Dr Betsy Parkinson, Purdue University
Natural Prodcast’s interview with Elizabeth “Betsy” Parkinson, from Purdue, about bacterial signaling molecules and regulation of biosynthetic pathways, student mental health, and getting kids interested in microbiology.
Links are available in the show notes below – you can jump to them here. Catch up on previous Natural Prodcast episodes here.
Transcript
DAN: All right. Welcome back to Natural Prodcast. I did it. I’m keeping to my schedule. This should be coming out on the first Thursday of the month, just like I promised. Now I just have to make this whole “on-time thing” a habit! I’m really not good at that, you guys. I’m trying really hard just for you. And the JGI Comms team. But mostly you.
Anyway…I’m really happy today to be handing over our interview with Dr Elizabeth (or Betsy) Parkinson from Purdue University. She’s in the Department of Chemistry and the Department of Medicinal Chemistry and Molecular Pharmacology there. We talked about several different pieces of her work, including bacterial quorum sensing and its effects on regulation of natural product biosynthetic pathways, which led her to a successfully funded JGI CSP project. And we also got to talk about work at her University on graduate student mental health, and an outreach program to get kids interested in microbiology and microbial chemistry. All good stuff, and I hope you enjoy it. And just to remind you, you can get transcripts, and show notes with links to papers around the science we talked about, at natural prodcast dot com.
So, here’s Betsy Parkinson!
JACKIE: Well, welcome. Dr. Betsy Parkinson is joining us today who is an assistant professor at Purdue University, and she has a joint appointment in the Organic Chemistry division, the Chemistry Department, as well as the Medicinal and Molecular Pharmacology Department. So welcome to today’s podcast.
BETSY PARKINSON: Awesome. Thank you so much for having me. Really excited to be here.
DAN: Happy to have you do it. So, I don’t know how we start out. Where are we going to go from here?
JACKIE: Well, how about you just give us a little bit of your background because you do– you’re classically trained as a synthetic chemist.
BETSY PARKINSON: Yes.
JACKIE: And then do you want to tell us a little bit about– you’re trained in chemistry, and what sparked your interest in natural products?
BETSY PARKINSON: Sure. Definitely. So, I got my PhD with Paul Hergenrother at the University of Illinois at Urbana-Champaign. And, when I was working with him, I was working on the natural product dioxin ubiquinone, which actually comes from a marine bacterium. And so, I was working on chemically synthesizing and making derivatives of this to test its anticancer agent properties. And on the one hand, it was really great training and I learned a lot. But oftentimes, it would be very frustrating how many steps it would take to actually get to that product. And–
DAN: So, this is like real synthetic chemistry–
BETSY PARKINSON: Yes.
DAN: –that sort of thing.
BETSY PARKINSON: Yeah. So, palladium catalyzed cross-coupling–
DAN: Got it.
BETSY PARKINSON: –all that jazz. But I was in the same Department as both Wilfred Van der Donk and Doug Mitchell. And so I got a lot of exposure to natural products and got really interested in thinking about how bacteria actually are able to make some of these really interesting molecules, oftentimes much more efficiently than we can in the lab. And so that’s how I got interested in natural product biosynthesis.
I then went on to do a postdoc with Bill Metcalf, also at the University of Illinois at Urbana-Champaign. I had a two body problem, and it was a really great opportunity to get a training in natural products and be able to stick around with my partner as well. And so, in Bill’s lab, I got great exposure to working with Streptomyces, learning more about genome mining, as well as isolation and a little bit of entomology as well.
DAN: Right. Yeah. No, yeah, Bill does it all. A lot of people I think– well, maybe I’m older, but– [LAUGHS] I feel like a lot of people hedge their way into natural products by starting out in synthesis and then discovering more– [LAUGHS] I don’t know, practical or interesting things that are happening with the molecules that you’re trying to build? Yeah.
BETSY PARKINSON: Yeah.
DAN: Yeah. Do you think your synthesis background influences a lot of what you do?
