Applied and Environmental Microbiology Publications

Ahanotu, E.N. and D.G. Ahearn. 2002. Association of Pseudomonas aeruginosa and Serratia marcescens with extended-wear soft contact lenses in asymptomatic paients. CLAO J. 28: 157-159.

Drago, G.K., Simmons, R.B., Price, D.L., Crow, S.A. and D.G. Ahearn. 2002. Effects of antiodor automobile air-conditioning system products on adherence of Serratia marcescens to aluminum. J. Ind. Microbiol. Biotechnol. 29: 272-375.

George, M., Ahearn, D., Pierce, G. and M. Gabriel. 2003. Interactions of Pseudomonas aeruginosa and Staphylococcus epidermidis in adhesion to a hydrogel.

Noble, J.A., Ahearn, D.G., Avery, S.V. and Sidney A. Crow, Jr. 2002. Phagocytosis affects biguanide sensitivity of Acanthamoeba spp. Antimicrob. Agents Chemother. 46: 2069-2076.

Price, D., Drago, G., Simmons, R., Crow, S. Jr. and D. Agearn. 2002. Rapid assessment of antimould efficacies of pressure-treated southern pine. J. Ind. Microbiol. Biotechnol. 29: 368-372.

Hauwaerts, D., G. Alexandre, S. K. Das, J. Vanderleyden, and I. B. Zhulin (2002) A major chemotaxis gene cluster in Azospirillum brasilense and relationships between chemotaxis operons in alpha-proteobacteria. FEMS Microbiol. Lett. 208:61-67.

Alexandre, G. and I. B. Zhulin (2003) Different evolutionary constraints on chemotaxis proteins CheW and CheY revealed by heterologous expression studies and protein sequence analysis. J. Bacteriol 185:544-522

Kotsyurbenko O.R., K.-J. Chin, M.V. Glagolev, S. Stubner, M.V. Simankova, A.N. Nozhevnikova A.N., and R. Conrad. 2004. Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian peat bog. Environ. Microbiol. 6: 1159-1173.

Glissmann, K., K.-J. Chin, P. Casper, and R. Conrad. 2005. Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: effect of temperature Microb. Ecol. 48:389-399.

Chidthaisong, A., K.-J. Chin, D. Valentine, and S.C. Tyler. 2002. A Comparison of isotope fractionation of carbon and hydrogen from paddy field rice roots and soil bacterial enrichments during CO2/H2 methanogenesis. Geochimica et Cosmochimica Acta 66:983-995

Chin, K.-J., A. Esteve-Nunez, C. Leang and D. R. Lovley. 2004. Direct correlation between rates of anaerobic respiration and levels of mRNA for key respiratory genes in Geobacter sulfurreducens. Appl. Environ. Microbiol. 70:5183-5189.

Chin, K.-J., T. Lueders, M. Friedrich, M. Klose, and R. Conrad. 2004. Archaeal community structure and pathway of methane formation on rice roots. Microb. Ecol. 47:59-67

Kemnitz, D., K.-J. Chin, P. Bodelier, and R. Conrad. 2004. Community analysis of methanogenic archaea within a riparian flooding gradient. Environ. Microbiol. 6:449-461

Wu, X.-L., Chin, K.-J., and R. Conrad. 2002. Effect of temperature stress on structure and function of the methanogenic archaeal community in a rice field soil. FEMS Microbiol. Ecol. 39:211-218

Chin, K.-J., and P.H. Janssen. 2002. Propionate formation by Opitutus terrae in pure culture and in mixed culture with a hydrogenotrophic methanogen, and implications for carbon fluxes in anoxic rice paddy soil. Appl. Environ. Microbiol. 68:2089-2092

Wu, X.-L., Chin, K.-J., and R. Conrad. 2002. Effect of temperature stress on structure and function of the methanogenic archaeal community in a rice field soil. FEMS Microbiol. Ecol. 39:211-218

Leang, C, L. A. Adams, K.-J. Chin, K. P. Nevin, B. A. Methé, J. Webster, M. L. Sharma, and D. R. Lovley. 2005. Adaptation to Disruption of Electron Transfer Pathway for Fe(III) reduction in Geobacter sulfurreducens. J. Bacteriol. 187:5918-5926

Erkel, C., D. Kemnitz, P. Ricke, M. Kube, K.-J. Chin, S. Dedysh, R. Reinhardt, R. Conrad, and W. Liesack. 2005. Retrieval of first genome data for rice cluster I methanogens by a combined approach of cultivation and molecular ecology techniques. FEMS Microbiol. Ecol. 53:187-204.

