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What's New in the UM-BBD?

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December 9, 1998
Two new pathways were added, for 1,2,4-trichlorobenzene and fungal 9S,10S penanthrene. The 9S,10S pathway is the UM-BBD's first fungal pathway. Reaction page ExPASy links have been changed. On the Useful Internet Resources page, a link has been added to Lignin Biodegradation by White Rot Fungi at Wageningen Agricultural University, The Netherlands and the link to the ExPASy Enzyme Database has been changed.

November 25, 1998
Two new pathways were added, for TNT and anaerobic DDT. The TNT pathway is the first pathway contributed by a student in the 1998 Biocatalysis and Biodegradation course, taught completely over the Internet. The 1998 students are completing their work and we plan to offer the course again in early 1999. It will again be limited to no more than 10 students. On the Useful Internet Resources page, a link has been added to TOXNET (Toxicology Data Network) from the National Library of Medicine and the Polyaromatic Hydrocarbon Database and Pesticide Database from Toyohasi University of Technology, Japan.

October 30, 1998
Two new pathways were added, for nicotine and phenanthrene. Ben Vickers and Jun Ouyang have been added to our Contributor's Page. All pathway maps which link to intermediary metabolism now link to a KEGG map with the compound common to the UM-BBD and KEGG pathways highlighted in red. On the Useful Internet Resources page, a link has been added to the searchable List of Designated Hazardous Substances from the Australian National Occupational Health and Safety Commission.

October 14, 1998
Two new pathways were added, for DDT and carbazole. Keywords have been added describing UM-BBD enzyme mechanism graphics. All microorganism links to external databases were updated. On the Useful Internet Resources page, a link has been added to In Situ Bioremediation: When Does It Work? from National Academy Press.

September 22, 1998
Two new pathways were added, for caprolactam and phenylpropionate. The phenylproprionate pathway is our first pathway to have its link to intermediary metabolism produce a KEGG map with the compound common to the UM-BBD and KEGG pathways highlighted in red. To see how this looks, try to find the red node for "succinate" in this KEGG map. This functionality will appear in all new UM-BBD pathways and will be added to older pathways as time permits. The UM-BBD Metapathway Map has been updated to include structures of compounds as well as their names. It is a good overview of UM-BBD contents. Its links to KEGG highlight the node for the linking compound in the KEGG pathway map. Thanh Trinh has been added to our Contributor's Page, and a 1998 group picture of UM-BBD Developers has been added to the Developer's Photo Gallery. On the Useful Internet Resources page, a link has been added to the MBGD: MicroBial Genome Database from the University of Tokyo and the link to the Groundwater Pollution Primer has been changed.

August 26, 1998
Two new pathways, for (+)-camphor and methionine and threonine, were added. All UM-BBD compound page links to EXTOXNET Pesticide Information Profiles have been updated. A new list can be dynamically generated of all UM-BBD reactions not studied enough to be assigned enzyme(s). There is a link to it on the UM-BBD Search page. Students in our 1998 Biocatalysis and Biodegradation class, offered completely over the Internet, have examined websites on the UM-BBD Useful Internet Resources and selected the most interesting ones. The Resources page now links to the list of these choices and the reason each site was selected. On the Useful Internet Resources page, links have been added to Thermodynamics of Enzyme-Catalyzed Reactions from the National Institute of Standards and Technology and the Sequence Retrieval Server at the European Bioinformatics Institute, and the link to Environmental Conferences has been removed.

July 23, 1998
Two new pathways, for fluorene and organomercury, were added and one new reaction was added to the 2,4-D pathway. The organomercury pathway is our first to include organometallic compounds. We were selected as HMS Beagle's "Web Pick of the Day" for July 20, 1998, and have added a link to them and their award graphic to our Awards page. The dreaded 404 Not Found message has been improved. Potential users have seen these more frequently since we reorganized the database and changed many URLs. It now includes links to the UM-BBD home, search, and other pages. To see the new message, try this Bad Link. On the Useful Internet Resources page, a link has been added to the Polycyclic Aromatic Hydrocarbons (PAHs) Database at Toyohashi University of Technology, Japan and the link to OSHA Chemical Information has been changed.