BETSY PARKINSON: Oh, it definitely influences a lot of what I do. I mean, it’s been really fun to merge the chemical synthesis with some of the biosynthesis, getting to get the best of both worlds because I feel like there’s some areas where chemical synthesis is actually– might be better, especially in really low-yielding products. We’re interested in some of the hormones that Streptomycetes use, and isolating those is not really terribly feasible. And so, in that sense, that allows us to do that. But on the other hand, we’re also really interested in enzymes to do some of the reactions that chemists find really challenging. So that balance is really fun.
JACKIE: Enjoy the best of both worlds. You can tackle it all.
BETSY PARKINSON: We’re trying to.
JACKIE: So I was reading on your website that– speaking of hormones, that you’re also using hormones as this chemical communication signal.
BETSY PARKINSON: Yes.
JACKIE: And using these hormones as a way that bacteria can talk to each other and then up-regulate or trigger some of these cryptic clusters or these biosynthetic clusters we don’t really know what they make. Do you want to talk a little bit about that?
BETSY PARKINSON: Yeah, definitely. So we are really interested in some of the gamma-butyrolactone (GBL) and butenolide type hormones. And so, these hormones actually oftentimes will bind to receptors within biosynthetic gene clusters. Specifically, these are Tet repressors that oftentimes turn off these biosynthetic gene clusters. And so we’ve been really interested in trying to find new hormones that can activate receptors and clusters that haven’t previously been explored.
And so we are chemically synthesizing these in order to then actually put them onto the bacteria to see if we can then see changes. And we’re primarily doing this by mass spec seeing different levels go up and down. We’re pretty early on in that project. I will fully admit that, but it’s been fun, so far, trying to play with that a little bit.
JACKIE: So I guess the organisms you’re working with, to see how they respond, where do they come from?
BETSY PARKINSON: Yeah, that’s a really great question. So we do a couple of different things. Most of them are actinobacteria. And so we get a lot of them from databases of organisms, so things like the NRL database – or online catalog, I guess. So we’ve also been able to get soils from Purdue campus itself and been able to actually have several undergrads from the lab go out and get soil from different areas around their dorm and things like that. And we’ve been able to isolate new bacteria from that as well.
DAN: So that I’m not ignorant, is there a difference in concept between– so we just talked to Aaron Puri [coming up in a future episode!] and we were talking about signaling molecules. And is there a difference between a hormone and a signaling molecule and a quorum sensing molecule or–
BETSY PARKINSON: Great question, yeah. They’re all the same thing. I mean, oftentimes these GBLs are also called quorum sensing–
DAN: There are ways that bacteria communicate with one another.
BETSY PARKINSON: Exactly. And they’re also involved– so they’re also involved in sporulation and other–
DAN: True.
BETSY PARKINSON: –aspects of the life cycle, but we’re just particularly interested in their connection to these biosynthetic gene clusters.
DAN: OK. So maybe if we talk in a really simple way, the idea here is then that the bacteria are growing. They’re, what, excreting at a base level these signaling molecules. And as they grow up, more signaling molecules are there. And so at a certain point, they’re more detectable to the other organisms and they– I don’t know hear each other. It’s chemistry, right? Not–
BETSY PARKINSON: Exactly, yeah. So chemicals are their way of talking. You bring up an excellent point though, and I think this is an area that is a little bit unclear whether for Streptomyces and actinomycetes, whether they can cross talk with these guys? And so there have been a couple of examples where they show cross talk. But oftentimes, what’s been shown today is it’s more a quorum sensing within a single species.
DAN: Within a species. Genus?
BETSY PARKINSON: So we don’t know yet.
DAN: Yeah, OK.
BETSY PARKINSON: I will fully admit.
DAN: OK. OK, cool.
JACKIE: So they’re very much developed their own language based on–
DAN: Sure.
JACKIE: Yeah, they’ve evolved. That’s pretty – that’s pretty amazing. I guess, I also have a pretty ignorant question. So if you have these organisms in a soil sample–
BETSY PARKINSON: Yes.
JACKIE: –how does that signal move from one– because, I mean, the organisms don’t necessarily move.
