Difference between revisions of "Template:Team:TU Eindhoven/Project Safety HTML"

 
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This year’s project is about Clickable Outer Membrane Biosensors (COMBs). The sensor is designed to become an aptamer-based approach to a universal and modular biosensor platform. Because of its modularity, is has a broad range of applications.  
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This year’s project is about Clickable Outer Membrane Biosensors (COMBs). The sensor is designed to become an aptamer-based approach to an universal and modular biosensor platform. Because of its modularity, it has a broad range of applications.  
 
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Beads
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Our sensor is expressed in the BioSafety level 1, E. coli K-12 strain. This strain cannot survive by itself outside the laboratory environment and is therefore not harmful. As additional precaution, the bacteria will be placed in a small enclosed device. The small enclosed device has been created by the used of alginate beads. <br />
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Alginate is an ionotropic hydrogel which shows immobilization of macromolecules and cells due to the chemical features of the gel. The material however does have the ability to do free diffusion of substrates and products.  The alginate solution is prepared by dissolving alginate into a NaCl solution. The bacteria are placed into the alginate solution. This solution is then slowly dropped into the CaCl2 solution. After being in contact with the Ca2+ the polysaccharides show crosslinking behavior causing beads to be formed. For a detailed description of the formation of alginate beads click <a href="https://static.igem.org/mediawiki/2015/4/4c/TU_Eindhoven_Protocols_Alginate_beads.pdf" target="_blank"> here</a>. <a name="reft1" href="#ref1" class="textanchor">[1]</a><br />
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The encapsulation makes sure that the beads are immobilized but still reachable by substrates. This property is needed for the modular sensor as the bacteria will not be able to cause any harm. However recent studies show that alginate beads have a low mechanical strength and a poor chemical durability. As the wish is to use the beads for a longer time they have to be durable so another coat of silicone is placed over the alginate beads. A siliceous polymeric structure is prepared to coat the alginate bead to improve the mechanical stability and to reduce leakage. Research confirms that entrapment in a double-layer matrix is a lot more effective. <a name="reft2" href="#ref2" class="textanchor">[2]</a>
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Thanks to the platform technique, almost everyone can become a user of our project. For Policy Practices a couple <a href="https://2015.igem.org/Team:TU_Eindhoven/Policy_Practices/Application_scenarios" target="_blank"> future applications</a> were deeply investigated. <br />
 
Thanks to the platform technique, almost everyone can become a user of our project. For Policy Practices a couple <a href="https://2015.igem.org/Team:TU_Eindhoven/Policy_Practices/Application_scenarios" target="_blank"> future applications</a> were deeply investigated. <br />
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The first worked out application is a system against the over usage of pesticides. In this case the bacteria will sense these disease markers and activates a pathway in the cell which produces pesticides. In this way no pesticides are used redundant and the environment will be less damaged.  
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The first worked out application is a system against the over usage of pesticides. In this case the bacteria will sense these pathogen markers and activate a pathway in the cell which produces pesticides. In this way no pesticides are used redundantly and the environment will be less damaged.  
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Another application is early diagnosis of Intestinal Cancer. Ideally, self-sustaining bacteria in the gut will be able to tell whether a person has colon cancer or not. Since the E.coli bacteria already naturally occur in the human intestines, it is ideal for diagnostic and treating purposes.
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Another application is the early diagnosis of intestinal diseases. Ideally, self-sustaining bacteria in the intestinal system will be able to tell whether irregularities are present. Since E. coli bacteria are natural inhabitants of the human intestines, our sensor is ideal for diagnostics and treatment purposes.
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Besides intestinal cancer, Q fever is also a disease which is investigated. Because its origin lies with animals, it would be a sensor for farmers to use to test if their animals are infected.  
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The last scenario described is about Q fever. Because its origin lies with animals, it would be a sensor for farmers to use to test whether their animals are infected.  
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A lot of stakeholders were contacted and interviewed and much of the reactions were positive.  
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A lot of stakeholders were contacted and interviewed and many positive reactions were received.  
  
 
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The modularity of the sensor is one of the greater strengths of this sensor. It creates a lot of possibilities to solve many problems. The modularity however should also be assessed on certain risks. One of the main concerns for this modularity is, if it is possible to perform harm with this system. Synthetic biology creates a database of small bricks which can be used to assemble new applications. One of the main fears is that it becomes too easy to assemble of virulent or hazardous microorganism. To asses this risk a couple of important questions need to be answered. Such as is it possible for a person to turn this platform technique into a harmful device? How easily accessible are the parts to construct this device? If wanting to do harm is this possible?
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The modularity of the sensor is one of the greater strengths of this system. It creates a lot of possibilities to solve many problems. The modularity however should also be assessed on certain risks. One of the main concerns for this modularity is, whether it is possible to perform harm with this system. Synthetic biology creates a database of small bricks which can be used to assemble new applications. One of the main fears is that it becomes too easy to assemble virulent or hazardous microorganisms. To asses this risk a couple of important questions need to be answered. Such as, is it possible for a person to turn this platform technique into a harmful device? How easily accessible are the parts to construct this device? If wanting to do harm is this possible?
 
