Model | TeamFreiburg:chAMBER

We, the iGEM-team Freiburg, would like to thank everyone for all the support we have received, big and small. For giving us the confidence to carry out our own research project, allowing us to work independently and to go beyond our limits . For accompanying us on this path with great advice and help of a financial, material, and mental nature. For standing by us from the beginning of our project with the first brainstorming sessions at the end of February 2022, to going to the lab and conducting experiments since the end of May, to the last minute at the Giant Jamboree.
In the following, we turn the spotlight on our external supporters, our supervisors, and our sponsors, without whom the project would not be possible. And we highlight, what each individual of our team excelled in.

Acknowledgements for help from outside the team
Acknowledgements
for help from outside
the team

Supervisors-Attribution
Supervisors-
Attribution

Team-Attribution

Sponsors

Acknowledgements for help from outside the team

Prof. Dr. Cheryl Kerfeld and the Kerfeld Lab, for providing us their bacterial microcompartment plasmids to work with and also to allow us to forward them to the iGEM registry. Their support expanded our toolbox for compartmentalisation.
Prof. Dr. Anthony Forster, for giving us an interview on the topics of research integrity and noncanonical amino-acids.
PD Dr. Joachim Boldt, for giving us an interview on the topic of research integrity with focus on ethics.
Dr. Chris van der Does, for giving us an interview on the topic of research integrity with focus on education.
Prof. Dr. Sonja-Verena Albers, for giving us an interview on the topic of research integrity with focus on detection and prevention of fake science at universities.
Piyush Gupta, for the public relations support of our project through inviting us to and performing an interview session.
Michele Garfinkel, for collaborating with us in our online workshop on "research integrity" for iGEM participants and giving a talk there.
Michal Rössler, for advice on how to present the video in the most comprehensible way possible.
Prof. Dr. Sonja-Verena Albers and Albers Lab, for sharing their plate reader and lab materials like plates with us when we were in need.
Prof. Dr. Barbara Di Ventura and Di Ventura Lab, especially Junsheng Liang and Büşra Merve Kırpat , for providing plasmids and bacteria and helping us with the fluorescence microscopy.
Dr. Nicole Gensch and Dr. Pavel Salavei from the Core Facility Signalling Factory & Robotics, for providing plasmids and all other kind of lab stuff. They always had an open door for us and helped where they could at any time.
Prof. Dr. Maja Köhn and Köhn Lab, for sharing their incubators with us.
Nico Höfflin, for performing NMR and HPLC-followed mass spectrometry with us for the analysis of Indigo and Indirubin and guided us on how to evaluate the results from these experiments. And for being a chemical advisor in general for us whenever we needed.
Ingmar Bauckhage, for writing a script to automatically convert plate-reader output in an evaluating-able excel sheet, saving us time to do that by hand.
Dr. Mehmet Ali Öztürk, for his ongoing help and advice with our modelling.
Dr. Irina Siegel, for the supervision of our human-practises survey and giving essential insights for making it better.
Anne Joost and Gudrun Reber, for inviting us to the Fashion Days to present there our work and assisting in the preparation of our spot.
Owusu Künzel of DASDING, for the possibility to present our work to a broad audience virtually by interviewing us and making a short video clip for Instagram on that.
Ariel Lindner and the iGEM-team Paris Bettencourt, for providing us the TEARS-plasmid to work with.
Vitor Bernardes Pinheiro, for sharing his plasmids with compatible origins of replications. Eventually, we did not come to use them in our project, but nonetheless we thank him for sending them to us so quickly!
Prof. Oliver Einsle, for allowing us to use PyMOL on his computer.
Wolf Hermann Martin Wildpret, for sharing his computational power and enabling us to run molecular dynamics for longer times.
Enoch Boasiako Antwi and Daniel Weis, for very good tips on how to design primers.
Professor Dr. Oliver Schilling, Dr. rer. nat. Stefan Tholen, and Lina Goncharenko, for advising on the detection of non-canonical amino acids introduced into the proteins and the possibility of detecting our samples using mass spectrometry.
Max Mundt from Insempra/OriginBio for an interesting interview.
PD Dr. Erik Schleicher, for doing an interview with us about unnatural amino acids and how they use them in the lab.
Dr. Stefan Schiller, for doing an interview with us about unnatural amino acids and giving advice on how to work with them.
Dr. Anja Störiko, for contacting us and offering to publish our project in BIOspektrum.
Dr. Eric Young, for assistance with questions about the wiffle ball and plasmids.
Prof. Anthony C. Forster, for giving us an interview on the topics of research integrity and noncanonical amino acids.
The Reski Lab, for supplying us with necessary lab equipment to start our lab work.
Dr. Marta Rodriguez-Franco, for doing EM with us and evaluating it.
AG Römer, especially Kai Stober, for using the SIM microscope with us.
Biorender, for giving us a premium account to create cool graphics.
iGEM Team Hamburg, for hosting the European Meetup.
Jannik Witte, for correcting the naming of the ncAAs.
Dr. Viviane Timmermann and Fabian Krause, for having a look in the last minutes at our failed pipeline and helping out with that bug.
Anne Zemella and the department of "Cell-Free and Cell-Based Bioproduction" at the Fraunhofer-Institute Potsdam, for providing us ncAAs we could start experimenting with while waiting on our deliveries.

