Difference between revisions of "Team:Berlin diagnostX/Description"

(Prototype team page)
 
 
(32 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
{{Berlin_diagnostX}}
 
{{Berlin_diagnostX}}
 
<html>
 
<html>
 +
<body>
  
 +
<!-- Head Image -->
  
 +
<div class="abstand_navbar conti_head">
 +
    <img class="head-img img-fluid" src="https://static.igem.org/mediawiki/2017/7/7c/T--Berlin_diagnostX--Header.jpg">
 +
    <h1 class="text-center head_us head-light">Description</h1>
 +
</div>
  
−
<div class="column full_size">
+
  <div class="container" id="inhalt">
−
<h1>Description</h1>
+
   
  
−
<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
+
    <!-- Schema 1 -->
 +
    <div class="row">
 +
        <div class="col-12">
 +
            <h3 class="text-center igem_blue mt-4"><strong>The healthcare background</strong></h3>
 +
        </div>
 +
    </div>
 +
    <div class="row mt-3">
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue pb-1"><strong>The tapeworm <em>Taenia solium</em></strong></h5>
 +
            <p class="text-justify"><em>Taenia solium</em>, otherwise known as pork tapeworm, is a parasite with potentially serious health effects in humans. It infects millions of people worldwide, leading to severe brain diseases, blindness, epilepsy, and death. Countries where pork production and consumption are coupled with poor hygiene are the worst affected, including large areas of Latin America, Sub-Saharan Africa, and South- and East-Asia, where over 14% of people have experienced an infection at some point <a class="igem_blue" href="#"> [1]</a>. However, a clear picture of how many people are currently infected by T. solium does not exist, due to the current difficulty in making a diagnosis. </p>
 +
        </div>
 +
        <div class="col-6">
 +
            <img class="img-fluid" src="https://static.igem.org/mediawiki/2017/0/03/T--Berlin_diagnostX--drawing_T.solium_Description.png">
 +
        </div>
 +
    </div>
 +
    <div class="row mt-1">
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue"><strong> Diagnosis: Difficult and Expensive</strong> </h5>
 +
            <p class="text-justify"> One of the most common diagnostic methods currently available is called enzyme-linked immunoelectrotransfer blot (EITB rES33). It is not only relatively expensive and requires a specialised laboratory setup, but it can only determine whether someone has had the infection at some point in their life, not whether they are currently carrying the parasite. Another method available involves checking faeces for tapeworm eggs under a microscope, which on top of requiring expensive equipment is relatively unreliable [2]. </p>
 +
        </div>
 +
        <div class="col-6"> </div>
 +
    </div>
 +
   
 +
    <!-- Seperator -->
 +
   
 +
    <div class="row"><div class="col"><hr class="mt-5 mb-5 igem_seperator mx-auto"></div></div>
  
  
−
<h5>What should this page contain?</h5>
+
<!-- Schema 2 -->
 +
   
 +
    <div class="row">
 +
        <div class="col-12">
 +
            <h3 class="text-center igem_blue mt-4"><strong>The Idea</strong></h3>
 +
        </div>
 +
    </div>
 +
    <div class="row">
 +
        <div class="col-6">
 +
            <p class="text-justify">Our goal is to develop a <em>cheap, practical, and effective diagnostic test</em> for the parasite T. solium in humans. By reliably identifying carriers of T. solium, treatment can be directed to those who need it, saving resources and avoiding unnecessary side effects. In this way the most dangerous health effects can be averted.
 +
The test will respond to RNA molecules from T. solium in order to detect a tapeworm infestation. RNA (Ribonucleic acid) is the basis of protein production, and every species, including T. solium, has specific RNA molecules which can be used to unambiguously identify it. We plan to take advantage of this in our diagnostic method.
 +
</p>
 +
        </div>
 +
        <div class="col-6">
 +
            <p class="text-justify">The test will be based on a newly developed method called <em>toehold switch sensors</em>. This method has already been successfully applied to the diagnosis of the Zika virus [3]. We are therefore convinced that toehold switch sensors will also be useful in detecting T. solium.
 +
In order to develop our test, we first need to achieve two things: </p>
 