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Our sensor is expressed in the BioSafety level 1 E.coli K-12 strain. This strain cannot survive by itself outside the laboratory environment and is therefore not harmful. As extra precaution, the bacteria will be placed in a small enclosed device. <img src="https://static.igem.org/mediawiki/2015/8/87/TU_Eindhoven_Ingeklapt.png" id="spoilerbutton1" class="spoilerbutton"><div class="spoiler" id="spoiler1">
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The risk of our project is the misusage of the parts. Fortunately, the use of the protein OmpX in the design limits the rates of using the device to E. coli strains only as this protein is a naturally occurring in the membrane of E. coli. However, there are some harmful E. coli strains which can be used, but the danger already lies in the strains themselves. The possibility to turn the sensing device into a harmful product is very unlikely. The harmful symptoms of those strains are diarrhea and a fever. It usually passes in 5 to 7 days but sometimes an infection can be severe.
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Information about the gel capsules!
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The risk of our project is the misusage of the parts. Fortunately, the use of the protein OmpX in the design limits the rates of using the device to E.coli strains only as this protein is a naturally occurring in the membrane of E.coli. However, there are some harmful E.coli strains which can be used, but the danger already lies in the strains themselves. The possibility to turn the sensing device into a harmful product is very unlikely. The harmful symptoms of those strains are diarrhea and a fever. It usually passes in 5 to 7 days but sometimes an infection can be severe.
 
 
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The modularity of the device is currently gained through the use of the clickable aptamers. The aptamers may be a potential risk as they are easily ordered. For the rest of the construct to order the proteins and DNA an institution is needed. This can only be done if the person who wants to do harm is included into an institution which has a license to work with GMOs. The internal components of the design can only produce a light and this is not harmful. A potential risk would occur if the system can be used to activate genes and used to produce harmful substances.
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The modularity of the device is currently gained through the use of the clickable aptamers. The aptamers may be a potential risk as they are easily ordered. For the rest of the construct to order the proteins and DNA an institution is needed. This can only be done if the person who wants to do harm is included into an institution which has a license to work with GMO’s. The inside of the design can only produce a light and this is not harmful.  
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Harms and benefits
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Harms &amp; Benefits
 
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Some of the many stakeholders are already described by the application examples of our device. There are however much more people who can receive harms and benefits, because of its modularity. The benefits will mostly be for the users and also for the producing companies. Additionally, the owners of the patents of dual aptamers or split aptamers can make more money with their patents. The possible harm will come to the companies with the competitive sensors, because our sensor can make them unnecessary. However, this chance is not very large, because they can still be wanted as additional tests for their higher accuracy.  
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At the page Talks, opinions of different stakeholders have been evaluated for the scenarios. However, there are many more people who would be affected by our system. For users and producing companies, our project influences them beneficially. Owners of the patents of dual or split aptamers will economically benefit from the system if the product is produced. The possible economic harm will come to the companies with the competitive sensors. However, the sensor systems can still be used together, only creating better and more accurate detection methods.
  
 
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The product needs to be collected as biological waste and be disposed of in the proper way. This includes sterilization. It is not possible to reuse our product itself, because the small device, in which our bacteria are kept, is too small.  
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To maintain the  durability of the biosensor, it should be stored at 4 °C. Under this condition, the bacteria will barely grow or divide and thus won’t need many nutrients and can live longer. When the sensor has reached its maximum durability or has completed its function, it should be collected as biological waste and be disposed in the proper way, including sterilization. The bacteria will die and no GMOs will be able to reach the environment. The materials of the device are already natural and can be degraded into smaller naturally occurring materials.  
  
 
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<a href="#reft1" name="ref1">[1]</a> Draget, K. I., Smidsrød, O., Skjåk-Bræk, G., Alginates from Algae, Biopolymers Online, 6, 2005 <br />
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<a href="#reft2" name="ref2">[2]</a>    E. Callone et al, “Immobilization of yeast and bacteria cells in alginate microbeads coated with silica membranes: procedures, physico-chemical features and bioactivity” Journal of materials chemistry, 18(40), pp. 4839-4848, Sep. 2008. <br />
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Latest revision as of 01:22, 19 September 2015





Project Safety



This year’s project is about Clickable Outer Membrane Biosensors (COMBs). The sensor is designed to become an aptamer-based approach to an universal and modular biosensor platform. Because of its modularity, it has a broad range of applications.


