Ecology Department

Ecology Department Publications 2007

 

  1. Ajo-Franklin, J. B., J. T. Geller, and J. M. Harris. 2007. Ultrasonic properties of granular media saturated with DNAPL/water mixtures. Geophysical Research Letters 34:5.
  2. Alkhalfioui, F., M. Renard, W. H. Vensel, J. Wong, C. K. Tanaka, W. J. Hurkman, B. B. Buchanan, F. Montrichard, F. Alkhalfioui, M. Renard, W. H. Vensel, J. Wong, C. K. Tanaka, W. J. Hurkman, B. B. Buchanan, and F. Montrichard. 2007. Thioredoxin-linked proteins are reduced during germination of Medicago truncatula seeds. Plant Physiology 144:1559-1579.
  3. Amos, B. K., Y. Sung, K. E. Fletcher, T. J. Gentry, W. M. Wu, C. S. Criddle, J. Zhou, F. E. Loffler, B. K. Amos, Y. Sung, K. E. Fletcher, T. J. Gentry, W.-M. Wu, C. S. Criddle, J. Zhou, and F. E. Loeffler. 2007. Detection and quantification of Geobacter lovleyi strain SZ: Implications for Bioremediation at tetrachloroethene- and uranium-impacted sites. Applied and Environmental Microbiology 73:6898-6904.
  4. Andreeva, I. S., N. I. Pechurkina, O. V. Morozova, E. I. Ryabchikova, S. I. Belikov, L. I. Puchkova, E. K. Emel'yanova, T. Torok, and V. E. Repin. 2007. The new eubacterium Roseomonas baikalica sp nov isolated from core samples collected by deep-hole drilling of the bottom of Lake Baikal. Microbiology 76:487-493.
  5. Bender, K. S., H. C. B. Yen, C. L. Hemme, Z. Yang, Z. He, Q. He, J. Zhou, K. H. Huang, E. J. Alm, T. C. Hazen, A. P. Arkin, and J. D. Wall. 2007. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibfio vulgatis hildenborough. Applied and Environmental Microbiology 73:5389-5400.
  6. Bozhkov, P., C. Jansson, P. Bozhkov, and C. Jansson. 2007. Autophagy and cell-death proteases in plants - Two wheels of a funeral cart. Autophagy 3:136-138.
  7. Bretschger, O., A. Obraztsova, C. A. Sturm, I. S. Chang, Y. A. Gorby, S. B. Reed, D. E. Culley, C. L. Reardon, S. Barua, M. F. Romine, J. Zhou, A. S. Beliaev, R. Bouhenni, D. Saffarini, F. Mansfeld, B. H. Kim, J. K. Fredrickson, K. H. Nealson, O. Bretschger, A. Obraztsova, C. A. Sturm, I. S. Chang, Y. A. Gorby, S. B. Reed, D. E. Culley, C. L. Reardon, S. Barua, M. F. Romine, J. Zhou, A. S. Beliaev, R. Bouhenni, D. Saffarini, F. Mansfeld, B.-H. Kim, J. K. Fredrickson, and K. H. Nealson. 2007. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Applied and Environmental Microbiology 73:7003-7012.
  8. Brodie, E. L., T. Z. DeSantis, J. P. M. Parker, I. X. Zubietta, Y. M. Piceno, and G. L. Andersen. 2007. Urban aerosols harbor diverse and dynamic bacterial populations. Proceedings of the National Academy of Sciences of the United States of America 104:299-304.
  9. Buchanan, B. B., and B. B. Buchanan. 2007. Thioredoxin: an unexpected meeting place. Photosynthesis Research 92:145-148.
  10. Buchanan, B. B., R. Douce, H. K. Lichtenthaler, B. B. Buchanan, R. Douce, and H. K. Lichtenthaler. 2007. Andrew A. Benson. Photosynthesis Research 92:143-144.
