At GIFS, Jaclyn Prystupa, Automation Specialist, programs and operates a growing number of automated liquid handlers that perform complex laboratory tasks with speed and precision.
Jaclyn Prystupa is an Automation Specialist at the Global Institute for Food Security (GIFS) at the University of Saskatchewan (USask).
It’s a dynamic role in which she leads the development, optimization, and troubleshooting of automated workflows and laboratory equipment within GIFS’ Omics and Precision Analytics Laboratory (OPAL).
Put more simply, she works with robots to expand the capabilities and throughput of GIFS’ genomics offerings.
Every day, she programs, operates, and maintains a growing number of automated liquid handlers, each one capable of executing complex laboratory tasks with speed and precision.
This work is central to OPAL — a PacBio Certified Service Provider and one of Canada’s largest sequencing and genotyping facilities. There, Prystupa combines genomics and computer science to accomplish big things in small timeframes.
How big is big? Think thousands of plant, animal, and microbial samples. By leveraging automation, these samples are efficiently prepared, processed, and sequenced to generate massive genomic datasets that help GIFS’ partners and customers accelerate research and product development.
“If you want to increase throughput, you have to move to automation … and as you further increase throughput, you just keep refining those automated workflows,” said Prystupa, MSc, whose work is critical to establishing and refining the technological capabilities that power GIFS’ programs and technical services.
From Bench Science to Automation
As is common, Prystupa’s career began at the bench performing hands-on experiments. That experience now informs her focus on automation, where manual protocols are translated into high-throughput automated workflows.
“A lot of what I do is optimizing and troubleshooting workflows at the bench, then adapting them for high-throughput automation,” said Prystupa, who draws on a diverse background, including degrees from USask and research experience in animal science, horticulture genomics, and human health.
In her role, Prystupa has embraced new technologies as GIFS expanded from a single Hamilton NGS STAR liquid handling system to a fleet of leading-edge instruments that assist in sample handling and library preparation.
“(Our lab’s) evolution has been really neat. I really enjoy learning the different variety of molecular technologies present at GIFS,” said Prystupa.
For each liquid handler, Prystupa writes scripts that adapt manual protocols, providing precise instructions for when the instrument should initiate a process, detect liquid levels, transfer samples, dispense reagents, move plates, and more.
Easier said than done.
Along the way, she works through challenges big and small to ensure the effective and reliable operation of each instrument, troubleshooting and optimizing mechanical quirks, fluid dynamics, software bugs, and more so that each workflow is effective and user friendly.
The work demands a blend of analytical thinking, creative problem-solving, and ingenuity.
“I really do like script writing…When you’re in it, you’re really in it,” she said.
“(But) sometimes what happens at the bench doesn’t easily translate to automation. If an instrument isn’t capable of spinning a plate on deck, then you have to work around that.”
Driving Innovation through Automation
Across GIFS’ laboratories, automated liquid handlers and other robotic systems are now powering at-scale capabilities typically reserved for industry — providing diverse stakeholders with access to world-class infrastructure.
In recent years, Prystupa has helped optimize automated workflows for long- and short-read whole genome sequencing, as well as Skim-Seq and RNA-seq.
“We definitely see projects that use multiple workflows,” said Prystupa. “Whatever question the clients have or need to answer, we have different workflows to help.”
This high-throughput capacity allows large quantities of genomic data to be generated and integrated into automated bioinformatics and visualization pipelines, delivering both highly accurate data and valuable analysis.
These services support plant improvement and other impactful research and product development activities, including collaborations through the FCC Breeding Acceleration Program. Through this initiative, GIFS is working with public- and private-sector breeders to accelerate genetic gain in commercial plant and livestock breeding programs.
To support these collaborations, Prystupa worked with colleagues to develop and optimize an automated workflow for genotyping by targeted sequencing. Unlike whole genome sequencing, in which information is acquired from the entire genome, this method captures information for specific desired regions of DNA.
This “capture” approach allows researchers to selectively target genes or markers related to a particular trait or breeding goal, offering greater efficiency than some other genotyping techniques and empowering breeders to make faster and more informed decisions.
This work, combined with other breeding acceleration strategies, can help breeders to more rapidly deliver new genetics and crop varieties that are more resilient and productive.
“We start with an established bench protocol. From there, I review each step of the protocol and identify any modifications needed for liquid handler compatibility,” said Prystupa, who assesses what steps require adjustments and evaluates whether the protocol can be executed as a single script or should be divided into smaller modules.
“Once the script(s) are written, they are then validated prior to being released as their own established automated workflow.”
At GIFS, the high-throughput genotyping by targeted sequencing workflow now runs dynamically, accommodating runs of varying sample sizes, while also integrating barcode reading for traceability.
For Prystupa, it was another opportunity to solve a complex problem and deliver a solution that helps researchers unlock the potential of new technologies.
Just another day for an Automation Specialist.
“A perfect day optimizing is when everything pipettes great, and that first validation run does what it’s supposed to. That’s always a win,” said Prystupa.