Team:TAU Israel/Collaborations
Collaborations
The Israeli HP team 2020- making inspiration videos for underrepresented groups in science
Following the Israeli meet-up that we held on 18/6 we have decided to collaborate together and make special videos in order to raise the awareness of the underrepresented groups in Israel’s science. We have decided to focus on three groups: Ethiopians, ultra-Orthodox and Arabs. In total we interviewed 8 people: 3 Ethiopians, 3 ultra-Orthodox and 2 Arabs who are involved in science.
We held some zoom meetings with the other israeli iGEM groups in which we discussed together how the videos would look like, how they would be presented, formulated questions for the interviewees and also presented the progress of each of the iGEM’s team.
Ben Gurion University, Israel
During the second Israeli meetup held on 18/6/20, we were exposed to the fascinating project of the BGU team from Ben-Gurion University, Israel. Their project aims to produce bacteria that will break down cellulose, using a plasmid containing a cellulase gene. These bacteria will allow the breakdown of wipes in sewers in the future. Therefore, the genomic stability of these bacteria as well as the plasmids plays a crucial role in the ability of those organisms to survive for a long time. We understood the potential for fruitful collaboration that will promote both projects- BGU team could receive an optimized sequence for their plasmid that would potentially increase its genomic stability. In return, we will receive empirical data about the comparison between the original sequence and the optimized sequence following BGU’s wet experiments. In addition, we asked for feedback on the output obtained from our optimizing tool.
BGU team sent us the sequences of the two relevant plasmids and we inserted them into our EFM optimizer. In a series of two sessions, we refined the results and gave an explanation about the output received. We then sent the final output by email.
Unfortunately, due to the Covid-19 crisis, BGU's wet lab work was stopped and we were unable to obtain empirical information about the comparison between the plasmids. However, the group sent us feedback on the output they received, feedback that helped us improve the user experience of our EFM optimizer.
Team BGU, it was a pleasure!!!
Marburg, Germany
On the 5/7/20 we were honored to conduct a workshop at the German iGEM meetup 2020. During the preparations for the workshop we had several zoom sessions with the Marburg team members, organizers of the meetup.
You can find out more about the workshop on our public engagement page.The meeting was enriching and instructive! The organizers thought of every detail.
Good job Team Marburg!
GO Paris Saclay, France
We heard about this ambitious team while we browse the iGEM community page on Slack. We were intrigued and excited to hear that our projects share a common theme - stabilizing synthetic circuits. Go Paris team strives to stabilize synthetic circuits by overlapping two genes that will be expressed in two different reading frames, using a software called Cameos.
On 19/8/20 we met with the group members. We started by presenting the two projects, during which we realized that although we share the same goal, our ideas are different. For example: one of the linkers our software offers (Super Linker) uses a gene overlap technique with -1 frameshift (pseudoknot), while maintaining the amino acid sequence. GO Paris team on the other hand, allows for certain changes in amino acids and later selects the genes that created functional proteins in the lab.
Both teams identified a potential for collaboration. We realized that the best way to collaborate would be by sharing information. We sent to the team information we collected regarding the overlap of the genes and the calculations we made. In return the team sent us information about cameos software, manuals for its installation and operation, and even offered us to continue the collaboration in the future and run for us a test in the software for sequences we choose.
We were very impressed with the team’s project. It is possible that in the future the knowledge we have acquired will be used to upgrade the way our software offers to connect two genes.
Gaston Day School, USA
The correspondence with George began towards the end of April following his publication on the "iGEM Slack" channel. In his post, he introduced his background and asked for help from a team with knowledge on MATLAB software, and our group picked up the glove :)
George explained his plan to implement a model that relies on differential equations from an existing article, run a simulation accordingly and perhaps make a curve fit. We briefly introduced him to the tools available in MATLAB for these purposes: the SimBiology tool and Curve Fitting tool respectively. We mentioned that in order to help him more, additional details were essential, such as the conditions in which he intends to hold the simulation, whether he has existing data (model parameters with which to simulate), and others. We decided to have another meeting later if needed. In addition, we presented our group's project and were delighted to hear George's impression of our idea. We sincerely hope that this meeting helped Gaston Day School team and his team is more than welcomed to contact us once again!
