Team:Austin UTexas/Attributions

Attributions

The UT iGEM team transformed 497 parts from the iGEM Registry into DH10B E. coli containing the burden monitor and assayed the growth rate and GFP expression rate of 330 of these parts. We then ran these measurements through our R pipeline and identified burdensome parts by observing percent reductions in growth rate. Additionally, we determined the type of burden created by each BioBrick using changes in genomic GFP expression.


We would like to thank the following individuals and organizations for all their help with our iGEM project throughout the year:

(Red names indicate team members while black names indicate non-members.)

Transforming BioBricks into E. coli

  • All team members participated in the transformations of BioBrick parts into E. coli.

Burden assays

  • Diya Bhat measured the burden of the Anderson series parts.
  • Noor Radde worked with Ginny Mortensen to complete our evolutionary stability experiments.
  • All team members participated in running burden assays.

Coding and Modeling

  • Dr. Jeffrey Barrick wrote the R Script code we used to analyze our burden measurements.
  • Ginny Mortensen made edits to the script to update it and fix potential errors. She completed all of the data analyses using the updated R scripts. Ginny also worked on the entire modeling aspect of our project.
  • All team members were trained to use the R code to run analyses of the burden assay results.
  • Sean Leonard helped the team troubleshoot some errors we encountered when running the code in R.

Next Generation Sequencing

  • Daniel Deatherage sequenced our parts using iSeq, allowing us to later verify our sequences against those provided on the iGEM Registry.
  • Angela Pak completed the Breseq analysis of our sequencing results.

Improving a Part

  • Kelsey Hu and the UT 2015 iGEM Team originally redesigned the SYFP2 plasmid. However, they never fully characterized the new part nor did they submit it to the registry.
  • Anna Bardenhagen measured the expressions of both the original and redesigned sequences and created the figures found on our "Improve a Part" page. Alex MacAskill wrote the wiki page and created new biobrick part pages in the iGEM registry.

Human Practices Support

  • Jordan Clements worked with Emily Garcia on the human practices aspect of our project. They contacted various members of the synthetic biology community in Austin to discuss the implications of our research.
  • Brian Renda offered his time to talk with us about the applications of synthetic biology. Specifically in the area of evolutionary stability.
  • Thinkery’s Building with Biology provided us with the opportunity to teach the Austin youth about synthetic biology. Shireen Shah and Jordan Clements volunteered at the Thinkery’s biology event.
  • Arts in Sciences and Painting provided us with the opportunity to talk about Synthetic Biology on our campus with students, staff, and faculty as a part of UT's Natural Science week. Emily Garcia and Michelle Chang volunteered at the natural science week event.

Wiki Support

  • All team members helped create our wiki.
  • Angela Pak created the template for the wiki.
  • Noor Radde and Diya Bhat took the lead in creating, updating, and finalizing our wiki pages.

Poster Presentation

  • Diya, Angela, Jordan, Ginny, Noor, Shireen and Alex all worked on the creation of our poster.

Oral Presentation

  • Shireen Shah created a presentation and shared our project at the UT Fall Undergraduate Research Symposium.
  • Noor Radde , Diya Bhat and the rest of our team offered support and advice regarding the presentation.
  • Dr. Dennis Mishler and Dr. Jeffrey Barrick mentored us for the oral presentation.

Collaboration

  • Jordan Clements , Ginny Mortensen and Noor Radde initiated our collaboration efforts with iGEM teams of the following universities:
    1. Texas Tech University
    2. Rice University
    3. Michigan State University
    4. University of Texas at Arlington
  • These four universities worked with us to exchange data and genetic parts for measuring burden.

Funding

  • BEACON and Barrick Lab provided the funds necessary for completing our work.

Project Advisor Support

  • Dr. Jeffrey Barrick, Dr. Dennis Mishler, Sean Leonard, and Matthew McGuffie advised us on our experiments and data analysis.

Lab Support

  • Barrick Lab provided its lab space and equipment for us to carry out our experiments.

We began brainstorming our iGEM project in January 2019. The University of Texas at Austin provided two courses (in the 2019 Spring and Fall semesters) to help guide our project development. The syllabus and course materials for these courses were released on Canvas for the participating students to reference. Wet lab work began in February 2019.