Team:Tec-Monterrey/projectresults/methods

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     <div class="panelcontent" style="">
     <div class="panelcontent" style="">
     
     
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        <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectoverview">overview</a></p>
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                  <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectoverview">overview</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectparts">parts</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectparts">parts</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectmodeling">genetic frame</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectmodeling">genetic frame</a></p>
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             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/safetypage">safety</a></p>
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             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectresults/methods">methods</a></p>
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            <p><a href="https://2011.igem.org/Team:Tec-Monterrey/teamha">human practice</a></p>
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            <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectnotebook">notebook</a></p>
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             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectresults">results</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectresults">results</a></p>
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            <p><a href="https://2011.igem.org/Team:Tec-Monterrey/teamha">human approach</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectprotocols">protocols</a><p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectprotocols">protocols</a><p>
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            <p><a href="https://2011.igem.org/Team:Tec-Monterrey/safetypage">safety</a></p>
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            <p><a href="https://2011.igem.org/Team:Tec-Monterrey/projectnotebook">notebook</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/sampledata">sample data</a></p>
             <p><a href="https://2011.igem.org/Team:Tec-Monterrey/sampledata">sample data</a></p>
           </div>
           </div>
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<a href="https://2011.igem.org/Team:Tec-Monterrey/projectmodeling">  
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<a href="https://2011.igem.org/Team:Tec-Monterrey/projectresults">  
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<img src="https://static.igem.org/mediawiki/2011/8/8f/Construct01.png"></a>
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<img src="https://static.igem.org/mediawiki/2011/1/13/Results002.png"></a>
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<a href="https://2011.igem.org/Team:Tec-Monterrey/projectmodeling/construct2" >
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<a href="https://2011.igem.org/Team:Tec-Monterrey/projectresults/methods" >
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<img src="https://static.igem.org/mediawiki/2011/f/fe/Construct02.png
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<img src="https://static.igem.org/mediawiki/2011/d/de/Methods01.png"></a>
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<a href="https://2011.igem.org/Team:Tec-Monterrey/projectmodeling/construct3" >
 
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<img src="https://static.igem.org/mediawiki/2011/f/f9/Construct03.png"></a>
 
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<center><img src="https://static.igem.org/mediawiki/2011/b/ba/Results01.png"> </center>
 
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<p class="textojustif"> There are several methods to prove the successful transportation of CelD and SacC on the outer membrane of <i>Escherichia coli</i>. In this project, SDS-PAGE of entire cell culture samples, SDS-PAGE of membrane fraction samples, and measurement of enzyme activity of whole-cell-system without chemical or enzymatical purification operation have been considered in order to confirm the presence of active enzymes on the external membrane of <i>E. coli</i>.
 
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<center><img src="https://static.igem.org/mediawiki/2011/9/9a/Results02.png"> </center>
 
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<style=bold>CelD + estA protein fusion profiles</style>
 
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In order to prove the presence of our proteic fusion (celD+estA) we ran several polyacrylamide gels to determine protein profiles on 6 different expression strains (BL21 SI, BL21 STAR, XL1 Blue, C43, BW 27783 and Rosetta Gami), to determine the correct variable combination, which would represent the best yield for our target protein. Said variables were time and induction temperature.
 
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<br><br>
 
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For our first assay, proteins were inducted in the BL21 SI, XL1 Blue, C43, BW 27783 and Rosetta Gami strains at 25°C for 12h. Once the induction time ended, cells were then lysed using the xTractor extraction kit, from Clontech, in order to obtain soluble and insoluble fractions.
 
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<br><br>
 
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The order of our polyacrylamide gels is as follows:
 
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As it is seen, lanes corresponding to the insoluble fraction on transformed and induced strains show a thick band at around 100kDa* according to our molecular weight marker (Bio-Rad). Said band is not found in lanes corresponding to negative controls (wild-types and non-induced transformed cells).
 
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<br><br>
 
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Based on our results, we can assure that our protein was translated just as planned. Nevertheless, there’s a chance of finding a fraction of our protein as a part of an inclusion body. Then, we ran activity essays to test the correct folding of our protein.
 
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<br><br>
 
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*Our protein’s molecular weight was calculated by means of a predictive program based on the amino-acid sequence codified for our protein (http://www.scripps.edu/~cdputnam/protcalc.html).
 
