Human Practices

We ask every team to think deeply and creatively about whether their project is responsible and good for the world. Consider how the world affects your work and how your work affects the world.

Introduction

The aspect of Human Practices goes beyond the scientific discovery of our project, and aims to attribute our contributions towards the betterment of the society. To do so, we first have to understand the needs of our community, thereby steering our research in meaningful ways to achieve a connection with the wider world.

Our approach towards Human Practices is divided into three aspects – individual, public, and the professional industry. In each aspect, we maintain an open-mindedness and listen attentively to the needs of the different community. This allows us to achieve a two-way feedback system, where we share with and learn from each community.

Approach towards Human Practices
Fig 1: Approach towards Human Practices



Individuals from the iGEM Team

The first target audience of our Human Practices aspect is ourselves.

Our team is composed of students from different backgrounds and major, from Chemistry to Biological Sciences to Bioengineering students. As student researchers, we perform the experiments and are ultimately responsible for the project's direction. As such, it is of utmost importance that we first reflect on our inspirations and goals leading up to the project. To accomplish this, we had an internal discussion to gather every member’s input on how we can ensure the integrity and safety of our project.

Scientific communication was also a key element of our project, as it allows us to convey our the findings of our project to individuals from different walks of life. By capitalizing on scientific communication, we are able to reach out to as many individuals from different backgrounds as possible. As such, we also wanted to gather every member’s idea on how scientific discoveries should be properly and effectively communicated to those outside the field.

• As a student researcher, how will I ensure the integrity of the results produced / collected during the project within all the teams I’m part of?

• As a student researcher, how will I ensure the safety of myself / other members when performing experimental protocols / during the project?

• Should I compromise the safety of myself / other members to produce experimental results? Elaborate further on the motivations behind your answer.

• In your opinion, what are some ethical concerns surrounding engineered RNA polymerase?

• When communicating scientific ideas to individuals outside of the scientific field, what do you think are some key pointers to take note of?

• In your opinion, what is one community that tends to be disregarded when publishing scientific discoveries? Why?



Our discussions led to meaningful insights which were summarized below. These valuable insights guided our experimental procedures, data presentation and other human practice initiatives.

• Fabrication of results should not be allowed to ensure consistency and credibility. All experimental results should be presented at it is, with clear and transparent documentations.

• All safety rules and regulations should also be strictly adhered to. Individual safety should be emphasised at all times (ie. wearing PPE) to prevent any accidents from occurring.

• Safety of any individuals should not be compromised to meet our experiment outcomes. All experiments should be carried out in a safe and regulated manner to prevent any accidents from occurring. Furthermore, experiments should be designed in a manner to include safety elements.

• When communicating scientific knowledge to individuals outside of the field, avoid using scientific jargons and terminology as they may lead to confusion. Simplification of the topic and analogies are key methods to convey our message across.



Engaging the Public

The second target audience of our Human Practices aspect is the public.

Fig 2: Collage of our Sharing Sessions; some pictures taken during the sharing session

We were privileged to collaborate with National Library Board (NLB) in organising two engaging sharing sessions aimed at creating awareness for our project among young adults and families. These sessions allowed us to gather valuable feedback and inputs from the general public, which further spurred the trajectory of our research.

Throughout both informative sessions, we shared about the motivations behind our research, inspiring younger students to explore the field of science and research. We also delved into the topic of RNA technologies, particularly the use of mRNA vaccines during the COVID-19 pandemic1, through a storybook written and designed by our team members. This creative approach not only informed but also captivated our audience, fostering a deep understanding of the topic.

Fig 3: Some Snippets from our storybook - Mary's Marvelous mRNA Adventure

One of the key elements which aided us in engaging the public was through a storybook that was written and illustrated by our team. Our storybook [Mary’s Marvelous mRNA Adventure] focuses on Mary, as she goes through a series of adventures to learn more about how mRNA vaccines work during the COVID-19 pandemic. The various illustrations used in the storybook help to simplify the complex mechanisms involved, allowing our readers to more easily understand the mechanics behind mRNA vaccines. Our illustrations were also of colourful and dynamic natures, making them more appealing and engaging to children of younger ages.

What We Learnt

One of the key takeways from the sharing session was to converse science effectively. In order to better communicate how mRNA vaccines work, analogies such as cooking following a recipe were used, allowing our attendees to easily follow along our presentation.

We were also able to engage in meaningful discussion with our attendees, as we address concerns regarding the "myths" of mRNA vaccines, and by extension, the relevance of other RNA therapeutics. We also received a few questions, some of which greatly influenced the trajectory our research. The most striking question we received, was perhaps:

"How can your research make the production of these mRNA vaccines safer?" - asked by one of our audiences

mRNA vaccines are typically synthesised by RNA polymerases (RNAP) through in vitro transcription, using unmodified nucleoside bases2. However, the introduction of exogenous mRNA can trigger several immunogenic responses via various pathogen recognition receptors3. One significant milestone in mRNA vaccine development was the incorporation of modified nucleosides4, which significantly reduced these immunogenic reactions.

