Team:British Columbia/Notebook/Brainstorming

Brainstorming

A week after the UBC iGEM 2011 team was formed, we got together at the beautiful Michael Smith Laboratories and brainstormed potential synthetic biology projects. These were some of the ideas and topics floating around:

• Optogenetics
• Chemo-signalling (using antibodies as signals)
• Re-routing networks (creating fusion proteins that make extra interactions to interfere with natural protein links)
• Eradicating bed bugs
• Eradicating pine beetles
• Tackling battery waste
• Photo-dynamic inhibition (bacteria are killed by light)
• Using bacteria to clean water
• Using probiotics to tackle cholera
• Temperature-sensitive inteins

Each team member brought an idea home and did background research to determine how feasible these ideas were. After more discussion, we came down to deciding between (1) cloning cholera receptors into probiotics and (2) transforming microbes with pine beetle pheromones to gather and eradicate pine beetles.

From left to right: an electron microscope image of Vibrio cholera, a view from Mount Fraser of the pine beetle infestation and dying red trees.

Everyone was passionate about the pine beetle project because of the relevant applications to the forests of British Columbia. Further, there is expertise close at home to collaborate with. Returning team members learned that it was difficult to obtain resources and hard to collaborate with scientists who were not in the same province (and country).

We established what we already know from the research we've done as well as gaps of knowledge. Some of our team members searched and contacted people relevant to our project to further discuss our project's feasibility. We also briefly discussed the objectives of our project.

May 9 2011

Dr. Joanne Fox begins a week of iGEM laboratory training in AMBL, the teaching lab in Michael Smith Laboratories. The training sessions run from 10am-4pm; Joanne provided short lectures so everyone understands the magic that goes on behind the actual bench work. Today, those present learned about restriction digests, and then set up restriction digests of the insert and vector in the morning. In the afternoon, we learned about purification kits, CIP assays, and ligation.

May 11 2011

Marianne and Vicki (returning team members) went over labeling etiquette, lab book organization, and the 3-antibiotic method in the morning.

In the afternoon, the team returned to AMBL to conduct transformation experiments on Monday's ligated parts.

May 12 2011

We did plate analysis, and started a culture for plasmid preps. Not everyone had colonies on their plates, so some had to steal others' colonies to start the culture.

In the afternoon, the team met up to discuss the pine beetle project in more detail - the objectives, the future applications/implications, the parts we need, the wet lab, modeling, and human practices components.

May 13 2011

We mini-prepped the plasmids.

May 16 2011

Mondays are when we have our weekly open lab meetings where interested faculty members/advisers as well as iGEM club members attend to hear about our project, provide any input/guidance. Today, we presented our project proposal to our advisers. The next step is to obtain all our necessary parts (Chris Keeling is generously giving us synthases) and to further develop our human practices and modeling routes.

May 18 2011

Our first iGEM team social = bonding time! We all went to the Indian Oven to have dinner, discuss our project, and watch a part of the hockey game (Go Canucks!). It was semi-productive (in terms of project discussion).

May 23 2011

We had our first modeling meeting at Blenz. Our modeling adviser, Shing, provided guidance on modeling the monoterpene production by yeast (model 1). Model 3 (google Earth) was briefly discussed and model 2 (protein homologue). Action items were established, and interested team members volunteered to work on a specific model: Gurpal and Sam will work on model 1 and 2, while Joe and Jacob work on model 3.

May 24 2011

Because Monday (the 23rd) was Victoria Day, we had our usual open lab meeting today. Prior to the usual lab meeting, Daisy presented Chris Keeling's 2011 Transcriptome Mining paper. We then discussed the methods section, and outlined the reagents, protocols, and any equipment that we may need. Sam and Gurpal found papers from Greece and France that used other genes (mutant erg20-2, IDI1) that may aid in increasing the yield of monoterpenes by yeast; they will e-mail the respective principal investigators.

May 27 2011

The team met up to discuss possible tracks, and came up with a "Synthase" track, and an "Extra parts" track. Marianne, Vicki, Daisy, Jacob, and Joe will be on the "Synthase" track, each taking on a different synthase; on the other hand, Laura, Gurpal, and Sam will be on the "Extra parts" track and will be in charge of liaising between us and the PI's in Greece and France in order to obtain the relevant plasmids/genes from them. Vicki will write up the sponsorship package so everyone can begin contacting potential sponsors to obtain more funding.

May 30 2011

We have finally secured a lab space (Thank you Ellis Lab!), and are in the process of moving equipment, unpacking, organizing, and ordering lacking supplies and/or reagents.

The sponsorship package is done, and we brainstormed potential companies/organizations to approach.

Gurpal has started working on model 1. He's found that Matlab would be the best program to use, and has gone through the SimBiology Kit Tutorials. He has also started writing out the biological pathways to produce monoterpenes.

Jacob and Joe have begun researching model 3 and started contacting relevant professors at UBC.