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<center>
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    <p><img src="https://static.igem.org/mediawiki/2011/5/5a/Gel_Chucho.jpg" alt="photo3" name="photo3" width="400" id="photo3" /><br />
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<b>1.1. CelD+estA Construction</b>
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<p class="textojustif">As our second experiment, the protein profile for 6 expression strains (BL21 SI, BL21 STAR, XL1 Blue, C43, BW 27783 and Rosetta Gami) was produced at a lower temperatura (15°C) for 36h, which attenuated our bacterial metabolism and thus our transcription and traduction rate as well, securing the safe and secure folding of our proteins.
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<p class="textojustif">
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The celD+estA construction was generated by joining the biobricks of the araC-P<sub>BAD</sub> promoter (<a href="http://partsregistry.org/Part:BBa_I13458">BBa_I13458 </a>and <a href="http://partsregistry.org/Part:BBa_K206000"> BBa_K206000</a>), RBS+phoA signal peptide+celD (<a href="http://partsregistry.org/Part:BBa_K633002">BBa_K633002</a>) and linker+estA (<a href="http://partsregistry.org/Part:BBa_K633001">BBa_K633001</a>) with the biobrick standard assembly protocol (<a href="http://ginkgobioworks.com/support/BioBrick_Assembly_Manual.pdf"> Manual</a>). The expected DNA fragment of the celD+estA construct was confirmed by several restriction endonuclease reactions, and used to transform the <i>Escherichia coli</i> strains BL21SI, Rosetta Gami, XL1 Blue, C43 and BW27783. The <i>E. coli</i> strains BL21SI, Rosetta Gami, XL1 Blue, and C43 were obtained from Invitrogen, Novagen, Agilent and Lucigen, respectively, and the strain BW27783 was donated by <a href="https://2010.igem.org/Team:Tec-Monterrey">Tec-Monterrey 2010</a>.
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The order of wells on our gel is as follows:
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    <p><img src="https://static.igem.org/mediawiki/2011/3/39/Gel_Chucho_2.jpg" alt="photo3" name="photo3" width="400" id="photo3" /><br />
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<b>1.2. CelD+estA Expression</b>
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      </p>
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</center>
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<p class="textojustif">In this gel we can see a wide, 100kDa band for the Induced BW27783 lanes in the insoluble fraction. This phenomenon happens on every induced strain. This suggests that the 15°C induction produces better protein folding and fusion, due to the slowdown on <i>E. coli </i>'s relative to its speed at 30 or 37°C.
 
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<p class="textojustif">
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The <i>E. coli</i> strains containing the celD+estA construct and non-transformed strains as negative controls were cultured in 6 mL of LB Miller Broth. The initial optical density at 600 nm (OD<sub>600</sub>) was 0.1, from there the batch cultures were incubated at 37°C until an OD<sub>600</sub> of 0.6 was attained. The expression was induced with 0.1mM of L-arabinose and the temperature of postinduction was changed to 30 °C. Culture samples collected from the bioreactor were harvested by centrifugation. Half the volume was used for the whole cell assay and the other half was processed with Clontech x-Tractor kit (Clontech) to obtain the soluble and insoluble fractions of each strain. Both fractions were separated by a 10% SDS-PAGE and visualized with GelCode Blue Stain Reagent (Thermo).
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<center><img src="https://static.igem.org/mediawiki/2011/4/40/Results03.png"> </center>
 
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<p class="textojustif"> Click here to read our pdf file with results!</p>
 
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<p class="textojustif"> <a href="https://static.igem.org/mediawiki/2011/8/8b/Roseta_results.pdf">Roseta Results pdf</a>
 
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<center>
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<b>1.3. CelD+estA Activity</b>
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</center>
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<p class="textojustif">
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The IUPAC Filter Paper Assay was used to determine the celD+estA activity.  The <i>E. coli</i> strain , Rosetta Gami, was used as a host for the expression of the chimeric protein because it has an improved protein folding system. The assay was applied to the whole-cells, but these were also lysated with x-Tractor Cell lysis Buffer (Clontech), which separated them into soluble and insoluble fractions. The negative controls (C-) of all the samples were non-transformed cells. In the whole-cell cellulase activity experiment and in the cellulase activity of cell-lysates experiment, a t-test was done  with an alpha of 0.05 to prove the hypothesis.
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The Escherichia coli strain, Rosetta Gami, was choosen as a host for the chimeric protein because it has an improved folding system.
 
