Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Wednesday, November 22, 2006

Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling by Li et. al in PLOS Biology uses boolean models to predict the modulators of Guard Cell closure in plants based on Abscisic Acid.
Guard Cells are the cells on the surface of plants that open and close for gas exchange. Here the authors use literature to build a boolean model of the system. As it stands the model does not seem that complex and is full of "intermediate" nodes which indicate that there are unkown elements to the system. Nevertheless, by coding the system with logical rules they simulate closure of the system and the effect of various knockouts in silico.
This paper is mostly a computational approach and their attempts at biological validation fall short of proving their point. Namely they show that fixing Calcium or pH modulates closure, this really only proves that these have an effect on closure, which was already known. What would have been more interesting is showing that the knockouts actually had the predicted effect.
In all this paper represents a valuable codification of the closure process but the effectiveness of the model is still up for debate. Perhaps other sources of information beyond literature can be incporporated to amke a much richer description of the process. Also they use a powerful tool called boolean models which have potential to be a powerful method of simulation when kinetic parameters are unknown; it may be worth keeping an eye on this method for future use.


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