Podcasts about qpcr

Matters Microbial #84: Detecting Pathogens — and Worse — in Wastewater March 27, 2025 Today, Dr. Rachel Poretsky, Associate Professor of Biological Sciences at the University of Illinois Chicago joins the #QualityQuorum to discuss how examining wastewater (and related water) can give insights into the presence of pathogen antimicrobial resistance genes and even microbial ecology. Host: Mark O. Martin Guest: Rachel Poretsky Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode A link to demonstrate the wonders of the Marine Biological Laboratories' Microbial Diversity course, which I know for a fact is life changing. Recommended by David Ranada, an article about water bottles and microbes.   An essay about the Chicago River and cholera, which led to the necessity of effective waste water treatment. An overview of the complexities of waste water treatment.  Here is a video on that topic.   An essay by Carl Zimmer about the microbial ecology of lakes…and human beings. How “recreational water quality” is determined. An article describing the microbiota associated with human biological waste with an amusing name (scroll down). How qPCR can be used to determine the prevalence of specific microbes. A recent article from Dr. Poretsky's research group, investigating how antimicrobial resistance genes can move through a hospital waste water system. A link to the Bacterial-Viral Bioinformatics Resource Center, for which Dr. Poretsky is a Principle Investigator. The Illinois state wastewater surveillance dashboard.  Fascinating! A Discovery Channel documentary on virus hunting and surveillance that includes Dr. Poretsky. Dr. Poretsky's faculty webpage. Dr. Poretsky's webpage for her research group. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

In this episode of Absolute Gene-ius, Dr. C. Dustin Rubinstein takes us inside the world of advanced genome editing, where cutting-edge tools like CRISPR and digital PCR are helping shape the future of biomedical research.As the Director of the Advanced Genome Editing Laboratory at the University of Wisconsin-Madison, Dr. Rubinstein shares how his lab develops genetically engineered pig models to study diseases like neurofibromatosis and cancer, providing researchers with more clinically relevant models than traditional small animals. He explains how digital PCR plays a crucial role in confirming genome edits with absolute precision, eliminating the ambiguity that often comes with qPCR and sequencing alone. The discussion dives into the advantages of dPCR for copy number variation analysis and gene editing confirmation, emphasizing the importance of multiple complementary technologies in modern molecular biology.Beyond the science, Dr. Rubinstein reflects on his career path, the value of mentors, and the unpredictable nature of scientific discovery. He also joins in on some lighthearted lab humor and shares his most embarrassing (and proudest) moments in research. Tune in for an insightful and entertaining look at the intersection of gene editing, career evolution, and the future of molecular biology.Visit the Absolute Gene-ius pageto learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. 

In this episode, we delve into the world of qPCR stool testing, with Dr Tom Fabian unravelling the common myths surrounding its validity and reliability. Throughout the episode, we explore the scientific evidence that underpins qPCR stool testing, addressing misconceptions and highlighting its role in clinical decision-making.Listeners will gain insights into the types of conditions that qPCR stool testing can effectively uncover and get an insight into the interpretation of test results, offering practical tips on integrating qPCR stool testing into routine clinical assessments. The episode also covers technological advancements that enhance test accuracy and reliability, demonstrating its effectiveness in clinical practice.Whether you're a seasoned healthcare professional or new to the field, this episode offers a deep dive into how qPCR stool testing can enhance patient care and decision-making, leaving you well-informed and equipped with the knowledge to make confident diagnostic choices.Meet Dr Tom Fabian, PhDDr. Fabian is a leading expert on the role of the microbiome in health, immune function, chronic disease, and aging. As a translational scientist, his primary focus is on the clinical application of microbiome research in the integrative and functional medicine space. He received his PhD in molecular biology from the University of Colorado, Boulder, and has worked as a biomedical researcher in the biotechnology industry, and more recently, as a consultant in the microbiome testing field. Currently, Dr. Fabian serves a consultant and science advisor with Diagnostic Solutions Laboratory, and he is also a Science Advisory Board member with Designs for Health. In addition, he is certified as a Nutrition Therapy Practitioner by the Nutrition Therapy Institute in Denver.Get in touch! Shownotes and references are available on the Designs for Health websiteRegister as a Designs for Health Practitioner and discover quality practitioner- only supplements at www.designsforhealth.com.au Follow us on Socials Instagram: Designsforhealthaus Facebook: Designsforhealthaus DISCLAIMER: The Information provided in the Wellness by Designs podcast is for educational purposes only; the information presented is not intended to be used as medical advice; please seek the advice of a qualified healthcare professional if what you have heard here today raises questions or concerns relating to your health

Season 2 of Absolute Gene-ius comes to a close with a look back at the topics and inspiring conversations that have defined the series. From exploring innovative uses of digital PCR to uncovering its synergy with other molecular tools, this season was packed with insights for scientists at all levels.Dive into the details as co-hosts Jordan Ruggieri and Christina Bouwens revisit memorable episodes, including using dPCR as a low-cost precursor to single-cell sequencing and its role in quantifying active mRNA in groundbreaking drug development. Hear from experts like Parker Wilson, Christian Cobaugh, and Raquel Munoz, who share how digital PCR is revolutionizing their workflows and complementing other tools like qPCR and NGS.Of course, it wouldn't be Absolute Gene-ius without a few puns! Stick around for some lighthearted banter as Jordan and Christina celebrate the season's success, share their favorite moments, and hint at what's coming in Season 3. Stay curious, and we'll see you next cycle!Visit the Absolute Gene-ius pageto learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. 

