![Page 1: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/1.jpg)
Application ofin silico genomic modeling in
bioremediation processes
![Page 2: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/2.jpg)
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.
![Page 3: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/3.jpg)
Mycoremdiation
![Page 4: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/4.jpg)
![Page 5: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/5.jpg)
![Page 6: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/6.jpg)
![Page 7: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/7.jpg)
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).
![Page 8: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/8.jpg)
QSAR model
![Page 9: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/9.jpg)
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),
![Page 10: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/10.jpg)
University of Minnesota Biocatalysis/Biodegradation Database (UMBBD)
• 177 metabolic pathways;
• 1220 reactions;
• 1133 compounds,
• 786 enzymes;
• 462 microorganisms of interest.
![Page 11: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/11.jpg)
BNICE BESS
![Page 12: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/12.jpg)
Biodegradative Strain Database (BSD)
![Page 13: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/13.jpg)
Ecological Structure Activity Relationships (ECOSAR)
Evaluates aquatic toxicity:
• Acute toxicity;
• Chronic toxicity.
Uses Structure Activity Relationships (SARs).
![Page 14: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/14.jpg)
Design of bacterial consortium
![Page 15: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/15.jpg)
Heavy metals reduction &radionuclides removal
Deinococcus geothermalis
![Page 16: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/16.jpg)
Biodegradation of pentachlorophenol (PCP)
Sphingobium chlorophenolicum
![Page 17: Application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · BNICE BESS. Biodegradative Strain Database (BSD) Ecological Structure Activity Relationships (ECOSAR)](https://reader033.vdocuments.net/reader033/viewer/2022060517/604a492c0f0c3347583ff883/html5/thumbnails/17.jpg)