Team:Rochester/Collaborations
UteRus
Collaborations
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Initiative: Biomarker Database
One of the issues our team faced while first looking into endometriosis was finding a good way to sort through literature and find biomarkers we might be interested in (e.g., IL-1b, TNF-a, CA125, etc.) . It was even more difficult to find out which of our biomarkers were novel for the iGEM competition. So, we came up with a solution. We created a Biomarker Database for iGEM teams to provide an easy and free way to search biomarkers for disease and see which teams workare working with which specific biomarker. The database contains information about various biomarkers from previous iGEM teams’ projects and serves to facilitate the development of future iGEM projects by determining what biomarkers have been used. For example, for each biomarker, the Database specifies the type of biological molecule a specific biomarker is, why a team did or did not select that biomarker for use in their project, what kindtype of sample the team used to measure or detect their biomarker, etc. Having thorough information about multiple biomarkers in one database may save time in designing an iGEM project and so help itsit’s development. We thank several iGEM teams, including Linköpings, MIT, Thessaly, and Queen’s University, at Kingston for adding their research information to our Biomarker database.
Teams: MIT, Thessaly, Linkopings and UR
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Initiative: Accessibility
Through social media, Slack Global, and the iGEM webpage, we discovered a few teams, including BITS Goa, IIT Madras, and IISER Berhampur, who were interested in exploring accessibility. Our team, along with BITS Goa and IIT Madras, co-presented our multifaceted approach to accessibility through language and art, discussed the possibilities and implications of incorporating accessibility in terms of language, and invited teams to collaborate with us on many initiatives. These initiatives included learning sign language phrases, participating in our Science As Art initiative, and collaboratively adding to Madras’ established language project. We reached over 40 teams through a presentation at the both the iGEM Global and India Meetups. Teams joined our initiatives through making their own videos to display common American Sign Language (ASL) phrases and posting them on social media, and participating in Science as Art. Furthermore, we added our Upward Bound synthetic biology educational materials to IIT Madras’ Language Project to expand the reach of our curriculum.
Teams: BITS Goa, IIT Madras, IISER Berhampur, and UR
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Initiative: Biomarker Sensing Group
Our team and Lambert High School in Georgia joined the Biosensor Working Group, which was organized and led by the Queen’s University at Kingston team. Our goal in joining this Group was to exchange biosensor knowledge and tips to improve our respective biosensors that we were creating. During a series of Zoom meetings, Queen’s University taught us how to use a number of synthetic biology softwares that are widely used in analytical aspects of biosensors and that could potentially be of interest to our team. We had stimulating discussions about the sciences behind our projects. These discussions helped us expand our approaches to solving modeling problems. For example, from Lambert High School we learned how we could search for kinetic parameters like reaction rates or transcription rates that we wanted to use for our ordinary differential equations. For Lambert High School, we gave input on their initial model development by suggesting that they divided the Pho Regulon signaling pathway into smaller modules and model those separately before connecting the pieces (since the pathway was very complex).When we finished meetings focused on biosensors, we talked to the other two teams about our human practice and outreach ideas. We received questions from Lambert High School and Queen's University with regards to these topics and shared with them our insights.
Our first meeting:
Teams: Queen’s University at Kingston, Lambert High School In Georgia, and UR
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Initiative: Outreach Workshop
Purdue University initially reached out to our team for a video collaboration about teaching synthetic biology to high school students. Their project aims to collect videos designed by various iGEM teams explaining different topics related to synthetic biology clearly and concisely and eventually presenting them to local high schools, similar to our Upward Bound educational program for high school students. Purdue University sought input and advice on establishing a virtual teaching program after hearing about our work. Incorporating the experiences and skills we have developed, we held a workshop for Purdue University. The purpose of this workshop was to present various lessons we learned from developing an interactive and effective online curriculum through the Upward Bound project. During the Zoom workshop, we shared what we learned from Dr. Hammond at the University of Rochester, who guided us in developing our online curriculum in the Upward Bound project. In the workshop for Purdue University, we addressed how virtual asynchronous teaching programs add another layer of difficulties in interacting with the students. We outlined several solutions. For example, to improve the interaction between the students, we created activities in the modules and reached out to coordinators and the students for feedback through anonymous google forms. We also shared the undeniable rewarding and fulfillment we received the Upward Bound program has brought to us. We answered questions from the Purdue team regarding teaching methods, delivery platforms, and interactive elements.