Tiny microbes have a big impact on wine quality. Aria Hahn, CEO and co-founder of Koonkie, Inc., discusses the exciting work her bioinformatics organization is doing in the field of metagenomics. Hahn explains the differences between genetics, genomics, and metagenomics. She shares insights from a project studying yeast populations in British Columbia's Okanagan region, revealing the diversity and distinct clades found on wine grapes. The conversation also covers the broader applications of bioinformatics in agriculture, including regenerative farming, soil health, and potential bioprotectants against wine spoilage. Hahn underscores the impact of microbiome management on wine terroir and the potential of bioinformatics in understanding and improving winemaking processes. Resources:         201: Balance Hot Climate, High Sugar Wine with Green Grape Juice aka Verjus 243: Microbial Communities in the Grapevine 251: Vine SAP Analysis to Optimize Nutrition Aria Hahn – Google Scholar Aria Hahn – LinkedIn Koonkie Make Better Wines with Bioinformatics The Microcosmos - Discover the World of Genomics Apple App Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade Vineyard Team Programs: Juan Nevarez Memorial Scholarship - Donate SIP Certified – Show your care for the people and planet   Sustainable Ag Expo – The premiere winegrowing event of the year Vineyard Team – Become a Member Get More Subscribe wherever you listen so you never miss an episode on the latest science and research with the Sustainable Winegrowing Podcast. Since 1994, Vineyard Team has been your resource for workshops and field demonstrations, research, and events dedicated to the stewardship of our natural resources. Learn more at www.vineyardteam.org.   Transcript [00:00:00] Beth Vukmanic: Tiny microbes have a big impact on wine quality. [00:00:09] Welcome to Sustainable Wine Growing with Vineyard Team, where we bring you the latest in science and research for the wine industry. I am Beth Vukmanic, Executive Director. [00:00:19] In today's podcast, Craig McMillan, Critical Resource Manager at Niner Wine Estates, with longtime SIP certified vineyard and the first ever SIP certified winery, speaks with Aria Hahn, CEO and co founder of Koonkie Inc. [00:00:35] She discusses the exciting work her bioinformatics organization is doing in the field of metagenomics. Hahn explains the differences between genetics, genomics, and metagenomics. [00:00:47] She shares insights from a project studying yeast populations in one of British Columbia's wine growing regions, revealing the diversity and distinct clades found on wine grapes. [00:00:58] The conversation also covers the broader applications. bioinformatics in agriculture, including regenerative farming, soil health, and potential bioprotectants against wine spoilage. [00:01:09] Hahn underscores the impact of microbiome management on wine terroir and the potential for bioinformatics in understanding and improving the winemaking process. [00:01:19] We know your customers are looking for sustainable wines. In a recent review of 30 studies, Customers reported a higher preference for eco label and social responsibility labels compared with nutrition labels. Achieving SIP certified gives you third party verification that your vineyard winery or wine has adopted and implemented stringent sustainable standards. Apply today at SIP certified. org. [00:01:46] Now let's listen [00:01:50] Craig Macmillan: Our guest today is Aria Hahn. She is the CEO and co founder of Koonkie, Inc., a bioinformatics organization, business, doing all kinds of exciting stuff. Thanks for being on the podcast, Aria. [00:02:02] Aria Hahn: Yeah, so excited to be here. Thanks for [00:02:04] Craig Macmillan: We're going to get into the thick of it But we were attracted to some work that you folks and your colleagues have done with bioinformatics and yeast, wild yeast. But I wanted to drop back. A little bit first to kind of give some context. All of this kind of comes under the umbrella of metagenomics, correct? [00:02:21] Aria Hahn: Yeah, absolutely. [00:02:22] Craig Macmillan: and what is metagenomics? [00:02:24] Aria Hahn: I'm going to take further step back and talk about genomics um, maybe the distinction between genomics and genetics. [00:02:32] So genetics is something I think most people kind of understand. They have this intuitive sense of it. um, that make up ourselves and all living creatures. But it actually turns out that in most organisms, and not bacteria, and we'll get there in a Most of your DNA is not in genes. It's in between genes. And so genomics is the study of genes and all of the things that are in between genes. So that's kind of the distinction between genetics and genomics. And then metagenomics is when we do that at the community level. [00:03:02] so you could do metagenomics of humans, but metagenomics refers to populations of bacteria, uh, microbes, archaea, viruses, things that you cannot see and I'll say interact with directly. [00:03:17] Craig Macmillan: And then bioinformatics is a subset or is a technique, is that correct? [00:03:23] Aria Hahn: Yeah, it's a technique, you know, it used to be even 10, 15 years ago that everyone kind of did their own bioinformatics. And so really what that means is when we sequence DNA or read that DNA, so it's only four letters, ATCs and Gs, we extract the DNA the sample is, could be the surface of grapes, uh, a human, anything. [00:03:42] Um, Then we put it on a sequencer. There's a bunch of different sequencing technologies right now. Um, But you end up with these like very gross files that aren't openable on regular computers and they're literally just ATCs and Gs. And so bioinformatics is the cross section of high performance computing and biology. And so we develop algorithms and processes and pipelines to really take those gross huge files of ATCs and Gs and make them human readable. make them interesting, figure out, you know, what are the genes that are there? Who is there? What are they doing? And who's doing what? [00:04:19] Craig Macmillan: Okay, and I think that's the important part here is you would take a sample from the environment. We'll talk about this one more in a second, but there are particular sequences that may be associated with a certain type of microbe or even a particular genus or particular species of microbe that can be detected. [00:04:39] Aria Hahn: Yes, absolutely. [00:04:40] So a genome is all of the DNA that makes up that organism. So you and I have distinct genomes, but of course, our genomes are going to be pretty similar to each other compared to a human genome, to a fish, to a plant, to a [00:04:55] Craig Macmillan: why the focus on microbes? [00:04:57] Aria Hahn: Yeah, that's a great question. It depends how philosophical You want to get You know, people are generally [00:05:02] familiar with the concept of like the Higgs boson particle. It's like the God particle that makes up everything and that's great and the physicists are gonna come for me. But when we think about our planet Earth, I always say like If there is a god particle on this planet that is alive and that we interact with, like, it's a microbe. [00:05:21] This is their planet. They were here long before us and they will surely be here long after us. So we think about microbes in terms of they are the destroyers of higher level populations. They keep us healthy. They make us I'm going to say it's a great example, but it wasn't a great thing. [00:05:40] So caveat that. But COVID was a great example about how this is not our planet where we had an of a virus in one location in a very particular place in the world. And all of a sudden it was across the planet. We are vectors for them. [00:05:58] You know, looking at those maps and showing the spread and how quickly it happened, I like to use that often in visual presentations to say, if you don't believe me, like, look at this. It's spread through us. [00:06:10] Craig Macmillan: Right. And I think also this gets to some other things we might talk about later on, but there are communities of microbes that are associated with certain macroorganisms. [00:06:23] Aria Hahn: uh, so are, they're everywhere, they're on your um, there's lots of research in the cosmetic industry that's looking at that. There was this crazy CEO years ago where he was I'm gonna slather this microbial laden cream on my skin and then I'm never gonna shower again and I'm not gonna smell. Not necessarily like my cup of tea, I love a good hot shower. But, you know, it can be there. The soil is the microbial diverse environment on the planet. , But your gut, like you, you as a human being, can't actually digest your food without those microbes. You can't get those vitamins and nutrients that you need without that community in your stomach. [00:07:03] Plants work the same We say charismatic macrofauna, eagles, whales, things that are very Um, They, they don't to, you the seaweed and the weeds and the grass and kind of everything in between. it's All supported by the microbiome, by these microbial communities. [00:07:20] Craig Macmillan: so let's talk about one microbiome in particular, and that would be populations of yeast that we find on wine grapes. [00:07:29] Aria Hahn: Yeah, yeah. So we've looked at yeast and bacteria and they're both cool. [00:07:34] Craig Macmillan: That is super cool. And so this one particular project where you looked at yeast on wine grapes in British Columbia Tell us a little bit about that project [00:07:41] Aria Hahn: there's, So I live in I'm, I'm right in the thick of, you know, BC wine country, which is a fantastic place to live, we were fortunate enough to work with the Wine Research Institute out of the University of British Columbia, Vivian Mease Day's group. them and They do very, very cool work, but they were trying to look at the yeast populations in wineries across the Okanagan region. [00:08:02] We know that the history of lots of commercial. Yeasts are actually from oak trees in Europe. So that's very cool. And what we wanted to see is how are the yeasts that are being used to produce wine in the Okanagan region distinct and similar to commercial yeasts and yeasts that have been characterized from across and so We did just that and we were actually able to sequence a whole bunch of yeast. And so, again, that's like reading the genome effectively there. so we found four distinct clades, um, in the Okanagan region. And a clade is they're related groups, and so it's not like you and you're a twin where you might have an identical, uh, genome to a twin. [00:08:50] It's more like you and your cousins and second cousins and second cousins twice removed and, you're, you're kind of vaguely related to each other. You kind of cluster over here, but you're not necessarily super We've kind of found four clades that the 75 yeast strains that we studied in that particular piece of work Really related to, then we looked at like what is different in their genomes. [00:09:12] So they're all the same species. That's the first thing to, to think about here. So just like you and I are the same species, they're all the same species, but just like you and I, we have different areas of, of specialties. Some people podcasters. Some people are, artists and scientists and, um, kind of everything in between. [00:09:33] And we need everybody. So, we're all the same species, but we have different specialties. And the yeasts work very similarly to that. [00:09:40] Craig Macmillan: all right, so this is interesting to me so You go out and you you said when you looked at 75 species of yeast or different types of yeast Those are ones that you, you found. It wasn't like you went in and said, I want to test for each of these 75. You got information, you got data in and said, Oh, look, here's 75 different types of [00:10:01] organism. Yes, that's a, that's a great Um, so, we And we uh, the ferment or the, the yeast skins and we extract the DNA and then we get rid of the great DNA, which could probably also be really cool, but we didn't look at it in this case. And kind of threw that into the and then said, okay, we're just going to focus on the Saccharomyces cerevisiae Latin term for a very common yeast strain, um, used in wine. And we said, we're going to look for it. [00:10:30] Aria Hahn: Then we found actually hundreds and . And then, um, and I didn't do this work, I don't do a lot of lab work myself, so, uh, this part is kind of the edge of my knowledge. But there is some ways to kind of do microsatellite clustering. And so you look, and you look for tiny differences in the genome, and you say, okay, maybe we found 500, but we actually want to look at ones that are distinct from one another. So we don't want to randomly pick 75, we want to pick 75. strains of this yeast that are different from one another. [00:11:01] And so you could use some lab techniques to make that happen. And then you take those hundreds and we say, these are the 75 that we know are different. We're going to dive deep into those 75 so that we can kind of get this breadth of genetic diversity from the region. [00:11:18] Craig Macmillan: And that was something I was thinking about. You mentioned you took samples from either fermenting wine or recently fermented wine or from skin material. How exactly is this collected so that you know that you're getting just [00:11:30] what you want? [00:11:31] Aria Hahn: Yeah. Painfully is the answer. So like when you do soil sampling, it's actually really And we tell people all the time sampling for yeast or microbes is not that complicated. I say every single time we talk to a client, I'm like, look, wash your hands with ethanol, you know, hand sanitizer, essentially between rinse your tools. And mainly you can't mess this up as long as you don't spit in the bag or bleed in the And I say this every time, and I will say one out of every few hundred samples is full of blood. Hands down like you always think we always the that and then hands down. We're like, this is full of And I think it's just like a matter of working in the field like people nick themselves They don't really realize that but really that kind of thing is really easy [00:12:15] When it comes to sampling a ferment that can also be fairly easy. [00:12:19] You have a lot of it You can kind and put it in a jar, but I will Um, Jay Marknack, who's done a lot of this work and developed a lot of these methods, he actually developed this method that is painstaking. Um, But you have like, he's got this method where he takes the grapes really carefully without touching them off of the and then washes just like very carefully with these like rinse solutions to really just get the microbes and yeast that are on that surface without touching it, without touching other surfaces. It's really just what was there in the field. And rinse all of that off. And you can imagine that's not that fun of a Um, And, and, and so, and it wasn't like he did it on his first try either. So he's now developed that we're copying and using, thank goodness. Uh, But it can be like that kind of painful where it's like washing individual grapes, collecting that rinse water, and then filtering that rinse water, like onto a physical filter, then extracting the DNA from that filter. [00:13:18] It's not fast. [00:13:19] Craig Macmillan: Nope, that's what I wanted to know. I've collected a lot of soil samples in my life for looking at soil microbiome. And you know, technique is everything. You know, contamination will mess you up pretty badly. [00:13:29] Aria Hahn: We had this one study I felt so bad, but they had collected these samples. They sent us the samples and we get the data back and it's, they're soil, they should be teeming with life, right? [00:13:38] And there's like one species basically in this thing, like there's a handful, but like one is dominating. So we go to them and we're like, what is going on here? And they're like, well, I don't see how that could have happened. , we've been storing these in a dark closet for a year. And we're like, that's why. You are studying bottle effects right here. And they're like, oh, we thought it'd be fine because it was dark and cool. And we're like, yeah, but it's not open to the air, and it doesn't have the plants and animals and bugs. You grew one guy. [00:14:07] Craig Macmillan: Yeah. We've been talking about bacteria, or the yeast. Are there other types of organisms, microorganisms, that you can use this technique with? [00:14:14] Aria Hahn: Totally. So you can use this technique on basically anything that's alive. So you could target viruses, uh, not something we've done on wineries, but could absolutely do it. You can target, , archaea, which are very similar to bacteria in that there are a single cell. But they are similar to eukaryotes. [00:14:32] So things that are bigger, um, like us, like mammals, like fish, Uh, but they are kind of small and invisible, , to the naked eye like bacteria. So those, we can, we can do that all the way up to, any animal that we can see, feel, touch, , and kind of anything in between. So it's a really powerful technique. As long as it has DNA, we can make this work. [00:14:53] Craig Macmillan: So you found these 75 types? of yeast organisms, but they fell into groups, they fell into clades. And I thought that was one of the most interesting things about this. Can you tell us a little bit about the natural history of behind these clades and kind of what that means? [00:15:09] Aria Hahn: We found these 75 different strains and they did group into four clades. So four kind of groups of more or less related organisms. So you can think of them as like clustering based on similarity. [00:15:22] The first one was one that is well known and well studied. So that's wine and European. And so those strains are more similar to these that we see in wines out of Europe and commercial strains. [00:15:35] And then the second clade we saw was the trans pacific oak. So a lot of wine yeast are very closely related to yeast that are found on oak trees. And so actually think that, , the original, , European wine yeast strains from, you know, the 1800s are from Mediterranean oak trees. And so it's not uncommon that we see these strains related to oak. [00:15:59] So that was the trans pacific oak. Then we see another group or clade that we called beer one mixed origin. And so we saw similarities to known previously studied yeast strains that are related to beer, sake, so other kind of fermented drinks. also kind of expected. [00:16:18] And then what was really exciting is that we found a new clade that we've designated the Pacific West Coast wine clade. it's always neat when you get to discover something new, of course. And so it has high nucleotide diversity. And so what that means is that even within this clade we do see a lot of genetic diversity kind of in there. [00:16:38] And what we do know is that that whole clade shares a lot of characteristics with wild North American oak strains, but, and this is kind of where like it all kind of comes full circle, but we also see that it has gene flow from the wine European and Ecuadorian clades. It can mean a couple of things. So it could mean that There is just so much selective pressure when you're, when you're trying to make good wine that these genes that are found in European wine strains, commercial wine strains, they're present in Saccharomyces cerevisiae in general, but then when we try to make good wine, we select for strains that have these, genes, , that we know produce good wine, because they produce good wine everywhere. [00:17:27] And so it could just be this process of natural selection. It also could be that most wineries , are not purists. It's not that. never in their history have other wine strains visited their their vineyards. They might have tried a commercial strain. They have wine from others, you know, people track things in, animals track things in. And so it could just be that there is this gene flow, quite literally from, from Europe, from these wine strains that just kind of comes into our population here in the Pacific West Coast. [00:18:00] And so there's kind of these, these two ways that we could have got these things, We do have some evidence to suggest that they were actually transferred in. [00:18:07] So it's called horizontal gene transfer. And my go to example on how horizontal gene transfer works is always , The Matrix, like the movie with Keanu Reeves. But what I've also learned is that if you talk to people that are like younger than me, they don't know that movie anymore, so this only lands with like a certain age of [00:18:23] Craig Macmillan: Right, I know, I know, [00:18:24] Aria Hahn: You know The Matrix where they like plug in and then they have all these new skills? [00:18:28] Bacteria can kind of do that, where you can just take genes from, , a relative, has to be like kind of closely related, and we take them and then we just put it into their genome, and in many cases, not all, but many, they're able to just kind of start making use of those genes right away. [00:18:43] And so that's horizontal gene transfer, which is pretty cool, because for us, the second that sperm hits the egg, that's it. That's all your genes. You're not getting more. You're not losing more. Like you're, you're set. But bacteria are more fluid. [00:18:57] So there is this cool thing called the wine circle, and it's a cluster of five genes that are associated with making commercial wine. [00:19:05] And we do think because we see this wine circle and these particular five genes in so many wine strains, and because of their location and a whole bunch of other kind of genomic characteristics of them, Um, we think that they are horizontally transferred. And so we do see this wine circle of these five genes in the majority of this new clade of British Columbia strains. [00:19:33] Craig Macmillan: So just talking about moving things around the world, you said like people have things on their bodies and whatnot. I, I was fascinated by the Ecuadorian group. And is that literally like it was growing on plants in Ecuador, kind of native to that area that is found its way up the West coast of North America. [00:19:53] Aria Hahn: that's really what we thought happened. I know it is amazing, right? Like does the amount and transfer and you know how you go through the airport and they're like, you and It's like the end of the world. It's like I get it because we don't want to like do that on purpose, but also the ecuadorian yeast like it's coming up here [00:20:12] Craig Macmillan: right, right. Exactly. [00:20:14] So what I think is of interest to winemakers, and also has potential beyond that that I'll ask you about winemakers are looking for increased complexity in their wines, and they're also looking for a sense of place. And I'm really happy to hear more and more people talking about terroir, not just in terms of rocks, but in terms of the whole picture. [00:20:33] The soil microbiome, the practices that are done, as well as light and climate and all those kinds of things. What are some of the things about what you found that indicate or that suggest a uniqueness to that Okanagan area that may make it stand out as different than other locations? How does this translate into sense of place? [00:20:54] Aria Hahn: That's a fantastic question. I'm going to give two answers first on the east side. We see that many of that nucleate. don't have all five of those wine circle genes. And so we see a lot of British Columbian strains have that, but there's this whole clade of these natural yeast used in wine that don't have all five of those. [00:21:17] So then you just have different genes to work with. And since you have different genes to work with, it's not just those genes, but it's all of the genes, and it's the rate that those specific strains are able to break things down. [00:21:28] You do get this added complexity when you're not using a standard commercial yeast. You just have this bigger variety of genes to choose from, and That's going to make the flavors more specific, and different. [00:21:44] It also introduces a certain, the disadvantage of using these is that, you know, they are gonna vary year to year, month to month. Uh, Potentially, and, and so you might get really, really amazing results one year and not the next year, and understanding why, why that might be is a whole exercise in and of itself, probably doable, but it's really exciting to think that these yeasts that are there naturally , they just have that genetic diversity and they want to live in these diverse communities, and so you are going to get that difference and terroir. [00:22:16] The other piece that was really exciting and was a different piece of work, but very similar groups and very similar, , samples, was looking at the microbiome, so the bacteria on the grapes. And we kind of found two things, and so there is some literature that shows if you look at a single farm, a single vineyard, and you look at different red varietals of grapes, you see actually a fairly similar microbiome signature on all of the different varietals. [00:22:46] Okay, but if we look at three distinct vineyards that are all within , one kilometer radius of one another. So they're very close. They have the same rock, to your point. They have the same weather. They have the same climate chaos happening, [00:23:01] but they're managed differently. We actually see very, very distinct signatures on all three that persists year after year. So we looked at two years, , this was again, Jay Martinek's work, , and we see that each one of those, even though it's the same varietal of grape, it is more similar to itself, year over year, than among the three farms. and and that's very interesting because what that suggests is Exactly what you're saying. [00:23:29] It's not the rock. It's not the climate that's driving the microbiome there. It's actually the practices of that vineyard that are changing that. And to me, that's so powerful, because what that means is that there's so much of that craft and art in the management of the vineyard that's then going to go and affect the terroir. , I know that's not the yeast answer, but that's the bacteria answer, and it's like, the power's in your hands. [00:23:54] Craig Macmillan: I'm on the Central Coast of California, and we've had some very hot vintages in this last , 2024 season. We had, and it was 2022 as well, we had these really hot stretches of over 100 Fahrenheit. Not very friendly to yeast in general. [00:24:09] Probably friendly to some, but not to others. And I had conversations with winemakers along the lines of like, could you even do a natural fermentation this year, a native fermentation? Are they there anymore? Or have they been selected against due to the heat? And I now have a total reset of the microbiome, the microflora in my world. this is the kind of thing that bioinformatics would be able to determine. [00:24:34] Aria Hahn: yeah, for sure. So we love that. We love when we get the baseline. We're like, show us your year that you were like, this is my typical year. This is my regular year. We'll live for that because as soon as you have the baseline, then we can go and answer those questions. So we can say, okay, great. We know what your baseline is when you typical year. [00:24:52] Now you have this heat wave that comes in. , Let's go and look. Let's go see who's survived. And I know I anthropomorphize all of these things a ton, but it really is, like, who's there, right? , is it the same bug, but very decreased? Are we getting different E strains coming in? are we seeing less overall diversity? [00:25:13] Do we see the same diversity, but Their population is a quarter of the size, and how does that affect the dynamics? Like, what do we see? And bioinformatics can absolutely absolutely answer these questions. And that can be really powerful. [00:25:26] Craig Macmillan: In my research I didn't pick up on this Can bioinformatics put a quantity on things? Can you quantify the relative size of these different populations? [00:25:34] Aria Hahn: We can, yes. So, you have to use some kind of special techniques. There's a couple of main ways we do them. One is called qPCR, so quantitative PCR. And so we literally take the DNA and we can count the copies of it in a very quantitative way. That's straightforward, pretty inexpensive. [00:25:52] Another way we can do it is a little bit more sophisticated, , but you don't have to know what you're looking for. So with quantitative PCR, we have to know, like, we want to go count saccharomyces cerevisiae. But if we don't know all of the microbes that are there, all of these that are there, then we can't go and target it with qPCR. So then what we have to do is use a spiken. the concept is pretty simple. You put a known quantity of a piece of DNA that we would not expect to appear in nature. And then when we sequence it, we know how many we got back. So if we know we put in a hundred copies of it and we get 200 copies back, now we have a pretty good idea of like, everything there was, sequenced twice or if we get 50 copies back, we're like, okay, well, however many we have, we're going to double that and we have a good idea and we do do this in like a little bit more sophisticated way where we put in like a whole bunch at different quantities so we can double check our math and make sure that it's all good. [00:26:49] But that's the concept is with a spike in so you can do it quantitatively. [00:26:53] Craig Macmillan: Talking about all the things that are out there, there's a lot of interest right now in bioprotectants for fermentation, where you introduce non fermentative yeast, and they kind of take up the ecological niche against foliage organisms, and then you can add a Cerevisiae strain to do that, to do your fermentation. [00:27:10] Would you be able to pick up those other genus, of yeast in a bioinformatic way and gives us a sense of what else is out there. [00:27:18] Aria Hahn: Yeah, for sure. So we sequence the whole community and then we kind of in a. Like a puzzle. I'm going to put together the individual genomes of everyone who's there. And so we can look at not just the targets, but the unknowns as well. And so often, especially in soils, what we get is sometimes up to 80 percent of the genomes that we're able to recover from that sample are totally novel. [00:27:43] So they're new to science. It's really exciting. and we hate it. We love it and we hate it. So, we love it because it's really fun. You, you discover these new species of bacteria, of yeast, or these new strains, and, and you get to name them. You don't have to name them after yourself anymore, you have to name them about the place that they're there. Which is a totally logical thing. But, would have been fun. , [00:28:06] So we get to name these things, it's really exciting. [00:28:09] But it also means it's so much work. Because now you have this genome that's so new. And so now you're trying to figure out. What are all the genes? Do we know the genes it has, but just not quite the way that they're arranged? Do we not know what many of these genes do? And if we don't know what these genes do, like what kind of uncertainty and questions does that bring up? And so it can be really exciting, that discovery phase, and also quite overwhelming, honestly. [00:28:36] Craig Macmillan: what other applications might there be for bioinformatics in wineries or in vineyards? [00:28:41] Aria Hahn: Yeah, that's fantastic. So definitely monitoring. You know, regenerative farming is a really big thing right now. how can we introduce additional species, cover crops, , you know, planting additional or different plants in between. Like, what can we do to really increase the soil health, sequester carbon, the biodiversity of the soil, of the land, and how does that affect it? So we can monitor all those things with environmental DNA or eDNA. [00:29:09] One thing that we've been thinking about a lot is this concept of smoke taint, which I think has kind of affected the whole west coast of North America. [00:29:18] Are there microbial treatments that can kind of mitigate smoke taint, , can we feed bacteria, the bacteria that we know [00:29:29] can kind of break down those volatile phenols that cause the smoke taint. Get them to kind of break that down first before we make the wine. Like we're kind of looking at applications like that. [00:29:40] Obviously those are, I would say further out in terms of technological development biodiversity, which we can absolutely go and do today. , but there's interest in that smoke taint. Application, and we're really interested in that. [00:29:52] Then there's also kind of everything in between. So can we the harvest? Can we increase the quality of the grape? Can we help with years that are dry? Can we help with years that are wet or cold or hot? as we, kind of committed to a certain number of effects of climate change, we have to start thinking creatively. [00:30:14] I was on this call with an unrelated company. They wanted to do similar things but in the mining space, in the reclamation space. And I don't know how it happened, but I was on this call with this man. It was his last day before it was dark where he was. He's in Quebec. He's three hours ahead. [00:30:29] , You know, it was winter. So it's very, the mood was very, like, dark and somber, and this was his final call of his final day of work. And he was so hopeful about microbes, and he spent his career working with them. And just before he signed off the call, he says, I hope microbes save us all. [00:30:50] And then he kills the call. And, and, for, the next few years, I titled every single talk I did, Microbes may save us all because I just, the weight of that conversation was so big and I know that's not what we're talking about here in terms of [00:31:08] smoke taint, but I do think, you know, to bring us full circle to this like omnipresent godlike presence of microbes that there's something to that idea in that I think that they have this potential to save us from ourselves. If we can learn more, [00:31:25] Craig Macmillan: I think what we're talking about is bioremediation and the potential there. And bioremediation would work by identifying an organism that's going to play a certain role and then actually introducing it into the environment. For instance, like introducing it to wine that may have smoke taint, for instance. [00:31:40] Aria Hahn: , so there's a three main approaches to that. [00:31:42] So the first is exactly what we're talking about. You introduce a micro that we know and you, and you put it in there. The main challenge of that is this, this word we call engraftment. We actually steal that word from organ transplants. So, when you put in a new heart, not that I know anything about heart transplants, but when you put in a new heart, you have to engraft it. [00:32:01] And so people need to be on immunosuppressants, is my understanding, to make that heart transplant like stick in their body, have their body accept it. Kind of the same challenge when you introduce a microbe into an open, wild environment where you need that new species to engraft in that community. If you can't do that, you just have to keep adding it. [00:32:21] You have to keep adding it, keep adding it, it's time consuming, it's expensive, all of these things. So engraffing is still a challenge in that field. But that is one way. [00:32:29] The second way is to bioengineer. And so the concept here is that you take species or strains that are naturally occurring, so they do well in that environment, and you change something in their genetics and then reintroduce that. It does get around the concept of, [00:32:50] of engraftment in theory. The major issue with it is, there's not a lot of people or companies that feel ready, I think, to take a biologically engineered synthetic genome and introduce it into the environment en masse. We just don't understand the risks of it, or, or not, we don't know, but I think that's the point, is that we don't know, and so people are a little bit like, Maybe we're not quite there yet. [00:33:19] And then the third way is to say, I'm going to look at who's already there. And I'm going to understand what they like to eat and what their competitors like to eat and I'm going to try to starve their competitors [00:33:31] and really feed the ones who have the capacity to degrade those volatile phenols. I'm going to like try to get their population to do super well and thrive. and and try to kind of starve out and make the populations that can't do the job that I want lesser and less prevalent in the community. [00:33:51] And that approach I think is kind of one of my favorites where we understand and then we put some selective pressures. So this could be adding more nitrogen, adding different carbon sources. [00:34:01] It could be watering less to create a more aerobic environment. It could be you know, kind of drowning them to create an anaerobic environment. It's kind of those bigger controls that we have working with the microbes that are already there. [00:34:17] Craig Macmillan: Yeah, in the same way that we're not afraid to play with plant communities in agricultural systems, with cover cropping or intercropping or anything like that, same kind of idea, where maybe I plant something that I think will out compete a weed. [00:34:28] Same kind of idea. And we're pretty comfortable with that. [00:34:32] And also things will have a way of finding their stasis, finding their, their It's just getting it kind of pushed in the right direction. I think that he's super, super cool. [00:34:44] A lot of interest and work in the soil microbiome in terms of soil health. We mentioned regenerative agriculture. I have put my toe in that, in, in my professional world extremely difficult, extremely confusing, lots of holes you know, and, and trying to find markers or metrics has been. challenging for instance, I was trying to figure out how healthy some soils were. It, healthy in quotes, and I wanted to do analysis of respiration. And this very good soil ecologist said, well, that tells you how many folks are in the room, but it doesn't tell you what they're doing or who they are. [00:35:21] And I was like, that's a really good Point I could have a lot of respiration from organisms. I don't want and I wouldn't know what was who and who was what? What world can bioinformatics play in that [00:35:33] Aria Hahn: , that's a great question. So I would say it's the opposite in general, without the spike ins and kind of specific things, what? we can tell pretty inexpensively, 50 to 100 a sample, is basically who's in the room and in what relative abundance. So it is come down a lot in price. It doesn't tell us a lot about their genetic capability. [00:35:55] So if we know them because they've been previously studied, then we can say like, oh, yeah, these guys are known to do X, Y, and Z. [00:36:02] If we don't know them, for that kind of price point in those methods, we're kind of just like, yeah, we know their names. But that's it. [00:36:08] Then we can do kind of a deeper dive, , to a different type of sequencing called whole genome sequencing. And you get the whole genome. And so there we can actually say not only who they are, but what they're doing. Or what they have the ability to do. And so that's where the limit of DNA is, is that it can tell us the potential. They can potentially do this, but it doesn't actually tell us if they're choosing to do that, so to speak. [00:36:33] There are other techniques that are very related. Metatranscriptomics, it's looking at the RNA, and you could do metabolomics. So you can actually look at the metabolites that they're producing, and then it tells you what they actually did. But we often can start at that base layer of DNA. and build up. So those questions we can answer. [00:36:51] And I think you're right about there are a lot of holes and it's confusing and it's complex. And we say this to clients all the time, like, if you know way to solve a problem, do that. Biology is messy. [00:37:03] But if you don't, like let's look at biology and let's enjoy the mess , there's a lot of beauty in that mess. And that's one of the things we've actually loved about interacting with wineries they are incredibly scientifically minded folks. They're data driven, the amount of innovation and technology they're using. never fails to impress, but you also get that love of the art and the craft from them. We love that. We see art and science as like in a circular spectrum. And so we love when, our clients in the, in the wine start talking to us about kind of their secret sauce and the things that they've tried and how, and they always get a little bit nervous. [00:37:49] And they would, if they always kind of start, they were like, you know what else I do? And we're like, tell us. And then they tell us something and they're like, we just know from experience. Experience that this works that this changes the ferment, but we don't have any evidence for that And and I think they're worried we're gonna judge them but we're like no that is like their science is all way of knowing but [00:38:09] my friend says art is science and love and and I love that idea that is something that's been really really fun about working with wineries and vineyards is they kind of get that they're like, yeah, this is the love piece here [00:38:22] Craig Macmillan: That's cool I think there's beauty in the mess. I might adopt that if you don't mind I mean, I may use that for some of my own stuff. I think that's great What is one thing you would tell growers or wineries, , [00:38:35] Aria Hahn: their choices are directly impacting the microbiome, so that's the bacteria and the yeast And that that is going to affect the terroir, the complexity, the quality of the wine, and it is knowable. [00:38:50] Craig Macmillan: there we go. And we also know that some of the things that we do may affect that and that is part of what makes us special. Where can people find out more about you? [00:38:58] Aria Hahn: We have a website, it is koonke. com, K O O N K I E dot com. can also look me up, Aria Hahn, , and on Google Scholar, the internet, I feel like I'm very findable. [00:39:10] Craig Macmillan: Yeah, you are very findable and we will have a lot of links and other things on the show page. So please check that out. Really fascinating stuff going even beyond this. I want to thank you for being on the podcast. [00:39:21] This has been a great conversation. [00:39:22] Aria Hahn: Yeah, thanks for having me. Super fun. [00:39:25] Craig Macmillan: So our guest today was Aria Hahn. She is CEO and co founder of Koonkie, a bioinformatics company, and is doing some really fascinating stuff, not only around yeast, but lots of other topics. [00:39:35] And I just got lost down the rabbit hole when I took a look at that website, all the different things you folks have been involved in, and it was really fun. [00:39:48] Beth Vukmanic: Thank you for listening. [00:39:49] Today's podcast was brought to you by Sunridge. For over 45 years, Sunridge nurseries has supplied premium quality grapevines. to grape growers worldwide. A pioneer in the industry with a focus on clean quality vines and personalized dedication to their partnered growers has led them to be the largest, most well respected grapevine nursery in the United States. Sunridge Nurseries continues to lead the industry having undergone several expansions to their modern state of the art facilities and is the first and only grapevine nursery to have implemented the most advanced greenhouse Horticulture water treatment technology in North America. [00:40:26] Make sure you check out the show notes for links to Aria, an article titled, make better wines with bioinformatics plus sustainable wine growing podcast episodes, 201 balance hot climate, high sugar wine with green grape juice, 243 microbial communities in the grapevine. And 251 vine sap analysis to optimize nutrition. [00:40:50] If you liked the show, do us a big favor by sharing it with a friend, subscribing and leaving us a review. You can find all of the podcasts at vineyardteam.org/podcast, and you can reach us at podcast at vineyardteam. org until next time, this is sustainable wine growing with the vineyard team.   Nearly perfect transcription by Descript

