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Modelling: Big Data and Society Conference
A new PhD student publication
Summer Intern Project 2010: Marta Dravecka
Project: Modelling Stress Response in Fission Yeast
Supervisors: Vera Pancaldi & Jürg Bähler (GEE) and Murad Banaji (Mathematics & Medical Physics)
Stress response in fission yeast (Schizosaccharomyces pombe) is a phenomenon extensively studied by the Bähler lab and is relevant to cancer research. The aim of the project was producing a Boolean (all genes/proteins involved in the pathway could only either be on or off at a particular step) and a continuous differential equation model of the stress response pathway, using information obtained from literature or experimental work done by the lab.
For this purpose, Marta performed simulations of single and double gene knock-outs in these models and compared them to results of her own experiments performed with the guidance of Jürg Bähler’s lab. In addition, Marta preformed stress assays to check for crossprotection between oxidative (H2O2) stress and heat stress. In this process, a weak stress of one kind was administered, followed at ranging intervals with a strong stress of the other kind. Marta then compared the survival of yeast to controls. Information obtained from these experiments can be used to make refinements to current models and add to the understanding of similarities between different stress responses.
Being supervised by a mathematician and a physist, while also getting support from the experimental biology lab, Marta gained valuable experience in the theoretical analysis of data, using modelling software and acquaintance with basic experimental techniques using fission yeast as a model organism.
Visualization of the Boolean model. The diagram shows all possible combinations of on/off modelled proteins and relations between them
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