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Inspiring stories and advice from dPCR gene-iuses
All of us want to be absolute “gene-iuses”, but how do we get there? Absolute Gene-ius is a podcast in which we interview trailblazing scientists about their career journeys, lab stories, and groundbreaking digital PCR research.
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Episode 12: The Poisson perspective—counting out false positives
We return to the topic of Poisson statistics and delve a bit deeper into how digital PCR (dPCR) handles topics like false positives or low-abundance and rare targets. Dave Bauer is once again our statistics and math guru who brings his easy-talking ways along with a depth of experience to give real-world examples that drive the concepts home.
About Dave Bauer
Dave Bauer, Ph.D., is a dPCR Product Applications Specialist at Thermo Fisher Scientific. He has a broad background in scientific education ranging from software programming to cell culture and quantum mechanics to evolutionary biology. Dave’s passion for dPCR relates to how it resides at an intersection between multiple scientific disciplines, complementing his background.
Prior to joining Thermo Fisher he obtained a Ph.D. in Molecular Biophysics, investigating the physical chemistry of viral genome packaging, worked as a researcher in DNA forensic science, and helped develop real-time PCR assays for cellular therapeutics. Outside of work he loves to spend time with his family and loving doggies, as well as routinely learning and tackling (with varying degrees of success) home renovation projects.
Episode notes
The statistics of Poisson distributions can seem complex at first but are simpler than you think, which is important to know given their relevance to dPCR. In short, they dictate the confidence you can have in the absolute quantification provided by dPCR.
Dr. Dave Bauer, Thermo Fisher Scientific’s very own dPCR Product Applications Specialist and statistics whiz, joins us once again for this short-but-sweet episode that’s a must-hear for those working with rare or low-abundance PCR targets. Dave and the hosts talk about applications like cancer research, where these types of samples are common, and then get into the details of how the QuantStudio Absolute Q Digital PCR System provides elegantly simple technologies like false positive rejection, background subtraction, low dead volume microfluidic array plates, and a master mix with chamber loading dye. Join us to learn about each of these technologies and how they help to provide confidence and reliability in results that matter for your precious samples.
Affiliation link
Publications
- Validating TrueAllele® Interpretation of DNA Mixtures Containing up to Ten Unknown Contributors https://pubmed.ncbi.nlm.nih.gov/31580496/
- Exploring the Balance between DNA Pressure and Capsid Stability in Herpesviruses and Phages https://pubmed.ncbi.nlm.nih.gov/26136570/
Guest fun fact
My dream job has always been to open my own distillery themed upon biology and chemistry education as part of the customer’s experience.
Episode 11: Somatic mosaic loss of sex chromosomes and kidney disease
Parker Wilson has taken a sometimes-unpredictable path to obtain his MD and PhD degrees and establish his physician scientist career, but he’s been quick to adopt and apply the molecular genetic pathology tools that are changing his field. Join us to hear about his exciting work where he uses digital PCR and NGS methods to identify and quantify rare mutations associated with kidney disease.
About Parker Wilson
Parker Wilson, MD, PhD, is a faculty member in the Division of Diagnostic Innovation in the Department of Pathology and Laboratory Medicine in the Perelman School of Medicine at the University of Pennsylvania. The Wilson laboratory uses single cell biology, spatial profiling, and computational biology as tools for investigating chronic kidney disease. Dr. Wilson did his undergraduate training in Biomedical Engineering with a concentration in Computer Science at Johns Hopkins University. He joined the Medical Scientist Training Program at the Medical University of South Carolina where he completed his MD and PhD in Molecular and Cellular Biology and Pathobiology. He did his residency in Anatomic and Clinical Pathology at Yale followed by a fellowship in combined Renal and Genitourinary Pathology, also at Yale. He did a second fellowship in Molecular Genetic Pathology at Washington University in St. Louis before joining the faculty in the Division of Anatomic and Molecular Pathology.
Dr. Wilson's clinical expertise is in Renal and Molecular Pathology where he provides histologic and genetic diagnoses for patients with kidney disease. Over the past several years, the Wilson laboratory has focused on detection of somatic mosaicism by digital PCR and single-cell sequencing. Mosaic chromosomal alterations (mCA) are a type of somatic mosaicism characterized by large chromosomal gains or losses and are associated with aging, heart disease, kidney disease, cancer and increased mortality. Mosaic loss of Y chromosome (LOY) is the most common mCA in aging men and is detectable in peripheral blood starting around the age of 40. LOY not only results in absence of Y chromosome genes but is also associated with senescence and changes in expression on other chromosomes. This Wilson lab has developed digital PCR assays and single-cell methods to measure LOY and other mCA in hundreds of thousands of cells to estimate cell-specific DNA damage and its effects on gene expression.
Episode notes
Same may think of the pathologist’s toolbox as only the microscope and their eyes, but in reality today’s pathologists are using more and more molecular methods ike NGS and PCR in additional to their traditional tools.
Meet Parker Wilson, MD, PhD. Parker is a faculty member Perelman School of Medicine at the University of Pennsylvania, focused on using modern molecular tools to investigate chronic kidney disease . He explains his work phenomenally, both from the general aspects, all the way down to the molecular methods, which include digital PCR. We learn about chronic kidney disease and the interesting genetic mutations associated with it, which Parker and his team are finding, include chromosomal loss. For this application, we hear how dPCR is adept at quantifying chromosome ratios within tissues, and is able to help them spot variations of only a single percent or two.
Our career corner portion uncovers an academic and career path with uncertainty and challenges one might not expect. Parker helps normalize these challenges and underscores the value of mentors in helping navigate them successfully. In the end, you have a phenomenally intelligent physician scientists sharing his exciting work and his insightful career development advice.
Affiliation link
Publications
- Wilson PC, Verma A, Yoshimura Y, Muto Y, Li H, Malvin NP, Dixon EE, Humphreys BD. Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease. Genome Biol. 2024 Jan 29;25(1):36
- Wilson PC, Muto Y, Wu H, Karihaloo A, Waikar SS, Humphreys BD. Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression. Nat Commun. 2022 Sep 6;13(1):5253
Guest fun fact
When the research gets tough, I like to practice my guitar. It makes the research seem easier in comparison.
Episode 10: Automating accuracy – an insider’s view
Automation is key to enabling high-throughput analysis for any analytical method, and automation of digital PCR (dPCR) is now a reality. Join us for this conversation with Dr. Clarance Lee, Senior Product Manger, about how Thermo Fisher is delivering the benefits of dPCR, along with high-throughput automation that saves time and enables diverse application areas.
About Clarence Lee
Clarence Lee is a Senior Product Manager with nearly 20 years of experience driving innovative solutions for the life sciences. His extensive background spans next-generation sequencing and now centers on cutting-edge digital PCR technology. Currently, Clarence leads efforts in assay and applications development to enable researchers and their scientific advancement.
Episode notes
Modern science, especially in the genetic and molecular biology spaces, generate vast amounts of data , and require vast amounts of data to be generated for thorough analysis. For example, finding a rare gene mutation such as BCR-ABL as a biomarker for chronic myeloid leukemia is like searching for a needle in a haystack. For a situation like this, dPCR is an ideal method, but high-throughput automation is also needed.
Dr. Clarence Lee, Senior Product Manger at Thermo Fisher Scientific, tells how the QuantStudio Absolute Q AutoRun dPCR suite helps make the benefits of digital PCR available in an easy-to-use high-throughput system. The conversation covers how automation benefits are provided by MAP16 plates, system software, and the AutoRun plate hotel and loading robot. Clarence also talks about customer applications where he sees automation like this being applied to innovate and drive science forward.
In the career corner portion, we learn about Clarence’s journey from chemist and biophysicist, to roles in industry and his current role as a product manager. He shares what he loves most about his job and what he’s most proud of over his career that has spanned several diverse roles.
