December 9, 1999
One pathway was added for anaerobic carbon tetrachloride. An image showing the mechanism of action of camphor 5-monooxygenase has been added to its reaction page. All mechanism (and other) UM-BBD graphics are listed on the UM-BBD Graphics Index. The UM-BBD conference web page has been removed. Biotechnology conferences are listed on the Elsevier Science BIOtech conference page. A link to it has been added to UM-BBD Useful Internet Resources. On the Useful Internet Resources page, links have been added for BRENDA: The Comprehensive Enzyme Information System and Elsevier Science BIOtech and a link has been updated for NBCI GenBank.
November 4, 1999
Two reactions and one compound were added to the 2,4,5-T pathway and one pathway was added for cyanamide. An image showing the mechanism of action of cyclohexanone 1,2-monooxygenase has been added to its reaction page. All mechanism (and other) UM-BBD graphics are listed on the UM-BBD Graphics Index. The Triazine Message Board has been removed due to very low use. If you have questions about triazines, or other UM-BBD pathways, reactions, or compounds, please first read the UM-BBD FAQs. If your question is not answered there, please send an email message to: BBDMaster@email.labmed.umn.edu. Jenny Kang was added to the UM-BBD Contributors page. On October 18, 1999, the UM-BBD was selected as SciWeb's Web Site of the Week. SciWeb is a web site designed to collate and present information and communication tools to the Life Science community. This and previous awards are shown on the Awards page. On the Useful Internet Resources page, links have been added for GenProtEC: E. coli genes and proteins at the Woods Hole Marine Biological Laboratory and Genamics JournalSeek: Molecular Biology, Biochemistry and Science Journals.
October 8, 1999
Two reactions were added to the PCP Family pathway, the atrazine pathway was updated, and one pathway was added for triethanolamine. This is another pathway developed by a student in this year's BioC/MicE 5309 class, offered completely over the Internet. This course will next be offered in Summer, 2000. A page was added which lists 42 organic functional groups found in UM-BBD compounds and links to at least one compound which contains each functional group. This page is linked to on the main UM-BBD Search page and on the UM-BBD Systematic List of Pathways. All ATCC search links on pathway maps and in the microorganism index were changed to their new format and the microorganism index was revised. It now has 258 entries. Sandra Wyman was added to the UM-BBD Contributors list. A link to the University of Minnesota Center for Biodegradation Research and Informatics was added at the bottom of the UM-BBD main menu.
September 1, 1999
One reaction was added to the fluorene pathway and one pathway was added for 1,4-dichlorobenzene. This pathway is the first developed by a student in this year's BioC/MicE 5309 class, offered completely over the Internet. Biodegradation enzymes often have great catalytic versatility. For example, the UM-BBD presently contains 7 reactions for the enzyme naphthalene 1,2-dioxygenase. But this versatile enzyme can catalyze many more; we now have a Reactions of Naphthalene 1,2-Dioxygenase page which lists 73 reactions. There is a link to this page on each of the 7 reactions the UM-BBD contains. If there are any reactions we have missed, please let us know. Jiangbi Liu and the Fall 1998 BioC 8-001 class at the University of Minnesota were added to the list of contributors. Members of this class started 33 reaction mechanism graphics. On the Useful Internet Resources page, a new section has been added on resources for Education, a link has been added to the Biodegradative Strain Database at Michigan State University, links have been updated for ChemConnect News and Research and the Hazardous Substances Research Centers, and the link to Fisher Scientific, Inc. has been deleted. There is now a web page for classes that use the UM-BBD as a required or supplemental Internet resources. It is linked to in the new Education section of the Useful Internet Resources. If you would like your class listed, please send the name of your school, the number and name of your class, your name, and, if you have a web page for your class, its URL.
August 2, 1999
One reaction was added to the nitrobenzene pathway, one reaction was added to the 2,4-dichlorobenzoate pathway, and two reactions were added to the thiocyanate pathway. With the growth in the number of pathways, a higher percentage of our time will be spent updating existing pathways rather than adding new ones. If you find changes that should be made to UM-BBD pathways, please let us know. Calling all teachers! Do you use the UM-BBD in your classes? If you do, let us know, and we'll put up a web page with the name of your school, the name of your class, your name, and, if you have a web page for your class, your URL. Do it now, and we can have the page up when school starts in September. All links to the ExPASy enzyme database on reaction pages have been changed to link to their new format NiceZyme pages. To see this, go to a reaction page which has an enzyme with a 4-digit EC code, such as the reaction from Acetylene to Ethylene which is catalyzed by nitrogenase, and click on "ExPASy". The FAQ page now answers several new questions. A search by page author has been added to the Search page. It will retrieve all compound and reaction pages authored by a specified UM-BBD contributor. Pathway statistics have been updated. We keep statistics on how many times each text pathway map is accessed and for the first seven months of this year, toluene was the winner. Check the popularity of your favorite pathway. The page stats are linked to from our main use statistics page. Our 1999 Developer Photo is now available on the UM-BBD Developer's Photo Gallery page. Students in our 1999 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 updated for Pathways and Controlling Factors in the Biodegradation of Energetic Wastes at the U.S. Army Construction Engineering Research Laboratories and Hazardous Substances for which exposure standards have been set, from the Australian National Occupational Health and Safety Commission.
