What's New in the UM-BBD?

December 19, 2005
The UM-BBD has moved to a new email list server. This move should be transparent to the UM-BBD email list members. To subscribe, unsubscribe, or change your subscription options, go to: http://lists.umn.edu/cgi-bin/wa?SUBED1=um-bbd&A=1

November 23, 2005
A pathway for fosfomycin (US) or (UK), was added. This pathway was developed by a student in the 2005 BioC/MicE 5309 class. The minireview: Lawrence P. Wackett, Anthony G. Dodge, Lynda B. M. Ellis (2004) "Microbial Genomics and the Periodic Table" Applied and Environmental Microbiology 70: 647-655, is one of the AEM's "Top 20" most requested articles, July - September 2005. This and other UM-BBD publicatons are found on our Publications page. On the Useful Internet Resources page, the link for PROCAT was replaced by the Catalytic Site Atlas, at EMBL-EBI.

October 21, 2005
A pathway for the nylon oligomer (US) or (UK), was added. This pathway was developed by a student in the 2005 BioC/MicE 5309 class. The Pathway Prediction System (PPS) web-based tutorial is now also available in a printer-friendly .pdf version. The UM-BBD was featured in Netwatch section of Science: Leslie, Mitch (2005) "DATABASE: Eating Pollution" Netwatch, Science, 309: 1795. This and other reviews and publications are found on our Publications page. On the Useful Internet Resources page, the link for Lignin Biodegradation by White Rot Fungi has been deleted.

September 12, 2005
Further implementation of suggestions made at the PredictBT workshop held May 6-7, 2005: Now the Pathway Prediction System (PPS) shows that a predicted compound is found in the UM-BBD by adding a "Cpd" button to the compound's MavinView applet. The About the PPS web page has been updated to include the Cpd button. PPS biotransformtion rules are being moved to ChemAxon's Reactor system as time permits. Btrules that have been so moved now display a Reactor pattern graphic on their web pages. For example, see the web page for bt0005, vic-unsubstitued benzenoid -> vic-dihydrodihydroxybenzenoid. The format of the btrule page is described on the About the BBD web page.

August 18, 2005
A pathway for Branched-Chain Dodecylbenzene Sulfonate, (US) or (UK), was added. This pathway was developed by a student in the 2005 BioC/MicE 5309 class. Further implementation of suggestions made at the PredictBT workshop held May 6-7, 2005: Now the Pathway Prediction System (PPS) shows the aerobic likelihood scores assigned at that workshop as a color bar to the left of each predicted compound. An About the PPS web page has been created that describes the PPS, including the new color bar, in more detail.

July 13, 2005
A PredictBT workshop was held May 6-7, 2005 to further develop the Pathway Prediction System (PPS). One complaint from users was that there were too many choices available at each step. To prioritize biotransformations for various environments, we started with aerobic conditions, in soil (moderate moisture) or water, at neutral pH, 25°C, with no competing or toxic other compounds. Two or more experts in biodegradation assigned an aerobic likelihood score to each btrule. More information on the rule prioritization process is available. Now btrule pages show their assigned aerobic likelihood scores. The scores are color coded, from green (very likely) to red (very unlikely). For example, bt0022, organoHalide -> Alcohol, is "neutral" (yellow). The format of a btrule page is described in About the UM-BBD. Each PPS pathway creation page shows a Rule button with each biotransformation choice. That button links to the btrule page for that biotransformation.

June 9, 2005
A pathway for Picric Acid (2,4,6-Trinitrophenol), (US) or (UK), was added. This pathway was developed by a student in the 2005 BioC/MicE 5309 class. American Type Culture Collection (ATCC) links work properly again on text pathway map pages, such as the 1,2-dichloroethane pathway map.

April 6, 2005
A pathway for Cyclohexane, (US) or (UK), was added and the one for Cyanuric Acid, (US) or (UK), was updated. The Cyclohexane pathway is based on the former Cyclohexanol pathway. The American Type Culture Collection (ATCC) is updating their website. UM-BBD links to them on the list of microorganisms have been updated; links to them on text pathway map pages, such as the 1,2-dichloroethane pathway map, work by redirection. We are fixing the problem as time permits. On the Useful Internet Resources page, the link for the Hazardous Substances Information System, from the Australian National Occupational Health and Safety Commission, has been updated.

March 2, 2005
A pathway for Cyclopropanecarboxylate degradation, (US) or (UK), has been added. On the Useful Internet Resources page, links for Chemical Entities of Biological Interest (ChEBI) at EBI, UK; PubChem, NCBI, NLM, NIH; and Biodegradation, from Environmental Inquiry, Cornell University, have been added.

February 18, 2005
A pathway for the oxidation of Hypophosphite, (US) or (UK), has been added. The links to the National Toxicology Program's database on UM-BBD compound pages have been improved and the number of compounds with such links has almost doubled. For an example, see the NTP link on the 1,2-dichloroethane page. A searchable list of compounds is available. In the Biochemical Periodic Tables, new entries were made for Curium (Cm), Niobium (Nb), Rhenium (Re) and Holmium (Ho). Some biological information is now available for almost all stable, non-noble-gas elements. On the Useful Internet Resources page, the link for IUBMB-Nicholson Metabolic Maps, Minimaps and Animaps at Trinity College, Dublin, Ireland has been updated.

January 12, 2005
A synthetic pathway for Valanimycin, (US) or (UK), has been added. This, the first synthetic pathway in the UM-BBD, includes synthesis of an azoxy compound, important in biocatalysis. Two new reaction mechanism graphics have been added. One is for the azoxy synthesis reaction in the Valanimycin pathway; the other is for the benzoylformate decarboxylation reaction in the Mandelate pathway. This brings the number of such graphics to 33. A list of all reaction mechanism graphics is available. In the Biochemical Periodic Tables, new entries were made for Zirconium (Zr), Hafnium (Hf), Tantalum (Ta), and Iridium (Ir). On the Useful Internet Resources page, links for ZINC, a free database of commercially-available compounds, and MetaRouter: Bioinformatics for Bioremediation, have been added, and the link to the Virtual Library of Microbiology and Virology has been removed. The What's New page restarts; 2004 activities have been archived.

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