What's New in the UM-BBD?

November 10, 2010
A pathway for syringate, an intermediate metabolite of lignin, (US), (CH), or (UK), was added, and the pathway for vanillin, (US), (CH), or (UK), was updated. In the UM Pathway Prediction System (UM-PPS), a non-exhaustive list of environmental reactions that the UM-PPS does not predict has been added. On the Links page, a link was updated for the DOE Office of Biological and Environmental Research, and a link was deleted for the Klotho database.

September 10, 2010
A pathway for phorate, a systemic insecticide, (US), (CH), or (UK), was added, and the pathway for parathion, (US), (CH), or (UK), has been updated. As each new pathway is added to the UM-BBD, interactions with existing pathways increase, leading to increasing numbers of "to the aaaa pathway" and "from the aaaa pathway" links. The start and end points of these pathways are arbitrary. Thus it is increasingly important for users to view pathways in a way that crosses these arbitrary borders. This was first offered to users as a "Generate a pathway starting from this reaction" function on each reaction page. This function has now been updated. The link to "Generate a Pathway" has been renamed "Display a Pathway" and now displays in graphical form a pathway of all UM-BBD reactions starting from the chosen reaction. For example, see the displayed pathway for the glyphosate dehydrogenase reaction. A help page for displayed pathways is available. On the Links page, a link was added for the KEGG PathPred server for biodegradation and biosynthesis pathway prediction, and a link was deleted for the BDP Server at the National Center for Biotechnology in Spain.

August 6, 2010
The pathway for benzoate, (US), (CH), or (UK), has been updated. UM-BBD ChemAxon applets (MarvinSketch used in UM-BBD structure searching and UM-PPS structure entry, and MarvinView used in UM-PPS results display) have been updated to version 5.3.4. These new applets require (free) Java 6 installed on user's computers. Users who have problems loading these applets should update their Java version. The Pathway Prediction System (UM-PPS) has been updated with version 2.0 software. This update, over one year in development, has undergone extensive beta testing by UM-BBD users representing many different user groups. New features include generation of multi-step predictions, visualization of predictions as directed acyclic graphs, removal of duplicate products, and grouping of co-products. A zoom feature permits easier viewing and printing of the predictions. UM-PPS version 2.0 is presently only available at the US site. The original version remains available at the Swiss UM_PPS site. On the Links page, a link has been updated for search of National Academy Press.

July 2, 2010
A pathway for 3-(4-sulfophenyl)butyrate, a model biodegradation product for linear alkylbenzenesulfonates, (US), (CH), or (UK), was added, and the pathways for azulam, (US), (CH), or (UK), and 4-carboxy-4'-sulfoazobenzene, (US), (CH), or (UK), were updated. On the Links page, a link has been updated for the Agency for Toxic Substances and Disease Registry (ATSDR) ToxFAQs.

June 2, 2010
A pathway for nitrofen, a pre- or post-emergence contact herbicide, (US), (CH), or (UK), was added, and the pathway for chlorobenzene, (US), (CH), or (UK), was updated. As shown by the above web links, UM-BBD now has a new mirror. It is hosted by ETH Zurich, in Switzerland. It mirrors not only the UM-BBD, but also its Biochemical Periodic Tables, and its Pathway Prediction System. Now there is redundancy for all UM-BBD resources. On the Links page, a link has been removed for the E. coli Index at the University of Birmingham, UK.

April 22, 2010
A pathway for cinnamic acid, produced in plants in stressful conditions and also a specialty chemical, (US) or (UK), was added. Version 2.0 of the Pathway Prediction System will undergo beta testing in May. Applications for beta testers are being accepted until Friday, April 23. Applicants will be informed if they have been chosen on or before Wednesday, April 28.

March 29, 2010
A pathway for desulfurization of benzothiophene, an organic sulfur compound found in petroleum, (US) or (UK), was added. A new publication is available: Wicker J, Fenner K, Ellis L, Wackett L, Kramer S (2010) Predicting Biodegradation Products and Pathways: A Hybrid Knowledge-Based and Machine Learning Based Approach. Bioinformatics. 2010 Mar 15;26(6):814-21. The full text of this paper is linked to on the publications page.

February 23, 2010
A pathway for 1,4-dioxane, a commercial dehydrating agent and polar solvent, (US) or (UK), was added. This pathway was started by a student in the 2009 Biocatalysis and Biodegradation class. On the Links page, a link was removed for Bioremediation Research Abstracts at the Hazardous Substances Research Centers.

January 13, 2010
A pathway for N-oleoyl-N-methyltaurine, a commercial amphoteric surfactant, (US) or (UK), was added, and the pathways for aerobic TNT, (US) or (UK), p-xylene, (US) or (UK), and naphthalene, (US) or (UK), were updated. The N-oleoyl-N-methyltaurine was started by a student in the 2009 Biocatalysis and Biodegradation class. A new publication is available: Gao J, Ellis, L.B.M., and Wackett, L.P. (2010) "The University of Minnesota Biocatalysis/ Biodegradation Database: improving public access" Nucleic Acids Research 38: D488-D491. The full text of this paper is linked to on the UM-BBD home page and publications page. Cite the database using this paper or its successors. The What's New page restarts; 2009 activities have been archived.

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