Zhang, S., R.N. Borazjani, J.C. Salamone, D.G. Ahearn, S.A. Crow, Jr., G.E. Pierce. 2005. In vitro deposition of lysozyme on etafilcon A and balafilcon A hydrogel contact lenses: Effect on adhesion and survival of Pseudomonas aeruginosa and Staphylococcus aureus. Contact Lens and Anterior Eye 28: 113-119

Mateus, C., S.A. Crow, Jr and D.G. Ahearn. 2004. Adherence of Candida albicans to silicone induces immediate enhanced tolerance to fluconazole. Antimicrobial and Chemotherapeutic Agents 48:3358-3366

Price, D. L., R. B. Simmons, S. A. Crow, Jr. and D. G. Ahearn. 2005. Mould colonization during use of preservative treated and untreated air filters, including HEPA types from hospitals. J Ind. Microbiol. Biotechnol. Submitted.

Zaidi, M.A. and S. A. Crow, Jr. 2004. Biologically active traditional medicinal herbs from Balochistan, Pakistan. J. Ethnopharmacology. in press

Zhang, S., D.G. Ahearn, C.Mateus, S.A. Crow, Jr. 2006. In vitro effects of Ag+ on planktonic and adhered cells of fluconazole-resistant and susceptible strains of Candida albicans, C. glabrata and C. krusei. Biomaterials. in press.

Fan, F., and Gadda, G. (2005) Oxygen- and Temperature-Dependent Kinetic Isotope Effects in Choline Oxidase: Correlating Reversible Hydride Transfer with Environmentally Enhanced Tunneling, J. Am. Chem. Soc. U.S.A., 127, 17954-17961.

Gadda, G. (2003) pH and Deuterium Kinetic Isotope Effects Studies on the Oxidation of Choline to Betaine-Aldehyde Catalyzed by Choline Oxidase, Biochim. Biophys. Acta 1650(1-2), 4-9.

Fan, F., Germann, M.W., and Gadda, G. (2006) Mechanistic Studies of Choline Oxidase with Betaine Aldehyde and its Isosteric Analog 3,3-Dimethylbutyraldehyde, Biochemistry, 45, 1979-1986.

Francis, K., Russell, B., and Gadda, G. (2005) Involvement of a Flavosemiquinone in the Enzymatic Oxidation of Nitroalkanes Catalyzed by 2-Nitropropane Dioxygenase, J. Biol. Chem., 280, 5195-5204.

Gadda, G., and McAllister-Wilkins, E.E. (2003) Cloning, Expression, and Purification of Choline Dehydrogenase From the Moderate Halophile Halomonas elongata, Appl. Environ. Microbiol. 69(4), 2126-2132.

Ghanem, M., and Gadda, G. (2006) Effects of Reversing the Protein Positive Charge in Proximity of the N(1) Flavin Locus of Choline Oxidase, Biochemistry, 45, 3437-3447.

Gadda, G., Fan, F., and Hoang, J.V. (2006) On the Contribution of the Positively Charged Headgroup of Choline to Substrate Binding and Catalysis in the Reaction Catalyzed by Choline Oxidase, Arch. Biochem. Biophys., web released May 3, 2006.

Fan, F., and Gadda, G. (2005) On the Catalytic Mechanism of Choline Oxidase, J. Am. Chem. Soc. U.S.A., 127(7), 2067-2074.

Fan, F., Ghanem, M., and Gadda, G. (2004) Cloning, Sequence Analysis, and Purification of Choline Oxidase from Arthrobacter globiformis: a Bacterial Enzyme Involved in Osmotic Stress Tolerance, Arch. Biochem. Biophys. 421, 149-158.

Ghanem, M., and Gadda, G. (2005) On the Catalytic Role of the Conserved Active Site His466 of Choline Oxidase, Biochemistry, 44, 893-904.

