Team:UGA-Georgia/Collaborations

• HOME
• TEAM
• PROJECT
  • Description
  • Experiments & Protocols
  • Results
  • Design
• PARTS
  • Team Parts
• NOTEBOOK
• ATTRIBUTIONS
• COLLABORATIONS
• HUMAN PRACTICES
• SAFETY
• MODELING
• MEASUREMENT
• SOFTWARE

Collaborations

ARCHAEAL COLLABORATION STUDY: HOW WE DID IT

STEP ONE: THE IDEA

We were interested in signing up for the E. Coli. collaboration study earlier this year, but were disappoint to learn that our archaeal study could not contribute to the Interlab’s framework. This led to our idea to create a new InterLab study of our own utilizing our labs methanococcus mCherry stocks.

STEP TWO: INITIAL PROPOSAL

Since early 2015, the University of Georgia iGEM team has been working on establishing a sound, effective, and universal protocol and logistics system to circulate mCherry samples on a largescale circuit for fluorescence measurements. We decided to contact iGEM headquarters officially early June 2015 with a formal proposal to motion for a new Archaeal InterLab study modeled after the current E. coli InterLab administered by iGEM. We suggested that we send out our own collection of mCherry protein extracts from our methanococcus experiments. iGEM Headquarters and the Measurement Division advised us to pursue a sort of ‘pilot’ InterLab, which we began calling the Archaeal Collaboration Study.

STEP 3: PREPERATION

After a few weeks of carefully refining our proposal, gaining proper clearance from the biosafety office, developing the shipment system, creating registration and data input forms, and creating a universal protocol for measuring mCherry protein florescence, we were ready to contact an assortment of iGEM research teams across the United States gauging general interest in our collaboration study.

STEP 4: GAUGE INTEREST

An assortment of teams across the United States were contacted with our proposal and an invitation to join the collaboration effort. We were truly inspired by the level of interest we received from the feedback and began to slowly build up the network of participating teams we have today. Slowly but surely, we built up a network of 9 participating teams: University of Georgia, Massachusetts Institute of Technology, Stony Brook University, University of California at San Francisco, Carnegie Mellon University, College of William & Mary, Genspace, Columbia University, and Vanderbilt University. We can’t thank our participating teams enough for their support and efforts toward our study.

STEP 5: DISTRIBUTION

STEP 6: STATISTICAL TESTS ON DATA

We standardized all team data inputs based on the average UGA M3Z1 flourescence unit data and created a matrix of this data. We then realized outliers were present in the matrix and ran an Extreme Studentized Deviate test to identify the outliers. After this was done, we created a new matrix similar to the initial matrix, with the numbers adjusted to ignore the outliers. Our data can be seen on our Measurement page.

STEP 7: WHAT THE DATA MEANS

From the collaboration study, we’ve gained priceless information about the reliability and reproducibility of our study, and cornerstones of the scientific method. Our collaboration study not only functions as a system of support that adds validity to our findings with the work we’ve done in the lab—it also only functions as an educational teaching tool that has brought awareness of the capabilities of methanococcus to anyone that read our proposal and knowledge of the methods of reading mCherry fluorescence. In addition, we believe it helps the scientific community as a whole. By creating the logistics and protocol schedule, we’ve created a system that can be used by anyone to distribute protein samples of any kind; provided minor alterations to the protocol be made if a group were working with another type of RFP or GFP. The information we’ve gained from this collaboration effort has been priceless and we’d encourage any team to try to implement our setup into their own study.

STEP 8: THE FUTURE

As for the future of the collaboration effort, we would like to send out recombinant cells for teams to observe the archaeal cells with a fluorescence microscope. Also, we would once again like to try to create an official iGEM Archaeal InterLab study to run side-by-side with the E. coli InterLab study. We strongly believe our ‘pilot’ collaboration study to be a huge success and would like to take it to the next step.