The First Sixteen Podcast - EP 005

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Chris: It is one of the cool feelings in science where, you know, when you are looking at something that nobody else has ever seen before.  And just understanding that I'm the only person who has ever seen this before. It's always very fun and makes know it always pushes you to to to make further discoveries.

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Sara: Welcome back to the First Sixteen. I’m Sara Boivin-Chabot.

Kirk: And I’m Kirk Finken. Today’s episode is going to blow your agricultural socks off.

Sara: We are dealing with that eternal, huge, double-sided challenge -- disease management in crops and saving nutrients in the food cycle.

Kirk: That’s a big challenge. And where are we finding the answer?

Sara: It’s in the smallest possible molecules. We are talking about enzymes.

Sara: An enzyme is a protein that exists in all living organisms – plants, animals, microorganisms. They are the workhorse molecules, nano-machines. They speed up the rate of virtually all chemical reactions in cells. In simplest terms – they help convert one chemical into another.

Kirk: They are like molecular change agents. Can they convert me into a better man?

Sara: They are doing it right now -- in every single cell of yours. But, don’t take me off topic. We spoke with one of our research scientists who specializes in enzymes.

Kirk: Yeah. He is using enzymes to detoxify disease-infected corn. He is working on a project that will have huge ramifications -- for corn producers, ethanol producers and livestock producers.

Sara: There are still a few years to go in the project. But they have made some important breakthroughs.

Kirk: This is novel, applied science that is happening here in the labs at Agriculture and Agri-Food Canada. Sara, are you ready? Get out your X-Ray Crystallographic Diffractometers.

Sara: I’ve got mine turned on.

Chris: My name is Chris Garnham, I'm a research scientist at Agriculture and Agrifood Canada in London, Ontario. And you're listening to the first 16.

Sara: Chris Garnham and his team have been working with industrial partners in the ethanol industry.

Kirk: Hold on. Hold on. Sorry. Before we get into speaking with him, I think we need a crash course in ethanol. Even before we talk about enzymes.

Sara: I think you’re right. Ethanol is a biofuel made with corn. It’s essentially like making alcohol. The majority of corn grown in southern Ontario is grown for bioethanol.

Kirk: And the byproduct of making ethanol is a delightful mash of corn that still holds a lot of nutrients. It is called dried distillers grains with soluble or DDGS.

Sara: That byproduct is fed mostly to pigs. So, it is a very valuable byproduct. It’s actually essential to the financially viability of the production of ethanol. And it is those nutrients that need to stay in the food cycle.

Kirk: The problem arises though when you have disease-infected corn.

Sara: There is a certain type of fungus that infects corn -- fusarium. That fungus is really cheeky. It creates its own protective armor in the form of a mycotoxin. But it has something even more special going on with its enzymes. I’ll let Chris explain…

Chris: What we identified is different strains of Aspergillus niger.  Which is a type of fungus.  This fungus, it produces fewmonosins which it uses as kind of a survival tool because it allows it to break down some of the living, I guess, some of the nutrients or I guess break down to the host on which it's growing.   But how do some of these fungi survive the toxic effects of their own toxins?  What we think we've potentially identified is, is a self-protection mechanism for this particular species of fungus, which is aspergillus Niger, where it can not only make its own toxin that allows it to, ah, I guess enhances its survival out in the wild.   But it also produces an enzyme that is capable of detoxifying this toxin so that it is no longer toxic to itself.

Kirk: Kirk: When we hear the words toxins and mycotoxins, it’s normal for alarm bells to go off. Important to note that mycotoxins are naturally occurring. They are produced by certain moulds (fungi) that grow on a variety of crops. And have been a part of the natural world way before humans appeared on the scene.

Sara: It’s brilliant in and of itself. But, listen to how it fits in to the solution.

Chris: You know this is kind of opened up some new research windows for us and trying to understand different types of protection mechanisms that these fungi have against their own toxins. And so we were fortunate enough to to identify what we think is one protection mechanism in this one fungus. And it's in its enzymatic nature, which is very interesting you know to me because I'm interested in the biochemistry and understanding how proteins function at the molecular level. But it has that added benefit of when it is an enzyme in terms of being applicable to solving contamination problems of food and feed that might have fewmonosins's in it.

Kirk: How do you figure out how they work?

Chris: It's kind of like anything in life where if you understand the structure of something, you get a much better understanding about how that thing functions. And say with even a shoe, if you have a shoe and you had no prior knowledge about what that shoe did, you could at least gain or infer some potential function for that shoe just based on its overall structure.  You see it’s in the shape of a foot.  On the underside there's kind of some rubber that's going to allow it to have some traction against a surface that you're potentially walking over. So it's the same thing when it comes to when it comes to enzymes. And if you can understand the structure of that enzyme at the molecular level it really gives you a solid understanding about how it functions. 

