Team:Calgary/Attributions

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Attributions

Accomplishements

Over January to April of 2017, our team got together for the first time over weekly meetings. As the majority of our team had no synthetic biology or iGEM experience, we spent a lot of this time learning about what synthetic biology is and how it works, as well as the infrastructure of iGEM. Over this period, our mentors (composed of some 2016 iGEM team members) held presentations to explain the parts registry, what human practices entails, Wiki requirements, and general iGEM advice. At this point we also began looking into previous team's projects to get an idea of what is possible. A portion of this time was also dedicated to each team member acquiring research funding for the summer.

In mid March, we decided on pursuing PHB production from E. coli to be used in wastewater systems, and the rest is history. Despite taking a large portion of April off for exams, we were able to do some literature search about our proposed methods to get a better idea of what our project will entail. In May, we began working full time, splitting our work between the lab, literature research, as well as all the other iGEM requirements such as human practices, fundraising, public engagement and Wiki design.

This is a paragraph about what the team accomplished!

General Support

Dr. Mayi Arcellana-Panlilio: Our fearless leader, Dr. Mayi was our primary supervisor over the summer. She guided us in every step of the project, from idea development to final result. Our team would not be where we are without her!

Dr. Elke Monika Lohmeier-Vogel:

Dr. Andres Nygren:

Dr. Craig Jenne:

Dr. Fabiola Aparicio-Ting:

Brad Prince: Provided us with the cost analysis of PHB production, specifically, how much media is required to produce one kilogram of plastic, and how profit it could make. Offered general support on presentation and design, as well as the user interface of the 3D PHB Simulator.

Rachelle Varga:

David Feehan:

Bruce Ramsay & Polyferm:

Deirdre Lobb: Helped ensure that all of our lab work was performed according to safety standards, and assisted in getting the whole team certified with all safety courses. Also collaborated with our team to keep lab risk at a minimum by encouraging us to look towards alternative forms of human feces - this led us to finding the NASA recipe for syn poo.

Elena Fekete, Sid Goutam, Syed Jafri, David Nguyen, Nishi Patel, Nilesh Sharma, and Dan Ziemianowicz: All members of the 2016 UCalgary team. They helped with the initial brainstorming of our project, general advice, and gave us need-to-know iGEM tutorials. These included how to use the parts registry, how to set up the Wiki, fundraising suggestions, and possible contacts that we may find useful.

Synthesis & Secretion Support

Dr. Isabelle Barrette-Ng: Assisted with troubleshooting transformation experiments, and also gave advice for proper cloning protocols.

Dr. Sui-Lam Wong: Donated E. coli BL21(DE3) to use as our chassis.

Dr. Richard Moore Donated competent E. coli DH5𝛼 and his competency protocol to make our own competent cells.

Process Support

Dr. Nashaat Nassar:

Matthew Bamsey: Advised

Dr. Peter Dunfield:

Christine Sharp, Marc Strous and the Solar Biocells Lab: Let us use HPLC! Woo!

Wiki Support

Patrick Wu: Provided us with wiki support, especially regarding how to set up templates as well as some formatting and layout troubleshooting.

Modelling Support

Dr. Justin MacCallum:

Dr. Jason de Koning:

Dr. Ian Lewis:

Human Practices Support

Chris Hadfield:

Derek Thomas:

Carol Nelson:

Pascal Lee:

Marko Markicevic: Provided us with detailed information about the regulation and testing performed during the wastewater treatment process, as well as the VFA concentrations. This information confirmed that using wastewater as a feedstock was feasible, but not the proper application for a pure culture of genetically engineered bacteria.

Minds in Motion: Gave us the platform to speak with Grades 4-6 and 7-9 campers about synthetic biology and expose them to some fun, hands on learning activities.

Pine Creek Wastewater Treatment Plant: After touring the plant and consulting with their employees, we realized that a synthetic biology application into existing wastewater treatment plants was not feasible. We started looking towards alternative applications after our visit.

