Team:Thessaly/Partnership
Overview
We decided to cooperate with two iGEM teams as partners because we shared mutual objectives
to our respective projects, moved towards engaging our communities and co-evolved our teams
throughout this iGEM season, with multiple meetings and a constant open dialogue with both
teams.
The collaboration with Team McMaster Synbio was a valuable asset for our Wet Lab brainstorming, establishing our safety mechanisms as well as guiding them through some of their troubleshooting. As for the collaboration with team Aalto-Helsinki, it was central to our project to create new ways of bridging the gap between mental health and microbiome physiology, enlarging our projects in all possible directions.
The collaboration with Team McMaster Synbio was a valuable asset for our Wet Lab brainstorming, establishing our safety mechanisms as well as guiding them through some of their troubleshooting. As for the collaboration with team Aalto-Helsinki, it was central to our project to create new ways of bridging the gap between mental health and microbiome physiology, enlarging our projects in all possible directions.
Team Aalto-Helsinki
Figure 1: Aalto-Helsinki team logo
Humble Beginnings
After team Aalto-Helsinki reached out to us in mid April, we were excited to learn that a
fellow iGEM team was working on the gut microbiome. The biggest surprise was the effort of
the Aalto-Helsinki team to correlate gut health with mental health, something that we were
completely unaware of at that point of time. And that worked as a catalyst for the development
of our longterm friendship and cooperation.
Their project
GutLux is an ingestible biosensor providing an understanding of the connection between the gut microbiota and the brain, by measuring the concentration of the metabolites in vivo, inside the gut. GutLux consists of two parts. The biological component responds to the concentration of metabolite by producing a light signal that can be measured quantitatively. The electronic component measures this signal and converts it to readable, wirelessly transmittable data.
How did Amalthea shape GutLux?
Figure 2: Aalto-Helsinki project logo
The conclusion on the free DNA safety mechanisms was made upon the description of our systems. And so we brainstormed and worked on this subject to propose ideas for its solution. Something that we also took into consideration was the capsule storage capabilities, a task that was set to take on by our Dry Lab teams.
Finally, we gradually elaborated and exchanged some ideas about our biosafety plans and proposed kill-switch mechanisms and how to ensure host, microbiome and environmental protection.
How did GutLux shape Amalthea?
The Aalto-Helsinki team was very helpful in sharing their findings about the semipermeable membranes. We discussed further about the components each team is interested in passing through this membrane and which molecules’ access needs to be prohibited. After that, they also enlightened us about the capsule coating properties that we are interested in and helped each other on overcoming the problem of pH variation throughout the gastrointestinal tract. This issue concerned both teams, as we both need to initiate our measurements as close to the site of interest as possible, without starting too early or too late.
What was also important for our mutual development was our collaboration on data encryption and privacy. Consequently, we decided that a workshop concerning data encryption and safety would be organized later in an active format. That will include breakout room discussion on safety, legislation and thoughts on medical data, all the subjects that would be covered by our predefined questions.
Figure 3: Flinga board with the Dry lab ideas
The two pillars of this discussion were “Improving Safety” and “Risk Detection”. In this conversation we address the main issues and concerns of our society on the premise of capsule endoscopy, GMO’s, personal health data, the pros and cons of our two respective ways of data transfer, safe practices, safe storage of medical data, etc.
Figure 4: Improving Safety section of question and answers
Figure 5: Risk Detection section of question and answers
Wet Lab 04/06/21
Team Thessaly-Team Aalto-Helsinki Meetings
On our first meeting, before getting into the details of our work, we took time to discuss the restrictions that COVID inflicted on both teams and the ways in which we considered dealing with this problem. After that, we briefly described our projects and our wet lab design. Our partnership is mainly based on the capsule and its mechanisms, by which we translate the biological signal to something we can measure and quantify, so our conversation developed on two capsule-related topics: The safety mechanisms for the containment of free DNA as well as other degradation products, and the possible ways of storing the capsule, upon its massive production.
