Team:Wageningen UR/Contribution
Contributions
As a team, we were aware of the great efforts of teams before us, from Wageningen University and Research (WUR) and internationally. We could benefit from tools developed within the iGEM community, such as the iGEMers guide to the future and the how to wiki guide of the WUR iGEM team of 2019. Therefore, Cattlelyst, the iGEM team of WUR in 2021, worked hard to contribute to the iGEM community and the community of Synthetic Biology (Synbio) in general. We produced two new guides and we developed a tool, the iGEM Pipeline for Improved Pathway Engineering (PIPE). The latter, combined with our new Wikibase of Biobricks, facilitates the design of synthetic pathways needed for both bioremediation and production of (high value) compounds. Find the link to our contributions in the tabs below.
Go to simulation of a stakeholder meeting to find out how the Cattlelyst team prepared for the real interstakeholder meeting.
Scroll to the section on this guide
Do you want to inspire children about SynBio and share with them your enthusiasm about iGEM? The Cattlelyst team had some experience with that and made a guide with tips for helping the organization of a science laboratory for primary school kids.
Go to the Junior Science Lab section
We found that the community of iGEM and synbio could benefit from a tool that helps in identifying metabolic pathways for the increased assimilation of polluting compounds. The iGEM PIPE does this while also suggesting engineering strategies for the production of target compounds. This is possible thanks to the combination with our new organised database of Biobricks.
Go to our software contributionStakeholder meeting simulation: Our guide
The stakeholder simulation that WUR iGEM team 2021 did was crucial in the iterative development of our technology. We gathered people not involved in the project and asked them to impersonate a stakeholder group in order to gather information of synergies and conflicts between them. This helps in obtaining a broader overview of the acceptance of the product than what is gained from interviewing single stakeholders. Our guide explains the advantages of the simulation in detail.
Jump to the guide!
Here a list of benefits from performing the simulation:
- It helped us identify shared concerns among stakeholder groups
- It is an opportunity to present the iGEM project to a non-expert audience.
- It prepares for bringing your human practices efforts to the next level.
This include for instance the need of external financing for the implementation of our biofilter. Therefore, we then knew what to focus our effort on: finding possible ways of easing the economical investment that would be required for farmers to use our biofilter.
This is needed, since the participant to the simulation should know the context and background of the Synbio innovation.
Performing such simulation gives a solid base that helps in organizing a real inter-stakeholder meeting.
Our guide explains what needs to be considered for the organization of such meetings. It provides tips, checklists of steps to be followed and examples. The stakeholder meeting simulation really brought our HP efforts to the next level and we wanted to help other teams in organizing such event. Groningen iGEM team 2021 already followed our advice and collaborated in the finalization of the guide. Their experience and feedback was implemented in the guide that is published in here.
WUR and Groningen iGEM teams 2021 really shared the energy and motivation boost given by performing a simulation of a stakeholder meeting. As WUR iGEM team 2021, we really wanted to share our very positive experience freshly and we did so in a post in our blog, “The Cattlelyst’s Journey”.
Go to our blog!
Junior Science Lab guide
Communication about Synthetic Biology and the specific topic of a project can be done at many educational levels as our team has proudly demonstrated.
Go to our Education page!Talking about science to children can be a bit more challenging than describing an iGEM project to fellow students. Our team was lucky to receive the support of enthusiastic people from the Wetenschapsknooppunt (Science Hub) of WUR in organising a science laboratory for children. This was called Junior Science Lab (JSL). The participants were enthusiastic 10-12 years-old children that voluntarily decided to spend a day of their Summer holiday in getting to know about Synbio and our project. We wanted to share our experience and what we learned from it with other iGEM teams. For this reason we wrote a guide!
In this guide we give you suggestions on how to organize a JSL, with practical tips especially on the structure. Two elements are at the core of the JSL:
- Lecture sessions
- Practical experiments
They can be seen as “input moments” when information is provided to the pupils;
These help the children to apply the knowledge gained during the lecture to a specific context.
The iGEM PIPE
Cattlelyst, the WUR iGEM team 2021 developed a Python-based tool, the iGEM Pipeline for Improved Pathway Engineering, (PIPE), that suggests how to engineer a microorganisms of interest for both bioremediation and bio-production purposes. It also facilitates the experimental testing of the engineering approaches by indicating which existing Biobricks should be used for constructing the synthetic strain experimentally.
iGEM teams often aim at targeting either the degradation of pollutants or the production of high value chemicals. Microorganisms can be used for the completion of both tasks. Many computational tools in synthetic biology focus on facilitating the production of high value compounds. But what about the degradation of pollutant that threaten us and the environment? Tools that suggest designs involving both addition and deletion of reactions exist only in the context of improved (growth-coupled) production. Thus, one of the novel aspects of the iGEM PIPE of WUR iGEM team 2021 is the suggestion of engineering strategies that allow the consumption of uncommon substrates (e.g. pollutants and xenobiotics).
Additionally, this Python package aims at facilitating the transition from in silico design of the engineering strategy to its application in vivo. The transition usually consists in using biological parts, Biobricks, to confer the new functionalities (e.g. gene knock-ins). The iGEM PIPE accelerates the otherwise time-consuming task of manually looking for Biobricks encoding the correct function. This search has been automated by making use of a new version of the Biobrick database, the Biobrick wikibase.
This tool was improved and validated with the help of two other iGEM teams:
Click here to learn more about our Collaborations!