Team:HKUST-Hong Kong/Characterization

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           <div><p align="center"><font size="20">CHARACTERIZATION</font></p></div>
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           <div><p align="center"><font size="20">Characterization</font></p></div>
  <div id="paragraph1" class="bodyParagraphs">
  <div id="paragraph1" class="bodyParagraphs">
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               <h1>Introduction</h1>
               <h1>Introduction</h1>
           </div>
           </div>
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           <p>In our project, we have characterized two promoters and the cell death device by different methods. This tells us that our parts are functional and we can quantitatively adapt their activity by changing the experimental conditions.</p>
+
           <p>In our project, we have characterized two promoters and the cell death device using different methods. The results indicate that our parts are functional and we can quantitatively control their activities by changing the experimental conditions.</p>
           </div>
           </div>
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          <div class="Section_Heading" align="center"><h3><p>Detailed Plan</p></h3></div>
 
  <div id="paragraph2" class="bodyParagraphs">
  <div id="paragraph2" class="bodyParagraphs">
           <div align="center">
           <div align="center">
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               <h1>Low Efficiency Constitutive Promoter pTms</h1>
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               <h1>Low Efficiency Constitutive Promoter <em>Ptms</em></h1>
           </div>
           </div>
           <p><strong>Background  Information <u><a href ="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Regulation_and_control" target="_blank" >(link to Regulation and Control Module)</a></u></strong><br />
           <p><strong>Background  Information <u><a href ="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Regulation_and_control" target="_blank" >(link to Regulation and Control Module)</a></u></strong><br />
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The basic reason of using this low  efficiency constitutive promoter is to enable our bacteria to express a low  level of antitoxin so that a certain amount of toxin can be balanced; thus the  BMP-2 whose expression is tightly linked with the toxin can be expressed at a  certain level as well.</p>
 
-
<p><strong>Objective</strong><br />
 
-
  Our objective for characterizing this promoter is to test whether pTms works in <i>E.coli DH10B</i> strain and determine the relative promoter units (RPU) of it to the standard constitutive promoter activity reference point given by part registry so that we and the subsequent IGEM teams may have an idea how efficient this promoter is.</p>
 
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 +
 +
 +
 +
  The key reason for using this low efficiency constitutive promoter in our construct is to enable our bacteria to express a low level of antitoxin so that the bacterial cell can only tolerate a certain amount of toxin. As the expression of BMP2 is tightly linked to the toxin, its expression can be regulated accordingly.</p><br>
 +
<p><strong>Objective</strong><br />
 +
  Our objective in characterizing this promoter is to test whether <em>Ptms</em> works in <i>E. coli</i> DH10B strain and determine its relative promoter unit (RPU) compared to the standard constitutive promoter (a promoter whose activity is arbitrarily valued at 1.0 by partsregistry.org).</p>
 +
<br>
<p><strong>Intended Result</strong><br />
<p><strong>Intended Result</strong><br />
-
   1. pTms should work in <i>E.coli</i>. This is supported by previous research (Moran et al., 1982). <br>
+
   1. <em>Ptms</em> should work in <i>E. coli</i>. This is supported by previous research (Moran et al., 1982). <br>
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2. The activity of pTms should be relatively low.
+
2. The activity of <em>Ptms</em> should be relatively low.
</p>
</p>
-
 
+
<br>
<p><strong>Method</strong><br />
<p><strong>Method</strong><br />
-
   Instead of measuring the absolute promoter activity, our characterization was generally based on measuring the relevant in vivo activity of this constitutive promoter. By adopting this method, we may be able to eliminate the error caused by different experimental conditions and give a relatively  more convincing result.<br />
+
   Instead of using the absolute promoter activity as the final result, our characterization was based on obtaining the in vivo activity of this constitutive promoter. Adopting this method enables us to eliminate errors caused by different experimental conditions and give a more convincing result.<br />
-
   By linking the promoter with GFP (BBa_E0240), the promoter activity was represented by the GFP synthesis rate which can be easily measured. E.Coli carrying the right construct was then cultured to log phase. During a time slot around the mid-log phase, the GFP intensity and OD595 value were measured to obtain the Relative Promoter Units (RPU).</p>
+
   By linking the promoter with GFP (BBa_E0240), the promoter activity was represented by the GFP synthesis rate which can be easily measured.<i> E. coli </i>carrying the right construct was then cultured to log phase. At a time point around the mid-log phase, the GFP intensity and OD595 values were measured to obtain the Relative Promoter Units (RPU).</p><br>
 +
 
 +
 
 +
<p align="center"> <img src="https://static.igem.org/mediawiki/2012/c/c3/Promoter_characterization_1.JPG" width="50%" /></p>
 +
 