BETSY PARKINSON: They’re not moving. No, they definitely aren’t. And so this is a really great question. I think that there is diffusion through the soil–
DAN: Sure.
BETSY PARKINSON: –but I think that that’s something we don’t have a great sense of how far they really can diffuse. These are generally very potent, so picomolar to nanomolar levels. So they don’t have to get a ton in order to sense that signal, but it’s a great question, not naive at all.
DAN: Right. Picomolar, you might have to tell people what that number is.
BETSY PARKINSON: So micromolar, 10 to the negative 6th. Nanomolar, 10 to the negative 9th. Picomolar, 10 to the negative 12th.
DAN: Yeah. So very–
BETSY PARKINSON: Very, very–
JACKIE: Very sensitive.
BETSY PARKINSON: Yeah.
DAN: Yeah.
JACKIE: It’s like whispering–
BETSY PARKINSON: Exactly.
JACKIE: –to each other.
BETSY PARKINSON: And that’s what they are. They don’t want other people to hear them talking, so other people – other bacteria probably.
DAN: Yeah. We’re really anthropomorphizing now. But that’s OK.
BETSY PARKINSON: I’m good with that.
JACKIE: So I guess when you get a new organism or a genome, let’s say, and you’re looking at clusters, is there something that kind of triggers to you like, oh, this one might need some special communication to turn it on so that you can see the resulting product?
BETSY PARKINSON: Yeah. So that’s a really good question. I think at this point, we can’t predict whether or not one’s going to be silent or not. So the example I think of is really actinorhodin and Streptomyces coelicolor versus Streptomyces lividans. They both have the genes. The genes are pretty much 100% identical. We don’t know why one is expressed over the other. As far as whether we’re interested in it or not, we are really looking for these Tet receptors.
And oftentimes, also, the biosynthetic genes for the hormones are also right next door to these receptors as well. And so oftentimes, the receptor– the hormone biosynthetic gene cluster and a gene cluster for natural product might be all together. And so that’s how we decide what we’re going to look at. But these have also actually been shown to– some of these hormones have been shown to regulate things very distal from them. So just because they’re nearby doesn’t necessarily mean they won’t. They’ve been turned these clustered situated regulons, but that might not be quite as true as we once thought it was.
DAN: So it’s very empirical then how you tackle this.
BETSY PARKINSON: Yeah.
DAN: OK.
JACKIE: Do you want to talk a little bit more what a Tet receptor might be?
BETSY PARKINSON: Sure.
JACKIE: If we’re looking through a genome, how–
BETSY PARKINSON: Yeah.
JACKIE: –what would that– what would that–
BETSY PARKINSON: So a TetR receptor, so those historically are tetracycline receptors. And so they were originally, I think, discovered in E. coli, but we can utilize blast searches or other things like that in order to find them. And so they have a– they have their own Pfam. And so oftentimes, we’ll just use blast and see other things with that Pfam and prioritize those. Does that answer your question?
JACKIE: I guess for a more generalizable, what does a TetR receptor do?
BETSY PARKINSON: Yeah, that’s a great question. So a TetR receptor, so these are typically repressors. So typically they are expressed, and then they will off– they usually serve as dimers, and then they will bind to certain sequences of DNA. And when they bind to those certain sequences of DNA, they essentially make it not possible for the RNA polymerase to bind and then express or transcribe whatever is downstream of that.
And so these typically are repressors, and then these hormones, when they get to a certain level are able to bind to these receptors. When they do that, they have a conformational change which causes them to essentially fall off the DNA allowing the RNA polymerase to come through and transcribe the genes downstream.
JACKIE: Very nice.
DAN: And then just to make this abundantly clear to our audience, so the goal here then is to understand these regulatory mechanisms so that you can turn on the natural product, say clusters or expression systems so that–
BETSY PARKINSON: Exactly.
DAN: –you get the molecules out of the organisms that you’re trying to do.
BETSY PARKINSON: Exactly. We want to understand, can we utilize sequences of these TetRs to identify what molecule might bind them and then allow for their release from the DNA and transcription of biosynthetic gene clusters?
