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− | <title>Experiment</title> | + | <title>Curcumin Experiment</title> |
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− | <img src="https://static.igem.org/mediawiki/2018/3/30/T--NCTU_Formosa--Experiment_design_title.png" class="title_title"> | + | <div class="title"><p>Introduction of Electrochemistry</p></div> |
| <div class="text"> | | <div class="text"> |
− | <p> Our system provided a way to regulate microbiota to an ideal balance . Since we focused our model on the excess PSB in soil, which is a large issue of agriculture in Taiwan, we chose antimicrobial peptide as the Bio-stimulator to limit the amount of PSB in soil. To express our target protein, we first designed BioBricks that contain sequences of these peptides. All the experiments we performed with BioBricks are mentioned below. | + | <p> After choosing α<sub>S1</sub>-Casein as our biosensor, we should choose the method to detect curcumin. We choose the electrochemical impedance spectroscopy (EIS) and Differential Pulse Voltammetry (DPV), the two detecting methods in electrochemistry.</p> |
− | </p> | + | <p> EIS is simple, convenient, and rapid, so that it is quite suitable for detecting whether the biosensor effective or not. This method uses the principle that impedance will be changed by charge transfer, and then measure the change of impedance by Alternate Current. Therefore, if we find out that our measured result has the stronger change than negative control, we can say our method could produce a fierce Redox reaction. However, because EIS is not a suitable method for detecting small molecule, the error will be very large if we choose it to perform formula computing. So we decide to use DPV to improve this problem.</p> |
| + | <p> DPV uses the difference between before and after the pulse application in order to solve the influence of background noise. This principle is difference from EIS. We hope we can find out which method is more sensitive to curcumin, and create more accurate formula.</p> |
| </div> | | </div> |
| </div> | | </div> |
| <div class="sec2" style="background-color:#FFFFFF;"> | | <div class="sec2" style="background-color:#FFFFFF;"> |
− | <div class="title"><p>BioBrick</p></div> | + | <div class="title"><p>Data Analysis</p></div> |
| <div class="text"> | | <div class="text"> |
− | <p> The BioBrick we designed contains a T7 promoter, induced by IPTG, and RBS with our target protein behind. We also added a intein-CBD (chitin binding domain) tag behind bacteriocin to better purify our peptide.</p> | + | <p> First of all, we use EIS to check whether our biosensor can detect curcumin. We have two samples. Red line is connected to general chip, and blue line is the chip connected with α<sub>S1</sub>-Casein(Fig 1). When our biosensor is connected with α<sub>S1</sub>-Casein to detect curcumin, impedance value become larger. That is our biosensor connected with α<sub>S1</sub>-Casein produce more fierce Redox reaction than another. This figure also represent that the biosensor connected with α<sub>S1</sub>-Casein have more effect of detecting curcumin than none.</p> |
| </div> | | </div> |
− | <img src="https://static.igem.org/mediawiki/2018/a/aa/T--NCTU_Formosa--biobrick.png" class="expression" style="display:block; margin:auto;" width="700"> | + | <img src="https://static.igem.org/mediawiki/2018/c/c9/T--NCTU_Formosa--curcumin_fig1.png" class="expression" style="display:block; margin:auto;" width="700"> |
| <div class="explanation"> | | <div class="explanation"> |
| <svg class="icon" aria-hidden="true" data-prefix="fas" data-icon="arrow-circle-up" class="svg-inline--fa fa-arrow-circle-up fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M8 256C8 119 119 8 256 8s248 111 248 248-111 248-248 248S8 393 8 256zm143.6 28.9l72.4-75.5V392c0 13.3 10.7 24 24 24h16c13.3 0 24-10.7 24-24V209.4l72.4 75.5c9.3 9.7 24.8 9.9 34.3.4l10.9-11c9.4-9.4 9.4-24.6 0-33.9L273 107.7c-9.4-9.4-24.6-9.4-33.9 0L106.3 240.4c-9.4 9.4-9.4 24.6 0 33.9l10.9 11c9.6 9.5 25.1 9.3 34.4-.4z"></path></svg> | | <svg class="icon" aria-hidden="true" data-prefix="fas" data-icon="arrow-circle-up" class="svg-inline--fa fa-arrow-circle-up fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M8 256C8 119 119 8 256 8s248 111 248 248-111 248-248 248S8 393 8 256zm143.6 28.9l72.4-75.5V392c0 13.3 10.7 24 24 24h16c13.3 0 24-10.7 24-24V209.4l72.4 75.5c9.3 9.7 24.8 9.9 34.3.4l10.9-11c9.4-9.4 9.4-24.6 0-33.9L273 107.7c-9.4-9.4-24.6-9.4-33.9 0L106.3 240.4c-9.4 9.4-9.4 24.6 0 33.9l10.9 11c9.6 9.5 25.1 9.3 34.4-.4z"></path></svg> |
