Difference between revisions of "Team:Vilnius-Lithuania/Implementation"

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                 <div class="h2 larger">Proposed Implementation</div>
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                 <p class="content-paragraph">According to the Food and Agriculture Organization of the United Nations, 35% of global aquaculture harvest is either lost or wasted<a href="#cit1" class="citation">1</a>. Considering that fish are purposefully killed for only two main
                <div class="h3">Detection</div>
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                    reasons - consumption and disease control - pathogens are responsible for a large portion of the economic losses<a href="#cit2" class="citation">2</a>. If an accurate treatment method would be applied as soon as the first infected
                 <p class="content-paragraph">Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi quis ante odio. Sed eleifend, eros at bibendum ullamcorper, nisl nisl mattis ligula, ut euismod lorem elit sit amet ipsum. Suspendisse scelerisque, odio vitae malesuada mattis, sem augue mattis velit, sit amet ornare lacus velit nec nibh. Curabitur sed lectus sapien. Suspendisse finibus urna volutpat mi consequat lacinia. In ut felis quis purus tempus gravida. Vestibulum eget gravida risus. Vivamus porta dui et nulla fringilla, nec fermentum felis placerat. Pellentesque dictum risus quis aliquam lacinia. Duis mauris arcu, rhoncus eu felis a, laoreet volutpat ipsum. Ut sed aliquam libero. Sed placerat sem nec hendrerit pellentesque.</p>
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                    fish is observed, there would be no need to kill potential carriers of the disease. The ability to detect the pathogens at the very start of an infection could help drastically minimize these numbers. Our pathogen detection kit was
                 <div class="h3">Treatment</div>
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                    created for exactly this reason.</p>
                 <p class="content-paragraph">Maecenas in orci non risus fringilla maximus. Morbi id erat commodo, feugiat ante a, ullamcorper urna. Interdum et malesuada fames ac ante ipsum primis in faucibus. Mauris ligula nunc, gravida in interdum non, pellentesque eget libero. Aliquam porta purus nec arcu sodales, eget sagittis purus lacinia. Aliquam dictum augue id lacinia lacinia. Ut et elementum nunc, nec tempus lacus. Fusce vel mauris ante. Suspendisse bibendum quam tortor, vitae congue urna facilisis at. Aliquam erat volutpat. Sed sit amet magna in nunc ullamcorper porta id et dui. Vestibulum in eros nisi. Proin cursus nisl eu justo laoreet interdum. Suspendisse eu tellus vel felis iaculis posuere.</p>
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                <img src="https://static.igem.org/mediawiki/2020/0/09/T--Vilnius-Lithuania--imp1.svg">
                 <div class="h3">Prevention</div>
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                 <p class="content-paragraph">In porttitor, est at porta luctus, dolor mi sollicitudin libero, id placerat urna ipsum vitae metus. Vivamus ornare rhoncus est, ut condimentum sem vulputate eget. Praesent et tortor non eros molestie interdum. Vivamus ut eros quis nulla gravida placerat viverra non libero. Sed feugiat sapien feugiat, gravida risus in, luctus dolor. Donec sed nibh arcu. Sed sollicitudin lorem eu magna eleifend molestie. Nulla eu urna quis nisl aliquam feugiat. Praesent semper nec sem ut ultricies. Ut sit amet pulvinar odio. In laoreet lectus nulla, a vulputate magna porta eget. Cras ac placerat libero. Donec sollicitudin bibendum ex, at pellentesque urna.</p>
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                 <p class="content-paragraph">To help <b>coldwater fish farmers</b> alleviate the burden, we propose them to be the <b>end users</b> of our <a href="https://2020.igem.org/Team:Vilnius-Lithuania/Software">detection system</a>. The test is especially relevant to them,
                 <div class="h3">Phase I</div>
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                    because most of the farms do not have access to expensive laboratory equipment, yet the pathogens need to be detected as fast as possible, in order to prevent further spread of the disease. The requirement for the testing systems to
                <p class="content-paragraph">Cu esse case euripidis qui. Nonumes mediocrem vel ut. At cum meis velit, nec at dissentias cotidieque, ea modus nulla lobortis ius. Cum timeam probatus persecuti eu, sea latine debitis id, qui dolor mandamus molestiae ei. In audiam impetus eam, ius an tamquam detraxit tincidunt. Epicurei interpretaris no eos. Ne habeo scaevola sapientem sed, unum inani ubique ius ex.</p>
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                    be user-friendly and inexpensive for the target customers are stated in the WHO guidelines<a href="#cit3" class="citation">3</a>, to which we referred to and complied with while developing the system.</p>
 +
                <img src="https://static.igem.org/mediawiki/2020/2/2e/T--Vilnius-Lithuania--imp2.svg">
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                <p class="content-paragraph"><b>The vision of user interaction</b> starts with a typical consumer of fish. As one reads about the health benefits of fish products and is influenced by the growing popularity of seafood, one naturally invests more into them. His/her
 +
                    friends and family are also influenced by the same factors and, together with the growing population of the world, they create a considerable demand. The aquaculture farmer adjusts their production rates accordingly. An increasing
 +
                    number of consumable fish suddenly starts to drop. There are noticeable changes in the behavior of some fish as well as physical differences. From the yellow accumulations around the gills it is clear that Flavobacterium has infected
 +
                    the farm. A farmer orders a <b>FlavoFlow testing kit</b>, takes a <b>sample from the gills</b> of the lethargic animals and within an hour or two knows <b>exactly which species of <i>flavobacterium</i></b> is causing the fluctuations
 +
                    in the production rate. Now, the most accurate treatment method can be chosen and applied.</p>
 +
                 <img src="https://static.igem.org/mediawiki/2020/3/36/T--Vilnius-Lithuania--imp3.svg">
 +
                 <p class="content-paragraph">In addition to this, we created a software tool <a href="https://2020.igem.org/Team:Vilnius-Lithuania/Software">OnFlow</a> to speed up the process of pathogen detection test development, as there are numerous pathogens in the industry
 +
                    that lack a quick testing system. Hence, another group of <b>end users</b> would be people working in the <b>industry of pathogen detection tests</b>. Our <b>vision</b> is that they could use our software for that purpose. Developers
 +
                    would put the information gathered from various articles into the system and it would then calculate specific parameters, such as test line distance, test reaction time and optimal volume of the sample, adjusted to the pathogen of
 +
                    interest. They could use the given information for the design of the test strip, saving a lot of time and resources necessary for the development.</p>
 +
                <img src="https://static.igem.org/mediawiki/2020/0/03/T--Vilnius-Lithuania--imp4.svg">
 +
 
