Abteilung Umwelttoxikologie


Wir sind aktiv in der Lehre an der ETHZ und der EPFL tätig.





Advanced Ecotoxicology (ETHZ)


Rik Eggen, Elisabeth Janssen,
Kristin Schirmer, Marc Suter, Ahmed Tlili
Praktikum Molecular Ecotoxicology (ETHZ)


Kristin Schirmer, Colette vom Berg, Stephan Fischer (Aquatox Solutions)

Introduction to Toxicology (ETHZ)752-1300-00L Rik Eggen
Ecotoxicology (EPFL)


Kristin Schirmer, Michael Burkhard, Julita Stadnicka
Chemistry of Aquatic Systems (ETHZ)701-0423-00L

Lenny Winkel, Ahmed Tlili

Computational Biology and Bioinformatics Seminar (ETHZ)636-0704-00L

Jörg Stelling, Manfred Claassen, Dagmar Iber, Tanja Stadler, Anze Zupanic
Grundlagen der Umweltchemie und Ökotoxikologie (ETHZ)529-0037-01L

Kathrin Fenner, Juliane Hollender, Colette vom Berg
Seminar für Bachelor-Studierende: Biogeochemie (ETHZ)701-0419-01L

Gerhard Furrer, Ruben Kretzschmar, Colette vom Berg


Prof. Dr. Kristin SchirmerAbteilungsleiterinTel. +41 58 765 5266E-Mail senden
Dr. Marc SuterStv AbteilungsleiterTel. +41 58 765 5479E-Mail senden

Aktuelle Master Projekte

Exploring the differences of fish cell lines in sensitivity toward chemical exposure

Background: Current environmental risk assessment for chemicals relies to a large part on experiments with fish. These tests are costly, lengthy, create large volumes of waste and are ethically questionable. In light of this unsatisfying situation, we are developing strategies to predict the impact of chemicals on fish using cell lines from different organs of fish, such as from rainbow trout. Cell line derived parameters alone or combined with computational approaches have been shown to successfully predict fish acute toxicity as well as fish growth and to improve predictions for bioaccumulation. It became apparent as well, that, indeed, cell lines from different organs respond differently to chemical exposure. Exploring such differences in more detail is therefore one of our current aims.

Aim: We offer Master thesis projects that explore the mechanisms by which fish cell lines from different organs respond to chemical exposure and what the causes of sensitivity differences are. Two hypotheses are being followed: (i) Differences stem from distinct toxicokinetic processes in the cells, particularly biotransformation; and (ii) Cells differ in their dynamic processes depending on the chemical structure and cell line origin.

Methods: Basic methods that the candidate will learn are the routine cell culture and how to work with different rainbow trout cell lines and performance of in vitro test assays upon chemical exposure. Depending on the specific project aims, expertise will be gathered in quantifying chemical uptake by the cells, biochemical and molecular effect- as well as computational analyses. 

Interested? If you are excited about this line of research, and have a background in cell biology, environmental toxicology and/or chemistry, please contact Kristin Schirmer (Kristin.Schirmer@eawag.ch) or Hannah Schug (Hannah.Schug@eawag.ch). The work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf.



Impact of nano- and microplastic fibers on a stream biofilm-grazer system

Particulate plastics (microplastics, fibers, and nanoplastics) are produced either intentionally for their commercial use in consumer products or unintentionally as breakdown fragments of larger synthetic materials (e.g. plastic bottles, polyester textiles, rubber tire wear). Currently, there is little information on the fate, transport and bioavailability of  nanoplastics and microplastic fibers in water bodies. Importantly, knowledge on their potential to interact with organisms and to impact food-webs is largely lacking.

AIMS: Here we aim to quantify interactions of nanoplastics and microplastic fibers with stream microbial biofilms, as well as their potential transfer from biofilms to grazers. Focus will be on examining for transgenerational effects on the snail offspring fitness. Unique metal-doped particulate plastics developed in-house will be used through all experiments, which will both expedite analysis times in determining biota-plastic burden and provide more precise and accurate quantification of plastics throughout the exposure system.

METHODS: The candidate can expect to learn (1) how to set up and maintain experimental mesocosms in a laboratory setting, (e.g. growth and sampling of biofilms and snails), (2) how to register changes in biofilm and snail biology (e.g. growth, respiration, reproduction), and (3) how to quantify particulate plastics in various media, including techniques for particle characterization (e.g. Dynamic light scattering, Nanoparticle tracking analysis, Transmission electron microscopy) and analytical chemistry (e.g. Inductively coupled plasma mass spectrometry)).

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline. For further information please contact Ahmed Tlili (ahmed.tlili@eawag.ch). This work will be performed at Eawag (Dübendorf) in the Department of Environmental Toxicology, and in collaboration with Denise Mitrano (denise.mitrano@eawag.ch) in the Department of Process Engineering.