Episode 9: Helping democratize access and use of mRNA technology
The use of mRNA as a vaccine platform has been mostly derisked and its speed to move from antigen discovery to drug product is impressive. However, high-purity mRNA can still be a challenge to make. Dr. Christian Cobaugh, CEO of Vernal Biosciences, is on a mission to make high-purity mRNA available to more researchers and drug developers to help realize even more potential from mRNA medicines.
About Dr. Christian Cobaugh
Christian Cobaugh, PhD, has been at the cutting edge of mRNA drug discovery for over fifteen years. He has extensive experience leading teams in mRNA technology and was the first Alexion Pharmaceuticals scientist working on their partnership with Moderna Therapeutics to develop mRNA therapeutics. He has directed critical discovery, delivery, development, manufacturing, and quality control in the mRNA sector, having led mRNA R&D at Arcturus Therapeutics and Translate Bio; and served as Vice President of Process Development and Manufacturing at Omega Therapeutics.
With 15 mRNA patent applications, Christian brings strong scientific expertise in mRNA and LNP with broad experience in all phases of mRNA therapeutic development and regulatory requirements. He has also authored CMC sections for briefing books and developed ICH Q7-compliant quality management systems.
Christian holds a PhD in cell and molecular biology from the University of Texas-Austin and completed a postdoctoral fellowship for Applied Biosystems in Redwood City, CA. In his spare time, Christian enjoys all that Vermont’s Green Mountains have to offer, including mountain biking, alpine and Nordic skiing with his family, and volunteering to build and maintain the local trail networks.
View LinkedIn profile ›
Vernal BioSciences ›
Episode notes
The potential of mRNA medicines was postulated for years, but it took the COVID pandemic and emergency use authorizations for that potential to be demonstrated. By now, most of us have received at least one mRNA based vaccine and the platform has been mostly derisked. However, if you’re not one of the major players in this space, generating high-purity mRNA, let alone a GMP-grade mRNA-based drug product , can still be quite challenging.
Dr. Chrisitan Cobaugh, CEO of Vernal Biosciences in Vermont, has been working in the mRNA field for more than a decade and is passionate about the potential of mRNA medicines. He’s also been in the field long enough to know firsthand the challenges of high-purity mRNA and lipid nanoparticle supply. Join us as Christian walks us through his story, the start of Vernal Biosciences, and their progress toward their mission of democratizing access to mRNA technology. Our conversation touches on the molecular biology of making mRNA, and the use of digital PCR and other methods in monitoring development and release of mRNA drug products, and the potential applications of mRNA as a platform (some of which you might not have guessed).
Whether you’re new to the technology, or have chosen mRNA as a focus area, you’re sure to find this conversation engaging and intriguing and our guest insightful.
Affiliation link
- Vernal BioSciences: https://www.vernal.bio/
Fun facts
I’m really passionate about molecular cloning and applying molecular analytical technologies more broadly.
Episode 8: Now that’s what I call a high-quality viral vector
We dive deep into gene therapy during this conversation with Dr. Cliff Froelich. He covers what vectors his team works with, what methods and technologies they use to monitor quality and safety, and he reminds us why it all matters. As always, you’ll get a bit of fun too!
About Cliff Froelich, PhD
Cliff grew up in a small town, New Braunfels, TX located between San Antonio and Austin. He attended Texas A&M University where he received two Bachelors of Science degrees, one in Nutritional Sciences and the second in Food Sciences and Technology. He stayed at Texas A&M University to receive a Master of Science in Nutrition where he studied the rate limiting amino acid, methionine, in Poultry Feeds and developing a rapid method biosensor method to rapidly assess and determine the amino acid profile of any feed. While at Texas A&M University, Cliff interned through Texas A&M University and Scott and White/VA Hospitals in Temple, TX as a Clinical Dietitian and became certified and licensed before working at the University of Texas Medical Branch – Galveston as a staff Clinical Dietitian. In this role Cliff oversaw the nutritional needs of the Medical ICU, neurology/neurosurgery, and orthopedics wards as well as providing support to Pediatric Endocrinology Outpatient care and periodic support to the Texas State Prison System hospital that is physically connected to the hospital. After a year Cliff found he missed research and moved on to graduate school at Louisiana State University Medical Center – Shreveport where he received a PhD in Biochemistry and Molecular Biology studying the single turnover kinetics and thermodynamics of Tyrosyl-tRNA Synthetase and its role in Charcot-Marie-Tooth disorder, a peripheral neuropathy. Following this, Cliff continued to St. Jude Children’s research Hospital where he held a postdoctoral fellowship exploring the structural characteristics of Mini-Chromosome Maintenance Proteins (MCM) by X-ray crystallography. After this experience Cliff moved to St. Jude Children’s Research Hospital’s Children’s GMP, LLC as a Senior Scientist in AD/QC developing assays and testing a large portfolio of early Phase clinical drug products. He was promoted shortly after starting to a manager role and stayed for 4.5 years before moving to Cognate BioServices, a CDMO for Cellular Therapies where for 2 years he was Director of Quality Control. Cliff was offered a challenge and moved to Massachusetts to take on the role of Senior Director to create and establish the BioAnalytics for new Gene and Cell Therapy division at Sanofi referred to the Genomic Medicine Unit. After 2.5 years Cliff wanted to go back into the lab and support the development of not just assays but the careers of his Team as the Senior Manager of Analytical Development within Thermo Fisher Scientific Viral Vector Services, the CDMO arm of Thermo Fisher producing clinical-grade gene therapies.
Episode notes
Viral vectors are a cornerstone of gene therapy and many employ experts in the viral vector services space to help design and produce their specialty vectors. These service providers are experts at making sure you get the vector you want with a titer and purity you need for your application.
We’re joined in this episode by Dr. Cliff Froelich, Head of Analytical Development for a viral vector services provider. Cliff and his team work with AAV, lentivirus, and other vectors to support multiple, and simultaneous, client projects. Specifically, we dive into how they use various analytical and molecular methods to monitor and assess identity, strength, purity, impurities, potency, efficiency, empty/full ratios, safety, and more. As you might expect, it’s not a one-method-does-it-all approach or solution. Yes, digital PCR is in the mix here, and Cliff does a great job of outlining where it shines relative to the other methods they use regularly in their GMP practice.
In our career corner portion, you’ll hear about Cliff’s circuitous career path, which includes stints in the poultry industry and time as a clinical dietitian. Through it all, and into his current role, Cliff brings a passion and genuine interest for the science and its potential to affect lives.
Affiliation links
Publications
- C.A. Froelich, A. Nourse, E.J. Enemark, MCM ring hexamerization is a prerequisite for DNA-binding, Nucleic Acid Research, Sept. 13, 2015.
- R. Kumar, C.V. Simpson, C.A. Froelich, B.C. Baughman, A.J. Gienapp, K.A. Sillay, Obesity and deep brain stimulation: an overview. Annals of Neurosciences 22(3), July 2015.
Fun facts
I was an Extra in a Denzel Washington and Meg Ryan movie “Courage Under Fire”.
Episode 7: Ch-ch-ch-ch-changes
Now that we’re 15 episodes deep into this series, and because life is forever changing, we thought we’d take a moment to reflect on where we are, how we got here, and talk about what’s to come. Witness the evolution of the series!
Episode notes
When you have a good thing going you often want it to last forever, but we know that can never happen. Life and the world around us are fluid, dynamic, and we’re always finding the balance of fighting or harnessing entropy and inevitable change.
As we encounter unexpected changes, we see them as chances to evaluate the foundations of our podcast's success while finding opportunities to evolve it and make it even better.
Join us for a reflection of where we are, how we got here, and a sneak preview at what’s to come. We’re here to assure you, evolution is a good thing!
Episode 6: What’s your vector, Victor?
Curious about cell and gene therapy and the viral vectors used in these applications? If so, join us for a conversation with a couple of resident experts that shed light on these topics.