The conclusion on the free DNA safety mechanisms was made upon the description of our systems. Team Helsinki worked on a cell-free system with fragments of DNA that could be released in the gut if the capsule broke and our team worked on a cell-based system that could also lead to the release of DNA fragments if our cells escaped the capsule and got killed by our kill-switches. Thus, we shared a common problem, and placed the task of researching the topic until our next meeting. The issue of the capsule’s storage is also something that we needed to do some research upon, as the electronic parts that the capsule is composed of, can be sensitive to extreme temperatures in which our bacterial and nonbacterial systems need to be to be inactive.
At the end of the meeting, we discussed the possibility of of our team participating in Team Helsinki’s podcast.
Figure 6: First wet lab meeting
Wet Lab 2/07/21
Team Thessaly-Team Aalto-Helsinki Meetings
OAt our second meeting, we exchanged some ideas about our biosafety plans and proposed kill-switch mechanisms. Our team proposed an AND gate kill-switch, activated by O2 and double regulated by a repressor protein and a binding molecule that we add to the system when we want to induce cell death. The mechanism is site-specific for the hypoxic environment of the gut and tightly regulated by the consumer of the bacteria. The consumer is able to decide the exact time of their death by consuming the repressor-binding molecule. Team Aalto proposed a stop-codon (TGA) optimization of their bacterial genes, so that the gene sequence could be read only by the modified enzymes they would add to the system. This way, they could ensure that in case the modified DNA escapes the capsule and enters another cell, it’s RNA would not be able to get translated by the natural ribosomes and thus, the synthetic gene products would not spread.
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After our discussion on the kill-switch, we sat two tasks for our next meeting:
- Searching for natural capsule coatings that are compatible with the gut environment (e.g. not causing inflammation).
- Searching for semipermeable membrane types.
Figure 7: Second wet lab meeting about kill switches
Wet Lab 06/08/21
Team Thessaly-Team Aalto-Helsinki Meetings
We started our third meeting, by sharing our findings about the semipermeable membranes. We discussed further about the components each team is interested in passing through this membrane and which molecules’ access needs to be prohibited. After that, we talked about the capsule coating properties that we are interested in and helped each other on overcoming the problem of pH variation throughout the gastrointestinal tract. This issue concerned both teams, as we both need to initiate our measurements as close to the site of interest as possible, without starting too early or too late.
Figure 8: Third wet lab meeting about semipermeable membranes
Dry Lab files
Dry Lab 15/06/21
Team Thessaly-Team Aalto-Helsinki Meetings
After breaking the ice by introducing ourselves to one another, we started our main meeting by discussing the Dry Lab goals for both teams: the safety of our mechanisms, the capsule design and important issues to address within the capsule design. We touched nearly all the subjects that were common ground for us, but we were particularly interested in collaborating on data encryption/privacy, and there also were suggestions on something similar for modeling, considering that modeling teams proposed collaboration themes as well (equations, software, capsule route). Consequently, we decided that a workshop concerning data encryption and safety would be organized later in an active format, the details of which would be discussed later that same week. We also established that it would be more entertaining and educational if other members than the Dry Lab were welcomed to join. We were really happy to collaborate with each other and had a great time meeting the Dry Lab team of Aalto-Helsinki for the first time!
Figure 9: First dry lab meeting
Dry Lab 05/07/21
Team Thessaly-Team Aalto-Helsinki Meetings
In this meeting, after our established introductory relaxed chat between our teams, we brainstormed and summarized our plans regarding the data privacy and encryption workshop. We planned to begin with 1-1.5 hours reserved for technical, exclusive to Dry Lab members discussion to answer predefined questions. To define the questions we were to answer, we had to give each other some additional insights of our project, so, through sorting out these questions, both teams gained a better knowledge of the other team’s project and noticed some flaws of their own. After that, we agreed on the second part of the workshop being open for all the members of both teams. That part would last 1 hour and include breakout room discussion on safety, legislation and thoughts on medical data, all the subjects that would be covered by our predefined questions. To make it more fun, we thought it would be nice to include interactive tools in the second part of our workshop, and thankfully the Aalto-Helsinki Dry Lab team had some interesting suggestions (Kahoot quiz, online whiteboard). Finally, we scheduled the workshop, as well as the test calls before that and we surely achieved a phenomenal organization of our workshop. Once again, it was a pleasure to collaborate with the Aalto-Helsinki Dry Lab team!
