The process of enzyme manufacturing has already been cracked ages ago, so the protocols of manufacturing polymerases is established. Our aim through this proof of concept isn’t to show you that we successfully produced the Pfu enzyme in a biofoundry, but to lay down the foundational proof (and motivation for future teams?) that a distributed team producing different parts of the enzyme production pipeline can indeed democratize biotechnology. The set-up and functioning of our project is a proof-of-concept that it will work in a real world scenario. Here, we outline how different components have helped us tackle various challenges in democratizing biotechnology and ways we’ve inched towards that goal.
Team:Open Science Global/Proof Of Concept
Proof of Concept
Introduction
Our Social Spirit
When Isaac Larkin, our student lead, had a vision of democratizing biotechnology, he knew it was a daunting and huge task that he wouldn’t be able to do alone. It was required to gather all possible help from everyone in the community, scientists and non-scientists alike. The international set-up of our team meant that there was a representation to address problems that different parts of the world faced which has lead to a low-bioeconomy. Which also meant that many of us lacked traditional biotechnology or engineering background and it would require people to learn a lot more about biotechnology to make it happen. Our current iGEM team consists of people with various skills and expertise and others lacking those. Educating each other was our internal step in bringing about equality in knowledge for us to cater this to the wider synthetic biology community. For that, we open sourced every aspect of our project as well as have detailed documentation to educate others (see education) and have proposed an entrepreneurship idea through which others can also set-up their own companies on top of our workflow.
We learnt a lot from each other in this iGEM journey and did things that wouldn’t have been possible locally.
Our team members from Brazil, some of whom (Giovanna, Isaac G) have participated in previous iGEM years and felt that the biggest hurdle of their project was the inaccessibilty to reagents due to bureaucratic issues. Even though they had excellent ideas, it was a shame that the resources restricted them to not execute the projects to their potential. But, as an international team we were able to do wetlab work in places like Vancouver and USA where the accessibility to resources is higher. They focused their attention on strengthening our software to minimize and automate a lot of physical lab work.
For our team members from the African subcontinent, the opportunity to do synthetic biology research wasn’t abundant. Even if there are other enthusiasts in the region, they are sparsely spread. This is mainly because of the inaccessibility of resources. Being part of the Friendyzmes team helped them to tackle that very problem. They were able to connect with people worldwide passionate about solving the problem. They focussed their attention on building the hardware as a lot of parts were available at a low price.
For people from Canada, creating connections with like-minded individuals outside an academic set-up, sharing resources, and getting inputs on improving their existing resources was very beneficial. They were able to carry out the actual research in the lab set-ups that were carefully planned out by the others.
For the others from around the world, the distributed team provided a platform to make an impact on a real-world pressing problem, inaccessibility to diagnostic capacities during the pandemic. They were able to learn and provide support to SciComm aspects of the project to make it widely known in their local communities.
We bridged the inaccessibility of each of our team members to create our team. To our knowledge, an internationally distributed team working in 4 community laboratories over 10 countries is one of the first in the history of iGEM. So, by participating in this iGEM season, coming so far as to finishing this Wiki at the stroke of the midnight hour, we have shown that a distributed synthetic biology team is possible and can be a great success to deal with international problems at an international scale. One such being, mobilizing people to contribute towards biotechnology.
Building our proof of concept from decoupling:
our wetware build and hardware efforts
The address of our team is the virtual space of Friendzymes Discord Server. While COVID has forcefully made people work virtually, the end-product of an enzyme produced cannot exist in cyberspace. Thus, we take as inspiration a very important engineering concept often applied to synthetic biology, called decoupling, which involves the decomposition of complicated problems into simpler ones, implemented by decomposing complex systems into their simplest components, and separating design from manufacturing. We broke down all the steps in an enzyme production pipeline and performed different tasks at different labs. So, each of our labs functioned as a ‘mini-foundry’.
Building our wetware constructs and making our frugal hardware designs were the bottlenecks and the most problematic parts of our project in our distributed enzyme manufacturing because this required us to solve many logistical issues of transferring physical biological constructs across the globe. We tried to tackle them by using B. subtillis as the model organism. The spores of this bacteria can be shared by embedding them on a paper and they are highly resistant to temperature fluctuations. Dan Zeigler’s patent-free and MTA-free B.subtillis protein expression strains were used to make our Bacillus subtillis toolkit. This would ensure that we can share it with anyone in any part of the world. We made this sharing feasible by uploading the Bacillus subtillis toolkit to the FreeGenes website. It then allowed other labs to order them via FreeGenes. The BioBlaze lab ordered this from FreeGenes and saw the growth of their gene of construct. More details can be seen on our BioBlaze wetware notebook.
Software, the only step in our proof of concept to be done remotely without issue, was also very important in minimizing the need to physically do many wetlab processes through smart wetlab designs and facilitated our distributed enzyme manufacturing.
We were generously sponsored by Opentrons and equipped with Opentrons liquid handler in all of our four labs [see Integrated Human Practices and Sponsors]. This was beneficial to reduce the molecular biology expertise needed to get started in the lab. Having the same liquid handler in all the labs meant that we could automise the same wetware protocols to be followed everywhere. If we knew that a protocol worked in one of the labs, it would would have many chances to work in the other three as well. Most of our wetlab work was done in BioBlaze and Vancouver due to their resource availability and accessibility. We adhered to wetware protocols uniformly in both the places.
We built two bioreactors, one in Peru and the other one in Chicago. In Chicago, as it was done in a community lab we were able to check the functionality using a fluorescent E. coli strain. In Peru, we weren’t capable of testing it with a living organism, because the team member building the bioreactor was not allowed to access the university lab (reserved only for students defending their thesis due to COVID limitations), but the important parameters (such as temperature) were meticulously thought out and we even managed to debug problems with intelligent solutions using circuits, using low-cost electronic components, such as transistors and optodevices. The sand based frugal chromatography column was made to purify the protein of interest. Our genes of interest contained silica binding domains and hence would bind to the sand in the frugal column. We tested this indirectly by setting up to separate and isolate plant pigments which bind to silica in sand as well. So, if it is feasible to purify complex plant pigments then it would be feasible to purify protein of interest tagged with silica binding domains! The frugal plate reader was done to take a measurement of the purity of the proteins secreted. We have documented it in Hardware section.
While we did different parts of the project at different places, we believe that our different modules, built in different parts of the world are robust and we will be joining efforts to integrate those well-established mini-foundries as a next step - just as modules are joined in engineering and as parts are joined with cloning.
Through each of these steps, we’ve attempted to make distributed enzyme manufacturing work in a parallel way and we’ve dealt with democratising biotechnology by frugalising in each step and enabling as many people as possible to be a part of it.