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Yiorgo Skiniotis (Stanford University)

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#3 — Yiorgo Skiniotis of Stanford University has been using cryoEM to study transmembrane receptors. In this episode of Cryo-Talk, Yiorgo joins Eva Amsen to chat about the potential of cryoEM to gather more information about signaling pathways. We also hear more about his love of cinema and classic literature, why he’d be a fisherman if he had to pick another job, and why it’s so important to have various research interests. Tune in to hear more!

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Eva Amsen interviews Yiorgo Skiniotis in episode #3 of Cryo-Talk

This is an automated transcript and may not be 100% accurate.

Intro/Outro (00:01):
Welcome to Cryo-Talk a Bitesize Bio podcast, sponsored by Thermo Fisher Scientific featuring conversations between your host, Eva Amsen and experts in the field of cryo-electron microscopy.

Eva Amsen (00:15):
Today on Cryo-Talk, we are joined by Yiorgo Skiniotis, Professor of Molecular and Cellular Physiology, Structural Biology and Photo Science at Stanford University. We’re talking about his research career.

Yiorgo Skiniotis (00:28):
I was always curious as to how we can bring different methods, sort of together

Eva Amsen (00:36):
Catching up on classic literature.

Yiorgo Skiniotis (00:38):
These are the days that I’m grabbing again with, with James Joyce.

Eva Amsen (00:42):
The surprising job he would choose if he wasn’t a scientist.

Yiorgo Skiniotis (00:46):
I often fantasize about being out there and catching fish.

Eva Amsen (00:50):
And the importance of cultivating diverse research interests.

Yiorgo Skiniotis (00:54):
None of us wants to do the same thing over and over again. It becomes, it becomes very boring

Eva Amsen (01:00):
All in this episode of Cryo-Talk. Hi and welcome to Cryo-Talk. I’m Eva Amsen and I’m here today with Yiorgo Skiniotis, Professor of Molecular and Cellular Physiology, Structural Biology and Photo Science at Stanford University. His research group uses Cryo-EM and 3D reconstruction techniques to study macromolecular complexes in cell signaling, such as transmembrane receptors. Yiorgo how are you today?

Yiorgo Skiniotis (01:32):
I’m good. Thank you very much for having me.

Eva Amsen (01:34):
Yeah, thanks for joining me. So as I told people, you’re at Stanford now, but can you tell me a little bit about your research background? So what, what brought you there?

Yiorgo Skiniotis (01:46):
Oh, what brought me there? Life, science. So I, I, I grew up in Greece. I studied though Biochemistry at the University of Leeds in the, in the UK. And then I did you know, two months sort of diploma thesis that was actually on electron microscopy to crystallography of all things and sort of that, you know, level of direct imaging that an electron microscope would provide you compared, let’s say to other structural biology techniques sort of pick my interest and it was one of the techniques that was definitely not as much in fashion as it is now. So I did my PhD at EMBL in Heidelberg at the European Molecular Biology Lab. And I actually did Cryo-EM of kinesin microtubule complexes, trying to understand how kinesin motors changed their confirmation as a function of their nucleotide state. And that enables sort of a walking mechanism on, on the microtubule. And then it was pretty clear at the time that you know, that was obviously Helical Reconstructions, because we were trying to select microtubules that you could apply helical averaging, but it, but it was clear that the, the next thing was actually, or it wasn’t, I, I shouldn’t call it next, but it was still in the earlier stages of development. It was single particle analysis, right. Without having the need for symmetry for example, in, in going after individual molecules and averaging them. So I, you know, decided to do a Postdoc at Harvard Medical School. I was actually in Tom Kirchhausen’s Lab and there I learned single particle Cryo-EM. I spent most of the time then to actually do negative stain analysis.

Eva Amsen (04:03):
Oh, wow.