Investigating behavioral consequences of neuroactive micropollutant exposure in zebrafish larvae

Selecting an appropriate behavioral response to a rewarding or threatening stimulus is critical for the survival of an animal. This innate ability of the animal might be severely affected by substances that act on the nervous system. Many neuroactive pharmaceuticals and insecticides are present in our water and aquatic non-target organisms are inevitably exposed to these substances, but the behavioral consequences of such potentially harmful exposure are not yet well understood.

AIM: In this Master thesis project we will investigate whether the presence of neuroactive substances in the water alters the animal’s behavior and neuronal activity. Specifically, we will measure whether the animals are attracted to the substance or avoid higher concentrated areas. Moreover, we are interested in the chemosensory system mediating such a response.

METHODS: We will use zebrafish larvae in this study, because behavioral responses can easily be measured and their transparent brain allows the use of imaging techniques for the measurement of neuronal activity. We have developed a behavioral set-up in which we deliver the substance on one side of the chamber and measure the animal’s space use with a fully automated video tracking system. Neuronal activity maps will be generated using whole mount immunohistochemistry of an endogenous activity marker followed by confocal imaging.

The candidate will learn how to 1) breed zebrafish and handle eggs and larvae; 2) measure and analyze zebrafish behavior; 3) perform fluorescent immunostainings and confocal microscopy.

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline and should have a genuine interest in neuroscience.

For further information please contact Colette vom Berg (Colette.vomberg@eawag.ch). This work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf.



Methods development for monitoring metal transporters in green algae Chlamydomonas reinhardtii

Silver is a heavy metal that is highly toxic. It exerts its toxicity by inhibiting enzymes and causing oxidative stress. How silver enters a cell is not completely understood, but there is evidence that it hitchhikes copper transporter proteins (CTRs), which are essential for metal homeostasis for instance in the green algae Chlamydomonas reinhardtii. 

AIM: In this project we will adapt existing targeted proteomics techniques for the selective detection of metal transporters in extracts of metal-exposed and control Chlamydomonas reinhardtii. In a first step, we will select peptides specific to the cytosolic transporters CTR3 and FOX1 and optimize mass spectrometric settings for their determination. Those transporters have been seen to be upregulated in silver-exposed algae. We will then extend our investigation to membrane proteins, such as DMT1, CTR1, CTR2. This will require an optimization of the extraction procedure. If time permits we will validate our results using gene-deletion clones, lacking the respective transporter.
METHODS: The candidate will learn (1) to culture green algae (2) to adapt LC-MS based targeted proteomics protocols for new target proteins and (3) to monitor specific metal transporters in metal-exposed and control green algae. 

Suitable candidates for this MSc thesis project are expected to hold a BSc degree in environmental sciences or a related discipline and to have experience in laboratory work. 

For further information please contact Marc Suter (marc.suter@eawag.ch). This research will be performed at the department of Environmental Toxicology, Eawag, in Dübendorf.



Molecular responses to herbicide exposures in stream biofilms

Stream biofilms are complex communities of algae, bacteria and fungi, which play a fundamental ecological role in aquatic ecosystems. Microorganisms composing biofilms are primary targets for herbicides, which can lead to structural and functional alterations of the community, with potential negative consequences for ecosystem functioning. Yet, molecular processes underlying functional and structural responses of biofilms to herbicides are still largely unknown.

AIM: By establishing a set of genes that are specifically regulated in biofilms upon exposure to herbicides, we aim in this project to (i) examine toxicity and adaptive cellular processes, on the transcriptome level, in aquatic biofilms and  (ii) link these processes to community functional and structural alterations.

METHODS: Candidates will learn (1) how to culture and sample biofilms both in the field and in laboratory mesocosms , (2) various techniques for gene expression (mRNA extraction and quantification, qPCR), molecular and functional diversity analyses (genomic DNA extraction and amplification, DGGE, flowcytometry), and (3) quantification of the herbicides in water and biofilms.

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline.

For further information please contact Ahmed Tlili (ahmed.tlili@eawag.ch). This work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf. 


Mathematical modeling of a novel in vitro system for measuring permeation
of hydrophobic and volatile chemical across a fish intestinal epithelial cell monolayer

Permeation of organic chemicals from the aquatic environment across cellular barriers is a critical step for accumulation in organisms, such as fish. To better understand the underlying processes, we aim to study the role of the fish intestine as barrier for hydrophobic and volatile chemicals. Therefore, at the department of environmental toxicology, we combined a recently developed in vitro epithelial barrier model using the rainbow trout (Oncorhynchus mykiss) intestinal cell line, RTgutGC, and a newly constructed chamber that enables stable chemical exposure concentrations.We estimated  the effective permeation of different chemicals across the intestinal epithelial monolayer and measured chemical mass in different biological and non-biological compartments of the system over time. Mathematical modeling of the experiment is now needed to determine which processes (passive diffusion, carrier-mediated influx/efflux, binding, biotransformation) are dominant for the measured chemicals and  what are their corresponding rates. 

AIM: The aim of the master project is to build a family of mathematical models that describe the permeation experiments, use model selection to find the dominant processes in the experiments with different chemicals and use the best fitting models to estimate the effective permeation coefficient.

