Difference between revisions of "Team:Cork Ireland/Achievements"

 
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<header>
 
<header>
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                <a href="https://www.igem.org/Main_Page">
 
                 <img src="https://static.igem.org/mediawiki/2014/d/d7/Sysuchina_igemdeLogo.png" id="igem_logo"/>
 
                 <img src="https://static.igem.org/mediawiki/2014/d/d7/Sysuchina_igemdeLogo.png" id="igem_logo"/>
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                </a>
 
<img src="https://static.igem.org/mediawiki/2015/d/dd/AchIrlCork.png" alt="Achieve Banner" id="banner_pic"/>
 
<img src="https://static.igem.org/mediawiki/2015/d/dd/AchIrlCork.png" alt="Achieve Banner" id="banner_pic"/>
 
<nav>
 
<nav>
−
<h1>Basehunter</h1>
 
 
<ul>
 
<ul>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland"><li>Home</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland"><li>Home</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Project"><li>Our Project</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Project"><li>Our Project</li></a>
 +
<a href= "https://2015.igem.org/Team:Cork_Ireland/Design"><li>Design</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Practices"><li>Outreach</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Practices"><li>Outreach</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Team"><li>Team</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Team"><li>Team</li></a>
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<div id="main_col">
 
<div id="main_col">
 
  <div id="achieve">
 
  <div id="achieve">
 +
                <div id="overall_results">
 +
                    <h2>Final Results</h2>
 +
                    <ul>
 +
                    <li>Awarded a gold medal</li>
 +
                    <li>Nominee for Best Integrated Human Practices.</li>
 +
                    </ul>
 +
                </div>
 
<div id="gold">
 
<div id="gold">
 
<h2>Gold Medal Achievements</h2>
 
<h2>Gold Medal Achievements</h2>
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<li>
 
<li>
−
Improved function of an existing Biobrick part (made by another Team / your team in a previous year)
+
Help any registered iGEM team from a high-school, different track, another university, or institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.
−
and document findings on that parts page of the Registry.
+
 
</li>
 
</li>
 
</ol>
 
</ol>
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<li>
 
<li>
−
Submitted this part (ii) to the registry.
+
<a href="http://parts.igem.org/Part:BBa_K1698001">Submitted</a> this part (ii) to the registry.
 
</li>
 
</li>
 
 
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<li>
 
<li>
−
Documented a new Biobrick part (I) and submitted to Registry.
+
Documented a new Biobrick part (I) and <a href="http://parts.igem.org/Part:BBa_K1698003">submitted</a> to Registry.
 
</li>
 
</li>
 
</ol>
 
</ol>
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<p>
 
<p>
−
Our team member Donnchadh went to Malawi for 6 weeks. He thoroughly explained the concept to the Medical Laboratory
+
Taking advantage of a medical summer elective at UCC, we decided as part of our project to send one of our members to an African hospital in Malawi. Donnchadh spent the month of June there investigating the usefulness and potential application of our detection system. While he was there he took this opportunity to explain the scientific concepts of synthetic biology and of our Basehunter System to the medical and laboratory staff. He spoke to the local people and at schools about the upcoming field of synthetic biology and our aims  
−
Scientists in the hospital, they also filled out a survey. He spoke to the local people about science and our aims  
+
with the iGEM project. He also spoke to a witchdoctor about modern science and the medicine it is capable of producing using synthetic biology.
−
with the iGEM project. He also spoke to a witchdoctor about modern science and the medicine it is capable of producing.
+
 
</p>
 
</p>
  
 
<p>
 
<p>
−
Donnchadh discovered in his survey of hospital workers in Malawi that there is a need for more rapid testing of certain  
+
While Donnchadh was in Malawi, he identified a potential application for our novel DNA detection system. He discovered through interviewing the laboratory staff at Nhkoma, spending time on the hospital wards and from our survey that there is a need for more rapid testing of certain  
 
diseases which can be done cheaply and simply. He found that running machinery in these countries can be expensive so a  
 
diseases which can be done cheaply and simply. He found that running machinery in these countries can be expensive so a  
−
low cost alternative such as BaseHunter is favourable.
+
low cost alternative such as Basehunter is favourable.
 
