Difference between revisions of "Team:UNebraska-Lincoln/Description"

 
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{{UNebraska-Lincoln}}
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<h3>How did we choose our project?</h3>  
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<p>We wanted our project to address a problem of significance on both global and local levels. Because Nebraska’s economy relies heavily on agriculture, a project devoted to an aspect of this industry was the obvious choice. Our objective is to reduce the nitrate levels in the waterways around Nebraska. Runoff from land treated with nitrate-containing fertilizers causes the accumulation of these compounds in waterways, where they are carried to the Gulf of Mexico. According to the National Oceanic and Atmospheric Administration, the Gulf of Mexico is the second-largest dead zone in the world, measuring approximately 5,500-6,500 square miles.</p>
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<p>A dead zone is a hypoxic area in a body of water where little marine life can survive. The excess nutrients in the water from fertilizers cause algal blooms at the surface. Because algae is not a good food source for other organisms in the ecosystem, it sinks and decomposes when it dies. The process of decomposition uses oxygen dissolved in the water, making the area uninhabitable for many species.</p>
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<p>We want to fix this problem by reducing nitrate levels in local rivers, addressing the problem at its source. We aim to engineer E. Coli to convert nitrate ions back into elemental nitrogen, a process called denitrification. Engineering E. coli to denitrify waters will involve introducing a nitrate-responsive promoter, corresponding bacterial ‘termination sequences’, and safety steps to ensure that the process can be controlled to the cells.</p>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/background">Background</a>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/modeling">Modeling</a>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/design">Design</a>
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<span class="sdt_link" style="">Laboratory</span>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/experiments">Experiments</a>
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<h5>Advice on writing your Project Description</h5>
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                                                        <a href="https://2016.igem.org/Team:UNebraska-Lincoln/Integrated_Practices">Integrated Practices</a>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/human_practices">Human Practices</a>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/collaboration">Collaboration</a>
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/industry">Industry</a>
  
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
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Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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<a href="https://2016.igem.org/Team:UNebraska-Lincoln/sponsors">Sponsors</a>
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                      <center><h2 style="height:100px; padding-top:5px"><font size="+10">Description</font></h2></center>
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                      <center><font color="silver">Our project, "Knockout Nitrate", is a developing project with the aim to use synthetic biology to balance the nitrogen cycle. </font></center>
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<p><center><font color="silver"><h2>Background</h2></font></center></p>
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<p><center><font color="silver">Nitrogen is a highly abundant element in the Earth’s atmosphere. Nitrogen is also essential for life. However, atmospheric nitrogen (N2) is not useful in living processes. Humans have developed processes to convert unreactive atmospheric nitrogen into a usable form of nitrogen such as Ammonia or Nitrate for plants and animals (reactive nitrogen). To maximize crop yield, many farmers add nitrogen based fertilizer to their crops. Oftentimes excess nitrogen in the soil is washed away by rain into other natural water systems. This nitrogen runoff can and does have devastating effects on the biodiversity in waterways.</font></center></p>
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<p><center><font color="silver">To read more background information about the nitrate problem, click the image below.</font></center></p>
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<center><a href="https://2016.igem.org/Team:UNebraska-Lincoln/background"><img src="https://static.igem.org/mediawiki/2016/6/67/T--UNebraska-Lincoln--background.png" style="width:40%; height:auto;" alt="image"/></a></center>
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<br><br>
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<p><center><font color="silver"><h2>Project Design</h2></font></center></p>
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<p><center><font color="silver">In order to combat the nitrate problem, we aimed to design a strain of <i>E. coli</i> capable of reducing these excess nitrate ions. By isolating a gene that codes of periplasmic nitrate reductases, we began the process of designing our synthetic organism.</font></center></p>
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<p><center><font color="silver">To read more information about the design of our system, click the image below.</font></center></p>
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<center><a href="https://2016.igem.org/Team:UNebraska-Lincoln/design"><img src="https://static.igem.org/mediawiki/2016/0/0f/T--UNebraska-Lincoln--design.png" style="width:40%; height:auto;" alt="image"/></a></center>
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<p><center><font color="silver"><h2>Experiments for Our System</h2></font></center></p>
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<p><center><font color="silver">Throughout the summer and into the fall, we implemented our design into the laboratory. We isolated and synthesized our periplasmic nitrate reductase genes, as well as developed a kill switch and safety-assurance cases</font></center></p>
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<p><center><font color="silver">To read more information on the application of our design, click the image below.</font></center></p>
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<center><a href="https://2016.igem.org/Team:UNebraska-Lincoln/experiments"><img src="https://static.igem.org/mediawiki/2016/1/16/T--UNebraska-Lincoln--experiments.png" style="width:40%; height:auto;" alt="image"/></a></center>
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<p><center><font color="silver"><h2>Recharacterization of K381001</h2></font></center></p>
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<p><center><font color="silver">In the design of our project, we implemented a nitrate-sensitive kill switch. This took advantage of the fact that the yeaR promoter, originally submitted by the Edinburgh iGEM Team in 2009 (<a href="http://parts.igem.org/Part:BBa_K216005">K216005</a>) was active only in the presence of nitrate ion. We decided to begin our project by determining sensitivity of this promoter the concentrations of nitrate that would be present in waterways. To do this, we recharacterized the composite part <a href="http://parts.igem.org/Part:BBa_K381001">K381001</a>, a PyeaR-GFP nitrate sensor.  You can read more about our rechracterization of the PyeaR-GFP Biobrick <a href="http://parts.igem.org/Part:BBa_K381001:Experience#UNebraska-Lincoln_2016">Here</a>.</font></center></p>
  
