Modelling Reoccurring Stimulations in Living Organisms

Julia Lischke

• Publisher: Shaker
• Year: 2025
• eBook ISBN:
  9783819102028
• Print ISBN:
  9783819101274
• Edition: 1

Modelling Recurring Stimulations in Living Organisms This thesis explores how living systems respond to periodically recurring environmental changes, combining wet-lab experiments and computational modelling. The first part focuses on E. coli, a key organism in industrial biotechnology. To investigate how oxygen gradients in large-scale bioreactors affect cellular behaviour, a novel scale-down bioreactor was developed. Transcriptome analyses revealed regulatory patterns in electron transfer, RNA, and amino acid metabolism and led to a distributed parameter model predicting complex cellular responses based on simpler switch experiments. This modelling approach supports targeted strain optimisation for improved industrial performance. The second part turns to humans, examining how individual genetic variation affects reactions to 5-fluorouracil (5-FU), a common chemotherapy drug. Using systems biology and optimisation methods, the study identifies fluoroacetate as a likely cause of severe side effects and proposes dietary countermeasures. It also highlights biomarkers that could one day help predict patient-specific drug tolerability and toxicity.

Table of contents

• 1 Introduction
• 2 Analysis of Transcriptional Response in E.coli after Repeated Oxygen Stimulation
• 3 5-FU - A Use Case for Model Development and Utilisation to Limit Adverse Side Effects
• 4 Conclusion
• A Appendix
• List of Figures
• List of Tables
• Abbreviations and Formula Signs
• Bibliography
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