  11. Buchanan, B. B., O. L. Frick, B. B. Buchanan, and O. L. Frick. 2007. Thioredoxin and food allergy. Journal of Allergy and Clinical Immunology 119:513-514.
  12. Caffrey, S. A., H. S. Park, J. K. Voordouw, Z. He, J. Zhou, G. Voordouw, S. A. Caffrey, H.-S. Park, J. K. Voordouw, Z. He, J. Zhou, and G. Voordouw. 2007. Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology 189:6159-6167.
  13. Clark, A. G., M. B. Eisen, D. R. Smith, C. M. Bergman, B. Oliver, T. A. Markow, T. C. Kaufman, M. Kellis, W. Gelbart, V. N. Iyer, D. A. Pollard, T. B. Sackton, A. M. Larracuente, N. D. Singh, J. P. Abad, D. N. Abt, B. Adryan, M. Aguade, H. Akashi, W. W. Anderson, C. F. Aquadro, D. H. Ardell, R. Arguello, C. G. Artieri, D. A. Barbash, D. Barker, P. Barsanti, P. Batterham, S. Batzoglou, D. Begun, A. Bhutkar, E. Blanco, S. A. Bosak, R. K. Bradley, A. D. Brand, M. R. Brent, A. N. Brooks, R. H. Brown, R. K. Butlin, C. Caggese, B. R. Calvi, A. B. de Carvalho, A. Caspi, S. Castrezana, S. E. Celniker, J. L. Chang, C. Chapple, S. Chatterji, A. Chinwalla, A. Civetta, S. W. Clifton, J. M. Comeron, J. C. Costello, J. A. Coyne, J. Daub, R. G. David, A. L. Delcher, K. Delehaunty, C. B. Do, H. Ebling, K. Edwards, T. Eickbush, J. D. Evans, A. Filipski, S. Findeiss, E. Freyhult, L. Fulton, R. Fulton, A. C. L. Garcia, A. Gardiner, D. A. Garfield, B. E. Garvin, G. Gibson, D. Gilbert, S. Gnerre, J. Godfrey, R. Good, V. Gotea, B. Gravely, A. J. Greenberg, S. Griffiths-Jones, S. Gross, R. Guigo, E. A. Gustafson, W. Haerty, M. W. Hahn, D. L. Halligan, A. L. Halpern, G. M. Halter, M. V. Han, A. Heger, L. Hillier, A. S. Hinrichs, I. Holmes, R. A. Hoskins, M. J. Hubisz, D. Hultmark, M. A. Huntley, D. B. Jaffe, S. Jagadeeshan, et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.
  14. Curley, C. M., E. L. Brodie, M. G. Lechner, A. H. Purcell, and C. Montllor Curley. 2007. Exploration for facultative endosymbionts of glassy-winged sharpshooter (Hemiptera : Cicadellidae). Annals of the Entomological Society of America 100:345-349.
  15. Dalevi, D., T. Z. DeSantis, J. Fredslund, G. L. Andersen, V. M. Markowitz, and P. Hugenholtz. 2007. Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. Bmc Bioinformatics 8.
  16. DeAngelis, K. M., M. K. Firestone, and S. E. Lindow. 2007. Sensitive whole-cell biosensor suitable for detecting a variety of N-acyl homoserine lactones in intact rhizosphere microbial communities. Applied and Environmental Microbiology 73:3724-3727.
  17. DeSantis, T. Z., E. L. Brodie, J. P. Moberg, I. X. Zubieta, Y. M. Piceno, and G. L. Andersen. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial Ecology 53:371-383.
  18. Dicksved, J., H. Floistrup, A. Bergstrom, M. Rosenquist, G. Pershagen, A. Scheynius, S. Roos, J. S. Alm, L. Engstrand, C. Braun-Fahrlander, E. von Mutius, J. K. Jansson, J. Dicksved, H. Floistrup, A. Bergstrom, M. Rosenquist, G. Pershagen, A. Scheynius, S. Roos, J. S. Alm, L. Engstrand, C. Braun-Fahrlander, E. von Mutius, and J. K. Jansson. 2007. Molecular fingerprinting of the fecal microbiota of children raised according to different lifestyles. Applied and Environmental Microbiology 73:2284-2289.
