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Interviewer: Aging on a microscopic scale, up next on The Scope.

Announcer: Examining the latest research and telling you about the latest breakthroughs. The Science and Research Show is on The Scope.

Interviewer: I'm talking with Dr. Adam Hughes, Assistant Professor of Biochemistry at the University of Utah. Dr. Hughes, when I think of aging, I think about getting wrinkles, going gray, slowing down, but you think of aging on a different scale. How do you think about aging?

Dr. Hughes: We think about aging, I'd say, more at an organismal level or even more specifically than that, the cell biology level. Sort of looking at not how aging affects the whole organism, but how it affects specific structures within our cells within different tissues.

Interviewer: A lot of your research focuses on one component of the cell, an organelle called the mitochondria. First of all, can you orient us to the mitochondria? What does it do?

Dr. Hughes: Sure. Mitochondria, they're known as the powerhouse of the cell. Historically, they're drawn as kidney-bean-shaped structures you see in all the textbooks, but mitochondria do a lot of different things in metabolism. They're a double-membraned structure that produces lipids, they're involved in oxidative phosphorylation, they basically make energy for cells and also participate in a large number of metabolic reactions.

Interviewer: Studying the mitochondria is actually a whole field in and of itself. What's some of the evidence that mitochondria is involved in aging?

Dr. Hughes: Mitochondria has drawn a lot of attention, not only for its role in changes in mitochondrial function affecting how long an organism lives but it's also become very clear that as mitochondria become faulty with age, which happens for a number of different reasons in a number of contexts, this is also been linked to driving the development of a large number of age-associated disorders as well.

Interviewer: And as it turns out, there's quite an elaborate system for getting rid of or repairing mitochondria that does not function well. You've just published some research about this in the journal "eLife."

Dr. Hughes: I haven't explained much of what we've been doing. We've been using yeast as a model system to understand the aging process. So it's pretty cool that the single-celled eukaryote, the simplest one, and a lot of labs have been using it for a very long time to understand lifespan regulation type processes. And so our lab actually uses this organism in it does, in fact, age. A yeast cell, we measure aging by the number of times a cell can divide before it dies. Now, it happens about 30 times before a cell dies. And so in these old cells, it started several years ago when I was a postdoc at the hutch in Dan Gotchling's lab, we found it in old cells there was damaged or dysfunctional mitochondria.

So we decided to use this system to try to see what we can learn about how cells handle this, how they respond, what can they do. And we went into it, at the time, wondering if we could model pathways that were already known in mammals, one of the most prominent being the autophagy-dependent or self-eating pathways that had already been fairly well characterized. And so when we went into this, we set out to see in an old cell, do we see pieces of mitochondria? And we're visualizing all this on the microscope, being ripped off and degraded after they're damaged/

And we saw that there was, in fact, this going on in old yeast cells and so we initially thought it was similar to what had been observed already. And that's how we got into it. We didn't go into it looking for new pathways, but eventually it sort of, as we got more into the details of what this is going on, we realized they totally new type of quality control that we discovered that was different than anything else that had been described before.

Interviewer: So what is it? What did you find and how is it different from what was there, what you knew before?

Dr. Hughes: In general, in this field, it was always thought as a mitochondria became damaged that these systems aren't very smart for a lack of a better word, that they would go to the damaged mitochondria and just degrade the entire thing. Which seems a bit wasteful and so when we came into this we thought the same thing and we were using a protein on the mitochondria. We are monitoring it by microscopy and we could see that it was being eaten. But what we did that went beyond these original studies and other systems was there are about 1000 different proteins in the mitochondria. And we just started looking at other ones too. So most of the studies in mammalian cells had only looked at one or two and made conclusions.

And so we went on and looked at all mitochondrial proteins to see how they were all being degraded. What we discovered, based on this, and this is the big crux of this study, is that the pathway we've uncovered now is the concept and idea that mitochondria actually, under these situations when they're damaged, don't just get totally degraded as a whole. They can actually be broken down piece by piece. And what I mean by that is certain proteins can be basically selectively sorted out and removed from the mitochondria and degraded and the rest of it can be left intact.

Interviewer: Do you have any ideas yet of whether this pathway relates to aging or how it relates to aging?

Dr. Hughes: We got into it looking at aging, but we think it's actually going to have many applications in other systems, especially sort of metabolic-related disorders. We've been working from the standpoint of seeing the structure and it forms, it's sort of very descriptive. It forms, it gets released, it gets degraded and certain proteins go into it and certain ones don't. But understanding what the importance of it is and why it happens has been a much more difficult question. And we are starting to get at that.

