Difference between revisions of "Team:Freiburg/Project/Overview"

 
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−
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+
<!-- BEGIN Responsive Layout -->
−
expand text s.t. it leads to system overview <br>
+
 
−
write appropriate content for slider: should present main subpoints of project in short sentence and link to them
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<div class="header_box">     
 
<div class="header_box">     
−
<h1>The DiaCHIP - A Versatile Detection System</h1>
+
<h1 class="headerbox">The DiaCHIP - A Versatile Detection System</h1>
 
</div>
 
</div>
  
−
<div class="image_box left" style="margin-bottom:10%;margin-left:-8%;margin-top:-10%;margin-right:-10%">
+
<div class="float_barrier"></div>
−
  <img align="left" alt="DiaCHIP_Sabi" src="https://static.igem.org/mediawiki/2015/a/af/Freiburg_DiaCHIP_Sabi.png" height="1430px">
+
−
</div>
+
  
−
<div style="width:120%;margin-bottom:22%">
+
<div class="floatcontainer">
−
<div class="content_box3" style="margin-right:20%;margin-left:30%">
+
−
<h2>Project Motivation</h2>
+
−
<p>
+
−
        Serological tests are a key element in modern medicine. Especially for detection and identification of infectious diseases, performing several blood tests is inevitable. Testing for more than one disease at a time or diagnosing a patient with diffuse symptoms usually requires more than one serological test. Every single test that is performed increases the time of waiting for a result as well as the bill. In case of dangerous infectious diseases every minute until the onset of the appropriate treatment is important for life. What if there was a possibility to combine all this testing in one single device which is affordable for everyone?
+
−
</p>
+
−
</div>
+
  
−
<div class="content_box3" style="margin-left:38%;margin-right:12%">
+
<div id='leftimage'>
−
<h2>Detecting Antigen-Antibody Interactions</h2>
+
  <img align="left" alt="DiaCHIP_Sabi" src="https://static.igem.org/mediawiki/2015/a/af/Freiburg_DiaCHIP_Sabi.png" height="1430px">
−
<p>
+
</div>
−
  The DiaCHIP is an innovative tool to screen for a broad range of antibodies present in serum. Antibodies serve indicator for an immune response towards an infection or a successful vaccination. They also play an important role in the diagnosis of autoimmune diseases. Spotting diseases by detecting correspondent antibodies in a patient's serum is an established method in  <a href="https://2015.igem.org/Team:Freiburg/Diagnostics" title="diagnostics_today">modern diagnostics</a>. <br>
+
−
Based on the very same principle, the DiaCHIP enables to simultaneously screen for multiple diseases at time, thereby reducing time and cost of a diagnosis. Especially the ability to differentiate between life threatening diseases and mild infections within a short time bears the potential to save lives. 
+
−
</p>
+
−
</div>
+
  
−
<div class="content_box3" style="margin-right:25%">
+
<div class="transparent_container">
−
<h2>The Concept</h2>
+
<div id="content_box1" class="content_box">
−
<p>
+
<h2>Project Motivation</h2>
−
  The key feature of the DiaCHIP concept is the combination of on-demand protein synthesis and a novel method for label-free detection packed into one device. The idea is to overcome challenges commonly found in protein array production and preservation. In addition, results can be obtained in a time- and cost-efficient manner; with a device simple enough to be rebuilt by future iGEM Teams.
+
<p>
−
</p>
+
    Serological tests are a key element in modern medicine. Especially for detection and identification of infectious diseases, the performance of several blood tests is inevitable. Testing for more than one disease at once or diagnosing a patient with uncertain symptoms usually requires far more than one test. Every single test that is required increases the time of waiting for a precise diagnosis. In case of dangerous infectious diseases every minute until the onset of an appropriate treatment is crucial for the patient's survival. What if there was a possibility to combine all these tests in one single chip which offers a fast diagnosis and is affordable for everyone?
−
</div>
+
</p>
 +
</div>
 +
</div>
 +
 