The Use of Immunohistochemistry vs. qPCR to Detect BRAFV600E in Thyroid Cancer- Kannitha Chek HTL (ASCP), Nicholas Hoo-Fatt, MS, HTL (ASCP), DP, Samantha Diamond, M.D., Haresh Mani, M.D., Myong Ho “Lucy” Nam, M.D. Introduction: This study aimed to validate the effectiveness of the Ventana anti-BRAFV600E antibody in detecting the BRAFV600E mutation in thyroid cancer using immunohistochemistry (IHC) as an initial screening test. The BRAFV600E mutation is a common genetic alteration in thyroid cancer, particularly papillary thyroid carcinoma (PTC), and detection is crucial for prognosis and treatment decisions. Methods: The research examined 12 thyroid cancer cases (11 PTC and 1 anaplastic thyroid carcinoma) and 12 non-cancerous thyroid cases. This study was conducted by using both the IHC BRAFV600E antibody as well as genetic testing methods including Next-Generation Sequencing (NGS) and the Biocartis Idylla rapid qPCR module for BRAF mutation. Results: The antibody successfully identified the BRAFV600E mutation in all cancer cases, aligning with results from other genetic testing methods, and as expected, non-cancerous cases showed no mutation-specific staining. The study highlighted important considerations in interpreting IHC results, such as the presence of non-specific brown staining due to colloid containing brown pigments in negative cases. It also emphasized the importance of proper tissue representation, as demonstrated by one case that initially lacked staining. While the research provides strong evidence for the accuracy of the Ventana anti-BRAFV600E antibody, it also identified limitations. The study lacked PTC cases negative for the BRAFV600E mutation, which would have provided a more comprehensive validation. Conclusion: The researchers suggest further investigation with a broader range of samples, including more anaplastic thyroid carcinoma cases and follicular variant of PTC, to explore potential correlations between tumor heterogeneity and staining intensity. This validation study contributes to improving thyroid cancer diagnosis and treatment by authenticating the reliability IHC methods in detecting a key genetic mutation. It also highlights the importance of continued research to optimize diagnostic methods in thyroid cancer.

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 digital PCR. 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 Applied Biosystems QuantStudio Absolute Q Digital PCR System works to provide 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 what each of these are all about and how they help to provide confidence and reliability in results that matter for your precious samples. Visit the Absolute Gene-ius pageto learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. 

The history of fermented foods like beer, bread, and other foods can be traced back thousands of years to ancient civilizations in China and Egypt. This ancient technology was originally used to preserve foods when refrigeration was not an option. While less common in modern industrialized civilizations, we're now realizing that fermented foods play a major role in gut microbiome diversity, which is a biomarker for overall health. Join our conversation with Dr. John Leech, Technologist at Teagasc in County Cork, Ireland to learn all about the history and how cutting-edge technologies are being applied to research in food fermentation. John shares his story of how he found this field of research and how he's now headlong into striving to understand and harness the power of fermented foods. We learn about the complex microbial communities that define and deliver the health benefits of these foods, but we also hear about how this biological complexity makes them inherently irreproducible. Foods like kimchi, sauerkraut, kombucha, tepache, milk kefir, and water kefir are produced from fermentation, facilitated by complex communities of microbes. Consumption of fermented foods can alter our gut microbiome, which has been shown to affect obesity, inflammation, longevity, and efficacy of drug treatments. John and his team are using qPCR, NGS, and other methods to characterize the microbial consortia used to produce these foods. They're now working to figure out how to simplify the consortium while still delivering health benefits, all while making the process reproducible and scalable Subscribe to get future episodes as they drop and if you like what you're hearing we hope you'll share a review or recommend the series to a colleague.  Download Transcripts: Speaking of Mol Bio Podcast | Thermo Fisher Scientific - US Visit the Invitrogen School of Molecular Biology to access helpful molecular biology resources and educational content, and please share this resource with anyone you know working in molecular biology.

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

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

Our hosts, Dom and John, are excited to welcome special guest, Carrie Vyhlidal, to discuss the topic of the 80th episode of “The Weekly Bioanalysis” podcast – The Rapid Evolution of PCR Assays. PCR (or Polymerase Chain Reaction) is like a copying machine for DNA. Scientists have found ways to measure the copies being made throughout the reactions, which is where they get their real-time, quantitative PCR (or qPCR). Carrie does a wonderful job of explaining not only why these advancements in the study of PCRs are so amazing – but also why they play (and will continue to play) such an important part in bioanalysis.“The Weekly Bioanalysis” is a podcast dedicated to discussing bioanalytical news, tools and services related to the pharmaceutical, biopharmaceutical and biomarker industries. Every month, KCAS Bio will bring you another 60 minutes (or so) of friendly banter between our two finest Senior Scientific Advisors as they chat over coffee and discuss what they've learned about the bioanalytical world the past couple of weeks. “The Weekly Bioanalysis” is brought to you by KCAS Bio.KCAS Bio is a progressive growing contract research organization of well over 250 talented and dedicated individuals with growing operations in Kansas City, Doylestown, PA, and Lyon, France, where we are committed to serving our clients and improving health worldwide. Our experienced scientists provide stand-alone bioanalytical services to the pharmaceutical, biopharmaceutical, animal health and medical device industries.

Biotherapeutics are transforming healthcare for over 350 million patients globally, tackling everything from cancer and diabetes to rare diseases. Human embryonic kidney (HEK) 293 cells play a key role in the manufacturing of many of these life-changing products. However, they are not without their challenges. In this episode of The Top Line, sponsored by Bio-Rad, Dipika Gurnani, Global Product Manager at Digital Biology Group, discusses the critical need to accurately quantify HEK293 DNA in biotherapeutics to ensure patient safety and regulatory compliance. Gurnani highlights the risks of residual DNA integrating into a patient's genome, potentially causing cancer or genetic abnormalities. She also addresses the limitations of traditional quantification methods like qPCR, which can be time-consuming and prone to errors. We also look at some key innovations in the field, such as Bio-Rad's Vericheck ddPCR HEK293 Residual DNA Quantification Kit that can minimize false positives by specifically targeting HEK293 DNA. For deeper insights into these challenges and innovations, listen to the full episode.See omnystudio.com/listener for privacy information.

"To find the most sensitive, accurate, reproducible, and reliable method for detecting and quantifying Legionella in a sample, qPCR is the best option.” - Michael Loewenstein In this much-anticipated episode highlighting the findings of Part 2 of Michael Loewenstein and Joe Benzinger's study,  Michael Loewenstein, Vice President of Scientific Consulting at Q Laboratories, returns to share their surprising discoveries. He offers valuable advice to water professionals on developing strategies for incorporating qPCR in a Water Management Plan (WMP). Join Trace Blackmore and Michael Loewenstein as they guide you through the latest advancements in Legionella detection methods, the nuances of traditional culture techniques versus modern qPCR, and the future of water management. What Are the Different Testing Methods for Legionella? Michael elaborates on the two primary methods for Legionella testing: traditional culture techniques (ISO 11731) and qPCR. Culture methods, while widely used, take a significant amount of time (7 to 14+ days) to yield results. In contrast, qPCR offers faster and more sensitive detection, identifying the presence and quantity of Legionella DNA in a matter of hours. Is There a “Gold Standard” for Legionella Testing? The term "Gold Standard" often pops up in discussions about Legionella testing, but as Michael points out, no regulatory body has officially designated a single best method. While ISO 11731 is a trusted standard, Michael argues that qPCR provides a more reliable, accurate, and sensitive approach for detecting and quantifying Legionella in samples. What Were the Findings from Phase 2 of His Study? Michael shares findings from a two-phase study comparing cultural methods with PCR and qPCR. Phase 1 focused on method validation, confirming the efficacy of commercially available PCR methods. Phase 2 moved to real-world samples, revealing that qPCR detected Legionella in about 67% of samples, far surpassing the detection rates of traditional culture methods. What Can qPCR Do and How Does It Differ from Culture Methods? qPCR is a powerful tool in Legionella testing. Unlike culture methods that rely on colony-forming units, qPCR measures the number of DNA copies present in a sample, providing a clear picture of the Legionella population. It can also distinguish between viable and non-viable cells, making it a comprehensive and efficient method for routine monitoring. How Would Michael Set Up His Water Management Plan (WMP)? When asked how he would set up his water management plan, Michael emphasizes the importance of frequent testing. He advocates for the use of qPCR due to its speed and sensitivity. However, he cautions that those uncomfortable with detecting any Legionella might find qPCR overwhelming, as it tends to reveal a higher positivity rate than traditional methods. How Does Pricing Compare Between Culture and qPCR Methods?Interestingly, Q Laboratories charges the same for both qPCR and culture methods. Despite higher costs for qPCR, it requires significantly less analyst time, making it a cost-effective choice for many labs. What's Next for Phase 3 of the Study? The next phase of Michael's study aims to explore additional factors such as UV light treatment. He encourages feedback from the community to ensure all relevant aspects are covered in the ongoing research. How Can I Get Involved with the AOAC Legionella Working Group? Please visit www.aoac.org/news/legionella-in-water-wg-volunteers-needed . If you would like to support this initiative or are interested in more information, please reach out to scienceprograms@aoac.org. Michael's key message is that qPCR is a viable, non-intimidating option for Legionella testing. He reassures listeners that the CDC does not mandate the use of culture methods exclusively. Embracing qPCR can lead to more accurate monitoring and better-informed water management decisions. Until next Friday's episode, stay curious, stay informed, and keep scaling up your Legionella knowledge! Your roadside friends as you drive from client to client, The Scaling UP! H2O Team Timestamps 01:00 - Trace Blackmore invites you to check out our Legionella Resources page 03:28 -  Upcoming Events for Water Treatment Professionals 05:00 - Interview with Michael Loewenstein, Vice President, Scientific Consulting at Q Laboratories 51:05 - Drop by Drop With James McDonald  Quotes “PCR detects whether Legionella DNA is present, while qPCR not only confirms its presence but also measures the quantity of Legionella DNA in a sample.” -  Michael Loewenstein “The CDC does not say you have to use culture.” - Michael Loewenstein “An increase in Legionella positivity with a qPCR test is a feature, not a bug.” - Michael Loewenstein Connect with Michael Loewenstein Phone: +1 513 207 4943 Email: MLoewenstein@qlaboratories.com Website: Scientific Consulting for Q Labs LLC LinkedIn: Michael Loewenstein Read or Download Michael Loewenstein's Press Release HERE Links Mentioned Ep 269 Ep 335 Read Michael Loewenstein's technical paper HERE The Rising Tide Mastermind Scaling UP! H2O Academy video courses Submit a Show Idea Drop By Drop with James In today's episode, I have a “What If.” What if acid is overfed to a cooling tower system and drops the pH to a 3. You heard it correctly, the pH is now 3 in your cooling tower system. What damage is being done right now. How do you recover from this low pH excursion? Should you just turn off the acid feed and wait for the system pH to slowly return naturally? What could be the impact of this approach? Should you take immediate action and raise the pH as quickly as possible? What could be the impact of this approach? Should you increase blowdown? What caused the acid over feed? How could this be prevented in the future? What alarms could be setup? What do you communicate all this to the end user? 2024 Events for Water Professionals Check out our Scaling UP! H2O Events Calendar where we've listed every event Water Treaters should be aware of by clicking HERE.

There are all sorts of molecular tests to tell if you're infected with something specific, but what do you use when you're not sure what you might have? You might use a thermometer as a first step, but wouldn't it be nice if that thermometer was a bit more high tech? In this episode we meet Dr. Nick Meyerson, CEO and co-founder of Darwin Biosciences, who's team is working to develop the “molecular thermometer of the future.” We hear about how this physicist transitioned into molecular biology and then latched onto saliva as a sample of choice to detect early molecular indicator of infection. Nick does a great job of explaining his path leading up to the founding of Darwin Bio, the challenges of founding a company in early 2020, why saliva is their sample of choice, the beautiful simplicity of isothermal amplification methods, and the lesser-known funding routes of working with government agencies like the Defense Threat Reduction Agency (DTRA). Join us as we dive into the molecular nature of non-specific detection of infections, how it's done using no electricity, it's potential applications, and what the future holds for this field. Nick also shares lessons learned and some insights on the value of mentors and a lifelong curiosity. Subscribe to get future episodes as they drop and if you like what you're hearing we hope you'll share a review or recommend the series to a colleague.  Download Transcripts: Speaking of Mol Bio Podcast | Thermo Fisher Scientific - US Visit the Invitrogen School of Molecular Biology to access helpful molecular biology resources and educational content, and please share this resource with anyone you know working in molecular biology.

