MEET A WHITEHEAD POSTDOC: Tomáš Pluskal

Postdoc Tomas Pluskal

Tomáš Pluskal is a postdoc in Whitehead Member Jing-Ke Weng’s lab investigating molecules of medicinal interest in plants and the genes that produce them. We sat down with Pluskal to learn more about him and his experiences in and out of the lab.

 

What do you investigate?

Our lab studies plant biochemistry. There is so much biochemistry in plants that we don't know about because when people have studied plants in the past, they made simple associations and often focused on one molecule per plant — like nicotine from tobacco, or salicin (related to aspirin) from willow bark. Actually, each plant contains tens of thousands of different molecules that have different activities, many of which haven't been studied. So, our lab is trying to look at these things more in depth, and identify the genes in the plants that produce these molecules. Then we can create new variations of the natural molecules that are even more effective using synthetic biology. I think that's really cool, and that globally synthetic biology is going to transform the way we do chemistry in the future.

My main project here is about a Pacific Island plant called kava. It's an herb that has been used for thousands of years to prepare a drink, also called kava, that has very relaxing and pleasant properties. Some clinical trials have shown that kava is effective in cases of mild anxiety or insomnia. We are studying the biosynthetic pathway that produces the active molecules in kava, which are called kavalactones. Because kava is not a model organism, there is no genome sequence available and there are no genetic tools tailored to it. We are using cutting-edge methods like de novo transcriptomics and metabolomics to figure out which enzymes are producing those molecules. Then we try to take the genes for those enzymes and put them into a controlled system like yeast so the yeast will mass produce the kavalactones or potentially produce new variations that we engineer. We create a kind of bio-factory.

 

How did you become interested in your field?

I entered the biology field sort of by accident. I started out in computer science, but after my master’s I was looking for a job. I was really interested in martial arts, and I wanted to go to Japan to do karate. The only job I could find there at the time was in a biology lab, so I took it. Then I realized I really enjoyed it, and I ended up doing a Ph.D. in biology there. While I was in Japan I started working on metabolomics, looking at molecules produced by yeast, so then it was a natural transition for me to look deeper into what genes are behind the metabolites that I was studying, and that's why I came to the Weng lab at Whitehead Institute. 

 

Why did you want to do karate in Japan?

I started doing karate seriously when I was 16. I wanted to move to Okinawa specifically because it has a more traditional approach to karate. As opposed to mainland Japan where karate became more of a competitive sport, the Okinawan forms of karate are a bit closer to their origins, when it was a self-defense art. They put more emphasis on the application of karate in real life, and I often say that the application is not really about fighting somebody physically. It's more about becoming a stronger person to fight any kind of obstacles that you have in your life. That aspect is very strong in Okinawan karate. I moved to Japan when I was 24 and I did karate for ten years over there, and I can recommend it to everyone.

 

Do you use things you’ve learned from your martial arts training in the lab?

Yes, I think it helps with the kind of perseverance and determination that one needs to do science. 

 

What was your experience of living in Japan?

There is no other country like Japan in the world. Its culture is unique, and they treat foreigners with great respect and hospitality. You can experience some challenges when you stay for a longer time as you become part of the social hierarchy there, which can be quite complicated. But overall, I have to say the ten years I spent in Japan were fantastic, and I think more researchers should study or do postdocs there.

 

What did you want to be when you were a kid?

I wanted to be a garbage man. When I was a kid I always saw the garbage men driving around, hanging onto the trucks as they drove, and I found that really cool.

 

How did you get into computer science?

I have been a technical type since I was a kid. I liked computers and playing computer games. I tried programming and found that I was fairly good at it, so computer science was a natural choice for me. But then when I was in computer science school, I realized that I wanted to do something more than just sit by the computer the whole day. After I finished my master's, most of my peers got jobs at big computer companies. Some are at Google now. I didn't see myself doing that. I wanted to try a different path, and I discovered that I found doing basic research quite fascinating and satisfying.

 

What do you enjoy about doing research?

You get to explore paths that no one has walked before. You're working on something completely new almost all the time, so you don't have the answers and you have to find them yourself. That can be quite confusing and challenging, but in the end when you put all the pieces together and you have the whole picture it's very exciting.

 

You created a popular software. Can you tell me about that?

I developed a software called MZmine 2, for mass spectrometry data processing and metabolomics, that is now quite popular worldwide. We published that in 2010 and the paper now has over 1100 citations, so it's been used by many labs. If a biologist wants to do something with metabolomics, that is fairly computationally intensive and requires some computer science knowledge. I think the reason why the labs like my software and use it is that, because I also work in biology, I could make the software in a way that biologists can understand.

 

What's the most expensive thing you've ever broken in the lab?

In my Ph.D. lab I broke a mass spec, which is about a million dollars. I was just trying to screw in an ion transfer capillary and it wouldn't go in, and I pushed a bit too hard, and then we had to exchange the whole front end of the mass spec. That was a bad day.

 

Has your career path been what you expected?

One thing that I see looking at my career is that I've taken some quite dramatic turns, like changing fields from computer science to biology, that at the time I didn't think about too much. It was challenging making the switch, especially at first, but looking back I realize how beneficial it was. I would really encourage people not to be afraid to make dramatic changes in their careers or their plans. Often people hesitate to make big changes because everything’s going okay, but if you want to become a PI with your own independent lab and do something new, you will really benefit from having experience entering new areas or fields and learning to do things a new way.

 

Where do you see yourself in ten years?

I’m moving to Prague next year to be PI of a lab there, and I hope I will stay there for the next ten years. I hope I will do some good work that will have an impact on the field. I want to merge the expertise that I have originally from computer science with the expertise that I have gained in biology and now biochemistry here, and find some exciting new area that other people haven't thought about yet. And when I move to Prague I'm planning to open my own karate school. That's going to be my hobby.

Whitehead Institute postdoctoral researcher Tomáš Pluskal

Image: Conor Gearin/Whitehead Institute

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