June 23, 1998
One new pathway, for m-cresol, was added and one new reaction was added to the tyrosine pathway. The chemical formula search on the Search page can now handle formulas in any order and you can search for organic acids using the formula for the neutral acid or any anionic form. On the Useful Internet Resources page, the link to Worksafe Australia has been removed.

May 27, 1998
Two new pathways were added, biphenyl and p-cymene. The Search page now includes a search for full or partial microorganism names. Generated pathways now include links to reactions for which enzymes have not yet been identified. These have an "X" instead of an enzyme name. For an example, here are two X'ed reactions. Generated pathways, where necessary, now link to the static C1 cycle pathway map rather than including it, and the generate pathway option has been removed from reactions in the C1 cycle and methanogenesis pathways.

May 12, 1998
One new reaction, for the biodegradation of 4-methoxybenzoate, was added to the 2,4-Dichlorobenzoate pathway. Annotated results of our Third Annual User Survey are found on our Use Statistic page. We have also updated other Use Statistics there. We have added two UM-BBD publications to our Publications page. On the Useful Internet Resources page, the link to the USGS Toxic Substances Hydrology Program has been updated.

April 21, 1998
Two new pathways were added: Benzonitrile and 1-Aminocyclopropane-1-carboxylate. The three last pathways were converted to our new format: 2,4-Dichlorophenoxyacetic Acid, Trichloroethylene, and Tyrosine. Our search and index pages have been combined and improved. From the the new Search page, you can search for UM-BBD compounds by full or partial name or synonym, CAS Registry Number, or chemical formula; or for UM-BBD enzymes by full or partial enzyme name or EC code. You can also view lists of all UM-BBD compounds, reactions, enzymes, pathways, graphics, or microorganisms. We have sent out our Third Annual User Survey. If you have not yet responded, please take a minute to fill it out and e-mail it back to help guide UM-BBD development. Results of past surveys are available. On the Useful Internet Resources page, the link to HInCyc has been removed.

April 7, 1998
Twelve pathways were converted to our new format: 2,4,5-Trichlorophenoxyacetic Acid, Naphthalene, Tetrachloroethene (anaerobic), Toluene-4-sulfonate, Naphthalenesulfonate Family, Pentachlorophenol Family, Methanogenesis, Toluene (anaerobic), Methanesulfonic Acid, Nitrobenzene, 2-Aminobenzoic Acid (anaerobic), and Methyl fluoride. The ad hoc pathway generator is now able to produce "partial pathways." To test this new functionality, go to the anthranilate-CoA ligase reaction page and click on "Generate a pathway starting from this reaction." A large pathway map is produced. To see a subset, enter "2" as the number of levels (reaction depth) and then press "return" or "enter." A new pathway, only two reactions deep, will be generated. Next either enter another number (for example, 3 or 4) to see another pathway starting at the same reaction and decending further, or click on "Next 2 levels" to move along the pathway, 2 reactions at a time. The e-mail address at the bottom of each UM-BBD page has changed to BBDMaster@email.labmed.umn.edu Use this address for general questions, comments or concerns; your message will be forwarded to the person best able to answer it. We will be soon be sending out our Third Annual User Survey. When you receive it, please take a minute to fill it out and e-mail it back. They help guide UM-BBD development. Results of past surveys are available.

