Difference between revisions of "Team:NYMU-Taipei/ttest"

 
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<p style="font-size:16px;">Our project is comprised of four parts,  the introduction, part design, prototype, and human practice. Let me introduce some background information regarding our project. The Oriental fruit fly is a serious agricultural pest. It can consume more than 150 types of vegetables and fruits and primarily affects tropical areas. According to research, in 2004, Asia produced 178 million tons of tropical fruits, amounting to 66% of the global production worth US$2.5 billion. Because Asia is mainly a tropical environment, these fruit flies can decimate the agricultural industry. They can cause 90% to 100% yield loss depending on the fruit fly population, locality, variety and season. In other words, the oriental fruit fly poses a great threat to our global food supply as it can destroy most of the global produce.</p>
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        <p style="font-size:16px;">Oriental fruit flies are wreaking havoc worldwide. It accounted for an annual loss of $176 million in California and billions worth of damage in Taiwan. Furthermore, it devastated fruit production in Africa, causing more than 80% of crop damage. As a result, various countries, out of fear, impose trade restrictions and refused imports of produce from Africa, leading to significant economic losses for Africa.</p>
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        <p style="font-size:16px;">The ravages of oriental fruit flies are also not limited to tropical areas. This is a global issue. They have plagued approximately 60 countries worldwide and the issue is worsened by international transportation, which can spread the oriental fruit fly eggs. This is why the issue of oriental fruit flies needs to be solved and our project aims to solve this problem.</p>
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        <p style="font-size:16px;">Here are a few traditional solutions to the oriental fruit fly, but each of them are far from perfect.</p>
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        <p style="font-size:16px;">#1: One of the most effective approach is contraception or male annihilation, which uses high-energy radiation to sterilize the male and in turn prevent reproduction. This is ineffective, however, as wild female flies can differentiate between sterilized males and non-sterilized males.</p>
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        <p style="font-size:16px;">#2: Another way is baiting, which uses pheromones like methyl eugenol to attract male oriental fruit flies into traps that kill them. This is still ineffective however, as the female fruit flies, being the one capable of reproducing, are the real problem but are unaffected by methyl eugenol. There are other more ways like bagging, spraying pesticides and early harvesting but none of these are perfect solutions.</p>
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        <p style="font-size:16px;">Our project aims to solve the shortcomings of these previous solutions. Our fungi is a biological agent that takes biosafety and environmental conservation into consideration.</p>
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        <p style="font-size:16px;">What is Metarhizium anisopliae?</p>
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        <p style="font-size:16px;">Metarhizium Anisopliae is an entomogenous fungi, Or a fungi that can act as a parasite and seriously harm them.It can infect over 300 hosts but different strands have highly specific hosts. Because various strains of Metarhizium Anisopliae already exist in soil, it doesn’t alter the environment, making it eco-friendly.</p>
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        <p style="font-size:16px;">M. Anisopliae however, is vulnerable to environmental stress like low humidity, temperature, UV exposure… Etc. Thus, scientists are currently genetically engineering M. Anisopliae to solve these shortcomings. But, because of certain laws and policies that bar GMO products from entering the market, biopesticides using M. Anisopliae is still uncommon.</p>
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        <p style="font-size:16px;">Traditionally, biosafety is achieved by selecting strains with low UV tolerance or low heat tolerance to ensure that it dies under uncontrolled environments. This, however, compromises on its virulence and applicability. Thus, our project aims to mitigate these GMO concerns without compromising its virulence and vitality.</p>
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          <li><a class="txttype" href="#ground"></a></li>
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          <li><a href="#Background">Background</a></li>
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          <li><a href="#Collaborations">Collaborations</a>
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            <ul class="nav">
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              <li><a href="#TAS-TAIPI"><span class="fa fa-angle-double-right"></span>TAS Taipei</a></li>
