This interview first appeared as an episode of the Science Positive podcast. You can check it out here on Youtube or here on Spotify!
Emma: Welcome to Science Positive, or SciPos for short. My name is Emma Guerrini-Romano, and I’ll be your host for today. Today, I’m joined by the wonderful Tori Armitage. Thank you for joining us.
Tori: Thank you for having me. This is a lovely setup.
Emma: Yeah, well, I’m so glad you’re here. OK, cool. So the setup for today, we’re going to talk a little bit about how you got into science to start. So Tori, tell us a little bit about your experience in science in your childhood, and how you got into doing science in your undergrad, and what that path was kind of like for you.
Tori: OK, I mean, I guess very broadly, I spent a lot of time outside when I was younger, because I grew up in a very rural area. So a lot of observing animals, if you count that broadly as science, and catching things, like terrorizing garter snakes. I don’t know why I felt so compelled to catch animals, too, it was not just enough to look at them. But I think going into undergrad, I was like, OK, I’m either going to major in biology or chemistry, because that’s what I’m interested in, but I had very little vision beyond that. And then I think they had this cool little thing at my undergrad, where some of the faculty gave lectures to the incoming freshmen on what research they were doing. And the professor that I ended up working with was giving this lecture on more like ecology and evolutionary biology in the hourglass tree frog. So I was like, OK, well, I’m more interested in molecular stuff, I’ll just go, because, you know, frogs, and there was nothing else that was more interesting at the time. So I had not that much intentionality to it. But then he was giving this lecture, and at the end, he was talking about this project that was looking at the gene expression patterns that underlie, it’s called predator-induced plasticity in these tadpoles, it’s really cool. And I just liked how you could connect something, like organism level, with something molecular. And I was like, OK, I guess I’ll see if I can get involved in that, and sent a very awkward email being like, hi, could I maybe, possibly, please join your lab? And then I think that was a pretty important experience, because it was a very non-intimidating environment. And it was like– I think that was kind of– there was a bunch of domino effects from that, like doing an REU and all that stuff.
Emma: Yeah, awesome. And just for people who might not know, what is plasticity?
Tori: OK, plasticity is a super broad term, but in the context of the hourglass tree frog, I don’t think they’re the only tree frog that does this, but their tadpoles have predator-induced morphological plasticity. So specifically, there’s two common predators in their environment. This is a very specific situation in which it would develop. So there’s two common predators that kind of demand opposite morphology. You have dragonfly larvae, which the most advantageous morphology for that is to have a really big red tail spot, because the dragonfly larvae–you can see this if you watch them hunt–they have really bad eyesight. And so if they see a large red spot, they’ll go for that, and they’ll miss the body of the tadpole. Versus the fish, it’s best to have a pretty invisible tail and just be able to get away as fast as you possibly can. So plasticity in this context refers to the fact that if the tadpoles encounter a certain chemical cue from the dragonfly larvae, they’ll develop those large red tails, because that’s advantageous, versus if they encounter a different chemical cue from the fish, they’ll develop the morphology that works best for that. And you can see it happening, which is so cool. If you put them in with the predator and the predator’s eating, which is a really interesting little detail that the predator has to actually be eating so probably the chemical cue comes from the predator actually consuming tadpoles. It’s not just the presence of the predator. But if you put them in there for a couple weeks, you can see it as early as three to five days.
Emma: Wow, that’s fascinating. So this was your undergraduate research, right? And you mentioned an REU briefly. Can you explain a little bit about what an REU is? When did you do that? And how did that kind of set you up for post-grad life?
