Difference between revisions of "Team:JMU Wuerzburg/Human Practices"

 
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            <p style="visibility: hidden;" id="workshops">&npsp;</p>
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            <h2>Workshops</h2>
 +
            <h3>iGEM Lecture Series</h3>
 +
            <div>
 +
                As a part of our project we actively contribute to our universitie’s teaching program by organizing a lecture series followed by an open discussion on specialized topics related to our project. Until now, we had talks on Norovirus, Malaria and Primer and Probe Design. Currently we are preparing the next talks for the following semester.
 +
                <br><br>
 +
                Our first lecture was held by our PI Prof. Dr. Jochen Bodem. As a professor of virology, he delivered interesting insights into the molecular biology of Norovirus. We discussed the mechanisms how the virus is infiltrating the human cells, its replication and the damage caused by an infection leading to the typical symptoms of a gastrointestinal disease.
 +
                <br><br>
 +
                Prof. Dr. Christian Janzen, an expert on protozoan parasites especially Trypanosoma, gave a fascinating talk on Malaria. He started with some basic facts about the historic background and the worldwide incidences of the disease followed by details about the biochemistry of plasmodium, the different subtypes of the pathogen and the varying characteristics and symptoms of Malaria. Furthermore, we discussed current methods to diagnose and treat Malaria.
 +
                <br><br>
 +
                For a talk on primer and probe design we invited experts from the company Thermo Scientific to our university. The lecture focused on the design of a probe-based assay for pathogens and how to achieve reliable and accurate results in qPCR experiments. Starting with an introduction to qPCR we also discussed the process of assay validation as well as potential pitfalls regarding primer and probe design.
 +
                <br><br>
 +
                By initiating our iGEM lecture series, we want to reach out to interested people from Würzburg and students of all faculties, draw attention to the topic of infectious and tropical diseases. Furthermore, we are able to introduce the iGEM competition and our research project to a lager audience, thereby attracting new members for our team. In the future we will further enrich the curriculum for many students by inviting speakers from the field of synthetic biology. We hope to have a conversation about the amazing possibilities but also the practical and ethical limits of biological engineering.
 +
            </div>
 +
 +
            <h3>Outlook</h3>
 +
            <div>
 +
                Since we are the first team of our university to participate in the iGEM competition, lot of effort has still to be invested to create a favourable environment and a close, far-reaching network for the iGEM initiative to grow and to expand at Wuerzburg. We will further intensify our relations to different faculties and institutes to conduct interdisciplinary research.
 +
                <br><br>
 +
                We have already published an article in an internal journal at our university, called “Einblick”. The next step to push our project forward and to gain local support is presenting our results to the public at our home town by newspaper articles and a discussion Forum. Our “Cake and Science” cake sale in the university hospital is our first step to reach out to the inhabitants of our city. Furthermore, we will present our research to biomedical students from all over Germany at the 13th Biomedical Students` Symposium in November.
 +
            </div>
 +
 +
            <img alt="fehlt" src="https://static.igem.org/mediawiki/2018/2/20/T--JMU_Wuerzburg--human-workshops.jpg" />
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 +
 +
            <hr id="education">
 +
            <h2>Education</h2>
 +
            <h3>Cake and science</h3>
 +
            <div>
 +
                Wondering about how we could bring our project in mind of people from our city who we wouldn’t meet at the university, we came up with a rather unusual idea: Why not have a piece of cake with people while introducing them to our project?  We organized two cake sales at the facilities of the university hospital in Wuerzburg. We were able to present our project to the public and we also gained some revenue selling the cakes.
 +
                <br><br>
 +
                People were attracted by our poster we had brought with us. Not only doctors were curious, but also the staff, visitors and the patients were asking questions about our work. Enlightening conversations about the development of diagnostic tests while eating a lovely piece of self-made cake created a less common, more extraordinary atmosphere, which was pleasant for our visitors and for ourselves. For the insatiable curious people, we provided handouts for further reading.
 +
            </div>
 +
 +
            <img src="https://static.igem.org/mediawiki/2018/b/b4/T--JMU_Wuerzburg--human-cake.jpg" alt="fehlt"/>
  