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

Discover the key considerations critical to the genetic analysis for advanced therapies, including qPCR and dPCR. Don't miss expert insights from Chandler Walker, Product Manager of Digital PCR Instruments at Thermo Fisher Scientific and Janelle Hart, managing editor at Citeline.

To understand fungicide resistance in the vineyard, a group of United States scientists formed the Fungicide Resistance Assessment Mitigation and Extension (FRAME). Sarah Lowder, Assistant Professor and Viticulture Extension Specialist at the University of Georgia describes a nationwide sampling project to test for resistance markers. To get samples, they are promoting a new collection method called glove sampling. This process leverages the time that fieldworkers are in the field running their hands through the vines. They collect samples by rubbing their gloved hands on a cotton swab and sending the sample to the lab. Research shows that glove sampling results are very similar to spore trapping, a process that samples the air flowing through the vineyard. Resources:         117: Grapevine Mildew Control with UV Light 219: Intelligent Sprayers to Improve Fungicide Applications and Save Money A Rapid Glove-Based Inoculum Sampling Technique to Monitor Erysiphe necator in Commercial Vineyard Fisherbrand™ Plastic Handled Cotton Swabs and Applicators Grape FRAME Networks Glove swab sampling tutorial for collecting grape powdery mildew (video) Glove Swab sampling tutorial for collecting grape powdery mildew - silent (video) Identification of Putative SDHI Target Site Mutations in the SDHB, SDHC, and SDHD Subunits of the Grape Powdery Mildew Pathogen Erysiphe necator Rapid sampling technique to monitor Erysiphe necator more effective than visual scouting Sarah Lowder Vineyard Team Programs: Juan Nevarez Memorial Scholarship - Donate SIP Certified – Show your care for the people and planet   Sustainable Ag Expo – The premiere winegrowing event of the year Sustainable Winegrowing On-Demand (Western SARE) – Learn at your own pace Vineyard Team – Become a Member Get More Subscribe wherever you listen so you never miss an episode on the latest science and research with the Sustainable Winegrowing Podcast. Since 1994, Vineyard Team has been your resource for workshops and field demonstrations, research, and events dedicated to the stewardship of our natural resources. Learn more at www.vineyardteam.org.   Transcript 2024-07-04_235_Sarah Lowder - glove sampling for mildew_Otter [00:00:00] Craig Macmillan: Our guest today is Sarah Lawder. She is Viticulture Extension Specialist and an Assistant Professor in the Department of Horticulture at the University of Georgia. And today we're going to talk about some exciting new advancements around monitoring for powdery mildew and other related topics. Welcome to the podcast, Sarah. [00:00:16] Sarah Lowder: Thank you very much, Craig. I'm very excited to be here. [00:00:18] Craig Macmillan: First though, I want to start with something I just found out about that applies to this, and that is the grape frame networks. Can you tell us exactly what that is and kind of how it came about and what it does? Okay. Thanks, Craig. [00:00:29] Sarah Lowder: Absolutely. Yeah, the FRAME Network is part of a USDA SCRI grant. This is a project that was funded several years ago, I believe in 2017, as part of the Specialty Crop Research Initiative Project System. And FRAME Networks literally stands for Fungicide Resistance Assessment Mitigation and Extension. networks. And so this was a grant that was really intended to look and learn so much more about how fungicide resistance works in the vineyard for powdery mildew specifically. But this was a group, a very large group of scientists from all across the country from a wide range of different disciplines looking into how we can better address fungicide resistance for vineyards and for powdery mildew specifically. [00:01:12] Craig Macmillan: But there's also applications either now or in the future for other fungal diseases like downy mildew, et cetera. [00:01:18] Sarah Lowder: Absolutely. Yep. They are currently working on getting a new iteration of this grant, Frame 2 as it were that will hopefully be able to address also resistance in Downy Mildew and Botrytis Bunch Rot. [00:01:29] Craig Macmillan: Fantastic. This is really exciting because what I saw was that there are people at Washington State, Oregon State in California, and then on the East Coast. So hopefully this work will continue. What exactly kinds of things does Frame do? [00:01:45] Sarah Lowder: Yeah, so we had a multi pronged approach for this project. One of the big parts that I was a part of is looking at the assessment of the fungicide resistance. So one of the things that we did was collect powdery mildew from all across the country, from states and vineyards all over, all over the place, and then look for different fungicide resistance markers in that mildew. That can hopefully help us much more quickly assess if we have fungicide resistance present in a sample. One of the big groups of fungicides that we looked at was the QOI fungicides, the Sturbulurins, also sometimes they're called or the FRAC Group 11, with FRAC is the Fungicide Resistance Action Committee. Is what the FRAC group would be for that and those just kind of group your different fungicides based on the mode of action. So how they work on the different diseases that they're attempting to control. And so we were looking at this group, this group 11, the QOI products which operate by attaching to the mitochondria, so the powerhouse of the cell. And just preventing them from being able to produce energy and so the, the spores die and you don't get any more growth of that disease. But because it's one of those products that works like a binding site if you get resistance presence it just means that your fungicide can no longer attached to the disease and then it can grow in the presence of that fungicide and then you can even no matter how much you spray that product it can still continue to grow. By looking at there's one particular mutation that occurs that causes that resistance in this group of products and we're able to run a test much more quickly than you can otherwise do a lot of different fungicide resistance testing And tell whether or not you had QOI resistant or sensitive Mildew in your field so you knew whether or not you could use that product or not [00:03:35] Craig Macmillan: What about frac group three? That's another one that we have known Resistance issues with the demethylation inhibitors. Is that part of the project as well? [00:03:43] Sarah Lowder: Absolutely Absolutely, the DMIs demethylation inhibitors, absolutely, the FRAC3 Group 3 are a group of products that have a little bit more complicated unfortunately of a resistance pattern rather than just having one particular mutation. There, there are a bunch of different things going on in those products. But we do have a marker that can help us get a sense for the resistance. It's not as necessarily reliable as the QOI. Frack Group 11 product resistant testing, but we can test that as well and give us an idea of whether or not we might have resistance to DMIs present in the field as well. [00:04:19] Craig Macmillan: Are there other frack groups that have potential or have found some resistant populations coming down the pike? [00:04:28] Sarah Lowder: Absolutely. Anything that has a very specific mode of action really has some potential for having a resistance develop in a population. [00:04:36] Craig Macmillan: Great. [00:04:38] Sarah Lowder: We're, we're looking at some of the modes of action. We have not heard as much of field failures due to resistance to a lot of other products, but we wanted to, like, kind of get a, get a jump on looking for some of those other modes of action to see if we can develop. Test to be able to monitor that, monitor that much more quickly before resistance becomes as much of an issue. And we were able to get a lot of that information for like the SDHI groups, which is the group 7 products. Although again, we're not really hearing too much yet of any field failures for powdery mildew control from the SDHIs. As well as looking much more into some of the mechanisms for how group 13, quinoxafen how well how the resistance might work in that system. All of those are stuff that we were able to do because of the Frame Network project team. [00:05:26] Craig Macmillan: That's really great. I hope that we can continue that. That's really important work. In order to do that kind of thing, you need to get samples. And you and your colleagues are promoting a new method for monitoring for powdery mildew and collecting, I guess, ASCA spores, I would imagine, is what you're collecting. Tell me about it. There's videos on YouTube. It's really exciting. [00:05:47] Sarah Lowder: Absolutely. [00:05:47] Craig Macmillan: It involves a glove. [00:05:49] Sarah Lowder: Indeed, we call them glove swabs, which is one of the projects that I was able to help lead as a part of the system. Because you hit the nail on the head when you are trying to monitor fungicide resistance. The first step that you have to do is actually find the mildew. And you want to find this before you have a control problem. You want to find it while there's still not very much mildew present in the field. We looked at, we looked at a bunch of different ways. Not everything worked very well. But one of the ideas that we had was, oh, We have vineyard workers moving throughout the field all the time. Could we potentially use these people who are already in the field doing normal stuff to also potentially collect powdery mildew? And we found that as you're moving through the vineyard, as you're moving your hands along the canopy, you're able to collect powdery mildew. Conidia spores, actually, it's generally, it's their summer spores. are collecting and you're able to take a, just a cotton swab. So many of us have taken a COVID test that you've had to stick up your nose. It's a very similar, similar swab that you take with your hands. And you can stick that in a tube and send it to the lab for processing. This system worked, I think, way better than any of us were expecting it to. It was actually much better than trying to go out there and look for it physically. And you can do it much faster because it's just literally, you can be walking through the vineyard with your hands in the canopy, take a swab. and collect it, and you can find that so much faster if you're already having to do a lab test for that product. [00:07:16] Craig Macmillan: And also the potential here is that, let's say I've got a crew out and we're doing a shoot thinning in the spring, so they're handling the canopy all the time, we could swab some gloves and then send that out to be tested and get an idea what's out there. [00:07:27] Sarah Lowder: Absolutely. Absolutely. And as you're already testing for whether the field is out there, you can also use the same test to tell whether or not you have resistant mildew to the QI fungicides. [00:07:38] Craig Macmillan: Is this quantitative? [00:07:41] Sarah Lowder: So, it is run on a quantitative quantitative PCR. So, in theory, it does give you some information on how much mildew is present. In the QI QPCR test, in the test that tests for the fungicide resistance pattern, it tests a piece of DNA in the mitochondria, and you can technically have different numbers of things. Mitochondria per cell, individual cell, and so the, the quantitative, it does give you that information, but it's not necessarily the most reliable information. So as, as a scientist, I'm always hesitant to say that, oh, you can get quantitative information, but it, in theory, it does give you a little bit of information about how many spores at least you were able to collect. You can tell a little bit of that information. [00:08:21] Craig Macmillan: Can it tell me something along the lines of, I can go out and sample at the very beginning of the season, maybe even post bud break, and say, oh, we have nothing there yet, and then come by later and test and say, oh, we have something there now. Is there a qualitative aspect to it? [00:08:41] Sarah Lowder: Absolutely. So we tested it and compared the glove swabs to visual scouting to compare it to someone actually physically going out and looking and found that the glove swabs were much more sensitive. They were able to find the powdered mildew much faster, and also much sooner than the OR than our visual eyes were able to do So. But we also tested it in comparison to impaction spore traps. So these are tests that actually had come out of a lot of the lab that I worked in the foliar pathology lab with Walt Mahaffey at the USDA for a couple years previously with like Lindsay Thiessen that they were able to test these impaction spore traps which sample the air that flows through the vineyard. We're collecting that many of the vineyards in the Willamette Valley of Oregon which we did a lot of the testing in that area as well as in Areas like Napa, California have a bunch of these spore traps present that we were able to test it in comparison to these spore traps, which have been used pretty widely in the system. And what we found was that our glove swabs were showing us very similar information to these impaction spore traps which was really cool because a lot of these growers absolutely do use already these impaction spore traps to look at when they're going to initiate their fungicide spray programs. So, in theory, yes. You could absolutely potentially use these glove swabs as a fungicide initiation indicator. [00:10:01] Craig Macmillan: Yeah, that's what I was getting at, and that's, that's a really exciting technology. Because obviously we're trying to control the amount of material we put out there, and obviously part of resistance management is being careful what you put out and when. And so having a good idea of what the timing should be, I think, is really important. And then of course, as everybody knows, People who listen to this podcast know, by the time you see it, it's too late, baby. [00:10:24] Sarah Lowder: Absolutely. [00:10:24] Craig Macmillan: You know, it's, it's, it's, you're chasing a ghost. And so, here's, here's our Ghostbuster tool, where we can catch that ghost before before it comes too much of a problem. Now you said, send these off for, to a lab for analysis. What what labs are we talking about? [00:10:39] Sarah Lowder: The initial frame grant project is technically at a, has come to an end and so the funding that originally funded a lot of this testing has ended, but now we're able to supply all of these protocols and testing materials and stuff to a lot of the different private labs elsewhere. So I know one of the private labs that does the impaction trap testing. service in the William Valley of Oregon has taken over that process, as well as I know a bunch of different labs like I know at UGA here, where I am currently, they have some tools and able to do some of those testings or do some of those tests as well with the qPCR. And so even if you, a lab where you send a lot of your materials, if they happen to have a qPCR present and you're strongly interested in doing it, you can talk to them to see if they might potentially be willing to add this into their repertoire. [00:11:24] Craig Macmillan: So, this technology is starting to make it out into the world of commercial plant pathology. [00:11:29] Sarah Lowder: Yes. [00:11:30] Craig Macmillan: I may have a plant pathology lab that I already work with, I can talk to them, I can make some phone calls, and for instance, a commercial lab in Oregon, they're a business, so they still may do samples from California or from Washington or from Ohio. [00:11:44] Sarah Lowder: Yeah, potentially. [00:11:45] Craig Macmillan: It's not limited by territory. [00:11:46] Sarah Lowder: Correct. You can send these samples and as long as you're not leaving your samples out in the sun and in the heat for a long period of time they can be shipped off elsewhere as well. [00:11:55] Craig Macmillan: Where do you see this technology going? What's, what's the future here? We, we, we've just kind of touched on it a little bit, but what, in your, when you close your eyes and imagine the long term impact of your work, where do you see this kind of thing going? [00:12:08] Sarah Lowder: One, I would love to see a lot of this information being used more regularly to be able to test this a little faster. And eventually, one day, we may be able to test for all of these different resistance genes, all of these different resistance patterns within the same sample. So you could be like, okay as a normal part of my practice, I'm going out and taking these glove swabs or whatever else that I'm looking to test. Even if I don't use a glove swab, but I can come in and take my powdery mildew sample and send it off to the lab and get a, just a score sheet of exactly what fungicide products could be used or could be not used. That would be really awesome, because no one wants to buy a product that it's not going to work, and no one wants to put a product out that's not going to work for any reasons, environmentally or financially. In the wallet or just for labor purposes. It's just a win, win, win situation. If you know, you don't have to use a product and instead you could choose a different one. [00:13:01] Craig Macmillan: Oh, this might be a related, very practical matter. So gloves, touching vines, no problem. I can have workers. I could have actually my VIT tech go down a row and then swipe the canopy. Where do I get the swabs because we're talking about something has to be a sterile protected swab, just like the COVID test swab. Where do I get those? [00:13:17] Sarah Lowder: Yeah so a lot of the times, or at least for a lot of this test that we did originally they were groups that we sent out, or like just kits that we would send out to the different cooperating practices. But essentially, it is literally the same tool. It's a polystyrene cotton swab tip and we normally will put them into these little half tubes that kind of keep their tip protected, and then you will stick it back into the plastic wrap that it came in, and then wrap it up so that it stays more protected. But it is, it is literally the same tool that you often will use for those COVID tests, which made it really hard to get that right at the beginning of the pandemic. [00:13:54] Craig Macmillan: Where, where can I get them? Where can I order them from? [00:13:56] Sarah Lowder: So I can send a link for the type of material that we're looking for. And then you can shop around for the same tip at a couple different locations and find the best price. [00:14:06] Craig Macmillan: That'd be perfect. We'll put a link to that in the show notes. So folks, you can go check that out and find the materials that you need. And then you can also shop around for the labs and see who's doing what. And again, if a lab is getting a lot of phone calls. That's going to encourage them to adopt this new technology. What is kind of the, the current state of the nation, if you will, in terms of fungicide resistance, what are the hot new topics, what's getting funded? What are people working on and where are they working on it? [00:14:33] Sarah Lowder: Fungicide resistance is certainly a hot topic that has a lot of different research happening in a lot of different areas. I could literally fill your entire podcast probably with talking about this topic. One thing that I'm very excited about is to hopefully see this Frame 2 iteration happen that is, being submitted for funding for this next funding cycle this year, but it is looking to hopefully also add in testing for downy mildew and betritis bunch rot, which are also two big diseases that can cause a lot of issues. Especially now that I'm over here in Georgia, I'm very excited to hopefully get to test much more of the downy mildew which can be quite the struggle in the vineyard. And we're getting much more information on a lot of the other modes of action that we're working with. I'm excited to see a lot of the information come out about some of the quinoxephins. Some of this information that we have started to work on and we haven't seen much field resistance to these products yet. But if we continue to use them, then they may still pop up. And so hopefully making sure that we can get ahead of the game for these other products. [00:15:37] Craig Macmillan: I'm very happy about that because I'm old enough to remember when the DMIs came out and it was like, Oh my god, it's a secret. It's the silver bullet. We're never gonna have to use sulfur again. Yay, and then it was literally within a couple of years they failed in some places. Now, the Fungicide Resistance Action Committee is publishing better information, more information, more accessible information every year about what's new about the different code groups. And they're also now putting a category in, or they have for a long time, but they have a category in there about the potential for resistance. So they'll say, yeah, there's known resistant populations for this. This one has got high potential, even if we haven't found it yet. And that's directing research in that direction. And I think that's really important that we stay ahead of these things. things, looking at where the potential is, as well as where there's known issues. So that's really fantastic. This is going on at what OSU, MSU, I think, Tim Miles in Michigan Walt Mahaffey in Oregon. I think Washington state. [00:16:35] Sarah Lowder: Mm hmm. Michelle Moyer is the viticulture specialist at Washington state university, who's been the project director for this project, led with Walt Mahaffey, who is the foliar plant pathologist at the USDA located in Corvallis. the horticultural crops units. And then a whole, a whole group of scientists from across the nation. There are people at UC Davis. There's people at Michigan State University. Even while I worked on this project in my role at Oregon State, I'm at with the USDA in Corvallis, Oregon. I'm now here at the University of Georgia working with Phil Brannon, who was the University of Georgia, Scientist working on this project and who actually was the person that convinced me to actually apply for the job that I currently now sit in. [00:17:20] Craig Macmillan: That's great. You know, we do still have a little bit of time left. This is a huge topic, but I found it interesting as I was doing research on you and looking at your publications. One of the things you've been involved in is research on collective action. and information transfer among growers related to disease management. And I am really fascinated by this topic. My background is in sociology. So my background is in people, talking to people, doing people stuff. And as we know, things, not just diseases, but also insects like mealybugs, etc. It's an area wide issue. And what you do or do not do on one farm affects what happens or doesn't happen on another farm. Can you tell us just a little bit about what that research was like, what you did? [00:17:57] Sarah Lowder: Absolutely. So that was really coming from how do we branch out from some of the fungicide resistance? Like how do we use a lot of this information that we are getting? One of the things that we were realizing is that some of the vineyards that we were working with, that we were getting some of these tests from, even organic vineyards who were not using any, they weren't using the QIs. They also weren't using any other synthetic product. We're still seeing sometimes very high rates. of the fungicide resistance to these different products. And what we really found was that a lot of the information that we were able to look at was really so much more useful on that larger scale when we were able to look at all of this data in the aggregate. And so one of the things, which I'm going to talk about my experience with the Oregon State, in the William Valley Vineyard growers especially, that they took all of this information, that they took the data, powdery mildew information that we are getting from their impaction spore traps. They were taking the fungicide resistance data that we were giving them, and they were sharing all this information with each other. And we're able to say, Hey, oh, I was using this product, you know, on my field this year and next year. And then I started to see a lot of issues. You didn't see it immediately, but you saw it pretty closely after I did, even though you followed the patterns elsewhere. And so they were able to take a lot of that information and aggregate it and share together and be able to use that much more quickly. I didn't talk too much about how much of the fungicide resistance that we were seeing. We definitely did see some differences in some of the states. that we were looking at, although it was generally pretty high rates of resistance to the QI products across the nation. That degree was less in a lot of the places in Oregon where a lot of this information started and where they shared a lot of this information from the get go. So one of the things that we wanted to look at was how does this information come across and then what do people do with that information? Absolutely. So when you get into the area wide management, when you, when you start talking about it, you're like, okay, while I manage my property, Unfortunately, a lot of these diseases aren't just staying on my property. If we could, if we could keep everyone isolated, then we wouldn't have to talk about a lot of this information management information management across all these different regions. What do we do once we have that knowledge and once we're sharing all of these spores back and forth even if we don't necessarily want to share that. But if we can also share some of the information on what we're all seeing, we can all manage it a little better. Even if it's just as simple as like, Oh, my sprayer was not calibrated correctly and I'm starting to see More powdery mildew in my vineyard blocks. If you communicate that to your neighbor, then they may be able to increase their spray intervals a little bit more in order to not lose their crop because they're going to have to deal with a much higher crop load. And they could be looking at the spore information. They could be looking at any of these monitoring effects that they're collecting. But if you can know that a source population nearby is going to be pushing more spores more readily, that's even before it's hitting your vineyard. So it's getting that information even a little faster than you would with some of the spore monitoring efforts, if that makes sense. [00:21:01] Craig Macmillan: That does make sense. And so, in terms of the collecting the information, this doesn't just have to be glove swabs or, you know, impaction traps. This simply can be people saying, hey, I'm seeing mildew pressure that's pretty intense, or I'm seeing it earlier, or whatever. Other people are saying, I'm not seeing it yet, but I know I'm downwind of you, for instance. Or, I know that my conditions are still very conducive, so I might be able to, like you said, increase my spray intervals, maybe check my calibration, check my coverage. It's a, it's a heads up. Basically from from one grower to another. How is this information shared? [00:21:34] Sarah Lowder: So there are lots of different ways that this information is shared One of the ways that we wanted to look is at just what did people find the most useful when they were Looking for different information on either new diseases or old diseases or all that kind of thing And some of the stuff that we were finding was that people really found their colleagues, just those person to person conversations that they were having to be the most useful information when managing any diseases. And while people certainly found, which I was happy to hear, that people found their viticulture specialists, their extension agents, to be extremely useful when helping to find this information, they really were still, the the most important part was their colleagues and their neighbors, the other growers in the area. And so you can look at different ways that people communicate, which we, one of the things that we did was look at a communication network. So just exactly how is that information flowing in the system? And there are certain people, which this may not necessarily be a huge surprise. But there are certain people that a lot of people go to, to learn more information about stuff, especially as someone that is looking at a region and be like, Ooh, I have one, this super great new tool, mate, I have something even cooler than the glove swabs. And now I need to tell. the growers about it. I need to see if we can actually use this in a commercial way that'll be viable. You can go to some of these more influential individuals within a region and then hopefully see that information spread a little bit more quickly than it might otherwise if you just kind of picked your people based on just where they were located or even just the closest ones you get your hands on. As it were. [00:23:09] Craig Macmillan: Gotta find the node. Gotta find the hub, [00:23:11] Sarah Lowder: find the node. . [00:23:14] Craig Macmillan: This is an interesting topic to me because one of the things that I think we've lost from a cultural standpoint is the coffee shop. People who are now retired growers have talked to me about how you're on your farm. You know, before sunup you get things running, you get going. People are doing what they're doing. Everything's fine. And then you go to the coffee shop about nine o'clock and everybody's there. And that's where the information would get transferred. And this goes back to the, you know, basic farming decades ago. We don't do that anymore. What we do is we're there at Sunup before Sunup, we get things running, we get done, then we're back in the truck and we're on the phone and we're going to the next ranch and we're not connecting with people. In that kind of social conversational way, the way that we used to. And so hopefully we can revive some of that either through meetings or through internet or through just simply networks, like you said, if there's a relationship, you can just simply call somebody and say, Hey, I'm starting to see this and hopefully we can build those social networks and see the collective benefits [00:24:12] Sarah Lowder: and find more ways to bring us together. [00:24:15] Craig Macmillan: Find more ways to bring us together in a world that seems to be forcing us apart, right? No. On this topic of managing diseases and monitoring diseases, is there one thing you'd recommend to our listeners around this? [00:24:27] Sarah Lowder: There are lots of different diseases in lots of different ways that a lot of things are managed and we talked a little bit about Collective action in the sense that a lot of times some diseases are more effectively managed on a much wider scale than an individual Farming unit so like you could do the best practices in your own vineyard but if you have Someone next door doing lawn best practices that could just mitigate all of the hard work that you just put into it. But it's hard to say anything on the large scale other than the fact that Talking more with those around you has a much wider benefit for disease management on all scales And just also grow better cultural practices, better more information on learning. I may be someone in the academia realm, but I always think that the more you can learn, the better. And your neighbors are in the same game as you are, especially in vineyards. I feel like the mantra of the rising tide lifts all boats is very much in effect. [00:25:24] Craig Macmillan: So we can learn from extension and from all that great stuff that's out there, but we can also learn from each other. Sarah, where can people find out more about you and your work? [00:25:31] Sarah Lowder: Yeah, so now that I'm over here at the University of Georgia, where I'm most easy to find is through the Viticulture Extension website. It's called the UGA Viticulture Blog. We post a lot of information relevant to those growers in the southeast, but we also have a blog posting that sometimes will go out via email if you would like to sign up for that, backlog of what we've posted. It's the easiest way to find me. I'm all around the University of Georgia system. [00:26:00] Craig Macmillan: Fantastic. Thank you so much. Our guest today was Sarah Lowdre. She's a Denture and Viticulture Specialist and Assistant Professor in the Department of Horticulture at the University of Georgia. Thanks for being here. This was a great conversation. [00:26:10] Sarah Lowder: Thank you, Greg. I had a great time. Nearly perfect transcription by Descript