Teams: Purdue University and UR
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Initiative: German iGEM Meetup
Marburg University organized the German iGEM Meetup, where iGEM teams around the world presented their projects to other teams and attended lectures presented by world-class biologists. Our team presented our progress thus far during the poster session. In this poster, we highlighted that our project is indeed unique in that we use biomarkers from menstrual effluent for the diagnosis of endometriosis and that this has not been done previously due to the lack of research funding and the lack of interest in the disease both by the public and medical professionals. Presenting our project to other iGEMers was beneficial for us as we had a discussion with the attendees during which we learned more about endometriosis diagnostic tools in different countries. For example, we learned that in France, the diagnosis of endometriosis is performed with echography only. Presenting our project to other teams was valuable for us also in that we received questions that allowed us to understand where we could explain certain parts of the project better. For instance, a member from iGEM Toulouse asked us why testing blood samples had not been done yet to diagnose endometriosis. We took this question into consideration when designing our project’s poster for the iGEM Giant Jamboree.
iGEM Marburg University poster for the German iGEM Meet Up
Participating in the iGEM2020 Manchester team’s poster session.
Our poster for the German Meet Up
During our presentation.
Our team is on schedule.
Teams: Marburg University and UR
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Initiative: Symposium on Global Challenges
Leiden iGEM team invited us to be guest speakers in their organized Symposium on Global Challenges - an online two-day symposium on how international iGEM teams have taken on the challenge to tackle global and local issues using synthetic biology. There were two other teams, the FCB-UANL team from Mexico and the Aalto-Helsinki team from Finland, who were guest speakers like us and presented their projects to a diverse audience that consisted of iGEMers, non-iGEMers, and other students. Participating in this event was a great opportunity for us to practice delivering scientific knowledge to the general public, spread awareness on endometriosis, and connect to other iGEM teams.
Teams: Leiden and UR
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Initiative: Journal initiative
The iGEM team at Maastricht University announced an initiative about collecting team-written research papers from other iGEM teams about their projects so they can all be published in an accessible database for the iGEM community. We participated in this initiative by writing and submitting our journal article for the Maastricht Journal Initiative. iGEM team Maastricht University provided us with feedback on our own journal draft and, in this way, helped us train our scientific writing skills. We contributed to the Journal initiative by providing feedback to two other iGEM teams, UPF Barcelona, and MIT. During the journal review for UPF Barcelona, for example, we addressed the journal in the writing structure and the connection between their project idea and the research they conducted. In COVID-19 circumstances and limited access to lab space, it can be challenging to connect the broad goals of a project with the actual research and designs that were created. We advised UPF Barcelona to improve their conclusions and discussion sections so that they clearly remain relevant to the research; we also encourage them to clearly lay out what the next steps would be to reach the full scope of the project idea.
Our journal
Teams: iGEM team Maastricht University and UR
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Initiative: iGEM video collaboration
TU Delft invited us to participate in their informative video initiative in which iGEM teams share their project to show the power of synthetic biology in science and medicine. We provided a clip of our project in which we explained the problem we are solving and how we were doing this. We are thankful to TU Delft for spreading the word about our project to the global iGEM community.
Teams: TU Delft and UR
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Initiative: Dance Collaboration
Our team worked with the BITS Goa and IIT Madras teams to design a movement collaboration to promote diversity. The activity had the participants put their team logo as their background, then pass a mask around while introducing themselves in their native language, during the Global Meetup in August. Our event was attended by multiple teams as well as iGEM global meetup organizers who were interested in our initiative during the planning period.
This activity demonstrates that although the pandemic has affected us all, we still persevere, and through dance, we can show the possibility of overcoming the global boundaries and challenges using science during difficult times through collaboration and embracing diversity. Through dance collaboration, we supported each other to use science and arts for self-expression and perseverance in times of uncertainty.
For the dance collaboration, all three teams met on through Zoom on a weekly basis throughout the summer to brainstorm ideas, plan the event and publicize it during the Indian Meetup. All three teams, which in total consisted of 15 iGEMers, also participated in choreographing dances that represent the different stages of Covid-19, as an additional event that related to passing, the mask activity.
Our team was in charge of leading the trial runs as well as the Indian Global Meetup. We also designed the poster for publicizing the event. Bits Goa team members video edited the preview video for the event.
Dance collaboration: featuring getting sick, having the virus and the recovery.
Teams: Bits Goa, IIT Madras and UR
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Initiative: The Transcriptome Blog
Our team participated in a blog initiative created by Team UNLausanne. The goal of this initiative was to increase science communication; specifically, scientific communication with text accessible to those without an extensive science background about a topic that we were interested in. We created accompanying graphics reflecting concepts in a written explanation of our topic: cytokines. We chose to add this topic to UNLausanne’s blog because cytokines are involved in signaling for many biological processes, including endometriosis, because of their role in inflammation. Furthermore, this blog post contributes to our efforts to spread awareness of endometriosis because we specifically discuss the role of cytokines in endometriosis. To learn more about the significance and importance of cytokines and their role in endometriosis, click here.
Teams: UNLausanne and UR
