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One response of microbes1 to stress is the formation of biofilms, which are ubiquitous and relevant medically, technically and (at least for plants) physiologically. How different microbes contribute to biofilm formation and maintenance is currently unknown, but can probably be predicted from DNA topology and it's change under stress. I am working on this prediction with Machine Learning tools (my favorite subject).

Two of the key questions are:

• which of the more than thousand topology features predict stress response well
• how to integrate the massive amount of microarray, gene expression, transcriptome and proteome data

The answers will provide new methods and insights into possible stress responses, virulence factors, microbe-microbe and host-microbe interactions and the metabolic structure of biofilm associated microbes.

1: Currently, prokaryotes are the main subject, since eukaryote and fungal stress response may differ dramatically from that of prokaryotes. DNA topology plays a role, too, but in a different way as they lack a key enzyme. They may still be incorporated later.
last updated on 2013-11-21