  19. Dong, M., H. Liu, S. Allen, S. Hall, S. Fisher, T. Hazen, J. Geller, M. Singer, L. Yang, J. Jin, M. Biggin, and H. E. Witkowska. 2007. Methodological refinements in iTRAQ reagent-based" tagless" strategy of identification and purification of soluble protein complexes in bacteria. Molecular & Cellular Proteomics 6:23-23.
  20. Flanagan, J. L., E. L. Brodie, L. Weng, S. V. Lynch, O. Garcia, R. Brown, P. Hugenholtz, T. Z. DeSantis, G. L. Andersen, J. P. Wiener-Kronish, and J. Bristow. 2007. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology 45:1954-1962.
  21. Fu, A., Z. Y. He, H. S. Cho, A. Lima, B. B. Buchanan, S. Luan, A. Fu, Z. He, H. S. Cho, A. Lima, B. B. Buchanan, and S. Luan. 2007. A chloroplast cyclophilin and maintenance of functions in the assembly photosystem II in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 104:15947-15952.
  22. Garczarek, F., M. Dong, D. Typke, H. E. Witkowska, T. C. Hazen, E. Nogales, M. D. Biggin, and R. M. Glaeser. 2007. Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris. Journal of Structural Biology 159:9-18.
  23. Garten, C. T., S. Kang, D. J. Brice, C. W. Schadt, J. Zhou, C. T. Garten, Jr., S. Kang, D. J. Brice, C. W. Schadt, and J. Zhou. 2007. Variability in soil properties at different spatial scales (1 m-1 km) in a deciduous forest ecosystem. Soil Biology & Biochemistry 39:2621-2627.
  24. Hajheidari, M., A. Eivazi, B. B. Buchanan, J. H. Wong, I. Majidi, G. H. Salekdeh, M. Hajheidari, A. Eivazi, B. B. Buchanan, J. H. Wong, I. Majidi, and G. H. Salekdeh. 2007. Proteomics uncovers a role for redox in drought tolerance in wheat. Journal of Proteome Research 6:1451-1460.
  25. He, J. Z., V. F. Holmes, P. K. H. Lee, and L. Alvarez-Cohen. 2007. Influence of vitamin B-12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Applied and Environmental Microbiology 73:2847-2853.
  26. He, Z. L., T. J. Gentry, C. W. Schadt, L. Y. Wu, J. Liebich, S. C. Chong, Z. J. Huang, W. M. Wu, B. H. Gu, P. Jardine, C. Criddle, J. Zhou, Z. He, T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, Z. Huang, W. Wu, B. Gu, P. Jardine, C. Criddle, and J. Zhou. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. Isme Journal 1:67-77.
  27. Hillson, N. J., P. Hu, G. L. Andersen, and L. Shapiro. 2007. Caulobacter crescentus as a whole-cell uranium biosensor. Applied and Environmental Microbiology 73:7615-7621.
  28. Hjort, K., A. Lembke, A. Speksnijder, K. Smalla, J. K. Jansson, K. Hjort, A. Lembke, A. Speksnijder, K. Smalla, and J. K. Jansson. 2007. Community structure of actively growing bacterial populations in plant pathogen suppressive soil. Microbial Ecology 53:399-413.
  29. Jernberg, C., S. Lofmark, C. Edlund, and J. K. Jansson. 2007. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. Isme Journal 1:56-66.
  30. Lee, P. K. H., M. E. Conrad, and L. Alvarez-Cohen. 2007. Stable carbon isotope fractionation of chloroethenes by dehalorespiring isolates. Environmental Science & Technology 41:4277-4285.
