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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                <h3 class="text-center">The Tapeworm <em>Taenia solium</em></h3>
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            <h1 class="text-center igem_blue">The fight against T. solium</h1>
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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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            <h3 class="text-center">The worldwide fight against Taenia solium
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(pork tapeworm) is facing three different challenges</h3>
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                <h4 class="text-center">Diagnosis: Difficult and Expensive</h4>
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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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            <h5 class="igem_blue text-center mt-4 mb-1 pb-1">HIGH PREVALENCE</h5>
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            <p class="text-center px-5 pt-2">Estimated billions are affected - the infection causing epilepsy, blindness and death</p>
 
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<h5 class="igem_blue text-center mt-4 mb-1 pb-1">INSUFFICIENT DRUG DISTRIBUTION</h5>
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                <h3 class="text-center">The Idea</h3>
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            <p class="text-center px-5 pt-2">Although affordable therapeutics exist, they don't reach patients in infectious hotspots </p>
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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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<h5 class="igem_blue text-center mt-4 mb-1 pb-1">EXPENSIVE DIAGNOSTICS</h5>
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            <p class="text-center px-5 pt-2">No methods suited for field use are yet available preventing the identification of infectious hotspots</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 igem_blue">The vision of diagnost-x</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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                <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 mb-4">Target Identification</h5>
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            <p class="text-justify mb-1">We sequenced 96 million RNAs  and mapped them against about 12.000 Genes of T. saginata,  T. asiatica and T. solium. The expression level of unique RNAs was analyzed. We identified 215 unique, potential diagnost-x targets.</p>
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<p class="text-justify mb-4">The colour intensity is proportional to the expression of each identified possible target.</p>
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            <p class="d-inline pl-3"> First RNA isolation from T. solium eggs avoiding hatching procedure </p>
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            <div class="mt-5 ml-1"><a class="btn btn-lg igem_but btn-primary red" href="https://2017.igem.org/Team:Berlin_diagnostX/Design" role="button">Discover More</a></div>
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            <h5 class="igem_blue pb-1">Sensor Design</h5>
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                <h3 class="text-center">Application</h3>
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            <p class="text-justify mb-4">Based on the analysis of the build-plan of different published toehold sensors, our In Silico Team generated a first generation of switches. Further optimisation based on testing results let us to the establishment of our software for in silico design. Selected Switches were furthermore tested in the following testing pipeline.</p>
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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="d-inline pl-3"> Refined preselection of promising sensors thanks to established software</p>
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            <div class="mt-5 ml-1"><a class="btn btn-lg igem_but btn-primary red" href="https://2017.igem.org/Team:Berlin_diagnostX/Design" role="button">Discover More</a></div>
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            <h5 class="igem_blue pb-1">Sensor Screening</h5>
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            <p class="text-justify mb-4">The designed switches from the In Silico Team were assembled using Extension PCR. Assembled Sensors passed all through the standard screening in liquid phase.</p>
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            <p class="d-inline pl-3"> 6 successfully working sensors detected thanks to our high flow-through Screening Pipeline</p>
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            <h5 class="igem_blue pb-1">Considerating future application from Day 1</h5>
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            <p class="text-justify mb-4">Developing a diagnostic test needs careful consideration of the circumstances in which the toll will be used - therefore we spared no expense and investigated local circumstances in India.</p>
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            <p class="d-inline pl-3"> Find out more about what the insight we gained in India!</p>
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            <h5 class="igem_blue pb-1">Raising awareness for T. solium </h5>
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            <p class="text-justify mb-4">Neglected Tropical Diseases have few platforms in the eastern world since they don't affect people directly. Our mission was to raise  awareness for NTDs and provide innovative impulses for the education of a new generation.</p>
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            <p class="d-inline pl-3"> Organisation of a congress with over 150 scientists, politicians & students </p>
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            <div class="mt-5 ml-1"><a class="btn btn-lg igem_but btn-primary red" href="https://2017.igem.org/Team:Berlin_diagnostX/HP/Silver" role="button">Discover More</a></div>
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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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            <h5 class="igem_blue pb-1">Route to the Future</h5>
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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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            <p class="text-justify mb-4">The 21st century leaves it's marks - new methods for intelligent assisted education are wanted - and we're on the track of time!
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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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Dynamic & new ways of solving problems will determine the success of social entrepreneurship - get started!</p>
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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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            <p class="d-inline pl-3">Development of an <strong>augmented reality app </strong> for innovative future education</p>
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Latest revision as of 01:15, 16 December 2017

The fight against T. solium

The worldwide fight against Taenia solium (pork tapeworm) is facing three different challenges

HIGH PREVALENCE

Estimated billions are affected - the infection causing epilepsy, blindness and death

INSUFFICIENT DRUG DISTRIBUTION

Although affordable therapeutics exist, they don't reach patients in infectious hotspots

EXPENSIVE DIAGNOSTICS

No methods suited for field use are yet available preventing the identification of infectious hotspots

The vision of diagnost-x

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

Target Identification

We sequenced 96 million RNAs and mapped them against about 12.000 Genes of T. saginata, T. asiatica and T. solium. The expression level of unique RNAs was analyzed. We identified 215 unique, potential diagnost-x targets.

The colour intensity is proportional to the expression of each identified possible target.

First RNA isolation from T. solium eggs avoiding hatching procedure

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Sensor Design

Based on the analysis of the build-plan of different published toehold sensors, our In Silico Team generated a first generation of switches. Further optimisation based on testing results let us to the establishment of our software for in silico design. Selected Switches were furthermore tested in the following testing pipeline.

Refined preselection of promising sensors thanks to established software

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Sensor Screening

The designed switches from the In Silico Team were assembled using Extension PCR. Assembled Sensors passed all through the standard screening in liquid phase.

6 successfully working sensors detected thanks to our high flow-through Screening Pipeline

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Considerating future application from Day 1

Developing a diagnostic test needs careful consideration of the circumstances in which the toll will be used - therefore we spared no expense and investigated local circumstances in India.

Find out more about what the insight we gained in India!

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Raising awareness for T. solium

Neglected Tropical Diseases have few platforms in the eastern world since they don't affect people directly. Our mission was to raise awareness for NTDs and provide innovative impulses for the education of a new generation.

Organisation of a congress with over 150 scientists, politicians & students

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Route to the Future

The 21st century leaves it's marks - new methods for intelligent assisted education are wanted - and we're on the track of time! Dynamic & new ways of solving problems will determine the success of social entrepreneurship - get started!

Development of an augmented reality app for innovative future education

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Many Thanks to our Sponsors!