Collaborations
Phototroph Community Collaboration
Hopkins x William & Mary x East Coast Biocrew Collaboration
Phototroph Community Collaboration
From the handbook: “The iGEM Phototroph Community was founded by the grandprize winning team, iGEM Marburg and top-ten ranking iGEM Bielefeld in 2021, with the aim of bringing together teams working with phototrophic organisms in the iGEM competition, including cyanobac- teria, microalgae and higher plants. Their vision was to open further dialogue and have teams support each other in troubleshooting, project ideation and more!
iGEM teams working with phototrophic organisms have been underrepresented overall within the competition. This is likely due to the slower growth rates and lack of standardization in protocols for engineering phototrophs. With this in mind, the community has worked on standardization in protocols for the most common phototrophic chassis in synthetic biology! In doing so, the goal is to make engineering and cultivation of these promising organisms less daunting and more accessible to everyone!
This Handbook was created as a large scale collaboration with several iGEM teams from all over the world, who worked together to create a global community of teams working with phototrophic organisms in the iGEM competition. Since working with phototrophs brings along with it some challenges, differing from work with heterotrophic organisms like bacteria or yeast, the iGEM Phototroph Community worked together to identify these challenges and lay the groundwork to overcome them.”
Hopkins iGEM contributed towards the development of a Phototroph Handbook with other iGEM teams (UBCO iGEM, ASU iGEM, HKU iGEM, UBC iGEM, Worldshaper-SH iGEM, iGEM Thessaly, Hopkins iGEM, SUNY Oneonta iGEM as well as other past contributors.) We wrote about the evolution and development of phototrophs as well as about the factors that differentiate phototrophs (dicots vs monocots etc.) We also covered ways that different phototrophs can be used and are being used in research.
The Phototrops Handbook Volume II can be found here , and will be uploaded to the iGEM Plant Subcommittee Webpage for future teams!
Hopkins x William & Mary x East Coast Biocrew Collaboration
Hopkins iGEM met with the East Coast Biocrew and William & Mary iGEM teams throughout the competition to get feedback from each other on our projects and work on collaboration activities.
At our first meeting on 7/16, the three teams presented their project ideas and looked for common ground and how we could benefit from sharing expertise. For their iGEM project, the East Coast Biocrew proposed to address PCB pollution by designing a device for sensing and degrading PCB. William & Mary decided to build a software tool for scientists to determine fieldability of synthetic biology designs. Their tool would answer questions like, “Is this the appropriate chassis for this problem?” Hopkins iGEM shared our idea of engineering roots to have magnetotropism so they could be directed in zero gravity spaceflight. While our projects addressed distinct scientific questions, we identified four areas for potential collaboration: general iGEM challenges, math modeling, hardware, and education.
iGEM Challenges
One of the general iGEM challenges we discussed was fundraising. East Coast Biocrew suggested seeking out corporate donations from local biotech companies, specifically targeting local sales representatives.
Math Modeling
Regarding math modeling, Hopkins iGEM was planning to model the iron concentration needed to have the roots sense the magnetic gradient field. East Coast Biocrew was interested in modeling the PCB concentration needed to create a response in their biosensor and also modeling the reactions in the bioreactor needed for PCB degradation. W&M described intentions to include a flux-balance analysis as a component of their software tool. One collaboration idea was to have W&M’s software tool be used by Biocrew to check the feasibility of their bioreactor by checking for limiting nutrients.
Hardware
By this meeting, Hopkins iGEM had already decided that hardware would be a core component of our project because we had some students with expertise on our team. We described to the other teams our idea for creating a device that spins the plants to simulate microgravity and powers coils to generate a magnetic field to direct the roots under magnetotropism. Biocrew described the hardware specifications needed for their biosensor device. In the presence of PCB, their genetic circuit would output luciferase and they would need a light detector to sense the luciferase and a small computer to transmit the signal from the light detector. Biocrew was considering utilizing a raspberry PI to connect to the light sensors, but Hopkins iGEM advised to Biocrew that obtaining a raspberry PI chip would be difficult because there is a chip shortage and raspberry PI isn’t necessary for something that doesn’t need to be wifi enabled. Hopkins iGEM suggested Biocrew instead use a Arduino with maybe a photodiode to detect the luciferase.
Education
The area that the three teams discussed that had the most potential for collaboration was education. William & Mary iGEM was working on writing a comparative review on environmental microbiome in the USA and India. Biocrew had been researching the history of PCB contamination and planning social media posts. Hopkins iGEM expressed interest in making video content similar to the previous year. We thought it could be a cool collaboration if all three teams, Biocrew, W&M, and Hopkins, worked together on a collection of educational videos. Hopkins set up a North America iGEM Discord so we could chat more about the collaboration ideas there.
At the next meeting on 7/31, East Coast Biocrew and Hopkins brainstormed topics for videos. Some of the proposed ideas included chassis selection, environmental justice, golden gate assembly, and experimental protocols.
On 8/12, W&M and Hopkins discussed more about the videos’ target audience and how to increase dialogue with the audience. Ideas for target audiences included new iGEM teams and people joining their first lab who could be too scared to ask their PI about troubleshooting experiments. To get feedback from video viewers, we decided to make a survey on effectiveness of video content.
By 8/19, the ideas were narrowed down to one video on chassis selection and a few videos on protocol bloopers (including PCR, gel electrophoresis, and minipreps).
The final videos and survey were completed in October and can be found on the Education page.