</p>
 
</p>
  
 
<p>
 
<p>
−
In our talks with experienced biomedical scientist, Dr. Brigid Lucey, we found that a niche exists even in developed labs  
+
In our talks with an experienced biomedical scientist, Dr. Brigid Lucey, we found that a niche exists even in developed labs  
−
for a rapid diagnostic for TB. As Mycobacterium tuberculosis is slow growing, it is difficult to culture. For this reason,  
+
for a rapid diagnostic for <i>Mycobacterium tuberculosis</i> (TB). As TB is slow growing, it is difficult to culture. For this reason,  
 
lab results are often delayed even weeks for a confirmation of results. Basehunter could provide a simple and rapid method  
 
lab results are often delayed even weeks for a confirmation of results. Basehunter could provide a simple and rapid method  
−
to identify M. tuberculosis in samples. For this reason we designed a Mycobacterium tuberculosis detector and began to verify  
+
to identify TB in samples. For this reason we designed a TB detector and began to verify  
 
that it functions as well as the other detectors. In this way, our Human practices investigations highlighted a real world problem  
 
that it functions as well as the other detectors. In this way, our Human practices investigations highlighted a real world problem  
 
that we sought to address.
 
that we sought to address.
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<p>
 
<p>
 
We demonstrated a functional prototype of our project in our own lab. We then collaborated with both TCD and UCL to see if the  
 
We demonstrated a functional prototype of our project in our own lab. We then collaborated with both TCD and UCL to see if the  
−
prototype would be functional in another laboratory setting.
+
prototype would be functional in another laboratory setting. Find our <a href="https://2015.igem.org/Team:Cork_Ireland/Design">design</a> here.
 
</p>
 
</p>
  
 
<h3>
 
<h3>
−
Improve function of an existing Biobrick part (made by another Team / your team in a previous year) and document findings on that
+
Help any registered iGEM team from a high-school, different track, another university, or institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.
−
parts page of the Registry.
+
 
</h3>
 
</h3>
  
−
<p>Improved GFP by adding a detector part to it.</p>
+
<p>In July we met with the <a href="https://2015.igem.org/Team:Cork_Ireland/Collaborations">Trinity College Dublin</a> iGEM team who are taking part in iGEM for the first time. We provided feedback on their project work and told them what to expect at the Jamboree. We were in contact with the team in its early days before the team members were selected and stressed the need for a diverse team from many backgrounds. This was something we learned at iGEM last year and knew it was important to relay this advice. We also suggested that the team should not focus entirely on lab work and that engaging with the community throughout their project is encouraged.</p>
 +
<p>Over the course of working on the projects, we kept in contact with the team and aided them in their efforts to create a <a href="https://www.youtube.com/channel/UCjPJThAlEuACPeOl_VLHlNw">Youtube Channel “iGEM Academy”</a>with videos of common lab protocols by providing a video tutorial of our “Detector Reaction” for use with our Basehunter parts.</p>
 
</div>
 
</div>
 
 
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<p>
 
<p>
−
HPV 55bp Detector Part was designed, constructed and validated over the course of the project. Its sensitivity and specificity was  
+
HPV 55bp Detector Part was designed, constructed and validated over the course of the project. Its sensitivity and specificity was determined and an optimised protocol for its construction and use was developed.
−
determined and an optimised protocol for its construction and use was developed.
+
 
</p>
 
</p>
 
 
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<p>
 
<p>
−
This year Cork iGEM identified intellectual property rights as an issue. We interviewed the (INSERT TITLE HERE) Cathal Garvey to  
+
This year Cork iGEM identified intellectual property rights as an issue. We interviewed <a href="https://2015.igem.org/Team:Cork_Ireland/Practices#interviews">Cathal Garvey</a> to  
 
investigate the issue and see his views on the issue.
 
investigate the issue and see his views on the issue.
 
</p>  
 
</p>  
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in a real life lab setting was investigated by Donnchadh as he visited hospital labs in Malawi where the detector may theoretically be used.  
 
in a real life lab setting was investigated by Donnchadh as he visited hospital labs in Malawi where the detector may theoretically be used.  
 
He surveyed staff members on the equipment and reagents they had and whether they believed such a detector was a viable and sustainable tool.  
 
He surveyed staff members on the equipment and reagents they had and whether they believed such a detector was a viable and sustainable tool.  
−
We considered this in the design of our prototype and what to include in kits sent to TCD &amp; UCL labs.
+
We considered this in the design of our prototype and what to include in kits sent to <a href="https://2015.igem.org/Team:Cork_Ireland/Collaborations">TCD &amp; UCL</a> labs.
 
