Difference between revisions of "Team:Harvard/Description"

 
(44 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
{{Harvard}}
+
{{Team:Harvard/NavBar}}
 +
 
 
<html>
 
<html>
  
 +
<!--Parallax scrolling-->
 +
<style>
 +
.parallax {
 +
    /* The image used */
 +
    background-image: url("https://static.igem.org/mediawiki/2017/3/3c/Harvard--High_Banner.jpeg");
  
  
−
<div class="column full_size">
+
    /* Set a specific height */
−
<h1>Description</h1>
+
    min-width: 100%;
 +
    min-height: 50%; 
 +
    height: 500px;
 +
    width: 100%;
 +
   
  
−
<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
 
  
 +
   
  
−
<h5>What should this page contain?</h5>
+
    /* Create the parallax scrolling effect */
−
<ul>
+
    background-attachment: fixed;
−
<li> A clear and concise description of your project.</li>
+
    background-position: center;
−
<li>A detailed explanation of why your team chose to work on this particular project.</li>
+
    background-repeat: no-repeat;
−
<li>References and sources to document your research.</li>
+
    background-size: cover;
−
<li>Use illustrations and other visual resources to explain your project.</li>
+
}
−
</ul>
+
  
 +
img {
 +
    max-width: 100%;
 +
    height: auto;
 +
    width: auto\9; /* ie8 */
 +
}
  
−
</div>
+
</style>
  
−
<div class="column full_size" >
+
<!-- make the above container -->
 +
<div class="parallax column full_size"></div>
  
−
<h5>Advice on writing your Project Description</h5>
+
<div class="column full_size description" style = "margin-top: 5%">
  
−
<p>
+
<h1>Project Description</h1>
−
We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.  
+
<h3>Overview</h3>
−
</p>
+
<br>
 +
Chemical synthesis is the most commonly used method of producing industrially relevant molecules, yet this practice is often accompanied by various environmental hazards. Biological synthesis, on the other hand, does not produce any toxic byproducts, nor does it require expensive starting materials. In the long run, it is a better manufacturing solution in many respects.
 +
<br><br>
 +
One strategy for biological synthesis is to adapt pre-existing systems already in nature. For instance, <i>E. coli</i> produces proteinaceous components in its biofilm called curli fibers. These fibers self-polymerize outside of the cell, forming a macroscopic agglomeration of material when isolated in sufficient bulk. The Joshi lab has already demonstrated how various functional peptide domains can be added to the self-polymerizing units of curli, so the polymers can form the basis of a variety of functional materials.
 +
<br><br>
 +
Our project focuses on optimizing curli production on two fronts as a first step to developing the curli system into a robust platform for producing materials at industrially relevant yields. First, we alter ribosome binding site strengths associated with proteins involved in the curli pathway to optimize the stoichiometric ratios of these molecules in the cell. The alterations are informed by a model of curli production and export that determines the optimum ratio of pathway components to maximize the production of our desired product, extracellular curli fibers, and minimize the aggregation of unwanted byproducts within the cell. This ensures that each cell becomes a more efficient curli export machine. The second component of the project aims to maximize cell densities within culture media through the development of a bioreactor that maintains higher dissolved oxygen concentrations than standard shaker flasks. Eliminating the limiting factor of insufficient oxygenation allows bacterial cells to produce more curli per unit of feedstock. This aspect of the project aims to optimize the conditions for protein-producing cell cultures. Our work along these two lines will inform the development of the curli system as a feasible biosynthetic platform for producing scalable and programmable materials.
  
