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Luke Lavis: Bright Ideas in Fluorescence Imaging
316 Plays3 months ago
In this episode of the Back of the Napkin, we dive into the world of fluorescence imaging with Luke Lavis. Known for his pioneering work at the Janelia Research Campus, Luke shares his unique journey from the woods of Oregon to the chemistry lab. Luke’s story illustrates how diverse experiences can lead to groundbreaking scientific achievements.
Discover how Luke’s work has pushed the boundaries of fluorescence imaging. Notably, his development of Janelia Fluor® dyes has significantly improved live-cell and super-resolution imaging capabilities. This episode reveals the intricate balance between fundamental research, application in drug discovery, and the collaborative culture at Janelia, emphasizing the importance of mentorship and interdisciplinary interactions.
- Follow Luke on X: @rhodamine110
- Explore the Janelia Research Campus’s Open Chemistry initiative for pre-commercial compounds: dyes.janelia.org
- Learn more about HHMI and the Janelia Research Campus: HHMI Janelia
- Janelia Fluor(R) dyes for super-resolution microscopy available at Bio-Techne Janelia Fluor® Dyes for Super Resolution Microscopy | Bio-Techne
- Follow Alex: @MoloneyAlex
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Transcript
Paths to Discovery
00:00:03
Speaker
A discovery is said to be an accident meeting a prepared mind but every story behind the discovery is different. Perhaps the idea is conceived in a light bulb moment or a brainstorming session or captured in scribblings on the back of a napkin.
Introduction to Podcast and Guests
00:00:21
Speaker
Here we introduce you to scientific pioneers taking you beyond their publications and into innovation corner to hear the untold stories behind their discoveries. This podcast is brought to you by Biotechny and I'm your host, Alex Maloney.
Fluorescent Dyes and Cellular Imaging
00:00:41
Speaker
Live and let die. The die who loved me, die another day. The field of fluorescence imaging is very much reliant on dyes. Fluorescent dyes. And apart from giving you fantastic James Bond-related paper titles, fluorescence imaging has been an enormously enabling method for unraveling cellular physiology and the specific location and concentration of cellular components. The Nobel Prize in Chemistry in 2008 acknowledged the impact of fluorescence imaging from the discovery of GFP, the green fluorescent protein from a Quora vitoria jellyfish. But fluorescence imaging has come further than this now, and small molecule fluorophores open up more possibilities and applications. You can tune their properties, make them cell permeable, use them for live cell imaging experiments, and even do super resolution imaging now.
Meet Dr. Luke Leavis
00:01:39
Speaker
And today's guest is one of the key people delivering the latest and greatest advancements in fluorescent dyes. Dr. Luke Leavis is a senior group leader and head of molecular tools and imaging at HHMI's Janelia Research Campus.
Innovative Environment at Janelia
00:01:58
Speaker
Now, if you haven't heard about Janelia, Campus, this is one of those extraordinary facilities that breeds innovation. Investigators don't have to worry about writing grants. Their focus is just on the science and the collaboration. And to quote Luke, they are let loose on a couple of big problems. And when you have an environment built to enable creative collisions, you bet there are some equally big solutions to these problems appearing.
00:02:31
Speaker
In this episode, we unpick how Luke created the next generation fluorescent dyes, the Janelia floors. Hear what they have unlocked, and we also discuss what the future looks like with these now in the imaging toolbox. I'm dying for you to listen to this one. Welcome to Back of the Napkin.
Dr. Leavis' Unconventional Path to Science
00:02:55
Speaker
Hi, Luke. Welcome to Back of the Napkin podcast. It's great to have you on as a guest. It's great to be here. I was just on your Twitter page actually and my kind of first observation here is you don't look like your your Twitter picture. Yeah, the Twitter picture is from a ah visit to my daughter's ah third grade class and um they wrote me a bunch of thank you notes and and one of them they drew a portrait of me. And so I use that as my as my Twitter portrait. Nice. And for the listeners who are probably wondering what this this looks like, I'd encourage you to go over and look on on Luke's Twitter and see this. It's very funny. They depicted you as some kind of evil scientist. Was that the? ah yeah That was the take. I showed up with ah you know with a lab coat and a bunch of glowing dyes.
00:03:51
Speaker
and you know showed them all about fluorescence and and stuff like that. it was It was really fun. Nice, nice. All right, Luke, let's go back to the the beginning then. How did you get into science? Yeah, I didn't come to science directly. So ah I grew up in Oregon. my My parents were actually hippies. They had moved up from California, my dad from Santa Cruz, and my mom from Orange County. and They met in in Oregon, and so I grew up way out in the sticks. I was a first-generation college student and really did didn't know what I wanted to do. so I kind of bounced around. I was an English major for a while, an anthropology major. I'd never really seen a scientist, but in college I sort of discovered chemistry.
00:04:43
Speaker
And ah originally it was it was a path to medicine, ah but ah ended up ah really loving this field and and stuck with it. huh ah And growing up with parents as hippies, you must have been surrounded by lots of colors. And is it kind of a coincidence that you've now ended up in sort of becoming an expert in fluorescence imaging and making dyes? Yeah, I think ah that upbringing um has ah colored my the way I do science, if I can use that. There were a lot of
00:05:20
Speaker
colors growing up, um you know, tie-dye is big in Oregon, especially back then. um But I think more so this idea of um giving stuff away and and trying to push ah science forward in more of a ah communal ah setting has has sort of been ah something that that I've carried with me ever since I was a kid. Uh-huh, uh-huh. All right, so talk me through then your time at college then. So you became interested in in chemistry then when you were at Oregon State University. So what was it about chemistry that kind of piqued your interest?