 +
 
<p><strong>Characterization Procedure</strong></p>
<p><strong>Characterization Procedure</strong></p>
<ol>
<ol>
-
   <li>Constructing BBa_K733009-pSB3K3 (pTms-BBa_E0240-pSB3K3); Transforming BBa_I20260-pSB3K3 (Standard Constitutive Promoter Activity Reference Point) from 2012 Distribution;</li>
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   <li>Constructing BBa_K733009-pSB3K3 (<em>Ptms</em>-BBa_E0240-pSB3K3); Transforming BBa_I20260-pSB3K3 (Standard Constitutive Promoter/Reference Promoter) from the 2012 Distribution Kit;</li>
   <li>Preparing supplemented M9 medium (see below); </li>
   <li>Preparing supplemented M9 medium (see below); </li>
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   <li>Culturing <i>E.coli DH10B</i> strain carrying BBa_K733009-pSB3K3 and <i>E.coli</i> carrying BBa_I20260-pSB3K3 in supplemented M9 medium and measuring the growth curve respectively;</li>
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   <li>Culturing <i>E. coli</i> DH10B strain carrying BBa_K733009-pSB3K3 and <i>E. coli</i> carrying BBa_I20260-pSB3K3 in supplemented M9 medium and measuring the respective growth curves;</li>
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   <li>Measuring the GFP intensity and ODA595 value every 15 minutes after <i>E.coli</i> carrying BBa_K733009-pSB3K3 and E.coli carrying BBa_I20260 are cultured to mid-log phase;</li>
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   <li>Measuring the GFP intensity and OD595 values every 15 minutes after the above mentioned<i> E. coli</i> strains are cultured to mid-log phase;</li>
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   <li>Calculating the Relative Promoter Unites (RPU) using the obtained data;</li>
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   <li>Calculating the Relative Promoter Units (RPU) using the obtained data;</li>
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   <li>Compiling the result.</li>
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   <li>Compiling the results.</li>
</ol>
</ol>
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<br>
<p><strong>Data Processing</strong></p>
<p><strong>Data Processing</strong></p>
<ol>
<ol>
-
   <li>After <i>E.coli</i> carrying the right construct was grown into mid-log phase, GFP intensity and ODA595 were measured every 15 minutes (up to 60min);</li>
+
   <li>After <i>E. coli</i> carrying the right construct was grown to mid-log phase, GFP intensity and OD595 were measured every 15 minutes (up to 60 mins);</li>
-
   <li>For GFP intensity, curve reflecting GFP expression change was plotted; for ODA595, average values was taken;</li>
+
   <li>For GFP intensity, curve reflecting GFP expression change was plotted; for OD595, average values were taken;</li>
-
   <li>GFP synthesis rate was then represented by the slope of the curve reflecting GFP expression change;</li>
+
   <li>GFP synthesis rate was then obtained by calculating the slope of linear regression line of the above mentioned curve;</li>
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   <li>Absolute promoter activity of pTms and I20260 were calculated by divide the corresponding GFP synthesis rate by the average ODA595 value;</li>
+
   <li>Absolute promoter activity of <em>Ptms</em> and BBa_I20260 were calculated by dividing the corresponding GFP synthesis rate over the average OD595 value;</li>
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   <li>Absolute promoter activity was then modified by taking the average value of all sets of data obtained;</li>
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   <li>Averaged absolute promoter activity was then obtained by averaging the respective sets of absolute promoter activity values;</li>
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   <li>Finally, R.P.U was calculated by dividing pTms absolute promoter activity by I20260 absolute promoter activity.</li>
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   <li>Finally, R.P.U was calculated by dividing the averaged <em>Ptms</em> absolute promoter activity over the averaged BBa_I20260 absolute promoter activity.</li>
</ol>
</ol>
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<br>
<p><strong>Result</strong><br />
<p><strong>Result</strong><br />
<div style="margin-left: 25px">
<div style="margin-left: 25px">
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   1. Suggested by the GFP expression curve we plotted, pTms functions in <i>E.coli DH10B </i>strain.
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   1. Suggested by the GFP expression curve we plotted, <em>Ptms</em> functions in <i>E.coli </i>DH10B strain.
   <br>
   <br>
  <p align="center"> <img src="https://static.igem.org/mediawiki/2012/d/d9/PTms_GFP.jpg" width="75%" /></p>
  <p align="center"> <img src="https://static.igem.org/mediawiki/2012/d/d9/PTms_GFP.jpg" width="75%" /></p>
  <br>
  <br>
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<i>            * GFP expression curve for one set of data</i>
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<i>            * Above: GFP expression curve for one set of data</i><br>
<br>
<br>
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2. The overall RPU was calculated as 0.046497. It has been shown that pTms has a very low promoter efficiency in <i>E.coli DH10B </i>stain.
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2. The RPU of <em>Ptms</em> obtained was 0.046497. This shows that <em>Ptms</em> has a very low promoter efficiency in <i>E.coli</i> DH10B strain.
<br>
<br>
<p align="center"> <img src="https://static.igem.org/mediawiki/2012/a/ae/PTms_Promoter.jpg" width="75%" /></p>
<p align="center"> <img src="https://static.igem.org/mediawiki/2012/a/ae/PTms_Promoter.jpg" width="75%" /></p>
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</div>
</div>
</p>
</p>
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<br>
<p><strong>Discussion</strong><br />
<p><strong>Discussion</strong><br />
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   Compared with I20260, it seems that bacteria carrying pTms had a rather low GFP expression. This may cause some difficulty upon deciding whether pTms functions in <i>E.coli</i> or not. However, since viewed from the curve, the GFP expression for pTms increased gradually in respect to time. These all give us good reason to say that pTms functions in <i>E.coli DH10B</i> strain, although with a low efficiency. Another reason for its low efficiency could be that pTms was originally got from <i>B.subtilis</i> and is only suggested to be functional in <i>E.coli</i>. While we haven’t got time to characterize the promoter in <i>B.subtilis</i>, we still hope that in the future we can actually achieve that.
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   Compared to BBa_I20260, it seems that <i>E. coli</i> carrying <em>Ptms</em>-GFP has a rather low GFP expression. This may cause some difficulties in deciding whether <em>Ptms</em> functions in <i>E. coli</i> or not. However, referring to the curve (for GFP Intensity), the GFP expression for <em>Ptms</em> increased gradually with respect to time. This suggests that <em>Ptms</em> functions in <i>E. coli</i> DH10B strain, although with a low efficiency. A possible reason for its low efficiency could be that <em>Ptms</em> was originally from <i>B. subtilis</i> but was functioning in a heterologous system when placed in <i>E. coli</i>. Due to time constraints, we were unable to characterize the promoter in <i>B. subtilis</i>, and we still hope that we can address this in the future.
</p>
</p>
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<br>
<p><strong>Reference</strong><br />
<p><strong>Reference</strong><br />
  Moran, C., Lang, N., LeGrice, S., Lee, G., Stephens, M., Sonenshein, A., et al. (1982). Nucleotide sequences that signal the initiation of transcription and translation in <i>Bacillus subtilis</i>..<i>Molecular and General Genetics MGG,186,</i> 339-346.
  Moran, C., Lang, N., LeGrice, S., Lee, G., Stephens, M., Sonenshein, A., et al. (1982). Nucleotide sequences that signal the initiation of transcription and translation in <i>Bacillus subtilis</i>..<i>Molecular and General Genetics MGG,186,</i> 339-346.
</p>
</p>
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<br>
<p><strong>Supplemented M9 Medium Composition</strong><br/>
<p><strong>Supplemented M9 Medium Composition</strong><br/>
1.  5X M9 Salt Composition (1L) <br>
1.  5X M9 Salt Composition (1L) <br>
<div style="margin-left:25px">
<div style="margin-left:25px">
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(1) 64g Na<font size="1"><small>2</small></font>HPO<font size="1"><small>4</small></font><br>
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(1) 64g Na<font size="1"><small>2</small></font>HPO<font size="1"><small>4</small></font>﹒7H<font size="1"><small>2</small></font>O<br>
(2) 15g KH<font size="1"><small>2</small></font>PO<font size="1"><small>4</small></font><br>
(2) 15g KH<font size="1"><small>2</small></font>PO<font size="1"><small>4</small></font><br>
(3) 2.5g NaCl<br>
(3) 2.5g NaCl<br>
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  <div id="paragraph3" class="bodyParagraphs">
  <div id="paragraph3" class="bodyParagraphs">
           <div align="right">
           <div align="right">
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               <h1>Xylose inducible promoter</h1>
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               <h1>Xylose Inducible Promoter</h1>
           </div>
           </div>
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<p><strong>Background  Information <u><a href ="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Regulation_and_control" target="_blank" >(link to Regulation and Control Module)</a></u></strong><br />
<p><strong>Background  Information <u><a href ="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Regulation_and_control" target="_blank" >(link to Regulation and Control Module)</a></u></strong><br />
-
  The reason of using xylose inducible promoter is to make the expression of toxin and BMP-2 controllable. Xylose is  not toxic and normally is not present in human colon. This provides us an easy  way to induce BMP-2 expression without disrupting normal human body function.</p>
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<p><strong>Objective</strong><br />
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  Upon characterizing xylose inducible promoter, we want to test whether xylose inducible promoter works in <i>E.coli DH10B</i> strain and if it works what is the absolute promoter activity under certain experimental condition.</p>
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 +
  The reason for using the xylose inducible  promoter is to enable control on the expression of toxin and BMP2. Xylose is not toxic and normally not present in the human colon. This provides us an easy way to induce BMP2 expression without disrupting normal human body function.</p><br>
 +
<p><strong>Objective</strong><br />
 +
  On characterization, we want to test whether the promoter works in <i>E. coli</i> DH10B strain and if it works, what is the absolute promoter activity under varied experimental condition (i.e. xylose concentration).</p>
 +
<br>
<p><strong>Intended Result</strong><br />
<p><strong>Intended Result</strong><br />
    
    
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1. Xylose inducible promoter is functional in <i>E.coli</i>.
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1. Xylose inducible promoter is functional in <i>E. coli</i>.
<br>
<br>
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2. After the inducer concentration has reached certain level, a relatively stationary GFP expression level should be observed.
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2. After the inducer concentration has reached a certain level, a relatively stationary GFP expression level (expression upper-limit) should be observed.
</p>
</p>
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<br>
<p><strong>Method</strong><br />
<p><strong>Method</strong><br />
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   The absolute promoter activity was measured in respect to induction time and xylose concentration. <br>
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   The absolute promoter activity was measured with respect to xylose concentration. <br>
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Here the same reporter gene (BBa_E0240) was used to indicate promoter activity. <i>E.coli</i> carrying the right construct was cultured to log phase. Following the addition of xylose at serial concentration, during a time slot around the mid log point, the GFP intensity and ODA595 were measured for every 30 min. A curve indicating the GFP intensity unit as a respect of time and xylose concentration was plotted.
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The same reporter gene (BBa_E0240) was used to indicate promoter activity. <i>E. coli</i> carrying the right construct was cultured to log phase. Following the addition of xylose at various predetermined concentrations, at a time point around the mid-log phase, the GFP intensity and OD595 were measured for every 30 mins (up to 120 mins). Independent curves indicating the GFP intensity units (of various xylose concentrations) with respect to time were then plotted, following which the respective absolute promoter activities were calculated.
</p>
</p>
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<br>
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<p align="center"> <img src="https://static.igem.org/mediawiki/2012/c/cf/Promoter_characterization_2.JPG" width="50%" /></p>
<p><strong>Characterization Procedure</strong></p>
<p><strong>Characterization Procedure</strong></p>
<ol>
<ol>
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   <li>Constructing xylR-PxylA-BBa_E0240-pSB1A2</li>
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   <li>Constructing <em>xylR-PxylA</em>-BBa_E0240-pSB1A2</li>
   <li>Preparing supplemented M9 medium (see below);</u></li>
   <li>Preparing supplemented M9 medium (see below);</u></li>
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   <li>Culturing <i>E.coli</i> carrying xylR-PxylA-BBa_E0240-pSB1A2 and <i>E.coli</i> without constructs in supplemented M9 medium and measuring the growth curve respectively;</li>
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   <li>Culturing <i>E. coli</i> carrying <em>xylR-PxylA</em>-BBa_E0240-pSB1A2 and <i>E. coli</i> without constructs in supplemented M9 medium and measuring the growth curve respectively;</li>
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   <li>Culturing the same bacteria in supplemented M9 medium to log phase;</li>
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   <li>Culturing the above mentioned bacteria in supplemented M9 medium to log phase;</li>
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   <li>Adding xylose at different concentration to different sets of culture medium;</li>
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   <li>Adding xylose at different concentrations to different sets of bacterial culture;</li>
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   <li>Measuring the GFP intensity and OD595 value across time for every sets of culture medium that are of different xylose concentration;</li>
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   <li>Measuring the GFP intensity and OD595 values across time for every set of bacterial culture containing different xylose concentrations;</li>
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   <li>Plotting a 3D figure about the GFP intensity unit in respect of xylose concentration and time;</li>
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   <li>Plotting independent curves showing the GFP intensity units of various xylose concentrations with respect to time;</li>
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   <li>Compiling the result.</li>
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  <li>Plotting a graph to demonstrate the absolute promoter activity under different inducer concentrations;</li>
 +
   <li>Compiling the results.</li>
   