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<div class="column full_size">
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            <h3>Lab intern pipetting test</h3>
 +
            <div>
 +
                The iGEM intern pipetting workshop was designed to provide first semester students an introduction to standard pipetting techniques. Also, the more experienced students were given an excellent opportunity to pass on their knowledge to younger students.
 +
                <br><br>
 +
                Taking part in the lab intern pipetting test also trained the participants in precise pipetting, which was a big advantage for the students of the wet lab team when they started their work in the lab later.
 +
                <br><br>
  
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<h1>Human Practices</h1>
+
                <h4>Protocol Bradfort protein assay</h4>
−
<p>
+
                <h5>Bradford solution</h5>
−
At iGEM we believe societal considerations should be upfront and integrated throughout the design and execution of synthetic biology projects. “Human Practices” refers to iGEM teams’ efforts to actively consider how the world affects their work and the work affects the world. Through your Human Practices activities, your team should demonstrate how you have thought carefully and creatively about whether your project is responsible and good for the world. We invite you to explore issues relating (but not limited) to the ethics, safety, security, and sustainability of your project, and to show how this exploration feeds back into your project purpose, design and execution.
+
                Dilute Bradford solution 1:5 with water.
−
</p>
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                Use for one 96 well plate 12 ml water and 3 ml Bradford solution.
  
 +
                <h5>BSA solution</h5>
 +
                Dilute BSA solution 1:20 with water.
 +
                Use 11µl BSA and 209 µl water for one 96 well plate.
  
 +
                <h5>Assay</h5>
 +
                Transfer 100µl Bradford solution and 2µl BSA solution in each well.
 +
                Mix the solution well and destroy all airbubbles with a pipette tip.
  
−
<p>For more information, please see the <a href="https://2018.igem.org/Human_Practices">Human Practices Hub</a>. There you will find:</p>
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                <h5>Measurement</h5>
−
+
                Measure absorption of the 96 well plate with a photometer at 580nm.
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<ul>
+
−
<li> an <a href="https://2018.igem.org/Human_Practices/Introduction">introduction</a> to Human Practices at iGEM </li>
+
−
<li>tips on <a href="https://2018.igem.org/Human_Practices/How_to_Succeed">how to succeed</a> including explanations of judging criteria and advice about how to conduct and document your Human Practices work</li>
+
−
<li>descriptions of <a href="https://2018.igem.org/Human_Practices/Examples">exemplary work</a> to inspire you</li>
+
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<li>links to helpful <a href="https://2018.igem.org/Human_Practices/Resources">resources</a></li>
+
−
<li>And more! </li>
+
−
</ul>
+
−
+
  
 +
                <br><br>
 +
                To pass the pipetting test the error rate of two following rows in a 96 microwell plate had to be less than 6 %.
 +
                If a student met this criterium, we decided by this calculation:
 +
                <br>
 +
                1. average for one row
 +
                <br>
 +
                2. deviation average – a single well plate (for every well plate in a row)
 +
                <br>
 +
                3. result of 2. / average for one row * 100
 +
            </div>
  
  
  
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<p>On this page, your team should document all of your Human Practices work and activities. You should write about the Human Practices topics you considered in your project, document any activities you conducted to explore these topics (such as engaging with experts and stakeholders), describe why you took a particular approach (including referencing any work you built upon), and explain if and how you integrated takeaways from your Human Practices work back into your project purpose, design and/or execution. </p>
 
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<p>If your team has gone above and beyond in work related to safety, then you should document this work on your Safety wiki page and provide a description and link on this page. If your team has developed education and public engagement efforts that go beyond a focus on your particular project, and for which would like to nominate your team for the Best Education and Public Engagement Special Prize, you should document this work on your Education and Education wiki page and provide a description and link here. </p>
 
