Team:Hong Kong UCCKE/Experiments
We have done 4 assays, which are Assay A, Assay B, Assay C and Assay D on the cultured cells to test whether part BBa_K2197300, BBa_K2197400, BBa_K2197500 and BBa_K2197502 are valid. Protocols are documented on the protocol page. The design and results will be discussed in detail below.
Assay A
Design
Assay A is an experiment designed to prove the validity of BBa_K2197300. By incubating engineered cells with different concentrations of uric acid and measuring the green fluorescence level in a plate reader, it is expected a positively proportional trend be shown. As theoretically, the higher the concentration is, the more the GFP will be expressed. It is because the strong repressor KRAB-HucR will stop the expression of GFP when there is no uric acid, or in very low concentration.
Steps and Result
We first pipette the cells into different concentrations of uric acid and incubate them in 96 well plate for 30 minutes. After that, we put it into the plate reader to measure the green fluorescence level.
The result is shown as below (Click me for raw data).
There is no significant trend shown. When higher concentrations of uric acid are added, the levels of green fluorescence measured are similar to that in lower concentrations. Therefore, we carry out another experiment, Assay B, after receiving the advice from 2017 team Hong Kong-CUHK.
Assay A
Assay A
Assay B
Design
Assay B is another experiment designed to prove the validity of BBa_K2197300. By growing engineered cells with different concentrations of uric acid and measuring the green fluorescence level in a plate reader, we expect a positively proportional trend will be shown. As theoretically, the higher the concentration is, the more the GFP will be expressed. It is because the strong repressor KRAB-HucR will stop the expression of GFP when there is no uric acid, or in very low concentration.
Steps and Result
We first grew cells in LB broth overnight. Then we cultured cells from the same tube with different concentrations of uric acid-LB mixed. We then incubate the cells for 1 hour and then pipette them into the 96-well plate. After that, we put it into the plate reader to measure the green fluorescence level.
The result is shown as below (Click to see raw data).
There is also no significant trend shown. When higher concentrations of uric acid are added, the amount of GFP measured is similar to that in lower concentration. Therefore, we tried to figure out the problem. After double checking the sequence, we found out that the DNA sequence we ordered from IDT is different from what we designed, in which the sequence 'tactagag' is missing. GFP E0040, Terminator B0010, K2197302 and K2197303 are affected. Referring to the mechanism of the promoter, if HucO is missing, the repressor protein mUTS can not bind to it. Thus, the amount of GFP expression cannot be restricted and no trend can be shown. Also, the GFP is seriously affected, therefore, GFP cannot be expressed.
Assay B
Assay C
Design
Assay C is an experiment designed to prove the validity of BBa_K2197400. By incubating engineered cells (BBa_K2197400) and Competent cells with different concentrations of uric acid, then adding engineered cells (BBa_K2197300) after 30 minutes, we measure the Green fluorescence level in a plate reader. We expect that the columns with engineered cells (BBa_K2197400) will have less green fluorescence expressed when comparing to the column containing competent cells. As theoretically, the higher the concentration is, the more the smUOX will be expressed and this will catalyse uric acid into allantoin. So by adding engineered cells (BBa_K2197300) which expresses more GFP when there is more uric acid, the green fluorescence level of the columns with engineered cells(BBa_K2197400) will be lower than the columns with competent cells although they were in the same concentration at the beginning
Steps and Result
We first pipette the cells (BBa_2197400, competent cells) into different concentrations of uric acid and incubate them in 96 well plate for 30 minutes. After that, we add in engineered cells (BBa_K2197300) into the wells and incubate them for another 30 minutes. Then, we put it into the plate reader for the measurement of green fluorescence level.
However, due to the problem of BBa_K2197300, in which there is no difference of the green fluorescence levels between the one with lower uric acid concentration and higher uric acid concentration, we cannot determine whether it can really lower the level of uric acid.
Assay D
Design
Assay D is an experiment designed to prove the validity of BBa_K2197500 and BBa_K2197502. By incubating engineered cells (BBa_K2197500), cells (BBa_K2197502) and Competent cells with different concentrations of uric acid, then adding engineered cells (BBa_K2197300) after 30 minutes, we measure the Green fluorescence level in a plate reader. We expect that the columns with engineered cells (BBa_K2197500) and engineered cells (BBa_K2197502) will have less green fluorescence expressed when comparing to the column containing competent cells. As theoretically, engineered cells (BBa_K2197500) will absorb uric acid into the cell and for engineered cells (BBa_K2197502), the higher the concentration is, the more uric acid will be absorbed into the cells. So by adding engineered cells (BBa_K2197300) which express more GFP when there is more uric acid, the green fluorescence level of the columns with engineered cells (BBa_K2197500 and BBa_K2197502) will be lower than the columns with competent cells although they were in the same concentration at the beginning.
Steps and Result
We first pipette the cells (BBa_2197500, BBa_K2197502, competent cells) into different concentrations of uric acid and incubate them in 96 well plate for 30 minutes. After that, we add engineered cells (BBa_K2197300) into the wells and incubate for another 30 minutes. Then, we put it into the plate reader for the measurement of green fluorescence level.
However, due to the problem of BBa_K2197300, in which there is no difference of the green fluorescence levels between the one with lower uric acid concentration and higher uric acid concentration, we cannot determine whether it can really lower the level of uric acid.
