Team:Northwestern/Notebook/June

Week 1

6/17 - We started our iGEM bootcamp by shadowing Will Bothfeld (our primary graduate student TA) during ligating, transforming and working with DNA software. In addition, we learned the fundamentals of primer design, colony PCR and gel electrophoresis. We ended by continuing research and discussing all of our projects of interest.

6/18 - To start our day, we narrowed down on project ideas to CRISPR-Cas system, quick quench GFP, and non-model organisms; we then discussed their individual pros and cons. During our meeting with Professors and graduate students, we had an in depth discussion on this topic as well as laboratory logistics such as lab equipment and our summer budget. With this information and guidance, we were able add to our initial thoughts on each of our potential projects by starting corresponding flowcharts of events.

6/19 - All team members finished necessary safety training modules online to partake in wet lab work. We then cleaned the lab and organized materials/equipment. Will proposed a problem to us regarding primer design that we worked on first individually and then collaboratively to compiled an answer to for later review.

6/20 - After learning the basics of and observing plate reading, we compiled a series of protocols that we felt would be important to have before getting starting on DNA cloning first-hand. We also updated our lab shelves and freezer inventory thoroughly to get a sense of what we should be ordering and asking in our sponsorship emails.

Week 2

6/23 - In the morning, we had a meeting with a TA, Karthik Sekar, to discuss the iGEM registry and parts along with how to use them. Following that, we had a meeting our professors and grad students in which we learned more about the project of non-model organisms. After our meeting, we made LB Mix and discussed which project to pick- non-model organisms or quenching GFP. In the end, we came to agreement to do our project on non-model organisms by having E Coli and yeast as our controls and other strains of bacteria and fungi as our non-model organisms. We would test out how promoters would differ in their activity across all these strains by the use of GFP.

6/24 - Throughout the day, we sent out emails to sponsors for lab supplies. We also worked on a problem that Karthik gave us to do in which we had to construct a plasmid with an origin of replication and a PhoP promoter controlling PFP expression as the insert using iGEM registry parts. We also started cloning with Will.

6/25 - We took an inventory of the chemicals we had from before in our lab and of the contents in our freezers. We met with Karthik again to discuss the solution we came up to the problem he gave us to do. In addition, we brainstormed project titles and created a tentative timeline for the summer. Lastly, we read a paper by Paul Freemont of the Imperial College of London that talked in detail about cell free systems being accurate representations of E Coli cells.

6/26 - This day had relatively more wet lab work. We started by running PCR, and then running a gel for 1000 base pairs to confirm if the PCR worked. After analyzing our results, we researched promoters that we could potentially use to test for our project. We also searched for professors and labs around campus from which we could get strains of non model organisms. The final task we did was shadow Dr. Jian Li, a member of Jewett lab who showed us how to collect cells for lysate preparation and observation.

6/27 - We started our day at the Jewett lab where a grad student, Rey Martin, showed us how to lyse E Coli cells and perform extract. We made another gel and tested for ladders. Meanwhile, some members of the team made M9 media and then autoclaved it. Two of our members met with a representative of IDT to talk about buying their products. Lastly, we continued researching promoters and reaching out to labs asking for non-model organisms.

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