December 5, 1997
One new pathway, for the biodegradation of dibenzofuran, was added. The compound and reaction pages for this pathway has a slightly different format. For example, the compound pages show which new-format UM-BBD reactions include the compound as a substrate or as a product. Functionality will continue to increase in the coming months as we improve the format and convert all compounds and reactions to it. On our Useful Internet Resources page, the link to Bioremediation Research Abstracts at the Hazardous Substances Research Centers was updated. Links to PROCAT: A database of 3D enzyme active site templates; the Enzyme Structures Database; SFB Biocatalysis, Institute for Organic Chemistry, Technical Institute Granz, Austria; and the U.S. EPA Citizen's Guide to Bioremediation were added.
November 20, 1997
Three new pathways, for the anaerobic biodegradation of gallate and the aerobic biodegradation of octane and pentaerythritol tetranitrate (PETN), were added. The compound and reaction pages for these new pathways have a slightly different format. For example, the compound pages show which new-format UM-BBD reactions include the compound as a substrate or as a product. Functionality will continue to increase in the coming months as we convert all compounds and reactions to this new format. The PETN pathway is the first one contributed by a student in our graduate-level Biocatalysis & Biodegradation course, offered completely over the Internet. The first group of students are completing their work and we plan to offer the course again in early 1998. It will again be limited to no more than 10 students. We have developed a new overview for the UM-BBD, called the UM-BBD Metapathway Map. It contains links to most UM-BBD pathways and graphically illustrates how they converge to relatively few intermediates, which continue to intermediary metabolism common to most organisms. On our Useful Internet Resources page, the links to Boehringer Mannheim Biochemical Pathways on the ExPASy server, Agricultural Research Service (ARS) Pesticide Properties Database, and BIOREP: Biotechnology Research Projects in Europe were updated. The EPA Chemical Substance Factsheets at the University of Virginia were replaced by the EPA Chemical Resources Index.
October 24, 1997
A metapathway map for s-Triazine compounds was added. This metapathway introduces a new UM-BBD triazine message board, for non-commercial discussion of microbial triazine catabolism. Take a look at the board and leave a message if you like. Two new pathways, for the anaerobic biodegradation of aminobenzoic acid and the aerobic biodegradation of naphthalene sulfonate family, were added. The reaction page links to Medline citations which link to tertiary structures of our enzymes were updated and several new ones were added. We also added these links to the UM-BBD EC index and search (though the EC code). Our prototype ad hoc pathway generator has moved to the UM-BBD server. This move will permit this functionality to be added to the entire UM-BBD as time permits. Try it out and let us know how you like it. On our Useful Internet Resources page, the link to Michigan State University's Microbe Zoo and the Zoo's Toxic Waste Site was updated and a links to the Agency for Toxic Substances and Disease Registry (ATSDR) ToxFAQs and INFOBIOGEN's DBCAT: Catalog of Biological Databases were added.
September 29, 1997
Two new metapathway maps for Benzene, Toluene, Ethylbenzene and Xylene (BTEX) compounds were added, one for aerobic and one for anaerobic metabolism. Users have asked for more information on microorganisms. We are finally able to meet that need. Search links have been added to microbial names, whenever genus and species are known, in the Microorganism Index and in pathway maps. The World Data Center for Microorganisms (WDCM)'s Hunting for Microbial Information for Bacteria search engine was used. Each search produces combined results from searches of the American Type Culture Collection (ATCC) Bacteria Database, the National Center for Biotechnology Information (NCBI) Taxonomy Database and the Belgian Co-ordinated Collections of Micro-organisms (BCCM) Bacteria Database. Searches may be slow. On our Useful Internet Resources page, the link to the University of Utah Material Safety Data Sheet database was updated. A Summer, 1997 group picture was added to the Developer's Photo Gallery.
