Natural Product Discovery: From Science Fiction to Reality

[Low, eerie music; SFX: low whirring, door opening]

00:00 PA Announcement: All personnel prepare for Black Alert. This is not a drill. Repeat, this is not a drill.

00:08 Computer Voice: Spore Drive online.

00:12 Paul Stamets (Actor: Anthony Rapp): Spore Drive is ready, Captain.

00:14 Saru (Actor: Doug Jones): Questions or concerns before we depart, Captain?

00:17 Captain Pike (Actor: Anson Mount): If you're telling me that this ship can skip across the universe on a highway made of mushrooms, I kind of have to go in faith. 

00:25 Captain Pike (Actor: Anson Mount): Be Bold. Be brave. Be courageous. Black Alert.

00:39 Rocky Lowenthal: While we may not be able to teleport using the mycelial network, as you just heard them do in Star Trek: Discovery, we may be able to use it for the next best thing. 

Welcome to the Lab Notebook podcast. Today, we'll be starting from page one and unraveling some of the science facts woven into Discovery's science fiction as we discuss just what fungi might really be capable of through the lens of natural products. I'm your host, Rocky Lowenthal, and soon I'll be joined by Dr. Michael Mullowney, a senior scientist at the Host Microbe Metabolomics Facility here at the University of Chicago– and lest I forget to mention this, he's also an artist. 

So I suppose we should rewind a little. I promised you starting from page one, but I think we should really back up to the prologue. Why fungi? What am I even doing with them? And who even am I and what are natural products? 

Okay, well, first I'm your host, but I'm also a researcher in the Snyder and Esser-Kahn labs at the University of Chicago. I'm a mycologist, a scientist who studies fungi, and I've been researching a species called turkey tail for over four years now.

Prior to all of this, when I first heard the clip that I played for all of you at the very beginning, something really stuck with me. And it wasn't really the teleporting, though that was certainly cool, but it was the scientist who said, “Spore Drive ready, Captain.” Now, that was a pretty bad impression, and unless you're as much a fan of the show as I am, you probably didn't catch that that character is Paul Stamets, an astromycologist. But what does a fictional scientist and his fictional job have anything to do with my research? 

Well, Paul Stamets certainly isn't fictional. I mean, the one you heard earlier, played by Anthony Rapp, is fictional, but the character is based on a real-life mycologist of the same name. Now, Mr. Paul Stamets, the real one, and his enthusiasm for fungi is the reason I'm here at all. And I don't mean in the recording studio, but instead in my research lab. 

In 2012, he published a study containing something frankly miraculous:

02:29 Paul Stamets: I have to say that my siblings, uh, look upon my research, eh- our research- a lot differently now. We have a lot more credibility because, you know, my- my mother did have stage four cancer. She was given less than three months to live, and, um, in combination with Taxol and Herceptin– two great drugs– and turkey tail, she now has no detectable tumors. She started in June of 2009, and a year later, her tumors had disappeared.

02:58 RL: Now, I didn't see this until 2019, by which point a bit more research had been done on turkey tail mushrooms and cancer, but I was floored. 

Naive and inspired makes a pretty great combination, so I sent out five emails to the heads of different institutions across Arkansas– I'm from Arkansas, by the way– and I was so excited to receive a response. Now, in retrospect, I'm truly floored that a few people responded, especially now that I know just how hard it can be to get in contact with even your college professors. But that was truly a pivotal moment for me where I got to step foot into the worlds of mycology and cancer research. 

My main goal was and still is to answer the question: what kind of anticancer properties do turkey tail mushrooms have and how can we harness them? But before I talk your ear off about the nitty gritty of how we actually go about asking and answering this question, let's talk about the field. Because at first glance, it almost seems like mycology and cancer research– or even medicine as a field– have about as much in common as Star Trek and Star Wars fans.

Okay, that was probably a really bad simile, but I didn't want to do the apples and oranges thing… Anyway, let's talk about this thing that I keep name dropping and not defining– natural products– with Dr. Michael Mullowney.

04:08 Michael Mullowney: I’m a senior scientist at the Duchossois Family Institute, specifically in the Host Microbe… What is it? 

RL: Metabolomics Facility?

MM: [Laughing] We don't ever use that internally.

RL: No? I've never known how to pronounce… Was it Dutch-wa? 

MM: Dutch-a-swa. I think.

RL: I’ve never- I've never pronounced that one. 

