Team:TU Darmstadt/Attributions
Starting this iGEM year we didn’t know that it would not be a normal iGEM year. Due to the COVID-19 pandemic we could not go to the lab and were not able to hold regular team meetings in person. Even though every year different problems arose, this year they were different and the team had to manage not only a special situation for iGEM but also had to deal with many new aspects in their regular lives. Despite many bad news we managed to have a great year and design a great project. This would not have been possible without many great people that helped us and supported us in every situation.
We want to use this opportunity to thank all these lovely people.
We want to use this opportunity to thank all these lovely people.
First of all there would be no iGEM at the Technical University of Darmstadt (TU Darmstadt) without Prof. Dr. Heribert Warzecha. We want to thank him for being our primary PI and for supporting us. Even during our struggles, he explained that if we wanted to participate in iGEM without much lab time, he would support us in every way possible. Also, we want to thank the whole working group of Prof. Dr. Heribert Warzecha for helping us. Especially when we were not allowed to go to the university they looked out for our packages at the central post station and answered all our questions. A special thank you goes to Simone Bartl-Zimmermann for having our backs, taking care of our letters and opening up important packages. Additionally, we want to thank Barbara Wolf for helping us with everything regarding sponsoring. Dr. Melanie Mikosch-Wersching also helped helped us with the correction of our sponsoring letters.
We want thank Prof. Dr. Johannes Kabisch for helping us with all questions regarding Bacillus subtilis (B. subtilis) and providing us information, protocols and strains and of course for being our secondary PI.
From the beginning until the end of this iGEM year we got helpful advice and feedback from our instructors. For helping us deal with this special situation, holding workshops about lab methods, the BioBrick system and SnapGene, helping with criticism and inspiring ideas we want to thank Sebastian Barthel, Alexander Gräwe, Leon Kraus and Maximilian Zander. Regarding the modeling part of our project, Fran Bacic Toplek has really helped us a lot with his experience from last year.
We want thank Prof. Dr. Johannes Kabisch for helping us with all questions regarding Bacillus subtilis (B. subtilis) and providing us information, protocols and strains and of course for being our secondary PI.
From the beginning until the end of this iGEM year we got helpful advice and feedback from our instructors. For helping us deal with this special situation, holding workshops about lab methods, the BioBrick system and SnapGene, helping with criticism and inspiring ideas we want to thank Sebastian Barthel, Alexander Gräwe, Leon Kraus and Maximilian Zander. Regarding the modeling part of our project, Fran Bacic Toplek has really helped us a lot with his experience from last year.
University
The staff of the TU Darmstadt was always here to help us and share their knowledge with us. We want to thank the working group of Prof. Dr. Johannes Kabisch for providing us with information about B. subtilis, plasmids and also protocols. Especially Peter Gockel helped us a lot with the plasmid design for B. subtilis. Additionally, we were able to use their laboratory to perform an assay with our flow chamber. For the media used in this assay PD Dr. Arnulf Kletzin provided us with some required substances and answered our questions. Marianna Karava and Benedict Spannenkrebs from the working group of Prof. Dr. Johannes Kabisch helped us to perfom the assay in the lab. Additionally Marianna Karava gave use useful input for the implementation of our kill switch in B. subtilis.
Prof. Dr. Viktor Stein answered our questions regarding the mutagenesis of EreB and mutagenesis strategies in general. We would also like to thank Dr. Agata Staniek for correcting several texts in English spelling, grammar and language. For the theoretical planning of the AFM (atomic force microscopy) measurement and offering us the possibility to perform the experiments in his laboratory, we want to thank Dr. Christian Dietz. Unfortunately we could not accept the offer due to the COVID-19 pandemic. Additionally, we would like to thank PD Dr. Stefan Immel and Prof. Dr. Boris Schmidt for answering our questions regarding the laccase assays. Also Prof. Dr. Boris Schmidt provided us information about our toxicity assay with Vibrio fischeri and offered us to perform the experiments in his laboratory with their cultures. Even though this was not possible due to the COVID-19 pandemic, we want to thank them for this offer.
Prof. Dr. Susanne Lackner from the TU Darmstadt, IWAR – Department of Wastewater Engineering, told us about her own project for wastewater treatment using laccases. She also showed us carrier for the biofilm, to apply it in wastewater treatment plants.