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We used the IUPAC Filter Paper Assay, to determine the activity of the cellulase. This method is based in the reduction of the DNS, generating a proportional colorimetric concentration.
 
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The assay was assest to the whole-cells, but also, we lysated the cells and separated them in two main fractions: soluble and insoluble. We were expecting more activity in the insoluble because our protein has a transmembranal domain.
 
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The negative controls of the assay were non-transformed cells.
 
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All samples were treated equally in the assay.
 
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<p class="textojustif">
 
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In the “ Whole-cell cellulase Activity” chart, is observed that there is a difference in the glucose concentration between the Negative Control cells (C-) and the CelD+ estA cells.
 
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A t-student was done (sigma = 0.05) . The result was the rejection of the null hypothesis (Ho), this meant that the difference was significant.
 
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<center><img src="https://static.igem.org/mediawiki/2011/f/f2/Graficathelma02.png"> </center>
 
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<br><p class="textojustif">
 
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In the “Cellulase Activity Cell Lysates” is analysed two fractions : Soluble ans Insoluble. As it can be seen, in both cases, there is a difference between the celD+estA cells and their respective Negative Controls (C-) . Also, it is noticed that there is a higher difference in the Insoluble fraction that in the Soluble one. A t-student was done (sigma = 0.05). The result was the rejection of the null hypothesis (Ho), this meant that the difference was significant.
 
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<center><img src="https://static.igem.org/mediawiki/2011/e/e9/Grafica01thelma.png" alt="photo3" name="photo3" width="400" id="photo3"/></center>
 
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Conclusions
 
<br>
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• The difference in the glucose concentration between the celD+esta and their Negative Control (C-) were significant.
 
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• The celD is ancher to the estA and it is active.<br>
 
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• The activity in the Negative Control (C-) is due to the background signal.<br>
 
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<b>2.1. SacC Amplification</b>
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</center>
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Future Work
 
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• Standarize all the variables of the UIPAC Filter Paper Assay and do more measurement with the samples.<br>
 
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• Change the LB medium to a Basal medium like M9 medium.<br>
 
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• Try another E. coli strain like XL1 Blue, C43, Bl21 SI and others<br>
 
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• Assest others activity assays like Benedict Method and HPLC.<br>
 
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<p class="textojustif">
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The SacC gene from <i> Zymomonas mobilis </i> was PCR amplified with the primers S1PSF: 5’-GAATT CGCGG CCGCT TCTAG AGGAG CTCAT GTTTA ATTTT AATGC CAGTC GC-3’, S1PSR 5’-CTGCA GCGGC CGCTA CTAGT AGCTA GCGTA TTTGC GACGA TCAGG G-3’. The amplification mixture for 50 mL contained 1U of Platinum Taq HF polymerase (Invitrogen), 60 mM Tris-SO<sub>4</sub>, 18 mM Ammonium Sulfate, 0.2 mM for each dNTP, 2 mM MgSO<sub>4</sub>, 2 mM of forward and reverse primers. PCR was performed in an MultiGene (Labnet) thermocycler using the following program: 94 ºC for 5 min, 35 cycles of 94 ºC for 45 s, 56.4 ºC for 30 s, and 68 ºC for 1 min, and finally an extension step at 68 ºC for 5 min. The PCR product was first sub-cloned in pGEM T Easy Vector (Promega) and added to the registry (<a href="http://partsregistry.org/Part:BBa_K633003">BBa_K633003</a>).
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<br><center><img src="https://static.igem.org/mediawiki/2011/1/1b/Results04.png"> </center>
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<b>2.2. OmpA+sacC Construction</b>
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</center>
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<p class="textojustif">
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The ompA+sacC construction was generated by joining the biobricks of the araC-P<sub>BAD</sub> promoter (<a href="http://partsregistry.org/Part:BBa_I13458">BBa_I13458 </a>and <a href="http://partsregistry.org/Part:BBa_K206000"> BBa_K206000</a>),  RBS (<a href="http://partsregistry.org/Part:BBa_B0034">BBa_B0034</a>), lpp+ompA (<a href="http://partsregistry.org/Part:BBa_K103006">BBa_K103006</a>), and sacC (<a href="http://partsregistry.org/Part:BBa_K633003">BBa_K633003</a>) with the biobrick standard assembly protocol (<a href="http://ginkgobioworks.com/support/BioBrick_Assembly_Manual.pdf"> Manual</a>). The expected DNA fragment of the ompA + sacC construct was confirmed by several restriction endonuclease reactions, and used to transform the <i>E. coli</i> strains BL21SI, Rosetta Gami, XL1 Blue, C43 and BW27783.
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<p class="textojustif"> Construction of genetic frame ompA + sacC was confirmed by several restriction endonuclease reactions and agarose gel electrophoresis.
 
