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.

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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

• www.thermofisher.com

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.  

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.  

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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

• https://pathology.med.upenn.edu/

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.  

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. 

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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.

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.

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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.

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.

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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

• https://www.patheon.com/us/en/our-capabilities/advanced-therapies/viral-vector-manufacturing-services.html

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 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!

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.

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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.

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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.

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.   

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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.

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.

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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

• https://www.rigshospitalet.dk/english/departments/centre-of-diagnostic-investigation/department-of-clinical-genetics/Pages/default.aspx

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.

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.

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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.

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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

• Rounak Feigelman
  https://scholar.google.com/citations?user=MCubbvkAAAAJ&hl=en&oi=ao

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.

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. 

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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”.

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.

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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

• EVMS
  https://www.evms.edu/

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.