Week 1

6/24/13
At the end of the weekend, we had a list of four separate ideas. Each of these ideas also had a rough timeline for each of them. Each of these ideas were discussed with our advisers, Dr. Siegel and Dr. Tagkopoulos. The first idea involved a more complicated idea of producing multiple pigments in bacteria with different wavelengths of light. We also proposed an idea involving riboswitches and TAL repressors, a protein batch reporter device, and a means of detecting multiple RNA transcripts with different RNA fluorophores. We narrowed down the number of possible projects to the riboswitch and TAL repressor idea and the protein batch reporter device. While recognizing the pitfalls of either idea, we tried to develop them further in order to better assess their feasibility.

6/25/13
We began researching different endoribonucleases that would function for our protein batch reporter idea. In addition, Amy spoke to Dr. Yokobayashi, an expert on riboswitches and gave further insight on either potential project. He did not see the incentive in pursuing the protein batch reporter project if GFP tagging could accomplish the same goal.

6/26/13
We began leaning towards using TAL repressors and riboswitches in a way that would provide a foundational advance for future iGEM teams. We continued reading the literature on the most reliable riboswitches. Ideally, we would like to use a riboswitch with the greatest amount of change in repression in the presence of a particular inducer. Dr. Tagkopoulos also gave us some input on computational modeling that could be carried out with our TAL repressor library.

6/27/13
After deciding on the TAL repressor and riboswitch idea, we began constructing a timeline and considered different lab protocols that would help us generate a library of different riboswitches. In addition, we further elaborated on the incentive of generating a library of riboswitches that would be in conjunction with different TAL repressors. First, three different TAL repressors will be used with the same theophylline riboswitch. Then, we plan on varying the theophylline riboswitch with different ribosomal binding sites. We also discussed different We were also given a tour of the lab and informed about the safety protocols that would have to be followed while working on the project.

6/28/13
On Friday, we clarified which Biobricks that we needed to hydrate for next week. In addition, we decided on which parts would be obtained from other labs in our facilities. We went over the general timeline and aims of our project with Dr. Facciotti. The hypothetical construct involving our TAL repressor and riboswitch was also drawn out with GFP as our reporter.