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<center>
<center>
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    <p><img src="https://static.igem.org/mediawiki/2011/1/14/Imagenpruebas01.png" alt="photo3" name="photo3" width="350" height="230" id="photo3" /><br />
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<b>2.3. OmpA+sacC Expression</b>
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      </p>
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</center>
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<p class="textojustif">
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The <i>E. coli</i> strains containing the ompA+sacC construct and non-transformed strains as negative controls were cultured in 6 mL of media M9 with glycerol as its unique carbon source. The initial optical density at 600 nm (OD<sub>600</sub>) was 0.1, from there the batch cultures were incubated at 37°C until an OD<sub>600</sub> of 0.6 was attained. The expression was induced with 0.1mM of L-arabinose and the temperature of postinduction was changed to 15 °C. Culture samples collected from the bioreactor were harvested by centrifugation. Half the volume was used for the whole cell assay and the other half was processed with Clontech x-Tractor kit (Clontech) to obtain the soluble and insoluble fractions of each strain. Both fractions were separated by a 10% SDS-PAGE and visualized with GelCode Blue Stain Reagent (Thermo).
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<p class="textojustif"> After transformations, the samples were processed with Clontech x-Tractor kit to obtain soluble and insoluble fraction of each strain.
 
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    <p><img src="https://static.igem.org/mediawiki/2011/2/20/Gel_1.jpg" alt="photo3" name="photo3" width="400" id="photo3" /><br />
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<b>2.4. SacC Enzymatic Assays</b>
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      </p>
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<p class="textojustif"> Expected MW of the fusion protein (ompA + sacC) was 62.8 kDa, but the expression could not be confirmed by SDS-PAGE with Coomassie blue method. However, as Lee <i>et al.</i> (2004) have proved that the fusion protein could hardly be detected by Coomassie blue staining because its expression level used to be very low, our result may be due to this reason. Further research should be focused on SDS-PAGE with more efficient staining/blotting technique, expression of sacC fusing it with estA protein fragments, and sacC enzymatic assay.
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To determine the ompA+sacC activity, EnzyChromTM Fructose Assay Kit (kindly donated by PhD. Fernández) was used. The <i>E. coli</i> BL21 SI was used for the expression of the fusion protein. The assay was applied to the whole-cells, and non-transformed cells were used as a negative control. A t-test was done with an alpha value of 0.05 to compare fructose concentrations of each sample.
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<center><img src="https://static.igem.org/mediawiki/2011/4/40/Results03.png"> </center>
 
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<center><img src="https://static.igem.org/mediawiki/2011/c/cf/Graficamin03.png"></center><br/>
 
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<p class="textojustif">Fructose concentrations in the samples were stimated with fructose standard curve.
 
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The difference between the negative control, which consist of non-transformed BL21SI strain, and the sample strain, transformed with sacC+ompA plasmid, can be observed in the graph. T- test with 2 tails and alpha value of 0.05 was carried out, and the null hypothesys of “the population means are the same” was rejected, indicating that there is difference between the fructose concentration in the control strain and those of the sample strain.
 
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<center><img src="https://static.igem.org/mediawiki/2011/6/66/Referencesimg.png" alt="" name="" width="200" height="50" id="tgo"></center>
 
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<p class="textojustif"> • Lee SH, Choi JI, Park SJ, Lee SY & Park BC (2004) Display of Bacterial Lipase on the Escherichia coli Cell Surface by Using FadL as an Anchoring Motif and Use of the Enzyme in Enantioselective Biocatalysis. Applied and Environmental Microbiology. Vol.70(9):5074–5080.
 
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