http://2010.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Mitu&year=&month=2010.igem.org - User contributions [en]2024-03-29T11:42:08ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T01:16:40Z<p>Mitu: /* 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 />
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====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 />
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====Pu+GFP (BBa_K270003)====<br />
[[Image:Pu_GFP.jpg | 650 px | center]]</div>Mituhttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-28T01:16:23Z<p>Mitu: /* 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>Mituhttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-27T02:51:30Z<p>Mitu: /* Results */</p>
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===Results===<br />
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[[Image:Ver2.jpg | 650 px | center]]<br />
</span></div>Mituhttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-27T02:51:14Z<p>Mitu: /* Results */</p>
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===Results===<br />
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[[Image:Ver2.jpg | 700 px | center]]<br />
</span></div>Mituhttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-27T02:51:02Z<p>Mitu: /* Results */</p>
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===Results===<br />
[[Image:Ver2.jpg | 700 px | center]]<br />
</span></div>Mituhttp://2010.igem.org/Team:UTDallasTeam:UTDallas2010-10-27T02:49:58Z<p>Mitu: </p>
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<div style="font-size:200%"> <center><br />
Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental pollutants <br />
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===Project Abstract===<br />
Recalcitrant pollutants such as petroleum constituents and nitrates are regularly introduced to the environment through oil spills, natural geological seepage and eutrophication. The UN’s flagship water protection initiative enumerates a host of health risks associated with these chemicals. UT Dallas iGEM addresses the eminent need to mitigate their circulation by developing novel whole-cell biosensors that can detect alkanes, aromatics and nitrates and execute combinatorial logic, feedback and noise-reduction functions inspired by synthetic biology. This work has wide ranging applications requiring a cheap chemical sensor that can dynamically process heterogeneous inputs and express a user-friendly output.<br />
===Track Selection===<br />
Top three track choices:<br />
#Environment<br />
#Foundational Advance<br />
#Information Processing<br />
</span><br />
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= Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental pollutants =<br />
<br />
<br />
===Project Abstract===<br />
Recalcitrant pollutants such as petroleum constituents and nitrates are regularly introduced to the environment through oil spills, natural geological seepage and eutrophication. The UN’s flagship water protection initiative enumerates a host of health risks associated with these chemicals. UT Dallas iGEM addresses the eminent need to mitigate their circulation by developing novel whole-cell biosensors that can detect alkanes, aromatics and nitrates and execute combinatorial logic, feedback and noise-reduction functions inspired by synthetic biology. This work has wide ranging applications requiring a cheap chemical sensor that can dynamically process heterogeneous inputs and express a user-friendly output.<br />
===Track Selection===<br />
Top three track choices:<br />
#Environment<br />
#Foundational Advance<br />
#Information Processing<br />
</span><br />
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</html></div>Mituhttp://2010.igem.org/Team:UTDallasTeam:UTDallas2010-10-27T02:43:38Z<p>Mitu: /* Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental pollutants */</p>
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Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental pollutant<br />
<br />
==Project Abstract==<br />
Recalcitrant pollutants such as petroleum constituents and nitrates are regularly introduced to the environment through oil spills, natural geological seepage and eutrophication. The UN’s flagship water protection initiative enumerates a host of health risks associated with these chemicals. UT Dallas iGEM addresses the eminent need to mitigate their circulation by developing novel whole-cell biosensors that can detect alkanes, aromatics and nitrates and execute combinatorial logic, feedback and noise-reduction functions inspired by synthetic biology. This work has wide ranging applications requiring a cheap chemical sensor that can dynamically process heterogeneous inputs and express a user-friendly output.<br />
==Track Selection==<br />
Top three track choices:<br />
#Environment<br />
#Foundational Advance<br />
#Information Processing<br />
</span><br />
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</html></div>Mituhttp://2010.igem.org/Team:UTDallasTeam:UTDallas2010-10-27T02:43:24Z<p>Mitu: /* Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental pollutants */</p>
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== Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental pollutants ==<br />
<br />
==Project Abstract==<br />
Recalcitrant pollutants such as petroleum constituents and nitrates are regularly introduced to the environment through oil spills, natural geological seepage and eutrophication. The UN’s flagship water protection initiative enumerates a host of health risks associated with these chemicals. UT Dallas iGEM addresses the eminent need to mitigate their circulation by developing novel whole-cell biosensors that can detect alkanes, aromatics and nitrates and execute combinatorial logic, feedback and noise-reduction functions inspired by synthetic biology. This work has wide ranging applications requiring a cheap chemical sensor that can dynamically process heterogeneous inputs and express a user-friendly output.<br />
==Track Selection==<br />
Top three track choices:<br />
#Environment<br />
#Foundational Advance<br />
#Information Processing<br />
</span><br />
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==Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental pollutants==<br />
<br />
==Project Abstract==<br />
Recalcitrant pollutants such as petroleum constituents and nitrates are regularly introduced to the environment through oil spills, natural geological seepage and eutrophication. The UN’s flagship water protection initiative enumerates a host of health risks associated with these chemicals. UT Dallas iGEM addresses the eminent need to mitigate their circulation by developing novel whole-cell biosensors that can detect alkanes, aromatics and nitrates and execute combinatorial logic, feedback and noise-reduction functions inspired by synthetic biology. This work has wide ranging applications requiring a cheap chemical sensor that can dynamically process heterogeneous inputs and express a user-friendly output.<br />
==Track Selection==<br />
Top three track choices:<br />
#Environment<br />
#Foundational Advance<br />