The talks with Prof. Dr. Nico van der Vegt and Angelina Folberth from the working group of Prof. Dr. Nico van der Vegt were very helpful for our Modeling, where they answered our questions to the molecular dynamic simulations and the need of copper ions for our enzymes.
We would like to thank Prof. Dr. Torsten Waldminghaus for giving us feedback in regard to our first podcast episode and also helping us with our kill switch design. To discuss our project ethically we talked with Prof. Dr. Andreas Jürgens from the ethics commitee at the TU Darmstadt and with Prof. Dr. Alfred Nordmann from the department of philosophy. They told us how to evaluate a project ethically and which considerations have to be made in order to design a responsible project.
Also, many professors (and staff) from the faculty of biology and chemistry came to our presentations. Their input was very helpful to reveal problems in our project design and they also provided advice to solve these problems.
Prof. Dr. Viktor Stein answered our questions regarding the mutagenesis of EreB and mutagenesis strategies in general. We would also like to thank Dr. Agata Staniek for correcting several texts in English spelling, grammar and language. For the theoretical planning of the AFM (atomic force microscopy) measurement and offering us the possibility to perform the experiments in his laboratory, we want to thank Dr. Christian Dietz. Unfortunately we could not accept the offer due to the COVID-19 pandemic. Additionally, we would like to thank PD Dr. Stefan Immel and Prof. Dr. Boris Schmidt for answering our questions regarding the laccase assays. Also Prof. Dr. Boris Schmidt provided us information about our toxicity assay with Vibrio fischeri and offered us to perform the experiments in his laboratory with their cultures. Even though this was not possible due to the COVID-19 pandemic, we want to thank them for this offer.
Prof. Dr. Susanne Lackner from the TU Darmstadt, IWAR – Department of Wastewater Engineering, told us about her own project for wastewater treatment using laccases. She also showed us carrier for the biofilm, to apply it in wastewater treatment plants.
The talks with Prof. Dr. Nico van der Vegt and Angelina Folberth from the working group of Prof. Dr. Nico van der Vegt were very helpful for our Modeling, where they answered our questions to the molecular dynamic simulations and the need of copper ions for our enzymes.
We would like to thank Prof. Dr. Torsten Waldminghaus for giving us feedback in regard to our first podcast episode and also helping us with our kill switch design. To discuss our project ethically we talked with Prof. Dr. Andreas Jürgens from the ethics commitee at the TU Darmstadt and with Prof. Dr. Alfred Nordmann from the department of philosophy. They told us how to evaluate a project ethically and which considerations have to be made in order to design a responsible project.
Also, many professors (and staff) from the faculty of biology and chemistry came to our presentations. Their input was very helpful to reveal problems in our project design and they also provided advice to solve these problems.
Experts
Our project includes a lot of topics and methods for which we found experts. Talking to them resulted in very helpful feedback and advice. The inclusion of this generated output, formed our project, and helped us to improve our methods and designs. The feedback received also helped us to adapt our project to the needs of the stakeholders. Therefore, we would like to thank everyone who discussed our project with us and gave us helpful feedback. For more information about the information we gained through talking to experts, please refer to our Integrated Human Practices.
Dipl. Ing. Udo Bäuerle, a civil engineer from Ellwangen, who helped design and plan many sewage treatment plants, helped us to get into the topic of wastewater treatment. He explained us the most important steps of the sewage treatment plant and told us about floating bodies, as Prof. Dr. Susanne Lackner had done before. We also spoke to stakeholders like Thomas Seeger, working in the management of the Weiterstadt sewage treatment plant. He was available to answer various questions and offered us to get a sample of activated sludge. Additionally, Florian Heyn, the manager of the wastewater treatment plant Alzenau, was available to answer our questions as a possible user of our biofilm. Furthermore, we visited the wastewater treatment plant in Darmstadt and were also able to record some scenes for our project promotion video. We would like to thank Wolfgang John from the Entega Abwasserreinigung (wastewater treatment) GmbH & Co KG at Darmstadt for having us. All of these talks helped us to adapt our project to the needs of the stakeholders and make a use in real live even more realistic.
