown are the images used to get the data. From left to right the image is the negative control to a 10mM concentration of the respective contaminants. The graph shows the average of all the maximum intensities of the cells in the image vs the concentration of nitrate/nitrite added to the sample. The data shows that PyeaR+GFP responds better to nitrates than nitrites. It also shows that the cell is more sensitive to aluminum nitrate nonahydrate, and therefore starts dying at a lower concentration. <br />
<br />
<br />
*PyeaR+GFP(BBa_K412000) Timelapse images<br />
[[Image:tileview.jpg | 650 px | center]]<br />
*The images above are timelapse images. The images were taken every ten minutes after the 10mM potassium nitrate was added to the sample. (It was not allowed to grow for two hours, like all the other images.) <br />
<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
*The images and the graph are from PyeaR+RFP incubated with potassium nitrite. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of nitrite added to the sample. <br />
<br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]<br />
*The data was taken using E. coli DH5α that was co-transformed with Pu+GFP and Pr+XylR.<br />
*The leftmost image is the negative control. The other six images are the other concentrations (10uM and 500uM) in the specific aromatic: xylene, benzene, and toluene. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of the aromatic added to the sample. We also took data from 10mM and 100mM concentrations of aromatics, but most of the cells died at these higher concentrations.<br />
<br />
<br />
*LacI+RFP, PyeaR+GFP (BBa_K412002)<br />
[[Image:LacI+RFP, PyeaR+GFP.jpg | 650 px | center]]<br />
*Preliminary measurements show that the PyeaR promoter does not work in combination with the LacI+RFP. The two right images is the sample incubated in 500uM potassium nitrite, and the two left images is the negative control. The LacI+RFP is constantly on (bottom images) while the PyeaR+GFP does not respond (top images).</div>Krishttp://2010.igem.org/File:OurLab.JPGFile:OurLab.JPG2010-10-28T02:43:20Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/File:Sameer.JPGFile:Sameer.JPG2010-10-28T02:39:28Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/File:Schedule.JPGFile:Schedule.JPG2010-10-28T02:37:55Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/File:LP.JPGFile:LP.JPG2010-10-28T02:34:33Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/File:Kristina.JPGFile:Kristina.JPG2010-10-28T02:30:59Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/Team:UTDallas/TeamTeam:UTDallas/Team2010-10-28T02:27:38Z<p>Kris: </p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
=Advisors=<br />
====Dr. Leonidas Bleris====<br />
I am an Assistant Professor with the Electrical Engineering Department of the University of Texas at Dallas.<br />
<br />
====Dr. Hyun-Joo Nam====<br />
I am an Assistant Professor with the Bioengineering Department of the University of Texas at Dallas.<br />
<br />
=Students=<br />
====Jacob White====<br />
<div style="clear:both;"></div><br />
I am a PhD student in Biomedical Engineering at UTD. I have a BS in Electrical Engineering and a BS in Biochemistry.<br />
<br />
====Sameer Sant====<br />
I am an sophomore molecular biology major at UT Dallas.<br />
<div style="clear:both;"></div><br />
<br />
====Kristina Ehrhardt====<br />
<br />
<div style="clear:both;"></div><br />
I am a senior Biochemistry undergraduate student at UTD.<br />
<br />
====Mitu Bhattatiry====<br />
<!--[[Image:NSERL_windows.PNG|left|100x200px]]--><br />
I am a high school student and a rising senior at Coppell High School. I am researching at UTD through the Nanoexplorers program at the Nanotech Institute. I think iGEM is a truly unique experience and I am looking forward to the iGEM Jamboree in November!<br />
<div style="clear:both;"></div><br />
<br />
====Lagnajeet Pradhan====<br />
I am doing my Masters in Biomedical engineering at UTD. <br />
<div style="clear:both;"></div><br />
</span><br />
<br />
=Pictures=</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T02:23:16Z<p>Kris: /* Results */</p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
<br />
===Results===<br />
*All images were taken with Olympus IX81 automated inverted microscope specially equipped for live cell imaging. All microscope images were taken from live DH5α E.coli cells. The filter sets we used are: 545/30x (excitation) and 620/60m (emission) filters for DsRed, 470/40x (excitation) and 525/50m (emission) for GFP. Data collection and processing was performed by the SlideBook software.<br />
*The data was taken using cells that were grown overnight in 2mL of LB broth that had 50ug/mL of the appropriate antibiotic at 37C and 220rpm. This was used in a 1:50 dilution. Each sample had 40uL from the broth grown overnight and 2mL of the LB broth with the appropriate antibiotic. These were allowed to grow until a predetermined OD. Then the contaminants were added and the cells were allowed to grow for another 2 hours, before the images were taken.<br />
<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
*The images shown are the images used to get the data. From left to right the image is the negative control to a 10mM concentration of the respective contaminants. The graph shows the average of all the maximum intensities of the cells in the image vs the concentration of nitrate/nitrite added to the sample. The data shows that PyeaR+GFP responds better to nitrates than nitrites. It also shows that the cell is more sensitive to aluminum nitrate nonahydrate, and therefore starts dying at a lower concentration. <br />
<br />
<br />
*PyeaR+GFP(BBa_K412000) Timelapse images<br />
[[Image:tileview.jpg | 650 px | center]]<br />
*The images above are timelapse images. The images were taken every ten minutes after the 10mM potassium nitrate was added to the sample. (It was not allowed to grow for two hours, like all the other images.) This shows that the promoter takes a few minutes to respond, but a few hours to respond well.<br />
