My Pint of Science talk

Added: 2026-05-27

[00:00:00]Assistant Professor at Loyola Marymount University, and this is my first year there, and I've been doing some really cool work. I think it's cool work with some really awesome students. I know they're awesome students.

[00:00:15]So, I'm going to tell you a bit about a protein from a bacteria. And that might sound really boring, and you're like, "I just want to drink."

[00:00:23]Um but, you can drink while you hear about this really cool protein from this really cool bacteria.

[00:00:29]And so, this really cool bacteria has this property where it can actually go and clean up the environment. And we're trying to figure out kind of how the proteins inside of this bacteria work.

[00:00:44]So, trivia time. Are there bar bar trivia as a thing, right? This is my first time at a bar, so I like don't know anything about bars other than what I see on the TV.

[00:00:55]I'm legal. I just don't don't care.

[00:00:58]Okay, so trivia time.

[00:01:01]The film Erin Brockovich surrounds a toxic heavy metal that got into ground water, causing a variety of health problems. What was that toxic heavy metal?

[00:01:14]Not lead.

[00:01:18]Yes. Yes, hexavalent something is definitely correct. I'm impressed.

[00:01:23]Hexavalent chromium.

[00:01:25]So, chromium six.

[00:01:28]And so, PG&E used this chromium six uh to prevent corrosion in their pipes, and then it uh leaked into unlined ponds, uh got into the ground water, not good stuff. Really not good stuff. Caused a direct or diverse array of health problems. Not good for the people, and ultimately also not good for PG&E. They had to pay $333 million.

[00:01:56]dollars. But, that is better than the effects that actually had to happen that actually happened to the people. And so, it affects a large variety of tissues um tissue systems. Pollution comes from a variety of sources. So, a lot of industrial processes, even though they don't line the pipes with that anymore, they're still um coming from various industrial processes as well as if you're like, "Oh, well, we just plant the industry." It also comes from natural sources. And the wildfires might be making things worse.

[00:02:33]So, thankfully, here we've got our superhero bacteria, Bacillus safensis. And so, Bacillus safensis is really awesome bacterium.

[00:02:43]And it has this property where it Well, it's got a lot of cool properties, but it's been proposed to be used for bioremediation.

[00:02:51]So, don't worry, there won't be too many big words, but bioremediation means break things down. We've got the bio, like life, so living organisms. And then remediation, let's clean up the messes that we've made. And so, bioremediation uses friendly organisms like Bacillus safensis, our superhero, in order to clean up the environment. And so, there's not a good lot of good solutions for actually cleaning up the chromium six from the environment. And so, typically, it just sits around there, and then that land can't be used for anything. But, what if we can bring in some really cool bacteria that are actually able to detox that environment and help plants grow in the process?

[00:03:33]And so, this bacterium Bacillus safensis is going to be our friendly bacteria.

[00:03:38]And now we need to talk about our friendly protein.

[00:03:44]And so, strains of this bacteria are able to adapt their metabolism in order to thrive in the presence of this chromium.

[00:03:53]When we talk about metabolism, we're just talking about the breaking and making of molecules. So, if you think about like a LEGO set, you can break it down and like a big LEGO thing and then break it down into smaller pieces and then build those into new things and then break those down and build new things. That's basically what metabolism is. But, you don't have a system like organisms can't just use a single thing like we are able to with our hands make a bunch of different things. But, in organisms, they have different enzymes that are kind of like the people who are doing the different steps.

[00:04:28]Um and so, if we think about what kind of needs to happen in order to detoxify this chromium, they've got to really adapt their metabolism.

[00:04:37]But, before I tell you about how they adapt their metabolism and the purchase at the heart of it, let's just talk a little bit more about how super cool this bacteria is.

[00:04:47]So, if we think about chromium, we talked about that we got hexavalent chromium. That's the chromium six state.

[00:04:53]That's a really toxic, really bad state.

[00:04:56]But, there's also this benign chromium three and that's a different version of chromium.

[00:05:02]And then that and so, the bacterium we're going to talk about is actually able to convert the chromium six, that toxic form, to the chromium three, the non-toxic form.

[00:05:14]And so, in order to actually convert it, first it needs to be able to survive in the presence of this chromium. And so, we need to make sure that these bacteria can actually survive there before we ask them, "Okay, well now detox it."