 +
                <p class="content-paragraph">To <b>implement</b> our project into the <b>real world</b> and make it easy to use in the aquaculture farm, we developed a <b>3D printed case</b> for the testing strip. The model can be printed out by anyone, who has access to a 3D printer,
 +
                    making the process even more effortless. In addition, a lyophilized mixture and a universal HDA methodology for the development of our product was used, which is easy to adapt and implement for different testing goals
 +
                    <a href="#cit4" class="citation">4</a>. IsoAmp is also known to have the smallest amount of pipetting steps, thus reducing human error. By combining the software, the case and universal methodologies we designed an overall <b>user-friendly</b>                    and <b>adaptable testing system</b>.</p>
 +
                 <img style="width: 100%;" src="https://static.igem.org/mediawiki/2020/2/29/T--Vilnius-Lithuania--imp5.svg">
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                 <p class="content-paragraph">Although the test is highly accurate, one of the primary <b>issues that would need to be considered</b> is the temperature at which the reaction takes place. The problem is that farmers might not have a device to keep the temperature at
 +
                    a constant level. This aspect should be taken into account when developing other tests and presumably considering providing a hardware device for temperature control for the farmers.</p>
 +
                <img src="https://static.igem.org/mediawiki/2020/2/26/T--Vilnius-Lithuania--imp6.svg">
 +
                <p class="content-paragraph">Concerning the <b>safety aspects</b> of this project, the bacteria that cause fish disease and can be detected with our test are <b>not pathogenic to humans</b>. Furthermore the samples for the test are taken from the gills of the fish,
 +
                    without harming the animal waiving the need to kill it.</p>
 +
                <img src="https://static.igem.org/mediawiki/2020/2/2a/T--Vilnius-Lithuania--imp7.svg">
 +
                <p class="content-paragraph">Briefly, we developed a <b>rapid testing kit</b>, that provides a quick and convenient pathogen detection solution for <b>fish farmers</b> and a <b>software tool</b> that enables other developers to <b>speed the process</b> of testing
 +
                    kit <b>development</b>.</p>
 +
                 <div class="references beforeWave">
 +
                    <h3>References</h3>
 +
                    <ol>
 +
                        <li id="cit1">FAO. The State of World Fisheries and Aquaculture 2020. <b>2</b> (FAO, 2020)</li>
 +
                        <li id="cit2">Hastein, T., Scarfe, A. & Lund, V. Evaluación por métodos científicos del bienestar de los animales acuáticos. <i>Revue Scientifique et Technique de l'OIE</i> <b>24</b>, 529-547 (2005)</li>
 +
                        <li id="cit3">Lorenzo-Ferreiro Carmen., et al. “Nucleic-Acid Lateral Flow Assay Optimization with Different Gold Nanoparticle Size for Detection of Pathogen after PCR, Using L. Monocytogenes as Model. <i>Acta Scientific Microbiology</i> <b>1.10</b>                            17-24 (2018)</li>
 +
                        <li id="cit4">Biolabs, N. How to design the primer and select the amplicon for IsoAmp II Universal tHDA Kit? | NEB. International.neb.com at '
 +
                            <https://international.neb.com/faqs/2011/07/17/how-to-design-the-primer-and-select-the-amplicon-for-isoamp-ii-universal-thda-kit>'</li>
 +
                    </ol>
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                </div>
 
