Pesticide mixtures and gene expression in gut organoids

Background

Farmers rely on pesticides to maximise their yields. However, some pesticides are potentially harmful to environmental, plant, animal, and human health. The effect of pesticides and pesticide mixtures on the intestinal epithelium is important to study because of the crucial barrier function of the intestine, restricting entry of harmful substances and microorganisms into the body. This project if part of SPRINT (https://sprint-h2020.eu/).

Objectives

Porcine gut organoids were exposed to (mixtures of pesticides. In this bioinformatics project, we will study the differences in gene expression induced by different pesticides, as well as the cumulative effects of pesticide mixtures (is the impact of a mixture more than the sum of the individual pesticides?), aiming to generate hypotheses on the cellular and molecular mechanisms underlying negative health effects of pesticide exposure.

Methodology

This is an in-silico project, without any wet-lab components. Available data includes RNA-Seq datasets of porcine organoids exposed to pesticides and pesticide mixtures. We will apply differential gene expression techniques (EdgeR, DESeq2), as well as supervised and unsupervised multivariate analysis (PCA, RDA). The analyses will be done in Linux with Python and / or R.

Requirements

We are looking for MSc students in the field of Biology, Bioinformatics, or related fields. Some experience with Python or R is required, while experience with Linux would be useful. The project will have a duration of 6 months.

Contact information

Supervisors are Maaike Gerritse (email:maaike.gerritse@wur.nl), PhD candidate, and Jos Boekhorst, staff scientist at Host-Microbe Interactomics, Wageningen University and Research. Visiting address: Room E1205, De Elst 1, 6708 WD, Wageningen.