DAN: And I don’t want to jump on your SIMB talk too– and I don’t– actually, I haven’t even looked at your title.
BETSY PARKINSON: No, you’re good.
[LAUGHTER]
DAN: Do you have a favorite example of this or of some situation where this has worked for you that you might want to talk about?
BETSY PARKINSON: So as far as– we are in very early days on this. So we are right now– we have just recently finished the synthesis of the first set of these molecules and are exploring the promiscuity of one of the previously best studied SVR receptors. And so previously, a lot of these have been studied– haven’t been able to be studied very well just because these hormones are produced at such low levels. It’s hard to isolate them. And previous syntheses of these typically were not enantio or diastereomeric pure. And so there were studies that were done previously with SVR. But because those molecules were oftentimes diastereomeric mixtures, that makes it really challenging to actually interpret the data. And so we’ve been able to get these–
DAN: In terms of concentration and–
BETSY PARKINSON: Exactly.
DAN: –the real details of it. Yeah.
BETSY PARKINSON: And so that that’s where we are right now with the gamma-butyrolactone story. But–
DAN: So then tell us how this ties into your JGI project.
BETSY PARKINSON: Yeah, that’s a fantastic question. And so with what we have been doing so far, we’ve primarily been working with previously characterized gamma-butyrolactone receptors, and now we really want to explore some of the ones that are unknown. And so we’ve done the sequence similallity network analysis where we look for other receptors with sequence similarity to some of these known ones. What’s really interesting is we have clusters that do cluster with known receptors, but we also have ones that are completely their own cluster. And so we’re hypothesizing that the ones in clusters with known receptors might bind similar ligands. And so one of–
DAN: OK. The similar proteins are going to bind similar molecules. Yeah, OK.
BETSY PARKINSON: Exactly. And so we’re working with the JGI to actually explore 92 of these receptors both from clusters with known and completely kind of orphan clusters, a different type of orphan clusters than we usually talk about–
DAN: Sure.
BETSY PARKINSON: –to see whether we can determine both the DNA they bind because that’s really useful in learning what biosynthetic gene clusters they might be regulating if they’re regulating something that’s distal from where they’ve actually produced. And once we figure that out, we have designed GFP based plasmids where we can actually then put these in E. coli and add in our compounds of interest to start to understand whether this hypothesis is correct and whether we can activate these, utilizing some of these already synthesized molecules.
DAN: OK. These receptors are coming from which organisms?
BETSY PARKINSON: So these receptors are coming from– it’s primarily actinobacteria. Mainly actinos. Yeah.
DAN: Yeah. I mean, those are the systems that are best understood right now. So yeah. If you can expand that repertoire, then yeah, you’re helping things a lot for sure.
JACKIE: So this will definitely add to the toolbox of ways that people are genome mining. You have all these unknown clusters that if you see these regulatory elements, that you might have a catalog of signals or molecules, hormones = you know, these forms of communication that you can just add in to your fermentation and try to see what happens.
BETSY PARKINSON: That’s exactly what we’re trying to do. And we’re also trying to generate syntheses of these molecules so that we can actually get enough to then be happy to send them out for people to actually test that.
JACKIE: Very nice.
DAN: Very cool. Yeah, so that’s a new JGI project. Just came out from a CSP this year.
BETSY PARKINSON: Yes.
DAN: So how long do you expect that’s going to take?
BETSY PARKINSON: Yeah. So it’s going to take a little bit of time. So we are starting with doing DAP-seq and we’re hoping I think to get the DAP-seq done in this next year. And then, probably, it’ll take another year or two to get all the screening done with the molecules and the plasmids.
DAN: Sure… My audience might not know what DAP-seq is. [Note: Check out this JGI story on DAP-Seq technology.]
BETSY PARKINSON: OK. DNA affinity purification sequencing. And so the way this essentially works is you will mix together your receptor of interest with genomic DNA, and then allow that to bind. Your receptor also typically has some tag so that you can then pull down the receptor with that DNA still bound, wash away any unbound DNA, and then release that DNA from your receptor and then sequence that in order to determine what sequences your receptor best binds.