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              <li><a href="#NCTU-Formosa"><span class="fa fa-angle-double-right"></span>NCTU Formosa</a></li>
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            </ul>
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          <li><a href="#Achievement">Achievement</a>
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              <li><a href="#Gold"><span class="fa fa-angle-double-right"></span>Gold</a></li>
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              <li><a href="#Silver"><span class="fa fa-angle-double-right"></span>Silver</a></li>
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              <li><a href="#Bronze"><span class="fa fa-angle-double-right"></span>Bronze</a></li>
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            </ul>
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          <li><a href="#Parts">Parts</a></li>
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        </ul>
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        <section id="Background">
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          <h2><span class="fa fa-edit"></span> Background</h2>
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            <p>Potatoes all over the world are in danger and this is not the first time in history. In the late 1840s, potato late blight epidemics caused the Great Famine in Ireland and one million people were starved to death. This devastating disease is caused by the plant pathogenic oomycetes, <i>Phytophthora infestans</i>. Even now, when potatoes are widely grown in 135 countries and consumed by 1 billion people, late blight is still causing serious problems, including food insecurity, economic losses, and environmental damages.</p>
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            <div style="margin-left:12.5%;width:75%;"><img src="https://static.igem.org/mediawiki/2015/e/eb/Nymu-overview-world.png" style="margin-left:13;padding-top:2%;padding-bottom:2%;width:90%;"><p style="font-weight:bold;font-size:14px;">Fig 1. Worldwide distribution of potato late blight caused by <i>P.infestans</i></p></div>
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            <br><br>
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            <p>Potato late blight costs an annual loss of 6.7 billion USD. Although late blight have only little impact on the food supply in some areas, crop loss can still force farmers out of business. To control late blight, fungicides are frequently used, up to once every 3 days. These fungicides have enormous costs financially, at $200 per acre of farmland. Moreover, these chemicals often seep underground or escape to nearby streams and contaminate water sources. Water samples from over the U.S. show that 75% of surface waters and 58% of groundwater wells contain at least one of the 33 potato fungicides.</p>
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            <br><br>
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            <p>In modern agriculture, the use of fungicides and genetically modified potatoes are inefficient in fighting against potato late blight. Most strains of <i>P. infestans</i> have developed resistance against fungicides used nowadays. <i>P. infestans</i> secretes some enzymes and form high turgor pressure inside its cell to penetrate and colonize in potato cells. <i>P. infestans</i> infect potato leaves and tubers; eventually the entire plant rots and dies. The 2015 NYMU-Taipei iGEM team aims to prevent potatoes from being infected by this devastating disease and ensure global food security.</p>
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          <button type="button" class="btn btn-primary">Learn More</button>
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        </section>
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        <section id="Collaborations">
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          <h2><span class="fa fa-edit"></span>Collaborations</h2>
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          <section id="TAS-TAIPI">
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              <h2>Collaboration with <a href="https://2015.igem.org/Team:TAS_Taipei/Collaborations">TAS Taipei iGEM team</a></h2>
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              <ul>
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              <li>We gave them the part with yebF, a motor protein that brings our product out of the cell. This was essential to their project because it allowed their protein, the granzyme B inhibitor, to be delivered out into the reservoir and to diffuse through the bandage.</li>
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              <li>Furthermore, NYMU hosted an educational summer camp welcoming members from the 2015 and 2016 TAS_Taipei iGEM teams to join and learn.</li>
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              <li>We have also been supportive for helping TAS_Taipei iGEM team with research and running the model for diffusion, bandage, and the ACT inhibition model.  We provided them with modeling expertise, literature values for our models and debugging expertise.</li>
