COLLABORATIONS

As the aim of our project is to construct a modular toolkit using co-cultures with three organism, we would have to conduct many experimental iterations to reach conclusive and reliable results. To avoid this tedious process, we, as many other scientists working in this field, turned our attention to computer based biological modeling to predict the behavior of our system.
In the realm of mathematical and computer based biology, scientist use algorithms, data structure and data visualization to create approximations of existing biological systems. This serves two important goals: One, to check whether the theoretical understanding of a process is correct. Of course, this can be done by constructing a model and checking if the cultures behave within reasonable correctness as the observations in the lab indicate.
The other goal of such modeling approach is to predict whether the behavior of the system is changed or other external influences are applied. This latter role is why we are using modeling in our project.
However, many of our team members lacked experience in this field. As such, we were happy to be offered the possibility of a collaboration with the iGEM team of Tec Monterrey. This team, unlike ours, is more knowledgable in modeling.
After we had a discussion with Professor Ebenhöh of the Institute of Quantitative and Theoretical Biology at our university, we agreed that we ask Team Tec Monterrey to provide us with a simple model to gain another perspective on our work.

The model they provided to us uses the following equations:

• $$d[A]/dt=c_A\ast <!--\; \ast \; -->[A]\ast <!--\; \ast \; -->i_A\ast <!--\; \ast \; -->(1-<!--\; -\; -->A/A_m)$$

Where [A] is the population of organism A, C_A is it’s consume constant, i_A is the Input resources available for A and A_m is the maximum sustainable population.

And:

• $$d[i_A]/dt=K_A[B]+K_A[C]-<!--\; -\; -->c_A\ast <!--\; \ast \; -->[A]\ast <!--\; \ast \; -->i_A\ast <!--\; \ast \; -->(1-<!--\; -\; -->A/A_m)$$

Where K_A[B] is the influence of organism B on the resource availability to A, K_A[C] the influence of organism C and the other variables are defined as above.

This is far more simple than our approach. It has however, also produced results that were useful to us. The model provided by Tec-Monterrey took a different approach to the concept of co-culture and it offered us new insights to our model. By allowing us to refocus our attention we were able to bring our own theoretical work to a point that is closer to reality than it had been previously.

We also collaborated with team Unesp Brasil, who also work with Quorum sensing. They characterised one of our quorum sensing plasmids and checked the amounts of acyl homoserine lactone to be added to achieve a certain amount of lysis. Moreover we also supplied them with n-3-oxohexanoyl-l-homoserine-lactone, a quorum sensing molecule that they required and were not able to synthesize themselves.
We were really happy to hear, that the AHL has helped them in characterising their system. It was able to induce at least one of their systems (Figure 1), showing that their iGEM project cannot only be used to test biological, but also chemical crosstalking. Moreover they also tested one of our construct, which we sent as well with the AHL molecule. They found out, that with concentrations of AHL from 0mM to 10^-4mM of AHL, barely a difference compared to the corresponding control was visible.This data is consistent with our findings, which show, that a minimum concentration of 0.05mM AHL was necessary to present a visual difference between the uninduced variant.
With this we did not only help a team to characterize a system, by supplying them with a missing molecule, but they also have supported us a lot, by confirming our achieved findings.

iGEM Manchester is working on characterisation of different promoters this year. They are creating an assembly of various promoters and asked us to add our promoter to their library. For this purpose we sent them the sequences of all of our synthesized promoters, mostly quorum sensing promoters, and therefore successfully achieved a further collaboration. We were really glad to have successfully collaborated with another team as well. Within already a few weeks, they have generated an optimised version of our promoter sequences, by once designing the promoter harbouring a decreased, and once an increased activity. They did so by running each sequences through an online algorithm which predicted the -10 and -35 sites of each promoter. Then they identified regions in our promoters that would benefit from a point substitution and recorded the likely change in activity associated with the sum of these changes via MatLab. Below you can find an overview with the optimised sequences. The parts that we sent and are optimised are signalized in yellow. In green are the sequences optimised for increased activity and in red are the sequences optimised for decreased activity.