Yiorgo Skiniotis (04:04):
Uh because the majority of the target, so I, I had done Cryo-EM for my PhD, but for, for most of my postdoc, I actually did negative stain because the targets that I selected were very, very small, like receptors, for example, small signaling cell-surface receptors. But that also, you know, negative stain is also a bit of an art, right? It has a lot of caveats, but you know, it’s, it’s, it’s, it’s art in imaging and you can extract very useful information. And, you know, when I moved to the university of Michigan as an assistant professor, I built a research program around signaling receptors, cytokine receptors at the time. Then we started slowly going after G Protein-Coupled Receptors. I got tenured in Michigan and then I, you know, moved to Stanford about five years ago.

Eva Amsen (05:09):
Wow. And how are you liking it there so far?

Yiorgo Skiniotis (05:12):
I like it. Stanford is a, is, is, is an interesting place you can’t beat the weather, you know?

Eva Amsen (05:18):
Yeah. I mean, I’m in London, so I, I can’t imagine good weather, yeah. So one of my questions, which you actually already answered was how did you get started with Cryo-EM? So I guess you, you started during your PhD.

Yiorgo Skiniotis (05:34):
I started during my PhD. And it was, it, it was a very interesting time. I mean, I, I have to say it was one of the most fulfilling times that I ever had. My background is actually in biochemistry, right? So when I chose a, a Cryo-EM project, I sort of had to do everything from A to Z, from the molecular biology, the protein biochemistry learn Cryo-EM understand many of these concepts that at, at the time were somewhat esoteric and often the, the, the doubt of disputes resolution and, and what have you. But I also feel that this prepared me well for, for what was to come because I, I think I’m fortunate in, I, in that I developed sort of more well rounded approach to a structural biologic project. Right. Which is not just the, electron microscopy not just the image processing, but perhaps even more importantly, the target preparation, right. What, what are you looking at? How do you purify it, what state is it when, when, when you’re purify it and how you can fine tune the system that you’re interested in in order to get, you know, reasonable information.

Eva Amsen (07:05):
Mm yeah. Cause what, what are some of the, the advantages that you’ve found of Cryo-EM when you’re looking at receptor structures in particular?

Yiorgo Skiniotis (07:15):
Well, so I started looking into cytokine receptors and, and these receptors have sort of a series of Ig-like domains to put it simply, you know, small round domains that are connected, like beats on a string. Mm. So when you actually purify them and you take a look, you realize that these are very flexible assemblies. And, and this is the reason why, besides some small parts of these molecules that, you know, were determined by x-ray crystallography, you know, this flexibility essentially hindered [inaudible] crystallography on the full ectodomains. So the entire receptor in complex with its, with its Ligon. So the advantage of, of single particle Cryo-EM is essentially that you don’t have to go through crystallization and you can obtain information from different classes that show different distinct confirmational states. And that of course is also crucial to understand biology. Things are not static. Things are moving left and right, and, and up and down because they need to execute a certain type of, of, of work. So this is the, the true power of single particle, which I would argue. It probably has not been fully realized yet.

Eva Amsen (08:48):
Hmm. That actually brings me to, to my next question which is a little bit about the future. So you’re also director of Stanford Cryo-EM center. So I’m sure you’ve got a bit of an overview of how Cryo-EM is being used beyond your own work. Now, if you think like five to 10 years in the future, what are some of the, the exciting applications that you think we can expect of Cryo-EM?