</p>
 
</p>
  
 
<p>
 
<p>
−
Also while in Malawi, Donnchadh evaluated resources in the lab and what diagnostics tests are available to patients of that hospital.  
+
While in Malawi, Donnchadh evaluated resources in the lab and what diagnostics tests are available to patients of that hospital.  
−
The issue of social justice arose as gaps were clear between the hospital described by Biomedical Scientist with experience working
+
Speaking to Dr.Bridget Lucey, a Biomedical Scientist in Ireland and the Biomedical Scientists working in Malawi- the issue of social justice was very clear regarding the standard of diagnostic tests available. With Basehunter, we can help bridge the gap between the inadequate resources and tests available in Malawi and those available in Ireland. This innovative Basehunter technology will make first world standard health care diagnostics available to all. Our project aims to bring first class molecular  
−
in Ireland, Dr. Brigid Lucey, and that described by the Malawi biomedical scientists. Our project aims to bring first class molecular  
+
 
diagnostics to areas where it currently is not by providing an alternative to expensive equipment such as PCR machines. With this in mind,  
 
diagnostics to areas where it currently is not by providing an alternative to expensive equipment such as PCR machines. With this in mind,  
−
we designed our kits to be low cost, easy to ship and practical for use in labs which may be small and under-resourced.
+
we designed our kits to be low cost, easy to ship and practical for use in labs which may be small and under-resourced. Blaine Doyle, CEO of GlowDx (which is a molecular diagnostic company), gave advised us on how to keep our costs as low as possible while ensuring an effective detector.  
 
</p>
 
</p>
  
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</div>
 
</div>
 
 
−
<div id="bronze_dis">
+
 
−
<h2>Bronze Medal Discussion:</h2>
+
−
+
−
</div>
+
−
+
 
</div>
 
</div>
 
</div>
 
</div>
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<li>Quick Links</li>
 
<li>Quick Links</li>
 
<a href="#gold"><li>Overview</li></a>
 
<a href="#gold"><li>Overview</li></a>
−
<a href="#gold_dis"><li>Gold Discussion</li></a>
+
<a href="#gold_dis"><li>Gold Medal Discussion</li></a>
−
<a href="#silver_dis"><li>Silver Discussion</li></a>
+
<a href="#silver_dis"><li>Silver Medal Discussion</li></a>
−
<a href="#bronze_dis"><li>Bronze Discussion</li></a>
+
 
</ul>
 
</ul>
 
</div>
 
</div>
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<a href= "https://2015.igem.org/Team:Cork_Ireland"><li>Home</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland"><li>Home</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Project"><li>Our Project</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Project"><li>Our Project</li></a>
 +
<a href= "https://2015.igem.org/Team:Cork_Ireland/Design"><li>Design</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Practices"><li>Outreach</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Practices"><li>Outreach</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Team"><li>Team</li></a>
 
<a href= "https://2015.igem.org/Team:Cork_Ireland/Team"><li>Team</li></a>

Latest revision as of 17:38, 9 November 2015

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Final Results

  • Awarded a gold medal
  • Nominee for Best Integrated Human Practices.

Gold Medal Achievements

  1. Integrated findings of Human Practices investigation into design and execution of project.
  2. Demonstrated a functional prototype of your project.
  3. Help any registered iGEM team from a high-school, different track, another university, or institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.

Silver Medal Achievements

  1. Experimentally validated that another new BioBrick Part (ii) of your own design and construction works as expected & document the characterisation of this part on the Registry.
  2. Submitted this part (ii) to the registry.
  3. Identified, investigated & addressed issues relating to ethics, sustainability, social justice, safety, security, and intellectual property rights (Human Practices) in the context of the project.

Bronze Medal Achievements

  1. Registered for iGEM 2015.
  2. Completed the Judging Form.
  3. Added project description to Wiki.
  4. Document team’s parts using Registry of Standard Biological Parts.
  5. Poster and presentation at Giant Jamboree.
  6. Work attributed as necessary on wiki.
  7. Documented a new Biobrick part (I) and submitted to Registry.

Gold Medal Discussion:

Integrate findings of Human Practices investigation into design and execution of project:

Taking advantage of a medical summer elective at UCC, we decided as part of our project to send one of our members to an African hospital in Malawi. Donnchadh spent the month of June there investigating the usefulness and potential application of our detection system. While he was there he took this opportunity to explain the scientific concepts of synthetic biology and of our Basehunter System to the medical and laboratory staff. He spoke to the local people and at schools about the upcoming field of synthetic biology and our aims with the iGEM project. He also spoke to a witchdoctor about modern science and the medicine it is capable of producing using synthetic biology.

