New York iGEM Team Meetup

As a part of 2021 Team SUNY Oneonta’s collaborative efforts, we participated in a regional meet up. The Teams that participated in this meet up were Team University of Rochester, Team Cornell and Team SUNY Oneonta. The goal of this meet up was to present our projects. We learned about the projects each team chose for this year’s competition, along with why they chose their topic. This served as a testament as to how synthetic biology can be used in a diverse array of fields and/or topics.

An additional goal of the meet up was to garner advice from other team advisors. The advisors provided individual feedback on each team’s project, along with advice on competition etiquette and helpful tricks. The advice served as helpful reminders as to how we would choose to present our own project to the best of its ability.

Below is a portion of the advice given to us by Team Cornell and Rochester:

• Showcase a farmer using our prototype
• Don’t link to outside pages on your wiki
• List all parts on your registry page
  • A mini wiki for each part (description, use, additional characterizations)
• When speaking to judges remain practical and professional, a little laid back is okay but not too much

Collaboration With Team Linkoping

Over the course of the summer, the iGEM team representing Linköping University in Sweden, reached out to our team asking to participate in a collaboration. Upon meeting, both teams jointly decided to partake in a series of collaborative efforts due to our project topics falling within agriculture. Our main goal was to gather background knowledge on the impact our respective issues have, in a country different from our own.

Interview Exchange:

To accomplish our goal, both teams decided to create a series of interview questions related to our topics. Team SUNY Oneonta drafted questions that touched on cattle diseases and genetic testing. Team Linköping drafted questions that spoke about water shortages and resources. We aimed to exchange the interview questions so that Team Linköping can gain insightful data about water shortages farmers experience in rural New York, and Team SUNY Oneonta can learn about the steps farmers in Sweden take when encountering cattle diseases and breeding decisions.

The interview questions were then promptly exchanged. However, both teams encountered difficulties in garnering responses to the questions, halting progress on the collaboration. Nonetheless, we have documented the process of our coll aboration, which can be seen below.

Collaboration With Team Rochester

As part of our search for new targets, we had difficulty accessing the sequence for the transposon ERV2-1, as this DNA sequence is not annotated on the NCBI database. This transposon has been inserted into the APOB gene, creating a new allele, APOB CD. APOB CD which causes cholesterol deficiency. We discovered another database which contains this sequence, Repbase (1). Our school does not have a subscription to this database.

Fortunately, we discovered that the University of Rochester does subscribe to Repbase. We asked Team Rochester to search Repase and download the sequence for the ERV2-1 transposon, and they were able to send us the file. Thanks to them, we were able to reconstruct the APOB CD allele using the APOB wildtype sequence from NCBI and the ERV2-1 sequence from Repbase. This allowed us to have a fragment of this allele synthesized for use as a positive control in our genetic testing system.

1. Bao W, Kojima KK, Kohany O. 2015. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile DNA. 6:11. doi: 10.1186/s13100-015-0041-9.

Lesson Plan Collaboration with Team TU Eindhoven & iGEM Aachen

For this year’s competition, we collaborated with Team TU Eindhoven & iGEM Aachen on creating a set of science lessons for elementary students. We contributed a lesson plan that we developed as part of our education outreach activities to this book. The goal of the book was to introduce children to some basic concepts in the field of chemistry and synthetic biology. Children can explore chemical phenomena in an interactive and fun way by conducting hands-on science experiments.

The SUNY Oneonta team was very excited to conduct an education outreach program called the “Liquid Nitrogen Ice Cream Lab”. This program’s target age group was fifth grade (10–11 years old). The hands-on program covers thermodynamics and how molecules are impacted to create a solid, liquid, or gas. Furthermore, predicting the outcome when the application of heat or pressure is added. Students were able to draw conclusions based on the trends observed in thermodynamics

Our objective was to spark interest in science while fulfilling New York State learning outcomes. Students exercised their understanding of the scientific method by observing, predicting, and recording results. The focus of the lesson was on understanding the different states of matter: solid, liquid, and gas, as well as comprehending changes of state in matter including melting, evaporation, sublimation, and freezing.

The program was divided into three components: a presentation, workshop stations, and a challenge. The presentation consisted of a slideshow that was presented to the students introducing the concepts demonstrated by the activities. Team members took turns presenting the different sections of the slideshow. The workshop section consisted of four demonstration experiments illustrating changes of physical state in matter. Student participants were divided up into four groups and rotated from station to station. At each station, students made observations, developed hypotheses, conducted experiments, drew conclusions, and reported their work in a worksheet for that station. The challenge consisted of a survey that was administered to the students before and after they participated in the presentation and workshop stations. The purpose of the survey was to assess prior understanding, and then measure any learning gains that were achieved through the program.

More information about this collaboration can be found in the science lesson plan document and in the Educational section of our wiki.