The Ontario Genetically Engineered Machine Network (oGEM)
Queen’s Canada attended the annual oGEM meeting hosted by the McMaster University. We had the pleasure of being in the company of iGEM teams from the Universities of Toronto, Guelph, Waterloo, Brock, Ottawa, and Western Ontario. McMaster iGEM Team directed the conversation on the awareness and challenges faced by the synthetic biology community in Canada. The lack of self and social awareness in the community was thought to be caused by the fact that synthetic biology is indeed an interdisciplinary subject and it requires expertise in all branches of science and engineering. It is quite difficult for such a large multidisciplinary group to recognize themselves, and other members as one of their own, leading to the absence of communication and combined resources. On top of that, as a newly emerging field of study, synthetic biology has yet to be clearly defined. The general public might have the foggiest idea what this community aims to achieve, and misconceptions about genetic engineering continue to cause fear and resistance in the society. The rest of the conversation was dedicated to devising solutions to these challenges. Firstly, it is important that the synthetic biology community finds a suitable definition for its work which would be agreed by all of its members. The second focus shall be improving education at the undergrad level to increase student interests in synthetic biology. All the iGEM teams present were very eager to share their experiences in recruitment and outreach, members from the University of Western have especially shared their path of creating a program for synthetic biology at their university. The discussion was concluded with remarks on actions to be taken to gather resources and suggestions for future Canada-wide conferences.
Team Stony Brook
Directed Evolution: Queens iGEM & Stony Brook iGEM Collaboration
This project sought to perform some sort of directed evolution on our constructs. While reading about other team’s projects, we came across a fellow iGEM team located at Stony Brook University in New York was evaluating the use of directed evolution of Synechococcus elongatus to create sustainable sucrose feedstocks for ethanol biofuel production. This discovery created the basis for further discussion about which protocols are most efficient when performing directed evolution. Upon speaking with our fellow iGEM team, we learned about other directed evolution techniques, such as UV mutagenesis and phage assisted continuous evolution. With these ideas in mind, we collectively decided that other teams may also be trying to determine the most effective type of directed evolution for their project and thought we could combine each of our groups’ knowledge and experiences to aid future iGEM teams. We believe that an effective route to convey this information would be in the format of a short, detailed video, that both of our teams could collectively contribute to, as well a pamphlet highlighting a variety of directed evolution techniques, available resources and current literature.
Check out our Directed Evolution pamphlet below and download it here.
University of Calgary Collaboration
Members of the University of Calgary iGEM team, and members of the Queens Canada team were selected as winners of the Canadian Reduced Gravity Experiment Design Challenge (CAN-RGX), a Canada-wide competition run by the Students for the Exploration and Development of Space (SEDS), in collaboration with the National Research Council, and Canadian Space Agency. This provided an unpresented opportunity to collaborate, and facilitate discussions on genetic engineering, engaging students in STEM research and competitions, and biomedical sciences education in Canada. Members of the University of Calgary team and Queen’s Canada teams have met up multiple times, and had skype calls to share ideas and troubleshoot problems, including strategies to synthesize complex gene fragments, accessing university funding, STEM research at Canadian universities, laboratory techniques, check-ins on each others progress, the difficulties of performing life sciences research in zero gravity, and plans for helping to share the fantastic learning opportunities that iGEM and CAN-RGX provide for ambitious science students. We have had nothing but great experience working alongside the University of Calgary Team, and we wish them success at the 2018 iGEM Jamboree!
After being graciously awarded an Opentrons OT-2 automatic pipetting robot, we were eager to find other teams that we could share protocols and tips with. Speaking with iGEM Makerere, we both had a lot of questions surrounding wet lab protocols, dry lab modelling, and practical applications of our respective projects that could be answered by the other team’s diverse knowledge and unique experiences. For example, the Makerere team stated that a metabolic by-product of the degradation of plastics by microbes is ethylene glycol, however they couldn’t decide on a practical use for this by-product. As Canadians, we know ethylene glycol well, as it is the major component of antifreeze for windshield frost in the winter! We suggested that their by-product could be used in cryopreservatives here in Canada. Above all, our teams agreed that because the distance between us would making sharing resources difficult, we could however proof-read each others work, give suggestions on standard operating procedures, and aid in general scientific dissemination. This has included presentations to each others teams, and providing feedback wherever needed. Ultimately, through various Skype calls and email exchanges, members of both our teams were able to assist the other with different aspects of the projects. Our outreach teams often had calls together to share our plans for outreach events, and public dissemination of current science that it would be easy accesible to the general public. Our dry lab teams were able to collaborate with various 3D modelling techniques in PyMOL, help with Opentrons OT-2 protocols, as well as wiki formatting.
University of Toronto
It's a warm feeling to have a great friend so close by. The University of Toronto, and Queens Canada teams became friends at the oGEM meeting (see above), and we continued conversations and support for one another all the way to the jamboree. The University of Toronto team were there for us for 1am cloning troubleshooting, theoretical conversations about synthetic biology, and selecting E. Coli strains. This friendship evolved into a collaboration when we provided the University of Toronto team with their Wiki, by providing the services of our graphic design and wiki teams. We developed graphics for them based off sketches they drew, which can be now seen on their homepage and throughout their wiki. In exchange, University of Toronto provided us with a gift of a pSB1C3 vector with a unique nucleotide sequence (UNS) flanking the Biobrick Prefix and Suffix. We are extremely grateful for this gift because it allows for easier Gibson Assembly, and therefore construction of biobricks. Gibson Assembely relies on overlaps of >15bp between the vector and the insert without majorly repetitive sequences. Since NotI is found in both the prefix and suffix, this can result in poor assembly of inserts. The UNS sequence designed and created by University of Toronto allows for PCR linearization of the vector, and then highly efficient Assembly. We are thankful to University of Toronto for their friendship and help, and we look forward to seeing them at the Jamboree!
Queen's Biomedical Innovation Team (QBiT)
The Queen’s Biomedical Innovation Team is an undergraduate student-run, interdisciplinary design team that focuses on biomedical device design and innovation. This year QGEM has collaborated with QBiT in the production of a pacifier devicer which will utilize our engineered protein construct for the detection of salivary analytes. Features of the pacifier design include:
- A one-way valve nipple to passively collect saliva from the infants mouth, while preventing any backflow of the engineered protein from the internal components towards the infants mouth.
- A circuit board containing a photon-counter chip, a battery, and a Bluetooth Low Energy Beacon. These three components allow for the detection of bioluminesce produced by active luciferase, the transmission of this data over Bluetooth Low Energy to a smartphone device.
- A 3D printer polylactic acid polymer casing.
Queen's Reduced Gravity Experimental Design Team
The Queen’s Reduced Gravity Experimental Design Team is an undergraduate student-run team which will be participating in an upcoming flight mission in collaboration with the National Research Council, Canadian Space Agency, and Students for the Exploration and Development of Space in July. QRGX are winners of the Canadian Reduced Gravity Experiment Design Challenge (http://seds.ca/projects) and have been selected to conduct an experiment comparing DNA Polymerase I processivity and error rate in microgravity vs normal gravity. This year QGEM will be accompanying them on their flight mission and providing them with technical expertise and access to our laboratory equipment.