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 the anticancer drug, paclitaxel, 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 paclitaxel in vitro, development of methods of quantitative analysis of paclitaxel by HPLC/MS, establishment of methods for genetic transformation and engineering of Taxus plant cell cultures, and elucidation of steps in the paclitaxel biosynthetic pathway. 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.

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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.

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).

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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.

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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.

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.

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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.

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.

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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

• 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/

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 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

• thermofisher.com

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.