METHODS: The candidate will use Matlab to build the models and perform parameter estimation, identifiability analysis and model selection, using algorithms available at the department for environmental toxicology. In case of extensive expertise of the student, shifting to a different modeling environment is an option.

Suitable candidates for this project are expected to hold a BSc degree in environmental sciences or a related discipline and to have sufficient experience in dynamic ODE modeling.

For further information please contact Anze Zupanic (anze.zupanic@eawag.ch). This research will be performed at the department of Environmental Toxicology in Dübendorf.



Characterization of Glutathione S-transferases Expression and Activity in Pac2 Zebrafish Cell Line

In vitro toxicity testing with cell culture is applied to screen chemicals and potential drug candidates for their efficacy and safety. However, the fate of chemicals within a biological system strongly depends on biotransformation reactions catalyzed by xenobiotic-metabolizing enzymes. Phase II enzymes, such as glutathione S-transferases (GSTs), can modify the chemical structure of the parent compound leading to an increase or decrease in its toxic potential. To avoid false positive or false negative results in chemical screening, it is therefore crucial to investigate possible differences in the biotransformation processes between in vitro and in vivo models.

Aim: By using established targeted proteomics methods, we aim to profile the expression of GSTs in zebrafish cell line to allow a comparison of the in vitro system with the existing data from zebrafish embryos. Furthermore, we aim to analyze the regulation of the GST isoforms on the protein level upon exposure to reference chemicals and to monitor the production of phase II metabolites (GSH-conjugates) via high resolution mass spectrometry.

Candidates will learn: (1) cell culturing techniques (2) how to prepare samples for proteomics analysis (protein extraction and tryptic digest) (3) how to carry out targeted proteomics analysis (4) exposure of cell lines to reference compounds (5) analysis of GSH-conjugates.

For further information please contact Marc Suter or Alena Tierbach  (marc.suter@eawag.ch; alena.tierbach@eawag.ch). This work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf. 



The impact of metal exposure on zebrafish: Investigating the mechanism of hair cell toxicity in zebrafish larvae by behavioral, structural and molecular analysis

Metals are widespread aquatic contaminants and affect aquatic wildlife in different ways. For instance, copper ions have been shown to specifically impair hair cells of the lateral line organ in fish. These cells are sensors of hydrodynamic flows helping the fish to orient, detect predators and prey and communicate with conspecifics. As a consequence, some behavioral responses, such as e.g. rheotaxis, a natural behavioral reaction of fish to orient counter-flow in order to hold a fixed position in a stream, are severely affected in copper-exposed fish.

AIM: The aim of this Master thesis is to investigate the effects of different metals on hair-cell mediated behavior of fish and to explore the mechanism by which these cells are specifically affected.

METHODs: To tackle this question, we are using zebrafish (Danio rerio) larvae, because of several reasons: genomic resources and genetic tools are available, their transparent larval stages enable different optical techniques and their small body size allows the continuous measurement of behavior with full control of the environment.

The impact of metals on hair cells will be elucidated from different angles: 1) Behavioral tests of metal-exposed zebrafish larvae will be performed, 2) hair cell structure and metal distribution will be investigated by different staining techniques followed by bright-field or confocal imaging and 3) the molecular basis of metal transport mechanisms will be studied by whole mount in situ hybridization in zebrafish larvae, which allows to localize gene expression of relevant transporters to specific tissues such as e.g. hair cells. Gene expression will form the basis for further loss-of-function experiments. Depending on the progression, the Master thesis could be extended with such functional tests.

Up to two Master thesis can be offered about this topic, and the project can be tailored to the candidate’s interests.

Suitable candidates for this project are expected to hold a BSc degree in biology, environmental sciences or a related discipline and to have experience in laboratory work.

For further information please contact Colette vom Berg (Colette.vomberg@eawag.ch) or Michael Burkard (Michael.Burkard@eawag.ch) . This work will be performed at Eawag in the department of Environmental Toxicology in Dübendorf.

Division Analytische Wissenschaften - Kursangebot

Marc Suter ist der aktuelle Präsident der Division Analytische Wissenschaften (DAS) der Schweizerischen Chemischen Gesellschaft (SCG), die eine breite Palette von Weiterbildungskursen in den Gebieten Trennmethoden, Spektroskopie, Analytische Anwendungen, Methoden der Liefe Sciences und Qualitätssicherung, Informationsbeschaffung anbietet.

Die Kurse werden in Zusammenarbeit mit unseren Industriepartnern angeboten und richten sich sowohl an Einsteiger wie auch an Experten.

Viele Kurse werden an der Eawag durchgeführt, wo sich auch das von Esther Wolff geführte Kursbüro befindet.


Die vollständige Liste der Kurse kann HIER gefunden werden.


Esther WolffTel. +41 58 765 5200E-Mail senden
Dr. Marc SuterStv AbteilungsleiterTel. +41 58 765 5479E-Mail senden