DAN: Beautiful explanation. Yeah. So the goal here then is to figure out exactly what sequences your receptors are binding to in the DNA. So then you can then go back into the genome and look where those sequences are, and then you can know what those regulators are regulating.
BETSY PARKINSON: Exactly, yeah.
DAN: Perfect. OK, great.
JACKIE: So another project I think you have in the lab right now is really bringing in, again, you talked about synthesizing the hormones. And I think there’s another project where you’re also using semisynthesis–
BETSY PARKINSON: Yes.
JACKIE: –with some of these cyclic molecules.
BETSY PARKINSON: Yes.
JACKIE: You want to talk a little bit about that?
BETSY PARKINSON: Sure, I’d love to. So coming from a synthetic background, when I started doing a lot of this natural product production within bacteria, they’re great at it, but it also– one of the things I got frustrated with is how little material you could get out. And so one of the things that I got really interested in is actually seeing whether we could go into the genomes and predict what the natural product might actually be.
And so we are specifically looking at non-ribosomal peptides, looking in genomes for ones that are cyclic. And so we do this– we’ve primarily been looking at NRPSs that are nearby what’s called a “PBP-like” thioesterase
DAN: OK.
BETSY PARKINSON: So in typical NRPSs, typically, they end in a thioesterase. And so that thioesterase at the end of this large multimodular protein allows for release from the DNA, either as a linear–
DAN: From the protein.
BETSY PARKINSON: Or from the protein, sorry. Thank you. So when you release this from the protein, essentially, you can release it in a couple of different ways. And so you can release it as a linear product, so just hydrolyzing, or alternatively, you can use one of the nucleophilic residues on your peptide to cyclize. You can use the N-terminus to get a head to tail peptide, or you can use a nucleophilic sidechain to make other ring sizes.
When we were starting off this project though, we wanted to be able to predict which one it was. And one of the challenges, at least right now with thioesterase on these NRPSs is that it’s actually pretty challenging to predict.
DAN: For sure. Yeah.
BETSY PARKINSON: And so start–
DAN: Every single one is unique, right?
BETSY PARKINSON: Exactly.
DAN: So you never really know exactly what you’re going to do. And often, you don’t even know the molecule that’s going to be produced by the NRPS in the first place. Right.
BETSY PARKINSON: Exactly.
DAN: Yeah.
BETSY PARKINSON: But what was really interesting is when I started my lab in 2018, several papers came out right in a row all about this cyclase called SurE. And so SurE cyclizes a cyclic peptide called the surugamides. And what’s interesting is that it’s a standalone enzyme, and it is, at least to date, all other kind of examples that have gene clusters with associated molecules that have these [penicillin binding protein] PBP-like thioesterases are all head to tail cyclized.
There are only about 10 examples, but we thought that was an interesting thing to start with. So we utilize these PBP-like thioesterases as what we initiated our search around. And so we found examples of those, and then looked for NRPSs nearby, and then we used both AntiSMASH and PRISM predictions to get an idea of what that NRPS peptide might actually look like. We fully admit that these are natural product inspired, not true natural products–
DAN: Sure.
BETSY PARKINSON: –because obviously those predictions are not perfect, but what we were able to do is we– from just an initial set of 500 of these PBP thioesterases, we were actually able to find approximately 300 with NRPSs nearby. And of those once we did the predictions, about 140 unique cyclic peptides. And from that, about 130 of them were not previously known. So
DAN: Very cool.
JACKIE: And those are all coming from actinobacteria or–
BETSY PARKINSON: Those are not all coming from actinos. So that, we have a little bit wider spread since we’re just doing bioinformatic searches. The majority of them are actinos, but not all of them are.
JACKIE: Interesting.
DAN: OK.
JACKIE: Interesting. Do you want to say a little bit about what a PBP is, a PBP binding protein?
BETSY PARKINSON: Yeah. So PBP is a Penicillin Binding Protein. And so most people think of this as the targets of penicillin, so very important in that peptidoglycan cross-linking. These enzymes show a lot of similarity to them in the primary structure. However, the reaction that they perform is different. So they’re not doing that cross linking, they’re instead doing a cyclization reaction.
