Berkeley Lab

2017 Publications

(Paper highlighted as: Impact factor >8.0, ** of outstanding interest, partial funding)

Jump to: Legacy and Synergistic External Research


  1. Baran, R.; R. Lau, B.P. Bowen, S. Diamond, N. Jose, F. Garcia-Pichel and T.R. Northen (2017) Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D(2)O) Stable Isotope Probing. American Chemical Society Chemical Biology. [doi]:10.1021/acschembio.6b00890 {PMID}:28068058
  2. Chakraborty, R.; H. Woo, P. Dehal, R. Walker, M. Zemla, M. Auer, L.A. Goodwin, A. Kazakov, P. Novichkov, A.P. Arkin and T.C. Hazen (2017) Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Standards in Genomic Sciences. [doi]:10.1186/s40793-017-0233-7 {PMID}:28194258 PMCID:PMC5299692
  3. de Raad, M.; T. de Rond, O. Rübel, J.D. Keasling, T.R. Northen and B.P. Bowen (2017) OpenMSI Arrayed Analysis Toolkit: Analyzing spatially defined samples using mass spectrometry imaging. Analytical Chemistry. [doi]:10.1021/acs.analchem.6b05004 {PMID}:28467051
  4. Erbilgin, O.; B.P. Bowen, S. Jenkins, S.M. Kosina, R.K. Lau and T.R. Northen (2017) Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. BioMed Central Bioinformatics. [doi]:10.1186/s12859-017-1478-2 {PMID}:28114881
  5. Huan, T.; E.M. Forsberg, D. Rinehart, C.H. Johnson, J. Ivanisevic, H.P. Benton, M. Fang, A. Aisporna, B. Hilmers, F.L. Poole, M.P. Thorgersen, M.W.W. Adams, G. Krantz, M.W. Fields, P.D. Robbins, L.J. Niedernhofer, T. Ideker, E.L. Majumder, J.D. Wall, N.J.W. Rattray, R. Goodacre, L.L. Lairson and G. Siuzdak (2017) Systems biology guided by XCMS Online metabolomics. Nature Methods. [doi]:10.1038/nmeth.4260 {PMID}:28448069 PMCID:PMC5933448
  6. Jenkins, S.; T.L. Swenson, R. Lau, A.M. Rocha, A. Aaring, T.C. Hazen, R. Chakraborty and T.R. Northen (2017) Construction of viable soil defined media using quantitative metabolomics analysis of soil metabolites. Frontiers in Microbiology. [doi]:10.3389/fmicb.2017.02618 {PMID}:29312276 PMCID:PMC5744445
  7. King, A.J.; S.P. Preheim, K.L. Bailey, M.S. Robeson II, T. Roy Chowdhury, B.R. Crable, R.A. Hurt Jr., T. Mehlhorn, K.A. Lowe, T.J. Phelps, A.V. Palumbo, C.C. Brandt, S.D. Brown, M. Podar, P. Zhang, W.A. Lancaster, F. Poole, D.B. Watson, M.W. Fields, J.-M. Chandonia, E.J. Alm, J. Zhou, M.W.W. Adams, T.C. Hazen, A.P. Arkin and D.A. Elias (2017) Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environmental Science & Technology. [doi]:10.1021/acs.est.6b04751 {PMID}:28112946
  8. Kothari, A.; Y.-W. Wu, M. Charrier, L. Rajeev, A.M. Rocha, T.C. Hazen, S.W. Singer and A. Mukhopadhyay (2017) Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes. bioRxiv. [doi]:http://biorxiv.org/content/early/2017/03/08/113860
  9. Majumder, E.L.-W.; and J.D. Wall (2017) Uranium Bio-transformations: Chemical or Biological Processes? Open Journal of Inorganic Chemistry: Actinide Special Issue. [doi]:10.4236/ojic.2017.72003
  10. Paradis, C.J.; L.D. McKay, E. Perfect, J.D. Istok and T.C. Hazen (2017) Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application. Hydrogeology Journal. [doi]:10.1007/s10040-017-1672-3
  11. Price, M.N.; and A.P. Arkin (2017) PaperBLAST: Text-mining papers for information about homologs. mSystems. [doi]:10.1128/mSystems.00039-17
  12. Ray, J.; M.N. Price, A.T. Iavarone, H.K. Carlson, E.M. Ryan, R.R. Malmstrom, A.P. Arkin and A.M. Deutschbauer (2017) Oxidative Pathway of Deoxyribose Catabolism. bioRxiv. [doi]:10.1101/205583
