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I was not always a member of the great Ettema-Lab. Before finding my way to the illustrious Thijs Ettema, I undertook the following academic career path:
After obtaining my high school diploma in 2006 in the Netherlands, I started on the bachelor program ‘Biology and medical laboratory research’ at the University of Applied Science Rotterdam. The program gave me the opportunity to work with academic research groups. And so I did: one ~5 months project with Plant-Microbe Interactions at Utrecht University, and one ~9 months project with Molecular and Developmental Genetics at Leiden University. Both of them were very positive experiences for me and gave me the feeling I wanted to work in academia.
Thus, after graduating in 2009, I decided to continue my studies with the master program ‘Molecular and Cellular Life Sciences’ at Utrecht University. Once more I had the opportunity to work with research groups. And again I did: for my major research project I worked with Jan Bogerd at the Developmental Biology group at Utrecht University for about 1 year. This project ultimately resulted in my first two publications as a co-author. And then for my minor research project, with help of funding from the Erasmus exchange program, I worked with Thijs for the first time at the Molecular Evolution research group at Uppsala University in Sweden for ~9 months. After a successful project and subsequent masters’ thesis, I graduated cum laude in June 2012.
I returned to Molecular Evolution and joined the Ettema-Lab in the beginning stages as a PhD-student in October 2012.
During the various stages of my research training I’ve been interested in a wide variety of topics. For example, for my very first project I was interested in the plant-pathogen interaction between the oomycete Hyaloperonospora arabidopsidis and Arabidopsis thaliana, while for my third project I was interested in the gene expression levels of relaxins and relaxin receptors in the fish Danio rerio. But since my last master project I have a strong interest in the evolutionary origins of eukaryotes and mitochondria.
Many different hypotheses have been suggested regarding their origins, and there is no real consensus. One of the hypotheses that has been gaining favor lately is a model in which ancestral archaea and bacteria establish a symbiotic relationship, and eventually evolve into the first eukaryotic-like cells. However, the nature of the archaeal and bacterial parent and their symbiosis remains mysterious. This can largely be attributed to the fact that no closely related lineages of these ‘parents’ have been found yet. By applying novel genomics approaches like single cell- and metagenomics on extreme environments like hydrothermal vents, black smokers and hot springs, we aim to expand the microbial genetic dataset and find these ‘parental’ lineages.
One aspect of the symbiotic model, sometimes referred to as ‘symbiogenesis’ or ‘fusion’, is that the bacterial parent is the progenitor of the mitochondria. Thus, the origins of eukaryotes and mitochondria are intertwined. It is generally accepted that this bacterial parent was an alphaproteobacterium, but what kind of alphaproteobacterium is far from certain. Currently, I’m looking at 5 novel Alphaproteobacteria, which are candidate members of new alphaproteobacterial lineages. By assembling, annotating and performing phylogenomics I’m trying to figure out what kind of bacteria they are and what their phylogenetic placement is in the Alphaproteobacteria tree. Furthermore, using the new lineages, it will be possible to estimate with greater accuracy the nature of the mitochondrial ancestor. In the near future I hope to find and analyze more novel Alphaproteobacteria and so shed light on the bacterial side of the origin of eukaryotes.
As a result of being in contact with evolutionary research, I also became generally interested in the process of evolution on the molecular level. Rather than the biology of a given organism, or mechanism of a given protein, I’m more interested in what happens in between generations of organisms or proteins. What kind of ‘forces’ are at play that cause the gradual change of nucleotides, proteins and eventually organisms over many generations? And how do we try to model this process? It’s not an active research interest, but I like to read books about it and take (online) courses. I can highly recommend this Coursera course and the Molecular Evolution Workshop in Woods Hole.
I’m also interested in how a given environment can cause similar evolutionary changes on many different organisms in that environment. For example the extensive reductive evolution of microbes living inside another cell, or the hypothesized genome streamlining in the nutrient poor upper layers of the ocean. Another recently published example (by Kasia) is the extremely low recombination versus mutation ratio in freshwater SAR11 compared to marine SAR11.
Martijn J, Schulz F, Zaremba-Niedzwiedzka K, Viklund J, Stepanauskas R, Andersson SGE, Horn M, Guy L, Ettema TJG; Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution; The ISME Journal, April 2015
Good S, Yegorov S, Martijn J, Franck J, Bogerd J; New insights into ligand-receptor pairing and coevolution of relaxin family peptides and their receptors in teleosts; International Journal of Evolutionary Biology, Volume 2012
Chen SX, Bogerd J, Schoonen NE, Martijn J, de Waal PP, Schulz RW; A progestin (17α,20β-dihydroxy-4-pregnen-3-one) stimulates early stages of spermatogenesis in zebrafish; General and Comparative Endocrinology, May 2013