DAN: Got it. Got it.
JACKIE: Interesting. Do they still have the active site serine?
BETSY PARKINSON: They do still have an active site serine. They have the full tetrad that are found in PBPs. So–
DAN: OK.
JACKIE: Well, that’s interesting. Well, I guess with these cyclic natural product inspired molecules that you have, what assays are you testing them in? Because a lot of these compounds are really bioactive.
BETSY PARKINSON: Yeah. So that’s a really great question. And so within the lab, we have both antibiotic assays for ESKAPE pathogens as well as anti cancer assays, and so we’ve screened them for both of those. And we’ve actually found a decent number with decent antibiotic activity. We haven’t found any with anti cancer, but it is what it is. We also are collaborating with others to screen in other assays. So if you have an assay you like, we’d love to send you a plate of cyclic peptides to test.
DAN: I’m sure there are people who listen to this who have assays.
JACKIE: Yes.
DAN: Oh, yes.
BETSY PARKINSON: Yeah.
JACKIE: No, I think that that’s remarkable, and then you have the capability and the flexibility to really alter residues and then also look to see, is it accepted? Can it be cyclized? And I think that really does a beautiful job of marrying synthetic chemistry, building these products that then you can then apply enzymatic reactions to form that product and then test it in appreciable yield.
DAN: Yeah.
BETSY PARKINSON: I guess the other thing that’s kind of exciting is we’ve actually been able to find ones that can do cyclic tetrapeptides, which are really challenging to make chemically. So that’s been a really exciting part of this journey, is finding these enzymes that are capable of making those strange ring systems.
JACKIE: Why? Is it just because of ring strain or is it– I guess, what’s the efficiency between maybe a tetrapeptide versus a pentapeptide?
BETSY PARKINSON: So for chemical synthesis, a pentapeptide is so much easier to make.
DAN: Really?
BETSY PARKINSON: Well, so one of the issues is in order to make the tetrapeptide, that’s a 12 membered ring. And there’s extreme ring strain in 12 membered rings. You also have to change the amide conformation. So cis versus trans in order to cyclize at that small of a ring, which is highly unfavorable.
DAN: Oh, I did not know that. That’s cool.
JACKIE: But nature can do this.
BETSY PARKINSON: But nature can do it much better than a lot of synthetic chemists. Don’t tell my colleagues.
JACKIE: We won’t, no. No, it’ll be our secret.
[LAUGHTER]
DAN: Yeah, with our hundreds of listeners.
[LAUGHTER]
JACKIE: No, but that’s interesting that nature has evolved an enzyme that actually can use that. So I guess for synthetic chemists though too, can you use the active site of that enzyme in catalysis or designing a synthetic reaction that kind of mimics what nature has evolved?
BETSY PARKINSON: Yeah, that’s a really good question. So you’re asking, could we try and do this with something that’s smaller than the enzyme – some bio-organic type catalyst? I’m not sure. That’s a good question. I will fully admit that we are still trying to figure out why this particular enzyme can do these small rings, and so I think we need a better understanding of that. We have a crystal structure, and we’re working on getting crystals to understand it. And maybe after that, when we have a better understanding of how it does this, it might be possible.
DAN: Sure. Yeah.
BETSY PARKINSON: I’m just trying to think because you are primarily wanting to focus on the research side of things, correct?
DAN: Why? What are you thinking?
BETSY PARKINSON: No, I just am thinking about– when I think about the other things that I do and just the other hats I wear. But–
DAN: What other hats do you wear?
JACKIE: What other hats– how many hats do you have?
BETSY PARKINSON: Well, obviously, I teach, but the other thing that’s been a big thing for me is thinking about mental health for graduate students. And so during the time that I have been an assistant professor with the support of my department head, we’ve actually made a graduate student mental health committee and we’re trying to help more with that, because I feel like that’s an area that’s really a huge area of unmet need within our community and thinking about how best to tackle these issues.
