Simulation of chemical metabolism for fate and hazard assessment. II CATALOGIC simulation of abiotic and microbial degradation

References

• Hermens , J , Balaz , S , Damborsky , J , Karcher , W , Müller , M , Peijnenburg , W , Sabljic , A and Sjöström , M . 1995 . Assessment of QSARs for predicting fate and effects of chemicals in the environment: An international European project . SAR QSAR Environ. Res. , 3 : 223 – 236 .
   PubMedGoogle Scholar
• Rorije , E , van Wezel , MC and Peijnenburg , W . 1995 . On the use of backpropagation neural networks in modeling environmental degradation . SAR QSAR Environ. Res. , 4 : 219 – 235 .
   PubMedGoogle Scholar
• Paris , DF , Wolfe , NL and Steen , DWC . 1982 . Structure–activity relationships in microbial transformation of phenols . Appl. Environ. Microbiol. , 44 : 153 – 158 .
   PubMed Web of Science ®Google Scholar
• Howard , PH , Boethling , RS , Stiteler , W , Meylan , W and Beauman , J . 1991 . Development of a predictive model for biodegradability based on BIODEG, the evaluated biodegradation database . Sci. Total. Environ. , 109–110 : 635 – 641 .
   PubMed Web of Science ®Google Scholar
• Tunkel , J , Howard , PH , Boethling , RS , Stiteler , W and Loonen , H . 2000 . Predicting ready biodegradability in the Japanese Ministry of International Trade and Industry test . Environ. Toxicol. Chem. , 19 : 2478 – 2485 .
   Web of Science ®Google Scholar
• Punch , B , Patton , A , Wight , K , Larson , B , Masscheleyn , P and Forney , L . 1996 . “ A biodegradability evaluation and simulation system (BESS) based on knowledge of biodegradation pathways ” . In Biodegradability Prediction , Edited by: Peijnenburg , WJGM and Damborsky , J . 65 – 74 . Dordrecht : Kluwer .
   Google Scholar
• Klopman , G , Zhang , Z , Balthasar , D and Rosenkranz , H . 1995 . Computer automated predictions of aerobic biodegradation transforms in the environment . Environ. Toxicol. Chem. , 14 : 395 – 403 .
   Web of Science ®Google Scholar
• Klopman , G , Saiakhov , R , Tu , MH , Pusca , F and Rorije , E . 1998 . Computer-assisted evaluation of anaerobic biodegradation products . Pure Appl. Chem. , 70 : 1385 – 1394 .
   Web of Science ®Google Scholar
• Ellis , LBM , Gao , J , Fenner , K and Wackett , LP . The University of Minnesota pathway prediction system: Predicting metabolic logic, Nucleic Acids Res. 36 (2008), Web Server issue W427–W432
   Google Scholar
• Gao , J , Ellis , LBM and Wackett , LP . The University of Minnesota Biocatalysis/Biodegradation Database: Improving public access, Nucleic Acids Res. 38 (2010), Database issue D488–D491
   Google Scholar
• Lhasa Limited, General information about Meteor: Demonstration. Available at https://www.lhasalimited.org/meteor/
   Google Scholar
• Patel , ML , Hobbs , MD , Judson , PN , Ott , MA , Ulyatt , M and Vessey. , JD . Consensus modelling of chemical degradation pathways, Presented at 8th International Conference of Chemical Structures, Noordwijkerhout, 2008
   Google Scholar
• Dimitrov , SD , Jaworska , JS , Nikolova , N and Mekenyan. , OG . Probabilistic biodegradation modeling based on catabolic pathways, 9th International Workshop on Quantitative Structure–Activity Relationships in Environmental Sciences (QSAR’2000), Bourgas, 2000
   Google Scholar
• Jaworska , J , Dimitrov , S , Nikolova , N and Mekenyan , O . 2002 . Probabilistic assessment of biodegradability based on metabolic pathways: CATABOL system . SAR QSAR Environ. Res. , 13 : 307 – 323 .
   PubMed Web of Science ®Google Scholar
• Schwarzenbach , RP , Qschwend , PM and Imboden , DM . 1993 . Environmental organic chemistry , New York : John Wiley & Sons .
   Google Scholar
• Gray , NF . 1992 . Biology of Wastewater Treatment , Oxford : Oxford University Press .
   Google Scholar
• Tippin , B , Pham , P and Goodman , MF . 2004 . Error-prone replication for better or worse . Trends Microbiol. , 12 : 288 – 295 .
   PubMed Web of Science ®Google Scholar
• van der Meer , JR , de Vos , WM , Harayama , S and Zehnder , AJ . 1992 . Molecular mechanisms of genetic adaptation to xenobiotic compounds . Microbiol. Mol. Biol. Rev. , 56 : 677 – 694 .
