Berkeley Lab

2014 Publications

Jump to: Books/Book Chapters | Legacy and Synergistic External Research

  1. Beer, K. D; E. J. Wurtmann, N. Pinel and N. S. Baliga (2014). Model organisms retain an “ecological memory” of complex ecologically relevant environmental variation. Applied and Environmental Microbiology 80(6):1821-1831. Epub 2014/01/15. [doi]:10.1128/AEM.03280-13 {PMID}:24413600
  2. Brileya, K. A; L. B. Camilleri, G. M. Zane, J. D. Wall and M. W. Fields (2014). Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy. Frontiers in Microbiology 5:693. [doi]:3389/fmicb.2014.00693 {PMID}:25566209
  3. Brileya, K. A; J. M. Connolly, C. Downey, R. Gerlach and M. W. Fields (2014). Taxis toward hydrogen gas by Methanococcus maripaludis. Scientific Reports 3:3140. Epub 2013/11/06. [doi]:1038/srep03140. {PMID}:24189441
  4. Brooks, A. N; D. J. Reiss, A. Allard, W.-J. Wu, D. M. Salvanha, C. L. Plaisier, S. Chandrasekaran, M. Pan, A. Kaur and N. S. Baliga (2014). A system-level model for the microbial regulatory genome. Molecular Systems Biology 10(7):740. Epub 2014/07/17. [doi]:15252/msb.20145160. {PMID}:25028489
  5. Brown, S. D; S. M. Utturkar, T. S. Magnuson, A. E. Ray, F. L. Poole, W. A. Lancaster, M. P. Thorgersen, M. W. W. Adams and D. A. Elias (2014). Complete Genome Sequence of Pelosinus Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology. Genome Announcements 2(5). Epub 2014/09/06. [doi]:10.1128/genomeA.00881-14. {PMID}:24155594
  6. Deutschbauer, A; M. N. Price, K. M. Wetmore, D. R. Tarjan, Z. Xu, W. Shao, D. Leon, A. P. Arkin and J. M. Skerker (2014). Towards an informative mutant phenotype for every bacterial gene. Journal of Bacteriology 196(20):3643-3655. Epub 2014/08/13. [doi]:1128/jb.01836-14. {PMID}: 25112473
  7. Figueiredo MCO, Lobo SAL, Sousa SH, Pereira FP, Wall JD, Nobre LS, Saraiva LM. (2014) Hybrid cluster proteins and flavodiiron proteins afford protection to Desulfovibrio vulgaris upon macrophage infection. Journal of Bacteriology [doi]:10.1128/JB.00074-13
  8. Hillesland, K. L; S. Lim, J. J. Flowers, S. Turkarslan, N. Pinel, G. M. Zane, N. Elliott, Y. Qin, L. Wu, N. S. Baliga, J. Zhou, J. D. Wall and D. A. Stahl (2014). Erosion of functional independence early in the evolution of a microbial mutualism. Proceedings of the National Academy of Sciences 111(41):14822-14827. Epub 2014/10/01. [doi]:1073/pnas.1407986111. {PMID}:25267659
  9. Hurt, R. A; Jr; M. S. Robeson, 2nd, M. Shakya, J. G. Moberly, T. A. Vishnivetskaya, B. Gu and D. A. Elias (2014). Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments. PLoS ONE 9(7):e102826. Epub 2014/07/18. [doi]:1371/journal.pone.0102826. {PMID}:25033199
  10. Keller, K. L; B. J. Rapp-Giles, E. S. Semkiw, I. Porat, S. D. Brown and J. D. Wall (2014). New Model for Electron Flow for Sulfate Reduction in Desulfovibrio alaskensis Applied and Environmental Microbiology 80(3):855-868. Epub 2013/11/19. [doi]:10.1128/AEM.02963-13. {PMID}:24242254
  11. Korte, H. L; S. R. Fels, G. A. Christensen, M. N. Price, J. V. Kuehl, G. M. Zane, A. M. Deutschbauer, A. P. Arkin and J. D. Wall (2014). Genetic basis for nitrate resistance in Desulfovibrio strains. Frontiers in Microbiology 5:153. Epub 2014/05/06. [doi]:3389/fmicb.2014.00153 {PMID}:24795702
  12. Korte H; A. Saini, V. V. Trotter, G. P. Butland, A. P. Arkin and J. D. Wall (2015). Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. Environmental Science and Technology. 2015, 49 (2), pp 924–931 [DOI]:1021/es504484m {PMID}:25534748
  13. Kuehl, J. V; M. N. Price, J. Ray, K. M. Wetmore, Z. Esquivel, A. E. Kazakov, M. Nguyen, R. Kuehn, R. W. Davis, T. C. Hazen, A. P. Arkin and A. Deutschbauer (2014). Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis mBio 5(3):e01041-01014. Epub 2014/05/29. [doi]:10.1128/mBio.01041-14. {PMID}:24865553
  14. Lancaster, W. A; A. L. Menon, I. Scott, F. L. Poole, B. J. Vaccaro, M. P. Thorgersen, J. Geller, T. C. Hazen, R. A. Hurt, Jr; S. D. Brown, D. A. Elias and M. W. Adams (2014). Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization. Metallomics 6(5):1004-1013. Epub 2014/04/08. [doi]:1039/c4mt00050a. {PMID}:24706256
  15. Meyer, B; J. V. Kuehl, M. N. Price, J. Ray, A. M. Deutschbauer, A. P. Arkin and D. A. Stahl (2014). The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environmental Microbiology 16(11):3463-3486. Epub 2014/01/23. [doi]:1111/1462-2920.12405. {PMID}:24447568
  16. Novichkov, P. S; X. Li, J. V. Kuehl, A. M. Deutschbauer, A. P. Arkin, M. N. Price and D. A. Rodionov (2014). Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environmental Microbiology 16(1):1-8. Epub 2013/10/15. [doi]:1111/1462-2920.12273. {PMID}:24118949
  17. Pedersen, K; A. Bengtsson, J. Edlund, L. Rabe, T. Hazen, R. Chakraborty, L. Goodwin and N. Shapiro (2014). Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2. Genome Announcements 2(3). Epub 2014/05/31. [doi]:1128/genomeA.00509-14. {PMID}:24874683
  18. Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS. (2014) Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. BMC Syst Biol. 2014 Nov 14;8:122.
  19. Price, M. N; J. Ray, K. M. Wetmore, J. V. Kuehl, S. Bauer, A. M. Deutschbauer and A. P. Arkin (2014). The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis Frontiers in Microbiology 5:577. Epub 2014/11/18. [doi]:10.3389/fmicb.2014.00577. {PMID}:25400629
  20. Rajeev, L; E. G. Luning, S. Altenburg, G. M. Zane, E. E. Baidoo, M. Catena, J. D. Keasling, J. D. Wall, M. W. Fields and A. Mukhopadhyay (2014). Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. Frontiers in Microbiology 5:382. Epub 2014/08/15. [doi]:3389/fmicb.2014.00382. {PMID}:25120537
  21. Rajeev, L; E. G. Luning and A. Mukhopadhyay (2014). DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. Journal of Visualized Experiments (89). Epub 2014/08/01. [doi]:3791/51715. {PMID}:25079303
  22. Ray, J; K. L. Keller, M. Catena, T. R. Juba, M. Zemla, L. Rajeev, B. Knierim, G. M. Zane, J. J. Robertson, M. Auer, J. D. Wall and A. Mukhopadhyay (2014). Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough Frontiers in Microbiology 5:77. Epub 2014/03/19. [doi]:10.3389/fmicb.2014.00077. {PMID}:24639670
  23. Shao, W; M. N. Price, A. M. Deutschbauer, M. F. Romine and A. P. Arkin (2014). Conservation of Transcription Start Sites within Genes across a Bacterial Genus. mBio 5(4):e01398-01314. Epub 2014/07/06. [doi]:1128/mBio.01398-14. {PMID}:24987095
  24. Shatsky, M; P. Arbelaez, B. G. Han, D. Typke, S. E. Brenner, J. Malik and R. M. Glaeser (2014). Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs. Journal of Structural Biology 187(1):66-75. [doi]:1016/j.jsb.2014.03.017. {PMID}:24694675
  25. Tu, Q; H. Yu, Z. He, Y. Deng, L. Wu, J. D. Van Nostrand, A. Zhou, J. Voordeckers, Y. J. Lee, Y. Qin, C. L. Hemme, Z. Shi, K. Xue, T. Yuan, A. Wang and J. Zhou (2014). GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Molecular Ecology Resources 14(5):914-928. [doi]:1111/1755-0998.12239. {PMID}:24520909
  26. Turkarslan, S; E. J. Wurtmann, W. J. Wu, N. Jiang, J. C. Bare, K. Foley, D. J. Reiss, P. Novichkov and N. S. Baliga (2014). Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Research 42(Database issue):D184-190. Epub 2013/11/26. [doi]:1093/nar/gkt1190. {PMID}:24271392
  27. Wurtmann, E. J; A. V. Ratushny, M. Pan, K. D. Beer, J. D. Aitchison and N. S. Baliga (2014). An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular Microbiology 92(2):369-382. Epub 2014/03/13. [doi]:1111/mmi.12564. {PMID}:24612392
  28. Zhou, J; Y. Deng, P. Zhang, K. Xue, Y. Liang, J. D. Van Nostrand, Y. Yang, Z. He, L. Wu, D. A. Stahl, T. C. Hazen, J. M. Tiedje and A. P. Arkin (2014). Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences 111(9):E836-845. Epub 2014/02/20. [doi]:1073/pnas.1324044111. {PMID}:24550501