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Revision as of 03:26, 28 October 2020

According to the Food and Agriculture Organization of the United Nations, 35% of global aquaculture harvest is either lost or wasted1. Considering that fish are purposefully killed for only two main reasons - consumption and disease control - pathogens are responsible for a large portion of the economic losses2. If an accurate treatment method would be applied as soon as the first infected fish is observed, there would be no need to kill potential carriers of the disease. The ability to detect the pathogens at the very start of an infection could help drastically minimize these numbers. Our pathogen detection kit was created for exactly this reason.

To help coldwater fish farmers alleviate the burden, we propose them to be the end users of our detection system. The test is especially relevant to them, because most of the farms do not have access to expensive laboratory equipment, yet the pathogens need to be detected as fast as possible, in order to prevent further spread of the disease. The requirement for the testing systems to be user-friendly and inexpensive for the target customers are stated in the WHO guidelines3, to which we referred to and complied with while developing the system.

The vision of user interaction starts with a typical consumer of fish. As one reads about the health benefits of fish products and is influenced by the growing popularity of seafood, one naturally invests more into them. His/her friends and family are also influenced by the same factors and, together with the growing population of the world, they create a considerable demand. The aquaculture farmer adjusts their production rates accordingly. An increasing number of consumable fish suddenly starts to drop. There are noticeable changes in the behavior of some fish as well as physical differences. From the yellow accumulations around the gills it is clear that Flavobacterium has infected the farm. A farmer orders a FlavoFlow testing kit, takes a sample from the gills of the lethargic animals and within an hour or two knows exactly which species of flavobacterium is causing the fluctuations in the production rate. Now, the most accurate treatment method can be chosen and applied.

In addition to this, we created a software tool OnFlow to speed up the process of pathogen detection test development, as there are numerous pathogens in the industry that lack a quick testing system. Hence, another group of end users would be people working in the industry of pathogen detection tests. Our vision is that they could use our software for that purpose. Developers would put the information gathered from various articles into the system and it would then calculate specific parameters, such as test line distance, test reaction time and optimal volume of the sample, adjusted to the pathogen of interest. They could use the given information for the design of the test strip, saving a lot of time and resources necessary for the development.

To implement our project into the real world and make it easy to use in the aquaculture farm, we developed a 3D printed case for the testing strip. The model can be printed out by anyone, who has access to a 3D printer, making the process even more effortless. In addition, a lyophilized mixture and a universal HDA methodology for the development of our product was used, which is easy to adapt and implement for different testing goals 4. IsoAmp is also known to have the smallest amount of pipetting steps, thus reducing human error. By combining the software, the case and universal methodologies we designed an overall user-friendly and adaptable testing system.

Although the test is highly accurate, one of the primary issues that would need to be considered is the temperature at which the reaction takes place. The problem is that farmers might not have a device to keep the temperature at a constant level. This aspect should be taken into account when developing other tests and presumably considering providing a hardware device for temperature control for the farmers.

Concerning the safety aspects of this project, the bacteria that cause fish disease and can be detected with our test are not pathogenic to humans. Furthermore the samples for the test are taken from the gills of the fish, without harming the animal waiving the need to kill it.

Briefly, we developed a rapid testing kit, that provides a quick and convenient pathogen detection solution for fish farmers and a software tool that enables other developers to speed the process of testing kit development.

References

  1. FAO. The State of World Fisheries and Aquaculture 2020. 2 (FAO, 2020)
  2. Hastein, T., Scarfe, A. & Lund, V. Evaluación por métodos científicos del bienestar de los animales acuáticos. Revue Scientifique et Technique de l'OIE 24, 529-547 (2005)
  3. Lorenzo-Ferreiro Carmen., et al. “Nucleic-Acid Lateral Flow Assay Optimization with Different Gold Nanoparticle Size for Detection of Pathogen after PCR, Using L. Monocytogenes as Model. Acta Scientific Microbiology 1.10 17-24 (2018)
  4. Biolabs, N. How to design the primer and select the amplicon for IsoAmp II Universal tHDA Kit? | NEB. International.neb.com at ' '