00:06:02
Speaker
yeah Chemistry is is a fantastic discipline because um you know you can dream up any molecule and then you go into the lab and make it. There's an intellectual component, but there's also this hands-on component. so You have to actually go in and build molecules. and You do so by using different reactions. You can't just take tweezers and put different atoms where you want them to be. You have to take this collection of of transformations and put them together in ah in a sequence where you can make these new
From Academia to Industry
00:06:36
Speaker
molecules. and So that really fascinated me. and I think the other thing that
00:06:42
Speaker
ah resonates with me and and why I got into chemistry is that the molecules that come out at the end can be useful. And originally, you know, the dream was to make ah pharmacological agents drugs. ah But then I fell into this field of fluorescent dyes where we're making molecules that can go inside cells and then tell us about what's going on there. Yeah, so let's take it back to this kind of early part of your career then. So after Oregon State and you spoke about this kind of, you know, the the kind of end applications, you do you move out of academia to ah into to industry? Tell me about this kind of transition. Was this all kind of focused around this idea of being a little more applied in what you are ah you were making?
00:07:34
Speaker
Yeah. So at Oregon State, I had the the privilege to work with a fantastic scientist, James D. White, and and we called him Jim. Jim was ah really a leader in the field of ah natural products, total synthesis. and So making molecules from nature that were very difficult to make and also had potential therapeutic applications. And so I learned a ton of chemistry in Jim's lab, but I also learned that I didn't just like making molecules because they were there and complex. And so ah after that um experience, after I graduated, I again, wasn't quite sure what I wanted to do. Do I go to medical school? Do I go to graduate school?
00:08:19
Speaker
And so I looked around for a job, and Oregon's not the the epicenter of biotechnology. And as a chemist, there was only one job I could get in the state, and that was at a a little company called Molecular Probes, which at the time was still owned by its founders, Dick and Rosaria Houghland. And so I showed up there and I remember distinctly in my interview ah learning about this field, which I i never really ah looked into ah making
00:08:54
Speaker
glowing dyes and then throwing them at at cells. And I realized you could make molecules pretty quickly and then deploy them. And they could report back really interesting information. And so the the feedback loop was much ah tighter than you would get with drug discovery. um And as an added bonus, these molecules were sort of flat. There wasn't a lot of stereochemistry. And so they were sort of fun to look at and and fun to play with. Nice. So this was your this was your introduction into fluorescence imaging then and and fluorescence dyes. And what happened next? Yeah, so I showed up and my first project was actually to make a commercial lot of this dye, Alexa Floor 633. And so that was the first rhodamine I ever made. They had developed the dye, discovered the structure
00:09:52
Speaker
ah but ah they were commercializing it and so I was tasked with making you know a gram of this material. And ah from then, you know i've i've they know we've we've continued to work on rhodamines now for almost 25 years. um I was at molecular probes for about a year, and then my boss moved down to the Bay Area ah to another company, Molecular Devices, and then he recruited me down. And that was a different experience, ah where we weren't just making molecules by themselves.
00:10:27
Speaker
and um ah just you know putting them in a catalog. ah We were actually working with biochemists and cell biologists to develop kits for drug discovery. So ah Molecular Devices was a company that was making a lot of instrumentation. And so we came down to help create a reagents division there and develop kits that would go along with these instruments that were being sold both to academics and to folks in the industry.
00:11:00
Speaker
Yeah, this must have been a really exciting time to be in science. Around the 2000s, this is like the dot-com boom, the human genome project all going on. So, yeah, how is that was that? Did it feel like you were in the right place?
Mentorship and Collaboration in Science
00:11:13
Speaker
it was Yeah, it was fantastic. um And at molecular devices, I had two great mentors. you know I'll say that really any success story in science is is all about mentorship. And so as an undergrad, I had great mentors.
00:11:33
Speaker
ah Jim White, and then as an industry, Zengin, he goes by Jack now, Zengin Di Wu, and Anagret Boge, who actually works now for Biotechnique. And so from them, I learned ah you know how to do chemistry, how to think about developing reagents, and Anagrad actually taught me how to ah do biochemistry as well. So it was a fun interdisciplinary ah team, and we were all just working together to try and develop the best kits for ah for drug screening.
00:12:11
Speaker
That's really interesting. But Summit must have piqued your interest for you to then head back into academia because your next chapter was to go to the University of Wisconsin, Madison. So tell me about this. Yeah, after about three years at Molecular Devices, I realized it was time to take the next step. And ah by then, the idea of going to medical school had sort of died down. I was you firmly interested in doing chemistry. You took another interest. Yeah, yeah. i um
00:12:52
Speaker
you know i the The funny story is I never ever really wanted to leave Oregon, but now I live on the other side of the country. And ah and so it was in small steps, though. It was first going down to California, and then I wanted to move somewhere interesting and different, but I couldn't quite make the leap to the East Coast. So we decided to go to Madison. And Madison Chemistry Department fantastic place. And I know you've had ah Laura Kiesling on ah this podcast. Laura was a really, and another really important mentor. And I actually ended up working ah for ah her husband, Ron Raines, joining his lab ah in the early 2000s. Interesting. And
00:13:47
Speaker
Is it true that you were known as the probe guy when you went into so Ron's lab? Tell me about this. Yeah, Ron didn't know my name at first. So I was referred to as the probes guy for a while. um And actually in Ron's lab, there for some reason, we just decided to give everyone nicknames. And so my nickname throughout my time there was Prober. And we just referred to everyone as as as nicknames. It was wasn't a Madison-wide thing or a department-wide thing. It was just just our lab, but it was something we did. So I still you know call people
00:14:29
Speaker
and call them by those nicknames now 20 years later. So when you were there, if someone had a ah problem that needed kind of sewing that was fluorescent space, they'd be like, go and speak to the prober. Was that kind of hard? Yeah, exactly. you It would just be like, hey, prober. And you and was it just became a ah thing. you know So yeah one of those charming things from graduate school, great, great memories. Yeah, a good camaraderie. um All right, and then ah the next chapter in your career, Luke, is where Janelia comes in. So talk to me about about this, because this is is obviously a ah huge part of your your career and where you are now still. So yeah, tell me about this.
