Down to the roots. The story of experimental botanist Matyáš Fendrych

After six years spent collecting experience in top-class Belgian and Austrian institutes, experimental botanist Matyáš Fendrych has returned home. Working in a lab at the Faculty of Science at Charles University in Prague, he – assisted by his team and buoyed by an ERC Starting Grant – constructed a unique vertical microscope and investigates cellular and intercellular processes and interactions mainly in connection with the root growth of plants. Observing the plant life-cycle in real time holds no end of fascination for him.

Read the story in Czech translation here.

We are chatting at a cultural and social hub in the Prague neighbourhood of Karlín. We move back and forth, switching between outdoors and indoors: the August weather is playing tricks on us – one moment it is raining cats and dogs, the next the sun is blazing down. Matyáš Fendrych’s face, too, sometimes lights up – when he is describing the fascinating processes in the roots of the thale cress that he observes under the microscope – or clouds over, even tempestuously so – when discussing the frustrations that bog down research and researchers at virtually every step. But let’s save such annoyances for later.

A microscope makes everything intimate

“What I see as the most beautiful part of my job is contact with living matter at an almost intimate level. We look inside the roots, the root cells, and we have real-time insight into what they do, how they react, how they grow. Most people have never seen anything like that: it’s fascinating. I love the intimacy of looking inside cells. I’m a microscopist through and through.”

It is these nifty tools, allowing members of the Faculty of Science to observe live cells in real time, that quite deservedly fill him with pride.

His one-of-a-kind vertical microscope makes it possible to observe the growth of a plant in its natural – i.e. vertical – position. It is combined with spinning disc technology, which in turn allows the researcher to single out and observe one particular layer of the object, and moreover, it does not scan line-by-line but all at once, so that the scanning is fast.

“There’re several vertical microscopes in the world, but – as far as I know – only our lab has this particular combination right now. It took a lot of effort to select the components and their supplier, secure the funding and get the machine up and running, but now it’s working round-the-clock, we’re getting the maximum mileage out of it.”

Still, just seeing is not enough. What is important is the ability to observe in the right way: in order to come closer to understanding all the processes, Fendrych and his team also have to make sure that the objects under observation enjoy the most suitable conditions. This is why he – in collaboration with Dominik Králík from the University of Chemistry and Technology in Prague – developed microfluidic chips, i.e. tiny chambers (“mini-greenhouses”) in which the test plants are mollycoddled while still being potentially exposed to a variety of stimuli and observed under a microscope.

The fruit fly among plants

Their model organism is the thale cress, Arabidopsis thaliana. “It’s ideal. It has everything a plant is supposed to have, but it’s delicate. The radius of the root has only ten cell layers – as opposed to mung beans, for instance, which have such thick roots that you wouldn’t be able to see anything. The cress is tiny, translucent – it’s a fruit fly among plants, it’s awesome,” enthuses Fendrych.

“The special transparent chambers allow us to give the plants various stimuli and watch how they respond. What’s going to happen if I add the plant hormone auxin? What if I dial back on potassium? I can see everything in real time. It’s just marvellous. Only a few people in the world can do this and we’re beginning to have some success with it, which makes me awfully happy. I’m all the more happy because my French postdoc got enthusiastic about the idea and teamed up with Dominik Králík to fine tune everything and make it run smoothly. As a boss, I have quite a lot of ideas, and it’s great when a team member adopts one of them – perhaps even overhauling and modifying it – but sinks their teeth into it and achieves some – even if partial – success. That gives us both a huge boost. The opposite scenario is frustrating.”

And back it comes. Frustration. We will get to the personal/scientific setbacks in due course, but for the time being let’s stay with plants. When under observation, they must not experience frustration: if a biologist wants to examine a plant, they should not stress it out, but rather make its living conditions as comfortable as possible.

“They need good care. They’re already in a very artificial environment: glass, agar jelly, silicone, strong lighting – these alone are a source of stress for them. Working with these plants requires sensitivity, so that you don’t damage them, so that they can prosper,” he describes.

Unless the aim is actually to observe what happens with the plant when it is under stress, right? “Well, sure. But that’s a job for other teams, not so much for us. Our main goal is to observe basic processes in cellular biology and physiology, which is why we need our plants to thrive and live in a natural and wholesome environment.”

