Berkeley Lab

2013 Publications

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

  1. Baran R., Bowen, B.P, Price, M.N, Arkin, A.P, Deutschbauer, A.M, Northen, T.R. (2013) Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype. ACS Chemical Biology 8(1): 189-199 [doi]:10.1021/cb300477w {PMID}:23082955 (Recommended by Faculty of 1000)
  2. Baran R and Northen TR. (2013) RAMSI: Robust Automated Mass Spectra Interpretation and Chemical Formula Calculation Using Mixed Integer Linear Programming. Analytical Chemistry. [doi]:10.1021/ac402180c {PMID}:24032353
  3. Brileya K.A., Connolly, J.M., Downey, C., Gerlach, R., Fields, M.W. (2013) Taxis toward hydrogen gas by Methanococcus maripaludis. Scientific Reports. 3:3140. [doi]:10.1038/srep03140
  4. Brown S.D., Utturkar, S.M., Arkin, A.P., Deutschbauer, A.M., Elias, D.A., Hazen, T.C., chakraborty, R. (2013) Draft Genome Sequence for Desulfovibrio africanus strain PCS. Genome Announcements (genomeA) vol. 1 no. 2 e00144-13 [doi]:10.1128/​genomeA.00144-13 {PMID}:23580709
  5. Chivian, D., Dehal, P.S., Keller, K., Arkin, A.P. (2013) MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic acids research. 41(Database issue): p. D648-54. (ENIGMA and KBase Collaboration) [doi]:10.1093/nar/gks1202. {PMID}:23203984
  6. Cipriano M.J., Novichkov, P.N., Kazakov, A.E., Rodionov, D.A., Arkin, A.P., Gelfand, M.S. , Dubchak, I. (2013) RegTransBase–a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics. 14(1):213. [doi]:10.1186/1471-2164-14-213. {PMID}:23547897
  7. Costa K.C., Yoon, S.H., Pan, M., Burn, J.A., Baliga, N.S., Leigh, J.A. (2013) Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. Journal of Bacteriology. [doi]:10.1128/JB.02141-12. {PMID}:23335420
  8. Fels S., G. Zane, S. Blake, and J.D. Wall. (2013) Rapid TnLE-seq for gene fitness evaluation in underdeveloped bacterial systems. Applied and Environmental Microbiology. 79(23):7510-7. [doi]:10.1128/AEM.02051-13. {PMID}:24077707
  9. Hazen, T. C. (2013) Opinion: The SuperChip for Microbial Community Structure, and Function from all Environments. Microbial Biotechnology. [doi]:10.1111/1751-7915.12045. {PMID}:23464831
  10. Hazen, T. C., A. M. Rocha, and S. M. Techtmann (2013) Advances in monitoring environmental microbes. Curr. Opinions in Biotech 24: 526-533. [doi]:10.1016/j.copbio.2012.10. {PMID}:23183250
  11. Kazakov A.E., Rodionov, D., Price, M.N., Arkin, A.P., Dubchak, I., Novichkov, P. (2013) Transcription factor family-based reconstruction of singleton regulons: Study of the Crp/Fnr, ArsR and GntR families in Desulfovibrionales genomes. Journal of Bacteriology. 2013, 195(1):29-38. [doi]:10.1128/JB.01977-12. {PMID}:23086211
  12. Kazakov AE., Rajeev, L., Luning, E.G., Zane, G.M., Siddartha, K., Rodionov, D.A., Dubchak, I., Arkin,A.P., Wall, J.D., Mukhopadhyay, A., Novichkov, P. S. (2013) A new family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. Journal of Bacteriology. [doi]:10.1128/jb.00679-13. {PMID}:23913324