About MinGin Kim, PhD
MinGin joined Thermo Fisher Scientific to continue pursuing advances in science and engineering technology after obtaining her PhD in Medical Science from Texas A&M University. She focuses on developing multiplex assays for the Absolute Q digital PCR system while also working on systems projects to further improve the instrument and consumables as well as work close to different functions in her division to help support the system in the field. Her doctorate studies focused on developing an affordable microfluidic PCR platform for point-of-care analysis based on convection. In 2008 she earned her BS in Material Science and Engineering at Yonsei University in Seoul, Korea. There, she also worked on developing new miniaturized molecular analysis platforms, especially focused on PCR systems, in both academia and industry. On her free time, you can find MinGin dancing, cycling, or completing puzzles to be framed on her wall. She also enjoys spending time with friends playing games, especially MMORPGs.
About Kimberly Gomez
Kimberly Gomez is a scientist at Thermo Fisher Scientific specializing in the development and release of dPCR and qPCR products for the cell and gene therapy field. With a background in biochemistry and molecular biology research, she brings experience in analytical verification and clinical validation testing as well as research and development for new products in the cell and gene therapy space.
Episode notes
The fields of Cell and gene therapy are booming and poised to change the treatment and prevention of disease. These research areas require the transfer of genetic material to cells, and viral vectors are commonly used here. Specifically, adeno-associated virus (AAV) and lentiviral vectors (LVV) are vectors of choice.
We’re joined for this episode by MinGin Kim and Kimberly Gomez, both scientists at Thermo Fisher. With backgrounds and expertise in the areas of cell and gene therapy, they help explain what all the excitement is about and how AAV and LVV are used. We hear about some of the challenges associated with viral vector work and get to hear about how digital PCR (dPCR) and good assay design are helping overcome many of these challenges to enable research and the biopharmaceutical industry. As you might expect from Absolute Gene-ius, you also get to hear their respective career path journeys and some really interesting lab stories.
Affiliation links
- MinGin Kim: https://www.thermofisher.com/us/en/home/life-science/pcr/digital-pcr/quantstudio-absolute-q-system.html
- Kimberly Gomez: https://www.thermofisher.com/us/en/home/life-science/pcr/digital-pcr/quantstudio-absolute-q-system.html
Publications
MinGin Kim
- Phagocytosis of antibody-opsonized tumor cells leads to the formation of a discrete vacuolar compartment in macrophages
https://pubmed.ncbi.nlm.nih.gov/29437282/ - Implementation of Compact and Low-Cost PCR Thermal Cycler
https://www.researchgate.net/publication/290604052_Implementation_of_Compact_and_Low-Cost_PCR_Thermal_Cycler
Kimberly Gomez
- Measuring rAAV Genomic Titer, Viral Particle Titer and Full/Empty Capsid Ratio on the QuantStudio Absolute Q dPCR System
https://assets.thermofisher.com/TFS-Assets/GSD/posters/measuring-full-vs-empty-capsid-ratio-by-dpcr-poster-2023.pdf this was the poster referenced in the interview. - High Throughput Sample Data Consistency for Adeno-Associated Virus Using an Automated Digital PCR System
https://www.thermofisher.com/us/en/home/global/forms/life-science/absolute-q-event-resources.html
Fun facts
- MinGin Kim: My doctorate research basically says we can do PCR using the principle of boiling water! One of my explorations during my career journey, I wanted to become an Astronomer or Dancer.
- Kimberly Gomez: I love a good escape room. Will not do ones with zombies. Never again.
Episode 5: A passion for cfDNA analysis is in her blood
This episode gets personal quickly when our guest talks about how her husband is now benefiting from methods her and her colleagues have developed over her career in developing organ transplantation compatibility assays.
About Dr. Lee Ann Baxter-Lowe
Dr. Lee Ann Baxter-Lowe is the Director of the HLA Laboratory at Children's Hospital Los Angeles and Clinical Professor at the Keck School of Medicine of the University of Southern California. Her research interests include understanding the role of HLA diversity in health and disease, investigating the impact of HLA mismatching in transplantation, and improving tests to monitor engraftment of blood and marrow transplants, determine HLA types, and measure transplant biomarkers. She is an author for more than 150 scientific publications and 250 abstracts. She holds 5 patents related to HLA typing. She has had a long-standing commitment to policy development and has served as Chair of the Histocompatibility Committee of the United Network for Organ Sharing (UNOS) and served as a chair or member of numerous professional committees related to transplantation and clinical laboratory testing. She is currently the Editor-in-Chief of the ASHI Quarterly, Associate Editor for Frontiers in Immunology and a member of the Editorial Board of Human Immunology.
Episode notes
Organ transplantation is a modern marvel, with more than 157,000 solid organ, and more than 9,000 marrow and blood transplants occurring worldwide in 2022. Organ donor and recipient matching and compatibility screening has progressed significantly in recent decades as molecular methods have progressed rapidly to support this and other fields. Specifically, typing of human leukocyte antigens (HLAs) has expanded to consider ethnic population variation and cell free DNA (cfDNA) monitoring is now being used to monitor recipients for biomarkers that indicate organ rejection.
Our guest for this episode, Dr. Lee Ann Baxter-Lowe, Director of the HLA Laboratory at Children's Hospital Los Angeles has been working in the field of transplantation science for virtually her entire career. Join us for a great explanation of the science and a first-hand recounting of developing the assays, from decades ago, before thermal cyclers existed, to her cutting-edge work using digital PCR to progress the field even further.
Lee Ann also shares very personal aspects of her career journey in her conversation with Cassie. This includes her describing the scientific “studies” of her and her cousin as children, her venturing into the world of HLA typing when it was emerging, and the role her family has played in her career, which gets personal quickly when she shares that her husband is currently dealing with a blood malignancy.
Affiliation link
- CHLA: https://www.chla.org/pathology-and-laboratory-medicine/laboratory-medicine
- Keck School of Medicine of USC: https://keck.usc.edu/pathology/
Publications
- The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside
https://pubmed.ncbi.nlm.nih.gov/34030895/ - HLA diversity in ethnic populations can affect detection of donor-specific antibodies by single antigen beads
https://pubmed.ncbi.nlm.nih.gov/38077376/ - CPRA for allocation of kidneys in the US: More candidates ≥98% CPRA, lower positive crossmatch rates and improved transplant rates for sensitized patients
https://pubmed.ncbi.nlm.nih.gov/27012168/ - Cell-free DNA as a solid-organ transplant biomarker: technologies and approaches
https://pubmed.ncbi.nlm.nih.gov/35195028/
Fun facts
Lee Ann would read scientific journals to her children as bedtime stories.
Episode 4: “Junk” RNA is anything but garbage
Good things come in little packages, is the theme for this episode. Join us to learn about micro RNA (miRNA) and how digital PCR is being used to understand its role is disease states.
About Dr. Guy Novotny
As the son of an American father and Danish mother, I lived in Minnesota, USA, until the age of 10, when we moved to Denmark. Here I received a MSc. in Molecular and Cellular biology, followed by a Phd in health sciences. After receiving my Phd degree in 2009 I have primarily worked in academia in research positions as post doc, and the last 11 years employed as a molecular biologist at pathological, hematological, and clinical genetic departments at hospitals in the capital region of Denmark.
Episode notes
Before the 1990s, small bits of RNA were considered junk by most, but the 1993 discovery of microRNA (miRNAs) began to reveal that bits of only 19-24 nucleotides of RNA can have an important gene regulation function in cells. Since their discovery, there has been a flurry of work to catalog known miRNAs and understand their functions, which include being tied to specific disease states such as leukemia.
According to our guest, Dr. Guy Novotny, Molecular Biologist at Herlev Hospital in Copenhagen, it’s now relatively easy to identify a miRNAs and follow their expression, but to figure out what they’re actually doing is a real challenge. We hear how he and his team have recently adopted digital PCR, and the benefits that come with it, to study microRNAs and figure out what proteins they’re regulating the expression of. This includes basic research, where Guy is “adding to the big pile of data that’s existing out there,” and he also does clinical research that has a closer connection to specific disease states and subject outcomes. As always, you’ll get to learn about his career journey and learn that there’s really not much that cake cannot fix.
