Partnership

“Teamwork makes the dreamwork” - John Maxwell

Next to all collaborations, we also participated in a partnership with iGEM team BOKU Vienna through the whole project. As iGEM team BOKU Vienna's project also revolves around intestinal disorders, we quickly got in touch to discuss the possibilities of a collaboration. BOKU Vienna is working on the production of a pill containing enzymes that can digest fructan in the intestines, thereby reducing the triggers for irritable bowel syndrome. For more information about the project of Vienna, please check their wiki.

iGEM BOKU Vienna -

iGEM TU-Eindhoven

After our first online meeting, we decided together to go for a partnership as we had many opportunities to collaborate. Therefore, we planned general and separate meetings with subgroups to determine exactly where we could collaborate on and both profit on. In these meetings, we discovered that we could collaborate together on human practices, lab, modeling, and wiki. We met every two weeks with iGEM team BOKU Vienna to review each other's projects progress and see where we could help each other. For easy communication outside those meetings and for sharing documents, we made a shared Google Drive and Slack together with a Whatsapp group. During the general meetings, we gave tips on how to keep track of the documentation of our wiki. Moreover, we aimed to make our wiki’s easier to follow and ensure a logical structure in our documentation by providing each other with feedback on multiple wiki texts. Additionally, we participated in Vienna's low FODMAP Cookbook collaboration whereas they participated in our lesson plan collaboration. Both can be found on our Collaboration page. Finally, we promoted each other's work on social media and mentioned each other in our end presentation video.

Figure 1: Fun activity during the meeting.

Human Practices

For Human Practices, we worked together on multiple topics throughout the project. These topics include the general survey, the patient interviews, the informed consent, the ethics professor, and the design of the pill, which will be described in more detail below.

General survey

Both teams were interested in the opinion of the general public on the willingness to use our products. Therefore, we decided to make a survey for the general public in order to reach as many people as possible. This survey included questions based on general knowledge and opinions. Important questions we included in the survey were:

1. What is your feeling about getting an endoscopy?

2. What is your feeling about getting an ultrasound measurement?

By spreading the survey together, we reached a larger public resulting in 344 people of different nationalities who filled in the survey. The results of this survey can be found on our Human Practices page segment The Need.

Patient interviews

iGEM team BOKU Vienna and we both wanted to hear about patient’s experiences with intestinal disorders. We discussed the possibility of distributing a survey or interviewing patients directly. From this discussion, it became evident that interviews were the best option, as they allow for a better understanding of the patients’ experiences. Because of the close relationship between our two target groups, we decided to work together on the patient interviews. Both teams included two questions of the other team in their interviews. The project of the other team was introduced to the patients, whereafter the questions were asked. The first question we included in their interview was based on the willingness of the patient to take in GMOs for the given purpose. In the second question the patients were asked if they have additional suggestions for the project. We interviewed five patients with IBD, whereas BOKU Vienna interviewed six patients with IBS, especially for us they interviewed a extra patient with IBD. In this way, a larger patient group was reached for both teams making the definition of the need in the field more valuable. The experience of the patients can be found on our Human Practices page segment The Need and The Medical Field.

Informed consent

iGEM team BOKU Vienna notified us that informed consent is of huge importance. Because they mentioned it early in the project, we could adapt at it by making informed consent documents for all patient interviews and expert meetings. In this informed consent, we asked the experts to approve of putting their full name, picture, and input on our wiki. The patients were requested to approve of sharing their experience on our wiki. With BOKU Vienna's advice, we were able to perform interviews and handle information in a responsible manner.

Ethics professor

We shared with iGEM team BOKU Vienna that we had a lot of difficulties finding an expert in the field of ethics. In turn, they told us that they had not even thought about interviewing an ethical expert. We emphasized that it is important to clarify the ethical consideration as both our projects require GMOs to go inside the body. Thereupon, iGEM team BOKU Vienna suggested a potential ethical expert. This ethical expert was willing to meet with both teams, so we decided to have a meeting with that ethical expert together. We set up a shared document with ethical questions related to our projects and arranged to meet with the ethical expert. After the meeting, we were both able to describe the ethical considerations of our projects, which can be found on our Human Practices page segment The Ethics.

