Getting Started 

The groundbreaking commonalities in our projects is that both teams share a common goal of designing a diagnostic kit to detect RNAs. While the implementation of both the projects is miles apart, synthetic biology found a way to unite us. This is how our partnership with Team Aboa. We reached out to themon Slack and we scheduled a meeting and discussed our projects in detail. 

Our discussions made us realise that both teams are planning to use NUPACK, a commonly used tool to design RNA/DNA toeholds and aptamers. It is useful in analysing secondary structures and determining useful parameters for the sequences. This was a very important team for both the teams and we shared struggles and difficulties faced by both teams. 

At this point we agree to help each other with the program and together figure out solutions to our problems. This made us think that there would be so many iGEM teams every year, who are not gifted with people from heavy computational backgrounds. So realising the immense potential of NUPACK in synthetic biology and keeping in mind the growing trend towards RNA research, we decided to create a guide for NUPACK, so more teams with little experience could feel comfortable tipping their toes into computational design and modelling.

Helping each other with 

APTASTELES, takes advantage of light-up aptamers like Spinach and Broccoli to detect proteins, hormones and miRNA biomarkers and produce fluorescent signals. WhileTeam Aboa’s project CropFold, utilises toehold switches to detect the target sequence in a pathogen’s genome to produce a visible signal. 

What do we share in common? Toehold switches for detection of RNA. 

Determining the functional aspects and implications of a sequence depends on its predetermined structure and motifs. As neither of our teams had any expertise in the field of RNA designing, we wanted to tackle the challenges posed by these requirements together. We both used NUPACK to design these RNA sequences and so we worked together closely to take advantage of the program’s functionalities.

NUPACK has a powerful web app, but the full benefits of the program can be utilised in the python module. Because the installation of this module can be confusing for novices, we worked together on this. When we had our first meeting, team Aboa had finally managed to install the module and so they helped us through the basics of the installation phase. After successful installation, we began discovering the properties of the program and we had regular chats and meetings when writing our programs and helped each other through many issues.

Let’s contribute towards a better future

Making our way through designing sequences and banging head to solve issues with NUPACK,we kept documenting all the steps we had to take to understand NUPACK web application and it’s Python module.The Python module of NUPACK is a tool that provides advanced computational tools but yet they can be quite intimidating for beginners. To lower the barrier of entry for novices, we wanted to create a guide for using the NUPACK python module and web app(Please visit Contribution). Although NUPACK provides a user guide which is extremely detailed and full of complex terms, we wanted to provide a simpler version in which we cover all the necessary information for starting and even provide example programs. The guide covers the basics of analysing and designing nucleic acid sequences with NUPACK and compiles different programs created by us and other life science researchers, so anyone could find inspiration for designing a program for their specific needs or even find one ready-made for them.

Although this guide was meant to help future teams in their endeavours, we also learnt a lot when compiling the guide. As we dove deeper into the user guide for NUPACK, we discovered new features that we did not think of implementing into our programs and therefore managed to improve their functionalities. Writing this guide together helped our projects and hopefully it will make the first steps easier for future iGEM teams.

Turning experience to reality 

While working with a lot of different types of aptamers, our team realised that there are few aptamers that are not well characterised in the iGEM Registry and there is a scope to improve these parts using NUPACK, along with other computational tools like MD simulations. They were able to produce in-silico results however, they were struggling to order and test these parts. So they discussed this with us and we realised that we could help them as our team has some experience with in-vitro transcription and handling RNA samples. Additionally, we realised that these light up aptamers could also be implemented in our project to improve and simplify the method of readout. So we proposed to help them in characterising these parts.

We discussed and prepared in detail the protocols and reagents required. This helped us understand the potential of aptamers in detail. 

Unfortunately, due to boundations of time and few reagents, we couldn’t perform the experiments. However, the brainstorming and troubleshooting we did during these meetings was extremely fruitful for both the teams.

Conclusion

Through our partnership during the whole year, we were able to learn new skills in computational design phases of our projects. We also helped each other to create the design programs, which play a key role in both of our projects. As we formed the partnership in the design phases in the spring, we were able to accelerate the creation of these programs and therefore progress into the later phases of the projects much faster. We stayed in contact through the year up until wiki freeze through regular video meetings and a WhatsApp group.

TEAM TeccCM 

Are you diagnosing for CRP too?

Team TeccCM grabbed our attention when we saw their message on Slack. We had a sigh of relief knowing that some other team is also working on detection of C-Reactive Protein. Both the teams share the same pattern. We instantly knew after the first meeting that Team TeccCM would be our long term collaborators.