Dry Lab 29/07/21
Team Thessaly-Team Aalto-Helsinki Meetings
This was our last meeting but also the workshop day. The last meeting was about a few last checks before the big meeting later. The nature of the workshop was from the beginning to give us the time to brainstorm together and progress together through questions, our respective projects. The dry lab part had a duration of 1.5 hours. In this time we discussed the following : “How to anonymise data”, “Power consumption and battery choices” and of course “What ways are there to encrypt the data we collect and transmit”. Some of the most valuable “answers” to these questions were, “Make use of the Amnesia tool”, “Delay times between data transmission” and “Use advanced encryption algorithms like AES/CCM that is used in bluetooth”, you can read all of our points in the image below. We moved on onto our next session where the rest of our team members would join to continue our discussion. The two pillars of this discussion were “Improving Safety” and “Risk Detection”. In this conversation we address the main issues and concerns of our society on the premise of capsule endoscopy, GMO’s, personal health data, the pros and cons of our two respective ways of data transfer, safe practices, safe storage of medical data, etc. At the end of this workshop we played a fun little game of questions and answers to test what we have learned from this experience.
Figure 10: Commemorate screenshot from the dry lab workshop
Working Together on Human Practices
After the first meeting we had as teams we started dividing our meetings, to the respective subteams.
So, we scheduled our first human practices between the heads of HP, Sofie and Kostas, where they decided
how the HP team would meet further down the road.We proposed to Aalto-Helsinki Team our idea of the Microbiome Day videos and the MicrobioCOSMOS event, on the basis that they would be interested to, firstly participate in the Microbiome Day event and secondly if they were interested to co-host the MicrobioCOSMOS event
MicrobioCOSMOS The first step we made to implement our idea of uniting all the teams that worked on the various microbiomes was a celebration about the World Microbiome Day. MicrobioCOSMOS was our most ambitious meetup this year as it had many moving parts and so many responsibilities from our part to deliver the best possible meetup about educating and bringing together the various microbiome teams.
After a brief lunch break we came back with the workshop of the day, named “Ethics and Values”. Based on questions on an interactive Flinga board, we then were split into different breakout rooms and talked about the ethics of our projects for about 25 minutes, which gave us the opportunity to discover each other's concerns, perspectives, etc. In the end it was a truly educational experience.
Lastly we had a super fun kahoot session. In the end we ended the day with smiles on our faces and filled with new knowledge and ideas!
Figure 11: Commemorate screenshot from the MicrobioCOSMOS event
Human Practices 16-06-2021
Team Thessaly-Team Aalto-Helsinki Meetings
Our first official joint Human Practices meeting was held on the 16th of June. After the ice was broken between us and we could talk more freely and openly, we proposed to Sofie our idea of the Microbiome Day videos and the MicrobioCosmos event, on the basis that they would be interested to, firstly participate in the Microbiome Day event and secondly if they were interested to co-host the MicrobioCOSMOS event. Moving on we discussed Sofie’s idea which had to do with mental health, an issue both of our projects are tackling. She proposed a webinar-like event about the correlation of the Gut-Brain axis between a gut microbiome expert and a mental health expert. Another big idea we had was to host a panel discussion for people with gastrointestinal disorders, this would entail that we would contact local authorities to try to find people and come in contact with them. Lastly, we uploaded to our common server our children's book so they can translate it to Finnish.
