The aptamer community in iGEM has been flourishing over the years, as iGEM 2021 saw about 12 teams working with aptamers. However, there was no platform to unify them. So our team joined hands with iGEM LiU, IISER Mohali and NU-Kazakhstan, to form the Aptamer club. The goal of Aptamer club is to build a community where iGEMers and ex-iGEMers can come together to share insights and help each other troubleshoot problems.

Upon discussion, we realised a common problem faced by us, which was lack of resources, databases and compilations about aptamers. So team LiU initiated the Aptamer book where all the teams in Aptamer club focused on curating a chapter to help future iGEMers find relevant information at a single place. This is the very first edition of the book, and we hope this will help the Aptamer community to grow and collaborations flourish. Go to Contribution to view the Aptamer book 
Click on the arrow to see the photos from our collaboration.

•  NU_Kazakhstan: The MAWS guys

Our collaboration with NU-Kazakhstan began with a Slack message. Our projects shared a lot in common. Their project, Viraless focuses on detection of biothreats caused by vaccina virus, by detection of B5R viral proteins using aptamers. They plan to use MAWS (Heidelberg 2015) and generate aptamers. AptaSteles share the same approach in terms of protein detection and identifying aptamers, although the techniques for detection used by both teams are different.

This led to conversations on all domains of the project. In our first meeting, we shared insights on how MAWS, MPDR and other in silico tools are difficult to deal with. We discussed in depth about the importance of stakeholder analysis while developing user-friendly detection kits and we brainstormed ways to increase accessibility in synthetic biology.

In the following meetings, we further discussed our detection systems and aptamer designs in detail. We discussed how our team would be using light-up aptamer while their idea to use aptamers on optic fibres was a really new and interesting idea for us.

During the next couple of months, team NU-Kazakhstan cracked how to use MAWS and simplified the pipeline to use the software, meanwhile our team was still struggling with the repetitive errors. Sakengali from their team sat with us to troubleshoot our problems and helped us understand and use MAWS. 

Apart from this, we also submitted an artwork for their Bio art exhibition and we collaborated in creating the Aptamer Book as part of the Aptamer.  Their MAWS Guide would be a useful reference for future teams. 

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•  Rochester: Saptasense

Our paths crossed with the lovely team of iGEM Rochester via Slack. Their project, Saptasense aims at developing a colourimetric kit to test the quality of Maple syrup using aptamers and electrochemical techniques. We discussed how even with different stakeholder pool, we have such similar ideas and outlook. We learnt from them how cheap 3D printing (1$ per chip) can be done. This made us think deeper on our hardware designs and feasibility of our kit. 

We kept in touch with them via our Slack workspace and attended the fabulous webinar series organised by them, “Disability Justice in STEM”.

•  AFCM_Eygpt: Detecting Phenylalanine

While troubleshooting MAWS, we saw their message on Slack about their project and we immediately got in touch with them. After discussions about our projects and difficulties faced by each team, they suggested us to use a direct-evolution method to identify aptamers, called CLADE (Closed Loop Aptamer Directed Evolution). It is a tool that uses SELEX and machine learning. However, we couldn’t incorporate due to challenges in using computational tools. With their  knowledge in microfluidics, they  helped us contemplate about  our designs and detection methods. Furthermore, we agreed to test the CLADE software their team is developing, if we’d have been able to run few cycles of SELEX.

SCIENCE FOR ALL!

•  iGEM Patras: The Accessibility Collab: iGEM IISERTVM, iGEM Heidelberg, IISER Mohali, iGEM TecCEM, ASU iGEM, HKUST iGEM 

In an attempt in lifting all social, cultural and linguistic barriers, seven teams from different regions collaborated to make “ The Accessibility Collab” series. Here we addressed what is synthetic biology, what is iGEM, and elaborated on applications of wetlab and drylab in over 5 languages.

iGEM Patras compiled all the videos and the result was just beautiful! It was a heart-filling moment to see all teams coming together and talking about one common thread that binds us all together, synthetic biology.

•  Synthetic biology in disease diagnostics: Collaboration with iGEM Patras Medicine, iGEM Aachen

Accurate and early detection of diseases is the key to their  treatment and cure, and over the last two decades, synthetic biology has paved the way to enormous diagnostic techniques. This leads to a healthier and safer future for all. Along with few other iGEM teams pursuing diagnosis of diseases, we compiled a video to elaborate on our motivation to work on AptaSteles and how we utilised synthetic biology principles in our project. We hope this would help future iGEMers realise how simple ideas can make a difference in the society.

•  VIT Vellore: Ethics in Synbio Podcast

Ethical practices in science is the most important instinct that drive our research and determines the validity of our future research and development. These practices need to be incorporated into our daily lifes and as iGEMers we realised that these small things, like showing tampered experimental results, could have a great impact on our projects. Hence, along with VIT Vellore we sought to find answers to what are ethics in science and synthetic biology, how do we avoid intentional or unintentional unethical practices, what impacts can ethics have on ourselves and our work, and ultimately the world. 