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</div>
 
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<div class="clear"></div>
 
  
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            <hr id="establishing">
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<div class="column full_size">
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            <h2>Establishing an iGEM-Team</h2>
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<div class="highlight decoration_background">
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            <h3>The beginning of our project </h3>
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<p>The iGEM judges will review this page to assess whether you have met the Silver and/or Gold medal requirements based on the Integrated Human Practices criteria listed below. If you nominate your team for the <a href="https://2018.igem.org/Judging/Awards">Best Integrated Human Practices Special Prize</a> by filling out the corresponding field in the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>, the judges will also review this page to consider your team for that prize.  
+
            <div>
−
</p>
+
                During a regular seminar of virology, we discussed about different possibilities to engage into scientific research as soon as possible. Annabel and Nicole came up with the idea to participate in the iGEM competition. We were motivated by the outlook to conduct our own research project with all tasks and responsibilities but with close supervision by experienced researchers. Mostly we were eager to gain experience working in the lab.
−
</div>
+
                <br><br>
−
</div>
+
                After collecting more information about the competition online and from other participants, we decided to bring iGEM to Wuerzburg and founded the first team of our university. Together with two additional bachelor students we motivated Prof. Jochen Bodem to become our PI. He also provided us with lab space to get started with the lab work. By advertising our project among friends, we soon got more and more students, until we were a huge group of 50 participants.
 +
                <br><br>
 +
                After various brainstorming sessions we decided to start exploring new methods in the detection of infectious diseases.  This led us to our project, designing a rapid diagnostic test to distinguish different types of Plasmodium, the pathogen which causes Malaria.  
 +
                <br><br>
 +
                Organizing the team in different subgroups meant that every student could contribute to the topic they liked the most. Unfortunately, many students did not spend as much time and passion on our project as necessary, so our team shrank to the final number of eleven student members and three advisors. Our final team consists of an interdisciplinary synergy of bachelor students from biology, biomedicine, medicine and mathematics.
 +
            </div>
  
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<div class="clear extra_space"></div>
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            <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
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                <img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/5/5f/T--JMU_Wuerzburg--human-establishing_beginning.jpg" alt="fehlt" style="display: block;">
 +
                <span style="text-decoration: underline;"></span> The Beginning of our project
 +
            </div>
  
 +
            <h3>German Meetup in Marburg</h3>
 +
            <div>
 +
                As a newly established team we were excited to get in contact with the other teams at the German meetup in Marburg. Especially, we exchanged some ideas about the different projects and talked about problems we had to face in the wet lab. This exchange of experience resulted in a huge benefit for our project in the following weeks.
 +
                <br><br>
 +
                We were introduced to team Marburg’s project for the first time. Later we established a collaboration with team Marburg by participating in their Vibrio natriegens InterLab Study. Moreover, we learned much more about the iGEM competition itself and got contacts to students more familiar to the iGEM competition who provided us with advice later on.
 +
            </div>
  
 +
            <h3>European Meetup in Munich</h3>
 +
            <div>
 +
                In July we attended the European Meetup in Munich.
 +
                It was a great experience to get in touch with so many teams.
 +
                For the first time we presented our poster to a greater audience and
 +
                were excited by all the positive comments and helpful advice we received.
 +
                We are thankful for the opportunity to get an insight into the other amazing projects.
 +
                Not only did we get to hear stunning talks about synthetic biology in current science issues,
 +
                but we also received important information by attending many workshops.
 +
                In the end we left a bit wistfully, but we also took home so many amazing impressions. 
 +
            </div>
  
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<div class="column full_size">
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            <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
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                <img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/7/74/T--JMU_Wuerzburg--human-european03.jpg" alt="fehlt" style="display: block;">
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<h3>Silver Medal Criterion #3</h3>
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                <span style="text-decoration: underline;"></span> Exploring Munich with team Bielefeld photo by team Bielefeld
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<p>Convince the judges you have thought carefully and creatively about whether your work is responsible and good for the world. Document how you have investigated these issues and engaged with your relevant communities, why you chose this approach, and what you have learned. Please note that surveys will not fulfill this criteria unless you follow scientifically valid methods. </p>
+
            </div>
  
 +
            <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
 +
                <img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/7/7a/T--JMU_Wuerzburg--human-european01.jpg" alt="fehlt" style="display: block;">
 +
                <span style="text-decoration: underline;"></span> Presenting our poster for the first time
 +
            </div>
  
−
<h3>Gold Medal Criterion #1</h3>
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            <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
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<p>Expand on your silver medal activity by demonstrating how you have integrated the investigated issues into the purpose, design and/or execution of your project. Document how your project has changed based upon your human practices work.
+
                <img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/1/10/T--JMU_Wuerzburg--human-european02.jpg" alt="fehlt" style="display: block;">
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</p>
+
                <span style="text-decoration: underline;"></span> We got to know many fellow iGEMers from all over Europe
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</div>
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            </div>
  
  
  