00:15:16
Speaker
Yeah, Janelia had just started. So Janelia is part of the Howard Hughes Medical Institute, HHMI. HHMI has been around for a long time since 1953. And ah in the early aughts, the leadership of HHMI decided to build their own research facility. So before, HHMI largely was supporting basic science by funding investigators at different universities around the country. So you'd have HHMI investigators at Harvard or Stanford or or wherever.
00:15:58
Speaker
And ah that was an effective way to fund science, and they still do that. There are around 300 investigators still today. But ah it's just I wanted to try a new experiment. And so their idea was to start their own research facility and then fill it up with a bunch of scientists from different disciplines and give them ah I always say more than adequate resources and and just turn them loose on a couple big problems. and And so this was coming up while I was in graduate school. It opened in 2006.
00:16:38
Speaker
And I'll be honest, i you know I was coming from industry to graduate school. I was thinking about ah my next step. Do I go back to industry? Do I do a postdoc? I was sort of an atypical candidate, so I was actually having a pretty hard time finding a postdoc. And so on a whim, I applied to this place called Janelia, right? I had heard about it it. There was some news stories. I thought it seemed interesting, especially because one of the main goals of Janelia was to push forward imaging technology. And so I applied on a whim and ah
00:17:23
Speaker
You know, HHMI doesn't really mess around. So I came in. I gave a 20-minute talk. The entire interview for eight people lasted exactly one day. And then I had an offer, a five-year term, a week later. So things moved quickly. um So I defended my PhD and then started here in early 2008, almost 16 years ago. Wow, I was looking on the Janelia campus website and ah they described the people there as idiosyncratic tinkerers and thinkers. I thought that was really i thought that was really cool.
00:18:08
Speaker
um So yeah. And the other thing I saw on there actually was that, uh, in the conception of this Gilia camp, Janelia campus, um, Jerry Rubin and Tom check were, and I don't know if this is true, but they were sketching the idea on the back of a napkin. Um, that was on the video. So I thought, wow, this is, uh, yeah. Yeah. Yeah. The idea was, uh, uh, yeah, started out with with Tom and and Jerry on the back of a napkin. And Janelia is really a ah sort of social experiment almost in science. And everything about this place is designed to maximize interactions. ah So the building is all glass. It's built into the side of a building. And and so you you can't hide.
00:19:04
Speaker
ah you know, my even my door is glass and there's actually glass to the next office a little bit. So, you know, you can't just sequester yourself in an office and and never be seen. ah There's only one place to get coffee. And there's free coffee, but you can only have coffee in that one place. And so the idea is everyone has to go there if they want a cup of coffee. And and that's designed to ah maximize these unexpected conversations about science. So I was getting tea there yesterday and ended up talking for 20 minutes about some new idea with a a postdoc from another lab. So you know it's those sorts of of things that make Janelia an interesting place
00:19:49
Speaker
to do science. it's It's a lot of thought went into how to to maximize the interactions between ah people who study different things. Yeah, how to create these creative collisions, I guess, I think I've seen it described as. Yeah, really interesting. And you know like looking back in kind of history at some of similar models that have been used like Bell Labs. These have been amazing environments that encourage innovation and discovery and collaboration. and um So is this kind of like the idea that Janelia was built on this sort of Bell Labs kind of model? Yeah, Bell Labs was one of the inspirations. the
00:20:40
Speaker
ah LMB, MRC is another. ah The idea is to give people freedom and resources and then kind of get out of their way. Janelia has a few other ah things, ah or maybe one way to to think about it is we try to take the best um ideas from all those different places and and put them all into to one. And so the labs here are quite small. So you start with just two people, including or in addition to yourself. And then a large lab here is six people. So my lab is is six people. um And the idea is with that small group, ah you focus on a particular thing and then you collaborate to do bigger things.
00:21:32
Speaker
ah you're almost forced to collaborate if you want to do something really significant. And so it's pretty common for folks to move in and out of of different labs, maybe not officially, but unofficially ah to learn new skills or to work closely together on different projects. So, you know for example, I have this longstanding collaboration with my colleague here, Eric Schreider, and together we've used the dyes developed in my lab and the proteins that he's developed combining those to make ah really useful indicators for things like a voltage or or calcium ah that can be deployed not just in cells, but in animals.