In our first meeting, we discussed how different subteams can collaborate to benefit both the teams and we scheduled future meetings. We established constant communication by creating a common WhatsApp group.

Protocol discussions

The goals of both the teams aligned in a streamline manner, with the only deviation that both teams were using different readout methods. They plan to do it by electrochemical assay, unlike our fluorescence assay. So we agreed to share our protocols, results, and help each other in troubleshooting our experiments. In the next few meetings, we discussed what experiments we were planning to perform and shared insights on how we could improve-improvise in our experiments to supplement each other's projects as well.

Unfortunately, none of the teams could perform our experiments with CRP before the wiki freeze due to lack of time and inability to get the protein in due time.

Biosafety first!

Team TeccCM told us that they would have a chance to get hands on biosafety training to for managing the principal risks and safety practices that should be followed while working in a biosafety level 1 and 2 (BSL1 and BSL2) laboratory, how to safely handle blood samples and general biosafety concern. We requested them to share the protocols and highlights of the workshop and they happily converted their entire workshop in English from Spanish. This was a huge step towards establishing and sharin meaningful work.

Troubleshooting Drylab

While we were facing difficulties in working with SELEX and MAWS, team TeccCM offered to help with the pipeline their team was using to obtain their own aptamer sequences via in silico design to avoid SELEX. We wanted to try this technique as well, but we realised that this could take a lot of time and won’t be feasible to complete this iGEM season. 

However, both drylab teams met continuously to discuss other modules of our projects and continued to find ways to collaborate. Both teams shared their mathematical models and equations with each other to receive invaluable feedback from the other team.These feedback sessions gave insights on aspects that we left unnoticed and we made suggestions to improve their model as well.

Why do we need aptamer databases?

Upon discussions both teams found that there are very limited sources and databases to find aptamers. We felt this necessity, like a lot of other teams who work on Aptamers every year. So in an attempt to understand the awareness about these databases and collect information on existing databases, we conducted a collaborative survey and shared it with iGEM teams from 2022 to the past few years, along with experts in this field. This was performed with the aim of creating a database in the future, which would gather all the necessary information for aptamers, and make it accessible to anyone around the world.

Conclusion

Team TeccCM and IISER Tirupati were sailing in the same boat at all times in the iGEM 2022 and we learnt from each other, be it in drylab, wetlab or science communication aspects of the project. We are glad to have the opportunity to collaborate with such amazing people across several continents, but united by a cause.

TEAM IISER TVM

The One where our first collaborators became our partners

Our collaboration with IISER TVM happened very organically at the beginning of the iGEM journey, thus it was only natural that they get together at least once to talk about their ideas and plans for the iGEM competition. We presented our project ideas to each other at the first meeting and realised the immense potential of collaboration, whether it is promoting our project idea and general public awareness given the shared themes of our project.

Given that both of our teams' projects are related to public health, we wanted to come up with creative ways to reach out to children and youth, so we decided to think outside the box to create events while staying true to the core theme of synthetic biology and addressing health issues with novel approaches.

After a few meetings, we realised that we could talk to them about everything, from troubleshooting our projects to commiserating about the stress we're under. We constantly stayed in touch over our WhatsApp group, given that we were collaborating on something or the other every 2 weeks. We had no idea that a collaboration meeting would result in such a wonderful partnership for the iGEM journey.

Syn - Vibe

It is widely accepted that teaching young children through musical means is highly effective. We've all used rhymes to learn the alphabet, count to ten, and identify the continents,

But there were hardly any songs about science aimed at higher-grade students.

Hence to bring forth our life as GAMers working with bacteria, our team, in collaboration with iGEM IISER Tirupati, present SynVibe, a musical that celebrates the monotonous routines in the lab with microorganisms, full of reading papers and repeating experiments.

It was a challenging piece of work to incorporate our "own" story through the medium of song lyrics, direct the scenes, and choreograph the fun part of being a scientist. Two extremely well-known songs, Dance monkey and I don't care served as the basic tracks for our synbio parody.

This parody focuses on showing the general struggles that iGEMers face in their project and how we overcome them with strong resilience. The audience enjoyed the song. It also honestly gave insights to the general audience about the life of a researcher and the struggles with our bacteria every day.

Come work with us!

