Berkeley Lab

2016 Publications

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

  1. de Raad, M.; C.R. Fischer, and T.R. Northen. (2016) High-throughput platforms for metabolomics. Current Opinions in Chemical Biology. 30: p. 7-13 [doi]: 10.1016/j.cbpa.2015.10.012. {PMID}:26544850
  2. Fischer CR, Ruebel O, Bowen BP. An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses. Arch Biochem Biophys. 2016;589:18–26 [doi]: 10.1016/ {PMID}:26365033
  3. Gao, J.; de Raad, M.; Bowen, B.; Zuckermann, R.N.; Northen, T.R. (2016) The Application of Black Silicon for Nanostructure-Initiator Mass Spectrometry.  Analytical Chemistry 88 (3), 1625–1630. [doi]:10.1021/acs.analchem.5b03452
  4. Hemme, C.L.; S.J. Green, L. Rishishwar, O. Prakash, A. Pettenato, R. Chakraborty, A.M. Deutschbauer, J.D. Van Nostrand, L. Wu, Z. He, I.K. Jordan, T.C. Hazen, A.P. Arkin, J.E. Kostka, and J. Zhou. (2016) Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. MBio. 7(2) [doi]: 10.1128/mBio.02234-15. {PMID}:27048805
  5. Kosina, S.M.; M.A. Danielewicz, M. Mohammed, J. Ray, Y. Suh, S. Yilmaz, A.K. Singh, A.P. Arkin, A.M. Deutschbauer, and T.R. Northen. (2016) Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. ACS Synthetic Biology [doi]: 10.1021/acssynbio.5b00236 {PMID}:26885935
  6. Kurczy, M. E.; E. M. Forsberg, M. P. Thorgerson, F L. Poole II, H. P. Benton, J. Ivanisevic, M. L. Tran, J. D. Wall, D. A. Elias, M. W. W. Adams, G. Siuzdak (2016) Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation in Pseudomonas. ACS Chemical Biology. [doi]:10.1021/acschembio.6b00082 {PMID}:27045776
  7. Lindemann, S.R.; H.C. Bernstein, H.-S. Song, M.W. Fields, W. Shou, D. Johnson, J.K. Fredrickson, and A.S. Beliaev. (2016) Engineering microbial consortia for controllable outputs.  ISME Journal (2016) 10, 2077–2084 [doi]: 10.1038/ismej.2016.26
  8. Louie, K.; B.P. Bowen, R.K. Lau, T.R. Northen (2016) Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI) bioRxiv. [doi]: 10.1101/050658
  9. Montenegro-Burke, J.R.; T. Phommavongsay, A.E. Aisporna, T. Huan, D. Rinehart, F. L. Poole, M. P. Thorgersen, M. W. W. Adams, G. Krantz, M. W. Fields, P. D. Robbins, L. J. Niedernhofer, H. P. Benton, G. Siuzdak (2016) Smartphone Science: Taking the Metabolomics Lab into the Cloud. Analytical Chemistry. 2016, 88 (19), pp 9753–9758 [doi]: 10.1021/acs.analchem.6b02676
  10. Olesen S.; S. Vora, S. Techtmann, J. L. Fortney, J. R. Bastidas-Oyanedel, J. Rodriguez, T. C. Hazen, and E. Alm. 2016. A novel analysis method for paired-sample microbial ecology experiments. PlosOne 11:e0154804, [doi]: 10.1371/journal.pone.0154804. (3.057, 2).*
  11. Price, M.N; K.M. Wetmore, R.J. Waters, M. Callaghan, J. Ray, J.V. Kuehl, R.A. Melnyk, J.S. Lamson, Y. Suh, Z. Esquivel, H. Sadeeshkumar, R. Chakraborty, B.E. Rubin, J. Bristow, M.J. Blow, A.P. Arkin, A.M. Deutschbauer. (2016) Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes. bioRxiv 072470;[doi]: 10.1101/072470
  12. Price M. N.; K. M. Wetmore, A. M. Deutschbauer, A. P. Arkin. (2016) A Comparison of the Costs and Benefits of Bacterial Gene Expression. PLoSONE [doi]: 10.1371/journal.pone.0164314
  13. Price, M. N.; and A. P. Arkin. (2016) Weakly deleterious mutations and low rates of recombination limit the impact of natural selection on bacterial genomes. MBio vol. 6 no. 6 e01302-15. [doi]: 10.1128/mBio.01302-15 {PMID}:26670382
  14. Price M. N.; and A. P. Arkin (2016) A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. Genome Biology and Evolution. [doi]: 10.1093/gbe/evw126 {PMID}:27289091
  15. Rhee, M.; Light, Y.K.; Meagher, R.J. and Singh, A.K. (2016) Digital Droplet Multiple Displacement Amplification (ddMDA) for whole genome sequencing of limited DNA samples (2016) PLoS ONE. [doi]: 10.1371/journal.pone.0153699 {PMID}:27144304
  16. Rocha, A.M; Q. Yuan, D. Close, K.B. O’dell, J. Fortney, J. Wu, and T.C. Hazen (2016) Rapid Detection of Microbial Cell Abundance in Aquatic Systems. Biosensors and Bioelectronics. Volume 85: 915–923. [doi]: 10.1016/j.bios.2016.05.098 {PMID}:27315516
  17. Shatsky, M.; M. Dong, H. Liu, L.L. Yang, M. Choi, M.E. Singer, J.T. Geller, S.J. Fisher, S.C. Hall, T.C. Hazen, S.E. Brenner, G.P. Butland, J. Jin, H.E. Witkowska, J.M. Chandonia, and M.D. Biggin. (2016) A quantitative tagless method to validate and identify protein‐protein interactions. Molecular & Cellular Proteomics. [doi]: 10.1074/mcp.M115.057117 {PMID}27099342
  18. Shatsky, M.; S. Allen, B.L. Gold, N.L. Liu, T.R. Juba, S.A. Reveco, D.A. Elias, R. Prathapam, J. He, W. Yang, E.D. Szakal, H. Liu, M.E. Singer, J.T. Geller, B.R. Lam, A. Saini, V.V. Trotter, S.C. Hall, S.J. Fisher, S.E. Brenner, S.R. Chhabra, T.C. Hazen, J.D. Wall, H.E. Witkowska, M.D. Biggin, J-M. Chandonia and G. Butland. (2016) Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported. Molecular and Cellular Proteomics. 2016 Feb 12. [doi]: 10.1074/mcp.M115.054692 {PMID}:26873250
  19. Spencer, S.J.; M.V. Tamminen, S.P. Preheim, M.T. Guo, A.W. Briggs, I.L. Brito, D. A. Weitz, L.K. Pitkanen, F. Vigneault, M.P. Virta, and E.J. Alm. (2016) Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME Journal. 10(2): p. 427-36 [doi]: 10.1038/ismej.2015.124 {PMID}:26394010
  20. Swenson, T.L; S. Jenkins, B.P. Bowen, and T.R. Northen. (2015) Untargeted soil metabolomics methods for analysis of extractable organic matter. Soil Biology & Biochemistry. 80: p. 189-198. [doi]:10.1016/j.soilbio.2014.10.007. {WOS}:000346545800022
  21. Thorgersen, M.P; M. W. (2016) Nitrite Reduction Assay for Whole Pseudomonas Cells. Bio-protocol. 6(10) [doi]
  22. Vaccaro, B.J.; M.P. Thorgersen, W.A. Lancaster, M.N. Price, K.M. Wetmore, F.L. Poole, A.M. Deutschbauer, A.P. Arkin, and M.W.W. Adams. (2016) Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Applied and Environmental Microbiology. 82(1): p. 51-61 [doi]: 10.1128/Aem.02602-15 {PMID}:26452555
  23. Vaccaro, B. J.; Lancaster, W. A.; Thorgersen, M. P.; Zane, G. M.; Younkin, A. D.; Kazakov, A. E.; Wetmore, K. M.; Deutschbauer, A.; Arkin, A. P.; Novichkov, P. S.; Wall, J. D. and Adams, M. W. W.  (2016) Novel metal cation resistance systems from mutant fitness analysis of denitrifying Pseudomonas stutzeri. Applied and Environmental Microbiology. 82(19) 6046-6056. [doi]: 10.1128/AEM.01845-16 {PMID}:27474723

