Come meet Patrick Hanington and learn about his work in parasitology. We talk about how dPCR is advancing his team’s work in monitoring public and recreational waters for parasites, including schistosomes, which cause swimmer’s itch. You’ll also get some great career advice, funny sample-collection stories, and some unexpected movie references and recommendations.
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.
Jordan Ruggieri 00:00
Invertebrate, invertebrae?
Cassie McCreary 00:02
Invertebrate.
Jordan Ruggieri 00:03
Invertebrate. Okay, invertebrate.
Cassie McCreary 00:06
Invertebrate.
Jordan Ruggieri 00:07
Invertebrate.
Cassie McCreary 00:07
Crushed it.
Jordan Ruggieri 00:20
Welcome to Absolute Gene-ius, a new podcast series from Thermo Fisher Scientific. I'm Jordan Ruggieri.
Cassie McCreary 00:26
And I'm Cassie McCreary. And for today's episode, we scratch our itch for talking all things digital PCR with Patrick Hanington.
Jordan Ruggieri 00:34
Patrick is a professor at the University of Alberta, where he earned his Bachelor of Science and PhD studying invertebrate animals, parasites, and immunology. His work today focuses on schistosome parasites and how they transmit swimmers itch in lake ecosystems.
Cassie McCreary 00:49
So quickly, if you need to get in the mood for this conversation, pause the podcast and go watch Alien, maybe Aliens Next, then The Last of Us.
Jordan Ruggieri 00:58
Go watch it.
Cassie McCreary 00:59
Go watch it, then come back to us, please. Don't leave us.
Jordan Ruggieri 01:06
Patrick, I'm just gonna dive right in. You know, talking about, you know, some of your background here. When it comes to detecting parasites in both public and recreational waters. What does that look like? What exactly do you do in terms of looking for parasites and things in water samples?
Patrick Hanington, PhD 01:25
We work on a group of parasites that are related to human schistosomes, which are parasites that can cause disease in tropical regions of the world. The ones that we work on though, in North America, cause swimmers itch. It looks like a bunch of mosquito bites on you. Can last for like two weeks and is very unpleasant, especially if it happens to young kids. We work on this group of parasites, and they are transmitted by freshwater snails. You have to have a snail to continue the lifecycle of the parasite. And for the ones that cause swimmer’s itch, usually it's waterfowl, that are the other host and the parasite lifecycle. So, we are actually interested in the larval stage of the parasite that comes out of the snail. And that's what causes swimmers itch. It's looking for a bird that's in the ecosystem. And it'll try to penetrate the skin of a bird. And if a swimmer is in the water, they're just sort of like a casualty of the process. Historically, the way that people would look for those parasites are to look at the snails. So they would collect a whole bunch of snails and look to see, you know, what, snails are releasing what parasites. It works, but it's a complicated process, and there's a lot of other parasites that go through those snails. So it's really difficult.
Jordan Ruggieri 02:37
You know, when you're looking at the snails is there, you know, do you look at the actual snail and kind of project, how much potential parasite there might be? Are you just looking to detect the parasite? What does that look like?
Patrick Hanington, PhD 02:48
It's actually a pretty cool process. So, the snail eventually is just hijacked by these parasites. And it becomes a little factory that produces the parasite. And, like, it can be a pretty insane process, like up to 25% of the snail’s biomass can be taken up by the parasite,
Cassie McCreary 03:07
Holy cow.
Patrick Hanington, PhD 03:07
After about a month. Yeah. And then they'll, these like larval stages, they look like microscopic tadpoles. And they, they'll just come out of the snail. Like they come like through the tissues, just like right out of the snail. And there'll be like, thousands of them.
Cassie McCreary 03:23
Yeah, that's really gnarly.
Patrick Hanington, PhD 03:26
You know, one of the things that I, when I teach parasitology to students is I usually use an analogy of the movie Alien. Where like the alien's like bursting out of Ripley's chest. And I've realized that like students nowadays, lots of them have not watched Alien. Like that movie is not on the like, must watch list of students now. And so that that analogy doesn't go anywhere. Like, they're always like, "What is he talking about?" But it's like a perfect analogy for what's happening to these snails because it's like, the parasites are just like tearing through them. I always feel like I need to put a lot of like a required set of moves use for the students to watch before coming to class. So that all of my, all of my stories make sense to them.
