Virtual Organism Reveals Secrets of Cellular Processes

Bioengineering researchers Stanford University have created a computational model of entire organism, according to a report in Cell.

This model them predict cellular behaviors that haven't observed, as well as new biological processes and parameters.

The organism modeled is Mycoplasma genitalium, or M. genitalium, the smallest genome that can constitute a cell.

"We synthesized research the literature, but we also performed our own experiments," team leader Markus Covert, assistant professor of bioengineering Stanford University, told TechNewsWorld.

The team went hundreds of reports, and the model also "points out aspects of what we know on the literature that are not internally consistent," Covert said. "These areas then become tagged as spots for further experimentation."

What the Researchers Did

The team used data more than 900 scientific papers to spell every molecular interaction known that takes place in the life of M. genitalium. It used that data, together its own experiments, to create a computational model of the organism incorporates more than 1,900 experimentally observed parameters.

The model integrates 28 submodels of cellular processes -- cell functions and variables -- grouped five categories indicated by colors: DNA represented by red; RNA by green; proteins by blue; metabolites orange; and all other processes by black. Colored lines the variables and submodels indicate the cell variables predicted by submodel.

The model was trained heterogeneous data and reproduces independent experimental data across multiple cellular functions and scales. It provides a global analysis the use and allocation of energy in the cell. It also identifies common molecular pathologies underlying single-gene disruption phenotypes.

A phenotype is the composite an organism's observable characteristics such development, biochemical or physiological properties, and behavior.

The Value of the Model

"I think the main contribution the paper is that it shows how models about different processes a cell can be integrated," Tao Jiang, a professor in the computer and engineering department of the University of California at Riverside, told TechNewsWorld. "But we're still far from understanding how these processes work, not to how they interact with each other."

As we learn more how a cell works, it "would be interesting to know if the cell model can adapted," said Jiang, who works in bioinformatics, a branch of biological science that studies methods storing, retrieving and analyzing biological data.

The Lowdown on M. Genitalium

M. genitalium, is the smallest genome that can constitute a cell, and the second-smallest bacterium. It's a parasitic bacterium that lives the ciliated epithelial cells of primates' genital and respiratory tracts.

Cilia are protuberances from the main body a cell. Think of them as small hairs. Epithelial cells line the cavities and surfaces of structures animal bodies. They also form many glands.

M. genitalium's genome consists of 521 genes in circular chromosome of nearly 583,000 base pairs.


Adapted and abridged from: Technewsworld, July 24, 2012.