Architecture for interoperable software in biology.

Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. To this end, simple flexible strategies are needed for interconnecting heterogeneous software tools and enabling data exchange between them. Drawing on our own work and that of others, we present several strategies for interoperability and their consequences, in particular, a set of simple data structures--list, matrix, network, table and tuple--that have proven sufficient to achieve a high degree of interoperability. We provide a few guidelines for the development of future software that will function as part of an interoperable community of software tools for biological data analysis and visualization.

Safety Evaluation of Glucose Isomerase Derived from Flavobacterium arborescens and Used in Production of High Fructose Corn Syrup.

Flavobacterium arborescens is a common rod-shaped, gram-negative bacterium which, when cultivated in a nutrient medium, is an efficient source of glucose isomerase (GI). GI is then used in the production of high fructose corn syrup. Studies were conducted to assure product safety and establish GRAS status for GI derived from F. arborescens . A viable cell suspension of F. arborescens and the cell-free medium in which the organism was cultured were administered i.v. to rats and rabbits. For feeding studies, the cells were immobilized using polycationic polymers and a crosslinking agent (i.e., chitosan, polyethylenimine and glutaraldehyde). GI, in the whole cell immobilized form, was offered at concentrations of 0, 1.5, 3.0 or 5.0% (wt/wt) of the diet to dogs for a minimum of 90 consecutive days and to rats over three generations. Animals were observed daily for signs of toxicosis; body weight and food consumption were monitored; biochemical tests, hematologic determinations, and urinalyses were done on blood and urine samples; and thorough gross and microscopic tissue examinations were performed at terminations. There were no signs of infection or toxicosis following i.v. administration of F. arborescens or the cell-free supernatant fluid. This, and the lack of toxicity in dogs and rats which received daily dietary concentrations of GI many times above the projected highest possible human exposure level, suggest that there should be virtually no risk of toxicity associated with the consumption of food and beverages containing high fructose syrup produced by GI derived from F. arborescens .