00:22:19
Speaker
And that's a good example. We've had postdocs who you know started out in my lab doing chemistry, but then essentially move into his lab so they can learn how to do ah protein engineering and vice versa. So it's it's a very fluid system where we're all just working together trying to do impactful things. Yeah, that sounds that sounds great, Luke. So tell me more about the work that
History and Development of Fluorescence
00:22:42
Speaker
you're doing then. We haven't really got into the kind of meat of um the dye work. so And I think we'll have some listeners here who are kind of more familiar than others with this kind of field of fluorescence imaging and fluorescence microscopy. so And it's moved so fast. So maybe if you could give a bit of an overview to the field and maybe um
00:23:04
Speaker
move towards where we are now and what the kind of state of the art is. That would be great. yeah The field of of fluorescence is is a little funny and because on one hand it's it's kind of old. ah A lot of these dyes were at least the core structures were first discovered in the 19th century. ah So, fluorescein, a famous molecule, 1871. The rhodamine dyes that I've mentioned and and we still work on, first developed in 1887.
00:23:42
Speaker
and so ah Over the years, there's been a lot of advances. So in the 40s, people realized you could put these dyes on antibodies and use them to stain structures. And then fluorescence microscopy ah came up um as a way to to look at these things. Also in the 60s and 70s, dye lasers came about. And that pushed the field of, ah fluorescence, you can use dye solutions to make finely tuned lasers. This field has kind of um gone away with ah solid state lasers, but it was really important in in and in those days. um And then in the 90s,
00:24:29
Speaker
different companies, including molecular probes that I mentioned, started making dyes that were sort of purpose built for different applications, whether labeling oligonucleotides or antibodies or or other things. um But when I started my lab, what we realized, looking at it from a a chemistry standpoint, is that we were building all these new fluorophores that had been going on for decades, but ah everyone was using pretty much the same chemistry that was in the original rhodamine work from you know the 1880s.
00:25:06
Speaker
And that had really limited the ah types of structures you could build. All but the simplest functional groups kind of fall apart in these conditions. Typically, how how people would make rhodamine dyes is you would ah stir together a few things in concentrated sulfuric acid or or other very harsh conditions and under very elevated temperature, like 180 degrees centigrade. so so you know i did that same reaction in graduate school, making rhodamine dyes. That's how we were making these rhodamine dyes back at molecular probes. and And so what we decided to do um when we came to Janelia was
00:25:48
Speaker
to bring modern chemistry to bear on on um some of these old structures. Because our idea is if we had new chemistry, we could make new dyes, and maybe we could um ah make better reagents that would ultimately enable new biological discoveries. and And so I was really fortunate um to recruit ah someone here at Janelia early on. he's He's been here over 13 years now, Jonathan Graham. So John was someone I knew in graduate school. ah He had gone on to Merck. So he was working in drug discovery. And so I was able to recruit him down. And together we decided, let's let's bring modern chemistry on some of these old old structures. And and you know we've been working on that for for over a decade now.
00:26:37
Speaker
That's really interesting. So there seems to be this people kind of over projects philosophy at Janelia as well. So I'm really interested to hear about this kind of recruitment process. How do you, you know, when you're looking for people to join the team, what is it you're you're looking for? Is it, you know, like a straight A resume or, you know, what what is it you're looking for people? And I guess, you know, you've spoke about John already, but your team's bigger now. So, um yeah, tell me about this. Yeah, the the team, ah you know my team is a ah mix of people. So we have um senior scientists, basically staff scientist positions who are here long term. That's another unique thing about Janelia. It's hard to do that and in a standard academic environment. But it's really useful because it ah preserves the tribal knowledge within the lab. So you have you know the all the the knowledge
00:27:34
Speaker
over the years isn't just in me, but it's also in some of these other long-term employees. um It also really facilitates collaboration because if you have ah a graduate student or a postdoc, they have their own project, you want them to be focused so they can move on and and take the next step. But staff scientists can take a little bit of time and and do these smaller projects ah that can be really impactful, um but may not result in in sort of first or or last authorship. And and so that's that's really important. um But in addition to these staff scientists, we also have postdocs in lab and technicians. And that's something that I've i've um felt very strongly about based on my background.
00:28:22
Speaker
having spent time in industry before going to graduate school, I think it helped. It really accelerated um my time in graduate school. I came in with with halfway decent hands. And so I've over the years given this opportunity to a number of ah students. And right now I have two fantastic technicians, ah Sarah and Carla, who are really just crushing it in terms of chemistry. there you know They're as good as any postdoc. That's awesome. That's really cool. And and you spoke about you know the question I asked you before about kind of where ah the field is is heading and the problems the biological questions and problems that you're trying to answer with ah what you're doing. like Tell me some more about this. What are the guys who are in the lab, all this fantastic chemistry they're doing?
Advancements in Imaging Technologies
00:29:10
Speaker
How are you applying these dyes now to these biological problems? Yeah, so in addition to you know over the last few decades, um
00:29:19
Speaker
you know, new fluorophores being made. ah There have also been tremendous advances in microscopy, ah some of that done here at Janelia. So my colleague Eric Betsik and Harold Hess developed localization microscopy to to break the or circumvent the diffraction limit um in standard imaging. ah We've also helped to push structured illumination, another high-resolution microscopy technique. And then ah technologies that allow folks to attach fluorophores, monomolecule fluorophores to proteins inside live cells also came out in the last 20 years or so. The snap tag system from Kai Johnson and and the halo tag system from
00:30:11
Speaker
folks at ProMega. And so now, with all these improvements in dyes, in microscopy, and in labeling technology, ah it's pretty routine to watch individual molecules move around inside ah live cells for a long time. And so that's, I think, where the field is going, ah watching individual molecules. You can get a bunch of statistics. um You're not just doing these these sort of bulk measurements or or measurements in vitro.
