Team:Peking/DataPage/Parts

From 2013.igem.org

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.Navbar_Item > ul > li {float:left; list-style:none; text-align:center; background-color:transparent; position:relative; top:10px; padding:0 10px;}
.Navbar_Item > ul > li {float:left; list-style:none; text-align:center; background-color:transparent; position:relative; top:10px; padding:0 10px;}
.Navbar_Item:hover{ border-bottom:1px solid #D00000; color:#D00000; background-color:#fafaf8;}
.Navbar_Item:hover{ border-bottom:1px solid #D00000; color:#D00000; background-color:#fafaf8;}
-
.Navbar_Item:hover > ul{ display:block;}
+
.Navbar_Item:hover > ul{zoom:1; display:block;}
.Navbar_Item:hover >a {color:#D00000; background-color:#fafaf8;}
.Navbar_Item:hover >a {color:#D00000; background-color:#fafaf8;}
.Navbar_Item > ul > li:hover {border-bottom:1px solid #D00000; color:#D00000; background-color:#fafaf8;}
.Navbar_Item > ul > li:hover {border-bottom:1px solid #D00000; color:#D00000; background-color:#fafaf8;}
.Navbar_Item > ul > li:hover >a {color:#D00000}
.Navbar_Item > ul > li:hover >a {color:#D00000}
 +
.BackgroundofSublist{position:absolute; left:-1000px; width:2000px; height:80px; background-color:#ffffff; opacity:0;}
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#DataPage_Sublist{position:relative; top:0px; left:-60px;}
#DataPage_Sublist{position:relative; top:0px; left:-60px;}
#Safety_Sublist{position:relative; top:0px; left:-180px;}
#Safety_Sublist{position:relative; top:0px; left:-180px;}
-
#HumanPractice_Sublist{position:relative; top:0px; left:-360px;}
+
#HumanPractice_Sublist{position:relative; top:0px; left:-470px;}
#iGEM_logo{position:absolute; top:30px; left:1090px; height:80px;}
#iGEM_logo{position:absolute; top:30px; left:1090px; height:80px;}
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#ProjectList{position:absolute; top:120px; left:5px; color:#ffffff; font-family: calibri, arial, helvetica, sans-serif;}
#ProjectList{position:absolute; top:120px; left:5px; color:#ffffff; font-family: calibri, arial, helvetica, sans-serif;}
#ProjectList > li {display:block; list-style-type:none; width:180px; height:30px; font-size:20px; text-align:left; background-color:transparent;}
#ProjectList > li {display:block; list-style-type:none; width:180px; height:30px; font-size:20px; text-align:left; background-color:transparent;}
-
#ProjectList a {color:#ffffff; text-decoration:none; line-height:30px;}
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.SensorsListItem>a {color:#ffffff; text-decoration:none;}
 +
.SensorsListItem:hover >a{color:#999999;}
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/*Parts Editing Area*/
/*Parts Editing Area*/
-
#PartsEditingArea{position:absolute; left:200px; top:340px; width:1000px; height:3000px; background-color:#ffffff; padding:60px 0;}
+
#PartsEditingArea{position:absolute; left:200px; top:340px; width:1000px; height:6150px; background-color:#ffffff; padding:60px 0;}
-
#PartsEditingArea a{color:#5cc33c}
+
#PartsEditingArea a{color:#5cc33c; font-weight:bold;}
.SmallBoxs{position:absolute; width:400px; height:300px; background-color:#eeeeee;}
.SmallBoxs{position:absolute; width:400px; height:300px; background-color:#eeeeee;}
#FavoritePart1{top:150px; left:80px;}
#FavoritePart1{top:150px; left:80px;}
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#ImprovedPart{position:absolute;top:890px; left:80px; width:840px; height:300px; background-color:#e5e5e5;}
#ImprovedPart{position:absolute;top:890px; left:80px; width:840px; height:300px; background-color:#e5e5e5;}
-
#OtherPart{position:absolute;top:1290px; left:80px; width:840px; height:1500px; background-color:#e5e5e5;}
+
#OtherPart{position:absolute;top:1290px; left:80px; width:840px; height:2050px; background-color:#e5e5e5;}
-
#Dataplot{position:absolute;top:2900px; left:80px; width:840px; height:0px; background-color:white;}
+
 +
#Dataplot{position:absolute;top:3450px; left:80px; width:840px; height:0px; background-color:white;}
 +
 +
#BiosensorFigure3{line-height:20px; text-align:justify; position:relative; top:20px ; left:10px; width:800px; border-bottom:0px; color:#1b1b1b; font-size:14px;font-family:arial,calibri,helvetica,sans-serif;}
 +
#Figure2{line-height:20px; text-align:justify; position:relative; top:20px ; left:10px; width:800px; border-bottom:0px; color:#1b1b1b; font-size:14px;font-family:arial,calibri,helvetica,sans-serif;}
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#Title2{position: absolute; top:810px; left:80px; width:200px; background-color:#5cc33c;font-size:25px; font-family:calibri,Arial, Helvetica, sans-serif;line-height:40px; text-align:center;font-weight:bold; font-style:Italic;height:60px;color:#ffffff;}
#Title3{position: absolute; top:1210px; left:80px; width:200px; background-color:#5cc33c;font-size:25px; font-family:calibri,Arial, Helvetica, sans-serif;line-height:40px; text-align:center; font-weight:bold; font-style:Italic;height:60px;color:#ffffff;}
#Title3{position: absolute; top:1210px; left:80px; width:200px; background-color:#5cc33c;font-size:25px; font-family:calibri,Arial, Helvetica, sans-serif;line-height:40px; text-align:center; font-weight:bold; font-style:Italic;height:60px;color:#ffffff;}
-
#Title4{position: absolute; top:2810px; left:80px; width:200px; background-color:#5cc33c;font-size:25px; font-family:calibri,Arial, Helvetica, sans-serif;line-height:40px; text-align:center; font-weight:bold; font-style:Italic;height:60px;color:#ffffff;}
+
#Title4{position: absolute; top:3360px; left:80px; width:200px; background-color:#5cc33c;font-size:25px; font-family:calibri,Arial, Helvetica, sans-serif;line-height:40px; text-align:center; font-weight:bold; font-style:Italic;height:60px;color:#ffffff;}
/*End of Parts Editing Area*/
/*End of Parts Editing Area*/
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<ul id="navigationbar">
<ul id="navigationbar">
<li id="PKU_navbar_Home" class="Navbar_Item">
<li id="PKU_navbar_Home" class="Navbar_Item">
 +
                       