  13. Keller, K.L., Rapp-Giles, B.J., Semkiw, E.S., Porat, I, Brown, S.D., Wall, J.D. (2013) The role of the Type I cytochrome c3 in electron flow for sulfate reduction and pyruvate metabolism in Desulfovibrio alaskensis G20. Appl. Environ. Microbiol. Appl. Environ. Microbiol. Appl. Environ. Microbiol. [doi]:10.1128/AEM.02963-13
  14. Krumholz, L. R; L. Wang, D. A. C. Beck, T. Wang, M. Hackett, B. Mooney, T. R. Juba, M. J. McInerney, B. Meyer, J. D. Wall and D. A. Stahl (2013). Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis. Microbiology 159(Pt 10):2162-2168. [doi]:1099/mic.0.063818-0. {PMID}:23842468
  15. Louie, K. B; B. P. Bowen, X. Cheng, J. E. Berleman, R. Chakraborty, A. Deutschbauer, A. Arkin and T. R. Northen (2013). “Replica-Extraction-Transfer” Nanostructure-Initiator Mass Spectrometry Imaging of Acoustically Printed Bacteria. Analytical Chemistry 85(22):10856-10862. [doi]:1021/ac402240q. {PMID}:24111681
  16. Meyer, B; J. Kuehl, A. M. Deutschbauer, M. N. Price, A. P. Arkin and D. A. Stahl (2013). Variation among Desulfovibrio Species in Electron Transfer Systems Used for Syntrophic Growth. Journal of Bacteriology 195(5):990-1004. [doi]:1128/JB.01959-12. {PMID}:23264581
  17. Meyer, B; J. V. Kuehl, A. M. Deutschbauer, A. P. Arkin and D. A. Stahl (2013). Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. Journal of Bacteriology 195(21):4900-4914. [doi]:1128/JB.00504-13. {PMID}:23974031
  18. Momeni, B., Brileya, K.A., Fields, M.W., Shou, W. (2013) Strong inter-population cooperation leads to partner intermixing in microbial communities. eLife. 00230;[doi]:7554/eLife.00230. {PMID}:23359860
  19. Novichkov, P.S., Kazakov, A.E., Ravcheev, D.A., Leyn, S.A., Sun, E.I., Kovaleva, G.Y., Sutormin, R.A., Novichkova, E.S., Kazanov, M.D., Reihl, W.J., Arkin, A.P., Dubchak, I., Rodionov, D.A. (2013) RegPrecise 3.0 – a resource for genome-scale exploration of transcriptional regulation in Bacteria. BMC Genomics. 14(1): 745 [doi]:10.1186/1471-2164-14-745. {PMID}:24175918
  20. Novichkov, P.S., Li, X., Kuehl, J.V., Deutschbauer, A.M., Arkin, A.P., Price, M.N., Rodionov, D.A. (2013) Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environmental Microbiology. [doi]: 10.1111/1462-2920.12273
  21. Orellana M.V., Pang, W.L., Durand, P.M., Whitehead, K. Whitehead, Baliga, N.S. (2013) A role for programmed cell death in the microbial loop. PLoS One [doi]:10.1371/journal.pone.0062595. {PMID}:23667496
  22. Pang, W.L., Kaur, A., Ratushny, A.V., Cvetkovic, A., Kumar, S., Pan, M., Arkin, A.P., Aitchison, J.D., Adams, M.W., Baliga, N.S. (2013) Metallochaperones regulate intracellular copper levels. PLoS Comput Biol 9(1): e1002880.[doi]:1371/journal.pcbi.1002880. {PMID}:23349626
