Unearthing the Roots of Life

Dr. Jan Kooter started with cultivating plants and ended up studying genetics. What was his journey from a future in horticulture to his current position at Vrije Universiteit (VU) Amsterdam? Before the well-known VU lecturer, education coordinator and life scientist Jan Kooter retires, we decide to go back to his roots.

By Sonja van Scheijen & Mette Oorthuijs

In light of Jan Kooter’s retirement in February 2020, we wanted to take this moment to get to know Jan a little better and look back at his career. Who is this man with a passion for (epi)genetics, who has been involved in university life in so many aspects? How did he end up being the kind, approachable master coordinator he is today? Let’s take a look back at the steps that Jan took throughout his career to become the man he is; a man with a mission to understand the world around him in more depth.

Off the Beaten Track

Jan’s childhood was centered around plants and biology, as his whole family worked and works in horticulture. Fruit growing was then mostly passed down from father to son and although at present only his allotment garden remains from all this, his career did start in the garden.

Even though his primary school teacher strongly advised Jan to go to the lyceum, he was more eager to go to gardening school. When thinking back on this choice, Jan talks enthusiastically about what a fantastic time he had here. He claims that the same enthusiasm was never reciprocated by his peers who attended the lyceum, therefore cementing his delight in his own choice. This experienced enthusiasm and passion are the reasons Jan often advises his students to always follow their heart, even if something does not seem like the right choice for others.

Jan’s positive experience at gardening school is one of the reasons he always advises to follow your heart.

Jan loved all the practical courses that concerned topics ranging from pruning trees to motor mechanics, and after a couple of years, he continued to the higher gardening school (nowadays known in the Netherlands as MBO). His vocational training contained more theoretical courses. Jan delved into the world of botany and discovered his love for manipulating and breeding plants.

After his graduation, he started working at the Royal van Zanten in Hillegom, where, besides growing flowers for quality control, he developed new strains through classical breeding. The attentive reader will probably not be very surprised by this turn of events, since genetics – with all its flavors – turned out to be the main focus of Jan’s scientific career…

Jan in his early twenties, in the lab of the Swammerdam Institute.

Jan moved to Amsterdam after one year in the horticultural industry. His desire for more in-depth knowledge increased during evening courses and he decided to continue studying. Inspired by an interview with Dr. Piet Borst about recombinant DNA, Jan decided that he also wanted to work with the molecules of life. With a gardening school degree, directly enrolling into a university study was not possible then, and therefore at 19 years old he decided to go to laboratory school to become a technician.

An Era of Discoveries

During laboratory studies (nowadays known in the Netherlands as HBO), Jan chose the Biochemical Analyst specialization, which, besides theoretical courses in the evening, consisted of a two-year internship. For this, he went to the very scientist he was previously inspired by, Piet Borst. In this department at the Swammerdam Institute (now SILS, UvA) he joined a group led by Prof. Richard (Dick) Flavell. Amongst other projects, Flavell was working with the then brand-new Southern blot technique, after hearing about it at an American congress. Together, Flavell and Jan further developed this technique so that they could map human hemoglobin genes and compare the structure of the hemoglobin region in normal and Hb Lepore DNA (1). Jan told us that he cherishes the fact that many scientific techniques, like the Southern blot, were developed early on in his career, since these aided further discoveries.

Jan started to want more. Looking at the interns, PhD students and postdocs he thought “I can do that as well!”.

Working alongside Flavell for two years taught Jan a lot, such as developing great experimental insight. However, most of the things Jan learned and published about were focused on practical work, and then he started to want more. He distinctly remembers looking at the interns, PhD students and postdocs, and thinking “I can do that as well!”, so he decided to study further. 

Back to the School Bench

Jan chose to study chemistry and specialized in biochemistry. At the time, this consisted of a “kandidaats” exam (BSc) and a “doktoraal” (MSc), lasting 5 years in total. During these years at the University of Amsterdam, Jan was introduced to many exciting new topics, such as quantum mechanics. It was there that Jan discovered he always wanted to understand things in-depth. Like a chemical chain-reaction, just as Jan’s understanding of trees and plants had led him to research DNA, now he turned to chemistry and physics.

The last 2 years of his doktoraal consisted mainly of internships. For his second internship, Jan returned yet again to Borst’s department at the Swammerdam Institute, who was now working on trypanosomes, which are unicellular parasites that cause sleeping sickness in humans. There he joined the group of (then) Dr. Titia de Lange, to study the mechanism of antigenic variation and how these parasites could alter their characteristics throughout an infection.  

A Leap Towards Oncology

After his graduation, Jan continued his PhD under the supervision of Borst, who was the director of the Netherlands Cancer Institute (NKI) at that time. At the NKI, Jan continued studying trypanosomes. Trypanosomes are able to perform DNA rearrangements, making them useful for tumor research. Jan mentions one of his proudest findings during this time was that the promotor, which was regulating genes that encode the variant surface glycoproteins, was actually situated 60.000 bp upstream of the gene of interest with several other important associated genes (2, 3). As during his technician days, laboratories then still used a lot of radioactivity and Jan jokingly posits that he “does not understand how he is still sitting here”, adding that he probably has many mutations himself as a result.

Jan had to do a lot of practical work and spent entire days at the lab.

Looking back at his PhD, Jan realizes he was really ‘at the right place at the right time’. A very stimulating environment, where he could do lots of experiments and was less distracted by all the literature because they only had access to articles on paper. This practical work was also right up his alley, due to his already gained experience and a certain dexterity, developed back in gardening school. He spent entire days at the lab performing cloning experiments, since at that time, the polymerase chain reaction technique was still being developed. It is stories like these that can make the modern-day science student speculate about current experimental procedures which could become less laborious for future researchers.