<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
*The images and the graph are from PyeaR+RFP incubated with potassium nitrite. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of nitrite added to the sample. We also took data from potassium nitrate and aluminum nitrate nonahydrate, but the cells were not responsive to these. <br />
<br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]<br />
*The data was taken using E. coli DH5α that was co-transformed with Pu+GFP and Pr+XylR.<br />
*The leftmost image is the negative control. The other six images are the other concentrations (10uM and 500uM) in the specific aromatic: xylene, benzene, and toluene. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of the aromatic added to the sample. We also took data from 10mM and 100mM concentrations of aromatics, but most of the cells died at these higher concentrations.<br />
<br />
<br />
*LacI+RFP, PyeaR+GFP (BBa_K412002)<br />
[[Image:LacI+RFP, PyeaR+GFP.jpg | 650 px | center]]<br />
*The images show that the PyeaR promoter does not work in this part. The two right images is the sample incubated in 500uM potassium nitrite, and the two left images is the negative control. The LacI+RFP is constantly on, and the PyeaR+GFP does not respond.</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T02:20:40Z<p>Kris: /* Results */</p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
<br />
===Results===<br />
*All images were taken with Olympus IX81 automated inverted microscope specially equipped for live cell imaging. All microscope images were taken from live DH5α E.coli cells. The filter sets we used are: 545/30x (excitation) and 620/60m (emission) filters for DsRed, 470/40x (excitation) and 525/50m (emission) for GFP. Data collection and processing was performed by the SlideBook software.<br />
*The data was taken using cells that were grown overnight in 2mL of LB broth that had 50ug/mL of the appropriate antibiotic at 37C and 220rpm. This was used in a 1:50 dilution. Each sample had 40uL from the broth grown overnight and 2mL of the LB broth with the appropriate antibiotic. These were allowed to grow until a predetermined OD. Then the contaminants were added and the cells were allowed to grow for another 2 hours, before the images were taken.<br />
<br />
<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
*The images shown are the images used to get the data. From left to right the image is the negative control to a 10mM concentration of the respective contaminants. The graph shows the average of all the maximum intensities of the cells in the image vs the concentration of nitrate/nitrite added to the sample. The data shows that PyeaR+GFP responds better to nitrates than nitrites. It also shows that the cell is more sensitive to aluminum nitrate nonahydrate, and therefore starts dying at a lower concentration. <br />
<br />
<br />
*PyeaR+GFP(BBa_K412000) Timelapse images<br />
[[Image:tileview.jpg | 650 px | center]]<br />
*The images above are timelapse images. The images were taken every ten minutes after the 10mM potassium nitrate was added to the sample. (It was not allowed to grow for two hours, like all the other images.) This shows that the promoter takes a few minutes to respond, but a few hours to respond well.<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
*The images and the graph are from PyeaR+RFP incubated with potassium nitrite. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of nitrite added to the sample. We also took data from potassium nitrate and aluminum nitrate nonahydrate, but the cells were not responsive to these. <br />
<br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]<br />
*The data was taken using E. coli DH5α that was co-transformed with Pu+GFP and Pr+XylR.<br />
*The leftmost image is the negative control. The other six images are the other concentrations (10uM and 500uM) in the specific aromatic: xylene, benzene, and toluene. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of the aromatic added to the sample. We also took data from 10mM and 100mM concentrations of aromatics, but most of the cells died at these higher concentrations.<br />
<br />
<br />
*LacI+RFP, PyeaR+GFP (BBa_K412002)<br />
[[Image:LacI+RFP, PyeaR+GFP.jpg | 650 px | center]]<br />
*The images show that the PyeaR promoter does not work in this part. The two right images is the sample incubated in 500uM potassium nitrite, and the two left images is the negative control. The LacI+RFP is constantly on, and the PyeaR+GFP does not respond.</div>Krishttp://2010.igem.org/File:LacI%2BRFP,_PyeaR%2BGFP.jpgFile:LacI+RFP, PyeaR+GFP.jpg2010-10-28T02:18:26Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T02:15:07Z<p>Kris: /* Results */</p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
<br />
===Results===<br />
*All images were taken with Olympus IX81 automated inverted microscope specially equipped for live cell imaging. All microscope images were taken from live DH5α E.coli cells. The filter sets we used are: 545/30x (excitation) and 620/60m (emission) filters for DsRed, 470/40x (excitation) and 525/50m (emission) for GFP. Data collection and processing was performed by the SlideBook software.<br />
*The data was taken using cells that were grown overnight in 2mL of LB broth that had 50ug/mL of the appropriate antibiotic at 37C and 220rpm. This was used in a 1:50 dilution. Each sample had 40uL from the broth grown overnight and 2mL of the LB broth with the appropriate antibiotic. These were allowed to grow until a predetermined OD. Then the contaminants were added and the cells were allowed to grow for another 2 hours, before the images were taken.<br />
<br />
<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
*The images shown are the images used to get the data. From left to right the image is the negative control to a 10mM concentration of the respective contaminants. The graph shows the average of all the maximum intensities of the cells in the image vs the concentration of nitrate/nitrite added to the sample. The data shows that PyeaR+GFP responds better to nitrates than nitrites. It also shows that the cell is more sensitive to aluminum nitrate nonahydrate, and therefore starts dying at a lower concentration. <br />
