Difference between revisions of "Team:IISc Bangalore/Description"

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IISc Bangalore
  
    <link rel="stylesheet" type="text/css" href="https://2016.igem.org/Template:IISc Bangalore header/CSS?action=raw&ctype=text/css">
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header/CSS?action=raw&ctype=text/css
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">
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    <link rel="stylesheet"
  
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type="text/css"
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href="https://2016.igem.org/Template:
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IISc Bangalore
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nav/CSS?action=raw&ctype=text/css">
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type="text/css"
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footer/CSS?action=raw&ctype=text/css
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type="text/css"
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type="text/css"
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href="https://2016.igem.org/Template:
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boxes/CSS?action=raw&ctype=text/css"
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>
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<script type="text/javascript"
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source
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src="https://2016.igem.org/Template:I
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 +
ISc Bangalore
 +
 +
sidebar/Javascript?action=raw&ctype=
 +
 +
text/javascript">
  
    <script type="text/javascript" source src="https://2016.igem.org/Template:IISc Bangalore sidebar/Javascript?action=raw&ctype=text/javascript">
 
 
 
 
<div class="navbar" id="top">
 
<div class="navbar" id="top">
          <ul class="navs">
+
     
             <li>Home
+
 
               <div class="drop">
+
  <ul class="navs">
                 <a href="#overview">
+
              
                   Overview
+
 
 +
<li>Home
 +
               <div  
 +
 
 +
class="drop">
 +
                 <a  
 +
 
 +
href="#overview">
 +
                    
 +
 
 +
Overview
 
                 </a>
 
                 </a>
              </div>
+
     
 +
 
 +
      </div>
 
             </li>
 
             </li>
            <li>Team
+
   
               <div class="drop">
+
 
                 <a href="">
+
      <li>Team
 +
               <div  
 +
 
 +
class="drop">
 +
                 <a  
 +
 
 +
href="">
 
                   Members
 
                   Members
 +
 
 +
 +
              </a>
 +
               
 +
 +
<a href="">
 +
                 
 +
 +
Collaborations
 
                 </a>
 
                 </a>
                <a href="">
+
                  Collaborations
+
 
                </a>
+
            </div>
              </div>
+
              
             </li>
+
 
 +
</li>
 
             <li>Project
 
             <li>Project
              <div class="drop">
+
     
                <a href="#description">
+
 
                  Description
+
      <div class="drop">
                </a>
+
         
 +
 
 +
    <a href="#description">
 +
       
 +
 
 +
          Description
 +
             
 +
 
 +
</a>
 
                 <a href="">
 
                 <a href="">
                  Design
+
 
                </a>
+
 
                <a href="">
+
              Design
                  Experiments
+
             
                </a>
+
 
 +
</a>
 
                 <a href="">
 
                 <a href="">
 +
 
 +
 +
              Experiments
 +
         
 +
 +
      </a>
 +
                <a
 +
 +
href="">
 
                   Proof
 
                   Proof
                </a>
+
   
                 <a href="">
+
 
 +
            </a>
 +
                 <a  
 +
 
 +
href="">
 
                   Demo
 
                   Demo
                </a>
+
   
                 <a href="">
+
 
 +
          </a>
 +
                 <a  
 +
 
 +
href="">
 
                   Results
 
                   Results
 +
 
 +
 +
              </a>
 +
               
 +
 +
<a href="">
 +
                 
 +
 +
Notebook
 
                 </a>
 
                 </a>
                <a href="">
+
     
                  Notebook
+
 
                </a>
+
      </div>
              </div>
+
 
             </li>
 
             </li>
            <li>Parts
+
   
               <div class="drop">
+
 
                 <a href="">
+
      <li>Parts
                   Basic parts
+
               <div  
 +
 