In four episodes of the podcast, we interview four experts from different aspects of science, but who have worked closely with ethics committees. We learnt mindblowing things, came across examples of the good and the evil of synthetic biology and tried to inculcate the best values in our teams. The tireless efforts by both teams made this a successful collaboration.

Find the podcast on Communication.

•  COME WORK WITH US!: Presented by IISER TVM, iGEM Patras, Tec CEM, ABOA Finland and IISER Mohali 

Accessibility remains an unsolved issue in appreciating the beauty of science. How exciting it would be to get an opportunity to explore the biolabs around the globe! We collaborated with 5 teams for a global lab tour video, covering the lab experience beyond the oceans that separate us. 

•  Stonybrook: Synthetic Biology Review : A Global Journal

iGEM Stony Brook proposed us an idea for creation of a scientific journal designed by them for the use and consumption by  the general public. Through this journal, we would sought to investigate social and health disparities, and address the societal implications of synthetic biology.  We submitted our article for the journal, along with eight other iGEM teams. 

LEARNING FROM EACH OTHER’S EXPERIENCE!

•  HKUST: Fisherly

The goal to create a cell-free kit which utilises fluorescence output upon detection on biomolecules brought us together to discuss and collaborate. We discussed various aspects of modelling and hardware. Insights from their modelling team helped us shape our deterministic models. Since both the teams shared the goal to make a concentration-based detection system, we realised that determining a threshold for the system would be extremely important. Together, we sought to discuss solutions for the same, using mathematical modelling and they introduced us to tools such as Sobol analysis and global sensitivity analysis.

Our discussions led to troubleshooting of technical issues in our projects.

•  iGEM Crete: Benefits of Buying Locally

On the World Environment Day (5th June 2022), we collaborated with iGEM Crete to convey the impact of local vendors, supermarkets and food carts in reducing waste, pollution and effective use of fresh products. We submitted pictures of local vendors and food places in our local area and posted in our social media to spread awareness.

•  iGEM Toulouse: Allergen Detection, Microfluidics

Microfluidics and multiple target detection were the two hot-topics of discussion in our meeting. Both teams presented their ideas and gave suggestions on blood test kits and tried to find ways to supplement each others microfluidics designs.

•  iGEM-Waseda_Tokyo: Achieving SDGs & Hormone sensing

iGEM Waseda reached out for our team because both teams are tackling women related issues and hormone detection in our projects. One of our team members, Shreyas was also a part of our iGEM 2021 team and has experience with progesterone detection. He shared his advices and suggestions to refine their project and experiments and our team also learnt from their results and tweaked our experiments, over the multiple meetings. We helped them conduct a survey on sex education and fertility treatment.

During our meetings, one of our major points of discussion was how both the teams are working towards developing a sustainable product and what sustainable development goals (SDGs), as set up by the United Nations, each team is targeting. We helped each other understand and internalise the meaning of relevant SDGs.
Click on the arrow to see the photos from our collaboration.

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•  iGEM Tokyo Tech: Fluorescence detection kit for dengue, Cre-Lox system; Serotype prediction

 With team iGEM Tokyo Tech, we discussed how both teams are utilising fluorescence readout for detection of biomarkers. Discussions on hardware designs, relevant experiments and kit operations using Raspberry Pi software , helped us plan future experiments for our prototype testing.

•  NCKU Taiwan: Presentation at ARS - Synthetic Biology & Protein Engineering conference

NCKU Taiwan organised the ARS - Synthetic Biology & Protein Engineering Symposium on 25-27th June 2022, which was a three-day event filled with flash talks by lots of iGEM teams and scientific researchers from various asian countries. Our team presented our idea at the symposium, and learnt from other iGEM teams. This also paved a path for future collaborations with other asian teams.
Click on the arrow to see the photos from our collaboration.

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•  Imperial College London: Outreach to unknown lands

With team ICL, we set out to find ways to reach out to stakeholders of projects from both our teams. We planned to conduct online and in-person surveys in each others regions to help the other team analyse the stakeholder base and variations in different parts of the world. However, we couldn’t conduct them due to inaccessibiltiy to remote areas and language barriers.

However, this collaboration helped us look into the difficulties that the team would face in the implementation of a novel test kit amongst local communities and we analysed how these issues could be tackled by us in the future. 

•  ICT Mumbai: Who’s the mentor and who’s the mentee?

Communication between Shreyas (IISER Tirupati) and Darsh (ICT Mumbai) began even before the teams were formed, as Darsh was initiating an iGEM team at their institute after a long break. Although the teams interacted with each other at AIIM’22, had loads of fun and learning chats, both teams shared a great relationship and our team helped ICT Mumbai in tackling iGEM related issues and shared our hacks with them (pun intended).