| iGEM Freiburg 2022 presents chAMBER
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Achievements

The iGEM experience was truly unforgettable for us! We learnt a lot, from how to come up with a project idea, how to perform experiments including the appropriate controls, to how to interpret our data, and even how to ask for help to the right people.

In the end we were rewarded for our efforts and the quality of our project as

the prize we won in the iGEM competetition 2022: best foundational advance project

the best foundational advance project 2022

and received a

gold-medal

Here a list of our most important achievements:

  • We were able to show the formation of the full and minimal wiffleballs in E. coli cells via transmission electron microscopy;
  • We could show recruitment of proteins to the wiffleballs using fluorescence microscopy;
  • We demonstrated the formation of the peptide bond between the T1 protein of the wiffleball and the cargo (mVenus2, mTurquoise2, XiaI and TnaA) via Western Blotting;
  • We showed the formation of encapsulins in living E. coli cells via fluorescence microscopy;
  • We showed the formation of SPD-5 liquid droplets in living E. coli cells via fluorescence microscopy;
  • We created the chAMBER toolbox, consisting of several biobricks that future iGEM teams can use to localize their proteins of interest in their compartment of choice;
  • We successfully incorporated two different ncAAs into sfGFP;
  • We created a collection with sfGFP mutants that can be used by future iGEM teams to detect incorporation of ncAAs;
  • We successfully incorporated two different ncAAs into the T1 and H proteins of the wiffleball;
  • We created a database and software, inCLUSIVE, that will make working with ncAAs easier for future iGEM teams;
  • We performed computational analyses showing that mutations could lead to the enlargement or shrinkage of the pore size of the wiffleball;
  • We successfully produced trehalose in E. coli cells;
  • We successfully produced indigo in E. coli cells;
  • We successfully produced indirubin in E. coli cells;
  • We investigated the effect of genome-reduction on the formation of compartments, ncAA incorporation and bioproduction;
  • We showed that more indigo and indirubin is produced when two of the enzymes in the pathway are localized into the wiffleballs.
  • We scaled-up production of indigo using medium-scale bioreactors.

Beyond the scientific results, we:

  • Arose awareness on scientific integrity and good scientific practice with a workshop co-organized with the EMBO publishing group and a survey;
  • Wrote a guideline for good scientific practice for future iGEM teams;
  • Explained synthetic biology in general and our project in particular to society through various initiatives (interviews with radio station, participation to the Fashion Days in Freiburg).

Bronze

bronze-medal
  • We completed all the competition deliverables.
  • We wrote an attributions page, where we clearly indicated everything that was not performed by us students. We clearly acknowledged all the people that helped us with our project on this page.
  • We wrote a description and inspiration for our project.
  • We contributed to iGEM in many ways: 1) by developing a guideline for future teams on how to tackle science integrity during their project; 2) by developing a database and a software (INCLUSIVE) that will facilitate working with ncAAs by future iGEM teams; 3) by creating the chAMBER toolbox, which will allow future iGEM teams to localize their protein(s) of interest in their compartment of choice; 4) by creating a collection of biobricks based on mutated sfGFP that future iGEM teams can use to test incorporation of ncAAs.

Silver

silver-medal
  • We went through several iterations of the engineering design cycle for multiple parts of our project, carefully described on the engineering success site for one case. On the judging form, we also gave another example;
  • We collaborated with several iGEM teams: iGEM Cambridge, Aachen, Münster and Edinburgh-UHAS_Ghana and hosted a workshop for fellow iGEM teams.
  • We discussed our project with the lay public and assessed their opinion on using GMOs to produce goods such as indigo.
  • Despite being mostly a foundational advance, we also have applications in our project with important societal impact. Therefore, we considered what we would have to do to apply our project in the the real-world and summarized our considerations on the proposed implementation site.

Gold

gold-medal
  • We engaged with specialists, professors and group leaders on science integrity and conducted a thorough survey on the topic to improve our project's good scientific practice. We also integrated into our project the feedback obtained by industrial leaders and by all the participants of our survey, which helped us shape and design our wiki;
  • We improved the existing BioBrick Bba_9832475 by adding the SpyCatcher to it, which now allows for the recruitment of proteins into the SPD-5 liquid droplets in E. coli;
  • We performed thorough modelling on wiffleball pore size and its possible effect on cargo import and export. We also collaborated with Cambridge on modelling bacterial growth with ODEs;
  • We conducted proof of concept experiments showing the functionality of our whole chAMBER system;
  • Throughout our project, we extensively collaborated with iGEM teams UNILausanne and Chalmers-Gothenburg by running their blog together, as we translated all their website pages and blog posts into German;
  • We engaged in many forms of education of the public, using the platforms of science communicators, talking to the broad public at the Freiburg fashion days and hosting the EMBO workshop.