Team:Groningen/Human Practices

1. Human Practices.

1.1 Introduction.

Our team has tried to attain two main goals with our project. Goal number one was making the process of sharing information safer. We tried to do this by translating sensitive information into a physical status: a QR code of bacteria that only grows when using the right conditions. Our second goal was familiarizing the public with a genetic engineering. We tried to do this by visiting several institutions, elementary and high schools. More on this can be read in education and engagement .

After embarking on our mission, we dare to say our project represents an accessible and fun way of genetic engineering. We wanted to work on something that would be easily understandable for the layman audience. The concept of using bacteria to make a QR code is an out of the box idea that could familiarize people with the principles of genetic engineering without being initially scary. Improving safety with the help of bacteria could be perceived as less ‘against nature’ in many people’s eyes, because people are not directly involved. We do not change nature, we merely use her in an applicable and fun way. Using our project, we aim to show the world that genetic engineering is not frightening. We present genetically engineering in a lightweight and acceptable matter, thereby pursuing our goal to educate people about the advantages of synthetic biology. When engaging in human practices, we have emphasized that genetic engineering offers many benefits and can and will be of great influence in the future.

To improve and optimize the technical part of our project we received input from a wide spectrum of experts in the fields of microbiology, molecular genetics, biotechnology and molecular systems biology.

In order to functionally and successfully transferring our message to the public, we talked to many people with different backgrounds. The more people take a look at our project, the more accurate our project becomes. We have assembled this feedback and used it to spread the word about synthetic biology. Taking this into account, we think our project is saving two birds with one stone.

1.2. RIVM Safety-by-design assignment.

We were invited by the Dutch Governmental Institute for Public Health and Environment (RIVM) to participate in their safety-by-design assignment. Every year the RIVM gives this assignment to the Dutch IGEM teams to stimulate the teams to carefully consider different safety measures while designing their projects. We found the RIVM assignment to be very helpful and it gave insight into safety issues that we otherwise probably would have overlooked.

At the beginning of our project, the main safety consideration was given to the bacterial strain that we use. We identified that, in the real-world scenario, the most critical part of our protocol was the delivery of the QR code to the recipient. During delivery, there is a risk of accident and possible spill of the bacteria to the environment. Therefore, we propose to engineer bacteria with auxotrophy for a certain amino acid. These bacteria will need the supplementation of a specific amino acid to grow and will not be able to grow in the environment without it. Secondly, the auxotrophy can be used as a marker, replacing the need for antibiotic use and thus, minimizing the risk of spreading antibiotic resistance among bacteria through horizontal gene transfer.

During our first Skype meeting with the RIVM, we spoke with Korienke Smit, a policy advisor for Safety and Innovation. Korienke pointed out a very important point: we need to consider not only the biological safety but also the safety of the data. As our QR code system is intended to exchange sensitive data, we need to also consider how these data can be protected. Therefore, we now have two important safety aspects: 1. Biological safety; 2. Data safety.

In between the first and the second RIVM meeting, we spoke to different stakeholders to gain more insight on how to better implement safety to our project. For biological safety, we spoke to the safety officer from our department, dr. Marleen Otzen, from whom we learned that it is important to consider how long the cells will keep being viable during delivery. She also provided the VMT course our dry lab took for the safety of our project and a manual on how the RUG sends biological packages. She also emphasized the importance of a solid packaging to minimize the risk of a spill during an accident. This remark was also supported by UPS, a courier company that we had the opportunity to talk to. They provided us with information on how they handle packages with GMO’s in them. In addition, we also learned that the courier companies, in general, are prepared to handle the delivery of biological material. However, it is important to note that trained officers are only located in some critical points while the delivery is done by regular drivers.

For the data safety, we spoke to the Dutch Cyber Security and a professor with expertise in encryption. From this encounter, we decided to implement the AES system and a special algorithm for the QR code. Details on the conversations with these experts can be found in the cybersecurity part.

During the second skype meeting, with RIVM, we spoke again with Korienke and Cecile. Mainly, we reported our efforts to speak with the stakeholders and how these encounters have shaped our project. By the end of the meeting, we concluded that we have thoroughly considered different safety aspects and have implemented them into the design of our project. The safety designs of our project are summarized in the infographic in the Safety tab.