  23. Preheim SP, Perrottaa AR, Martin AM, Gupta A, Alm EJ. Distribution-Based Clustering: Using Ecology to Refine the Operational Taxonomic Unit. Applied Environmental Microbiology. (2013) 79(21): 6593-6603. [doi]:1128/aem.00342-13. {PMID}:23974136
  24. Price M.N., Deutschbauer, A.M., Skerker, J.M., Wetmore, K.M., Ruths, T., Mar, J.S., Kuehl, J.V., Shao, W., Arkin, A.P. (2013) Indirect and suboptimal control of gene expression is widespread in bacteria. Molecular Systems Biology 9:660 [doi]:10.1038/msb.2013.16. {PMID}:24987095
  25. Somenahally A.C., J.J. Mosher, T. Yuan, M. Podar, T.J. Phelps, S.D. Brown, Z.K. Yang, T.C. Hazen, A.P. Arkin, A.V. Palumbo, J.D. Van Nostrand, J. Zhou and D.A. Elias. (2013). Hexavalent chromium reduction under fermentative conditions with lactate stimulated microbial communities. PloS One. [doi]:10.1371/journal.pone.0083909. {PMID}:24376771
  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 (2013). Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Research 42(Database issue):D184-190. [doi]:1093/nar/gkt1190. {PMID}:23271269
  27. Tu Q, He Z, Deng Y, Zhou J. (2013) Strain/Species-specific probe design for microbial identification microarrays. Appl Environ Microbiol. 79(16):5085-8. [doi]:10.1128/AEM.01124-13. {PMID}:23747703
  28. Wang, L., X. Wang, A.P. Arkin, and M.S. Samoilov, Inference of gene regulatory networks from genome-wide knockout fitness data. Bioinformatics (2013) 29(3): p. 338-46.[doi]:10.1093/bioinformatics/bts634. {PMID}:23271269
  29. Yoon S.H., S. Turkarslan, D.J. Reiss, M. Pan, J.A. Burn, K.C. Costa, T.J. Lie, J. Slagel, R.L. Moritz, M. Hackett, J.A. Leigh, and N.S. Baliga. (2013) A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Research. 23(11): 1839-51 [doi]:10.1101/gr.153916.112. {PMID}:24089473
  30. Zhou, A., Baidoo, E., He ,Z., Mukhopadhyay, A., Baumohl, J.K., Benke, P., Joachimiak, M.P., Xie, M., Song, R., Arkin, A.P., Hazen, T.C., Keasling, J.D., Wall, J.D., Stahl, D.A., Zhou, J. (2013) Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME J . 7, 1790–1802. doi:10.1038/ismej.2013.60 (ENIGMA & KBase collaborative project) [doi]:1038/ismej.2013.60. {PMID}:23575373
  31. Zhou, A.F., He, Z., Qin, Y., Lu, Z., Deng, Y., Tu, Q., Van Nostrand, J.D., Wu, L., Hazen, T.C., Arkin, A. P., Zhou, J. (2013) StressChip as a High Throughput Tool for Assessing Microbial Community Responses to Environmental Stresses. Environ Sci Technol. [doi]:10.1021/es4018656. {PMID}:23889170
  32. Zhou, J.-Z., Liu, W., Deng, Y., Jiang, Y., Xue, K., He, Z., Van Nostrand, J. D., Wu, L., Yang, Y. Wang, A. (2013) Stochastic assembly leads to alternative communities with distinct functions. mBio 4(2):). [doi]:10.1128/mBio.00584-12. {PMID}:23462114
  33. Zhou, J.Z., Jiang, Y., Deng, Z, Shi, Y, Zhou, Y., Xue, K., Wu, L., He, Z., Yang, Y. (2013) Random sampling process leads to overestimation of β-diversity of microbial communities. mBio 4: e00324-13 (doi:10.1128/mBio.00324-13). (Editor’s Choice) [doi]:10.1128/mBio.00324-13. {PMID}:23760464.