  31. Lee, S. C., W. Z. Lan, B. G. Kim, L. G. Li, Y. H. Cheong, G. K. Pandey, G. H. Lu, B. B. Buchanan, S. Luan, S. C. Lee, W.-Z. Lan, B.-G. Kim, L. Li, Y. H. Cheong, G. K. Pandey, G. Lu, B. B. Buchanan, and S. Luan. 2007. A protein phosphorylation/dephosphorylation network regulates a plant potassium channel. Proceedings of the National Academy of Sciences of the United States of America 104:15959-15964.
  32. Letain, T. E., S. R. Kane, T. C. Legler, E. P. Salazar, P. G. Agron, and H. R. Beller. 2007. Development of a genetic system for the chemolithoautotrophic bacterium Thiobacillus denitrificans. Applied and Environmental Microbiology 73:3265-3271.
  33. Luo, F., Y. Yang, J. Zhong, H. Gao, L. Khan, D. K. Thompson, J. Zhou, F. Luo, Y. Yang, J. Zhong, H. Gao, L. Khan, D. K. Thompson, and J. Zhou. 2007. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. Bmc Bioinformatics 8:17.
  34. Lynch, S. V., L. Dixon, M. R. Benoit, E. L. Brodie, M. Keyhan, P. Hu, D. F. Ackerley, G. L. Andersen, and A. Matin. 2007. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrobial Agents and Chemotherapy 51:3650-3658.
  35. MacLean, L. C. W., T. J. Pray, T. C. Onstott, E. L. Brodie, T. C. Hazen, and G. Southam. 2007. Mineralogical, chemical and biological characterization of an anaerobic biofilm collected from a borehole in a deep gold mine in South Africa. Geomicrobiology Journal 24:491-504.
  36. Mahendra, S., C. J. Petzold, E. E. Baidoo, J. D. Keasling, and L. Alvarez-Cohen. 2007. Identification of the intermediates of in vivo oxidation of 1,4-dioxane by monooxygenase-containing bacteria. Environmental Science & Technology 41:7330-7336.
  37. Marin-Spiotta, E., R. Ostertag, and W. L. Silver. 2007. Long-term patterns in tropical reforestation: Plant community composition and aboveground biomass accumulation. Ecological Applications 17:828-839.
  38. McGrath, P. T., H. Lee, L. Zhang, A. A. Iniesta, A. K. Hottes, M. H. Tan, N. J. Hillson, P. Hu, L. Shapiro, H. H. McAdams, P. T. McGrath, H. Lee, L. Zhang, A. A. Iniesta, A. K. Hottes, M. H. Tan, N. J. Hillson, P. Hu, L. Shapiro, and H. H. McAdams. 2007. High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nature Biotechnology 25:584-592.
  39. Moissl, C., S. Osman, M. T. La Duc, A. Dekas, E. Brodie, T. DeSantis, K. Venkateswaran, C. Moissl, S. Osman, M. T. La Duc, A. Dekas, E. Brodie, T. DeSantis, and K. Venkateswaran. 2007. Molecular bacterial community analysis of clean rooms where spacecraft are assembled. FEMS Microbiology Ecology 61:509-521.
  40. Mukhopadhyay, A., A. M. Redding, M. P. Joachimiak, A. P. Arkin, S. E. Borglin, P. S. Dehal, R. Chakraborty, J. T. Geller, T. C. Hazen, Q. He, D. C. Joyner, V. J. J. Martin, J. D. Wall, Z. K. Yang, J. Zhou, and J. D. Keasling. 2007. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgatis Hildenborough. Journal of Bacteriology 189:5996-6010.
  41. Oliver, M. J., D. Petrov, D. Ackerly, P. Falkowski, O. M. Schofield, M. J. Oliver, D. Petrov, D. Ackerly, P. Falkowski, and O. M. Schofield. 2007. The mode and tempo of genome size evolution in eukaryotes. Genome Research 17:594-601.
