joran.html

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		<title>Joran Martijn</title>
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								<h1>People</h1>
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							<h3>Joran Martijn</h3>
							<h6 style="font-weight: lighter;">Research Associate</h6>
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						<p>Hi! I’m currently a research associate in the lab of Andrew Roger and I've been here since August 2019, originally as a Swedish Research Council postdoctoral fellow.</p>
						<h3>My research interests</h3>
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							My research is mainly focused on the evolutionary histories of the Metamonada, a group of anaerobic protists, and their mitochondria. More on that below. I've also become quite interested in the odd nuclear and mitochondrial genome biology of <i>Blastocystis</i>. More on that below, as well! Other than the biological aspects of these projects I’m particularly fascinated by the methods by which we can study these evolutionary histories. These include the very latest DNA sequencing technologies and the continuously evolving bioinformatics algorithms. These algorithms allow us to amongst other things assemble entire genomes <i>de novo</i>, predict where on those genomes the genes and other elements are located, and reconstruct the evolutionary histories of these genes.
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						<h3>The Metamonada, odd little protists who aren't exactly fans of oxygen</h3>
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							The Metamonada are a clade of anaerobic protists for which the exact phylogenetic position in the tree of life remains unclear. The most well known metamonads are perhaps <i>Trichomonas vaginalis</i>, the causative agent of sexually transmitted trichomoniasis, and <i>Giardia intestinalis</i>, the causative agent of gastrointestinal tract disease giardiasis. They additionally include <i>Monocercomonoides</i>, the very first organism discovered that has completely lost its mitochondria. Compared to typical aerobic organisms like humans, yeast and plants, the metamonads house substantially reduced mitochondria called mitochondria related organelles (MROs). They differ most notably in their mode of ATP production: whereas aerobic mitochondria execute oxidative phosphorylation, MROs often use anaerobic substrate level phosphorylation. The exact pathways differ between most metamonad species. The aim of the project is to infer the complete evolutionary history of the metamonads and identify all gene gains and losses that occurred on branches associated with important evolutionary transitions such as (i) the switch to anaerobic lifestyle, (ii) adaptation to host-associated lifestyle and (iii) reduction and complete loss of mitochondria. We do this by sequencing the complete genomes and transcriptomes of novel Metamonads with a mix of Oxford Nanopore and Illumina sequencing and compare them with the publicly available genomes and transcriptomes with the latest bioinformatics algorithms.
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						<h3><i>Blastocystis</i>, human and animal gut protists with a peculiar way of making STOP codons</h3>
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							<i>Blastocystis</i> protists were originally thought to be a genus level group, but after many isolates had their DNA sequenced, it turned out they were much more genetically diverse than meets the eye. They inhabit the guts of humans and many animals, and are suspected to contribute to various gut ailments, though their exact level of pathogenicity (if any) remains to be determined. To me, their most interesting feature is that roughly a third of their genes encode incomplete canonical STOP codons. That is, they end with 'T', 'TA' or 'TG'. The STOP codons are completed by the addition of the polyA tail. We are currently investigating how this mechanism evolved, and why it is that only Blastocystis exhibits this phenomenon.
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						<h3>My road to the Roger lab</h3>
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							Being from the Netherlands, I did most of my undergraduate studies in Rotterdam (bachelors) and Utrecht (masters), focusing primarily on molecular and cellular biology. In 2012 I moved to Uppsala, Sweden and started my PhD studies at the -just founded- lab of Thijs Ettema, in the field of evolutionary microbiology. I learned bioinformatics and used metagenomics and single-cell genomics to discover and reconstruct genomes from completely unexplored branches of the tree of life. In particular, we assembled genomes from many novel lineages of Alphaproteobacteria and used those to study the alphaproteobacterial ancestry of mitochondria. See <a href="https://www.the-scientist.com/daily-news/mitochondrias-bacterial-origins-upended-33345">https://www.the-scientist.com/daily-news/mitochondrias-bacterial-origins-upended-33345</a> for a popular science article describing the work. In 2017 I obtained my PhD degree and decided I would like to continue my research in the lab of Andrew Roger. I managed to get funding through the Swedish ‘VR International Postdoc’ grant and arrived in Halifax in August 2019.
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