Berkeley Lab

2016 Publications

Jump to: Submitted/In Review Manuscripts | 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 Opinion in Chemical Biology. 30: p. 7-13 [doi]:10.1016/j.cbpa.2015.10.012. {PMID}:26544850
  2. Fischer CR, Ruebel O, Bowen BP. (2016) An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses. Arch Biochem Biophys. 2016;589:18–26. [doi]:10.1016/j.abb.2015.08.021
  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]: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. Cold Spring Harbor Labs Journals; [doi]:10.1101/050658
  9. 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
  10. Price M. N; K. M. Wetmore, A. M. Deutschbauer, A. P. Arkin. (2016) A Comparison of the Costs and Benefits of Bacterial Gene Expression. PLoS ONE Accepted. [doi]:10.1101/038851
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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. [doi]:10.1074/mcp.M115.054692 {PMID}:26873250
  17. 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
  18. Thorgersen, M.P; M. W. (2016) Nitrite Reduction Assay for Whole Pseudomonas Bio-protocol. 6(10) [doi]:www.bio-protocol.org/e1818.
  19. 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


Submitted/In Review Manuscripts

  1. Chakraborty, R; H.Woo, P.S. Dehal; R. Walker, M. Zemla, M. Auer, L.A. Goodwin, A. Kazakov, P. Novichkov, P. Arkin, T.C. Hazen. (2016) Complete genome sequence of Pseudomonas stutzeri strain RCH2. Standards in Genomic Sciences. In revision
  2. de Raad, M; T. de Rond, O. Rübel, J.D. Keasling, T.R. Northen, B.P. Bowen. (2016) OpenMSI Arrayed Analysis Toolkit: Analyzing spatially defined samples using mass spectrometry imaging. Analytical Chemistry
  3. Erbilgin, O.; B.P. Bowen, S. Jenkins, S.M. Kosina, R.K. Lau, T.R. Northen (2016) Dynamic substrate preferences and predicted metabolic properties of a simple microbial consortium. BMC bioinformatics. Submitted
  4. Justice, N.B; A. Sczesnak, T.C. Hazen, A.P. Arkin. (2016) Environmental Selection, Random Dispersal, and Organism Interactions Shape Community Assembly in High Throughput Enrichment Culturing. ISME J. Submitted
  5. 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 Analytics: Mobilizing the Lab into the Cloud for Omic Scale Analyses. Analytical Chemistry. Accepted
  6. Thompson A.W; S. Turkarslan, C.E. Arens, A.L. García de Lomana, A.V. Raman, D.A. Stahl, and N.S. Baliga. (2016) The robustness of a microbial community emerges from population structure among single cells of a clonal population. Environmental Microbiology and Environmental Microbiology Reports. Submitted
  7. Turkarslan S; Raman A. V; Thompson A. W; Hillesland K. L; Arens C. E; Stolyar S; Reiss D. J; von Netzer F; Gorman-Lewis D; Zane G. M; Wall J; Stahl D. A; Baliga N. S. Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology MSB-16-7058. In revision
  8. von Netzer F; Gorman-Lewis D; Shock E. L; Stahl D. A. Working title: Understanding the thermodynamic foundations of microbial growth efficiencies via microcalorimetry. In prep
  9. Zhang, P; Z. He, J.D. Van Nostrand, Y. Qin, Y. Deng, L. Wu, Q. Tu, J. Wang, C.W. Schadt, M.W. Fields, T.C. Hazen, A.P. Arkin, D.A. Stahl, and J. Zhou. (2016) Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environmental Science and Technology. In revision
  10. Zhou A; Lau R; Baran R. B; Ma J; Shi W; He Z; Tu Q; Qin Y; Shi Z; Kempher M. L; Zane G. M. Z; Wu L; Bowen B; Northen T; Hillesland K. L; von Netzer F; Gorman-Lewis D; Stahl D. A; Wall J. D; Arkin A. P; Zhou J. Working title: Mostly restored basal changes and altered adaptation-derived salt stress response and genomic changes in experimentally evolved Desulfovibrio vulgaris Hildenborough. In revision

Books/Book Chapters

  1. 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


Legacy and Synergistic External Research

  1. 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. (2016) Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. mBio, 2016. 7(3) [doi]:10.1128/mBio.00714-16.
  2. 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.
  3. 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.
  4. 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.