Supervisor attributions

Prof. Dr. Barbara Di Ventura, Prof. for biological signalling research at the University of Freiburg / BIOSS

Barbara brought a lot of impulses to the project, but at the same time she was also a critical voice who questioned in the right places whether things were feasible in the way we imagined them. With her many years of experience, she was also a great help in interpreting unexpected results. She could also hand us over to experts from her lab and beyond when specific questions came up.

Dr. Nicole Gensch, Labmanager at the CIBBS

Nicole was always at hand. No matter whether the ligase ran out, the plasmid design stalled or something else went wrong. You could ask Nicole and Nicole helped you, both with materials and with her expertise around the lab. She was also a great help with the finances, had good tips for fundraising and knew the possibilities to save money when shopping materials.

Dr. Pavel Salavei, Postdoc in protein laboratory at the CIBSS

As an expert in protein purification, Pavel was able to provide us with many useful tips on how best to produce and quantify our substances (e.g Indigo, Trehalose, BMCs). He was also able to introduce us to the equipment needed for this, such as Plate Readers and FACs. Pavel was also enthusiastic in helping us with our first upscaling-trials! He provided us his bioreactor, assisted us in using it and also had a helping hand to dye fabric with our self-produced Indigo.

Paulina Kaas, M.Sc. Mol.Medicine student at the University of Freiburg

Since Paulina used to participate in iGEM herself, she had useful tips about what to pay special attention to in this competition. Especially in improving and creating BioBricks, she was able to give important advice on what is required of them and how to submit and register. She was also a diligent reader of our wiki and other public texts and gave helpful feedback on how to phrase them better.

Team attributions

Everyone in our team has put a lot of time, energy, and effort into our project this summer.
And it has been worth it! We gathered much experience and had a lot of fun. And we can be proud what we achieved in one summer with our project chAMBER!
Many aspects of the project involved the whole team. The most important are:

Brainstorming to find and flesh out the project topic at the beginning
Researching literature on the topic
Making sure safety rules were followed
Participating in lab maintenance (preparing plates, media, pipette tips, cleaning, etc.)
Writing texts for the wiki

For the wet lab, we divided ourselves into three subgroups (Pathways, Compartments, ncAAs), each of which organised itself. In weekly full team meetings, we informed each other about the news of the subgroups. Each subgroup planned their experiments, conducted and evaluated them and wrote/visualised their results independently. But of course, we also helped each other between the subgroups :)
In addition, some team members did extra work for the project. These additional efforts, as well as subgroup affiliation are listed below as bullet points for each team member.

Nikita Edel, B.Sc. Biology student