<a href="https://2013.igem.org/Team:Peking">Home</a>
<a href="https://2013.igem.org/Team:Peking">Home</a>
<ul id="Home_Sublist" >
<ul id="Home_Sublist" >
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</li>
</li>
<li id="PKU_navbar_Team" class="Navbar_Item">
<li id="PKU_navbar_Team" class="Navbar_Item">
-
<a >Team</a>
+
<a href="">Team</a>
<ul id="Team_Sublist">
<ul id="Team_Sublist">
 +
                                <div class="BackgroundofSublist"></div>
<li><a href="https://2013.igem.org/Team:Peking/Team/Members">Members</a></li>
<li><a href="https://2013.igem.org/Team:Peking/Team/Members">Members</a></li>
<li><a href="https://2013.igem.org/Team:Peking/Team/Notebook">Notebook</a></li>
<li><a href="https://2013.igem.org/Team:Peking/Team/Notebook">Notebook</a></li>
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<a href="https://2013.igem.org/Team:Peking/Project">Project</a>
<a href="https://2013.igem.org/Team:Peking/Project">Project</a>
<ul id="Project_Sublist">
<ul id="Project_Sublist">
 +
                                <div class="BackgroundofSublist"></div>
                                 <li><a href="https://2013.igem.org/Team:Peking/Project/SensorMining">Biosensor Mining</a></li>
                                 <li><a href="https://2013.igem.org/Team:Peking/Project/SensorMining">Biosensor Mining</a></li>
<li><a href="https://2013.igem.org/Team:Peking/Project/BioSensors">Biosensors</a></li>
<li><a href="https://2013.igem.org/Team:Peking/Project/BioSensors">Biosensors</a></li>
-
<li><a href="https://2013.igem.org/Team:Peking/Project/Plugins">Adapters</a></li>
+
<li><a href="https://2013.igem.org/Team:Peking/Project/Plugins">Adaptors</a></li>
<li><a href="https://2013.igem.org/Team:Peking/Project/BandpassFilter">Band-pass Filter</a></li>
<li><a href="https://2013.igem.org/Team:Peking/Project/BandpassFilter">Band-pass Filter</a></li>
 +
                                <li><a href="https://2013.igem.org/Team:Peking/Project/Devices">Devices</a></li>
</ul>
</ul>
</li>
</li>
<li id="PKU_navbar_Model" class="Navbar_Item">
<li id="PKU_navbar_Model" class="Navbar_Item">
-
<a href="https://2013.igem.org/Team:Peking/Model">Model</a>
+
<a href="">Model</a>
<ul id="Model_Sublist">
<ul id="Model_Sublist">
 +
                                <div class="BackgroundofSublist"></div>
 +
                                <li><a href="https://2013.igem.org/Team:Peking/Model">Band-pass Filter</a></li>
 +
                                <li><a href="https://2013.igem.org/Team:Peking/ModelforFinetuning">Biosensor Fine-tuning</a></li>
</ul>
</ul>
</li>
</li>
                         <li id="PKU_navbar_HumanPractice" class="Navbar_Item" style="width:90px">
                         <li id="PKU_navbar_HumanPractice" class="Navbar_Item" style="width:90px">
-
<a >Data page</a>
+
<a href="">Data page</a>
-
<ul id="DataPage_Sublist">
+
<ul id="DataPage_Sublist">
 +
                                <div class="BackgroundofSublist"></div>
                                 <li><a href="https://2013.igem.org/Team:Peking/DataPage/Parts">Parts</a></li>
                                 <li><a href="https://2013.igem.org/Team:Peking/DataPage/Parts">Parts</a></li>
<li><a href="https://2013.igem.org/Team:Peking/DataPage/JudgingCriteria">Judging Criteria</a></li>
<li><a href="https://2013.igem.org/Team:Peking/DataPage/JudgingCriteria">Judging Criteria</a></li>
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<li id="PKU_navbar_HumanPractice" class="Navbar_Item" style="width:120px">
<li id="PKU_navbar_HumanPractice" class="Navbar_Item" style="width:120px">
<a href="https://2013.igem.org/Team:Peking/HumanPractice">Human Practice</a>
<a href="https://2013.igem.org/Team:Peking/HumanPractice">Human Practice</a>
-
<ul id="HumanPractice_Sublist">
+
<ul id="HumanPractice_Sublist">
-
                                 <li><a href="https://2013.igem.org/Team:Peking/HumanPractice/Questionnaire">Questionnaire</a></li>
+
                                <div class="BackgroundofSublist"></div>
-
<li><a href="https://2013.igem.org/Team:Peking/HumanPractice/FactoryVisit">Factory Visit</a></li>
+
                                 <li><a href="https://2013.igem.org/Team:Peking/HumanPractice/Questionnaire">Questionnaire Survey</a></li>
-
                                 <li><a href="https://2013.igem.org/Team:Peking/HumanPractice/iGEMWorkshop">Team Coummunication</a></li>
+
<li><a href="https://2013.igem.org/Team:Peking/HumanPractice/FactoryVisit">Visit and Interview</a></li>
-
<li><a href="https://2013.igem.org/Team:Peking/HumanPractice/ModeliGEM">Model iGEM</a></li>
+
                                 <li><a href="https://2013.igem.org/Team:Peking/HumanPractice/ModeliGEM">Practical Analysis</a></li>
 +
<li><a href="https://2013.igem.org/Team:Peking/HumanPractice/iGEMWorkshop">Team Communication</a></li>
 +
 