Jordan Ruggieri 04:10
Do you make them watch Contagion as well? Is that on the list?
Patrick Hanington, PhD 04:15
I should put that on there.
Jordan Ruggieri 04:17
When I was in virology in college Contagion was the movie that that we were required to watch. So it was that I remember pretty vividly.
Patrick Hanington, PhD 04:27
Yeah, you know, the one that I think it came became before Contagion - Outbreak - and it had like Cuba Gooding Jr. and Dustin Hoffman in it. And that one was like an awesome movie to use as a sort of a reference point for how technically specific a movie could get about scientific procedures because there's this part where they find out that it's like a monkey that's brought this virus into the United States and Cuba Gooding Jr., he's playing a scientist in the show, and he's like, "We've got to get this back to the lab and do an ELISA." And it's like such a specific scientific test that he's talking about. But like, that's the only movie I could think of where they actually ever said "I'm gonna go back and do an ELISA."
Cassie McCreary 05:12
So, I'm relatively ignorant when it comes to like parasites and anything really about it. But like, I mean, you say that these things sort of like burst out of the snails and what but like, what's that really like? Are they harmful to the, I mean, are the snails like exploding or are they like it isn't harmful is not really anything?
Patrick Hanington, PhD 05:28
There is certainly some negative effects on the snail. But when we bring a snail that's infected into our lab, and we have like a whole room that's just for maintaining snails, we can keep them alive for like, for months. Like, they'll live like that and produce parasites like almost every morning. So the parasites coming out of the snail when the sun comes up. And they're positively phototactic. So they'll, they'll rise up to the surface of the water. And they'll just sit there and if they encounter a bird, or a swimmer, for that matter, they'll penetrate through your skin. And it only takes a couple like within a minute, they'll be in your skin, so it doesn't take a long time for them to get in. And then there's a lot of like, you know, if you're working with human parasites, then the parasite will enter the bloodstream and move around and develop into an adult worm and all this kind of stuff. But for the ones that cause swimmers itch, they just get killed in your skin. And then there's this a local sort of inflammatory response. Our goal was really to try to find a better way to evaluate the risk of swimmer’s itch at a recreational water site. That's sort of what got us into this track of applying, I guess, like a recreational water quality monitoring lens that is often used for monitoring for things like enteric bacteria. Using PCR, qPCR, to swimmer’s itch and we were able to, to piggyback off of an existing publication that developed a test that would detect, like all of the species of swimmers itch causing parasite from a water sample. And then what we did as we further validated that test to allow us to quantify those parasites and standardize sample collection. 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 so you, 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 qPCR to now 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.
Jordan Ruggieri 07:58
When you're using PCR for things like this, you know, do you have to have multiple different targets that you're that you're looking at to identify these parasites? Or is it one that's kind of a species conserved region that you're looking at?
Patrick Hanington, PhD 08:11
Yeah, it's, it is a single gene target that we look for. But we're often looking at slightly different regions of that gene for each of the different species of the parasite. So far, that's worked out, okay. And luckily, these parasites are relatively distinct within an aquatic ecosystem compared to like all the other things that are in a water sample. And that's, you know, one of the biggest challenges for us doing this sort of level of environmental microbiology or parasitology, is we have to be really careful that we're not cross reacting with all the other possible organisms that are leaving behind DNA or present in that water sample. So, there's a lot of test validation that has to be done. And we need to have you known quantities. So, we have to have pure specimens of each of the different species that we're trying to detect and all the ones that might cross react. And that's taken a lot of time for us to developing sort of accumulate all that sample material that allows us to go in and develop these tests now. But we have now we have like almost 100 different species of flatworm parasite, like DNA samples. That's really helpful because we can then use those to confirm that we're not going to get false positives or false negatives or things like that on our tests.
Jordan Ruggieri 09:23
Now, ultimately, what are your goals when you're when you're looking at this? It's just to kind of understand and research more of the parasite. Or you know, what, what exactly is kind of that that ultimate goal for your research?