[00:05:27]So, let's think about some of the limits of chromium. So, the EPA has a limit of 100 parts per billion in drinking water. And this is total chromium, so the good stuff and the bad stuff. It's harder to measure them separately, so they're just like, "Okay, well let's measure it all and then say 100 parts per billion." Where a part per billion is about a drop in an Olympic size swimming pool. And so that's the limit for the EPA, that red arrow.

[00:05:55]Now, if we think about in California, they're actually like, "Okay, well, now let's actually just measure the really bad stuff and put a limit on that." And so that's 10 parts per billion. So again, that's like 10 drops in an Olympic swimming pool is the level that is like the legal limit.

[00:06:14]This bacteria we were growing it over 100 parts per million. So now we're talking about like 100 cups of chromium.

[00:06:24]This had this toxic metal in an Olympic swimming pool.

[00:06:28]So this bacteria is able to live there.

[00:06:31]And it's not just able to live there and thrive there, but it can actually reduce that chromium.

[00:06:39]And so I'm not going to go into all the details. I'm happy to answer any questions, but we've got a couple of different experimental techniques that we can use in order to measure both that total chromium and the chromium six. I mean, and yeah.

[00:06:56]And so what you can see here is just um So on this side of things, you see the total chromium if you don't have bacteria, that's that black bar.

[00:07:09]And then when you have these different strains of bacteria, you can see that on the right side is the total chromium and then you can see both when you put the bacterium in there, the total the amount of that toxic form goes down. Perfect. Okay. So these bacteria are able to live in the chromium, they're able to detox that chromium.

[00:07:31]And now we want to think about, "Okay, well, how might they be doing that?"

[00:07:36]Getting back to the idea of could we use these bacteria, these nice friendly bacteria, can we stick them in environment and get them to help clean up chromium.

[00:07:47]So, as we this is back to our talking about the metabolism. So, our interconverting of all those Lego Lego building stuff. Um and so, we these bacteria are going to need to adapt their metabolism in order to carry out all these processes.

[00:08:05]And so, this is not to scare you. Don't worry.

[00:08:10]This is kind of just This is just part of the metabolism that happens in an organism. And now we're going to quiz you. No, no we're not going to quiz you on this. Don't worry. Don't worry. Okay.

[00:08:21]I'm going to make things easier for you, okay? So, we've got this road map of metabolism. We're just going to go to a single stop, so the citric acid cycle.

[00:08:32]Sometimes you might know that it's just the Krebs cycle, the the tricarboxylic acid cycle.

[00:08:40]We're going to go here. This is kind of like the heart of metabolism.

[00:08:44]And then we're not just going to go through this whole thing. We're just going to take you a single enzyme in there, okay? So, we're looking at the heart of the citric acid cycle, this enzyme malate dehydrogenase. And the citric acid cycle was at the heart of metabolism. So, what you need to understand is this protein is really really important for this bacteria to do all this metabolism. And its metabolism is really important for it to be able to detox that chromium.

[00:09:12]And the chromium in the environment is really really bad, and there's not good ways to clean it up. But, this bacterium offers one of those ways that you can clean it up.

[00:09:24]Okay. So, malate dehydrogenase, or MDH, it's so important in not just bacteria, but in all organisms. And it's so important in us, as well as in other like eukaryotic cells, so basically animals, plants, this sort of thing. In humans, we have two versions of malate dehydrogenase. That's how important it is.

[00:09:47]But, in bacteria, they only get one.

[00:09:52]And this is true for the bacteria that have to do things like produce the chromer and live in the presence of the chromer and all that stuff.

[00:10:01]So, this and that's not the only difference for some of the bacterial versions of this protein.

[00:10:09]So, the versions of malate dehydrogenase that are mostly studied are the versions like we have where they're this kind of a dimer. And so, basically, malate dehydrogenase is kind of made up of multiple copies. And so, if you think about I don't have any props here, but you can kind of think about like two two subunits, so one copy of the protein, one copy of the protein hanging out.

[00:10:36]That's a dimer. You get two of those together, now you got four copies of the protein working together, that's a tetramer. And that's what we have with these bacterial this malate dehydrogenase we're working with.

