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ISB, NYU Team Use Genomic, Proteomic Tools to Create Model for Improving Genetic Engineering

NEW YORK (GenomeWeb News) — Scientists at the Institute for Systems Biology and New York University have developed a model that can characterize and predict how a free-living cell responds on the molecular level to genetic and environmental changes.
The model, called EGRIN, for Environmental and Gene Regulatory Influence, used data from genome-wide binding-location analyses for eight transcription factors; mass spectrometry-based proteomic analysis; protein-structure predictions; computational analysis of genome structure; and protein evolution.
The results of their study may enable researchers to perform “more complex” genetic engineering with “fewer unintended consequences,” the scientists said in a statement.
Writing in the online edition of the current issue of the journal Cell, the researchers showed that EGRIN was able to link biological processes with previously unknown molecular relationships. They also showed that it could predict new regulatory powers of know biological processes as well as how more than 1,900 genes respond to “novel” genetic and environmental experiments.
To arrive at their results, the researchers studied the “poorly characterized” archaeon Halobacterium salinarum NRC-1. They perturbed the organism by altering 10 environmental factors and 32 genes, characterizing the resulting growth and/or survival phenotype, and quantitatively measuring steady state and dynamic changes in mRNA.
Their next step will be to applying EGRIN to more complex organisms or networks and to “actually reengineer organisms based on knowledge obtained” through the model.
"It will take a lot more effort before the EGRIN model can be applied in a practical fashion," Nitin Baliga, an associate professor at ISB and a study author, said in a statement. “At this point we've basically proven that we can develop a comprehensive understanding of how complex biological systems work, which has been an open question to this point.”

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