Kristin Ellis recently visited Biomarin Pharmaceuticals’ headquarters in San Rafael, California. There, she spoke with Elaine Phan, a senior research associate in protein biochemistry at Biomarin. Elaine Phan has been using the OT-1 PRO for protein quantification.
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Kristin: I'm really excited to hear how Biomarin is utilizing the OT-1 PRO, so first of all, can you share your experience with Opentrons?
Elaine: Excellent! The agreement you provided allowed me to execute smoothly. So far, I've mainly based it on the automation you guys gave me a> and then look on your website for details on how to write the protocol. I assume you have a dedicated page for people to learn from?
Kristin: You mean Opentrons' Open source API documentation?
Elaine: Yes, there is also the Python learning platform SoloLearn recommended by Artyom. At first, I learned based on the JSON protocol shared by Will on his blog, which made it easier for me to understand Python related content.
Kristin: Oh, really? Why do you think so?
Elaine: Because at the beginning, I thought Python looked more complicated. But by reading the JSON instructions you provided, I was able to better understand and write the various commands. Once I got the hardware, I was able to quickly assemble the machine and tweak the existing Bradford Assay code. For me, I have been doing dosing work for over a decade and this device really takes the load off my arms.
Kristin: Can you briefly introduce what your team does?
Elaine: We focus on protein purification and belong to the protein science research team. Our workflow is huge, and I'm still in the early stages of research. We obtain many fractions and need to determine the purity of each fraction. This means we need to do gel electrophoresis, Bradford experiments, etc., and then gather all the required materials. Next, we need to prepare enough material for use in preclinical samples to demonstrate the efficacy of the drug. In short, we need to make enough of the drug to make it available to other teams for experimentation. Once these experiments are completed, we give the drug to mouse models and observe its effects. Having Opentrons robots can significantly speed up this process, making it more efficient.
Kristin: Where do you originally get the proteins you test?
Elaine: We have another team dedicated to cell culture. They grew the cells I needed. We used both mammalian cells and E.coli cells. Currently, I'm mainly working on E. coli and expressing His-tag on it. The process is relatively simple. The location of the protein can be visualized by binding it through a His binding column, then eluting it, and placing it in a fraction.
Kristin: So you can observe the expression of the protein.
Elaine: Yes, the process is roughly like this. First, there is a loading step, where the sample is loaded into the instrument and any material not bound to the column flows out. This way, all unwanted impurities can be removed. Next comes a wash step to rinse the column. The material is then eluted through an imidazole gradient so that ultimately only the material I want to bind binds to the column. These materials bound to the column are collected and separated into fractions. Its purity is then analyzed by gel electrophoresis. I will also perform a Bradford experiment to quantify all proteins and show recovery. Afterwards, each fraction can be subjected to gel electrophoresis, or several fractions can be combined and subjected to gel electrophoresis, and the location of the protein can be observed by Western blot. This is what we usually do!
Our ultimate goal is to enable OT-1 to perform ELISAs experiments. We need to display data such as activity. I personally don't work on ELISAs, but others do. So once they figure out the workflow, I can get ELISAs and other activity detection methods from them and try to apply them to the robot.
Kristin: Yes, this is one of the projects we are currently working on with several other groups - we want to automate various types of ELISAs. Not just a single ELISA, but MSD plates, Luminex, anything we can develop. This is an area we want to enter.
Elaine: Great! I will ask you more questions once I decide to start researching this.
Kristin: Of course! This is why we exist and why we built this community!
You’ve been using the OT-1 PRO for a month and a half. You said you have been working in biology and manual pipetting for 10 years. Then you get the OT-1 PRO and start learning how to program and how to build experiments around automation. How does programming experimentation impact your lab work experience compared to manual work?