<br />
<br />
*PyeaR+GFP(BBa_K412000) Timelapse images<br />
[[Image:tileview.jpg | 650 px | center]]<br />
*The images above are timelapse images. The images were taken every ten minutes after the 10mM potassium nitrate was added to the sample. (It was not allowed to grow for two hours, like all the other images.) This shows that the promoter takes a few minutes to respond, but a few hours to respond well.<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
*The images and the graph are from PyeaR+RFP incubated with potassium nitrite. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of nitrite added to the sample. We also took data from potassium nitrate and aluminum nitrate nonahydrate, but the cells were not responsive to these. <br />
<br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]<br />
*The data was taken using E. coli DH5α that was co-transformed with Pu+GFP and Pr+XylR.<br />
*The leftmost image is the negative control. The other six images are the other concentrations (10uM and 500uM) in the specific aromatic: xylene, benzene, and toluene. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of the aromatic added to the sample. We also took data from 10mM and 100mM concentrations of aromatics, but most of the cells died at these higher concentrations.<br />
<br />
*LacI+RFP, PyeaR+GFP (BBa_K412002)<br />
[[Image:LacI.jpg | 650 px | center]]<br />
*The images show that the PyeaR promoter does not work in this part. The two right images is the sample incubated in 500uM potassium nitrite, and the two left images is the negative control. The LacI+RFP is constantly on, and the PyeaR+GFP does not respond.</div>Krishttp://2010.igem.org/File:Tileview.jpgFile:Tileview.jpg2010-10-28T02:05:02Z<p>Kris: </p>
<hr />
<div></div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T02:04:18Z<p>Kris: </p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
<br />
===Results===<br />
*All images were taken with Olympus IX81 automated inverted microscope specially equipped for live cell imaging. All microscope images were taken from live DH5α E.coli cells. The filter sets we used are: 545/30x (excitation) and 620/60m (emission) filters for DsRed, 470/40x (excitation) and 525/50m (emission) for GFP. Data collection and processing was performed by the SlideBook software.<br />
*The data was taken using cells that were grown overnight in 2mL of LB broth that had 50ug/mL of the appropriate antibiotic at 37C and 220rpm. This was used in a 1:50 dilution. Each sample had 40uL from the broth grown overnight and 2mL of the LB broth with the appropriate antibiotic. These were allowed to grow until a predetermined OD. Then the contaminants were added and the cells were allowed to grow for another 2 hours, before the images were taken.<br />
<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
*The images shown are the images used to get the data. From left to right the image is the negative control to a 10mM concentration of the respective contaminants. The graph shows the average of all the maximum intensities of the cells in the image vs the concentration of nitrate/nitrite added to the sample. The data shows that PyeaR+GFP responds better to nitrates than nitrites. It also shows that the cell is more sensitive to aluminum nitrate nonahydrate, and therefore starts dying at a lower concentration. <br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
*The images and the graph are from PyeaR+RFP incubated with potassium nitrite. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of nitrite added to the sample. We also took data from potassium nitrate and aluminum nitrate nonahydrate, but the cells were not responsive to these. <br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]<br />
*The data was taken using E. coli DH5α that was co-transformed with Pu+GFP and Pr+XylR.<br />
*The leftmost image is the negative control. The other six images are the other concentrations (10uM and 500uM) in the specific aromatic: xylene, benzene, and toluene. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of the aromatic added to the sample. We also took data from 10mM and 100mM concentrations of aromatics, but most of the cells died at these higher concentrations.</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T02:01:13Z<p>Kris: /* Results */</p>
<hr />
<div>{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
{{Template:UTDallasTop}}<br />
{{Template:UTDallasMenu}}<br />
<span style="color:#EDE8E8"><br />
===Results===<br />
*All images were taken with Olympus IX81 automated inverted microscope specially equipped for live cell imaging. All microscope images were taken from live DH5α E.coli cells. The filter sets we used are: 545/30x (excitation) and 620/60m (emission) filters for DsRed, 470/40x (excitation) and 525/50m (emission) for GFP. Data collection and processing was performed by the SlideBook software.<br />
*The data was taken using cells that were grown overnight in 2mL of LB broth that had 50ug/mL of the appropriate antibiotic at 37C and 220rpm. This was used in a 1:50 dilution. Each sample had 40uL from the broth grown overnight and 2mL of the LB broth with the appropriate antibiotic. These were allowed to grow until a predetermined OD. Then the contaminants were added and the cells were allowed to grow for another 2 hours, before the images were taken.<br />
<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
*The images shown are the images used to get the data. From left to right the image is the negative control to a 10mM concentration of the respective contaminants. The graph shows the average of all the maximum intensities of the cells in the image vs the concentration of nitrate/nitrite added to the sample. The data shows that PyeaR+GFP responds better to nitrates than nitrites. It also shows that the cell is more sensitive to aluminum nitrate nonahydrate, and therefore starts dying at a lower concentration. <br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