1.3. Education and engagement.

We have been extensively involved in education and engagement of the public in order to change the outlook of genetic engineering, as it is commonly regarded as ‘scary’ or ‘against nature’. In order to introduce it as a technology that we can use to our advantage, we developed an educational curriculum, for both primary and secondary schools. We aim to make the ground principles understandable and seizable for these children so they can grab the relevance of genetic engineering for the future. Besides explaining genetic engineering, we focused on the importance of the healthy balance between malignant and benignant bacteria on both your body as in the environment.

We have partnered with three different Dutch foundations for science and education, namely: Science linX, Scholieren Academie and the Jonge Onderzoekers, in order to reach kids and young adults. We helped Science linX to organize the "Night of Arts and Science" as well as "Zpannend Zernike", two science festivals aimed to raise the interest of young adults in science. With Scholieren Academie we visited primary schools to familiarize kids and young adults with the basics of genetic engineering, and in return they visited our lab to observe genetic engineering work in real life. We also gave a workshop on genetic engineering as part of the Jonge Onderzoekers for kids. The following sections of this page will outline in more detail the work done with the previously mentioned organizations and how we used the opportunity of IGEM to educate future potential scientists.

1.4. IGEM Project Search Engine

As part of human practices we have developed a tool to easily look through past IGEM Projects. We hopw this tool will help future iGEM teams find inspiration quickly for their projects. Learn more about "IGEMdb" in it's respective page

2. Integrated Human Practices

The human practices integrated in our project can be divided into 4 categories:

1. Safety
2. Wet lab
3. Dry lab
4. Outreach

Because we are not experts in most topics, information and advice from several experts from different institutions was needed. Here we describe how their information and advice shaped our project at different stages.

2.1. Wet Lab Experts.

The Wet lab has overcome many challenges. In order to optimize our project we got in contact with a lot of experts. Due to the advice, suggestions and feedback of many experts, we were able to design, develop and improve our QR code project.

2.1.1. The New organism. Vibrio Natriegens

There is no experts at our university working with our go to organism: V. natriegens. Still, we were optimistic to implement and learn new techniques. Also, many methods and seemed to be similar to the familiar E. coli procedures. To ensure success, it was very important for us to reach out to experienced people that could help us form our project. We have talked to Tanya Tschirhart, a postdoctoral research fellow at the Naval Research Laboratory in Washington DC. She discussed with us the different aspects of our V. natriegens related work and provided us with important insights to help form our project. We experienced a few issues trying to work with a new organism and her advice and personal protocols supported us a lot. She discussed with us using the mannose inducible promoter in our CRISPR design pointing out that mannose cannot be utilized in this organism. In her own work she had characterized the use of arabinose and tetracycline inducible promoters, both seemed to be less sensitive than in E. coli. As a consequence, we designed the synthetic promoter library for BBa_R0040 and BBa_K808000 with the aim to optimize their function in V. natriegens. Moreover, Tanya advised us to use mCherry as a reporter gene instead of RFP, because of the intense fluorescence evene in the high salt concentrations used for V. natriegens.
(“You are doing worthwhile research in natriegens” - about our experimental designs)
Additionally, we got a lot of helpful suggestions from Matthew Weinstock, group leader at AbSci in Vancouver and Enoch Yeung, assistant professor at the University of California Santa Barbara, concerning especially the transformation of V. natriegens. Thanks to all the experts for sharing their protocols and insights on our procedures and troubleshooting.

Tanya Tschirhart Matthew Weinstock Enoch Yeung

2.1.2. The backbone of synthetic biology: molecular cloning

Many experts that work with cloning strategies every single day have helped us design our experiments and enable us to overcome struggles. Harma Karsens from the Molecular Genetics group supported us with many suggestions during troubleshooting our procedures. Sonja Billerbeck is an assistant professor at the University of Groningen and an expert in the field of synthetic biology. She reviewed many of our experimental designs and constructs. For the synthetic promoter library she suggested the design of a PCR that would amplify the whole plasmid and would not need additional assembly steps.