Design of the pill

The target of both iGEM team TU Eindhoven and iGEM team BOKU Vienna is to deliver a pill to the intestine. Therefore, the design of both pills can be practically made the same. Our current design is based on a pH-responsive and time-dependent coating that releases the GMOs inside the intestine. This, however, comes with some ethical concerns. Therefore, we wanted to have an alternative pill design that might be implemented in the future. For this reason, we had a meeting with BOKU Vienna about their pill design. The biocompatible pill that iGEM team BOKU Vienna created has pores that let the enzymes out but let the GMOs stay in. Furthermore, the coating of the pill is able to attach to the intestinal mucosa resulting in a longer residence time in the intestine. As they also work with lactic acid bacteria, their obtained results will most probably also apply to our system.

Laboratory

Physical partnerships in the lab are perhaps the most convenient, but the considerable distance between Vienna and Eindhoven made it difficult for us to achieve this. At the start of July we had a first meetup with the labteams, where we presented the biological design of both our projects and created a discussion about possibilities for the partnership. Fortunately, several online meetings were possible to profit from each other. These meetings were focused on troubleshooting, safety, and additionally we discussed the possibility of testing our GMO’s on Vienna’s gut-on-a-chip.

Troubleshooting

We had a troubleshooting meeting with the team's supervisors in which we discussed several problems that were encountered in the lab. For instance, the results of our experiments on Augustus 25th, which can be found on our Results and Engineering Success pages,. Furthermore, we talked about the problems with the golden gate assembly of their composite parts.

Safety

Next to our troubleshooting meeting, we had a meeting in which we discussed the safety measures designed and safety precautions that should be considered for safely introducing GMOs in healthcare. From this meeting it became clear that the incorporation of a proper kill switch is important for controlling the area where GMOs can survive. This control is in our opinion a term which has to be fulfilled before any experiments can be performed outside a safe and controlled environment such as a lab. Additionally, it is important to not only consider the safety after ingesting the pills. The safe production, transportation and storage of the pills (and thus the GMOs) are at least as important. You can read on this on our Implementation page.

Gut-on-a-chip

Lastly, iGEM team BOKU Vienna offered to test our GMOs on a synthetic gut-on-a-chip to simulate the effect of our cells to the gut. Due to the large distance between Eindhoven and Vienna the transport of our GMOs towards Vienna was not executed and our cells were not tested on the gut-on-a-chip.

Model

Even though the genetically engineered systems in our bacteria differ quite a bit, iGEM team BOKU Vienna and us were still able to support each other in modeling our systems. We did this through several troubleshooting meetings, and in addition collaborated on a SimBiology Guide to assist future iGEM teams who want to build a kinetic model.

Troubleshooting

For our modeling collaboration, we met regularly with the modeling subteam of iGEM team BOKU Vienna to discuss our progress. During these meetings we focused on troubleshooting, and helped each other on how our models might be improved. At the start of our partnership, iGEM team BOKU Vienna was still undecided on the program they were going to use to build and simulate their kinetic model. We shared with them the advice that we had gotten from our supervisor to use MATLAB in combination with the SimBiology toolbox, and they adopted this recommendation. By using the same program for our models, it was very easy to detect errors in each other's models and give suggestions for improvement. These regular meetings were very useful for us as they often resulted in new insights. For instance, iGEM team BOKU Vienna pointed us to the possibility of using an online tool to determine protein degradation rates.

SimBiology Guide

During our discussions on the models both teams agreed that the available documentation on SimBiology is quite limited, aside from the iGEM webinars and basic getting started guides. Because of the struggles we had during our work with SimBiology, we decided we wanted to make it easier for the future iGEM teams by sharing our experiences in a guide that is a supplementation on the available documentation. Together, we collected our best tips and tricks, and compiled these in a SimBiology Tips & Tricks guide, which can be found on our Contribution page.

Wiki

Although the partnership with the Wiki wasn’t as extensive as for example human practices or the lab, that doesn’t mean that we didn’t benefit from each other. During our meetings, we discussed what pages were to be filled, what roughly should be on each page and what link - provided by the competition - should be used. We discussed this mainly to find out if we both understood the information given by iGEM in the same way, as there is so much information on different sites provided to the teams.

Next, we discussed how you could easily transfer your page text to html, by means of a html converter website. Also, another website was shared on how to easily transfer tables to html for the wiki. Both sites made uploading content to our team's wiki pages much easier. Later on, iGEM team BOKU Vienna shared their inclusivity article on how they plan to make their wiki available for individuals with impaired vision. Sadly, this was too late for us to implement this on our wiki.

Team:TU-Eindhoven/Partnership

iGEM BOKU Vienna -

iGEM TU-Eindhoven

Human Practices

General survey

Patient interviews

Informed consent

Ethics professor

Design of the pill

Laboratory

Troubleshooting

Safety

Gut-on-a-chip

Model

Troubleshooting

SimBiology Guide

Wiki