Meet the team

TOP: Tommy Xu, Brent Weatherall, Danny Salem, Matt Chandrawan, Yara Abou-Hamde, Abdus Anwar, Katie Harrison MIDDLE: Lloyd Mai, Kaitlyn Kharas, Nicholas Huang, Sarah Mohand-Said, Linda Dam, Joanne Joseph, Alex Huluta, Peter Doan, BOTTOM: Huy Tran, Dylan Siriwardena, Jenna Khawas, Cory Lefebvre, Martin Hanzel

Wet lab

Dylan Siriwardena, Alex Tzahristos, Shihab Sawar, Sarah Mohand-Said, Martin Hanzel

Dry lab

Lloyd Mai, Peter Doan, Matt Chandrawan

Modelling

Cory Lefebvre, Alex Huluta, Joey Irani, Danny Salem

Policy and Practices

TOP: Abdus Anwar, Nick Huang, Alex Huluta, Katie Harriman BOTTOM: Joanne Joseph, Yara Abou-Hamde, Jenna Khawas, Kaitlyn Kharas, Linda Dam

Graphic Design

Cory Lefebvre, Sarah Mohand-Said, Jenna Khawas, Huy Tran

Shihab

I'm bringing sexy back

Safety

Would any of your project ideas raise safety issues?

Researcher safety: Our lab is a relatively safe one, as the only organisms we use are E. coli and S. cerevisiae, which are considered level 1 Biosafety Containment Agents so are not pathogenic. We do handle Bunsen burners, chloroform and phenol. Therefore, the largest risks that are presented within the lab include potential fires or exposure to fumes. However, the chloroform and phenol are only ever handled in a fume hood so the risk of exposure to fumes is minimized. In addition, all members must pass the university courses for WHMIS, general laboratory safety, biosafety and autoclave handling prior to entering in the lab.

Public safety: The strains that we use in the lab are non-pathogenic. Although we do genetically modify the organisms that we use, they never could possibly make it into the external environment due to the fact that we use decontamination techniques such as autoclaving and bleaching. The organisms that we modify may contain genes that are less advantageous than those seen in wild type strains, as we occasionally knock out genes that have an impact on the metabolism of the organism, such as genes that pertain to adenine metabolism. There are no risks to the biosecurity of different groups of people. The modifications that we make to the organisms that we use in the lab could not possibly cause the organisms to become pathogenic.

Environmental safety: The genes that we modify in the organisms that we use typically impact their metabolic processes such that they are not as "fit" as the same strains in the external environment. The wastes that we dispose are autoclaved first before they are disposed of. The phenol and chloroform waste that our lab produces is shipped to another facility that is designed to handle chemical waste. Overall, the amounts of phenol and chloroform that are used within the lab are so small that there should not be any environmental repercussions if they were to escape from the lab without being sent to a chemical handling facility first.

In order to reduce these risks, we only work with organisms that are of a level one biosafety containment, meaning that they are non-pathogenic. In order to fully assure that the organisms that we do use within the lab do not make their way out of it, we decontaminate any live samples that are used once we are finished with them. This also includes antibiotics, which we sterilize in order denature them so that they do not have any harmful effects on the environment. We do so through the use of sterilization techniques such as autoclaving. Our lab in general is very secure (ie. An access card is required to get into the lab, any side-entrances into the building are locked after hours, and there are security guards stationed within the building,) so there is a very low chance that any malicious persons will obtain access to the genetically modified organisms that are present within our lab.

View the About our Lab and Safety sheets for uOttawa iGEM 2014.

Is there a local biosafety group, committee, or review board at your institution?

The University of Ottawa has a Biosafety Committee that works with the Office of Risk Management and the Vice President of Research to ensure that all biosafety regulations are met. A lengthy description of their role can be found here.

