Fun fact

“In my free time I sing in a choir in Seattle, and have been singing with choirs since I was in undergrad.”

Sarah is a postdoctoral research associate with the Wastewater Surveillance for SARS-CoV-2 and Emerging Public Health Threats Research Coordination Network at the University of Notre Dame. She received her PhD in Environmental Health from the University of Washington School of Public Health in Seattle. Her PhD research focused on wastewater surveillance for SARS-CoV-2 and antimicrobial resistance, and she is excited to continue working in this area with the Wastewater Surveillance RCN. She has a BS in Biological Sciences from the University of Notre Dame (2016) and an MS in Global Health from Duke University (2018).

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Wastewater-based epidemiology (WBE) has been around for a while and has been used to track drugs of abuse, chemical waste, and pathogens alike. It may not be the most glorious of samples to work with, but wastewater has proven to be a valuable way to do community-wide monitoring. The COVID pandemic brought new attention and focus to WBE once it was shown it could be used to detect the SARS-CoV-2 virus to alert public health officials to outbreaks, often before clinical symptoms presented.

Our gene-ius guest for this inaugural episode is Dr. Sarah Philo, a postdoctoral research associate with the Wastewater Surveillance for SARS-CoV-2 and Emerging Public Health Threats Research Coordination Network at the University of Notre Dame. In our conversation, Sarah talks about how she found this area of research and the “joys” of working with wastewater samples. We learn about how she and her team have used both qPCR and dPCR to detect and quantify SARS-CoV-2 and antimicrobial resistance genes in wastewater.

The conversation also touches on several other interesting and informative topics that include a “one health” approach to public health, the importance of teamwork in academics, considerations when selecting a graduate research program, the importance of passion in science, and how science is the “punk rock” discipline within academia.  Join us for this fun start of the series and this first season!

Affiliation links 

• Website for Sarah’s project: https://sites.nd.edu/rcn-wastewater-sarscov2/ 
• Website for the lab of Sarah’s primary appointment: https://germlab.nd.edu 
• Website for the College of Environmental Engineering and Earth Sciences where the lab is based: https://ceees.nd.edu

Publications 

• Philo SE, Ong AQW, Keim EK, Swanstrom R, Kossik AL, Zhou NA, Beck NK & Meschke JS (2022) Development and Validation of the Skimmed Milk Pellet Extraction Protocol for SARS-CoV-2 Wastewater Surveillance. Food Environ Virol. https://pubmed.ncbi.nlm.nih.gov/35143035/ 
• Philo SE, Keim EK, Swanstrom R, et al. (2021) A comparison of SARS-CoV-2 wastewater concentration methods for environmental surveillance. Science of The Total Environment 760: 144215. https://pubmed.ncbi.nlm.nih.gov/33340739/

Fun fact

“I own a farm called Perkiomen Creek Ranch.   Note the initials:  PCR.   Yeah, that was on purpose. ”

Marcia Slater is a Senior Technical Specialist for real-time PCR and digital PCR at Thermo Fisher Scientific. Over the past 26 years, Marcia has held various technical roles with Applied Biosystems/Life Technologies/ThermoFisher Scientific. Her passion is PCR, especially qPCR and dPCR and she has trained many scientists on these technologies. She was awarded a patent for using qPCR for HLA typing in 2007. Prior to joining Applied Biosystems, she was a research scientist at the Schering-Plough Research Institute (now Merck) in Kenilworth NJ. She holds a BS from Penn State and MS from Rutgers.

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The details of what make digital PCR (dPCR) different from real-time, or quantitative PCR (qPCR) are relatively simple but not always explained very well. Likewise, it’s not always clear which use cases are a good fit for dPCR, and which others simply don’t require the power of dPCR. The power of digital PCR is real, if you understand it.

In this episode we enlist Marcia Slater, a self-described “PCR guru” to explain digital PCR and its power. She covers the basic differences between dPCR and qPCR and then delves into the details of where dPCR derives its power and where it shines. With over 20 years’ experience in helping customers troubleshoot PCR, Marcia makes is easy to understand key terms and concepts related to dPCR, including:

• Sub-reactions
• Poisson statistics
• Statistical power and confidence intervals
• Controls and false negatives vs. true negatives
• Dead volume
• Dynamic range
• Multiplexing

Marcia also covers some great examples of where the absolute quantification of dPCR is a great fit and how it’s even used to qualify and quantify standards for qPCR. Multiplexing and how its used to do molecular integrity evaluations for gene therapy applications is also discussed.

