Team:JMU Wuerzburg/Human Practices
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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.
Exploring Munich with team Bielefeld photo by team Bielefeld
Presenting our poster for the first time
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.