</ul>
</ul>
</li>
</li>
</ul>
</ul>
-
         <a href="https://igem.org/Team_Wikis?year=2013"><img id="iGEM_logo" src="https://static.igem.org/mediawiki/igem.org/4/48/Peking_igemlogo.jpg"/></a>
+
         <a href="https://2013.igem.org/Main_Page"><img id="iGEM_logo" src="https://static.igem.org/mediawiki/igem.org/4/48/Peking_igemlogo.jpg"/></a>
</div>
</div>
<!--end navigationbar-->
<!--end navigationbar-->
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           <h1 id="ProjectListTitle">Data Page</h1>
           <h1 id="ProjectListTitle">Data Page</h1>
           <ul id="ProjectList">
           <ul id="ProjectList">
-
                 <li><a href="https://2013.igem.org/Team:Peking/DataPage/Parts">Parts</a><li>
+
                 <li class="SensorsListItem"><a href="https://2013.igem.org/Team:Peking/DataPage/Parts">Parts</a><li>
-
                 <li><a href="https://2013.igem.org/Team:Peking/DataPage/JudgingCriteria">Judging Criteria</a><li>
+
                 <li class="SensorsListItem"><a href="https://2013.igem.org/Team:Peking/DataPage/JudgingCriteria">Judging Criteria</a><li>
                 </ul>
                 </ul>
     </div>
     </div>
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<p id="Favoritecontent1" style="position:absolute; top:20px; width:360px; left:20px;font-size:18px; font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>XylS</b></br>
<p id="Favoritecontent1" style="position:absolute; top:20px; width:360px; left:20px;font-size:18px; font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>XylS</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031911">Main Page-BBa_K1031911</a>
<a href="http://partsregistry.org/Part:BBa_K1031911">Main Page-BBa_K1031911</a>
-
</br>XylS is a &sigma;<sup>70<sup>-dependent transcriptional factor, which may activate <i>Pm</i> promoter when benzoate acid and its homologous compounds’ binding. We constructed constitutive promoter <i>Pc</i> library to tune its performance. Adaptor of this biosensor can also improve the detection efficiency.   
+
</br>XylS is a &sigma;<sup>70</sup>-dependent transcriptional factor that activates <i>Pm</i> promoter when benzoate acid or its derivative is present. It is used to build a XylS biosensor circuit. <a href="https://2013.igem.org/Team:Peking/Project/Plugins">Adaptor</a> for this biosensor will improve the performance of XylS in detection.   
</br>
</br>
<a href="https://2013.igem.org/Team:Peking/Project/BioSensors/XylS">Visit Wiki</a>
<a href="https://2013.igem.org/Team:Peking/Project/BioSensors/XylS">Visit Wiki</a>
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<p id="Favoritecontent2" style="position:absolute; top:20px; width:360px; left:20px;font-size:18px; font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>HbpR</b></br>
<p id="Favoritecontent2" style="position:absolute; top:20px; width:360px; left:20px;font-size:18px; font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>HbpR</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031300">Main Page-BBa_K1031300</a>
<a href="http://partsregistry.org/Part:BBa_K1031300">Main Page-BBa_K1031300</a>
-
</br>HbpR is a &sigma;<sup>54</sup>-dependent transcriptional factor, which may activate its promoter when 2-Hydroxybiphenol and 2-aminobiphenol’s binding. Tuning <i>Pc</i> constitutive promoter was insufficient for this biosensor, so the RBS library before reporter gene was constructed and remarkably improved the performance.
+
</br>HbpR is a &sigma;<sup>54</sup>-dependent transcriptional factor, which activates <i>P<sub>C</sub></i> promoter in the presence of 2-hydroxybiphenol or 2-aminobiphenol. We built a HbpR biosensor circuit and fine-tuned its performance in <i>E.coli</i>.
</br>
</br>
<a href="https://2013.igem.org/Team:Peking/Project/BioSensors/HbpR">Visit Wiki</a>
<a href="https://2013.igem.org/Team:Peking/Project/BioSensors/HbpR">Visit Wiki</a>
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<p id="Favoritecontent3" style="position:absolute; top:20px; width:360px; left:20px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>NahF</b></br>
<p id="Favoritecontent3" style="position:absolute; top:20px; width:360px; left:20px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>NahF</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031620">Main Page-BBa_K1031620</a>
<a href="http://partsregistry.org/Part:BBa_K1031620">Main Page-BBa_K1031620</a>
-
</br>NahF is the salicylaldehyde dehydrogenase to transform salicylaldehyde into salicylic acid (salicylate) using NAD<sup>+</sup>. We tested NahF in <i>E.coli</i> and it showed that the NahF can work as an adaptor for biosensor NahR, meaning that NahF notably improve the performance and range of detection.   
+
</br>NahF is the salicylaldehyde dehydrogenase to convert salicylaldehyde into salicylic acid (salicylate) using NAD<sup>+</sup>. We tested NahF in <i>E.coli</i> and showed that the NahF works as an <a href="https://2013.igem.org/Team:Peking/Project/Plugins">Adaptor</a> for the NahR biosensor <a href="https://2013.igem.org/Team:Peking/Project/BioSensors/NahR">NahR</a>, significantly improving the performance and range of detection.   
</br>
</br>
-
<a href="https://2013.igem.org/Team:Peking/Project/Plugins#PageTitle2">Visit Wiki</a>
+
<a href="https://2013.igem.org/Team:Peking/Project/Plugins#ContentHbpR7">Visit Wiki</a>
</p>
</p>
     </div>
     </div>
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<p id="Favoritecontent4" style="position:absolute; top:20px; width:360px; left:20px; font-size:18px; font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>Hybrid Promoter</b></br>
<p id="Favoritecontent4" style="position:absolute; top:20px; width:360px; left:20px; font-size:18px; font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:25px;"><b>Hybrid Promoter</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031021">Main Page-BBa_K1031021</a>
<a href="http://partsregistry.org/Part:BBa_K1031021">Main Page-BBa_K1031021</a>
-
</br>The hybrid promoter is constructed for the band-pass filter. A band-pass filter can be theoretically summarized as an incoherent feed forward loop, consisted of a positive loop and a negative loop. As for the reporter node, a special promoter is used so that the reporter should be controlled by the activator and inhibitor at the same time.
+
</br>The hybrid promoter was constructed for Band-pass Filter. The reporter sfGFP was controlled by both the activator and the inhibitor at the same time. We tested this hybrid promoter and built a model to describe its performance.  
</br>
</br>
-
<a href="https://2013.igem.org/Team:Peking/Project/BandpassFilter">Visit Wiki</a>
+