[00:10:49]It's this one of those cool like four-part ones.

[00:10:53]And we don't know that much about those ones, especially compared to the two-part ones.

[00:10:59]So, we want to learn more about these.

[00:11:02]And so, we have some questions. So, this is my first semester uh my first year at LMU, we actually just had our first semester like literally just finished today. Or even though Thank you. Thank you. Okay. And so, we've been starting to answer some questions, but we don't have answers to all the questions yet, but here are some of the questions that we're thinking about.

[00:11:27]What effect does that tetramerization have on MDH function? So, why is it like does it matter that it's four-part instead of two-part?

[00:11:40]Do the subunits communicate with one another? So, are like the two halves talking to each other? And what are they talking about?

[00:11:48]Are they like what talking about that cool drink that they had at the bar?

[00:11:53]Okay.

[00:11:54]What specific parts do what?

[00:11:58]So, in order to do this, we kind of want to start with a baseline.

[00:12:04]I like to think about this kind of like doing a sibling study. So, the one that we really really are interested in is this Bacillus safensis.

[00:12:12]But Bacillus safensis, there's not much known about it.

[00:12:15]And there is more There is more known about Bacillus subtilis. And so, Bacillus subtilis is another bacteria that's really similar to Bacillus subtilis. It's not quite as cool, but scientists know a lot more about it. It's often used in the lab as a kind of model for bacteria species as a whole.

[00:12:39]Um and it is also used in biotech to make various products and things.

[00:12:46]So, it's cool. It's cool. Don't get me wrong. But Bacillus safensis is is the really cool one.

[00:12:52]But we want to be able to compare the two of them. And so, we're going to take the proteins, the malate dehydrogenase protein, the version that's in the subtilis and the version that's in the safensis.

[00:13:04]They're almost identical in their sequence. And so, if we can compare their properties, we can try to figure out like where those differences between them are coming from.

[00:13:15]Kind of like when you have sibling studies, you know that their genetic makeup is really similar, and so that makes it easier to kind of find the differences.

[00:13:28]Okay.

[00:13:29]So, we're going to do a couple times of characterization.

[00:13:32]So, we're going to do biophysical characterization, which is basically what the protein looks like, how it kind of moves around, and stuff.

[00:13:42]As well as enzymatic characterization.

[00:13:44]So, malate dehydrogenase is an enzyme.

[00:13:47]An enzyme is a protein that can kind of interconvert pieces. So, going back to our LEGO kit, the enzymes are the things that are actually making taking things apart and putting them together in different ways.

[00:14:01]And so, we want to look at how this protein does the does this conversion of these two molecules called malate and oxaloacetate.

[00:14:10]Don't need to worry about that. Just know it's kind of like interconverting some LEGO pieces in a really important way.

[00:14:17]Okay. So, this is we actually just the other day put this online. So, this is a preprint. So, it means that basically it's not a public peer-reviewed paper yet, but it's up there online for anybody to go and read.

[00:14:35]And so, this is my wonderful team or some of my wonderful team. Some of the So, this is Haley and Nicholas. They were doing work with me at my previous institution.

[00:14:47]And then we've got Karina, Alice, Brian, and Liam, who are part of my team at LMU. And then we've got some collaborators, Chris Bernstein and Julia Thomas at James Madison University. And sorry, this slide kind of cut off.

[00:15:03]But, this is kind of some of the work that they've collected, and I wanted to show you all show you all their faces because they did some really awesome work, and I'm really proud of them. This is This is a team of undergraduates. So, undergraduates often don't get to do research. And so, I think it's really important. That's one of the privileges of my life is being able to um work with undergraduates and have their work um get out there.

[00:15:32]Okay. So, we can't do everything though, so that's why we have collaborators. And so Dr. Bernstein and Juliet, what they did was a technique called sex sacks.

[00:15:42]Now, that sounds really dirty, but it's small angle X-ray scattering.

[00:15:46]Um but bottom line is you shine some light at some solution that has some proteins and then the light interacts with the proteins and then depending on how the proteins are shaped, you'll get a different shape signal.

[00:16:01]And so I'm not going to take you through how to interpret this and we don't need to worry about that. All you need to worry about is that the red and the black seem to be like overlaying each other pretty nicely. One of those is funces, one of those is subtilus. So, basically the proteins have really similar shapes is what this is showing you.