#Information Processing<br />
</span><br />
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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_Research Research]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Details Details]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
==References==<br />
[1] [http://www.britannica.com/EBchecked/topic/454269/petroleum Petroleum; Encyclopedia Britannica; 2010]<br />
<br />
[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 />
<br />
[3] [http://www.eoearth.org/article/Deepwater_Horizon_oil_spill Cleveland, C. Deepwater Horizon oil spill; Encyclopedia of Earth. 23 June 2010.]<br />
<br />
[4] [http://www.eoearth.org/article/Oil_spill Patin, S. Oil Spill. Encyclopedia of Earth. 23 June 2010.]<br />
</span></div>Mituhttp://2010.igem.org/Team:UTDallas/Project_DetailsTeam:UTDallas/Project Details2010-10-27T02:41:57Z<p>Mitu: </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_Research Research]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Details Details]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
<br />
==Project Details==<br />
Details of the project</div>Mituhttp://2010.igem.org/Team:UTDallas/Project_ResearchTeam:UTDallas/Project Research2010-10-27T02:41:44Z<p>Mitu: </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_Research Research]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Details Details]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
<br />
==Research==<br />
Any articles that are relevant to our project and project goals<br />
<br />
#Paper entitled [http://www.jbioleng.org/content/pdf/1754-1611-2-5.pdf '''Engineering BioBrick vectors from BioBrick parts'''] describing how to make BioBricks using existing parts in the registry - useful for constructing parts necessary for alkane and nitrate sensors.</div>Mituhttp://2010.igem.org/Team:UTDallas/Project_IntroductionTeam:UTDallas/Project Introduction2010-10-27T02:41:30Z<p>Mitu: </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_Research Research]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Details Details]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
|}<br />
==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 />
<br />
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>Mituhttp://2010.igem.org/Team:UTDallas/Project_ProjectOverviewTeam:UTDallas/Project ProjectOverview2010-10-26T23:09:03Z<p>Mitu: </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_Research Research]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Details Details]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_Components Components]<br />
!align="center"|[https://2010.igem.org/Team:UTDallas/Project_References References]<br />
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== Project Overview ==<br />
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The University of Texas, Dallas iGEM team will develop a new generation of biosensors for contaminants. These sensors will be engineered in bacteria and will be able to combine heterogeneous inputs, process the incoming information dynamically, and release accordingly a reporter. <br />
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We are mainly interested in producing biosensors for use in disasters such as the recent Deepwater Horizon Spill. Even though the rig was recently closed, the World Water Assessment Program (WWAP) warns of health risks associated with the presence and circulation of such pollutants. Therefore, there is an urgent need for cheap and reliable contaminant sensors. Chemical sensors can have wide-ranging environmental applications, but can be very expensive depending on the technology. On the other hand, bacterial biosensors offer a cheaper alternative to existing systems. We will use Synthetic biology to implement gene circuits responsible for combinatorial logic, feedback and noise-reduction functions in a similar manner to electronic devices.We will employ molecular biology techniques to develop new and modify existing BioBricks that respond to the following contaminants:<br />
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''Crude oil:'' Commercial oil spills release millions of gallons of toxic chemicals into the ocean, which severely implicate wildlife and their habitats. These chemicals comprise several oil fractions including light ends, naphtha, kerosene, fuel oil, PGO and residual oil fractions. Crude oil is a complex mixture of hydrocarbons consisting primarily of alkanes, cycloalkanes and aromatic hydrocarbons. The alkane series are saturated hydrocarbons with linear or branched chains. The cycloalkane series are saturated hydrocarbons that include non-aromatic rings. The aromatic series are unsaturated hydrocarbons that include six-carbon benzene rings. We will engineer novel BioBricks to convert straight-chain alkanes into aldehydes. Existing parts sensitive to aldehydes would then indicate the presence of alkanes. We will also modify parts submitted by the Glasgow 2007 team, which are inducible by aromatic compounds benzene, toluene, ethylbenzene and xylene.<br />
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''Nitrates:'' Nitrates are a common ingredient in fertilizers, whose use is widespread and often excessive. Nutrient-rich runoff enriches water sources such as lakes, rivers and aquifers with the nitrates in a process called eutrophication, which facilitates the onset of algal blooms that deprive the water of oxygen and essential nutrients. Afflicted water sources are difficult and expensive to cleanse and the process would severely implicate the native wildlife. <br />
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We have several options for the sensor’s output. One possibility is for each contaminant sensor to activate the transcription of a pigment protein. For example, aromatics could produce red, nitrates purple, and alkanes green. When used in conditions with multiple contaminants, this would produce a specific color. A second possibility is using logic functions in a gene network implementation. For example, the presence of aromatics OR nitrates OR alkanes produces green. We will explore both options.</div>Mituhttp://2010.igem.org/Team:UTDallas/ResultsTeam:UTDallas/Results2010-10-26T19:51:03Z<p>Mitu: </p>
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===Results===<br />
[[Image:Ver2.jpg | 500 px | center]]<br />
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<div>===Results===<br />
[[Image:Ver2.jpg | 500 px | center]]</div>Mituhttp://2010.igem.org/Team:UTDallas/PartsTeam:UTDallas/Parts2010-10-26T19:49:32Z<p>Mitu: </p>
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===Parts===<br />
<groupparts>iGEM010 UTDallas</groupparts><br />
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===Results===<br />
====Data====<br />
[[Image:Ver2.jpg | 500 px | center]]<br />
===Parts===<br />
<groupparts>iGEM010 UTDallas</groupparts><br />
</span></div>Mituhttp://2010.igem.org/Team:UTDallas/PartsTeam:UTDallas/Parts2010-10-26T19:47:23Z<p>Mitu: </p>
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<groupparts>iGEM010 UTDallas</groupparts><br />
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