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<h5>Inspiration</h5>
 
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<p>See how other teams have described and presented their projects: </p>
 
  
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<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
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<center><a href="https://2016.igem.org/Team:UNebraska-Lincoln/laboratory"><img src="https://static.igem.org/mediawiki/2016/9/9c/T--UNebraska-Lincoln--tothelab.png"  style="width:60%;height:auto;" transform:scale(0.2)></a></center>
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Latest revision as of 02:55, 20 October 2016

<!DOCTYPE HTML> Elements - Solid State by HTML5 UP

Description

Our project, "Knockout Nitrate", is a developing project with the aim to use synthetic biology to balance the nitrogen cycle.

Background

Nitrogen is a highly abundant element in the Earth’s atmosphere. Nitrogen is also essential for life. However, atmospheric nitrogen (N2) is not useful in living processes. Humans have developed processes to convert unreactive atmospheric nitrogen into a usable form of nitrogen such as Ammonia or Nitrate for plants and animals (reactive nitrogen). To maximize crop yield, many farmers add nitrogen based fertilizer to their crops. Oftentimes excess nitrogen in the soil is washed away by rain into other natural water systems. This nitrogen runoff can and does have devastating effects on the biodiversity in waterways.

To read more background information about the nitrate problem, click the image below.

image


Project Design

In order to combat the nitrate problem, we aimed to design a strain of E. coli capable of reducing these excess nitrate ions. By isolating a gene that codes of periplasmic nitrate reductases, we began the process of designing our synthetic organism.

To read more information about the design of our system, click the image below.

image

Experiments for Our System

Throughout the summer and into the fall, we implemented our design into the laboratory. We isolated and synthesized our periplasmic nitrate reductase genes, as well as developed a kill switch and safety-assurance cases

To read more information on the application of our design, click the image below.

image

Recharacterization of K381001

In the design of our project, we implemented a nitrate-sensitive kill switch. This took advantage of the fact that the yeaR promoter, originally submitted by the Edinburgh iGEM Team in 2009 (K216005) was active only in the presence of nitrate ion. We decided to begin our project by determining sensitivity of this promoter the concentrations of nitrate that would be present in waterways. To do this, we recharacterized the composite part K381001, a PyeaR-GFP nitrate sensor. You can read more about our rechracterization of the PyeaR-GFP Biobrick Here.