−
<p>
 
−
Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
 
−
</p>
 
  
−
</div>
+
<h3>Curli System</h3>
  
 +
<br>
 +
Curli fibers are the main proteinaceous component of <i>E. coli</i> biofilms, which are aggregates of microorganisms embedded in a self-produced matrix of various polymeric substances. Biofilms are often associated with pathogenicity, but they also provide opportunities for development as platforms for biological synthesis of functional materials. The secretion and polymerization pathway of curli fibers is well-documented, and is depicted here in this diagram:
  
−
<div class="column half_size" >
+
<br>
  
−
<h5>References</h5>
+
<center>
−
<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you thought about your project and what works inspired you.</p>
+
<img src="https://static.igem.org/mediawiki/2017/2/25/Harvard_--_Curli_Pathway.jpeg" alt="Curli_Pathway.jpg" width="300" height="600"><br>
 +
<div align="middle" style="font-size:80%"> Goyal, Parveen, et al. (2014) </div>
 +
</center>
  
−
</div>
+
<br>
  
 +
There are a number of chaperone and membrane proteins involved in this pathway:
  
−
<div class="column half_size" >
+
<br>
−
<h5>Inspiration</h5>
+
<center>
−
<p>See how other teams have described and presented their projects: </p>
+
<table>
 +
  <tr>
 +
    <th>Protein</th>
 +
    <th>Function</th>
 +
  </tr>
 +
  <tr>
 +
    <td>csgA</td>
 +
    <td>Major subunit that aggregates and self-polymerizes to form curli fibers</td>
 +
  </tr>
 +
  <tr>
 +
    <td>csgB</td>
 +
    <td>Interacts with csgF to initiate nucleation of csgA fibers</td>
 +
  </tr>
 +
  <tr>
 +
    <td>csgC</td>
 +
    <td>Chaperone protein that interacts with csgA and csgB and prevents them from polymerizing inside the cell</td>
 +
  </tr>
 +
  <tr>
 +
    <td>csgE</td>
 +
    <td>Periplasmic protein that interacts with csgG at the outer membrane</td>
 +
  </tr>
 +
  <tr>
 +
    <td>csgF</td>
 +
    <td>Periplasmic protein that interacts with csgG at the outer membrane</td>
 +
  </tr>
 +
  <tr>
 +
    <td>csgG</td>
 +
    <td>Outer membrane lipoprotein that is required for stability and secretion of csgA and csgB</td>
 +
  </tr>
 +
</table>
 +
</center>
 +
 
 +
<br>
 +
 
 +
We are particularly interested in curli fibers because they are extremely robust and can withstand exposure to extreme conditions like boiling in detergents or incubation in solvents. Thus, they present great potential for use in harsh environments.
 +
 
 +
<br><br>
 +
 
 +
Additionally, the Joshi lab has demonstrated that it is possible to fuse functional proteins to the csgA subunit and have both csgA retain its secretion and polymerization properties while having the fused protein maintain its primary function. For instance, the Joshi Lab successfully showed GFP fused to csgA retains its fluorescent properties, and enzymes can be immobilized on csgA to form catalytic biofilms. Proteins fused to csgA will not only be secreted using <i>E. coli</i> ’s natural secretion machinery, but it will also be embedded within a physical material that can be handled and applied in a variety of ways.
 +
 
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2017/e/e5/Harvard--Curli_fusions.png" alt="Curli_Fusions.jpg" width="600" height="300"><br>
 +
<div align="middle" style="font-size:80%"> Nguyen, Peter Q., et al. (2014) </div>
 +
</center>
 +
 
 +
 
 +
<br>
 +
<h3>References</h3>
  
 
<ul>
 
<ul>
−
<li><a href="https://2016.igem.org/Team:Imperial_College/Description">2016 Imperial College</a></li>
+
  <li>Goyal, Parveen, et al. "Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG." Nature 516.7530 (2014): 250-253.</li>
−
<li><a href="https://2016.igem.org/Team:Wageningen_UR/Description">2016 Wageningen UR</a></li>
+
  <li>Nguyen, Peter Q., et al. "Programmable biofilm-based materials from engineered curli nanofibres." Nature communications 5 (2014).</li>
−
<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> 2014 UC Davis</a></li>
+
−
<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">2014 SYSU Software</a></li>
+
 
</ul>
 
</ul>
 +
 +
<br><br><br>
 
</div>
 
</div>
  
 +
</html>
  
−
 
+
{{Team:Harvard/Footer}}
−
</html>
+

Latest revision as of 03:23, 2 November 2017

Harvard OPTI POLY

Project Description

Overview


Chemical synthesis is the most commonly used method of producing industrially relevant molecules, yet this practice is often accompanied by various environmental hazards. Biological synthesis, on the other hand, does not produce any toxic byproducts, nor does it require expensive starting materials. In the long run, it is a better manufacturing solution in many respects.

