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After our conversation with David we visualised our project in an entirely different manner. We decided to make some changes to our project: | After our conversation with David we visualised our project in an entirely different manner. We decided to make some changes to our project: | ||
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We no longer focused on the spider silk aspect of the project. We decided inteins would be at the core of the project. | We no longer focused on the spider silk aspect of the project. We decided inteins would be at the core of the project. | ||
Revision as of 18:19, 19 November 2018
Overview
Science and society work best in sync - it is important to realise that the development of technology is a two way conversation between scientists and stakeholders. With this in mind, we made sure to work closely with people outside of our lab. These conversations influenced our design, our lab project, our public engagement and our understanding of bio-safety. Through engagement with scientists, the biotechnology industry, and the public, we decided to develop SETA, a tool that benefits the great scientific community and makes BioBricks more accessible. We also conducted a short psychological survey on art as a tool for synthetic biology education. Our results indicated that the public is more engaged through art as opposed to purely text-based communication. We integrated this finding into the way we communicated our project.
Bolt Threads
Bolt Threads is a world-leader in spider silk scale up for use in the fashion industry. Our Skype conversation with David Breslauer, the CTO and co-founder of the company, gave us an insight on the impact our project will have on the world but also forced us to rethink some of our ideas and redesign the project. Below is a summary of key topics discussed:
We learnt about the benefits of using synthetic spider silk for textiles. Since the biomaterial is durable, it will last longer and cause less waste. The carbon dioxide emissions are lower compared to the current textile industry which relies on the use of fossil fuels. We considered whether the use of growth media was a major drawback. Food crops, for example, have to be substituted to produce a food source for the microbes synthesising spider silk. However, we may solve this issue by cultivating more productive engineered crops. This made us wonder about the future perspectives of our project. We envisaged the possibility of creating our biomaterial in cyanobacteria or algae due to their relatively low carbon footprint, requiring just carbon dioxide, water and light. With more time we would have liked to investigate the possibility of cultivating our spider silk in algae. Another biomaterial Bolt Threads has recently developed is mycelium leather, a replacement for natural leather. By using synthetic materials, they remove the need for animal cruelty. Our work would remove the need to harm spiders directly. Some spider silk is spun by pulling threads out of the spiders spinneret, the organ responsible for silk extraction. This process is also inefficient and requires a lot of time, therefore using synthetic spider silk will help scale up the production.
David informed us about the use of chimeric proteins and their functionalization. For example, hydrophobic proteins could be bound to spider silk to enable waterproof clothing. However, one of the greatest hurdles in designing chimeric proteins is the difficulty in predicting their behaviour. Due to steric hindrance caused by large molecules, chimeric silks to not always behave in an ideal manner. David was familiar with intein proteins. We decided to replace SpyTag and SpyCatcher proteins with inteins entirely. This is because SpyTag and SpyCatcher are large proteins which may prevent the spider silk from behaving correctly. This was doubly confirmed after we performed a small literature review, which showed the benefits of inteins for this purpose.
Protein engineering can benefit from models capable predicting behaviour. We were informed that computational modelling may help predict the polymerisation pattern of fibres. This would enable scientists to design protein polymers with greater ease. We thought about designing a model which would enable a user to test the polymerisation of different proteins when bound by inteins.
Other protein biopolymers exist in nature too - collagen, keratin and elastin are some of the most common. These proteins are often studied for tissue engineering applications but, we found that synthesising them and getting them approved for medical applications is often a challenge. Rigorous testing and expensive trials are often needed for the development of these biomaterials. We were told that a tool that enables rapid functionalisation of fibres would be beneficial to people working with polymers. This led us to take our project in an entirely different direction. Instead of focusing on spider silk, we decided to shift our focus to intein polymerisation which would benefit a much larger community of people. SapI sites were inserted so that any biomaterial could be substituted for more efficient manufacturing.
In order to spin spider silk, we require high concentrations of the material. We were told that the easiest way to spin silk is to dissolve it in high concentrations of acid and extrude the product into an ethanol bath. Although this technique is simple, it would require the use of harsh chemicals that would eventually find their way into the environment. Another popular method is electrospinning which requires an extremely high voltage. David hadus look into alternative methods of spinning spider silk and it made us think about the environmental implications each one would have.