As always with the Gene-ius series, you’ll also get to learn about more than Marcia’s science chops. We learn about her unlikely career path from growing up on a livestock farm to her storied role in helping produce “data so beautiful it should be framed.” We even get into her rediscovered love of raising animals, including her beloved panda alpaca with a name you cannot forget!

Affiliation links 

• Affiliation Link: www.thermofisher.com

Fun fact

"A substantial portion of my research group works on parasites that require snails to complete their life cycle. To study many of these parasites, we maintain a snail facility in our lab. This room is often the highlight for any visitors to our lab space. I find snails fascinating and name them as my favourite animal when my 6-year old daughter asks. However, slugs, which are close relatives of snails, are among my most reviled animals - to the point where I shiver just thinking about them (especially the larger ones). I really can’t explain why the shell makes the difference."

Patrick is an associate professor in the School of Public Health at the University of Alberta. He is a trained parasitologist and immunologist, and his research focuses on studying the interface between animals, parasites/pathogens, and freshwater environments. This research often focuses on understanding three aspects of biology: the specific interactions underpinning host and parasite/pathogen compatibility, how host and parasite populations influence each other within a freshwater ecosystem, and how species invasions can disrupt the balance between hosts and parasites. Patrick and his research group often approach these topics using multiple approaches that combine large-scale field surveys with large-scale spatial and temporal studies, molecular biology and specific host-parasite association investigations. Patrick and his team have formed partnerships with the Government of Alberta, non-government organizations, industry, schools/educational groups, and community partners to undertake these ambitious studies. These partnerships have coalesced into an incredible collaboration that advances research objectives and our understanding of important health issues related to freshwater ecosystems. 

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Parasites may bet a bad rap overall, but they play a vital role in healthy ecosystems. In this episode, we focus on the role parasites play in freshwater ecosystems. Specifically, we’re talking about the role of avian schistosomes, a very interesting parasite that infects waterfowl, but that also uses snails as a host in its larval stage. Larvae also infect humans to cause what’s know as swimmer’s itch.

To guide this conversation we have Dr. Patrick Hanington, associate professor in the School of Public Health at the University of Alberta. As a self-described parasitologist and immunologist he and his team focus on developing multiplexed PCR-based tests to detect freshwater parasites, including avian schistosomes. Their work benefits locals in his area by monitoring pubic and recreational waters for swimmer’s itch outbreaks, but their work also serves as a model for informing human schistosome research, where Schistosomiasis is the second most prevalent disease worldwide, behind malaria.  

In our conversation with Patrick we learn about how they design their assays, why they’re increasingly using dPCR instead of qPCR. Beyond the technical work, we get into how Patrick’s career path developed, how what he loves most about his job has changed and evolved over time, his lessons learned in the lab, and how his research and hobbies have blended over time. And because it’s Absolute Gene-ius, you know we keep it fun with some unexpected movie references and a bit of discussion about how science is represented in television and film. 

Patrick Harrington additional information

Affiliation links

• University of Alberta, School of Public Health 
• www.ualberta.ca

Publications 

• qPCR-based environmental monitoring of Myxobolus cerebralis and phylogenetic analysis of its tubificid hosts in Alberta, Canada. https://pubmed.ncbi.nlm.nih.gov/34196282/ 
• Non-resident definitive host presence is sufficient to sustain avian schistosome populations. https://pubmed.ncbi.nlm.nih.gov/35007566/
• Coordination of humoral immune factors dictates compatibility between Schistosoma mansoni and Biomphalaria glabrata. https://pubmed.ncbi.nlm.nih.gov/31916937/
• Species-specific qPCR assays allow for high-resolution population assessment of four species avian schistosome that cause swimmer's itch in recreational lakes. https://pubmed.ncbi.nlm.nih.gov/31061794/