One strategy for biological synthesis is to adapt pre-existing systems already in nature. For instance, E. coli produces proteinaceous components in its biofilm called curli fibers. These fibers self-polymerize outside of the cell, forming a macroscopic agglomeration of material when isolated in sufficient bulk. The Joshi lab has already demonstrated how various functional peptide domains can be added to the self-polymerizing units of curli, so the polymers can form the basis of a variety of functional materials.

Our project focuses on optimizing curli production on two fronts as a first step to developing the curli system into a robust platform for producing materials at industrially relevant yields. First, we alter ribosome binding site strengths associated with proteins involved in the curli pathway to optimize the stoichiometric ratios of these molecules in the cell. The alterations are informed by a model of curli production and export that determines the optimum ratio of pathway components to maximize the production of our desired product, extracellular curli fibers, and minimize the aggregation of unwanted byproducts within the cell. This ensures that each cell becomes a more efficient curli export machine. The second component of the project aims to maximize cell densities within culture media through the development of a bioreactor that maintains higher dissolved oxygen concentrations than standard shaker flasks. Eliminating the limiting factor of insufficient oxygenation allows bacterial cells to produce more curli per unit of feedstock. This aspect of the project aims to optimize the conditions for protein-producing cell cultures. Our work along these two lines will inform the development of the curli system as a feasible biosynthetic platform for producing scalable and programmable materials.

Curli System


Curli fibers are the main proteinaceous component of E. coli biofilms, which are aggregates of microorganisms embedded in a self-produced matrix of various polymeric substances. Biofilms are often associated with pathogenicity, but they also provide opportunities for development as platforms for biological synthesis of functional materials. The secretion and polymerization pathway of curli fibers is well-documented, and is depicted here in this diagram:
Curli_Pathway.jpg
Goyal, Parveen, et al. (2014)

There are a number of chaperone and membrane proteins involved in this pathway:
Protein Function
csgA Major subunit that aggregates and self-polymerizes to form curli fibers
csgB Interacts with csgF to initiate nucleation of csgA fibers
csgC Chaperone protein that interacts with csgA and csgB and prevents them from polymerizing inside the cell
csgE Periplasmic protein that interacts with csgG at the outer membrane
csgF Periplasmic protein that interacts with csgG at the outer membrane
csgG Outer membrane lipoprotein that is required for stability and secretion of csgA and csgB

We are particularly interested in curli fibers because they are extremely robust and can withstand exposure to extreme conditions like boiling in detergents or incubation in solvents. Thus, they present great potential for use in harsh environments.

Additionally, the Joshi lab has demonstrated that it is possible to fuse functional proteins to the csgA subunit and have both csgA retain its secretion and polymerization properties while having the fused protein maintain its primary function. For instance, the Joshi Lab successfully showed GFP fused to csgA retains its fluorescent properties, and enzymes can be immobilized on csgA to form catalytic biofilms. Proteins fused to csgA will not only be secreted using E. coli ’s natural secretion machinery, but it will also be embedded within a physical material that can be handled and applied in a variety of ways.
Curli_Fusions.jpg
Nguyen, Peter Q., et al. (2014)

References

  • Goyal, Parveen, et al. "Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG." Nature 516.7530 (2014): 250-253.
  • Nguyen, Peter Q., et al. "Programmable biofilm-based materials from engineered curli nanofibres." Nature communications 5 (2014).