04:29 RL: Natural products. We're talking about those. Those are really cool. And I could just take out a textbook definition of that, but that would be super boring. So I was just wondering, what is your definition of natural products?

04:42 MM: Yeah, so natural products are chemicals that are produced by biological organisms. So anything from microbes all the way up to eukaryotes, like even humans. So it would be small molecules besides the molecules that people would be familiar with in central metabolism, like amino acids and fats and sugars, those kinds of things. And they often have a specialized function. 

So, I mean, of course, the complexity is vast– just like most everything else in biology. So, yeah, natural products, it’s like the universal language of all living things.

05:22 RL: Awesome. Do you have a favorite natural product? Class or specific one or just?

05:26 MM: Oh, well– it’s really– I’m highly biased. I think my favorite might be just like the project I had in grad school. I discovered and elucidated the structures of this class called the diazaquinomycins. They're these small molecules that are produced by actinomycete bacteria. I think I would probably be sick of hearing that name. I mean, it's been a while now, but like during my PhD, it was just like diazaquinomycin this, diazaquinomycin that.

RL: There’s no abbreviation? They just…

MM: D-A-Q, so we call them the DAQs sometimes. The DAQs. 

05:59 MM: Yeah, I'm a big fan. I mean, the structures are interesting. They were very active against mycobacterium tuberculosis. So we were– a lot of my time during grad school was exploring that application. I guess it's just a nostalgia thing. They're really cool. Because like otherwise, it's hard to have a favorite because they're just, I don't know, they're all special in their own way.

06:22 RL: And you're picking between your children.

06:23 MM: Yeah, exactly. They're all really interesting. So it's all just like a personal, you know, my personal story. That's a big part of it.

06:30 RL: Yeah, that's perfect. I've already talked a little bit about how I got into natural products, but– so you did natural products for grad school. Can you tell me just a little bit more about how you even got into that field?

06:40 MM: Yeah, so in my late 20s, I was working in restaurants and recording music for bands and singer-songwriters and recording some of my own music. And I was also doing art for– like I was making posters. So yeah, I was doing a lot of creative work and waiting tables and I got interested in environmental conservation and ecology and stuff. 

So I was reading books about environmentalism. And I started reading E.O. Wilson's book, it's called The Future of Life. And it was like three pages in, you know, chapter three or four– I don't know. It was talking about people that go to the Amazon and meet up with Shaman and collect plants and search for, you know, anticancer molecules. 

And it reminded me of the movie Medicine Man, which came out in the 80s, I think. And like those two pieces of media were like the only exposure I had to the idea of natural products and I just had never really thought about it. And I was like shocked to learn that the majority of the medicine that we use, it wasn't just this niche thing. I thought maybe it was just like really, this strange guy going into the jungle and it's not like a normal thing. But like, no, like most of our medicine is based on small molecules from nature, whether used directly or synthetically modified. So, yeah, I read about that and it just blew my mind and I was like...

Wow, nature is really creative. Like plants are doing all this chemistry, bacteria are also doing this chemistry. It's all around us. 

RL: Hey, fungi are there too!

08:19 MM: Sorry, yeah, fungi too. Yeah, of course, of course. Yeah, so I was just floored and I was like, man, I need to get involved in this. There's still plenty out there that we just, you know, there's limited time and resources. We haven't gotten around to all of them. So my thought was like, yeah, I'll discover new chemicals from nature and show the world that, you know, there's value here.

Like if you can't find it intrinsically just by taking a walk in the woods, then you know, [you] can sit in your condo in the middle of the city and be cured of your disease and be thankful that the trees are out there somewhere.

08:48 RL: Yeah, and then you did find them. You did find those natural products.

08:52 MM: Yeah, and then I got into it. Like, but okay, at that point, I did not have any real, like, scientific background because I had gone to art school and I went to audio engineering school. And so I was just like an art kid. I just decided pretty quickly I needed to enroll in a bachelor, college level chemistry and biology and get the prereqs I needed to get into grad school to get deep into research. So I did. I enrolled at DePaul University in Chicago.

And it took me four years and I took a break for a semester, I think, because I was just busy. I had two little kids also. There's a lot going on. But yeah, I got my prerequisites, applied to... I really just wanted to go to one program and it happened to also be in Chicago. So yeah, I applied to that program and I applied to a couple other ones as backup because that's what you're supposed to do. But I didn't really care. I wanted to go to UIC and I got in. Yeah, and I contacted an advisor that I wanted to work with, Brian Murphy.

