From 2014.igem.org

Revision as of 03:59, 31 July 2014

BYU 2014 Notebook Edit July August

Home Team Official Team Profile Project Parts Modeling Notebook Safety Attributions

Week of July 5th

June 30, 2014

--BRK--I chose one colony of E.coli from four separate LB and CAM plates containing transformed bacteria with EreB and a promoter of either 101, 108, 111, or 119. These four colonies were streaked on four separate LB, CAM, and Erythromycin plates and grown overnight at 37C.

--CS-- We got our new reverse primers in today so I first checked all of the sequences to make sure they were correct and then ran Q5 PCR for all 4 genes. Julie then ran a gel of the PCR products. It looked like this:

The lanes are, from left to right, nirS, the DNA ladder, norB, norC, and nosZ. The most prevalent bands in each lane appear to be in the appropriate places based on length so it looks good to continue.

July 1, 2014

--BRK--The streaked colonies grew well on the LB/CAM/Erythromycin plates, indicating that the plasmid with the EreB gene had been successfully transformed. I took pictures of all the plates to compare the growth and use in the future to determine the effect of the different promoters.

--CS-- Today I did PCR cleanup, the restriction digest (XbaI and SpeI), the low-melt gel, the ligation, and the transformation of all 4 of the denitrification genes since we got the new reverse primers yesterday. My low-melt gel looked like this:

The lanes are, from left to right, the DNA ladder, nirS, norB, norC, nosZ and pIG91. I put my plates in the 37°C incubator overnight.

July 2, 2014

--CS-- Today we went to the wastewater reclamation facility in Park City. I learned a lot about the entire treatment process; I almost wish that we had gone to see the facility even earlier on to get a better idea of what actually happens. The visit gave me some more hope about the feasibility and importance of adding the denitrification pathway to N. multiformis. At first the worker who gave us the tour made it seem that the majority of the ammonia was converted to nitrogen during the activated sludge carousel stage, but the algal bloom observed in the final effluent stage and the high proportion of nitrite/nitrate released in the effluent show that there certainly is a need for improvement in nitrate removal. The readings they took in March (they provided us a copy of their report sheet) showed that of the 34 mg/l ammonia that enter the facility, about .5 mg/l ammonia and 25 mg/l nitrite/nitrate leave the facility. This shows that although the ammonia is removed very effectively (99%) there is still quite a bit of room for improvement in removing the nitrate from the effluent to reduce the occurrence of eutrophication. We got some pictures of the water leaving the facility where algae was growing all over despite the rather low flow of water. Another thing that I learned was that the conditions of the activated sludge carousel might actually be in favor of forcing N. multiformis to do both nitrification and denitrification since it might not be too favorable from a metabolic standpoint. As the waste water enters the carousel it is aerated to activate it. As it moves around the carousel though the oxygen supply is depleted, resulting in a portion of the carousel in which the conditions are anoxic. Denitrification occurs during this stage. Here is a diagram:

This change from activated to anoxic conditions works well with our project since, as Dr. Breakwell discussed when I met with him last week, this will help convince our engineered N. multiformis to undergo both nitrification (aerobic) and denitrification (anaerobic) since the different pathways are favorable under different oxygen conditions.

July 3, 2014

--BRK--Our team went to the wastewater treatment plant to learn more about the entire treatment process. I collected the biofilm and effluent water run-off from the plant to bring back to the lab for testing.

Week of July 12th

July 7, 2014

--BRK---Searched for a process to detect antibiotics in water. A few processes were discussed in a powerpoint written by Dr. Rosenfeldt from the University of Massachusetts. http://k12s.phast.umass.edu/sess/emerging/

Week of July 19th

Week of July 26th