Difference between revisions of "Team:Consort Alberta/Collaborations"

 
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<li class="navitaion_right_border_CON"><a href="https://2015.igem.org/Team:Consort_Alberta">Home</a></li>
 
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<li><a href="https://2015.igem.org/Team:Consort_Alberta/project">Parts</a></li>
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<li><a href="https://2015.igem.org/Team:Consort_Alberta/Parts">Parts</a></li>
<li><a href="https://2015.igem.org/Team:Consort_Alberta/project">Collaborations</a></li>
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<li><a href="https://2015.igem.org/Team:Consort_Alberta/Design">Design</a></li>
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<li><a href="https://2015.igem.org/Team:Consort_Alberta/Collaborations ">Collaborations</a></li>
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                                                                                 <li><a href="https://2015.igem.org/Team:Consort_Alberta/Modeling">Modelling</a></li>
 
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<li><a href="https://2015.igem.org/Team:Consort_Alberta/humanpractices#outreach">Practices</a></li>
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<li class="navitaion_right_border_CON"><a href="https://2015.igem.org/Team:Consort_Alberta/notebook">Notebook</a></li>
 
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<li><a href="contact">Contact Us</a></li>
 
<li><a href="contact">Contact Us</a></li>
 
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<h1 class="left_heading_CON">ECOS</h1>
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<h1 class="left_heading_CON"><div id="collaboratoins">Collaborations</div></h1>
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<p>ECOS is a BioBrick designed to detect xylene. Xylene is a carcinogen in crude oil that is closely associated with two other aromatic hydrocarbons, benzene and toluene,that are the more dangerous compounds in crude oil. In Consort, Alberta, our economy is based almost entirely on agriculture and the oil industry. These two portions of the economy coexist side by side; oil wells are drilled on land adjacent to crops and cattle. This poses an issue if oil spills occur. While oil companies have strict regulations and protocols that they follow, it is always important that we increase our environmental stewardship. There is not a test currently that can check for contamination on site. There is little one can do after sending a sample to a lab and not receiving results back for weeks at a time. In order to properly monitor these sites, farmers and oil companies alike need the tools to do so. This is where we come it. ECOS will provide an on-site test that is cheap, efficient and easy. After talking to many community members we believe that our project could be used for semi-annual testing of sites, water monitoring and post spill monitoring.</p>
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<p>This year, we collaborated with Canmore. Our goals was to get the opinion of another team in order to get an impartial and unbiased analysis of each others projects. We wanted to get another opinion on the usefulness of our biobrick along with any concerns about practicality or safety. Below are the write ups down by both teams.<p/>
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<p>Canmore:<p/>
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<p>Canmore’s project deals primarily with the issue of hair and feather build up in the water treatment systems. This is clearly a major issue and can use extensive amounts of money and time to remedy. There is an extreme amount of inconvenience to unclog the water treatment systems once they get to this point. Creating a BioBrick to produce keratinases could be an effective and cheap solution to the problem and also in preventing the problem. </p>
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<p>Our concerns for Canmore lie in the prototype and safety. The specific engineering and prototyping of a bioreactor is extremely important. The conditions required to keep the bacteria alive, the amount of keratinases that would need to be produced, and the length of time this process will take are all aspects to look into when designing the bioreactor. Their plan to use the membrane bioreactor is a very good and easily applicable idea but the research as to optimum conditions concerning the production of the gene is incredibly important. Having a viable analysis of the cost, time and resources required to make this something we can implement is society is also an important consideration. The time frame of how long it takes to break down the keratin is also something to look into. The comparison of the time requirements to break down other pollutants in the bioreactor chamber compared with the time to break down keratin. Knowing this will allow a design maximizing potential. </p>
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<p>Other thoughts for them to consider include: what types of bacteria are already being used in the bioreactor? What are they breaking down? Is there a way to genetically modify bacteria already in use to contain the kera or karus gene? This would eliminate the need to introduce another species and readjust conditions while allowing maximum productivity.
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Overall, I believe this project could introduce a valid and much needed solution to the issue of hair build up and could be quite effective, quick and safe. As the bioreactor is not connected to the main water line and is completely contained, contamination of water with E. coli would not be an issue. The proposed prototype also utilizes the current system and technologies used making it as easy as possible for implementation. Canmore has done an excellent job in looking at the practical portions of their project and with more research their project could do a lot of good in our world. (-Sam Davies)</p>
  