00:30:46
Speaker
There seems to be this key paper that came out from from your lab in 2015, the Nature Methods paper that introduced this new toolbox of dyes that enabled live cell imaging. um Tell me about about this and tell me kind of the story that that led up to this this podcast back in the napkin where really keen to hear the stories of innovation and these ah have kind of changed the field. So yeah, tell me tell me about this work. We had developed a a few new chemical methods for making fluorophores and so suddenly we we can make almost anything. And then the question is, well, what what do we make? ah And um we had this ongoing collaboration with
00:31:37
Speaker
A few folks here, ah Bob Tijen, who was president of HHMI and had a a small lab here. ah He's you know a biochemist who's been working on transcription factors. And ah there are a few other labs here interested in this idea of ah imaging individual molecules ah inside cells, typically transcription factors, and watching them as they bind ah DNA, et cetera. And so we we really wanted to to provide ah new fluorophores that would be brighter and more photo stable to improve these experiments. And we had all this chemistry, so technically you know we we could we could make any fluorophore we wanted. And the story of the Janelia fluorodyes really begins with me just kind of goofing off with a few very simple calculations.
00:32:30
Speaker
And I thought, what if what if we put ah a little four-membered ring and a Zetitine ring on ah on a die? and It seemed a little crazy because there's one thing you remember from organic chemistry, it's ring strain, and so a little four-membered ring doesn't seem that stable, at least on paper. But zenidines are found in some natural products and even some pharmacological agents, so it didn't seem i' too crazy. ah so i I ran that calculation, came in in the morning, and you know
00:33:01
Speaker
predicted to be planar and you could sort of ah squint and and and see that the bond links and everything suggested, maybe maybe this dye would be okay. So I showed John this this the of that that experiment and John said, okay, ill I'll give it a try. So he he made that dye, I think that week. and um You know, I remember this distinctly, I was working in the lab, you know, Janelia group leaders tend tend to work in the lab ah because we have at the time and desire to do so. So I was working in the lab and and John was purifying this this new dye that he just made on our property of HPLC and he pulled out the racquet tubes and it was just so bright.
00:33:43
Speaker
and We just looked at each other and we said, okay, this this might be interesting. This is a good one. I think that day I you know stayed late and measured the the spectral properties and realized that just by this little tiny adjustment, ah this little four-membered ring, which is only two carbon atoms different than a classic fluorophore from the 1880s, ah we could improve the brightness and photostability substantially. um And we tried this out in live cells. It gave more photons. Photons are really the currency of any imaging experiment. And so that started us on this path. And and since then, we've developed a large number of Janelia floor dyes. We've figured out how to
00:34:28
Speaker
ah change the color. ah We've figured out how to adjust the chemical properties so they work in you not just cells but in animals. um And we've pushed things even farther. We've ah ah made used use sort of similar ideas incorporating deuterium and other things to improve ah brightness and photostability and bioavailability. Yeah, really impressive work, Luke. I said I was on your Twitter and I saw that that meme where you've got Bilbo Baggins saying, why shouldn't I put an azetidine on it? That really made me laugh. I think the chemists will appreciate that. Yeah, we we have put azetidine on a lot of things. Sometimes it works. I mean, it it doesn't work all the time, but um
00:35:19
Speaker
It works, it works more often than not. And so it's, it's been a really nice thing. The the other great thing about this is, as I mentioned, um, you know, there are as editing in a lot of pharmacological agents. And so, uh, the building blocks are commercially available. And so that's really helped us explore things. We can use simple chemistry and make um you know small sets of dyes and then test them, fine tuning their structure in different ways. Yeah, OK. Luke, let me ask you then about, ah so you now have an entrepreneurial string to your bow and co-founded.
Bridging Imaging and Drug Discovery
00:36:05
Speaker
with some of the your colleagues who already discussed Eric Baitsig and ah Bob Tijan. So tell me about tell me about this. like At what point did you think, well, we've got something great here. We've got tools that work in live sales. Let's apply this to ah to a drug discovery problem. Can you can you tell me about this? Yeah. So, so, you know, we had, we had created these dyes and, um, we can talk about this later, but we, you know, we were giving them away to this, the, the basic research, uh, community, hu the, uh, at the same time, you know, I, I still had my experience in industry, uh, developing kits for, for drug discovery. And so teach and I would talk about, um, you know, wouldn't it be cool if we could use this, uh, to,
00:37:01
Speaker
ah do drug screening, right? It's it's pretty amazing. you can just You get all these great statistics. that you know A lot of drug screening is really about being able to tell hits from non-hits. And so ah you get a ton of molecules. You get a ton of data from this type of experiment. you can look at very subtle changes. And so we thought it would be an interesting potential assay. And so, you know, Tij and I would talk about it from time to time. When Tij stepped down from being president of HHMI and went back to Berkeley, ah he decided to to think about this more seriously. And and so we ah decided to found a company with Eric Betsik and
00:37:46
Speaker
uh, Xavier Darzak, uh, a biologist. So we had a chemist, a microscopist, a biochemist and a cell biologist. And, uh, so we sort of, uh, you know, started talking to VC firms. It was an interesting time because everyone else was at Berkeley. Eric Betsik had moved there by that time. And so I was on the East Coast. And so I would fly out sometimes on frequent fire miles just to meet with VC and then take the red eye back um because I had responsibilities here at Janelia or sleep on Xavier's couch. um But eventually you know we got
00:38:27
Speaker
ah a couple of people to bite. And we founded the company in late 2019. um And then ah a little while later, Teach was able to recruit Roger Pullmutter to run the company. ah Roger had previously run Merck Research Labs. and And so that really opened the floodgates. And um ah we got a little bit more investment. And now the company's ah
00:38:58
Speaker
500 employees, and it's going strong ah with a lot of ah different things, including this single particle tracking based primary screen. um But it it has branched out into a a few other um areas as well. Yeah, this is this is really interesting. I mean, the first company that you kind of co-found, and I was looking at some of the stats on it, um one of the most funded, or the second most funded pre-IPO other than Moderna. So wow, what you know what a thing to be a part of. Like how is this kind of entrepreneurial side, how does it feel having kind of, um yeah, I know you've kind of, you obviously did have your time in industry, but then transitioned back into a more kind of academic focus. So ah yeah, how do you feel about this?