We didn't get into a lot of it in this currently published paper, but some of our certain experiments are directed in the range of one thing that we did include here. And one big clue to us is the identity of the proteins that are actually degraded by the system. So again, the mitochondria has about 1000 proteins in yeast and when we looked at the proteins that are degraded by the system that we discovered, it's only about 10% of those proteins. And it turns out it's very selective for one particular group, which is a group of proteins called the mitochondrial nutrient carrier protein.

So the role of this group of proteins, there are about 30 of them, in the in the mitochondria, they basically facilitate the transport of all nutrients into and out of the mitochondria. So we're working from the fact that these are the main targets of this pathway and we think that giving us a big clue as to what might be its role. And so clearly, they're metabolite transporters. They're very heavily involved in all aspects of metabolism. And so we're testing the idea now, a hypothesis that this pathway may be very important for actually protecting mitochondria in times of changes in cellular metabolic state.

Interviewer: It's also kind of amazing to me that, especially in something as simple as a yeast, that there are still entire processes that we're still discovering.

Dr. Hughes: Yeah, I think that's definitely a really cool point. Sometimes, yeast in this day and age will get a bad rap. You hear all kinds of things that yeast research is done and things that we used to only be able to do in yeast, now we can do them in humans and other organisms. But what's sort of the big arena right now, I'd say, in the yeast field is cell biology. And it's been very limiting for a long time, the ability to look at all different proteins and all different things within the cell.

And what's really cool in the yeast field is that many, many years ago now, probably 10 years ago, a lab developed a collection of all yeast proteins tagged with a fluorescent protein, GFP. So it's about 6000 proteins in yeast. And so we have strains that contain every single one of them. And so there are a number of labs across the country, including ours, that are essentially using this collection to look at how the entire protium changes not in terms of levels, but in terms of localizations in cells.

And people are discovering a lot of new things that no one had ever noticed simply because we have the tools to do it now. And this is what's really nice in yeast. And we still don't have the ability to do this in mammalian systems yet. So I think the future will get there and we'll be able to start looking at these. But there's a lot of new, I'd say, cellular structures, cellular compartments that form under very particular conditions that people just hadn't seen before.

Announcer: Interesting, informative, all in the name of better health. This is The Scope Health Sciences Radio.

Announcer: Examining the latest research and telling you about the latest breakthroughs. The Science and Research Show is on The Scope.

Interviewer: When you look in the mirror, your reflection is essentially the same but everything is reversed. My guest, Professor of Biochemistry, Dr. Michael Kay, has figured out how to make mirror images of the proteins in our bodies. These small changes can have big impacts and his discovery has exciting applications in disease therapeutics.
Dr. Kay, your research involves making mirror images of proteins. Can you explain what you mean by that?

Dr. Kay: Proteins come in both left-handed and right-handed versions, and for reasons we don't understand, early in evolution nature picked left-handed. But in theory, they could have been right-handed and these are proteins that would be the mirror images of natural proteins. Just like your hands, they're structurally the same, they look the same, but they have a different handedness to them.

Interviewer: Why would you want to make mirror images of proteins?

Dr. Kay: Proteins and their smaller cousins, peptides, are extremely useful as therapeutics. There are many of them available against all sorts of diverse diseases, but they generally suffer from a problem that they get degraded in the body pretty rapidly by a process called proteolysis, so they're broken down into their component amino acids and then they stop working. This makes these drugs relatively expensive. It means they don't last very long in the body, and you have to give frequent doses of relatively large amounts.
It turns out that these mirror image proteins, because nature has never seen them before, they're not degraded this way. They have the potential to last essentially indefinitely in the body.

Interviewer: How do you go about making a mirror image protein?

Dr. Kay: A normal protein is made just naturally in a cell. A mirror image protein, since nature doesn't know how to make these proteins, we have to make them ourselves chemically from scratch. That process means taking the amino acids that make up a protein and stitching them together, one by one, individually to make up a protein. Once the protein is actually made, there's this second step where you have to fold it into a precise 3D geometry that's the functional state of the protein so that the protein is active.
The way we like to think about it is when a protein is made, both in the cell or in the lab, it basically looks like a limp piece of spaghetti. It's just a long string, and then that has to be folded up into a ball of yarn that's the particular shape that really dictates the function of the protein. In a cell, that process is handled by a set of machines called chaperones, and these take that spaghetti as its being synthesized and assist that to fold to the proper configuration. These are really essential machines in the cell without which life is not possible.

Interviewer: What were you able to figure out with this work that has not been done before?