Affiliation link
Publications
- Therapeutic Cancer Vaccination With a Peptide Derived From the Calreticulin Exon 9 Mutations Induces Strong Cellular Immune Responses in Patients With CALR-Mutant Chronic Myeloproliferative Neoplasms
https://pubmed.ncbi.nlm.nih.gov/33718228/ - Improved Variant Detection in Clinical Myeloid NGS Testing by Supplementing a Commercial Myeloid NGS Assay with Custom or Extended Data Filtering and Accessory Fragment Analysis
https://pubmed.ncbi.nlm.nih.gov/33687704/
Fun facts
Back in 2014 we decided to buy an American produced car and imported a Tesla model S. I still enjoy driving it but finding a parking lot at my work…not so much. So my wife drives the car, while I take the train, and in the quite hours commuting between home and work, I enjoy reading books by authors such as Douglas Adams, Peter Hamilton, Terry Goodkind and recently, Sarah Maas.
Episode 3: The bioinformatic artistry behind PCR assay design
Come get your assay on with us. If you’ve never designed one yourself or considered how PCR assays are designed and developed, this episode will help you appreciate the skill and artistry involved.
About Kimi Ong
Kimi is an aspiring bioinformatician supporting qPCR and dPCR assay design at Thermo Fisher Scientific. She has been working on assay design for one and a half years as she makes the transition from wet lab scientist to bioinformatician.
About Rounak Feigelman
Rounak is a seasoned bioinformatician supporting dPCR and qPCR custom assay designs at Thermo Fisher Scientific. She received B.Tech in Bioinformatics from VIT university in India, and then moved to Switzerland to complete her postgraduate (ETH Zurich) and doctoral studies (University of Zurich). Her research utilized next generation sequencing (NGS) data for applications such as reconstructing ancient microbial genomes and analyzing lung microbiome from Cystic Fibrosis patients.
In 2017, Rounak moved to the Bay Area to support the discovery of novel microbes for developing live bio-therapeutics that treat gut dysbiosis and received her first patent after identifying a novel microbe species. At the start of pandemic, she pivoted to designing NGS panels that targeted viral respiratory pathogens, including SARS CoV2 emerging variants. She is passionate about leveraging computational tools to advance molecular testing methods. In her free time, Rounak likes to hike in the hills of east bay with her two dogs and kids.
Episode notes
Designing a successful PCR assay is all about selecting the right primers to deliver the sensitivity and selectivity for which PCR is known for. But anyone that’s designed an assay themselves will know that doing so successfully is a lot harder it sounds.
We’re joined by two PCR assay design pros for this episode. Kimi Ong, and Dr. Rounak Feigelman, both from Thermo Fisher Scientific, shine a light on the many factors that must be considered to design a winning PCR assay. From the level of fragmentation of nucleic acids in the sample, to what other species’ genomes that may be present in the sample, to what the sample matrix may contain, to the PCR master mix being used, if multiplexing is required, to what assay controls will be, and more! These two practiced bioinformaticians cover these challenges and then tell us how their team overcomes challenges to develop winning assays for both qPCR and dPCR applications. Our conversation uncovers the level of skill and artistry that goes into this craft.
As always, you get to learn a bit more about our guests’ backgrounds and career paths in the Cassie’s Career Corner portion of the interview. They share how they both chose a bioinformatics path over wet lab work, while also acknowledging how important the wet lab work is to what they do. They also share some great advice and resources for anyone looking to explore a career in bioinformatics.
Affiliation link
- Thermo Fisher Scientific
thermofisher.com
Publications
Fun facts
Kimi Ong
A fun fact about me is that I love baking and often claim that I would work in a bakery for free.
Rounak Feigelman
About myself: I was a competitive swimmer for a decade, going as high as all India national level, then I decided to finally focus on science during high school J
About my research: I was trying to study what ancient Germanic mummies ate by analyzing DNA from their dental plaque.
Episode 2: CAR-T loads of immunology insights
We cross the pond for this episode, which focuses on CAR-T cell therapy. Join us and meet Raquel Munoz and learn what she thinks will be future of cancer research.
About Raquel Munoz
I was born in Lucena, a city in the south of Spain, 30 years ago. Since I was a child, I was curious to know how the human body works and why it gets sick, so I studied Biomedicine and specialized in Immunology. I have collaborated in research about CAR-T therapy, and I am currently carrying out my doctoral thesis on autoinflammatory diseases.
Episode notes
Blood is a symbol of life, which makes sense given that it plays such an important role in so many body functions, including our immune system. Blood makes up approximately 8% of your normal body weight and unfortunately, cancers of the blood, including lymphoma and leukemia, account for ~10% of all diagnosed cancers in the U.S. each year.
CAR-T cell therapy has emerged as a promising method to engineer a subject’s own immune cells to fight bloodborne cancer. Our guest for this episode, Raquel Munoz from the Hospital Universitario Virgen del Rocío in Seville Spain, is doing research in this exciting CAR-T cell therapy space. Specifically, she is working to develop methods to help better quantify and understand the expansion of CAR-T cells in the body to help monitor treatment and predict outcomes. We learn about why digital PCR was selected for her work and how it’s helped raise confidence in the results they’re getting. We even hear about how she believes this treatment will find success in treating solid tumor cancers.
In Cassie’s career corner, we learn how Raquel found her career path and love of immunology and working in a hospital setting. Raquel also shares some great career advice, stories of lab mishaps, and the dangerous hobby that she says is some of the only time she’s not thinking about work or problems.
Affiliation link
- Junta de Andalucía
https://hospitaluvrocio.es/
Publications
- Monitoring of kinetics and exhaustion markers of circulating CAR-T cells as early predictive factors in patients with B-cell malignancies
https://pubmed.ncbi.nlm.nih.gov/37122702/ - Variants in autoinflammatory diseases-related genes in a family with cold-induced autoinflammatory syndrome
https://pubmed.ncbi.nlm.nih.gov/35383566/
Fun facts
In the lab, Dr. Munoz is sometimes referred to as the “digital PCR girl”.
Episode 1: A couple of reproductive biology experts
Kicking off Season 2, in this episode, a married couple share their collaborative work in reproductive biology aimed at understanding the role of RNA degradation in oocytes. They share insights on how oocytes are so unique, why they’re so important, and how better understanding them can provide insights to improve women’s health and lead to potential therapies. Join us to meet this interesting couple and hear how they’ve built a marriage in reproductive science.
About Dr. Nehemiah Alvarez
I began my independent tenure track position as an assistant professor two years ago at Eastern Virginia Medical School, in the Department of Physiological Sciences. I am also Director of the Advanced Sequencing Program at EVMS. My research program focuses on understanding the role of RNA modifications in cellular processes that impact ovarian function in women. I have an extensive research background in computational, molecular, and cellular biology as it relates to investigating mechanisms of post-transcriptional gene regulation in physiology and disease. My research program leverages advanced computational sequencing technologies to address emerging areas of research involving RNA modifications and disease.
About Dr. Pavla Brachova
I got my Ph.D. at the University of Iowa, studying ovarian cancer and the tumor suppressor p53, and had postdoctoral training at the University of Kansas Medical School, studying ovarian physiology. I started my tenure-track appointment in the Physiological Sciences Department at Eastern Virginia Medical School (EVMS) two years ago. The main objective of my research includes characterizing the cellular and molecular events necessary for the function and quality of the oocyte and egg, such that this knowledge may provide insight into improving women’s health.
Episode notes
We are all the product of a reproductive process, yet reproductive biology, or the study of the processes and mechanisms involved in reproduction, is not well understood. Deepening our understanding of reproductive biology is crucial to advancing assistive reproductive technologies (ART) and advancing our collective comprehension of inheritance and evolution.
Our guests for this episode are a couple, and we mean a literal married couple, of reproductive biology experts. Dr. Pavla Brachova and Dr. Nehemiah Alvarez, both working in the Eastern Virginia Medical School’s Department of Physiological Sciences. In their collaborative work they aim to better understand and characterize the role of RNA and cellular events that impact ovarian function in women. We learn about their work with oocytes, which are single cells that grow and mature within the ovary and once fertilized provide the foundations of an embryo capable of maturing to a new individual. They outline how they use digital PCR (dPCR) and other methods to monitor RNA regulation in single cells and how progressing this work and lead to potential RNA-based therapies.
