Short summary
Experts
Overview
ChImp Report
Conference on Expanding the Genetic Code
Figure 1: Excerpt of the program for our workshop EGC: Expanding the Genetic Code.
While the CeBiTec has an excellent reputation as a center for genome research and biotechnology, there is no research related specifically to the expansion of the genetic code. Scientists from the CeBiTec and from Bielefeld University were invited to our workshop. Since there is just basic research on this topic in Bielefeld, the staff benefited from our conference, and gave us very positive feedback regarding the workshop. Moreover, we invited interested students to increase the popularity of iGEM and the knowledge about synthetic biology on the campus of Bielefeld University.
Figure 2: Guest speakers and part of the iGEM team “Bielefeld-CeBiTec 2017”: (left to right, back) Prof. Dr. Nediljko Budisa, Iker Valler Aramburu, Yannic Kerkhoff, Saskia Dymek, Christopher Whitford, (left to right, front) Markus Haak, Michelle Liebers, Olga Schmidt, Denise Kerkhoff
Research in the Budisa Lab, Berlin
Figure 3: From left to right: Huan Sun, Professor Nediljko Budisa, Olga Schmidt and Fabian Schildhauer.
Based on the first positive selection round, problems that may occur in handling the selection process as a whole were explained. The problems compromise for example low transformation rates or low incorporation efficiency of the non-canonical amino acid provided. These particular problems are tried to be eradicated by preparing a fresh batch of competent cells for each selection step and by lowering the concentration of the antibiotic which corresponds to the resistence gene with the blank codon while prolonging the incubation time, respectively.
We decided to study the selection process using two non-canonical amino acids we also use in our toolbox, namely 2-Nitro-L-phenylalanine (2-NPA) and Nε-L-cysteinyl-L-lysin (CL). We were lucky to use existing tyrosyl and pyrrolysyl synthetase libraries provided by the lab, respectively. We were made aware that the selection may not be as efficient as it could be utilizing those libraries, because the synthetases were evolved to bind the distinct non-canonical amino acids we are working with.
Figure 4: Olga at work in Berlin.
Figure 5: Plates with colonies for first positive selection step for 2-NPA. Because 2-NPA is photo cleavable, the plates could not be scanned as usual. (A) and (B) show the plates with added non-canonical amino acid. (C) shows the negative control plate without 2-NPA. Individual colonies could not be counted due to dense growth of the cells.
Figure 6: Plates with colonies for first positive selection step for CL. Plates were scanned. (A) and (B) show the plates with added non-canonical amino acid. (C) shows the negative control plate without CL. Individual colonies could not be counted due to dense growth of the cells.
Figure 7: Plate for first negative selection for CL. Plate was scanned. Colonies are difficult to see due to the plate being scanned.
Merck
Figure 8: iGEM Bielefeld-CeBiTec 2017 team members Olga Schmidt and Markus Haak presenting our project in front of the Merck scientists.
Figure 9: iGEM Bielefeld 2017 team members Olga Schmidt and Markus Haak with representatives from the iGEM Bielefeld 2016 team and Merck.
Discussion with Cell Product Purification Experts
Meeting with Prof. Dr. Dirk Lütkemeyer, General Manager of BIBITEC GmbH
Figure 10: Meeting with Prof. Lütkemeyer. Prof. Dirk Lütkemeyer (BIBITEC GmbH) and team member Yannic during a meeting at the Center for Biotechnology. A detailed discussion provided us with useful advices and opinions about our elution technique and purification column.
Meeting with Dr. Benjamin Müller, CEO of Biofidus AG
Figure 11: Meeting with Dr. Benjamin Müller Meeting of Yannic Kerkhoff with Dr. Benjamin Müller at his office on the 6th of September to discuss the light-induced elution technique.
Meeting with Prof. Dr. Thomas Noll and Ole Weigelt
Figure 12: Meeting with Prof. Thomas Noll and Ole Weigelt Group picture after a beneficial meeting about possible marketing and commercialization strategies for our EluX technology.From left to right: Yannic Kerkhoff, Prof. Thomas Noll (co-founder of Xell AG), Ole Weigelt (co-founder of Xell AG, lawyer and tax consultant) and Christopher Whitford.
Talk on single molecule real time sequencing
Figure 13: Members of the team talking to the invited experts prior to the talk. Interested members of the CeBiTec and our team within the audience.
Nagoya-Protocol
The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization (ABS) to the Convention on Biological Diversity” entered into force on October 12th, 2014 in Nagoya. It is an international environmental agreement to implement the objectives of the 1993 UN Convention on biological diversity: “the fair and equitable sharing of benefit arising out of the utilization of genetic resources” [2]. Especially developing countries which often have a manifold biodiversity are affected by bio piracy. The Nagoya Protocol intends to ensure that these countries at least profit financially or non-financially by the resulting research and products of their genetic resources. In addition to accessing genetic resources, it covers traditional knowledge concerning these resources. Contracting countries are bound to take action to guarantee informed consent prior to any course of action, as well as impartial benefit-sharing, respecting local laws as well as customary use and exchange.
Today, 100 countries signed the Nagoya Protocol [3]. To succeed, every partner nation should establish ABS National Focal Points, competent national authorities, legislative administrative, national databases, and checkpoints for information.
Germany signed the Nagoya protocol on July 20th, 2016. Our donor of the isoG-metabolism-pathway is Croton tiglium, which is a herb in traditional Asian medicine. Its original occurrence is in the Asian region. To make sure we do not infringe upon the Nagoya Protocol regulations, we clarified the origin of our plant as we got it from the botanical garden of the Phillips University Marburg. Croton tiglium is originally from an undocumented old stock of the botanical garden Giessen. In 1986, the botanical garden Marburg received seeds from this stock. The date on which the EU regulation entered into force was October 2014. All resources collected before this date are not subject to reporting requirements of the Nagoya Protocol in Germany. Thomas Greiber (Federal Agency for Nature Conservation, Head of Division Div I 1.4 “Competent National Authority for the Nagoya Protocol”) confirmed “[..]Therefore, the respective areas of application are not touched by this EU-regulation, and the mentioned regulations are not relevant.”
Therefore, we are allowed to work with the plant and publish information and results about gene sequences and metabolism pathways without violating applicable law.