How will this benefit humankind?

I am complimenting Mat (the short form of Matyáš he prefers using) on his talk from the lecture series ‘Biology Thursdays at Viničná’ (Viničná 7 is the seat of the Faculty of Science, Charles University). I really enjoyed the way he used visualisations and videos to draw his audience into the fascinating life of plants – especially the part that takes place underground.

“Granted, popularising science is important, but I was quite worried about the lecture; I’ve got to admit that I’m never sure how to speak in public about the stuff we do, because in most cases the question ‘What’s the use?’ is looming over the auditorium. And I can’t give a simple answer to that – and I don’t want to, either. I do basic research because I find it interesting and because it’s still unknown how this stuff works. I don’t need to see a cure for cancer waiting in the wings.”

In Belgium, he says, plant-themed talks would typically begin with the words: “There are more and more people in the world and we need to feed them…”

“But that’s rubbish, I hate that,” he counters.

That being said, the basic research findings of plant cellular biologists do indeed help – in the search for more resilient crops, for instance. “Well, yeah, that’s right. Plant pathogens, for example, are a huge problem and unless we’re familiar with basic cellular biology, we don’t know how pathogens work or how to deal with them. We’re learning to understand the processes and fellow researchers can use our findings. If I wanted to do applied research, I might choose a particular pathogen and focus on that, but personally, I don’t need to see such straightforward benefits in what I do. I look for what’s interesting for me. Like situations when we know that something’s happening in the plant, but we don’t know how it’s happening, how the plant does what it does.”

He poses himself questions – and behind each of them more peer out. “Fortunately, grant agencies don’t insist that we set precise goals and write down exactly what we want to find out. If I knew what exactly I’m supposed to find out, there’d be no point in actually doing it!” he laughs.

Messenger in the plant world

He is interested in cell growth in thale cress in response to the hormone auxin – a field that has been studied for a century, yet still contains fairly large blanks. “There’s a huge number of things that’ll perhaps remain unknown to science; the question is whether we really need to know them. But where auxin is concerned, I believe that it is important to know, and that finding out as much as we can about its influence is a no-brainer.”

Auxin is a hormone produced by all higher plants. It plays a key role in regulating the plant’s development, it establishes organs, it directs the growth of vessels. It is responsible for communication between cells, working as a ‘messenger’ that gives plant cells signals on how to behave, which of them and where they are supposed to blossom or put down roots.

“And with respect to roots, it’s responsible for the so-called ‘gravitropic response’, an issue I’m particularly interested in. Auxin sends a message and the cells receive it on the side where the root is supposed to curve towards the Earth’s centre, switching off its growth, whereas the cells on top carry on growing as before, forming a bend. It’s still unknown what’s between the auxin molecule and the response. For a while it was thought that the mechanism had been explained, but it hadn’t. And the response, too, is different than what was assumed.”

The work of experimental botanists includes switching genes on and off. “Our predecessors in the 1980s and 90s were able to measure ion flows with electrodes, weigh dry matter – they tended to use physics-based methods and found out a lot that way. However, we’ve got the ability to regulate gene functioning and we’re also able – with the help of fluorescence proteins – to see processes inside cells in real time. Inside living cells.”

The discovery of the green fluorescence protein was a milestone in the research of processes inside organisms – it hardly comes a surprise that its discoverers were awarded the Nobel Prize in 2008. It is not used just in botany, but also in neurobiology and elsewhere. The protein was isolated from jellyfish and when exposed to blue light (the kind of light emitted by ordinary fluorescent tubes, although lab experiments use laser light with a precisely set wavelength) it gives off green luminescence. It is used for tracing the expression of proteins as well as their precise localisation. And, amazingly, the plant – once it has been spliced with the gene that concerns us here, the one that is related to the GFP code sequence – produces the protein by itself.

“You can modify it in various ways, so that it reacts, for instance, to calcium or acidity – the more calcium-rich or the more acidic the environment, the more light it gives off. This helps us measure what’s happening in each cell, and even in its components. We can prick the root on one side and see a wave of calcium spreading from one cell to another.”