In Cassie’s career corner we hear childhood stories from each guest and learn about their respective career paths, which eventually collided and merged. They share insights on the importance of having mentors experienced in your field, the challenges of shared job searching, and the joys of collaborating as a couple with shared scientific interests
Affiliation link
Publications
- Brachova, P*, Alvarez NS*, Lane K. Christenson. Loss of Cnot61 impairs inosine RNA modifications in mouse oocytes. Int. J. Mol. Sci.2021, 22(3), 1191; https://doi.org/10.3390/ijms22031191. *Co-first Author. https://pubmed.ncbi.nlm.nih.gov/33530472/
- Brachova P*, Alvarez NS*, Hong X, Vincent KA, Latham KE, Christenson LK, Inosine RNA modifications are enriched at the codon wobble position in mouse oocytes and eggs. Biol Reprod. 2019 July 26. Doi:10. 1093/biolre/ioz130. *Co-first author https://pubmed.ncbi.nlm.nih.gov/31346607/
Fun facts
Dr. Brachova and Dr. Alvarez have worked together since they were postdoctoral trainees, where they shared the same bench (and pipettes, gasp!). Now as tenure track faculty, in the same department, they run a joint laboratory and a joint NIH supported research program. They still share pipettes.
Episode 1: Tales of a pandemic PhD
The season kicks off with a conversation with Dr. Sarah Philo, a recent PhD graduate working in wastewater-based epidemiology to track SARS-CoV-2 and antimicrobial resistance. We talk about the science, the joys of working with sewage samples, pandemic-era academics, career development, and more!
Episode notes
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!
About Sarah Philo
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).
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 facts
“In my free time I sing in a choir in Seattle, and have been singing with choirs since I was in undergrad.”
Episode 2: Insights from a PCR whisperer
For this episode we keep things in house with Marcia Slater. Her more than 20 years of experience in PCR are evident in how well she covers the history of power of digital PCR. Join for some dPCR fundamentals, the ever-present Gene-ius gems on career development, and stories about alpaca farming!
Episode notes
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!
About Marcia Slater
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.
Affiliation links
- Affiliation Link: www.thermofisher.com
Publications
- High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR. https://pubmed.ncbi.nlm.nih.gov/27929456/
- US Patent: WO-02077285-A2 Methods of determining the presence of polynucleotides employing amplification. https://patents.google.com/patent/WO2002077285A2/en?oq=+b.US+Patent:+WO-02077285-A2
Fun facts
“I own a farm called Perkiomen Creek Ranch. Note the initials: PCR. Yeah, that was on purpose. ”
Episode 3: Avoiding the itch with digital PCR
Come meet Patrick Hanington and learn about his work in parasitology. We talk about how dPCR is advancing his team’s work in monitoring public and recreational waters for parasites, including schistosomes, which cause swimmer’s itch. You’ll also get some great career advice, funny sample-collection stories, and some unexpected movie references and recommendations.
Episode notes
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.
About Patrick Harrington
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.
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/
Fun facts
"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."
Episode 4: Raising the fish that spawn our insights
For this episode we host two guests: Zoltan Varga and Corbin Schuster from the Zebrafish International Resource Center at the University of Oregon who join us to talk about why zebrafish are an ideal model organism for genetic studies and to tell us about some of the challenges of creating and maintaining thousands of genetically unique lines of the animal. The Career Corners part of this conversation is also super inspiring and insightful.
About the guests
Zoltan Varga
I was born in Düren Germany and went to elementary and high school in Grenzach-Wyhlen (Germany, until 1986). I did my undergraduate studies, Diploma, and Ph.D. at the Biocenter Basel (Switzerland, 1986-1995). My Ph.D. work (1992-1995) was under the supervision of Prof. John G. Nicholls. I studied the regenerative capacity of an immature mammalian central nervous system in vitro, with the South American opossum (Monodelphis domestic). This was followed by a post-doc in Prof. Monte Westerfield’s laboratory at the Institute of Neuroscience, University of Oregon, Eugene, OR (1995-1999). I studied patterning, regionalization, and cell fate decisions in the anterior neural plate of zebrafish embryos (Danio rerio) and the cellular movements underlying normal eye development or cyclopia. After that time, I moved back to Germany and started my own laboratory in Freiburg at the Institute of Biology 1, Department of Developmental Biology, under Prof. Wolfgang Driever. During this time (1999-2004), I focused on the development of the ventral neural plate and forebrain and the development of the pituitary placode (hypophysis), lens, and hypothalamus (also in zebrafish embryos). I then moved back to Eugene (2004) where I started my current position directing the Zebrafish International Resource Center at the UO (until present).
Corbin Schuster
Corbin Schuster grew up in the Yakima Valley in the heart of the Yakama Nation Reservation. He completed his B.S. in Biomedical Sciences at Heritage University and completed his Ph.D. in Microbiology at Oregon State University. During his doctoral training he studied microsporidian infections in laboratory zebrafish and concentrated on the development of environmental assays for detection of important zebrafish pathogens. He then completed a post-doc at the Zebrafish International Resource Center (ZIRC) focusing on the expansion of environmental zebrafish assays for large zebrafish facilities. He is now an assistant professor of Biology at his Alma Mater, Heritage University, where he teaches general biology, microbiology, and environmental microbiology, while also continuing to do research in assay development for zebrafish and salmonid pathogens.
LinkedIn profiles
- Zoltan Varga: https://www.linkedin.com/in/zoltan-m-varga-74373b7/
- Corbin Schuster: https://www.linkedin.com/in/corbinjschuster
Affiliation links
- Zoltan Varga: https://zebrafish.org/home/guide.php
- Corbin Schuster: https://heritage.edu
Publications
Zoltan Varga
- Jennifer L Matthews, Joy Murphy, Andrzej Nasiadka, Zoltan M Varga (2022) A Simple Method for Inducing Masculinization of Zebrafish Stocks Using 17α-Methyltestosterone. Zebrafish 19(6):241-244. doi: 10.1089/zeb.2022.0029. Epub 2022 Nov 1. PMID: 36318811; PMCID: PMC9810344. https://pubmed.ncbi.nlm.nih.gov/36318811/
- Langa, X., Neuhaus, P., Lains, D., Stewart, T.J., Borel, N., Certal, A.C., Monteiro, J.F., Aleström, P., Diaz, E., Piragyte, I., Bräutigam, L., Vázquez, R., Hlushchuk, R., Gfeller, L., Mestrot, A., Bigalke, M., Varga, Z.M., Mercader, N. (2021) A Systematic Analysis of Metal and Metalloid Concentrations in Eight Zebrafish Recirculating Water Systems. Zebrafish. 18(4):252-264. https://pubmed.ncbi.nlm.nih.gov/34227897/
- Yang H, Hu E, Tiersch T, Carmichael C, Matthews J, Varga ZM. Temporal and Concentration Effects of Methanol on Cryopreservation of Zebrafish (Danio rerio) Sperm. Zebrafish. 2020 Aug;17(4):233-242. doi: 10.1089/zeb.2019.1849. Epub 2020 Jun 27. PubMed PMID: 32598236, PMCID: PMC7455470 https://pubmed.ncbi.nlm.nih.gov/32598236/
- Matthews JL, Murphy JM, Carmichael C, Yang H, Tiersch T, Westerfield M, Varga ZM. Changes to Extender, Cryoprotective Medium, and In Vitro Fertilization Improve Zebrafish Sperm Cryopreservation. Zebrafish. 2018 Jun;15(3):279-290. doi: 10.1089/zeb.2017.1521. Epub 2018 Jan 25. PubMed PMID: 29369744, PMCID: PMC5985902 https://pubmed.ncbi.nlm.nih.gov/29369744/
Corbin Schuster
- Schuster, C.J., Murray, K.N., Sanders, J.L., Kent, M.L. (2023) Application of an eDNA assay for the detection of Pseudoloma neurophilia (Microsporidia) in zebrafish (Danio rerio) facilities. Aquaculture 564:739044. https://doi.org/10.1016/j.aquaculture.2022.739044
- Schuster, C.J., Kent, M.L., Peterson, J.T., Sanders, J.L. (2022) Multi-state occupancy model estimates probability of detection of an aquatic parasite using environmental DNA: Pseudoloma neurophilia in zebrafish aquaria. J Parasitol 108:527–538. https://doi.org/10.1645/22-21
- Schuster, C. J., Leong, C., Kasschau, K. D., Sharpton, T. J., & Kent, M. L. (2023). Early detection of Pseudocapillaria tomentosa by qPCR in four lines of zebrafish, Danio rerio (Hamilton 1882). Journal of Fish Diseases, 00, 1– 9. https://doi.org/10.1111/jfd.13773
Fun facts
Zoltan Varga
"It is family first, then working at ZIRC (or with zebrafish in general). In my free time I love reading about history, fly-fishing, playing music (guitar, piano, church/pipe-organ, and synthesizers), archery, cycling, hiking, and swimming. My family background allowed me to speak Hungarian, German, French and English, and understanding (rather less than more) a few languages due to Latin in High-School. - Aut viam inveniam, aut faciam."
