PhD: Development of a zebrafish metabolome atlas and bridging to EDC exposure

We are looking for an enthusiastic and motivated PhD candidate to join us.

Your function

This PhD project is part of the EU MSCA Doctoral Network NeXED (www.nexed.eu). It will be hosted by the section Chemistry for Environment and Health at the Amsterdam Institute for Life and Environment of Vrije Universiteit Amsterdam (https://vu.nl/en/about-vu/faculties/faculty-of-science/more-about/chemistry-for-environment-health). The main objective of this project is to determine the effects of EDC mixture exposure on thyroid hormone transport to the developing brain in novel human in vitro models and compare these effects to changes observed in cerebrospinal fluid thyroid hormone levels observed in humans and zebrafish. Selected real-life mixtures from the case studies will be tested for their effect on thyroid hormone transmembrane transporters (THTMTs) in dedicated THTMT-overexpressing cell lines as well as in human blood-cerebrospinal fluid barrier (BCSFB) organoid models and zebrafish embryos.

This 3-year PhD project is supervised by Pim Leonards. The objective of this project is to investigate at a molecular level (metabolome) the developmental and neurotoxic effects of endocrine disruptors in whole zebrafish embryos with a focus on specific organs (e.g. brain, liver, heart, gills, kidney, eyes), study at high time resolution the development of the normal zebrafish metabolome until 5 dpf and link these to the development of organs and tissues using advanced mass spectrometry techniques including tissue imaging techniques (MSI). This will provide comprehensive information on the effects of EDCs on the metabolome and link these to developmental and neurotoxic adverse effects (e.g. behaviour).

The following external research stays are planned:

  • Interdisciplinary secondment: Henrik Holbech (2 months) at University of Southern Denmark (SDU, Denmark)
  • Intersectoral secondment: Michael Rodamer (2 weeks) at Agilent (Company, Germany)
  • Interdisciplinary secondment: Dries Knapen (2 months) at University of Antwerp (UA, Belgium)

Your profile

You will

  • Perform metabolomics experiments with zebrafish and further develop tissue imaging mass spectrometry for zebrafish.
  • Enrol in the PE&RC graduate school (https://www.pe-rc.nl) and comply with the doctoral training requirements
  • Write project reports on a regular basis, and publish high-quality research results related to the research project in international conference proceedings and peer-reviewed scientific journals.
  • Participate actively in the NeXED training, dissemination, communication and exploitation activities.
  • Work actively on the preparation and defence of a doctoral thesis in the field of Environmental Chemistry
  • Engage with and further support a limited number of teaching activities for the section Chemistry for Environment and Health of the Amsterdam Institute for Life and Environment

In addition to the general eligibility and selection criteria of the NeXED Doctoral Network,

  • A 3-year PhD trajectory at Vrije Universiteit Amsterdam is only possible if:
    - The candidate has completed an accredited Research Master prior to the PhD trajectory or the candidate has comparable qualifications, as demonstrated by their curriculum.
    - This requires that the Master's degree amounts to at least 120 ECTS and that at least 60 ECTS has been spent on research preparation within the programme that ties in with the theme of the PhD trajectory to be followed.
  • Master’s degree in analytical chemistry
  • Familiar with metabolomics or tissue imaging mass spectrometry is a plus 

We realise that each individual brings a unique set of skills, expertise and mindset. Therefore, we are happy to invite anyone who recognises themselves in the profile to apply, even if you do not meet all the requirements.

What do we offer?