<ul>
 
<ul>
−
<li> A clear and concise description of your project.</li>
+
<li> 1. Production of toehold switch sensors to detect RNA specific to T. solium </li>
−
<li>A detailed explanation of why your team chose to work on this particular project.</li>
+
<li> 2. Creation of model RNA molecules to test Wormspotter </li>
−
<li>References and sources to document your research.</li>
+
−
<li>Use illustrations and other visual resources to explain your project.</li>
+
 
</ul>
 
</ul>
 +
            <p class="text-justify">Once these stages are complete, they will need to be brought together so that we can test whether Wormspotter can recognise and react to RNA from T. solium. We aim to achieve this in a cell-free system.
 +
            </p>
 +
        </div>
 +
    </div>
 +
    <div class="row">
 +
        <div class="col-12">
 +
            <p class="summarybox p-4"><strong>Our goal: Developing a simple, cost-effective and rapid diagnostic tool for infection with tapeworm T. solium</strong> using an innovative new method - <em>toehold switch sensors</em> - in a cell free expression system</p>
 +
        </div>
 +
    </div>
 +
   
 +
<!-- Seperator -->
 +
   
 +
    <div class="row"><div class="col"><hr class="mt-5 mb-5 igem_seperator mx-auto"></div></div>
  
−
 
+
<!-- Schema 3 -->
−
</div>
+
   
−
 
+
   
−
<div class="column full_size" >
+
<div class="row">
−
 
+
        <div class="col-12">
−
<h5>Advice on writing your Project Description</h5>
+
            <h3 class="text-center igem_blue mt-4"><strong>The Experiments</strong></h3>
−
 
+
        </div>
−
<p>
+
    </div>
−
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.  
+
    <div class="row">
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue pb-1">Production of Toehold Switch Sensors </h5>
 +
            <p class="text-justify">Toehold switch sensors are based on synthetic biology. Essentially, they are RNA molecules which code for a reporter protein. They consist of a specific toehold sequence, a ribosome-binding site (which is important for the production of proteins) and a sequence for the reporter protein. The reporter protein can only be produced if the sensor has bonded with its specific target RNA sequence [4]. When producing the sensors, we can select both the toehold sequence and the reporter protein with complete flexibility to match our needs. In this way we can fashion our Wormspotter so that it only sends a desired signal when it binds to RNA molecules specific to T. solium.
 +
We are planning to use T. solium-specific RNA sequences for the toehold sequence and beta-Galactosidase as a reporter protein.
 
</p>
 
</p>
 +
        </div>
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue pb-1">Toehold Switch Sensor Test</h5>
 +
            <p class="text-justify">We will then combine the toehold switch sensors and model RNA molecules in a cell-free expression system. These systems can produce proteins, just like in a normal cell. However, they are completely synthetically produced, and therefore provide extremely controlled reaction conditions
 +
We will subsequently be able to verify whether the reporter protein beta-Galactosidase was produced in the cell-free system. If it is present after adding our model RNA molecules, this will serve as proof that the toehold switch sensor reacts specifically to T. solium RNA.</p>
 +
        </div>
 +
        <div class="row large_image_element mt-4">
 +
            <div class="col-12">
 +
                <img src="https://static.igem.org/mediawiki/2017/5/54/T--Berlin_diagnostX--_switch_prinzipNEU.png" class="img-fluid">
 +
            </div>
 +
        </div>
 +
       
 +
        <!-- Seperator -->
 +
        <div class="row"><div class="col"><hr class="mt-5 mb-5 igem_seperator mx-auto"></div></div>
  
−
<p>
+
        <!-- Schema 3.5 -->
−
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.
+
    <div class="row">
−
</p>
+
        <div class="col-12">
−
 
