2/16/2021Karen Serrano
Andrew Saintsing: You're tuned into 90.7 FM KALX Berkeley. I'm Andrew Saintsing, and this is The Graduates, the interview talk show where we speak to UC Berkeley graduate students about their work here on campus and around the world. Today, I'm joined by Karen Serrano from the Department of Plant and Microbial Biology. Welcome to the show, Karen.Karen Serrano: Thanks, thanks for having me.Saintsing: Karen is actually about to be our newest host of The Graduates, so you can look forward to new interviews hosted by Karen. Are you excited to be hosting The Graduates, Karen?Serrano: Yeah, I'm super excited. It'll be nice to be on the other side of this soon.Saintsing: Have you ever done anything like interviewing before? What made you get interested in The Graduates?Serrano: I've been interviewed for a show like this, but I haven't been the interviewer, so I thought it would just be kind of interesting to be on the other side and then get to hear about all the cool research that's going on that I never really get to hear about, so yeah, that's kind of what made me decide.Saintsing: Nice. Oh, you have been interviewed before? When were you interviewed?Serrano: As an undergrad we had like a similar program at the University of Arizona, and it was called Thesis Thursday with the local radio show, so I was interviewed a couple of times about my research on that. It was pretty cool.Saintsing: So, you've been doing research, you were doing research all throughout undergrad to have enough to get a couple interviews?Serrano: I did have like basically the same interview. One year I was part of this research program called the Undergraduate Biology Research Program, and one of the requirements was to do a radio interview each summer. And so yeah, every summer I would get interviewed. I only did research for two years, but I got to be interviewed twice, so that was fun.Saintsing: Oh, that's cool. They had a requirement that you had to be interviewed?Serrano: They had to do a radio interview, yeah, and they also had a requirement that you had to write like a small like press release about your research, so that was also fun. Yeah, just like some activities to get you into communication.Saintsing: Oh, cool, so you're like well-versed in science communication now. Sounds like this...Serrano: I'm a beginner.Saintsing: But, well, you know, you have a good starting point relative to some other people. This is just like a thing at the University of Arizona where you went to undergrad?Serrano: It was kind of like a summer program that you had to apply for, but yeah, it was fun. I was happy to be a part of it.Saintsing: Well, let's put those science communication skills to the test. So, you are in the Department of Plant and Microbial Biology. So, you are studying, I guess, some kind of interaction between plants and microbes or something along those lines?Serrano: Yeah, so I'm a plant biology PhD student, but I do study an interaction between plant and microbes. I study the interaction between plants and a fungus called arbuscular mycorrhizal fungi.Saintsing: Can you repeat that one more time?Serrano: Yeah, it's a mouthful. It's called arbuscular mycorrhizal fungi.Saintsing: Okay, and what are those?Serrano: Yeah, so to kind of break down the name: mycorrhizae. They're called ‘fungus root’ because they're fungi that live in plant roots. And then, they're also called arbuscular because they form these little structures called arbuscules when they get into the plant root.Saintsing: What is an arbuscule?Serrano: It's kind of just like a little fungal structure that serves as kind of a hub for metabolite exchange. So, the fungi will like crawl into the plant root, and when they get there the plant will like entirely rearrange its whole cell to let the fungi grow this arbuscule.Saintsing: What do you mean by crawl?Serrano: They actually like seep into the plant cell walls.Saintsing: Okay, so the fungus, they're moving like an animal? Like they are controlling their movements? Or, I guess I'm wondering: is it kind of like how plants roots grow through the soil? Is that kind of how the fungi are moving?Serrano: Yeah, it's exactly like that. They just grow longer and longer in a certain direction.Saintsing: Okay, cool. Sorry, I interrupted, though. And you got to tell us more about how the plant rearranges itself to accommodate the fungus.Serrano: Yeah, so the fungus actually provides a lot of nutrients and water for the plant, and so the plant actually accommodates them like by rearranging its entire cell wall to let them fit in there. So, it's like a symbiotic relationship the plant gets more nutrients and water out of the soil because of the fungi, and the fungi gets a house and carbon from the plant.Saintsing: So, what kind of nutrients are the plants getting out of the relationship?Serrano: So, they've been shown to provide like, I don't know, so many nutrients. The main ones are phosphorous and some like small micronutrients that the plant usually has to scavenge for. Yeah, these fungi are really, really, really good at taking up phosphorus. Usually because phosphorus is present in like a non-available form in the soil that plants have to like work really hard to convert to an available form that they can use. And these fungi do it really easily, and so that's kind of a mechanism that yeah allows them to get more nutrients from these fungi.Saintsing: Do you know more about the like why is it unavailable to the plants or like what what's going on with the phosphorus? What, it's like energetically costly to convert it?Serrano: Yes and no, but the kind of hard part about phosphorus is that there's a lot of phosphorus