In this Season 2 recap our hosts revisit some highlights, from using dPCR for low-cost screening in single-cell sequencing to mRNA quantification breakthroughs. They reflect on guest insights, the complementary roles of dPCR and qPCR, and their growing synergy in molecular workflows. Join the team as they celebrate another successful season and add primers for the upcoming Season 3.
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.
Jordan Ruggieri00:12
Welcome to Absolute Gene-ius, a Thermo Fisher Scientific podcast series. I'm one of your hosts. Jordan Ruggieri, here with my co-host, Christina Bowens.
Christina Bouwens 00:20
Thanks, Jordan, and welcome listeners. Today, we want to button up season two of the series and quickly revisit some of the topics that we covered. And I have to tell you, Jordan, I was a little bit nervous jumping in mid-season as a co-host, but I really think I've settled in, and I've really been enjoying co-hosting this with you.
Jordan Ruggieri00:35
I don't even believe that based on how much I've seen you talk publicly prior to this. Super surprised, but what was it that had you nervous?
Christina Bouwens 00:45
Just in general, getting started with podcasts can feel kind of daunting. But you know, you and the team, and honestly, the guests who all join really fresh themselves, make it super easy to relax and just talk science, which is honestly what I really love talking about.
Jordan Ruggieri00:57
I'm really glad to hear that. I'm glad you've settled and found a place that really feels like home. And since we've wrapped up season two, and you've been part of more than half of our episodes, it seems like a really good time to talk about the topics we've covered and some of our takeaways. I'm curious, Christina, what was your favorite interview or episode so far, and why?
Christina Bouwens 01:16
It is so hard to pick, especially from the ones that I've been on. I feel like all of them have been such great conversations, but one of them that I really enjoyed and keep going back to, is Parker Wilson. I think it was episode eleven. I thought it was really clever how he was using dPCR’s sensitivity and specificity to do some low-cost screening as a precursor to single cell sequencing, which is kind of a new technique that I hadn't really considered before his conversation.
Jordan Ruggieri01:40
That was a really good one. Let's actually listen to a clip from that conversation.
Parker Wilson, MD PhD 01:44
We're interested in developing an assay to develop loss of X chromosome in the kidney or the blood or other tissues and animal models. So, if we know that loss of X chromosome happens much less frequently than loss of Y chromosome, are we looking for samples that have 1% or less? Is it possible to find that by digital PCR is a is a question that we're interested in pursuing. We think we can see it by single cell sequencing, but we want to push the boundaries with the digital PCR, because then you could use digital PCR as a quick, low-cost, very effective assay to screen tissues or disease models, and then you could move on to a more expensive assay if you wanted to really dive deeper.
Christina Bouwens 02:25
Yeah, exactly. That's such cool work, and it's really refreshing to hear someone talk about dPCR as the low-cost screening option. One of the other conversations that really did stand out to me was in episode nine, we had a conversation with Christian Cobaugh from Vernal Biosciences. mRNA is beginning to emerge, you know, as a really prominent drug modality, and I enjoyed hearing how they're using digital PCR to quantify complete and active mRNA materials from incomplete or truncated synthesis products. I think we can hear a little bit more about that conversation here.
Christian Cobaugh, PhD 02:56
We're very excited about using dPCR to quantify the active mRNA. One of the issues with RNA synthesis is you get a lot of truncation products. It could, may only be may only be 5% could only be 10% and for a lot of folks that's considered a success, but the current analytical methods don't do a great job sorting those out as separate from the main product. If we design dPCR assays to land on the right spot of the mRNA, we get a lot closer to the truth in terms of what is the active material. This is not something you're going to find in the USP, and I'm not sure you're going to find any other company that's doing this. And so, we're super excited about that because, I mean, we've got, again, some orthogonal data, including sequencing data, that's showing us that we're heading in the right direction. We still need to move this into a qualified environment. But you know, this is very differentiated, and honestly, I'm not sure of any other technology that can be that accurate in its ability to evaluate the active component of your DS (drug substance) in mRNA medicine.
Jordan Ruggieri04:22
Yeah, I agree, Christina. Christian was a really fun guest to talk with. I also remember him talking about how they started with only digital PCR in their lab but have since added qPCR into the mix too. He actually noted that they do a good bit of their assay development on both platforms and how they complement each other nicely.
Christina Bouwens 04:41
That's a really great point. In fact, it's one of the things I've been most impressed with talking to all the guests we've had on this season. As users of dPCR, they understand that dPCR has a lot of great advantages, but they also still utilize other tools like qPCR for their strengths as well. It seems to be like they're all really using all the tools at their disposal.
Jordan Ruggieri 04:59
I agree, Christina. This season, we heard from a lot of guests about how they use more than one technology in their toolbox. And to me, it makes a lot of sense, I suppose. I mean, the method section of a paper is rarely just a few sentences and one technology, after all.
Christina Bouwens 05:15
Let's check out another clip that stands out for really exactly this reason. This one comes from episode two, in the conversation that we had with Dr. Raquel Munoz, talking about the diversity of methods that she and her team use in their work understanding CAR-T cell therapies.
Jordan Ruggieri05:31
We talked a lot about digital PCR and even qPCR. Do you use any other methods, any cell culturing or next generation sequencing, or what a day, what does a day in the lab look like for you?
Raquel Munoz, PhD 05:46
Yeah, it depends on the area. For example, in histocompatibility, we use a lot of molecular biology, like NGS. In autoimmunity, we use more cell culture and IFF, it's the acronym of immunofluorescence, in direct immunofluorescence, and in immunodeficiency, we use a lot of flow cytometry.
Jordan Ruggieri06:19
Christina, I have to ask, are you ever going to ask about my favorite episode of the season?