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              </ul>
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              <h4>In addition to our help on TAS, we also collaborated with TAS</h4>
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              <ul>
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              <li>To provide us with the LuxR part which is pivotal for our oscillator. LuxR is essential for our oscillator which is used to report the presence of a malicious spore in the device part of the project.</li>
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              <li>TAS also helped us by running the initial experiments for our microbial fuel cell prototype. We were provided by TAS_Taipei with initial test results of the prototype for our project so that we found the correct soil to water to bacteria ratios(August 2015).</li>
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              <li>Three members of TAS (Alvin, Fiona and Huiru) are members of both NYMU and TAS teams. They worked at NYMU over the summer for the NYMU_Taipei team and are presenting with the team at the Giant Jamboree!</li>
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              </ul>
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              <button type="button" class="btn btn-primary">Learn More</button>
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          </section>
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          <section id="NCTU-Formosa">
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              <h2>Joining the Meetup hosted by NCTU_Formosa iGEM team</h2>
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              <p>We joined the meetup hosted by NCTU this summer. Many other teams from Taiwan and China gathered to have a seminar of their projects.</p>
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              <button type="button" class="btn btn-primary">Learn More</button>
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          </section>
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        </section>
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        <section id="Achievement">
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          <h2><span class="fa fa-edit"></span> Achievement</h2>
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          <section id="Gold">
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          <h2>Gold</h2>
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              <ul>
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              <li> Expand on our silver medal Human Practices activity and demonstrate an innovative Human Practices activity that relates to our project by hosting a bootcamp for high school students and work with International Cooperation Development Foundation(ICDF) to help control potato diseases in Republic of Honduras. <a href="https://2015.igem.org/Team:NYMU-Taipei/Practices">Our policy and practices</a></li>
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              <li>Help <a href="https://2015.igem.org/Team:NYMU-Taipei/Collaborations">TAS Taipei</a> , a high-school iGEM team, by debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.</li>
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              <li>We characterized a previously existing inducible promoter J61051 and entered the information in the part's page on the Registry.(<a href="http://parts.igem.org/Part:BBa_J61051">BBa_J61051</a>) </li>
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              <li>Demonstrate a functional prototype of our project and show that the system working under real-world conditions simulated in the lab.<a href="https://2015.igem.org/Team:NYMU-Taipei/Design">Our functional prototype</a> </li>
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              </ul>
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          <button type="button" class="btn btn-primary">Learn More</button>
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          </section>
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          <section id="Silver">
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          <h2>Silver</h2>
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            <ul>
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            <li>Experimentally validate new BioBricks Part or Device of our own design and construction works as expected and document the characterization of the parts in the Main Page section of the Registry entry for that Part/Device.(<a href=""http://parts.igem.org/Part:BBa_K1769009">BBa_1769009</a> <a href="http://parts.igem.org/Part:BBa_K1769002">BBa_K1769002</a>) </li>
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            <li>Submit the new parts to the iGEM Parts Registry.(<a href="http://parts.igem.org/Part:BBa_K1769009">BBa_K1769009</a>