in soil, but it gets tied up with metals just because it likes to interact with them more. So, it's not existing in like a free form that plants can just like suck up when they suck up water. It's tied up with other things, and so the work is trying to get it to untie from those other things.Saintsing: And the fungus just has like good metabolic pathways or something that let it break those interactions down?Serrano: Yeah, exactly. I don't study the fungus specifically, so I don't know more about it, but I’m assuming, yeah, they do. Plants also release like little, small like metabolites that convert the phosphorous, but it takes a lot more for them to do that than for the bacteria and fungi to do that.Saintsing: I see, so you don't study the fungus. You study the plant, I guess. Like the how the plant does this interaction.Serrano: Yeah, um so this fungus is actually like the worst behaved lab specimen ever. It's really hard to study the fungus specifically because it's multikaryotic. So, what that means is that each of the cells can have like hundreds of nuclei.Saintsing: Wait, so like the cell are like fusing together you mean? Or like what what's going on there?Serrano: So, the fungus is like eukaryotic. There are multiple cells that make up the organism. Those cells instead of just having one nucleus, it has like hundreds of them.Saintsing: So, it just like has a bunch of DNA that it can make its proteins with.Serrano: Exactly. So, it's really hard to actually genetically study them, and then there's like recent research has shown that like those nuclei will just like divide and multiply kind of at will. So, that makes it increasingly hard.Saintsing: Interesting, so wait, but I mean that seems like you have a bunch of DNA to study, right?Serrano: It’s hard to tell exactly like what DNA comes from what cells, which is pretty important.Saintsing: I see. Yeah, so like a cell could have slight deviations in DNA within the cell.Serrano: Exactly, yeah so just as like we have millions of cells but some of our cells are like eye cells and some of our cells are only expressing you know finger things (I don't know much about humans) but the fungi also like kind of separate these functions, and so, if we want to study them, we just get like hundreds of DNA we don't know actually where they're coming from.Saintsing: So, the fungus is poorly behaved. It's not something that's easy to study.Serrano: Right and they will die outside of the plant host, like they have to be studied within the plant, and so, it's really hard to separate like to get really clean fungal tissue first also. So, anyway they're just really hard to study, and so, we kind of have to get creative, and so, my research is trying to apply a transcriptomics technique that was developed for human biology and trying to use this technique and apply it to the symbiotic system.Saintsing: What is transcriptomicsSerrano: Transcriptomics… you've probably heard of genomics (the study of all the DNA within an organism). Transcriptomics takes a step further and only studies the genes that are actually being expressed.Saintsing: So, it's a transcript because it's like been transcribed.Serrano: Yeah, exactly right,Saintsing: Because you're not worried about genes or you're not worried about all the DNA that like doesn't get transcribed is basically the idea behind this, right?Serrano: Exactly, if you want to know like, for example, I only want to know about the genes that are related to the symbiosis, so I don't really care about everything else or the DNA that's not being transcribed at the moment. And it's kind of a new field, but it's developing really rapidly, and now we've gotten to the point where we can tell exactly what genes are being expressed and exactly what cells so it's pretty crazy.Saintsing: Oh, cool, so that's why the fungus is useless. Kind of like: what are you doing with that because you can't differentiate cells, so it doesn't really help you, right?Serrano: Exactly, and this company 10x Genomics has taken it a step further, so now they created this slide, which is what I'm going to be using, and it basically… like you can take a little slice of tissue and then like paste it on the slide that has DNA markers on it which will capture the DNA that's released, and so, you can take the plant tissue that's been infected with this fungus and then you stick it on the slide and you apply some chemicals that will let you see what like cells there are and what structures within the cells and if the structure is fungal or plant and then you release the DNA onto the slide and then you get information from a computer which I don't know actually much more about, but it will tell you exactly what DNA is coming from exactly what part on the slide. And so, you basically get like a picture and then all the DNA information next to it.Saintsing: Wait, wow, so you're saying that like essentially all you – I mean I'm not saying it's not work, but like all you have to do is take a slice of the plant, the root that you're looking at and just put it on slide and then you're just going to get all of this data about DNA?Serrano: Basically.Saintsing: Wow, yeah, that's really cool. Is this really new, the technology?Serrano: Yeah, it's really new. So, it was developed actually for like human cell biology, so like histologists that would take like – I don’t know, whatever histologists do. And they take like human tissue, and they try to study like what genes are being turned on which cells like for cancer or something. So, it was developed for that, and then a couple of scientists I think in 2016 applied it first to plant tissue, and they got some really good results. So, this