[00:16:21]And then over here we're showing you that it matches the modeled um size of a tetramer. So, all good. We've confirmed it's got tetramers and got really similar shapes.

[00:16:32]And they've got really similar enzyme activity. So, basically when you see the lines go over here, that's just showing, "Okay, we're building up some we're converting those molecules." And again, they're pretty similar to one another.

[00:16:47]Okay, so now you might be like, "Okay, this is like a bait and switch. I got here and you're like, 'Oh, this really cool enzyme in this really cool bacterium.' And now you're like, 'Okay, well they're the same.' Well, don't you yet.

[00:17:05]Okay, because it's time for the wiggle test.

[00:17:13]Oh, the wiggle test is the exciting part. I did the sofi dance.

[00:17:18]Okay, so we're going to make these proteins do the Scooby dance and see if they dance differently.

[00:17:26]To do this, we're going to be using a technique with another fancy name. We're just going to abbreviate it to DSF.

[00:17:33]And so the DSF is a way that you take your proteins and you make them do the Scooby dance and see how eager they are to do the Scooby dance.

[00:17:44]And so basically heat gives protein.

[00:17:47]Heat makes proteins wiggle. The more heat you they have, the more wiggling they're going to do.

[00:17:53]Proteins are kind of held together.

[00:17:56]Their like overall shape is held together based on these kind of like weak bonds and interactions. So if you think about holding hands with someone and now you're doing the Scooby dance together, if you start dancing too vigorously, you're going to come apart.

[00:18:11]That's what happens with the proteins, too. When they start dancing too vigorously cuz you give them too much heat, then they're going to unfold.

[00:18:19]And the tighter they were holding hands with one another, the more heat it's going to take them to unfold, to come apart.

[00:18:27]And so the more stable a protein is, the more heat it'll take to get them to to come apart.

[00:18:34]And then we can go and look and see how much heat it took for them to come apart.

[00:18:40]What we found was that if we're at a pH of eight, we take both those proteins and they they have the same like tendency to to come apart. So they take the same amount of heat for them to un- unlock their hands.

[00:18:55]But if we lower the pH, we make things more acidic, well now we see a differences. And so now you can see that these these dots are no longer overlying. We found something that's different between them and we see that now for the subtilis, it's a lot sturdier than it was before. It's a lot sturdier than the subtilase.

[00:19:20]So, now we have even more questions. Cuz now we want to say, "Okay, how is the pH affected?"

[00:19:29]And so, so far we know that the BSAP and BSAP MDH are tetrameric, so they've got the four subunits that they have very similar overall shapes and similar enzyme activity.

[00:19:47]And we know that the BSAP MDH shows pH-dependent changes that were not seen with the subtilase.

[00:19:57]And we've got a lot of cool stuff that I just don't have time to go into here, but we we've got cool stuff.

[00:20:06]Okay, and we still have a lot of questions, though.

[00:20:10]But, we're on the way to finding answers.

[00:20:14]And hopefully those could be then applied for societal benefit.

[00:20:19]So, I've been talking about our work, what we've been doing like in a test tube and stuff, but our kind of we're hoping that we could take these findings from a test tube and then kind of take those and use that to help optimize the use of these bacteria.

[00:20:38]And so, I want to thank my team. And so, in addition to the authors that I showed you before, I've had a couple of other students recently join my lab. So, we've got Brooke and Alby up there. And then I want to thank the previous students from my other institution, um everybody at LMU.

[00:21:01]And our collaborators, the Malagasy Probiotic Yogurt Community, uh which allows undergraduates to get experience doing research, like authentic research throughout the course of the year.

[00:21:14]And they've been really great, too.

[00:21:19]Uh if anyone wants to learn more about my lab, it's got a cool website.

[00:21:25]And thank you all. I know this is probably not what you came to a bar for, but hopefully you took a little bit away from it. Um and if you have any questions, I'm happy to answer now, or you feel free to email me. I'm also online and stuff as the Bumbling Biochemist. So, I really just have a passion for helping people learn. And so, I really appreciate you all uh giving me the opportunity to talk to you. And uh yeah, so happy drinking.

[00:22:03]Thank you.