Gene fishing

The holy grail of experimental botany is – to put it a little bluntly – the use of gene activation and deactivation in search for the genes and proteins that regulate the process. “But it’s like fishing. Plants have thirty thousand proteins. There are proteins that might be fundamental for the auxin response. You switch them off and examine how it impacts the response. And quite often, nothing happens. Signalling pathways and protein interactions in a cell are non-linear and they’re so complex that there’s still a lot of things left for us to unravel. And who knows if we ever will. Progress is very slow.”

And here it comes again. Frustration.

“Research is incredibly frustrating. Lots of people are frustrated. PhD students are frustrated. Postdocs are frustrated. Molecular biology is time-consuming, a single experiment can easily take six months. Say you have an idea that a particular protein might be interesting. You place an order for a mutant – that is, thale cress seeds in which the gene for your protein is switched off – you grow the plants and then you test what exactly happens in the mutants compared to plants that do produce the protein. And six months down the line you might perhaps find out that nothing happens, nothing at all!”

He says that in this respect he’s going through the roughest period right at this moment, now that he has a start-up team of his own. “I sense all the tensions, insecurities, disappointments in each of my staff. There are seven people on my team. It’s non-stop stress. On the whole, lots of people leave research because the results just fail to materialise. None of mine have left so far, but I feel hugely responsible for them. When they leave I want them to have a decent publication record, I don’t want them to bury their careers on my watch, to hit a brick wall, which is always a risk with a new group. I’ve been given a chance to start up my own research and the next few years will show whether I come through – whether we come through – or not,” he says. “It’s slow going, but luckily – luckily, it’s working out quite well for us.”

In his opinion, the magic cure for all negative feelings comes in the form of a published paper. “It gives you an incredible boost. Once we’ve got one out, I’ll rest easy. We haven’t had a publication yet, but we’re in the process of drafting a paper and I hope it ends well,” trusts Fendrych, who has a few publications under his belt (Nature Plants, Current Biology, eLife), but none so far as head of a research team.

“Seeing your paper published is a huge rush. But it’s preceded by a drawn-out process. You send your paper to a journal, they show you the door; you try a different one, no response. Some people spend years submitting their work to journals before they find one that accepts it. Just imagine you write an article and nobody runs it for two years. By that time you’ve started to hate the text, the constant re-writes to make it conform to different formats,” he describes the pre-publication drama.

Still, he himself has been lucky. “So far it seems we’ve been choosing the journals well – aiming neither too high nor too low – so all of our papers have been accepted.”

Down to the roots of the family tree

Matyáš’s father is Martin Fendrych, a well-known Czech journalist, commentator and also a mid-1990s Deputy Minister of the Interior. In an interview for a lifestyle magazine, he spoke about a “hereditary condition”, a drive to know and influence the world around himself. Apparently, his father had the same drive, as did his grandfather.

And the son?

“Everybody has that, don’t they? Well, alright then, to a certain extent. Perhaps it runs stronger in my family. So I try my best. Influencing students around me. And my children. Lecturing. Going to demonstrations and voting. It’s one of the reasons I’ve come back home, to Prague, although since then I’ve told myself a few times: ‘What an idiot!’” laughs Matyáš.

His father is a journalist, his mum works in the social services. Nothing in his family, nor in his childhood and teens suggested that, in the future, Matyáš would fall in love with science, of all things. “Plants weren’t a huge draw for me either. At secondary school I had no inkling about what I might do after graduation. A little hint came during a science class: I remember the shock of learning that the sex cells of some plants – such as ginkgo and moss – have flagellae, that their gametes can move, so that ‘static’ plants behave differently than you’d expect. I found that very interesting. But I was more interested in animals, especially their behaviour. Ants.”

He enjoyed reading books by Konrad Lorenz on animal ethology. “People kind of examine themselves that way, don’t they? Through extremes manifested in animal behaviour. We keep an eye out for parallels and differences.”

His classmates (Fendrych says the more ambitious ones) went on to study law or medicine. “And I kind of couldn’t make up my mind. I’d hang around pubs, smoking. I was no swot; to tell you the truth, I didn’t spend much time revising. I didn’t have to, I didn’t need it. Looking back, I think I may have missed out. I have poor memory, but I honed it somehow – when I was examined in front of the class, I’d always talk my way out of it, figure stuff out on the spot.”

I remark that it is quite a valuable skill to have. But he sees it as a handicap, too. “The scientists in my field are really super smart, they know a lot. I can do only what I understand, I’m essentially pretty ignorant.”