 +
 
 +
<div class="transparent_container">
 +
<div id="content_box2" class="content_box">
 +
<h2 style="text-align:left">Detecting Antigen-Antibody Interactions</h2>
 +
<p>
 +
The DiaCHIP is an innovative tool to screen for a broad range of antibodies in serum. Their presence serves as an indicator for an immune response towards an infectious disease or a successful vaccination. They also play an important role in the diagnosis of autoimmune diseases. Identifying diseases by detecting disease associated antibodies in a patient's serum is an established method in modern diagnostics. <br>
 +
Based on the very same principle, the DiaCHIP enables to screen for multiple diseases simultaneously, thereby reducing time and costs of a diagnosis. Especially the ability to differentiate between life threatening diseases and mild infections within a short time bears the potential to save lifes. 
 +
</p>
 +
</div>
 +
</div>
 +
 
 +
<div class="transparent_container">
 +
<div id="content_box3" class="content_box">
 +
<h2>The Concept</h2>
 +
<p>
 +
  The key feature of the DiaCHIP concept is the combination of on-demand protein synthesis and a novel method for label-free detection - all this packed into one device. The idea is to overcome challenges commonly found in protein array production and preservation. By cell-free expression of disease-related antigens, the protein array can be produced right when it is needed. In addition, results can be obtained in a time- and cost-efficient manner using a device simple enough to be rebuilt by future iGEM teams.
 +
</p>
 +
              <div class="link_button link_button_arrow">
 +
                <p><a href="https://2015.igem.org/Team:Freiburg/Project/System" title="System Overview">Step by Step Overview</a></p>
 +
              </div>
 +
</div>
 +
</div>
  
 
</div>
 
</div>
 +
 +
<div class="float_barrier"></div>
 +
 +
  
 
<!---------------BEGIN SLIDER------------------>
 
<!---------------BEGIN SLIDER------------------>
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         <div id="mask">  <!-- Mask -->
 
         <div id="mask">  <!-- Mask -->
 
           <ul>
 
           <ul>
 +
 
             <li id="first" class="firstanimation">  <!-- ID for tooltip and class for animation -->
 
             <li id="first" class="firstanimation">  <!-- ID for tooltip and class for animation -->
 
               <div class="artboard">
 
               <div class="artboard">
−
               <div class="sliderimage">
+
               <div class="sliderimage" style="margin-top:10%">
−
                 <img src="https://static.igem.org/mediawiki/2015/8/89/Freiburg_Slider-DIY_scaled.png" width="350px">
+
                 <img src="https://static.igem.org/mediawiki/2015/6/6a/Freiburg_DiaCHIP_overview_scaled.jpg" width="350px">
 
               </div>
 
               </div>
 
               <div class="slidertext">
 
               <div class="slidertext">
−
                 <h1>Building our own device</h1>
+
                 <h1>The DiaCHIP - System Overview</h1>
−
                 <p>The device originally used, in collaboration with AG Roth, is an expensive machine based on rather simple components. Therefore, we decided to build our apparatus in a cost-efficient manner. We were able to produce reliable results with it and provide a <a href="https://2015.igem.org/Team:Freiburg/Results/Own_Device#how_to_build_your_own_device">construction plan</a>. This plan will make it possible for future iGEM generations to build and use their own label-free protein array analysis tool.</p>
+
                 <p>The core of our new diagnostic device consists of two slides that form a microfluidic chamber. Therein, an antigen array can be generated on demand by cell-free copying of a DNA template array. By flushing the chamber with a blood sample, antibodies present in the sample bind to corresponding antigens. This interaction is detected in real-time using the optical detection method iRIf.</p>
 +
                <p style="margin-top:10px">
 +
              <div class="intro_button menu-arrow">         
 +
                <a href="https://2015.igem.org/Team:Freiburg/Project/System" title="System Overview">Step by Step Overview</a>
 
               </div>
 
               </div>
−
              <div class="slidertext indent">
 
−
                <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/OwnDevice">more</a>?
 
