Human Practices (Gold & Integrated)

Aims and Rationale

Sensynova was a project founded in Human Practices. Each branch of our project is rooted in a barrier to biosensor implementation identified by in-depth conversations with stakeholders. We identified not only technical issues, but also societal issues, as these are equally important in ensuring successful implementation of biosensor projects.

The aims of our human practices were to:
1 - Determine how current biosensor developers design, produce and implement biosensor projects
2 - Use these talks to determine the common barriers to biosensor development and implementation
3 - Create novel solutions to identified problems, producing frameworks and guidelines to aid future researchers

To achieve these aims, we emailed, skyped and attended conferences to speak to stakeholders in biosensor development, from the early research stage to the end-user.

Introduction

Synthetic Biology biosensors have a number of advantages over traditional methods. They are cost-effective (after the research stages, production of the biosensor relies only on the maintenance of a population of cells expressing an engineered system); can produce a variety of sophisticated behaviours, such as signal amplification and logic gates; and often have no reliance on additional equipment and therefore are ideal for onsite diagnosis.

Each year a plethora of useful biosensors are developed, both by iGEM researchers and in the broader synthetic biology community. We now have access to biosensors for applications ranging from water contamination to fruit ripeness. In fact, we had originally decided on the development of a biosensor for herbicides as our iGEM project. However, our research for this project unearthed an interesting fact: despite the large number of synthetic biology biosensors that have been developed over the years, there is a distinct lack of synthetic biology based biosensors in everyday use. Despite their advantages over methods like immunoassays and mass spectroscopy (which are expensive and often rely on additional equipment), these traditional methods are much more widely used by researchers. Also, day-to-day usage by non-scientists, who are often the target end-user for a biosensor, has not yet materialised. In fact, not one synthetic biology based biosensor has been approved for use outside of a laboratory setting by the EU.

This led to the question which shaped not only our human practices work, but our project as a whole: what are the barriers facing synthetic biology biosensors, and what can we do to help?

The Issues

Issue #1: Parts Reusability

“Each generation of scientists keeps reinventing the wheel” - Dr Martin Peacock

The Issue

When talking to experts about biosensor development, a common theme that came up was the rediscovery and work done on commonly used biosensor parts which lengthened the development process, as well as limited resources for novel findings. We talked to Dr Martin Peacock, a hardware biosensor developer, about this and he mentioned how this limits his hardware development and that having common part reusability would combat this problem.

Our Solution

Our solution to this problem was the creation of the modularity aspect of the Sensynova biosensor development platform. As part of the platform, developers can switch in and out different components of each device (adaptor, detector, processor and reporter) isolated in different cells, and co-culture these together so there is an easy switch in-switch out system. Variants of the devices could then be distributed in agar slabs, as a biosensor development kit.

Issue #2: Range of Analytes and Outputs

“Main bulk of the work in developing a biosensor is the deduction of the mechanistic process of substrate-circuit interaction” - Dr Oliver Purcell

The Issue

The majority of work done in the research and development around biosensor development is the deduction of native interactions between a target molecule and binding site. There are also many substrates which don’t have a known binding site. Upon discussion with biosensor developer Dr Oliver Purcell, he told us that this took up a large chunk of time during development.

Our Solution

To combat this issue, we have created a synthetic promoter library which a large number of substrates that don’t have a known binding sequence can be screened against. The screening would find a promoter that was induced by that substrate. This takes the focus from the biological knowledge and onto the engineering of the biosensor. Also, we have developed an adaptor module, which can link a substrate like the ones above into our system by breaking it down into a compound that has a known binding sequence.

Issue #3: Legislation

“The main problem with using biosensors outside the lab is legislation” - Dr Chris French

The Issue

The use of synthetic biology based biosensors is limited in the field due to restrictions around the use of genetically modified organisms outside controlled areas. Speaking to Dr Chris French on this matter, he told us about his experience with this issue when trying to get clearance for the use of the arsenic biosensor in the field. It became clear that this was the only hurdle in the arsenic biosensor project and that it was the reason the project has come to a stand still.

Our Solution

During our discussions with Dr French, he pointed us in the direction of the Workshop on Biosensorsthat took place in April 2017. This report said that “a possible solution to getting around legislative restrictions is the use of cell free systems”. After reading this and along with our discussions with experts, we went forward and created a mixed cell free system, informed by a design of experiments model to be able to implement our system in a cell free manner, in the future.

Issue #4: Extensive Optimisation

“Optimisation of a system is another time consuming step in development” - Dr Chris French

The Issue

Tighty coupled whole cell biosensors require extensive genetic engineering to optimise the system, for example breaking apart the components and reassembly including changes to optimise the system.

Our Solution

Our development platform allows the interchangeability of parts across the full biosensor, and the modularity aids easy optimisation. This is because changes can be made to one part if necessary, or the part can be swapped out for another, by relating it with the new device in a different cell, then reculturing.