will be the first time that's applied to both plant and fungal tissueSaintsing: Wow, yeah and the… So, it recognizes DNA. So, does that mean it, you have to program it in whatever way you program it? With the knowledge of the genes that you’re like… You already know what genes you're looking for essentially? So, you're trying to say like when are genes that you're interested in are activated? Or, are you actually going to find genes from this?Serrano: Yeah, so it'll actually just capture like everything that it's expressed. So, you don't need any prior knowledge about the genes and then from the data that'll give you that's when you kind of look at okay which genes were the most expressed in which areas and it'll give you kind of like a list of candidates that you can now go through each gene one by one and see okay does this gene actually do something.Saintsing: So you're going to maybe find a bunch of genes that people haven't ever seen before or like is this pretty well studied, and so, you'll find things that people have been talking about for a while now?Serrano: Hopefully a bit of both. So, there have been transcriptomic studies done on the system before, but it hasn't been… so, this kind of technique that I described to you, it's called “spatially resolved.” So, other techniques, they'll have single cell data, but they won't know exactly where the data came from, like which cells it came from because they have to pool them all together. So, this will be the first time that we get like both all the data and then where exactly it came from in the tissue. It can be used to validate other people's work, but we're hoping to actually find some new genes as well. It sounds very easy, but it'll take years. The slicesSaintsing: Yeah, have you started already?Serrano: Yeah, so COVID kind of threw a wrench in things, but this summer we mainly focused on getting the staining techniques down. So, there's a couple of different staining techniques that will allow us to see like exactly where the fungus is in the root tissue which is what we'll have to do for the slide to be visualized correctly. So, that's kind of what I've been focusing on, and then COVID also kind of delayed my training on the device that lets you actually slice the tissue so thinly. So, I hope to be doing that next week.Saintsing: Oh, cool. Nice. Are you looking at a particular plant?Serrano: Yeah, so I work with Medicago sativa, which is more commonly known as alfalfa.Saintsing: Is there a reason why?Serrano: It's kind of the model plant that's been used for this just because it's a legume and legumes tend to form these relationships more than other plants.Saintsing: Do you know why that is?Serrano: I think they were the – I don't know why exactly, but if I can remember I think it's because they were the first ones to evolve this interaction. This actually is the oldest like symbiotic interaction between plants and microbes.Saintsing: So, this interaction between this fungus and legumes is the oldest interaction because they were the first one to develop it?Serrano: I don't know about legumes specifically. This fungus and plants is the oldest known like interaction. Arbuscular mycorrhizal fungi are actually living fossils because identically similar fungi were found to be like associated with the oldest plant fossils we have. So there's a lot of research that basically points towards these fungi being the things that actually allowed plants to colonize land.Saintsing: How widespread is this? Is it like all plants are doing this?Serrano: It's about 80% of land plants, so it's pretty common.Saintsing: And what's up with the other 20?Serrano: Yeah, I don't know. That's probably something I should know, but they just have their own thing.Saintsing: Okay, so that's… so you're working towards like really getting into data collection at this point, and so you'll be hopefully like actually getting data maybe next semester even.Serrano: Yeah, hopefully.Saintsing: That's cool. So, you're in your second year. What brought you to Berkeley? How did you end up deciding Berkeley was the school for you, and this program, the Plant Microbial Biology program was the program for you?Serrano: Yeah, so in undergrad I did a lot of research in mining reclamation, so helping mines re-vegetate their land. Through that I got to kind of not only do like plant-related research but also like interact with like the mining companies themselves. And like getting to know like what the actual industry side of things was like, that's kind of what attracted me to Berkeley because we have so many partnerships with industry here, and that's what led me to my lab specifically. I work with Henrik Scheller at the Joint Bioenergy Institute, and so, it's like just a really collaborative environment, and that's exactly what I wanted. I wanted to be like working side by side with like industry scientists.Saintsing: And now, I guess the industry scientists that you're working with would be more like agricultural sciences or people that are involved in agriculture, right?Serrano: Yeah, and a lot of like bioenergy scientists.Saintsing: Oh, right. You said bioenergy. So, you're trying to help people improve like corn ethanol, things like that. Like the production of that.Serrano: Yeah, exactly. We have like another project that I work on which is studying the same interaction but in sorghum, which is a really important biofuel crop. So, hopefully the research I do with Medicago, like the model plant, will be translatable into sorghum also, so we can start trying to use this fungus to help us grow biofuel crops.Saintsing: So, you said like 80% of plants have these interactions, and sorghum is one of