Difference between revisions of "Team:Groningen/Integrated Practices"

Social

Originally our idea was to send exclusively the key encrypted in bacteria, and once the receiver decrypted the key he could use it to access to the sensitive information previously stored in internet. However, immediately we figured out a drawback; if the information is already digitally accesible, it might be target of leaking. So we decided to send both, the original message encrypted and the key in the same package using the DNA of bacteria.

With that idea in mind, we contacted the Cyber Security Centre from the Ministry of Security and Justice from the Netherlands, institution in charge of the cyber security in our country, to know what would be possible drawbacks of our idea, and what are the real challenges that they have to face in the field of encryption. This Institution made comments on our project, they told us that generally when a system is intended for the sending rather than just storing it, two questions are important:

The first one, what do we do with key and how we keep it safe?

This question changed deeply our project; the National Institution told us that when the message and the key are sent together in the same package the probability that the information is intercepted and decrypted is really high, therefore it must be ensured that either, the key, the message or both are safe and cannot be accessed easily if the package is intercepted. To overcome that, we propose the idea of using of biological security layers to provide an extra lock to access to the information; you and your receiver agreed on a biological key beforehand. This biological lock comprises the proper germination conditions for the key spores. A wrong treatment will cause the loss of the desired DNA sequence and therefore the message cannot be read anymore. Only with the biological key, the right treatment of the spores, the DNA of the Bacillus subtilis culture can be harvested and the genome will be sequenced.

The second question that the experts face when sending encrypted information is that how do we ensure that the information is securely decrypted?

By thinking in this problem, we came out with a simple solution. To make it especially hard for unauthorized parties to access our key, the key-spores will be sent in a mixture of decoy spores. The decoy is present in a much higher ratio than the key-spores. The key-spores have to be recovered using a specific selection mechanism. We have developed a ciprofloxacin resistance cassette that can be integrated into the B. subtilis genome. Only the knowledge of this specific selection antibiotic will allow the recovery. Even better: This resistance cassette also provides resistance against spirofloxacin which is a conjugate of the regular antibiotic ciprofloxacin and a spiropyrin photoswitch. In case of using the photoswitchable antibiotic, spirofloxacin, in its inactivated state, could be already added to the spore mixture. The recipient simply has to activate it by shining UV light of the right wavelength on it.

After shaping our project based on those two real challenges faced by the experts in the sending of sensitive information, we realized that not only governments but also private companies could be interested in using our system. But, which requirements? Would private companies or institutions be interested in using CryptoGErM? Would be able to adapt our system to the conditions required for real users? Is it our system better in comparison with current technologies for the storing and sending of information?

To answer this we interview a potential user, the Groningen Archives; they store the entire historical information related with the province of Groningen in the Netherlands. As a result of this interview, we learned that paper (it is often the medium used for the storing of historical information) requires specific conditions that sometimes are not suitable for long-term storing, because they consume a lot of resources to preserve it. In addition to that, paper it is a suitable for information storage just for a couple of hundred of years. Actually, this Institution has been prepared for the change from physical to digital storing for the last years. The advantages of storing information in DNA is that spores are highly resistant entities that can survive harsh environments; actually spore of Bacillus subtilis can be found after several million years, as shown for the discoveries done in the last years. Besides that, DNA can store up to 10⁹ GB/mm³ which is a regally high density compared with the current technologies that can store only 10 GB/mm³; furthermore, the spores do not need strict environment for their conservation in comparison with paper or digital storage.

We learned also that a system intended for the long-term storing of information must be ensure its storability and accessibility, i. e. the nature of the medium used for the storing does not matter as long as it is insured that the stored information is completely preserved. He told us that DNA is a considerable option if the information does not though mutations.

So here, we found another problem: how we could be sure that the DNA would not suffer mutations or that the potential mutations? After this interview, we realized how important is to know the mutation probability in the DNA of Bacillus subtilis spores, we explored in the literature the mutation rate in Bacillus subtilis spores concluding that each line of B. subtiliswill have around one mutation by the time we want to read the message; however, this mutation does not have to be necessarily inside our message because it is random

We modelled how many times the random mutations could be present in our message by using computational tools, and after the modelling we concluded that for that we applied that for our specific case the impact of the random mutations influencing our project was extremely low and that we could have safely saved our message

Additionally to the experts and the potential users, we started a survey to know what is the current perception of the society about the storing and sending of information. We wanted to achieve an extensive and broad range of people from different backgrounds and nationalities; however, though the years we have found out that most of the survey conducted by iGEM teams are in English which excludes people that do not speak this language. We were interested in a broader sample of the population and not limit our survey to English-speakers to have a real data from the general public; therefore, we developed versions of our survey in different languages together with iGEM Teams who shared it in their social media. These surveys gave us the opportunity to reach more general audience making easier for them to understand the questions. Originally the survey was developed together with a psychologist to assure that the questions and the structure were correct to obtain the information intended.