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            <a href="http://parts.igem.org/Part:BBa_K1769002">BBa_K1769002</a> <a href="http://parts.igem.org/Part:BBa_K1769000">BBa_K1769000</a> <a href="http://parts.igem.org/Part:BBa_K1769004">BBa_K1769004</a>
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            </li>
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            <li>Demonstrate how our team has identified, investigated and addressed one or more of these issues in the context of our project. <a href="https://2015.igem.org/Team:NYMU-Taipei/Practices">Our human practice</a></li>
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            </ul>
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          <button type="button" class="btn btn-primary">Learn More</button>
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          </section>
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          <section id="Bronze">
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          <h2>Bronze</h2>
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            <ul>
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            <li>Register for iGEM, have a great summer, and attend the Giant Jamboree.</li>
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            <li>Complete the <a href="https://igem.org/Judging_Form.cgi?id=1769">Judging form.</a></li>
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            <li>Create and share a Description of the team's project using the iGEM wiki, and document the team's parts using the Registry of Standard Biological Parts.(<a href="http://parts.igem.org/Part:BBa_K1769005">BBa_K1769005</a> <a href="http://parts.igem.org/Part:BBa_K1769006">BBa_K1769006</a> <a href="http://parts.igem.org/Part:BBa_K1769008">BBa_k1769008</a>)</li>
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            <li>Present a poster and a talk at the iGEM Jamboree.</li>
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            <li>Attributions:<a href="https://2015.igem.org/Team:NYMU-Taipei/Attributions">https://2015.igem.org/Team:NYMU-Taipei/Attributions</a></li>
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            <li>Parts:<a href="https://2015.igem.org/Team:NYMU-Taipei/Parts">https://2015.igem.org/Team:NYMU-Taipei/Parts</a></li>
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            </ul>
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          <button type="button" class="btn btn-primary">Learn More</button>
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          </section>
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        </section>
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        <section id="Parts">
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          <h2><span class="fa fa-edit"></span> Parts</h2>
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            <p>In the table below, all of our BioBricks can be found. These BioBricks are sent in pSB1C3.</p>
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            <table class="wikitable" style="margin-left:10%"><tbody> <tr>
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              <th> Part Number </th> <th> Type </th> <th> Description </th> <th> Length(bp) </th> </tr> <tr> <td> <a href="http://parts.igem.org/Part:BBa_K1769000">BBa_K1769000</a> </td> <td> composite </td> <td> Dimeric FYVE </td> <td> 426 </td> </tr> <tr> <td> <a href="http://parts.igem.org/Part:BBa_K1769001">BBa_K1769001</a></td> <td> composite </td> <td> Dimeric FYVE+GFP </td><td> 1152</td>  </tr> <tr> <td><a href="http://parts.igem.org/Part:BBa_K1769002">BBa_K1769002</a> </td> <td> composite </td> <td> J61051+RBS+LuxR+Ter+pLUX+RBS+LuxI+Ter+pLux+RBS+Aiia+Ter+pLux+RBS+GFP+Ter </td> <td> 5050 </td> </tr> <tr> <td><a href="http://parts.igem.org/Part:BBa_K1769003">BBa_K1769003</a></td> <td> reporter </td> <td> J61051+RBS+GFP+Ter </td> <td> 2154 </td> </tr> <tr> <td><a href="http://parts.igem.org/Part:BBa_K1769004">BBa_K1769004</a>  </td> <td> coding </td> <td> Monomeric FYVE </td> <td> 204 </td> </tr> <tr> <td><a href="http://parts.igem.org/Part:BBa_K1769005">BBa_K1769005</a> </td> <td> coding </td> <td> mtrB </td> <td> 2094 </td> </tr> <tr> <td> <a href="http://parts.igem.org/Part:BBa_K1769006">BBa_K1769006</a></td> <td> coding </td> <td> Dimeric FYVE (without stop codon) </td> <td> 423 </td> </tr> <tr> <td><a href="http://parts.igem.org/Part:BBa_K1769007">BBa_K1769007</a> </td> <td> reporter </td> <td> Monomeric FYVE+GFP fusion protein </td> <td> 1067 </td> </tr> <tr> <td><a href="http://parts.igem.org/Part:BBa_K1769008">BBa_K1769008</a>  </td> <td> coding </td> <td> MtrB+LVA tag </td> <td> 2127 </td> </tr> <tr> <td><a href="http://parts.igem.org/Part:BBa_K1769009">BBa_K1769009</a>  </td> <td> composite </td> <td> T7+RBS+defensin </td> <td> 196 </td> </tr> <tr> <td> <a href="http://parts.igem.org/Part:BBa_K1769010">BBa_K1769010</a> </td> <td> composite </td> <td> J61051+RBS+LuxR+Ter+pLUX+RBS+LuxI+Ter+pLux+RBS+Aiia+Ter+pLux+RBS+Ter </td> <td> 4301 </td> </tr></tbody></table>
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Latest revision as of 11:17, 22 September 2016