these plants, so what are you trying to improve? The interaction between the fungus and the plant? What is the ultimate goal there that could actually be an improvement on the industry?Serrano: Yeah, so as I mentioned before, there's so many benefits that these fungi bring to plants. They're improving their nutrient status; they help them survive better in drought… And so, we're hoping that we could like strengthen the interaction between these plants, between like these important crop plants and the fungi so that in field conditions you know, as climate change happens and we get worse soil and hotter and hotter weather, the fungus will better help the plant to survive in those conditions. And we'll have to put less input into the system.Saintsing: Okay, and by input you mean like fertilizer?Serrano: Yeah, fertilizer, water.Saintsing: So, ideally the ultimate goal of this would be to have improvements that you could genetically engineer into the fungus, or into the plant, or both?Serrano: Yeah, probably easier to do the plant.Saintsing: And these would just help it be a better host or something for the fungi, or help it to get the most it can out of the fungus?Serrano: Yeah, one of the things that we're looking at is the first interaction between the fungus and the plant. So, when it you know first kind of crawls into the cell wall, there's a lot of cell wall engineering that we could do to help the fungus kind of penetrate that wall. So, that's an example of something that we could engineer.Saintsing: I see, and if the… well, I guess I'm just wondering… because the fungus does ultimately penetrate that wall, that cell wall, right? Like, these interactions are occurring, so having that improvement would maybe make that interaction happen faster and speed up the plant growth. Is that the idea?Serrano: I don't know if speed is a factor but definitely the extent of colonization.Saintsing: I got you. Like maybe some plants that aren't growing as well or don't look as healthy don't have as much colonization in their roots of these symbiote relationships?Serrano: Right, exactly, yeah, the extent of colonization differs a lot across even just like different varieties of sorghum. And so, if we could make that more consistent, or if we could find a way to make it… if we could find a way to increase that colonization, it would really help the plant.Saintsing: I got you. So, you're improving yield, and then you'll have more source for fuel.Serrano: Exactly. With less input, which is important.Saintsing: Right, yeah. Well, that sounds really interesting. I'm also really interested in the mining reclamation. So, what, kind of briefly, were you doing there?Serrano: Yeah, so I worked with, it's called the Center for Environmentally Sustainable Mining, which is also a mouthful. And I worked with three southern Arizona copper mines, and two of them were legacy sites. So, those are mining sites that have kind of been abandoned and need to be revegetated. And then, one was an active site, and I worked more closely with the active site. And they basically had these gigantic mountains of just waste soil/rock. More rock than soil. And it was on national forest land actually, and so, they had this really tight deadline to get that stuff revegetated. But, as I said earlier, it's like mostly rock, so it's really hard to revegetate that stuff, and so what our lab did was we basically did a lot of soil sampling, vegetation sampling. And we wandered patterns across the mountains and tried to come up with ways that they could like cost effectively revegetate that area.Saintsing: And were you doing similar things? Like thinking about the genetics of the plants you were interested in and ways you could improve how, you know, well they grew in different situations?Serrano: I was actually looking at phosphorus really specifically. Which is kind of why I started getting into arbuscular mycorrhizal fungi because they're so good at scavenging phosphorus. But we were really focused on kind of just sampling everything we could just to get a better sense of: okay what are these slopes made out of? Because this is just like material that the mine dumps there from all of their other activities. And so, we would just sample and then try to analyze trends. So, over years, like, is the pH going down? How is the phosphorus different? Is carbon different? What plants are associated with different carbon? Different phosphorus? Different soil nutrients? Stuff like that. And then we would try to piece together what was actually happening.Saintsing: And I guess the interest there is like figuring out what the best way to colonize this area with plants was? Like maybe you would figure out which plants to introduce first or something like that?Serrano: Exactly. For example, we had we had two different slopes that we looked at. One, they had previously tried to seed, so there was like a few plants that they planted themselves. And then one they left alone. And the pH on the slope that they seeded was a lot lower and a lot more optimal for plant growth than the other slope that they had left alone. And so, one of the questions we were asking was: was the pH of that slope brought down by the plants, or did that pH just happen to be lower to begin with? And so, those were the kind of questions that we asked there. Because if it had just been lower to begin with, they would just have to wait a few years for the other slope to go down before planting.Saintsing: That sounds super interesting. So, when you got to undergrad, did you start like doing research as an undergrad like right when you got to undergrad?Serrano: Oh, no. Definitely not. I was a very lost freshman. I