Week Five - 15 July to 21 July


Advisor meeting 12- 1:30 pm today
discussion points:

  1. Proper design of the primers
  2. Synthesizing the entire A. niger phytase vs. using gBricks
  3. Updated timeline including key deadlines
  4. Updated budget information
  5. Access to the google drive folder for the advisors

To do list:

  • Is using gBricks more cost effective than synthesizing the entire phytase gene?
  • Give the advisors access to google drive
  • Create a presentation for the advisor meeting

We decided on utilizing the gBlocks to construct the Aspergillus Niger phytase gene rather than have the entire gene synthesized


Yuan worked on designing the website. A final design layout was decided on utilizing an easy layout
Grant researched modeling. Specifically, he looked over the past winning iGEM modeling projects to get a feel for what a good modeling project should have.

Lajja, Tae and Sarah made overnight stocks to be used for miniprepping the following morning.


Lajja, Tae and Sarah mini-prepped RFP colonies (refer to the miniprepping protocol in the protocol notebook)
Jen discussed how to use the NanoDrop to correctly measure whether the miniprep was done correctly. As shown in the figure below, the concentration of DNA is relatively high [concentration] and the ratio of DNA to protein is [1.82], meaning that the miniprep was done properly and the DNA obtained is likely good for use.

Lajja, Tae, and Sarah plan on retransforming the DNA obtained from the miniprep back into bacteria to make sure the DNA obtained still has the RFP plasmid in it.

Grant continued researching modeling projects and is contacting Adam from Jewett’s lab in order to possibly get help with modeling. Grant also found a webpage that helps with writing and solving biochemistry differential equations. Specifically, the differences between the different orders of kinetics reactions and how that affects the writing of the ODEs.

We decided to take our miniprepped DNA and prepare it for gel electrophoresis:

  • 20 microliters of miniprepped DNA solution was prepared with restriction enzymes (we decided to use the DNA with a lower concentration for practice)
  • 20 microliters of miniprepped DNA solution without restriction enzymes was prepared as a control
  • These samples were placed in a 37 degree C water bath overnight to be used the next morning

Yuan made overnight stocks of bacteria that had been previously transformed with GFP for miniprepping the next day.


Tae and Lajja miniprepped the bacteria that had been transformed with GFP previously from the overnight stocks. They followed the miniprep protocol as described earlier.

Yuan and Sarah made a gel for gel electrophoresis following the gel electrophoresis protocol. The gel will be used to separate the bands of DNA that were digested the previous night that came from bacteria with a plasmid with RFP in them.

Grant talked to Jennifer and decided making sequencing primers for all of the parts would be a good idea to check work. Grant worked on finishing up making the primers to sequence all of the parts.

Tae, Grant and Brian ran a gel for the miniprepped bacteria from the morning.
Yuan and Sarah eluted the DNA from the gel following the gel extraction protocol


Grant and Brian met with Adam from Jewett’s lab to discuss modeling the system.