Applied Experimental Evolution and Bioinformatics

What it is about

In this module you work with a mushroom model (in the summer semester Zymoseptoria tritici, in the winter semester a different fungal species) and learn experimental evolution, laboratory techniques and bioinformatic analysis of NGS data. At the end you can design experiments and statistics, perform microbiological and molecular biology experiments, and evaluate genomic data (Quality Control, Mapping, SNP analysis) and report scientifically.

What you will be able to do

• Experiment design and statistical planning (e.g. with R)
• Acquisition and access to NGS raw data and reference genomes
• Knowledge of common genome file formats (e.g. BAM, VCF)
• Basic Linux and cluster usage for bioinformatics
• Perform quality control, trimming, read-mapping and SNP-calling
• Microbiology: Cultivation of fungi on plates and in liquid culture
• Molecular biology: DNA/RNA extraction, cDNA synthesis, sample preparation for NGS
• Interpretation of the evolutionary mechanisms of fungicide resistance
• Integration of NGS techniques in field diagnostics and experimental studies
• Creation of a scientific report from experiment to analysis

What the module consists of

• VorlesungIntroduction to fungicide resistance, experimental design and case studies
• Praktikum / LaborMicrobiological and molecular biology experiments: fungal cultures, DNA/RNA extraction, cDNA synthesis, sample preparation for NGS
• Übung / ComputerpraktikumBioinformatics and statistics exercises: NGS quality control, trimming, read-mapping, SNP-calling and analysis
• PräsentationPresentation and discussion of published articles on fungicide resistance and resistance management

Teaching method

• Vorlesung (PowerPoint)Conveying the theoretical foundations of experimental design and fungicide treatment
• LaborpraktikumAcquisition of practical microbiological and molecular biological skills
• ComputerübungenLearning and applying bioinformatics and statistics tools
• Fallpräsentationen und DiskussionApplication of what has been learned to real examples and critical reflection