March 27, 1998
Seven pathways were converted to our new format: Dibenzothiophene Desulfurization, C1 Metabolic Cycle, Styrene, Ethylbenzene, Ethylbenzene (anaerobic), 3-Chloroacrylic Acid, and Toluene. All new format pathway maps (both text and graphical) now have a new format "Compounds and Reactions" menu which replaces the previous two separate "Compound" and "Reaction" menus. To check this, go to any of the above pathways and click on [Compounds and Reactions]. The ad hoc pathway generator now handles more complex pathways, including those which contain multiple products or metabolic cycles. Some of these generated pathway maps are quite large and we will add ways to generate partial maps as time permits. To test the new pathway generator functionality, go to the ethylbenzene dioxygenase reaction page and click on Generate a pathway starting from this reaction. On the Useful Internet Resources page, the links to Hunting for Microbial Information for Bacteria, Bioremediation Bibliography 1/92-7/94, and U.S Department of Energy Office of Energy Research, were updated, the link to TOXTALK was replaced by a link to Newsletters from the Canadian Network of Toxicology Centers, and the link to "Processing Organic Solid Wastes and Remediating Hydrocarbon Contaminated Soils" was replaced by a link to "Pathways and Controlling Factors in the Biodegradation of Energetic Wastes"

March 10, 1998
One new reaction, for the biodegradation of resorcinol, was added to the 4-nitrophenol pathway. Seven pathways were converted to our new format: Dimethyl Sulfoxide & Organosulfide Cycle, o-Xylene, m-Xylene, p-Xylene, 2-Aminobenzenesulfonate, s-Triazine Metabolism, and 4-Nitrophenol.

February 20, 1998
Two new pathway, for the biodegradation of cyclohexanol and methyl ethyl ketone, were added. Three pathways were converted to our new format: anaerobic benzoate, chlorobenzene, and dichloromethane. GenoBase links on reaction pages have been replaced by equivalent links to the ExPASy ENZYME database. The About the UM-BBD page has been updated to reflect the new format of our pathway, reaction, and compound pages. The Guided Tour page has been updated to reflect the many changes of the past year. On the Useful Internet Resources page, the link to the Ligand Chemical Database has been updated and a link to the ExPASy ENZYME database was added.

February 10, 1998
One new pathway for the biodegradation of mandelate was added. Six pathways were converted to our new format: 4-chlorobiphenyl, 2,4-dichlorobenzoate, dibenzothiophene, phthalate family, phenol, and atrazine. On our Useful Internet Resources page, the links to EcoCyc, HinCyc, and the EPA Envirofacts Master Chemical Integrator have been updated and a link has been added to the journal Bioinformatics (formerly CABIOS). We have been added to the peer-reviewed SciCentral and InterNIC Academic Guide to the Internet websites. Our Awards page contains links to all such honors.

January 20, 1998
Three new pathways, for the biodegradation of 1,3-dichloro-2-propanol, 3-methylquinoline, and parathion, were added. The 3-methylquinoline and parathion pathways are contributed by students in our graduate-level Biocatalysis & Biodegradation course, taught completely over the Internet. The first group of students are completing their work and the course will be offered again in early 1998, again limited to no more than 10 students. Six pathways were converted to our new format: 1,2-dichloroethane, orcinol, glyphosate, acrylonitrile, beta-1,2,3,4,5,6-hexachlorocyclohexane, and dimethyl ether. All new format reaction and compound pages now have a white background, to help differentiate them from the grey static pages they replace. The link to the prototype ad hoc pathway generator was removed from the home page. Ad hoc pathways can now be generated from many new- format reaction pages. To test this, go to the haloalkane dehalogenase reaction page and click on "Generate a pathway." The ad hoc pathway generator will increasingly handle more complicated reactions as we progress with the conversion to the new format. All enzyme mechanism graphics now include the reference(s) on which the mechanism is based. A complete list of these graphics is found in the UM-BBD Graphics Index. 1997 Student Papers on Selected UM-BBD Enzymes, from the University of Wisconsin, Eau Claire, are now linked to on the appropriate UM-BBD text pathway maps. The Useful Internet Resources page contains a link for a list of those papers. On our Useful Internet Resources page, the link to the GenoBase server at NIH has been removed. GenoBase will be unavailable for at least the next several months and perhaps forever, so links to it have been removed from new-format reaction pages.

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