Christina Bouwens 06:27
Okay, sure, Jordan. What’s has your favorite interview of the season been? Or, really, I guess, the entire series.
Jordan Ruggieri06:33
You know, even after making you ask me that question, I don't know if I can pick a favorite interview or episode if I'm being honest. For me, it's really about how our guests routinely understand and concisely summarize just how dPCR fits in relative to other technologies like qPCR. With dPCR being a relatively newer technology to the scene, I still find that a lot of scientists don't quite know how it fits in their toolbox or how it can be used to answer questions they're trying to research.
Christina Bouwens 07:04
Nicely avoided question, Jordan, but I totally agree with you. You know, something that we find outside of the podcast, especially to people who are new to dPCR is they're always looking for a reason to use one technology or the other, and all of our guests have a ton of experience in dPCR, but you know, it didn't always start that way. They've built it into their workflows. So, I really love to see how each of them really use multiple technologies like qPCR and dPCR to complement each other to really complete their, you know, their research goals.
Jordan Ruggieri07:33
Exactly. I mean, we can go all the way back to season one, episode three, with Patrick Hannington, who I think of as the “swimmer's itch and parasite guy.” Let's dig up some clips from that conversation where he talks about qPCR and dPCR for environmental monitoring.
Patrick Hanington, PhD 07:49
So when we go out and sample now, what we do is we use a 20-micron zooplankton collecting net. So it's like a, like a, you know, maybe like, three foot long mesh net with a cup at the bottom and see we pour a set volume of water through that, and then it all collects into this bottom cup that we can then pass through a smaller filter that concentrates everything that was in that water sample onto a little filter disk that we can extract DNA from. Then we just run, we would run a qPCR to analyze that sample and quantify the number of parasites. What we've tried to do is evolve from the test that just allows us to quantify all the swimmer’s itch causing parasites to get down to the level of species identification using PCR. Like I mentioned earlier, you know, we have a lot of experience using qPCR, quantitative polymerase chain reaction and it was a just a few years ago now that we realized, you know, that some of the limitations of using qPCR in an environmental context. Alot of them have been addressed by digital PCR. The big one that we often struggle with is PCR inhibitors in a sample, because we're often working with either water samples. And I mean, you guys probably haven't been to Alberta before, but the lakes here are pretty gunky. I don't want to, like, I don't want to bash them too badly.
Christina Bouwens 09:16
That one was before my time, but I do remember it, and it's one that I actually bring up often. I thought it was such a great conversation about both of those technologies. Another episode that was before my time, but from a guest we had on again this season was from Dave Bauer, where he brought up some really good points on when and why to use dPCR. And I think that was in season one.
Dave Bauer, PhD09:35
Yeah, I think if I had to kind of give like an elevator pitch for digital PCR, there'd be a couple bullet points. One, of course, is quantification, absolute quantification. If you want to know the concentration of a target, digital PCR is the gold standard. Real time PCR can do it, we can talk about some of the nuances there, but absolute quantification is a critical value for digital PCR. Another one is precision. We talked about before, you get better precision with digital PCR, generally than you would with real time PCR. Also, if you have a really low concentration, if you want to quantify at the lower end of concentrations, digital PCR usually is going to outperform real time PCR. And finally, another point I like to make on it is looking for rare targets that are kind of in a sea of wild type, or a sea of sequences that are really similar. In that case, digital PCR can often get better resolution than real time PCR would.
Jordan Ruggieri10:33
Yeah, it is always a pleasure talking with Dave and a really nice, concise summary from him there. Christina, I want to come back to the idea of wrapping up season two together. It's been a real pleasure co-hosting with you. I really appreciate the digital PCR experience and expertise you bring to the table in our conversations. I'm just really grateful and thankful for you joining the series.
Christina Bouwens 10:55
Thanks, Jordan. I so appreciate being a part of this. I think this has also been one of the most fun projects that we've worked on this year. So I'm really excited to continue doing more of this next season and to interview a lot more guests. But you know, we're not quite there yet, so as our newest team member, I'll take care of a couple housekeeping items.
I think it's really important that we thank our listeners, because both you and I know that without them, we don't get to do this. So thank you to our loyal listeners, and we welcome any new listeners too. We really do appreciate you tuning in this season, and we hope you enjoyed it and got as much out of it as we did. If you are, in fact, enjoying the series, there are a couple of things I'll be so bold as to ask you to consider doing for us. First, if you're not already subscribed, please subscribe. This helps us and ensures that new content is downloaded and ready for your ears as soon as we drop it. The second thing we ask you to consider doing is either to provide feedback or to share the series with a friend or colleague. We're always eager to hear from you, so a rating or feedback is always welcome in whatever platform you listen on. As far as sharing the series goes, we know that a personal referral is the best compliment that can be shared. If you know someone considering dPCR or working in an application where you know digital PCR would be beneficial. We hope you share the series with them.
Jordan Ruggieri12:07
All great points, Christina, thanks for covering all of those. With that. Let's officially button up and close the door on season two of Absolute Gene-ius. One might even say we've reached the last cycle for this season but stay tuned for a whole new run coming soon. Oh man, I love our puns. On behalf of all of us at Absolute Gene-ius, thanks for listening, and stay tuned for more info on season three, coming soon. Until then, stay curious. Absolute Gene-ius is produced by Matt Ferris, Sarah Briganti and Matthew Stock.
Jordan Ruggieri12:41
One might even say our season has amplified all the way to the end but stay tuned as we prepare to analyze new genes next season.
Christina Bouwens 12:49
I thought that was gonna say, analyze new gene-iuses. And I was like, "Ooh."