Team:Heidelberg/Attributions


Attributions





Project Attributions

Principal Investigator

The head of our project is our PI Prof. Dr. Stefan Wölfl who supports us during the implementation of the project and is always available with advice and encouragement. He organized all bureaucratic challenges reagarding the iGEM competition.

Advisors

Lucas Arnoldt, a first-year master student in Molecular Biotechnology, was one of our advisors. He supported us when we had a problem with our code. Also, he supervised the development of our logistic regression and the interpretability maeasures as well as the graph neural network.

Fabian Bradic, a last-year bachelor student in Molecular Biotechnology, was one of our advisors. Whenever we had a problem with our code we asked Fabian. He supported us in the development of our logistic regression, the graph neural network and the modeling of our results in the wetlab.

Faculty Support

Saskia Schmitteckert supported us by learning the basic techniques for working with bacterial cultures like streaking out, making competent bacteria or with heat shock protocols.

Dr. Suzan Can was postdoc and our contact to the working group of Prof. Dr. Wölfl. She gave us safety instructions to the laboratories and machines like plate reader or Nanodrop. Additionally, she helped us with ordering new lab material and discussing results.

Christiane Graffy gave us the centrifuge instructions and helped us with all problems that arise in the laboratory regarding the machines.

Consults

Wetlab

Prof. Dr. med Stefan Kölker is the head of section neuropediatrics and metabolic medicine at the university hospital of Heidelberg. He has agreed to talk with us about metabolic single-gene diseases like phenylketonuria, that are included in the German newborn screening as well. THis ointerview helped to broaden our horizon to integrate our treatment idea for other microbiome diseases.

Xinglin Jiang, PhD is postdoc at the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark. He is an expert for natural transformation. We had an online meeting early in the year in February to lay the project's foundation. He told us how to increase the natural transformation efficiency with transforming the DNA to a multicopy and linear DNA double strand. He supported us very friendly and later on answered our questions via email contact.

Keith Edward Jaggard Tyo, PhD was our second contact to a working group which had expertise in natural transformation with A. baylyi ADP1. He answered our question by email about the pBWB162 plasmid and its new origin of replication. With his help we performed the first successful natural transformation.

Dr. Rainer Beck was always available whenever we needed advice for the wetlab. He was motivated to answer quickly all our questions regarding for example, cloning methods. Furthermore, he provided plasmids we used especially in the beginning of the project.

Dr. Ilka Bischofs-Pfeifer was a great support for our project by providing the Bacillus subtilis 168 strain with integrated GFP (BIB1574). Additionally, she gave us insights in the Bacillus research about which cloning methods are more or less efficient and how the main cloning strategies are.

Dr. Holger Schäfer is a member of the IPMB which is responsible for the molecular biotechnology studies in Heidelberg. He helped us a lot by discussing the cloning method by changing the restriction enzyme frames of our insert. Additionally, he provided us with our first Bacillus subtilis DSM 10 strain.

Dr. Mila Leuthold is working in the IPMB and helped us with the protein detection methods SDS-PAGE and western blot as well as the suitable staining methods. She provided us access to the french press machine which was also needed for the AvPAL in vitro assay.

Jannik Berger was a iGEM Team member from Heidelberg 2020. He has an enormous knowledge about the software Geneious Prime 8, cloning strategies such as Golden Gate Cloning and was always available with helping in with questions that arise in the wetlab. Additionally, he helped us with the concepts for proof of concept versus proposed implementation text.

Education & Communication

Gisa Wilhelm is a trainee teacher for biology and sports. She helped us extensively with the preparation of the workshop, especially with regard to the level of difficulty and the structure. She gave us insights into the curriculum of biology lessons from the 7th to 10th class in our federal state Baden-Wüttenberg. She is a young and motivated teacher and supported us by trying to get a connection between school and university.

Dr. Dorothea Kaufmann gave us new insights into the world of online and distance learning universities. She was our student coordinator for the molecular biotechnology students and now works for the Fernuni Hagen. We met in an online meeting to discuss our workshop for schools and how to improve the interaction.

Sagithjan Surendra is the founder of the "Aelius Förderwerk" and gave us great advice for future workshops. We discussed state-of-the-art methods to get the attenstion of students in online workshops as well as meetups in presence. He has close contact to innovative startup companies who tried to establish virtual reality in schools or gaming associated learning. He gave us a completely different perspective on learning.

Drylab

Dr. Carl Hermann is a group leader of the DKFZ Heidelberg while also having been a lecturer for mathematics and informatics for the degree course molecular biotechnology for several years. He specialises in data evaluation, linear/logistic regression and building of GNNs and has also been working on data with Covid. He gave us detailed information on how much work each step would consist of, starting from data acquisition until the final models.

Dr. Georg Zeller leading a team at the EMBL Heidelberg and works on the contribution of the human microbiome to health health, disease progression and treatment success, which is essentially the topic of our project the only difference being that we chose a very specific topic which was phenylketonuria. He had a big impact foremost regarding the choice of our topic since he reassured us by saying that there are several big databases when working with the human microbiome e.g. HMP or MDB, just to name a few.

Prof. Dr. Robert Bruce Russell is currently employed as the vice-dean of the faculty of biosciences at the University of Heidelberg. His specialty lies in bioinformatics in general while having a special focus on proteins. While this was sadly not our project he possesses a vast knowledge in the bioinformatics field in general and gave us tips whether some of our ideas would be viable at all.

Team Members

Name Major Involved Helping
Elizaveta Bobkova Coordination Safety Expert Interview with Dr. Kölker, Safety and Security Science communication
Duc Thien Bui Coordination Drylab, Finances, Wiki Eurofins Article, Logistic Regression Model, MicrobioCOSMOS, Student Workshop, Sponsors communication, Wiki Human Practices, Science Communication
Michelle Emmert Coordination Design, Drylab, Human Practices BaWü Meetup, Expert interview Dr. Kaufmann and Sagithjan Surendra, Logo and Proposal Design, Promotion & Presentation Video, Student Workshop, Wiki Design Social Media
Franziska Gießler Human Practices, Wetlab, Science communication AvPAL Assay, β-Agarase Assay, Biospektrum Article, Co-culture, Eurofins Article, Expert Interview with Dr. Kölker, Natural Transformation, Primer Design, Registry documentation, Selective Advantage Finances
Jonathan Herth Wiki Capsule elaboration, Wiki design Wetlab
Silja Malkewitz Coordination Wetlab, Human Practices AvPAL Assay, Co-culture, Expert Interview with Dr. Kölker, Dr. Kaufmann and Sagithjan Surendra, MicrobioCOSMOS, MNase Assay, Natural Transformation, Primer Design, Registry, Risk assessment lecture, SCU Collaboration, Selective Advantage, Sponsors communication, Student workshop Finances
Kamil Moskal Science Comunication Biospektrum Article Drylab
Laura Sanchis Coordination Social Media, Design BfR Risk assessment lecture, MicrobioCOSMOS, MTU collaboration, Promotion Video, Social Media Science communication
Nick Wehrwein Finances BaWü Meetup, "Dietmar Hopp Metabolic Center" communication, MicrobioCOSMOS, Risk assessment lecture, Sponsors communication Wetlab
Helena Weinig Human Practices, Social Media Biospektrum Article, Logo and Proposal Design Wetlab
Marilena Wittmaack Human Practices, Wetlab AvPAL Assay, β-Agarase Assay, Co-culture, Expert Interview with Dr. Kölker, Model, Natural Transformation, Selective Advantage, Student Workshop, Wetlab Figures Design, Drylab