Team:NUS Singapore-A/Collaborations

Collaboration Header


NUSGEM is delighted to have interacted with so many teams around the world! We believe that collaborations have made our project more meaningful, and we are excited to share with you about our collaborations with the following teams!

NUSGEM initially wanted to explore using RNA aptamers as a reporter system for our stress promoter (PhtpG1) and blue light repressible promoter. However, we faced many difficulties in constructing our aptamers reporter system and we could not get a successful construct for many months. However, we read that the Team CUHK was working on aptamers. Hence our team leader, Nanda, met up with them in Hong Kong.

Nanda (far left) with the members from CUHK iGEM team

After an exciting discussion in Lee Woo Sing College at the Chinese University of Hong Kong, both teams saw a great collaboration opportunity between us, discovering many aspects of our projects which we could collaborate in - wetlab, modelling and hardware.

Selfie on a beautiful Sunday morning!

The two teams concluded our meeting by agreeing to keep in contact, and we continued to discuss intensively on our collaboration even after Nanda returned to Singapore. Eventually, we decided to collaborate on wetlab!

As the CUHK team worked on a RNA-based project, they were urgently looking for a particular strain of E. coli, BL21 Star. It is an RNase-knockout strain that will allow them to maximize RNA production. They asked whether our lab has this E. coli strain - we do! Without any hesitation, we shipped the strain over to them.

On the other hand, NUSGEM needed help on RNA aptamers constructions. Team CUHK kindly offered their expertise by redesigning our RNA aptamer constructs, as well as designing suitable primers to increase the chances of successful construction. In addition, they incorporated the RNA aptamer that they aimed to characterise, tRNALys3-iSpinach, with our stress promoter (BBa_K2819010), for us to characterise. Both teams agreed on constructing the constructs from both teams simultaneously, using the set of primers which Team CUHK has designed. They advised us to use overlap PCR in our constructions, a technique that we don’t usually use in our lab. We took their advice and were delighted to find out from our gel electrophoresis results that our overlap PCR was successful!

CUHK and NUSGEM results
Gel Electrophoresis of PhtpG1-RNA aptamers

With their help, we eventually succeeded in constructing the RNA aptamer plasmids! We managed to successfully construct our plasmids, as well as Team CUHK’s parts. Subsequently, NUSGEM assisted CUHK in characterising their parts. We measured the fluorescence intensity given off by the RNA aptamers under different temperatures according to the assay protocol provided by them. After we obtained the results, we sent them the data obtained from our characterization. They subsequently found that that tRNALys3-iSpinach-D5 gives off a higher fluorescence reading than tRNALys3-Spinach 2.1, a previous biobrick! Figure 1 refers to the graph which they have obtained from their analysis.

Figure 1: Graph was plotted and provided by Team CUHK

Last but not least, CUHK also hoped to carry out their survey with a wider audience, so NUSGEM did the survey and spread the word of their survey to help them with gathering responses in Singapore.

What started out as a informal discussion session between Team Toulouse-INSA-UPS and Team ULaval developed into a exciting collaboration opportunity between three groups from different parts of the world. All three teams wanted to bring to light how matters synthetic biology touches different aspects of our quotidian life in an interesting and educational manner.

After weeks of discussion and deliberation, the three main subjects we chose to discuss were bioethics in synthetic biology, economic aspects, and societal perspectives of synthetic biology. We are excited to present to you our Collaborative Report - please check it to learn more about the issues surrounding synthetic biology!

Skype call with them

With Team NTU just being next door in sunny Singapore, how could we not collaborate with them? Both teams first met in our SG iGEM Meetup, and we subsequently met up several times to finalise our collaboration plans.

Team NTU made a trip down to the BioMakerSpace for discussion!

NUSGEM helped Team NTU in 2 ways. Firstly, we gave them some CoE1 plasmids. Secondly, we validated their Adenine Base Editing project. We co-transformed 2 plasmids into the strain, sgRNA Kan* plasmid and ABE-dCas9 plasmid, and validated the constructs under 4 different inducer conditions: No inducer, IPTG, Arabinose, IPTG+Arabinose. Their system has the following proposed working mechanism: sgRNA Kan*, induced by IPTG, is a construct with a mutated kanamycin gene attached to sgRNA, while ABE-dCas9, induced by arabinose, is capable of editing and correcting the mutation on Kan* to restore the plasmid’s antibiotic (kanamycin) resistance.