Beads


Our sensor is expressed in the BioSafety level 1, E. coli K-12 strain. This strain cannot survive by itself outside the laboratory environment and is therefore not harmful. As additional precaution, the bacteria will be placed in a small enclosed device. The small enclosed device has been created by the used of alginate beads.
Alginate is an ionotropic hydrogel which shows immobilization of macromolecules and cells due to the chemical features of the gel. The material however does have the ability to do free diffusion of substrates and products. The alginate solution is prepared by dissolving alginate into a NaCl solution. The bacteria are placed into the alginate solution. This solution is then slowly dropped into the CaCl2 solution. After being in contact with the Ca2+ the polysaccharides show crosslinking behavior causing beads to be formed. For a detailed description of the formation of alginate beads click here. [1]
The encapsulation makes sure that the beads are immobilized but still reachable by substrates. This property is needed for the modular sensor as the bacteria will not be able to cause any harm. However recent studies show that alginate beads have a low mechanical strength and a poor chemical durability. As the wish is to use the beads for a longer time they have to be durable so another coat of silicone is placed over the alginate beads. A siliceous polymeric structure is prepared to coat the alginate bead to improve the mechanical stability and to reduce leakage. Research confirms that entrapment in a double-layer matrix is a lot more effective. [2]




Usage


Thanks to the platform technique, almost everyone can become a user of our project. For Policy Practices a couple future applications were deeply investigated.
The first worked out application is a system against the over usage of pesticides. In this case the bacteria will sense these pathogen markers and activate a pathway in the cell which produces pesticides. In this way no pesticides are used redundantly and the environment will be less damaged. Another application is the early diagnosis of intestinal diseases. Ideally, self-sustaining bacteria in the intestinal system will be able to tell whether irregularities are present. Since E. coli bacteria are natural inhabitants of the human intestines, our sensor is ideal for diagnostics and treatment purposes. The last scenario described is about Q fever. Because its origin lies with animals, it would be a sensor for farmers to use to test whether their animals are infected. A lot of stakeholders were contacted and interviewed and many positive reactions were received.


Risks


The modularity of the sensor is one of the greater strengths of this system. It creates a lot of possibilities to solve many problems. The modularity however should also be assessed on certain risks. One of the main concerns for this modularity is, whether it is possible to perform harm with this system. Synthetic biology creates a database of small bricks which can be used to assemble new applications. One of the main fears is that it becomes too easy to assemble virulent or hazardous microorganisms. To asses this risk a couple of important questions need to be answered. Such as, is it possible for a person to turn this platform technique into a harmful device? How easily accessible are the parts to construct this device? If wanting to do harm is this possible?

The risk of our project is the misusage of the parts. Fortunately, the use of the protein OmpX in the design limits the rates of using the device to E. coli strains only as this protein is a naturally occurring in the membrane of E. coli. However, there are some harmful E. coli strains which can be used, but the danger already lies in the strains themselves. The possibility to turn the sensing device into a harmful product is very unlikely. The harmful symptoms of those strains are diarrhea and a fever. It usually passes in 5 to 7 days but sometimes an infection can be severe.

The modularity of the device is currently gained through the use of the clickable aptamers. The aptamers may be a potential risk as they are easily ordered. For the rest of the construct to order the proteins and DNA an institution is needed. This can only be done if the person who wants to do harm is included into an institution which has a license to work with GMOs. The internal components of the design can only produce a light and this is not harmful. A potential risk would occur if the system can be used to activate genes and used to produce harmful substances.


Harms & Benefits


At the page Talks, opinions of different stakeholders have been evaluated for the scenarios. However, there are many more people who would be affected by our system. For users and producing companies, our project influences them beneficially. Owners of the patents of dual or split aptamers will economically benefit from the system if the product is produced. The possible economic harm will come to the companies with the competitive sensors. However, the sensor systems can still be used together, only creating better and more accurate detection methods.


Disposal


To maintain the durability of the biosensor, it should be stored at 4 °C. Under this condition, the bacteria will barely grow or divide and thus won’t need many nutrients and can live longer. When the sensor has reached its maximum durability or has completed its function, it should be collected as biological waste and be disposed in the proper way, including sterilization. The bacteria will die and no GMOs will be able to reach the environment. The materials of the device are already natural and can be degraded into smaller naturally occurring materials.

[1] Draget, K. I., Smidsrød, O., Skjåk-Bræk, G., Alginates from Algae, Biopolymers Online, 6, 2005
[2] E. Callone et al, “Immobilization of yeast and bacteria cells in alginate microbeads coated with silica membranes: procedures, physico-chemical features and bioactivity” Journal of materials chemistry, 18(40), pp. 4839-4848, Sep. 2008.