First Computer Simulated Model of an Organism Achieved
For the first time ever, Scientists from the Stanford University and the J Craig Venter Institute have developed a complete model of an organism, a breakthrough in a field that raises expectations of combating diseases and stash uncertainties of biological engineering.
The first model to be completely simulated by computer software is 'Mycoplasma Genitalium', the world's smallest free living bacterium that lives in the genital and respiratory tracts of humans and other primates. This organism is responsible causing sexually transmitted disease.
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The experiment was possible after considering the data from over 900 scientific papers. The team led by Professor Markus Covert was able to account for every single molecular interaction which takes place in Genitalium with 525 genes. If compared to the human genes, they have about 20,500 genes.
Covert stated, "The answer is simply cancer is not a one-gene phenomenon, it's thousands of genes interacting together, and other factors interacting in complicated ways. The fact is we won't be able to understand how those things interact together unless we use a rational, computer-based approach."
Modeling of an organism as tiny as Genitalium was a challenging task. The simulation was designed to model a whole cell, including all of its molecular components and their interactions. The final virtual cell model made use of more than 1,900 experimentally determined parameters, with computational models making sense of 'enormous' amounts of data, according to the scientists.
The simulation of the Genitalium bacteria runs on a cluster of 128 computers, and shows the interactions of 28 categories of molecules, including DNA, RNA, proteins, and small molecules called metabolites that are generated by cell processes.
The concept of simulation software will multiply the early stages of screening for new compounds especially for the medical researchers and biochemists. And for molecular biologists, models that are of sufficient accuracy will yield new understanding of basic cellular principles.
This kind of modeling is already in use to study individual cellular processes like metabolism. But Dr. Covert said: "Where I think our work is different is that we explicitly include all of the genes and every known gene function. There's no one else out there who has been able to include more than a handful of functions or more than, say, one-third of the genes."
This is one of the long standing goals for the biological fraternity. It not only allows scientists to investigate how cell works but also offers good platform for future avenues of research which could use computer aided design in bioengineering and medicine.
James M. Anderson, director of the National Institutes of Health Division of Program Coordination, Planning and Strategic Initiatives states, "this achievement demonstrates a transforming approach to answering questions about fundamental biological process. Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and ultimately to inform new approaches for the diagnosis and treatment of diseases."
The simulation of the complete life cycle Genitalium, was presented Friday in the journal Cell.