To get to know more about the environmental problem we want to solve, we talked with an expert in aquatic ecotoxicology. Prof. Dr. Jörg Oehlmann from the Institute for Ecology, Evolution and Diversity from the Goethe University Frankfurt explained the effects of various micropollutants to the environment and contributed ideas for our project. For example, he told us that a floating body made out of plastic would be not the best idea because of the microplastic pollution.
Additionally, Dr. Patrick Schröder from the General Environment Agency in Germany told us about many problematic pollutants in wastewater and explained the right handling of drugs.
Since the problem was clear, we got help in designing our project by many experts from the university (see above) and also from external experts. Our friends from Kaiserslautern talked to Dr. Dietmar Schlosser, group leader of environmental mycology at the Helmholtz Centre for environmental research in Leipzig. He answered questions about laccases and told us what the optimal copper concentration is. In addition, Dr. Sabine Sané from the University Freiburg informed us about laccases since she also uses them for the purification of wastewater. She told us the optimum pH range for the laccase and answered questions regarding the ABTS-assay. This interview was also conducted from Kaiserslautern.
Regarding the use of B. subtilis, Prof. Dr. Jörg Stülke from the University Göttingen has been very helpful. He provided us with a B. subtilis strain where tasA and sinR are knocked out and looked at our protocols for the handling and experimental details regarding B. subtilis. We have been confirmed in the idea to use TasA for the enzyme immobilization by PhD Yunrong Chai. He is assistant professor at the College of Science at the Northeastern University in Boston and an expert in microbial genomics and biofilm formation. Furthermore, he told us that the knockout of sinR and σF would be good to prevent sporulation.
Besides the design, it is very important to have a closer look at the project from an ethical point of view. Therefore, we received help from experts form the university (see above), but also from Prof. Dr. Sibylle Gaisser from the University Ansbach, who answered our questions about the ethical aspects of our project. These contributions helped us to take a closer look at our project regarding ethical aspects and to think about important safety and security aspects.
Dr. Ulrich Ehlers, Federal Office for Consumer Protection and Food Safety (BVL) explained to us, which regulations we have to consider, when we want to implement our project in wastewater treatment plants and how to deal with these regulations. Through Prof. Dr. Ralf Möller we became aware of another possible implementation of our project beside wastewater treatment plants: we could use our biofilm in space travel.
Dipl. Ing. Udo Bäuerle, a civil engineer from Ellwangen, who helped design and plan many sewage treatment plants, helped us to get into the topic of wastewater treatment. He explained us the most important steps of the sewage treatment plant and told us about floating bodies, as Prof. Dr. Susanne Lackner had done before. We also spoke to stakeholders like Thomas Seeger, working in the management of the Weiterstadt sewage treatment plant. He was available to answer various questions and offered us to get a sample of activated sludge. Additionally, Florian Heyn, the manager of the wastewater treatment plant Alzenau, was available to answer our questions as a possible user of our biofilm. Furthermore, we visited the wastewater treatment plant in Darmstadt and were also able to record some scenes for our project promotion video. We would like to thank Wolfgang John from the Entega Abwasserreinigung (wastewater treatment) GmbH & Co KG at Darmstadt for having us. All of these talks helped us to adapt our project to the needs of the stakeholders and make a use in real live even more realistic.
To get to know more about the environmental problem we want to solve, we talked with an expert in aquatic ecotoxicology. Prof. Dr. Jörg Oehlmann from the Institute for Ecology, Evolution and Diversity from the Goethe University Frankfurt explained the effects of various micropollutants to the environment and contributed ideas for our project. For example, he told us that a floating body made out of plastic would be not the best idea because of the microplastic pollution.
Additionally, Dr. Patrick Schröder from the General Environment Agency in Germany told us about many problematic pollutants in wastewater and explained the right handling of drugs.
Since the problem was clear, we got help in designing our project by many experts from the university (see above) and also from external experts. Our friends from Kaiserslautern talked to Dr. Dietmar Schlosser, group leader of environmental mycology at the Helmholtz Centre for environmental research in Leipzig. He answered questions about laccases and told us what the optimal copper concentration is. In addition, Dr. Sabine Sané from the University Freiburg informed us about laccases since she also uses them for the purification of wastewater. She told us the optimum pH range for the laccase and answered questions regarding the ABTS-assay. This interview was also conducted from Kaiserslautern.