He had just gotten a job there as an assistant professor and he was doing natural products research by diving in the oceans and collecting bacteria and growing them in the lab and exploring their natural products, which are also called specialized metabolites or secondary metabolites. So yeah, that's where I got into the diazaquinomycin project. And then from there– that was like two sentences to sum up four years of immense growth in my life.

But that's what it was. Yeah, my PhD was a huge deal. I feel like I grew so much. And then, yeah, again, I wanted to do a postdoc. So I ended up at Northwestern in Neil Kelleher's lab. I was also co-advised by Regan Thomson, who's a synthetic chemist. So the two of them are working on a similar thing. They're doing natural products discovery research, looking at bacteria from the soil, which is actually a very old source. Like some of the first antibiotics are from soil bacteria– in addition to the fungi, like penicillin comes from fungi. 

So we were using bacteria, even bacteria that had been like in repositories and in freezers for decades, but what we were doing was applying high tech, new metabolomics and genomics technology to explore the natural products system. So like the genes that produce the natural products and the natural products themselves. 

And then after that, I got the job here at University of Chicago in the Duchossois Institute, where we focus on the human gut microbiome. I mean, if you think about the beginning of my story, the idea was like, I want to show the world that there's value in nature and, you know, nature produces these molecules. They're like a universal language between all of biology. And there's like some philosophical level of this too, where I was like just really interested in the idea that like humans can take the chemistry of other organisms and sort of like, and use them for our purposes. Like sometimes we don't even know why the fungus or the bacteria is making the particular metabolite, but we find that it works for us to kill cancer cells or modulate our immune system or something like that. There's this connection between us and nature where we're borrowing these chemicals from microbes and plants and that is super interesting because the only reason it works is because our biology– there's similarities in our biology. There's homology between our systems and the systems that are out in the natural world. 

And now I'm working in the gut microbiome and it's kind of like, it brings the whole thing full circle. It's like not only, you know, we can borrow from nature, but nature, like it's within us and there are bacteria in our bodies that are producing these natural products that are made to be in the environment that is the human being. And so it's like integral to our own biology already. There's this tie between bacteria in the environment, bacteria in our bodies, and how those chemicals modulate our physiology, our health. And yeah, those connections have always been really fascinating to me.

13:03 RL: Would you consider yourself to be working in the field of natural products? Do you- like, how would you- how would you phrase that? Cause I- cause I was always talking about- I was like, it's the field of natural products. I don't really know if that's a thing. The field of natural products.

13:14 MM: Oh, it is. Oh, yeah, yeah. Yeah, so if you find yourself at a natural products conference, you realize it is a thing. It's a relatively small field. I mean, like the annual conference that's pretty well known as the American Society of Pharmacognosy meeting every year. And I think they're usually like 300 to 500 people. And you know, there's a lot of students and then there's always like I've made a lot of friends at those conferences. I've been to, I don't know, six or seven of them. Yeah, but like if you go back multiple times, like there's the usual cast of characters. It's like, it's really like a world of its own where it is definitely a field. And there's a journal of natural products, which is dedicated to natural products. And there are other journals that are similarly dedicated to natural products discovery– one's called Marine Drugs. So as you imagine, natural products for marine organisms specifically.

14:11 RL: But it definitely– it sprawls a little further, like there's journal for– I mean there's organic chemistry where we're doing like full total synthesis of those natural products it's just like it touches, I feel like almost every other journal you could come up with it's like natural products could be found somewhere in there.

14:31 MM: Oh absolutely, yeah so, so there are journals that are completely dedicated to the idea of discovering new chemistry from biological organisms. But yeah, like you said, there's plenty of nodes in the network that are connected.

14:44 RL: Yeah. No, I don't know, I just really like natural products, especially because I can just kind of go through what seems like different fields. Like, but like, I don't know. I mean, I'm not– I don't do immunoengineering, but one of my labs is immunoengineering because they do related things for natural products or like, or again, total synthesis for organic chemistry. Like I don't do total synthesis, but natural products are so involved in total synthesis projects that it's like, okay, well can go there as well and get more knowledge. I just really like that interdiscipline– I don't know if it's interdisciplinary, but just kind of...