   
</ol>
</ol>
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<br>
<p><strong>Data Processing</strong></p>
<p><strong>Data Processing</strong></p>
<ol>
<ol>
-
   <li>After <i>E.coli</i> carrying the right was growing into mid-log phase, GFP intensity and ODA595 were measured every 30 minutes (up to 120min);</li>
+
   <li>After <i>E. coli</i> carrying the right construct was grown to mid-log phase, GFP intensity and OD595 were measured every 30 minutes (up to 120 mins);</li>
-
   <li>For GFP intensity, curve reflecting GFP expression change was plotted; for ODA595, average value was taken;</u></li>
+
   <li>For GFP intensity, curve reflecting GFP expression change was plotted; for OD595, average value was taken;</u></li>
-
   <li>GFP synthesis rate was then represented by the slope of the curve reflecting GFP expression change;</li>
+
   <li>GFP synthesis rate was then obtained by calculating the slope of linear regression line of the above mentioned curve;</li>
-
   <li>Absolute promoter activity for the promoter under different inducer concentrations were calculated by divide the corresponding GFP synthesis rate by the average ODA595 value;</li>
+
   <li>Absolute promoter activity for the promoter under different inducer concentrations were calculated by dividing the corresponding GFP synthesis rate over the average OD595 value;</li>
-
   <li>Absolute promoter activity was then modified by taking the average value of all sets of data obtained.</li>
+
   <li>Averaged absolute promoter activity was then obtained by averaging the respective sets of absolute promoter activity values.</li>
   
   
</ol>
</ol>
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+
<br>
<p><strong>Result</strong></p>
<p><strong>Result</strong></p>
<ol>
<ol>
-
   <li>Shown by our figure below, under the addition of xylose, GFP expression increased. This tells us that xylose inducible promoter is functional in <i>E.coli DH10B</i> strain.</li>
+
   <li>Shown in the figure below, with the addition of xylose, GFP expression increased. This tells us that the xylose inducible promoter is functional in <i>E. coli</i> DH10B strain.</li>
-
   <li>When no xylose was added, a little amount of GFP was expressed. This suggests that xylose inducible promoter is to some extent leaky.</li>
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   <li>When no xylose was added, a limited amount of GFP was expressed. This suggests that the xylose inducible promoter is to some extent leaky.</li>
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   <li>A relatively stationary GFP expression was observed after xylose concentration increased to 1% up to 5%. Despite some other variables (see discussion for more detail), we would say that the minimum inducer concentration for triggering full induction should lie in somewhere between 0 and 1%</li>
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   <li>A relatively stationary GFP expression level was observed at xylose concentrations of 1% to 5%. Despite some other variables (see discussion for more details), the data suggests that the minimum inducer concentration for triggering a full induction should lie somewhere between 0% and 1%</li>
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   <li>For 10% inducer concentration, the GFP expression was relatively lower. There could be several reasons for that, such as xylose metabolism by bacteria. (see discussion for more detail)</li>
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   <li>For 10% inducer concentration, the GFP expression was relatively lower. There could be several reasons for this occurence, such as suboptimal growth conditions due to high osmotic pressure. (see discussion for more details)</li>
</ol>
</ol>
<p align="center">
<p align="center">
<img src="https://static.igem.org/mediawiki/2012/4/4c/PXylGFP.jpg" width="75%" />
<img src="https://static.igem.org/mediawiki/2012/4/4c/PXylGFP.jpg" width="75%" />
</p>
</p>
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<br>
<p><strong>Discussion</strong></p>
<p><strong>Discussion</strong></p>
<ol>
<ol>
-
   <li>It is quite obvious that addition of xylose apparently induces the GFP expression. However, problem lies in that even when no xylose was added, a detectable amount of GFP was still expressed. This means that xylose inducible promoter was leaky. Reason for this could be that three mutagenesis had been done to the repressive gene of this promoter. Although we have adopted the most frequently used codon in <i>B.subtilis </i>for the mutagenesis, this may not work as our expectation in<i> E.coli.</i></li>
+
   <li>It is quite obvious that addition of xylose induces GFP expression in this construct. However, a slight issue remains: even when no xylose was added, a minute but detectable amount of GFP was still expressed. This shows that the xylose inducible promoter is leaky. It should be noteworthy that this version of the xylose inducible promoter has undergone mutagenesis on 3 different sites on the repressive gene for standardization purposes. Even so, the mutagenesis is done while preserving an identical codon translation. As such, similar to the <em>Ptms</em> promoter, activity of the <em>xylR-PxylA</em> promoter might be different in <i>E. coli</i> from that of <i>B. subtilis</i> due to expression in a heterologous system. Further characterization on this promoter in <i>B. subtilis</i> would be our future aim as time was limited.</li>
-
   <li>For the observation of full induction. Our biggest problem is that the E.coli strain we used contains the xylose metabolic operon, which means xylose might be metabolized by the bacteria. To eliminate error caused by this factor, we chose to use relatively higher concentration for experiment. This further caused another problem on determining the minimum xylose concentration for full GFP induction as when xylose concentration increased to 1%, the observed GFP expression level already entered a relatively stationary phase. Therefore, based on this result, we would say that due to bacterial metabolism of xylose, we are not sure whether the real GFP maximum level is higher than our current observation. However, since for a xylose concentration above 1%, a relative stationary level of GFP was observed, we would say that the minimum xylose concentration to trigger the full induction lies below 1%. We hope that in the future we can confirm the exact concentration.</li>
+
   <li>Another interesting fact to note is that the <i>E. coli</i> strain used is one in which it's xylose metabolic operon remains active. As such, one might assume that the observed GFP expression upper-limit ("stationary expression level"),particularly at 1% or 2% is not the "true" upper-limit, since there should be underlying metabolism of xylose. In order to eliminate this possible error, higher concentrations of xylose was used and the promoter activity does not appear to vary greatly, suggesting that the stationary expression level reflects the maximum promoter activity. While this problem is solved, due to the relatively large concentration difference of inducer, it appears that the maximum promoter activity was achieved at 1% xylose, implying that we are unable to determine the exact minimum inducer concentration requirement for maximum activity. Based on the current result, it is safe for us to make a conjecture that the minimum concentration required lies between 0% and 1% xylose.</li>
-
   <li>For the GFP expression decrease at 10% xylose concentration, one possible reason is that the high osmotic pressure caused by the medium may inhibit the growth and metabolism of bacteria, thus reducing the GFP expression. Another possible reason could be that the over expression of induced GFP expression may disturb the normal bacteria function, leading to a low overall GFP expression.</li>
+
   <li>For the decreased GFP expression at 10% xylose concentration, one possible reason is that the high osmotic pressure caused by the xylose in the medium may inhibit the growth and metabolism of bacteria, thus reducing the bacterial population and/or its GFP expression. Another possible, but unlikely reason could be that the over-expression of induced GFP expression may disturb the normal bacterial function, leading to a low overall GFP expression.</li>
-
</ol>
+
</ol><br>
<p><strong>Supplemented M9 Medium Composition</strong><br/>
<p><strong>Supplemented M9 Medium Composition</strong><br/>
1.  5X M9 Salt Composition (1L) <br>
1.  5X M9 Salt Composition (1L) <br>
<div style="margin-left:25px">
<div style="margin-left:25px">
-
(1) 64g Na<font size="1"><small>2</small></font>HPO<font size="1"><small>4</small></font><br>
+
(1) 64g Na<font size="1"><small>2</small></font>HPO<font size="1"><small>4</small></font>﹒7H<font size="1"><small>2</small></font>O<br>
(2) 15g KH<font size="1"><small>2</small></font>PO<font size="1"><small>4</small></font><br>
(2) 15g KH<font size="1"><small>2</small></font>PO<font size="1"><small>4</small></font><br>
(3) 2.5g NaCl<br>
(3) 2.5g NaCl<br>
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           <div align="center">
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               <h1>ydcD-E Cell Death Device</h1>
+
               <h1>YdcDE Growth Inhibition Device</h1>
           </div>
           </div>
-
<p><strong>Background  Information <u>(link to construct page)</u></strong><br />
+
<p><strong>Background  Information <u><a href ="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Regulation_and_control" target="_blank" >(link to Regulation and Control Module)</a></u></strong><br />
 +
The rationale for including this growth inhibition device is that over-dose of BMP2 can possibly cause unexpected proliferation of healthy colon epithelial cells (Zhang et al., 2012). Thus, a growth inhibition device is introduced and will be characterized.
</p>
</p>
<p><strong>Objective</strong><br />
<p><strong>Objective</strong><br />
-
  Upon characterization, we want to know what  concentration of xylose can induce the death of cells carrying our ydcDE device. It does not necessarily need to be a minimal thresh hold, as long as a  concentration for killing the bacteria is defined, we can come to the  conclusion that xylose concentration which is above the point can kill the cell  or at least inhibitory the cell growth.</p>
+
The objective of this characterization is to determine the minimal concentration of xylose necessary to inhibit the growth of our B. hercules.
 +
</p>
<p><strong>Method</strong><br />
<p><strong>Method</strong><br />
-
   We assembled ydcD and ydcE into the same  plasmid as our artificial operon. Bacteria carrying the right construct were then cultured in supplemented M9 medium of serial xylose concentration. By  comparing the turbidity of experimental group with the negative control, we got a concentration of xylose above which cells would dye.</p>
+
<i>I. Construct </i> <br>
-
<p><strong>Procedure</strong></p>
+
<div style="margin-left: 30px">
-
<ol>
+
   <p align="center"><img src="https://static.igem.org/mediawiki/2012/0/08/CGIDchar.JPG" width="50%" /></p>
-
  <li>Constructing ^^^^;</li>
+
<br>
-
  <li>Culturing bacteria carrying the right construct in supplemented M9  medium of serial xylose concentration;</li>
+
<em>xylR</em>: The transcriptional regulator for the xylose inducible promoter. <br>
-
  <li>Checking the turbidity of cell culture after ^^ hours;</li>
+
<em>PxylA</em>: The xylose inducible promoter. <br>
-
  <li>Doing several more round of experiment and modifying the result.</li>
+
<em>ydcE (ndoA)</em>: The toxin gene encoding EndoA. <br>
 +
<em>Ptms</em>: The low efficiency constitutive promoter. <br>
 +
<em>ydcD (endB)</em>: The antitoxin gene encoding YdcD. <br>
 +
</div>
 +
<br>
 +
 
