Team:SDU-Denmark/safety-d

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(The watermark)
(Useful ideas for Improving Safety)
 
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==Watermarking==
==Watermarking==
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To increase public safety we propose to introduce a water-marking standard
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To increase public safety we propose to introduce a water-marking standard. <br>
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Following the example of J. Craig Venter, who, in may 2010, created the first watermark in a bacteria, containing several readable messages, we propose to create a watermarking standard to increase the safety of the environment, as well as the safety of the community at large.  
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Following the example of J. Craig Venter, who, in may 2010, created the first watermark in a bacteria, containing several readable messages, we propose to create a watermarking standard to increase the safety of the environment, as well as the safety of the community at large. <vr>
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But why should we consider creating and using a watermarking standard for work in synthetic biology? Let us consider the following example. <br />
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But why should we consider creating and using a watermarking standard for work in synthetic biology? Let us consider the following example: <br>
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A company has created a synthetic organism capable of absorbing harmful substances from the ground. The government, eager to help clean polluted ground, releases the bacteria into the wild, confident that the bacteria will not pose any threat to the environment. These bacteria do not, however, react as planned. Instead of absorbing only the harmful substances from the ground, they transfer the substances to other organisms, or simply run amok spreading themselves in an uncontrolled manner, causing harm instead of good. Let us imagine that this happens close to the border. The government in the neighboring state finds itself with a unexplained biological phenomenon, possibly causing great harm. <br />
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A company has created a synthetic organism capable of absorbing harmful substances from the ground. The government, eager to help clean polluted ground, releases the bacteria into the wild, confident that the bacteria will not pose any threat to the environment. These bacteria do not, however, react as planned. Instead of absorbing only the harmful substances from the ground, they transfer the substances to other organisms, or simply run amok spreading themselves in an uncontrolled manner, causing harm instead of good. Let us imagine that this happens close to the nation's border. The government in the neighboring state finds itself with a unexplained biological phenomenon, possibly causing great harm. <br />
Should the rogue bacteria contain engineered, watermarked parts, it would be a small matter to have the parts sequenced, thus the government would be able to easily access all the relevant information on the rogue bacteria, contact the manufacturers and would know how to stop it.
Should the rogue bacteria contain engineered, watermarked parts, it would be a small matter to have the parts sequenced, thus the government would be able to easily access all the relevant information on the rogue bacteria, contact the manufacturers and would know how to stop it.
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==Placing the watermark==
==Placing the watermark==
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The initial thought was to insert the watermark into the genome of the bacteria, as to increase the stability of the watermark in the bacteria. However, as all parts inserted into the bacteria are placed in plasmids, it would make no sense to insert the watermark into the genome. The bacteria could transfer their plasmids to other bacteria, and retain their watermark, and the watermark would have become useless, persisting in bacteria that have no modified material at all. <br />
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The initial thought was to insert the watermark into the genome of the bacteria, so as to increase the stability of the watermark in the bacteria. However, as all parts inserted into the bacteria are placed in plasmids, it would make no sense to insert the watermark into the genome. The bacteria could transfer their plasmids to other bacteria, and retain their watermark, and the watermark would have become useless, persisting in bacteria that have no modified material at all. <br />
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Also the thought was to mark the bacteria, and not the parts. Thus we could have a single watermark to cover the entire modified organism. However, this presents us with many of the above problems. Should anyone encounter  a rogue bacteria which has lost some of its plasmids, the watermark would be useless. It would only cover the entire modified system, and should some, or all bacteria have discarded the plasmids, the watermark would be useless. We therefore propose to mark every plasmid, before and after the coding sequence. The watermark will therefore be split into two separate components. The team creates a watermark for every part, and inserts it into the plasmid, before and after the coding sequence. <br />
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Also, the thought was to mark the bacteria, and not the parts. Thus we could have a single watermark to cover the entire modified organism. However, this presents us with many of the above problems. Should anyone encounter  a rogue bacteria which has lost some of its plasmids, the watermark would be useless. It would only cover the entire modified system, and should some, or all bacteria have discarded the plasmids, the watermark would be useless. We therefore propose to mark every plasmid, before and after the coding sequence. The watermark will therefore be split into two separate components. The team creates a watermark for every part, and inserts it into the plasmid, before and after the coding sequence. <br />
We chose to divide the code into two separate parts for two reasons. Firstly, being split into two equally long parts at each end of the coding sequence ensures symmetry , which again should help make insertion of a watermark easy, as this will reduce the complexity of the primers we need to design to insert them. Secondly this ensures that identification is done easily, since the combination of nucleotides of the sequence from E to X and from S to P is known. Thus we effectively increase the sequence we search for from 6 to 26 nucleotides. Also this means that the risk of a naturally occurring combination of nucleotides, identical to the synthetically created one decreases.  
We chose to divide the code into two separate parts for two reasons. Firstly, being split into two equally long parts at each end of the coding sequence ensures symmetry , which again should help make insertion of a watermark easy, as this will reduce the complexity of the primers we need to design to insert them. Secondly this ensures that identification is done easily, since the combination of nucleotides of the sequence from E to X and from S to P is known. Thus we effectively increase the sequence we search for from 6 to 26 nucleotides. Also this means that the risk of a naturally occurring combination of nucleotides, identical to the synthetically created one decreases.  
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Every team, and lab / company which works with synthetic biology will be assigned a specific “license plate”, unique to them and being their ‘ID’ on parts-registry. An extension to parts registry’s search function should then be added. If its database contains information on each “license”, one could easily find information on a foreign organism, in case they found it in the wild (that is, anywhere else than the lab), and had it sequenced afterwards. Upon entering the parts-registry, one should then be able to enter the license and gain access to information on the parts that the team / lab / company has created. Anyone should be able to enter the license code into the parts-registry and gain access to all information on the creating team, the parts created by the team, and of course some contact information, in order to seek advice.
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Every team and lab/company which works with synthetic biology will be assigned a specific “license plate”, unique to them and being their ‘ID’ on parts-registry. An extension to parts registry’s search function should then be added. If its database contains information on each “license”, one could easily find information on a foreign organism, in case they found it in the wild (that is, anywhere else than the lab), and had it sequenced afterwards. Upon entering the parts-registry, one should then be able to enter the license and gain access to information on the parts that the team / lab / company has created. Anyone should be able to enter the license code into the parts-registry and gain access to all information on the creating team, the parts created by the team, and of course some contact information, in order to seek advice.
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The above list of question is more or less derived from a more throughout list of questions relevant to assessing the safety and securty of the parts, see appendix II
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The above list of question is more or less derived from a more throughout list of questions relevant to assessing the safety and securty of the parts, see appendix II.
==Further Information==
==Further Information==

Latest revision as of 21:46, 26 October 2010