Difference between revisions of "Team:ETH Zurich/Results"

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<h1 class="headline">Results</h1>
 
<h1 class="headline">Results</h1>
  
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<section class="emphasize">
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<section class="emphasize first">
−
<h1>Achievements</h1>
+
    <h1>Achievements</h1>
−
<ul>
+
    <ul>
−
    <li>We integrated 5 distincts functions in <im>E. coli</im> Nissle to build an autonomous, specific and controllable anti-tumor treatment.</li>
+
        <li>We integrated 5 distincts functions in <span class="bacterium">E. coli</span> Nissle to build an autonomous, specific and controllable anti-tumor treatment.</li>
−
    <li>We designed our parts according to a preliminary modeling phase to optimize from start our system.</li>
+
        <li>We designed our parts according to a preliminary modeling phase to optimize from start our system.</li>
−
    <li>We experimentally and analytically characterized these modules.</li>
+
        <li>We experimentally and analytically characterized these modules.</li>
−
    <li>We fitted a comprehensive model with our experimental data and are able to assess its performance <im>in silico</im>.</li>
+
        <li>We fitted a comprehensive model with our experimental data and are able to assess its performance <em>in silico</em>.</li>
−
</ul>
+
    </ul>
 
</section>
 
</section>
  
 
<section>
 
<section>
 +
    <h1>Tumor Sensor</h1>
 +
    <ul>
 +
        <li>Designed parts rationally, according to a preliminary functioning point search thanks to our model.</li>
 +
        <li>Designed and realized the most relevant experiments to precisely characterize our quorum-sensing system.</li>
 +
        <li>Designed a hybrid promoter that implements AND-gate logic evaluation of L-lactate and AHL and successfully demonstrated its operation.</li>
 +
        <li>Characterized several versions of this hybrid promoter and improved the model of the hybrid promoter from the observed experimental behavior.</li>
 +
        <li>Step by step fitting of the most relevant parameters controlling the lactate and bacterial cell density sensing.</li>
 +
        <li>Using our model, we could choose the best version of AND-gate such that it is capable of distinguishing lactate levels and bacterial population densities associated with healthy and tumor tissue. </li>
 +
    </ul>
  
−
<h1>Tumor Sensor</h1>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fa_Tumor_Sensor">Description</a></p>
 +
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Tumor_Sensor">Experiments</a></p>
 +
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Model/Environment_Sensing">Model</a></p>
 +
</section>
  
−
<ul>
+
<section>
−
    <li>Designed parts rationally, according to a preliminary functioning point search thanks to our model.</li>
+
    <h1>MRI Contrast Agent</h1>
−
    <li>Designed and realized the most relevant experiments to precisely characterize our quorum-sensing system.</li>
+
    <ul>
−
    <li>Designed a hybrid promoter that implements AND-gate logic evaluation of L-lactate and AHL and successfully demonstrated its operation.</li>
+
        <li>Characterized the expression of a genetically encoded MRI contrast agent bacterioferritin in <span class="bacterium">E. coli</span> Nissle 1917.</li>
−
    <li>Characterized several versions of this hybrid promoter and improved the model of the hybrid promoter from the observed experimental behavior.</li>
+
        <li>Participated in parameter fitting of our model.</li>
−
    <li>Step by step fitting of the most relevant parameters controlling the lactate and bacterial cell density sensing.</li>
+
        <li>Showed that the contrast agent indeed leads to a marked decrease in the MRI signal which demonstrates its usability as an MRI contrast agent in vitro and confirms the potential to use it as an in vivo reporter of tumor sensing.</li>
−
    <li>Using our model, we could choose the best version of AND-gate such that it is capable of distinguishing lactate levels and bacterial population densities associated with healthy and tumor tissue. </li>
+
    </ul>
−
</ul>
+
  
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fa_Tumor_Sensor">Description</a></p>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fb_MRI_Contrast_Agent">Description</a></p>
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Tumor_Sensor">Experiments</a></p>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/MRI_Contrast_Agent">Experiments</a></p>
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Model/Environment_Sensing">Model</a></p>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Model/Environment_Sensing/parameter_fitting#luxr_fit">Model</a></p>
 +
</section>
  
−
<h1>MRI Contrast Agent</h1>
+
<section>
 +
    <h1>Anti-Cancer Toxin</h1>
 +
    <ul>
 +
        <li>Developed an assay to characterize killing of cells in a cell line when supplemented with supernatant of lysed bacteria expressing azurin.</li>
 +
        <li>Expressed it successfully in our bacteria.</li>
 +
        <li>Quantified the potential treatment efficiency of our system.</li>
  
