27 research outputs found

    Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

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    © The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium

    Possible Savings Achievable by Recipients of Training and Software Provided by the U.S Department of Energy’s Industrial Technologies Program

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    Through its Save Energy Now (SEN) Initiative, the U.S. Department of Energy’s (DOE’s) Industrial Technologies Program (ITP) disseminates information on energy efficient technologies and practices to U.S. industrial firms to improve the energy efficiency of their operations. Among other things, Save Energy Now conducts training sessions on a variety of energy systems that are important to industry (i.e., compressed air, steam, process heat, pumps, motors, and fans) and distributes software tools on those same topics. A recent Oak Ridge National Laboratory (ORNL) study collected information from recipients of SEN training and software regarding how much their total annual plant energy costs could be reduced by implementing the measures that they identified since receiving SEN services. Those same individuals were also queried regarding the portion of potential savings that were actually achieved. The responses revealed both similarities and differences between training and software recipients as well as substantial variation in the savings associated with the diverse energy systems addressed

    Mining Credit Card Data for Decision Support (Extended Abstract)

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    June M. Donato, Jack C. Schryver, Nancy W. Grady, Gregory C. Hinkel, Richard L. Schmoyer Jr., Michael R. Leuze Oak Ridge National Laboratory Oak Ridge, Tennessee 37831 USA For more information contact: [email protected] 1 Introduction While it is widely recognized that data can be a valuable resource for any organization, extracting information contained within the data is often a difficult problem. Attempts to obtain information from data may be limited by legacy data storage formats, lack of expert knowledge about the data, difficulty in viewing the data, or the volume of data needing to be processed. The rapidly developing field of Data Mining or Knowledge Data Discovery is a blending of Artificial Intelligence, Statistics, and HumanComputer Interaction. Sophisticated data navigation tools to obtain the information needed for decision support do not yet exist. Each data mining task typically requires a custom solution that depends upon the character and quantity of the data. A probl..
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