Regarding the use of B. subtilis, Prof. Dr. Jörg Stülke from the University Göttingen has been very helpful. He provided us with a B. subtilis strain where tasA and sinR are knocked out and looked at our protocols for the handling and experimental details regarding B. subtilis. We have been confirmed in the idea to use TasA for the enzyme immobilization by PhD Yunrong Chai. He is assistant professor at the College of Science at the Northeastern University in Boston and an expert in microbial genomics and biofilm formation. Furthermore, he told us that the knockout of sinR and σF would be good to prevent sporulation.
Besides the design, it is very important to have a closer look at the project from an ethical point of view. Therefore, we received help from experts form the university (see above), but also from Prof. Dr. Sibylle Gaisser from the University Ansbach, who answered our questions about the ethical aspects of our project. These contributions helped us to take a closer look at our project regarding ethical aspects and to think about important safety and security aspects.
Dr. Ulrich Ehlers, Federal Office for Consumer Protection and Food Safety (BVL) explained to us, which regulations we have to consider, when we want to implement our project in wastewater treatment plants and how to deal with these regulations. Through Prof. Dr. Ralf Möller we became aware of another possible implementation of our project beside wastewater treatment plants: we could use our biofilm in space travel.
Former iGEMers
As every year, many former iGEMers were interested in the progress of our project. They provided us with information and shared their knowledge from previous years. Sometimes they joined our team meetings or helped our student leaders regarding organization aspects. Therefore, we would like to thank Jonathan Funk, Jamina Gerhardus, and Peter Gockel. Bea Marie Spiekermann, Christian Sürder and Leon Werner held presentation trainings for the team and gave us feedback on our final presentation. Christian Sürder also supported Rosi Krebs and Max Schäfer with the project monitoring.
For giving instructions regarding the programming of the wiki and the TU Darmstadt website we want to thank Marius Wollrab. Fran Bacic Toplek and Benjamin Mayer took care of our server. Hannah Rainer helped us with the planning of the podcast and took part in two episodes. Furthermore, Klara Eisenhauer, Jonathan Funk, Jamina Gerhardus, Peter Gockel, Thea Lotz, Jean Victor Orth, Hannah Rainer, Bea Marie Spiekermann, Lara Steinel and Leon Werner came to our presentations and gave us feedback for the improvement of our project and to our performance of presenting our project.
Many people helped with the proof reading of our wiki texts. For this we want to thank Klara Eisenhauer, Jonathan Funk, Jamina Gerhardus, Peter Gockel, Robin Johannson, Thea Lotz, Tim Maier, Hannah Rainer, Bea Marie Spiekermann, Lara Steinel and Leon Werner.
For giving instructions regarding the programming of the wiki and the TU Darmstadt website we want to thank Marius Wollrab. Fran Bacic Toplek and Benjamin Mayer took care of our server. Hannah Rainer helped us with the planning of the podcast and took part in two episodes. Furthermore, Klara Eisenhauer, Jonathan Funk, Jamina Gerhardus, Peter Gockel, Thea Lotz, Jean Victor Orth, Hannah Rainer, Bea Marie Spiekermann, Lara Steinel and Leon Werner came to our presentations and gave us feedback for the improvement of our project and to our performance of presenting our project.
Many people helped with the proof reading of our wiki texts. For this we want to thank Klara Eisenhauer, Jonathan Funk, Jamina Gerhardus, Peter Gockel, Robin Johannson, Thea Lotz, Tim Maier, Hannah Rainer, Bea Marie Spiekermann, Lara Steinel and Leon Werner.
Others
We received further help from some other people. We would like to thank Jörg Kalkowski for taking our pictures. Aleksa Zecevic did the programming of the videogame we designed for reaching out to younger people. We also had help for our technical requirements. We want to thank Dipl.-Soz. Felix Heinemann from the HDA of the TU Darmstadt for providing us with a microphone and the webteam of the TU Darmstadt, especially Tobias Thalmann, for helping with the release of our podcast. For additional advice on how to produce and upload a podcast we want to thank the people from “Krautnah”. Also we want to thank Alba Stabile for recording our presentation video and showing us how to edit the video. Last but not least, David Adamson lent us equipment for the video shoot, like a green screen and lights.