Dr. Kay: In this work, we synthesized the largest protein that has ever been made by synthetic means. It's a 312 amino acid protein. The specific question we were asking is the chaperones in a cell, could they be used to fold these mirror image proteins even though they've never seen them? Do they have that kind of secret ability to handle this?
Initially that sounds kind of crazy. Things in the cell generally don't perform functions that they're not designed to perform, but we thought this might be possible because chaperones are a very special machine. They're extreme generalists. Basically, the particular chaperone we're working with folds hundreds or maybe even thousands of different proteins of all different shapes and sizes. Because it's such a generalist and it can't grab onto any very specific feature of any one protein, we thought it might be such a generalist that that would even extend to these mirror image proteins. The chemistry just didn't exist to do this previously. Now, with this paper, it's finally gotten to the point where we can make these large proteins that do depend on chaperones and then test whether the natural chaperone has this secret ability to fold mirror image proteins. And in fact, it does.

Interviewer: How do you know when you have a right-handed protein? It's not like you can look at it in a microscope.

Dr. Kay: It's extremely difficult, actually. Just like if you're looking at your image in a mirror or looking at your left and right hands, what's really different about them? The answer is almost nothing. They're the same size. They look the same. They have the same chemistry. Everything is basically identical except this somewhat difficult to describe property of handedness. You can tell your left from your right hand. There's just something that's different about them.
There are a few very specialized techniques, mostly spectroscopy techniques, that can be used that actually can tell the difference, and it just turns out through some very esoteric science that you can have a type of light that interacts differently with a left-handed versus a right-handed sample and then we can detect that using this advanced spectroscopy.

Interviewer: What are the next steps?

Dr. Kay: We need these mirror image proteins to do mirror image drug discovery, to discover these mirror image peptides and proteins that are not degraded by the body. We've been limited to relatively small targets in the past, but now we're really interested in expanding mirror image drug discovery to common cellular targets, things like cancer receptors, proteins involved in inflammation, heart disease, diabetes. These tend to be in that 300 amino acid range. Now that we can make these kinds of proteins and fold them, those types of targets are now available. Now we're excited to start attacking those types of targets with mirror image drug discovery.

Interviewer: One thing that I was really struck by is that you're interested in making a mirror image organism and you give the example of a D. coli, which would be the mirror image of an E. coli. Why would you want to do that?

Dr. Kay: That's right. That is a very good question. We may be a little crazy on this, but the idea is if we can make an organism that was completely synthetic and had all of its components that are mirror image to a natural organism, it would function exactly the same way as the natural organism, except it would eat mirror image food and it would produce mirror image proteins. This would allow us to get around having to manually synthesize individual proteins, so then hundreds or thousands of targets would become readily available using standard cell expression of proteins rather than this tedious individual synthesis by chemistry.

Interviewer: So it would be a little mirror image factory.

Dr. Kay: Exactly.

Interviewer: Fascinating.

Dr. Kay: Then there are some kind of spacier applications as well as we get into this deeper. Further ahead, if you have a mirror image organism, it's interesting, just like your hands in the mirror, it would function exactly the same way, but the mirror image organism would not be able to interact with the environment. We're very interested in this idea of coming up with mirror image organisms to allow us to study very dangerous pathogenic organisms or toxins in the lab in a safe way, because they wouldn't be able to attack our body. They'd only be infectious to a mirror image human, which doesn't exist yet.
Bring up Ebola, which has been so important recently. We talk about this idea of Debola. A huge problem with the Ebola virus is it's so dangerous to study that it really slows research down. For instance, our lab, we can't study the virus directly. There are no facilities in Utah that are sufficient for studying Ebola, so we work on individual pieces that are much safer and we collaborate with the US Army, which has a lab that's capable of handling Ebola. But these labs are very specialized, very expensive, and they really slow down the research. So if there was a way to work with something that had all the same properties of Ebola but was completely safe and noninfectious to humans, we could do our research on that kind of mirror image organism and then flip it back to the original left-handed version to test against the real virus at late stages. We could do drug discovery, mechanism, really do some interesting studies that right now are just too difficult from a safety point of view.

Announcer: Interesting, informative, and all in the name of better health. This is The Scope Health Sciences Radio.

Interviewer: What is a physician trying to find when they look into your eyes? That's next on The Scope.

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Interviewer: A lot of times on TV you'll see, or if you've ever even gone to the doctor yourself, they got the little flashlight and they start looking in your eyes and I've always wondered, what are they looking for? We're with Dr. Troy Madsen, emergency medicine at the University of Utah Hospital. In your particular situation, in the emergency room, if you get out the light and are looking into somebody's eyes, what are you trying to figure out?