15:14 MM: No you’re– yeah, you bring up a really good point. That was– that– when I was in grad school and you know, people are graduating and looking for jobs and– that was one of the things that was always impressed upon us was like, remember, like, your training is very interdisciplinary. Like, two natural products students in grad school are not, they're not using the same technologies necessarily. You could be working, like you're saying, you could be building bioassays for some immune modulatory system, or you could be running a mass spectrometer to analyze the chemicals from your extracts or elucidating structures using NMR. I mean, that's only a few things, there's genomics involved. There's everything. Yeah, that is a really interesting aspect of it for sure… and valuable for like a trainee.

16:00 RL: How do you think the field of natural products is changing? Kind of a big question, but...

16:04 MM: It is. I mean, there are new technologies and new platforms for accelerating discovery all the time. Like, and those words will be used in the title and the abstract in the last sentence of the conclusion of the papers for those technologies all the time. It's like, that's like, everyone's trying to find, like, the faster way to get to new natural products that can potentially be turned into real medicine used in hospitals.

So yeah, I– the current state is like, I really think that we may be in sort of a lag phase, not that it's like, there's still really valuable things happening. I don't want to give the impression that that's not the case, but I think like in the last decade, as a field, natural products has come up against, I mean, this is probably the same for a lot of different fields. It come up against the fact that we can generate just an enormous amount of data and it takes…

You know, there are some programming technologies people have developed to try to sift through it, find what, you know, rises out of the noise as like significant signals. And those have been very useful. But also, I mentioned earlier, too, biology is just so complex. Like the complexity is mind-boggling. And I think that, you know, as the world is welcoming in machine learning and AI technologies, like that is the integration of AI into natural products discovery is going to be, like, critical. There's going to be a boom when AI really locks in with everything and we'll be able to truly accelerate the discovery process.

17:40 RL: So I was talking with Dr. John Jumper two weeks ago. He won the Nobel Prize in chemistry, I think last year for AlphaFold. Total coincidence, he went to my high school. Or rather, I went to his high school. 

MM: [Laughing] That’s amazing.

18:00 RL: But what's really unique about AlphaFold is that it, well, I mean, AlphaFold is great. We could talk about that forever, but it does protein structures. And the thing that it really struggles with is small molecules. Like you… couldn't really feed it small molecules and like get out structures in the way that we would really hope to. It just fascinated me how much small molecules seem to be like a whole different beast than proteins in that sense.

18:19 MM: Yeah, I think the massive challenge with a more like predictive or automated pipeline for elucidating structures in the way that AlphaFold can or predicting structures in the way that AlphaFold can is that natural products aren't based on a limited set of monomers like proteins are based on the 20 amino acids. But so, it's kind of like two levels. It's like natural products are not based on a limited set of monomers but then they're also highly modified after the fact. So… there's just many layers of modification and changes and many different types of machinery that can be involved in producing what we consider natural products.

18:57 RL: So if you went in a time capsule and you woke up in 100 years, do you think that they would, do you think we figured out how to AlphaFold small molecules or do you think that's just kind of a different beast?

19:08 MM: Yeah, you know, I think we probably will. I don't want to like– it's a massive task, but I mean, 100 years ago from now, like, there were not many cars on the road, you know? So like, we've come a long way. So yeah, I think in 100 years, there probably would be some way to do like an AlphaFold for natural products.

19:19 RL: I– that would be really ideal. I don't have to stare at my data for like hours on end and just kind of get nowhere with it, but–

19:39 MM: Right, and I hope it does take that long because I want a job at least.

19:43 RL: [Laughing] Then I have no job. So, okay, so we know natural products, what natural products are and what the state of the field kind of is. But, so I kind of started this with Star Trek Discovery. I showed you like that intro clip. They weren't, I don't know how much we...

MM: They zoom along the mycelial network.

RL: Yeah, I don't know how much we'll be able to, I don't think in a hundred years we'll get there, but...

MM: Well, they can definitely use AI to do some of the after products if they're like, traveling–

20:08 RL: Maybe I should ask the producers of Star Trek if they have any ideas… Do you ever, like does seeing natural products in just kind of the world like a little bit outside of science, like how does that feel as a researcher?

20:20 MM: Well, it's usually vastly simplified, obviously like traveling on a mycelial network. Like I don't know what are you talking about? [Laughing] ]But yeah, seeing Natural Products and popular media, I mean it's exciting, but yeah, it's always a little bit simplified. It wouldn't be fun to show it how it really is. 

