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

© 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

Technology Development, Evaluation, and Application (TDEA) FY 1998 Progress Report Environment, Safety, and Health (ESH) Division

This progress report presents the results of 10 projects funded ($504K) in FY98 by the Technology Development, Evaluation, and Application (TDEA) Committee of the Environment, Safety, and Health Division. Nine projects are new for this year; two projects were completed in their third and final TDEA-funded year. As a result of their TDEA-funded projects, investigators have published 19 papers in professional journals, proceedings, or Los Alamos reports and presented their work at professional meetings. Supplemental funds and in-kind contributions, such as staff time, instrument use, and work space were also provided to the TDEA-funded projects by organizations external to ESH Division. Products generated from the projects funded in FY98 included a new extremity dosimeter that replaced the previously used finger-ring dosimeters, a light and easy-to-use detector to measure energy deposited by neutron interactions, and a device that will allow workers to determine the severity of a hazard

Comparison of Low-Cost 5G Electromagnetic Field Sensors.

This paper compares different low-cost sensors that can measure (5G) RF-EMF exposure. The sensors are either commercially available (off-the-shelf Software Defined Radio (SDR) Adalm Pluto) or constructed by a research institution (i.e., imec-WAVES, Ghent University and Smart Sensor Systems research group ((SR)-R-3), The Hague University of Applied Sciences). Both in-lab (GTEM cell) and in-situ measurements have been performed for this comparison. The in-lab measurements tested the linearity and sensitivity, which can then be used to calibrate the sensors. The in-situ testing confirmed that the low-cost hardware sensors and SDR can be used to assess the RF-EMF radiation. The variability between the sensors was 1.78 dB on average, with a maximum deviation of 5.26 dB. Values between 0.09 V/m and 2.44 V/m were obtained at a distance of about 50 m from the base station. These devices can be used to provide the general public and governments with temporal and spatial 5G electromagnetic field values