*The images and the graph are from PyeaR+RFP incubated with potassium nitrite. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of nitrite added to the sample. We also took data from potassium nitrate and aluminum nitrate nonahydrate, but the cells were not responsive to these. <br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]<br />
*The data was taken using E. coli DH5α that was co-transformed with Pu+GFP and Pr+XylR.<br />
*The leftmost image is the negative control. The other six images are the other concentrations (10uM and 500uM) in the specific aromatic: xylene, benzene, and toluene. The graph is of the average of all the maximum intensities of the cells in the picture vs the concentration of the aromatic added to the sample. We also took data from 10mM and 100mM concentrations of aromatics, but most of the cells died at these higher concentrations.</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T01:04:40Z<p>Kris: /* Results */</p>
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===Results===<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
We used our fluorescence microscope to take all of the images and to get the intensity data. Our results show that the part works as intended. When the concentration of nitrate or nitrite is increased the intensity of the fluorescence increases, up to the point where it is killing the E. coli. These results also show that PyeaR works better on nitrates, then nitrites, again as expected. The graph is of the mean intensity of all the cells in the picture at each concentration with the standard deviations shown.<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
We used our fluorescence microscope to take all of the images and to get the intensity data. Our results show that the part works partially as intended. Unlike the PyeaR promoter and the PyeaR+GFP only the nitrites worked for this part. The graph shows the mean intensity of all of the cells in the picture at each concentration with the standard deviations shown. <br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T00:57:41Z<p>Kris: /* Results */</p>
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===Results===<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
<br />
*Pu+GFP (BBa_K270003)<br />
[[Image:Pu_GFP.jpg | 650 px | center]]</div>Krishttp://2010.igem.org/File:Pu_GFP.jpgFile:Pu GFP.jpg2010-10-28T00:56:46Z<p>Kris: </p>
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<div></div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T00:56:12Z<p>Kris: /* Results */</p>
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===Results===<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
<br />
*Pu+GFP (BBa_K270003)</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T00:34:51Z<p>Kris: /* Results */</p>
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===Results===<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
<br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T00:32:58Z<p>Kris: /* Results */</p>
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===Results===<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
</span><br />
<br />
*PyeaR+RFP (BBa_K412001)<br />
[[Image:Pyear_RFP.jpg | 650 px | center]]<br />
</span></div>Krishttp://2010.igem.org/File:Pyear_RFP.jpgFile:Pyear RFP.jpg2010-10-28T00:17:57Z<p>Kris: </p>
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<div></div>Krishttp://2010.igem.org/Team:UTDallas/SafetyTeam:UTDallas/Safety2010-10-27T23:50:39Z<p>Kris: /* Safety */</p>
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==Safety==<br />
<br />
Please use this page to answer the safety questions posed on the [[Safety | safety page]].<br />
<br />
Safety Questions: <br><br />
'''1. Would any of your project ideas raise safety issues in terms of researcher, public, or environmental safety?''' <br><br />
*Materials that pose a safety risk (i.e. cell cultures, ethidium bromide, UV transilluminator, etc) are handled according to standard lab safety protocol and Materials Safety Data Sheets. Materials containing safety hazards are disposed in separate containers with “biohazard” designations. Appropriate protective gear, such as gloves, is worn at all times. Our bacterial chassis, E. coli DH5α, is disabled to where it is nonpathogenic and cannot survive outside of lab conditions. In addition, all exposed counters are disinfected using 70% ethanol after each use of the lab. All lab equipment is thoroughly cleaned and autoclaved after use and access to the lab is limited by cardkey. <br />
'''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?''' <br><br />
*We worked with genes encoding known properties and utilized safety measures to ensure that biohazardous materials including antibiotic-resistant cells are contained within the lab and are appropriately disposed. Therefore, we assess that none of our submitted parts raise safety issues.<br />
'''3. Is there a local biosafety group, committee, or review board at your institution?''' <br><br />
*UT Dallas has an Institutional Biosafety Committee (http://provost.utdallas.edu/policy/utdpp1016) that manages all safety responsibilities under NIH “Guidelines for Research Involving Recombinant DNA Molecules”. Throughout the course of this work, we ensured that all lab activity respected safety measures. <br />
'''4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?''' <br><br />
*The iGEM plasmid backbone could be programmed to include both resistance markers and a suitable inactivation pathway (i.e. apoptosis) whose induction can be altered to meet user requirements. However, while this would enable the user to more effectively regulate the activity of cells endowed with BioBrick parts, disseminating pertinent safety information through the Registry is a more practical alternative to engineering biosafety measures into parts, devices and systems. <br />
