Exploring the virtual plant cell
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| Julie Dickerson and Eve Wurtele |
Picture this: A biologist sits down at a computer and logs into a virtual Arabidopsis plant to see how knocking out a gene affects the plant. Or, he or she creates a model that maps out the network of chemical reactions that take place in photosynthesis.
Creating a computerized plant that lets users make predictions before heading to the field is the goal of the MetNet (Metabolic Network Exchange) software being developed at Iowa State.
The project, headed up by Eve Wurtele, member of the Center for Designer Crops, and Julie Dickerson, member of the Laurence H. Baker Center for Bioinformatics and Biological Statistics, embodies an emergent field of study called systems biology—how molecular components within an organism interconnect and are related, with a focus on plant systems.
Dickerson describes MetNet as a suite of software that takes enormous amounts of information out of databases and makes it useable by placing it in a biological context. "A lot of these tools are designed to look at pathways," said Dickerson.
Pathways are sequences of chemical reactions that happen within a plant. These pathways control plant development and composition and are actually intricate networks as opposed to linear pathways.
The software allows users to visualize, analyze and model different pathways, creating a "roadmap" of sorts. That "roadmap" can be used to track the synthesis and fate of various chemicals or proteins. Users can also see how different pathways interconnect and affect one another.
"Change one thing and it doesn't just change one pathway," said Wurtele. "There's all sorts of signaling that goes on. For example, if you block one enzyme or add another enzyme, different chemical intermediates can be built up. And these intermediates may go back and signal some genes to be active or others to shut down. We want to be able to predict what will occur."
Other MetNet tools allow the pathway information to be combined with the gene expression profiling data, information that tells if a gene was expressed, when it was expressed and under what conditions.
While the software is still being refined, Wurtele said it is already being used by biologists to develop hypotheses about gene function and recently was used to predict a particular gene important in starch regulation. The function of this gene was independently identified experimentally by scientists in another lab.
The MetNet software development group includes three other faculty members, a postdoctoral scientist and students, bringing together computer scientists, mathematicians and biologists. The project is funded by the National Science Foundation, Arabidopsis 2010. This NSF effort has the goal of determining the functions of all Arabidopsis genes by 2010.