RL: No?

MM: I mean, it's too complicated.

20:43 RL: But if you wanted to be a little true to life but also make it fun, what would you do?

20:50 MM: Well, okay, yeah, so it would for sure involve like, you know, the whole fantasy that started my career was this, you know, Medicine Man going out into nature kind of idea. And so that would be an aspect of it. That would be like a character aspect, right? Like these like medicine research people that just like are sort of like straddling the line between like foragers and high tech, like laboratory guru scientists, geniuses.

So it'd be like that, those would be the characters. And I think like then the sci-fi element of it would be, like I was talking about how natural products are like just like this common chemistry that all of biology has.. it's like a universal language. So if you were to take that statement literally, these characters would be these natural product medicine people that could like communicate with all of biology through chemistry.

RL: That’s awesome– they’re the translators?

21:47 MM: Like the way that like the Star Trek is traveling on the mycelial network these people could like speak to and like bend biology at their will by like sending chemicals through the earth and into the plants and into the bacteria and make forests grow or you know tell things to do what they want them to do through like the chemical signal.

22:06 RL: I'm there. I'm contacting Netflix. This is great. Okay, yeah, so in public kind of popular media, we get this perception of natural products and kind of just science in general. It's definitely not as complex as it is because that's impossible, you said. we can't do that. 

MM: It doesn’t make for good entertainment.

RL: I'm not going to in my living room and watch someone–

22:30 MM: You don't wanna watch me pipette. Oh yeah, yeah, so when I say it's simplified, you know, I don't have a problem with it. I don't feel offended. Go ahead and simplify it and make it fantastic and make it look more easy than it is and make it look heroic. You know, that's great. Yeah, cause then we got other people, there's kids, you know, after school watching Star Trek or Medicine Man or whatever and thinking like, man, this is great. This is something I wanna do. Like I've been looking. Yeah, yeah, so that's inspirational. And there's a huge amount of value in that.

22:58 RL: Were you disappointed like it wasn't the Medicine Man?

23:01 MM: Well, actually, I mean, I really did have that experience, though. That's the thing. Like, I mean, part of the reason I was targeting the particular lab I went to for a few reasons. I mean, I recognize that marine natural products were a new– newer field, newer than soil, like natural products from soil bacteria or natural products from plants. Like the marine environment was like a front, - has been a frontier. So I wanted to get in for that reason. But also, like, I saw pictures of him diving and I was like, oh, man, I need to be there

Yeah, like, traveling the world and diving, and so, like I said about getting into that lab, and, like, did everything I could to, like, you know, do interesting, good research. And then also, I was like, I need to get myself on a plane and then on a boat and in a dry suit with goggles on, and get into the water and find some interesting samples, you know. 

So I ended up doing that, you know, over the course of a couple summers, or it was in the spring, I traveled with my advisor to Iceland, and we, yeah, we drove all the way around the island those two different times, visiting different sites, and both in the fjords, like out in the ocean, and then also in inland lakes. And there's even, like, a fissure in the middle of the the island, because Iceland is like, you know, it's a volcanic island that is situated right on top of where the North American and the Eurasian plates meet. And so there's like this fissure that has like this super clear, like crystal blue water that has like a current. You just float through it, and it's like magic. And, yeah, so like– I did get to realize the fantasy.

RL: Ok well now I have to go… that’s awesome.

24:41 MM: And, you know, now, and I also, and along the way, I got to appreciate the magic of the, you know, the actual bench work. And, like, writing, I didn't know I was a writer. I feel like I can write, like I'm pretty good at it. And then, and that was like, a realization, like, wow, I can do this. And, you know, give presentations. And there's, like, all these different skills you learn in science, which I like. I wasn't aware that we're all necessarily involved. And then it's just really great that there's such variety in the daily work. It's not like one thing every day. And that was also a draw, like, I can dive with the seals and then also write a paper and publish it like what I don't know, there's just a lot of cool stuff going on. So yeah, now I'm working in the gut microbiome, the fantasy and romance of being out in the world. It's kind of on the other end of the spectrum, actually, but I mean the in those terms, but the actual bench work, the science is, it's, I think it's actually, it has some there's some areas where it is more interesting, because the natural products that are being produced by the bacteria that are in our guts are already relevant to human biology, because they're there now, right?