Yiorgo Skiniotis (09:15):
Yeah. Well, I’m, I’m afraid I’m not gonna be able to tell you any, anything new here. You know, I think Joachim, in the first podcast that, that you hosted talked about time resolved Cryo-EM, this is definitely one of the next frontiers and, you know, our approaches are at their infancy. I would argue that Cryo-EM, single particle Cryo-EM is still not used to its full capabilities. And what I mean by that is that we’re still going after one or two structures at high resolution. And we don’t take full advantage of the ability of the technique to look at the entire end symbol, right? Because these, these are single particle single molecule measurements. I, if you wish part of the problem is that our approaches to the, to the whole sort of methodology come from, crystallography where we try to purify as well as possible macromolecular complexes in a single state, right? But the question is what would happen if we start in a controlled way, of course, inducing states. And instead of going after steady state samples, let’s say samples that are all in the same state, we see them in flux. And then we take advantage of these wonderful sort of classification methods that have been developed much more rigorously in the last few years to actually see how things move the entire dynamics. And how can you go from A, to, you know, B and seeing all the intermediate states, B C D for example. So time resolved Cryo-EM is definitely one of the next frontiers, of course, looking at more complex assemblies that somewhat recapitulate better. If, if you will, what happens inside the cell  is definitely one of the next frontiers as well. And what I mean by that, let’s take, for example, our own work on G Protein-Coupled Receptors, you see hundreds of you have seen hundreds of structures now, right now, you know, published, and this is a GPCR and a G protein, but, you know, a GPCR and G protein are not there on their own there are downstream effectors. There is a membrane environment, there are additional players into this whole system. So the question is, can we sort of individual or recapitulate higher order assemblies that give us a more pragmatic view, if, if, if you will, of how these things work. And of course, this is also the connective tissue with the other big player, which is, which is tomography cellular tomography, you know, looking at macromolecular complexes in, in C2. And there’s definitely a lot of development that is required in, in, in that space, particularly when we are targeting, you know, complexes that are beyond sort of the model complexes, you know, whether it’s ribosomes that are very easily distinguishable and you might have a lot to other ads or proteasomes, or, or, or what have you, how can we go after lower occupancy targets that are also more difficult to recognize, and this is where you’re having the interplay with fluorescence microscopy and doing correlative Cryo Electron Microscopy, light microscopy. So there’s gonna be an explosion of, of new developments there in terms of how do we go, how do we even go in a rational way after said targets?

Eva Amsen (13:27):
Yeah. That’s, that’s going to be very exciting once we get to that point. That’s yeah. Cause yeah, of course in biology, everything, everything is dynamic. It’s not just a, a snapshot of one or two molecules at a time. I guess speaking of dynamics let, let’s talk a bit about your own career and research again. Has there ever been a moment where things took a surprising turn for you in your career?

Yiorgo Skiniotis (13:57):
You know, I, I, I have to tell you, there is there was never really an aha moment that, you know, you wake up one day and you’re like, I have to change direction completely. You know, my positioning in all this, or, or, or, or my view is I’m, I’m, I’m trying to, to, to tell a story, right. And, and all these stories interconnect, and one story takes you to, to the next and the plot is, is very often very difficult to sort of plan ahead. Yes. I mean, you can plan the next couple of, of, of steps, but suddenly, especially as let’s say, you become a little bit more senior and you have been involved for a number of years in, in many different projects, then you start drawing connectivities between all these different plots. And this is what, this is where the new thing comes essentially, but yeah, to give you sort of a as, as straight answer as possible, I never had like, oh my God, you know I have to change completely direction. You hone, you, you hone your skill right slowly, and you see again how all these connectivities build and, and how you can bring additional. I mean, I always approach things from a more holistic perspective, if, if, if you wish. And I, I, I, I was always curious as to how we can bring different methods sort of together and see how they, they communicate with each other and, and tell part of this story, you know, whether it is Cryo-EM and molecular dynamic simulations, or more sophisticated biochemical experiments. And how can we go after dynamics with through single molecule biophysical measurements, let’s say threat for example,

Eva Amsen (16:21):
Hmm. It sounds like you’ve, you, you’re pretty in control then of, of like what’s happening next. So what do you think will be next for you in, in your career over the next few years? Do you have any exciting plans?

Yiorgo Skiniotis (16:35):
Well, I never said I was in control.

Eva Amsen (16:38):
But it sounds like you are.

Yiorgo Skiniotis (16:44):
I’m just, you know, I guess through the years I have become a little bit more paced mm-hmm if you wish, with what I’m doing. You know, part, part of being a scientist is, is also having, you know, developing an intuition and also the, the quick reflexes, if there is something interesting to, to, to follow, follow it up. And, and still I’m, I’m very, I’m, I’m convinced that there’s many things that we kind of leave behind because we don’t have the capacity to focus on everything. Right. I’m not quite sure about the, the next steps in my career now that Cryo-EM, has become much more mainstream maybe it’s time for me to do something else? I don’t know.