−
<ul>
+
    </ul>
−
    <li>Characterized the expression of a genetically encoded MRI contrast agent bacterioferritin in <i>E. coli</i> Nissle 1917.</li>
+
−
    <li>Participated in parameter fitting of our model.</li>
+
−
    <li>Showed that the contrast agent indeed leads to a marked decrease in the MRI signal which demonstrates its usability as an MRI contrast agent in vitro and confirms the potential to use it as an in vivo reporter of tumor sensing.</li>
+
−
</ul>
+
−
   
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fb_MRI_Contrast_Agent">Description</a></p>
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/MRI_Contrast_Agent">Experiments</a></p>
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Model/Environment_Sensing/parameter_fitting#luxr_fit">Model</a></p>
+
  
 +
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fc_Anti_Cancer_Toxin">Description</a></p>
 +
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Anti_Cancer_Toxin">Experiments</a></p>
 +
    <p><a href="https://2017.igem.org/wiki/index.php?title=Team:ETH_Zurich/Model/In_Vivo#InVivo_Killing">Model</a></p>
 +
</section>
  
−
<h1>Anti-Cancer Toxin</h1>
+
<section>
 +
    <h1>Heat Sensor</h1>
 +
    <ul>
 +
        <li>Built and characterized a thermoresponsive system that induces expression of a controlled gene at 45 °C but not at 37 °C.</li>
 +
        <li>Validate with a thermal diffusion model the clinical feasibility of a 45°C induction in the context of our application.</li>
 +
        <li>Built an RBS library for the Heat Sensor, whereby we reduced leakiness far enough to transform the potent lysis-inducing protein E under its control.</li>
 +
    </ul>
  
−
<ul>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fd_Heat_Sensor">Description</a></p>
−
<li>Developed an assay to characterize killing of cells in a cell line when supplemented with supernatant of lysed bacteria expressing azurin.</li>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Heat_Sensor">Experiments</a></p>
−
<li>Expressed it successfully in our bacteria.</li>
+
    <p><a href="https://2017.igem.org/wiki/index.php?title=Team:ETH_Zurich/Model/Heat_Sensor">Model</a></p>
−
<li>Quantified the potential treatment efficiency of our system.</li>
+
</section>
  
−
</ul>
+
<section>
−
 
+
     <h1>Cell Lysis</h1>
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fc_Anti_Cancer_Toxin">Description</a></p>
+
    <ul>
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Anti_Cancer_Toxin">Experiments</a></p>
+
        <li>Showed that we can induce lysis of the bacteria when transformed with protein E under the thermosensitive promoter and induced at 45° C.</li>
−
<p><a href="https://2017.igem.org/wiki/index.php?title=Team:ETH_Zurich/Model/In_Vivo#InVivo_Killing">Model</a></p>
+
    </ul>
−
 
+
−
<h1>Heat Sensor</h1>
+
−
 
+
−
<ul>
+
−
<li>Built and characterized a thermoresponsive system that induces expression of a controlled gene at 45 °C but not at 37 °C.</li>
+
−
<li>Validate with a thermal diffusion model the clinical feasibility of a 45°C induction in the context of our application.</li>
+
−
<li>Built an RBS library for the Heat Sensor, whereby we reduced leakiness far enough to transform the potent lysis-inducing protein E under its control.</li>
+
−
</ul>
+
−
 
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fd_Heat_Sensor">Description</a></p>
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Heat_Sensor">Experiments</a></p>
+
−
<p><a href="https://2017.igem.org/wiki/index.php?title=Team:ETH_Zurich/Model/Heat_Sensor">Model</a></p>
+
−
      
+
−
<h1>Cell Lysis</h1>
+
−
 
+
−
<ul>
+
−
<li>Showed that we can induce lysis</a> of the bacteria when transformed with protein E under the thermosensitive promoter and induced at 45° C.</li>
+
−
</ul>
+
−
   
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fe_Cell_Lysis">Description</a></p>
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Cell_Lysis">Experiments</a></p>
+
−
 
+
−
<h1>Human Practices</h1>
+
  
−
<ul>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Circuit/Fe_Cell_Lysis">Description</a></p>
−
<li>Brought synthetic biology and bacterial cancer therapy closer to a broad range of people.</li>
+
    <p><a href="https://2017.igem.org/Team:ETH_Zurich/Experiments/Cell_Lysis">Experiments</a></p>
−
<li>Learned from various experts to think about aspects of our project that go beyond the lab.</li>
+
−
</ul>
+
−
   
