PhD: Endocrine disruption of zebrafish brain and sensory organ development

This PhD project is part of the EU MSCA Doctoral Network NeXED (www.nexed.eu). It will be hosted by the section Environmental Health and Toxicology at the Amsterdam Institute for Life and Environment of Vrije Universiteit Amsterdam (https://vu.nl/en/about-vu/faculties/faculty-of-science/more-about/environmental-health-toxicology). The section focuses on understanding the influence of environmental factors on human and environmental health. Its interdisciplinary approach integrates (eco)toxicology, risk assessment, and epidemiology to study contaminants from the molecular level to populations and society. The work includes toxicological hazard characterization through toxicity profiling and studies on toxicological mechanisms using in vitro, cell-based assays and zebrafish embryo and nematode models.

This 3-year PhD project is supervised by Lisa Baumann and will investigate how thyroid hormone system disruptors (THSDs) (and their mixtures) can interfere with neurodevelopment, namely brain and sensory organs, in zebrafish embryos. Impaired neurodevelopment is the priority adverse health effect of THSDs in humans, while it has not been sufficiently addressed from that perspective in fish. Previous has demonstrated that zebrafish eye development is sensitive to THSDs (see AOP#363). Within this project, this previous work will be substantially extended by investigating the impact of THSDs on other sensory organs like the lateral line and the olfactory epithelium of zebrafish. Moreover, the effects of THSDs (and their mixtures) on brain development and specific nervous cells will be studied. The work will include exposure experiments with transgenic zebrafish embryos and subsequent analyses of brain and sensory organ development using (confocal) microscopy, histopathology, behaviour assays and different molecular techniques.

The following external research stays are planned:

• Interdisciplinary secondment: Jean-Baptiste Fini (2 months) at CNRS (Centre National de la Recherche Scientifique, France)
• Intersectoral secondment: David Du Pasquier (2 weeks) at Watchfrog (Private contract laboratory, France)
• Intersectoral secondment: Ellen Hessel (1 month) at RIVM (Rijksinstituut voor Volksgezondheid en Milieu, Netherlands)

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

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)

PhD position: Disruption of thyroid hormone transport to the brain

This PhD project is part of the EU MSCA Doctoral Network NeXED (www.nexed.eu). It will be hosted by the section Environmental Health and Toxicology at the Amsterdam Institute for Life and Environment of Vrije Universiteit Amsterdam (https://vu.nl/en/about-vu/faculties/faculty-of-science/more-about/environmental-health-toxicology). The section focuses on understanding the influence of environmental factors on human and environmental health. Its interdisciplinary approach integrates (eco)toxicology, risk assessment, and epidemiology to study contaminants from the molecular level to populations and society. The work includes toxicological hazard characterization through toxicity profiling and studies on toxicological mechanisms using in vitro, cell-based assays and zebrafish embryo and nematode models.

This 3-year PhD project is supervised by Timo Hamers. The main objective of the 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.

The following external research stays are planned:

• Interdisciplinary secondment: Terje Svingen (2 months) at DTU (Technical University of Denmark)
• Intersectoral secondment: Ellen Hessel (1 month) at RIVM (National Institute for Public Health and the Environment, Netherlands)

PhD Evaluating the Transformative Impact of Sustainability-oriented Experiments

De complexe uitdagingen rondom voedsel, landbouw, natuur, klimaat en welzijn vragen om nieuwe manieren van kennis delen, samenwerken en samenleven. Maatschappelijke experimenten creëren ruimte om die nieuwe manieren uit te proberen en ervan te leren. Specifieke ontwerpkenmerken van dergelijke experimenten kunnen leren bevorderen, maar daardoor juist het creëren van impact ‘in de echte wereld’ belemmeren (de 'pilot paradox'). Om voorbij deze paradox te komen en de maatschappelijke impact van experimenten te vergroten zoekt het Athena Instituut kandidaten voor een PhD positie in het EXTRA project “From EXperiment to sustainable change. TRAnsformatieve methodologieën voor innovatie en leren”. EXTRA is een samenwerking tussen meerdere universiteiten en publieke en private partners om experimentele leeromgevingen in kaart te brengen en te verbeteren. Dit promotieonderzoek binnen EXTRA richt zich op het ontwikkelen van nieuwe methoden en instrumenten voor het monitoren van de (duurzame, transformatieve) impact van maatschappelijke experimenten in hun directe omgeving en daarbuiten, op de middellange en langere termijn.

Het onderzoek resulteert in een proefschrift. Voor meer informatie over het project, zie: EXTRA

In het PhD traject is de taakverdeling 85% onderzoek en 15% onderwijs. Jaarlijks zul je binnen 1 of 2 cursussen een werkgroep begeleiden binnen het onderwijs van het Athena Instituut, waarvoor je didactische training en begeleiding krijgt.

Jouw taken

• samenwerken met de onderzoekers en andere teamleden in EXTRA om een overzicht te maken van verschillende soorten maatschappelijke experimenten (leeromgevingen) op de thema’s klimaat, circulariteit, energie en biodiversiteit
• een typologie ontwikkelen van impactmodellen en -indicatoren (CO2, biodiversiteit, sociaaleconomische factoren, inclusie enz.) en databronnen die nu gebruikt worden in de experimenten voor het meten van impact
• bestaande modellen en indicatoren verbeteren, en nieuwe ontwerpen voor impact assessment en evaluatie van maatschappelijke duurzaamheidsexperimenten
• dataverzameling en -analyse met behulp van kwalitatieve en kwantitatieve methoden
• schrijven en publiceren van wetenschappelijke artikelen
• presenteren van onderzoeksbevindingen op (inter)nationale conferenties en aan de betrokken partners en organisaties van het consortium
• toepassen van onderzoeksbevindingen via actie-onderzoek in de praktijk van maatschappelijke partners

PhD student in Machine Learning

We are looking for a new PhD student who will do research in the area of machine learning (ML) and in particular on reinforcement learning (RL) and the application of these techniques in a large health project (CAREPATH). The EU funded CAREPATH project focuses on improving medication adherence and persistence for patients with chronic conditions across six European countries. The position is embedded in the Quantitative Data Analytics (QDA) group of the VU in close collaboration with the Amsterdam University Medical Center and companies developing the interventions tools. The QDA group focuses on both fundamental and application-driven research in ML while the Amsterdam University Medical Center has a wealth of experience in applying complexity science to health intervention development. We are looking for candidates with experience in the area of machine learning, with a special preference for those having expertise in one or more of the following areas: reinforcement learning, the utilization of domain knowledge in ML, and data efficient ML methods. We are interested in attracting a PhD student that is able to perform ground-breaking research in fundamental aspects of machine learning and reinforcement learning, with a willingness to deploy the models in real-life applications.. The goal within the project is to apply the developed algorithms in an app and use them to personalize medication adherence interventions.

Your duties

• Perform research in machine learning and publish in top ML conferences
• Develop and deploy reinforcement learning algorithms for personalization in the CAREPATH app
• Work with multidisciplinary teams across the six pilot countries, including academic and industry partners
• Contribute to teaching activities and supervise Bachelor/Master students (20% of time)
• Help evaluate algorithm effectiveness in real-world healthcare settings