<br />
</span></div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-27T23:48:56Z<p>Kris: /* Results */</p>
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===Results===<br />
*PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
</span></div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-27T23:48:43Z<p>Kris: /* Results */</p>
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===Results===<br />
<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
</span><br />
*PyeaR+GFP (BBa_K412000)</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-27T23:47:50Z<p>Kris: /* Results */</p>
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===Results===<br />
<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
</span><br />
PyeaR+GFP (BBa_K412000)</div>Krishttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-27T23:47:15Z<p>Kris: /* Results */</p>
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<span style="color:#EDE8E8"><br />
===Results===<br />
PyeaR+GFP (BBa_K412000)<br />
[[Image:Ver2.jpg | 650 px | center]]<br />
</span></div>Krishttp://2010.igem.org/Team:UTDallas/Background_ReferencesTeam:UTDallas/Background References2010-10-27T23:44:12Z<p>Kris: </p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Background_EnvironmentalBiosensors Environmental Biosensors]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_OilSpills Oil Spills]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizon Deepwater Horizon]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizonUpdates Deepwater Horizon Timeline]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_References References]<br />
|}<br />
=References=<br />
[1] [http://en.wikipedia.org/wiki/Biosensor Wikipedia, ''Biosensor''.]<br />
<br />
[2] [http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.133.6222&rep=rep1&type=pdf Rodriguez-Mozaz, S., Marco, M., de Alda, M. L., & Barceló, D:"Biosensors for environmental applications: Future development trends", ''Pure and Applied Chemistry'', 76(4):723-752, 2004.]<br />
<br />
[3] [http://books.nap.edu/openbook.php?record_id=10388&page=29 Oil in the Sea, Ocean Studies Board and Marine Board of the National Academy of Sciences (2003)]<br />
<br />
[4] [http://www.nature.com/scientificamerican/journal/v303/n1/full/scientificamerican0710-16.html Scientific American 303, 16-18 doi:10.1038/scientificamerican0710-16; July 2010.] <br />
<br />
[5] [http://www.sciencedaily.com/releases/2010/06/100629122948.htm National Oceanic and Atmospheric Administration (2010, June 29). NOAA- supported scientists predict 'larger than average' Gulf dead zone. ScienceDaily. Retrieved July 5, 2010, from http://www.sciencedaily.com/releases/2010/06/100629122948.htm ]<br />
<br />
[6] [http://pubs.acs.org/cen/coverstory/88/8824cover.html Johnson, J., & Torrice, M. (2010, June 14). BP's Ever-Growing Oil Spill | Cover Story | Chemical & Engineering News. C & EN: Chemical & Engineering News. Retrieved July 6, 2010, from http://pubs.acs.org/cen/coverstory/88/8824cover.html]<br />
<br />
</span></div>Krishttp://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizonUpdatesTeam:UTDallas/Background DeepwaterHorizonUpdates2010-10-27T23:43:32Z<p>Kris: </p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Background_EnvironmentalBiosensors Environmental Biosensors]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_OilSpills Oil Spills]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizon Deepwater Horizon]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizonUpdates Deepwater Horizon Timeline]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_References References]<br />
|}<br />
=Deepwater Horizon Oil Spill Timeline=<br />
The following information is taken from the [http://www.doi.gov/ '''Department of the Interior'''] and the [http://topics.nytimes.com/top/reference/timestopics/subjects/o/oil_spills/gulf_of_mexico_2010/index.html?scp=1-spot&sq=BP%20Oil%20Spill&st=cseupdates/ '''New York Times'''] on the updates of the BP Oil Spill. To look for more detailed information regarding the BP Oil Spill visit the [http://www.bp.com/extendedsectiongenericarticle.do?categoryId=40&contentId=7061813/'''BP Global Site Oil Spill Response'''].<br />
<br />
<br />
'''August 8'''<br />
*cement plug had been successfully put in place after a procedure to seal the leaking well in the Gulf of Mexico<br />
*next step will be a relief well<br />
<br />
'''August 4'''<br />
*Static Kill of Gulf Oil well is deemed a success<br />
*Carol Browner, the president's energy and climate adviser, will visit Panama and Florida for discussion<br />
*scientists react with skepticism at federal government's report over extent of spill cleanup<br />
<br />
'''July 30:'''<br />
*Effort to Permanently Plug Well Is Progressing<br />
*State and federal biologists released 13 laughing gulls, two royal terns and one sandwich tern at Rockefeller State Wildlife Refuge<br />
<br />
'''July 27:'''<br />
*bill intended to tighten environmental and safety standards for offshore drilling introduced<br />
*BP increased the money set aside for spill-related costs to $32.2 billion on Tuesday<br />
*wellhead off southeastern Louisiana was spewing oil and gas up to 100 feet into the air on Tuesday<br />
<br />
'''July 26:'''<br />
*Admiral Allen said workers could begin the procedure called a static kill on Aug. 2<br />
*Robert Dudley expected to replace Hayward as BP chief<br />
<br />
'''July 25:'''<br />
*quick turnaround for continuing oil cleanup in the Gulf<br />
*endangered baby sea turtles released back into the Gulf<br />
<br />
'''July 24:'''<br />
*28.3 percent of gulf oil production and 10.4 percent of natural gas output has stopped because of storm<br />
*emergency alarm on oil rig partly disabled - new discovery<br />
<br />
'''July 21:'''<br />
*bad weather could cause delays in BP's work at the Deepwater Horizon oil well<br />
*Exxon Mobil, Chevron, Conoco Phillips plan to commit $1 billion to set up a rapid-response system to deal with oil spills<br />
<br />
'''July 20:'''<br />
