From Biolog_Inc from mail.vresp.com Thu Sep 20 12:02:44 2007 From: Biolog_Inc from mail.vresp.com (Biolog, Inc.) Date: Thu Sep 20 14:46:43 2007 Subject: [Biofilms] PM Newsletter Message-ID: Bacillus subtilis Metabolism and Gene Regulation Studied in Two Recent Applications of Phenotype MicroArray Technology Genome-scale reconstruction of metabolic network in bacillus subtilis based on high-throughput phenotyping and gene essentiality data. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S3E5. http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/7c51f6e3de/Db=pubmed&Cmd=ShowDetailView&TermToSearch=17573341&ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum This landmark paper is the first example of a careful and thorough use of Phenotype MicroArray data to challenge and improve a whole-cell bioinformatics model of Bacilllus subtilis. Network gap analysis was used to identify 48 essential reactions missing from the genome annotation. Detailed growth rate analysis revealed incorrect modeling outcomes which were subsequently improved by adding 75 reactions. Simulation of growth phenotypes of knock-out strains were verified in 720 of 766 cases. Overall, the integrated analysis of substrate utilization and gene essentiality data led to identification of 80 required enzymes and improved the genome annotation for Bacillus subtilis. Regulatory Overlap and Functional Redundancy Among Bacillus subtilis Extracytoplasmic Function (ECF) (sigma)-Factors. Mascher T, Hachmann AB, Helmann JD. Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA. http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/9b32985aba/Db=pubmed&Cmd=ShowDetailView&TermToSearch=17675383&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The biological role of extracytoplasmic function sigma factors in Bacillus subtilis was examined in this paper. Seven genes encode these sigma factors, so the authors constructed strains with multiple gene knockouts and then used Phenotype MicroArray technology to test the phenotypes of their strains. A triple mutant in sigM, sigW, and sigX exhibited greatly increased sensitivity to detergents, polymyxin B, B-lactams, and D-cycloserine. Printable PDF http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/4897aa48fa Useful links For more information on PM technology http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/d19e32d630 For information on Biolog's Phenotype MicroArray Services http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/6d4131a8fc To view Biolog's PM publications and bibliography http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/5d951f3fdd To request sales information mailto:pmmarketing@biolog.com Register with Biolog to receive regular updates on your area of interest. http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/ba76c46c4a New Biolog Press Releases http://cts.vresp.com/c/?BiologInc./ffaa8a4ebe/cace00508f/2b3034eb83 "Forward-to-a-friend" link can be found at the bottom of the page. Brief description of PM technology Phenotype MicroArray? technology tests cellular phenotypes. Included in the tests are assays of basic cellular nutritional pathways for C, N, P, and S metabolism, osmotic and pH and sensitivity, and sensitivity to chemical agents. The most common application is to assess the phenotypic effects of mutations. A change in genotype of a cell should lead to one or more changes in phenotype. PMs allow testing of knock-out or knock-in mutants to help discern the biological changes that occur consequent to genetic changes. Another common application is phenotypic characterization of a collection of related strains. For example, it is possible to determine the phenotypic relatedness of a collection of isolates of a given species. PM analysis has been successfully implemented for a wide variety of model microbial cells including Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Pseudomonas putida, Sinorhizobium meliloti, Saccharomyces cerevisiae, Bacillus subtilis, Bacillus cereus, Shewanella oneidensis, Proteus mirabilis, and many other species. In the last year, Biolog has successfully developed universal protocols that allow us to test most species of interest. Contact us for details. Phenotype MicroArray? technology uses Biolog's OmniLog? instrument, which is also used for microbial identification. The OmniLog? automatically incubates, reads and interprets the Biolog Phenotype MicroArray MicroPlates?. It continuously processes samples but allows the user complete access at any time during a sample run. Samples can be loaded when ready and removed when complete without disturbing other samples still in-process. Inside the Reader there are 25 trays. Each tray holds 2 MicroPlates, giving the Reader a total capacity to incubate and read 50 MicroPlates. Before the user inoculates the appropriate MicroPlates, they log the MicroPlate information into the OmniLog? software. By simply following the software's instructions, the user then opens the door of the OmniLog? Reader and places each MicroPlate in the appropriate tray slot indicated by the software. Once all the MicroPlates are loaded and the door of the Reader is closed, the OmniLog? software takes over the responsibility for incubating, reading, saving, and printing the results. The OmniLog? PM System utilizes Windows-based software with an elegantly simple user interface. The status of all the samples can be observed by simply looking at the Read menu screen of the OmniLog? PM System software. All of the information for a specific MicroPlate is contained on a single line of this screen. Once the system has completed a specific MicroPlate it indicates this status with a check mark icon. A clock icon is used for those samples that are still incubating because a result has not yet been determined. The OmniLog? PM System's software is extremely flexible and can be integrated into virtually any laboratory's workflow. New MicroPlates can be entered into the Reader and MicroPlates that have already completed can be removed from the Reader at almost any time. This allows the user to either perform experiments one at a time or batch them. PM Technology and the OmniLog? instrument are ideal for a core facility or for purchase under a shared equipment grant. All content copyright Biolog, Inc. 2005. All trademarks and registered trademarks are the property of their respective companies. Use of this web site indicates that you accept the Terms and Conditions. Please see our User Privacy policy. 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