Amongst the modified nucleotides used in the production of mRNA vaccines against COVID-19, psuedouridine is notable5. As such, we designed an extra experiment to determine if the RNAP variants that we developed were able to incorporate these modified nucleosides, and whether they would affect the transcriptional strength.



Interview with Professionals from Leading Industries

The third target audience of our Human Practices aspect is professionals.

We also had the opportunity to interview professional scientists from leading industries and research institutessup>*.These interactions allowed us to learn more regarding the standard practices and the difficulties faced, in both novel protein engineering and mRNA production. We were also able to discuss ethical concerns with regards to emerging fields of therapeutics.

• How do small-scale reactions that are performed in laboratory settings differ from those that are carried out in large-scale in biopharmaceutical companies?

• What are some of the common techniques utilised in product purification?

• How has COVID-19 influenced the development of mRNA therapeutics?

• What are some difficulties faced during novel protein engineering?

• What are some of the ethical concerns regarding emerging therapeutics? What are some key areas we should look out for?



• There are multiple complexities involved when scaling up biotechnological processes. These include protein recovery, and reducing waste during the mRNA production process. There are also other challenges such as achieving purity in enzyme-mediated mRNA synthesis and reducing undesirable by-products such as double-stranded RNA.

• Product purification is crucial in both chemical and enzymatic mRNA synthesis, as contaminants like double-stranded RNA can elicit immune responses. Methods such as high-performance liquid chromatography (HPLC) and continuous manufacturing can help improve the purity. Furthermore, there is also a need for innovative methods to address the production of other forms of RNA (eg. circular RNA).

• The COVID-19 pandemic was a catalyst for increased focus on mRNA research. However, with the emerging fields of oligonucleotide therapeutics, extra measures and regulations should be put in place to ensure the safety of these researches.

• One of the main issues related to novel protein engineering ties in with intellectual property (IP). There are incentives for patenting a novel sequence, especially for biopharmaceutical companies. However, one of the key factors in deciding the patentability of a particular protein lies with its sequence similarity, with lower sequence similarity usually being easier to patent.



*The identity of our interviewees are kept annonymous to prevent any conflict of interest.

What We Learnt

One of the key takeaways from our interview was the difficulties faced in novel protein engineering. Generating functional proteins with a sequence similarity low enough proves to be difficult due to the unpredictability of unknown seqeunces. Conventional methods such as random mutagenesis via error-prone PCR (EP-PCR)6 usually yield limited variability, thereby requiring large mutant libraries to be screened before identifying better-performing variants.

The slight limitations involved in random mutagenesis thus prompted us to utilise other de novo protein sequence generation methods and tools such as ancestral reconstruction7 and Progen28 respectively.

References

1 Lamb Y. N. (2021). BNT162b2 mRNA COVID-19 Vaccine: First Approval. Drugs, 81(4), 495–501. https://doi.org/10.1007/s40265-021-01480-7

2 Rosa, S. S., Prazeres, D. M. F., Azevedo, A. M., & Marques, M. P. C. (2021). mRNA vaccines manufacturing: Challenges and bottlenecks. Vaccine, 39(16), 2190–2200. https://doi.org/10.1016/j.vaccine.2021.03.038

3 Karikó, K., Ni, H., Capodici, J., Lamphier, M., & Weissman, D. (2004). mRNA is an endogenous ligand for Toll-like receptor 3. The Journal of biological chemistry, 279(13), 12542–12550. https://doi.org/10.1074/jbc.M310175200

4 Karikó, K., Buckstein, M., Ni, H., & Weissman, D. (2005). Suppression of RNA Recognition by Toll-like Receptors: The Impact of Nucleoside Modification and the Evolutionary Origin of RNA. Immunity (Cambridge, Mass.), 23(2), 165–175. https://doi.org/10.1016/j.immuni.2005.06.008

5 Nance, K. D., & Meier, J. L. (2021). Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines. ACS central science, 7(5), 748–756. https://doi.org/10.1021/acscentsci.1c00197

6 McCullum, E. O., Williams, B. A., Zhang, J., & Chaput, J. C. (2010). Random mutagenesis by error-prone PCR. Methods in molecular biology (Clifton, N.J.), 634, 103–109. https://doi.org/10.1007/978-1-60761-652-8_7

7 Joy, J. B., Liang, R. H., McCloskey, R. M., Nguyen, T., & Poon, A. F. (2016). Ancestral Reconstruction. PLoS computational biology, 12(7), e1004763. https://doi.org/10.1371/journal.pcbi.1004763

8 Nijkamp, E., Ruffolo, J. A., Weinstein, E. N., Naik, N., & Madani, A. (2023). ProGen2: Exploring the boundaries of protein language models. Cell Systems, 14(11), 968-978.e3. https://doi.org/10.1016/j.cels.2023.10.002