What's New in the UM-BBD?

November 17, 2003
The pathway for 2,4-dichlorotoluene (US) or (UK), has been added. This pathway was developed by a student in the 2003 Biocatalysis and Biodegradation class, offered completely over the Internet. Registration is now open for the 2004 offering of this class. The class will be offered from January 20 to May 7, 2004. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. There are now 252 rules. A list of all rules is available. The system can now handle 357 (63%) of the 571 pathway branches from 114 UM-BBD compounds containing C and H, O, N, P, S and/or halides that initiate pathways containing two or more reactions. In Biochemical Periodic Tables, there are new entries for Hydrogen (H) and major cations, and an updated entry for Iodine (I). This completes the first update of the Biochemical Periodic Tables. Let us know of any errors or omissions in this or any other part of the UM-BBD.

October 20, 2003
The pathway for n-hexane (anaerobic) (US) or (UK), has been added. This pathway was developed by a student in the 2003 Biocatalysis and Biodegradation class, offered completely over the Internet. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. There are now 237 rules. A list of all rules is available. On the Useful Internet Resources page, a link has been added to ChemSpy Environment News and a link has been updated for the US Department of Energy, Office of Science, Biology and Environmental Research.

September 22, 2003
The pathway for benzyl sulfide, (US) or (UK), has been added. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. There are now 227 rules. A list of all rules is available. In Biochemical Periodic Tables, there are new entries for Europium (Eu), Praseodymium (Pr), Protactinium (Pa), Neodymium (Nd), Promethium (Pm), Neptunium (Np), Samarium (Sm), Americium (Am), Terbium (Tb), Dysprosium (Dy), Erbium (Er), and Ytterbium (Yb). There is a new way to contact UM-BBD staff. A "Contact Us" link at the bottom of most UM-BBD web pages links to a web form that sends questions and comments to the people most able to respond to them. Join the UM-BBD Email List to receive periodic UM-BBD Progress Reports and Announcements. On the Useful Internet Resources page, the link to the Database for Environmental Fate of Chemicals from the Japanese Agency of Industrial Science and Technology has been deleted.

August 20, 2003
The pathway for 1,1,1-trichloroethane (an/aerobic), (US) or (UK), has been added, and the phthalate family, (US) or (UK), the beta-1,2,3,4,5,6-hexachlorocyclohexane (an/anerobic), (US) or (UK), the benzoate, (US) or (UK), and the phenanthrene (fungal 9S,10S) (US) or (UK), and (fungal 9R,10R) (US) or (UK), pathways have been updated. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. There are now 233 rules. A list of all rules is available. In the Biochemical Periodic Tables, there are new entries for Cerium (Ce) and Thorium (Th). On the Useful Internet Resources page, the links to the Centraalbureau voor Schimmelcultures (CBS) Bacteria/Plasmids Database and The Microbial World at University of Edinburgh, have been updated.

July 23, 2003
The pathway for pyrene, (US) or (UK), has been added. This pathway was developed by a student in the 2003 Biocatalysis and Biodegradation class, offered completely over the Internet. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. There are now 222 rules. The system can now handle 324 (58%) of the 557 pathway branches from 108 UM-BBD compounds containing C, H, O, N, P, S and/or halides that initiate pathways containing two or more reactions. A list of all rules is available. Reaction pages that exemplify up to three rules now list all of them. For an example, see the page for the reaction: cis-3-Chloroacrylic acid to Malonate semialdehyde. In Biochemical Periodic Tables, there is a new entry for Plutonium (Pu) and updated entries for Copper (Cu), Zinc (Zn), Flourine (F), Chlorine (Cl), Bromine (Br), and Iodine (I). On the Useful Internet Resources page, a link to the National Safety Council Chemical Backgrounders has been added and the links to the Agricultural Research Service (ARS) Pesticide Properties Database, Thermodynamics of Enzyme-Catalyzed Reactions from the National Institute of Standards and Technology and GenProtEC: E. coli genes and proteins at the Woods Hole Marine Biological Laboratory, have been updated.

June 26, 2003
The pathway for pyrrole-2-carboxylate, (US) or (UK), has been added. This pathway was developed by a student in the 2003 Biocatalysis and Biodegradation class, that is offered completely over the Internet. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. There are now 209 rules. A list of all rules is available. The Search and Browse page has been updated to improve the accuracy and ease of use of the searches. The List of All Microorganisms has a new URL and can now accept Boolean operators (AND, OR, NOT) in the microorganism name search. In Biochemical Periodic Tables, there are updated entries for (Pb), Arsenic (As), Tellurium (Te), Gadolinium (Gd), Vanadium (V), Chromium (Cr), Molybdenum (Mo), Tungsten (W), Manganese (Mn), Iron (Fe), Cobalt (Co), and Nickel (Ni).