 +
class="drop">
 +
                 <a  
 +
 
 +
href="">
 +
                   Basic  
 +
 
 +
parts
 
                 </a>
 
                 </a>
                <a href="">
+
         
                   Composite
+
 
                </a>
+
      <a href="">
                <a href="">
+
                    
                  Part collection
+
 
 +
Composite
 
                 </a>
 
                 </a>
 +
     
 +
 +
          <a href="">
 +
             
 +
 +
  Part collection
 +
               
 +
 +
</a>
 
               </div>
 
               </div>
            </li>
+
         
 +
 
 +
</li>
 
             <li>Safety</li>
 
             <li>Safety</li>
            <li>Attributions</li>
+
 
            <li>Practices</li>
+
 
            <li>Awards</li>
+
          <li>Attributions</li>
 +
   
 +
 
 +
      <li>Practices</li>
 +
         
 +
 
 +
<li>Awards</li>
 
           </ul>
 
           </ul>
        </div>
+
   
  
 +
    </div>
  
        <div class="content">
 
  
              <span class="cellfiefuge">
+
        <div
                Cellfiefuge
+
              </span>
+
              <p class="tagline">
+
                An auto-pelleting system
+
              </p>
+
  
 +
class="content">
  
 +
             
  
 +
<span class="cellfiefuge">
 +
         
  
             <div class="wrap">
+
      Cellfiefuge
               <svg height="60" width="320" xmlns="http://www.w3.org/2000/svg">
+
             
                <rect class="shape" height="60" width="320" />
+
 
                <div class="calltoaction">
+
</span>
                  <a href="#description">Description</a>
+
              <p
                </div>
+
 
               </svg>
+
class="tagline">
 +
                An
 +
 
 +
auto-pelleting system
 +
             
 +
 
 +
</p>
 +
 
 +
 
 +
 
 +
 
 +
             <div  
 +
 
 +
class="wrap">
 +
               <svg  
 +
 
 +
height="60" width="320"  
 +
 
 +
xmlns="http://www.w3.org/2000/svg">
 +
 +
 
 +
              <rect class="shape"  
 +
 
 +
height="60" width="320" />
 +
         
 +
 
 +
      <div class="calltoaction">
 +
   
 +
 
 +
              <a  
 +
 
 +
href="#description">Description</a>
 +
 +
 
 +
              </div>
 +
                
 +
 
 +
</svg>
 
             </div>
 
             </div>
           </div>
+
            
 +
 
 +
</div>
  
 
           <!--boxes  -->
 
           <!--boxes  -->
  
        <div class="boxes" id="description">
+
 
          <p class="header">Description</p>
+
          <div class="bara_dabba">
+
  
            <div class="semi_dabba" id="first">
+
    <div class="boxes"
               <div class="chotta_dabba">
+
 
                <p class="glimpse">
+
id="description">
                 <a href="#overview">Overview</a><br><br>
+
          <p
 +
 
 +
class="header">Description</p>
 +
     
 +
 
 +
    <div class="bara_dabba">
 +
 
 +
     
 +
 
 +
    <div class="semi_dabba"  
 +
 
 +
id="first">
 +
               <div  
 +
 
 +
class="chotta_dabba">
 +
             
 +
 
 +
<p class="glimpse">
 +
                  
 +
 
 +
<a  
 +
 
 +
href="#overview">Overview</a><br><br
 +
 
 +
>
  
 
                 </p>
 
                 </p>
              </div>
+
           
 +
 
 +
</div>
  
  
 
             </div>
 
             </div>
            <div class="semi_dabba" id="second">
+
       
              <div class="chotta_dabba">
+
                <p class="glimpse">
+
                  <a href="#design">Design</a><br><br>
+
  
                 </p>
+
    <div class="semi_dabba"
               </div>
+
 
 +
id="second">
 +
              <div
 +
 
 +
class="chotta_dabba">
 +
             
 +
 
 +
<p class="glimpse">
 +
                  
 +
 
 +
  <a
 +
 
 +
href="#design">Design</a><br><br>
 +
 
 +
 
 +
 
 +
              </p>
 +
                
 +
 
 +
</div>
 
             </div>
 
             </div>
           </div>
+
            
  
          <div class="bara_dabba">
+
</div>
  
            <div class="semi_dabba" id="third">
+
          <div  
              <div class="chotta_dabba">
+
                <p class="glimpse">
+
                  <a href="#protein">Protein production module</a><br><br>
+
  