  24. Books/Book Chapters

  25. Hazen, T. C. and G. S. Sayler.  2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, 4th Edition. ASM Press, Washington, DC.  [doi]: 10.1128/9781555818821.ch5.1.6
  26. Lubbe, Andrea and Trent R. Northen. (2016) Exometabolomics for Linking Soil Carbon Dynamics to Microbial Communities. Microbial Metabolomics: Applications in Clinical, Environmental, and Industrial Microbiology. Springer Press. Editors: Beale, D.; Kouremenos, K.; Palombo, E. ISBN 978-3-319-46326-1 [doi]: 10.1007/978-3-319-46326-1_5
  27. Rabus, R.; S.S. Venceslau, L. Wöhlbrand, G. Voordouw, J.D. Wall, and I.A.C. Pereira. (2015) A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Advances in Microbial Physiology. 66: p. 55-321. [doi]:

  28. Legacy and Synergistic External Research

  29. Blaser, M.J.; Z.G. Cardon, M.K. Cho, J.L. Dangl, T.J. Donohue, J.L. Green, R. Knight, M.E. Maxon, T.R. Northen, K.S. Pollard, and E.L. Brodie, Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. MBio, 2016. 7(3) [doi]: 10.1128/mBio.00714-16.
  30. Bouskill, N.J.; T.E. Wood, R. Baran, Z. Ye, B.P. Bowen, H. Lim, J. Zhou, J.D. Nostrand, P. Nico, T.R. Northen, W.L. Silver, and E.L. Brodie. (2016) Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism. Frontiers in Microbiology. 7: p. 525 [doi]: 10.3389/fmicb.2016.00525.
  31. Bouskill, N.J.; T.E. Wood, R. Baran, Z. Hao, Z. Ye, B.P. Bowen, H.C. Lim, P.S. Nico, H.Y. Holman, B. Gilbert, W.L. Silver, T.R. Northen, and E.L. Brodie. (2016) Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Frontiers in Microbiology. 7: p. 323 [doi]: 10.3389/fmicb.2016.00323.
  32. Paradis, C.J.; S. Jagadamma, D.B. Watson, L.D. McKay, T.C. Hazen, M. Park, and J.D. Istok. (2016) In situ mobility of uranium in the presence of nitrate following sulfate-reducing conditions. Journal of Contaminant Hydrology. 187: p. 55-64
    [doi]: 10.1016/j.jconhyd.2016.02.002.