College of Engineering
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The College of Engineering at Montana State University will serve the State of Montana and the nation by fostering lifelong learning, integrating learning and discovery, developing and sharing technical expertise, and empowering students to be tomorrow's leaders.
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Item Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas sp. Strain JS666(American Society for Microbiology, 2009-06) Jennings, Laura; Chartrand, Michelle; Lacrampe-Couloume, Georges; Sherwood Lollar, Barbara; Spain, Jim C.; Gossett, James M.Polaromonas sp. strain JS666 is the only bacterial isolate capable of using cis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. The primary cellular responses of JS666 to growth on cDCE were explored using proteomics and transcriptomics to identify the genes upregulated by cDCE. Two-dimensional gel electrophoresis revealed upregulation of genes annotated as encoding glutathione S-transferase, cyclohexanone monooxygenase, and haloacid dehalogenase. DNA microarray experiments confirmed the proteomics findings that the genes indicated above were among the most highly upregulated by cDCE. The upregulation of genes with antioxidant functions and the inhibition of cDCE degradation by elevated oxygen levels suggest that cDCE induces an oxidative stress response. Furthermore, the upregulation of a predicted ABC transporter and two sodium/solute symporters suggests that transport is important in cDCE degradation. The omics data were integrated with data from compound-specific isotope analysis (CSIA) and biochemical experiments to develop a hypothesis for cDCE degradation pathways in JS666. The CSIA results indicate that the measured isotope enrichment factors for aerobic cDCE degradation ranged from −17.4 to −22.4‰. Evidence suggests that cDCE degradation via monooxygenase-catalyzed epoxidation (C═C cleavage) may be only a minor degradation pathway under the conditions of these experiments and that the major degradation pathway involves carbon-chloride cleavage as the initial step, a novel mechanism. The results provide a significant step toward elucidation of cDCE degradation pathways and enhanced understanding of cDCE degradation in JS666.Item Cytoprotective Nrf2 pathway is induced in chronically txnrd 1-deficient hepatocytes(2009-07) Suvorova, Elena S.; Lucas, Olivier; Weisend, Carla M.; Rollins, MaryClare F.; Merrill, Gary F.; Capecchi, Mario R.; Schmidt, Edward E."Background Metabolically active cells require robust mechanisms to combat oxidative stress. The cytoplasmic thioredoxin reductase/thioredoxin (Txnrd1/Txn1) system maintains reduced protein dithiols and provides electrons to some cellular reductases, including peroxiredoxins. Principal Findings Here we generated mice in which the txnrd1 gene, encoding Txnrd1, was specifically disrupted in all parenchymal hepatocytes. Txnrd1-deficient livers exhibited a transcriptome response in which 56 mRNAs were induced and 12 were repressed. Based on the global hybridization profile, this represented only 0.3% of the liver transcriptome. Since most liver mRNAs were unaffected, compensatory responses were evidently effective. Nuclear pre-mRNA levels indicated the response was transcriptional. Twenty-one of the induced genes contained known antioxidant response elements (AREs), which are binding sites for the oxidative and chemical stress-induced transcription factor Nrf2. Txnrd1-deficient livers showed increased accumulation of nuclear Nrf2 protein and chromatin immunoprecipitation on the endogenous nqo1 and aox1 promoters in fibroblasts indicated that Txnrd1 ablation triggered in vivo assembly of Nrf2 on each. Conclusions Chronic deletion of Txnrd1 results in induction of the Nrf2 pathway, which contributes to an effective compensatory response."Item Water Vapor Profiling using a Widely Tunable, Amplified Diode Laser Based Differential Absorption Lidar (DIAL)(2009-04) Nehrir, Amin R.; Repasky, Kevin S.; Carlsten, John L.; Obland, Michael D.; Shaw, Joseph A.A differential absorption lidar (DIAL) instrument for automated profiling of water vapor in the lower troposphere has been designed, tested, and is in routine operation at Montana State University. The laser transmitter for the DIAL