You know what? Join us!

His interest in ethology brought him to the science faculty, but it was not long before he put animal behaviour out of his mind. That is because he was fascinated by lectures on plant anatomy given by Olga Votrubová. “Many of my schoolmates thought hers was the most boring course ever, but for me she was like an epiphany. Then I knocked on her door to discuss my graduation thesis… And just like with most things in my life, blind chance intervened. Ms. Votrubová wasn’t in her office, sitting there was Jana Albrechtová, who was researching the response of spruce trees to increased CO2 levels, which appealed to me as well. I was quite into environmental issues back then.”

His graduation thesis discussed experiments with spruce trees and their reactions to various fungal symbiotes, but he did not want to pursue this direction in his postgraduate studies. He contemplated a radical change of field, but first went to consult experimental botanist Viktor Žárský (“He had a reputation as someone who knew everything.”).

“Yeah, that’s an excellent idea,” Žárský told him. “But you know what, why don’t you join me for a while and have a look around our lab!”

And so he did. He went to the district of Lysolaje on the outskirts of Prague, location of the Institute of Experimental Botany (IEB) of the Czech Academy of Sciences. And he stayed there. “That’s when I started to do molecular biology. I got hooked, I had to learn my way around PCR, cloning, RNA and DNA isolation, splicing genes into plants,” he enumerates. And it was there, too, that he fell in love with microscopes.

He did a six-month internship in Durham, England, at the lab of Patrick Hussey, working with Mike Deeks. “He sat me down at a confocal microscope – a machine worth tens of millions – and asked me: ‘Do you know how to handle this?’ I said I did, because I felt stupid admitting I had only minimum experience with it. He demonstrated something to me and left. So I sat there, not really sure what to do. Then I started fiddling with it – and it worked. I learned on that machine. To this day when I’m sitting at a microscope, I hear the words of Mike Deeks ringing in my ears – that every image has to be usable for publication, it has to be technically sound. Otherwise you’ll be writing a paper one day and suddenly you realize you really need a picture… But because you were lazy that one time, the photo has the resolution of a cell phone snapshot, and that’s crap.”

His PhD studies at IEB involved cell division. “I was enthralled by it. A plant cell divides differently than an animal one, which simply strangulates down the middle and splits into two. The plant cell is surrounded by a solid wall, solid as steel. The cell divides everything inside nicely and evenly, just like the animal one, but then it builds a new wall between the two bundles of stuff.”

Plant cells keep multiplying, but each one stays squarely next to its sister/neighbour throughout its life. “It’s a fascinating process. It was an exciting moment for me when I watched the dynamic under the microscope for the first time.”

There is also enormous pressure within the cell. “I’d compare it to a well pumped-up bike tyre. The plant works with the pressure: you can see this quite clearly when you don’t water a plant – it goes limp. When you water it, it re-inflates and perks up. And this is also directed by auxin.”

Auxin. Judging from the number of times I have heard plant biologists utter the name of the green hormone, I should regard it as a mighty wizard. Matyáš puts a damper on my excitement: “That may be a bit of an optical illusion. It’s the most famous one, it’s been studied for ages and while it does have a lot of responsibilities, other hormones are probably similarly efficient, only we haven’t studied them quite as much yet.”

Resistance to failure

“Early into my PhD, I’d already decided that I’d carry on doing research, although I knew by then how mentally draining it could be. A realisation that is still borne out to this day. There are also long spells when nothing goes your way, when you just can’t seem to catch a break. You sink into frustration, which can have fatal results.”

He thinks that one of the most important qualities in a researcher ought to be resistance to failure. “It’s make or break. I keep seeing it with students and PhDs – when something isn’t working for them for a long time, they just ditch it and do a different experiment instead – but they get no answers that way. The more resistant ones last it out. When a good researcher asks themselves a question, they have to persist. Either they arrive at an answer – when one approach isn’t working, they take a step back and go at it from a different angle – or they recognize the right moment when it’s really impossible to make any headway, and ask a different question,” he describes.

Fresh from his PhD, he decided to try his luck abroad.