And I think they were really brought about– we all became more aware of it during COVID. But even pre-COVID–
JACKIE: It was– yeah.
BETSY PARKINSON: It was–
JACKIE: –creeping in I think–
DAN: Oh, yeah. I mean–
JACKIE: –really high.
DAN: Yeah. Graduate school is a pressured environment, right?
JACKIE: Yes.
DAN: And so there’s always– yeah. It’s tough. Yeah, it’s definitely tough. I mean, I have my own issues. Right? So what is a committee — or what do you do for that?
BETSY PARKINSON: Yeah. So we’re doing a couple of different things. So one of the things that I’m really proud of is we’ve been able to bring a CAPS therapist– CAPS, y’all don’t know what CAPS is. [Note: Counseling and Psychological Services (CAPS) at Purdue.] We’ve been able to bring therapists from the University to actually come to our Department once a week and have– they’re called Let’s Talk sessions where grad– well, any student, grad student or undergrad, can go and actually have their 15 minute blocks. And so they’re not true– they’re not therapy. They’re times to go and talk to someone about what might be going on in your life and what options you have to seek.
DAN: Yeah.
BETSY PARKINSON: So that’s one of the things we’ve done. And one of the other things we’re working on doing right now is actually developing a set of mental health advisors. So these would be faculty members, staff members, and senior graduate students who want to participate who obviously are not therapists, but are trained in mental health awareness by the Mental Health America first aid training. And be people that students can go and talk to if they are having issues and can help them find the right resources.
DAN: Find the help they need, yeah. For sure. Yeah, that’s amazing. OK.
JACKIE: That’s a great resource to have. I mean–
DAN: That’s so important.
JACKIE: Really, really important. And it’s a great the Department supports that and recognizes that. And because it is– I mean, with COVID, I just– like Dan was saying, grad school is difficult. And that just add a whole other level of complexity and–
BETSY PARKINSON: I guess the other thing that is kind of fun that we’ve started that is a different subject is from microbes to medicine labs. So this is– we’ve been working with both high schools as well as local children’s museums so that kids can actually isolate bacteria from their own backyards.
DAN: Oh, OK.
BETSY PARKINSON: It’s been really fun to work with them. So we do these lab-kit-in a boxes that we’ve sent around the country. So we’ve sent them to schools in Alabama, Illinois, Indiana, Tennessee so that high school students can get a chance to actually learn a little bit more about how these microbes are isolated, but also learn a little bit more about where antibiotics actually come from. And so–
DAN: Very cool.
BETSY PARKINSON: –that’s been really fun. And so if you have a high school that wants to do this, but–
DAN: Where can they– where can these high schools go to learn more about this?
BETSY PARKINSON: They can go to my website.
DAN: OK.
BETSY PARKINSON: So parkinsonlaboratory.com.
DAN: Perfect. Great. OK.
JACKIE: Is it just kids that can get those or only the high schools?
[LAUGHTER]
BETSY PARKINSON: We are focusing on high schools and children’s museums. We unfortunately cannot send elsewhere at this point due to restrictions on money.
JACKIE: Got it.
DAN: Fair enough. Yeah. OK, great. I guess, tell me about the step wise process on this learning experience.
BETSY PARKINSON: Yeah. So there are two different processes. So for the children’s museums and things like that, it really is– we give them a plate. They bring in their soil. They plate it, and then they take it home.
DAN: Got it.
BETSY PARKINSON: And they watch it.
DAN: The Petri dish.
BETSY PARKINSON: And the Petri dish, they take home. And essentially, for the younger students, we obviously can’t put any antibiotics or antifungals in there. So they get just a smattering.
JACKIE: That would be an introduction to natural products right there.