Previously, you know, I'm looking for novel metabolites in nature, but there, there are so many natural products that have been discovered in nature, that have been tested against cancer cell lines, or, as you know, other against bacteria or fungi as anti fungal or antibacterials, and no one's found any decent activity for them. So they're, they're kind of like another note in the catalog of natural products, and that's still valuable. Like everyone's research is built on everyone else's research is, you know, we're all standing on the shoulders of giants and all that. So there's every contribution. Contribution is worthwhile, and I've made plenty of those contributions. That's most of it, right? So yeah, but yeah, I just find it really fascinating that the things that we're studying now are immediately relevant to human biology, because they're a part of it already.

26:40 RL: Yeah, okay, so… the only other thing I think I have is how would you sign off your lab notebook? This is the lab notebook podcast.

26:49 MM: [chuckling] It would be something along the lines of, you got enough done today. 

RL: [Laughing] That's great, that’s really good.

MM: …and you're overestimating what you're going to do tomorrow.

26:58 RL: That's also true. How did you see– Did you see my pages for today?

27:04 MM: [Laughing] And that’s fine because that’s every single day, that's everything I do. I'm like, I'm gonna do 300 of XYZ. And it's like, 

RL: I got three-

MM: I’m 33 in and it's 5pm, right? 

27:15 MM: And it's just like, yeah, again, persistence and patience on the whole path. It's gonna be hard. It's gonna take a long time. That's why we're here. If it was easy, everyone would be doing it, the problems would already be solved. So, yeah. 

27:33 RL: Thank you so much. This has been really awesome. Thank you. 

27:37 RL: That was Dr. Michael Mulowney of the DFI Metabolomics Facility on natural products, their place in medicine and science fiction, and so much more. So now that we're on the same page about natural products, let's dive into my lab notebook and explore what it's really like to research them. 

As a fun lab fact, your lab notebook is technically property of the lab. So unfortunately, I can't actually read anything off of my first or second lab notebooks since my previous labs aren't in Chicago, I’ll paraphrase. 

All right, book one. At UAMS– the University of Arkansas for Medical Sciences– under Dr. Alicja Urbaniak, I was actually able to test turkey tail against skin cancer. And I found that through a variety of different experiments, turkey tail does actually have some impressive anti-cancer properties. Nothing crazy novel there, but we didn't just look at them to make that conclusion. No, we found that with this line of melanoma, SK-MEL-5 for all the other cancer researchers out there, turkey tail extract, is basically just blended up alcohol-based mushroom juice, actually induced programmed cell death, or apoptosis. 

It also had anti-migratory effects, which we discovered through a wound healing assay. And this is one of my favorites. It's basically where you grow these skin cancer cells in a dish, and then you make two huge cuts down the middle, making kind of a plus sign through the petri dish. And when we treated the cancer cells with turkey tail extract, they were way less able to move into that cut area.

And by way, I do mean with a statistically significant margin. Now, this has some pretty significant implications for metastasis, which is a sign of your cancer becoming more aggressive since it can move and relocate throughout the body. If you're interested in learning more about these findings, please feel free to read the paper linked in the show notes. But as a synopsis, we found, just like Paul Stamets did, that turkey tail mushrooms combat cancer, specifically skin cancer. An exciting first step, but a first step nonetheless.

29:22 RL: When I first started this project, I imagined that figuring out a bit more about turkey tail and cancer was kind of all I needed to do, and then I'd be satisfied. But as you do research, more and more questions pop up, and answering one question generally leads you down a new path of, yeah, you guessed it, discovery, in an attempt to answer new questions. So how can we even take natural products out of turkey tails? What specific part of them is even contributing to their anticancer properties? Like, do we have to use the whole mushroom juice or is it more efficient if we can just use a really small part of it? 

To answer those questions, let's jump into book two. At the Marine Biological Laboratory under Dr. Andrew Gillis, I got to look at turkey tail mushrooms through a slightly different lens, that being one of a microscope. When I first got to Cape Cod, that's where the lab is, it's actually really beautiful if you get a chance to visit, but when I first got there, I wanted to know something that I thought would be pretty easy to answer. Do turkey tail mushrooms have immune cells? 