Ladies and gentlemen, scientists and skeptics alike, today we are thrilled to announce a scientific project that will rock the very foundations of virology. In an unprecedented effort led by Jamie Andrews and sponsored by The Way Forward, a team of independent biologists are conducting the most exhaustive virological control experiments ever. This brave team of scientists have completely dismantled virology's so-called "evidence," rendering the foundational aspects of virology totally pseudoscientific and fraudulent. And the good news is, we're just getting started... And we're asking for your help to finish the job. We've finished Phase 1 and 2, but we'll need help funding Phases 3 and 4. Phases 3 and 4 of the control experiments will focus on genetics — Polymerase Chain Reaction (PCR) and Full Genome Sequencing.  To fully understand the truth about PCR related to so-called "viral genetics," we need to purchase a QPCR machine and a few other bits of equipment. We'll need to send samples to CROs for Full Genome Sequencing, and we'd like to conduct a more comprehensive Transmission Electron Microscopy (TEM).  In order to finish, we need your help to raise funds to continue these vital experiments. Any amount helps, and we are so grateful for your contributions.  To donate to the project, click here or visit https://www.thewayfwrd.com/donate Additional Resources: Link to Kidney 360 EM Study mentioned by Jamie. Link to Duck Study mentioned by Jacob Jamie's Thread on Forensics Frauds Jamie's Thread on Dr. Lanka's control experiment Mike Stone's Avian Flu Article Stay Updated: Scroll to the bottom of our homepage and sign up for The Way Forward newsletter to receive important project updates. Sign up here  Other episodes to get you up to speed: Ep 85: Can You Catch a Cold? Ep 66: It Came From a (Computer-Lab) Ep 91: Bio-labs, Anthrax, and Gain of Fiction  Ep 35: The Show is Over The Way Forward podcast is sponsored by: NEW BIOLOGY CLINIC: Experience individually tailored terrain-based health services with virtual consults, practitioner livestreams, movement classes, and more. The New Biology Clinic's motivation is to make you healthy and keep you that way. Visit https://NewBiologyClinic.com and enter code TheWayForward for $50 off your activation fee. Members of The Way Forward get the full activation fee waived. Become a member of The Way Forward here: https://thewayfwrd.com/membership-sign-up/ ————————— ORGANIC MUSCLE: Organic Muscle is revolutionizing sports nutrition by exclusively utilizing non-GMO ingredients from USDA Organic farms. Experience the fusion of organic purity and scientific excellence at https://organicmuscle.com, and unlock a 15% discount with code "FORWARD15" at checkout. ————————— Visit our online marketplace for discounts on a variety of the best holistic health brands and products: https://thewayfwrd.com/store/ Click here for all of our links, and to watch or listen to The Way Forward on other platforms. Join The Way Forward to connect with like minded men and women near you, businesses near you, and more! The best part? You pay whatever you want!: https://thewayfwrd.com/membership-sign-up/ Are you a natural health practitioner? Join our private, natural-health practitioner database here: https://thewayfwrd.com/directory-form/ ————————— *This material may not be published, broadcast, rewritten or redistributed in whole or in part without expressed written permission from The Way Forward, LLC. The purpose of this presentation is to convey information. It is not intended to diagnose, treat or cure a condition; nor is it to be considered medical or legal advice, opinion or recommendation. This information is presented in the spirit of service for all.*   1:45 - Introduction 5:00 - Importance in Dispelling Virology PART 1, BIRD FLU:  8:12 - “Isolation” of Bird Flu Virus 17:30 - Bird Experiments and Misrepresentation of Nature  30:00 - When 29 Million Chickens Die  35:20 - 462 Deaths Related to “Bird Flu” Worldwide PART 2, VIROLOGY CONTROL EXPERIMENTS: 49:33 - Important Project Announcement  53:09 - Project Overview and Details 1:00:55- Objections to Stefan Lanka's Work and Replications 1:10:08 - Importance of Strong Cell Lines 1:18:30 - Fetal Bovine Serum and Cytopathic Effects 1:27:05 - Pulling Aspects of Virology Apart 1:28:28- CDC Images vs Controlled Experiments  1:37:37 - Claims Supporting Viruses Being Real  1:44:13 - Project Moving Forward and Help Needed 1:55:24 - Where to Donate  

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!

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. 

In the fifth episode of The New Frontier podcast, we're joined by Paul Byrne, Senior Director of Genomics from ProtaGene (MA, USA). Paul describes his experience working with qPCR vs digital and digital droplet PCR assays and advises on their pros and cons, as well as when it's best to use each. We discuss how these assays can be optimized for cell and gene therapy targets and get a peek into the tips and tricks he's picked up over his 30 years of experience.

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. 

BUFFALO, NY- February 13, 2024 – A new #research paper was #published in Aging (listed by MEDLINE/PubMed as "Aging (Albany NY)" and "Aging-US" by Web of Science) Volume 16, Issue 2, entitled, “IL-17 promotes IL-18 production via the MEK/ERK/miR-4492 axis in osteoarthritis synovial fibroblasts.” The concept of osteoarthritis (OA) as a low-grade inflammatory joint disorder has been widely accepted. Many inflammatory mediators are implicated in the pathogenesis of OA. Interleukin (IL)-18 is a pleiotropic cytokine with versatile cellular functions that are pathogenetically important in immune responses, as well as autoimmune, inflammatory, and infectious diseases. IL-17, a proinflammatory cytokine mainly secreted by Th17 cells, is upregulated in OA patients. However, the role of IL-17 in OA progression is unclear. In this new study, researchers Kun-Tsan Lee, Chih-Yang Lin, Shan-Chi Liu, Xiu-Yuan He, Chun-Hao Tsai, Chih-Yuan Ko, Yuan-Hsin Tsai, Chia-Chia Chao, Po-Chun Chen, and Chih-Hsin Tang from National Chung-Hsing University, Taichung Veterans General Hospital, Shin-Kong Wu Ho-Su Memorial Hospital, Mackay Medical College, China Medical University, Show-Chwan Memorial Hospital, Fu-Jen Catholic University, National Taiwan Normal University, Asia University, and China Medical University Hsinchu Hospital used synovial tissues collected from healthy donors and OA patients to detect the expression level of IL-18 by immunohistochemistry stain. “Elucidation of the molecular mechanisms and main factors involved in OA pathogenesis may help with the development of novel therapeutic targets that relieve OA pain or prevent the disease from progressing.” The OA synovial fibroblasts (OASFs) were incubated with recombinant IL-17 and subjected to Western blot, qPCR, and ELISA to examine IL-18 expression level. The chemical inhibitors and siRNAs which targeted signal pathways were used to investigate signal pathways involved in IL-17-induced IL-18 expression. The microRNAs which participated IL-18 expression were surveyed with online databases miRWalk and miRDB, followed by validation with qPCR. This study revealed significantly higher levels of IL-18 expression in synovial tissue from OA patients compared with healthy controls, as well as increased IL-18 expression in OASFs from rats with severe OA. In vitro findings indicated that IL-17 dose-dependently promoted IL-18 production in OASFs. Molecular investigations revealed that the MEK/ERK/miR-4492 axis stimulated IL-18 production when OASFs were treated with IL-17. “This study provides novel insights into the role of IL-17 in the pathogenesis of OA, which may help to inform OA treatment in the future.” DOI - https://doi.org/10.18632/aging.205462 Corresponding authors - Po-Chun Chen - pcchen@ntnu.edu.tw, and Chih-Hsin Tang - chtang@mail.cmu.edu.tw Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts About Aging-US Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging-US go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways. Please visit our website at https://www.Aging-US.com​​ and connect with us: Facebook - https://www.facebook.com/AgingUS/ X - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Spotify - https://open.spotify.com/show/1X4HQQgegjReaf6Mozn6Mc Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

BUFFALO, NY- February 12, 2024 – A new research paper was published in Oncotarget's Volume 15 on February 5, 2024, entitled, “Differential expression of Mad2 gene is consequential to the patterns of histone H3 post-translational modifications in its promoter region in human esophageal cancer samples.” Raw areca nut (AN) consumption increases esophageal squamous cell carcinoma (ESCC) due to overexpression of securin (pituitary tumor transforming gene1), causing chromosomal instability. Mitotic arrest deficient protein 2 (Mad2), a crucial spindle assembly checkpoint protein, is at risk of aneuploidy and tumor development when overexpressed or underexpressed. In this new study, researchers Chongtham Sovachandra Singh, Nabamita Boruah, Atanu Banerjee, Sillarine Kurkalang, Pooja Swargiary, Hughbert Dakhar, and Anupam Chatterjee from The Assam Royal Global University, University of Pennsylvania, LN Mithila University, University of Chicago Medicine, Nazareth Hospital, Laitumkhrah, and North-Eastern Hill University evaluated Mad2 status in human ESCC with AN consumption habits, revealing unclear molecular mechanisms. Human ESCC samples (n = 99) were used for loss of heterozygosity analysis at 4q25-28, while 32 samples were used for expression analysis of Mad2, E2F1 genes, and Rb-phosphorylation. Blood samples were used for metaphase preparation. The Mad2 deregulation was assessed using chromatin immunoprecipitation-qPCR assay in the core promoter region, establishing its association with the pRb-E2F1 circuit for the first time. “The study revealed overexpression and underexpression of Mad2, premature anaphase, and chromosome missegregation in all the samples.” LOH pattern identified a deletion in D4S2975 in 40% of ESCC samples. The study reveals the deregulation of pRb-E2F1 circuit in all samples. 4q27 disruption could be a factor for Mad2 underexpression in AN-induced esophageal carcinogenesis, while overexpression may be due to the deregulation of the Rb-E2F1 circuit and consequently elevation of H3K4me3 and H3K9ac. “Mad2 expression levels with chromosomal abnormalities can be a clinical biomarker, but further research is needed to understand pRb's role in Mad2 down-regulation.” DOI - https://doi.org/10.18632/oncotarget.28554 Correspondence to - Anupam Chatterjee - achatterjee@rgu.ac, chatterjeeanupam@hotmail.com Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.28554 Subscribe for free publication alerts from Oncotarget - https://www.oncotarget.com/subscribe/ Keywords - cancer, Mad2 gene, histone methylation, histone acetylation, Rb-phosphorylation; esophageal cancer About Oncotarget Oncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science. To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us: Facebook - https://www.facebook.com/Oncotarget/ X - https://twitter.com/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/@OncotargetJournal LinkedIn - https://www.linkedin.com/company/oncotarget Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget/ Spotify - https://open.spotify.com/show/0gRwT6BqYWJzxzmjPJwtVh Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

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.  

