Researchers at Stanford University and the J. Craig Venter Institute (the group who made the first
"synthetic" bacterium) have produced a computational model that tracks the activities of every single gene in the bacterium
Mycoplasma genitalium during its cell cycle (the researchers chose to model this bacterium because it has the smallest number of genes of any known organism). Here's the abstract from their paper, published in the journal
Cell:
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Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery.
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Karr et al. 2012. A Whole-Cell Computational Model Predicts Phenotype from Genotype.
Cell, 150: 389.
doi:10.1016/j.cell.2012.05.044.
NY Times summary:
https://www.nytimes.com/2012/07/21/s...-software.html
The model, of course, is far from perfect and even the authors acknowledge that the model represents more of a "first draft" than a complete model. Indeed,
M. genitalium is not particularly easy to work with experimentally, so much of the data used to model the genes in
M. genitalium came from studies of similar genes in other bacteria. Nevertheless, the paper represents an interesting proof of principle that could lead to some very interesting work in the future.
Science Advisor
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