May 28, 2003
The pathways for anaerobic trichloroethane, (US) or (UK), nicotine, (US) or (UK), and alpha-pinene, (US) or (UK), have been updated. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. With 172 rules, the PPS could correctly predict known metabolism for 97 (90%) of the 108 compounds containing C, H, O, N, S, P and halides that initiate UM-BBD pathways of two or more reactions. There are now 180 rules. A list of all rules is available. Reaction pages now list btrules, if any, that are in accord with the reaction. For example, see the page for the reaction: 1,2-dichloroethane to 2-chloroethanol. The format of UM-BBD pathway, reaction, enzyme and compound pages is described in About the UM-BBD. In Biochemical Periodic Tables, there are new entries for Polonium (Po), Uranium (U) and Cadmium (Cd) and updated entries for Technetium (Tc), Bismuth (Bi), Ruthenium (Ru), Rhodium (Rh), Palladium (Pd), Platinum (Pt), Gallium (Ga), Indium (In), Thallium (Tl), Tin (Sn) and Germanium (Ge). The results of the Seventh User Survey are now available.

April 10, 2003
The pathways for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), (US) or (UK), and nitroglycerin, (US) or (UK), have been updated. The Pathway Prediction System (PPS) biotransformation rules have been added to and updated. There are now 146 rules. The current PPS can correctly predict known metabolism for 77 (71.3%) of the 108 compounds containing C, H, O, N, S, P and halides that initiate UM-BBD pathways of two or more reactions. A list of all rules is available. An organic functional group name contains search for biotransformation rules is now available on the UM-BBD Search page and the all rules page. In Biochemical Periodic Tables, the entries for Strontium (Sr), Cesium (Cs), Barium (Ba), Scandium (Sc), Yttrium (Y), Lutetium (Lu), Lanthanum (La), and Mercury (Hg) have been updated. A new publication is available on the UM-BBD Publications Page: Hou, B.K., Wackett, L.P., and Ellis, L.B.M. (2003) "Predicting Microbial Catabolism: A Functional Group Approach" Journal of Chemical Information and Computer Sciences, ASAP Web Release Date: April 4, 2003.

March 11, 2003
The pathways for 2-chloro-N-isopropylacetanilide (US) or (UK), and limonene (US) or (UK), have been updated. The Pathway Prediction System's biotransformation rules have been added to and updated. There are now 110 rules. Existing rules have been generalized where possible to include compounds containing substituents. A list of all rules is available. In Biochemical Periodic Tables, the entry for Rubidium (Rb) was updated. Students in our 2003 Biocatalysis and Biodegradation class, offered completely over the Internet, have examined websites on the UM-BBD Useful Internet Resources page and selected the most interesting ones. The Useful Internet Resources page now links to the list of these choices and the reason each site was selected. The What's New page restarts; 2002 activities have been archived.

February 3, 2003
The pathways for iprodione, (US) or (UK), and trichloroethylene, (US) or (UK), have been updated. The TCE update adds one more UM-BBD reaction for toluene dioxygenase. A list, (US) or (UK), of the 109 reactions known for this enzyme is available. The TCE update also updates reaction mechanisms, for a total of 29. A list of these is available. Biotransformation rules have been added and updated in the Pathway Prediction System (PPS). There are now 80 rules. Each rule now includes a list of all UM-BBD reactions that exemplify that rule. Rules with more examples have stronger support. A list of all rules is available. The current PPS can correctly predict known metabolism for 60% of the 84 compounds containing C, H, O, N, and halides that initiate UM-BBD pathways of two or more reactions. In the Biochemical Periodic Tables, entries for: Boron (B), Carbon (C), Nitrogen (N), Oxygen (O), Fluorine (F), Silicon (Si), Sulfur (S) Chlorine (Cl), Selenium (Se), Litium (Li), Beryllium (Be), and Arsenic (As), were updated. BioC/MicE 5309, Biocatalysis and Biodegradation, a University of Minnesota class offered completely over the Internet, is full and registration has closed. The class runs from January 21 to May 17, 2003. A new publication is available: Ellis, L.B.M., Hou, B.K., Kang, W., and Wackett, L.P. (2003) "The University of Minnesota Biocatalysis/Biodegradation Database: Post-Genomic Datamining" Nucleic Acids Research 31: 262-265. The full text of this paper is linked to on the UM-BBD main menu and publication page. Cite the database using this paper or its successors.

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