While Donnchadh was in Malawi, he identified a potential application for our novel DNA detection system. He discovered through interviewing the laboratory staff at Nhkoma, spending time on the hospital wards and from our survey that there is a need for more rapid testing of certain diseases which can be done cheaply and simply. He found that running machinery in these countries can be expensive so a low cost alternative such as Basehunter is favourable.

In our talks with an experienced biomedical scientist, Dr. Brigid Lucey, we found that a niche exists even in developed labs for a rapid diagnostic for Mycobacterium tuberculosis (TB). As TB is slow growing, it is difficult to culture. For this reason, lab results are often delayed even weeks for a confirmation of results. Basehunter could provide a simple and rapid method to identify TB in samples. For this reason we designed a TB detector and began to verify that it functions as well as the other detectors. In this way, our Human practices investigations highlighted a real world problem that we sought to address.

Demonstrate a functional prototype of your project:

We demonstrated a functional prototype of our project in our own lab. We then collaborated with both TCD and UCL to see if the prototype would be functional in another laboratory setting. Find our design here.

Help any registered iGEM team from a high-school, different track, another university, or institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.

In July we met with the Trinity College Dublin iGEM team who are taking part in iGEM for the first time. We provided feedback on their project work and told them what to expect at the Jamboree. We were in contact with the team in its early days before the team members were selected and stressed the need for a diverse team from many backgrounds. This was something we learned at iGEM last year and knew it was important to relay this advice. We also suggested that the team should not focus entirely on lab work and that engaging with the community throughout their project is encouraged.

Over the course of working on the projects, we kept in contact with the team and aided them in their efforts to create a Youtube Channel “iGEM Academy”with videos of common lab protocols by providing a video tutorial of our “Detector Reaction” for use with our Basehunter parts.

Silver Medal Discussion:

Experimentally validate that another new BioBrick Part (ii) of your own design and construction works as expected & document the characterisation of this part on the Registry:

HPV 55bp Detector Part was designed, constructed and validated over the course of the project. Its sensitivity and specificity was determined and an optimised protocol for its construction and use was developed.

Submit this part (ii) to the registry:

Submitted

Identify, investigate & address issues relating to ethics, sustainability, social justice, safety, security, and intellectual property rights (Human Practices) in the context of the project:

This year Cork iGEM identified intellectual property rights as an issue. We interviewed Cathal Garvey to investigate the issue and see his views on the issue.

Issues relating to the safety of the system for use as a diagnostic were identified. As with all diagnostics, this system must be optimised, standardised and deemed as good as or better than current procedures. The use of live cells in a diagnostic system is a unique feature which may lead to unforeseen complications such as unsuitable growth conditions in some settings or the impact of contaminating growth on results. To address this, we investigated suitable controls and validates our results by having outside labs (TCD & UCL) carry out our tests. We also sought the advice of experienced Biomedical Scientist, Dr. Brigid Lucey on the issue.

Another aspect of our human practices work was that done by team member Donnchadh in Malawi. The issue of sustainability of our detector in a real life lab setting was investigated by Donnchadh as he visited hospital labs in Malawi where the detector may theoretically be used. He surveyed staff members on the equipment and reagents they had and whether they believed such a detector was a viable and sustainable tool. We considered this in the design of our prototype and what to include in kits sent to TCD & UCL labs.

While in Malawi, Donnchadh evaluated resources in the lab and what diagnostics tests are available to patients of that hospital. Speaking to Dr.Bridget Lucey, a Biomedical Scientist in Ireland and the Biomedical Scientists working in Malawi- the issue of social justice was very clear regarding the standard of diagnostic tests available. With Basehunter, we can help bridge the gap between the inadequate resources and tests available in Malawi and those available in Ireland. This innovative Basehunter technology will make first world standard health care diagnostics available to all. Our project aims to bring first class molecular diagnostics to areas where it currently is not by providing an alternative to expensive equipment such as PCR machines. With this in mind, we designed our kits to be low cost, easy to ship and practical for use in labs which may be small and under-resourced. Blaine Doyle, CEO of GlowDx (which is a molecular diagnostic company), gave advised us on how to keep our costs as low as possible while ensuring an effective detector.

Knowledge of synthetic biology was also limited in Malawi and this may hinder acceptance of our detector. To address this, Donnchadh explained our project and gave detail on what exactly synthetic biology is to workers in the hospital lab. We also learned of a culture of seeking medical care from witch doctors in Malawi. Donnchadh explained the concept of synthetic biology to this figure in the community where he worked, and got her approval of this and an acknowledgment that other advancements in science and medicine can aid in healing also.