September 5, 1997
Three new pathways were added, for the biodegradation of 2-aminobenzenesulfonate, methyl fluoride, and dimethyl ether. The glyphosate pathway was updated. Doug Hershberger, a new contributor, has been added to our Contributor's Page. A new search for and index of microbial names have been added. Use these to see what organisms are presently known to initiate UM-BBD pathways. Other organisms may carry out later steps and organisms yet unstudied may also initiate pathways. The UM-BBD graphic banner at the top of the home page is now a clickable graphic with links to Kyoto University's Ligand Chemical Database and to EMBL's Nucleotide Database. On the Useful Internet Resources page, links were added to the Centraalbureau voor Schimmelcultures (CBS) Bacterial Database, the World Data Center for Microorganisms Hunting for Microbial Information for Bacteria, and the Groundwater Pollution Primer from Virginia Tech.
August 18, 1997
The first graphical metapathway map was added, for C1 microbial metabolism. A metapathway map is a pathway map of pathway maps. It is an attempt to graphically organize selected UM-BBD pathways, show how they are related, and how they relate to other pathways not presently in the UM-BBD. It is included on the UM-BBD Graphical Index. Four new pathways were added, for methanogenesis, the C1 cycle, and the biodegradation of methanesulfonic acid and toluene-4-sulfonate. Other related UM-BBD pathways will be updated to link to the C1 cycle as time permits, but until then redundant links may be returned by searches for some of its reactions and compounds. Jian Ma, a new student contributor, has been added to our Contributor's Page.
August 6, 1997
The UM-BBD has a new URL. The old one will still work for the present, but the new one is shorter and eliminates the tilde (~). It is http://www.labmed.umn.edu/umbbd/index.html One new pathway was added, for the anaerobic biodegradation of tetrachloroethene. The atrazine pathway has been updated with more recent information. This latter pathway is used to demonstrate microbial biodegrative diversity. The organisms which are known to carry out each reaction of this pathway are listed. Where an organism is not listed for a reaction, the organism(s) listed for the preceding reaction(s) also carry it out. Other, yet unstudied, organisms may also carry out each reaction. This diversity is also present in most other pathways, even if not specifically shown. When they are known, organism names have been added for the inital steps of all text pathway maps. On the Useful Internet Resources page, a link was added to the National Biotechnology Information Facility.
July 25, 1997
One new pathway was added, for the biodegradation of o-xylene. The UM-BBD also contains pathways for m-xylene and p-xylene. On our Useful Internet Resources page, the link to the NCBI PubMed Bibliographic and Sequence Databases was updated.
July 10, 1997
Two new pathways were added, for the biodegradation of p-xylene and m-xylene. o-xylene is under development. Students in our Biocatalysis and Biodegradation class, which is offered completely over the Internet, have each examined from 6 to 20 of 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. The link to the Hazardous Chemical Database at the University of Akron was updated. Science, in the July 4, 1997 issue, favorably reviews the UM-BBD in the Webwatch section [Voss, D. (1997) Science 277(5322): 53]. We thank you, our users, for your help in making us a resource deserving of this honor. The review has been added to the "mentioned in passing" section on our publications page. More compounds have been added to our prototype ad hoc pathway generator. The font size used for the resulting pathways has been reduced, to reduce the overall size of the pathways. Try it and let us know what you think.
June 25, 1997
Two new pathways were added, for the anerobic degradation of phenol and for the biodegradation of 3-chloroacrylic acid. A HELP graphic which links to "Work on Enzyme Nomenclature Needs Your Help" was removed from our home page. The committee which assigns EC codes is still disbanded, but the webpage which provided further information no longer exists.
June 2, 1997
One new pathway was added, for the anerobic degradation of benzoate. The format of the 2,4-D text pathway map has been improved. A link to a prototype UM-BBD Pathway Generator was added. This prototype allows a user to select a UM-BBD compound and generate an ad hoc pathway from this compound to intermediary metabolism. It contains only a few compounds now and will undergo frequent change based on your comments. On the Useful Internet Resources page, a link was added to the American Society for Microbiology Journals and to Searchable Biology Journal Tables of Contents, the link to Material Safety Data Sheets from University of Utah was updated, and the link to the journal Biodegradation was deleted.