Patrick Hanington, PhD 09:37
Yeah, so well one of them, one of them is just to understand more about the specific swimmer’s itch causing parasites these avian schistosomes. And the reason for that is A, because I think they're interesting parasites but they also, working on those parasites, allows us to make a lot of inferences about the human parasites which we also work on in my lab. From an ecosystem perspective, we can test a lot of hypotheses about environmental factors and different drivers of the abundance of those parasites in an aquatic ecosystem. Where we can test that using swimmers itch causing parasites, which are much lower consequence, and a lot easier to design experiments on than human causing, human disease-causing parasites, which you know, you have to go to a tropical area to research and they cause human infection. So, so it's a nice system to test hypotheses about how these parasites behave in an aquatic ecosystem. And then I think, more broadly, at a sort of a bigger picture level, it's really emerging that we're able to use these parasites more broadly, not just the schistosomes, but all the flatworm parasites that are in a sample as an indication of aquatic ecosystem biodiversity. So, we can, like I was saying, we can predict the birds that are present, and we can predict the mammals that are present. And often, some of those parasites are going through aquatic invertebrates. And so, as we piece together all of the species that we have in our aquatic environments, then we can use something like eDNA meta-barcoding to create a parasite profile for that aquatic ecosystem, and then predict what the aquatic ecosystem biodiversity is. And it's, it's a way of unifying around a single sort of sampling strategy. But you get this huge, comprehensive profile.
Cassie McCreary 11:27
Something like, say you had like some sort of invasive species come in or something like that, would that like greatly shift the meta-barcoding and everything like, I'm assuming these things would change over time, depending on how the ecosystem itself will change. Yeah?
Patrick Hanington, PhD 11:39
Yeah. And that's actually like, it's, we just got a grant from one of our provincial funding organizations to look at exactly that question about how invasive species, aquatic invasive species, influence the sort of aquatic ecosystem broadly. And so, it relies on eDNA meta-barcoding. And we compare it actually to digital PCR assessments of the presence or absence of those aquatic invasive species. And so we kind of are comparing the very high sensitivity, high specificity of digital PCR assessment to what is probably slightly lower sensitivity and specificity of meta-barcoding, just because you have some organisms are going to be very abundant in an aquatic ecosystem eDNA sample and you might lose that signal from what is a rare invasive species. For like an early detection type of an approach it could be a really powerful tool, especially I think, the digital PCR if you have the right information, and you can continue to survey for those organisms using digital PCR. I think it's a really exciting tool.
Jordan Ruggieri 12:44
I was just gonna say it is the perfect segue. Patrick, I know, you know, we are big digital PCR fans here at Absolute Gene-ius. Can you kind of elaborate a little more how you utilize digital PCR in your workflow?
Patrick Hanington, PhD 12:56
Like I mentioned earlier, you know, we have a lot of experience using qPCR, quantitative polymerase chain reaction. And it was just a few years ago, now that we, we realized, you know, the, some of the limitations of using qPCR in an environmental context. A lot 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. They, I don't want to like I don't want to bash them too badly.
Jordan Ruggieri 13:38
Why even for clear water, I can imagine you get you get mud, you get sediment, you get plants, you get, you know, lots of stuff in there?
Cassie McCreary 13:46
I'm from New Jersey, our beaches are the definition of gunky like.
Patrick Hanington, PhD 13:53
Well, we have cyanobacterial blooms, like blue green algae blooms in every one of our central Alberta lakes. We're always wrestling with PCR inhibitors, cyanobacteria. And you know, we can do cleanup procedures of the DNA when we do the DNA extraction, we can try to clean that sample up a little bit. And often those work pretty well to get rid of inhibitors, but it doesn't take much to impact the qPCR reaction. And digital PCR, one of the big advantages, from our perspective anyways, is that it does a much better job of minimizing the impact of inhibitors on your reaction. That is the number one big advantage for us in the environmental space, I think. And then the other is that we've actually found that it's a little bit easier to multiplex than the qPCR reactions are. So, that's become really advantageous for this invasive species work that we're doing. This idea that we can create these customized digital PCR panels for particular invasive species groups, and just run a single digital PCR plate to assess for all four of them is really, it's really exciting.
Jordan Ruggieri 15:02
What benefits does digital PCR allow in that in that multiplexing area?