We found out that our survey respondents send sensitive information through digital means but they do not trust it, because they feel their information is not secure from digital hacking. Our survey respondents also agree that ours system could be used by them for the storing of sensitive information that has not to be necessarily accessed immediately. Based on those results, we can trust that our system could be use also by general public. Thanks to this survey we found out the applications that normal citizens would give to our system, which includes the storing of medical records, family information, etc. However, as a result of this survey we also found out that an important percentage of our survey respondents do not actually what bacteria are. So we dedicated our Education and Outreach sections to reach as much general public as possible to promote concepts of synthetic biology and our project.

Legal

Once the system fulfilled the requirements from experts, users and society; the next step was to explore the shipping of our spores containing the encrypted information.

For that, we contacted the iGEM Teams from Eindhoven and Wageningen in the Netherlandsto collaborate with us by decrypting our message… The bacteria would be sent to the iGEM Teams by post.

The idea of our system is that the encrypted information contained on bacteria can be shipped freely around the world. So, the next important step for the Human Practices and was to look for the national and international legislations that regulate the sending of GMOs. This is crucial for our project, because we cannot send the spores of Bacillus subtilis without following regulations because it might be that we put in the risk the environment or society. Since the legislations were really extensive, we contacted the for guidance in the Dutch Regulations for the sending of modified bacteria. We read all those regulations to find out what is the correct way for the sending of GMOs using conventional methods, such as post. We found out that the GMOs received a classification according to its nature, focusing on the fact if the GMOs pretending to be sent meet the definition of infectious substances; in our case, the Bacillus subtilis spores with the message are not within the concept of infectious substance and they are assigned to the labelling UN3245. Besides that, we found out that for the shipping of GMOs we must use packings with strict specifications, for example, we used an leakproof envelopment using the labelling mentioned before. We discussed explicitly this in our legal section of Human Practices.

The next step was looking for international regulations for the shipping of GMOs, because the perspectives of our system is the free shipping of encrypted information in our system around the world. We consulted the Cartagena Protocol. However, we realized that the International shipping of GMOs is regulated from different legislations depending on the country that is intended for the access of the GMOs. We consulted the three more important guidelines and regulations for the sending to America, Europe and Asia of our system, the Cartagena Protocol in Biosafety, the national legislations from non-parties of the Cartagena Protocol and the guidelines of the World Health Organisation. We followed a strict protocol for the sending of our spores to our Dutch iGEM Collaborators obeying the national and international recommendations.

Future scenarios

We decided to explore different aspects of our project and the repercussions of its introduction as a daily-used system in the near and long future. These scenarios were based on current evidence.We explore the applications of our project that may result of the advantages that DNA has over others storage medium, such as minimal physical space and high density of storing; for example, we can store 10⁹ GB/mm³ in DNA leading to a decrease in the physical space required for the storing. This also leads to a high capacity to store large amount of data in DNA of bacteria.

in our future scenarios we explored the cost and speed of sequencing DNA and the predictions made for those two in the upcoming years. The last step of our project includes the sequencing of the DNA that contains the key and the message, so it was important for us to know the current price and time required for reading our message. We found that the current price for sequencing a Megabase (less than one dollar) of DNA and that the time to read our message would be two hours if the laboratory have the required. One thing that support the use of our system in the near future is that the experts predict that in the near future the techniques used for the DNA sequencing will become better, cheaper and faster

In addition, we created a fictional scenario where we explore the potential application of our system for the long-term information storage, because researches have shown that Bacillus subtilis spores can last intactly for thousands or even million of years. This fact give the opportunity for our system to be used as a capsule time

Finally we also did an extensive research about the current type of information that has been stored in DNA, and we found out that a company has successfully stored this year images in DNA; besides that we have successfully stored a complete message in the DNDA of Bacillus subtilis; as a result of that we present fiction al scenarios where a movie is stored in Bacillus subtilis