Sonja Billerbeck Harma Karsens

2.2. Dry Lab Experts.

Over the course of our project it became increasingly clear that combining different fields requires an immense amount of knowledge and expertise. The work of one researcher in particular caught our eye. Anne Meyer and colleagues have published several papers in recent years on bioprinting and on how to make your own do-it-yourself bioprinter. To realize our end-goal, we reached out for a fruitful discussion on the progress and struggles we faced during our project. Anne was really helpful and interested in our project and we would like to thank her for her collaboration. She said that our project was really fun interesting. Particularly interesting was the use of high precision bio-printing with different strains. The take-home messages we got from our talk are shown below: a dot is what we concluded from the talk and after a dash is shown how the former point affected our project.

Anne S. Meyer

1. The bacteria are not completely fixed in the sodium alginate hydrogel and they can move around
2. Indeed, when we added inducers on the hydrogel, bacteria moved outside of the edges of the printed alginate gel. This can potentially decrease the consistency in readability of our printed QR code.
3. It would be interesting to see if the bacteria would move in between different lines that are printed in close proximity of each other.
4. if this is the case, and it interferes with the readability of the QR code, it might be interesting to induce biofilm forming agents inside the bacteria to further fixate them.
5. “These findings suggest that a considerable amount of nutrients is needed for formation of such a biofilm. More importantly, these findings show that substances inside the alginate gel can diffuse from the printing substrate into the alginate gel and exert an effect on the resident bacteria”. For the experiment see the results page.

Furthermore, Anne referred us to Srikkanth Balasubramanian who worked on the bioprinter with her Srikkanth showed great interest in our work and was willing to provide us with the plasmids for biofilm formation.
Gert Jan advises companies on the implementation of their technical ideas. He provided us with insights on Stamping and Replica plating, for transferring bacteria from one plate to another. Also, he provided us with a Laser CNC and a 3D printer and was so kind to allow us to convert them into bio printers. Gert Jan has been a part of iGEM Groningen for years. He was one of the supervisors for Groningen’s winning team in 2012!
Simon has his expertise in the field of Computer Science (Hardware & Architecture) and Engineering (Electrical & Electronic). He was very helpful in providing a workspace in his Electronics and Robotics lab and also helping our dry team in cross checking and refining their ideas.

Prof. Dr. Gert Jan Euverink Simon Busman

2.3. Outreach Experts.

In order to increase the accuracy of our second goal, we have contacted several institutes which are involved in promoting science to the audience. The experts in this specific field have given us feedback and advice in promoting our project. Additionally, these well-trained outreach experts have given us comments and suggestions on how we should spread the word about an in general less understandable and acceptable subject, as genetic engineering is. We have attained teaching workshops and improved our skills in educating the public. The experts have triggered us to think and brainstorm about our project and to look to our project from different perspectives. Based on these insights, we have learned how to improve the underlying message we want to communicate to the public and subsequently, in what way we should do it.
Scholierenacademy pursues the goal to get kids acquainted with the Rijksuniversiteit Groningen and as an extension, the scientific world. Scholierenacademie, as part of the RUG, facilitates scientific activities for schools including varied excursions, lessons, and workshops.
After we prepared and developed a curriculum for synthetic biology for both primary and secondary school students, we presented it to the educational department of Scholieren Academie. They criticized our curriculum and we received a lot of feedback. Because the curriculum is made for children, the information has to be limited. However, the information we want to communicate, has to be loud and clear. We have learned a lot about teaching kids and especially, making an effective and interesting curriculum. As part of our human practices, we taught at five different primary schools in the province of Groningen and arranged a lab excursion for those classes. We learned them about bacteria and the manipulation of them. The scholierenacademy helped us with perfecting our lectures by providing the opportunity to give them a practice lecture on which they would provide feedback. They made it clear to us that we need to focus on the fact that bacteria are mostly good, we do not want the children to be afraid of them.

Douwe van der Tuin

2.3.1. Science linx & Discovery Truck.

Theo Jurriens is a communications advisor at the faculty of Science and Engineering and part of the RUG Discovery. He provided us with the opportunities to have a stand at Zpannend Zernike and to teach high school kids about genetic engineering. We talked with him a lot about everything we could do at Zpannend Zernike and the high schools. He gave us a lot of ideas on fun things to do where students could also learn something. With his help, we created a game for Zpannend Zernike (and the Jonge Onderzoekers) and a discussion session at the high schools.

