JEROEN NOORDHOEK

ECOLOGY - ECOTOXICOLOGY - GENETICS - SOIL QUALITY - PHOTOGRAPHY

News and Publications

Exploring DNA methylation patterns in copper exposed Folsomia candida and Enchytraeus crypticus

Exploring DNA methylation patterns in copper exposed Folsomia candida and Enchytraeus crypticus

October 13, 2017: My first article as first author has been published in Pedobiologia - Journal of Soil Ecology.

Tea consumption leads to epigenetic changes in women

Tea consumption leads to epigenetic changes in women

May 31, 2017: Epigenetic changes are chemical modifications that turn our genes off or on. In a new study, researchers show that tea consumption in women leads to epigenetic changes in genes that are known to interact with cancer and estrogen metabolism. Source: ScienceDaily

Study pinpoints when the Galápagos Islands developed their unique ecology

Study pinpoints when the Galápagos Islands developed their unique ecology

December 20, 2016: A new study shows the geologic formation of one part of the Galapagos Islands archipelago -- the one responsible for the biodiversity -- formed roughly 1.6 million years ago. Source: ScienceDaily

Like father like son: Epigenetics in wild guinea pigs

Like father like son: Epigenetics in wild guinea pigs

December 23, 2015: Fathers are able to adjust to increasing temperatures within their own lifetime and do transmit this information to their offspring. This has now been shown for the first time in a wild animal. Source: ScienceDaily

Ecology buys time for evolution: Climate change disrupts songbird's timing without impacting population size (yet)

Ecology buys time for evolution: Climate change disrupts songbird's timing without impacting population size (yet)

April 25, 2013: Songbird populations can handle far more disrupting climate change than expected. Density-dependent processes are buying them time for their battle. But without (slow) evolutionary rescue it will not save them in the end, says an international team of scientists. Source: ScienceDaily

Ants have big impact on environment as 'ecosystem engineers'

Ants have big impact on environment as 'ecosystem engineers'

February 4, 20011: Research on the impact of ants on their local environment has revealed they play an important role. They have a dual effect on their local ecosystem which affects both the density and diversity of other species around them, including animals much higher up the food chain. Source: ScienceDaily

ABOUT ME

Biography

As a child I spent most of my days outside catching frogs and picking flowers and I knew that one day I would become the greatest veterinarian of all times. And for many years becoming a vet was my dream. However, as a high school student it became clear that I needed a back-up plan. Back in the day I wasn't so much the math and science guy. I did, however, realize that everything that had to do with nature fascinated me. So, some serious changes needed to be made in order to get anywhere close to the dream I'd been having for so many years. Luckily, spending time in South Africa doing voluntary work opened up my eyes and helped me making the change. I got back from South Africa and decided to do a bachelor in Wildlife Management. During these years my interest for nature and ecology evolved. Therefore, it didn't take long for me to come to the decision that I wanted to become an ecologist. I enrolled for the masters programme Ecology at the VU University in Amsterdam and two years later I earned my MSc degree. Now, with an increased knowledge and passion about evolution, molecular ecology, and genetics, I was certain to become a scientist. I applied for a PhD position in ecotoxicology and genetics at the VU University in Amsterdam, and I was given the position in november 2013. I hope that I will be able to unravel a fraction of the incredible complexity that is life, by focusing my research on genomic changes caused by stress exposure. By observing changes I hope to understand how organisms are coping with an ever changing environment.

Personal Info

  •   VU University, Dept. of Animal Ecology, De Boelelaan 1085, 1081 HV Amsterdam
  •   jeroen.noordhoek@vu.nl.

CONTACT

FOR ANY QUESTIONS PLEASE COMPLETE YOUR DETAILS BELOW

RESEARCH

Research interest

I am broadly interested in the interaction between evolution, genetics, epigenetics, and ecology. For instance, I find it fascinating to understand what shapes genetic and phenotypic diversity in natural populations and how organisms adapt to their environment. Also, the many ways in which the genetic environment may affect gene evolution. For example, factors such as the pattern of inheritance, the level of recombination, and the presence of selection at nearby genes can have significant consequences for how a gene responds to selection.

I am also interested in the genetic basis of ecologically important traits and how evolutionary forces such as selection and gene flow may interact in the processes of adaptation and speciation.

Although my research interest is broad and diverse, I focus my current research around the molecular response of organisms to environmental factors. I study the multigenerational effect of engineered nanoparticles (ENPs) in several soil invertebrates. The fascinating part about my project is that I get to combine the two emerging fields of nano-ecotoxicology and epigenetics.

Current

From bacteria that sense the earth’s magnetic field using ‘nanomagnets’ to the facilitated transport of radionuclides in groundwater, nanoparticles are central to many natural processes. The behavior of these naturally occurring materials result from their physical size, tunable properties and large and accessible inorganic surfaces. These same features can be optimized in engineered nanoparticles tailored for the requirements of diverse technologies. However, as society begins to use nanomaterials in greater quantities and in consumer products, interest in the broader implications of this emerging technology has grown. The central question is whether the unknown risk of engineered nanoparticles, in particular their environmental impact, outweigh their established benefits for society.