Drs. John Sweetenham and Fred Locke discuss the FDA investigation on the risk of cancer from CAR T-cell therapy and share insights on the known number of cases and the potential implications on clinical research and patient care. TRANSCRIPT Dr. John Sweetenham: Hello, I'm Dr. John Sweetenham from the UT Southwestern Harold C. Simmons Comprehensive Cancer Center and host of the ASCO Daily News Podcast. CAR T-cell therapies have been game changers for treating certain cancers including lymphomas and leukemias, as well as multiple myeloma, since the vast majority of patients who have received CAR-T do not have other curative options with conventional non-cellular, anti-cancer therapies. But on November 28, the U.S. Food and Drug Administration announced that it is investigating whether CAR T-cell therapy can, in rare cases, cause secondary cancers. The FDA launched the probe after receiving reports from clinical trials and other data sources of T-cell malignancies in patients who received CAR T-cell immunotherapies. Joining me to discuss the investigation and its implications for the field is Dr. Fred Locke, a medical oncologist and translational researcher and a senior member and chair in the Department of Blood and Marrow Transplant and Cellular Immunotherapy at the Moffitt Cancer Center in Tampa, Florida. Dr. Locke is an internationally renowned clinical research leader in the field of CAR T-cell therapy. You'll find our disclosures in the transcript of this episode, and disclosures of all guests on podcasts are available at asco.org/DNpod. Fred, it's great to have you on the podcast today. Dr. Fred Locke: Thanks, John, I'm really glad to be here. Dr. John Sweetenham: So, T-cells are the backbone of CAR T-cell therapies, and there are currently 6 CAR-T products approved by the FDA. As our listeners will know, CAR T-cell therapies manipulate a patient's T-cells, enabling them to recognize and attack antigens on cancer cells and induce potential long-standing changes in the immune system. In its statement on November 28, the FDA said it determined that the risk of T-cell malignancies is applicable to all of the currently approved BCMA- and CD19-directed, genetically modified, autologous CAR T-cell immunotherapies. Fred, could you comment for us on the investigation: How many patients are reported to have developed second malignancies from CAR T-cell therapy, and whether there are likely to be more secondary cancers reported? Dr. Fred Locke: Yes, so the FDA and the reports are coming out that there are 19 cases of T-cell malignancy that we're aware of that have occurred after the current FDA-approved CAR T-cell therapies were administered for the treatment of leukemia, lymphoma, or multiple myeloma. The majority of those cases were reported through the FDA Adverse Event Reporting System. And we don't know a lot of details of those 19 cases. We think that there's probably about 13,000 to 14,000 patients who've been treated with the commercial CAR T-cell therapies. So if you kind of do some crude math, you can come up with 19 out of say, 13,500; we're at about 0.1% of patients who could have developed T-cell lymphoma after treatment with these CAR T-cell therapies. It's not entirely out of the realm of possibility that T-cell lymphoma could develop from gene-modified T-cells, and these are all the patient's own T-cells that have been modified outside of the body. But I would still posit that this is a really low incidence of T-cell lymphomas in these patients who really are without other great treatment options. Dr. John Sweetenham: Yeah, and I think that's a point that we'll return to a little bit later on in the conversation around the fact that you know, clearly, there are major benefits that have been associated with CAR T-cell therapy and hematologic malignancies so far. And of course over the years, I think that many of us have become familiar with and learned a great deal about how to manage some of the more serious side effects of CAR T-cell therapy. And you, of course, have led several pivotal national trials of anti-CD19 CAR-Ts for lymphoma. Can you comment at all on whether you've seen previous data from your own practice or others on the risk of second malignancy from CAR T-cell therapy? And can you share your insights on the data and any new emerging data that warrants our attention for the concern or risk of second malignancy? And I guess to round up that series of questions, is there anything currently in yours or others research into CAR-T to explain what's happening and why this is going on? Dr. Fred Locke: I think what may have prompted the FDA's announcement of this is that on the same date that they came out with announcing their investigation, there was the release of the abstracts for the American Society of Hematology Annual Meeting. And within those abstracts, and unfortunately it was not selected for poster or oral abstract presentation, but discovered within those abstracts was one on a CAR+ T-cell lymphoma after ciltacabtagene autoleucel therapy for relapsed refractory multiple myeloma. And what these investigators and the company were reporting is that a patient with refractory multiple myeloma received the cilta-cel BCMA-directed CAR T-cell therapy and developed a stringent complete response, and about 5 months later developed a nasal facial plaque and PET+ cervical lymph nodes. And both the lymph nodes and the plaque were biopsied and showed a T-cell lymphoma in which 90% to 100% of the cells were positive by qPCR for the CAR construct and immunohistochemistry for the CAR protein. So this was a T-cell lymphoma growth where the cells were expressing the inserted protein, the chimeric antigen receptor protein, which is obviously not natural. And when they looked a little bit deeper at these patients, 91% of the cells have the same T-cell receptor sequence. So this was really a clonal sort of process. They did CAR integration analysis to see how the insertion of the CAR, the chimeric antigen receptor gene, could have potentially disrupted a gene within the T-cells. And what they found is that there were some dominant sort of insertions within certain genes suggesting monoclonality, but it wasn't within any sort of obvious activating genes that would be expected to lead to the T-cell lymphoma. They went on and did some additional analysis, and they showed that there was some existing TET2 mutations in the T-cells of this patient, prior to probably prior to the CAR T-cell manufacturer, and they weren't associated with clonal insertion. And I think, you know, it's possible that this patient who had a pre-existing mutation may have been susceptible to the development of a T-cell lymphoma prior to the CAR T-cell treatment. And TET2 was previously shown a number of years ago in a CLL patient treated with CD19 CAR T-cell therapy; it was shown that there was insertional mutagenesis, silencing the TET2 gene, and that associated with clonal expansion of the CAR T-cells in that patient and corresponded with remission of the CLL. However, the difference here is that that patient's T-cell clone went back down and contracted, and the patient remained in remission 5 years later with their T-cells still in the blood, but the minority of those T-cells had that that TET2 mutational insertional mutagenesis. All this is something we thought was theoretically possible, that T-cell lymphoma could develop after car T-cell therapy. And in fact, a prior trial using a different method of delivery of a CAR gene; instead of using a virus to insert the car into the into the T-cells, a transposon system called piggyBac was used. And in that trial, again, CD19 CAR trial, but in this case, it was allogeneic donor cells for patients who had relapsed after an allogeneic transplant. So it's sort of an autologous, you know, analogy, but it's using the donor cells. And in that trial, 2 out of like 10 patients developed clonal T-cell lymphoma, which was CAR+, but they weren't able to identify a clear insertional mutagenesis event in those cases. So, we've known this is possible, and it would have been great if this poster or if this abstract at ASH was presented as an oral or a poster so we could get more detail, but it's possible that that's the likely reason for the FDA's announcement. Dr. John Sweetenham: Thanks. The bottom line, I guess, is that for now, the jury's still out on exactly what's underlying these observations, but something which I'm sure is going to be the subject of a lot of discussion during the ASH meeting this year and moving forward. I'd like to inform our listeners that ASCO released a statement on the FDA investigation, stating that the risk of T-cell malignancies due to CAR T-cell therapy appears to be very low. And we've just heard from Dr. Locke that, of the several thousand patients who've received CAR Ts, there are 19 cases so far, it's been reported, which puts us into some type of proportion. The ASCO statement goes on to say that based on available data, and while such malignancies have occurred in patients who have received CAR T-cell therapy, the causal relationship, whether these cases are spontaneous or are caused by the therapy, needs to be investigated further, and we've just heard a little about the detail of that. ASCO added that by issuing a warning but not revoking approval of these therapies, the FDA clearly believes that the current available evidence suggests the overall benefits of these products, used within their approved label, continue to outweigh the potential risks. So Fred, the risk of secondary malignancies is already included as a class warning in the U.S. prescribing information for these CAR T-cell therapies. But do you think that the CAR-T products could eventually be taken off the market, and how would your research be impacted if this were to happen? And maybe finally, how long will patients on CAR T-cell therapy need to be monitored moving forward? Dr. Fred Locke: I don't believe that CAR T-cell therapy will be taken off the market. As we've already talked about, the incidence is extraordinarily low and the causality is unclear. It would certainly impact my research, as I'm doing clinical trials with CAR T-cell therapies, but it would more importantly impact the way we treat patients. We did over 300 CAR T-cell therapy treatments last year here at Moffitt Cancer Center. We're one of the busiest programs in the world giving CAR T-cell therapy, and it is truly a transformative therapy for all the diseases that we administer these FDA-approved therapies for. For example, in diffuse large B-cell lymphoma, we participated in the ZUMA-7 clinical trial and recently reported that patients randomized to CAR T-cell therapy had improved overall survival. They were living longer than patients randomized in the second-line setting to get conventional chemotherapy and autologous transplant. This is clearly a therapy that can work. I would also add that the risk of secondary malignancies is real, but that's a risk for all cancer patients, particularly patients with hematologic malignancies, and for example, lymphoma patients who've gotten an autologous stem cell transplant are at a relatively high lifetime risk of developing a secondary myeloid malignancy, most commonly, treatment-related MDS or AML. And that risk is also present after CAR T-cell therapy. The degree of attribution of CAR-T versus the condition of chemotherapy for CAR-T versus the previous chemotherapy is all unclear, and more analysis needs to be done. But the risk of developing treatment-related MDS or leukemia is certainly higher than the small number of T-cell lymphomas reported. The other thing I want to point out is that there was an analysis of the SEER database that patients with B-cell lymphomas are at about a 5-fold higher risk of developing a T-cell lymphoma than the otherwise healthy population; and vice versa, by the way, T-cell lymphoma patients are at risk for developing B cell lymphoma. And in fact, in that SEER database, it's not a wildly different percentage chance of developing a T-cell lymphoma after a B-cell lymphoma. And this data came out before the advent of CAR T-cell therapy. So I really think we need more science to be done to understand what's happening for these patients. Will this impact the field? Well, certainly, there are treatments that are not CAR T-cell therapy that compete with CAR T-cell therapy or could; I'm a strong believer that they don't offer the same outcomes for patients, but we will certainly see people talking about this for some time. Then the other place where this could be relevant, I think, is as we look at CAR T-cell therapy for autoimmune disorders, and we're starting to see studies of that for lupus and other diseases, the risk to benefit ratio could be different in those cases. So this is something we really need to consider as we move forward with CAR T- cell therapy. Dr. John Sweetenham: Yeah, thanks, Fred. And as a major clinical investigator in the field of CAR-T at the moment, do you see any potential concerns about difficulties in getting patients onto the trials of CAR T-cell in the light of this information? Dr. Fred Locke: No, I really don't. We're not seeing hesitancy, at least in the patients who are referred in for CAR T-cell therapy. Again, it may give ammunition for those who are already predisposed to not refer patients in for CAR T-cell therapy, but I don't think it should. I think that these are low risks, and these therapies clearly have benefits to patients. And we should give their patients an opportunity to get these therapies, and I don't see it impacting our clinical trials at this point. Dr. John Sweetenham: Yeah, and your comments address what was going to be my final question to you and that is, as a referring oncologist, how would you advise a referring oncologist to talk with their patients about these data and their implications moving forward? Dr. Fred Locke: If the patient brings it up, I think the response should be that these are very few cases of very low incidence and very low risk. There are other risks to CAR T-cell therapy that are greater, and really speaking with a cell therapist who administers the treatment is probably the best way to give the patient the option to get CAR T-cell therapy if they want to, knowing all the risks and benefits. So, I would leave it up to the CAR-T treatment center to discuss those risks with the patient.   Dr. John Sweetenham: Well, thanks, Fred, for sharing your insights with us on these concerning developments in CAR T-cell therapy, and I think also for putting them into context in terms of the sort of magnitude of this problem in the context of the overall number of patients who are benefiting from this therapy right now. We truly appreciate your time, and thanks for sharing your thoughts with our listeners. Dr. Fred Locke: Thanks, John, my pleasure. Dr. John Sweetenham: And thank you to our listeners for your time today. If you value the insights you hear on ASCO Daily News Podcast, please take a moment to rate, review, and subscribe wherever you get your podcasts. Disclaimer:  The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions. Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity or therapy should not be construed as an ASCO endorsement.    Find out more about today's speakers:      Dr. John Sweetenham Dr. Fred Locke @DrFredLocke     Follow ASCO on social media:         @ASCO on Twitter     ASCO on Facebook     ASCO on LinkedIn         Disclosures:        Dr. John Sweetenham:    Consulting or Advisory Role: EMA Wellness     Dr. Fred Locke: Consulting or Advisory Role: Novartis, Celgene, Calibr, Allogene, Gerson Lehrman Group, EcoR1, Amgen, Bluebird Bio, Bristol Myers Squibb, Iovance Biotherapeutics, Legend Biotech, Cowen, Kite (Gilean), Umoja Biopharma, Takeda, Sana Biotechnology, Daiichi Sankyo/UCB Japan, Bristol-Myers Squibb/Celgene, Janssen, A2 Biotherapeutics, Mittenyi Biotec, Caribou Biosciences, Takeda, Umoja Biopharma Research Funding: Kite Pharma, Allogene, Novartis, Bluebird Bio, Bristol-Myers Squibb/Calgene Patients, Royalties, Other Intellectual Property: Double Mutant Survivin Vaccine. US010414810B2 CAR T Cells with Enhanced Metabolic Fitness; Serial Number: 62/939,727 Methods of Enhancing CAR T Cell Therapies. Serial Number: 62/892,292. Evolutionary Dynamics of Non-Hodgkin Lymphoma CAR-T cell therapy.  Serial Number: 62/879,534. Travel, Accommodations, Expenses: Kite Pharma, A2 Biotherapeutics