Theo Jurriens

2.3.2. The Ubbo Emmius fund: Derk Bosker.

The Ubbo Emmius fund is the crowdfunding website of the RUG. We contacted Derk Bosker to help us create our crowdfunding page. We have been informed by this foundation how to pronounce our project in an attractive way. He helped us come up with the idea to present our subject as a way to safely distribute delicate information. By having it physically as well as digitally encrypted, it will be double encrypted and therefore much safer. The process of getting the information is slower because you have to grow the bacteria, this may also be an advantage for safety. Derk Bosker gave us a lot of information on how to effectively gather crowdfunding and in what way to promote our project.

Derk Bosker

2.3.3. Communications Officer Faculty of Science and Engineering bij Rijksuniversiteit Groningen.

Daniek helped us to spread the word about iGEM. As part of the communication department of the faculty of Science and Engineering (FSE), Daniek is responsible for promoting and supporting faculty involved programs and projects. During our project, she closely accompanied and helped us with the aspects involved in communicating iGEM to students, professors and companies connected to our faculty. She helped us by improving our promoting strategy, for instance by making a planning of all the promoting events we have to take in account. Additionally, she gave us tips and tricks about sharing information on social media. By arranging an official video for us, we were able to promote our iGEM project in a more professional matter on social media. Due to Daniek, the TV screens, spread around all faculty buildings, daily show an update of our project. Summarized, she has given us the opportunity to explain the iGEM competition and our project itself to facultairy people via both social media as via different network channels.

Daniek Gortmaker

2.4. Cybersecurity.

In terms of encryption and how to make our QR code more secure, we came up with several ideas: changing the function that generates the masking, symmetric encryption, asymmetric encryption using a digital signature. In order to establish the best approach, we reached out to specialists from the cybersecurity.

We made contact with Mr. Tjarko, an expert from NSCS (Nationaal Cyber Security Centrum). We learned from him the optimal value of the encryption as in the following:

“Breaking the encryption yourself is fairly impossible. There is also a principle. You can break a key code if you have enough time and computer power. But when you break a code, you hung your time on a supercomputer. The idea is, when you encrypt information, it should be a vector of 10 less valuable that would cost the supercomputer to break the code... If I tell you a secret and it is worth a $1000, I will encrypt it with a technique that costs $10000 to decrypt."

Regarding the encryption methods, we learned from the same expert that by using the standard computers, they are relatively safe, but a major question will be put forward in the case of quantum computers. As he mentioned “That [quantum computer] could be a be a real threat for the modern encryption that we use today. We don`t really understand, we don`t really know if a quantum computer can exist, because there is also discussion about that, but for now, our encryption methods are quite safe”.

Thus, our approach and the use of the QR code encryption can be considered at a reasonable degree of safety. We tried to find out the optimal algorithm that can be used in our project and apparently we learned that: “Development of encryption mostly happens in university. The theoretical part and development part of the encryption is for the mathematicians. The more practical make of use is done by the bigger security corporations”.

Therefore, there is a theoretical part, done by members of the academia and the practical one, of implementing it, done by cybersecurity companies. Having this found out, we decided to contact a member of academia. While browsing through articles that could help us shape our process of encryption in the most suitable way, we came across a paper written by professor Tilman Wolf from the University of Massachussetts. There he explored the idea of encrypting sensitive information from medical patients using QR code on a paper, but the similarity to our approach determined us to contact him. Via a Zoom call, he provided us with the process that we have implemented namely:

So instead of changing the masking function, thus making it more complicated to break, he advised us on using the encryption method before creating the QR code. This translated into the fact that our message was first converted into a string of fixed characters and then this string was used to generate the QR code. Hence, if a person would manage to scan and retrieve the info, it would be only comprised of the random characters that would not make sense for that person.

Another useful aspect that we put into practice from this conversation was the encryption method, AES. After presenting him with the options we had at that point (symmetric and asymmetric encryption), he recommended the AES due to its relative easiness to implement, but also due to the safety it provides for our purpose. In the end, both experts, when presented with our iGEM project concept, found it complex and fascinating:

“Your project I think it is very interesting.” (Tjarko)

“This physical support to encode information is quite interesting. I am curious to see how this will develop further…”(Prof. Tilman Wolf)