Kirk: I like the shoe analogy. So you go to figure out the structure of the enzyme or the protein.

Chris: Understanding the structure of a protein can be a very laborious process sometimes but when you finally do solve the structure of it, it's kind of that eureka moment where what was previously all blurry is now in kind of crystal clear resolution.  So it's almost like with when they first had the Hubble telescope and it was up in space and they realized like, oh, all the images that are coming back are blurry.  We need to go and do a couple of tweaks.
And once they finally fixed those issues with it, all of a sudden there they were getting back these crystal-clear, images of beautiful constellations and stars and everything up in space. And it's somewhat similar when we're doing some structural biology on various enzymes.

It's kind of struggle, struggle, struggle, until you kind of get the right conditions and then all of a sudden everything will lock into place. And now you have this crystal clear image of of this molecule that is almost incomprehensibly small but now all of a sudden you can see it. 

Sara: And how do you see it? How did you get the breakthrough?

Chris : That's part of the frustration of science, but then also part of the beauty of it as well, is that you can work on something for a really long time and once you finally do make that breakthrough, it kind of makes all of that struggle worthwhile.  When you're working with the protein, you can't see it with your own eyes. It's extremely small. Like we're talking nanometers in size, like you think of a human hair we are orders of magnitude smaller than the width of a human hair when it comes to when it comes to protein.
But there are tools and techniques that are available that allow us to potentially see what that protein looks like at the molecular level. And one of the main techniques that that I use in my lab is X-ray crystallography.

Kirk: Okay. X-Ray Crystallography. I made a joke about it at the start. It’s not really  household terminology. I am assuming it is just a fancy way of getting an image of the enzyme once it has taken a crystallized form. Is that right?

Sara: Exactly. It's a very fancy way to do those models we use to make in highschool chemistry class with sticks and play dough. You basically do an XRay of the enzyme and see things you have never seen before. So, I asked Chris, what he sees at that point, because it sounds like it is this exact point where the truth is revealed about these enzymes.

Chris: The eureka moment is when you get this diffraction pattern that all of a sudden you can you can see the electron density of an enzyme where in months and months of research before where you're trying to grow protein crystals, but maybe they're just not quite regular enough that it doesn't give you a very strong diffraction pattern or for one reason or another, it's just not quite working as good as you want it. Once you finally do crack it and you get a really strong and well result diffraction pattern, you can do a little bit of mathematics on it that allows you to all of a sudden instantly see the structure of that enzyme at the molecular level. And so I can always remember every time that I've done that for any protein that that I've solved the structure of, I will remember or I can remember where I was when I did that. And that's and it's it is one of the cool feelings in science where, you know, when you've done that, you are looking at something that nobody else has ever seen before. And so this is kind of the first time, first time knowledge, first time I've ever seen it, obviously. And just just understanding that I'm the only person who has ever seen this before. It's always very fun and makes know it always pushes you to make further discoveries.  So I guess when we say we can we can identify an enzyme that performs a specific function, but if we if we say we want to use that enzyme as a tool to remediate contaminated food or feed, we're just saying what is the best way that we can identify?  

Kirk: How do you figure out how they work?

Chris: And so it's kind of like anything in life where if you understand the structure something, you get a much better understanding about how that thing functions with even a shoe. If you have a shoe and you had no prior knowledge about what that shoe did, you could at least infer some potential function for that shoe just based on its overall structure.

You see what's in the shape of a foot on the underside. There's kind of some rubber that's going to allow it to have some traction against a surface that you're potentially walking over.

So it's the same thing when it comes to the enzymes. And if you can understand the structure of that enzyme at the molecular level, it really gives you a very solid understanding about how it functions.

Kirk: I like the shoe analogy.  So you go and figure out the structure…

Chris: Understanding the structure of a protein can be a very laborious process sometimes, and it's a lot of trial and error. But when you finally do solve the structure of it's kind of that eureka moment where what was previously all blurry is now in a crystal clear resolution.
So it's almost like with when they first had the Hubble telescope and it was up in space and they realized like, oh, all the images that are coming back are blurry. We need to kind of go do a couple of tweaks. And once they finally fixed those issues with it, all of a sudden there they were getting back these crystal clear images of beautiful constellations and stars and everything up in space. And it's somewhat similar when we're doing some structural biology on various enzymes.
It's kind of struggle, struggle, struggle until you kind of get the right conditions and then all of a sudden everything will lock into place and now you have this crystal clear image of this molecule that is almost incomprehensibly small. But now all of a sudden you can see it.

Sara: How did you see it?  How did you get the breakthrough?