Now, I don't know if this question is the next one that most people would ask, but I was thinking, okay, so we know that the immune system fights off cancer as best as it can, and we found that some of the same markers were triggered when I tested turkey tail. So maybe they're behaving in the same way because some of their cells are kind of immune cells. Now, Dr. Gillis was totally on board, which was awesome. And so when I got there, that was the idea that I had for the main part of my summer. But lo and behold, you can't answer that question about immune cells if you don't know what kind of cells they have at all…

30:54 RL: Now, I hope it hit you as much as it did me in that moment when I realized that we, as in the scientific community in general, just had no idea about anything that was going on in this fungus. I kind of just sat down for a while, and then when I was sitting, I kind of wrote an email or two, and I ended up with a new procedure for staining mushroom cells, but that's later down the line. So I pivoted, and I asked the question, do turkey tail mushrooms have different kinds of cells? And if so, at what point do they develop them?

As you heard from Star Trek Discovery, the mycelial stage is pretty much like the root network– that part is true– and I found that those are all pretty much the same type of cell, at least structurally. But then as it grows into the adult stage, we call this the fruit body of a mushroom. It's kind of what you see if you hit that mushroom emoji, for example, though of course, turkey tails look like turkey tails and not like the little button fungi. But I digress. In the fruit body stage, we found that turkey tails do in fact have different kinds of cells. 

Now, unfortunately, I was using a stain that had been developed for vertebrate animals. Vertebrates, fungi, something about that 1.5 billion years of evolutionary gap makes it pretty hard to draw real conclusions about the data. But under the microscope, the best we can say is that they're different. So at this point, it was time to circle back. Immune type cells should probably have some kind of immunomodulatory or immune regulating kind of proteins.

And before proteins comes mRNA, which are way easier and cheaper to look at. Basically, I found three different immunomodulatory mRNA sequences, one of which had actually never been found in turkey tails before. And I ordered probes for each of these. Now, something that they don't tell you when you get into science is that companies are apparently allowed to just not tell you how things are made. So when I had asked how those mRNA transcripts were made, everyone in my lab just looked at me as if I had asked if anyone knew the nuclear launch codes.

So, though I don't know exactly how they were made, I fortunately was the one to use them, so I can tell you for sure that 1) they all worked, (yay!) and that 2) these mRNA transcripts were everywhere. 

Now, I know you're not really supposed to have these biases and all that, but I really just wanted to see one super bright cell under the microscope so I can jump up and down in that tiny dark room and triumphantly announce to all of the shells of the old microscope slides that yes, turkey tails do have immune cells, and that if we just use those cells, then we can use these fungi to cure cancer one million times more effectively than before. 

33:20 RL: But no, they're everywhere, which is really curious. And in a way, I suppose this is pretty great, despite my initial disappointment. As Enrico Fermi said, “there are two possible outcomes. If the result confirms the hypothesis, then you've made a measurement. If the result is contrary to the hypothesis, then you made a discovery.” And since discovery is our guiding light from Star Trek to anticancer drugs, it was discovery that I would follow. I mean, ‘Star Trek: Measurement’ would be a way less catchy title anyway.

So if I couldn't get to my goldmine of cancer cures under the microscope, I decided to pivot and approach the problem from the field of chemistry. Specifically, organic chemistry. Now, before you groan and shut this off, I promise not to tell you about all the specific reagents and mechanisms and pathways. If you want to know about that, you can read a textbook or even the pages of my third lab notebook.

But this is the Lab Notebook podcast, so we're going to focus on the bigger picture. And I don't mean the doodles I have all over my table of contents or anything, which I admit to being really bad at keeping up to date, but I digress. So what am I doing now with the same species that I got hooked on nearly four years ago, now thinking about how I can get the natural products out of turkey tails from the lens of organic chemistry? 

Let me reframe that: How can I access the natural products of turkey tail in a way that brings its anticancer compounds out of the realm of science fiction and into reality? In the Snyder and Esser-Kahn Labs at the University of Chicago, I am working on extracting, isolating, and characterizing the components of turkey tail mushrooms, all while doing bioactivity screening to make sure that those are the compounds of interest. 

34:49 RL: One cool technique that you might be tangentially familiar with is called sonication. I use a sonicator, which is basically a machine that yells at your sample to break it down.

Now, though that was kind of a joke, it is technically how it works, since a sonicator uses sound energy to form cavitation bubbles inside of fungal cells. Cavitation bubbles are vapor bubbles in the liquid surrounding the mushroom, which are at low pressure and high velocity. Now, I use an ultrasonicator, which is the same principle and is very effective at forming these cavitation bubbles using ultrasonic waves. As these pulse, the cells get damaged and their contents, those awesome proteins and small molecules of interest, get let out into the solution, which I then concentrate down, just like a beverage company might do for apple juice or something, to get my turkey tail extract. 

