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What's New in the UM-BBD?

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December 20, 2002
Biotransformation rules have been added and updated in the Pathway Prediction System. There are now 55 rules. A list of all rules exists. In the Biochemical Periodic Tables, entries for Phosphorus (P), Silver (Ag), and Aluminum (Al) were updated. Registration continues for BioC/MicE 5309, Biocatalysis and Biodegradation, a University of Minnesota class offered completely over the Internet. There are still a few openings; registration will close when the class limit is reached. The class will run from January 21 to May 17, 2003. On the Useful Internet Resources page, a link to EPA Persistent, Bioaccumulative, and Toxic (PBT) Profiler has been added and the link to the Centraalbureau voor Schimmelcultures (CBS) Bacterial Database has been updated.

November 15, 2002
A pathway for isoproturon, (US) or (UK), has been developed. In Biochemical Periodic Tables, the page for Gold (Au) was updated.

October 30, 2002
A pathway for quercetin (US) or (UK), has been developed. All reaction and enzyme page GenBank and GenPept searches have been reviewed. 35 GenBank searches have been added, and some searches have been updated to increase their proportion of good hits. Lists of all reactions and all enzymes are available.

September 18, 2002
A pathway for anerobic biodegradation of tetrachloroethene (PCE) (US) or (UK), has been updated. A prototype Pathway Prediction Engine has been added. It contains 40 rules for biodegradation of organic functional groups and can handle simple aliphatic and aromatic compounds. User comments on rules, suggestions for new rules, or limits to existing rules, are encouraged. Multimedia Educational Resources for Learning and Online Teaching (MERLOT) reviewed the UM-BBD and awarded it high scores: Content Quality: 5/5; Potential Effectiveness as a Teaching Tool: 4/5; Ease of Use for Students and Faculty: 5/5. The review is linked to on the UM-BBD Publication page. On the Useful Internet Resources page, the link to Klotho has been updated.

August 26, 2002
Pathways for the aerobic and anerobic biodegradation of trifluoroacetate (TFA) (US) or (UK), and chromium reduction (US) or (UK), have been added. The chromium pathway is another in our series of metal, metalloid and metal chelator pathways. A list of these is available. Two new Biochemical Periodic Tables have been developed. Both contain links to web pages for elements that are transformed by, bound by, or are otherwise important in, biological systems. All search links to ATCC microbial strains have changed. A list of all microbial strains exists. The UM-BBD Contributor's page was updated with new members of its International Scientific Advisory Board. On the Useful Internet Resources page, the link to Centraalbureau voor Schimmelcultures (CBS) Bacterial Database has been updated, and links to ChemConnect News and Research, Pathways and Controlling Factors in the Biodegradation of Energetic Wastes, and Biotechnology in Waste Management, have been removed.

July 11, 2002
Pathways for the biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), under aerobic (US) or (UK), or anerobic (US) or (UK) conditions, have been added. All search links to ATCC are changing. Most have been updated on the Microbiology Index, and the ones on pathway maps are being updated as time permits. The UM-BBD has moved its data to a MySQL database. Searches are faster and more complete. The freely-available MySQL database management system is linked to on the UM-BBD Tools page. A recent review of the UM-BBD: Burgard A.P.; Maranas C.D. "Review of the University of Minnesota Biocatalysis/Biodegradation Database" Metabolic Engineering (2002) 4(2): 111-113, has been added to our publications page. On the Useful Internet Resources page, the links to BioCyc and Bioremediation Research Abstracts at the Hazardous Substances Research Centers have been updated, and a link to a list of DSMZ microorganisms which degrade chemical compounds has been added.