<h1 class="left_heading_CON">Our Biobrick:</h1>
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<p>Consort:</p>
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<p>This year the iGem team from Consort is continuing with their ECOS project, bacteria designed to detect the presence of aromatic hydrocarbons in order to prevent any harm to the environment. Consort’s ongoing project is a great concept for many reasons. Firstly it is something that is a local problem in their community and especially hits home for some of the team members, which means that they devote themselves fully to the project. Secondly because the outcome of this project could be very helpful for surrounding communities and possibly could hold some wealth in it. Finally because this project could help save countless amounts of crops and livestock from what is a major threat to them.</p>
<p>ECOS consists of the following parts:</p>
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<p>The science behind the project is very intriguing as well. The indicator protein is atoned to xylene, which is a very volatile liquid hydrocarbon, which in itself is a good thing to find and remove but it is tied to other dangerous compounds. When these compounds are detected the proteins emit a color indication that would alert the user to the presence of said dangerous compounds. Whilst this all seems simple the biobrick is not, and they have spent years developing this to perfection to start with their prototypes.</p>
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<p>The prototype and models of prototypes look to be a very effective method of using ECOS. I was able to see one of the prototypes and it looked good even though I was unable to see it in action, this shows great promise for the team in their upcoming endeavors. I can see much success in the future if this team especially if they have a working prototype at the giant Jamboree, I personally wish them the best (-Joshua Lamb)</p>
<p>(Pic of sequence without reporter)</p>
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J23100 - which is a constituent promoter.<br />
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B0034 - the RBS for our XylR gene.<br />
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I723017 - the XylR coding region which encodes for the transcriptional regulator XylR protein.<br />
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B0015 - the double stop codon for this sequence.<br />
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I723020 - This is the Pu promoter.<br />
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B0030 - RBS.1 strong.<br />
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<p>We also attached the Reporter AmilCP in the backbone pCB1C3 to give us an output in correspondence to the level of xylene present.</p>
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<p>(pic of whole sequence) </p>
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<h1 class="left_heading_CON">Our Prototypes</h1>
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<h2>Prototype 1:Animation</h2>
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<p>Alginate beads!  We were hoping we were going to be able to trap our E.coli containing ECOS in the matrix of alginate beads. Alginate is easy to manipulate, it is cheap, light and safe. It would also be extraordinarily simple to operate as you simply place the beads in the soil or water and wait. We did several trials with alginate; experimenting with different protocols to form the beads. Unfortunately the beads ended up being totally opaque. With our trials with ECOS, we had to spin the cells down to see the AmilCP. You could not detect a colour change when the cells were suspended in the LB. With this information, there is no way we would be able to tell if the protein was being produced or not in the alginate beads. We also looked into making beads out of agar. Agar is too porous though and would not be able to hold the bacteria within the matrix.</p>
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<p>(pic of both beads with labels)</p>
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<h2>Prototype 2: (Animation)</h2>
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<p>While this prototype is slightly more complicated, at this point we may have to sacrifice simplicity for something that will give us results. We designed this prototype so that it has a positive pressure source which creates a current for our xylene to travel from our sample, which is in a heated container so that the xylene is vaporized, to our ECOS container in which we bubble it through the E.coli culture to get results. This was a plausible idea, as it would require fairly non-expensive materials and could be maintained by the average business person.</p>
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<h2>Our Results</h2>
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<p>We were able to successfully create two parts. The first being just ECOS and the second having AmilCP attached. We did a lab on the part including AmilCP and did have positive results!</p>
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<p>(Photo’s with labeling guide attached)</p>
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<p>For more details please view our lab write up on the part!</p>
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<p>(LAB WRITE UP goes here… it’s referred to in the notebook a lot)</p>
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<h2>Our Future Plans</h2>
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<p>As AmilCP is hard to see, we plan to look into finding a different reporter which will be easier to work with. Protein Paintbox has many different and vibrant proteins that may work better with ECOS. We have also discussed improving our prototype to make it as efficient as possible. A “seek and destroy” idea has also been brought up. This would mean we could not only detect the oil but also break down the harmful carcinogens contained in it.</p>
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Latest revision as of 19:50, 18 September 2015

