Difference between revisions of "Team:Hong Kong UCCKE/Experiments"
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| − | <p style="text-align:left !important;">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 included in the protocol page and | + | <p style="text-align:left !important;">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 included in the protocol page. The design and results will be discussed in detail below.</p> |
<h3 class="sectiontitle">Assay A</h3> | <h3 class="sectiontitle">Assay A</h3> | ||
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<p><font size="4">Design</font></p> | <p><font size="4">Design</font></p> | ||
| − | <p style="text-align:left !important;"> Assay A is the experiment designed to prove the validity of BBa_K2197300. By incubating engineered cells with different concentration of uric acid and measure the | + | <p style="text-align:left !important;"> Assay A is the experiment designed to prove the validity of BBa_K2197300. By incubating engineered cells with different concentration of uric acid and measure the green fluorescence level in a plate reader, it is expected a positively proportional trend will be shown. As theoretically, the higher the concentration is, the more 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.</p> |
<p><font size="4">Steps and Result</font></p> | <p><font size="4">Steps and Result</font></p> | ||
| − | <p style="text-align:left !important;">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 | + | <p style="text-align:left !important;">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. </p><br> |
<p style="text-align:left !important;">The result is shown as below (Click to see raw data). </p> | <p style="text-align:left !important;">The result is shown as below (Click to see raw data). </p> | ||
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| − | <p style="text-align:left !important;">There is no significant trend shown. | + | <p style="text-align:left !important;">There is no significant trend shown. When higher concentrations of uric acid are added, the levels of green fluorescence measured are similar to the lower concentration ones. Therefore, we carry out another experiment, Assay B, after receiving the advice from team Hong_Kong_CUHK. |
</p><br> | </p><br> | ||
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<p><font size="4">Design</font></p> | <p><font size="4">Design</font></p> | ||
| − | <p style="text-align:left !important;"> Assay B is another experiment designed to prove the validity of BBa_K2197300. By growing engineered cells with different | + | <p style="text-align:left !important;"> 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 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.</p> |
<p><font size="4">Steps and Result</font></p> | <p><font size="4">Steps and Result</font></p> | ||
| − | <p style="text-align:left !important;">We first | + | <p style="text-align:left !important;">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. </p><br> |
<p style="text-align:left !important;">The result is shown as below (Click to see raw data). </p> | <p style="text-align:left !important;">The result is shown as below (Click to see raw data). </p> | ||
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</a> | </a> | ||
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| − | <p style="text-align:left !important;">There is also no significant trend shown. | + | <p style="text-align:left !important;">There is also no significant trend shown. When higher concentrations of uric acid are added the amount of GFP measured is similar to the lower concentration ones. Therefore, we tried to figure out the problem. After double checking the sequence, we found out that the DNA we ordered from IDT is different from what we designed, which the operating site HucO is missing. 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. However, it is possible that the GFP itself is not working or the repressor KRAB-HucR is not strong enough to repress it. And more experiments should be done to figure out the answer. |
</p><br> | </p><br> | ||
Revision as of 14:27, 31 October 2017
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 included in the protocol page. The design and results will be discussed in detail below.
Assay A
Design
Assay A is the experiment designed to prove the validity of BBa_K2197300. By incubating engineered cells with different concentration of uric acid and measure the green fluorescence level in a plate reader, it is expected a positively proportional trend will be shown. As theoretically, the higher the concentration is, the more 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 to see 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 the lower concentration ones. Therefore, we carry out another experiment, Assay B, after receiving the advice from team Hong_Kong_CUHK.
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 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 the lower concentration ones. Therefore, we tried to figure out the problem. After double checking the sequence, we found out that the DNA we ordered from IDT is different from what we designed, which the operating site HucO is missing. 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. However, it is possible that the GFP itself is not working or the repressor KRAB-HucR is not strong enough to repress it. And more experiments should be done to figure out the answer.
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 concentration of uric acid, and adding engineered cells (BBa_K2197300) after 30 minutes, we measure the Green fluorescence in a plate reader. We expect that the columns with engineered cells(BBa_K2197400) will have less green fluorescence while comparing it to the column containing competent cells. As theoretically, the higher the concentration is, the more smUOX will be expressed and this will catalyse uric acid into allantoin. So by adding engineered cells (BBa_K2197300) which express more GFP when there is more uric acid, the green fluorescence 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 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.
However, due to the problem of missing the operating site in K2197300, which there is no difference of the green fluorescence 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 concentration of uric acid, and adding engineered cells (BBa_K2197300) after 30 minutes, we measure the Green fluorescence in a plate reader. We expect that the columns with engineered cells(BBa_K2197500) and engineered cells(BBa_K2197502) will have less green fluorescence while comparing it 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 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.
However, due to the problem of missing the operating site in K2197300, which there is no difference of the green fluorescence 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.