*Testing of oil cap extended another 24 hours with officials considering killing the well entirely<br />
*speculations of other seeps occur<br />
<br />
'''July 19:'''<br />
*Subsea containment efforts continue with the capping stage<br />
*408 controlled burns<br />
<br />
'''July 15:'''<br />
*5,000 personnel are currently responding to protect the shoreline and wildlife<br />
*32.9 million gallons of an oil-water mix have been recovered<br />
*1.84 million gallons of total dispersant have been applied<br />
*581 miles of Gulf Coast shoreline are currently oiled<br />
<br />
'''July 14:'''<br />
*31.8 million gallons of an oil-water mix have been recovered<br />
*348 controlled burns<br />
*572 miles of Gulf Coast shoreline are currently oiled<br />
*1.82 million gallons of total dispersant have been applied<br />
<br />
'''July 13:'''<br />
*31.4 million gallons of an oil-water mix have been recovered<br />
*330 controlled burns have been conducted<br />
*550 miles of Gulf Coast shoreline are currently oiled<br />
<br />
'''July 6:'''<br />
*ensure the safety of seafood coming from the Gulf, the Food and Drug Administration (FDA), National Oceanic and Atmospheric Administration (NOAA), and state authorities have agreed upon a shared protocol<br />
*BP also has begun connecting a floating riser pipe to third vessel, the Helix Producer, which will increase collection capacity to an estimated 53,000 barrels per day<br />
*45,700 personnel are currently responding to protect the shoreline and wildlife<br />
*484 miles of Gulf Coast shoreline are currently oiled<br />
*1.72 million gallons of total dispersant have been applied<br />
<br />
'''July 5:'''<br />
*NOAA expanded the closed fishing area in the Gulf of Mexico to include portions of the oil slick<br />
*Tar balls collected from the Crystal Beach on the Texas coast were from the'' Deepwater Horizon'' Oil Spill with approximately 35 gallons of sand/seaweed/tar balls collected<br />
*45,000 personnel are currently responding to protect the shoreline and wildlife<br />
*31.3 million gallons of an oil-water mix have been recovered<br />
*492 miles of Gulf Coast shoreline are currently oiled<br />
<br />
'''July 4:'''<br />
*making progress on new oil that washed because of bad weather in Hurricane Alex<br />
<br />
'''July 1:'''<br />
*42,700 personnel are currently responding to protect the shoreline and wildlife<br />
*1.61 million gallons of total dispersant have been applied<br />
*428 miles of Gulf Coast shoreline are currently oiled<br />
<br />
'''June 30:''' <br />
*EPA Releases First Round of Toxicity Testing Data for Eight Oil Dispersants<br />
*42,700 personnel are currently responding to protect the shoreline and wildlife<br />
*1.61 million gallons of total dispersant have been applied<br />
*423 miles of Gulf Coast shoreline are currently oiled<br />
<br />
'''June 29:'''<br />
*Vice President Biden Travels to Gulf Coast to Assess Response Efforts<br />
*Fish and Wildlife Service and Coast Guard, released more than 70 rehabilitated brown pelicans back to the wild from the USCG station in Brunswick, Ga.<br />
*38,900 personnel are currently responding to protect the shoreline and wildlife and cleanup vital coastlines<br />
*1.6 million gallons of total dispersant have been applied<br />
*413 miles of Gulf Coast shoreline are currently oiled<br />
<br />
'''June 28:'''<br />
*NOAA-Supported Scientists Predict Increase in Area Containing Depleted Oxygen or the “dead zone”<br />
*38,600 personnel are currently responding to protect the shoreline and wildlife<br />
*28.2 million gallons of an oil-water mix have been recovered<br />
*213 miles of Gulf Coast shoreline are currently oiled<br />
<br />
'''June 25:'''<br />
*37,000 personnel, more than 4,500 vessels engaged<br />
*275 controlled burns have been carried out to date, removing about 239,000 barrels of sea surface oil</div>Krishttp://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizonTeam:UTDallas/Background DeepwaterHorizon2010-10-27T23:31:25Z<p>Kris: </p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Background_EnvironmentalBiosensors Environmental Biosensors]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_OilSpills Oil Spills]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizon Deepwater Horizon]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizonUpdates Deepwater Horizon Timeline]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_References References]<br />
|}<br />
=Deepwater Horizon Oil Spill=<br />
The ''Deepwater Horizon'' Oil Spill, referred to also as the BP Oil Spill and the Gulf Oil Spill, is a large oil spill in the Gulf of Mexico that is currently the largest oil spill in America’s history with hundreds of millions of gallons of oil spilled. Following a deep oil rig explosion occurring on April 20, 2010 killing 11 workers, the leak has been gushing oil. <br />
<br />
Follow the link to watch a short and interesting video relating to the [http://www.youtube.com/watch?v=XLiqvZOP8TY/ '''''Deepwater Horizon'' Oil Spill mechanics'''].<br />
<br />
The'' Deepwater Horizon'' Oil Spill had caused serious backlash and worry over the environment surrounding the impacted oil rig, and the toxic compounds and environmental hazards of oil have been looked into again in order to create an efficient clean up of the oil spill. <br />
<br />
The toxic compounds in oil vary, but some of the most worrisome of compounds are the polycyclic aromatic hydrocarbons (PAHs) including napthalenes, benzene, toluene, and xylenes not only to the environment but to humans as well. According to experts, the ecology nearest to the spill and in the upper water column will be greatly affected and “contamination could ultimately end up having cascading effects up the food chain.” According to the article, “when an oil spill occurs, there are no good outcomes.” [[Team:UTDallas/Background_References|[4] ]]<br />
<br />
