Our collaborations for this season include: 1) a partnership, 2) one major collaboration, 3) attendance of two meetups hosted by other iGEM teams, 4) participation in the iGEM InterLab Study, and 5) seven minor collaborations.
- Partnership: Our partnership with GastonDay-Shangde iGEM involved modeling their genetic circuit designed to convert L-phenylalanine to cinnamaldehyde in E. coli. As part of this partnership, we incorporated three new reactions and four new metabolites into a genome-scale metabolic model through the use of a COBRA toolkit, and provided GastonDay-Shangde iGEM with the code for this model with the new reactions and metabolites incorporated. Through this experience, their team gained a model for analysis of their circuit, and our team gained an opportunity to experiment with ways of incorporating circuits directly into GEMs, a future direction for our project. This partnership goes beyond a Silver medal collaboration as it is central to both our team’s project and GastonDay-Shangde iGEM’s project, and involved multiple interactions between our teams. For more information about this partnership, please visit the partnership page of our wiki.
- Major Collaboration: Our team was involved in one major collaboration this year with the Hopkins and East Coast BioCrew iGEM teams. We contributed a video on chassis selection to a collaborative educational YouTube channel.
- Attendance of iGEM Meetups: We attended two meetups hosted by other iGEM teams this year: the MidAtlantic Meetup hosted by UMaryland iGEM for teams in the MidAtlantic region, and an online conference hosted by the Pui_Ching Macau and UM Macau iGEM team on aquaponics and hydroponics.
- iGEM InterLab Study: Our team was part of this year’s Sixth International InterLaboratory Measurement Study alongside many other iGEM teams. The results of this study can allow for analysis of the reproducibility of procedures as well as the inherent measurement errors present in biological studies.
- Minor Collaborations: We participated in seven minor collaborations including IISER-Pune iGEM’s World Environment Day challenge, an educational picture book created by iGEM teams from McGill, Cornell, and Queens, a global seafood cookbook developed by iGEM MIT MAHE, UNSW iGEM’s compilation of synthetic biology articles, NTHU Taiwan iGEM’s project “iGEM Map: Navigation of Synthetic Biology,” IISER-Pune iGEM’s survey on desertification and drought, and iGEM MSP’s puzzle book for iGEM projects.
Detailed Descriptions of Each Collaboration
1. Partnership
GastonDay-Shangde iGEM and William and Mary iGEM:
Image above: Logo of GastonDay-Shangde iGEM, sourced from GastonDay-Shangde iGEM.
This year, we partnered with GastonDay-Shangde iGEM, a team consisting of members from Gaston Day School, a high school located in North Carolina, and Shangde Experimental School, a boarding school located in Shanghai, China. GastonDay-Shangde iGEM’s 2022 project involves engineering E. coli to more readily produce cinnamaldehyde from L-phenylalanine (Kure et al., 1997; Tada et al., 1969) by upregulating transcription of three key enzymes: phenylalanine-ammonia lyase, 4-coumarate:CoA ligase, and cinnamoyl-CoA reductase (Bang et al., 2016). We contributed to their project by incorporating their genetic circuit into a genome-scale metabolic model (GEM) through the use of a COBRA toolkit. This model provided GastonDay-Shangde iGEM with important information about the feasibility and burden of their circuit, and provided our team with an opportunity to explore ways to incorporate genetic circuits into our software, which is a future direction of our project. This partnership goes beyond a Silver medal collaboration as it is more central to both our team’s project and GastonDay-Shangde iGEM’s project, and involved multiple interactions between our teams. For more information about this partnership, please visit the partnership page of our wiki.