Collaborations

This year, we collaborated with Canmore. Our goals was to get the opinion of another team in order to get an impartial and unbiased analysis of each others projects. We wanted to get another opinion on the usefulness of our biobrick along with any concerns about practicality or safety. Below are the write ups down by both teams.

Canmore:

Canmore’s project deals primarily with the issue of hair and feather build up in the water treatment systems. This is clearly a major issue and can use extensive amounts of money and time to remedy. There is an extreme amount of inconvenience to unclog the water treatment systems once they get to this point. Creating a BioBrick to produce keratinases could be an effective and cheap solution to the problem and also in preventing the problem.

Our concerns for Canmore lie in the prototype and safety. The specific engineering and prototyping of a bioreactor is extremely important. The conditions required to keep the bacteria alive, the amount of keratinases that would need to be produced, and the length of time this process will take are all aspects to look into when designing the bioreactor. Their plan to use the membrane bioreactor is a very good and easily applicable idea but the research as to optimum conditions concerning the production of the gene is incredibly important. Having a viable analysis of the cost, time and resources required to make this something we can implement is society is also an important consideration. The time frame of how long it takes to break down the keratin is also something to look into. The comparison of the time requirements to break down other pollutants in the bioreactor chamber compared with the time to break down keratin. Knowing this will allow a design maximizing potential.

Other thoughts for them to consider include: what types of bacteria are already being used in the bioreactor? What are they breaking down? Is there a way to genetically modify bacteria already in use to contain the kera or karus gene? This would eliminate the need to introduce another species and readjust conditions while allowing maximum productivity. Overall, I believe this project could introduce a valid and much needed solution to the issue of hair build up and could be quite effective, quick and safe. As the bioreactor is not connected to the main water line and is completely contained, contamination of water with E. coli would not be an issue. The proposed prototype also utilizes the current system and technologies used making it as easy as possible for implementation. Canmore has done an excellent job in looking at the practical portions of their project and with more research their project could do a lot of good in our world. (-Sam Davies)

Consort:

This year the iGem team from Consort is continuing with their ECOS project, bacteria designed to detect the presence of aromatic hydrocarbons in order to prevent any harm to the environment. Consort’s ongoing project is a great concept for many reasons. Firstly it is something that is a local problem in their community and especially hits home for some of the team members, which means that they devote themselves fully to the project. Secondly because the outcome of this project could be very helpful for surrounding communities and possibly could hold some wealth in it. Finally because this project could help save countless amounts of crops and livestock from what is a major threat to them.

The science behind the project is very intriguing as well. The indicator protein is atoned to xylene, which is a very volatile liquid hydrocarbon, which in itself is a good thing to find and remove but it is tied to other dangerous compounds. When these compounds are detected the proteins emit a color indication that would alert the user to the presence of said dangerous compounds. Whilst this all seems simple the biobrick is not, and they have spent years developing this to perfection to start with their prototypes.

The prototype and models of prototypes look to be a very effective method of using ECOS. I was able to see one of the prototypes and it looked good even though I was unable to see it in action, this shows great promise for the team in their upcoming endeavors. I can see much success in the future if this team especially if they have a working prototype at the giant Jamboree, I personally wish them the best (-Joshua Lamb)