Team:Siberia/Collaborations
Korea_HS
We have collaborated with team Korea_HS starting from the 4th July up until the end of this year’s competition. This was done both via several zoom calls updating us with our respective projects’ progress and in written form via Instagram. One thing that unites our projects is the use of cell-penetrating peptides. Team Korea_HS offered to forward our questions regarding LWMP to their professor, an expert in this field. We were wondering how to predict the influence of the CPP in our fusion protein on binding with the necessary receptor, how to model such an impact and what motifs can be used to reduce its membrane permeability. We plan to use the insight provided by the professor to further improve our in vitro model after iGEM. In our initial meeting, Artemii suggested they look into long dsRNA, as an alternative to siRNA, as siRNA had some disadvantages when it came to delivery and silencing of the target protein in cancer cells. They looked into the idea, but after some consideration, they decided against this. In our final meeting on the 17th of September, we gave them some advice regarding what they could do with the modelling aspect of their project, as they were having some trouble with deciding what to model and how.
CityU
Though thematically our projects didn’t have much in common, our collaboration with VarieCure was very productive. Firstly, we helped each other with collecting data we could analyse for human practices. We translated our respective surveys and the other team shared them in their country. Thus we provided team CityU with statistics regarding Russia, and they provided us with statistics from Hong Kong. To reiterate, this wasn’t limited to us just filling out each others’ survey, but actually actively sharing the other team’s survey in our own circles. This allowed both teams to have a larger sample size, that was also more representative of public opinions on an international scale.
Secondly, on a zoom call, one of the team members mentioned that they’ve found an in vitro model of the blood-brain barrier to use in their project. At the time, we were still considering doing murine in vivo experiments, provided we managed to demonstrate the secretion of our fusion protein by modified bacteria first. This significantly impacted our project, as we decided to step away from in vivo experiments completely for the time being, and instead look into researching and designing an in vitro model of the mucosal barrier in the nasal epithelium, suitable for our goals. More on our in vitro model can be found on the project implementation page of our wiki.
Thirdly, we continued to actively stay in touch via email, and team CityU kindly shared their PCR and Western Blot protocols with us. In turn, we offered to help them model variecolin derivatives, as we know an expert in quantum chemistry, should they decide to continue developing their project after iGEM.
UTEC_Peru
UTEC_Peru was the first team we collaborated with in iGEM. Our projects both involved fusion proteins and we arranged a zoom call on the 27th of June. We discussed the modellingof fusion proteins and circuit design. It was interesting to compare the different software we used for this (they used Modeller, we, on the other hand, carried out our alignment inPyMol and modelled the protein in trROSETTA).
One non-research-related aspect that impressed us, was thedesign of their presentation and the clarity of its’ delivery. This prompted us to make our own presentation more detailedthan it was originally and breaking it into smaller understandable blocks.
While UTEC_Peru ended up carrying their project as part ofthe iGEM Design League, and thus we couldn’t continuecollaborating to discuss lab-related aspects of our projects,we are still extremely grateful to them as our meeting andemail exchange significantly impacted how we deliver ourideas across. This was also reflected in our educationalprojects, as clarity and good design are imperative when itcomes to teaching someone something new.
Multi-team collaborations
Engineering Biology Problem Book
Although there are some problems when it comes to synthetic biology-related education in Russia, there are specialists who greatlycontribute to developing the field and bringing cutting-edge scienceinto the classroom. As synthetic biology is a very rapidly developingfield, we felt that students from all across the world should have accessto materials relevant to the current age of science. As part of a multi-team collaboration between Russian teams, Danil and Daria assisted with the translation of the Engineering Biology Problem Bookby Dr. Kablukov of MSU from Russian into English and helped to thinkof new questions to add to the English edition. The work on thistranslation was done over the period of roughly 3 weeks, starting withthe end of September, with all the participating teams keeping in touch via video calls on Google Meet or in written form on the specially made group chat on Telegram.
The 1st Russian Meet-up. Moscow, Moscow City, LMSU and others.
On July 3rd, three of the Moscow teams had organised a meet-up in which all willing iGEM teams from all around the could share their iGEM projects and discuss potential areas of improvement and find teams with similar concepts for future collaborations. Andrei Kalinichenko from LMSU asked a great question about our project, regarding our choice of Sec and Tat secretion pathways. We’re were limited to these secretion pathways, which only secrete into the periplasm, due to the fact that in our fusion protein, the N and C termini were uncleavable as they were blocked by Myc-Tag and LMWP sequences respectively. Andrei suggested looking into self-cleaving peptides, which may have potentially solved our issue. Unfortunately, after doing some research we ended up concluding that this option wasn’t suitable for us, but the question itself prompted us to look into other potential secretion pathways and consult with our mentor on this issue. As a plan B we ended up using YebF which provides secretion into the culture medium, but occupies the N-terminus of the secreted protein. Either way, we were very impressed with the astute observation and did end up collaborating with LMSU on the Engineering Biology Problem Book project.
BioDoodle
iBowu China
The BioDoodle Challenge was a great collaborativeoutreach project from iBowu China. The “BioDoodle”is a colouring book that acts as an introduction of biological concepts to schoolchildren (which is also technically great fun for any age). Our team memberAnna did a wonderful drawing of a neural synapse in combination with an easy-to-understand explanationof how it works. As most of our educational projects were aimed at high school students, university students and educators, this was a nice change ofpace and we felt it was great to use a more intuitivevisual format for a younger audience.
SIBIRIA