<a href="https://2013.igem.org/Team:Peking/Project/BandpassFilter#Legend7">Visit Wiki</a>
</p>
</p>
     </div>
     </div>
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Pre-existing Part: <a href="http://partsregistry.org/Part:BBa_J61051">Main Page-BBa_J61051</a>
Pre-existing Part: <a href="http://partsregistry.org/Part:BBa_J61051">Main Page-BBa_J61051</a>
</br>
</br>
-
BBa_K1031610 is upgraded from previous part BBa_J61051 designed by Arkin Lab.  
+
BBa_K1031610 is upgraded from original part BBa_J61051.  
-
NahR is a 34 kDa transcription factor mined from <i>Pseudomonas putida</i> which binds to <i>nah</i> and <i>sal</i> promoters to activate transcription in response to the inducer salicylate. We constructed a Psal/NahR biosensor circuit using sfGFP as reporter gene. Adaptor of this biosensor not only improves detection efficiency but also expands detection profile.
+
NahR is a transcription factor mined from <i>Pseudomonas putida</i> which binds to <i>nah</i> and <i>sal</i> promoters to activate transcription in response to the inducer salicylate. We constructed a Psal/NahR biosensor circuit using sfGFP as reporter gene and systematically characterized its performance . <a href="https://2013.igem.org/Team:Peking/Project/Plugins">Adaptor</a> of this biosensor not only improves the detection efficiency but also expands the detection profile.
</br>
</br>
<a href="https://2013.igem.org/Team:Peking/Project/BioSensors/NahR">Visit Wiki</a>
<a href="https://2013.igem.org/Team:Peking/Project/BioSensors/NahR">Visit Wiki</a>
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</p>
</p>
<p style="position: relative; top:0px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>DmpR</b></br>
<p style="position: relative; top:0px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>DmpR</b></br>
-
<a href="http://partsregistry.org/Part:BBa_K1031221">BBa_K1031221</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031221">BBa_K1031221</a>,
-
<a href="http://partsregistry.org/Part:BBa_K1031222">BBa_K1031222</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031222">BBa_K1031222</a>,
-
<a href="http://partsregistry.org/Part:BBa_K1031223">BBa_K1031223</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031223">BBa_K1031223</a> and
-
<a href="http://partsregistry.org/Part:BBa_K1031224">BBa_K1031224</a> are the RBS library of DmpR biosensor's reporter. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031224">BBa_K1031224</a> are the DmpR biosensors using different RBS preceding sfGFP. </br>
 +
<a href="http://partsregistry.org/Part:BBa_K1031211">BBa_K1031211</a> is the DmpR transcriptional factor under a constitutive promoter.<br/>
</p>
</p>
<p style="position: relative; top:20px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>HbpR</b></br>
<p style="position: relative; top:20px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>HbpR</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031300">BBa_K1031300</a> is the coding sequence of HbpR with terminators. </br>
<a href="http://partsregistry.org/Part:BBa_K1031300">BBa_K1031300</a> is the coding sequence of HbpR with terminators. </br>
<a href="http://partsregistry.org/Part:BBa_K1031301">BBa_K1031301</a> and
<a href="http://partsregistry.org/Part:BBa_K1031301">BBa_K1031301</a> and
-
<a href="http://partsregistry.org/Part:BBa_K1031302">BBa_K1031302</a> are the RBS library of HbpR biosensor's reporter. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031302">BBa_K1031302</a> are HbpR biosensors using different RBS preceding sfGFP. </br>
 +
<a href="http://partsregistry.org/Part:BBa_K1031311">BBa_K1031311</a> is the HbpR transcriptional factor under a constitutive promoter.<br/>
</p>
</p>
<p style="position: relative; top:40px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>HcaR</b></br>
<p style="position: relative; top:40px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>HcaR</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031410">BBa_K1031410</a> is the coding sequence of HcaR with terminators. </br>
<a href="http://partsregistry.org/Part:BBa_K1031410">BBa_K1031410</a> is the coding sequence of HcaR with terminators. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031441">BBa_K1031441</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031441">BBa_K1031441</a>,
-
<a href="http://partsregistry.org/Part:BBa_K1031442">BBa_K1031442</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031442">BBa_K1031442</a>,
<a href="http://partsregistry.org/Part:BBa_K1031443">BBa_K1031443</a> and
<a href="http://partsregistry.org/Part:BBa_K1031443">BBa_K1031443</a> and
-
<a href="http://partsregistry.org/Part:BBa_K1031444">BBa_K1031444</a> are the Pc library of HbpR to tune its performance . </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031444">BBa_K1031444</a> are HcaR transcriptional factors with different constitutive promoters (<i>Pc</i>). </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031420">BBa_K1031420</a> and
+
<a href="http://partsregistry.org/Part:BBa_K1031420">BBa_K1031420</a>,
-
<a href="http://partsregistry.org/Part:BBa_K1031421">BBa_K1031421</a> are the RBS library of HcaR biosensor's reporter. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031421">BBa_K1031421</a> and
 +
<a href="http://partsregistry.org/Part:BBa_K1031422">BBa_K1031422</a>  are HcaR biosensors using different RBS preceding sfGFP. </br>
</p>
</p>
Line 360: Line 378:
<a href="http://partsregistry.org/Part:BBa_K1031100">BBa_K1031100</a> is the coding sequence of CapR transcriptional factor. </br>
<a href="http://partsregistry.org/Part:BBa_K1031100">BBa_K1031100</a> is the coding sequence of CapR transcriptional factor. </br>
<a href="http://partsregistry.org/Part:BBa_K1031111">BBa_K1031111</a> and             
<a href="http://partsregistry.org/Part:BBa_K1031111">BBa_K1031111</a> and             
-
<a href="http://partsregistry.org/Part:BBa_K1031112">BBa_K1031112</a> are basic sensor construction with different CapR expression level.   </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031112">BBa_K1031112</a> are CapR transcriptional factors under different constitutive promoters (<i>Pc</i>). </br>
<a href="http://partsregistry.org/Part:BBa_K1031113">BBa_K1031113</a> and
<a href="http://partsregistry.org/Part:BBa_K1031113">BBa_K1031113</a> and
<a href="http://partsregistry.org/Part:BBa_K1031114">BBa_K1031114</a> are reporters with different RBS for the CapR biosensor. </br>
<a href="http://partsregistry.org/Part:BBa_K1031114">BBa_K1031114</a> are reporters with different RBS for the CapR biosensor. </br>
Line 377: Line 395:
<p style="position: relative; top:80px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>PaaX</b></br>