2. Major Collaboration
Educational YouTube Channel - Hopkins iGEM, East Coast BioCrew iGEM, and William and Mary iGEM:
One of our collaborations this season involved two iGEM teams based in Maryland, a state bordering Virginia that shares some of the same important ecosystems, such as the Chesapeake Bay. These teams include Hopkins iGEM and East Coast BioCrew iGEM. Hopkins iGEM is an undergraduate team from Johns Hopkins University, while East Coast BioCrew iGEM is a high school team made up of students from multiple schools across the eastern United States, based in the Baltimore Underground Science Space (BUGSS), a publicly funded, non-profit laboratory. We had a virtual meeting with both teams to discuss our projects this year, help each other troubleshoot problems, offer advice, and discuss collaborations on potential educational deliverables. The most substantive part of our collaboration was our contribution to an educational YouTube channel developed by Hopkins iGEM on synthetic biology and bioengineering lab techniques. Our team created a video on chassis selection as part of this educational video collection, while Hopkins iGEM contributed three videos on various lab techniques, including minipreps, PCR, and gel electrophoresis. Baltimore BioCrew iGEM took a survey created by Hopkins iGEM to gain feedback on their YouTube channel, and helped to distribute this survey. Our video on chassis selection defines the Central Dogma of biology, describes synthetic biology, defines a chassis in the context of synthetic biology, provides examples of chassis, and explains the importance of chassis selection, especially in relation to the development of fieldable synthetic biology systems. It explains why ‘fieldable’ chassis selection is currently so difficult, and also discusses the role of computational tools in addressing major roadblocks to fieldability. After receiving feedback from viewers through the Hopkins iGEM survey, we will be able to gain information on any improvements we can make to our educational videos in the future.
3. Attendance of Meetups
3a) MidAtlantic Meetup - UMaryland iGEM, Virginia iGEM, Hopkins iGEM, East Coast BioCrew iGEM, and William and Mary iGEM:
We attended the 2022 MidAtlantic Meetup hosted by UMaryland iGEM on August 13. The MidAtlantic Meetup is an annual meetup held by an iGEM team in the MidAtlantic region of the United States to provide an opportunity for other MidAtlantic iGEM teams to meet, present their work, and receive feedback on their projects. Along with presenting our project and hearing about the projects of several other iGEM teams, including the Virginia iGEM team, the Hopkins iGEM team, the East Coast BioCrew iGEM team, and the UMaryland iGEM team, we were also provided the opportunity to attend the presentation given by keynote speaker Yeesin Yeung from the iGEM Engineering Committee, and participate in a collaboration workshop.
From left to right (on top row): Logos for UMaryland iGEM, Baltimore BioCrew iGEM, Virginia iGEM, and Hopkins iGEM. Logos were sourced from each of these teams, respectively. On bottom row: Logo for William and Mary iGEM, sourced from William and Mary iGEM.
3b) iGEM Online Conference - PuiChing Macau iGEM, UM Macau iGEM, TecCEM iGEM, NNU-China iGEM, and William and Mary iGEM:
We also attended an online conference on aquaponics and hydroponics hosted by the PuiChing Macau and UM Macau iGEM team on September 10 (Eastern Time). Other attendees included the TecCEM and NNU-China iGEM teams. Each attending team was asked to propose a method for improving the aquaponic system developed by team PuiChing Macau and UM Macau iGEM, and to submit a document outlining their proposed improvement method. Prior to the conference, each team submitted a survey in which they provided their team name, number of team members attending the conference, contact information, a brief project description, their presentation slides, and which part of the aquaponic system they were interested in proposing an improvement for. As part of this conference, each team presented their project and their proposed improvement method to the aquaponic system. Our proposed method involved the use of our chassis selection software to select the optimal bacterial chassis for their aquaponic system. The improvement methods proposed by all attending teams were compiled into a flow chart and posted on PuiChing Macau and UM Macau iGEM’s social media platforms.
Poster for PuiChing Macau and UM Macau iGEM’s online conference on aquaponics and hydroponics, sourced from PuiChing Macau and UM Macau iGEM.
Images above, from left to right: PuiChing Macau iGEM logo, sourced from PuiChing Macau iGEM; UM Macau iGEM logo, sourced from UM Macau iGEM; William and Mary iGEM logo, sourced from William and Mary iGEM; TecCEM iGEM logo, sourced from TecCEM iGEM; Nanjing Normal University logo; sourced from Nanjing Normal University.