Dr. Shannon Westin and her guest, Dr. Nanda Horeweg and Dr. Carien Creutzberg, discuss the paper "Molecular Classification Predicts Response to Radiotherapy in the Randomized PORTEC-1 and PORTEC-2 Trials for Early-Stage Endometrioid Endometrial Cancer" recently published in the JCO. TRANSCRIPT  The guest on this podcast episode has no disclosures to declare. Shannon Westin: Hello everyone, and welcome to another episode of JCO After Hours, the podcast where we get in-depth on manuscripts published in the Journal of Clinical Oncology. I'm your host Shannon Westin, Social Media Editor for the JCO and GYN Oncologist by trade. And I'm so excited about today's topic because it is a GYN Oncologist dream. Before I start, please note that none of the authors have any conflict of interest. We are going to be discussing molecular classification predicts response to radiotherapy in the randomized PORTEC-1 and PORTEC-2 trials for early-stage endometrioid endometrial cancer. And this was published in the JCO on September 20th, 2023. And we're going to be speaking to two of the lead authors. First is Nanda Horeweg. She's a senior researcher in the Department of Radiation Oncology at the Leiden University Medical Center in the Netherlands. Welcome. Nanda Horeweg: Thank you. Happy to be here. Shannon Westin: And Dr. Carien Creutzberg. She's professor at the Department of Radiation Oncology at the Leiden Medical Center as well. Carien Creutzberg: Thank you. Shannon Westin: So, let's get into it. And I want to really level set because we have a mixed audience here. So, why don't you start by speaking about the incidents and mortality of endometrial cancer? Nanda Horeweg: Yes, of course. Endometrial cancer is the sixth most common cancer in women with around 400,000 new diagnoses made globally each year. And a woman's lifetime risk to get endometrial cancer is around 3%, and the median age, the diagnosis is 61 years. Most of the women who are diagnosed with endometrial cancer are diagnosed at an early stage, around two thirds, and they have an excellent prognosis. Actually, the five-year survival rates are around 92%. For stage 2 disease, this is actually already going down a bit to 74%. Therefore, stage 3 disease is only 48%. Women that are diagnosed with advanced disease have only a five-year survival, 15%. Shannon Westin: So, given that we know the majority of endometrial cancers are diagnosed at this early stage, prior to your evaluation, what was known about the optimal way to treat this early-stage patient population? Carien Creutzberg: Well, of course, the PORTEC trials were done … were started PORTEC-1 in the 19th of the last century, and PORTEC-2 in 2002. So, at that time, there were still many, many women treated adjuvantly with external beam radiation therapy. And we just developed risk factors to decide on their risk and the incidents for radiotherapy. And in PORTEC-2, because in PORTEC-1 we had seen that most of the recurrences in these early stage cancers were in the vaginal fold, we compared local vaginal brachytherapy only three sessions within full course of pelvic radiotherapy and showed that it had similar pelvic control and survival. Of course, this study, which Nanda conducted, was a long-term analysis with many new factors known from the translational research in the tissue samples of these patients who participate in PORTEC-1 and 2. And in the meantime, we've developed much more knowledge on the molecular factors and other important factors such as LVSI, which tell us much more about the individual prognosis to patients. So, the treatment has been developing greatly in the past 20 years. Shannon Westin: Yeah, and I think this is a great case of less is more, right? We were doing so much for so many people that really didn't need it. And so, really tailoring who needs less treatment, who doesn't need any treatment, and then also, conversely, who may need more treatment that would be missed by the traditional risk factors that you're speaking of. So, I think that brings us right into my next question, which is just bringing the audience up to date on the cancer genome atlas and how that's changed the way we classify endometrial cancer. Nanda Horeweg: Yes, I think the molecular classification of the TCGA has shaped the way we think about endometrial cancer, and has huge impact on decisions on adjuvant treatments in the years to come. The TCGA performed an extensive characterization of the endometrial cancers and found that in fact, this disease exists of four different groups. And the first of the groups I'd like to discuss is the ultra-mutated group, which is characterized by POLE mutations. And this group is shown to have an excellent prognosis in many independent studies. A second group that also has a high mutational burden is characterized by microsatellite instability, and mismatch repair deficiency and has shown to have an intermediate prognosis. Then there's another group that has a low mutational burden with high copy number alterations and frequent TP53 mutations, and these have a poor prognosis. And then lastly, there's a group that does not have any of the classifying features and is often called non-specific molecular profile or TP53 wild type. And this group also has an intermediate prognosis. And then finally, there's a small group of cancers that has more than one of these classifying features, the so-called multiple classifiers. And the WHO 2020 has developed an algorithm which can be used to classify them into the four groups. And that's first on the POLE status. And for the POLE wild type tumors, they are assigned according to mismatch repair deficiency status. And for those that are mismatch repair proficient than POLE wild type, they are classified according to the TP53 status into NSMP or p53 abnormal. Carien Creutzberg: Yeah, that is because of in the ultra-mutated and hyper mutated groups, many of the other mutations are secondary mutations in the context of the ultra-mutated stage, and they behave like the first molecular group. Shannon Westin: Yeah. So, that POLE mutation is going to trump anything else, and it's so important. And I will just say as a sidebar, it's been challenging with the price of next gen sequencing sometimes to get that for everyone. So, sometimes for us when we see a p53 mutation, we actually go back and do the full next gen sequencing to make sure that we're not going to act on that core prognostic feature when it really is in the setting of that more simplistic or that more positive prognostic place. So, this is great, we already kind of highlighted a little bit PORTEC-1 and 2, but if you don't mind, I would love to get the audience a little bit more information just maybe about the populations that were included as we were figuring out how aggressive to be with radiation just to remind people of that, or to teach them that if they haven't gotten a chance to look at those studies. Carien Creutzberg: Yeah, that's important to know because PORTEC-1 was still in the era that we also treated intermediate risk stage 1 endometrial cancer patients. So, deep invasion with grade 1 and 2 or superficial invasion with grade 2 and 3. That's what we defined at that point. Then we compared external beam radiation or no further treatment, showing no survival difference, but a higher risk of recurrence with higher risk being older age over 60, grade 3 for deep myometrial invasion. And we kept those high intermediate risk factors as also similarly found by GOG-99 at the time to do PORTEC-2. So, at the time, about 50% of patients did not have an indication for adjuvant therapy anymore, and with a high intermediate risk population for PORTEC-2, we compare external beam or vaginal brachytherapy and found the benefit of vaginal brachytherapy. A simple outpatient treatment, very short with almost no side effects ensuring local control. And nowadays, using the molecular classification of PORTEC-4a, we've compared achieving treatment with or without use of the molecular factors to designated treatment. So, the standard arm is vaginal brachytherapy and investigational arm is first, a molecular risk profile. And then we give no radiotherapy for those with a favorable profile, then a brachytherapy for the intermediate ones, and for the small group is either extensive LVSI or TP53 mutation or L1 chem overexpression external beam. And we hope to show that less overtreatment and less undertreatment will benefit these patients. Shannon Westin: Yeah, I'm very much looking forward to the results of PORTEC-4a. But let's circle back and talk a little bit about your amazing work here. So, how did you leverage those patient populations from PORTEC-1 and 2 for the current study? Nanda Horeweg: Yes. Well, the PORTEC-1 and 2 study provided a unique opportunity to look into differential treatment effects for radiotherapy. And that is because these are randomized trials, so the groups are comparable, and we have long-term follow-up data that's of very high-quality. In addition, as Carien said earlier, she had the vision already back in the nineties to directly ask the patients permission for the collection of the tissue. So, we have a broader complete biobank for both of these trials, which is quite unique. And our colleagues, Professor Smit and also Charlene Goseff from the pathology department, they have done extensive work on molecular classification, and have molecularly characterized all these cases. So, this allowed us to include 880 patients in this study, which is the largest so far. And besides like the very good starting point that we have of PORTEC-1 and 2 is that we also chose a design that was optimized to conduct like real causes, the causal effects of the molecular class on radiotherapy response. So, we tried to preserve this randomization effect, the exchangeability of the groups as much by working with the intention to treat population and not excluding any patients, except for when they did not have the molecular classification assessed. And also, we looked at areas in the body that were irradiated in one group and not in the other one to really observe the effect of radiotherapy as much as possible. So, looking to the entire pelvis, so local and regional recurrences in PORTEC-1 and looking at pelvic recurrences in PORTEC-2. Shannon Westin So, how were the intervention outcomes in this study different based on the TCGA classifiers? Nanda Horeweg: Before I tell you the results of biomolecular group, I think it's good to have the starting point of the analysis here. So, the no hypothesis of my study was to see whether there was any difference, and no hypothesis is that there's no difference. So, if we find a significant effect, then we can actually say that we found something. And if we start with the POLE group, we did not find any significant difference between the groups allocated to radiotherapy or not. But we did see not a single recurrence in any of the patients that we included from both of these trials. So, technically speaking, we did not find a predictive effect of the molecular classifier, but a prognostic effect. There's no one's having recurrence, so we can deduct from that, that radiotherapy is probably over treatment. Then for the MMRd group, we did observe some recurrences, but these were not significantly different between these three groups. So, based on this study, we cannot draw conclusions on which type of radiotherapy we should give to the patients or whether we should give radiotherapy at all. This was very different for the p53 group. There, the patients had lots of recurrences, unfortunately, as we expected, but we saw a big difference in outcome compared between no radiotherapy at all if it's vaginal brachytherapy where we still had lots of recurrences, and EBRT where we hardly saw any recurrences in the pelvis. And that difference was significantly different. So, that's an indication that these patients need more than just vaginal brachytherapy, even though it's only stage 1 endometrioid endometrial cancer. And then in the last group, the NSMPs, we saw even a different pattern where patients who had had external beam radiotherapy or vaginal brachytherapy, both had an excellent local regional control, and the ones that did not receive any treatments had more recurrences. And this was also very significant. So, there, you would conclude that both therapies are appropriate, but of course, the toxicity profile for vaginal brachytherapy is much more favorable than that of EBRT. Shannon Westin: We really are getting kind of consistent data around p53 needing more treatment. And I think the natural question that comes here, for me at least, and I know we can't answer it with the work, is would chemo be — would that be that extra treatment, when we saw with PORTEC-3 that the group needed the chemotherapy the most. So, I think we'll have to continue to work through that and determine is any more treatment what we need or specific treatments really the best. So, this is so intriguing and it's nice that it's consistent, that we're seeing that across these different studies that really kind of lends strength and validity, I think to what we're finding. So, one of the actions that we're kind of moving towards and that you advocate certainly in your paper is omitting therapy for patients with POLE mutations. Are there any ongoing studies around that that will help us confirm that this is safe for our patients? Nanda Horeweg: Yeah, that's a very good point. I think the evidence is strong enough now to conduct prospective trials. And of course, these are ongoing, the PORTEC-4a trial was already briefly mentioned there. The patients with poor mutations will be randomized between observation and vaginal brachytherapy. So, that will give us a good indication whether in this high intermediate risk early-stage group omission is safe. And in addition to that, we are also conducting with the RAINBO Consortium, the RAINBO-BLUE trial, wherein patients also with high-risk features, so non-endometrioid isotypes, LVSI and higher stages are included. And also in those patients, we investigate whether the de-escalation of treatment is safe. So, we're definitely looking forward to those results to be able to transfer this knowledge to clinical practice later on. Carien Creutzberg: And maybe it's nice to add that RAINBO BLUE is connected to the Canadian Taper trial. Taper being a general de-escalation trial where the POLE patients in that trial are also feeding into the RAINBO-BLUE. And I know that in North America, many centers will participate in the Taper trial. Shannon Westin: Yes, I think everyone is very excited and I think it'll be nice to have these two very strong studies that will help us really confirm that that is 100% a test that needs to be done, cost are not — and that will help avoid overtreatment of patients. So, in line of that, have you all experienced any challenges with implementing molecular testing across patients with endometrial cancer? Any thoughts on how we could potentially simplify? You talked about the rational promise algorithm, which I think is excellent, but I'm just curious to hear your thoughts on this. Nanda Horeweg: The implementation of the molecular classification can be challenging. We have to be honest about that. And usually, it's the assessment of the POLE status that's causing the problems because that's usually done with NGS, which is quite expensive. It requires a lot of knowledge in the laboratory and it's also a bit time-consuming. So, that is the bottleneck for most laboratories and for most settings. But this is already changing in a couple of places, like in the UK and the Netherlands, it's being reimbursed by healthcare insurances, and also, in many tertiary care centers in other countries, they're already systematically performing this test. But of course, there will always be places where this is not feasible. And luckily, there are also cheaper alternatives coming up and are already available at the moment. So, one of them is, for example, standard sequencing, which is not so expensive, but a bit labor intensive. Some colleagues we work with from India have implemented that in their clinical practice and are perfectly able to molecularly classify the endometrial cancers in daily practice. Another alternative is a test that we've developed in Leiden that's called the QPOLE test, which is based on qPCR, so that's a technology which we use for our COVID test around the world, so that can be done almost anywhere. And with that, you have a very high accuracy to detect unknown pathogenic variants. And this is also published in JCO Global Oncology, and can be implemented in any center after a local validation step. And even like more companies nowadays are realizing that this is important. So, I think commercial tests are already becoming available and very more on the market soon. So, I am really hoping that it'll be more available to endometrial cancer patients. Carien Creutzberg: And they'll offer them at a very low cost and also a rapid turnaround because NGS can take like 10 days. But realizing on a more national level, if you have found one patient with a POLE mutation, the omission of cycles of chemotherapy with all of the patient care around in the hospital is worth much more than just a few POLE tests. So, we have to look at this and that's I think why our healthcare reimbursement came through that if you look at a population level, it is cheaper, and we'll do an extensive cost analysis in PORTEC-4 just to show this. Shannon Westin: That is such a good point. I love that and all of the downstream issues that happen potentially with radiotherapy or with chemotherapy, that's really brilliant. And I'm going to take that back, I love these podcasts. I always learn stuff that I immediately start to use. So, I guess then the last question is, what's next for this particular research and how might we validate what you found? Nanda Horeweg: Yes. Well, as mentioned earlier, for POLE, we have already put the next step in place. So, PORTEC-4a has completed accrual almost two years ago, and we're very much looking forward to do the final analysis within one to one and a half years. So, that will be one of the important next step. And of course, the POLE-BLUE trial is open at the moment, and within a couple of years, we also hope to learn more about this group. So, that's very exciting. Then for the mismatch repair deficient group, while we did not find any particular sensitivity for radiotherapy, and I also don't think that we will conduct another large randomized radiotherapy trial in this group — I think the results that we've observed in the metastasized setting, were really impressive results with immunotherapy are the way forward for this molecular class. And I think the next thing we should do now is prove whether this works or not in the adjuvant setting. And if that's starting with the high-risk patients, which is something we are currently doing in the MMRd-GREEN trial, which is ongoing in the Netherlands, and soon, will open internationally. And from there on, we can work forward if we see that also in this setting the immunotherapy works well. Shannon Westin: And I think GY020 also — NCI trial is also looking at the addition of immunotherapy to radiotherapy in that irony at risk. Carien Creutzberg: Absolutely. Nanda Horeweg: Yeah. And the KEYNOTE-B21 as well — oh, well, already complete accrue. Shannon Westin: The B21, yeah. So, I think those are good. Yeah, that's a really good point for that MMRd group that the immunotherapy really is the way to go, and then more work to be done with the no specific molecular profile. Nanda Horeweg: The NSMP, I think like for the early-stage group, it's quite clear that vaginal brachytherapy is a therapy of choice. But you can of course, try to identify those at such a low risk that you could deescalate treatment. And that's of course what's being done in the Taper trial and also in part, investigated in the PORTEC-4a trial. Carien Creutzberg: And those with higher risk NSMP that we are revisiting hormonal treatments because 90% are estrogen receptor positive, and they have a clearly better prognosis than those with estrogen receptor negative tumors. So, those with estrogen receptor positive tumors can in RAINBO-ORANGE, which will be run led by the UK group, see if we can improve quality of life with less intensive adjuvant treatment. And then you came to the p53 group, that's a good one to stop with. Nanda Horeweg: Yeah, we have very good indications that radiotherapy and chemotherapy is working well for this group. And this is also in line with the guidelines that have been issued in the last few years by many societies. So, I don't think we should change this base of the treatment consisting of radiotherapy and chemotherapy. But since the prognosis is still rather poor, we need to add systemic agents to reduce the risk of metastasis. And preferably, this should be like well-designed based on a proper biological underpinning, plus something that's not too toxic since we're combining the three therapies together. So, this is what we try to do in the RAINBO-RED trial where we will investigate the addition of a PARP inhibitor to chemoradiation in the p53 group. Shannon Westin: Oh, I love that. That's been my whole career, is adding PARP inhibitors wherever I can. Carien Creutzberg): We might also want to mention the HER2 inhibitors, which are also in about 20% of the p53 group has HER2 overexpression. And there is a trial being set up in NCI with trastuzumab and pertuzumab. Shannon Westin: My only concern with that one is I think that the antibody drug conjugates are so much more powerful, the TDX data that we just saw from DESTINY is so impressive. And so, I do wonder, like if we need to move on from kind of some of the older HER2, and get with the program and use some of these more powerful drugs. But with that, I just want to thank Dr. Creutzberg and Horeweg. This was such a great discussion, and obviously, near and dear to my heart talking about endometrial cancer, but I hope our audience enjoyed as well. Just as a reminder, this was a discussion on molecular classification predicts response to radiotherapy in the randomized PORTEC-1 and PORTEC-2 trials for early stage endometroid endometrial cancer, published in the JCO on 9.20.23. I am your host, Shannon Westin, and I hope you'll check out more JCO After Hours wherever you get your podcasts. Have an awesome day. The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care, and is not intended for use in the diagnosis or treatment of individual conditions. Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement.    

Bill Graham is the Founder of Microcline Tissue Culture, a company that provides tissue culture kits, consulting, and training to cannabis cultivators. With hands-on expertise, he retailed and distributed hydroponics supplies, sourced grow lights globally, created Biojuice nutrients, designed Phresh filter air quality systems, and simplified micropropagation cloning - creating the leading Microclone tissue culture kits in 2005. During our conversation we discussed: The basics of tissue culture Tissue culture as propagation alternative to cloning How mother plants can lead to pathogen infections and loss of vigor Combining tissue culture and qPCR to eliminate pathogens, such as hop latent viroid and more! Thanks to This Episode's Sponsor: Cambium Analytica Cambium Analytica, provides analytical, product development, and quality assurance services for the natural foods, botanical products, natural pharmaceutical, and dietary supplement industries. Cambium is a leading research organization that is focused on leveraging its expertise on drug discovery and method development, to be a research partner of choice for new innovative companies in the burgeoning botanical medicines space. Their focus on applying analytical techniques in combination with sensory, product development, and consumer research is driving advancement in natural product quality and innovation. Learn more at cambiumanalytica.com Additional Resources microclone.com Microclone on YouTube Register for CannMed 24 Submit an Abstract for CannMed 24 Review the Podcast! CannMed Archive CannMed Community Board [Facebook Group]

When it comes to assessing the microbiome, technology continuously evolves. With that, our understanding of the microbiome deepens. There is a lot of confusion out there regarding technology. Companies use marketing spin to lead you to believe the newest is the best when in fact, every technology has its strengths and weaknesses. No one method can capture the entire dynamic of the microbiome. Here at Genova, we use many methods to give you the most complete look at overall gut health. Today we simplify the science behind laboratory assays used to study the microbiome – culture, qPCR, metagenomics, and transcriptomics. Every method has its advantages and disadvantages. We're cutting through the confusion with no marketing spin, just the facts. Today on The Lab Report: 3:30 So much confusion around laboratory methods - why should we care? 7:45 Culture technology is old but still so important 11:10 Conventional PCR and qPCR (aka Real-Time PCR) 15:40 Beware of these qPCR shortcomings 19:50 Next-Gen Sequencing 21:40 Metagenomics – not all labs are created equally!! 26:55 The vital role of taxonomy libraries 30:30 Transcriptomics and assessing RNA Additional Resources: GI Effects Microbiomix Genova Connect               PROMO CODE:  TheLabReport20 for 20% off Subscribe, Rate, & Review The Lab Report Thanks for tuning in to this week's episode of The Lab Report, presented by Genova Diagnostics, with your hosts Michael Chapman and Patti Devers. If you enjoyed this episode, please hit the subscribe button and give us a rating or leave a review. Don't forget to visit our website, like us on Facebook, follow us on Twitter, Instagram, and LinkedIn. Email Patti and Michael with your most interesting and pressing questions on functional medicine: podcast@gdx.net. And, be sure to share your favorite Lab Report episodes with your friends and colleagues on social media to help others learn more about Genova and all things related to functional medicine and specialty lab testing. To find a qualified healthcare provider to connect you with Genova testing, or to access select products directly yourself, visit Genova Connect. Disclaimer: The content and information shared in The Lab Report is for educational purposes only and should not be taken as medical advice. The views and opinions expressed in The Lab Report represent the opinions and views of Michael Chapman and Patti Devers and their guests.See omnystudio.com/listener for privacy information.