  13. Sagawa, S.; M.N. Price, A.M. Deutschbauer and A.P. Arkin (2017) Validating regulatory predictions from diverse bacteria with mutant fitness data. Public Library of Science ONE. [doi]:10.1371/journal.pone.0178258 {PMID}:28542589 PMCID:PMC5443562
  14. Thompson, A.W.; S. Turkarslan, C.E. Arens, A. López García de Lomana, A.V. Raman, D.A. Stahl and N.S. Baliga (2017) Robustness of a model microbial community emerges from population structure among single cells of a clonal population. Environmental Microbiology. [doi]:10.1111/1462-2920.13764 {PMID}:28419704
  15. Thorgersen, M.P.; W.A. Lancaster, X. Ge, G. Zane, K.M. Wetmore, B.J. Vaccaro, F.L. Poole, A.M. Deutschbauer, A.P. Arkin, J.D. Wall and M.W.W. Adams (2017) Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown Under Anaerobic Nitrate-Reducing Conditions. Environmental Microbiology. [doi]:10.3389/fmicb.2017.01529 {PMID}:28848534 PMCID:PMC5554334
  16. Thorgersen, M.P.; W.A. Lancaster, L. Rajeev, X. Ge, B.J. Vaccaro, F.P. Poole, A.P. Arkin, A. Mukhopadhyay and M.W.W. Adams (2017) A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium. Applied and Environmental Microbiology. [doi]:10.1128/AEM.03044-16 {PMID}:27913415 PMCID:PMC5288816
  17. Turkarslan, S.; A.V. Raman, A.W. Thompson, C.E. Arens, M.A. Gillespie, F. von Netzer, K.L. Hillesland, S. Stolyar, A. López García de Lomana, D.J. Reiss, D. Gorman-Lewis, G.M. Zane, J.A. Ranish, J.D. Wall, D.A. Stahl and N.S. Baliga (2017) Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology. [doi]:10.15252/msb.20167058 {PMID}:28320772 PMCID:PMC5371734
  18. Warth B.; N. Levin, D. Rinehart, H.P. Benton, J. Teijaro and G. Siuzdak (2017) Metabolizing Data in the Cloud. Trends in Biotechnology. [doi]:10.1016/j.tibtech.2016.12.010 {PMID}:28117091
  19. Wu, X.; A.M. Deutschbauer, A.E. Kazakov, K.M. Wetmore, B.A. Cwick, R.M. Walker, P.S. Novichkov, A.P. Arkin and R. Chakraborty (2017) Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announcements. [doi]:10.1128/genomeA.00582-17 {PMID}:28663297 PMCID:PMC5638281
  20. 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 (2017) Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environmental Science and Technology. [doi]:10.1021/acs.est.6b02980 {PMID}:28300407
  21. Zeng, L.; E. Wooton, D.A. Stahl and P.J. Walian (2017) Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. [doi]:10.1128/JB.00286-17 {PMID}:28874410 PMCID:PMC5686591
  22. Zhou, A.; R. Lau, R. Baran, J. Ma, F. von Netzer, W. Shi, D. Gorman-Lewis, M.L. Kempher, Z. He, Y. Qin, Z. Shi, G.M. Zane, L. Wu, B.P. Bowen, T.R. Northen, K.L. Hillesland, D.A. Stahl, J.D. Wall, A.P. Arkin and J. Zhou (2017) Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium, Desulfovibrio vulgaris. mBio. [doi]:10.1128/mBio.01780-17 {PMID}:29138306 PMCID:PMC5686539
  23. Zhou, J.; and D. Ning (2017) Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiology and Molecular Biology Reviews. [doi]:10.1128/MMBR.00002-17 {PMID}:29021219 PMCID:PMC5706748

  24. Legacy and Synergistic External Research

  25. McKay, L.J.; R. Hatzenpichler, W.P. Inskeep and M.W. Fields (2017) Occurrence and expression of diverse methane cycling genes by multiple archaeal phyla in hot spring sediments. Nature Scientific Reports. [doi]:10.1038/s41598-017-07354-x
  26. Rand, J.M.; T. Pisithkul, R.L. Clark, J.M. Thiede, C.R. Mehrer, D.E. Agnew, C.E. Campbell, A.L. Markley, M.N. Price, J. Ray, K.M. Wetmore, Y. Suh, A.P. Arkin, A.M. Deutschbauer, D. Amador-Noguez and B.F. Pfleger (2017) A metabolic pathway for catabolizing levulinic acid in bacteria. Nature Microbiology. [doi]:10.1038/s41564-017-0028-z