instrument uses a widely tunable external cavity diode laser (ECDL) to injection seed two cascaded semiconductor optical amplifiers (SOAs) to produce a laser transmitter that accesses the 824–841-nm spectral range. The DIAL receiver utilizes a 28-cm-diameter Schmidt–Cassegrain telescope; an avalanche photodiode (APD) detector; and a narrowband optical filter to collect, discriminate, and measure the scattered light. A technique of correcting for the wavelength-dependent incident angle upon the narrowband optical filter as a function of range has been developed to allow accurate water vapor profiles to be measured down to 225 m above the surface. Data comparisons using the DIAL instrument and collocated radiosonde measurements are presented demonstrating the capabilities of the DIAL instrument.Item Detachment, surface migration, and other dynamic behavior in bacterial biofilms revealed by digital time-lapse imaging(2001) Stoodley, Paul; Hall-Stoodley, Luanne; Lappin-Scott, H. M.Item Development of a standardized antibiofilm test(2001) Zelver, NickItem Characterization of extracellular chitinolytic activity in biofilms(2001) Baty, Ace M.; Diwu, Zhenjun; Dunham, G.; Eastburn, Callie C.; Geesey, Gill G.; Goodman, Amanda E.; Suci, Peter A.; Techkarnjanaruk, SomkietItem Biofilms in the new millennium: musing from a peak in Xanadu(2000) Costerton, J. WilliamItem Microbial detachment from biofilms(2000) Moore, G. F.; Dunsmore, B. C.; Jones, S. M.; Smejkal, C. W.; Jass, J.; Stoodley, Paul; Lappin-Scott, H. M.Item Modeling biocide action against biofilms(2000-03) Stewart, Philip S.; Hamilton, Martin A.; Goldstein, B. R.; Schneider, B. T.A phenomenological model of biocide action against microbial biofilms was derived. Processes incorporated in the model include bulk flow in and out of a well-mixed reactor, transport of dissolved species into the biofilm, substrate consumption by bacterial metabolism, bacterial growth, advection of cell mass within the biofilm, cell detachment from the biofilm, cell death, and biocide concentration-dependent disinfection. Simulations were performed to analyze the general behavior of the model and to perform preliminary sensitivity analysis to identify key input parameters. The model captured several general features of antimicrobial agent action against biofilms that have been observed widely by experimenters and practitioners. These included (1) rapid disinfection followed by biofilm regrowth, (2) slower detachment than disinfection, and (3) reduced susceptibility of microorganisms in biofilms. The results support the plausibility of a mechanism of biofilm resistance in which the biocide is neutralized by reaction with biofilm constituents, leading to a reduction in the bulk biocide concentration and, more significantly, biocide concentration gradients within the biofilm. Sensitivity experiments and analyses identified which input parameters influence key response variables. Each of three response variables was sensitive to each of the five input parameters, but they were most sensitive to the initial biofilm thickness and next most sensitive to the biocide disinfection rate coefficient. Statistical regression modeling produced simple equations for approximating the response variables for situations within the range of conditions covered by the sensitivity experiment. The model should be useful as a tool for studying alternative biocide control strategies. For example, the simulations suggested that a good interval between pulses of biocide is the time to minimum thickness.Item Confocal laser microscopy on biofilms: Successes and limitations(2008-07) Pitts, Betsey; Stewart, Philip S.Imaging of bacterial biofilms with microscopes has been an essential and transformative method in biofilm research. Fluorescence microscopy can elucidate specific biofilm components and cellular activities that cannot be separated otherwise. In particular, confocal fluorescence microscopy extends that examination through the thickness of a fully hydrated, in-situ biofilm, affording the potential for 3D, non-invasive, time-lapse imaging. This article discusses some striking examples of the insight provided by confocal fluorescence microscopy into biofilm structure, composition, and heterogeneity, and will also enumerate some limitations of this imaging process.