Patrick Hanington, PhD 15:06
Related to that question, one of the really big advantages that we find with the Absolute Q system is that we can use a qPCR assay on the Absolute Q system. So, we can do a lot of the sort of traditional validation steps for, you know, the assay performance and all that kind of stuff. And then we move it on to the Absolute Q system, and it works fine. In terms of multiplexing, we always struggle A, with the presence or absence of inhibitors, but then B, like part of the part of our challenge sometimes is that we're, we'll be working with assays that that can be, you know, depending on the fluorophore, depending on what we're amplifying can cause challenges when we multiplex. And so we've, we've often defaulted to just always running a single fluorophore assay with the qPCR. It's not that we can't multiplex on the qPCR platforms. But there's a lot more that we have to do in terms of compensation and figuring out exactly, you know, how the two different assays performed with each other. The thing that we found with the Absolute Q was that that's essentially set up so that the three, three of the fluorophores for sure are like very distinct, and then the fourth one is usually like also pretty good. And so we find that it's a lot easier to just run those four and we can, we can confirm that there's no bleed over a lot easier with that software. So, it's just a very simple multiplexing platform. And because of the simplicity of the way that the system works, generally, it's just really easy for us to just load it up and run the samples with four different fluorophores in there and then get the data we need from all four. With the qPCR, we often found that we had to, we had to work on optimizing enzyme amount versus DNA that we loaded into the reaction, versus the presence of like all the different components of the reaction, and Absolute Q system just works a lot easier to do that multiplexing. Like we've played around with how much DNA we load versus water versus enzyme and all that stuff, and we basically found that like, the amount that it says to use is just the right amount to use. So, it's a lot it's a lot easier that way. And that's like that's helpful just because often within our lab we're you know, it's it's MSc students or PhD students or sometimes even undergrad students that are working on this stuff. And it's helpful just to know that you can multiplex with these four things and often that you're going to be okay, and that it's really easy for them to go in and know whether or not there's a problem rather than having to have like all that technical background of understanding how it works, the qPCR system, part of it is that it's a lot easier.
Cassie McCreary 17:47
Taking a quick break from our conversation to tell you about Applied Biosystems™ QuantStudio™ Absolute Q™ dPCR system. This instrument enables quantification of your targets without the need for standard curves in only 90 minutes. Digital PCR can be as simple as preparing your samples, loading onto the plate, and running the instrument.
Jordan Ruggieri 18:07
Unlike other digital PCR systems, the Absolute Q dPCR instrument does not use emulsion or other droplet-based methods to compartmentalize reactions. In fact, the microfluidic array plate (MAP) technology enables consistent delivery of more than 20,000 micro-chambers. It's a great solution for anyone looking to quantify gene.
Cassie McCreary 18:28
And Thermo Fisher Scientific has a suite of dPCR assays for applications like AAV viral titer quantification, liquid biopsy analysis, and wastewater surveillance. You can learn more at www.thermofisher.com/absoluteq or visit the Absolute Gene-ius webpage. Again, that's www.thermofisher.com/absoluteq or visit the Absolute Gene-ius webpage.
Jordan Ruggieri 18:55
The Applied Biosystems™ QuantStudio™ Absolute Q™ dPCR system is for Research Use Only. Not for use in diagnostic procedures. Let's get back to our conversation.
Cassie McCreary 19:08
It's clear that like, you're very passionate about this stuff, you care a lot about this stuff. But is this, I mean, has it always been like what you wanted to do? Is this the route that you thought your career would take? Like has it always been parasites and water quality and like the environment and swimmer’s itch.
Patrick Hanington, PhD 19:24
That's a funny question. Like when I, if you were to ask me that at the end of my undergraduate degree, I had no idea what I was gonna do. And it was really, it was really just, I took a fourth-year parasitology course I really enjoyed it. The instructor for that course ended up being my PhD advisor. And I actually I started in that lab wanting to do parasitology. But the guy was working for was like, “No, I think you're gonna work on immunology instead.” So I did a PhD on fish immunology. But then yeah, then I, I was faced with a decision of like, what I wanted to do after like my PhD. And I really wanted to get back into the parasite stuff that was kind of what initially attracted me to going into research in the first place. And then I didn't mind doing the immunology part, but I really wanted to get back into parasitology. And so I actually merged the two things together. So I, I worked on snail immunology to the human schistosome. And so I moved to New Mexico. And I was there for about three years and worked on snail immunology to human schistosome infections. And we still, I still actually do work on that now as a dimension to the research that I do in the lab. Yeah, then I just started applying for jobs. And I actually thought that the University of Alberta, which is where I had done my undergraduate degree and my PhD, I thought for sure, like, that was gonna be a no go, because I had been there for so long. And I was like, there's no way they're gonna offer me a job to come back there. I thought, you know, this idea of getting diverse experiences and stuff like that would prevail. But the School of Public Health offered me a position and so I came in started up a lab. And then then the rest of it really just came as I thought about, what is it that I actually know how to do?