<p style="position: relative; top:80px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>PaaX</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031710">BBa_K1031710</a> is the coding sequence of PaaX with terminators. </br>
<a href="http://partsregistry.org/Part:BBa_K1031710">BBa_K1031710</a> is the coding sequence of PaaX with terminators. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031742">BBa_K1031742</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031742">BBa_K1031742</a>,
<a href="http://partsregistry.org/Part:BBa_K1031743">BBa_K1031743</a> and
<a href="http://partsregistry.org/Part:BBa_K1031743">BBa_K1031743</a> and
-
<a href="http://partsregistry.org/Part:BBa_K1031744">BBa_K1031744</a> are the Pc library of PaaX. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031744">BBa_K1031744</a> are PaaX transcriptional factors under different constitutive promoters (<i>Pc</i>). </br>
</p>
</p>
<p style="position: relative; top:90px; left: 20px; width:800px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>XylS</b></br>
<p style="position: relative; top:90px; left: 20px; width:800px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>XylS</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031911">BBa_K1031911</a> is the coding sequence of XylS transcriptional factor with terminators. </br>
<a href="http://partsregistry.org/Part:BBa_K1031911">BBa_K1031911</a> is the coding sequence of XylS transcriptional factor with terminators. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031912">BBa_K1031912</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031912">BBa_K1031912</a>,
-
<a href="http://partsregistry.org/Part:BBa_K1031913">BBa_K1031913</a> and            
+
<a href="http://partsregistry.org/Part:BBa_K1031913">BBa_K1031913</a>,            
-
<a href="http://partsregistry.org/Part:BBa_K1031916">BBa_K1031916</a> are the Pc library of XylS. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031916">BBa_K1031916</a> and
 +
<a href="http://partsregistry.org/Part:BBa_K1031917">BBa_K1031917</a>
 +
are XylS transcriptional factors under different constitutive promoters (<i>Pc</i>).  </br>
 +
<a href="http://partsregistry.org/Part:BBa_K1031941">BBa_K1031941</a> is the reporter for the XylS biosensor. </br>
</p>
</p>
<p style="position: relative; top:100px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>XylR</b></br>
<p style="position: relative; top:100px; left: 20px; width:800px;  font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>XylR</b></br>
<a href="http://partsregistry.org/Part:BBa_K1031803">BBa_K1031803</a>
<a href="http://partsregistry.org/Part:BBa_K1031803">BBa_K1031803</a>
-
<a href="http://partsregistry.org/Part:BBa_K1031804">BBa_K1031804</a> are the RBS library of XylR biosensor's reporter. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031804">BBa_K1031804</a> is the XylR biosensor library using different RBS. </br>
</p>
</p>
Line 399: Line 420:
<p style="position: relative; top:110px; left: 20px; width:800px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>NahF</b></br>
<p style="position: relative; top:110px; left: 20px; width:800px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>NahF</b></br>
-
<a href="http://partsregistry.org/Part:BBa_K1031620">BBa_K1031620</a> is the coding sequence of XylS transcriptional factor with terminators. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031620">BBa_K1031620</a> is the coding sequence of the enzyme NahF with terminators. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031621">BBa_K1031621</a>  
+
<a href="http://partsregistry.org/Part:BBa_K1031621">BBa_K1031621</a>,
-
<a href="http://partsregistry.org/Part:BBa_K1031622">BBa_K1031622</a>  
+
<a href="http://partsregistry.org/Part:BBa_K1031622">BBa_K1031622</a>,
-
<a href="http://partsregistry.org/Part:BBa_K1031623">BBa_K1031623</a>  
+
<a href="http://partsregistry.org/Part:BBa_K1031623">BBa_K1031623</a>,
<a href="http://partsregistry.org/Part:BBa_K1031624">BBa_K1031624</a> and           
<a href="http://partsregistry.org/Part:BBa_K1031624">BBa_K1031624</a> and           
-
<a href="http://partsregistry.org/Part:BBa_K1031625">BBa_K1031625</a>are the Pc library of NahF. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031625">BBa_K1031625</a> are coding sequences of enzyme NahF under different <i>Pc</i>. </br><br/>
 +
<b>XylC</b></br>
 +
<a href="http://partsregistry.org/Part:BBa_K1031931">BBa_K1031931</a> is the coding sequence of enzyme XylC under <i>Pc</i>. </br>
 +
</br>
 +
<b>XylB</b></br>
 +
<a href="http://partsregistry.org/Part:BBa_K1031922">BBa_K1031922</a> and         
 +
<a href="http://partsregistry.org/Part:BBa_K1031923">BBa_K1031923</a> are coding sequences of enzyme XylB under different <i>Pc</i>. </br><br/>
</p>
</p>
Line 410: Line 437:
<b>Parts for Band-Pass Filter</b>
<b>Parts for Band-Pass Filter</b>
<p style="position: relative; top:90px; left: 20px; width:800px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"></br>
<p style="position: relative; top:90px; left: 20px; width:800px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"></br>
-
<a href="http://partsregistry.org/Part:BBa_K1031021">BBa_K1031021</a> is the hybrid promoter for the reporter node, which can be activated as well as inhibited. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031021">BBa_K1031021</a> is the hybrid promoter which can be activated and inhibited at the same time by two different transcriptional factors. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031011">BBa_K1031011</a> is the transcriptional factor that can activate its cognate promoter, which is used as the activate node in the band-pass filter. </br>
+
<a href="http://partsregistry.org/Part:BBa_K1031011">BBa_K1031011</a> is the ϕR73δ activator used in the Band-pass Filter. </br>  
-
<a href="http://partsregistry.org/Part:BBa_K1031013">BBa_K1031013</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031017">BBa_K1031017</a> is the coding sequence of activator ϕR73δ under <i>Pc</i>. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031014">BBa_K1031014</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031018">BBa_K1031018</a> is the coding sequence of activator ϕR73δ under Promoter <i>pSal</i>. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031015">BBa_K1031015</a>
+
<a href="http://partsregistry.org/Part:BBa_K1031019">BBa_K1031019</a> is the coding sequence of activator ϕR73δ Regulated by the biosensor NahR. </br>
-
<a href="http://partsregistry.org/Part:BBa_K1031016">BBa_K1031016</a> are RBS library to tune the expression of C1, under the control of pSal promoter, which is a crucial part for band-pass filter. </br>
+
 