Issue #5: Uptake of Technologies

“Only the top 5% of an industry will pick up new technologies, and we rely on them feeding it down" - Dr David George

The Issue

When researching a concept for the project, we attended the N8 Crop and Agriculture Innovation Conference, where we heard a talk by Dr David George, who was speaking about the uptake of new technologies among agriculture industries. He said that only a small percentage of the top of an industry will pick up a new technology, then it is relied to filter down the industry. Professor Rick Mumford also spoke on the long process from lab to field and that improvements of the innovation pipeline can be made at every level, including deployment.

Our Solution

We have looked at this issue from a communication angle and extensively analysed the current profile of SynBio in the media, as well as producing guidelines for future science communication. We did this to help future teams and scientists on how to best communicate their work and help deployment of technologies to the public.

Further Stakeholder influences and feedback

During our extensive talks with stakeholders, we took other ideas and advice on board and directed our project's direction accordingly. At the N8 Crop and Agriculture Innovation Conference, we spoke to many experts in the agriculture industry, including organic farmers. They were interested in the detection of herbicides such as Glyphosate. This lead to use looking for a detection module we could incorporate into our system that could detect it. There was no known binding sequence for Glyphosate and this lead to us developing Sarcosine Oxidase, an adapter module that broke down Glyphosate into formaldehyde as this has a known biosensor.

During talks with Dr Karen Polizzi from Imperial College, she told us about her work with biosensors in bioprocessing and bioreactors. From this, she told us a particular problem industry is questions over reliability; is it as reliable as a non biological mechanism for detecting things? they have access to any analytical equipment they want- how does the performance and reliability of your biosensor compare to that? We kept this in the forefront of our minds when carrying out extensive characterisation and optimisation process.

It was important to use to complete the design circle and revisit our stakeholders after our initial conversations. At the end of our laboratory work, we recontacted all the experts that helped us on the way, to get their feedback on our work. Dr Martin Peacock was impressed with the problems we had addressed and commended us on our novel approach to solving them. We’d like to thank Dr Chris French, Dr Martin Peacock, Dr Karen Polizzi and Dr Oliver Purcell for their invaluable insight into biosensor development and their help in influencing our project.

Conclusion

The possibilities of synthetic biology biosensors are wide reaching, from diagnostic applications to bioremediation, and their advantages include low equipment requirements and portability in the field. However, there are still many issues in their development and deployment. As a team, from all our skype calls, emails, conferences, and own research we have identified five main issues, which have influenced how we addressed our project. We recognise there are other issues in biosensor development which were not able to be considered in the scope of this project; sample backgrounds and speed are two problems which, in the future, can be tackled. On the whole, we focused on problems that we had established were the major concerns and offered our solutions to each.

Our project demonstrates the importance of early stage human practice discussions. Through attendance at a crop improvement conference and early discussions of the specific herbicide biosensors in our original project plan, we gained an understanding of the broader biosensor issues. It was through these realisations and subsequent discussions with stakeholders in biosensor development that we were able to confirm that these were real issues, and changed the focus of our project accordingly - shifting from production of a specific biosensor to a broader study of synthetic biology produced biosensors. A willingness to facilitate honest discussions about the advantages of a synthetic biology approach whilst reviewing the limits of the current technology is essential for progress. Teams starting to integrate human practices at a later stage in their project development, having invested time and resources into a project, may find themselves at risk of having to “sell” their project to potential stakeholders, preventing opportunity for open and honest discussion.

We hope that in addressing the barriers outlined here, we have facilitated the progression of synthetic biology biosensors, bringing us closer to a future in which the broad range of biosensors developed are utilised and have impact on our lives on a day-to-day basis. Encouragingly, we found that all the biosensor developers we approached were very open to discussion of the limits of current technology, and excited about potential improvements.

Advice to future teams

We advise future iGEM teams to begin early with human practice discussions. We approached stakeholders in our project within a month of settling on a project idea: well before the summer had started and wetlab work began. This means that projects still have the plasticity to adjust following discussions, even if that means a complete change of project, as was the case for us.

It is important to maintain lines of communication with stakeholders. The easiest way of determining if you have correctly addressed a concern is to ask the person who posed it in the first place. However, many teams fail to do this. We contacted many of the people we had originally engaged at the beginning of the project again at the end to discuss the final framework. Not only did we get some great positive feedback, we also were able to discuss areas for future improvement, which would enable further iterations of the design-build-test cycle.

Finally, do not be afraid to ask the difficult questions. As new inductees to the field of synthetic biology, iGEM team members are perhaps some of the best suited for identification of bigger issue problems in the field of synthetic biology. For us, this was the inability to be able to point to an example of a synthetic biology produced biosensor in use in everyday life. Closer inspection of other applications of synthetic biology are likely to pose their own unique challenges. Therefore, we encourage other teams to follow our example: iGEM teams have been hugely successful in identifying problems in many areas - we propose that turning this insight on our own field of synthetic biology is equally important.