Tori: Yes. Oh my gosh. I would promote REUs until the end of time. It was such a positive experience. So an REU is federally funded undergrad research, where they will not only pay you to do research as an undergrad, but usually they provide room and board, and you get a cool little cohort of people. They are pretty selective, I think I applied to 10 or 11 of them, but it’s good practice for the application process. But yeah, I applied to 10 or 11, got into one that was in Idaho, of all places, which Idaho is actually a very beautiful state so it was nice to be there in the summer. And yeah, basically, that was also a good experience. I think it’s especially good if you’re at a primarily undergraduate institution, because for my undergrad research, I was never around grad students. And then for the REU, it’s at a larger university. And so I was mentored by a grad student and actually did more of a dry lab project. They always make sure it’s projects that you can fit in into eight to 10 weeks. And so I learned how to analyze transcriptome data in R, which was really good practice. And yeah, it was also a good chance to get a project other than my primary undergrad project, which when I was interviewing here, I was kind of relieved that I had more than one undergrad project to talk about, because I feel like there’s only so much you can say about your main undergrad research. So yeah, it was a very useful experience.
Emma: That’s awesome. And then so after your undergraduate work, I know that you worked in the industry for about a year. Is that right?
Tori: I think it was two years.
Emma: Two years. OK. So how did you make the decision to start working in industry? And what in the industry sparked you to now then pursue graduate school?
Tori: So I feel like I was more or less planning on grad school, but also the advice that I got from literally everybody was, if you don’t feel strongly about going right away, don’t go right away. And I was kind of tired after undergrad and also had student loans to pay. So I was like, OK, I’m going to work. And I think originally I wasn’t set on it being industry. I think it was good that it was, because I feel like my other goal with working after undergrad was to get a sense of the different options out there before going into grad school, because I feel like people obviously always tell you once you’re in grad school that you need to gear what you’re doing towards your plans afterward. But I was like, I think I want to go into industry afterwards, but I don’t want to make that huge decision without trying it out first. So yeah, I applied to a whole bunch of different companies. And I ended up getting one that was my first choice just based on the research and also the benefits. We love health insurance and paid time off. But yeah, so that’s how I ended up– it was called Singular Genomics. It’s a midsize company, which I feel like that was another good piece of advice that I got for working in industry. There’s a whole bunch of options all the way from a startup with 20 people to these companies, like, I don’t know, like Sigma that have thousands and thousands of employees. And I feel like I had heard, OK, midsize is good, because you’re not going to be expected to do everything. But also, at a really large company, you’re going to have such a niche role that you might not learn as much, or there’s a higher chance that you won’t really enjoy the thing that you’re being asked to do all day, every day. So I think it was a good balance of those two things, because I feel like, especially straight out of undergrad, I don’t know if all startups are exactly like this, but I don’t think I would have done well in an environment where somebody was just like, OK, take care of all of this stuff. I did not have the lab skills necessary for that, so I think it was good that it was kind of a midsize company.
Emma: Yeah, so you had support and some sort of freedom, too.
Tori: Yeah, exactly.
Emma: So all of this experience, right, your undergraduate research, your REU, your work experience, led you to pursuing graduate school. And so knowing everything that you’ve done before grad school and now being in the same lab, I do know what you do in your current research. But let’s talk about now what you do as a PhD student. So what is your research topic? What is your study system? And what are the kinds of questions that you’re looking at?
Tori: OK, I feel like this is a very good time to have this interview because we’re all just starting to write our proposals. I feel like I’m about to regurgitate the intro to my proposal right now. So ammonia transporters are very broadly important because in animals, if you get a buildup of ammonia, that’s toxic to cells. And mosquitoes are pretty interesting because they have a really wide variety of ammonia transporters. So we’re looking specifically at Aedes aegypti (dengue mosquito), which is a vector for dengue and other arboviruses. We’re looking at the transporters AMT1 and AMT2. This is like building off of our PI, Andrea’s, work because she did a lot of work with the AMTs in larva because larva can survive in really ammonia rich environments and so it’s like cool to look at–and I don’t know as much about what allows the larva to survive and like AMT expression in the larva–but we’re looking at adults. And basically, AMT1, based on a type of knockdown that Andrea did during her PhD, it’s pretty likely that if you fully knock out AMT1, meaning like break the gene, probably most of the sperm won’t survive, which is something I talked about a lot in the DOD application because like sterile insect technique and stuff, that’s way down the line. So we’re interested in AMT1 primarily in the context of reproduction, but like who knows. So for AMT1, it’s not like it’s only expressed in the sperm. There’s like expression in other tissues, and so there’s a chance that there could be some other phenotypes. But that’s like– I mean, you don’t want to just be like knocking out AMT1 and being like, I wonder what phenotypes we’ll see. So that’s our like more hypothesis driven thing.