 +
<i>II. Culture Medium </i> <br>
 +
Supplemented M9 minimal medium (M9 salt, 1 mM thiamine hydrochloride, 0.2% casamino acids, 0.1 M MgSO<font size="1"><small>4</small></font>, 0.5 M CaCl<font size="1"><small>2</small></font>, 0.4% glycerol) was used for our characterization. The reason for using this medium with 0.4% glycerol (instead of glucose) as a sole carbon source is that glucose can repress the induction of xylose (Kim, Mogk & Schumann,. 1996). 25 mg/mL chloramphenicol stock was diluted 100 times and added to the medium to select for bacterial cells carrying our intended vectors. The final concentration gradient of xylose in the supplemented M9 minimal medium is: 0.05%, 0.10%, 0.15%, 0.20% and 0.25%.<br>
 +
<br>
 +
 
 +
<i>III. Control and Experiment Group </i> <br>
 +
Control Group: <i>E. coli</i> DH10B without any transformed plasmid was used as the control. It was inoculated in the supplemented M9 minimal medium with xylose concentrations: 0.00%, 0.05%, 0.10%, 0.15%, 0.20%, 0.25%. Note that in the control group, the medium does not contain chloramphenicol.<br>
 +
Experiment Group: <i>E. coli</i> DH10B cells containing our cell growth inhibition device were inoculated in the supplemented M9 minimal medium with the following xylose concentrations: 0.00%, 0.05%, 0.10%, 0.15%, 0.20%, 0.25%. The total volume of the culture was 2mL for each test tube.<br><br>
 +
 
 +
<i>IV. Experiment </i> <br>
 +
The bacterial cultures were incubated at 37 degree Celsius, shaken at 200 rpm for exactly 16 hours. After the 16-hour incubation, the turbidity each culture tube was checked and photographed. Later on, 50uL of culture from one set of the experiments was aliquoted and spread on LB plate containing chloramphenicol (25 ug/mL) for overnight incubation. <br><br>
 +
 
 +
</p>
 +
 
 +
 
 +
<p><strong>Result</strong> </p>
 +
<p>
 +
<div style="margin-left":40px>
 +
  <img src="http://partsregistry.org/wiki/images/f/f9/CGIDC.png" width="50%" /><br>
 +
Note that after spreading the bacterial liquid cultures on the plates, bacterial growth was observed in all the tubes belonging to the experiment groups. However, there was distinguishable difference in the extent of bacterial growth between cultures given 0.00%, 0.05% and 0.10% of xylose and those given 0.15%, 0.20% and 0.25% of xylose. That is, in the left three tubes (see picture), the number of bacterial cells (as indicated by culture turbidity) was much greater than that in the right three ones. This result indicates that our<i> E. coli </i> had its growth inhibited but did not die from the xylose- induced toxin expression.<br>
 +
</div>
 +
</p>
 +
<br>
 +
<p><strong>Reference</strong><br />
 +
Pellegrini O, Mathy N, Gogos A, Shapiro L, and Condon C. "The<i> Bacillus subtilis </i>ydcDE operon encodes an endoribonuclease of the MazF/PemK family and its inhibitor.." <i>Molecular microbiology.</i> 56.5 (2005): 1139-1148. Print.<br>
 +
Kim, L., Mogk, A., & Schumann, W. (1996). A xylose-inducible <i>Bacillus subtilis</i> integration vector and its application.. <i>Gene, 181</i>(1-2), 71-76. <br>
 +
Zhang J, Ge Y, Sun L, Cao J, Wu Q, Guo L, Wang Z. Effect of Bone Morphogenetic Protein-2 on Proliferation and Apoptosis of Gastric Cancer Cells.<i> Int J Med Sci </i>2012; 9(2):184-192.
 +
</p>
 +
 
 +
</div>
 +
  <div id="paragraph5" class="bodyParagraphs">
 +
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 +
              <h1>Colon Tumor Binding System</h1>
 +
          </div>
 +
<p><strong>Abstract <u><a href ="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Target_binding" target="_blank" >(link to Target Binding Module)</a></u></strong><br>
 +
A phage displaying peptide, RPMrel, was reported to have the ability to bind to poorly differentiated colon cancer cells while having significantly lower binding affinity to well-differentiated colon cancer cell and other normal tissues including lung, liver and stomach.  (Kelly & Jones, 2003). Displaying RPMrel peptide on <em>B. subtilis</em> cell wall is expected to enable vegetative <em>B. subtilis</em> binding to colon cancer cell line specifically without adhering to other normal epithelial cell. In this characterization, <em>B. subtilis</em> was transfected with integration plasmid pDG1661-BBa_K733007 in order to display RPMrel on its cell wall. Empty vector pDG1661 is also transformed into <em>B. subtilis</em> as negative control. HT-29 (cancer adenocarcinoma) and HBE16 (Human Bronchial epithelial cell) are utilized for adherence test to compare the binding affinity of experiment and control <em>B. subtilis</em> on cancer cell. The binding specificity of RPMrel displaying <em>Bacillus subtilis</em> was also investigated in this characterization.</p><br>
 +
<strong>Materials and Method</strong><br>
 +
<li><strong>Constructing part for <em>B. subtilis</em> characterization</strong><br>
 +
In order to characterize biobrick BBa_K733007 and demonstrate that it functions as expected in <em>Bacillus subtilis</em>, the recombinant DNA constructed needs to be inserted into integration plasmid pDG1661. Therefore, K733007 was first inserted into pBluescript II KS+ through <em>EcoRI</em> and <em>PstI</em> site. The construct in pBluescript II KS+ was further digested with <em>EcoRI</em> and <em>BamHI</em> site in order to insert into the integration vector pDG1661. pDG1661-K733007 was transformed into <i>E. coli</i> DH10B and selected on Ampicillin plate (150 μg/ml). After replicating in <i>E. coli</i>, pDG1661-K733007 was extracted and transformed into <em>B. subtilis</em>. LB plate containing 5μg/ml Chloramphenicol is used to select transformed <em>B. subtilis</em>. All <i>E. coli</i> and <em>B. subtilis</em> transformation were performed strictly follow the protocol uploaded in the protocol section. </li><br>
 +
<li><strong>Mammalian cell culture</strong><br>Colon adenocarcinoma (HT-29) was cultured in McCoy’s 5A medium supplemented with 10% FBS in 5% CO2, 37℃ incubator. Normal human bronchial epithelial cell (HBE16) was cultured in MEM medium supplemented with 10% FBS in 5% CO2, 37℃ incubator. 12-well plate was used to culture both cells to confluent. </li><br>
 +
<li><strong><i>Bacillus subtilis</i> culture</strong><br>
 +
<em>Bacillus subtilis</em> transformed with pDG1661-K733007 and the one transformed with pDG1661 empty vector were cultured separately in LB medium. Overnight cultures were diluted to OD650=0.1 and sub-cultured for another 3 hours until OD650 reached 1. Bacteria were washed in 0.1M PBS 3 times and then re-suspended in McCoy's 5A (without FBS) and MEM medium (without FBS) respectively.</li> <br>
 +
<li><strong>Co-culture <i>Bacillus subtilis</i> with mammalian cell: </strong><br>
 +
Confluent mammalian cells were washed with 0.1M PBS once before adding bacteria. 1ml <em>B. subtilis</em> suspensions were added into each well of mammalian cell culture plate. After co-culturing the mammalian cell with bacteria, 5 times washing with 0.1M PBS was then performed to wash away the free unattached bacteria and proceed further in characterization.</li><br>
 +
<li><strong>Gram staining for detecting the binding between <i>Bacillus subtilis</i> and colon cancer cell:</strong><br>
 +
Cells were fixed with 1% paraformaldehyde for 15 minutes at room temperature. After fixation, 0.0007 % crystal violet was used to stain cells overnight. Stains were washed away the next day with water and observed under inverted microscope with 400X magnification.</li><br>
 +
<li><strong>Adherence assay through CFU calculation</strong><br>
 +
0.1% Triton X-100 in 0.1M PBS was added into the well after PBS washing and incubated for 10 minutes. Cells were then pelleted and re-suspended in LB medium, plating on LB plate to determine CFU. (Sheng et al, 2011)</li><br>
 +
<strong>Result</strong><br>
 +
<p><li><strong>Gram staining </strong><br>
 +
Co-cultured <i>Bacillus subtilis</i> with RPMrel peptide on HT-29 and controlled <i>Bacillus subtilis</i> on HT-29 were stained and observed under inverted microscope with 400X magnification. As shown in Figure 1, <i>Bacillus subtilis</i> and nucleus of HT-29 cell were stained purple and both types of <i>B. subtilis</i> can be detected on HT -29 cell.</li>
 +
 