Daubner,S.C., Gadda,G., Valley,M.P., and Fitzpatrick,P.F. (2002) Cloning of nitroalkane oxidase from Fusarium oxysporum identifies a new member of the acyl-CoA dehydrogenase superfamily. Proceedings of the National Academy of Sciences , 99, 2702-2707.

Gadda, G. (2003) Kinetic Mechanism of Choline Oxidase from Arthrobacter globiformis, Biochim. Biophys. Acta 1646(1-2), 112-118.

Gadda, G., Powell, N.L.N., and Menon, P. (2004) The Trimethylammonium Headgroup of Choline is a Major Determinant for Substrate Binding and Specificity in Choline Oxidase, Arch. Biochem. Biophys., 430, 264-273

Ghanem, M., Fan, F., Francis, K., and Gadda, G. (2003) Spectroscopic and Kinetic Properties of Recombinant Choline Oxidase from Arthrobacter globiformis, Biochemistry 42, 15179-15188.

Niu, C., J. Graves, F. Mokuolu, S. E. Gilbert and E. S. Gilbert. 2005. Enhanced swarming of bacteria on agar plates containing the surfactant Tween 80. Journal of Microbiological Methods. J Microbiol Methods 62:129-32.

Chang, I., E. S. Gilbert, N. Eliashberg, and J. D. Keasling. 2003. A three-dimensional, stochastic simulation of biofilm growth and transport-related factors that affect structure. Microbiology. 149:2859-2871.

Gilbert, E., and J. Keasling 2004. Bench scale flow cell for nondestructive imaging of biofilms, p. 109-118. In J. Spencer, and A. Ragout de Spencer (eds), Environmental Microbiology Methods and Protocols. Humana Press, Totowa, NJ.

Niu, C., and E. S. Gilbert. 2004. A colorimetric method for identifying plant essential oil components that affect biofilm formation and structure. Appl Environ Microbiol 70:6951-6956.

Niu, C., S. Afre and E. S. Gilbert (2006). "Subinhibitory concentrations of cinnamaldehyde interfere with quorum sensing." Lett Appl Microbiol 43(5): 489-94.

Gilbert, E. S., A. W. Walker, and J. D. Keasling 2003. A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion. Appl Microbiol Biotechnol. 61:77-81.

O'Connell, H. A., C. Niu and E. S. Gilbert (2007). "Enhanced high copy number plasmid maintenance and heterologous protein production in an Escherichia coli biofilm." Biotechnol Bioeng. 97(3): 439- 446.

Belkasim, S., J. Gu, G. Derado, E. Gilbert, H. O'Connell 2004. Multi resolution image segmentation for quantifying spatial heterogeneity in mixed population biofilms, p. 197-203. The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '04), Las Vegas, NV, USA.

Belkasim, S., G. Derado, E. Gilbert, H. O'Connell. 2004. "The effectiveness of multi resolution image segmentation for measuring spatial heterogeneity in mixed population biofilms", accepted for publication on the proceedings of the 47th IEEE International Midwest Symposium on Circuits and Systems, July 25-28, 2004, Hiroshima, Japan.

O'Connell, H. A., G. S. Kottkamp, J. L. Eppelbaum, B. A. Stubblefield, S. E. Gilbert and E. S. Gilbert (2006). "Influences of biofilm structure and antibiotic resistance mechanisms on indirect pathogenicity in a model polymicrobial biofilm." Appl Environ Microbiol 72(7): 5013-9.

Lopanik, N., N. Lindquist, and N. Targett. 2004. Potent cytotoxins produced by a microbial symbiont protect host larvae from predation. Oecologia 139:131-139.

Lopanik, N. B., N. M. Targett, and N. Lindquist. 2006. Ontogeny of a symbiont-produced chemical defense in Bugula neritina (Bryozoa). Mar. Ecol. Prog. Ser. 327:183-191.

Lopanik, N. B., N. M. Targett, and N. Lindquist. 2006. Isolation of two polyketide synthase gene fragments from the uncultured microbial symbiont of the marine bryozoan Bugula neritina. Appl. Environ. Microbiol. 72:7941-7944.