Cassie McCreary 21:12
Something, and this isn't necessarily career related, but it's something that's been like it's weighing on me, based on our conversation. With all of your years of like, this research that you've done with, like having to collect water and things like that, what is the most interesting, or maybe the strangest location that you've had to collect water from?
Patrick Hanington, PhD 21:31
I think like, when I go collecting myself, my most interesting collecting experience was actually really close to Edmonton. They are actually having a swimmer’s issue, which is rare like that we would go out to that here in Alberta. It's actually like a lot of our swimmer’s itch work is in Michigan. And in Alberta, it's like, it doesn't come up that often. And so this lake that had a private beach out of there, they called, and they asked if I would come up just sample to confirm whether or not they had swimmer’s itch or not. And normally, my default answer is like just, “Yes, you do have swimmer’s itch. So you don't need me to go out and tell you that.” But I was like, “Well, it'd be good to like go and check in stuff.” So I went and I sampled the beach. And normally the snails are living in like the vegetation off to the sides of the beach. So, I was just like, okay, I'll just go check out those things. And there was all these, like red wing blackbirds that were nesting in the vegetation. So I realized I was kind of in a midst like a whole bunch of nests, and they just like dive bomb at me. And so I realized there wasn't welcome there really quickly. So I was like, well, I'll just leave and there's this other pond that was behind the main lake. And the people who had asked me to come, they said, oh, well, we know a lot of the birds are over there. So, I thought maybe there'd be a lot more infected snails over there. So, I went in and like I said earlier, our lakes here are not the nicest lakes. So the shoreline is often pretty muddy and like it's like a lot of it is like decayed vegetation and stuff so it's really can get pretty stinky when you like first go in and so we have to wear waders and all this stuff to go collecting. So, I went in and like I took two steps and then like just sank like three feet into the mud. And I was like, “Oh man, this isn't going to be good.” And so I was trying to like wiggle like myself to free myself from the mud. And I was like, well, like I didn't want to call for help. But I was like, “I'm not gonna get out of this without getting dirty.” And the more I wiggled I realized like I probably should have like applied some of my movie knowledge that I was mentioning earlier to my situation because like, I like that's not how you should get out of quicksand and that's what I was doing. And I was like, “This is not getting any better, because I just kept on going further down.” And I was like, I'm gonna have bail on the waders and just kind of like, like mudskipper along the shore to get out. So I just like had to, I had to unclip the waders, and I just like, extracted myself out, and just pulled myself along with the vegetation and just, like, pulled myself along the mud to the shore, and just left them there. So the waders are still they're still in the water, they're like, there buried there. Eventually I get to the car and like, got in, and I drove just like out of the area, and then just like, pulled off to the side of the highway. And then like, my phone was luckily okay. And I just emailed them back and just said, like, “Sorry, I had to go really quick, but I'll do it. I'll analyze your samples, and it'll be fine. Like, don't worry about it.” I was like, phew.
Cassie McCreary 24:39
We just we just took a journey there. So has your love of some of this stuff, like spilled over into like, your personal life, or like hobbies that you do. So with, like, the swimmer’s itch thing, are you a swimmer? Or you know,
Patrick Hanington, PhD 24:52
I mean, I love going to lakes, and, and doing stuff there. But it's, it's like, it's funny, because my daughter who's six years old, she knows that snails are my favorite animal. And so she loves to go to the lakes and like collect snails and like, grab and look at them and stuff like that. So she's always like, “I found a snail I found a snail.” It's like a little shell and stuff like that. So, so yeah, it's definitely spilled over into, like, into what we do. And, and yeah, so I always just enjoy if I go, I don't swim, but I'll like wander along the shoreline and just like pick stuff up and look at what's there. Investigate things. So yeah, it's fun. It's like it's a good, it's a good way to keep your curiosity high.
Cassie McCreary 25:33
We were talking about Contagion and things like that earlier on and like so do you enjoy picking out like fallacies in like, films that have to do science or anything like that?