The northern Gulf of Mexico hypoxic zone, an “underwater area with little or no oxygen known commonly as the ‘dead zone”’[[Team:UTDallas/Background_References|[5] ]], has been predicted to grow and be negatively affected by the growing crisis with the Gulf Oil spill. There is evidence of underwater oil plumes which could be attributed to BP’s injection of chemical dispersants at the source of the leak. “These reports found that the high pressure of oil released from a deepwater blowout causes droplets and bubbles to form. Natural gas also rushes into the ocean, joins the crude, and helps form a buoyant plume of oil and gas. As this plume rises, it pulls in dense water from the ocean’s depths. Eventually, the denser water in the mixture slows the plume’s ascent.” [[Team:UTDallas/Background_References|[6] ]] The more time that oil spends in the water, the more time the components of oil – including the more toxic compounds such as the PAHs and aromatic compounds – have to dissolve into the water and affect the aquatic ecosystem. Also, there are reports over the actual values of biodegradation occurring in the ocean environments. Typically, biodegradation occurring in marine environments is measured through the depletion of oxygen; however, some critics of dispersant use claim that the decreased oxygen use could actually be caused by oil- eating microbes consuming particles of the dispersant rather than the intended petroleum.</div>Krishttp://2010.igem.org/Team:UTDallas/Background_OilSpillsTeam:UTDallas/Background OilSpills2010-10-27T23:28:28Z<p>Kris: </p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Background_OilSpills Oil Spills]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizon Deepwater Horizon]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizonUpdates Deepwater Horizon Timeline]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_References References]<br />
|}<br />
=Oil Spills=<br />
Because of the recent [[Team:UTDallas/Background_Deepwater Horizon Oil Spill|'''''Deepwater Horizon Oil Spill''''' ]] disaster and the resulting implications of oil contamination in the environment, we hope to provide you a thorough informational resource for learning about not only the current oil spill, but also general information regarding oil spills because of its direct connection to the one of the main goals of our project. <br />
<br />
Facts: <br />
*The United States uses 700 million gallons of oil a day [[Team:UTDallas/Background_References|[3] ]]<br />
*Oil has many uses in human activities: fuel source, lubricate machinery, make plastics, make medicines and pesticides, make asphalt [[Team:UTDallas/Background_References|[3] ]]<br />
*Natural seepage of crude oil from geologic formations below the seafloor is estimated to exceed '''47,000,000''' gallons in North American waters and '''180,000,000''' gallons globally every year [[Team:UTDallas/Background_References|[3] ]]<br />
<br />
Oil spills cause the oil to float on the saltwater of the ocean, spreading out rapidly across the surface of the water to create a thin sheen. The methods of clean up for oil spills include booms, floating barriers to oil, skimmers, sorbents, dispersants, in-situ burning, vacuum trucks, and washing. [[Team:UTDallas/Background_References|[3] ]]<br />
<br />
There are four major sources of pollution: naturally occurring oil seeps, extraction, transportation, consumption. Despite popular thought, the oil spills caused by transportation and disasters only constitute a small portion of the oil that enters marine environments every year. The following charts based on information provided by the Ocean Studies Board and Marine Board of the National Academy of Sciences, show the percentage of oil contamination as per each category of source of pollution. [[Team:UTDallas/Background_References|[3] ]]<br />
<br />
[[Image:North American Waters.png |484px | center]]<br />
<br />
[[Image:World Marine Waters.png | 484px | center]]<br />
<center> '''Source:''' From Oil in the Sea, Ocean Studies Board and Marine Board of the National Academy of Sciences (2003). </center><br />
<br />
<br />
Similarly, oil spills have differing impacts depending on a variety of factors including location, size, and temperature. However, the size of an oil spill does not necessarily dictate the impact that an oil spill will have on a marine environment; rather, the impact of an oil spill depends on its location.</div>Krishttp://2010.igem.org/Team:UTDallas/Background_EnvironmentalBiosensorsTeam:UTDallas/Background EnvironmentalBiosensors2010-10-27T23:26:44Z<p>Kris: </p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Background_EnvironmentalBiosensors Environmental Biosensors]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_OilSpills Oil Spills]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizon Deepwater Horizon]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_DeepwaterHorizonUpdates Deepwater Horizon Timeline]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Background_References References]<br />
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=Environmental Biosensors=<br />
A biosensor is any “device for the detection of an analyte that combines a biological component with a physicochemical detector component” [[Team:UTDallas/Background_References|[1] ]] consisted of a sensor, a detector, and a signal processor. The use of biosensors is important in the detection of varying chemicals that induce reactions on promoters in gene sequences thus emitting a form of measurable output. The advantages of environmental biosensors over the current methods are the portability, relatively low cost, and environmentally friendly characteristics of microorganisms over bulky equipment. Biosensors have potential to be maintained on-site able to monitor conditions continuously in the soil or marine environments without significant effort being placed into the maintenance as is<br />
customary in expensive equipment that must be maintained and used by skilled workers. <br />