00:39:52
Speaker
Uh, it's nice to have, um, a little toehold in that world, uh, simply because, uh, you know, industry, and I know you know this, uh, industry is nice because you're, you're really trying to develop products. Um, and in basic science, you're, you're really trying to tell stories too, right? We try and develop useful reagents, but then, you know, part of our output is papers. um And sometimes it's it's nice to just be part of of something that the the main goal is to develop a reagent and not
00:40:31
Speaker
really have to tell a huge story around it. And and so i I sometimes miss those days from industry where it was like, OK, let's do this thing. OK, we got it. We got it. And then I'll move on to the next exciting ah thing where where you don't have to write this big paper. So it's it's nice to see that. um Part of things, I think the other nice thing about industry is it really is team science. Everyone's pulling together in the same direction. and And so um it's more a focused effort ah where in academic science you play a little bit more, you make ah interesting discoveries that are unexpected, um but you know everyone is is sort of um ah steering their own little ship rather than all working together to to ah steer a big ship.
00:41:22
Speaker
Yeah, that's a really nice way of putting it. And I i completely completely agree. So this idea then of using super as imaging in in drug discovery or applying it in drug discovery problems, is this you know is this the is this a future? Is this ah what more people are going to be doing? how How can we enable more people to do this? I think in general, um ah imaging is the future of drug discovery and that can mean a bunch of different things. It doesn't mean just single particle tracking. Uh, that's just going to be one, uh, type of imaging that is quite useful. Uh, but I think, uh, you know, when I was in, in this field 20 years ago, you know, there was a big push
00:42:16
Speaker
moving from in vitro assays with just purified biochemical components to doing things in cells. um But you know these were typically bulk fluorescence measurements, you know looking at calcium flux or something. And then this idea of high content screening ah was just coming online. Now, I think all the advances in microscopy are just waiting to be applied to drug discovery. and the single particle tracking idea with icon therapeutics is is just one example. But we're seeing that with a lot of other places too, with cell paint ah so painting assays and other things, right really doing
00:43:03
Speaker
you know, super high content screening and drug drug discovery is going to be the future. And so we've, you know, we talked to different companies and and we're actually working now with Promega um more closely to ah bring some of our reagents ah to folks in industry. And so I think ah those will be ah and increasingly useful and important as the field progress progresses. and kind of relatedly, but what excites you most or what motivates you most about what you think is to to look forward to in the field? I think, um you know, we
00:43:47
Speaker
We went from biochemical assays to cell-based assays. I think the future is probably going to be either a tissue or even intact animals. And then that's really the the challenge. um And that' that's for drug discovery, but it's also just for for basic science. right um you know there's There's been a push from purified proteins to ah cells and now um you know the future of really all biology, whether it's an industry doing drug discovery or or basic science, is going to be ah in tissue or animals. and so as As chemists, we have to figure out how to make the tools that are going to enable those types of assays, those types of discoveries. and and so it's It's been fun for us to now go back ah to some of the literature on
00:44:41
Speaker
on you know but medicinal chemistry, what do you put on ah on a molecule to make it more bioavailable or more soluble or stuff like that and start designing dyes that ah show these improved properties in in intact animals or in tissue? Yeah, that's interesting. I think you know, working towards being able to solve these problems in the native systems is going to help to reduce the chance of failure and have more productive and more beneficial outputs. That's really exciting. Yeah. So I've been reading a lot about, you know, you start reading that other side of the literature ah where, you know, how do you design a thing um that will work in ah in an animal, right?
00:45:31
Speaker
ah We're starting to measure different pharmacokinetic properties of our fluorophores, which is is sort of new territory yeah um the four for a dichemist, where we're just making these these flat molecules that glow quite brightly. But now we have to think about how they're going to behave in an intact system. Yeah, interesting. I never even really thought of it. Do the dyes, are they in like a rule of five space? for How far out? Yeah, that's what we're that's what that's what we think about, right? And so yeah you know are there motifs that we can put on that both improve the spectral properties of the dyes as well as yeah ah the chemical properties? What are the rules around these molecules? We've we figured out a few. We have ah compounds that will work in animals. We can do cool experiments. like
00:46:23
Speaker
pulse chase in Devo to look yeah at protein lifetimes in the brain. And you can do that across across the whole animal. I mentioned this before, but we can make sensors that have a small molecule component and a genetically encoded component. And we build those things in an intact animal and that use of The synthetic fluorophore gives you many more photons. You can image for longer or or pick up really low signals. um But I think there's a lot more work to be done. We've just scratched the surface on on you know making tools than that work in Vivo.