– Colvin, 2003

During this project we will investigate the multi-generational response of soil invertebrates to nanoparticles, starting from an F0 exposure to several compounds that differ in core structure and surface functionalization. We will perform long-term experiments including repeated exposures over multiple generations on Folsomia candida and Enchytraeus crypticus. This study will be used to develop tools to quantify hazard at the epigenetic level. ENPs may in two scenarios cause changes over multiple generations (1) genome integrity damage through enhanced mutation (genotixicity), (2) transcriptional plasticity changed over multiple generations without affecting DNA structure, e.g. via shifts in methylation status.

Therefore, with this project I will address the following questions:

  • Does multigenerational exposure of soil invertebrates to ENPs cause phenotypic effects increasing with subsequent generations?
  • Do ENPs cause inherited mutations in future invertebrate generations when the F0 has been exposed to ENPs?
  • Is CpG methylation an epigenetic factor in F. candida and E. crypticus and if so, can this be influenced by exposure to ENPs?
  • Can we correlate gene expression with changes in methylation pattern (when present)?

 
The results from this project will be used to develop a first fully probabilistic ecological Risk Assessment tool, including probabilistic evaluation of environmental distribution, exposure scenarios, and species sensitivity distributions.

Research projects

If we knew what it was we were doing, it would not be called research, would it?

– Albert Einstein

 

Metagenomic analysis of mycoflora in Dutch dune and forest habitats – 2013

Fungi are major determinants for the functioning and stability of terrestrial ecosystems. Still there is a large lack of knowledge about the true diversity of fungal communities. With this study, we provide a genetic diversity assessment of mycoflora in Dutch forest and dune habitats. We analyzed ITS 2 rDNA sequences from soil fungal communities using Ion Torrent sequencing, OTU delimitations and ordinations to compare fungal communities in different vegetation types and to investigate the effect of plant/tree hosts and soil acidity on these communities.

Climate change induced phenological shifts in migratory birds – 2013

The climate is now changing at a rate faster than birds have experienced in the past and the evolutionary adjustments by birds may not be able to keep pace with this change. Several studies have shown that many migratory birds exhibit a high degree of ecological and evolutionary adaptability and that many are now showing rapid adjustments to climatic changes. However, for other species, climate change can severely constrain or prevent full ecological and evolutionary adjustment, putting their survival at risk. With this literature study I reviewed which characteristics of migratory birds make them more or less susceptible to climatic changes by investigating the general effects of environmental change on migratory birds, the risks involved for migratory bird populations that are adjusting to new environmental changes and what mechanisms play an important role here, and the effects that birds experience at the start and at the end of the season.

Genetic variation within and between populations of Betula and their hybrids – 2012

The past few decades a substantial number of population genetic studies were performed on plants and trees using molecular tools, to investigate genetic diversity, gene flow, genetic differentiation and introgressive hybridization. From an ecological point of view the Betula (Birches) genus is interesting, because, population boundaries as well as species boundaries are highly unclear. Due to introgression and hybridization even the number of species the genus contains is uncertain and the genus is considered “taxonomically problematic”. With this project I aimed to investigate the genetic diversity and differentiation within and between populations of Betula pendula and Betula pubescens distributed in the Netherlands. Aspects that were analyzed were allelic diversity within and between populations, genetic variation between diploids and tetraploids, and genetic population structuring.

CV

EDUCATION AND TRAINING

VU University Amsterdam
PhD Candidate
Department of Ecological Science
November 2013 - Present
Supervisors: N.M. van StraalenD. RoelofsC.A.M. van Gestel

Project title: Genomic consequences of multigenerational exposure to ENPs in soil invertebrates

VU University Amsterdam
Ecology
Master of Science (MSc)
2010-2013

Van Hall Insitute, Leeuwarden
Wildlife Management
Bachelor of Science (BSc)
2007-2010

RESEARCH PROJECTS

Naturalis Biodiversity Center, Leiden
Trainee Scientist
February 2014 - July 2014

Project title: Metagenomic analysis of mycoflora in Dutch dune and forest habitats

Skills: Analyzing fungal diversity using Ion Torrent sequencing and ordination techniques

VU University Amsterdam
Literature study
October 2012 - April 2013

Project title: Climate change induced phenological shifts in migratory birds

Skills: Studying the characteristics of migratory birds which makes them more or less susceptible to climatic changes

Netherlands Forensic Institue, The Hague
Trainee Scientist
Januari 2012 - September 2012

Project title: Genetic variation between populations of Betula and their hybrids

Skills: Genetic analyses using PCR, fragment length determination, Genemapper, Genalex, Genepop, AUTOTET, GDA

TEACHING

Mabula Ground Hornbill Project, South Africa
January 2013 - Present

Creating lesson plans and materials for the education programme

For more information about the project, click here

WESSA / WWF Eco-Schools Programme, South Africa
2009

Environmental education at rural South African primary and secondary schools in Limpopo, South Africa

For more information about the Eco-Schools Programme, click here