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

(Prototype team page)
 
Line 1: Line 1:
 
{{Berlin_diagnostX}}
 
{{Berlin_diagnostX}}
 
<html>
 
<html>
 +
<body>
  
 +
    <!-- Head Image -->
 +
<div class="abstand_navbar headimage" id="background_description_head"> <h1 class="text-center head_us head-light">Experiments</h1> </div>
  
 +
  <div class="container" id="inhalt">
 +
   
  
 +
    <!-- Schema 1 -->
 +
    <div class="row">
 +
        <div class="col-12">
 +
            <h3 class="text-center igem_blue mt-4"><strong>The preliminary work</strong></h3>
 +
        </div>
 +
    </div>
 +
    <div class="row mt-3">
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue pb-1">RNA isolation </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 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://placekitten.com/550/400">
 +
        </div>
 +
    </div>
 +
    <div class="row mt-5">
 +
        <div class="col-6">
 +
            <img class="img-fluid" src="https://placekitten.com/550/400">
 +
        </div>
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue">RNA sequencing </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 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>
 +
   
 +
    <!-- Seperator -->
 +
   
 +
    <div class="row"><div class="col"><hr class="mt-5 mb-5 igem_seperator mx-auto"></div></div>
  
−
<div class="column full_size">
+
    <!-- Schema 1 -->
−
<h1>Design</h1>
+
    <div class="row">
−
<p>
+
        <div class="col-12">
−
Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
+
            <h3 class="text-center igem_blue mt-4"><strong>The bioinformatics behind our switch design</strong></h3>
−
</p>
+
        </div>
 +
    </div>
 +
    <div class="row mt-3">
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue pb-1">In silico design </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 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://placekitten.com/550/400">
 +
        </div>
 +
    </div>
  
−
<p>
+
<!-- Seperator -->
−
This page is different to the "Applied Design Award" page. Please see the <a href="https://2017.igem.org/Team:Berlin_diagnostX/Applied_Design">Applied Design</a> page for more information on how to compete for that award.
+
   
−
</p>
+
    <div class="row"><div class="col"><hr class="mt-5 mb-5 igem_seperator mx-auto"></div></div>
  
−
</div>
+
<!-- Schema 1 -->
 +
    <div class="row">
 +
        <div class="col-12">
 +
            <h3 class="text-center igem_blue mt-4"><strong>The switch synthesis</strong></h3>
 +
        </div>
 +
    </div>
 +
    <div class="row mt-5">
 +
        <div class="col-6">
 +
            <img class="img-fluid" src="https://placekitten.com/550/400">
 +
        </div>
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue">Extension PCR </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 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>
 +
    <div class="row mt-3">
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue pb-1">Nested PCR</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 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://placekitten.com/550/400">
 +
        </div>
 +
    </div>
 +
    <div class="row mt-5">
 +
        <div class="col-6">
 +
            <img class="img-fluid" src="https://placekitten.com/550/400">
 +
        </div>
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue">Colony PCR </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 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>
 +
<div class="row mt-3">
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue pb-1">DNA Clean Up (via column & gel extraction) </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 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://placekitten.com/550/400">
 +
        </div>
 +
    </div>
 +
    <div class="row mt-5">
 +
        <div class="col-6">
 +
            <img class="img-fluid" src="https://placekitten.com/550/400">
 +
        </div>
 +
        <div class="col-6">
 +
            <h5 class="text-left igem_blue">Gel electrophoresis </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 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>
 +
<!-- Seperator -->
 +
   
 +
    <div class="row"><div class="col"><hr class="mt-5 mb-5 igem_seperator mx-auto"></div></div>
  
−
<div class="column half_size">
+
<!-- Schema 2 -->
−
<h5>What should this page contain?</h5>
+
   
−
<ul>
+
    <div class="row">
−
<li>Explanation of the engineering principles your team used in your design</li>
+
        <div class="col-12">
−
<li>Discussion of the design iterations your team went through</li>
+
            <h3 class="text-center igem_blue mt-4"><strong>The Idea</strong></h3>
−
<li>Experimental plan to test your designs</li>
+
        </div>
−
</ul>
+
    </div>
−
 
+
    <div class="row">
−
</div>
+
        <div class="col-6">
−
 
+
            <h5 class="text-left igem_blue pb-1">The Tapeworm <em>Taenia solium</em> </h5>
−
<div class="column half_size">
+
            <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 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>
−
<h5>Inspiration</h5>
+
        </div>
−
<ul>
+
        <div class="col-6">
−
<li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
+
            <p class="text-justify">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.
−
<li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
+
            In order to develop our test, we first need to achieve two things:  
−
<li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
+
            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.
−
</ul>
+
            In order to develop our test, we first need to achieve two things:  
−
</div>
+
            </p>
 +
        </div>
 +
    </div>
 +
    <div class="row">
 +
        <div class="col-12">
 +
            <p class="summarybox p-4"><strong>Summary</strong>: Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum.</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 class="row">
 +
        <div class="col-12">
 +
            <h3 class="text-center igem_blue mt-4"><strong>The Experiments</strong></h3>
 +
        </div>
 +
    </div>
 +
    <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"><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 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">
 +
            <h5 class="text-left igem_blue pb-1">Toehold Switch Sensor Test</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 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="row large_image_element mt-4">
 +
            <div class="col-12">
 +
                <img src="https://static.igem.org/mediawiki/2017/4/4f/T--Berlin_diagnostX--toehold_easy.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>
  
 +
        <!-- Schema 3.5 -->
 +
    <div class="row">
 +
        <div class="col-12">
 +
            <h3 class="text-center igem_blue mt-4"><strong>Application</strong></h3>
 +
            <h5 class="igem_blue pb-1">Überschrift</h5>
 +
            <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> 
  
 +
     
 +
</body>
 
</html>
 
</html>
 +
{{Berlin_diagnostX2}}

Revision as of 23:02, 29 October 2017

Experiments

The preliminary work

RNA isolation

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 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.

RNA sequencing

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 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.

The bioinformatics behind our switch design

In silico design

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 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.

The switch synthesis

Extension PCR

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 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.

Nested PCR

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 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.

Colony PCR

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 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.

DNA Clean Up (via column & gel extraction)

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 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.

Gel electrophoresis

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 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.

The Idea

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 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.

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: 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:

Summary: Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum.

The Experiments

Production of Toehold Switch Sensors

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 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.

Toehold Switch Sensor Test

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 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.

Application

Überschrift

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.