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For traditional “offsite” laboratory testing, the samples must be sent in, proving to be a costly and ineffective method. The new trend towards biosensors aims to “provide fast, reliable, and sensitive measurements with lower cost; many of them aimed at on-site analysis.” [[Team:UTDallas/Background_References|[2] ]]Most biosensor systems have focused on the use of bacterial organisms, while the use of eukaryotic organisms is rare. One particular concern is the presence of water-soluble aromatic components of petroleum products in drinking water that often persist in the environment. [[Team:UTDallas/Background_References|[2] ]]<br />
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'''According to The Department of Environmental Biochemistry in Barcelona, “Genetic engineering provides an elegant way not only for providing unlimited amounts of biorecognition molecules, but also for the alteration of existing properties and the supplementation with additional functions”, which addresses our [[Team:UTDallas/Project_ProjectOverview|project ]] directly.'''[[Team:UTDallas/Background_References|[2] ]]</div>Krishttp://2010.igem.org/Team:UTDallas/Project_ReferencesTeam:UTDallas/Project References2010-10-27T23:21:41Z<p>Kris: </p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Project_ProjectOverview Project Overview]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Introduction Introduction]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
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==References==<br />
[1] [http://www.britannica.com/EBchecked/topic/454269/petroleum Petroleum; Encyclopedia Britannica; 2010]<br />
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[2] Idem, R.; Simanzhenkov, V. Nature and Classification of Crude Oil. In Crude Oil Chemistry; 1st Ed. Marcel Dekker: New York, 2003; pp 5-13.<br />
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[3] [http://www.eoearth.org/article/Deepwater_Horizon_oil_spill Cleveland, C. Deepwater Horizon oil spill; Encyclopedia of Earth. 23 June 2010.]<br />
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[4] [http://www.eoearth.org/article/Oil_spill Patin, S. Oil Spill. Encyclopedia of Earth. 23 June 2010.]<br />
</span></div>Krishttp://2010.igem.org/Team:UTDallas/Project_IntroductionTeam:UTDallas/Project Introduction2010-10-27T23:21:27Z<p>Kris: </p>
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!align="center"|[https://2010.igem.org/Team:UTDallas/Project_ProjectOverview Project Overview]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Introduction Introduction]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
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==Introduction==<br />
Petroleum, a nonrenewable resource valuable as a fuel source, plays a pivotal role in the economies and environments of countries. The United States as one of the top oil-producing nations in the world participates in the production and refining of crude oil. However, over one quarter of the United States’ crude oil is produced offshore in the Gulf of Mexico bringing up hazards to the marine environment. With the recent news of the Deepwater Horizon Oil Spill occurring in the Gulf of Mexico, the issue of safe and effective cleanup of the oil comes into greater concern. Oil spills, usually resulting from tanker spills, penetrate the surface of sea water as well as decreasing fauna populations affecting the food chain of marine ecosystems. [[Team:UTDallas/Project_References|[1] ]]<br />
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Crude oil consists of many different types of hydrocarbons including alkanes, cycloalkanes, and aromatic compounds. The alkanes (C<sub>n</sub>H<sub>2n+2</sub>), either straight or branched, consist of a chain of carbons and hydrogen molecules, while cycloalkanes (C<sub>n</sub>H<sub>2n</sub>) are composed of carbon rings and hydrogen molecules, and aromatic compounds are hydrocarbons consisting of benzene rings. [[Team:UTDallas/Project_References|[2] ]] Crude oil is immiscible with water and is lighter than water, causing it to float on top of the water surface. Based on the crude oil’s specific gravity, the ratio of the weight of equal volumes of oil and pure water, it is categorized into types such as tar sands, heavy oils, and light oils. [[Team:UTDallas/Project_References|[1] ]]<br />
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Past oil spills such as the Gulf War Oil Spill occurring in the Persian Gulf reveal the truly detrimental and potentially long-term impacts of oil spills in aquatic environments. The oil spill which began in January of 1991 has been found to contain truly significant long term effects on the environment. The lack of shoreline cleanup caused a large amount of oil sediment remaining even 12 years after the spill, and the oil penetrated so deeply that it cannot be retrieved now. A method to detect the presence of oil even after visible oil is removed from an area is necessary to aid the recovery of oil-affected ecosystems.<br />
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The Exxon Valdez spill occurring near Prince William Sound, Alaska resulted in unprecedented damage to the fragile Arctic ecosystem and a large portion of the oil from the massive oil spill of the Exxon Valdez in 1989 remained retained in the land. However, the oil spill occurring in Prince William Sound revealed not only the potentially deleterious effects of a large oil spill on the aquatic environment, but the harmful effects of large, cleanup machinery. [[Team:UTDallas/Project_References|[3] ]] When oil reaches the shoreline, some components of the oil evaporate leaving behind the heavier components of oil. In rocky shores, the heavier components will convert into tar and will eventually be washed away through wave action; in marsh areas, however, the oil can sink down below the surface and remain for years. Low energy environments such as marshes are the highest risk areas because the marsh areas are the most vulnerable to the effects of oil. [[Team:UTDallas/Project_References|[4] ]]</div>Kris