Absolute Gene-ius

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. Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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. Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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. Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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 Soohoo 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. Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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. Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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. Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

Welcome back Gene-iuses! Jordan and Cassie kick us off with a fun teaser of what’s to come in Season 2 of the Absolute Gene-ius series. We’ll be featuring another great season of interesting guests, all using dPCR to progress their diverse research applications. This includes conversations about reproductive biology, liquid biopsy and transplantation research, CAR-T research, the role of bioinformatics in PCR assay design, micro-RNA analysis, differential gene expression analysis, and of course Cassie’s Career Corner, where we get to learn about people behind the science. This teaser, like every episode of Absolute Gene-ius, has the fun baked in to keep it all light and interesting too. You might even hear some digital PCR jokes! Visit the Absolute Gene-ius page to access the entire first season and to learn more about the hosts and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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! Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. This episode includes the following sound effects from freesound.org, licensed under CC BY-ND 4.0:

Polymerase chain reaction (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 clear-cut way. Dave Bauer, PhD, is an Application Scientist at Thermo Fisher Scientific that specializes in real time PCR (qPCR) and digital PCR (dPCR). He has an educational background in physics, mathematics, and biology, but what’s more important is that Dave loves to help others learn and to break down a topic’s complexities to make it more 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 unexpectedly working in forensics after his PhD, and how he eventually landed in his current Application Scientist role. Dave shares 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. Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. This episode includes the following sound effects from freesound.org, licensed under CC BY-ND 4.0:

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. Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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 seemingly 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 is 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. Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

This mid-season message from Cassie includes the announcement of the arrival of Jordan’s first baby, which will mean a short delay in production of the second half of the season. We will be back soon though with more great conversations with the Gene-iuses using dPCR to progress their science. In the meantime, we hope you’ll constructive feedback via absolute.geneius@thermofisher.com or in a review on whatever service you stream us through. We also hope you’re tell a friend about us so that they can catch up on back episodes during the break. Stay curious!

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 known 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 about miscalculations while providing advice to help other avoid similar missteps. Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

The use of model organisms in science dates to ancient Greece and represents an important way humans have progressed our collective understanding of biology and disease. We’ve probably all heard of using mice, rats, or even Drosophila melanogaster (i.e., fruit flies) in the lab, but zebrafish have surged in their use as a model organism. Zebrafish are small, more cost effective to maintain, have a fast generational lifecycle, and have clear embryos that enable direct observation of their development. As is the case with any model system used across the globe, standards matter and help make results transferrable to other studies. This is where our guests come into the picture. For this unique episode we’re joined by both Corbin Schuster and Zoltan Varga of Zebrafish International Resource Center (ZIRC) at the University of Oregon. In their roles, they help raise and maintain over 12,000 genetically unique zebrafish lines for use in studies across the globe. We learn about the health monitoring they conduct on a regular basis to maintain their colony and support their own and partner studies using their zebrafish. The conversation touches on: As always, you’ll also get to know our guests on a more personal level. We learn about how they each got into this line of work, what they love about it, and how they both value human relationships and helping their communities. Through the audio alone you’ll get a sense of the positive, kind, and collaborative attitudes that have helped them both be successful in their careers. Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

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. Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System.

Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. 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: 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!

Visit the Absolute Gene-ius page to learn more about the guest, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. 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 her conversation with Jordan and Cassie, 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 team and 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!

This series and season 1 intro is a perfect bite-sized taste of the Absolute Gene-ius podcast series. You get to meet the hosts, Jordan and Cassie, and hear about their backgrounds while sampling their hosting style and sense of humor. They cover what their goals are for the series and some of the interesting digital PCR topics and applications that will be covered in the inaugural season of this new series. Tune in to become an Absolute Gene-ius!