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/Human_Practices">Overview</a></p>
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/HP/Gold_Integrated">Integrated Practices</a></p>
+
−
<p><a href="https://2017.igem.org/Team:ETH_Zurich/HP/Silver">Public Engagement</a></p>
+
 
</section>
 
</section>
  
−
 
−
<!--
 
 
<section>
 
<section>
−
<h1>Future Perspectives</h1>
+
    <h1>Human Practices</h1>
  
−
     <h2>DIY FUS Transducer</h2>
+
     <ul>
−
    <p>To test the <a href="/Team:ETH_Zurich/Circuit/Fd_Heat_Sensor">Heat Sensor</a>, we had initially thought of building a Magnetic Resonance-guided Focused Ultrasound transducer (MRgFUS).</p>
+
        <li>Brought synthetic biology and bacterial cancer therapy closer to a broad range of people.</li>
 +
        <li>Learned from various experts to think about aspects of our project that go beyond the lab.</li>
 +
    </ul>
  
−
     <p>This was motivated by some recent articles like <a href="#bib1" class="forward-ref">[1]</a> by the FUS Foundation that talks about an open source DIY – MRIgFUS device proposed by Vanderbilt University <a href="#bib2" class="forward-ref">[2]</a>, and shares access to detailed instructions on the hardware and software requirements for building it. Compared to commercial options, this is much cheaper although less powerful in terms of precision and less sensitive in terms of control. The idea was to demonstrate a proof-of-concept that would contribute to the <em>cost-effectiveness</em> and <em>feasibility</em> of the bacterial cancer therapy CATE.</p>
+
     <p><a href="https://2017.igem.org/Team:ETH_Zurich/Human_Practices">Overview</a></p>
−
 
+
     <p><a href="https://2017.igem.org/Team:ETH_Zurich/HP/Gold_Integrated">Integrated Practices</a></p>
−
     <p>However, as advised by our very own <i><font color="red">`FUS-man´</font></i>, Beat Werner, a FUS-compatible test-bench requires proper material (acoustic impedance, thickness, etc.) and appropriate-containment for the test-sample. Also, adding MRI steerability increases the cost exponentially; typical MRI compatible FUS machines cost around <span title="&#36;&#36;&#36;">&#36;200,000</span>.
+
     <p><a href="https://2017.igem.org/Team:ETH_Zurich/HP/Silver">Public Engagement</a></p>
−
    Due to lack of dedicated expertise in the team in this field, this idea was kept very low priority as far as iGEM was concerned. Instead, the FUS test conditions were emulated using an incubator at 45&deg;C.</p>
+
−
 
+
−
     <p>Moreover, due to requirement of an MRI compatible transducer, amplifier and waveform generator, the Vanderbilt University open-source system costs around &#36;10,000 <a href="#bib3" class="forward-ref">[3]</a>, which was not feasible in the scope of the funding we received, but more importantly not critical to the demonstration of the idea of CATE, as a bacterial cancer therapy, in the time scope of this competition.</p>
+
−
 
+
−
 
+
−
 
+
−
    <h2>CATE, FUS and Beyond</h2>
+
−
 
+
−
    <p>For future development of a bacterial cancer therapy such as CATE, it would be logical to develop a high intensity FUS curved-transducer phased-array, for triggering the thermal switch that lyses the cells and releases the cancer-toxin. Popular FUS transducers (like from Sonic Concepts Co.) cost around &#36;4500 and could be used with front-end sensing solutions such as from Texas Instruments (for eg. TDC 1000), that would overall be much cheaper than an MRIgFUS. </p>
+
−
 
+
−
    <p>Moreover, according to recent developments in MRI science <a href="#bib4" class="forward-ref">[4]</a>, <a href="#bib5" class="forward-ref">[5]</a>, the near-future will very likely see cheaper and better accessible MRIgFUS devices. Recent research for gadolinium replacement for MRI <a href="#bib6" class="forward-ref">[6]</a> will also possibly lead to cheaper MRI solutions in the future, and thus could potentially lead to more economically-feasible MRIgFUS technology. </p>
+
−
 
+
−
    <p>As per Beat Werner, radio frequency (RF) is better than FUS for heating a larger volume and thus a better solution for us, to heat the whole bacteria layer while maintaining a temperature of 45&deg;C for 3 hours to trigger expression of protein E. However, currently RF allows lesser control than FUS. But with rapid progress in this field, using sound/RF as a non-invasive tool used in medicine would become better, cheaper and more accessible with time.</p>  
+
 
