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Data mining algorithm explains complex temporal interactions among genes
Date:6/24/2010

ral metabolic and cell cycle relationships in the datasets studied. "Through our temporal models, we have shown that S. cerevisiae reacts in a somewhat unified fashion, with cellular fate depending on core metabolism and cell division," the authors write in their paper.

"The metaphor that emerges from this analysis is that the metabolic state of the cell is essentially a fuel gauge, and there must be enough 'fuel in the tank' before permitting another key biological process, such as reproduction, to commence," said Helm. "The availability of energy controls whether a yeast cell divides or not."

"Our tools bring out the nature of temporal 'hardwiring' manifest in biological processes," said Ramakrishnan.

Helm adds: "In particular, they open up questions related to whether it would be possible to manipulate the system to adopt an aberrant cell state or make it proceed along a desired temporal order. The identification of well-defined states, such as found in hydrogen peroxide treatments, suggests that at this stage it may be possible to force the organism to adopt aberrant states."

For instance, the biotechnology industry currently employs microbes for a number of important commodity and specialty compounds, ranging from biofuels to pharmaceutical products. If cell division could be unlinked from metabolism, the microbial system would only need nutrients for maintaining metabolism, with fewer resources diverted to cell division. "This scenario would reduce overall bioproduction costs for the chemical of interest," said Helm.

Ramakrishnan, Mishra, and co-author Marco Antoniotti, associate professor of computer science with the University of Milan, are also inventors on a US patent application about GOALIE for which a notice of allowance has been issued. "We hope in the future our work can become key to understanding other important phenomena, like disease progression, aging, host-pathogen interactions, stress responses, an
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Contact: Susan Trulove
strulove@vt.edu
540-231-5646
Virginia Tech
Source:Eurekalert

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