                 </p>
+
class="bara_dabba">
 +
 
 +
           
 +
 
 +
<div class="semi_dabba" id="third">
 +
 +
 
 +
            <div
 +
 
 +
class="chotta_dabba">
 +
             
 +
 
 +
<p class="glimpse">
 +
                  
 +
 
 +
  <a href="#protein">Protein
 +
 
 +
production module</a><br><br>
 +
 
 +
     
 +
 
 +
          </p>
 
               </div>
 
               </div>
            </div>
+
            <div class="semi_dabba" id="fourth">
+
  
              <div class="chotta_dabba">
+
          </div>
                <p class="glimpse">
+
            <div
                  <a href="#aggre">Auto Aggregation module</a><br><br>
+
  
                 </p>
+
class="semi_dabba" id="fourth">
 +
 
 +
   
 +
 
 +
          <div
 +
 
 +
class="chotta_dabba">
 +
             
 +
 
 +
<p class="glimpse">
 +
                  
 +
 
 +
  <a href="#aggre">Auto Aggregation
 +
 
 +
module</a><br><br>
 +
 
 +
               
 +
 
 +
</p>
 
               </div>
 
               </div>
            </div>
+
         
 +
 
 +
</div>
 
           </div>
 
           </div>
  
  
         </div>
+
          
        <div id="sidebar" class="sidebar">
+
  
          <a href="javascript:void(0)" class="closebtn" onclick="closeBar()">&times;</a>
+
</div>
          <a href="#overview">Overview</a>
+
        <div id="sidebar"  
          <a href="#design">Design</a>
+
          <a href="#protein">Protein</a>
+
          <a href="#aggre">Aggregation</a>
+
          <a href="#ref">References</a>
+
          <a href="#top">Back to top</a>
+
  
               <a href="https://facebook.com/iiscbangaloreigem/" >
+
class="sidebar">
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onclick="closeBar()">&times;</a>
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      <a
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href="#overview">Overview</a>
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  <a href="#design">Design</a>
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    <a href="#protein">Protein</a>
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        <a
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href="#aggre">Aggregation</a>
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Line 177: Line 5,242:
  
  
        </div>
+
     
 +
 
 +
</div>
 
         <span >
 
         <span >
<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
+
<svg  
        </span>
+
 
         <div id="overview" class="sub">
+
class="panel" onclick="openBar()"  
           <div class="header">
+
 
             Overview
+
enable-background="new 0 0 128 128"  
          </div>
+
 
          <div class="text">
+
height="40px" id="Layer_1"  
            <p>Since the advent of rDNA technology in the late 1970s, the use of recombinant protein has been on the rise, starting from insulin and hormones all the way through to monoclonal antibodies and one hundred and fifty-one FDA approved protein based recombinant pharmaceuticals by the year 2009[1]. Despite being in high demand, recombinant proteins have heavy price tags, thanks to the significant manufacturing costs. One of the important steps in the manufacturing process is Centrifugation but on an industrial scale, it is an economic nightmare. [2] Further, existing industrial setups use complex sensors to monitor cell density to determine the point at which to begin separation of the cells from the cell culture. One can immediately see the humongous relief that would be associated with finding a way to deal with the above problems. Hence, we came up with the idea of our project, the Cellfifuge.</p>
+
 
 +
version="1.1" viewBox="0 0 128 128"  
 +
 
 +
width="40px" xml:space="preserve"  
 +
 
 +
xmlns="http://www.w3.org/2000/svg"  
 +
 
 +
xmlns:xlink="http://www.w3.org/1999/
 +
 
 +
xlink"><g><g><path  
 +
 
 +
d="M64,0C28.656,0,0,28.656,0,64s28.6
 +
 
 +
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 +
,64,0z M64,120     
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fill="#B0BEC5"/></g></g><g><g><path  
 +
 
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fill="#8BC34A"/></g></g></svg>
 +
     
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 +
  </span>
 +
         <div id="overview"  
 +
 