Patrick Hanington, PhD 25:43
I sometimes, it's like, a little bit disappointing because I feel like sometimes the movie gives you like a bit of a false impression of how, how science works. And I don't feel like it, they need to. Like I feel like science is can be pretty cool on its own if you just are honest about it. You know, I always enjoy watching like the BBC documentaries with David Attenborough and stuff like that. And those are always super impressive. Like just to see the natural world and its existence. And I feel like right now is there's more and more of those that are focusing on the organisms like that I like better. There's never those their shows are never about the parasites. They're never about the little worms that live in the gunky mud and stuff like that. But I feel like there's more of those coming around now and I feel like that's, that's kind of cool. Like, I don't expect there to ever be like a blockbuster movie about that stuff. But I mean, you know, right now we're like in the thrall of Last of Us. And now, like I was just on Twitter a couple days ago and Cordyceps was one of the trending things that people were looking for. And I was like, I never thought I would see the day, that Cordyceps fungus would be one of the things trending on Twitter. So you know, that's pretty cool. And those mind-altering parasites are like, they're really awesome. They're not quite the same as Cordyceps. But but you know, there's lots of parasites that we have here in North America that do really cool stuff like that, to that changing the behavior of the host and all that kind of thing, which are really, it's really cool.
Cassie McCreary 27:09
We've talked about the waders you left behind. We talked about getting dive bombed by birds. I want to know in the lab, what is your biggest oops, moment, and also maybe your best lab moment.
Patrick Hanington, PhD 27:21
The oops that I always tell my own students is actually way back from when I first started working in the lab, I did my PhD in. I had just started, and I was actually my project that I did as an undergraduate summer student was just to do PCR. Like endpoint PCR screening of, at the time what was a macro array library. So like, that's a whole other thing about what those even are now. But this macroarray library I was screening I would run the PCRs on like in a 96-well PCR machine. And each of them would be a separate tube, though. So, we didn't have like the 96-well plates for running into machine we had individual tubes, 96 individual tubes, and then I'd have to run them out on this huge agarose gel that held 120 different samples. So, it was like this like massive undertaking to do that stuff and I made two oopses, but one of them is the story that's more appropriate to tell. And so the first oops was like the person who was working under, he and the rest of the lab, they all went on a conference. So I got like, maybe a couple days of training, and then they were like, “Okay, just like, just keep doing this, just do this.” And so I said, “Sure. Okay.” So I did that. And then I got to the point where I had to load the gel, and I loaded the loading buffer into each of the different tubes, and then loaded it all. And then I went and took a picture. And the picture was just like, like hundreds of bands in every lane, everything was like a total look like a total mess. And I was like, I don't know what's going on. And so I ran it again and did it all over again. And then finally, I had to email the guy, the student that I, the grad student I was paired with, and I was like, “I've run out of the loading buffer.” And he was like, “How did you run out of the loading buffer.” And the TLDR of this, as it turns out, I was using like the ladder for the like, the DNA gels as the loading buffer. So, every one of my samples was just like, all loading buffer ladder. And so there was like, 240 samples that just like we couldn't use that of the entire macro array, because they, we’d used up the entire thing. Like the phage that had been picked. I amplified it all, like ran the entire thing out, I supposed to cut out each of those bands so that we can sequence them and stuff like that, and all gone because I couldn't figure out what the band was. Like I was trying to try to look and like, see if I could figure out like which one it was in the ladder. But it didn't work. And so I use that as like an example for my own students now that like, you know, I learned my lesson. So I was like, I made a mistake. But I never did that again. So like, it's okay to make mistakes, but just don't do them multiple times in a row.
Cassie McCreary 30:00
Either inside or outside of the lab, then what is your, your best moment or your proudest moment in your career?
Patrick Hanington, PhD 30:07
Yeah, I guess like inside the lab, it's that it's tough. Like, if I think about it, personally, the answer would be very different than if I think about it at a career level. Because I think at the career level, I got given a piece of advice when I started my position back at the University in the School of Public Health. And that was that, like, “You have to stop thinking about your own contributions as your metric of success, once you become a PI, and that it's really your student’s contributions are really what you're going to, that's your legacy.” Now, it's just facilitating others at being successful. And I think that, I think that's like, maybe the part where I'm most proud, is really, in all the success of this, that the students and trainees I've had, are getting. You know, when a student graduates or you see somebody, like, overcome some problem that like I, I can only maybe partly help solve, and then they, they go through it and figure it out. And, and then you get a paper on that, or they defend their thesis. Like, all that stuff is really, it's all it's all awesome. And it's like, it's the main reason that I really enjoy the job is just like, you get to interact with these, like really enthusiastic, you know, curious people who are asking questions that I think are cool, but they're answering them in ways that I would have never come up with. Like, I can help guide some of that process. But it's really exciting just to say, like, see how they decide to tackle problems.
