Customer Interview | University of Calgary Arianna postdoctoral researcher uses OT-2 to run magnetic bead cleaning automation

Arianna Morosetti studies anthelmintic resistance at the University of Calgary. She performs a large number of PCRs using an Opentrons OT-2 pipetting robot.

University of Calgary is one of Canada's top universities. Arianna Morosetti is a molecular biologist. Studying drug resistance in parasitic nematodes in the Gilleard Laboratory at the University of Calgary. The laboratory purchased its first Opentrons OT-2 in March 2019 and hopes to add another one specifically for PCR applications.

Arianna Morosetti pictured with their OT-2 at the Gilleard Laboratory at the University of Calgary. Photo credit: Arianna Morosetti

Opentrons: Please introduce your research background.

ARIANNA MOROSETTI: I am a molecular biologist employed as a postdoctoral researcher in the Gilleard Laboratory at the University of Calgary. I work in a large research group. The members of our group have different research backgrounds. Some are working in bioinformatics, some are new to this academic field, and some have never touched a pipette. But we finally succeeded in giving everyone the ability to do molecular biology experiments.

Prior to this role, I had been in the corporate world, so I knew what was going on in terms of laboratory automation. In my role at the University of Calgary, I use the OT-2 to validate new protocols and streamline our standard procedures.

Opentrons: What is your research project?

AM: I work on amplicon sequencing. We use molecular genetics and genomics approaches to study parasitic nematodes that harbor a large number of important pathogens. A core project of our laboratory is to study resistance to anthelmintic drugs and to study the generation and spread of potentially causal mutations in parasitic nematode populations. Our goals are to improve diagnostics, identify new control targets and provide an evidence base for the sustainable management of drug resistance.

Opentrons: What is your daily work like in the laboratory?

AM: Our protocol for amplification sequencing has many established elements within a very specific workflow. We went through a more complex PCR setup: sometimes we used 4 well plates with 96 samples, using 96 unique primer combinations. Handling such work manually is very troublesome and time-consuming, so we hand over these manual processes to the OT-2 pipetting robot Execute.

Opentrons: Why did you choose OT-2?

AM: We already have a device from another brand in our lab and we considered using it, but we didn't use it much and the company was slow to respond to support requests. We also need to purchase an additional magnetic module to implement our scheme. Since we work separately in the PCR pre-room and PCR post-room, this means we will have to purchase a new robot and magnetic module, which will incur high costs. Opentrons OT-2 and magnetic modules are affordable and cost-effective, and can meet the experimental functions we need. This is an important reason why we finally chose OT-2 after comparing multiple products.

Opentrons: What exactly do you use OT-2 for? How does it fit into your workflow?

AM: We use OT-2 to dispense small amounts of primers. We have a simple solution that I designed using the simple tool Opentrons Protocol Designer. Now it works great and we use it regularly, but we faced a lack of proven filter tips in the beginning. I tried using a different brand of filter tips, but this caused delays in protocol development. Now that the filter tip is available, the problem is solved.

In our amplicon sequencing workflow, we use magnetic beads to clean up our PCR products, which requires a lot of time and manual work. In order to improve cleaning efficiency and save labor costs, we used Opentrons magnetic modules to automate magnetic bead cleaning. After doing some research in Python, I created our automation protocol. We are very strict about avoiding cross-contamination (because this step is critical to our library preparation process), but the Opentrons support team gave us a lot of helpful help. We had a lot of questions but they were patient enough to help us out. Next we will verify everything using PCR samples.

Opentrons: How is your experience running OT-2?

AM: One of our P10 pipettes was leaking, but Opentrons' customer support team quickly replaced it with a new one and so far everything is going smoothly. Beyond that, I did a lot of testing on the robot by using various colors of food coloring and then running the program to make adjustments. That's what I do, just by observing and adjusting the program based on what we want to achieve.

Opentrons: Before you used the OT-2, had you used other laboratory automation equipment? What are your expectations for laboratory automation processes?

AM: This is my first time using laboratory automation equipment. I was expecting some setbacks, so when something went wrong, I took a deep breath and tried again. I'm not afraid of new things; usually when a new device comes out, I'm more than happy to try it out.

In my experience, setting up any pipetting robot takes time. No matter what the machine is, no matter how intuitive its operating software is, it requires a person to take the time to learn all the features of their lab robot and truly understand how the software works.

Opentrons: What are the pros and cons of your OT-2?

AM: OT-2 Automation makes our lives easier. For professional researchers, using the OT-2 helps save time in experiments.

We also have many students and visitors to our lab who come to learn about the techniques used by our group. We have integrated the OT-2 into our laboratory procedures so that students and visitors can start their experiments by simply removing the pre-portioned well plates from the freezer. They are also easy to learn.

Opentrons: Do the current modules meet your needs? Are you considering adding other functional modules?

AM: We have looked at Opentrons' thermal cycling module and thought it would integrate well with our bead cleaning unit. The thermal cycle module was something we needed within our plans to provide more functionality while making efficient use of deck space.

I think for myself, in order to run routine DNA extractions, I might need to add a temperature control module, but the limiting factor is the centrifugation step that needs to be performed outside of the robot. The most important thing for us is to deal with the most time-consuming parts of our workflow, which are the PCR setup and cleanup steps.

Opentrons: How do you feel about robotic automation?

AM: As a user, I wish there were more tutorials on using the API. I have a little experience with Python, but not enough since my applications are more focused on using objects for design and programming. I think most experts in the field of biology are not proficient in Python, and the existing tutorials are not very helpful. I think a webinar or video would be more helpful.

Another expectation I had when using the OT-2 was to be able to use different labware and materials. If we use products that haven't been tested on the OT-2, getting them to work is a bit more problematic. But I know you're integrating Labware Creator, which will help us a lot. Especially our filter tips.

I think bots are very helpful. A lot of people think you have to suffer in the lab, but I disagree. I work in many labs with varying funding capabilities, and I often have to do things manually. I agree with the spirit of hard study and research, but with the advancement of science and technology, the efficiency of scientific research should be improved, and the development of automation technology can also make our research process less boring.

I don't think you should spend too much time on repetitive steps that add no value to your research. If you have a way to do this—pipetting—that is both clean and practical, then you should move toward using it, even though the initial investment in time and labor may be high.