00:47:01
Speaker
Yeah, really interesting. and this kind of All the synthetic capabilities that you have now seem to be tremendously enabling for this. um Let me switch it a sec, Luke. so so There's been some fantastic discoveries in fluorescence imaging. you know reference GFP and Roger Chen. like This is a discovery that comes from nature. Have you ever looked to nature to kind of for inspiration or or ideas around fluorescence problems or solutions?
00:47:37
Speaker
yeah the you know i I am quite inspired by the work from ah Promega, as well as Kai Tronson's work, you know using enzymes to ah capture dyes. That's a technology that really all are our work rests on. ah So looking for nature there, we've also ah tried to engineer enzymes that will unmask fluorophores and pharmacological agents in specific cells. That's another arm.
00:48:13
Speaker
of work ah in the lab. ah And we have dabbled in ah different ideas of of um using enzyme cascades to ah have cells build their own small molecule fluorophores. That hasn't worked so well. Some of these enzymes are from weird organisms that don't immediately translate into, say, i'm a mammalian cell. but But it's something, I think, to to consider, right? the The world of enzymes is amazing. There are so many transformations that you can do. And if you can then add, say, a slightly different synthetic substrate, maybe you can have the cell do some amazing chemistry. Yeah, I agree. I mean, my background is molecular body and enzyme engineering. So maybe I'm a little biased, but ah yeah, totally, totally agree. Did I hear that you were doing some ink on a starfish?
00:49:11
Speaker
Yeah, the starfish project. Yeah, so one of the wonderful things about Janelia is you can just wake up one morning and decide to try a crazy experiment.
Exploration and Creativity in Science
00:49:23
Speaker
So this is with my colleagues and and another fantastic mentor, Lauren Lugar. So there are these brittle stars that when they're poked, ah they ah show this bioluminescence effect, and then um that region of the arm also becomes fluorescent. And so we thought that would be an amazing reporter. And and so ah this involved chartering boats in Florida to collect specimens and grinding up a lot of stuff and running one of my HPLCs.
00:50:07
Speaker
around the clock for many months and um and then, you know, fractionating out this stuff and and trying to figure out what's going on. We we never quite got there, um but it's a good example of, you know, Janelia allows one to swing for the fences sometimes. You don't always hit a home run, but, you know, if you have a good idea, ah you can ah push it forward. and And they're quite flexible about, ah you know giving you the resources to do what it takes to to ah try something new that could be impactful. Again, it didn't work, but ah but it was a you know it was a fun ah fun experiment. We learned a lot about other things along the way.
00:50:52
Speaker
Yeah, I love that. you know Having the capability to go and try these ideas and test those ideas, where otherwise you know people are relying on on grants and getting these getting these funded, you can actually just go and and do it. I think that's amazing. um Let me ask you about Janelia, because I know you've started your family or grown your family anyway while you've been at Janelia. So how how is that? How do does the Janelia campus cater to kind of being a family person? Yeah. So my, um, you know, my, my wife and I like say my wife is amazing. And if it wasn't for her, I would probably be laying concrete and in Oregon still. Um, uh, the,
00:51:41
Speaker
Yeah, so i I met my wife actually in in junior high, but we didn't date until senior year of college. And really the decision to move to California to take the job at molecular devices and the decision to come to Janelia. was ah largely her saying, come on, we have to do this. This will be fun. right so So she's ah really helped this first generation college student kid who never wanted to leave Oregon to kind of step out of my shell. And so you know we
00:52:16
Speaker
We did graduate school in Madison and then we came here and and started a family. And, you know, Janelia is a great place to start a family. So we have an in-house daycare. So when my son was in in daycare, I would just go eat lunch with him every day. It's just, you know, on the other side of the building. um You know, we have a playground, it's ah it's a fantastic campus, a lot of different things. Another ah fun thing that that amenity that Janelia has is is a pub, it's called Bob's Pub, named after one of the architects at Hughes that helped design the building.
00:52:53
Speaker
and And so really, for my kids' entire life, they've spent almost every Friday evening at Bob's for dinner. And that has become just a traditional place where all the parents bring their kids, and we just hang out and and have a good time. And so it's been ah a really positive experience ah balancing this science job with having a family ah because of of just the openness that Janelia has ah to kids and and all the amenities that it has.
00:53:29
Speaker
That's awesome. That's really cool. I think there'll be a lot of people who are very envious of that um you know having that facility or resource to you know be able to do what you love and to have you your kids around you. but You mentioned this before when we were talking offline about the earthquake that happened. you tell Can you tell that story? Yeah. I think my son was under a year old and you know we're on here on the i you know grew up on the West Coast. I lived in California, so I ah knew I'd experienced earthquakes before. But you know i was after lunch, and I was just
00:54:08
Speaker
you know, chilling with my infant son and and all of a sudden, you know, there's an earthquake. It was a small earthquake, ah sort of, it was almost a joke around here of, you know, everyone freaked out, but it wasn't wasn't that big of a deal. um But yeah, it was just nice that we were, you know, I happened to be with my son during this event, um you know, because ah our daycare center is you know in the same building as my lab. so um it's it's it was But yeah but then since then, that that earthquake has become sort of a meme. People say never forget you know this earthquake because it knocked down some plastic chairs or something. right It wasn't wasn't that big of a deal um in the grand scheme of things compared to some of the earth earthquakes on the West Coast.