 +
Each of
 +
<a href="http://partsregistry.org/Part:BBa_K1031013">BBa_K1031013</a>,
 +
<a href="http://partsregistry.org/Part:BBa_K1031014">BBa_K1031014</a>,
 +
<a href="http://partsregistry.org/Part:BBa_K1031015">BBa_K1031015</a> and
 +
<a href="http://partsregistry.org/Part:BBa_K1031016">BBa_K1031016</a> is the coding sequence of cI with different RBS and <i>pSal</i> as its promoter, which is a crucial component for the Band-pass Filter. </br>
</div>
</div>
<div id="Dataplot">
<div id="Dataplot">
 +
<img src="https://static.igem.org/mediawiki/2013/a/a8/Peking2013_Biosensorfig3.png" style="position:relative; left:120px; width:600px;"/>
 +
<p id="BiosensorFigure3"><b>Figure 1. The aromatics spectrum showing the aromatics-sensing profiles of our individual biosensors.</b>
 +
</br>
 +
Each color segment in the central spectrum represents the detection profile of a biosensor. Structural formulas highlighted in color stand for the aromatic compounds that can be detected by our biosensors. The "plug" icon stands for <a href="https://2013.igem.org/Team:Peking/Project/Plugins">Adaptors</a>, enzymes that convert the undetectable compounds into the detectable compounds, thus to reinforce the detection capacity of some biosensors. <a href="https://static.igem.org/mediawiki/igem.org/2/24/Peking2013_Chemicals_V3%2B.pdf">Click Here</a> for the summary of the aromatics spectrum and aromatics-sensing profiles of individual biosensors. </br>
 +
<a href="https://2013.igem.org/Team:Peking/Project/BioSensors">Visit Our Wiki</a>
-
<img src="https://static.igem.org/mediawiki/igem.org/a/a8/Peking2013_Biosensorfig3.png"/ style="position:relative; left:120px; width:600px;">
+
</p>
-
<table border="1" id="XylSTable"; style="position:relative; top:40px;">
 