Dr. Madsen:It's going to vary depending on who I'm looking at. But it's just part of a standard physical exam that when I see a patient I will document something that says on the chart, PERRL. What that stands for is the pupils are equal and reactive to light. And the pupil is the black part of your eye so I'm looking at that. I'm looking at are they the same size, and when I shine a light into it does it close? Does it react to that light and constrict like you'd expect?

And the relevance of that kind of varies from person to person. I mean, in the average person, it's not really a big issue. I can just kind of look at you and look at your eyes and say, "Oh, yeah, they look fine." But in different situations I'm looking for different things.

So if someone comes in after a head injury and they've been in a trauma, I really want to get a good look at those eyes to make sure the pupils are equal, because if they're not, that can be the sign of potentially something very serious in the brain that is affecting the brain's ability to send that message to the eye to have that pupil squeeze down and constrict. That can be a sign of some kind of bleeding in the brain, which is the more serious thing I'm really looking for there. So that's kind of the number one thing I'm looking when I do that.

The other thing I'm looking for often times, and this is a tough thing to do sometimes in the E.R., but sometimes I'll try and get a look at the back of the eye at what's called the fundus of the eye, called a fundoscopic exam, where I'm looking at optic nerve, so where the nerve inserts into the back of the eye. And if a person has a lot of pressure in their brain from bleeding in the brain or something like that, I can actually see swelling on that nerve. So that for me says this person potentially has something that's raising the pressure in their brain, like bleeding, a tumor, something like that. So that's kind of the other big thing I'm looking for when I do that.

Interviewer: All right. So two reasons you would look into somebody's eyes, none of them related to the eyes. Are there things you're looking in somebody's eyes for if they have an eye issue?

Dr. Madsen: Oh, certainly. Yep. And that's one of these things where if someone . . . and usually there I need to have something that's going to push me toward that, someone saying I'm having a lot of pain in my eye or I feel like just something is scratching my eye. And there, I'm going to do an even more detailed exam. I'll kind of flip their eyelid out, kind of like kids do to gross people out. So I'm doing that to look for some kind of piece of dirt or a splinter or something like that in the eyelid itself that's scratching the eye.

Interviewer: And that actually happens?

Dr. Madsen: It does.

Interviewer: That's gross.

Dr. Madsen: Oh, it does, yeah. And then I'm looking at the cornea, so the front part of the eye and sometimes you'll look at that, you'll see little pieces of metal that are stuck on there, say, from a welder or someone who is working with metal. I can see that. Sometimes I'll see a rust ring there. You can actually see rust on the eye itself from a piece of metal that may have been there and then came off.

And then I'll do a very detailed exam, something called a slit lamp exam. It's basically a microscope where I'm sitting down kind of with this microscope that focuses right on the person's eye. I'm looking in the front part of the eye for any, what we call just any cells, any inflammation there that would suggest a lot of irritation in the eye itself. And then I actually put a little thing on the eye that's kind of like a dye that will light up to look for any scratches.

Interviewer: Okay.

Dr. Madsen: Which is what's called a corneal abrasion.

Interviewer: Sure.

Dr. Madsen: So lots of different things you're looking for there on the eye.

Interviewer: So any of these tricks that people can try at home? For example, taking the flashlight and if a person's pupils aren't dilating properly, knowing that you might potentially have an issue?

Dr. Madsen: Yeah, and that's something you can do. If you've had a head injury and you feel comfortable looking at that, you can even look at your own eyes in a mirror and just say, "Do my pupils look like they're the same size?" If you have a family member who's had a head injury, you can shine a light in their eye, just watch, does that pupil squeeze down? And at the same time that one squeezes down does the other one do the same thing? And if it's not, those are concerning things.

Interviewer: Is time of the essence for any sort of eye injuries, generally?

Dr. Madsen: It is, yeah. So time is really of the essence for eye injuries if you actually have something that cuts the eye open. So if we have what's called an open globe injury, so the globe being the eye, the big eyeball, if something actually gets in there and cuts that where there's fluid coming out, time is absolutely of the essence. You need to get to the emergency department. We call our ophthalmologist and they'll oftentimes get you to the operating room to repair that emergently.

Interviewer: All right. Any final thoughts on the eyes?

Dr. Madsen: Final thoughts on the eyes. Obviously, a lot of these things are things we are going to need to do in the E.R. but, like you said, you can kind of take a look at the eyes at home. And certainly if anything comes up, make sure you come in so we can evaluate you further.

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updated: October 31, 2018
originally published: March 19, 2014