Life on a chip

According to an article in the journal Cell, scientists have devised a computer simulation of single-celled organisms named "Halobacterium salinarum NRC-1". The model accurately predicts the activity of Halobacterium's 2,400 genes, in silico.

In all living cells, genes are constantly switched on and off by so-called "transcription factors" (the Halobacterium has 72 of them). When a gene is active, it acts as a micro-scale protein factory. The resulting proteins are then used by the cell as building materials, signaling devices, and new transcription factors.

The computer model accurately simulated the behavior of roughly 80 percent of the Halobacterium's gene regulatory and functional interrelationships (called "networks" or "pathways"). The Halobacterium cell is genetically hard-wired to respond to 9 external environmental factors (EFs).

Gene activity in the Halobacterium cell is highly interconnected. (Like pressing a bag of marbles with your finger, you don't know where it will bulge out, since all the pieces are connected.) By perturbing one or more genes (perhaps by a change in the environment), scientists can test how well their computer simulation of the cell is working.

Yet, 38 percent of the Halobacterium's genes seem to do little or nothing.  That may be because scientists have yet to explore other gene regulatory mechanisms (small RNAs, epigenetic modifications, post-translational modifications, metabolite-based feedback) in their computer simulation.