Plux_oh_FB old
atcgGGTCTCGCGCTACTATTGTATCGCTGGGAATACAATTACTTAACATAAGCACCTGTAGGATCGTACAGGTTTACGCAAGAAAATGGTTTGTTATAGTCGAATATTACTCGAGACCatcg

Plux_oh_FB new
atcgGGTGTACCGCTACTATTGTATCGACCATATACCTAGAACTTAACATCAACTCATGTAGGATCGTACAGGTT TACGCAAGAAAATGGTTTGTTATAGTCGAATATTACTCGAGACCatcg
Relative increase = 426.25 miller units

atcgGGTAGTTTGCTACTATTGTATCGGTATCGCCATCCTTACTTAACATAGCCCCCGCAGTATCGTACAGGTT TACGCAAGAAAATGGTTTGTTATAGTCGAATATTACTCGAGACCatcg
Relative decrease = 162.07 miller units

Plas_oh_FB old
atcgGGTCTCTCGCTcctttccgaaacgaaacaagttggattttgcacctaccagaactggtagttctgacctgtggctatcttcgaaggcatcgatattatgcacattggaactcttcatgacataacgccgagTACTAGAGACCatcg

Plas_oh_FB new
atcgGGTCTCTCGCTcctttccgaaacgaaacaagttggattttgcacctaccagaACTGTACCTTCTGACCTGTCGCTACCATAAACCTAGACGATATTATGAACTTTGGAACACttcatgacataacgccgagTACTAGAGACCatcg
Relative increase = 197.61 miller units

atcgGGTCTCTCGCTcctttccgaaacgaaacaagttggattttgcacctaccagaACTAGTTTTTCTGACCTGTGGCTTTATCGCCATCCTTCGTTATTATG-GCCATGGAAGTCttcatgacataacgccgagTACTAGAGACCatcg
Relative decrease = 168.11 miller units

Postcards

As we all know iGEM is not only about experiments and labwork but also about bringing the topic “synthetic biology” closer to the public. In order to do so the previous iGEM teams of the Heinrich-Heine-University of Duesseldorf created a postcard exchange project to promote synthetic biology in public using self-designed postcards. Each year a bunch of iGEM teams decided to join which is why the campaign was a huge success with a lot of beautiful and funny postcards as a result.
Of course we wanted to continue this tradition as well. How does this postcard exchange work? Every participating team had to design a postcard which shows an image related to synthetic biology or their topic on the front and a small informational text on the back. Specific rules included:

• Image related to your project or (synthetic) biology in general on the front
• Small informational text on the back
• Standard postcard format (A6; 14,8cm x 10,5cm)

We reached a lot of iGEM Teams by showing off postcards from the previous years on Instagram and other social media accounts and were also the first ones to post on the Collaboration page of iGEM 2018. A lot of iGEM Teams responded who wanted to channel their inner creativity and design their own postcard about their project or synthetic biology in general. A few had to cancel last minute but in total we had 37 participating teams. In addition to that we also collaborated with iGEM TU Delft who introduced our postcard project on their Eurasian meetup in Shenzhen, China. A lot of iGEM Teams brought their postcards to the meet up.
The first postcards arrived on July 18 from iGEM Tiapei, Taiwan. From then on, every day we eagerly awaited for the mail to arrive and were often rewarded with packages containing new, beautiful postcards from all over the world. One time we had to go all the way to the custom service since one team forgot to declare their content. Another time we received an empty package without any postcards! Unfortunately the postcards had fallen out during shipment or delivery. But luckily (!!!) the team had some postcards left which they were able to send to us - and finally they arrived.

After we had received postcards from (mostly) every team, we started sorting them, glueing addresses on them and putting them into packages. Each participating team received one stack of postcards from other teams and another stack which included their own postcards with the addresses of the other teams.
Afterwards each team’s postcards were exchanged with other iGEM-teams so that every team received postcards from all over the world. The shared postcards were then shared with people in the neighborhood, during public events etc.