test a.txttype{ color: red; }

Background

Potatoes all over the world are in danger and this is not the first time in history. In the late 1840s, potato late blight epidemics caused the Great Famine in Ireland and one million people were starved to death. This devastating disease is caused by the plant pathogenic oomycetes, Phytophthora infestans. Even now, when potatoes are widely grown in 135 countries and consumed by 1 billion people, late blight is still causing serious problems, including food insecurity, economic losses, and environmental damages.

Fig 1. Worldwide distribution of potato late blight caused by P.infestans



Potato late blight costs an annual loss of 6.7 billion USD. Although late blight have only little impact on the food supply in some areas, crop loss can still force farmers out of business. To control late blight, fungicides are frequently used, up to once every 3 days. These fungicides have enormous costs financially, at $200 per acre of farmland. Moreover, these chemicals often seep underground or escape to nearby streams and contaminate water sources. Water samples from over the U.S. show that 75% of surface waters and 58% of groundwater wells contain at least one of the 33 potato fungicides.



In modern agriculture, the use of fungicides and genetically modified potatoes are inefficient in fighting against potato late blight. Most strains of P. infestans have developed resistance against fungicides used nowadays. P. infestans secretes some enzymes and form high turgor pressure inside its cell to penetrate and colonize in potato cells. P. infestans infect potato leaves and tubers; eventually the entire plant rots and dies. The 2015 NYMU-Taipei iGEM team aims to prevent potatoes from being infected by this devastating disease and ensure global food security.

Collaborations

Collaboration with TAS Taipei iGEM team

  • We gave them the part with yebF, a motor protein that brings our product out of the cell. This was essential to their project because it allowed their protein, the granzyme B inhibitor, to be delivered out into the reservoir and to diffuse through the bandage.
  • Furthermore, NYMU hosted an educational summer camp welcoming members from the 2015 and 2016 TAS_Taipei iGEM teams to join and learn.
  • We have also been supportive for helping TAS_Taipei iGEM team with research and running the model for diffusion, bandage, and the ACT inhibition model. We provided them with modeling expertise, literature values for our models and debugging expertise.

In addition to our help on TAS, we also collaborated with TAS

  • To provide us with the LuxR part which is pivotal for our oscillator. LuxR is essential for our oscillator which is used to report the presence of a malicious spore in the device part of the project.
  • TAS also helped us by running the initial experiments for our microbial fuel cell prototype. We were provided by TAS_Taipei with initial test results of the prototype for our project so that we found the correct soil to water to bacteria ratios(August 2015).
  • Three members of TAS (Alvin, Fiona and Huiru) are members of both NYMU and TAS teams. They worked at NYMU over the summer for the NYMU_Taipei team and are presenting with the team at the Giant Jamboree!

Joining the Meetup hosted by NCTU_Formosa iGEM team

We joined the meetup hosted by NCTU this summer. Many other teams from Taiwan and China gathered to have a seminar of their projects.

Achievement

Gold

  • Expand on our silver medal Human Practices activity and demonstrate an innovative Human Practices activity that relates to our project by hosting a bootcamp for high school students and work with International Cooperation Development Foundation(ICDF) to help control potato diseases in Republic of Honduras. Our policy and practices
  • Help TAS Taipei , a high-school iGEM team, by debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.
  • We characterized a previously existing inducible promoter J61051 and entered the information in the part's page on the Registry.(BBa_J61051)
  • Demonstrate a functional prototype of our project and show that the system working under real-world conditions simulated in the lab.Our functional prototype

Silver

  • Experimentally validate new BioBricks Part or Device of our own design and construction works as expected and document the characterization of the parts in the Main Page section of the Registry entry for that Part/Device.(BBa_1769009 BBa_K1769002)
  • Submit the new parts to the iGEM Parts Registry.(BBa_K1769009 BBa_K1769002 BBa_K1769000 BBa_K1769004
  • Demonstrate how our team has identified, investigated and addressed one or more of these issues in the context of our project. Our human practice

Bronze

Parts

In the table below, all of our BioBricks can be found. These BioBricks are sent in pSB1C3.

Part Number Type Description Length(bp)
BBa_K1769000 composite Dimeric FYVE 426
BBa_K1769001 composite Dimeric FYVE+GFP 1152
BBa_K1769002 composite J61051+RBS+LuxR+Ter+pLUX+RBS+LuxI+Ter+pLux+RBS+Aiia+Ter+pLux+RBS+GFP+Ter 5050
BBa_K1769003 reporter J61051+RBS+GFP+Ter 2154
BBa_K1769004 coding Monomeric FYVE 204
BBa_K1769005 coding mtrB 2094
BBa_K1769006 coding Dimeric FYVE (without stop codon) 423
BBa_K1769007 reporter Monomeric FYVE+GFP fusion protein 1067
BBa_K1769008 coding MtrB+LVA tag 2127
BBa_K1769009 composite T7+RBS+defensin 196
BBa_K1769010 composite J61051+RBS+LuxR+Ter+pLUX+RBS+LuxI+Ter+pLux+RBS+Aiia+Ter+pLux+RBS+Ter 4301