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