Every day, scientific research skyrockets on the wings of progress. We are uncovering the huge potential with the help of new breakthrough fields such as synthetic biology. However, most of the time, these intriguing and new ideas and technology are restricted to the research community. Children who do not have the financial means to continue their education in college never get to experience how the questions that arise from curiosity are addressed. Even students at our local institutions do not have access to sophisticated equipment. Science and laboratory accessibility has been a source of concern for a long. We clearly realised that this regional and linguistic divide in science needed to be addressed. This thought urged us to come up with the concept for a global lab tour video, combining the lab facilities and techniques throughout iGEM labs worldwide.

It was an attempt to appreciate the differences in our approach to research, the accessibility of science is varied across the globe and we wanted to let people know how different our facilities are yet we work towards the same goal of engineering biology.

We - Talk

Team IISER TVM proposed an event on a topic very personal to us, and we couldn’t deny it. Our We - Talk organising meetup sessions turned out to be a blend of four Indian iGEM teams sharing ideas. From the talk series it turned into a 3 day forum with talks on cervical and breast cancer, menstrual hygiene and challenges in adolescent girls, an interview with founder of OncoStem Diagnostics, panel discussion and a fun quiz session. Hosting any event with IISER TVM was always super fun with them!

All India iGEM Meet

AIIM has been an amazing opportunity to interact, incorporate suggestions and critically analyse the iGEM projects of Indian teams. During AIIM we got an opportunity to meet the IISER Tirupati team in person, an indeed moment of joy! We discussed the plan for Syn-Vibe, the collaborative music video during AIIM. AIIM had a session where the teams presented their projects to a panel of judges.

Conclusion

Our team cherished all moments of fun, learning and creating opportunities to collaborate beyond the usual. The most exciting partnership, and the longest one. We are thankful to the team for always keeping the spirits high and keeping us on our toes to work harder.

TEAM HEIDELBERG

Meet the RNA Club Members

Our teams met because of our love for RNAs. Team Heidelberg’s project Csi:RNA focuses on developing a siRNA based therapeutic, while our project AptaSteles focuses on a diagnostic kit. So RNA-based technologies were the common ground for our discussions.

Our initial contact started on the Global iGEM Slack Account, where both our team and the team IISER Tirupati got in touch as we both were looking into microfluidics systems as well as RNA-based technology. We soon realised we had many things in common, and we both wanted to at the end of the project create a semi-automatic microfluidics system for our respective goals of application. 

After the initial meeting, we stayed in constant contact over our shared Discord server and helped each other, initiated discussions and had fun chats which created a stronger connection between the teams.

Optimising our kits 

Team Heidelberg’s expertise in microfluidics and diagnostics instigated our meetings to go on for long stretches of time. In our initial meetings, we bombarded Marcel from their team with tons of questions, we explained our kit designs and microfluidics and they’d answer all our questions. It helped us to make initial designs for our kit, as they share with us a lot of relevant literature and advice on our designs. We also learnt newer methods while learning about their microfluidic device.

Designing Aptamers

Team Heidelberg aims to deliver vesicle trapped siRNAs to the brain. For experimental and application purposes, their team wanted to detect free siRNAs in the solution after their encapsulation and they reached out to us, if we can do this using Aptamers. This was a wild and fun challenge for our team. Both the teams discussed this idea on our common Discord channel, we explore all possibilities from detecting proteins associated with siRNAs, to developing aptamers detect small overhangs or double stranded structure of siRNAs.After lot of brainstorming, we couldn’t find a way to directly detect free siRNAs but we realised few tweaks to their system in the future can help us in detecting siRNAs.

In an ideal scenario, we would have used in-silico tools like MAWS, NUPACK to identify or design aptamers for their system. However, we couldn’t do it due to technical difficulties. 

Contemplating on Human Practices

Johann’s questions on HP were always thought provoking. We discussed about Human practices, and how our device could be designed to be user-friendly, safe and environmentally friendly. We discussed safe disposal of our kits, how reusability could be beneficial and we looked at seeking expert opinions for the same. Both teams received valuable input from this discussion and implemented these aspects into their final product design.

Conclusion

Our partnership with Team Heidelberg acted as a bridge in crossing challenges we faced throughout the iGEM season. We were enthralled to have such enthusiastic and helping partners. With both our team focusing on developing RNA-based technology, we could share insights on all aspects of our projects. Both teams worked hand in hand for developing microfluidics and verifying models in monthly meetings. Team Heidelberg advised us on in-vivo expression and purification of RNA, while we designed aptamers to sense siRNA for their project and shared our knowledge on in-vitro systems. Our discussions on human practices and biosafety issues inspired us to reflect upon risks