  • The selected candidate will be employed full-time by Vrije Universiteit Amsterdam on the MSCA-DN project for a period of 36 months.
  • Doctoral candidates are offered an employment contract for full-time employment, with a competitive remuneration based on the MSCA allowances in line with the MSCA WP 2023-2025.
  • The gross monthly amount at Vrije Universiteit Amsterdam corresponds to minimum € 3,378 and maximum € 3,707 (PhD) in the third (last) year. Fringe benefits include a maximum of 41 days of annual leave based on full-time employment, 8% holiday allowance and 8.3% end-of-year bonus.
  • Funding is available for technical and personal skills training and participation in international research events.
  • The expected start date is between July-September 2025. Last-year master students expected to graduate by this time are encouraged to already apply.
  • Read more about working at Vrije Universiteit Amsterdam here: https://workingat.vu.nl

About us

NeXED is a Marie Skłodowska-Curie Actions (MSCA) Doctoral Network, funded by the European Union. NeXED will in total recruit 15 enthusiastic, talented and driven Doctoral Candidates (DCs) who are highly motivated to be part of a new generation of cross-disciplinary toxicologists specialised in using harmonised approaches in a One Health framework to develop and support the implementation of innovations in the field of endocrine disruptor assessment. This vacancy is one of those 15 opportunities. Make sure to also read the general eligibility and selection criteria! See: www.nexed.eu.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 5,500 staff work at the VU and over 30,000 students attend academic education.

Diversity
Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding. We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.

Faculty of Science
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

Amsterdam Institute for Life and Environment (A-LIFE)
A-LIFE brings together the groups of Molecular Microbiology, Systems Biology, Environment & Health, and Ecological Sciences, with the aim to advance the fundamental understanding of the interplay between life and its environment. A-LIFE seeks to connect properties and emergent behaviours across all scales, from molecules to ecosystems, including human populations. The research of the department covers a broad range of research topics, including ecology and evolution, microbiology, (eco)toxicology and analytical chemistry of pollutants, global change biology, and biotechnology, and the associated state-of-the-art methods and technologies, both computational and experimental.

Interested

Applications must be submitted through the NeXED job application platform: www.nexed.eu

Deadline for applications: April 21, 2025, 23:59 CET. More information about the application procedure for NeXED PhD positions can be found here.

For additional information about this vacancy, please contact Pim Leonards ([email protected]).

Your function

This PhD project is part of the EU MSCA Doctoral Network NeXED (www.nexed.eu). It will be hosted by the section Chemistry for Environment and Health at the Amsterdam Institute for Life and Environment of Vrije Universiteit Amsterdam (https://vu.nl/en/about-vu/faculties/faculty-of-science/more-about/chemistry-for-environment-health). The main objective of this project is to determine the effects of EDC mixture exposure on thyroid hormone transport to the developing brain in novel human in vitro models and compare these effects to changes observed in cerebrospinal fluid thyroid hormone levels observed in humans and zebrafish. Selected real-life mixtures from the case studies will be tested for their effect on thyroid hormone transmembrane transporters (THTMTs) in dedicated THTMT-overexpressing cell lines as well as in human blood-cerebrospinal fluid barrier (BCSFB) organoid models and zebrafish embryos.

This 3-year PhD project is supervised by Pim Leonards. The objective of this project is to investigate at a molecular level (metabolome) the developmental and neurotoxic effects of endocrine disruptors in whole zebrafish embryos with a focus on specific organs (e.g. brain, liver, heart, gills, kidney, eyes), study at high time resolution the development of the normal zebrafish metabolome until 5 dpf and link these to the development of organs and tissues using advanced mass spectrometry techniques including tissue imaging techniques (MSI). This will provide comprehensive information on the effects of EDCs on the metabolome and link these to developmental and neurotoxic adverse effects (e.g. behaviour).

