Load and Go: LogPhase 600 Simply Confirms Yeast Activity
University of British Columbia
Shortly after the first full genome sequence of the yeast Saccharomyces cerevisiae was completed in the mid-1990s, Dr. Corey Nislow remembers feeling a bit disheartened that this information didn’t shed any additional light on how the yeast actually works. Rather than remaining downcast, he and his scientific and life partner, Dr. Guri Giaever, decided to approach yeast from the angle of functional studies. With this in mind, they and other like-minded yeast researchers worked together to delete each gene from the yeast genome and insert a molecular barcode to note the resulting mutation.
This undertaking resulted in the creation of about 21,000 barcoded yeast mutants (both mating types, and diploid strains) that could be used to understand gene function, especially in the context of external stimuli and environmental factors. As yeast and humans share about half of their genes, this information can help to guide new drug treatments. These strains have been featured in over 1000 publications since 1999.
Today, as a Professor in the Faculty of Pharmaceutical Sciences at the University of British Columbia (UBC) in Vancouver, BC, Canada, Drs. Nislow and Giaever continue to leverage this novel, barcoded mutant yeast collection to understand how the organism works, and how it interacts with drug compounds and other external stimuli. Dr. Nislow’s commitment to this goal has earned him a Tier 1 Canada Research Chair (CRC) in Translational Genomics.
Drs, Guri Giaever (left) and Corey Nislow (right) in their lab at the University of British Columbia.
Sometimes, customers provide assay methods, but in most cases, ABL has to develop a new assay for each compound in addition to method development and validation. De Jonge notes, “ABL’s staff of 36 people are involved in the entire process; their challenge is to find solutions. Everyone’s work is appreciated, which culminates in good results and low staff turnover.”
A deep passion drives his ambition to shoot for the moon in his research goals, both figuratively and literally. In addition to sending yeast mutants to the International Space Station to investigate micro-gravity effects, his yeast mutant library will be included in an upcoming 48-day NASA mission, where an unmanned space capsule will travel to the moon and back. The effects of cosmic radiation on these yeast samples will be analyzed and used to develop treatments that protect future space explorers from radiation harm.
Back on Earth in the Nislow-Giaever lab, drug-gene interaction experiments are performed as a pooled screen, where all 6,000 mutants at equal abundance are grown together and challenged with a drug compound. Mutants impacted by the drug exhibit slower growth rates than unimpacted mutants which creates a rank order, of sorts, based on drug sensitivity. The mutants are then separated based on sequencing of their unique barcodes. While this genomic snapshot helps to characterize the impact of that drug, the real power is found when screening thousands of drugs, concentrations, and conditions and uncovering patterns in the resulting data.
Dr. Nislow relies on a number of BioTek products to assist his research, including the EL406 Washer Dispenser for plate loading, Precision 2000 Microplate Pipetting System for assay development, and Cytation 5 Cell Imaging Multimode Reader for mammalian cell studies and imaging. But it’s the LogPhase 600 Microbiology Reader that propels his research forward every day.
The LogPhase 600 is used to confirm data collected from the pooled screen. This reader features consistent temperature control and robust shaking of up to four standard 96-well microplates at once. In Nislow’s workflow, stock mutants are grown with and without drug exposure in the LogPhase 600 and assessed in relation to data from the pooled screen. Most confirmation studies last 24 hours, with optical density (OD) readings automatically taken every 15 minutes.
Reproducibility of the LogPhase 600 demonstrated on a first run. Columns 1-4 have clonally identical yeast. Columns 7-10 are set of clonally related yeast variant strains. No-cell controls are in columns 5,6, and 11,12.
“We’ve had the LogPhase 600 for less than a year, but we’ve got about two decades of experience with these growth curves, so we have a good sense of whether something will or won’t work in constant use,” says Dr. Nislow. “We have very good karma with this device; it does one thing – reading OD – day in and day out, and it does that extremely well.”
Four team members use the LogPhase 600 every day, and others use it weekly or bi-weekly. Everyone appreciates the simplicity of the reader’s operation. They can just load plates and walk away, use the onboard software to check on progress during the run, and even easily transfer data for analysis using the lab’s in-house growth curve analysis software.
Some yeast mutants have a propensity to adhere to other cells in the culture, which can result in aberrant data points. Fortunately, LogPhase 600 ensures thorough shaking to prevent clumping. Dr. Nislow notes, “We don’t see aberrant data points with LogPhase 600, which shows me that these cells are very well suspended and uniform.”
He’s so pleased with the LogPhase 600 performance, in fact, that he’s preparing to purchase a second unit, and has also convinced two other UBC laboratories, including one at UBC’s prestigious Life Sciences Institute, to purchase units as well.
The Nislow-Giaever lab members. Front: Mina and Marjan. Second row, left to right: Rutuja, Divya, Sam, Joseph, Credo, Kipling, and Hamid. Bold type indicates members using the LogPhase 600.
To learn more about Drs. Nislow and Giaever's lab (GCN), visit their web site.
Thanks to Drs. Nislow and Giaever for sharing their BioTek experience.
For Research Use Only. Not for use in diagnostic procedures.