 +
class="sub">
 +
           <div  
 +
 
 +
class="header">
 +
              
 +
 
 +
Overview
 
           </div>
 
           </div>
 +
         
 +
 +
<div class="text">
 +
           
 +
 +
<p>Since the advent of rDNA
 +
 +
technology in the late 1970s, the
 +
 +
use of recombinant protein has been
 +
 +
on the rise, starting from insulin
 +
 +
and hormones all the way through to
 +
 +
monoclonal antibodies and one
 +
 +
hundred and fifty-one FDA approved
 +
 +
protein based recombinant
 +
 +
pharmaceuticals by the year 2009[1].
 +
 +
Despite being in high demand,
 +
 +
recombinant proteins have heavy
 +
 +
price tags, thanks to the
 +
 +
significant manufacturing costs. One
 +
 +
of the important steps in the
 +
 +
manufacturing process is
 +
 +
Centrifugation but on an industrial
 +
 +
scale, it is an economic nightmare.
 +
 +
[2] Further, existing industrial
 +
 +
setups use complex sensors to
 +
 +
monitor cell density to determine
 +
 +
the point at which to begin
 +
 +
separation of the cells from the
 +
 +
cell culture. One can immediately
 +
 +
see the humongous relief that would
 +
 +
be associated with finding a way to
 +
 +
deal with the above problems. Hence,
 +
 +
we came up with the idea of our
 +
 +
project, the Cellfifuge.</p>
 +
       
 +
 +
  </div>
 
         </div>
 
         </div>
         <span >
+
          
<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
+
 
        </span>
+
<span >
         <div id="design" class="sub">
+
<svg class="panel"  
           <div class="header">
+
 
           Our Bioreactor Design
+
onclick="openBar()"  
 +
 
 +
enable-background="new 0 0 128 128"  
 +
 
 +
height="40px" id="Layer_1"  
 +
 
 +
version="1.1" viewBox="0 0 128 128"  
 +
 
 +
width="40px" xml:space="preserve"  
 +
 
 +
xmlns="http://www.w3.org/2000/svg"  
 +
 
 +
xmlns:xlink="http://www.w3.org/1999/
 +
 
 +
xlink"><g><g><path  
 +
 
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d="M64,0C28.656,0,0,28.656,0,64s28.6
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 +
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 +
 
 +
fill="#B0BEC5"/></g></g><g><g><path  
 +
 
 +
d="M96,56H72V32c0-4.414-3.586-8-8-8s
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fill="#8BC34A"/></g></g></svg>
 +
     
 +
 
 +
  </span>
 +
         <div id="design"  
 +
 
 +
class="sub">
 +
           <div  
 +
 
 +
class="header">
 +
           Our  
 +
 
 +
Bioreactor Design
 
           </div>
 
           </div>
          <div class="large">
+
 
          <div id="left" class="text">
+
            <p>We realized that manufacturing units use expensive and energy expensive machinery [3]. Hence, we engineered our bacteria in such a way that it could do most of the work done by these monstrous machines so that we no longer have to buy them and pay their bills.
+
To increase the yield of the product, we came up with the idea of separating cell growth and target protein production so that when the cells have grown up to a high enough cell density, they shuttle all their energy towards the required protein production.[4] Based on the above ideas, we came up with the design of our bioreactor. (Figure 1)</p>
+
  
<p>We realized that we would not be able to work on the whole idea this summer so, we focussed on two modules of our design: the Protein production module and the auto-aggregation module leaving the arresting of cell growth for future iGEM teams as a seed for their ideas.</p>
+
        <div class="large">
 +
       
 +
 
 +
<div id="left" class="text">
 +
     
 +
 
 +
    <p>We realized that
 +
 
 +
manufacturing units use expensive
 +
 
 +
and energy expensive machinery [3].
 +
 
 +
Hence, we engineered our bacteria in
 +
 
 +
such a way that it could do most of
 +
 
 +
the work done by these monstrous
 +
 
 +
machines so that we no longer have
 +
 
 +
to buy them and pay their bills.
 +
To
 +
 
 +
increase the yield of the product,
 +
 
 +
we came up with the idea of
 +
 
 +
separating cell growth and target
 +
 
 +
protein production so that when the
 +
 
 +
cells have grown up to a high enough
 +
 
 +
cell density, they shuttle all their
 +
 
 +
energy towards the required protein
 +
 
 +
production.[4] Based on the above
 +
 
 +
ideas, we came up with the design of
 +
 
 +
our bioreactor. (Figure 1)</p>
 +
 
 +
<p>We realized that we would not be  
 +
 
 +
able to work on the whole idea this  
 +
 
 +
summer so, we focussed on two  
 +
 
 +
modules of our design: the Protein  
 +
 
 +
production module and the  
 +
 
 +
auto-aggregation module leaving the  
 +
 
 +
arresting of cell growth for future  
 +
 
 +
iGEM teams as a seed for their  
 +
 
 +
ideas.</p>
  
 
           </div>
 
           </div>
          <div >
+
       
             <img class="image" src="designa.jpg" />Figure 1: The bioreactor design of Cellfifuge
+
 
