Jenny Molloy studied Zoology and is now a Shuttleworth Fellow at the University of Cambridge. She is a director of Biomakespace, and much of her work aims to make research more open and globally accessible.
Q: Can you describe in one sentence what this project is about?
The goal of the project is to produce a toolkit for making enzymes, specifically enzymes that are critical biological research tools, as cheaply and easily as possible.
Q: How did the idea for the project come about?
I’ve collaborated with a lot of scientists from the global South and during my PhD research on mosquito control I was very aware that the biological experiments I was doing were extremely expensive. I learned that in many parts of the world, reagents are not affordable and take a long time to arrive which limits the science that can be done and the application of that science to solving local and global problems. I also have experience volunteering and working on open-source biology projects where we aimed to make science more accessible, so I wanted to use that knowledge and experience to make molecular and synthetic biology research more accessible to researchers in underfunded laboratories.
This project is part of my fellowship at the University of Cambridge but volunteers and students at Biomakespace have been helping a lot. It’s also not just laboratories in poorer regions that could really benefit from the toolkit but also community laboratories like Biomakespace. We want people to be able to play with the technology, to try and fail, and expensive enzymes are one of the things that makes this cost-prohibitive.
Q: Can you explain the project in more detail?
We plan to create an open-source toolkit for the production of enzymes (which are specific kinds of proteins) for people working in low-resource laboratories. The toolkit will consist of hardware designs, the DNA required to make E. coli bacteria produce the enzymes of interest, protocols, and quality-control guidance. It will be as readily-available as possible and we are co-developing and piloting it with colleagues in Ghana and Cameroon.
It’s definitely a longer-term project because we want to offer all of the most important enzymes in the toolkit, not just one or two! The types of enzymes we have in mind are: DNA polymerases, ligases, reverse transcriptases, as well as restriction enzymes. What we want to create is an essential toolkit to cheaply produce good-quality enzymes that most molecular biologists and synthetic biologist would be using on a daily basis. This is the goal, and the number of enzymes will vary depending on how much time and funding we have to optimise the protocols. We are co-developing the project with the Kumasi Hive BioLab in Ghana and the Mboa Lab in Cameroon since the toolkit can really make a difference there. We collaborate closely and share designs, which has been great!
Open Bioeconomy Lab team members during a meeting in Cameroon. Stephane Fadanka and Lenchina Agbor from the MboaLab, Chiara Gandini from University of Cambridge, and Anne-Pia from the University of Geneva.
This single large project consists of several smaller projects that start with obtaining the DNA sequence of the enzyme you want to make. The first step is to search through patents for expired ones as they may contain the sequences of enzymes of interest. You then test these sequences against research papers to see whether you’ve got the right sequence to get the actual enzyme. A lot of sequences sadly are not easy to find and there are lots of steps involved to get a well-expressing construct for E. coli.
When you then finally get protein expression working in E. coli, you need to worry about the costs of expression. IPTG is the (expensive!) chemical generally used to induce protein expression in this organism. We instead like to let biology do the work by selecting promoters that auto-induce or are activated by something readily available and cheap, like light, which James Sanders, our summer intern, currently works on. Hannah Norbäck, our other Biomakespace intern, is working on tags that are needed to precipitate the protein out of the solution in order to do away with standard purification and instead only require a centrifuge. Pia Marty, who recently completed an internship at Biomakespace as part of her Master’s degree, is currently working on removing reliance on antibiotics which are usually used to keep the DNA plasmid stable in the bacteria as we do not want to risk releasing antibiotics or antibiotic-resistant genes into the waste and environment.
Flowchart of protein expression and purification in E. coli. 1: The protein of interest is identified/selected; 2: a plasmid (circular DNA) with the genetic information for a bacterium to produce the protein is created; 3: the plasmid is introduced in E. coli cells; 4: the bacteria culture is grown in a bioreactor to create large numbers of bacteria; 5: the protein produced by the bacteria is purified.
So for every single part of the pathway of creating an enzyme we are trying to find ways to do it cheaper, faster, and easier. For example, Chiara Gandini is optimising periplasmic expression of the enzyme so that instead of the enzyme being expressed inside the cell, it is expressed in between the cell membranes of the bacterium. We then use osmotic shock to release the protein into the solution and we found that for this, sugar from the supermarket works just as well as the sugar we got from a well-known chemicals provider (despite the vast difference in price)!
Another ongoing project is the open-source bioreactor which will be one part of the toolkit. This project was started last year as part of the Biomaker Challenge and will continue during this year’s challenge with the goal of improving the design and adding new modules.
The end result we envision right now is a set of protocols people can use to produce the enzymes plus the necessary DNA collection and hardware designs. We will then delve into how to make this toolkit as available as possible.
Q: Do you currently have all the experience/skills you need to start (and complete) this project or are you planning to learn these through Biomakespace?
We certainly don’t have all of the skills right now. That is why it has been so great to work with others at the space for things like 3D printing and electronics.
With regards to the biology, we have most of that covered but it’s been really good to work with the interns and there’s always more to do! It’s great to have access to people with various skills at Biomakespace and I think everyone involved learns something new, including and especially me!
Q: Are you looking for others to join you on this project?
We are always happy for people to join in on the project since there are lots of things to do. We are already working with people from other community laboratories, such as Scott Pownall from the Open Science Network lab in Vancouver. He is working on coming up with suggestions for enzymes and developing a pipeline for people to suggest enzymes to add to the collection.
We are especially interested to hear from people with expertise or experience in protein expression, electronic or mechanical engineering, and people who have skills in creating websites or databases. There are opportunities to work with our partner laboratories in Ghana and Cameroon, so if you are interested in this project, irrespective of where you currently are, please do get in touch!
Q: I know this is a tough question, but what is your current timeline?
This is an ongoing project so there are several stages with smaller milestones. We are starting with DNA polymerases because they are the easiest to work with: they’re robust and stable enzymes and are used the most in most labs. Our current goal is for production of DNA polymerases to be working in Ghana and Cameroon by October 2019. There will be improvements we need to make after this, but we hope to be supplying local researchers by then.
The open-source bioreactor project is constantly improving. We hope to have a really good prototype and documentation by October 2019 and we’re working with an engineering company to pick up on the quality testing and documentation.
Q: What do you expect from completing this project?
Each project that we do is taking us a little bit closer to this toolkit for a low-cost and easy way for people to manufacture their own research tools. With every smaller project we are lowering the cost or making the process easier, and we are opening up opportunities for different enzymes to be expressed.
We want to provide molecular-biology researchers across the world with rapid and affordable access to molecular-biology tools. The reason for that comes down to knowing that if you don’t have the resources to be creative, take risks and to fail quite a lot, you don’t get the chance to innovate. So in the end, you then do not have the ability so shape biotechnology to shape the future. We want to give people the freedom to innovate on their own terms.
By creating tools we are allowing hundreds if not more researchers to better solve problems they want to solve or discover what they want to discover, so the downstream effects of this project could be quite profound.
Q: Could you provide some resources to more information on the topic of your project?
Prof. Lisa Hall’s group at the Department of Chemical Engineering and Biotechnology where I’m based have a project focused on diagnostics where they are purifying enzymes using silica which can itself be purified from sand. This is a great example of the approach we are also taking (Henderson et al., 2019).
We’re inspired by the work of many groups across the world who are trying to find more-accessible ways of doing science, like a group in India who investigated using rice flour to purify enzymes (Neissi et al., 2013).
I love working in communities and I’m fortunate enough to be part of the Global Open Science Hardware Community, the Global Community Biosummit, and many other groups who inspire our work every day and have a similar vision for ensuring that science can be performed by more people in more places.