After our conversation with David we visualised our project in an entirely different manner. We decided to make some changes to our project:
- We no longer focused on the spider silk aspect of the project. We decided inteins would be at the core of the project.
- The inteins became a modular platform for protein polymerisation. We decided to test the polymerisation of RFP and GFP, two different proteins, instead of spider silk. This introduced a more novel concept (as spider silk polymerisation has been done before).
- We considered the use of an alternative chassis, algae or cyanobacteria, to make the product even more eco-friendly in the future.
- Our model for spider silk polymerisation changed to intein polymerisation by creating new parameters which allowed the model to act in a more modular fashion. The protein being polymerised, for example, was one of the parameters the user can now select.
Modularity in Biology
Following our conversation with Bolt Threads we met with Chris Myers, a professor who has avidly combined electrical engineering and genetic circuits in support of standardisation. We discussed standards in synthetic biology and integrating them effectively. Our conversation made us think about the importance of modularity and how BioBricks could be improved. We looked into the BioBrick standard and the issues that accompany it. The BioBrick registry provides a great array of genetic sequences for DNA assembly, however combining DNA using BioBrick assembly is not as effective. One problem we regularly encountered was assembling spider silk. The sequence of spider silk is repetitive, and the protein structure is glycine and alanine rich which leads to further instability in the cell. A better way of constructing the long sequence was needed. Constructing spider silk using BioBrick assembly is inefficient. Chris Myers gave us a firmer grip on standardisations which we applied in constructing our final brick. We found an efficient way to apply Gibson and Golden Gate while maintaining the BioBrick standard.
WASE-Tech
WASE is an organisation devoted to providing sanitation and energy to developing regions. When we went to visit them at Open Cell, we had the pleasure of talking to the CTO, William Gambier. The team was developing a decentralised wastewater treatment which we understood involved applying a bacterial biofilm to clear water naturally. We found the use of microbes to clear water to be clever, however from a synthetic biology perspective, if GMOs were to ever be applied it would open an entirely different ethical debate. We saw the need for a less biohazardous method of filtering water. Due to its high strength, a spider silk filter would provide a long lasting method of cleaning water. The silk proteins could be functionalised with heavy metal binding proteins for the removal of toxic compounds, for example. A spider silk filter would benefit local communities, which may apply decentralised wastewater treatment, however the cost of manufacturing at the moment would be infeasible for poorer regions.
Thanks to WASE we thought about implementing a spider silk filter in our project:
- We looked at decentralised wastewater treatments as a way of applying the spider silk filter in society.
- We looked into functionalising spider silk with proteins capable of binding different toxic elements, like heavy metals.
IndiCo
IndiCo is a company which originated from a past iGEM idea - patterning bacteria onto clothing. We had an interesting conversation with one of their representatives about the use of bacteria for creating patterns on clothing. The idea relied on bacteria covering a fabric and releasing a pigment on it. It was interesting to hear that customers did not find the product off-putting, although microbes had been on it. We spoke about our spider silk project and how we can use synthetic textiles to help the environment and living animals. Although the textiles would be plain white, we thought about functionalizing spider silk to provide colour. Chromoproteins are proteins which contain pigments, such as hemoglobin which makes blood appear red. Our project would be able to create coloured clothing by functionalising silks with chromoproteins. We found out that this is very environmentally friendly because the dye industry causes serious harm through the release of harsh chemicals for the manufacture of natural fabrics. Chromoprotein functionalised spider silk would prevent this issue.
IndiCo taught us about dyes in the textile industry and made us think about potential functionalization applications:
- Functionalising spider silk with chromoproteins is something we’d look into in the future.
Art in SynBio
Keeping designers and artists at the core of our project, we decided to investigate the effectiveness of art as a tool in science communication. With the support of psychologist Elena Petrovskaya, we conducted a short psychological study. Using appropriate study designing platforms and validated methodologies, we discovered that art is more engaging and enjoyable than text alone in the communication of synthetic biology. To support future iGEM teams and researchers to build on this new study, we decided to write a white paper for others to use our results. To integrate these findings into our project, we decided to apply art to our extensive education and public engagement strategy. We held an art competition, created novel art postcards and designed an art exhibition keeping artists close to our work. We also investigated Da Vinci’s role as a mediator in art and science.
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