 
                 </p>
 
                 </p>
 +
 
               </div>
 
               </div>
 
               </div>
 
               </div>
 
             </li>
 
             </li>
 +
 +
 
             <li id="second" class="secondanimation">
 
             <li id="second" class="secondanimation">
 
               <div class="artboard">
 
               <div class="artboard">
−
               <div class="sliderimage">
+
               <div class="sliderimage" style="margin-top:12%">
−
                 <img src="https://static.igem.org/mediawiki/2015/b/b8/Freiburg_Slider-HumanPractice_scaled.png" width="350px">
+
                 <img src="https://static.igem.org/mediawiki/2015/9/94/Freiburg_furture_slider.png" width="350px">
 
               </div>
 
               </div>
 
               <div class="slidertext">
 
               <div class="slidertext">
−
                 <h1>Communicating science</h1>
+
                 <h1>Outlook</h1>
−
                 <p>Diagnosing diseases fast and reliable is not only an issue among medical staff, it is also subject to public interest. This has lead us to ask for people's opinions regarding the DiaCHIP. Although the method is based on synthetic biology, which is a problematic term for the broad public according to a survey initiated by the Leopoldina (National academy of science), we received a lot of positive feedback. </p>
+
                 <p>Our results provide a proof of concept that the functional principle of the DiaCHIP is suitable for antibody detection in complex samples. Although further improvements have to be done in terms of reliablitiy and quantification, various additional applications are conceivable. Representing a way to reduce time and cost required for diagnosing a single patient, the DiaCHIP holds the potential to enhance and enlighten future diagnostics.  
−
              </div>
+
</p>
−
               <div class="slidertext indent">
+
            <p>
−
                <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/Practices">more</a>?</p>
+
               <div class="intro_button menu-arrow">        
−
              </div>
+
                <a href="https://2015.igem.org/Team:Freiburg/Project/Future_Directions" title="Future_Directions">DiaCHIP in the <br>Future</a>
 
               </div>
 
               </div>
 +
                </p>
 
             </li>
 
             </li>
 +
 +
 
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+
                 <img src="https://static.igem.org/mediawiki/2015/d/db/Freiburg_iRiF_slider.png" width="70%">
 
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               <div class="slidertext">  
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                 <h1>Modeling cell-free expression</h1>
+
                 <h1>Optical Detection: iRIf</h1>
−
                 <p>In order to optimize the DiaCHIP for future applications, we optimized the process of cell-free expression and diffusion over time. Making use of xxx parameters and xxx ordinary differential equations, we computed the size of the resulting antigen spots on the protein array and identified the factors limiting cell-free expression in the DiaCHIP. </p>
+
                 <p>One disadvantage of currently available serological tests is the need for secondary labels that allow the detection of disease markers. Making use of an optical method based on the interference of light, the DiaCHIP can detect specific binding events on a protein microarray without further labeling. Read more about this innovative tool and the physics behind it.  
 +
                </p>
 +
 
 +
                <p style="margin-top:15px">
 +
              <div class="intro_button menu-arrow">         
 +
                <a href="https://2015.igem.org/Team:Freiburg/Project/iRIf" title="Optical Detection">iRIf Principle and Physics</a>
 
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                 <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/Modeling">more</a>? </p>
+
 
 
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                 <h1>Measuring our blood</h1>
+
                 <h1>Surface Chemistry</h1>
−
                 <p>One of the most promising results was obtained from the detection of anti-tetanus antibodies in human blood serum. The DiaCHIP analysis made it possible for us to distinguish serum samples from a team member before and after vaccination. Samples taken two weeks after vaccination produced higher signals, compared to those prior to antigen exposure.</p>
+
                 <p>The production of a customized protein microarray in the DiaCHIP is based on selective immobilization of antigens on a glass slide. Therefore, a specific surface chemistry was established to reduce the proportion of unspecific binding of non-target proteins to a minimum.
 +
                  Read more about the different layer compositions we tested on our way to high specificity.
 +
                </p>
 +
 
 +
                <p style="margin-top:15px">
 +
              <div class="intro_button menu-arrow">         
 +
                <a href="https://2015.igem.org/Team:Freiburg/Project/Surface_Chemistry" title="Surface Chemistry">Establishing a Specific Surface</a>
 
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                 <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/Results">more</a>?</p>
+
 
 
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                 <h1>DNA Engineering</h1>
+
                 <h1>Protein Purification</h1>
−
                 <p>Genetic fusion of different antigens and tags is a really basic requirement of our project. To enable many people to work on our DNA constructs in parallel we designed a cloning strategy easy to follow and additionally easy to expand for further needs.
+
                 <p>Protein expression in the DiaCHIP is mediated by cell-free expression. As this is an advanced method dependent on the optimization of many parameters, we got back to conventional protein purification in <i>E. coli</i> for being able to compare the results of both techniques. <br>
−
                                <br>
+
Read more about overexpression and purification of several antigenic peptides. 
−
Read more about how we combined different cloning methods to reduce our efforts in <a href="https://2015.igem.org/Team:Freiburg/Methods/Cloning" class="wikilink1">DNA Engineering.</a>
+
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 +
                <a href="https://2015.igem.org/Team:Freiburg/Project/Protein_Purification" title="Protein Purification">Purification of Antigens</a>
 