+
            <h3 class="text-center igem_blue mt-4"><strong>Application</strong></h3>
−
</div>
+
            <p class="text-justify">The synthetic biology experiments described here are particularly important for participation in the iGEM competition. Simultaneously, a second team will work on the recovery of T. solium-RNA from patient stool samples in order to make our test applicable for medical purposes. We are currently forming the necessary partnerships for this goal: A working group in Nairobi has already committed to providing us with relevant material. However, these experiments will be conducted in a properly equipped laboratory, independent from the previously described experiments.</p>
−
 
+
        </div>
−
 
+
    </div>
−
<div class="column half_size" >
+
</div>  
−
 
+
−
<h5>References</h5>
+
−
<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>
+
−
 
+
−
</div>
+
−
 
+
−
 
+
−
<div class="column half_size" >
+
−
<h5>Inspiration</h5>
+
−
<p>See how other teams have described and presented their projects: </p>
+
−
 
+
−
<ul>
+
−
<li><a href="https://2016.igem.org/Team:Imperial_College/Description">2016 Imperial College</a></li>
+
−
<li><a href="https://2016.igem.org/Team:Wageningen_UR/Description">2016 Wageningen UR</a></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>
+
−
</div>
+
−
 
+
  
 +
   
 +
        <div class="row dark normal_box" id="references">
 +
            <div class="col-12">
 +
                <h5 class="text-center">References</h5>
 +
                <p class="text-justify"> [1] Coral-Almeida M, Gabriël S, Abatih EN, Praet N, Benitez W, et al. (2015). <i>Taenia solium</i> Human Cysticercosis: A Systematic Review of Sero-epidemiological Data from Endemic Zones around the World. PLoS Negl Trop Dis 9(7): e0003919. doi: 10.1371/journal.pntd.0003919<br>
 +
                [2] O'Neal SE, Moyano LM, Ayvar V, Rodriguez S, Gavidia C, et al. (2014) Ring-Screening to Control Endemic Transmission of <i>Taenia solium</i>. PLoS Negl Trop Dis 8(9): e3125. doi: 10.1371/journal.pntd.0003125<br>
 +
                [3] Pardee, K. et al. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 165, 1255–1266 (2016).<br>      [4] Green, A. A., Silver, P. A., Collins, J. J. &amp; Yin, P. Toehold Switches: De-Novo-Designed Regulators of Gene Expression. Cell 159, 925–939 (2014).<br>     
 +
                [5] Gomez, S. et al. Genome analysis of Excretory/Secretory proteins in <i>Taenia solium</i> reveals their Abundance of Antigenic Regions (AAR). Sci. Rep. 5, 9683 (2015).<br>
 +
                [6] Mayta, H. et al. Nested PCR for Specific Diagnosis of <i>Taenia solium</i> Taeniasis. J. Clin. Microbiol. 46, 286–289 (2008).<br>
  
 +
               
 +
                </p>
 +
            </div>
 +
        </div>
 +
</body>
 
</html>
 
</html>
 +
{{Berlin_diagnostX2}}

Latest revision as of 21:08, 1 November 2017

Description

The healthcare background

The tapeworm Taenia solium

Taenia solium, otherwise known as pork tapeworm, is a parasite with potentially serious health effects in humans. It infects millions of people worldwide, leading to severe brain diseases, blindness, epilepsy, and death. Countries where pork production and consumption are coupled with poor hygiene are the worst affected, including large areas of Latin America, Sub-Saharan Africa, and South- and East-Asia, where over 14% of people have experienced an infection at some point  [1]. However, a clear picture of how many people are currently infected by T. solium does not exist, due to the current difficulty in making a diagnosis.

Diagnosis: Difficult and Expensive

One of the most common diagnostic methods currently available is called enzyme-linked immunoelectrotransfer blot (EITB rES33). It is not only relatively expensive and requires a specialised laboratory setup, but it can only determine whether someone has had the infection at some point in their life, not whether they are currently carrying the parasite. Another method available involves checking faeces for tapeworm eggs under a microscope, which on top of requiring expensive equipment is relatively unreliable [2].