Corbin Schuster
"I enjoy fishing and outdoor activities in my downtime or anytime I can get away from the office/lab. I travel a lot, but the reason I do so is as a food enthusiast as I love trying out new and different cultural dishes of the places and peoples I visit."
Episode 5: Shrimp-ly amazing science
In this easy-to-listen-to episode we talk with Ray Ketchum from Agrinos and learn about how he and his team are using microbial consortia to produce products that improve plant health and crop yields. The conversation covers how dPCR helps them quantify individual species within a complex mixture of more than 20 bacteria that are a mix of aerobes and anaerobes. Ray also shares his career path journey and some insightful lessons learned along the way.
About Ray Ketchum
My career has involved working with many different technologies relating to plants and plant natural products and working with many different types of plants, in particular medicinal plants. I worked for 20 years on all aspects of the production of an anticancer drug derived from plant cell cultures of yew trees (Taxus sp.). My research encompassed nearly all disciplines of plant biotechnology, including the establishment of plant cell cultures, selection and elicitation of cell cultures to produce high levels of this compound in vitro, development of methods of quantitative analysis by HPLC/MS, establishment of methods for genetic transformation and engineering of Taxus plant cell cultures, and elucidation of steps in the biosynthetic pathway leading to the compound's production. I received a B.A. in Botany and Biochemistry from Connecticut College; received a Ph.D. in Botany, specializing in Developmental Plant Physiology with Prof. Murray Nabors, from Colorado State University; worked as a post-doctoral researcher with Dr. Donna Gibson at USDA-ARS, Cornell University; worked as a visiting scientist with Prof. Mike Shuler in the College of Engineering at Cornell University; worked with Prof. Rod Croteau at Washington State University as an Assistant Research Professor; and was the Director of the Bioinformatics and DNA Sequencing Core at the University of Idaho immediately prior to joining DianaPlantSciences
Episode notes
Microbial consortia are groups of diverse microorganisms that have the ability to act together in a community. Such consortia are common in nature and are known to play important roles in many ecosystems but are not always well understood. Soil management and nutrient mobilization are one area where complex communities of microbes are know to be important, whether it be a naturally occurring consortium, or a man-made consortium.
In this episode of Absolute Gene-ius Jordan and Cassie talk with Dr. Ray Ketchum form Agrinos about the microbial consortia he and his team cultivate and produce to improve plan health and increase crop yields. We learn about the challenges of fermenting mixtures of more than 20 diverse microorganisms to reproducibly make products that improve plant health and mobilize nutrients in a completely organic way. As you might expect, digital PCR plays in important role in Ray’s R&D and quality control process. Here, they use dPCR to titer each of the species within their consortia for quality and regulatory purposes, a task that cannot be done by cell culture methods given the range of bacteria involved.
Cassie’s career corner gets Ray sharing his full career development story from undergraduate through grad school and postdoc positions and into his professional career. Ray is generous in sharing his early misconceptions and miscalculations while providing advice to help other avoid similar missteps.
Affiliation link
- AMVAC/Agrinos, Inc
http://www.agrinos.com
Publications
- Fischedick J, Johnson S, Ketchum R, Croteau R, Lange B. 2015. NMR spectroscopic search module for Spektraris, an online resource for plant natural product identification–Taxane diterpenoids from Taxus × media cell suspension cultures as a case study. Phytochemistry. 113: 87-95. (DOI:10.1016/j.phytochem.2014.11.020)
https://pubmed.ncbi.nlm.nih.gov/25534952/ - Cuthbertson DJ, Johnson SR, Piljac-Žegarac J, Kappel J, Schäfer S, Wüst M, Ketchum RE, Croteau RB, Marques JV, Davin LB, Lewis NG, Rolf M, Kutchan TM, Soejarto DD, Lange BM. 2013. Accurate mass–time tag library for LC/MS-based metabolite profiling of medicinal plants. Phytochemistry 91: 187-197. (DOI:10.1016/j.phytochem.2013.02.018)
https://pubmed.ncbi.nlm.nih.gov/23597491/ - Kaspera, R., Cape, J.L., Faraldos, J.A., Ketchum, R.E.B., Croteau, R.B. 2010. Synthesis and evaluation of Taxol oxetane ring D precursors. Tet. Lett. 51: 2017-2019 (DOI:10.1016/j.tetlet.2010.02.033)
https://pubmed.ncbi.nlm.nih.gov/20305723/ - Ketchum, R.E.B., Wherland, L., and Croteau, R.B. 2007. Stable transformation and long-term maintenance of transgenic Taxus cell suspension cultures. Plant Cell Rep 27: 1025-1033 (DOI:10.1007/s00299-007-0323-x).
https://pubmed.ncbi.nlm.nih.gov/17333018/ - Ketchum, R.E.B., Horiguchi, T., Qiu, D., Williams, R.M., and Croteau, R.B. 2007. Administering cultured Taxus cells with early precursors reveals a bifurcation in the taxoid biosynthetic pathway. Phytochemistry 68: 335–341 (DOI:10.1016/j.phytochem.2006.10.019).
https://pubmed.ncbi.nlm.nih.gov/17157336/ - US Patent 20150150784 - Dermatological composition containing cultured Theobroma cacao cells or its extracts and related methods
https://patents.google.com/patent/US20150150784A1/en?oq=US%20Patent%2020150150784
Fun facts
Avid hiker, backpacker, downhill and cross country skier, and jazz saxophone player.
Episode 6: PCR on ‘zombie’ organisms in extreme environments
We once again welcome two guests to this episode where we talk about using digital PCR and other methods to study microbial life and survivability in extreme environments. Dr. Brandi Kiel Reese and Lydia Hayes-Guastella from the Dauphin Island Sea Lab at the University of South Alabama tell us all about their work collecting and analyzing samples from places as remote as Antarctica and the Mariana Trench. They share what working in such unique locations is like, how samples are collected and analyzed, and what they hope to glean from their studies. As always, you’ll also get to know a bit more about them and hear their personal stories!
About the guests
Brandi Kiel Reese, PhD
Brandi Kiel Reese received a BS in Geology with a concentration in biogeochemistry from Southern Methodist University. She went on to complete her MS in Soil and Water Sciences at University of California, studying sulfur biogeochemistry of the Salton Sea, California. After completing her MS, she went on to complete her PhD in Oceanography at Texas A&M University, combining her background in geochemistry with molecular microbial ecology. Her current research is widely interdisciplinary, combining geology, biogeochemistry, and molecular microbiology to provide a more integrated examination of aquatic and sediment biogeochemical cycling. When examining various environments, she is guided by fundamental questions such as: Who is alive? What are they doing? What are the global implications of microbial life within Earth systems? Specifically, her lab specializes in combining state-of-the-art culture-independent molecular techniques (including metatranscriptomics and metagenomics) with high throughput culturing and advanced geochemical analysis to describe the total microbial environment. This systems biology approach to understanding microbial ecology has spanned marine and freshwater, shallow sediments within estuaries and coastal hypoxic zones, deeply buried continental mines and caves, and marine subsurface sediments through the International Ocean Discovery Program (IODP).
