Team:Bielefeld-CeBiTec/Collaborations

Collaborations

Overview

The main idea of iGEM is an easy way of biological engineering realized by standard biological parts (BioBricks) and an open source database. These make synthetic biology accessible to everyone. The whole concept of BioBricks is based on sharing parts freely across the community. The community connects different iGEM teams to help each other, learn from each other and finally to achieve their desired goals. The collaboration of individual teams is one of the most important aspects in iGEM. For our iGEM project we worked with several other iGEM teams. We collaborated extensively with the iGEM team UNIFI 2017 and CU Boulder 2017. Team UNIFI participates for the first time in the iGEM competition and our aim was to help them getting jump started into the iGEM competition and coaching them in order to direct them towards a successful project. iGEM UNIFI helped us with the characterization of the transporter ptNTT2, using their more precise equipment to recording growth rates. Next to this collaboration we sent plasmids from former iGEM Bielefeld-CeBiTec Teams to iGEM SDU Denmark 2017 and to several other researchers worldwide.

Collaboration – Mentoring iGEM team UNIFI 2017

The iGEM team UNIFI is representing the University of Florence and is participating for the first time in the iGEM competition. As the only Italian team this year, they took the chance to collaborate with other iGEM teams beyond their own country borders. We met the iGEM team UNIFI at the European iGEM Meetup in Delft on 7th to 8th July and initiated the mentoring. Afterwards, we started this collaboration, with weekly skype conferences (Figure 1) in addition to intensive communication via email.

Figure 1: Skype meetings with iGEM UNIFI for a two-way collaboration.

During the mentorship we picked certain topics for every skype meeting. Those topics covered technical and practical advices concerning the wiki and important points for human practice among others. Together we discussed all the gold medal criteria and gave tips how to fulfill them. Furthermore we discussed organizational aspects of travel and stay in Boston. During one skype call our HTML programming expert Maximilian Edich answered questions concerning HTML coding.
In return for the mentorship, iGEM UNIFI helped us characterizing two BioBricks. To make sure that Escherichia coli is able to take up the unnatural nucleoside triphosphates from the cultivation media we had to introduce a heterologous transporter. This is due to a lack of nucleotide transporters in E. coli. One of the BioBricks encodes a complete nucleotide transporter PtNTT2 (BBa_K2201000) originated from the algae Phaeodactylum tricornutum. The second BioBrick is a truncated version missing the N-terminal signal peptide (BBa_K2201001). This N-terminal signal peptide leads to some kind of toxicity in E. coli. Through cultivation experiments we wanted to investigate the extent of the toxicity by comparing the growth of the strain expressing the full version of PtNTT2 to the ones expressing the truncated version.
We started to cultivate the different strains in 50 mL media using flasks and measured the OD600 every 30 minutes during the exponential growing phase. Due to manual measurements our results showed big error values for the maximum growing rate µmax. This makes it hard to get a valid conclusion. iGEM UNIFI has the capacity to do the same cultivation experiment using a microscale bioreactor. This ensures automatic measurements for OD600 values which would decrease errors concerning µmax. This characterization from iGEM UNIFI would lead to a more accurate estimation of the toxicity of a full length version compared to a truncated version of PtNTT2.

Collaboration - CU Boulder 2017

The iGEM team CU Boulder works with artificial compartments which consist of shell proteins containing a photoswitch amino acid. These compartments are supposed to break up into separate shell proteins releasing the protein captured inside the compartment. This could potentially act as next-generation drug delivery systems, biosensors, or as a solution to sequester diffuse and harmful environmental toxins. The iGEM team CU Boulder 2016 submitted the BioBrick containing the aminoacyl tRNA synthetase (aaRS) for the photoswitch amino acid. This year’s team helped us to realize our photoswitching project by sending us their aaRS and a small amount of the amino acid AzePhe. In return, we performed lokalization studies by fluorescence microscopy for their compartments labeled with GFP using their plasmids.

Figure 2: Animation of the EutS FusRed cotransformants from CU Boulder.