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Life in extreme environments

U.S. biologists have developed a model mapping the control circuit governing a bacteria named Halobacterium salinarum, which can live in extremely salty environments, and that can survive to radiation which would be deadly to most other organisms. Their model shows how these bacteria adapt themselves in response to their environment. According to the biologists, 'this study marks the first time researchers have accurately predicted a cell's dynamics at the genome scale.' This research effort is 'an important milestone for the new field of systems biology,' but could also lead to new ways of engineering biofuels and pharmaceuticals.

U.S. biologists have developed a model mapping the control circuit governing a bacteria named Halobacterium salinarum, which can live in extremely salty environments, and that can survive to radiation which would be deadly to most other organisms. Their model shows how these bacteria adapt themselves in response to their environment. According to the biologists, 'this study marks the first time researchers have accurately predicted a cell's dynamics at the genome scale.' This research effort is 'an important milestone for the new field of systems biology,' but could also lead to new ways of engineering biofuels and pharmaceuticals.

Halobacteria in San Francisco bay salt ponds

According to MicrobeWiki, "halobacteria are halophilic microorganisms, which means they grow in extremely high salinity environments. Halobacteria can be found in highly saline lakes such as the Great Salt Lake or the Dead Sea." You can also find other details on Wikipedia. But the picture above shows that these bacteria also can appear in San Francisco bay salt ponds. This picture is one of the 6,383 public photos posted by aroid on Flickr. Here is a link to the original photo. Thanks, aroid!

This research effort was led by New York University Assistant Biology Professor Richard Bonneau, who describes this project in this Regulatory network inference page. The other main author of the study was Nitin Baliga of the Institute for Systems Biology (ISB) in Seattle, WA. You'll find more information at ISB by visiting the Bonneau Group and the Baliga Group.

Now, let's look at their research results. This is not the first time that researchers have attempted to discover how cell components are connected. But this "study went beyond previous scholarship and accurately modeled how Halobacterium, an important organism in high-salt environments such as the Dead Sea or Utah's Great Salt Lake, functioned over time and responded to changing environmental conditions. The researchers were, for the first time, able to predict how over 80 percent of the total genome (several thousand genes) responded to stimuli over time, dynamically rearranging the cell’s makeup to meet environmental stresses."

And here are some comments from Bonneau about how the team worked on Halobacterium salinarum. "This organism is amazingly versatile and tolerates lots of different extreme environmental stresses, said Bonneau. It does this by making decisions and dynamically changing the levels of genes and proteins; if it makes incorrect decisions it dies. Our model shows how these decisions get made, how the bug responds. This is also a good model to explain how, in general, cells make stable decisions as they move through time scales. If you want to understand how cells respond to their environments, the model offers a clearer window than previously existed for this domain of life."

For more information, this research work has been published in the Cell journal under the title "A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell" (Volume 131, Pages 1354-1365, December 28, 2007). Here is the beginning of the abstract. "The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological networks. We have constructed a model for this process in Halobacterium salinarum NRC-1 through the data-driven discovery of regulatory and functional interrelationships among ~80% of its genes and key abiotic factors in its hypersaline environment. Using relative changes in 72 transcription factors and 9 environmental factors (EFs) this model accurately predicts dynamic transcriptional responses of all these genes in 147 newly collected experiments representing completely novel genetic backgrounds and environments."

Sources: New York University news release, December 27, 2007; and various websites

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