Lydia Hayes-Guastelladf
Lydia Hayes-Guastella graduated with her BS in Microbiology from Michigan State University, working with microbial communities in ophiolite serpentinizing systems. She went on to obtain her MS in Marine Biology from Texas A&M University-Corpus Christi, where she studied nitrogen cycling in restored and natural wetlands influenced by wastewater treatment plants. Currently, she is working toward her PhD in Marine Science at University of South Alabama studying under her advisor Brandi Kiel Reese. She is investigating microbial communities in the extreme high pH environments of the serpentinite mud volcanoes of the Mariana Forearc, as well as the nutrient and energy limited deep subsurface sediments of the South Atlantic Gyre through culture independent methods including metagenomic and metatranscriptomic analysis, as well as culture dependent isolation and ecophysiological studies, looking at what is living there, how they are surviving, and what is their role in their environment. Her research interests are microbial communities’ survivability in extreme environments and how those communities relate to nutrient cycling dynamics.
Episode notes
There are very few remaining locations on Earth that are untouched by humans, and those that do remain are in very extreme environments that are difficult to access. However, accessing and studying life in these extreme environments can provide unique insights to the biology of life. Understanding how simple organisms adapt and survive in seeming unlivable conditions is a unique field of study with the potential to inform and affect the human condition.
We’re joined in this episode by Dr. Brandi Kiel Reese and Lydia Hayes-Guastella from the Dauphin Island Sea Lab at the University of South Alabama. They are both geomicrobiologists that study microbial life in extreme environments like the Mariana Trench and Antarctica. They do an excellent job of painting a picture of how extreme conditions are in these environments and how they manage to collect and preserve samples from such harsh conditions. We learn about the various methods they use to analyze the microbial samples they collect, including the use of digital PCR (dPCR) to detect and quantify transcripts that would otherwise not be detectable given how few cells they’re able to collect.
Brandi and Lydia also share their unpredictable career path journeys, while sharing some insights and learnings from their respective experiences. We learn what they each love about their work and what qualities it takes to be successful at what they do. Once again, we’re reminded of what a small world it is, especially when you’re in a specialty field such as geomicrobiology of extreme environments.
Affiliation links
Brandi Kiel Reese
- Dauphin Island Sea Lab Website: https://www.disl.edu/
- Kiel Reese Geomicrobiology Lab Website: https://geomicrobiology.weebly.com/
- University of South Alabama Stokes School of Marine and Environmental Sciences- https://www.southalabama.edu/colleges/artsandsci/marinesciences/
Lydia Hayes-Guastella
- Dauphin Island Sea Lab Website: https://www.disl.edu/
- Kiel Reese Geomicrobiology Lab Website: https://geomicrobiology.weebly.com/
Publications
Brandi Kiel Reese
- Kiel Reese, B., Sobol, M. S., Bowles, M. W., & Hinrichs, K.-U. (2021). Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment. Frontiers in Fungal Biology, 2. https://doi.org/10.3389/ffunb.2021.727543
- Kiel Reese, B., Zinke, L. A., Sobol, M. S., LaRowe, D. E., Orcutt, B. N., Zhang, X., Jaekel, U., Wang, F., Dittmar, T., Defforey, D., Tully, B., Paytan, A., Sylvan, J. B., Amend, J. P., Edwards, K. J., & Girguis, P. (2018). Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank. Geomicrobiology Journal, 35(6), 468–483. https://doi.org/10.1080/01490451.2017.1392649
- Mullis, M. M., Selwyn, J. D., Kevorkian, R., Tague, E. D., Castro, H. F., Campagna, S. R., Lloyd, K. G., & Kiel Reese, B. (2023). Microbial survival mechanisms within serpentinizing Mariana forearc sediments. FEMS Microbiology Ecology, fiad003. https://doi.org/10.1093/femsec/fiad003
Lydia Hayes-Guastella
- Hayes, L. (2020). Assessment and Valuation of Nitrogen Mitigation Ecosystem Services in Natural and Restored Wetlands of the Texas Coastal Bend (Masters Thesis, Texas A&M University-Corpus Christi).
Fun facts
Brandi Kiel Reese
- When a member of the lab travels to a new country, it is tradition to send a postcard back to the lab. We currently have postcards from 22 different locations.
- The oldest sediment that we have worked with in the Kiel Reese lab is approximately 175 million years old.
- I have sent microorganisms to the International Space Station.
Lydia Hayes-Guastella
- I love to collect rocks and use them to make wire wrapped jewelry. I have also played piano since I was 8.
Episode 7: Bioinformatics—the bridge to understanding biology
This episode features an easygoing bioinformatics expert. Our conversation with Nikhil Ram Mohan, Staff Scientist at the Stanford University School of Medicine, is an easy entry into the dry-lab work of bioinformatics and how this informs and augments wet-lab molecular biology work. He tells us about his use of digital PCR to analyze biobank samples, how his first visit to another country was his move to the U.S. for grad school, about his love of teaching, and about being a new father. Check out this interesting episode, fueled by an interesting guest!
About Nikhil Ram Mohan, PhD
I am a computational biologist working in Dr. Samuel Yang’s lab in the Emergency Medicine Department at Stanford University. We work on developing technologies for rapid identification and antibiotic susceptibility testing of bacteria. My research focuses on developing predictive models for susceptibility and minimum inhibitory concentration to antibiotics based on morphological changes in imaging data. In parallel, I am also developing classification models to detect susceptibility based on nucleic acid levels in populations using cycle threshold levels from qPCR.
I received my PhD from the University of Connecticut under the supervision of Dr. R Thane Papke working on the mechanisms driving speciation in halophilic archaea. I surveyed the role of biogeographic distribution, temporal stability, and extensive homologous recombination in populations of halophilic archaea that drive the genesis of new species within the archael domain. My first postdoctoral training was with Dr. Michelle Meyer in Boston College studying non-coding RNAs in bacteria, including discovery of novel ones, definition of transcriptional boundaries, and their roles in periodontitis in the oral microbiome and the pathogenicity of Streptococcus pneumoniae. For my second postdoctoral training, I moved to Stanford to work with Dr. Yang where I used ATAC-seq, Hi-C, and RNA-seq to determine insult-specific epigenetic regulation in neutrophils. Subsequently, I led multiple collaborative COVID-19 studies during the pandemic.
Episode notes
Bioinformatics is a relatively new field of science that is very interdisciplinary in nature. Its practitioners use a mixture of biology, chemistry, physics, statistics, and computer science to develop methods and software aimed at helping integrate and understand biological and other data.
Our guest for this episode is Nikhil Ram Mohan, Staff Scientist at the Stanford University School of Medicine. He describes bioinformatics as the bridge to understanding biology. We learn about his international studies and path that brought him to this current role and field of study, and then dive into some of his recent work. Here he and his team analyze biobank samples using digital PCR (dPCR) and quantitative PCR (qPCR) and compare results from the two while correlating results with additional data available for each sample to determine if SARS-CoV-2 RNA detection and quantification in blood can serve to help predict potential for patient coinfection. Their work found that dPCR was able to detect SARS-CoV-2 in samples that were negative when evaluated by qPCR and that a series of biomarkers can help predict coinfection.
We also get to hear a bit of Nikhil’s interesting personal story, which includes his undergraduate engineering studies in India and leaving his native country for the first time when he moved to the U.S. for graduate school. We learn how he managed changes in culture, what he loves about teaching, and about him being a new father.
