Integrated Human Practices

Overview

Our team values the importance of connecting Science and the Society together and bringing about a human-centred design. Human practices was an important way for us to interact with the outside world to find out more about the real-world problems and understanding the needs of those who were affected by these problems. As our team was delving deeper into studying RNA-RNA interactions, it was imperative for us to speak to people who can advise us on our project and whom we thought would benefit greatly from our technology. Our Human Practices page would take you through our journey of interactions and engagment with people from diverse backgrounds and expertise and how their perspectives have shaped our project into what it is today.

Who did we talk to?

Experts

Organizations

Experts

This group of people was important for they provided us with valuable inputs and guidance to overcome challenges in our project. They also often had deep understanding of current trends and emerging technologies in their own fields which helped us understand whether our project was on par with current technology. They have also provided us with tailored advice based on their knowledge which has helped us understand information that we were not aware of before and assisted us in adapting our project accordingly. Look through our interviews below to find out whom we spoke to and what we learnt from them!

Organisations

This group of people was also equally important for us to understand how wouls our project be implemented in their workflow and whether it would benefit them. In fact, getting their endorsement and approval for our project would show others that our project indeed has potential to be used in a wide variety of applications.

Prof Roger Foo, Dr Ben Tan

Consultants @ National University Hospital

19 Mar 2023 - 22 Mar 2023

Why did we approach Prof Roger Foo and Dr Ben Tan?

After researching, we decided to focus on stroke due to its significance for Singaporeans. We decided to consult specialists to grasp their views on stroke, current detection, diagnosis, treatment methods, and assess the need for more efficient biomarker detection in the healthcare industry.

What did we learn from them?

We proposed a non-invasive sweat biomarker detection method for stroke to Dr. Ben and Prof. Roger Foo. They explained that stroke is multifaceted with no established blood-based biomarkers, making sweat biomarker detection challenging due to its intermittent nature. Dr. Ben Tan also introduced RapidAI for immediate CT scan data transfer and suggested exploring RNA-based biomarkers.

What is our next course of action?

After discussions with Prof. Foo and Dr. Tan, we recognized the complexity of biomarker research, necessitating rigorous validation before clinical adoption. Understanding stroke's multifaceted nature and numerous influencing factors, we decided not to pursue this topic. Instead, inspired by biomarkers, we decided to focus on sensors and RNA regulatory elements for our project.

Mr Alawn Koh

Head of Business Development @ Rong Yao Fisheries (Open-Cage Sea Farming)

19 May 2023

Why did we approach Mr Alawn Koh?

As our team started to focus on developing sensors, we wanted to know whether local fish farms would benefit from our technology, especially since Singapore has a goal of becoming self-sufficient by 2030 and we wanted to know whether viral infections can hinder farms from having more yield.

What did we learn?

Smaller fish farms, like Rong Yao, face significant delays of two to three weeks in obtaining fish health and disease status results. This delay hinders timely disease containment and appropriate treatment, potentially causing unnecessary antibiotic use and financial wastage. Immediate testing is vital for efficient disease management and cost-effective treatment.

What is our next course of action?

Insights from the discussions led to exploring two solutions: a rapid testing system to minimize economic losses from mass mortality events and continuous monitoring for real-time health tracking, enabling swift responses to disease outbreaks.

Dr Sunita Awate

Research Director @ UVAXX

24 May 2023

Why did we approach Dr Sunita Awate?

We consulted aquaculture expert Dr. Awate to gain insights into virus testing in aquaculture farms and understand disease management perspectives. We presented our aforementioned proposed solutions to assess their viability and gather expert input.

What did we learn?

Detecting diseases is difficult due to virus mutations. Early warning systems, including water bacterial load monitoring, are important. However, farmers hesitate to invest in new, costly technology due to traditional mindsets and financial concerns.

What is our next course of action?

The team recognized the need for an affordable, variant-specific test kit to tackle virus mutation challenges. The idea of a continuous monitoring system was dropped due to cost concerns for farmers. Further, consulting more aquaculture researchers about using e-DNA for water pathogen sampling was deemed necessary.

Dr Giana Bastos Gomes

Aquatic Veterinarian Researcher @ Temasek Life Sciences

31 May 2023

Why did we approach Dr Giana Bastos Gomes?