4. iGEM InterLab Study
Our team elected to participate in the Sixth International InterLaboratory Measurement Study, alongside many other iGEM teams. For the InterLab Study, teams from around the world complete the exact same experiment following the exact same procedure and then submit their quantitative results to iGEM, allowing researchers at iGEM to analyze the reproducibility of procedures as well as the inherent measurement errors present in biological studies. This year, the study focused on fluorescence testing using a plate reader, using both single- and dual- colored devices in Escherichia coli DH5-alpha. InterLab Studies, which typically are published in scholarly journal articles, contribute greatly to the field as they elucidate major issues with biological experimentation—variability and error. We are anticipating this year’s study to be published and widely distributed, as previous studies have been. We are very grateful for this major collaboration opportunity provided by iGEM.
Image above left: iGEM logo, attributed to iGEM Foundation and Justin Knight.
5. Minor Collaborations
5a) World Environment Day Collage - IISER-Pune iGEM and William and Mary iGEM:
IISER-Pune (India)’s iGEM team facilitated the creation of a World Environment Day themed collage in early June, filled with pictures of 2022 iGEM teams from around the world taking action to restore the health of their local environment. For this multi-team, environmentally conscious collaboration, William and Mary iGEM team members Walker and Megan collected a bag of litter from around William and Mary’s campus. As ecological health is so vitally important to the planet, and central to our project, we were really excited to participate in this collaboration.
Image to the right: Walker Knapp, member of the William and Mary iGEM team, participating in World Environment Day. Photo courtesy of Megan Fleeharty, member of William and Mary iGEM.
Images above: Images posted by iGEM IISER-Pune on their social media thanking all of the teams that participated in their World Environment Day challenge. Sourced from iGEM IISER-Pune iGEM.
5b) Educational Picture Book - McGill iGEM, Cornell iGEM, Queens iGEM, and William and Mary iGEM:
Images above from left to right: Logos for McGill, Cornell, Queens, and William and Mary iGEM, sourced from these teams respectively.
iGEM teams from McGill (Canada), Cornell (United States), and Queens (Canda) co-designed an educational picture book about bacteria, and asked other iGEM teams to help them create it by describing their favorite microbe. In order to raise awareness about synthetic biology’s amazing potential to remediate environmental pollutants, we submitted information about our favorite soil bacteria: Pseudomonas putida. We highlighted P. putida’s ability to degrade detrimental compounds, such as crude oil, and survive in antagonistic environments, which is part of what makes it such a promising chassis. We chose to participate in this collaboration because we hope that educational materials introducing students to the wide range of applications of bacteria will generate interest towards the field of synthetic biology, and to emphasize the potential for environmental bioremediation through the use of bacteria.
5c) Geo Book - MIT MAHE iGEM and William and Mary iGEM:
Moreover, the iGEM team MIT MAHE (India) proposed a collaboration for the assembly of a Geo Book, or global seafood cookbook highlighting local ecosystems and cuisine, and invited teams around the world to highlight a dish important to their culture. Ultimately, this project aims to educate the public about unsustainable practices pertaining to aquatic organisms and ecosystems. We submitted information about Eastern oysters (Crassostrea virginica), which are a native species in the Chesapeake Bay, located in Virginia. Eastern oysters have a crucial role economically, culturally, and environmentally in this region. However, the Eastern oyster population has experienced a major decrease due to overfishing, disease, and pollution. In completing this collaboration, we hope to propagate information about the important role that Eastern oysters play in our community, while also promoting their restoration as an issue that could potentially be addressed through synthetic biology.
Download MIT MAHE iGEM's Geo Book Below:
- To download the Geo Book, please click here.
Image above left: Header for MIT_MAHE’s Google Form for their Geo Book collaboration. Image above right: Photo of one of our team member’s favorite seafood dish, which we submitted as part of our entry for the Geo Book. Photo courtesy of Lin Fang, member of William and Mary iGEM.
5d) Compilation of Synthetic Biology Articles - UNSW iGEM and William and Mary iGEM:
We participated in UNSW iGEM’s project to compile short articles (300-500 words) on synthetic biology projects written by iGEM teams in different languages, either on their own projects or on projects of interest to them. We wrote a brief article in English on our chassis selection software to be included as part of this multilingual compilation of articles on synthetic biology projects.