May 12, 1997
Two new pathways were added, for the phthalate family and dimethyl sulfoxide and the organosulfide cycle. This last pathway is our first to contain a metabolic cycle (in this case, for organosulfide). The phthalate pathway is the first to be designated a "family" pathway, since besides phthalate, it includes the closely related compounds 4-hydroxyphthalate and terephthalate. The word "family" was also added to the name of the recently updated pentachlorophenol family pathway, since from the beginning of the UM-BBD, along with pentachlorophenol, it also has included 2,4,6-trichlorophenol and 2,6-dichlorophenol. The Fall 1996 BioC 8-001 class at the University of Minnesota was added to the list of contributors. Members of this class started 26 reaction mechanism graphics. These have already begun to be added to the UM-BBD. More will be added as they are checked for accuracy and updated where necessary. Reaction mechanism graphics are listed in our Index of Graphical Pathway Maps and Reaction Mechanisms. A HELP graphic which links to Work on Enzyme Nomenclature Needs Your Help was added to our home page. The disbanding of the committee which assigns EC codes seriously inhibits linkage between and among enzyme and metabolic databases such as the UM-BBD. On the Useful Internet Resources page, a link was added to Bugs 'n Stuff: the National Center for Genome Research Microbial Genome Site, the link to DSM was replaced by a link to DSM Bacterial Nomenclature Up-To-Date, the link to Microbiology Jump Station was replaced by a link to the Virtual Library of Microbiology and Virology, and the link to Biotechnology in Waste Management was updated. The second annual survey of the UM-BBD e-mail users list has been analyzed. The response rate was 67/364 (18%) and we thank all who responded. Results and our comments on them are found on a link from our use statistics page. The script behind the scrollable list of pathways on our home page has been improved. Users may notice faster processing of their pathway selections.
April 25, 1997
One new pathway was added, for the anerobic biodegradation of toluene. Reaction substrates and products were added to the EC Code Index to distinquish multiple reactions of the same enzyme. Reaction substrates and products will also be returned when a search for an EC code returns more than one hit. On the Useful Internet Resources page, links to BIOREP: Biotechnology Projects in Europe, NIST Chemistry WebBook, and In Situ Microbial Filters at the Lawrence Livermore National Laboratory were added and links to OSHA Chemical Sampling Information and the World Center for Microorganisms were updated.
April 11, 1997
Two new pathways were added, for the aerobic biodegradation of ethylbenzene and of dibenzothiophene. These are distinct from the UM-BBD anerobic ethylbenzene and dibenzothiophene desulfurization pathways. The pentachlorophenol pathway was updated based on new information. A reaction mechanism graphic was added to the dichloromethane dehalogenase reaction page. An Index of Graphical Pathway Maps and Reaction Mechanisms was developed and linked to the general Index of Compounds, Reactions and Pathways. Stephen Stephens was added to our contributors page and Alfred Spormann, Stanford University, was added to our International Scientific Advisory Board. A section on "How Accurate is UM-BBD Information?" was added to the About the UM-BBD page. On the Useful Internet Resources page, links to Sigma Chemical Company and Conferences - Environment were updated, a link to HinCyc: H. Influenzae Genes and Metabolism was added, and the link to Maxygen Bioremediation Page was deleted.
March 17, 1997
Two new pathways, for the biodegradation of acrylonitrile and the anerobic biodegradation of ethylbenzene, were added. On the Useful Internet Resources page, the link to OSHA Computerized Information Service was updated and a link was added to TOXTALK from the Canadian Network of Toxicology Centers.
February 10, 1997
One new pathway, for the biodegradation of dichloromethane, was added. The 1996 What's New entries were archived. The UM-BBD home page list of pathways is now scrollable. The "name contains" search on the search page now includes the Boolean operators AND, OR, and AND NOT, and an instruction page on their use.
January 27, 1997
Two new pathways, for the biodegradation of nitrobenzene and styrene, were added. Vanillin and vanillate were added to the dichlorobenzoate pathway map. On the Useful Internet Resources page, the links to Klotho and GenBank were updated and a link to Molecular Models in .pdb format from the Chemistry Department at Okanagan University College, Kelowna, British Columbia, Canada, was added. Andrea Marconi was added to our Contributors Page.
December 30, 1997 Lynda Ellis
Copyright (C) 1997, University of Minnesota. All rights reserved. http://www.labmed.umn.edu/umbbd/whatsnew/whatsnew97.html