− | Figure 1: BioBrick: T7 promoter + RBS + target peptide + intein-CBD | + | Figure 1: The method EIS has poor sensitivity for curcumin detection. |
| </div> | | </div> |
| <div class="text"> | | <div class="text"> |
− | <p> Intein is a protein segment that is able to excise itself from the larger protein it binds to. Therefore, it is also called “ protein introns”. We utilized intein-CBD tag to purify our peptides.<br>Although affinity tags have been widely used to purify recombinant proteins, it must removed by protease in the final purification. In contrast, intein-CBD tag will undergo the cleavage reaction with DTT (1,4-dithiothreitol) or cysteine, which will not cause the structure changes of our short peptide. | + | <p> After we prove that adding α<sub>S1</sub>-Casein can detect curcumin, we hope we can use more accurate method to show our data. We choose DPV to replicate the experiment above, and determine which method is sensitive. Comparing with fig1 and fig2, we can find out that chips with α<sub>S1</sub>-Caseinis almost no change in EIS experiment, and change a lot in DPV experiment in contrast. In this way, we can explain that DPV is more sensitive and has better signal than EIS.</p> |
− | </p> | + | |
| </div> | | </div> |
| + | <img src="https://static.igem.org/mediawiki/2018/8/83/T--NCTU_Formosa--curcumin_fig2.png" class="expression" style="display:block; margin:auto;" width="700"> |
| <div class="explanation"> | | <div class="explanation"> |
| <svg class="icon" aria-hidden="true" data-prefix="fas" data-icon="arrow-circle-up" class="svg-inline--fa fa-arrow-circle-up fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M8 256C8 119 119 8 256 8s248 111 248 248-111 248-248 248S8 393 8 256zm143.6 28.9l72.4-75.5V392c0 13.3 10.7 24 24 24h16c13.3 0 24-10.7 24-24V209.4l72.4 75.5c9.3 9.7 24.8 9.9 34.3.4l10.9-11c9.4-9.4 9.4-24.6 0-33.9L273 107.7c-9.4-9.4-24.6-9.4-33.9 0L106.3 240.4c-9.4 9.4-9.4 24.6 0 33.9l10.9 11c9.6 9.5 25.1 9.3 34.4-.4z"></path></svg> | | <svg class="icon" aria-hidden="true" data-prefix="fas" data-icon="arrow-circle-up" class="svg-inline--fa fa-arrow-circle-up fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M8 256C8 119 119 8 256 8s248 111 248 248-111 248-248 248S8 393 8 256zm143.6 28.9l72.4-75.5V392c0 13.3 10.7 24 24 24h16c13.3 0 24-10.7 24-24V209.4l72.4 75.5c9.3 9.7 24.8 9.9 34.3.4l10.9-11c9.4-9.4 9.4-24.6 0-33.9L273 107.7c-9.4-9.4-24.6-9.4-33.9 0L106.3 240.4c-9.4 9.4-9.4 24.6 0 33.9l10.9 11c9.6 9.5 25.1 9.3 34.4-.4z"></path></svg> |
− | Figure 2: Procedure of intein-mediated protein splicing | + | Figure 2: The sensitivity test of curcumin Biosensor in Dpv. |
| </div> | | </div> |
− | <div class="title_1"><p>1. Protein expression</p></div> | + | <div class="text"> |
− | <div class="title_2"><p>Cloning:</p></div>
| + | <p> Doing same experiment by using two different kinds of methods, we know that DPV is more sensitive. Then, we want to know what condition is more suitable to detect curcumin. We use PB and PBS, two buffers, as curcumin solvent. In fig3, blue line is use PB Buffer, and red line is use PBS Buffer. In the result, LOD (limit of detection) of curcumin in PB buffer is 10pM and in PBS buffer is 1nM. This means that the sensitivity by using PB buffer is one hundred times than using PBS buffer. We also can confirm that NaCl will increase noise in our method. In the conclusion, we use the PB buffer as our solvent rather than the PBS buffer.</p> |
− | <div class="textnew">
| + | |
− | <p>We cloned the insert gene into pSB1C3 backbone and transform into <i>E. coli</i> DH5α. <a href="https://2018.igem.org/Team:NCTU_Formosa/Parts parts"><br>These</a> have been submitted to iGEM.</p> | + | |
| </div> | | </div> |
− | <div class="title_2"><p>Expression:</p></div> | + | <img src="https://static.igem.org/mediawiki/2018/3/31/T--NCTU_Formosa--curcumin_fig3.png" class="expression" style="display:block; margin:auto;" width="700"> |
− | <div class="textnew"> | + | <div class="explanation"> |