The Idea

Our goal is to develop a cheap, practical, and effective diagnostic test for the parasite T. solium in humans. By reliably identifying carriers of T. solium, treatment can be directed to those who need it, saving resources and avoiding unnecessary side effects. In this way the most dangerous health effects can be averted. The test will respond to RNA molecules from T. solium in order to detect a tapeworm infestation. RNA (Ribonucleic acid) is the basis of protein production, and every species, including T. solium, has specific RNA molecules which can be used to unambiguously identify it. We plan to take advantage of this in our diagnostic method.

The test will be based on a newly developed method called toehold switch sensors. This method has already been successfully applied to the diagnosis of the Zika virus [3]. We are therefore convinced that toehold switch sensors will also be useful in detecting T. solium. In order to develop our test, we first need to achieve two things:

  • 1. Production of toehold switch sensors to detect RNA specific to T. solium
  • 2. Creation of model RNA molecules to test Wormspotter

Once these stages are complete, they will need to be brought together so that we can test whether Wormspotter can recognise and react to RNA from T. solium. We aim to achieve this in a cell-free system.

Our goal: Developing a simple, cost-effective and rapid diagnostic tool for infection with tapeworm T. solium using an innovative new method - toehold switch sensors - in a cell free expression system

The Experiments

Production of Toehold Switch Sensors

Toehold switch sensors are based on synthetic biology. Essentially, they are RNA molecules which code for a reporter protein. They consist of a specific toehold sequence, a ribosome-binding site (which is important for the production of proteins) and a sequence for the reporter protein. The reporter protein can only be produced if the sensor has bonded with its specific target RNA sequence [4]. When producing the sensors, we can select both the toehold sequence and the reporter protein with complete flexibility to match our needs. In this way we can fashion our Wormspotter so that it only sends a desired signal when it binds to RNA molecules specific to T. solium. We are planning to use T. solium-specific RNA sequences for the toehold sequence and beta-Galactosidase as a reporter protein.

Toehold Switch Sensor Test

We will then combine the toehold switch sensors and model RNA molecules in a cell-free expression system. These systems can produce proteins, just like in a normal cell. However, they are completely synthetically produced, and therefore provide extremely controlled reaction conditions We will subsequently be able to verify whether the reporter protein beta-Galactosidase was produced in the cell-free system. If it is present after adding our model RNA molecules, this will serve as proof that the toehold switch sensor reacts specifically to T. solium RNA.

Application

The synthetic biology experiments described here are particularly important for participation in the iGEM competition. Simultaneously, a second team will work on the recovery of T. solium-RNA from patient stool samples in order to make our test applicable for medical purposes. We are currently forming the necessary partnerships for this goal: A working group in Nairobi has already committed to providing us with relevant material. However, these experiments will be conducted in a properly equipped laboratory, independent from the previously described experiments.

References

[1] Coral-Almeida M, Gabriël S, Abatih EN, Praet N, Benitez W, et al. (2015). Taenia solium Human Cysticercosis: A Systematic Review of Sero-epidemiological Data from Endemic Zones around the World. PLoS Negl Trop Dis 9(7): e0003919. doi: 10.1371/journal.pntd.0003919
[2] O'Neal SE, Moyano LM, Ayvar V, Rodriguez S, Gavidia C, et al. (2014) Ring-Screening to Control Endemic Transmission of Taenia solium. PLoS Negl Trop Dis 8(9): e3125. doi: 10.1371/journal.pntd.0003125
[3] Pardee, K. et al. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 165, 1255–1266 (2016).
[4] Green, A. A., Silver, P. A., Collins, J. J. & Yin, P. Toehold Switches: De-Novo-Designed Regulators of Gene Expression. Cell 159, 925–939 (2014).
[5] Gomez, S. et al. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR). Sci. Rep. 5, 9683 (2015).
[6] Mayta, H. et al. Nested PCR for Specific Diagnosis of Taenia solium Taeniasis. J. Clin. Microbiol. 46, 286–289 (2008).