Figure 12: Sofie, Kostas, Anna and George the first Human Practices meeting
Human Practices 30-06-2021
Team Thessaly-Team Aalto-Helsinki Meetings
OWe met again on the 30th of June to discuss the upcoming Microbiome consortium (MicrobioCOSMOS) that took place on the 20th of August(you can read more about it ). At the beginning of the meeting, we set out to address some of our key concerns regarding the planning of the upcoming event. Who are the key speakers? What are the roles that each team would have and finally when can we finalize the date of the consortium. Moreover we took it upon ourselves to create a server on Discord for all the teams that would potentially participate in the upcoming Microbiome related events in the hopes that we would have more of a direct communication. Finally we scheduled the entirety of next for a potential meeting with all the teams that would participate. The meeting ended after we created a shared .docx file in order to start writing the draft of the schedule that would be finalized on the 5th of July when we would start contacting experts to talk to our consortium.
Figure 13: Sofie and Kostas in the second Human Practices meeting
Human Practices 07-07-2021
Team Thessaly-Team Aalto-Helsinki Meetings
Getting in the habit of our weekly meeting with the wonderful Aalto/Helsinki HP subteam, our main and only focus of this meeting was about the MicrobioCOSMOS event that we were planning. We started off things easy by introducing the girls to the server and by scheduling invites to the other teams to join the server. Next, we moved things right along to the draft of the schedule. It had been created and one of our jobs in this meeting was to comment on it and progress it to its final version. Finally we sent the HP team some resources that Leandros, one of iGEM’s Europe Ambassadors sent us regarding our search for a microbiome expert. Our last thing to do as Thessaly, was to create the presentation template that we would like the teams to use, when the time comes to present us their projects.
Figure 14: Sofie, Vilma, Kostas and George in the third Human Practices meeting
Human Practices 14-07-2021
Team Thessaly-Team Aalto-Helsinki Meetings
This meeting was mostly about our upcoming visit to the Aalto-Helsinki podcast. We were scheduled to attend on Wednesday the 21st of July at 1pm. We briefly discussed and covered the interview questions that the girls wrote for us and who’s final version would be sent by the end of the week. We then moved on to MicrobioCOSMOS updates. Where we had created the presentation template and had sent the invitations to the other teams. Now that our program had been created we informed the Aalto-Helsinki team of our idea to contact Dr. Vasiliadis on whether he would be interested to present his work in the event. We also were informed by Leandros, that he will be contacting the safety committee for any availability of their members to come present. We also proposed a new idea for collaboration, that would potentially include a scientist from YouTube that is a trained clinical psychologist and is also familiar with the microbiome. If that was to happen it would be a joint integrated interview.
Figure 15: Sofie, Iris, Kostas and George in the fourth Human Practices meeting
Human Practices 04-08-2021
Team Thessaly-Team Aalto-Helsinki Meetings
Continuing our-mostly- weekly meetings on the 4th of August we discussed mainly about the MicrobioCOSMOS event and the updates we had. More teams were joining the server, an email at HQ was sent to be posted in the events page, performed a test run on our ethics workshop, etc.) We also suggested a new collaboration. Its theme was about the differences between the beliefs of people from our respective countries about GMO’s and their diet. We would implement it with the help of two questionnaires that we had created.
- MicrobioCOSMOS
- More teams are joining server yipee!! MIT is possibly joining as well
- Thessaly has now sent out invitations and registrations formed
- Waiting replies from HP people for second guest speaker, if don’t respond by Friday Tessa will be the 2nd guest speaker
- Leandros added guides to the shared drives
- Send detailed program to teams by August 11th
- Perform ethics workshop test run on team Thessaly and Aalto-Helsinki
- See if Flinga can have restrictions implemented to prevent people adding inappropriate photos
- Make a chill and slow Kahoot for fun at the end.
