Difference between revisions of "Team:Berlin diagnostX"

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                <h1 class="text-center">diagnost-X Berlin</h1>
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                <p class="text-justify">One morning, when Gregor Samsa woke from troubled dreams, he found himself transformed in his bed into a horrible vermin. He lay on his armour-like back, and if he lifted his head a little he could see his brown belly, slightly domed and divided by arches into stiff sections. The bedding was hardly able to cover it and seemed ready to slide off any moment. His many legs, pitifully thin compared with the size of the rest of him, waved about helplessly as he looked. "What's happened to me?" he thought. It wasn't a dream. His room, a proper human room although a little too small, lay peacefully between its four familiar walls. A collection of textile samples lay spread out on the table - Samsa was a travelling salesman - and above it there hung a picture that he had recently cut out of an illustrated magazine and housed </p>
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            <h1 class="text-center">The Challenge</h1>
 
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            <p class="text-justify p-5">Millions are affected by infection with T. solium which can cause severe diseases</p>
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                <h3 class="text-center">The Tapeworm <em>Taenia solium</em></h3>
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                <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 href="#references">[1]</a>. However, a clear picture of how many people are currently infected by <em>T. solium</em> does not exist, due to the current difficulty in making a diagnosis.</p>
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                <h4 class="text-center">Diagnosis: Difficult and Expensive</h4>
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            <p class="text-center p-5">Affordable Therapeutics exist</p>
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                <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 <a href="#references">[2]</a>.</p>
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             <p class="text-center p-5">Until now: no affordable diagnostic test</p>
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                <h3 class="text-center">The Idea</h3>
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                <p class="text-justify">Our goal is to develop a cheap, practical, and effective diagnostic test for the parasite <i>T. solium</i> in humans. By reliably identifying carriers of <i>T. solium</i>, 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.</p>
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                <p class="text-justify">The test will respond to RNA molecules from <em>T. solium</em> in order to detect a tapeworm infestation. RNA (Ribonucleic acid) is the basis of protein production, and every species, including <em>T. solium</em>, has specific RNA molecules which can be used to unambiguously identify it. We plan to take advantage of this in our diagnostic method.</p>
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                <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 <a href="#references">[3]</a>. We are therefore convinced that toehold switch sensors will also be useful in detecting <em>T. solium</em>.</p>
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                <p>In order to develop our test, we first need to achieve two things:</p>
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                    <li> Production of toehold switch sensors to detect RNA specific to <em>T. solium</em></li>
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                    <li> Creation of model RNA molecules to test Wormspotter </li>
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                <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 <em>T. solium</em>. We aim to achieve this in a cell-free system</p>
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                <h3 class="text-center">The Experiments – Production of Toehold Switch Sensors</h3>
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            <h1 class="text-center">Our Premisse</h1>
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                <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 <a href="#references">[4]</a></p>
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            <h4 class="text-center">Developing a low cost, easy-to-handle diagnostic test for infection with the tapeworm Taenia solium</h5>
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                <img style="padding-bottom: 20px" class="img-fluid" src="https://static.igem.org/mediawiki/2017/4/4f/T--Berlin_diagnostX--toehold_easy.png" alt="Schematic of Toehold Switch">
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                <p class="text-justify">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 <em>T. solium</em>.</p>
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                <p class="text-justify">We are planning to use <em>T. solium</em>-specific RNA sequences for the toehold sequence and beta-Galactosidase as a reporter protein.</p>
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                <h3 class="text-center">The Experiments – Toehold Switch Sensor Test</h3>
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                <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</p>
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                <p class="text-justify">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 <em>T. solium</em> RNA.</p>
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            <h5 class="igem_blue pb-1">Target Identification</h5>
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                <h3 class="text-center">Application</h3>
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                <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 <em>T. solium</em>-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>
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                <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>
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                [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>
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                [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>    
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                [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>
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                [6] Mayta, H. et al. Nested PCR for Specific Diagnosis of <i>Taenia solium</i> Taeniasis. J. Clin. Microbiol. 46, 286–289 (2008).<br>
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Revision as of 18:05, 29 October 2017

The Challenge

Millions are affected by infection with T. solium which can cause severe diseases

Affordable Therapeutics exist

Until now: no affordable diagnostic test

Our Premisse

Developing a low cost, easy-to-handle diagnostic test for infection with the tapeworm Taenia solium

Target Identification

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Punkt 1

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Target Identification

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Punkt 1

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Target Identification

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Target Identification

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Target Identification

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Target Identification

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