mean I've always known that I was interested in science, and I really liked genetics. But I started out with like human stuff and quickly realized I didn't like human stuff. It wasn't until I kind of randomly volunteered to be like a mountain guide with really no experience (I'm from the suburbs of Dallas). So, I don't know. They kind of just accepted me. They paired me up with a graduate student who happened to be a graduate student studying plant biology, and he was just like absolutely infectious with like his love of plants. And I just really got into plants after that. And especially because in Tucson there are so many weird desert plants that it's kind of like impossible to miss them. And so, yeah that was that was kind of the story of how i got into plants. And I just started reaching out randomly to professors, and like: do you work on plants? Can I work with you?Saintsing: Wow, yeah that's really cool. So, this grad student was really like when you figured out what… or talking to him was really when you figured out you like really were interested in plants?Serrano: Yeah, exactly. He had this ability to just like look at a field and be like: this is that plant. That's that plant. This is how they interact. This is why they're cool. And I was like: yeah, I totally see that now.Saintsing: Are you at that level now?Serrano: You know my friends always try to get me to identify plants, and I'm like, that's not really what plant biologists do. I work with one plant, who I forget the common name of.Saintsing: So, you're going to be… you're always on trips with your friends, and then that one time, you're going to be like: that is alfalfa.Serrano: Yes, exactly. That's Arabidopsis.Saintsing: So, what turned you off of working with people? Were you going to be a doctor?Serrano: That was my initial thought. Or like a genetic counselor. I was also thinking about doing that. And then I was trying to be proactive, and so, I signed up for this health skills clinic that the university was offering, and you could do like a suture lab, and they had like this fake human tissue that you could practice like sewing on. And I just got like, just so very creeped out by that. And I remember I was like walking home from the place, and I called my mom, and I was like: yeah, I don't know about this. I got that creeped out by like fake tissue. I don't think I could handle it if it was actually bleeding.Saintsing: Yeah, that makes sense.Serrano: Yeah, and plants don't bleed, so you can't really – I mean, you can hurt plants, but they won't sue you.Saintsing: Yeah, that's true. So, okay you figured out you wanted to do plant biology, and then you went to your undergrad research experience, and you found these cool opportunities where you could work with industry partners, and you had all these collaborations. So, do you think after graduate school that you're kind of interested in more like the industrial side, actually working at these companies and doing the reclamation project yourself? Or do you want to pursue academic research, do you think? Or maybe something else entirely?Serrano: Yeah, I'm more leaning on the industry side just because I've always kind of just thrived in that environment. But I am interested in teaching, so I'm kind of torn right now because I love both.Saintsing: Why do you think you thrive in the industrial side of things?Serrano: I kind of like application-based problems. There's like an immediate kind of solution to a problem right in front of you, which is a little different than like doing science for science’s sake.Saintsing: So, you really enjoy teaching. What are you teaching?Serrano: I'm teaching intro bio right now. Bio1B.Saintsing: Is this the first time you've taught?Serrano: Yes.Saintsing: Did you know beforehand that you would be interested in teaching? Or you just found out you like teaching now, this semester?Serrano: I was interested in teaching prior to this, but I didn't expect liking it so much. So, as an undergrad, I served as like an undergraduate TA. It's kind of like the TA's helper. And I always found that really fun and like a good way to practice like learning concepts on my own. Like keeping refreshed with the material. I guess I had really been missing that personal component of things, like interacting with the students every day and like learning more about their lives. Because as an undergraduate you kind of just like go over concepts and like hold reviews and stuff. You don't really get to like make those connections. So, I've really enjoyed that and like learning about what makes them excited and like telling them probably way too much about my research. So, yeah, I think that's kind of why I like it.Saintsing: All right, well it looks like we're actually running out of time now. Usually at the end of the interview we have a moment where guests can take an opportunity to directly address the audience. Is there anything you'd like to leave us with?Serrano: I’d just like to say if you are interested in these fungi, you can actually buy these products yourself now. There's a lot of companies that sell like little inoculants for your own garden that you can try out and see if they help your own vegetables or anything like that. So, if you're interested just Google them: arbuscular mycorrhizal fungi. And you can buy them for yourself and try them out.Saintsing: Oh, cool. A way to minimize the amount of fertilizer you have to use in your own gardening.Serrano: Exactly.Saintsing: Today's guest was Karen Serrano, and she will also soon be a host. Thank you, again, Karen.Serrano: Thanks for having me. I'm so excited.Saintsing: Tune in in two weeks for the next episode of The Graduates.