  34. Books/Book Chapters

  35. He, Z., J. D. Van Nostrand, and J.-Z. Zhou. (2013) GeoChip-based metagenomics technologies for analyzing microbial community functional structure and activities. Encyclopedia of Metagenomics, edited by Karen E. Nelson
  36. Northen, Trent R (2013). Harnessing Microbial Metabolism for Biofuels and Biomaterials. Fundamentals of Materials for Energy and Environmental Sustainability. David Ginley and David Cahen, Cambridge Press
  37. Preheim SP, Perrotta AR, Friedman J, Smillie CS, Brito IL, Smith MB, Alm EJ. (2013) Computational methods for high-throughput comparative analyses of natural microbial communities. Methods in Enzymology. Volume 531, 2013, Pages 353–370. Microbial Metagenomics, Metatranscriptomics, and Metaproteomics. [doi]:10.1016/ B978-0-12-407863-5.00018-6
  38. Stahl, D.A., Flowers, J.J., Hullar, M., Davidson, S. (2013) The structure and function of microbial communities. In: E. Rosenberg, E.F. DeLong, F. Thompson, S. Lory, and Erko Stackebrandt (Eds.) The Prokaryotes. 4th Edition. Springer-Verlag, New York, New York
  39. Van Nostrand, J., Terry, D., Gentry, J., Zhou, J.-Z. (2013) Microarray-Based Microbial Identification and Characterization. In Y.-W. Tang and C. W. Stratton (eds) Advanced Techniques in Diagnostic Microbiology, 2nd ed., Springer, New York, NY (Invited)

  40. Legacy and Synergistic External Research

  41. De León, K; R. Gerlach, B. M. Peyton and M. W. Fields (2013). Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park. Frontiers in Microbiology 4:330. Epub: 2013/11/28. [doi]:3389/fmicb.2013.00330. {PMID}:24282404
  42. Figueiredo MCO, SAL. Lobo, SH. Sousa, FP. Pereira, JD Wall, LS. Nobre, and LM. Saraiva. (2013) Hybrid cluster proteins and flavodiiron proteins afford protection to Desulfovibrio vulgaris upon macrophage infection. Journal of Bacteriology. [doi]:10.1128/JB.00074-13
  43. Fischer, C. R; B. P. Bowen, C. Pan, T. R. Northen and J. F. Banfield (2013). Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific. ACS Chemical Biology 8(8):1755-1763. Epub: 2013/05/30. [doi]:1021/cb400210q. {PMID}:23713674
  44. Kang, S; J. D. Van Nostrand, H. L. Gough, Z. He, T. C. Hazen, D. A. Stahl and J. Zhou (2013). Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments. FEMS Microbiology Ecology 86(2):200-214. Epub 2013/05/29. [doi]:1111/1574-6941.12152. {PMID}:23710534
  45. Ivanisevic, J., Zhu Z., Plate L., Tautenhahn R., Chen S., O’Brien P.J., Johnson C.H., Marletta M., Patti G.J., Siuzdak G. (2013) Toward ‘omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. Analytical Chemistry 85 (14), pp 6876–6884; [doi]:10.1021/ac401140h
  46. Patti G.J., Tautenhahn R., Rinehart, D, Cho, K.Shriver L., Manchester M., Nikolskiy, I.Johnson, C. H. Mahieu, N. G. Siuzdak G. (2013) A view from above: cloud plots to visualize global metabolomic data. Analytical Chemistry. 85(2):798-804 [doi]:10.1021/ac802587r
  47. Rübel O., A. Greiner, S. Cholia, KB. Louie, EW. Bethel, TR. Northen, and BP. Bowen (2013) OpenMSI: High-performance web-based visualization, analysis and management of mass spectrometry imaging data. Analytical Chemistry. 85(21): 10354-10361. [doi]:10.1021/ac402540a
  48. Sim MS, Wang DT, Zane GM, Wall JD, Bosak T, & Ono S (2013) Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c 3. Front Microbiol 4:171 [doi]: 10.3389/fmicb.2013.00171
  49. Sun, E; S. Leyn, M. Kazanov, M. Saier, P. Novichkov and D. Rodionov (2013). Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics 14(1):597. [doi]:1186/1471-2164-14-597. {PMID}:24060102
  50. Zhu, Z. J; A. W. Schultz, J. Wang, C. H. Johnson, S. M. Yannone, G. J. Patti and G. Siuzdak (2013). Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nature Protocols 8(3):451-460. Epub 2013/02/09. [doi]:1038/nprot.2013.004. {PMID}:23391889