Eva Amsen (17:43):
Do something very surprising. And then the next time you’re on a podcast and I ask you about a surprising change in your career. You can talk about that.

Yiorgo Skiniotis (17:53):
Well, I guess, I guess what I’m trying to tell you though, is that, you know, whatever changes we decide to do are never, like, always smooth as every scientist, you know, you struggle with things, you, you try to figure out what is worth doing, how is it worth spending the next 10 years of, of your life in this particular space, in the scientific space, what questions are worth asking? Right. We, none of us wants to do the same thing over and over again, it becomes, it becomes very boring and yeah, I’m, I’m not quite sure I’m, I’m, it’s something that I’m, I’m grappling with on a regular basis. What is worth doing and where should I go next? Yeah. Right. And, and there are periods that I’m much more calm about what I’m doing. And there are other periods that I just wanna change everything around me.

Eva Amsen (18:52):
It’s it it’s like that for me, I don’t like doing the same thing over and over. And, and I notice a bike behind you is that is cycling one of your hobbies?

Yiorgo Skiniotis (19:03):
Cycling is one of my hobbies. I used to cycle much more indoors, especially at the start of the pandemic. Mm. But quite frankly, the weather is so nice around here that it was silly. I found myself staring for too long in front of a screen, you know? Cycling virtually. So I haven’t used it in months. To be honest with you, I’m just biking outside.

Eva Amsen (19:28):
And, and what else do you like to do for fun?

Yiorgo Skiniotis (19:35):
Yeah, it’s a good question. You know, I, I mean, I, it, it, it sounds mundane that it’s like, you know, I watch the occasional movie and catching up with cinema that is, is, is not the cinema that it used to be. I grew up with, you know, European cinema and, and, and movies. And I’m somewhat disappointed about what has been happening more, more recently. I’m not big into cooking. I, I, I suggested that you might ask me something

Eva Amsen (20:09):
Yeah.

Yiorgo Skiniotis (20:11):
This, I like looking for other people. I, I would like having friends around and of course the, the whole pandemic phase limited quite a bit. I like traveling. I, I, I travel you know, I started traveling again and I’m just like a kid, because we’ve all been so confined.

Eva Amsen (20:34):
Yeah.

Yiorgo Skiniotis (20:34):
For the last couple of years that now that traveling is opening up again, it just makes me very, very happy. And, you know, I spent time with, with, with my kid. That is my joy.

Eva Amsen (20:47):
That all sounds really nice. Yeah. Traveling, everyone has been traveling this year. I don’t know if the airline industries can keep up with it. So yeah. You mentioned that you love films. Do you have anything you can recommend us? Anything we need to watch?

Yiorgo Skiniotis (21:11):
I, I, I did watch and you can watch it on Netflix. Actually. I, I did watch The Power of the Dog by Jane Campion and, and I thought it was exceptional.

Eva Amsen (21:21):
I still that’s on my two watch list. I still need to see that. Yeah. I’ve got a couple of other quick questions for you. Do you prefer the city or the countryside?

Yiorgo Skiniotis (21:36):
Oh, I’m of two minds. I grew up in Athens and I think you know, it was, it it’s a chaos of a city, but once you know, it is an amazing environment, right. You have so much, so much input and different kinds of, of influences. And in a way I’ve been thinking about this, about my kid, because I would also like him to have the experience of, of, of the city. But I, I feel that I have also reached the point in my life that I like visiting cities. I don’t necessarily need to live in them. Cause I enjoy, so, you know, I, I live very close to, to campus and here it is just like I don’t know. It’s, it’s, it’s very quiet. It’s, it’s, it’s very green. There is no traffic. You don’t stress with anything else other than work. So I, I, I’ve learned to appreciate that. I’ve learned to appreciate the, the easiness of, of living in such an environment more countryside, if you will. But, but I always love visiting cities and, and tasting what they have to offer.