 +
<p align="center"> <img src="https://static.igem.org/mediawiki/2012/e/ea/HKUST_Characterization_of_RPMrel_construct_and_BMP2_construct.jpg" width="40%" style="float:left"/><img src="https://static.igem.org/mediawiki/2012/6/68/HKUST_Characterization_of_RPMrel_construct_and_BMP2_construct-2.jpg" width="40%" style="float:left"/></p>
 +
 
 +
 
 +
<p style="clear:both">
 +
Figure 1: Gram stain of <i>B. subtilis</i> on confluent HT-29 cell.<br>
 +
A: Gram stain of HT-29 co-cultured with <i>B. subtilis</i> with RPMrel peptide.<br>
 +
B: Gram stain of HT-29 co-cultured with control bacteria, <i>B. subtilis</i> without RPMrel peptide.<br></p>
 +
<p><li><strong>CFU calculation </strong><br>
 +
Serial dilutions were performed before plating and plates with colonies between 25~300 were counted to calculate the CFU/ml. As shown in Table 1 and Figure 1, more <i>Bacillus subtilis</i> with empty vector pDG1661 was detected on HT-29 cell line than the one of <i>B. subtilis</i> with RPMrel peptide on HT-29. Comparing the number of <i>Bacillus subtilis</i> with RPMrel retained on HT-29 and HBE16, more <i>Bacillus subtilis</i> can be detected on HBE16 cell. Two rounds of T-tests were further performed and it showed that no significant differences in the binding affinity between <i>Bacillus subtilis</i> with or without RPMrel to HT-29 cell (P>0.05) but the number of <i>Bacillus subtilis</i> with RPMrel peptide binding to HBE16 cells is significantly higher than the same bacteria bind to HT-29.</li>
 +
<p align="center"> <img src="https://static.igem.org/mediawiki/2012/a/aa/HKUST_table_for_colon_cancer_binding_steven.jpg" width="50%"/></p>
 +
 
 +
Table 1: Number of <i>Bacillus subtilis</i> retained on different mammalian cell line.<br>
 +
<p align="center"> <img src="https://static.igem.org/mediawiki/2012/3/30/HKUST_Number_of_Bacillus_subtilis_retained_on_mammalian_cell.jpg" width="50%"/></p>
 +
Figure 2: Number of Bacillus subtilis retained on different mammalian cell line</p><br>
 +
 
 +
<p><strong>Discussion</strong></p>
 +
<p><li><strong>Experiment results to some extent reject our hypothesis but no solid conclusion can be made at this stage:</strong><br></p>
 +
<p>Based on the results from Table 1 and Figure 2 and the two t-tests performed, it can be stated that <i>B. subtilis</i> with RPMrel displaying have no significant increase in binding ability to cancer cell line and the peptide displaying results in significant improvement in binding to normal epithelial tissue. <br></p>
 +
<p>However, the statement above is just based on the incomplete evidence we have currently. Because of time limitations, we haven’t demonstrated that LytC system can facilitate the display of RPMrel on the cell wall successfully. Therefore, we can hardly tell whether the unexpected result is caused by the unexpected structural changes of RPMrel when displaying on cell wall or because of the failure of the LytC system in transporting and localizing RPMrel on the cell wall.<br></p>
 +
<p>In addition, the Gram staining method used in our characterization is not consistent during our one-month characterization work. Over staining happened from time to time and the cell layers were easily detached from the bottom of the well after adding crystal violet.<br></p>
 +
<p>Besides, more proper control group is needed for our experiment. Because of the limitation of resources and time we had, no normal epithelial cell line from the digestive system can be obtained and used in our work. Substituting with HBE16 cells in the experiment is the best compromise we have so far. If possible, we will try to utilize other cell lines in our experiment in order to draw solid conclusions in the future. <br></p>
 +
<p><li><strong>Future work</strong></li></p><ol>
 +
<li>Using BBa_K733008 (LytC system with FLAG-tag on its C terminus) to verify the proper functioning of the cell wall binding system.</li>
 +
<li>Developing some more reliable staining method to demonstrate the adherence between <i>B. subtilis</i> and mammalian cell.</i>
 +
<li>Proper control bacteria and proper control cell line need to be added in our characterization in order to obtain reliable and solid conclusions. </i>
</ol>
</ol>
-
<p><strong>Result</strong></p>
+
<br>
 +
<p><strong>Reference</strong></p>
 +
<p>Haiqing Sheng, Wang Jing, Lim Ji Youn, Davitt Christine, Minnich Scott A. & Hovde Carolyn J. 2012. Internalization of <i>Escherichia coli</i> O157:H7 by bovine rectal epithelial cells. <i>Frontiers of Microbiology.</i> (2012.2.32)</p>
 +
<p>Kimberly A. Kelly & Jones David A.2003. Isolation of a Colon Tumor Specific Binding Peptide Using Phage Display Selection. <i>Neoplasia.</i> 5: 437 – 444</p>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
</p>
 +
 
