Knowledge base biodegradation

The biodegradation knowledge base of META includes 37 enzyme classes (Table 1 lists the 19 most important ones) providing a total of 120 transformations. 

CATABOL is a knowledge-based expert system for the prediction of biotransformation pathways. It works in tandem with a probabilistic model that calculates the probabilities of the individual transformations and overall biochemical oxygen demand (BOD) and extent of C02 production (Jaworska et al., 2002). The model assesses biodegradation based on the entire pathway and not,... 

META [22,23] was developed by Gilles Klopman and coworkers. The mammalian model covers a wide range of reactions promoted by 26 types of enzymes. Metabolic products can be assessed automatically for potential carcinogenicity and the results reported to the user. Separate knowledge bases cover aerobic biodegradation, anaerobic biodegradation, and photodegradation. 

In any case, biodegradable fibres based on polyesters while investigated and developed by researchers, should be considered seriously by industry and consumers. A knowledge concerning the properties and new techniques of production of the fibres should bring new ideas for applications of these materials followed by development of production technology. 

In addition to the knowledge base dictionary for biodegradation, the program also has access to a repair module that evaluates each structure for stability and, when necessary, rearranges the products to reflect molecular rearrangements and other product stability requirements. This capability is apparently unique to META. 

The METABOLEXPERT system uses almost the same knowledge base organization as BESS. How ever, it is not known to us whether the program currently has the ability to deal with microbial biodegradation. 

GAMBETAL makes its biodegradability prediction for a new compound by checking the three simple rules of its knowledge base. 

Surveying our present knowledge about the enzyme activities in PVA biodegradation, a trend toward increasing integration can be seen. There are free enzymes working in the extracellular space of the cells, including also the periplasmatic volume, and there are membrane-associated enzymes that are presumably Unked to the cellular cytochrome-based electron transport chains. 

Punch, B., Patton, A., Wight, K., Larson, R.J., Masscheleyn, P., and Forney, L., A biodegradability evaluation and simulation system (BESS) based on knowledge of biodegradation pathways, in Biodegradability Prediction, Peijnenburg, W.J.G.M. and J. Damborsky, J., Eds., Kluwer, Dordrecht, The Netherlands, 1996, pp 65-73. 

Boethling, R.S. and Sabljic, A. (1989). Screening-Level Model for Aerobic Biodegradability Based on a Survey of Expert Knowledge. Environ.Sci.Technol.,23,672-679. 

As the measurement of TOC is not sufficient for the determination of the biodegradable fraction of organic matter, the knowledge of which is very useful, a parameter based on the measurement of dissolved organic carbon (TOC after 1- xm filtration),... 

Pea is a renewable reservoir for functional macromolecules. Pea proteins or starches can be used for packaging applications, such as films, foams and controlled release systems. The functionality of the biopolymers is influenced by technological treatments and altered by physical, enzymatic or chemical modifications. This work is aimed at obtaining detailed knowledge about the structure-property relationships of pea-based biodegradable plastics. 

A critical factor currently limiting the exposure assessment of transformation products for substance classes other than pesticides is the lack of information on transformation schemes. Various computer tools exist whose goal it is to predict aerobic biodegradation pathways [63-66], but to the best of our knowledge, only CATABOL [65] (see chapter by Howard) and the University of Minnesota Pathway Prediction System (UM-PPS) (see chapter by Wackett Ellis) [66] are presently under constant development. In both systems, pathway prediction is based on an extensive collection of known enzymatic reactions, based on which transformation rules have been compiled that translate a substrate substructure into a product substructure. 

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