We had come across a research paper that talked about using eDNA for virus testing [1]. Hence, we wanted to gain more insights into this paper and whether eDNA can be a potential way for us to do virus testing.

What did we learn?

We discussed with Dr. Giana on using eDNA for water testing, emphasizing qPCR/digital PCR for specificity. Challenges in eDNA implementation due to contamination, logistics, and farmer engagement were noted. We were planning an on-site testing system similar to COVID ART kits was mentioned but it was seen as optional for farmers unless made mandatory. Dr. Giana emphasized quantifying water pathogens over simple presence/absence testing.

What is our next course of action?

After the fruitful discussion with Dr Giana, the team started to plan for the utilization of RNA regulatory elements as a tool in the aquaculture industry and also explore broader applications beyond aquaculture.

Mr Alrik Tan

Research and Product Development Member @ Natural Trace

31 May 2023

Why did we approach Mr Alrik Tan?

We connected with Natural Trace, a company focused on using DNA for tracing applications, aligning well with the detection aspect of our project. This alignment prompted us to arrange a meeting with Mr. Alrik Tan to gain a deeper understanding of the technology employed by Natural Trace and explore potential synergies that could mutually benefit our respective initiatives.

What did we learn?

From our discussion with Mr Alrik Tan, we have understood that they use PCR-based detection, which is specific and provides known and specific input-output values and their current detection pipeline takes around 4 hours to obtain results from PCR. We have also learnt that Natural Trace is open to the idea of a nucleic acid-based test kit if it provides comparable accuracy and speed.

What is our next course of action?

As a result, our team has decided that DNA tracing can be one other application other than aquaculture where we believe that our RNA regulatory elements can play a part in the future.

Dr Moses, Dr Kelvin Ho, Dr Zhang

NParks Animal Veterinarians

1 Jun 2023

Why did we meet with NParks?

As we started brainstorming applications where our technology may be useful, we decided to explore the applicability of our technology in Zoology and animal science. Specifically, we sought to determine if our technology could detect zoonotic viruses in animals before they affect humans.

What did we learn?

NParks effectively manages zoonotic disease risks in wildlife. PCR is standard for virus confirmation; rapid tests complement but can't replace it. Rapid testing may aid border checks for imported animals. Unlike aquaculture, wildlife industry prioritizes virus presence over quantification in testing.

What is our next course of action?

Our technology could enhance animal virus testing at borders, complementing PCR. Recognizing diverse industry needs, we continue to aim to assist multiple sectors effectively.

Dr Jacqueline Valeri

Author of "Sequence-to-function deep learning frameworks for engineered riboregulators"

7 Jun 2023

Why did we approach Dr Jacqueline Valeri?

Dr. Valeri's paper on deep learning for engineered riboregulators is our starting point to model RNA switches [2]. We're investigating challenges in implementing deep learning due to limited high-throughput datasets for RNA switches.

What did we learn from her?

Dr. Jacqueline Valeri explored fast-activating RNA toehold switches for viral detection, tolerant to small genetic differences. Benefits of them included freeze-drying for diagnostics, design improvements. Challenges included limited dynamic range, often requiring CRISPR or amplification. Commercialization was hindered by technology adoption reluctance. Deep learning models need a rich dataset for training.

What is our next course of action?

As a team, we have made the decision to focus on improving the design rules for RNA switches and exploring their potential as versatile tools with substantial improvements in component orthogonality for various applications.

Dr Nicolaas Manuel Angenent-Mari

Scientist, Author of "A deep learning approach to programmable RNA switches"

9 Jun 2023

Why did we approach Dr Nicolaas Manuel Angenent-Mari?

Alongside Dr. Valeri’s paper, “A deep learning approach to programmable RNA switches” was another reference point for us [3]. We wanted to learn more about how they generated and characterised 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors.

What did we learn from him?

We discussed toehold switch challenges with Dr. Nicolaas, highlighting low interest and commercial value in prokaryotic gene circuits. This inspired plans to emphasize gene circuit importance in our education initiatives. Dr. Nicolaas emphasized difficulties in library generation for our deep learning model, proposing Shine-Dalgarno sequence modifications to enhance variant yield. He also explored the rationale behind choosing first-generation toehold switches for a comprehensive library, ensuring diverse representation despite potential performance improvements with forward-engineered variants.

What is our next course of action?