Regenerating passion

Near the end of his PhD, Jan realized that he wanted to work with plants again, as it was demonstrated that you could genetically modify them easily. He decided to follow a postdoc at the Salk Institute for Biological Studies in San Diego, in the lab of Prof. Chris Lamb. At this institute, a variety of topics was studied, which meant that his girlfriend – who is still his partner today – could easily find a lab to work there too.

A photograph of the Salk Institute for Biological Studies, framed in Jan’s office.

Jan’s research focused on tobacco plants since this plant can easily be regenerated from a single cell, a feature that is beneficial when performing genome modifications. Lamb’s research focused on the immune system of plants. In response to infection, plants can secrete certain substances and Jan studied the activation of the genes involved, and the location of their promoters in the genome (4).

From Scientist to Program Coordinator 

In 1990, Jan moved back to the Netherlands and as a KNAW fellow, he started working at the VU, where he got a permanent position to do both research and teaching. Here he remained close to plant research and studied the mechanism of gene expression in petunias, which the VU then was renowned for. Interestingly, when Jan’s group attempted to make their petunias more vibrant, the flowers turned white!

It was discovered then that it was aberrant produced RNAs that could alter gene expression through a mechanism now known as RNA interference. It was the concept of RNA interference changing DNA that sparked Jan’s interest in epigenetics (5). To study this, he worked together with many European research consortia in (epi)genetics, both inside academia as well as industry (6). This resulted in many special friendships, many of which he still holds today.

Jan in his office, where his door is always open to his students.

Next to his research, Jan became increasingly active in teaching at the VU, starting with evolutionary genetics, and he will even continue lecturing in some courses after his retirement as education coordinator. Currently, he teaches many genetics courses in the bachelor, honors and master programs for the VU life sciences students, as well as an epigenetics course at Amsterdam University College.

Jan will miss helping students, as this has always given him a great sense of satisfaction.

Jan loves helping students to reduce the chaos and stress of studying, and he thinks it is important to be easily approachable for students. When he has the impression that he has really helped a student, he returns home with a great sense of satisfaction. When we ask Jan about his retirement, he said that he will miss his job as a master coordinator, and the personal contact with his students. However, he has faith that the new program coordinator, Dr. Jurgen Haanstra, will do an excellent job. 

A timeline of Jan’s life.

Jan has had a special career and he certainly did not take the shortest route to grow into the scientist he is today, of course this article could easily be twice as long. But all the steps in his career were driven by Jan’s exponentially growing passion to understand the world around him in more depth. Through following his passions, he also followed his heart. Jan will most definitely continue to learn new things and share them with others, even in retirement. Besides his science, Jan has a love for music, especially blues rock and jazz, and sports, namely: cycling. He encourages everyone to make time for physical activity, because he sees it as a big contributor to his ability to keep his head cool during stressful moments. 

We feel privileged that we were able to speak at length about Jan’s life and career before his retirement. We think we can say that many life sciences students at the VU are going to miss Jan dearly. In all, we think his career truly shows us all that there is more than one path to a successful, fulfilling career in science. Driven by his enthusiasm for genetics, Jan’s story demonstrates how one can truly flourish, by simply following their heart.

Do you have a message for Jan Kooter before his retirement?

We can imagine that more of our readers will miss Jan and so we would like to invite you to write something in this online guestbook. Please share your appreciation for Jan, and take a look to see what other students and Jan’s colleagues have to say.

About the writers

Sonja is studying both the Biomolecular Sciences and the Philosophy, Bioethics, and Health master degree at VU. She enjoys doing many things at the same time: her interests range from the influence of literature on society (and vice versa) to the molecular basis of rare genetic diseases.

Mette is a second year student in the Biomolecular Sciences master at VU. After a bachelor in neuroscience, she has chosen this master to study the molecular basis that underlies every organ in the body.

Further reading

1. Flavell, R. A., Kooter, J. M., De Boer, E., Little, P. F. R., & Williamson, R. (1978). Analysis of the β-δ-globin gene loci in normal and Hb Lepore DNA: direct determination of gene linkage and intergene distance. Cell, 15(1), 25-41.

2. Kooter, J.M., van der Spek, H.J., Wagter, R., d’Oliveira, C.E., van der Hoeven, F., Johnson, P.J., and Borst, P. (1987). The anatomy and transcription of a telomeric expression site for variant-specific surface antigens in T. brucei. Cell 51, 261-272.

3. Johnson, P. J., Kooter, J. M., & Borst, P. (1987). Inactivation of transcription by UV irradiation of T. brucei provides evidence for a multicistronic transcription unit including a VSG gene. Cell, 51(2), 273-281.

4. Faktor, O., Kooter, J. M., Dixon, R. A., & Lamb, C. J. (1996). Functional dissection of a bean chalcone synthase gene promoter in transgenic tobacco plants reveals sequence motifs essential for floral expression. Plant molecular biology, 32(5), 849-859.

5. Stam, M., Viterbo, A., Mol, J.N.M., and Kooter, J.M. (1998). Position-dependent methylation and transcriptional silencing of transgenes in inverted T-DNA repeats: Implications for posttranscriptional silencing of homologous host genes in plants. Mol. Cell. Biol. 18, 6165-6177.

6. Matzke, M., Matzke, A.J.M., and Kooter, J.M. (2001). RNA: Guiding gene silencing. Science 293,1080-1083.

Mette Oorthuijs took the photos for this article (except for the photo from Jan’s own collection) and created the timeline.