phd project available: modelling chronic toxicity in small mammals (fully funded)

Toxicokinetics & toxicodynamics
Toxicokinetics & toxicodynamics

Small mammals (e.g. field voles, wood mice) contribute to ecosystem services both in their own right and as prey for iconic predators such as birds of prey. It is important to understand how different pesticide exposure patterns lead to ecotoxicological effects under field conditions. We will develop a toxicokinetic-toxicodynamic (TKTD) model to simulate and predict toxic effects of pesticides on growth of small mammals. Existing laboratory toxicity studies with rats and mice will be used to develop and calibrate the model. In this PhD you will:

  • Develop, calibrate and test a computer model to predict toxicity in small mammals
  • Perform in-vitro laboratory tests on cell cultures with pesticides
  • Use the computer model to perform ecological risk assessment of wildlife
ModTox - CASE studentship - v02.pdf
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PSR2016-001 Syngenta BBSRC CASE - modell
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Modelling survival: exposure pattern, species sensitivity and uncertainty

The General Unified Threshold model for Survival (GUTS) integrates previously published toxicokinetic-toxicodynamic models and estimates survival with explicitly defined assumptions. Importantly, GUTS accounts for time-variable exposure to the stressor. We performed three studies to test the ability of GUTS to predict survival of aquatic organisms across different pesticide exposure patterns, time scales and species. Firstly, using synthetic data, we identified experimental data requirements which allow for the estimation of all parameters of the GUTS proper model. Secondly, we assessed how well GUTS, calibrated with short-term survival data of Gammarus pulex exposed to four pesticides, can forecast effects of longer-term pulsed exposures. Thirdly, we tested the ability of GUTS to estimate 14-day median effect concentrations of malathion for a range of species and use these estimates to build species sensitivity distributions for different exposure patterns. We find that GUTS adequately predicts survival across exposure patterns that vary over time. When toxicity is assessed for time-variable concentrations species may differ in their responses depending on the exposure profile. This can result in different species sensitivity rankings and safe levels. The interplay of exposure pattern and species sensitivity deserves systematic investigation in order to better understand how organisms respond to stress, including humans. (open access, Nature Scientific Reports)


Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS)

Fast calibration of GUTS proper parameters
Correlations between parameter posterior samples computed by MCMC

The General Unified Threshold model of Survival (GUTS) provides a consistent mathematical framework for survival analysis. However, the calibration of GUTS models is computationally challenging. We present a novel algorithm and its fast implementation in our R package, GUTS, that help to overcome these challenges. We show a step-by-step application example consisting of model calibration and uncertainty estimation as well as making probabilistic predictions and validating the model with new data. Using self-defined wrapper functions, we show how to produce informative text printouts and plots without effort, for the inexperienced as well as the advanced user. The complete ready-to-run script is available as supplemental material. We expect that our software facilitates novel re-analysis of existing survival data as well as asking new research questions in a wide range of sciences. In particular the ability to quickly quantify stressor thresholds in conjunction with dynamic compensating processes, and their uncertainty, is an improvement that complements current survival analysis methods. PLoS Comput Biol 12(6): e1004978.


Toxicology across scales: Cell population growth in vitro predicts reduced fish growth

Rainbow trout gill cells. Phot credit: Vivian Lu Tan/Eawag
Rainbow trout gill cells. Phot credit: Vivian Lu Tan/Eawag

Environmental risk assessment of chemicals is essential but often relies on ethically controversial and expensive methods. We show that tests using cell cultures, combined with modeling of toxicological effects, can replace tests with juvenile fish. Hundreds of thousands of fish at this developmental stage are annually used to assess the influence of chemicals on growth. Juveniles are more sensitive than adult fish, and their growth can affect their chances to survive and reproduce. Thus, to reduce the number of fish used for such tests, we propose a method that can quantitatively predict chemical impact on fish growth based on in vitro data. Our model predicts reduced fish growth in two fish species in excellent agreement with measured in vivo data of two pesticides. This promising step toward alternatives to fish toxicity testing is simple, inexpensive, and fast and only requires in vitro data for model calibration. (Published in Science Advances, open access)