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<div class="clear extra_space"></div>
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            <hr id="collabs">
 +
            <h2>Collaborations for our laboratory work</h2>
 +
            <h3>Genomic DNA of cultured <span style="font-style: italic">Plasmodia</span></h3>
 +
            <div>
 +
                Our primers were first established with synthetic DNA templates. Apart from that we urged to figure out if our primers work for the detection of real <span style="font-style: italic;">Plasmodium</span> DNA. We did not want to work with the parasite itself to exclude the risk of infection. This is why we reached out to laboratories who work with cultured <span style="font-style: italic;">Plasmodium</span> who could provide us extracted DNA that we could use for our experiments. This led to collaborations with the Center of Infectiology and Parasitology in Heidelberg (AG Portugal) and the Institute of Tropical Medicine, University of Tuebingen (AG Kreidenweiss) who provided us genomic DNA of their cultured <span style="font-style: italic;">Plasmodium</span> strains.
 +
            </div>
  
  
  
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<div class="column full_size">
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        </div>
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<h3>Best Integrated Human Practices Special Prize</h3>
+
  
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<p>To compete for the Best Integrated Human Practices prize, please describe your work on this page and also fill out the description on the judging form. </p>
 
  
−
<p>How does your project affect society and how does society influence the direction of your project? How might ethical considerations and stakeholder input guide your project purpose and design and the experiments you conduct in the lab? How does this feedback enter into the process of your work all through the iGEM competition? Document a thoughtful and creative approach to exploring these questions and how your project evolved in the process to compete for this award!</p>
 
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<p>You must also delete the message box on the top of this page to be eligible for this prize.</p>
 
  
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</div>
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</html>

Latest revision as of 15:41, 17 October 2018

Workshops

iGEM Lecture Series

As a part of our project we actively contribute to our universitie’s teaching program by organizing a lecture series followed by an open discussion on specialized topics related to our project. Until now, we had talks on Norovirus, Malaria and Primer and Probe Design. Currently we are preparing the next talks for the following semester.

Our first lecture was held by our PI Prof. Dr. Jochen Bodem. As a professor of virology, he delivered interesting insights into the molecular biology of Norovirus. We discussed the mechanisms how the virus is infiltrating the human cells, its replication and the damage caused by an infection leading to the typical symptoms of a gastrointestinal disease.

Prof. Dr. Christian Janzen, an expert on protozoan parasites especially Trypanosoma, gave a fascinating talk on Malaria. He started with some basic facts about the historic background and the worldwide incidences of the disease followed by details about the biochemistry of plasmodium, the different subtypes of the pathogen and the varying characteristics and symptoms of Malaria. Furthermore, we discussed current methods to diagnose and treat Malaria.

For a talk on primer and probe design we invited experts from the company Thermo Scientific to our university. The lecture focused on the design of a probe-based assay for pathogens and how to achieve reliable and accurate results in qPCR experiments. Starting with an introduction to qPCR we also discussed the process of assay validation as well as potential pitfalls regarding primer and probe design.

By initiating our iGEM lecture series, we want to reach out to interested people from Würzburg and students of all faculties, draw attention to the topic of infectious and tropical diseases. Furthermore, we are able to introduce the iGEM competition and our research project to a lager audience, thereby attracting new members for our team. In the future we will further enrich the curriculum for many students by inviting speakers from the field of synthetic biology. We hope to have a conversation about the amazing possibilities but also the practical and ethical limits of biological engineering.

Outlook

Since we are the first team of our university to participate in the iGEM competition, lot of effort has still to be invested to create a favourable environment and a close, far-reaching network for the iGEM initiative to grow and to expand at Wuerzburg. We will further intensify our relations to different faculties and institutes to conduct interdisciplinary research.

We have already published an article in an internal journal at our university, called “Einblick”. The next step to push our project forward and to gain local support is presenting our results to the public at our home town by newspaper articles and a discussion Forum. Our “Cake and Science” cake sale in the university hospital is our first step to reach out to the inhabitants of our city. Furthermore, we will present our research to biomedical students from all over Germany at the 13th Biomedical Students` Symposium in November.
fehlt

Education

Cake and science

Wondering about how we could bring our project in mind of people from our city who we wouldn’t meet at the university, we came up with a rather unusual idea: Why not have a piece of cake with people while introducing them to our project? We organized two cake sales at the facilities of the university hospital in Wuerzburg. We were able to present our project to the public and we also gained some revenue selling the cakes.