Have a look!

Marburg

Bielefeld-CeBiTec

TU Darmstadt

Bulgaria

Duesseldorf

Sorbonne U Paris

Leiden

Waterloo

Tec-CEM

TUDelft

Pasteur Paris

Tec-Chihuahua

Aachen

UPF-CRG Barcelona

Hamburg

Vilnius-Lithuania

TU-Eindhoven

AFCM-Egypt

Virginia

Tuebingen

MSU-Michigan

Aix-Marseille

Linkoping Sweden

Stony Brook

TAS Taipei

Melbourne

Evry Paris-Saclay

UAlberta

Alto-Helsinki

RHIT

Toulouse-INSA-UPS

Chalmers-Gothenburg

GO Paris-Saclay

BGU Israel

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

Opentrons

In spring of this year a producer of robots for pipetting automatisation, Opentrons, announced an event, where iGEM teams from around the globe would get a chance to win in a giveaway of 10 free OT-2 robots. The condition was sending an abstract of our project and arguing how exactly our team would benefit from this addition. We sent our freshly written scientific abstract and - completely unexpected - we were among the 10 winners of 77 teams who had applied. We were more than happy to get our hands on an OT-2 and very thankful to Opentrons for giving us such an amazing opportunity!

We also had the great honor to personally skype with one of the Opentron and iGEM Measurement Committee members and this year’s judge, Kristin Ellis. She was very kind and offered us help with anything we might need in the next few months. In addition to that we were invited to subscribe to the Opentron forum and stay in touch not only with other iGEM teams who won the same roboter, but also with the Opentron community.

Working with teams

iGEM Tec-CEM wants to bring joy to the world and simultaneously educate the public by making a cover song of “Girls like you” from Maroon Five with funny lyrics about science and the iGEM competition. We are glad to be a part of this very cool project!

A great way to educate kids is through pictures and a story. Since we knew about OUC China’s idea to create a comic book about synthetic biology we were on fire to help translating everything into German and Italian. The final comic book is really cute and explains the basics of Synthetic Biology in an easily understandable and educational way.

Since we use the same organism S.elongatus it was easy for us to exchange our knowledge in a Skype interview. The iGEM team of Stony Brook sent us helpful papers and we gave them some insight into our work with cyanobacteria.

The first time Team Bielefeld-CeBiTec visited us we immediately knew there was a special relationship between us. We had a lot of fun and talked in deep about our projects. The second time we met was at a discussion event organised by the team Bielefeld with the topic “Dual use”.
The iGEM Team of Bielefeld also wanted to use a part from the iGEM Distribution Kit, but some problems occurred while they used it. So we helped them by retransforming and sequencing this part, so they can troubleshoot a little bit better and solve their problems.

We met Team Eindhoven at the European Meet Up in Munich and their topic immediately caught our attention, since during our initial brainstorming sessions at iGEM, we thought about a similar project as well. However we encountered many difficulties when thinking about possible challenges and therefore did not decide to chose that topic. However all those brainstorm sessions about the challenges that we had allowed us to help team Eindhoven and advised them to think about upcoming problems. They were really glad that we supported them with those thoughts and we stayed in touch throughout the iGEM session.

They work with S.elongatus as well so we decided to get in touch and talk about this organism. Team Kazakhstan had some troubles transforming their Cyano so we took a look at their transformation protocol to find possible adjustments and also included some of our good working protocols.

Team Team Toulouse came up with the iGEM teams worldwide Instagram account where every interested iGEM Team was able to post for a week to show everyone their project and team. We took initiative and posted pictures for one week.

The iGEM Team FAU Erlangen wants to enlighten the world about their project through a short video. They asked us to help translate this video to italian so the video can reach out even further to all the interested people in the world.

iGEM Surveys

Surveys are a great method to collect a lot of opinions or the knowledge of the society about a certain topic. We have designed our own survey and are very pleased with the advantages of this method. For this reason, it was very important to us to participate in many other surveys of other iGEM teams to help them.