 +
  <div >
 +
             <img  
 +
 
 +
class="image" src="designa.jpg"  
 +
 
 +
/>Figure 1: The bioreactor design of  
 +
 
 +
Cellfifuge
 
           </div>
 
           </div>
         </div>
+
          
 +
 
 +
</div>
 
         </div>
 
         </div>
  
         <span >
+
         <span  
<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
+
 
        </span>
+
>
         <div id="protein" class="sub">
+
<svg class="panel"  
           <div class="header">
+
 
           Protein Production Module
+
onclick="openBar()"  
 +
 
 +
enable-background="new 0 0 128 128"  
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 +
height="40px" id="Layer_1"  
 +
 
 +
version="1.1" viewBox="0 0 128 128"  
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width="40px" xml:space="preserve"  
 +
 
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xmlns="http://www.w3.org/2000/svg"  
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xmlns:xlink="http://www.w3.org/1999/
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 +
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 +
 
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 +
,64,0z M64,120     
 +
 
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C33.125,120,8,94.875,8,64S33.125,8,6
 +
 
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 +
 
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fill="#B0BEC5"/></g></g><g><g><path  
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 +
 
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 +
 
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fill="#8BC34A"/></g></g></svg>
 +
     
 +
 
 +
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 +
         <div id="protein"  
 +
 
 +
class="sub">
 +
           <div  
 +
 
 +
class="header">
 +
           Protein  
 +
 
 +
Production Module
 
           </div>
 
           </div>
          <div class="text">
+
 
            <p>Induction synthesis of protein of interest is another important step. Microorganisms in bioreactors are induced at the OD, at which the protein production is maximum. [5] Because of this, factories install sophisticated machinery to keep track of the OD value of the culture so as to know when to induce the production. We wanted our bacteria to know when to start protein production and start it by itself. Hence, we used the lux quorum sensing system to sense this cell density. [6] We have expressed the gene for our protein of interest under the luxI gene so that protein of interest is produced in significant quantities only when the quorum is achieved.(Figure 2) We also wish to tune the quorum sensing system by tweaking with the strength of the promoters involved in quorum sensing.
+
 
 +
        <div class="text">
 +
         
 +
 
 +
  <p>Induction synthesis of protein  
 +
 
 +
of interest is another important  
 +
 
 +
step. Microorganisms in bioreactors  
 +
 
 +
are induced at the OD, at which the  
 +
 
 +
protein production is maximum. [5]  
 +
 
 +
Because of this, factories install  
 +
 
 +
sophisticated machinery to keep  
 +
 
 +
track of the OD value of the culture  
 +
 
 +
so as to know when to induce the  
 +
 
 +
production. We wanted our bacteria  
 +
 
 +
to know when to start protein  
 +
 
 +
production and start it by itself.  
 +
 
 +
Hence, we used the lux quorum  
 +
 
 +
sensing system to sense this cell  
 +
 
 +
density. [6] We have expressed the  
 +
 
 +
gene for our protein of interest  
 +
 
 +
under the luxI gene so that protein  
 +
 
 +
of interest is produced in  
 +
 
 +
significant quantities only when the  
 +
 
 +
quorum is achieved.(Figure 2) We  
 +
 
 +
also wish to tune the quorum sensing  
 +
 
 +
system by tweaking with the strength  
 +
 
 +
of the promoters involved in quorum  
 +
 
 +
sensing.
 
             </p>
 
             </p>
            <img class="image" src="lux.jpg" />Figure 2 : The lux quorum sensing system. Note the gene of interest "geneX*" downstream of the luxI gene. Image Courtesy: ETH Zurich 2013, iGEM team.
+
         
          </div>
+
 
 +
<img class="image" src="lux.jpg"  
 +
 
 +
/>Figure 2 : The lux quorum sensing  
 +
 
 +
system. Note the gene of interest  
 +
 
 +
"geneX*" downstream of the luxI  
 +
 
 +
gene. Image Courtesy: ETH Zurich  
 +
 
 +
2013, iGEM team.
 