Now, my use of the Sonicator is pretty typical in natural products, but for everyone else, it's a bit weird. If you ever see a Sonicator at, say, the tattoo or piercing parlor, where they'll hopefully be using one for disinfecting and cleaning tools, think of all the mushroom extract that you could be making in there. But please don't, we totally wanna keep those sanitary. 

So after extracting the contents by sonication, I start separating and isolating, with interspersed bioactivity screens to focus in on those anti-cancer agents, and... 

36:00 RL: Now, I suppose I should have predicted this one once I started talking about what I did yesterday, but the rest of the pages are blank. So I guess that means I should probably head back to lab and get to work. I actually have on the schedule for tomorrow to meet up with Michael, the same Michael that I interviewed earlier, for some data processing, but you never know. Like he said, you've done enough today, and you probably won't get all that you want to get done tomorrow. But tomorrow, it will still have been enough. 

Stay tuned for the next update of The Lab Notebook Podcast, where we'll cover more research highlights and discoveries. 

That's all for today's Lab Notebook entry, dated the 11th of March, 2025, signed by Rocky Lowenthal.

If we name dropped someone or something in the episode and you’re curious to find out more, you’re in the right place! In this episode…

00:00  Introduction

Audio clip from Season 2, Episode 2 of Star Trek: Discovery (Star Trek® and Star Trek: Discovery™ is a trademark of CBS Television Studios INC. No copyright infringement intended.)

02:58 Turkey Tail Mushrooms

Check out the Snyder and Esser-Kahn Labs at the University of Chicago: 

https://snyder-group.uchicago.edu/

https://www.esser-kahnlab.org/ 

See the full interview with Mr. Paul Stamets: 

“Mushrooms helping to Cure Cancer?” CNN Interview, 2 February, 2012. https://www.youtube.com/watch?v=uuL_faveAnw.  

04:00 Natural Products- Interview with Dr. Michael Mullowney

Find more about Dr. Michael Mullowney on his website: 

https://www.michaelmullowney.com/

Explore the DFI Metabolomics, at which Dr. Mullowney is a senior scientist: https://dfi.uchicago.edu/hmmf 

Learn more about the diazaquinomycins that Dr. Mullowney researched in graduate school by visiting his paper: 

https://pubs.acs.org/doi/full/10.1021/acsinfecdis.5b00005 

Explore E.O. Wilson’s The Future of Life to learn more about what inspired Dr. Mullowney: 

https://books.google.com/books/about/The_Future_of_Life.html?id=UrQkGOUbPfIC 

Check out the Medicine Man, which actually came out in 1992, for more insight into Dr. Mullowney’s inspiration: 

https://www.imdb.com/title/tt0104839/ 

Find out more about Dr. Brain Murphy’s lab at UIC:

https://www.murphylabuic.com/home-1 

Explore the Kelleher and Thomson research groups at Northwestern, where Dr. Mullowney did his post-doc: 

https://www.kelleher.northwestern.edu/# 

https://sites.northwestern.edu/thomson/ 

Check out the American Society of Pharmacognosy, which has a meeting this year: https://aspmeetings.pharmacognosy.us/ 

Explore the Journal of Natural Products and the journal, Marine Drugs: https://pubs.acs.org/journal/jnprdf 

https://www.mdpi.com/journal/marinedrugs 

If you’re interested in our brief conversion about AI, feel free to check out Dr. John Jumper’s paper on AlphaFold as well as Dr. Mullowney’s paper on AI in natural product drug discovery:

https://www.nature.com/articles/s41586-021-03819-2

https://www.nature.com/articles/s41573-023-00774-7 

27:37 Research at the University of Arkansas for Medical Sciences 

Learn more about turkey tails and their anticancer properties in our paper: 

https://pmc.ncbi.nlm.nih.gov/articles/PMC10147383/

Find out more about my first research mentor, Dr. Alicja Urbaniak at UAMS:

https://medicine.uams.edu/biochemistry/faculty/primary/alicja-urbaniak-ph-d/ 

29:30 Research at the Marine Biological Laboratory

Check out the Gillis Lab at MBL: https://www.gillislab.org/