The review resulting from the 2019 Lorentz workshop on predicting evolution, entitled: Towards evolutionary predictions: current promises and challenges has now been published in Evolutionary Applications.
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Another DNA walk
A photo of the DNA walk I did with my colleagues at the Leiden Centre for Applied Biosciene Leiden in Octber 2022. A DNA walk is a guided tour, in this case through the Hortus Botanicus in Leiden, during which I tell stories about the DNA of the plants and animals that we encounter.
DNA walk for curious citizens
On April 25th 2022 everyone with an interest in DNA could join me during a walk through the parks of Leiden, The Netherlands. The trees, birds and flowers seen during the walk each have their own DNA stories to tell.
New citizen science project
A new citizen science project has launched in which we will look at the soil microbiome around Tulip bulbs
Preprint on predicting evolution
The manuscript of the review resulting from the 2019 Lorentz workshop on predicting evolution, entitled: The why, what and how of predicting evolution across biology: from disease to biotechnology to biodiversity is now in preprint.
How to turn a wasp asexual
Photo: Herman Berkhoudt
In this project, we aim to gain deeper insight into the molecular mechanisms of Wolbachia-induced parthenogenesis, using the parasitoid wasp Asobara japonica as a model system. We employ a range of sequencing techniques, including whole-genome, IsoSeq and small RNA sequencing.
Collaborators:
- Leo Beukeboom, Groningen University
- Elzemiek Geuverink, Groningen University
tRNA evolution
Front cover PhD thesis Peter van der Gulik
Transfer RNAs (tRNA) are an integral component of translation in the three domains of life (Archaea, Bacteria and Eukaryotes). In this project, we are searching for domain-specific patterns in the set of tRNAs that are used.
We are also investigating whether these patterns can help assess the completeness of newly assembled genome sequences.
Collaborators:
- Wouter Hoff, Oklahoma State University
- Peter van der Gulik, Centrum Wiskunde & Informatica, Amsterdam
- Astrid Groot, University of Amsterdam
- Martijn Egas, University of Amsterdam
- Jenna Gallie, Max Planck Institute for Evolutionary Biology
A sustainable soil for Tulip industry
This soil metagenomics project at the Leiden Centre for Applied Bioscience is studying the soil microbiome of Tulip fields as part of an effort to transform this industry towards more sustainable practices.
Black Rhinoceros genome
The “Rhinoceromics” project at the Leiden Centre for Applied Bioscience is studying health issues in captive black rhino’s using various omics techniques, including metagenomics. As a sideline, we wanted to see whether we could assemble a large eukaryotic genome using only nanopore reads. This produced an assembly of comparable size and contiguity to the current reference genome for this species. Our assembly will be used as reference assembly in the metagenomics project.
Dré Kampfraath
co-supervised with Jacintha Ellers at the Vrije Universiteit Amsterdam
In his PhD work, Dré is using comparative genomics to study the loss of traits due to interactions between the springtail Folsomia candida and bacteria Wolbachia pipientis. This springtail has become dependent on Wolbachia for its reproduction. Using a combination of lab-experiments and genomics he searches for the phenotypic and genotypic loss of traits that led to this obligate relationship.