Arianna Morosetti is a molecular biologist studying the drug resistance of parasitic nematode worms in the Gilleard Lab at the University of Calgary. The lab purchased its first Opentrons OT-2 in March 2019, and are hoping to purchase another one dedicated to PCR.
Arianna Morosetti in the University of Calgary’s Gilleard Lab with their OT-2, Stuart. CREDIT: Arianna Morosetti
Opentrons: Please tell us about your background.
ARIANNA MOROSETTI: I am a molecular biologist, hired as a postdoctoral fellow at the Gilleard Lab at the University of Calgary. I work in a big research group with people from very different backgrounds: some work in bioinformatics, some go into the field, some never touch a pipette. But, in the end, everyone ends up doing molecular biology.
Before this position, I worked at a company, so I know what’s out there in terms of lab automation. Here at the University of Calgary, my work includes validating new protocols and streamlining our standard procedures—which is where the OT-2 comes in.
Opentrons: What kind of research do you do?
AM: I work with amplicon sequencing. We utilize molecular genetic and genomic approaches to study parasitic nematode worms which include a large number of important pathogens. The main focus of our lab is to study the mechanisms of anthelmintic drug resistance, and investigate how underlying causal mutations arise and spread in parasitic nematode populations. Our aim is to improve diagnosis, identify new targets for control, and provide an evidence base for sustainable management of resistance.
A microscope image of worm larvae. CREDIT: Gilleard Lab
Opentrons: What’s a typical day in the lab for you?
AM: The protocol we use for amplification sequencing has a lot of established elements in a very specific workflow. We go through a big PCR setup step: sometimes we work with 4 plates of 96 samples, with 96 unique combinations of primers. Processing them by hand is a lot of work, especially if you’re not very handy with a pipette; if you turn your head you can mix up everything. It’s time-consuming, too, so we delegate that to the Opentrons OT-2 pipetting robot.
Opentrons: Why did you choose the OT-2?
AM: The lab already had a robot from a different vendor and we considered using it, but it hadn’t been used much and the company wasn’t very responsive to support requests. We also needed to buy an additional magnetic module to do our protocol. Because we work separately in pre- and post-PCR rooms, that meant we would have to buy a new robot plus the module, and that would have been quite expensive. The fact that the Opentrons OT-2 and Opentrons Magnetic Module are affordable was a great motivation to purchase.
Opentrons: What specifically do you use the OT-2 to do, and how does it fit into your workflows?
AM: We use the OT-2 to dispense small volumes of primer. We have an easy protocol that I designed using the Opentrons Protocol Designer, the easy drag and drop tool. Now it works well and we use it routinely, but we faced the challenge of not having validated filter tips, at first. I tried to use different brands of tips but that created a delay in the development of the protocol. Now that filter tips are available, the issue is solved.
In our amplicon sequencing workflow, we use magnetic beads to clean up our PCR products. That takes a lot of time and manual work, so people are frustrated with it. That is why we thought of using the Opentrons Magnetic Module and the Opentrons API. I had to do a little studying with Python to work it into the protocol, which was good for me. It was somewhat difficult because we are very particular about cross-contamination (it is critically important in our library construction), but I must say your team was very helpful: Chaz Childers built a protocol and a new type of plate for it. We gave him a lot of work, but he was very patient. The next step will be to validate everything with PCR samples.
Opentrons: What was it like to get your Opentrons robot up and running?
AM: We had a problem with one of the P10 pipettes leaking, but it was quickly replaced and everything was fine. Other than that, I did a lot of playing with the robot, taking colorful food dye and running the protocol and tweaking from there. That’s how I did it, just by observing and adjusting protocols according to what we wanted to achieve.
Opentrons: Had you used any lab automation before your OT-2? What did you expect the process of lab automation to be like?
AM: This was my first experience with lab automation. I was expecting a little frustration, so when problems happened I took a big breath and tried again. I’m not afraid of new things; usually when there’s a new toy, I’m like “Yes!”
In my experience, setting up any pipetting robot will take time. It doesn’t matter what the machine is; it takes time for a person to learn all the features of their lab robots and really understand how the software works, even if it’s intuitive.
Opentrons: What else is good or bad about your OT-2?
AM: It is going to make our lives so much easier. For expert users, it helps to save time in the lab.
We also have many students and visitors in the lab that come to learn the techniques used by our group. Since we have the OT-2 integrated in our lab routines, they can just take a plate from the freezer that’s pre-dispensed and go and run their experiments. It’s easy for them to learn.
Opentrons: Are you planning any other automation?
AM: We’ve seen the Opentrons Thermocycler and we’re thinking it might be good to integrate with our magnetic beads unit. We have to think about it and plan, because it’s so many tips and you only have so much space on the deck of the OT-2.
I think for myself, doing classical DNA extraction, I’d maybe buy a thermoblock, but the limiting factor is the centrifugation steps that would need to be performed out of the robot. The main thing for us is to take care of the most time consuming part of our workflow, which are the PCR setup and cleanup steps.
Opentrons: Is there anything else you’d like to say about using the OT-2?
AM: As a user, I would like more tutorials on using the API. I have a little bit of experience with Python, but it didn’t really help me because my application was more object-oriented. Plus, you must know the lingo of OT-2. I don’t think everyone in biology is proficient in Python, and the tutorials you have didn’t help me much. I think a webinar or videos would be more helpful.
Another desire I had while working with the OT-2 is just being able to work with different labware materials. If we’re not using products that have been tested on the OT-2, it’s a little more problematic to get them to work—even the plate Chaz made us. But I see you incorporating this with the Labware Creator, and that will help us a lot. Especially with our filter tips.
All that said, I think the robot has been very helpful. A lot of people think you have to suffer in the lab, but I disagree. I worked in many labs, with different funding, and often I had to do things manually. It was really good for me to learn principles. But as technologies and processes develop, science gets easier and problems like this become less tedious.
I think you shouldn’t spend too much time on repetitive steps that don’t add anything to your research. If you have a way to do this thing—pipetting—that is just as clean and functional, you should move toward using it, even if the initial time and labor investment may be demanding.
Gilleard examining a container of worms. CREDIT: Gilleard Lab