BETSY PARKINSON: Obviously not. We can’t do that. So they get interesting things that grow, but it’s fun. They can send in pictures if they want and things like that. But for the high school students, we actually do put in some antibiotics. And we put [an antifungal,] cycloheximide, in there. They know that that’s in there, obviously, and we take the proper safety precautions. But they can choose if they want to send it back to us, and we actually will do a little bit further evaluation actually. Grow up extracts and test it. Because one– For the high school students, they have an extra step, a couple extra steps actually. So they plate it, but then they choose one or two colonies to re-streak and try to actually get a pure culture. And then the last step of it is, actually, they do a competition. So they choose two people, and they actually do a cross streak to see whether one of their bacteria can kill the other.
DAN: Make them fight. Yeah.
BETSY PARKINSON: Exactly.
JACKIE: We do that in our lab.
DAN: I know. We did, yeah.
BETSY PARKINSON: Yeah, Exactly.
JACKIE: And they take bets on the side, and you just– makes a day go by faster.
BETSY PARKINSON: But it also makes it more fun because it’s a competition. And I mean–
JACKIE: In more than one way.
BETSY PARKINSON: Exactly. And they can then, if they wish, send them back to us and we’ll do a PCR analysis to sequence the 16S and things like that to figure out what they actually might be.
DAN: Very cool. All right.
JACKIE: Yeah, that’s really neat. So do you follow up with the students to say, hey– if they do send you back the plates and say, oh, we found these really cool molecules, just to keep them going and–
BETSY PARKINSON: Yeah. We definitely follow up with them afterwards. And so we don’t always have the ability to find the exact molecule that’s active. But if we do, we try and keep them informed about it, and we definitely tell them what type of organism they found and all of that.
DAN: For sure.
JACKIE: So what if a student, the high school student, gets your kit, finds this really, really interesting. Is there an opportunity potentially for them to come work in the lab and actually do some of these experiments themselves in an actual lab setting?
BETSY PARKINSON: For students in Indiana, I’m going to say we could definitely probably do that, because of the travel to and from. It’s something that we would like to be able to offer that to anyone. There’s obviously limitations with resources and things like that.
DAN: Sure.
BETSY PARKINSON: But if a student was really interested in it, sure, we’d love to have them come and–
JACKIE: That’d be really a neat thing to leverage with Societies based on what component they might be interested in like genomics, metabolomics, just basic chemistry, natural products chemistry, and seeing about fellowships or something. Just to get high school students really active and then bring them into the fold into natural products.
BETSY PARKINSON: Yeah
DAN: Are you familiar with Tiny Earth?
BETSY PARKINSON: I am familiar with Tiny Earth, yeah. It’s very similar. They’re doing it at the college level. So–
DAN: Yeah, for sure. And JGI is sequencing quite a few of the things that end up–
BETSY PARKINSON: Oh, I didn’t realize that.
DAN: Yeah.
BETSY PARKINSON: OK. Oh, awesome.
DAN: So yeah. If you get any cool strains you need some help, we’ll probably be able to help out.
BETSY PARKINSON: We’ll probably take you up on that. So be careful what you offer.
[LAUGHTER]
DAN: Yeah, I’ll bend Nigel’s ear and we’ll get that to happen.
BETSY PARKINSON: Awesome. Sounds good.
[LAUGHTER]
JACKIE: Nigel, make it happen.
[LAUGHTER]
BETSY PARKINSON: Yeah.
DAN: Very cool. OK. Betsy, it was so awesome to talk to you today. This was a big, wide ranging conversation. I’m really glad that we got a chance to do it.
BETSY PARKINSON: Yeah. Thank you so much. It’s been a lot of fun.
DAN: Yeah.
JACKIE: Thank you. And congrats on the project, and this is just exciting the full gamut of everything. And thank you for what you do for the community.
BETSY PARKINSON: Of course. Thank you.
DAN: Great. Thanks.
Show Notes
Some of the topics we talked about:
- Synthetic Natural Product Inspired Cyclic Peptides
- Synthesis of Gamma-Butyrolactone Hormones Enables Understanding of Natural Product Induction
- Betsy’s lab webpage and the page on the From Microbes to Medicines outreach program
- JGI Release on DAP-Seq: Enlarging Windows into Understanding Gene Functions
- Purdue’s page on mental health resources. It might not be fully applicable to your University, but full of good advice. If you need help, please seek it out.