The following external research stays are planned:

  • Interdisciplinary secondment: Henrik Holbech (2 months) at University of Southern Denmark (SDU, Denmark)
  • Intersectoral secondment: Michael Rodamer (2 weeks) at Agilent (Company, Germany)
  • Interdisciplinary secondment: Dries Knapen (2 months) at University of Antwerp (UA, Belgium)

Your profile

You will

  • Perform metabolomics experiments with zebrafish and further develop tissue imaging mass spectrometry for zebrafish.
  • Enrol in the PE&RC graduate school (https://www.pe-rc.nl) and comply with the doctoral training requirements
  • Write project reports on a regular basis, and publish high-quality research results related to the research project in international conference proceedings and peer-reviewed scientific journals.
  • Participate actively in the NeXED training, dissemination, communication and exploitation activities.
  • Work actively on the preparation and defence of a doctoral thesis in the field of Environmental Chemistry
  • Engage with and further support a limited number of teaching activities for the section Chemistry for Environment and Health of the Amsterdam Institute for Life and Environment

In addition to the general eligibility and selection criteria of the NeXED Doctoral Network,

  • A 3-year PhD trajectory at Vrije Universiteit Amsterdam is only possible if:
    - The candidate has completed an accredited Research Master prior to the PhD trajectory or the candidate has comparable qualifications, as demonstrated by their curriculum.
    - This requires that the Master's degree amounts to at least 120 ECTS and that at least 60 ECTS has been spent on research preparation within the programme that ties in with the theme of the PhD trajectory to be followed.
  • Master’s degree in analytical chemistry
  • Familiar with metabolomics or tissue imaging mass spectrometry is a plus 

We realise that each individual brings a unique set of skills, expertise and mindset. Therefore, we are happy to invite anyone who recognises themselves in the profile to apply, even if you do not meet all the requirements.

What do we offer?

  • The selected candidate will be employed full-time by Vrije Universiteit Amsterdam on the MSCA-DN project for a period of 36 months.
  • Doctoral candidates are offered an employment contract for full-time employment, with a competitive remuneration based on the MSCA allowances in line with the MSCA WP 2023-2025.
  • The gross monthly amount at Vrije Universiteit Amsterdam corresponds to minimum € 3,378 and maximum € 3,707 (PhD) in the third (last) year. Fringe benefits include a maximum of 41 days of annual leave based on full-time employment, 8% holiday allowance and 8.3% end-of-year bonus.
  • Funding is available for technical and personal skills training and participation in international research events.
  • The expected start date is between July-September 2025. Last-year master students expected to graduate by this time are encouraged to already apply.
  • Read more about working at Vrije Universiteit Amsterdam here: https://workingat.vu.nl

About us

NeXED is a Marie Skłodowska-Curie Actions (MSCA) Doctoral Network, funded by the European Union. NeXED will in total recruit 15 enthusiastic, talented and driven Doctoral Candidates (DCs) who are highly motivated to be part of a new generation of cross-disciplinary toxicologists specialised in using harmonised approaches in a One Health framework to develop and support the implementation of innovations in the field of endocrine disruptor assessment. This vacancy is one of those 15 opportunities. Make sure to also read the general eligibility and selection criteria! See: www.nexed.eu.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 5,500 staff work at the VU and over 30,000 students attend academic education.

Diversity
Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding. We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.

Faculty of Science
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

Amsterdam Institute for Life and Environment (A-LIFE)
A-LIFE brings together the groups of Molecular Microbiology, Systems Biology, Environment & Health, and Ecological Sciences, with the aim to advance the fundamental understanding of the interplay between life and its environment. A-LIFE seeks to connect properties and emergent behaviours across all scales, from molecules to ecosystems, including human populations. The research of the department covers a broad range of research topics, including ecology and evolution, microbiology, (eco)toxicology and analytical chemistry of pollutants, global change biology, and biotechnology, and the associated state-of-the-art methods and technologies, both computational and experimental.

Questions about the vacancy?

Please contact

Pim Leonards

Hoogleraar

Interested

Applications must be submitted through the NeXED job application platform: www.nexed.eu

Deadline for applications: April 21, 2025, 23:59 CET. More information about the application procedure for NeXED PhD positions can be found here.

For additional information about this vacancy, please contact Pim Leonards ([email protected]).

Questions about the vacancy?

Please contact

Pim Leonards

Hoogleraar

Application procedure

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