           </div>
 
           </div>
 +
 
 +
 +
      </div>
 
         </div>
 
         </div>
  
        <span >
+
     
<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
+
 
        </span>
+
<span >
         <div id="aggre" class="sub">
+
<svg class="panel"  
           <div class="header">
+
 
           Auto-aggregation Module
+
onclick="openBar()"  
           </div>
+
 
 +
enable-background="new 0 0 128 128"  
 +
 
 +
height="40px" id="Layer_1"  
 +
 
 +
version="1.1" viewBox="0 0 128 128"  
 +
 
 +
width="40px" xml:space="preserve"  
 +
 
 +
xmlns="http://www.w3.org/2000/svg"  
 +
 
 +
xmlns:xlink="http://www.w3.org/1999/
 +
 
 +
xlink"><g><g><path  
 +
 
 +
d="M64,0C28.656,0,0,28.656,0,64s28.6
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 +
 
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 +
 
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fill="#B0BEC5"/></g></g><g><g><path  
 +
 
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 +
 
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 +
 
 +
,56z"  
 +
 
 +
fill="#8BC34A"/></g></g></svg>
 +
     
 +
 
 +
  </span>
 +
         <div id="aggre"  
 +
 
 +
class="sub">
 +
           <div  
 +
 
 +
class="header">
 +
            
 +
 
 +
Auto-aggregation Module
 +
            
 +
 
 +
</div>
 
           <div class="text">
 
           <div class="text">
            <p>
+
To achieve cellular aggregation, we use the famous auto-transporter protein, Antigen43 (Ag43). [7] It has shown to cause auto-aggregation of cells when overexpressed. (Figure 3) We plan to exploit this property of Ag43 to substitute centrifugation. We acknowledge previous iGEM teams who have worked on Ag43 (Hokkaido University, 2012; Aberdeen Scotland, 2014 and some more) as we got the BioBricks for Ag43 readily available.  We intend to express Ag43 only when the cells have made the product of interest. Hence, we use the diauxic shift in the media to act as a switch for the expression of Ag43.
+
 
             </p>
+
          <p>
             <img class="image" src="tube.jpg" />Figure 3: a) Cell culture without expression of Ag43 b) Cell culture overexpressing Ag43
+
To achieve cellular  
Source: MarjanW. van derWoude et al, 2008
+
 
 +
aggregation, we use the famous  
 +
 
 +
auto-transporter protein, Antigen43  
 +
 
 +
(Ag43). [7] It has shown to cause  
 +
 
 +
auto-aggregation of cells when  
 +
 
 +
overexpressed. (Figure 3) We plan to  
 +
 
 +
exploit this property of Ag43 to  
 +
 
 +
substitute centrifugation. We  
 +
 
 +
acknowledge previous iGEM teams who  
 +
 
 +
have worked on Ag43 (Hokkaido  
 +
 
 +
University, 2012; Aberdeen Scotland,  
 +
 
 +
2014 and some more) as we got the  
 +
 
 +
BioBricks for Ag43 readily  
 +
 
 +
available.  We intend to express  
 +
 
 +
Ag43 only when the cells have made  
 +
 
 +
the product of interest. Hence, we  
 +
 
 +
use the diauxic shift in the media  
 +
 
 +
to act as a switch for the  
 +
 
 +
expression of Ag43.
 +
              
 +
 
 +
</p>
 +
             <img class="image"  
 +
 
 +
src="tube.jpg" />Figure 3: a) Cell  
 +
 
 +
culture without expression of Ag43  
 +
 
 +
b) Cell culture overexpressing  
 +
 
 +
Ag43
 +
Source: MarjanW. van derWoude  
 +
 
 +
et al, 2008
  
 
           </div>
 
           </div>
        </div>
+
     
 +
 
 +
</div>
  
 
         <span >
 
         <span >
<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
+
<svg  
        </span>
+
 
         <div id="ref" class="sub">
+
class="panel" onclick="openBar()"  
           <div class="header">
+
 
           References
+
enable-background="new 0 0 128 128"  
 +
 
 +
height="40px" id="Layer_1"  
 +
 
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version="1.1" viewBox="0 0 128 128"  
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 +
 
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 +
 
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 +
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 +
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 +
 