Cassie McCreary 31:30
A lot of our listeners, or at least we're hoping a lot of our listeners, are people who are maybe a little bit earlier in their career, and they're actively at the bench, and they're working everything else. Or even people who are just considering going the route of science and research and everything. What would be your biggest piece of advice for them? Or even if you could go back and give yourself like your younger self, like a piece of advice when you were just starting like down this path?
Patrick Hanington, PhD 31:50
Yeah, I think that one of the things that I mentioned earlier, maybe relates to this, which is this idea that I have my research passion, and that I think, is what keeps me really excited about things and always engaged. And I mean, you know, I feel like an academic career, it has like, tons of really awesome advantages, like, the flexibility and all that stuff. But you're also kind of like a, your own driver of stress. So you know, like, I decide I need to apply for this grant, I decide I need to do this. And, and so you, you kind of are always feeling like you have to do the next thing because if you don't, then the whole thing falls apart. But I think it was it was really when I realized that it was it was the skill set that I had learned, sort of the methodological skill set, that was really what I could use to ask the questions that I thought were exciting and move into spaces that I, you know, hadn't traditionally thought of myself as being part of. Like water microbiology, and, you know, that's gotten us into this, this, like conservation ecology stuff and invasive species work. That I that isn't my area of expertise from my background, but the methods that I know how to design digital PCR assays or qPCR assays or do meta-barcoding. Those allow me to think of creative ways to enter into those spaces and ask questions that I think are exciting and cool. And learn about some of the stuff that I think is sort of my foundation of what got me here in the first place. And so, I don't know if it's like really advice, but I think that it's like “Don't, don't be afraid to think of your of your real skill set as being that methodological foundation and use that to explore interesting things.” I feel like sometimes people are afraid to apply for something that they like, why did you know maybe in my example, “I did fish immunology, so I can't do invasive species work and digital PCR analysis.” But you can, you know how to do all those things. It's just, you just have to, you know, get yourself into that headspace to be able to think of a creative question to ask in that area.
Cassie McCreary 35:26
And I think you said something that I really, really liked too, which is, just don't be afraid to ask the questions that interest you. Like, it's, it's okay to ask things that might seem a little, I don't know, out there or out of the box or something to somebody else that you're talking to, but chances are, they might be able to give you an answer that you really like, or you really need to know, and you can apply it in one way or another. So I think that's, I think people can be a little, like gun shy about that are like afraid of looking silly, if they're going to ask something and they don't know. And so I think I think it's, that's good advice.
Patrick Hanington, PhD 34:28
I would also say that one of the things has been almost as rewarding as sort of the publishing of papers and, you know, like, the sort of traditional academic milestones that happen as you go along is, has been engaging more with the public. People want to know more science, and they want to know how science works, and how you ask questions and science and stuff. But often, I feel like the language barrier is really sometimes challenging to talk to people who have no idea what it is you're talking about and try to get it across to them. And, like, as a good example, just this last weekend, I was, I was in the mountains here at Alberta at a thing for high school students talking to them about PCR, and trying to communicate to them like they we want them through extracting DNA. So, we got the group of 30 students to extract DNA from a water sample. And so it's like, you got to put yourself in the headspace of somebody who maybe knows a bit about DNA, but maybe isn't that interested in that right now. So you want to get them excited, tell them about like, why it's cool. But then have them be able to technically do it and understand, you know, what each step was really all about. And doing that I think is really rewarding when you can talk to somebody who you know, does not know why you would do digital PCR over qPCR or what even what digital PCR is, and leave that room after 20 minutes and say like, I think that they kind of get it.
Cassie McCreary 35:55
That was Patrick Hannington, Professor in the School of Public Health at the University of Alberta. Thank you so much for joining us for today's episode of Absolute Gene-ius. Stay curious, and we'll see you next time.
Jordan Ruggieri 36:07
Did I say schistosome correctly?
Cassie McCreary 36:10
I have no idea.
Jordan Ruggieri 36:12
See this is a YouTube video. Schistosome. No, that's not right.