Berkeley Lab

2013 Publications

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

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 (Recommended by Faculty of 1000)

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

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

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

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)

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

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

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

Hazen, T. C. (2013) Opinion: The SuperChip for Microbial Community Structure, and Function from all Environments. Microbial Biotechnology. doi:10.1111/1751-7915.12045

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.2012.10.020

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

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 JB.00679-13 Epub PMID: 23913324

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

Krumholz, L.R., Wang, L., Beck, D.A.C., Wang, T., Hackett, M., Mooney, B., Juba, T.R., McInerney, M.J., Meyer, B., Wall, J.D., Stahl, D.A. (2013) Membrane protein complex of APS reductaseand Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis. Microbiology. doi: 10.1099/mic.0.063818-0

Louie, K.B., Bowen, B.P., Cheng, X., Berleman, J., Chakraborty, R., Deutschbauer, A., Arkin, A., Northen, T.R. (2013) Replica-extraction-transfer’ for nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria and microbial communities; Analytical Chemistry. 85 (22), 10856-10862. PMID:24111681. doi:10.1021/ac402240q

Meyer, B., Kuel, J., Deutschbauer, A.M., Arkin, A.P., Stahl, D.A. (2013) Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. Journal of Bacteriology. Vol. 195, No. 5, p. 990-1004

Meyer, B., Kuehl, J., Deutschbauer, A.M., Price, M.N., Arkin, A.P., Stahl, D.A. (2013)Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. Journal of Bacteriology. Vol. 195, No. 5, p. 990-1004

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:10.7554/eLife.00230

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

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

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

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:10.1371/journal.pcbi.1002880

Preheim S.P., Perrotta, A.R., Friedman, J., Smillie, C.S., Brito ,I.L., Smith, M.B., Alm, E.J. (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

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: 10.1128/AEM.00342-13

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

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

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

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

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

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)

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

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

Zhou, J, W Liu, Y Deng, Y-H Jiang, K Xue, Z He, JD Van Nostrand, L Wu, Y Yang, A Wang. (2013) Communities with Distinct Functions in a Bioreactor Microbial Community. mBio 4(2): doi:10.1128/mBio.00584-12

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)


Books/Book Chapters

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

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. http://dx.doi.org/10.1016/ B978-0-12-407863-5.00018-6

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

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)


Legacy and Synergistic External Research

De León, K., R. Gerlach, B.M. Peyton, and M.W. Fields. (2013) Archaeal and bacterial communities in alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park. Frontiers in Extreme Microbiol. 4:330

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

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

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

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

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

Sun, EI, SA Leyn, MD Kazanov, MH Savier, PS Novichkov and DA Rodionov. (2013) Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics 2013, 14:597 doi:10.1186/1471-2164-14-597

Zhu Z-J., Schultz A.W., Wang J., Johnson C.H., Yannone S.M., Patti G.J., Siuzdak G. (2013) Quadropole-Time-of-Flight Mass Spectrometry Characterization of Metabolites Guided by the METLIN Database. Nature Protocols. 8(3):451-60. doi: 10.1038/PMID:23391889