Biology Graduate Student Association and Beakerhead:

Telus Spark:

Team Involvement

Alex: Worked on development of applied design through exploration of NASA’s Baseline Values and Assumptions document and process assumptions through the Equivalent System Mass toolkit. Conducted experiments on the solid-liquid separation and PHB fermentation stages of process design. Led Minds in Motion summer camp workshops and Contributed to human practices by developing the education material and lesson plans for the grade 5-6 and 7-9 Syn Bio workshops.
Alina: Alina worked on process development, conducted experiments to determine the optimal operating temperature and duration for the VFA fermentation stage and to test PHB production under different fermentation conditions, and worked on quantification of VFA and PHB using HPLC and titrations. Alina has also helped with flux balance analysis using MATLAB and organized meetings with experts in the space industry.
Amy: Part of the synthesis and modelling subgroups. Contributed to the background literature search to design genetic constructs. Helped design the genetic constructs used for synthesis. Cloned constructs into pET29b(+) vectors and, performed confirmation digest and confirmation sequencing. Synthesized and extracted PHB to be used in HPLC analysis. Ran SDS-PAGE experiments to confirm the production of protein in the transformed E. coli. Provided insight into the biological pathways to include and manipulate for mathematical modelling.
Atika: Part of synthesis and modelling subgroups. Worked on ligation of IDT geneBlocks and cloning the DNA into E. coli (BL21). Carried out experiments for synthesis of PHB. Looked into flux-balance analysis for synthesis of PHB and developed an initial model, which contained phaCBA genes to predict the optimal pathway for PHB production.
Bilal: Worked on securing corporate sponsorship for the team, and helped secure donations for the Space Slam fundraising event. Researched solid-liquid separation and PHB extraction, as well as liaising with experts and sponsors.
Helen: Part of the Synthesis group and helped to design and codon optimize constructs for synthesis and cloned constructs into pET29b(+) vectors. Took charge of iGEM team collaborations including the first Canadian iGEM newsletter and wet-lab work with iGEM McMasterU..Delivered a Synthetic Biology talk at Sir Winston Churchill High School, as well as the Minds in Motion workshops.
Jacob: Worked on the development and implementation of the PHB secretion phasin-HlyA Biobrick. Cloned secretion parts into the appropriate plasmids, assisted with PHB production and extraction, and performed the InterLab study.
Kaitlin:Helped design the secretion parts and clone them into our E. coli. Created a “super” plasmid with both PHB-producing and PHB-secreting genes, which was used to carry out secretion assays. Conducted research to identify barriers to synthetic biology for human practices, participated in the Minds in Motion workshops, Beakerhead Petri Dish Picasso, and the Telus Spark Adults Only Night.
Lalit: Helped design and codon optimize the parts for the phasin-hemolysin secretion construct. Conducted SDS-PAGE experiments to identify the production of the phasin proteins. Attended various meetings for integrated human practises and public engagement activities through high school visits and the Telus Spark Adults Only Night.
Maliyat: Researched possible extraction methods for PHB and ran lab experiments to test these methods as well as possible quantification methods. Worked on developing and testing lab protocols for measuring volatile fatty acids and PHB on an High Performance Liquid Chromatography column.
Michaela: Designed and programmed the wiki. Created the 3D PHB Simulator program in Unreal Engine, and participated in outreach activities such as the Minds in Motion summer camp. Led the team in fundraising efforts, particularly the Space Slam fundraiser, and worked with the Human Practices team to organize tours to the wastewater treatment plants, and as well as interviews for various industry professionals.
Preetha: Helped to codon optimize constructs, clone constructs into PET29B vectors, and ran experiments to characterize constructs for the synthesis subgroup. Led the team in human practices efforts: attended interviews with experts, organized outreach events (such as TELUS Spark Adults Only Night showcase and the Master’s Academy talk), and identified barriers to accessing synthetic biology. Also organized the production of the iGEM Manual video series script.
Sam: Designed, codon optimized and removed restriction sites from the hemolysin-phasin secretion construct. Cloned in the DNA and performed assays to measure PHB secretion. Completed the interlab study (including its affiliated wiki pages) and performed general lab duties such as creating competent cells and preparing empty plasmid backbones. Participated in the high school outreach component of human practices.
Tricia:Helped design the synthesis constructs. Developed branding for the team and project including logos, uniforms and promotional material. Designed graphics for the presentation, wiki, poster, and the deliverables used in workshops to engage and educate the public about synthetic biology. Designed the cover pages for the Canadian and International iGEM Newsletters and created a Sponsorship Package design with a template that is open to the public to use. Participated in a Minds in Motion Workshop during the summer.