In pre-work for the MicrobioCOSMOS meetup we made a video in which we briefly presented our project and talked about the microbiome. We dived into the world of filming for the first time and were able to prepare ourselves for the upcoming videos. The result can be seen in the instagram page from iGEM Thessaly.
MicrobioCOSMOS-Meetup
We, the iGEM Team Heidelberg, took part at the MicrobioCOSMOS meetup on 20th of August. The workshop was hosted by iGEM Thessaly and iGEM Aalto-Helsinki and apart from us iGEM Ilser Tirupati and iGEM MIT did join the online meeting. All iGEM teams have one thing in common, as we all have a project that is connected to the microbiome. We wanted to share our thoughts and ideas during this workshop.
The workshop began with each team delivering a presentation about their iGEM project. The audience had the opportunity to ask questions and give feedback afterwards.
One member of the iGEM Aalto-Helsinki team asked whether our idea of a treatment with a capsule against one-gene diseases is a one-time treatment or whether a patient has to take up our capsula regularly. We explained that we aimed for a one-time treatment with additional dietary supplements, because as discussed in the expert interview with Prof. Dr. med Kölker. More questions and feedback from the other iGEM teams followed which was helpful to further develop our project. The next part of the agenda was a presentation about the concept and the main idea of the iGEM competition by an official iGEM Judge from Italy. We learned that the iGEM competition has the power to create beautiful products as well as ideas which can change the world in the future but also about the responsibility of a scientist in this modern world. After the great presentation we had a short break for lunch. Hence, all participants were split into small groups in several breakout rooms. The task of each breakout room was to discuss one project that wasn’t their own in regards to ethics.
New about our project was the discussion about the cold shock kill switch system in which the bacteria die when they leave the body at 37°C and reach a temperature below 30°C. In our in our latitudes this system works successfully, but there are regions in the world that have longer periods where the average temperature is above 30°C. Second, we discussed intensively about the red flag of treating children, which we also discussed with Dr. Kölker. Therefore we planned to include children’s treatment as a major task in our project (Excellence in another area).
Additionally, we talked about the possible risks for the iGEMers, for society and whether the gain of the project is high enough to outweigh them. In these sessions, there was extensive discussion and we were obliged to look at the iGEM projects from all possible angles, which gave us new perspectives on our task. Then a member of every breakout room gave a short presentation about the risks of every project so every team had the possibility to note down the aspects and new insights. These notes could be used to improve their own projects. As this was the last former agenda item, followed by a kahoot in which all could compete against one another.
We were asked questions about the wetlab, drylab, funding and human resources and had to choose the most difficult aspect. All iGEM Teams got the opportunity to share more ideas and talk freely about iGEM and the current stage of their project. Moreover, we talked about how the other iGEM teams dealt with problems and if they have any suggestions for our project which could be interesting to further explore and do more research in this field.
Overall, we really enjoyed the MicrobioCOSMOS and we were happy to get the opportunity to receive new input about our project.
Picture 1: MicroBioCosmos-Meetup
BaWü-Meetup
Another collaboration in which we participated during this year's iGEM competition was hosted by the iGEM-Stuttgart. Apart from us the iGEM teams of Patras and Tübingen were invited on the 16th of October for the BaWü-Meetup. Sadly the iGEM team of Tübingen was not able to participate as they still needed the time for writing their texts for the wiki-page. The iGEM team Stuttgart started the BaWü-Meetup by introducing their team and continued with a presentation of their project “TardiSUN”. Secondly team Patras presented their project named “PGasus” , which is about comprehensive workflow for the identification and functional characterization of PGx variants. After every presentation we had the opportunity to ask questions about the projects itself, their methods and their workflow in order to give the other team constructive feedback and to learn more about the other projects. We were the last that presented their project. During our 20 minute presentation we talked about prior therapies for the gut microbiome, how to personalize a treatment of one's gut microbiome, a selective advantage without antibiotics and our work in the wetlab. Team Stuttgart asked about the legal situation of our project as we try to actively modulate the microbiome of a patient. We told them that our project does not fall under the GMO laws as we try to change the microbiome via natural transformation and therefore the bacterias do not necessarily take up the plasmids. The bacterias simply choose whether they want to take up the plasmids but in e.g. the CRISPR/Cas-method the DNA of bacterias could be changed and therefore the change would be forced.
We enjoyed listening to all iGEM teams that participated at the BaWü-Meetup and are happy for the useful feedback we got.
SCU-China Collaboration
As it is already proposed on the official iGEM page, filling out a survey is not counting collaboration. But still we would like to mention the survey from the iGEM Team SCU-China because it gave us a new perspective on our bacterial organism Acinetobacter baylyi ADP1. SCU-China is trying to introduce a new cloning model chassis with Vibrio natriegens. This was a great opportunity to compare their points for final implementation with our bacterium as a new model chassis. They took the following short form: “Vibrio natriegens is a kind of non-pathogenic marine microorganism that can complete replication in 7-10min. It also has the characteristics of diversified carbon source utilization and easy transformation. Based on these properties, Vibrio natrius shows great potential for efficient biosynthesis and directed evolution” iGEM 2021 SCU-China, as their starting point to discover Vibrio natriegens as a new biotechnological chassis. In our point of view we are exploring an easy transformation and comparable handling to E. coli which is our starting point. They are taking into account convenient transformation, perfect component characterization data, stable gene expression, efficient gene regulation, that it can be effectively separated from miscellaneous bacteria as well as stable conditions for expression and purification of protein. We would like to follow their example and pre-work and discuss on our cloning with natural transformation page as well the possibilities of A. baylyi as a new chassis model organism.