Affiliation link
- Stanford profile: https://profiles.stanford.edu/216728
Publications
- Rapid Molecular Phenotypic Antimicrobial Susceptibility Test for Neisseria gonorrhoeae Based on Propidium Monoazide Viability PCR
https://doi.org/10.1021/acsinfecdis.3c00096 - Using a 29-mRNA Host Response Classifier To Detect Bacterial Coinfections and Predict Outcomes in COVID-19 Patients Presenting to the Emergency Department
https://doi.org/10.1128/spectrum.02305-22 - SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19
https://doi.org/10.1093/cid/ciab394
Fun facts
I am not sure what to say here. I lead a pretty mundane life.
Episode 8: Let’s make a bet—Poisson statistics of digital PCR
For this episode we host another of Thermo Fisher Scientific’s own. Dave Bauer is a PhD-educated Application Scientist specializing in qPCR and digital PCR. His knack for using analogies to explain difficult concepts helps illuminate the benefits of digital PCR and the statistical aspects of this analytical method. This is a great overview episode that also touches on specific applications such as SNP detection. We also learn about Dave’s career path, hear some valuable advice, and get a sense of how poorly most us are at evaluating probabilities.
About Dave Bauer
Dave Bauer, PhD, is a Field Application Scientist for real-time PCR and digital PCR at Thermo Fisher Scientific. He has broad experience and scientific education ranging from software programming and cell culture to quantum mechanics and evolutionary biology. Dave’s passion for digital PCR relates to it residing at an intersection between multiple scientific disciplines, providing a complement to his background. Prior to joining Thermo Fisher he obtained a PhD in Molecular Biophysics investigating the physical chemistry of viral genome packaging, worked as a researcher in DNA forensic science, and helped develop real-time PCR assays for cellular therapeutics. Outside of work he loves to spend time with his family and loving doggies, as well as routinely learning and tackling (with varying degrees of success) home renovation projects.
Episode notes
PCR was discovered in 1983 by Kary Mullis and Michael Smith, who were jointly awarded the Nobel Prize in Chemistry in 1993. Since then, PCR has been a cornerstone method that has been a pillar of discovery and applied science. The various types of PCR are sometimes confusing, and the relative pros and cons of each method are not always clear, which is why it’s so great to have this episode’s guest explain them all in a simple and clearcut way.
Dave Bauer, PhD, is an Application Scientist at Thermo Fisher Scientific who specializes in real time PCR (qPCR) and digital PCR (dPCR). He has an educational background in biophysics, mathematics, and biochemistry, but what’s more important is that Dave has a real knack for using analogies to make complex topics understandable and approachable. In this episode we hear Dave explain the difference between qPCR and dPCR, the importance of Poisson statistics to dPCR, dead volume, reaction chamber volume consistency, and more. We learn how qPCR and dPCR complement each other and how they relate to sequencing methods for applications like single nucleotide polymorphism (SNP) detection.
As you’ve come to expect from Absolute Gene-ius, you also get a good sense of who Dave is and how he got to his current role. We learn about how he knew right away that academia wasn’t for him, how he ended up in a forensics job straight out of school, and how he eventually landed in his current Application Scientist role. Dave shared some great insights and advice, including how students should care less about their degree’s name and more about what techniques they’re learning and using in their studies.
Affiliation link
Publications
- Validating TrueAllele Interpretation of DNA Mixtures Containing up to Ten Unknown Contributors https://pubmed.ncbi.nlm.nih.gov/31580496/
- Exploring the Balance between DNA Pressure and Capsid Stability in Herpesviruses and Phages https://pubmed.ncbi.nlm.nih.gov/26136570/
Fun facts
My dream job has always been to open my own distillery themed upon biology and chemistry education as part of the customer’s experience.
Episode 9: An introspective retrospective
We close this season with our hosts sharing a retrospective conversation about the start of the Absolute Gene-ius series, the wonderful guests hosted, favorite moments, and lessons learned. In addition to the season recap, Cassie and Jordan also interview each other to extract some “Cassie’s Career Corner” insights about their respective backgrounds and how they each ended up in their current roles. Join us to get to know your hosts a bit better and to reflect on this amazing inaugural season.
Episode notes
It’s not every day that you discover a new podcast series you like, and it’s not every day that you start hosting a podcast series either! To bookend this inaugural season of Absolute Gene-ius, Jordan and Cassie interview each other to provide a retrospective look at the season and to learn more about each other and their respective career paths.
In their recap of the season, we revisit the diversity of applications that guests used digital PCR to progress, from monitoring wastewater for infectious diseases like SARS-CoV-2, to monitoring zebrafish populations to ensure research organizations around the world have reliable model organisms, to looking characterizing microbial diversity in some of the Earth’s most extreme environments. We also get to hear about each hosts’ favorite moments, biggest surprise, what they’re proud of, and what they love most about the series they’re helping build.
Jordan and Cassie also share a bit more about their individual career paths and journey within science. We learn how Jordan parlayed a childhood connection to a Claymation elf dentist into being a published author his career in marketing life science products. We learn how Cassie’s had several jobs that led to eye-opening experiences that eventually led to her finding a home in technical marketing and communication. Don’t miss this season 1 recap to get to know your hosts a bit better and to hear about what’s coming soon!
Affiliation link
Publications
Jordan Ruggieri
- Techniques for Nucleic Acid Purification from Plant, Animal, and Microbial Samples, Springer Publications http://link.springer.com/protocol/10.1007/978-1-4939-3185-9_4
- Enzymology and Protein Engineering Heterologous Expression and Characterization of the Manganese-Oxidizing Protein from Erythrobacter sp. Strain SD21, Applied Environmental Microbiology http://aem.asm.org/content/80/21/6837.full
Fun fact
Jordan Ruggieri
I have never had a cavity, was born without wisdom teeth, had 9 teeth pulled as a kid, had braces for 6 years, and have two dental implants. If you can’t tell, I LOVE going to the dentist.
Cassie McCreary
One of my proudest moments is that I won a Magic Tree House book competition when I was 7. My story suggestion was chosen from more than 3,000 entries! It was about Amelia Earhart, one of my personal heroines.
Digital PCR Academy
This webinar will cover dPCR basics and the differences between dPCR and qPCR and provide an overview of the QuantStudio Absolute Q dPCR System.
IdentiFIND: The digital PCR game
Are you up for the challenge? Play IdentiFIND to search for and find your target items and molecules.
Jordan Ruggieri
Jordan Ruggieri, while not a self-proclaimed “gene-ius”, received his B.S. in Biological Sciences from Cal State Fullerton and his MBA from Cal State Monterey Bay. At Cal State Fullerton he served as a President’s Scholar and spent three years in a research lab studying manganese oxidation in bacteria for potential bioremediation purposes. He has spent ten years working in the biotechnology industry holding positions in both research & development and product marketing across the life science and clinical diagnostics markets. Jordan is currently a Regional Marketing Manager at Thermo Fisher Scientific overseeing the digital PCR product line. He loves telling stories about how scientists use these technologies for incredible applications that enable positive change across the globe. Jordan is a nerd at heart and loves to read, his favorite series being The Wheel of Time, The Stormlight Archive, and The Lord of the Rings.
Publications
- Techniques for Nucleic Acid Purification from Plant, Animal, and Microbial Samples, Springer Publications, http://link.springer.com/protocol/10.1007/978-1-4939-3185-9_4
- Enzymology and Protein Engineering Heterologous Expression and Characterization of the Manganese-Oxidizing Protein from Erythrobacter sp. Strain SD21, Applied Environmental Microbiology, journals.asm.org
Christina Bouwens
Christina Bouwens is the Global Market Development Manager for Digital PCR at Thermo Fisher Scientific, and has a passion for all things digital PCR. She received her bachelor's of science in Molecular and Cellular Biology from Santa Clara University which then led her to join an oncology research group at Stanford University where she spent the next 6 years studying cancer biology with a focus on circulating tumor DNA detection and monitoring using digital PCR technology. Her experience there and proximity to innovative tools and technologies led her to follow that passion for digital PCR tool and assay development to Thermo Fisher Scientific. Outside of work she enjoys all the typical things you would expect a good California native to enjoy including hiking, biking, gardening, and camping!
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