Team:Calgary/Partnership
Partnership with iGEM Bonn
Overview:
This year, iGEM Calgary embarked on a partnership with iGEM Bonn, collaborating throughout the year in both our wet lab, dry lab, and educational initiatives. These efforts informed and shaped our work at several key stages, proving instrumental in the success of our project. Here’s to our partners across the Atlantic!
Figure 1.Screenshot of a Zoom meeting with both iGEM Calgary and iGEM Bonn.
STAGE 1: Setting the Stage
In late spring 2021, iGEM Calgary identified an overlap of our project aims with iGEM Bonn, as both teams planned to utilize the same REE-binding protein, lanmodulin, in order to solve the rare earth element (REE) scarcity problem. With this in mind, we reached out to iGEM Bonn to schedule a preliminary meeting to discuss the possibilities of a partnership. In this preliminary meeting, we decided to differentiate our projects by utilizing different feedstocks as our source of REEs. By exploring two unique avenues of REE reservoirs, we felt that we could cover a larger ground, thereby making more contributions to this relatively new field. Hence, iGEM Calgary decided to focus on utilizing lanmodulin to recycle REEs from electronic waste (e-waste), while iGEM Bonn focused on extracting REEs from raw minerals. After this initial meeting, each team then conducted independent human practices and literature review to characterize our respective feedstocks. The key to any successful partnership is to not only share the same values, but also to clearly define each partner’s roles and responsibilities, so in this stage, we also established open channels of communication and outlined guidelines for our collaborations. One such guideline was that each team would have an open door to support and help one another with troubleshooting when needed. Another key guideline was that both teams agreed to provide each other with transparent, consistent communication on our collaborative initiatives. As we moved forward, this set of guidelines helped keep each team on track and allowed us to stay accountable to our partnership. In this initial stage, we also outlined our key partnership goals. Goal-setting allowed us to maintain clear objectives and project values. The three major goals we identified are:
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Raise awareness about the significance and urgency of the rare earth element scarcity problem
Develop sustainable alternatives for existing REE extraction processes
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Characterize the novel lanthanide binding protein, lanmodulin, for different feedstocks
STAGE 2: Obtaining Data
With our respective feedstocks in mind, we moved on to data collection, where both teams worked in their respective labs to produce and characterize landmodulin, with the eventual aim of sharing our successes (and failures) with each other.
As iGEM Calgary encountered many obstacles in our wet lab experimental workflow, we were unable to generate lanmodulin during this stage. Despite this wet lab roadblock, our dry lab team was able to make major strides in developing software and hardware components to support our project.
During this stage, iGEM Bonn reported strong success in their lab, as they were able to recombinantly produce lanmodulin and begin developing purification methods. In addition, iGEM Bonn was able to apply their extraction process to their mineral ore substrate.
At the end of this phase, we met briefly to plan an educational collaboration that would complement each project’s overarching goals. Through this discussion, we decided to launch a social media collaboration in the fall that would contain a series of posts dedicated to explaining the pertinence of the REE scarcity problem.
STAGE 3: Troubleshooting and Sharing Resources
After both teams made sufficient progress on their respective experimental workflows, we held another meeting to provide each other key updates. This meeting proved instrumental to helping us overcome our roadblock in the wet lab, as we were able to collaborate on troubleshooting our wet lab issues. For instance, iGEM Bonn tried to advise us by sending us their vector sequences and sharing with us details of their experimental workflow. iGEM Bonn also lent us a protocol for the purification of lanmodulin using an acidification approach.
Although iGEM Calgary did not directly employ Bonn’s vector sequences or protocols, this troubleshooting meeting was helpful in comparing and contrasting our respective workflows, which enabled us to better reflect on our own laboratory procedures and troubleshooting practices. Shortly after this troubleshooting meeting, we were successful in heterologously producing LanM!