Our lab falls under BSL-1, meaning that no special design and practice features are necessary as we are not working with organisms which are dangerous if ingested or airborne. The sections of the guide dealing with recombinant DNA and genetic manipulation state that most recombinant DNA work is safe, but containment level and pathogenicity should be considered. Containment level is addressed above, and none of the strains we worked with was pathogenic. Therefore, we did not need to discuss our project with the biosafety committee.

All lab members are required to take both a biosafety course and a lab safety course prior to getting their access card for the lab. Each course consists of a full day of lecture outlining risks and necessary precautionary measures followed by a take home exam that is marked by the lecturer. Upon passing the exam, lab members received certificates to verify that they had passed and could work in the lab.

In addition, the Government of Canada has issued a lengthy set of guidelines pertaining to biosafety.

Attributions and Collaborations

uOttawa

The wet lab undergraduate team consists of Dylan Siriwardena, Shihab Sarwar, Alexandra Tzahristos, Sarah Mohand-Said and Martin Hanzel. All members helped construct all biobricks, promoter test constructs, and the final network. Flow cytometry was conducted by all members, with a majority done by Shihab Sarwar and Dylan Siriwardena. Martin Hanzel constructed and tested all E. coli strains used for the Measurement interlab-study. Dylan Siriwardena completed the network designs for the tri-stable switch, with the significant assistance of team advisor Ian Roney and supervisor Dr. Mads Kaern.

The many test strains created for each novel promoter were based upon Ian41, a strain created by Ian Roney. Ian Roney also provided significant assistance with training, day-to-day troubleshooting, and technical advice on many protocols. Our lab technician, Mila Tepliakova, assisted in training, gave indispensible advice on improving our methods, and provided stock solutions throughout the year. Finally, Dr. Mads Kaern provided the team with resources, including reagents, machines, and access to a flow cytometer, as well as providing extensive advice and support.

In fact, the entire Kaern lab provided support for the undergraduate wet lab, including Ian Roney, Afnan Azizi, Hilary Pheonix, Nada Elnour, and Vaibhav Gupta.

The entirety of the web application "Brick Builder" has been created from scratch by Mohammed Chamma, Kevin Rutkay, Peter Doan, Matthew Chandrawan, and Khama Hastick. They are the ones who have enabled the completion of Brick Builder. Mohammed set up the basics of the web app and helped bring iGEM's search tools into Brick Builder. Kevin set the basics of presenting search results and saved parts in the "Brick Bin" in a table. Peter translated RFC methods into computer programming codes and created a GUI for the construction of parts. Matthew helped reorganise the tables and paginated them so as to easily sort and search for parts. Khama created a tool tip for ease of understanding the functions of Brick Builder.

The members of the modeling team Cory Lefebvre, Danny Salem, Joey Irani and Alex Huluta designed, implemented and analyzed the models of our system. Cory Lefebvre was responsible for the design of the deterministic ODE models with the help of Sam Hirniak and John Drake from the Waterloo iGEM team, and Danny Salem was responsible for the design of the stochastic model. Joey Irani performed the model fitting of promoter data from the wet lab and parameterization. Cory Lefebvre, Joey Irani and Alex Huluta performed stability and sensitivity analyses of the deterministic models and Danny Salem did the same for the stochastic models.

Waterloo collaboration

This year, we had the opportunity to collaborate with the iGEM team from the University of Waterloo. We were asked to aid in the construction of three large DNA cassettes into one plasmid.

In order to do so, the uOttawa iGEM team designed a set of primers (6 total) to amplify out each of the DNA cassettes, with overhangs to be used for our labs version of overlap extension PCR. A protocol was written for the uWaterloo team. We also were able to discuss and advise its design and construction.

In return, Sam Hirniak and John Drake from the uWaterloo team helped us design ODE deterministic models for our inducible switch.

Queens collaboration

For the Queens iGEM team, we sent the fusion inducer GEV (gal4 binding domain, human estrogen receptor, and VP16 transactivator) to aid in their design, accompanied with detailed sequence data. We also provided some advice on its use.