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Application ofin silico genomic modeling in
bioremediation processes
Clean up nature from pollutants
Conventional methods- expensive;
- non-specific;
- release of intermediate toxic compounds.
Bioremediation
- ecologically focused process;
- an alternative to physical-chemical processes;
- detoxification and degradation of toxic pollutants either by intracellular accumulation or by enzymatic transformation.
Mycoremdiation
In silico toxicity of compounds
✓More than 70 million compounds have been identified by May 2013;
✓ Quantitative structure-activity relationship model;
✓OSIRIS;
✓SuperToxic database, contains information about multiple toxic compounds (about 60,000).
QSAR model
In silico biodegradation of toxic compounds
➢University of Minnesota Biocatalysis / Biodegradation Database (UMBBD)
➢BESS (Biodegradability Evaluation and Simulation System);
➢Biochemical Network Integrated Computational Explorator (BNICE);
➢The CATABOL software;
➢The MetaRouter System;
➢Biocatalysis Assignment Tool (BAT);
➢KEGG (Kyoto Encyclopedia of Genes and Genomes),
University of Minnesota Biocatalysis/Biodegradation Database (UMBBD)
• 177 metabolic pathways;
• 1220 reactions;
• 1133 compounds,
• 786 enzymes;
• 462 microorganisms of interest.
BNICE BESS
Biodegradative Strain Database (BSD)
Ecological Structure Activity Relationships (ECOSAR)
Evaluates aquatic toxicity:
• Acute toxicity;
• Chronic toxicity.
Uses Structure Activity Relationships (SARs).
Design of bacterial consortium
Heavy metals reduction &radionuclides removal
Deinococcus geothermalis
Biodegradation of pentachlorophenol (PCP)
Sphingobium chlorophenolicum