 +
class="sub">
 +
           <div  
 +
 
 +
class="header">
 +
            
 +
 
 +
References
 
           </div>
 
           </div>
          <div class="text">
+
       
 +
 
 +
<div class="text">
 
         <ol>
 
         <ol>
          <li> Ferrer-Miralles N, Domingo-Espin J, Corchero JL, Vazquez E, Villaverde A. Microbial factories for recombinant pharmaceuticals, Microbial Cell Factories, 2009:8:17. </li>
+
   
          <li> Medipally S.R., Yusoff F. Md., Banerjee S., Shariff M. Microalgae as sustainable renewable energy Feedstock for Biofuel Production, BioMed Research International, 2015. </li>
+
 
          <li> Felo M., Christensen B., Higgins J., Process cost and facility considerations in the selection of primary cell culture clarification technology, AIChE, 2013. </li>
+
      <li> Ferrer-Miralles N,  
          <li> Motoo Suzuki, Rohini Roy, Haiyan Zheng, Nancy Woychik, Masayori Inouye, Bacterial Bioreactors for High Yield Production of Recombinant Protein. The Journal of Biological Chemistry, 2006.</li>
+
 
          <li> Rosano G.L., Ceccarelli E. A., Recombinant protein expression in Escherichia coli: advances and challenges, Frontiers in Microbiology, 2014.</li>
+
Domingo-Espin J, Corchero JL,  
          <li> Miller M.B., Bassler B.L., Quorum Sensing in Bacteria, Annual Review of Microbiology, 2001.</li>
+
 
          <li> Marjan W. van der Woude, Ian R. Henderson, Regulation and Function of Ag43 (Flu), Annu. Rev. Microbiol., 2008.
+
Vazquez E, Villaverde A. Microbial  
 +
 
 +
factories for recombinant  
 +
 
 +
pharmaceuticals, Microbial Cell  
 +
 
 +
Factories, 2009:8:17. </li>
 +
       
 +
 
 +
<li> Medipally S.R., Yusoff F. Md.,  
 +
 
 +
Banerjee S., Shariff M. Microalgae  
 +
 
 +
as sustainable renewable energy  
 +
 
 +
Feedstock for Biofuel Production,  
 +
 
 +
BioMed Research International, 2015.  
 +
 
 
</li>
 
</li>
         </ol>
+
          <li> Felo M.,
 +
 
 +
Christensen B., Higgins J., Process
 +
 
 +
cost and facility considerations in
 +
 
 +
the selection of primary cell
 +
 
 +
culture clarification technology,
 +
 
 +
AIChE, 2013. </li>
 +
          <li>
 +
 
 +
Motoo Suzuki, Rohini Roy, Haiyan
 +
 
 +
Zheng, Nancy Woychik, Masayori
 +
 
 +
Inouye, Bacterial Bioreactors for
 +
 
 +
High Yield Production of Recombinant
 +
 
 +
Protein. The Journal of Biological
 +
 
 +
Chemistry, 2006.</li>
 +
          <li>
 +
 
 +
Rosano G.L., Ceccarelli E. A.,
 +
 
 +
Recombinant protein expression in
 +
 
 +
Escherichia coli: advances and
 +
 
 +
challenges, Frontiers in
 +
 
 +
Microbiology, 2014.</li>
 +
         
 +
 
 +
<li> Miller M.B., Bassler B.L.,
 +
 
 +
Quorum Sensing in Bacteria, Annual
 +
 
 +
Review of Microbiology, 2001.</li>
 +
 
 +
 
 +
         <li> Marjan W. van der
 +
 
 +
Woude, Ian R. Henderson, Regulation
 +
 
 +
and Function of Ag43 (Flu), Annu.
 +
 
 +
Rev. Microbiol., 2008.
 +
</li>
 +
       
 +
 
 +
</ol>
 
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     Cellfiefuge
             

An auto-pelleting system



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height="60" width="320"

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             <a 

href="#description">Description</a>



</svg>




Description




<a href="#overview">Overview</a>





<a href="#design">Design</a>






<a href="#protein">Protein production module</a>




<a href="#aggre">Auto Aggregation module</a>




       

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Overview



Since the advent of rDNA technology in the late 1970s, the use of recombinant protein has been on the rise, starting from insulin and hormones all the way through to monoclonal antibodies and one hundred and fifty-one FDA approved protein based recombinant pharmaceuticals by the year 2009[1]. Despite being in high demand, recombinant proteins have heavy price tags, thanks to the significant manufacturing costs. One of the important steps in the manufacturing process is Centrifugation but on an industrial scale, it is an economic nightmare. [2] Further, existing industrial setups use complex sensors to monitor cell density to determine the point at which to begin separation of the cells from the cell culture. One can immediately see the humongous relief that would be associated with finding a way to deal with the above problems. Hence, we came up with the idea of our project, the Cellfifuge.



