COLLABORATIONS

Overview

Duke iGEM is committed to the open and collaborative environment of iGEM. Throughout Phase I and II of our project, we have actively encouraged the growth and development of meaningful relationships with other iGEM teams in our community and across the world.

Phase I Collaborations

Duke x DKU Mini Jamboree

During Phase I, Duke iGEM collaborated with the Duke Kunshan iGEM to host the Duke x DKU Mini Jamboree, which was an opportunity for teams to meet, present their projects, and learn more about synthetic biology. Aiming to facilitate cooperation, we invited 5 iGEM teams from around the world to participate in this virtual meetup:

  1. Wright State (USA)
  2. Ulink College of SIP (China)
  3. Northeast Yucai Foreign Language School (China)
  4. Liverpool (China)
  5. IISER Berhampur (India)

During our conference, we presented a synthetic biology word cloud, facilitated a networking session, and created a synthetic biology Pictionary game via skribbl.io. We also collaboratively created SYN BIO, an educational outreach booklet featuring key synthetic biology terms to introduce beginners to the emerging field of synthetic biology. See our Phase I Partnerships Wiki Page for more details.

Figure 1. Duke x DKU iGEM Mini Jamboree

Additional Collaborations

In addition to collaborating with Duke Kunshan University, we also worked with the following institutions on various education and outreach initiatives (See our 2021 Collaborations Wiki Page for more details):

  1. Warwick iGEM
  2. Wisconsin Lutheran College iGEM
  3. Aix-Marseille iGEM
  4. iGEM Brawijaya
  5. iGEM MIPT
  6. iGEM NITW

Phase II Collaborations

NCSU Education Drive

The NCSU Education Drive focused on talks from local experts in the area. The topics of these talks included whole exome sequencing, gene therapies and CRISPR technology, biosafety, neuroethics, and quantum computing. Kishan Patel and Robert Kaptur from the Duke iGEM team presented about genomics and various -omics technology, gene delivery, and transfection at the iGEM Education Drive.

Figure 2. Duke iGEM participating in NCSU Education Drive

TriGEM - Hosted by Duke University

TriGEM was a joint hybrid research symposium in collaboration with Duke University, North Carolina State University (NCSU), and The University of North Carolina at Chapel Hill (UNC) iGEM teams. Undergraduates from each respective iGEM team presented their progress and plans within the field of synthetic biology. We hosted this “mini-jamboree” to unite the synthetic biology community in the Research Triangle Park area and uplift one another and celebrate the current successes in our research, human practices endeavors, and educational outreach. Watch the Zoom recording of TriGEM here!

Figure 3. TriGEM Flyer

The event started with a synthetic biology networking icebreaker bingo. Attendees had to collect signatures from various people in the room that matched the specific description in each bingo box. They could only have 2 bingo boxes signed off by someone they know, ensuring that attendees would meet new people.

Figure 4. TriGEM attendees participating in synthetic biology networking bingo

After the bingo, Duke, UNC, and NCSU teams presented their iGEM projects. The presentations were done Jamboree style, with a 20-minute time slot given to each team to serve as a practice run before the official competition in October. After each presentation, questions from the Zoom and in-person attendees were answered.

Figure 5. Duke iGEM team presenting

After the presentations from each iGEM team were completed, expert guest speakers gave presentations:

  • Dr. Pranam Chatterjee is an Assistant Professor of Biomedical Engineering at Duke University, Co-Founder at UbiquiTx, Inc, and Co-Founder at Gameto, Inc. He gave a talk about programmable genomes, proteomes, and cell engineering.
  • Dr. Cameron Kim is the Assistant Professor of the Practice in the Department of Biomedical Engineering at Duke University, Assistant Director of Undergraduate Studies in BME, and the faculty advisor for Duke iGEM. He presented about the history of synthetic biology.
Figure 6. Dr. Pranam Chaterjee (left) and Dr. Cameron Kim (right) presenting at TriGEM

The final component of TriGEM was the Synthetic Biology Designathon where attendees split into diverse teams with representatives from each university. Each team was tasked to design an infographic explaining a synthetic biology concept. More information can be found in the Education & Communication section of the Wiki.

Duke & DKU's PCR Troubleshooting Guide

Part 1: Nonspecific Binding

Problem Observation: Too much nonspecific binding in every sample.

Analysis: Possible reasons mainly coming in three flavors:

  1. The primers do not bind specifically in the genome of target organisms. Running alignments between primers and target genome helps identifying if there is other binding site outside our desired region.
  2. The primers bind specifically, whereas the DNA tested contains contamination DNAs that the primers can bind to. In this case efforts should be given to examine the sources of contamination.
  3. The annealing temperature is not optimal. Generally, nonspecific binding takes play when annealing temperature is too low so that the hydrogen bond still forms at the ends even though there are gaps or mismatches in the middle.

DKU:

In our experiments, we hypothesized that nonspecific binding coming from extraneous DNA contamination as aligning primers to yeast genome does not give any strong hit. Combined with the observation that bacteria often grow into lawn on the ampicillin agar plate disregard the concentration we added, we conjectured that the ampicillin is ineffective so that there is extraneous bacteria contamination.

Figure 7. Gel Picture with Nonspecific Binding (DKU)

Duke:

We ran a gradient of 8 temperatures, and we noticed that the band for the highest temperature was the brightest, and that for the lowest tempearture was the faintest. We therefore decided that the highest temperature was the most optimal melting temperature of the sample.

Figure 8. Unfavorable PCR Result with Nonspecific Binding (Duke)
Figure 9. PCR Gradient Used (Duke)

Part 2: Band Brightness

Problem Observation: Band is too bright or too dim.

Analysis: Optimize the amount of DNA loaded into the gel. The problem may be either an overly bright band or a relatively dim band.

DKU & Duke:
Problem Example: Oversaturation of template DNA (results in too many bright, nonspecific bands).
Solution: Dilute template DNA (add ~5ng total). Run a Nanodrop test after extraction and before loading to obtain concentration.

Figure 10. Overly Bright Bands (DKU)

Summary

Similar negative results can be caused by vastly different reasons. Troubleshooting is not an easy process. However, it is important to understand each step of the experiment and do step-wise trouble shooting, after brainstorming the different possible reasons. Collaboration is essential when encountering trouble shooting. When different mindsets combat the same problem, it might open a new perspective!