Chris: That's part of the frustration of science, but then also part of the beauty of it as well, is that you can work on something for a really long time once you finally do make that breakthrough it kind of makes all of that struggle worthwhile. When you're working with the protein you can't see with your own eyes, it's it's extremely small.  Like we're talking nanometers in size, like you think of a human hair or orders of magnitude smaller than the width of a human hair when it comes to when it comes to protein. But there are tools and techniques that are available that allow us to potentially see what that protein looks like at the molecular level.
And one of the main techniques that that I use in my lab is X-ray crystallography.

Kirk: Kirk: Okay. X-Ray Crystallography. I made a joke about it at the start. It’s not really a household terminology. I am assuming it is just a fancy way of getting an image of the enzyme once it has taken a crystallized form. Is that right?

Sara: Exactly. It's a very fancy way to do those models we use to make in highschool chemistry class with sticks and play dough. You basically do an XRay of the enzyme and see things you have never seen before. So, I asked Chris, what he sees at that point, because it sounds like it is this exact point where the truth is revealed about these enzymes.

Chris: The Eureka moment is when you get this diffraction pattern that all of a sudden you can you can see the electron density of an enzyme once you finally do crack it and you get a really strong and well result diffraction pattern, you can do a little bit of mathematics on it that allows you to all of a sudden instantly see the structure, that enzyme at the molecular level. I can always remember every time that I've done that for any protein that that I've solved the structure of.

Sara: that’s so exciting! How does that feel?

Chris: Any time you make a discovery in science, that's what drives you.  There's different levels of discoveries that you can make and sometimes you can set an experiment up and you get the expected result and it's good. But every now and then you can make a discovery where you realize that we are the first people to understand this out of anybody in the world. I've been fortunate enough to have a handful of those types of of discoveries in in my career that I can always kind of remember where I was for each one of those. And in particular, for sure, this case. We have been struggling a little bit in trying to identify this enzyme. And we had finally we thought we've got everything figured out here. And we said our reaction up and let it go overnight. And we ran it on a on the machine the next day. And the result was kind of as clear as day. And we do OK here. We can see the starting product now. We treated it with our enzyme and converted it into the end product. This is doing exactly what we're expecting it to do. That allowed us to kind of fully appreciate the potential impacts that this enzyme might have later on.

Kirk:  What are the benefits of using enzymes instead of chemical means to detoxify the DDGS?

Chris: They're very cost effective in terms of their ability to decontaminate food and feed, and that's because when you have an enzyme, it's very good at doing that reaction over and over and over again. And so you only need to add a very small amount of an enzyme in order to clean what could potentially be very large amounts of toxin that are present in solution. And so it's always interesting in talking to people who maybe aren't as educated in terms of the biochemistry of some of these tools and letting them know that just a very small amount of protein or enzyme can have a very big effect on the end product of the food or feed that we're trying to treat. And so in this case, with the one enzyme that we have found, it's very specific for the particular mycotoxins that we're interested in, in converting into a less toxic form. And we don't have to worry about this enzyme targeting other types of molecules that are present within those food or feed samples, because the enzyme has evolved to be very specific for this one toxin that we're interested in. So we can use low amounts, very small amounts of this enzyme, which makes it economically feasible to detoxify very large amounts of contaminated food or feed.

Sara: This sort of work can take years.  From test to trails to commercialization.  Where are you at with this project?

Chris: So we're working with our industrial partners to test our various enzyme candidates out in their production systems, and so they are checking to see if it's going to be feasible to actually make this enzyme within saccharomyces, which is the yeast that they use for fermentation and bioethanol production. And if so, can produce to a high enough level so that it's actually going to be effective in detoxifying contaminated feed.  In terms of kind of an end date where we will know is it is it are we going to have a commercial product? We're not sure, hopefully within a couple of years of rigorous testing and understanding what are the best conditions for this enzyme to function at a at an industrial scale?

Kirk: This type of research takes time. But this discovery of this specific enzyme has quite a lot of potential. Like so many things in agriculture and food, there is a domino effect. Yes, it detoxifies the corn. And when scaled up, we are talking about saving waste, reducing greenhouse gas emissions. There are potential money savings, too. And all of those benefits far outweigh the time put into the research.  It would be nice to follow up with him later and speak with the industrial partners too.

Sara: Yes and in the meantime we are working on some great episodes.  We will be speaking with the young and dynamic next generation of food producers and processers of our sector.   

Kirk: and we are going to be speaking to a number of leading women about how the role of women is evolving in our sector.  The youth, the women all agents of change. 

Sara: If anybody wants to get in touch with us they can use #thefirstsixteen on social media to get in touch with us and in the mean time you know what to do.

Kirk:  Try something new.