Elaine: This machine completely overturned my understanding. I had been working in biology and manual pipetting for 10 years and never imagined that I would be exposed to this completely new field. Now, this machine has almost become my experimental assistant. It helps me handle a lot of my daily experimental work, such as running Bradfords and other routine experiments, which saves me a lot of time. Now, I can devote more energy to reading literature, understanding experimental principles and improving experimental methods. In addition, after learning to program, I seemed to have opened the door to a new world. My mind is full of ideas right now, I just haven’t fully expressed them yet because there is still so much to learn.
And there are so many possibilities with this machine – like using different pipettes. Even though you guys said this machine might not work with Rainin pipettes, I still wanted to give it a try. I don't give up easily and always want to challenge new things!
Kristin: Of course we won’t stop you! That's one of the reasons we keep the Opentrons platform open source, so that when we say to you, "Oh, you know what, we don't do that here," you can figure it out yourself!
I know you think the programming part is cool and you've started tweaking the hardware. So, what are your thoughts on hardware modularity and being able to combine things however you want?
Elaine: This is awesome because I can put anything on the platform! I hadn’t even thought about these nice things before (pointing to tip holder with Beckman Coulter reservoir) because we usually use disposable plastic tip holders, but now I can think of a million ways to put them Liquid in there.
Biomarin has repurposed Opentrons tip racks into holders for Beckman Coulter reservoirs.
Elaine: I would also like to meet other people working in this area and get their thoughts. I know you have small communities on Slack channels, but if I can meet with people and explain what I'm doing and they explain to me what they're doing, then those ideas really come together.
Kristin: It sounds like you're also interested in the community aspect. As someone experienced in science, do you think this kind of community is important to develop and build?
Elaine: I think so, especially for me because now I'm the only one in the company using it. So I don't really know who to talk to other than you guys about the broader scope of what this machine can do. For example, you mentioned today that some people are using magnetic beads, Amazon’s Alexa, etc. In fact, my programming skills are still in the early stages. How much more programming can I do? How should I start studying?
Kristin: This is what we are behind Protocol Library concept. We recently relaunched the library, and part of the reason why we say, "We developed the Bradford Assay in partnership with Biomarin," is so that people can see the protocol in the library. Then, if they have questions about the solution, they can go into the community channel and ask you, "Hey, how did you develop this solution?" Also, the more users, the more solutions we add. You can then download them to look at the code and start understanding it, just like you did when you first started.
Elaine: Yes, that would be very helpful. Being able to ask questions to them after seeing a protocol makes the Protocol Library a starting point for conversation as well. We actually planned to introduce a platform, and I started to realize that you guys could do all the things they could do. They have some great ideas, and they're just drag and drop, which is really easy for someone who doesn't know programming...but if I could learn to program, I could get the OT-1 to do it, and it would The cost is very low, which makes me very excited.
Kristin: This is actually a very interesting point of view! So, if you look back at the beginning of your career, let's say you started out with a tool like an OT-1, like this and a 3D printer, what possibilities does that open up?
Elaine: That would be great! I think about it now, if this tool had been available at that time, I could have used it to write many experiments. A lot of things, especially separations... you know, sometimes you have to work late to get something done because you can't wait and you can't put it in the refrigerator or the protein will precipitate. So, you can only get to a certain stage and then stop or freeze. In many of these situations, it would be great to have an assistant to help.
Kristin: How did you decide to start with the Bradford Assay? Is this an urgent need in your laboratory?
Elaine: Yes, this is an experiment that everyone has to run, and it is the basic knowledge that every new person has to learn, because everyone needs to know the concentration of the protein at all times. So we thought, if the machine can run this Bradford Assay, then it can also run ELISAs, it can do gel preparations, it can do standard curves. The Bradford Assay is just the basic pipetting experiment that everyone must do at the beginning of the lab. If you can do these very accurately, then you can probably do all the experiments we need in the lab.
Elaine started out with no programming experience, but through learning, she has now grown into an Opentrons power user! Her feedback helps us improve the user experience, and her contributions to the Protocol Library make science more reproducible for everyone.