-
<tr>
 
-
  <th>Biosensors</th>
+
<img id="FigurePic3" src=" https://static.igem.org/mediawiki/igem.org/c/c7/Peking2013_Figure3ab.jpg " style="position:relative; top:50px; left:0px; width:840px"/>
-
  <th>NahR</th>
+
<img id="FigurePic4" src=" https://static.igem.org/mediawiki/igem.org/9/96/Peking2013_MAFigure3cd.jpg " style="position:relative; top:20px;left:0px;  width:840px"/>
-
  <th>XylS</th>
+
<img id="FigurePic5" src=" https://static.igem.org/mediawiki/igem.org/4/44/Peking2013_MAFigureef.jpg " style="position:relative; left:0px;  width:840px"/>
-
  <th>HbpR</th>
+
<img id="FigurePic6" src=" https://static.igem.org/mediawiki/2013/f/fb/Peking2013_Orthogonality_Fig._4%28g-h%29.png " style="position:relative; left:0px; width:840px"/>
-
  <th>DmpR</th>
+
<img id="FigurePic7" src=" https://static.igem.org/mediawiki/2013/4/46/Peking2013_Orthogonality_Fig._4%28i-j%29.png " style="position:relative; left:0px; width:840px"/>
-
</tr>
+
<img id="FigurePic8" src=" https://static.igem.org/mediawiki/2013/1/15/Peking2013_Orthogonality_Fig._4%28k-l%29.png " style="position:relative; left:0px; width:840px"/>
-
<tr>
+
-
  <th>NahR</th>
+
-
  <td>Broader aromatics-sensing profiles with high induction ratio</td>
+
-
  <td>Arg<sup>45</sup><Code>&rarr;</Code>Thr</td>
+
-
  <td>SaA; 4-EtBzO; BzO; 2-MeBzO; 4-MeBzO</td>
+
-
  <td>SaA; 4-EtBzO; BzO; 2-MeBzO; 4-MeBzO</td>
+
-
</tr>
+
-
<tr>
+
-
  <th>XylS</th>
+
-
  <td>Constitutive <i>Pm</i> promoter activation</td>
+
-
  <td>Trp<sup>88</sup><Code>&rarr;</Code>Leu</td>
+
-
  <td>Not mentioned, this mutant causes constitutive expression of <i>Pm</i> promoter</td>
+
-
  <td><img src="https://static.igem.org/mediawiki/igem.org/c/c7/Peking2013_Figure3ab.jpg"</td>
+
-
</tr>
+
-
<tr>
+
-
  <th>HbpR</th>
+
-
  <td rowspan="5">Broader aromatics-sensing profiles with lower induction ratios</td>
+
-
  <td>Arg<sup>152</sup><Code>&rarr;</Code>Gly</td>
+
-
  <td>BzO; 2-MeBzO; 2-,3-ClBzO; 2-,3- and 4-MeOBzO</td>
+
-
  <td>BzO; 2-MeBzO; 2-,3-ClBzO; 2-,3- and 4-MeOBzO</td>
+
-
</tr>
+
-
<tr>
+
-
  <th>DmpR</th>
+
-
  <td>Arg<sup>41</sup><Code>&rarr;</Code>His</td>
+
-
  <td>BzO; 3-MeBzO; 3-ClBzO; 3-BrBzO; 3-MeOBzO</td>
+
-
  <td>Asp<sup>288</sup><Code>&rarr;</Code>Val</td>
+
-
  <td>BzO; 3-MeBzO; 4-MeOBzO; 4-BrBzO; 2,4-MeBzO; 2,5-MeBzO; 3-ClBzO</td>
+
-
</tr>
+
-
 
+
-
</table>
+
 +
<p id="Figure2">
 +
<b>Figure 2.</b> Linear fitting of the data obtained from the orthogonality assay showing the orthogonality between the 4 representative biosensors. The experiments and data processing were performed as described in <b>Fig. 2</b> and <b>Fig. 3</b>.The black dashed line denotes slope=1 as the reference line. These fittings showed the orthogonality between biosensors, (<b>a, b</b>) XylS and NahR; (<b>c, d</b>) XylS and HbpR; (<b>e, f</b>) NahR and HbpR, (<b>g, h</b>) XylS and DmpR, (<b>i, j</b>) NahR and DmpR, and (<b>k, l</b>) HbpR and DmpR. The experiment data, linear fitting curves of biosensor, and cognate inducers are in different colors: XylS in red, NahR in green, HbpR in orange and DmpR in dark cyan.
 +
(For more details, please <a href="https://2013.igem.org/Team:Peking/Project/BioSensors/MulticomponentAnalysis">Click Here</a>)
 +
</p>
 +
</br>
</div>
</div>
Line 477: Line 487:
</div>
</div>
<div id="Title4">
<div id="Title4">
-
<p>Data Plot</p>
+
<p>Data Summary</p>
</div>
</div>

Latest revision as of 18:17, 28 October 2013

Parts


XylS
Main Page-BBa_K1031911
XylS is a σ70-dependent transcriptional factor that activates Pm promoter when benzoate acid or its derivative is present. It is used to build a XylS biosensor circuit. Adaptor for this biosensor will improve the performance of XylS in detection.
Visit Wiki

HbpR
Main Page-BBa_K1031300
HbpR is a σ54-dependent transcriptional factor, which activates PC promoter in the presence of 2-hydroxybiphenol or 2-aminobiphenol. We built a HbpR biosensor circuit and fine-tuned its performance in E.coli.
Visit Wiki