And then for AMT2, it’s like, in my opinion, the more interesting one, because basically in Drosophila (the fruit fly), it’s like confirmed that AMT, which is like a homolog of AMT2, is an olfactory receptor, which is really atypical. Because for example in mosquitoes, the two main like families of olfactory receptors are ORs and IRs. And our thought is that AMT2, we know that it’s expressed in neurons in Aedes aegypti. And our thought is that it might also be functioning as an olfactory receptor, which would be pretty different. They actually say in the paper where they first talk about AMT’s in Drosophila, they’re like, this is the only known instance of a transporter acting as an olfactory receptor in animals. So it would be cool to see if that generalizes, so that’s what we’re thinking, and because it’s especially relevant in mosquitoes because they like use volatile cues, so smells that come off of humans, to find humans. And one of the most important smells for them is ammonia. And so like there’s a lot of interest in what receptors are they using then to smell ammonia and like seek out humans.
Emma: Yeah, that’s really interesting. So your project is basically split into looking at AMT1, which is a transporter of ammonia that basically you think has to do with reproduction, and AMT2, which has a lot to do with like how mosquitoes sense humans potentially. So I guess in the process of exploring AMT1 versus AMT2, you kept saying the word knockdown. So what kind of work are you doing in lab regularly? And what does knocking down mean within a genetics component?
Tori: That is such a good question. Yeah, OK. So with that like literature background, one way that people explore function a lot is with gene knockouts, so we’re using CRISPR-Cas9. Technically, and I don’t think probably we have the time to get into why technically what we’re doing is a knock-in, but we’re trying to basically break these genes and see what happens, which it’s not like perfect, right? Because let’s say AMT2 is an olfactory receptor for ammonia. But there’s redundancy and there’s another olfactory receptor. Maybe we wouldn’t see as much of a phenotype, especially with olfaction. I think that tends to happen because like if you’re a mosquito and you only have one ammonia receptor, and you happen to be born with a messed up copy of that ammonia receptor, you’re in trouble. So there’s a lot of redundancy. But in general, like we’re doing a knockout because it can be a good way to like look at function. So do you want me to get into like microinjecting?
Emma: That’s up to you. I guess like let’s think a little bit more broadly. So the techniques that you use are primarily genetic techniques, right, in lab. So what are some techniques, including microinjecting, that you’ve learned throughout the course of your graduate studies that maybe you weren’t doing just before when you were working in industry?
Tori: Oh my God, like everything. I feel like I came in knowing like PCR and how to run a gel, basically. And it’s been a lot because basically for CRISPR Cas9, what we’re doing is like injecting DNA into these mosquito embryos and then hoping that the gene edit happens. So you do everything yourself. You have to make the DNA, which is like molecular cloning, which I hadn’t done before and had to learn, and then you have to actually inject it, which is microinjecting, which is also kind of tricky, and then there’s also like all of the mosquito care and like making them not die, which probably Elisa will also tell you is like harder than it seems.
Emma: Yeah, I mean in our lab we have boxes of mosquitoes in massive incubators all the time.
Tori: If anyone wants mosquitoes, yeah, we have like an abundance always.
Emma: Yeah. So throughout this genetic work that you’re doing, I’m sure that, you know, there’s different types of labs. There’s wet labs, dry labs. And so with a lot of genetic work, cleanliness and like making sure everything’s very tidy is super important. Have you had any sort of situations where you’ve run into a problem that’s been accounted for based off of like something that happened throughout your methodology or something that maybe went wrong that could be explained by a technique that maybe you didn’t have before or a practice that you didn’t have before while doing your experiments?