People were attracted by our poster we had brought with us. Not only doctors were curious, but also the staff, visitors and the patients were asking questions about our work. Enlightening conversations about the development of diagnostic tests while eating a lovely piece of self-made cake created a less common, more extraordinary atmosphere, which was pleasant for our visitors and for ourselves. For the insatiable curious people, we provided handouts for further reading.
fehlt

Lab intern pipetting test

The iGEM intern pipetting workshop was designed to provide first semester students an introduction to standard pipetting techniques. Also, the more experienced students were given an excellent opportunity to pass on their knowledge to younger students.

Taking part in the lab intern pipetting test also trained the participants in precise pipetting, which was a big advantage for the students of the wet lab team when they started their work in the lab later.

Protocol Bradfort protein assay

Bradford solution
Dilute Bradford solution 1:5 with water. Use for one 96 well plate 12 ml water and 3 ml Bradford solution.
BSA solution
Dilute BSA solution 1:20 with water. Use 11µl BSA and 209 µl water for one 96 well plate.
Assay
Transfer 100µl Bradford solution and 2µl BSA solution in each well. Mix the solution well and destroy all airbubbles with a pipette tip.
Measurement
Measure absorption of the 96 well plate with a photometer at 580nm.

To pass the pipetting test the error rate of two following rows in a 96 microwell plate had to be less than 6 %. If a student met this criterium, we decided by this calculation:
1. average for one row
2. deviation average – a single well plate (for every well plate in a row)
3. result of 2. / average for one row * 100

Establishing an iGEM-Team

The beginning of our project

During a regular seminar of virology, we discussed about different possibilities to engage into scientific research as soon as possible. Annabel and Nicole came up with the idea to participate in the iGEM competition. We were motivated by the outlook to conduct our own research project with all tasks and responsibilities but with close supervision by experienced researchers. Mostly we were eager to gain experience working in the lab.

After collecting more information about the competition online and from other participants, we decided to bring iGEM to Wuerzburg and founded the first team of our university. Together with two additional bachelor students we motivated Prof. Jochen Bodem to become our PI. He also provided us with lab space to get started with the lab work. By advertising our project among friends, we soon got more and more students, until we were a huge group of 50 participants.

After various brainstorming sessions we decided to start exploring new methods in the detection of infectious diseases. This led us to our project, designing a rapid diagnostic test to distinguish different types of Plasmodium, the pathogen which causes Malaria.

Organizing the team in different subgroups meant that every student could contribute to the topic they liked the most. Unfortunately, many students did not spend as much time and passion on our project as necessary, so our team shrank to the final number of eleven student members and three advisors. Our final team consists of an interdisciplinary synergy of bachelor students from biology, biomedicine, medicine and mathematics.
fehlt The Beginning of our project

German Meetup in Marburg

As a newly established team we were excited to get in contact with the other teams at the German meetup in Marburg. Especially, we exchanged some ideas about the different projects and talked about problems we had to face in the wet lab. This exchange of experience resulted in a huge benefit for our project in the following weeks.

We were introduced to team Marburg’s project for the first time. Later we established a collaboration with team Marburg by participating in their Vibrio natriegens InterLab Study. Moreover, we learned much more about the iGEM competition itself and got contacts to students more familiar to the iGEM competition who provided us with advice later on.

European Meetup in Munich

In July we attended the European Meetup in Munich. It was a great experience to get in touch with so many teams. For the first time we presented our poster to a greater audience and were excited by all the positive comments and helpful advice we received. We are thankful for the opportunity to get an insight into the other amazing projects. Not only did we get to hear stunning talks about synthetic biology in current science issues, but we also received important information by attending many workshops. In the end we left a bit wistfully, but we also took home so many amazing impressions.
fehlt Exploring Munich with team Bielefeld photo by team Bielefeld
fehlt Presenting our poster for the first time
fehlt We got to know many fellow iGEMers from all over Europe

Collaborations for our laboratory work

Genomic DNA of cultured Plasmodia

Our primers were first established with synthetic DNA templates. Apart from that we urged to figure out if our primers work for the detection of real Plasmodium DNA. We did not want to work with the parasite itself to exclude the risk of infection. This is why we reached out to laboratories who work with cultured Plasmodium who could provide us extracted DNA that we could use for our experiments. This led to collaborations with the Center of Infectiology and Parasitology in Heidelberg (AG Portugal) and the Institute of Tropical Medicine, University of Tuebingen (AG Kreidenweiss) who provided us genomic DNA of their cultured Plasmodium strains.