           </div>
           </div>
 +
  <div id="paragraph6" class="bodyParagraphs">
 +
          <div align="left">
 +
              <h1>Anti-tumor Molecule Secretion</h1>
 +
          </div>
 +
  <strong>Abstract <u><a href ="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Anti_tumor" target="_blank" >(link to Anti-tumor Molecule Secretion Module)</a></u></strong><br />
 +
  This characterization is intended to  demonstrate that <em>B. subtilis </em>transformed  with BMP2 expression and secretion construct can trigger the apoptosis of colon  cancer. In this characterization, <em>B.  subtilis</em> was co-cultured with HT-29 cell. MTT assay which is widely used as a cell proliferation and viability assay was performed in our experiment to investigate  the growth suppression effect on colon cancer cell.</p>
 +
<p><strong>Material  and Method</strong></p>
 +
<ul>
 +
  <li><strong>Constructing part for <em>B. subtilis</em> characterization  </strong></li>
 +
</ul>
 +
<p align="left">In order to characterize this  construct in <em>B. subtilis</em>, the K733017 was inserted into integration vector  pDG1661. Detailed methods can be referred to the characterization of  BBa_K733007. </p>
 +
<ul>
 +
  <li><strong>Mammalian cell culture</strong></li>
 +
</ul>
 +
<p>Colon adenocarcinoma (HT-29) was cultured in McCoy&rsquo;s 5A medium  supplement with 10% FBS in 5% CO2, 37℃ incubator. They were seeded in 96-well plates for further characterization.</p>
 +
<ul>
 +
  <li><strong><em>Bacillus  subtilis</em></strong><strong> culture </strong></li>
 +
</ul>
 +
<p><em>Bacillus subtilis</em> transformed with pDG1661-K733017 and another  transformed with pDG1661 empty vector were cultured separately in LB medium.  Overnight cultures were diluted to OD650=0.1 and subculture to OD650  reaching 1.0.<em> B. subtilis</em> were washed  three times with 0.1M PBS and diluted to OD=0.1, 0.01, 0.001 and 0.0001 in  McCoy&rsquo;s 5A medium with 10% FBS supplementation. </p>
 +
<ul>
 +
  <li><strong>Co-culture <em>Bacillus subtilis</em> with mammalian cell </strong></li>
 +
</ul>
 +
<p>3000 HT-29 cells in 100μl were seeded in 96-well plates. After overnight incubation, 100μl <em>B. subtilis</em> suspension is added into each well and co-cultured with  HT-29 cell for 48 hours. </p>
 +
<ul>
 +
  <li><strong>MTT assay </strong></li>
 +
</ul>
 +
<p>Cells were washed 5 times with 0.1M PBS. 0.5% MTT solution was  added and incubated at 37℃ for 4 hours. After incubation, 100ul DMSO was  added into each well, shaking for 5 minutes in order to obtain a homogenized  solution. A570 was measured then to reflect the  viability of cells. Percentage of viability was calculated through the equation <img width="342" height="26" src="https://static.igem.org/mediawiki/2012/b/bb/Clip_image002.png" /> <br />
 +
  <strong>Result </strong><br />
 +
  A declining trend of cell  proliferation can be clearly observed when more bacteria were co-cultured with HT-29  cell as shown in Figure 1. Comparing the proliferation rate of HT-29 cells which  were co-cultured with BMP2 producing<em> B.  subtilis</em> and non-BMP2 producing <em>B.  subtilis</em>, a significant decline can be detected when initial OD650 of <em>B. subtilis </em>equaled to 0.1 and 0.01.  (P&lt;0.05 ). No significant difference can be detected when OD650 decreased to  0.001. When the OD650 reaches 0.0001, significant increase in cell  proliferation rate can be detected in the experiment group. </p><p align="center"><img width=80% src="https://static.igem.org/mediawiki/2012/7/7f/Mmm.jpg"></p>
 +
 +
 +
<p>Figure 1: The viability of HT-29 cell after co-cultured with <i>B. subtilis</i></p>
 +
 +
<p style="clear:both"><strong>Discussion </strong><br />
 +
In this characterization, <em>Bacillus subtilis</em> transformed with plasmid pDG161-K733017 exert  significant growth inhibition effect when OD650 is above 0.01. However, no extra supporting experiments like Western Blot has been successfully carried out to  confirm the expression of BMP2 in <em>B.  subtilis</em>. Therefore, more experiments need to be done in order to fully  characterize this BioBrick.</p>
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<li><p><a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Project_Abstraction">Abstract</a></p></li>
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<li><p><a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Background_and_Motive">Motive</a></p></li>
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<li><p><a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Design_Overview">Design - Overview</a></p></li>
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<li><p><a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Design_Module">Design - Module</a></p></li>
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<p>-- <a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Target_binding">Target Binding Module</a></p>
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<p>-- <a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Anti_tumor">Anti-tumor Molecule Secretion Module</a></p>
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<p>-- <a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Module/Regulation_and_control">Regulation and Control Module</a></p>
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<li><p><a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Design_Chassis">Design - Chassis</a></p></li></ol>
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<li><p><a href="https://2012.igem.org/Team:HKUST-Hong_Kong/Characterization">Characterization</a></p></li>
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Latest revision as of 00:41, 27 September 2012

Team:HKUST-Hong Kong - 2012.igem.org

Characterization

Introduction

In our project, we have characterized two promoters and the cell death device using different methods. The results indicate that our parts are functional and we can quantitatively control their activities by changing the experimental conditions.

Low Efficiency Constitutive Promoter Ptms

Background Information (link to Regulation and Control Module)
The key reason for using this low efficiency constitutive promoter in our construct is to enable our bacteria to express a low level of antitoxin so that the bacterial cell can only tolerate a certain amount of toxin. As the expression of BMP2 is tightly linked to the toxin, its expression can be regulated accordingly.


Objective
Our objective in characterizing this promoter is to test whether Ptms works in E. coli DH10B strain and determine its relative promoter unit (RPU) compared to the standard constitutive promoter (a promoter whose activity is arbitrarily valued at 1.0 by partsregistry.org).


Intended Result
1. Ptms should work in E. coli. This is supported by previous research (Moran et al., 1982).
2. The activity of Ptms should be relatively low.


Method
Instead of using the absolute promoter activity as the final result, our characterization was based on obtaining the in vivo activity of this constitutive promoter. Adopting this method enables us to eliminate errors caused by different experimental conditions and give a more convincing result.
By linking the promoter with GFP (BBa_E0240), the promoter activity was represented by the GFP synthesis rate which can be easily measured. E. coli carrying the right construct was then cultured to log phase. At a time point around the mid-log phase, the GFP intensity and OD595 values were measured to obtain the Relative Promoter Units (RPU).


Characterization Procedure

  1. Constructing BBa_K733009-pSB3K3 (Ptms-BBa_E0240-pSB3K3); Transforming BBa_I20260-pSB3K3 (Standard Constitutive Promoter/Reference Promoter) from the 2012 Distribution Kit;
  2. Preparing supplemented M9 medium (see below);
  3. Culturing E. coli DH10B strain carrying BBa_K733009-pSB3K3 and E. coli carrying BBa_I20260-pSB3K3 in supplemented M9 medium and measuring the respective growth curves;
  4. Measuring the GFP intensity and OD595 values every 15 minutes after the above mentioned E. coli strains are cultured to mid-log phase;
  5. Calculating the Relative Promoter Units (RPU) using the obtained data;
  6. Compiling the results.

Data Processing

  1. After E. coli carrying the right construct was grown to mid-log phase, GFP intensity and OD595 were measured every 15 minutes (up to 60 mins);
  2. For GFP intensity, curve reflecting GFP expression change was plotted; for OD595, average values were taken;
  3. GFP synthesis rate was then obtained by calculating the slope of linear regression line of the above mentioned curve;
  4. Absolute promoter activity of Ptms and BBa_I20260 were calculated by dividing the corresponding GFP synthesis rate over the average OD595 value;
  5. Averaged absolute promoter activity was then obtained by averaging the respective sets of absolute promoter activity values;
  6. Finally, R.P.U was calculated by dividing the averaged Ptms absolute promoter activity over the averaged BBa_I20260 absolute promoter activity.

Result

1. Suggested by the GFP expression curve we plotted, Ptms functions in E.coli DH10B strain.


* Above: GFP expression curve for one set of data

2. The RPU of Ptms obtained was 0.046497. This shows that Ptms has a very low promoter efficiency in E.coli DH10B strain.



Discussion
Compared to BBa_I20260, it seems that E. coli carrying Ptms-GFP has a rather low GFP expression. This may cause some difficulties in deciding whether Ptms functions in E. coli or not. However, referring to the curve (for GFP Intensity), the GFP expression for Ptms increased gradually with respect to time. This suggests that Ptms functions in E. coli DH10B strain, although with a low efficiency. A possible reason for its low efficiency could be that Ptms was originally from B. subtilis but was functioning in a heterologous system when placed in E. coli. Due to time constraints, we were unable to characterize the promoter in B. subtilis, and we still hope that we can address this in the future.


Reference
Moran, C., Lang, N., LeGrice, S., Lee, G., Stephens, M., Sonenshein, A., et al. (1982). Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis..Molecular and General Genetics MGG,186, 339-346.


Supplemented M9 Medium Composition
1. 5X M9 Salt Composition (1L)

(1) 64g Na2HPO4﹒7H2O
(2) 15g KH2PO4
(3) 2.5g NaCl
(4) 5.0g NH4CL
2. Minimal 1X M9 medium (1L)
(1) 200ml of 5X M9 Salt
(2) 2ml of 1M MgSO4
(3) 100μl of 1M CaCl2
(4) 5ml of 40% glycerol
3. Supplement (for the final medium)
(1) 1mM thiamine hydrochloride
(2) 0.2% casamino acids

Xylose Inducible Promoter

Background Information (link to Regulation and Control Module)
The reason for using the xylose inducible promoter is to enable control on the expression of toxin and BMP2. Xylose is not toxic and normally not present in the human colon. This provides us an easy way to induce BMP2 expression without disrupting normal human body function.


Objective
On characterization, we want to test whether the promoter works in E. coli DH10B strain and if it works, what is the absolute promoter activity under varied experimental condition (i.e. xylose concentration).


Intended Result
1. Xylose inducible promoter is functional in E. coli.
2. After the inducer concentration has reached a certain level, a relatively stationary GFP expression level (expression upper-limit) should be observed.


Method
The absolute promoter activity was measured with respect to xylose concentration.
The same reporter gene (BBa_E0240) was used to indicate promoter activity. E. coli carrying the right construct was cultured to log phase. Following the addition of xylose at various predetermined concentrations, at a time point around the mid-log phase, the GFP intensity and OD595 were measured for every 30 mins (up to 120 mins). Independent curves indicating the GFP intensity units (of various xylose concentrations) with respect to time were then plotted, following which the respective absolute promoter activities were calculated.