Tori: Yeah, like troubleshooting? Yeah I mean, honestly, when we were like building the plasmids, so like basically sticking these pieces of DNA together, there were a lot of times that something didn’t work and then I either realized it was a really silly math mistake or I just did it again and then it somehow worked. So I feel like that’s not the most useful answer. We also, because we’re not the only ones that have these like genetically modified mosquitoes and we’re sharing lab space with other labs that have like genetically modified mosquitoes, we have to be careful that we don’t get them mixed up because the only way that you can tell that they’re modified is that they fluoresce in the eye. It would be great if there were like 20 different possible colors, right? That way you could say, oh, this one is like dark red, so that’s my AMT1 mosquito, but unfortunately, there’s not, you can only have so many like lenses on your–I don’t know if lens is the right word, I’ll say lenses–on your microscope to screen. So basically like you can use YFP, you can use RFP, which is yellow fluorescent protein, red fluorescent protein or BFP. But then you might have two lines that have the exact same color. And in that case, if they get mixed up, you can fix it, but it’s like kind of a huge nightmare. And we did actually have some contamination. We basically had positives in the BFP channel, which made no sense because that wasn’t the marker we were using, so we knew it came from somewhere else. So we had to like basically screen all of our mosquitoes, like all of our wild type, take the ones that were BFP, or at least all the ones we wanted to get eggs from, and just like kill those and then move forward with cages that were screened and we knew didn’t have contamination.
Emma: Yeah. So when you’re saying screening, just for context, you’re looking at every single individual mosquito. And how many mosquitoes are you screening?
Tori: Yeah, it takes a while. I guess it depends on the marker you use, unfortunately. We chose an eye marker, it’s in the eyelet. So we screen them as pupae because you don’t like want to work with them as adults if you can help it. So we take the pupae and basically screening involves like putting them on a dish, looking at them under a fluorescent scope and saying, ah, this one either has it in the eye or doesn’t have it, which, you know, that’s also like been kind of a process is developing the dexterity to flip a pupae and do it fast. We inject a lot of mosquitoes and then we screen the offspring of the injected ones. So on a typical day, you could be screening like hundreds of pupae.
Emma: Yeah. So you’re looking for this tiny, basically glowing little piece in the pupae of the eye of the mosquito.
Tori: Yes, yeah, and hopefully, I think when you have established lines, you can pick the individuals that have very clear eye fluorescence and you can move forward with those, but especially when you’re first setting up a line, my understanding is that, yeah, it can be very subtle. So it’s also kind of a process of sitting there and being like, “Is that fluorescence, or am I just seeing what I’m hoping to see, you know?”
Emma: Yeah, that’s very interesting. Well, I guess now that we’ve talked about a little bit of troubleshooting within your own project and the questions that you’re asking, what is something that you’re looking forward to within your research project that is perhaps something that you’re super excited to try or really scared to try, but think that the results are going to be really great?
Tori: I think once we have the AMT2 lines, I’m just personally very curious, because I think the AMT1 lines will be cool, it’ll be really awesome if knocking out AMT1 reduces reproductive fitness, but I do think that with AMT2, I really think it could go either way, because yes, in Drosophila, it is an olfactory receptor for ammonia, but then also there’s two papers where in Anopheles, they were looking at the Anopheles gambiae, which is another mosquito species, the Anopheles AMT, and they basically concluded that it was not an olfactory receptor for ammonia. So I think this could kind of go either way. It’s not like Aedes and Anopheles are super closely related, but either way, I think it’ll be exciting to get those knockout lines made for AMT2 and then we actually can do calcium imaging, which I think oh gosh, it’ll probably be really hard to get it going, but once we do, I mean, I don’t know, knock on wood, I think that could look very cool.
Emma: What does calcium imaging tell you?