Risk Assessment Webinar
Throughout our project, we noticed how important safety was for science, and how necessary it is for a project to consider all possible risks and issues, in order to ensure the protection of its users. In our case, it would be the patients that take up our therapeutic pill. Because of this, we became growingly interested in the process of risk assessment, and wanted to learn more about it, if possible directly from experts. Consequently, we wrote to the German National Risk Assessment Institute, and asked them if they were willing to do a presentation about their tasks and how danger evaluation works. They were very open to our proposal, and kind enough to offer us doing a Webinar.
However, we didn’t want to be the only ones profiting from this great opportunity, as collaboration is at the heart of science, and a very important value of the iGEM competition. Because of this, we invited other iGEM Teams to our Webinar, and organized a collaboration.
On Friday, the 15th of October, we held the Risk Assessment Webinar. The other teams that participated in our collaboration were iGEM Aachen, iGEM MTU and iGEM Saint Joseph.
The Webinar started with the presentation of Mr. Frederic Müller, the invited speaker from the BfR. He explained the functions of his institute, and how they were an independent organization, which conducts studies to evaluate health issues no matter the parties involved. And although they are a public organization, they do not depend on the government.
Still, for their assessment tasks they cannot only use their own research, as their capacities to conduct studies are reduced, so they also take other studies into account. Besides, they might get help from experts in the field, however, the assessment task is done solely by the BfR.
Mr. Müller explained that the BfR does not check medicines, which in Germany is done by other institutes (like the BfArM, the Federal Institute for Drugs and Medical Devices). Instead, they focus on the risks in food, chemicals and everyday products. The focus of the BfR lies in the process of risk analysis, which consists of hazard identification, risk assessment and risk management.
During these steps, the experts must first identify a hazard, a possible danger, and characterize it. It is important to consider how high the exposure to this danger is, how probable it is to affect the general public, and the different sources of it. Only then can an effective exposure assessment take place. When this is all taken into account, the risk is characterized and managed. Here comes the legal team to action, and regulates the permitted concentrations of a certain chemical, or publishes a general recommendation.
After this general introduction to the process of risk assessment, Mr. Müller focused on the topic of the Webinar, which were genetically modified organisms (GMOs). We asked the BfR about their work in this area because we saw it as the most closely related to the iGEM competition, where teams use synthetic biology to modify organisms and must consider all possible resulting safety issues.
As already mentioned, the BfR focuses on the non-medicinal applications of GMOs, so mostly food and feed. We learned the requirements for these GMOs to be accepted and be considered safe. They must not have any adverse effects on the consumer, and they should not be misleading, for example through correct labelling. Some examples are products with a positively altered nutrient content, an herbicide tolerance (like glyphosate) or protection against insect pests. These are the phenotypic changes, but the genomic alterations have to be investigated into the detail as well. The genetic modifications need to be characterised on a molecular level. This means that the new proteins are investigated to understand their changed function and interactions.
Additionally, as GM food and feed are consumed by humans and animals, their health risks need to be evaluated, e.g. their toxicity, allergenicity, and overall effects on nutrition.
Finally, the environmental hazards are considered. Because GMOs are in contact with the ecosystem they are in, it is key to evaluate their effects on non-target organisms, if they are more persistent or invasive than the conventional form of that organism, and their general impact on the biodiversity.
After the very interesting presentation of Mr. Müller, the teams got the opportunity to ask questions. It was inquired how the impact of GMOs on their ecosystem is controlled, and if the BfR expects a certain safety method, like a killswitch, which is a solution typically implemented in the iGEM competition. For the GMOs to be approved, their effects need to be studied beforehand, so that by the time they are allowed, the impact they could have on other organisms is very reduced and not negative.
Another question was how long the process of risk assessment might take in these cases, compared to the arduous procedure of passing clinical trials and getting a medicine approved. Mr. Müller described how different cases vary in their duration, and although they do not need to do as exhaustive health checks as the ones needed for medicaments, they still might take a long time, because there are many aspects that have to be considered and long-term effects which extend the evaluation process.
This Webinar provided us with an interesting insight to the risk assessment process, as it allowed us to speak to an expert on this topic.
Picture 2: A picture of the webinar.
MTU Collaboration
We also took part in a collaboration organized by iGEM MTU, which consisted of a very fun challenge in which our team had to colour a character, “Martina”, they had created and write a slogan or phrase that defined our project.
It was a fun task with which we could present our project in an impactful and easy way to other iGEM teams, and we thank MTU for the invitation and the opportunity!
Here is the final image with our version of "Martina":