Characterization Procedure

  1. Constructing xylR-PxylA-BBa_E0240-pSB1A2
  2. Preparing supplemented M9 medium (see below);
  3. Culturing E. coli carrying xylR-PxylA-BBa_E0240-pSB1A2 and E. coli without constructs in supplemented M9 medium and measuring the growth curve respectively;
  4. Culturing the above mentioned bacteria in supplemented M9 medium to log phase;
  5. Adding xylose at different concentrations to different sets of bacterial culture;
  6. Measuring the GFP intensity and OD595 values across time for every set of bacterial culture containing different xylose concentrations;
  7. Plotting independent curves showing the GFP intensity units of various xylose concentrations with respect to time;
  8. Plotting a graph to demonstrate the absolute promoter activity under different inducer concentrations;
  9. Compiling the results.

Data Processing

  1. After E. coli carrying the right construct was grown to mid-log phase, GFP intensity and OD595 were measured every 30 minutes (up to 120 mins);
  2. For GFP intensity, curve reflecting GFP expression change was plotted; for OD595, average value was taken;
  3. GFP synthesis rate was then obtained by calculating the slope of linear regression line of the above mentioned curve;
  4. Absolute promoter activity for the promoter under different inducer concentrations were calculated by dividing the corresponding GFP synthesis rate over the average OD595 value;
  5. Averaged absolute promoter activity was then obtained by averaging the respective sets of absolute promoter activity values.

Result

  1. Shown in the figure below, with the addition of xylose, GFP expression increased. This tells us that the xylose inducible promoter is functional in E. coli DH10B strain.
  2. When no xylose was added, a limited amount of GFP was expressed. This suggests that the xylose inducible promoter is to some extent leaky.
  3. A relatively stationary GFP expression level was observed at xylose concentrations of 1% to 5%. Despite some other variables (see discussion for more details), the data suggests that the minimum inducer concentration for triggering a full induction should lie somewhere between 0% and 1%
  4. For 10% inducer concentration, the GFP expression was relatively lower. There could be several reasons for this occurence, such as suboptimal growth conditions due to high osmotic pressure. (see discussion for more details)


Discussion

  1. It is quite obvious that addition of xylose induces GFP expression in this construct. However, a slight issue remains: even when no xylose was added, a minute but detectable amount of GFP was still expressed. This shows that the xylose inducible promoter is leaky. It should be noteworthy that this version of the xylose inducible promoter has undergone mutagenesis on 3 different sites on the repressive gene for standardization purposes. Even so, the mutagenesis is done while preserving an identical codon translation. As such, similar to the Ptms promoter, activity of the xylR-PxylA promoter might be different in E. coli from that of B. subtilis due to expression in a heterologous system. Further characterization on this promoter in B. subtilis would be our future aim as time was limited.
  2. Another interesting fact to note is that the E. coli strain used is one in which it's xylose metabolic operon remains active. As such, one might assume that the observed GFP expression upper-limit ("stationary expression level"),particularly at 1% or 2% is not the "true" upper-limit, since there should be underlying metabolism of xylose. In order to eliminate this possible error, higher concentrations of xylose was used and the promoter activity does not appear to vary greatly, suggesting that the stationary expression level reflects the maximum promoter activity. While this problem is solved, due to the relatively large concentration difference of inducer, it appears that the maximum promoter activity was achieved at 1% xylose, implying that we are unable to determine the exact minimum inducer concentration requirement for maximum activity. Based on the current result, it is safe for us to make a conjecture that the minimum concentration required lies between 0% and 1% xylose.
  3. For the decreased GFP expression at 10% xylose concentration, one possible reason is that the high osmotic pressure caused by the xylose in the medium may inhibit the growth and metabolism of bacteria, thus reducing the bacterial population and/or its GFP expression. Another possible, but unlikely reason could be that the over-expression of induced GFP expression may disturb the normal bacterial function, leading to a low overall GFP expression.

Supplemented M9 Medium Composition
1. 5X M9 Salt Composition (1L)

(1) 64g Na2HPO4﹒7H2O
(2) 15g KH2PO4
(3) 2.5g NaCl
(4) 5.0g NH4CL
2. Minimal 1X M9 medium (1L)
(1) 200ml of 5X M9 Salt
(2) 2ml of 1M MgSO4
(3) 100μl of 1M CaCl2
(4) 5ml of 40% glycerol
3. Supplement (for the final medium)
(1) 1mM thiamine hydrochloride
(2) 0.2% casamino acids

YdcDE Growth Inhibition Device

Background Information (link to Regulation and Control Module)
The rationale for including this growth inhibition device is that over-dose of BMP2 can possibly cause unexpected proliferation of healthy colon epithelial cells (Zhang et al., 2012). Thus, a growth inhibition device is introduced and will be characterized.

Objective
The objective of this characterization is to determine the minimal concentration of xylose necessary to inhibit the growth of our B. hercules.

Method
I. Construct


xylR: The transcriptional regulator for the xylose inducible promoter.
PxylA: The xylose inducible promoter.
ydcE (ndoA): The toxin gene encoding EndoA.
Ptms: The low efficiency constitutive promoter.
ydcD (endB): The antitoxin gene encoding YdcD.

II. Culture Medium
Supplemented M9 minimal medium (M9 salt, 1 mM thiamine hydrochloride, 0.2% casamino acids, 0.1 M MgSO4, 0.5 M CaCl2, 0.4% glycerol) was used for our characterization. The reason for using this medium with 0.4% glycerol (instead of glucose) as a sole carbon source is that glucose can repress the induction of xylose (Kim, Mogk & Schumann,. 1996). 25 mg/mL chloramphenicol stock was diluted 100 times and added to the medium to select for bacterial cells carrying our intended vectors. The final concentration gradient of xylose in the supplemented M9 minimal medium is: 0.05%, 0.10%, 0.15%, 0.20% and 0.25%.

III. Control and Experiment Group
Control Group: E. coli DH10B without any transformed plasmid was used as the control. It was inoculated in the supplemented M9 minimal medium with xylose concentrations: 0.00%, 0.05%, 0.10%, 0.15%, 0.20%, 0.25%. Note that in the control group, the medium does not contain chloramphenicol.
Experiment Group: E. coli DH10B cells containing our cell growth inhibition device were inoculated in the supplemented M9 minimal medium with the following xylose concentrations: 0.00%, 0.05%, 0.10%, 0.15%, 0.20%, 0.25%. The total volume of the culture was 2mL for each test tube.

IV. Experiment
The bacterial cultures were incubated at 37 degree Celsius, shaken at 200 rpm for exactly 16 hours. After the 16-hour incubation, the turbidity each culture tube was checked and photographed. Later on, 50uL of culture from one set of the experiments was aliquoted and spread on LB plate containing chloramphenicol (25 ug/mL) for overnight incubation.

Result


Note that after spreading the bacterial liquid cultures on the plates, bacterial growth was observed in all the tubes belonging to the experiment groups. However, there was distinguishable difference in the extent of bacterial growth between cultures given 0.00%, 0.05% and 0.10% of xylose and those given 0.15%, 0.20% and 0.25% of xylose. That is, in the left three tubes (see picture), the number of bacterial cells (as indicated by culture turbidity) was much greater than that in the right three ones. This result indicates that our E. coli had its growth inhibited but did not die from the xylose- induced toxin expression.


Reference
Pellegrini O, Mathy N, Gogos A, Shapiro L, and Condon C. "The Bacillus subtilis ydcDE operon encodes an endoribonuclease of the MazF/PemK family and its inhibitor.." Molecular microbiology. 56.5 (2005): 1139-1148. Print.
Kim, L., Mogk, A., & Schumann, W. (1996). A xylose-inducible Bacillus subtilis integration vector and its application.. Gene, 181(1-2), 71-76.
Zhang J, Ge Y, Sun L, Cao J, Wu Q, Guo L, Wang Z. Effect of Bone Morphogenetic Protein-2 on Proliferation and Apoptosis of Gastric Cancer Cells. Int J Med Sci 2012; 9(2):184-192.

Colon Tumor Binding System

Abstract (link to Target Binding Module)
A phage displaying peptide, RPMrel, was reported to have the ability to bind to poorly differentiated colon cancer cells while having significantly lower binding affinity to well-differentiated colon cancer cell and other normal tissues including lung, liver and stomach. (Kelly & Jones, 2003). Displaying RPMrel peptide on B. subtilis cell wall is expected to enable vegetative B. subtilis binding to colon cancer cell line specifically without adhering to other normal epithelial cell. In this characterization, B. subtilis was transfected with integration plasmid pDG1661-BBa_K733007 in order to display RPMrel on its cell wall. Empty vector pDG1661 is also transformed into B. subtilis as negative control. HT-29 (cancer adenocarcinoma) and HBE16 (Human Bronchial epithelial cell) are utilized for adherence test to compare the binding affinity of experiment and control B. subtilis on cancer cell. The binding specificity of RPMrel displaying Bacillus subtilis was also investigated in this characterization.