Tori: So we know it’s expressed in neurons, and so we’re going to hopefully look at the neurons that AMT2 is expressed in, and then basically–Okay, oh no, now I have to see whether I understand. I think, okay, basically I think there is a fluorescent indicator that binds to calcium, and if the neuron fires, you should have an influx of calcium. So if you see a bit of fluorescence, that’ll tell you that the neuron fired. And so if you expose them to ammonia, and in the neurons that express AMT in normal mosquitoes, you see them fire, and then you take your knockout mosquitoes and you expose them to ammonia and you don’t see those neurons fire, then that would be pretty solid evidence in combination with other things that the transporter was necessary to get those neurons to fire and to send the signal to the mosquito brain that’s like, “Hey, we just smelled ammonia.”
Emma: Yeah, yeah. Awesome. Well, I guess a lot of genetic work is basically doing something to a plasmid and then trying to find very circular ways of realizing, “Did I do this correctly or not?”
Tori: Yeah, never being totally certain.
Emma: Also, for context, Tori, I see you all the time in lab, and I feel like your thumb pipetting muscle must be really, really strong now because you’re doing that a lot.
Tori: Yeah, overuse injuries.
Emma: Carpal tunnel syndrome from pipetting.
Tori: I’ve heard of that happening to people, actually.
Emma: I have too. I’ve heard it too with scopes.
Tori: Oh, really?
Emma: Focusing.
Tori: I could see that, especially if you’re there for a long time and it’s not ergonomically set up right.
Emma: Exactly. So we’re going to pivot a little bit. So we’re talking a lot about your research now in grad school, but the big thing about grad school is that being a PhD student is an entire beast of its own, right? We all get into grad school thinking, “Okay, I’m just going to ask my research questions, do my project, and everything’s going to be fine and dandy,” but we have this entire program to go through, which is typically five or more years. So being in grad school, I guess, what is some sort of advice that you would give to someone who is looking to be in graduate school? Or, yeah, what’s your advice for people who are just starting grad school, want to get into grad school?
Tori: Oh, man. I feel like I got so much good advice and just kind of listened to it at the time and was like, “Okay,” and now I’m kind of living through it, and I’m like, “Wow, that was really solid advice.” So the one that you hear from everybody that I think is the most solid piece of advice is that you have to have a good mentor/mentee fit with your PI, because I don’t know, it’s like any other job, right? You want to work well with the people around you, right? I think different people have different mentorship needs, right? I think some people do want more supervision, some people want somebody that’s hands-off, so I think that was something that I paid a lot of attention to when I was first talking to PIs and then interviewing and everything. It was just like really even just asking directly, “What’s your mentorship style?” I don’t know, trying to get at those things. Ideally even one piece of advice that I got is speaking to current or former students of a PI and being like, “How do you feel like they are as a mentor? Has that worked for you?” et cetera, that kind of thing. So yeah, I feel like that’s the piece of advice that I got from almost everybody that I think really has held up, and I’m so glad that I heard that.
Emma: Yeah, totally. I guess with your previous experience in industry, you had some sort of mentorship experience. Did that kind of give you a gauge as to how you wanted to be mentored in grad school, or is that something that you developed in a different way?
Tori: Oh, that’s a really good question. Yeah, I think that was another benefit of having my gap years, because I did have a PI in undergrad, but I feel like it’s a little bit different when you’re an undergrad. Not totally different. My undergrad PI was pretty hands-off, and that was an informative experience, right? But yeah, it’s totally different when you’re working full-time with somebody. And I think there were, okay, first of all, I want to preface this by saying that I really liked my boss in industry.
Emma: Yes, of course.
Tori: We got along very well. But especially towards the end of that job, I was like, “Okay, maybe I could work with somebody who’s a little bit more hands-off, but is still available when I need them.” Yeah, yeah, yeah. Although it’s a very fine balance. And it was also, it was nice to have a boss that was a little bit younger, because I felt like we could kind of relate, and we’re in a similar-ish life stage. So yeah, I think that definitely informed my decision about who I wanted to work with going to grad school.