Images above from left to right: Logo for UNSW iGEM 2022, sourced from UNSW iGEM; logo for William and Mary iGEM, sourced from William and Mary iGEM.
5e) iGEM Map: Navigation of Synthetic Biology - NTHU Taiwan iGEM and William and Mary iGEM:
We took part in NTHU Taiwan iGEM’s project “iGEM Map: Navigation of Synthetic Biology,” in which iGEM teams were asked to design a character to represent their project, and complete a brief survey in which they provide their team name, email address, school, location, a brief project description, an explanation of what their character represents, a file containing their character, and links to their social media pages. Our character (shown on the right) represents our software toolkit for chassis selection. Each team’s character was used to mark their location on a map of the Earth.
Image on the right: The character we designed to represent our project as part of NTHU_Taiwan iGEM’s “iGEM Map: Navigation of Synthetic Biology” project.
5f) Desertification and Drought Survey - IISER-Pune iGEM and William and Mary iGEM:
Images above from left to right: logo for IISER-Pune iGEM; sourced from IISER-Pune iGEM; logo for William and Mary iGEM, sourced from William and Mary iGEM.
We completed a brief survey for the IISER-Pune (India) iGEM team on desertification designed to provide information on the awareness and involvement of the public regarding desertification and drought, and ways to address them. We answered questions about what we thought the word “desertification” implied, approximate estimates of how many people globally we thought were affected by drought each year, what percent of total global land surface we thought consisted of drylands, which top three human activities we thought were major causes of desertification, which top three environmental phenomena we thought were major causes of desertification, which solutions for drought or desertification we thought were most effective, whether we would propose any other solution to desertification or drought, and an explanation of how our project relates to desertification (if applicable).
Google Form header for survey created by IISER-Pune iGEM on desertification and drought.
5g) Puzzle Book for iGEM Projects - MSP iGEM and William and Mary iGEM:
iGEM MSP invited other iGEM teams to participate in creating a puzzle book containing information about the projects of various teams in order to inform the general public about iGEM and the field of synthetic biology as a whole. As participants, we provided them with a project description, 10 words or phrases that described our project, an explanation of why we selected these 10 words or phrases to describe our project, and our logo.
Images above from left to right: MSP iGEM logo, sourced from MSP iGEM; William and Mary iGEM logo, sourced from William and Mary iGEM.
Download MSP iGEM's Puzzle Book Below:
- To download the Puzzle Book, please click here.
Conclusion
Overall, our collaborations include:
- Partnership with GastonDay-Shangde iGEM
-
One major collaboration
- Hopkins and East Coast BioCrew iGEM: Educational YouTube Channel
-
Seven minor collaborations
- IISER-Pune iGEM’s World Environment Day challenge
- McGill, Cornell, and Queens iGEM teams’ educational picture book
- iGEM MIT MAHE’s global seafood cookbook
- UNSW iGEM’s compilation of synthetic biology articles
- NTHU Taiwan iGEM’s “iGEM Map: Navigation of Synthetic Biology”
- IISER-Pune iGEM’s survey on desertification and drought
- iGEM MSP’s Puzzle Book for iGEM projects
- Participation in iGEM InterLab Study
- Attendance of two meetups
- UMaryland iGEM’s MidAtlantic Meetup
- PuiChing Macau and UM Macau iGEM’s Online Conference
References
Bang, H. B., Lee, Y. H., Kim, S. C., Sung, C. K., & Jeong, K. J. (2016). Metabolic engineering of Escherichia coli for the production of cinnamaldehyde. Microbial Cell Factories, 15(1). https://doi.org/10.1186/s12934-016-0415-9
Kure, S., Tada, K., & Narisawa, K. (1997). Nonketotic hyperglycinemia: biochemical, molecular, and neurological aspects. The Japanese journal of human genetics, 42(1), 13–22. https://doi.org/10.1007/BF02766917
Tada, K., Narisawa, K., Yoshida, T., Konno, T., & Yokoyama, Y. (1969). Hyperglycinemia: a defect in glycine cleavage reaction. The Tohoku journal of experimental medicine, 98(3), 289–296. https://doi.org/10.1620/tjem.98.289