Materials and Method
  • Constructing part for B. subtilis characterization
    In order to characterize biobrick BBa_K733007 and demonstrate that it functions as expected in Bacillus subtilis, the recombinant DNA constructed needs to be inserted into integration plasmid pDG1661. Therefore, K733007 was first inserted into pBluescript II KS+ through EcoRI and PstI site. The construct in pBluescript II KS+ was further digested with EcoRI and BamHI site in order to insert into the integration vector pDG1661. pDG1661-K733007 was transformed into E. coli DH10B and selected on Ampicillin plate (150 μg/ml). After replicating in E. coli, pDG1661-K733007 was extracted and transformed into B. subtilis. LB plate containing 5μg/ml Chloramphenicol is used to select transformed B. subtilis. All E. coli and B. subtilis transformation were performed strictly follow the protocol uploaded in the protocol section.

  • Mammalian cell culture
    Colon adenocarcinoma (HT-29) was cultured in McCoy’s 5A medium supplemented with 10% FBS in 5% CO2, 37℃ incubator. Normal human bronchial epithelial cell (HBE16) was cultured in MEM medium supplemented with 10% FBS in 5% CO2, 37℃ incubator. 12-well plate was used to culture both cells to confluent.

  • Bacillus subtilis culture
    Bacillus subtilis transformed with pDG1661-K733007 and the one transformed with pDG1661 empty vector were cultured separately in LB medium. Overnight cultures were diluted to OD650=0.1 and sub-cultured for another 3 hours until OD650 reached 1. Bacteria were washed in 0.1M PBS 3 times and then re-suspended in McCoy's 5A (without FBS) and MEM medium (without FBS) respectively.

  • Co-culture Bacillus subtilis with mammalian cell:
    Confluent mammalian cells were washed with 0.1M PBS once before adding bacteria. 1ml B. subtilis suspensions were added into each well of mammalian cell culture plate. After co-culturing the mammalian cell with bacteria, 5 times washing with 0.1M PBS was then performed to wash away the free unattached bacteria and proceed further in characterization.

  • Gram staining for detecting the binding between Bacillus subtilis and colon cancer cell:
    Cells were fixed with 1% paraformaldehyde for 15 minutes at room temperature. After fixation, 0.0007 % crystal violet was used to stain cells overnight. Stains were washed away the next day with water and observed under inverted microscope with 400X magnification.

  • Adherence assay through CFU calculation
    0.1% Triton X-100 in 0.1M PBS was added into the well after PBS washing and incubated for 10 minutes. Cells were then pelleted and re-suspended in LB medium, plating on LB plate to determine CFU. (Sheng et al, 2011)

  • Result

  • Gram staining
    Co-cultured Bacillus subtilis with RPMrel peptide on HT-29 and controlled Bacillus subtilis on HT-29 were stained and observed under inverted microscope with 400X magnification. As shown in Figure 1, Bacillus subtilis and nucleus of HT-29 cell were stained purple and both types of B. subtilis can be detected on HT -29 cell.
  • Figure 1: Gram stain of B. subtilis on confluent HT-29 cell.
    A: Gram stain of HT-29 co-cultured with B. subtilis with RPMrel peptide.
    B: Gram stain of HT-29 co-cultured with control bacteria, B. subtilis without RPMrel peptide.

  • CFU calculation
    Serial dilutions were performed before plating and plates with colonies between 25~300 were counted to calculate the CFU/ml. As shown in Table 1 and Figure 1, more Bacillus subtilis with empty vector pDG1661 was detected on HT-29 cell line than the one of B. subtilis with RPMrel peptide on HT-29. Comparing the number of Bacillus subtilis with RPMrel retained on HT-29 and HBE16, more Bacillus subtilis can be detected on HBE16 cell. Two rounds of T-tests were further performed and it showed that no significant differences in the binding affinity between Bacillus subtilis with or without RPMrel to HT-29 cell (P>0.05) but the number of Bacillus subtilis with RPMrel peptide binding to HBE16 cells is significantly higher than the same bacteria bind to HT-29.
  • Table 1: Number of Bacillus subtilis retained on different mammalian cell line.

    Figure 2: Number of Bacillus subtilis retained on different mammalian cell line


    Discussion

  • Experiment results to some extent reject our hypothesis but no solid conclusion can be made at this stage:

    Based on the results from Table 1 and Figure 2 and the two t-tests performed, it can be stated that B. subtilis with RPMrel displaying have no significant increase in binding ability to cancer cell line and the peptide displaying results in significant improvement in binding to normal epithelial tissue.

    However, the statement above is just based on the incomplete evidence we have currently. Because of time limitations, we haven’t demonstrated that LytC system can facilitate the display of RPMrel on the cell wall successfully. Therefore, we can hardly tell whether the unexpected result is caused by the unexpected structural changes of RPMrel when displaying on cell wall or because of the failure of the LytC system in transporting and localizing RPMrel on the cell wall.

    In addition, the Gram staining method used in our characterization is not consistent during our one-month characterization work. Over staining happened from time to time and the cell layers were easily detached from the bottom of the well after adding crystal violet.

    Besides, more proper control group is needed for our experiment. Because of the limitation of resources and time we had, no normal epithelial cell line from the digestive system can be obtained and used in our work. Substituting with HBE16 cells in the experiment is the best compromise we have so far. If possible, we will try to utilize other cell lines in our experiment in order to draw solid conclusions in the future.

  • Future work
    1. Using BBa_K733008 (LytC system with FLAG-tag on its C terminus) to verify the proper functioning of the cell wall binding system.
    2. Developing some more reliable staining method to demonstrate the adherence between B. subtilis and mammalian cell.
    3. Proper control bacteria and proper control cell line need to be added in our characterization in order to obtain reliable and solid conclusions.

    Reference

    Haiqing Sheng, Wang Jing, Lim Ji Youn, Davitt Christine, Minnich Scott A. & Hovde Carolyn J. 2012. Internalization of Escherichia coli O157:H7 by bovine rectal epithelial cells. Frontiers of Microbiology. (2012.2.32)

    Kimberly A. Kelly & Jones David A.2003. Isolation of a Colon Tumor Specific Binding Peptide Using Phage Display Selection. Neoplasia. 5: 437 – 444

    Anti-tumor Molecule Secretion

    Abstract (link to Anti-tumor Molecule Secretion Module)
    This characterization is intended to demonstrate that B. subtilis transformed with BMP2 expression and secretion construct can trigger the apoptosis of colon cancer. In this characterization, B. subtilis was co-cultured with HT-29 cell. MTT assay which is widely used as a cell proliferation and viability assay was performed in our experiment to investigate the growth suppression effect on colon cancer cell.

    Material and Method

    • Constructing part for B. subtilis characterization

    In order to characterize this construct in B. subtilis, the K733017 was inserted into integration vector pDG1661. Detailed methods can be referred to the characterization of BBa_K733007.

    • Mammalian cell culture

    Colon adenocarcinoma (HT-29) was cultured in McCoy’s 5A medium supplement with 10% FBS in 5% CO2, 37℃ incubator. They were seeded in 96-well plates for further characterization.

    • Bacillus subtilis culture

    Bacillus subtilis transformed with pDG1661-K733017 and another transformed with pDG1661 empty vector were cultured separately in LB medium. Overnight cultures were diluted to OD650=0.1 and subculture to OD650 reaching 1.0. B. subtilis were washed three times with 0.1M PBS and diluted to OD=0.1, 0.01, 0.001 and 0.0001 in McCoy’s 5A medium with 10% FBS supplementation.

    • Co-culture Bacillus subtilis with mammalian cell

    3000 HT-29 cells in 100μl were seeded in 96-well plates. After overnight incubation, 100μl B. subtilis suspension is added into each well and co-cultured with HT-29 cell for 48 hours.

    • MTT assay

    Cells were washed 5 times with 0.1M PBS. 0.5% MTT solution was added and incubated at 37℃ for 4 hours. After incubation, 100ul DMSO was added into each well, shaking for 5 minutes in order to obtain a homogenized solution. A570 was measured then to reflect the viability of cells. Percentage of viability was calculated through the equation
    Result
    A declining trend of cell proliferation can be clearly observed when more bacteria were co-cultured with HT-29 cell as shown in Figure 1. Comparing the proliferation rate of HT-29 cells which were co-cultured with BMP2 producing B. subtilis and non-BMP2 producing B. subtilis, a significant decline can be detected when initial OD650 of B. subtilis equaled to 0.1 and 0.01. (P<0.05 ). No significant difference can be detected when OD650 decreased to 0.001. When the OD650 reaches 0.0001, significant increase in cell proliferation rate can be detected in the experiment group.

    Figure 1: The viability of HT-29 cell after co-cultured with B. subtilis

    Discussion
    In this characterization, Bacillus subtilis transformed with plasmid pDG161-K733017 exert significant growth inhibition effect when OD650 is above 0.01. However, no extra supporting experiments like Western Blot has been successfully carried out to confirm the expression of BMP2 in B. subtilis. Therefore, more experiments need to be done in order to fully characterize this BioBrick.