   Google Scholar
• Springael , D and Top , EM . 2004 . Horizontal gene transfer and microbial adaptation to xenobiotics: New types of mobile genetic elements and lessons from ecological studies . Trends Microbiol. , 12 : 53 – 58 .
   PubMed Web of Science ®Google Scholar
• West , I . 1997 . “ Molecular and physicochemical aspects ” . In Channeling in Intermediary Metabolism , Edited by: Aguis , L and Sheratt , H . London : Portland Press .
   Google Scholar
• Huang , X , Holden , H and Raushel , F . 2001 . Channeling of substrates and intermediates in enzyme-catalyzed reactions . Ann. Rev. Biochem. , 70 : 149 – 180 .
   PubMed Web of Science ®Google Scholar
• Hoppert , M and Mayer , F . 1999 . Principles of macromolecular organization and cell function in bacteria and archaea . Cell Biochem. Biophys. , 31 : 247 – 284 .
   PubMed Web of Science ®Google Scholar
• Conrado , RJ , Varner , JD and DeLisa , MP . 2008 . Engineering the spatial organization of metabolic enzymes: Mimicking nature's synergy . Curr. Opinion Biotech. , 19 : 492 – 499 .
   PubMed Web of Science ®Google Scholar
• Walckett , LP . 1996 . Co-metabolism: Is the emperor wearing any clothes? . Curr. Opin. Biotech. , 7 : 321 – 325 .
   PubMed Web of Science ®Google Scholar
• Grady , CPL . 1985 . Biodegradation: Its measurement and microbial basis . Biotech. Bioeng. , 27 : 660 – 674 .
   PubMed Web of Science ®Google Scholar
• Matsumura , F . 1987 . “ Comparative metabolism of mixtures of chemicals by animals, plants, and microorganisms and their significance in alteration of pollutants in the environment ” . In Methods for Assessing the Effects of Mixtures of Chemicals , Edited by: Vouk , VB , Butler , GC , Upton , AC , Parke , DV and Asher , SC . 509 – 522 . John Wiley and Sons, Chichester : SCOPE .
   Google Scholar
• Daughton , CG and Hiesh , DPH . 1977 . Parathion utilization by bacteria symbionts in a chemostat . Appl. Environ. Microbiol. , 34 : 175 – 184 .
   PubMed Web of Science ®Google Scholar
• Slater , JH and Bull , AT . 1982 . Environmental microbiology: Biodegradation . Phil. Trans. R. Soc. Lond. B , 297 : 575 – 597 .
   Web of Science ®Google Scholar
• Moore , JK , Braymer HD , HD and Larson , AD . 1983 . Isolation of a Pseudomonas sp. which utilizes the phosphonate herbicide glyphosate . Appl. Environ. Microbiol. , 46 : 316 – 320 .
   PubMed Web of Science ®Google Scholar
• Havel , J and Reineke , W . 1993 . Microbial degradation of chlorinated acetophenones . Appl. Environ. Microbiol. , 59 : 2706 – 2712 .
   PubMed Web of Science ®Google Scholar
• Furukawa , K and Matsumura , F . 1975 . Microbial metabolism of PBCs: Studies on relative degradability of PBC components by Alkaligenes sp. . J. Agric. Food Chem. , 24 : 251 – 256 .
   Web of Science ®Google Scholar
• Painter , HA . 1983 . “ Metabolism and physiology of aerobic bacteria and fungi ” . In Ecological Aspects of Used-water Treatment , Edited by: Curds , CR and Hawkes , HA . Vol. 2 , 11 – 85 . London : Academic Press .
   Google Scholar
• Dimitrov , S , Pavlov , T , Veith , G and Mekenyan , O . Simulation of chemical metabolism for fate and hazard assessment. I. Approach for simulating metabolism, SAR QSAR Environ. Res. 2011, published in this issue
   Google Scholar
• Dimitrov , S , Dimitrova , G , Pavlov , T , Dimitrova , D , Patlevisz , G , Niemela , J and Mekemyan , O . 2005 . A stepwise approach for defining the applicability domain of SAR and QSAR models . J. Chem. Inf. Model. , 45 : 839 – 849 .
   PubMed Web of Science ®Google Scholar
• Chemicals Inspection and Testing Institute . 1992 . Biodegradation and Bioaccumulation data of existing chemicals based on the CSCL Japan , Tokyo : Chemical Industry Ecology-Toxicology & Information Centre .
   Google Scholar
• Marquardt , DW . 1963 . An algorithm for least-squares estimation of non-linear parameters . J. Soc. Ind. Appl. Math. , 11 : 431 – 441 .