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         Our 

Bioreactor Design




We realized that manufacturing units use expensive and energy expensive machinery [3]. Hence, we engineered our bacteria in such a way that it could do most of the work done by these monstrous machines so that we no longer have to buy them and pay their bills. To increase the yield of the product, we came up with the idea of separating cell growth and target protein production so that when the cells have grown up to a high enough cell density, they shuttle all their energy towards the required protein production.[4] Based on the above ideas, we came up with the design of our bioreactor. (Figure 1)

We realized that we would not be able to work on the whole idea this summer so, we focussed on two modules of our design: the Protein production module and the auto-aggregation module leaving the arresting of cell growth for future iGEM teams as a seed for their ideas.


           <img 

class="image" src="designa.jpg"

/>Figure 1: The bioreactor design of

Cellfifuge


       

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         Protein 

Production Module



Induction synthesis of protein of interest is another important step. Microorganisms in bioreactors are induced at the OD, at which the protein production is maximum. [5] Because of this, factories install sophisticated machinery to keep track of the OD value of the culture so as to know when to induce the production. We wanted our bacteria to know when to start protein production and start it by itself. Hence, we used the lux quorum sensing system to sense this cell density. [6] We have expressed the gene for our protein of interest under the luxI gene so that protein of interest is produced in significant quantities only when the quorum is achieved.(Figure 2) We also wish to tune the quorum sensing system by tweaking with the strength of the promoters involved in quorum sensing.


<img class="image" src="lux.jpg" 

/>Figure 2 : The lux quorum sensing

system. Note the gene of interest

"geneX*" downstream of the luxI

gene. Image Courtesy: ETH Zurich

2013, iGEM team.


       </div>



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Auto-aggregation Module



To achieve cellular aggregation, we use the famous auto-transporter protein, Antigen43 (Ag43). [7] It has shown to cause auto-aggregation of cells when overexpressed. (Figure 3) We plan to exploit this property of Ag43 to substitute centrifugation. We acknowledge previous iGEM teams who have worked on Ag43 (Hokkaido University, 2012; Aberdeen Scotland, 2014 and some more) as we got the BioBricks for Ag43 readily available. We intend to express Ag43 only when the cells have made the product of interest. Hence, we use the diauxic shift in the media to act as a switch for the expression of Ag43.

           <img class="image" 

src="tube.jpg" />Figure 3: a) Cell

culture without expression of Ag43

b) Cell culture overexpressing

Ag43 Source: MarjanW. van derWoude

et al, 2008


       

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fill="#8BC34A"/></g></g></svg>


 


References


  1. Ferrer-Miralles N, Domingo-Espin J, Corchero JL, Vazquez E, Villaverde A. Microbial factories for recombinant pharmaceuticals, Microbial Cell Factories, 2009:8:17.

  2. Medipally S.R., Yusoff F. Md., Banerjee S., Shariff M. Microalgae as sustainable renewable energy Feedstock for Biofuel Production, BioMed Research International, 2015.
  3. Felo M., Christensen B., Higgins J., Process cost and facility considerations in the selection of primary cell culture clarification technology, AIChE, 2013.
  4. Motoo Suzuki, Rohini Roy, Haiyan Zheng, Nancy Woychik, Masayori Inouye, Bacterial Bioreactors for High Yield Production of Recombinant Protein. The Journal of Biological Chemistry, 2006.
  5. Rosano G.L., Ceccarelli E. A., Recombinant protein expression in Escherichia coli: advances and challenges, Frontiers in Microbiology, 2014.

  6. Miller M.B., Bassler B.L., Quorum Sensing in Bacteria, Annual Review of Microbiology, 2001.

  7. Marjan W. van der Woude, Ian R. Henderson, Regulation and Function of Ag43 (Flu), Annu. Rev. Microbiol., 2008.



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