NahF
Main Page-BBa_K1031620
NahF is the salicylaldehyde dehydrogenase to convert salicylaldehyde into salicylic acid (salicylate) using NAD+. We tested NahF in E.coli and showed that the NahF works as an Adaptor for the NahR biosensor NahR, significantly improving the performance and range of detection.
Visit Wiki

Hybrid Promoter
Main Page-BBa_K1031021
The hybrid promoter was constructed for Band-pass Filter. The reporter sfGFP was controlled by both the activator and the inhibitor at the same time. We tested this hybrid promoter and built a model to describe its performance.
Visit Wiki

NahR
Main Page-BBa_K1031610
Pre-existing Part: Main Page-BBa_J61051
BBa_K1031610 is upgraded from original part BBa_J61051. NahR is a transcription factor mined from Pseudomonas putida which binds to nah and sal promoters to activate transcription in response to the inducer salicylate. We constructed a Psal/NahR biosensor circuit using sfGFP as reporter gene and systematically characterized its performance . Adaptor of this biosensor not only improves the detection efficiency but also expands the detection profile.
Visit Wiki

Parts for Biosensors

DmpR
BBa_K1031221, BBa_K1031222, BBa_K1031223 and BBa_K1031224 are the DmpR biosensors using different RBS preceding sfGFP.
BBa_K1031211 is the DmpR transcriptional factor under a constitutive promoter.

HbpR
BBa_K1031300 is the coding sequence of HbpR with terminators.
BBa_K1031301 and BBa_K1031302 are HbpR biosensors using different RBS preceding sfGFP.
BBa_K1031311 is the HbpR transcriptional factor under a constitutive promoter.

HcaR
BBa_K1031410 is the coding sequence of HcaR with terminators.
BBa_K1031441, BBa_K1031442, BBa_K1031443 and BBa_K1031444 are HcaR transcriptional factors with different constitutive promoters (Pc).
BBa_K1031420, BBa_K1031421 and BBa_K1031422 are HcaR biosensors using different RBS preceding sfGFP.

CapR
BBa_K1031100 is the coding sequence of CapR transcriptional factor.
BBa_K1031111 and BBa_K1031112 are CapR transcriptional factors under different constitutive promoters (Pc).
BBa_K1031113 and BBa_K1031114 are reporters with different RBS for the CapR biosensor.

HpaR
BBa_K1031510 is the coding sequence of HpaR transcriptional factor.
BBa_K1031520 and BBa_K1031521 are reporters with different RBS for the HpaR biosensor.

NahR
BBa_K1031610 is the NahR biosensor circuit.

PaaX
BBa_K1031710 is the coding sequence of PaaX with terminators.
BBa_K1031742, BBa_K1031743 and BBa_K1031744 are PaaX transcriptional factors under different constitutive promoters (Pc).

XylS
BBa_K1031911 is the coding sequence of XylS transcriptional factor with terminators.
BBa_K1031912, BBa_K1031913, BBa_K1031916 and BBa_K1031917 are XylS transcriptional factors under different constitutive promoters (Pc).
BBa_K1031941 is the reporter for the XylS biosensor.

XylR
BBa_K1031803 BBa_K1031804 is the XylR biosensor library using different RBS.

Parts for Adaptors

NahF
BBa_K1031620 is the coding sequence of the enzyme NahF with terminators.
BBa_K1031621, BBa_K1031622, BBa_K1031623, BBa_K1031624 and BBa_K1031625 are coding sequences of enzyme NahF under different Pc.

XylC
BBa_K1031931 is the coding sequence of enzyme XylC under Pc.

XylB
BBa_K1031922 and BBa_K1031923 are coding sequences of enzyme XylB under different Pc.

Parts for Band-Pass Filter


BBa_K1031021 is the hybrid promoter which can be activated and inhibited at the same time by two different transcriptional factors.
BBa_K1031011 is the ϕR73δ activator used in the Band-pass Filter.
BBa_K1031017 is the coding sequence of activator ϕR73δ under Pc.
BBa_K1031018 is the coding sequence of activator ϕR73δ under Promoter pSal.
BBa_K1031019 is the coding sequence of activator ϕR73δ Regulated by the biosensor NahR.
Each of BBa_K1031013, BBa_K1031014, BBa_K1031015 and BBa_K1031016 is the coding sequence of cI with different RBS and pSal as its promoter, which is a crucial component for the Band-pass Filter.

Figure 1. The aromatics spectrum showing the aromatics-sensing profiles of our individual biosensors.
Each color segment in the central spectrum represents the detection profile of a biosensor. Structural formulas highlighted in color stand for the aromatic compounds that can be detected by our biosensors. The "plug" icon stands for Adaptors, enzymes that convert the undetectable compounds into the detectable compounds, thus to reinforce the detection capacity of some biosensors. Click Here for the summary of the aromatics spectrum and aromatics-sensing profiles of individual biosensors.
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Figure 2. Linear fitting of the data obtained from the orthogonality assay showing the orthogonality between the 4 representative biosensors. The experiments and data processing were performed as described in Fig. 2 and Fig. 3.The black dashed line denotes slope=1 as the reference line. These fittings showed the orthogonality between biosensors, (a, b) XylS and NahR; (c, d) XylS and HbpR; (e, f) NahR and HbpR, (g, h) XylS and DmpR, (i, j) NahR and DmpR, and (k, l) HbpR and DmpR. The experiment data, linear fitting curves of biosensor, and cognate inducers are in different colors: XylS in red, NahR in green, HbpR in orange and DmpR in dark cyan. (For more details, please Click Here)


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