</section>
 
</section>
−
-->
 
−
 
−
<!--
 
−
<section class="references">
 
−
    <h1>References</h1>
 
−
    <ol>
 
−
        <li id="bib1">“Open source Focused Ultrasound system now available to researchers around the world.” <cite>Focused Ultrasound Foundation</cite>, 24 May 2016. <a href="https://www.fusfoundation.org/news/1762-open-source-focused-ultrasound-system-now-available-to-researchers-around-the-world">URL</a></li>
 
−
        <li id="bib2">Poorman, Megan E., et al. “Open-Source, Small-Animal Magnetic Resonance-Guided Focused Ultrasound System.” <cite>Journal of Therapeutic Ultrasound</cite>, BioMed Central, 5 Sept. 2016, <a href="https://jtultrasound.biomedcentral.com/articles/10.1186/s40349-016-0066-7">doi.org/10.1186/s40349-016-0066-7.</a></li>
 
−
        <li id="bib3">“DIY Guide Converts Imaging Machines into Focused Ultrasound.” <cite>EDN Asia</cite>, 5 July 2016. <a href="https://www.ednasia.com/news/article/diy-guide-converts-imaging-machines-into-focused-ultrasound">URL</a></li>
 
−
        <li id="bib4">Dalton, L. “Engineers Use Two Magnets Instead of One to Build a Lower-Cost MRI Scanner.” <cite>Stanford Report</cite>, 21 Mar. 2001. <a href="https://news.stanford.edu/news/2001/march21/mri-321.html">URL</a></li>
 
−
        <li id="bib5">Pacella, Rena M. “Affordable DIY MRI Shows How We Really Breathe.” <cite>Popular Science</cite>, 22 Oct. 2010. <a href="https://www.popsci.com/technology/article/2010-10/diy-mri-shows-how-we-really-breathe">URL</a></li>
 
−
        <li id="bib6">Chandler, David L. “A New Contrast Agent for MRI.” <cite>MIT News</cite>, 14 Feb. 2017. <a href="http://news.mit.edu/2017/iron-oxide-nanoparticles-contrast-agent-mri-0214">URL</a></li>
 
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{{ETH_Zurich/Footer_N}}
 
{{ETH_Zurich/Footer_N}}

Revision as of 01:16, 2 November 2017

Results

Achievements

  • We integrated 5 distincts functions in E. coli Nissle to build an autonomous, specific and controllable anti-tumor treatment.
  • We designed our parts according to a preliminary modeling phase to optimize from start our system.
  • We experimentally and analytically characterized these modules.
  • We fitted a comprehensive model with our experimental data and are able to assess its performance in silico.

Tumor Sensor

  • Designed parts rationally, according to a preliminary functioning point search thanks to our model.
  • Designed and realized the most relevant experiments to precisely characterize our quorum-sensing system.
  • Designed a hybrid promoter that implements AND-gate logic evaluation of L-lactate and AHL and successfully demonstrated its operation.
  • Characterized several versions of this hybrid promoter and improved the model of the hybrid promoter from the observed experimental behavior.
  • Step by step fitting of the most relevant parameters controlling the lactate and bacterial cell density sensing.
  • Using our model, we could choose the best version of AND-gate such that it is capable of distinguishing lactate levels and bacterial population densities associated with healthy and tumor tissue.

Description

Experiments

Model

MRI Contrast Agent

  • Characterized the expression of a genetically encoded MRI contrast agent bacterioferritin in E. coli Nissle 1917.
  • Participated in parameter fitting of our model.
  • Showed that the contrast agent indeed leads to a marked decrease in the MRI signal which demonstrates its usability as an MRI contrast agent in vitro and confirms the potential to use it as an in vivo reporter of tumor sensing.

Description

Experiments

Model

Anti-Cancer Toxin

  • Developed an assay to characterize killing of cells in a cell line when supplemented with supernatant of lysed bacteria expressing azurin.
  • Expressed it successfully in our bacteria.
  • Quantified the potential treatment efficiency of our system.

Description

Experiments

Model

Heat Sensor

  • Built and characterized a thermoresponsive system that induces expression of a controlled gene at 45 °C but not at 37 °C.
  • Validate with a thermal diffusion model the clinical feasibility of a 45°C induction in the context of our application.
  • Built an RBS library for the Heat Sensor, whereby we reduced leakiness far enough to transform the potent lysis-inducing protein E under its control.

Description

Experiments

Model

Cell Lysis

  • Showed that we can induce lysis of the bacteria when transformed with protein E under the thermosensitive promoter and induced at 45° C.

Description

Experiments

Human Practices

  • Brought synthetic biology and bacterial cancer therapy closer to a broad range of people.
  • Learned from various experts to think about aspects of our project that go beyond the lab.

Overview

Integrated Practices

Public Engagement