Emma: Yeah. Awesome. And having a good mentor sets up a large part of your attitude throughout your PhD, your success. So yeah, we have it in common that we do have a great mentor, which is great.
Tori: Yeah, we are lucky, for sure.
Emma: Well, Tori, another question I have for you is, it’s a very tumultuous time for science, for pursuing STEM, and there’s a lot of barriers for scientists now. What is something that you turn to to give you hope or to give you happiness, especially, even if it’s just in grad school, if you’re really bogged down by the research, what is something that makes you feel good?
Tori: I would be interested in hearing what other people have said for this, because I’m always looking for new things. I don’t know, I feel like you could take this question in a lot of different directions. You mean if you’re really struggling with, “Oh my gosh, my experiment’s not working,” or also the world is on fire, how you cope?
Emma: Yeah. Let’s do how you cope with it in work and how you cope with it in life.
Tori: Okay. I feel like in work, I don’t know, I feel like for me something that has also been a challenge is just a lot of monotony. So I think lots and lots of yapping with other people and podcasts, because I don’t want to be sitting here doing work and having nothing going on. Outside of work, yeah, I think it’s important to be around other people. You know what I mean? Not just as a distraction, but just as a reminder that there are good things. That would be one of my primary strategies. Also just physically spending time outside of the lab, because I swear, I don’t know, any more than eight or nine hours under the fluorescent lights, I’m like, “Okay, I need to touch grass.”
Emma: Yeah, you walk in at 9 a.m., 8 a.m., and then you walk out, especially here in Seattle. Our sun is setting around four o’clock, 4:15 now, so it’s tough to get that sunlight. But yes, a lot of people who have been on this podcast before have emphasized the importance of community. And so how have you built community throughout grad school?
Tori: Gosh, I would also be interested in hearing what other people have said for this one, because it can be hard. I feel like one thing that I’ve heard a lot as an adult, this is actually veering away from grad school a little bit and more just into existing, but I feel like in undergrad you kind of have default friendships, and it’s a little bit harder as a grad student, because we have our cohort and our program, but so much of what you do is individual, and that can kind of inherently feel a little isolating. So I think for me, especially outside of work, I don’t know. I also think taking the gap year helped with this, because when I first moved to San Diego, I was like, I’m going to make friends through any means necessary. Literally, I met my best friend in San Diego because we were in a Discord channel for people in their 20s who wanted to make friends, and I showed up to a hangout and she was the only other girl there. I think honestly, literally doing whatever it takes, even if you’re like, oh, this is awkward and embarrassing, and I’m not having a good time in the short term, because it’s like, I don’t know you might not click with everybody, but the way I see it is it’s like you will be lucky. You’ll be lucky eventually and find people that you vibe with. And then the pros of that weigh out the cons of any awkwardness.
Emma: Yes, that’s great advice. Well, we’re going to wrap up. Anything else you want to say to the viewers in your last moments? It could be avoid mosquitoes.
Tori: Oh my god, yeah, avoid mosquitoes. Don’t keep standing water in and around your house. I don’t know.
Emma: There we go.
Tori: That’s the conclusion. That’s the ultimate lesson. No, but yeah, thank you for having me on. This is a really nice setup that you guys have.
Emma: Well, thanks, Tori. Hopefully we’ll talk to you post-general exam too and get some more updates about AMT1 and AMT2.
Tori: You’re going to do a post-general? That’ll be interesting.
Emma: Oh, let’s do a little debrief of the general exam.
Tori: I feel like it’ll be everyone being like, I thought it was going to be horrible and then it wasn’t.
Emma: Hopefully. Let’s channel that energy.
Tori: Imagine all the professors are like, oh, don’t stress, and then you go in and it’s like–no, I don’t think it’ll be horrible.
Emma: No, I think it will be fine. Cool. Thank you so much, Tori, for joining us and we’ll see you soon.
Tori: Okay. Thank you.
Check out the previous SciPos Podcast interview with Leigh West here!