− | <p>We expressed the proteins by <i>E. coli</i> ER2566 and <i>E. coli</i> BL21 Rosetta-Gami.</p> | + | <svg class="icon" aria-hidden="true" data-prefix="fas" data-icon="arrow-circle-up" class="svg-inline--fa fa-arrow-circle-up fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M8 256C8 119 119 8 256 8s248 111 248 248-111 248-248 248S8 393 8 256zm143.6 28.9l72.4-75.5V392c0 13.3 10.7 24 24 24h16c13.3 0 24-10.7 24-24V209.4l72.4 75.5c9.3 9.7 24.8 9.9 34.3.4l10.9-11c9.4-9.4 9.4-24.6 0-33.9L273 107.7c-9.4-9.4-24.6-9.4-33.9 0L106.3 240.4c-9.4 9.4-9.4 24.6 0 33.9l10.9 11c9.6 9.5 25.1 9.3 34.4-.4z"></path></svg> |
| + | Figure 3: The improvement test of curcumin Biosensor in Dpv. |
| </div> | | </div> |
− | <div class="title_2"><p>SDS-PAGE:</p></div> | + | <img src="https://static.igem.org/mediawiki/2018/2/26/T--NCTU_Formosa--curcumin_fig7.png" class="expression" style="display:block; margin:auto;" width="700"> |
− | <div class="textnew"> | + | <div class="explanation"> |
− | <p>We checked the expression result through SDS-PAGE.</p> | + | <svg class="icon" aria-hidden="true" data-prefix="fas" data-icon="arrow-circle-up" class="svg-inline--fa fa-arrow-circle-up fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M8 256C8 119 119 8 256 8s248 111 248 248-111 248-248 248S8 393 8 256zm143.6 28.9l72.4-75.5V392c0 13.3 10.7 24 24 24h16c13.3 0 24-10.7 24-24V209.4l72.4 75.5c9.3 9.7 24.8 9.9 34.3.4l10.9-11c9.4-9.4 9.4-24.6 0-33.9L273 107.7c-9.4-9.4-24.6-9.4-33.9 0L106.3 240.4c-9.4 9.4-9.4 24.6 0 33.9l10.9 11c9.6 9.5 25.1 9.3 34.4-.4z"></path></svg> |
| + | Figure 4: Curcumin concentration take natural logarithm to acquire polynomial. |
| + | </div> |
| + | <div class="text"> |
| + | <p> Now, we know that connecting our biosensor with α<sub>S1</sub>-Casein and using PB buffer are the best condition to detect curcumin by DPV. We use the data in this condition to curve fit. Fig4 easily shows that it is the Logarithmic function so we put the curcumin concentration into the Natural logarithm, and do the polynomial curve fitting. We can obtain the result in Figure 5, R<sup>2</sup> =0.9995. This represents our curve is really close to real value and get the following formula.</p> |
| + | </div> |
| + | <img src="https://static.igem.org/mediawiki/2018/1/1f/T--NCTU_Formosa--curcumin_fig8.png" class="expression" style="display:block; margin:auto;" width="700"> |
| + | <div class="explanation"> |
| + | <svg class="icon" aria-hidden="true" data-prefix="fas" data-icon="arrow-circle-up" class="svg-inline--fa fa-arrow-circle-up fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M8 256C8 119 119 8 256 8s248 111 248 248-111 248-248 248S8 393 8 256zm143.6 28.9l72.4-75.5V392c0 13.3 10.7 24 24 24h16c13.3 0 24-10.7 24-24V209.4l72.4 75.5c9.3 9.7 24.8 9.9 34.3.4l10.9-11c9.4-9.4 9.4-24.6 0-33.9L273 107.7c-9.4-9.4-24.6-9.4-33.9 0L106.3 240.4c-9.4 9.4-9.4 24.6 0 33.9l10.9 11c9.6 9.5 25.1 9.3 34.4-.4z"></path></svg> |
| + | Figure 5: The detection result of real samples from turmeric. |
| + | </div> |
| + | <div class="text"> |
| + | <p> We use our biosensor and estimated formula to detect curcumin. We mill the turmeric and divide into two groups to detect. One adds water and isn’t extracted, and another adds water and is extracted. The sample which isn’t extracted cannot be detected. It is true because curcumin exist in cell. Actually, this result also represent our sensor have strong specificity. That is our sensor will not be disturbed even if taking the whole turmeric to detect.</p> |
| </div> | | </div> |
− | <div class="title_1"><p>2. MIC test</p></div>
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− | <div class="title_2"><p>Inhibition zone:</p></div>
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− | <div class="title_2"><p>Minimum Inhibitory Concentration Broth Microdilution:</p></div>
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− | <div class="title_1"><p>3. Growth curve experiment</p></div>
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− | <div class="title_1"><p>4. Soil experiment</p></div>
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| </div> | | </div> |
− | | + | <div class="sec3" style="background-color:#ffffff;"> |
| + | <div class="title"><p>Conclusion</p></div> |
| + | |
| + | </div> |
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