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               </div>
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                 <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/Results">more?</a></p>
+
 
 
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                 <h1>Protein purification</h1>
+
                 <h1>Cell-Free Expression</h1>
−
                 <p>Protein expression in the DiaCHIP is mediated by cell-free expression. As this is an advanced method dependent on the optimization of many parameters, we got back to conventional protein purification in <i>E. coli</i> for being able to compare the results of both techniques. <br>
+
                 <p> A key feature of the DiaCHIP is the capability to produce protein arrays on demand via cell-free expression. To reduce the cost of a DiaCHIP measurement, we produced a cell-free expression system based on an <i>E. coli</i> lysate ourselves. This system is also capable of expressing immobilized DNA sequences. See how this sensitive system was established and optimized.  
−
<a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Project/Protein_Purification">Read more</a> about the overexpression and purification of many antigenic peptides.  
+
 
</p>
 
</p>
 +
            <p style="margin-top:30px">
 +
              <div class="intro_button menu-arrow">         
 +
                <a href="https://2015.igem.org/Team:Freiburg/Project/Cellfree_Expression" title="Cell-Free expression">Cell-free Antigen Expression</a>
 
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               </div>
−
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+
                 </p>
−
                 <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/Results">more?</a></p>
+
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                 <img src="https://static.igem.org/mediawiki/2015/b/b2/Freiburg_DNAengineering_slider.png" width="350px">
 
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               <div class="slidertext">  
 
               <div class="slidertext">  
−
                 <h1>Measuring our blood</h1>
+
                 <h1>DNA Engineering</h1>
−
                 <p>One of the most promising results was obtained from the detection of anti-tetanus antibodies in human blood serum. The DiaCHIP analysis made it possible for us to distinguish serum samples from a team member before and after vaccination. Samples taken two weeks after vaccination produced higher signals, compared to those prior to antigen exposure.</p>
+
                 <p>Genetic fusion of different antigens and tags is a basic requirement of our project. In order to enable several people to work in parallel we designed a cloning strategy easy to follow and additionally easy to expand for further needs.
 +
Read more about the combination of different cloning methods to reduce efforts in DNA Engineering and the design of an expression vector meeting iGEM requirements.
 +
</p>
 +
 
 +
                <p style="margin-top:30px">
 +
              <div class="intro_button menu-arrow">         
 +
                <a href="https://2015.igem.org/Team:Freiburg/Methods/Cloning" title="DNA Engineering">DNA <br>Engineering</a>
 
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                 </p>
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                 <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/Results">more?</a></p>
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                 <h1>Measuring our blood</h1>
+
                 <h1>Diagnostics Today</h1>
−
                 <p>One of the most promising results was obtained from the detection of anti-tetanus antibodies in human blood serum. The DiaCHIP analysis made it possible for us to distinguish serum samples from a team member before and after vaccination. Samples taken two weeks after vaccination produced higher signals, compared to those prior to antigen exposure.</p>
+
                 <p>Currently used serological tests are available for a broad range of infectious diseases. However, they meet limitations that restrict an early onset of appropriate treatments which could be life-saving. The necessity of performing several tests to check for more than one disease is not only time-consuming but also costly. The DiaCHIP tackles these issues by providing a fast and affordable method for simultaneous testing.
−
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+
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                <p> Want to read <a href="https://2015.igem.org/Team:Freiburg/Results">more?</a></p>
+
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 +
               <div class="intro_button menu-arrow">        
 +
                <a href="https://2015.igem.org/Team:Freiburg/Design" title="Diagnostics today">Limitations and Solutions</a>
 
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Latest revision as of 21:42, 18 September 2015

""

The DiaCHIP - A Versatile Detection System

DiaCHIP_Sabi

Project Motivation

Serological tests are a key element in modern medicine. Especially for detection and identification of infectious diseases, the performance of several blood tests is inevitable. Testing for more than one disease at once or diagnosing a patient with uncertain symptoms usually requires far more than one test. Every single test that is required increases the time of waiting for a precise diagnosis. In case of dangerous infectious diseases every minute until the onset of an appropriate treatment is crucial for the patient's survival. What if there was a possibility to combine all these tests in one single chip which offers a fast diagnosis and is affordable for everyone?