00:54:55
Speaker
Yeah, but still, you know, a cool experience and a cool story, I guess, to be able to recount um yeah in the in the future. Luke, I was reading through a couple of your papers and I loved that, you know, there was that one that kind of touched on the James Bond theme, I think you called it, i Die Another Day. And I thought, for instance, everything is such a great um a great area to make these kind of James Bond bond puns. um I was trying to kind of think up of some some funny James Bond titles myself, but none of them were quite as good as as there was it. Toby, what inspired you to write that that paper? Yeah, I you know i i think we you know another important mentor for me was um ah this this person, Winford Dank, who he developed two-photon microscopy. And
00:55:51
Speaker
And so he spent a considerable amount of time, he was he was moving um labs in Germany, and and so he was here, and he would just talk to, this was early in the and in our careers, and he would just spend a lot of time really drilling down and and giving us to think critically about our science. And I remember at one point, I said, oh, I'm just like goofing off in the lab. And and he said, you know there's not enough goofing off in science. And and I think that's true ah you know because of the way grants work and because of the time constraints. ah you know We can't just play. And and so Janelia is a place where you can kind of play or goof off.
00:56:33
Speaker
And I've tried to do that even when I'm writing perspective pieces. So this was was one. I said, let's just do something crazy. And it actually came about because I got my first COVID shot and I was sort of amped up from the experience of going to this abandoned department store and weaving through the line to get my my first COVID vaccination. And so I came home and I just wrote that um ah live or let die piece in an afternoon right after giving that that shot. So it just sort of came out. And it you know it was very easy because of all the the die ah things that are in James Bond titles and our dies. Yeah, it was very good. i'll give you I'll give you the one I came up with, which is pretty terrible. But um but given you guys have just
00:57:24
Speaker
published or just released that bio-archive paper with the hydroxymethylsiliconrodamines. I thought you could do ah The Spy Who Loved Methydroxysiliconrodamines.
00:57:39
Speaker
Four out of 10, but I think you wrote that as well. You appreciate that, jokes. Yeah, but you know it only it only works in ah you know with the English accent, the methyl. Yeah. Oh, yeah. Yes, I'll have to say it if it's funny ah funny for me. okay yeah um It kind of just prompted me to think lou when you're talking about you know getting these vaccines and you know this big ah interest people have now in studying ah RNA in the transcriptome and even imaging ah RNA, is this a problem that you've um you've thought about? Yeah, I i do wonder if
00:58:23
Speaker
um Chemistry can play a larger role in some of these ah imaging technologies. so A lot of folks in that field will get quite creative using the things that they can buy from DNA synthesis companies. and so I wonder if chemists, chemical biologists should take another look at some of these things. and And just with some simple chemistry tricks, accelerate how you know spatial genomics um assays can run.
00:59:02
Speaker
again you know You talk to a lot of people here and they're like, well, i can only you know I can buy this thing. I can have this thing made. So that's why I use it. And I think their opportunity is there to accelerate this. um Again, it may be hard to get funding for that sort of thing because
00:59:22
Speaker
funders may think it's a solved problem, but you know places like Janelia and others um should allow folks to um take a second look at some of these technologies and and maybe make them better. Yeah, well, thank goodness for places like Tunisia that can enable this type of stuff to ah happen. um Luke, we're kind of getting towards the end of the podcast. But I did want to ask you, like what did your parents make of this this career that you've taken? You described them as hippies. So what was it? what was it you what What did they say about you taking this this career in science? Yeah.
01:00:00
Speaker
Yeah, my parents are amazing, super supportive of everything that I've done, but you know, it was, it was sort of different, right? We had no reference, you know, I mean, originally, you know, we were thinking, I was thinking about becoming a teacher or a physician because I knew teachers and physicians and we, you know, we didn't know a scientist growing up. And, and, and so, uh, it was, it was a bit of an unknown and, uh, And you know it it took them, I think, a few years ah into the Janelia job to realize, oh, this is actually a career. right Because they saw me in this limbo period during industry and then as a you know poor graduate student. And so they're they're like, you know what what are you doing? But now I think they're fully on board with everything that's happened. And they see the value.
01:00:54
Speaker
And so, you know, for for folks who have um little experience or don't have a reference for scientists, you know, it's it's ah it's a fantastic career. It's a fun job, even if you you know didn't grow up around a lot of scientists. Yeah, ah so that's awesome. um Okay, Luke, so this is back of the napkin. Hopefully you've received some napkins in the post, so I'm gonna ask you if you'll leave your personalized scribbling or mark on the napkin at some point when you get time, and we can pin that up on the wall and post it on socials as a memento of your your time on the the episode. How can people follow you, Luke? Yeah, so I'm on Twitter at Rotamine110.
01:01:41
Speaker
Rotomene 110, that was the first ever Rotomene, so that's why that's why I have that. um and ah um And then you can also always contact me just via email. I'm actually pretty good at responding. I will say that you know a lot of the pre-commercial compounds that my lab develops are being shared with the research community through an initiative called Open Chemistry. And so you can go to dyes.genelia dot.org and register and request things there if you want to try some stuff out.
01:02:18
Speaker
Awesome. We'll leave some links in the description. Thanks so much, Luke. It's been a pleasure to have you on the show. Yeah, it's great chatting with you, Alex. Thank you so much. Thanks for listening to this episode of Back of the Nutkin. To hear more stories of innovation and discovery just like this, subscribe to Back of the Nutkin on Apple Podcasts, Spotify, Stitcher, or wherever you get your podcasts from. If you enjoyed this episode, please consider sharing it with your friends, colleagues, or lap mates.
01:02:52
Speaker
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01:03:24
Speaker
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