Week of July 24 - 28
Early Monday morning, we had a Skype call with Team SCU China while we were visited by REM (our lab had no major infractions!). In the wet lab, we continued our preservation protocol, inoculated for the interlab study and hardware testing, miniprepped, digested, and ran a gel of the upper operon. We also tested our chloramphenicol and ampicillin antibiotics to ensure they are working efficiently, as we have had contamination issues in the past few weeks. In the dry lab, we combined all parts of the mathematical model into one Python script and completed the Interlab Study Day 1 Survey. Additionally, our Experiment campaign was extended by a week!
Tuesday, we continued the preservation protocol, performed a Gibson PCR check on the AtpIp promoter, and miniprepped and digested the lower and upper operons. We met with Dean Fernandez to update him on our progress before lunch and in the afternoon we set up the Interlab Study samples to be checked by the plate reader overnight. In the dry lab, we created a framework for the mathematical model to contain all the parameters for the full-scale model, which will soon be filled in by what we find in our experiments and in further literature searches.
On Wednesday, we continued the preservation protocol and finished adding all content from our old website to our new one! Though it is still under construction, click around and check out the work so far! Our survey was distributed via Amazon MTurks and we started receiving responses. In the wet lab, we transformed the upper and lower operons and gBlock 4 and miniprepped GFP and the upper operon. We ran a gel for the products and performed an MIC50 iteration. Finally, we tested our nebulizer again. In dry lab work, we re-introduced a varying time step into the mathematical model and incorporated data from the preservation protocol. We also used Cotter’s Method to determine the most sensitive parameters of the model.
Thursday, we worked on the preservation protocol and inoculating colonies from both the upper and lower operon. We analyzed the hardware testing results and began documenting survey responses in an excel spreadsheet. Additionally, we miniprepped the GFP, digested it, and ran it through a gel. Finally, we modifed the model to allow for a constant benzene uptake from the lung and bacteria.
On Friday, we continued the preservation protocol, worked on the calibration curve for the Interlab Study, and looked to improve the MIC50 assay. We inoculated RFP and GFP and miniprepped
thirteen tubes!!! In the dry lab, we researched the relationship between biomass and growth rate along with glucose and benzene uptake. Finally, we analyzed the survey responses.