  42. Parton, W., W. L. Silver, I. C. Burke, L. Grassens, M. E. Harmon, W. S. Currie, J. Y. King, E. C. Adair, L. A. Brandt, S. C. Hart, and B. Fasth. 2007. Global-scale similarities in nitrogen release patterns during long-term decomposition. Science 315:361-364.
  43. Pollock, J., K. A. Weber, J. Lack, L. A. Achenbach, M. R. Mormile, and J. D. Coates. 2007. Alkaline iron(III) reduction by a novel alkaliphilic, halotolerant, Bacillus sp isolated from salt flat sediments of Soap Lake. Applied Microbiology and Biotechnology 77:927-934.
  44. Prosser, J. I., B. J. M. Bohannan, T. P. Curtis, R. J. Ellis, M. K. Firestone, R. P. Freckleton, J. L. Green, L. E. Green, K. Killham, J. J. Lennon, A. M. Osborn, M. Solan, C. J. van der Gast, and J. P. W. Young. 2007. Essay - The role of ecological theory in microbial ecology. Nature Reviews Microbiology 5:384-392.
  45. Quinn, N. W. T. 2007. Environmental Risk and Emergency Management - Preface. Environmental Modelling & Software 22:415-415.
  46. Sharp, J. O., C. M. Sales, J. C. LeBlanc, J. Liu, T. K. Wood, L. D. Eltis, W. W. Mohn, and L. Alvarez-Cohen. 2007. An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp strain RHA1. Applied and Environmental Microbiology 73:6930-6938.
  47. Steger, K., A. M. Sjogren, A. Jarvis, J. K. Jansson, and I. Sundh. 2007. Development of compost maturity and Actinobacteria populations during full-scale composting of organic household waste. Journal of Applied Microbiology 103:487-498.
  48. Stolyar, S., Q. He, M. P. Joachimiak, Z. L. He, Z. K. Yang, S. E. Borglin, D. C. Joyner, K. Huang, E. Alm, T. C. Hazen, J. Z. Zhou, J. D. Wall, A. P. Arkin, and D. A. Stahl. 2007. Response of Desulfovibrio vulgaris to alkaline stress. Journal of Bacteriology 189:8944-8952.
  49. Sun, C. X., K. Ridderstrale, A. S. Hoglund, L. G. Larsson, C. Jansson, C. Sun, K. Ridderstrale, A.-S. Hoglund, L.-G. Larsson, and C. Jansson. 2007. Sweet delivery - sugar translocators as ports of entry for antisense oligodeoxynucleotides in plant cells. Plant Journal 52:1192-1198.
  50. Tang, Y., F. Pingitore, A. Mukhopadhyay, R. Phan, T. C. Hazen, and J. D. Keasling. 2007. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry. Journal of Bacteriology 189:940-949.
  51. Tang, Y. J. J., R. Chakraborty, H. G. Martin, J. Chu, T. C. Hazen, and J. D. Keasling. 2007. Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Applied and Environmental Microbiology 73:3859-3864.
  52. Thrash, J. C., J. I. Van Trump, K. A. Weber, E. Miller, L. A. Achenbach, and J. D. Coates. 2007. Electrochemical stimulation of microbial perchlorate reduction. Environmental Science & Technology 41:1740-1746.
  53. Unell, M., N. Kabelitz, J. K. Jansson, H. J. Heipieper, M. Unell, N. Kabelitz, J. K. Jansson, and H. J. Heipieper. 2007. Adaptation of the psychrotroph Arthrobacter chlorophenolicus A6 to growth temperature and the presence of phenols by changes in the anteiso/iso ratio of branched fatty acids. Fems Microbiology Letters 266:138-143.
  54. Yergeau, E., S. Kang, Z. He, J. Zhou, G. A. Kowalchuk, E. Yergeau, S. Kang, Z. He, J. Zhou, and G. A. Kowalchuk. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. Isme Journal 1:163-179.