Detecting Antigen-Antibody Interactions

The DiaCHIP is an innovative tool to screen for a broad range of antibodies in serum. Their presence serves as an indicator for an immune response towards an infectious disease or a successful vaccination. They also play an important role in the diagnosis of autoimmune diseases. Identifying diseases by detecting disease associated antibodies in a patient's serum is an established method in modern diagnostics.
Based on the very same principle, the DiaCHIP enables to screen for multiple diseases simultaneously, thereby reducing time and costs of a diagnosis. Especially the ability to differentiate between life threatening diseases and mild infections within a short time bears the potential to save lifes.

The Concept

The key feature of the DiaCHIP concept is the combination of on-demand protein synthesis and a novel method for label-free detection - all this packed into one device. The idea is to overcome challenges commonly found in protein array production and preservation. By cell-free expression of disease-related antigens, the protein array can be produced right when it is needed. In addition, results can be obtained in a time- and cost-efficient manner using a device simple enough to be rebuilt by future iGEM teams.

Step by Step Overview

  • The DiaCHIP - System Overview

    The core of our new diagnostic device consists of two slides that form a microfluidic chamber. Therein, an antigen array can be generated on demand by cell-free copying of a DNA template array. By flushing the chamber with a blood sample, antibodies present in the sample bind to corresponding antigens. This interaction is detected in real-time using the optical detection method iRIf.

    Step by Step Overview

  • Outlook

    Our results provide a proof of concept that the functional principle of the DiaCHIP is suitable for antibody detection in complex samples. Although further improvements have to be done in terms of reliablitiy and quantification, various additional applications are conceivable. Representing a way to reduce time and cost required for diagnosing a single patient, the DiaCHIP holds the potential to enhance and enlighten future diagnostics.

    DiaCHIP in the
    Future

  • Optical Detection: iRIf

    One disadvantage of currently available serological tests is the need for secondary labels that allow the detection of disease markers. Making use of an optical method based on the interference of light, the DiaCHIP can detect specific binding events on a protein microarray without further labeling. Read more about this innovative tool and the physics behind it.

    iRIf Principle and Physics

  • Surface Chemistry

    The production of a customized protein microarray in the DiaCHIP is based on selective immobilization of antigens on a glass slide. Therefore, a specific surface chemistry was established to reduce the proportion of unspecific binding of non-target proteins to a minimum. Read more about the different layer compositions we tested on our way to high specificity.

    Establishing a Specific Surface

  • Protein Purification

    Protein expression in the DiaCHIP is mediated by cell-free expression. As this is an advanced method dependent on the optimization of many parameters, we got back to conventional protein purification in E. coli for being able to compare the results of both techniques.
    Read more about overexpression and purification of several antigenic peptides.

    Purification of Antigens

  • Cell-Free Expression

    A key feature of the DiaCHIP is the capability to produce protein arrays on demand via cell-free expression. To reduce the cost of a DiaCHIP measurement, we produced a cell-free expression system based on an E. coli lysate ourselves. This system is also capable of expressing immobilized DNA sequences. See how this sensitive system was established and optimized.

    Cell-free Antigen Expression

  • DNA Engineering

    Genetic fusion of different antigens and tags is a basic requirement of our project. In order to enable several people to work in parallel we designed a cloning strategy easy to follow and additionally easy to expand for further needs. Read more about the combination of different cloning methods to reduce efforts in DNA Engineering and the design of an expression vector meeting iGEM requirements.

    DNA
    Engineering

  • Diagnostics Today

    Currently used serological tests are available for a broad range of infectious diseases. However, they meet limitations that restrict an early onset of appropriate treatments which could be life-saving. The necessity of performing several tests to check for more than one disease is not only time-consuming but also costly. The DiaCHIP tackles these issues by providing a fast and affordable method for simultaneous testing.

    Limitations and Solutions