Some people in the cannabis industry are questioning whether it is appropriate or necessary to test inhaled cannabis products for pathogenic Aspergillus.  Full disclosure, we at Medicinal Genomics sell qPCR testing kits designed to detect pathogenic Aspergillus on cannabis products. We have also published several resources on our website that describe the potential harms that can be caused by inhaling pathogenic Aspergillus spores and cite with more than 2 dozen Aspergilosis cases in cannabis users.  We have also recommended that states that are considering cannabis testing regulations adopt pathogenic Aspergillus testing. Not because we sell Aspergillus tests, but because we want to protect patients.  By almost any measure, cannabis is one of the most safe and effective medicines available. And in many cases, the potential harms that can come from using cannabis are not caused by the plant, but rather contaminants. And although cases are rare, The documented cases describing Aspergillosis deaths from contaminated cannabis vastly outnumber the published clinical risks for every other contaminant for which the cannabis industry tests. There are no documented deaths for cannabis-derived heavy metals, mycotoxins, pesticides or incorrect cannabinoid labeling. The same cannot be said  So that is our position, but of course we acknowledge that we are biased, and we are not experts on pathogenic fungi; however, our guest today is.  David W. Denning is a Professor of Infectious Diseases in Global Health at the University of Manchester in the United Kingdom. He was the founding president, executive director, and CEO of Global Action For Fungal Infections, an organization dedicated to reducing the worldwide burden of fungal disease. In 2016, he became the director of the National Aspergillosis Centre in Manchester, which treats patients with chronic pulmonary aspergillosis (CPA), and led the committee that developed the first CPA guidelines. He chairs the editorial board of a website which focusses on aspergillus and he leads an organisation which provides education on fungal diseases.  In short, Dr. Denning is the leading authority on all things Aspergillus, and we asked him many of the questions that have been debated on social media recently, including:  Should cannabis be tested for pathogenic Aspergillus Should there be an allowable limit for pathogenic Aspergillus? Is Apergillosis only a concern for immunocompromised patients?  Are the number of Aspergillosis cases under reported?  How difficult is Aspergillosis to diagnose and treat?  How ubiquitous is Aspergillus in the air we breathe?  and so much more.  Thanks to This Episode's Sponsor: Modern Canna Modern Canna is regarded as Florida's first medical cannabis laboratory and one of the most trusted third party testing providers in the United States. The company's mission is to help set the standard for cannabis testing labs worldwide by providing the most accurate and efficient testing services, delivered with a sense of compassion, integrity, and moral obligation; and to attract and attain clients who value quality data that is verifiable, reproducible, and legally defensible. Modern Canna is the only Leafly Certified laboratory in the eastern United States and adheres to the industry's strictest SOPs and quality control standards. Modern Canna offers a wide variety of testing, rapid turnaround times, and consulting services to Florida Medical Marijuana Treatment Centers (MMTC's) and hemp businesses throughout the US. Learn more at moderncanna.com Additional Resources Too Many Mouldy Joints – Marijuana and Chronic Pulmonary Aspergillosis The Aspergillus website https://en.fungaleducation.org/ Submit an Abstract for CannMed 24 Review the Podcast! CannMed Archive CannMed Community Board [Facebook Group]

In this issue, we will review the applications of PCR analysis for your gene therapy programs, and present two case studies. Click to read this audiobook: https://www.altasciences.com/sites/default/files/2023-10/the-altascientist-issue-37-pcr_4.pdf Gene therapy continues to accelerate through preclinical and clinical research arenas. These programs are developed with targeted and personalized medicines in mind. The goal of gene therapy is to safely deliver and incorporate a genetic alteration to restore or repair the protein of a missing or faulty gene. Preclinical assessments of gene therapies consider the general absorption, distribution, metabolism, and excretion of the drug, as well as data from tailored assessments to evaluate delivery and cell incorporation. Gene therapies require, by design and definition, DNA and/or RNA delivery and analysis. While most ongoing research involves gene therapies being delivered in vivo via adeno-associated viral (AAV) vectors, new in vivo delivery mechanisms are on the rise, such as other types of delivery vectors including lipid nanoparticles. CHAPTESR: - 0:05 — About Issue 37 - 1:20 — Introduction to qPCR, dPCR, and RT-PCR - 5:58 — Utility of qPCR, ddPCR, and RT-PCR - 8:19 — PCR Applications - 10:01 — Advantages and Applications - 17:45 — Case Study 1 - 20:20 — Case Study 2 - 22:47 — Conclusion About Altasciences: Altasciences is an integrated drug development solution company offering pharmaceutical and biotechnology companies a proven, flexible approach to preclinical and clinical pharmacology studies, including formulation, manufacturing, and analytical services. For over 25 years, Altasciences has been partnering with sponsors to help support educated, faster, and more complete early drug development decisions. Altasciences' integrated, full-service solutions include preclinical safety testing, clinical pharmacology and proof of concept, bioanalysis, program management, medical writing, biostatistics, clinical monitoring, and data management, all customizable to specific sponsor requirements. Altasciences helps sponsors get better drugs to the people who need them, faster.

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:“Sax Jazz” by alonart“Crowd Cheering” by SoundsExciting“Drum Roll, Please!” by HoBoTrails

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:“Sax Jazz,” by alonart“Balloon Pop / Christmas cracker / Confetti Cannon,” by Breviceps“Crowd Cheering,” by SoundsExciting

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. 

Scientists commonly use qPCR applications in molecular diagnostics to detect pathogens, assess viral loads, or uncover mutations. While the qPCR assay itself may seem straightforward, other aspects such as data collection and security, and following regulatory guidelines, present challenges. In part one of this episode, Gloria Lam, the associate director of qPCR software for Thermo Fisher Scientific, discusses concerns surrounding molecular diagnostic data collection, analysis, cybersecurity, and more.   Welcome to Molecular Diagnostics: An Eye Toward the Future, a special edition podcast series produced by The Scientist's Creative Services Team. This series is brought to you by Thermo Fisher Scientific, a world leader in serving science. Their mission is to enable customers to make the world healthier, cleaner, and safer. Whether their customers are accelerating life sciences research, solving complex analytical challenges, and improving clinical research workflows, Thermo Fisher Scientific is here to support them. Scientists continuously develop new assays to fill unmet diagnostic needs. While methods such as quantitative PCR have emerged as essential tools in molecular diagnostics, scientists developing and administering these assays still must overcome technical challenges. In this podcast series, The Scientist's Creative Services Team talks to experts about their experiences designing and implementing assays and protocols for future molecular diagnostics.

Scientists commonly use qPCR applications in molecular diagnostics to detect pathogens, assess viral loads, or uncover mutations. While the qPCR assay itself may seem straightforward, other aspects such as data collection and security, and following regulatory guidelines, present challenges.   In part two of this episode, Fernando Beils, vice president and general manager of Thermo Fisher Scientific's qPCR Instruments, Assays, and Digital group, introduces an innovative software that streamlines molecular diagnostic testing by facilitating automation and connectivity in qPCR workflows.   Welcome to Molecular Diagnostics: An Eye Toward the Future, a special edition podcast series produced by The Scientist's Creative Services Team. This series is brought to you by Thermo Fisher Scientific, a world leader in serving science. Their mission is to enable customers to make the world healthier, cleaner, and safer. Whether their customers are accelerating life sciences research, solving complex analytical challenges, and improving clinical research workflows, Thermo Fisher Scientific is here to support them. Scientists continuously develop new assays to fill unmet diagnostic needs. While methods such as quantitative PCR have emerged as essential tools in molecular diagnostics, scientists developing and administering these assays still must overcome technical challenges. In this podcast series, The Scientist's Creative Services Team talks to experts about their experiences designing and implementing assays and protocols for future molecular diagnostics.

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: Environmental DNA (eDNA) methods they employ Assay development and method selection based on their need for sensitivity and specificity The use of qPCR and dPCR in their work Studies and monitoring of parasites and pathogens that affect their colony How zebrafish have helped shift research from forward genetic studies to reverse genetic studies 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.

As a winner in the 2023 MP Corrosion Innovation of the Year Awards, the GeneCount Voyager is a deployable, 16-well qPCR thermal cycler instrument that LuminUltra has paired with a portfolio of GeneCount qkits for sample preservation, DNA purification, and and qPCR assaying of microbial targets associated with microbiologically influenced corrosion (MIC). Quantifying MIC-associated microorganisms in a sample can give insight into a system's corrosion risk and the efficacy of its management programs. In this interview, Dr. Jordan Schmidt — senior director of technology and innovation at LuminUltra — explains the evolution of their winning innovation and where it stands today. Other topics include his perspective on market trends and demands; feedback by end users and clients; and an outlook for the future.

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:Sub-reactionsPoisson statisticsStatistical power and confidence intervalsControls and false negatives vs. true negativesDead volumeDynamic rangeMultiplexingMarcia 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!

Welcome to Olink Proteomics in Proximity Podcast! Below are some useful resources from this episode: Highlighted publication: Grasberger H, Magis AT, Sheng E, Conomos MP, Zhang M, Garzotto LS, Hou G, Bishu S, Nagao-Kitamoto H, El-Zaatari M, Kitamoto S, Kamada N, Stidham RW, Akiba Y, Kaunitz J, Haberman Y, Kugathasan S, Denson LA, Omenn GS, Kao JY. DUOX2 variants associate with preclinical disturbances in microbiota-immune homeostasis and increased inflammatory bowel disease risk. J Clin Invest. 2021 May 3;131(9):e141676. doi: 10.1172/JCI141676. PMID: 33651715; PMCID: PMC8087203. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8087203/Highlighted platform that was used to measure proteins in this study with a qPCR readout (Olink® Target 96): https://olink.com/products-services/target/ Learn more about the Crohn's & Colitis Foundation, which is non-profit, volunteer-fueled organization dedicated to finding cures for Crohn's disease and ulcerative colitis: https://www.crohnscolitisfoundation.org/aboutIn the fall of 2021, Dr. Andrés Hurtado-Lorenzo spoke at a Boston Olink event, and his 25-minute presentation is available here where he discusses the discovery and follow-up work with both RNA and protein biomarkers for Crohn's Disease: https://7074596.fs1.hubspotuserconten...Olink® Insight is an open-access resource, which aims to support the user throughout the Olink user journey, starting from product selection and study setup to post-run analysis and visualization of data output. Features include a pathway browser to reveal and understand connections between proteins and human biology, a publication browser, automatic annotations, and access to exclusive data sets. Sign up for free: https://insight.olink.com/ Here is general information about inflammatory bowel disease (IBD) from the U.S. Centers for Disease Control and Prevention (CDC): https://www.cdc.gov/ibd/what-is-IBD.htm#:~:text=Inflammatory%20bowel%20disease%20(IBD)%20is,damage%20to%20the%20GI%20tract. Here is general information from GeneCards about DUOX2, one of the protein biomarkers identified in this study: https://www.genecards.org/cgi-bin/carddisp.pl?gene=DUOX2Here is general information from GeneCards about IL-17C, one of the protein biomarkers identified in this study: https://www.genecards.org/cgi-bin/carddisp.pl?gene=IL17C&keywords=il17cWould you like to subscribe to the podcast on your favorite player or app? You can do so here: Apple Podcasts: https://apple.co/3T0YbSm Spotify Podcasts: https://open.spotify.com/show/2sZ2wxO... Google Podcasts: https://podcasts.google.com/feed/aHR0... Amazon Music: https://music.amazon.com/podcasts/d97... Podcast Addict: https://podcastaddict.com/podcast/409... Deezer: https://www.deezer.com/show/5178787 Player FM: https://player.fm/series/series-3396598 In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here: https://bit.ly/3Rt7YiY For any questions regarding information Olink Proteomics, please email us at info@olink.com or visit our website: https://www.olink.com/ WHAT IS PROTEOMICS IN PROXIMITY?Proteomics in Proximity discusses the intersection of proteomics with genomics for drug target discovery, the application of proteomics to reveal disease biomarkers, and current trends in using proteomics to unlock biological mechanisms. Co-hosted by Olink's Dale Yuzuki, Cindy Lawley and Sarantis Chlamydas.

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!

Dr. Sherman Hom is the Director of Regulatory Affairs at Medicinal Genomics where he provides recommendations to regulatory officials that are tasked with drafting or modifying microbial testing regulations for cannabis, hemp, and psychedelic mushrooms to ensure safe products for patients and consumers. Before Medicinal Genomics, he was at the New Jersey Department of Health, where he led teams that started the Cannabis Testing Laboratory, the Cannabis Microbial Testing Unit, and created the “All States Medical Cannabis Program Required Testing Compendium”. At CannMed 23 Sherman will share the latest update to the “All States Cannabis Microbial Required Testing Compendium” to elucidate the present landscape, and identify a consensus set of required tests to lower public health risk. During our conversation we discuss How concerned cannabis consumers should be about microbial contamination How microbial regulations differ from state to state How growers in certain jurisdictions struggle to meet microbial regulations The difference between presence-absence and total count microbial tests qPCR vs platingand more Thanks to This Episode's Sponsor: Labware Labware is recognized as the global leader in providing enterprise-scale laboratory automation solutions with over 40 offices across 6 continents. LabWare's Enterprise Laboratory Platform is a unique and proven suite of product capabilities that encompass LIMS, ELN, LES, method execution, and SDMS in an integrated and enterprise-ready solution. Learn more at labware.com.  Additional Resources Cannabis Microbial Testing Regulations by State [Interactive Tool]Request an Invitation to CannMed 23Review the Podcast!CannMed ArchiveCannMed Community Board [Facebook Group]Healthcare Provider Medical Cannabis Research Study

Stephen Clawson, CFM, QPCR, FMP, FMG, joins the podcast as this weeks guest!  Stephen has spent the better part of a decade consulting in Facilities Management.  As a Consultant, Stephen brings an outside perspective to his clients to help identify opportunities for optimization. What does optimization look like?  What is the desired end state?  How can I achieve these objectives?  Finding the answers to these questions is a unique journey for each organization. On this episode, Stephen discusses the importance of taking a step back, asking the right questions, and being your own 'consultant' in this never-ending pursuit of optimization. Enjoy! 

Welcome to a Farm4Profit episode Remind people to hit SUBSCRIBE – REMEMBER TO LEAVE REVIEWS Share their ideas at farm4profitllc@gmail.comThe listener review today is brought to you by Geringhoff.  Head of the class no matter the cropTwitter message Anonymous : Listened to the two Shows with Elaine while baling hay.  You could hear the Hayes boys squirming, I know I would.  Thanks for bringing it up!515.207.9640 – let us know why you listen to Farm4ProfitNative Microbials - Purpose built microbial solutions for your animal, from your animal.Lisa Marotz, PhDMicrobiome Scientist, Native MicrobialsLisa obtained her PhD in Biomedical Sciences from UC San Diego in 2020. During her graduate research she developed novel protocols and computational tools to elucidate complex microbial communities through next-generations sequencing which led to more than 20 peer-reviewed publications. After graduating she spent a year as a postdoctoral fellow where she focused on scaling up rapid qPCR testing at the start of the COVID-19 pandemic and identify the microbial communities co-associated with the SARS-CoV-2 virus. Lisa joined Native Microbials in early 2021 where she designs and analyses both commercial and academic studies to validate novel dairy cow endomicrobials.Who is Native Microbials founded in 2015 with a simple mandate to extend proprietary technical advancements in genomics, microbiology, and bioinformatics into Animal Health and Nutrition. now have a global team of scientists, technicians, and commercial support personnel that works tirelessly to ensure our world's animals can receive the best microbes earth has to offerWe have talked with BW Fusion about microbes in crop production, but Why use microbials in livestock?Microbes that are native to animals are safer, more sustainable, and vastly superior influencers of the environmental phenomena happening in animals than anything humanity has already discovered or designed.What is an endomicrobial?What ways can microbials be delivered to animals or livestock?Feed, water, what else?What animals can microbials work for??How can feeding microbials to livestock increase profitability?What types of things can microbials achieve in livestock?DairyBeefPoultrySwineEquinePetsHow do you go about discovering what is going to work for each animal?Decode the Interactions (what research is done to figure out what works)The Native Microbials Technology Platform transforms the analysis of microbial communities with a unique identification of microbial strains that are the most efficacious for desired mechanisms of commercial, health, environmental, and societal value.Biomass (how do we track the amount needed and not “overdose”)Microbial populations and systems are not static—they are dynamic and constantly responding to changes in their environment. The number of cells in a microbial community can change significantly over time for any multitude of reasons within different microbe Why does this matter?At Native Microbials we have pioneered the incorporation of absolute cell counts into microbial community analysis to measure the overall system more directly and how it shifts in response to random or induced perturbations.Activity Layers (What is really working in these combinations)Although microbial communities are incredibly diverse, only a portion of the community members will be active at any given time. this is done through the activation and deactivation of specific metabolic processes. Delivery (How do we get the microbial to our livestock)Moist feed rations, containing free radicals and endogenous bioburden and feed sanitation practices such as steam pelleting, can all negatively impact viability of a novel microbial solution. Mixing procedures on-farm or in your animals feed can also be a challenge. Native Microbials partners with many farms and industries to understand and incorporate the details of these on-farm challenges into the engineering of our microbial solutions through product formulations, specific and customized administration protocols, and value-added services like mixing studies thus enabling our customers to extract maximum value out of the products What is the best advice you have every been given? SummaryChallenge