 Books/Book Chapters

  1. Van Nostrand JD and J Zhou. (2014) Applications of functional gene microarrays for profiling microbial communities. In: Applications of Advanced Omics Technologies: From Genes to Metabolites, edited by V Garcia-Cañas and A Cifuentes. Elsevier. Print ISBN : 9780444626509/ eBook ISBN : 9780444626691


Legacy and Synergistic External Research

  1. Gowda, H; J. Ivanisevic, C. H. Johnson, M. E. Kurczy, H. P. Benton, D. Rinehart, T. Nguyen, J. Ray, J. Kuehl, B. Arevalo, P. D. Westenskow, J. Wang, A. P. Arkin, A. M. Deutschbauer, G. J. Patti and G. Siuzdak (2014). Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Analytical Chemistry 86(14):6931-6939. Epub 2014/06/18. [doi]:1021/ac500734c. {PMID}:24934772
  2. Rinehart, D; C. H. Johnson, T. Nguyen, J. Ivanisevic, H. P. Benton, J. Lloyd, A. P. Arkin, A. M. Deutschbauer, G. J. Patti and G. Siuzdak (2014). Metabolomic data streaming for biology-dependent data acquisition. Nature Biotechnology 32(6):524-527. Epub 2014/06/10. [doi]:1038/nbt.2927. {PMID}:24911492