The editor system is only supposed to work when both IPTG and Arabinose are present, as both SgRNA and dCas9 must be induced. SgRNA provides a guide sequence to direct dCas9 to target its plasmid, to perform adenine editing on sgRNA Kan*. To demonstrate this, we plated the cells from each condition into 2 types of agar plates with different antibiotics composition, one with kanamycin+gentamycin+chloramphenicol, and the other with gentamycin+chloramphenicol.

Results of our characterisation experiment
Top row: Agar plates with gentamycin+chloramphenicol (control)
Bottom row: kanamycin+gentamycin+chloramphenicol
Left to right: No inducer, IPTG only, Arabinose only, IPTG + Arabinose

We verified that their system works as proposed. As shown in the picture above, only the system induced by both inducers had colonies growing on the agar plate with kanamycin+gentamycin+chloramphenicol, while no colonies were observed for the other 3 induction conditions.

As our labs lack the necessary equipment to conduct RT-qPCR, we were unable to study the level of mRNA expression of our constructs. Fortunately for us, Team NTU is well-versed in this technique, having provided assistance to many teams previously. We gratefully accepted their offer to help and passed them several of our dye-synthesizing constructs for RT-qPCR analysis and characterization.

The RT-qPCR results showed that mRNA transcribes were produced from our constructs. Moreover, we also gained further insights into the design of our plasmids and how we can improve on them.

On 11 June 2018, all three Singaporean iGEM teams met up at the National University of Singapore, for the first ever Singapore iGEM meet!

iGEM participants mingling over everyone’s favourite food - pizza!

The goal of our inaugural meet-up was to provide an opportunity for all Singaporean iGEM participants to get to know each other, network, and spark fruitful discussion on potential collaborations. This meeting was the first official platform for all three teams (NUS_Singapore-Sci, NUS_Singapore-A and NTU-Singapore) to share with each other our respective team projects, and discuss possible avenues for collaboration. Hearteningly, members from all three teams felt the meet-up was fruitful, and we made many exciting plans for collaborations!

Deep in thought during our meeting

No meeting is complete without food! All of us had a great time socialising and discussing our iGEM experience over a pizza party! The meetup was indeed a great opportunity to get to know members from other teams, and even our own team members better, and perhaps more importantly, many memories were made that night!

Group photo featuring all three Singaporean iGEM teams!

On 18 July 2018, NUSGEM was privileged to host 2 members from the Jiangnan iGEM team!

A group photo with Team Jiangnan in front of the BioMakerSpace's signage!

The Jiangnan iGEM team members were in Singapore for a summer exchange programme, and they chanced upon our project. They took the initiative and wrote to us about the possibility of a meet-up to share our respective team’s iGEM experience, and learn more about the problems we have encountered, and how we managed to overcome them.

Without hesitation, we agreed to meet up with the Jiangnan iGEM team members! In fact, we were all so excited about the meet-up that we planned an engaging day of activities for our fellow iGEM-ers!

Firstly, we invited them to the BioMakerSpace, which is where our NUSGEM team carries out most of our experiments. At the BioMakerSpace, we brought them on a lab tour, which culminated in a fruitful sharing session on our projects, where we even exchanged solutions on the problems we faced. After the laboratory tour, we brought them on a NUS campus tour, visiting the various libraries (there are more than 6!) in our school, as well as the biofoundry in SynCTI (Synthetic Biology for Clinical and Technological Innovation).

The two teams had a great time interacting with each other and we can’t wait to see each other again in the Jamboree!

Other potential collaborations were discussed over Skype sessions with Team Michigan State, Team US AFRL CarrollHS, Team Newcastle, Team TUDelft, as well as Team Uppsala. We shared and discussed ideas about genetic circuit designs, modelling, human practices, fund-raising. We were happy to chat and make friends all over the world, and we were so happy to finally see one another at the Giant Jamboree!

Skype calls with various teams!