Partnership Wageningen

Overview

As both our team and the iGEM team from Wageningen projects are based on creating a bacterial biosensor to detect colorectal cancer, we decided to form a partnership. We held several online meetings where each of our teams explained their projects to the other team. It was very interesting seeing how each of our teams took relatively different approaches to the same topic. After some discussion, we decided that the most beneficial way for us to form a partnership would be to collaborate on human practices and on dry lab/wet lab.

Dry Lab Collab

After much discussion with the iGEM team from Wageningen about the details of each of our projects, we realized that their wet lab team had generated data that could potentially be beneficial for our dry lab team’s model. In return, we would be able to help iGEM Wageningen with the leakiness of their data. We had a few online meetings regarding this collaboration in which iGEM Wageningen explained their detailed 2 component system to our team and we exchanged ideas on different solutions to their problem. For example, we suggested implementing a riboswitch in their design to limit the amount of transcription happening at low concentrations. This exchange of ideas didn't only helped iGEM Wageningen solidify a plan of action to improve this part of the project in the future, but it also helped us understand 2 component systems in much greater detail, giving us more clarity about the different parameters in our project and model.

We also tested out the data given by iGEM Wageningen on our model for the Shoot part of our project, to see if it would help us train our model. Since the beginning we had already expected that the data obtained would not fit our model well. Nevertheless, we still wanted to investigate the flexibility of our model and make improvements in areas that would benefit both us and team Wageningen. Leakiness was one of these latent variables which occurred in both our models and we could attenuate using the same techniques. We therefore applied several types of filters: autoagressive model, a moving averages model, and an ARMA model. We used these filters to try to limit the noise present in these signals. This technique provided great results as it seemed that the response Wageningen had obtained was not as noisy as expected. For example, the photo below is a demonstration of the time series data provided by iGEM Wageningen with the ARMA filter, which is a combination of both an autoagressive filter and moving averages filter.

It can be observed that the dataset was most likely not being substantially affected by the leakiness. Although more insight on the effect of the leakiness is required since the polynomials of the ARMA can be tailored based on the suspected noise function. So TLDR; the data didn’t show signs of noise but this was only an estimation.

Overall, despite the fact that the data provided by iGEM Wageningen didn’t directly help us with our model, we benefitted greatly from our idea exchanges and learning about 2 component systems, which helped both our teams adjust our teams’ project details and make improvements for the future.

Human Practices

Once we heard from the iGEM team from Wageningen that they had conducted surveys in the Netherlands regarding colorectal cancer and GMOs, we thought it would be interesting for our teams to observe the difference in the results between our countries. In our surveys, in addition to asking questions about colorectal cancer and how people felt about genetically modified bacteria to detect colorectal cancer, we wanted to place certain emphasis on patients of colorectal cancer and if they felt that their concerns were being heard regarding their treatment. On the other hand, iGEM Wageningen focused their questions more on GMOs, to truly understand how both patients of colorectal cancer and the general public think about intaking a genetically modified bacterial biosensor in order to detect colorectal cancer. We aimed our survey towards three different target groups: the general public, healthcare workers, and patients of colorectal cancer. We conducted our surveys in 3 different languages: English, Spanish and Dutch. The summary of our surveys is as follows:

“In order to get a thorough notion on the perspective of different groups of people in colorectal cancer (CRC) and their opinion on ingesting a bacterial biosensor for CRC, we conducted a survey divided into 3 sections aiming: healthcare workers, patients of CRC and general public.

In the section aimed at healthcare workers, we focused on their opinion on current detection methods and the possibility of a genetically engineered bacteria as a detection method. Around 60% of them considered today’s methods not sufficient because of invasiveness, non-specificity and cost. 72% of them would recommend a pill containing the biosensor to their patients. However, they would first like to get more details such as: cost, side effects, efficiency and biosafety.

We only managed to get one patient with CRC (Spanish survey), who considered their concerns were not heard during treatment/diagnosis and was willing to take our biosensor, believing it would be efficient and present less side effects than conventional methods. They would like to know when should they take it and if its dependent on the symptoms.

Regarding the general public, the vast majority was familiar with CRC (from friends, family who had it), even though their knowledge about it wasn’t quite accurate (location, symptoms, prevention). A great number of them (56%) consider they would need more information beforehand in order to take our biosensor, the rest (44%) would take it nevertheless. That is interesting, considering only 23% of them knew what a biosensor is. Big majority believes it would be efficient and present less side effects than conventional methods.

Things we didn’t mention and people considered relevant: study CRC trigger, asked if it was genetic, contraindications of taking our biosensor while having other pathologies, long-term side effects, different effect in gender/family history/habits.”

After comparing the results that we obtained from the surveys to the results from iGEM Wageningen’s surveys, we realized that most people would be willing to take in a genetically modified bacteria to diagnose themselves with colorectal cancer. From our surveys we saw that more people would be willing to take in a genetically modified bacteria to detect colorectal cancer if they had more information available regarding the risks and side effects associated with this GMO. It was very interesting to see the different types of questions that each of our teams asked, and by exchanging our results we got to obtain even more knowledge about how people feel about GMOS. For example, the Wageningen team asked more questions about extra precautions taken regarding GMOs, while we placed more emphasis on the current detection methods of colorectal cancer and trying to find out how much the general public knew about colorectal cancer.

Partnership Vienna

Overview

Despite having completely different projects, we had a fruitful and mutually beneficial partnership with the iGEM team from Vienna. Our partnership started off after meeting in real life with a member from iGEM Vienna in real life. In this meeting, we first explained our teams’ projects to each other to see if we could find common ground to partner up on. After some discussion, we realized that both of our teams were having some troubles with starting up dry lab. That is why we decided to assist each other with dry lab concerns. In addition, since we were very interested in each other’s project ideas, we also decided to collaborate on the bioethical approach.

Dry Lab Collab

We had several meetings afterwards in which each of our teams updated the other on the progress of our model, especially after receiving advice from more experts in the field of modelling. It was quite comforting collaborating on dry lab with a team that also had a slow start on the model, showing us that we were not alone in this iGEM journey.

Ethics Collab

In order to ensure that each of our teams were taking into account all the ethical considerations associated with their projects, we decided to do a bioethics collab. To begin with, each team had to send the other team a summary of their project to the other team. Afterwards, each of our teams came up with a list of ethical considerations for the other team’s project. iGEM Vienna’s project was about creating bricks that contained bacteria that performed carbon fixation, so we encouraged them to think about the bacteria contained within the brick and its effects on human health. We also said they should make sure that the bacteria in the bricks doesn’t create a foul smell to harm human health. On the other hand, since our project involves creating a bacterial biosensor to detect colorectal cancer, iGEM Vienna also pointed out important things for us to keep in mind. For example, they asked us questions such as how will we ensure that the bacteria will kill itself once it leaves the body. They also emphasized the importance of making sure the genetically modified bacteria didn’t cause any harm or side effects on the human body. Overall, it was very interesting hearing about ethical considerations regarding our project that we hadn’t thought of ourselves.