Eva Amsen (22:53):
Yeah. And you’re close to a city, so you can just. Whenever you need to. Yeah. I, I also see a bookcase behind you and I can’t see what’s in it, but do you have any books you can recommend us?

Yiorgo Skiniotis (23:06):
Oh you know, my, my perspective about books keeps on oscillating. Right? There are books that I, you know, adored as in, in, in my twenties that I could then look back again, you know, let later on so it it’s something that keeps on evolving. I definitely don’t read even half of how much I, I, I used to read you know, I, I feel that I’m, I’m doing a return though. I’m, I’m, I’m going back to more classical content if, if, if you wish, so, you know, these are the days that I’m grappling again with, with James Joyce that I, I, I think is not gonna be to the taste of the majority of your audience.

Eva Amsen (24:05):
Not light reading. And do you like music?

Yiorgo Skiniotis (24:13):
I like music, but not in a very sort of targeted way. I operate better with music on, on, on in the background, but you know, as, as long as it is not something very offensive to my ears and I can listen to many different styles.

Eva Amsen (24:41):
Yeah. Background music is a [inaudible].

Yiorgo Skiniotis (24:45):
There’s, there’s always a mix. There is always a mix between, you know I, I could, I could listen from, you know Iron Maiden to Depeche Mode go to something much more jazzy a a again, you know, it’s not about the style of, of, of music. I think it’s particular style has certain things to offer depending on how you feel and, and the time of the day. But usually I try to have music around, it keeps me calm.

Eva Amsen (25:24):
Mm-Hmm it’s nice to have some sound in the background. Um and, and this is always a hard question for, well, it maybe you’ve thought about it before, but if you’re not a scientist, what would you be? What is your ultimate reality career?

Yiorgo Skiniotis (25:42):
If I was not a scientist, I think I would be a fisherman.

Eva Amsen (25:45):
Oh, why?

Yiorgo Skiniotis (25:50):
Many different reasons, actually. So I, I, I grew up next to the sea. My parents were Islanders, so I used to spend many summers on, on islands and I’ve, I’ve grown this sort of very deep connection to blue. To the sea, [inaudible], the arid landscape of the Cyclades complex where my parents came from and being a fisherman is a very, very tough job, but is also a job that you’re always out there. And there is a lot of science behind it. There is a lot of science and, and, and the skills and, and the tricks. Like I, you know, I was noticing as a kid, you know, these people, they were really good fishermen and there’s some horrible fishermen than everyone else in between, but the good fishermen really had a system. I mean, they were thinking about things. It wasn’t just instinct or experience. Right. They knew where, where to go. They were doing their calculations and they had the ability to be out there and not be sort of enclosed within four walls. So, you know, that’s my, cause as all of us, we’re spending a lot of time in front of a computer. I often fantasize about being out there and catching fish.

Eva Amsen (27:22):
That sounds amazing. Now, now I wanna go outside and fish . And, and finally, do you have any advice for early career researchers?

Yiorgo Skiniotis (27:41):
You know, I have a very close friend, Roger Sunahara, who is a professor at UCSD. And you know, at, at the bottom of his email, he has this saying, just go crazy and do it, or just, just get crazy and do it. And, you know, I, I, I think, you know, the usual advice is be persistent and go after your dreams. You know, my advice is like, just, just get crazy and do it. You know, life is short, experience, go after new experiences and, and, and, and see what comes stop, stop, calculating everything.

Eva Amsen (28:28):
That’s, that’s amazing advice. And on that note, thank you so much for joining us today. That brings us to the end of today’s episode. So thank you everyone. Yeah. Thank you very much. Thanks everyone for listening. We’re watching Cryo-Talk today and have a great day Yiorgo.

Yiorgo Skiniotis (28:49):
Bye-Bye. Thank you.

Eva Amsen (28:51):
Bye.

Intro/Outro (28:53):
Thank you for listening to Cryo-Talk a Bitesize Bio Podcast, sponsored by Thermo Fisher Scientific to view all audio and video recordings from this series, please visit bitesizebio.com/cryotalk.

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