- Email of the event was sent to HQ and event is now posted on events page
- Thessaly suggested a new collaboration
- hessaly has developed 3 questionnaires/surveys about GMOs, mediterranean diet, and gastrointestinal disorders)
- Consulted gastroenterologist experts and nutritionist
- Would like Aalto-Helsinki to share these in Finland at offices and what not
- Surveys will be uploaded on slack (GMO one) and google drive
Figure 16: Vilma, Kostas and George in the fifth Human Practices meeting
Human Practices 11-08-2021
Team Thessaly-Team Aalto-Helsinki Meetings
We met with the team again for our weekly debriefing. The things that we discussed about were the following:
We talked about MicrobioCosmos and where we are with the obligations for the event (we were good). We also talked about the teams that registered for the event and how we will be able to handle them. After that we talked about our surveys and how we can share them with the team to get the best results. We agreed to share them now and, in a month, come together again to run over the results and arrive at some conclusions.
Figure 17: Sofie, Kostas and George in the sixth Human Practices meeting
Raising Awareness
Aalto-Helsinki Podcast
Since our projects have many similarities we were invited to the team’s podcast series and had a wonderful discussion. We talked about our projects and specifically the gut microbiome which we both are working on and how we are tackling similar issues but with different methods. We also tapped upon mental health issues, the state of acceptance of them in both of our countries and how gut microbiome health can affect our mental health! Our goal was to engage in a mutually beneficial dialogue and raise awareness on mental health issues.
Sharing Thoughts With Team Thessaly
Figure 18: Aalto/Helsinki podcast
Foresight Report
To finalise our initiative, we urged the participating teams to document their experience and our effort to ensure the evolution of microbiome research in iGEM and of course its importance. After the end of the event, we started writing our foresight report which was collaboratively documented by the Aalto/Helsinki, Heildeberg and IISER Tirupati teams. We hope that this report will act as an inspiration for future iGEM teams that want to be engaged and discover the world of microbiomes.
Team McMaster SynBio
Figure 19: McMaster Synbio logo
Figure 20: McMaster first meeting
Understanding the problems we face
Due to our mutual interest in engineering the gut microbiome aiming to improve people’s wellbeing and
in parallel bearing in mind the fact that our society lacks basic knowledge on gut research innovations,
we decided to hold “New Frontiers In Gut Research'', an online lecture to further understand the modern
tendencies in microbiome research.We decided to host a panel discussion with Dr Brian Coombes, aProfessor in Biochemistry & Biomedical Sciences and Dr Alexandra Meziti, a Postdoctoral Researcher at the Department of Nutritional Sciences and Dietetics.
Figure 21: Screenshot from our panel discussion, top left is Dr. Meziti, top righ is Dr. Coombes, bottom left is Par( Mcmaster Synbio member) and bottom right is our very own Pericles member of the wet lab team.
We were able to interact together with credible stakeholders, receive feedback to some of our project-related questions and overall begin building our common foundation in moving forward in our iGEM season.
“New Frontiers in Gut Research”
Our Guidance and Mentorship
Being a two-phase project, we were privileged with scientific and more technical expertise through our last year's efforts. We were glad to share our experiences and help out our fellow iGEMers throughout this season in their troubleshooting and wet lab development
Figure 22: First wet lab meeting.
Figure 23: Second wet lab meeting.
- Select a suitable plasmid backbone to conduct their experimental design, using the pSEVA library
- Golden braid Cloning troubleshooting
- Snap gene4
Vector selection for designing genetically modified probiotics; shared results for chassis selection
Assistance on our Human Practices
In our broader collaboration efforts, the McMaster team managed to provide us contact information for
experts surrounding the capsule engineering industry. We tried contacting them but unfortunately didn’t
receive any reply for future interviewing.Moreover, after our team developed questionnaires for patients suffering gastrointestinal disorders, not only did we share our surveys to receive feedback from the Canadian Society but also shared some of our findings with McMasters Team.
Finally, they gave us feedback on our GMO applications and usage surveys to understand public perceptions surrounding their development and how friendly Canadian society is towards them.
For detailed surveys analysis, visit our Education and Public Engagement page