   Google Scholar
• Version , EPI Suite™ . 4.10, 2011. Available at http://www.epa.gov/opptintr/exposure/pubs/episuitedl.htm
   Google Scholar
• website , NITE . Biodegradation and bioconcentration of the Existing Chemical Substances under the Chemical Substances Control Law. Available at, http://www.safe.nite.go.jp/data/hazkizon/pk_e_kizon_data_input.home_list
   Google Scholar
• Wackett , LP and Hershberger , CD . 2001 . Biocatalysis and Biodegradation: Microbial Transformation of Organic Compounds , Washington , DC : ASM Press .
   Google Scholar
• Gibson , DT . 1984 . Microbial Degradation of Organic Compounds , New York : Marcel Dekker .
   Google Scholar
• Neilson , AH and Allard , A-S . 2008 . Environmental Degradation and Transformation of organic Chemicals , New York : CRC Press, Taylor & Francis Group .
   Google Scholar
• Ellis , LBM , Hershberger , CD and Wackett , LP . 1999 . The University of Minnesota Biocatalysis/Biodegradation Database: Specialized metabolism for functional genomics . Nucleic Acids Res. , 27 : 373 – 376 .
   PubMed Web of Science ®Google Scholar
• Ellis , LBM , Hershberger , CD and Wackett , LP . 2000 . The University of Minnesota Biocatalysis/Biodegradation Database: Microorganisms, genomics, and prediction . Nucleic Acids Res. , 28 : 377 – 379 .
   PubMed Web of Science ®Google Scholar
• Ellis , LBM , Hershberger , CD , Bryan , EM and Wackett , LP . 2001 . The University of Minnesota Biocatalysis/Biodegradation Database: Emphasizing enzymes . Nucleic Acids Res. , 29 : 340 – 343 .
   PubMed Web of Science ®Google Scholar
• Lobos , JH , Leib , TK and Su , T-M . 1992 . Biodegradation of bisphenol A and other bisphenols by gram-negative aerobic bacterium . Appl. Environ. Microbiol. , 58 : 1823 – 1831 .
   PubMed Web of Science ®Google Scholar
• Casellas , M , Grifoll , M , Bayona , JM and Solanas , AM . 1997 . New metabolites in the degradation of fluorine by Arthrobacter sp. strain F101 . Appl. Environ. Microbiol. , 63 : 819 – 826 .
   PubMed Web of Science ®Google Scholar
• van der Werf , MJ , Swarts , HJ and de Bont , J . 1999 . Rhodococcus erythropolis DCL14 contains a novel degradation pathway for limonene . Appl. Environ. Microbiol. , 65 : 2092 – 2102 .
   PubMed Web of Science ®Google Scholar
• Cook , AM and Hrsak , D . 2000 . The complete degradation of LAS is becoming better understood with pure cultures of bacteria . CLER Rev. , 6 : 46 – 53 .
   Google Scholar
• Ellis , DA , Hanson , ML , Sibley , PK , Shahid , T , Fineberg , NA , Solomon , KR , Muir , DCGM and Mabury , SA . 2001 . The fate and persistence of trifluoroacetic and chloroacetic acids in pond waters . Chemosphere , 42 : 309 – 318 .
   PubMed Web of Science ®Google Scholar
• US Environmental Protection Agency . 2000 . Interim Guidance for Using Ready and Inherent Biodegradability Tests to Derive Input Data for Multimedia Models and Wastewater Treatment Plants (WWT) Models , US EPA, Washington , DC : Exposure Assessment Tools and Models . Available at http://www.epa.gov/opptintr/exposure/pubs/halflife.htm
   Google Scholar
• Dimitrov , S , Pavlov , T , Nedelcheva , D , Reuschenbach , P , Silvani , M , Bias , R , Comber , M , Low , L , Lee , C , Parkerton , T and Mekenyan , O . A kinetic model for predicting biodegradation, SAR QSAR Environ. Res. 18 (2007), pp. 443–457
   Google Scholar
• Reuschenbach , P , Hermann , U , Silvani , M , Schwarz , H and Dimitrov , S . Validation of a QSAR model for predicting biodegradation with OECD Guidelines 301 data, Poster MO 084, SETAC Europe 19th Annual Meeting, Gothenburg, 2009
   Google Scholar
• Dimitrov , S , Nedelcheva , D , Dimitrova , N and Mekenyan , O . 2010 . Development of a biodegradation model for the prediction of metabolites in soil . Sci. Total Environ. , 408 : 3811 – 3816 .
   PubMed Web of Science ®Google Scholar
• European Food Safety Authority, ‘Rapporteur Member State assessment reports submitted for the EU peer review of active substances used in plant protection products’. Available at http://dar.efsa.europa.eu/dar-web/provision
   Google Scholar