A secondary wet lab meeting was also held to reflect on each team’s analytical techniques for REE detection. While iGEM Calgary was using and characterizing the Arsenazo-III assay for REE detection, iGEM Bonn was focusing on the xylenol-orange assay. We advised iGEM Bonn that Arsenazo III would not be suitable for detection from their feedstock (mineral ores), as Arsenazo III reacts strongly to calcium ions, which happens to be the main cation present in mineral ores [1]. Both teams also discussed using traditional instrument-based methods of REE measurement, such as inductively coupled plasma mass spectrometry (ICP-MS). iGEM Bonn informed us of their difficulties in accessing an ICP-MS. As such, we recommended that they try to utilize a similar analytical method using ICP-OES (inductively coupled plasma optical emission spectrometry).
With wet lab discussions underway, both teams also were curious to learn about dry lab progress and updates. Having developed numerous software modeling, process engineering, and hardware subprojects to support our project in Stage 2, we held several meetings with iGEM Bonn to provide them with a detailed overview of our dry lab workflow. At this time, iGEM Bonn informed us that they had not yet been able to develop much computational modeling to support their project, as their primary focus was their wet lab workflow. We were more than happy to help support their interests in modelling by providing them with access to our dry lab expertise and protocols. For instance, we discussed the addition of binding motifs to lanmodulin to make it more efficient, as well as the possibility of introducing mutations so that lanmodulin binds at a lower pH. Our Autodock workflow for modelling binding affinity was of particular interest to iGEM Bonn, as they wanted to see how lanmodulin would work in their complex mineral ore feedstock. Furthermore, iGEM Calgary’s dry lab team provided Bonn with an overview of software such as AlphaFold and PyMol so that they could experiment with computational approaches relevant to their project.
STAGE 4: Wrapping it up
As mentioned before, iGEM Calgary and Bonn wanted to supplement their similar experimental goals by developing an educational outreach collaboration. Since both projects aimed to target the REE scarcity problem, both teams thought it would be important to educate the general public about the significance of REEs, REE applications, and REE scarcity. Given that iGEM Calgary and Bonn are not geographically located close to each other, we thought a social media collaboration would be an appropriate way to present our educational material. We began ideating the content of our educational collaborations in Stage 2, and began working to design posts and find ways to creatively display facts that would educate our target audience during stage 3. Finally, in October, our educational collaboration materials were complete, and the series debuted on social media.
Figure 3. Gallery of posts developed and shared on social media as part of the iGEM Calgary x Bonn collaboration to raise awareness about REEs.
Although our partnership activities drew to a close as the end of the iGEM season approached, we discussed a variety of future partnership activities in which both teams could partake. For example, we discussed collaborating on the development of a financial model for the scaled-up usage of lanmodulin in industrial settings. Additionally, we also discussed the potential exchange of feedstocks so that both teams could test their respective solutions on the other team’s feedstock. This exchange could highlight the versatile nature of our synbio solutions and strengthen our industrial applications. Although we were unable to accomplish these two goals during the time frame of the iGEM season, these activities would be useful avenues to explore as a partnership in the future.
Partnership Summary and Outcomes
Early in the summer, we discovered that REEs are vital to many everyday technologies, but, with the annual demand for REEs predicted to double by 2035, we realized there was an urgent need for a new sustainable stream of REEs to help meet the needs of the future. As such, both iGEM Calgary and Bonn have both developed unique synthetic biology solutions to solve the REE scarcity issue by creating sustainable alternatives to existing industrial REE extraction processes. In summary, refer to the table below to see an overview of the key collaborations underwent in this partnership:
References
Stosch H-G, Romer RL, Daliran F, Rhede D. Uranium–lead ages of apatite from iron oxide ores of the Bafq District, East-Central Iran. Mineralium Deposita 2010 46:1. 2010 [accessed 2021 Oct 19];46(1):9–21. https://link.springer.com/article/10.1007/s00126-010-0309-4. doi:10.1007/S00126-010-0309-4