April 16, 2002
Pathways for the biodegradation of bisphenol A, (US) or (UK), tetrabromobisphenol A, (US) or (UK), and technetium, (US) or (UK), have been added, and the pathway for Mordant Yellow 3, (US) or (UK), has been updated. Mechanism graphics were drawn for three reactions in the bisphenol A pathway, bringing to 30 the number of such graphics. A list of these is available. The tetrabromobisphenol A pathway was developed by a student in the 2001 Biocatalysis and Biodegradation class, offered completely over the Internet. The technetium pathway brings to ten the number of metal, metalloid and metal chelator pathways in the UM-BBD. A list of these is available. A second form of structure-based searching has been added to the UM-BBD. You can draw the compound you wish to search for using a Java applet. Then enter the type of structure search (similarity, substructure or exact) you wish to do, the similarity threshold to use, the maximum time to search and the maximum number of hits. Images of matching structures in the UM-BBD are returned. Clicking on "More info" leads to the corresponding UM-BBD compound page, and from there to reactions of, and biodegradation pathways for, the compound. This is a step towards predicting biodegradation pathways for compounds the UM-BBD does not contain. The biodegradation pathways for UM-BBD compounds that are similar to the query compound can suggest ways the query might be degraded. This Java applet does not work with all browsers. If you have problems with it, please use the text-based simple structure search. Both structure searches are linked to on the main search page and are based on the JChem toolkit from ChemAxon, Ltd., listed on the UM-BBD Tools page. On the Useful Internet Resources page, the link to Chemfinder from CambridgeSoft has been updated.

March 20, 2002
Pathways for the biodegradation of 1,2,3,4-tetrachlorobenzene (US) or (UK), and Mordant Yellow 3 (US) or (UK), have been added, and the pathway for propylene (US) or (UK) has been updated. The 1,2,3,4-tetrachlorobenzene and Mordant Yellow 3 pathways were developed by students in the 2001 Biocatalysis and Biodegradation class offered completely over the Internet. The Mordant Yellow 3 pathway includes another reaction of the versatile enzyme, naphthalene 1,2-dioxygenase, bringing to 76 the number of reactions known for this enzyme. A list of these is available. Structure-based searching has been added to the UM-BBD. Enter the SMILES string of the compound to search for, the type of structure search (similarity, substructure or exact) to do, and the similarity threshold to use. Images of matching structures in the UM-BBD are returned. Clicking on the image of a returned compound leads to the corresponding UM-BBD compound page. From a compound page, one can go to reactions of and biodegradation pathways for the compound. This is a first step towards predicting a biodegradation pathway for compounds the UM-BBD does not contain. The biodegradation pathways for UM-BBD compounds that are similar to the query compound can suggest ways the query might be degraded. This structure search is linked to on the main search page. It is based on the JChem toolkit from ChemAxon, Ltd., listed on the UM-BBD Tools page.

February 27, 2002
Pathways for the biodegradation of cyanuric acid (US) or (UK), N-cyclopropylmelamine (US) or (UK), selenate (US) or (UK), and 1,2-dichloroaniline (US) or (UK), have been added. The N-cycloproplymelamine, selenate and 1,2-dichloroaniline pathways were developed by students in the 2001 Biocatalysis and Biodegradation class offered completely over the Internet. The selenate pathway brings to nine the number of metal, metalloid and metal chelator pathways in the UM-BBD. A list of these is available. On the Useful Internet Resources page, the link to Biotechnology in Waste Management from AusBiotech, Ltd. has been updated.

January 23, 2002
Pathways for the biodegradation of 4-hydroxyacetophenone, (US) or (UK), o-nitrobenzoate, (US) or (UK), and methylarsonate, (US) or (UK), have been added and the pathway for atrazine (US) or (UK), has been revised. The methylarsonate pathway was developed by a student in the 2001 Biocatalysis and Biodegradation class offered completely over the Internet. This pathway brings to eight the number of metal, metalloid and metal chelator pathways in the UM-BBD. A list of these is available. On the Useful Internet Resources page, the link to Metabolic Pathway Minimaps at Trinity College, Dublin, Ireland has been updated and the link to ERGO at Integrated Genomics, Inc. has been removed. The What's New page restarts; 2001 activities have been archived.

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