Post-interview, the team discussed the challenges of library generation and acknowledged potential variant loss. Toeholds were recognized as insufficiently sensitive switches but we decided to work with forward-engineered toehold switches for their superior performance compared to the first generation. Additionally, we opted not to pair amplification with toeholds, focusing on generating a comprehensive toehold library database.

Mr Aidan Riley

Graduate Research Fellow @ Boston Univrsity

16 Jun 2023

Why did we approach Mr Aidan Riley?

We wanted to seek further clarifications about toehold switches from the first paper that was published - “De Novo Designed Riboregulators of gene expression”[4]. We were directed to Mr. Aiden Riley to seek his opinion as we were entertaining a generative approach for toehold switches at that time which coincided with Mr. Riley’s work.

What did we learn from him?

We discussed generative toehold sequence approaches with Mr. Aidan Riley, affirming our research direction. Mr. Riley validated our idea and advised on dataset size for generative models. He suggested mathematical or piecewise modeling for specific toehold switch regions due to dataset limitations.

What is our next course of action?

Post-interview, we realized generative modeling might be data-intensive. Hence, we're exploring transfer learning and simpler models initially. Our next steps involve reviewing literature on DNA/RNA sequence models and pursuing dual paths: simpler models (linear regression, random forest) and complex encoder/decoder models. Success in these will lead us to consider generative modeling.

Dr Chayasith Uttamapinant

Scientist

21 Jun 2023

Why did we approach Dr Chayasith?

We were introduced to Dr Chayasith Uttampinant as he has worked on toehold switches on mammalian cells and we wanted to learn more about his work to understand the challenges he has faced and gather his advice for our experiments.

What did we learn from him?

Dr. Chayasith highlighted toeholds' limited sensitivity and incompatibility with mammalian cells, reducing their usability. He noted that CRISPR-based methods with amplification offer potentially greater sensitivity due to multiple signal amplification rounds, unlike toehold-mediated strand displacement, which typically has a single round. We discussed leaky toeholds and informed him of our strategy to address this by implementing a negative selection marker like the gene sacB, which he validated.

What is our next course of action?

Post-interview, we recognized toehold issues like low sensitivity and leakiness. We plan to address this using sacB as a negative selection marker, aiming to remove leaky toeholds. Additionally, we'll utilize these leaky toeholds, along with functional ones, to train our deep-learning model for a diverse toehold library.

Dr Ling Hua

Synthetic Biology Scientist

29 Aug 2023

Why did we approach Dr Ling Hua?

We were introduced to Dr Ling Hua due his expertise on metabolic engineering. Through him, we wanted to know the feasibility of our project in bioproduction to see if this can be another potential application of RNA-RNA interactions.

What did we learn from him?

In discussions with Dr. Ling Hua, we explored challenges in precise gene expression control within metabolic pathways. Gene expression is condition-dependent, posing tuning difficulties. Balancing high yields with organism health in metabolic engineering is complex, considering potential strain limitations and toxicity of intermediate products. We inquired about using transcriptional and translational control, learning both have distinct advantages and can be effective based on conditions, providing flexibility in their application.

What was our next course of action?

We were very happy to learn from Dr Ling Hua that our project, indeed, has potential in the area of bioproduction although more research needs to be done into this area. Dr Ling Hua had also mentioned that our machine-learning model needs to be user-friendly in order for researchers in bioproduction to become more receptive to adopt our model.

References

[1] Giana Bastos Gomes a et al., “Use of environmental DNA (Edna) and water quality data to predict protozoan parasites outbreaks in fish farms,” Aquaculture, https://www.sciencedirect.com/science/article/pii/S0044848617307615 (accessed Oct. 4, 2023).

[2] J. A. Valeri et al., “Sequence-to-function deep learning frameworks for engineered riboregulators,” Nature Communications, vol. 11, no. 1, 2020. doi:10.1038/s41467-020-18676-2

[3] N. M. Angenent-Mari, A. S. Garruss, L. R. Soenksen, G. Church, and J. J. Collins, “A deep learning approach to programmable RNA switches,” Nature Communications, vol. 11, no. 1, 2020. doi:10.1038/s41467-020-18677-1

[4] A. A. Green, P. A. Silver, J. J. Collins, and P. Yin, “Toehold switches: De-novo-designed regulators of gene expression,” Cell, vol. 159, no. 4, pp. 925–939, 2014. doi:10.1016/j.cell.2014.10.002