June 28, 1999
One new pathway was added, for tri-n-butyltin. There are two new reviews of the UM-BBD: Fluet, Amy (1999) "Pathways to Enlightenment" HMS Beagle, Reviews In Situ, Issue 55, and Boulay, Jean-Louis (1999) "Web Alert: Biochemical Technology" Current Opinion in Biotechnology 10: 113. They appear on the Publications page. The list of microorganism entries has been updated and corrected. There are now 254 entries. On the Useful Internet Resources page, links have been updated for the Journal of Biochemistry Online, Biotechnology in Waste Management from the Australian Biotechnology Association and Biocatalysis at the Institute for Organic Chemistry, Technical University Granz, Austria.
June 10, 1999
Two new pathways were added, for arsonoacetate and organosilicone, and one reaction was added to the benzoate pathway. The organosilicone pathway contains both anerobic and aerobic reactions. We now designate such pathways as (an/aerobic). This term can be seen in our pathway lists or searched for in pathway searches. An/aerobic pathways presently include organosilicone, beta-1,2,3,4,5,6-hexachlorocyclohexane and nitrilotriacetate. The pathway narrative explains which part of the pathway is anerobic and which is aerobic. A new pathway list ordered by functional groups found in the starting compound is now available, to complement the alphabetical pathway list. There are links to both of them on our main Search page. On the Useful Internet Resources page, a link has been added for the Chemical Information Page at the National Library of Medicine and a link has been changed for the Agency for Toxic Substances and Disease Registry (ATSDR) ToxFAQs.
May 12, 1999
Two new pathways were added, for aerobic benzoate and anaerobic 2,4,6-trinitrotoluene (TNT). These two pathways complement existing pathways for anerobic benzoate and aerobic TNT. We have added the full citation for each Medine reference to each of our reaction pages. As an example, see the atrazine chlorohydrolase reaction page. BioC/MicE 5309, a course on Biocatalysis/Biodegradation offered completely over the Internet, is now open for registration. The course will start on Monday, June 7 and will run through Friday, September 17, 1999. It will be limited to no more than ten students; a few places are still available. On the Useful Internet Resources page, links have been changed for the ExPASy ENZYME Database at the University of Geneva and In Situ Bioremediation: When Does It Work? (1993) from the National Academy Press and links have been deleted for MSDS at the University of Utah, Hunting Microbial Information for Bacteria at the World Data Center for Microorganisms, Searchable Biology Journal Tables of Contents, and Pedro's List of Bio/Chemical Journals and Newsletters.
April 21, 1999
Two new pathways were added, for bromoxynil and methyl tert-butyl ether. These two pathways are the final ones completed by students in the 1998 offering of BioC/MicE 5309, Biocatalysis and Biodegradation, a course taught completely over the Internet. This course will again open for registration in May 1999 and will run from June 7 to September 17, 1999. It will again be limited to no more than 10 students. All microorganism links have been changed to ATCC or, if the organism is not found there, to DSMZ. This change was carried out on pathway maps and the microorganism index. On the Useful Internet Resources page, a link has been added for the Taxonomy Browser at the National Center for Biotechnology Information.
March 17, 1999
Three new pathways were added, for acetylene, dodecyl sulfate, and thiocyanate, and one reaction was added to the 4-carboxy-4'-sulfoazobenzene pathway. A new list can be dynamically generated of all UM-BBD compounds whose further biodegradation has not yet been determined. If there is further biodegradation for any of these compounds, please let us know. There is a link to the list on the Search page. Recent publication: Ellis, L.B.M., Hershberger, C.D., and Wackett, L.P. (1999) "The University of Minnesota Biocatalysis/Biodegradation Database: Specialized metabolism for functional genomics" Nucleic Acids Research 27: 373-376. It is linked to on the UM-BBD main menu and the publications page. Use this paper or its successors to cite the database. KEGG links were updated on all generated and static pathway maps. Kyoto (Ligand) links were updated on all reaction pages. Time to load compound and reaction pages was significantly decreased. A postdoctoral position is available working with the UM-BBD for a US citizen or permanent resident with a PhD in the life sciences and skill in object-oriented programming. For further information, contact BBDMaster@email.labmed.umn.edu. On the Useful Internet Resources page, the link has been changed for WIT, now at Argonne National Laboratories.
February 10, 1999
Three new pathways were added, for nitrilotriacetate, 2-nitropropane and dibenzo-p-dioxin. The Dibenzo-p-Dioxin Pathway is another one completed by a student in BioC/MicE 5309, Biocatalysis and Biodegradation, a course taught completely over the Internet. This course is again open for registration. Registration will close and the class will begin no later than March 1, 1999, or earlier if the limit of 10 students is reached. Chemfinder links were updated on all compound pages. On the Useful Internet Resources page, links have been changed for Chemfinder, Bacterial Nomenclature Up-to-Date and Sigma Chemical Company.
February 3, 1999
Two new pathways were added, for phenanthrene (fungal 9R,10R) and 4-carboxy-4'-sulfoazobenzene. The 9R,10R pathway, the UM-BBD's second fungal pathway, completes the third and final UM-BBD pathway devoted to this compound. BioC/MicE 5309, Biocatalysis and Biodegradation, a course taught completely over the Internet, is now open again for registration. Registration will close and the class will begin no later than March 1, 1999, or earlier if the limit of 10 students is reached. On the Useful Internet Resources page, a link has been added to The Microbial World at University of Edinburgh.
January 20, 1999
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