Caps in Ghent

For his ‘walkabout’, Mat chose an institute in the Belgian city of Ghent, the lab of a group recently formed by Moritz Nowack, who was investigating programmed cell death within the context of evolutionary biology. He moved to Belgium along with his wife. “Lenka is a social geographer, back then she was studying the phenomenon of farmers’ markets, so she just carried on with her research in Belgium.”

He was excited about Ghent. He (supported by his boss) slightly modified the topic of his research. Originally, he was supposed to work on seeds, but eventually he went down to the roots. And then came a revelation. “A developing root has this kind of tissue, a ‘cap’, and I noticed the cells there periodically die off; when I put the cell death markers there, it kept lighting up. I went to see Moritz. ‘Hey, we may be on to something here!’ Seeking an ideal model system for the study of programmed cell death, we were focusing mainly on leaves and seeds. It takes the Arabidopsis four weeks before it starts producing seeds, it’s hard to work with – but its root pops out in four days! And right away, the cells start dying off there. Well, nowadays working with cell death on root caps is one of the staples at Moritz’s lab.”

The root cap protects the surface of the root during its growth. Once it has served its purpose, its cells commit suicide – and more than that: they dispose of their own remains, too. “While growing, these cells engineer their own self-destruction mechanism. The cell breaks down its membrane system, it cuts up its nucleus to avoid leaving mess on the surface, so that others don’t have to worry about it – basically, it arranges and conducts its own funeral,” comments Fendrych on the considerate nature of root cap cells.

Along with his coworkers in Ghent, he identified the gene that triggers production of the protein that ‘cuts up’ the nuclei. When they switched off the gene – i.e. the protein production – cellular nuclei stayed longer on the surface. And voilà! A paper in Current Biology. “The holy grail would be discovering a gene that would stop the whole suicide process, so that the cells stick around. No joy so far. And maybe it’ll never be done, the process has lots of components,” he thinks.

Like something out of a science movie

He remembers the time spent in Ghent as “something out of a science movie”. “It was intense. I was constantly discussing stuff with Moritz, and other team members, I even slept over at the lab a few times. I didn’t have kids back then, and then later I had one, but I could still sink huge amounts of time into it. Moreover, Ghent is a great place and the institute was top notch.”

Three years later, however, the time was ripe to move on. He said goodbye and, with his wife and child (two more were to come later) in tow, he took up a post at IST (Institute for Science and Technology) in the Austrian town of Klosterneuburg, at the lab of Jiří Friml, a world-renowned Czech experimental botanist.

Originally, Matyáš’s main project was to figure out how so-called ‘auxin channelling’ works in lower plants – the model organism was moss, but during the work he felt he was the one gathering moss. “It grows terribly slowly, not my cup of tea, I returned to my pet, thale cress.”

And so (although not without patient work), he scored another success. And since it is not right to blow one’s own trumpet, let’s hear what Jiří Friml has to say: “In our lab, the bigger discoveries occur about once a year. The most recent of those was made by Mat, that is my former postdoc Matyáš Fendrych. One of the main functions of auxin is inhibition of root growth and for years scientists thought it happened in a certain way, long since described in textbooks. But we found out that it happens in an entirely different manner,” said Friml in an interview for Deník N.

Another published paper saw the light of day (in Nature Plants), as did Matyáš’s second child. And he felt ready to hit the road again.


“Over time, having a boss got annoying. Jiří is cool, I like him, he can be a brute, he’s what you’d call ‘a big boss’, but he cares for his people, keeps in touch, and underneath that hard shell he’s a really nice guy. Still, when you’re thirty-five, it rubs you the wrong way to be told: ‘That’s nonsense, don’t do that.’ Or when visitors come: ‘Look after them, will you.’ I started yearning to have a team of my own and I felt ready for it. Also, I kind of wanted to return home.”

That was because of his children and because of Prague. “I wanted to live again in an environment where I speak the language well, and where I can participate in social life, although I’ve got to admit that, at the end of the day, I don’t do that a lot. But the institutes both in Austria and in Ghent were far outside the city, they were a world unto themselves. Working there had a lot going for it, but I missed the chance to be part of civil society. I kept reading Czech newspapers anyway… So I decided to return. And try bringing some of what I’d learned abroad back here with me,” he says.

The author is an editor of Deník N.
Translated by Petr Ondráček.

Vlajka Evropské unie

This project has received funding from European Union's Horizon 2020 research and innovation programme under grant agreement No 955326.