Steven David Brown

Steven D. Brown

Microbial Ecology & Physiology Group
BioSciences Division
Oak Ridge National Laboratory
Oak Ridge, TN 37831-6342
Phone: (865)576-2368
Fax: (865)241-1187
brownsd@ornl.gov

Research Interests

Systems biology studies than integrate genomics (e.g. resequencing) and functional genomics techniques such as transcriptomics (e.g. RNA-Seq), proteomics, and metabolomics and genetics for insights in microbial physiology and regulation.

Capabilities

Laboratory for controlled cultivation (e.g. pH, temperature, level, dissolved oxygen tension (DOT) and thermal mass flow) using New Brunswick Scientific Bioflo110 1.3 L and 7.5 L fermenters.

Aerobic and anaerobic Bioscreen C machines for growth and high-throughput screen of 200 individual cultures at one time.

Clean-room facilities for in-house microarray fabrication

Laboratories for microarray data generation and analysis

  Equipment includes Nimblegen 12-bay hybridization station, automated array washing system and 2um-resolution scanner for high-density DNA microarrays.
  Software includes NimbleScan, SignalMap, JMP Genomics, Pathway tools and KnowledgeBases

Next-Generation DNA Sequencing

  Equipment includes GS FLX running Titanium chemistry (454 Life Sciences), GAIIx and HiSeq2000 (Illumina) instruments. In addition, two ABI 3730xl 96-plate based DNA sequencers are available.

A variety of software are being used and on an available cluster and being assessed.

Education  [ Top ]

Professional Experience  [ Top ]

2009 Adjunct Faculty Member; Genome Sciences and Technology (GST) Graduate School, University of Tennessee, Knoxville, Tennessee
2008 Staff Research Scientist; Microbial Ecology & Physiology Group; ORNL
2005 R&D Associate Staff Scientist; Microbial Ecology & Physiology Group; ORNL
2002-2005 Postdoctoral Research Associate; Environmental Sciences Division; ORNL.
2001 Demonstrator for “Hands on Science“ course for high school students.
1997-2001 Undergraduate laboratory Demonstrator (including Biol115, Gene211, Micr211).
1995 Laboratory Assistant, Professor Gerald Tannock (part-time).

Patents

Brown, S., Guss, A., Yang, S., Karpinets, T., and Lynd, L. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol. Provisional patent application 61/346,660.

Yang, S. & Brown, S.D. 2009. Microorganisms having enhanced resistance to acetate. Non-provisional patent application 61/173,649.

Yang, S. & Brown, S.D. 2009. Microorganisms having enhanced tolerance to inhibitors and stress. Non-provisional patent application. No. 61/184,961.

Selected Publications  [ Top ]

  1. Brown SD, Guss A, Karpinets T, Parks J, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwad A, Rodriguez JM et al: Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci USA 2011:Accepted.
  2. Yang S, Keller M, Brown SD: Genomics on pretreatment inhibitor tolerance of Zymomonas mobilis. In: Microbial stress tolerance: from genomics to biofuels Microbiology monographs (Springer series). Edited by Liu ZL. Heidelberg, Germany: Springer; 2011: In press.
  3. Shao X, Raman B, Zhu M, Mielenz JR, Brown SD, Guss A, Lynd LR: Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum. Appl Microbiol Biotechnol 2011:Accepted.
  4. Raman B, McKeown CK, Rodriguez MJ, Brown SD, Mielenz JR: Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation. BMC Microbiol 2011, 11:134.
  5. Vishnivetskaya TA, Mosher JJ, Palumbo AV, Yang ZK, Podar M, Brown SD, Brooks SC, Gu BH, Southworth GR, Drake MM et al: Mercury and other heavy metals influence bacterial community structure in contaminated tennessee streams. Appl Environ Microbiol 2011, 77:302-311.
  6. Torres-Garcia W, Brown SD, Johnson RH, Zhang W, Runger GC, Meldrum DR: Integrative analysis of transcriptomic and proteomic data of Shewanella oneidensis: missing value imputation using temporal datasets. Mol BioSyst 2011, 7:1093-1104.
  7. Kalamorz F, Keis S, McMillan DGG, Olsson K, Stanton J-A, Stockwell P, Black MA, Klingeman DM, Land ML, Han CS et al: Draft genome sequence of thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1. J Bacteriol 2011, 193:4290-4291.
  8. Hauser LJ, Land ML, Brown SD, Larimer F, Keller KL, Rapp-Giles BJ, Price MN, Lin M, Bruce DC, Detter JC et al: The complete genome sequence and updated annotation of Desulfovibrio alaskensis G20. J Bacteriol 2011, 193:4268-4269.
  9. Gilmour CC, Elias DA, Kucken AM, Brown SD, Palumbo AV, Schadt CW, Wall JD: Sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation. Appl Environ Microbiol 2011, 77:3938-3951.
  10. Chauhan A, Layton AC, Williams D, Smartt AE, Ripp S, Karpinets TV, Brown SD, Sayler GS: Draft genome sequence of the polycyclic aromatic hydrocarbon-degrading, genetically engineered bioluminescent bioreporter Pseudomonas fluorescens HK44. J Bacteriol 2011:JB.05530-05511.
  11. Brown SD, Wall JD, Kucken AM, Gilmour CC, Podar M, Brandt CC, Teshima H, Detter JC, Han CS, Land ML et al: Genome sequence of the mercury-methylating and pleomorphic Desulfovibrio africanus strain Walvis Bay. J Bacteriol 2011, 193:4037-4038.
  12. Brown SD, Gilmour CC, Kucken AM, Wall JD, Elias DA, Brandt CC, Podar M, Chertkov O, Held B, Bruce DC et al: Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132. J Bacteriol 2011, 193:2078-2079.
  13. Brown SD, Begemann MB, Mormile MR, Wall JD, Han CS, Goodwin LA, Pitluck S, Land ML, Hauser LJ, Elias DA: Complete genome sequence of the haloalkaliphilic, hydrogen-producing bacterium Halanaerobium hydrogeniformans. J Bacteriol 2011, 193:3682-3683.
  14. Yang SH, Pelletier DA, Lu TYS, Brown SD: The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Microbiol 2010, 10:135.
  15. Yang SH, Land ML, Klingeman DM, Pelletier DA, Lu TYS, Martin SL, Guo HB, Smith JC, Brown SD: Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2010, 107:10395-10400. F1000 post-publication review as a “must read”
  16. Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang L, Drake MM, Podar M, Brown SD et al: Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microbial Ecol 2010, 60:784-795.
  17. Pelletier DA, Suresh AK, Holton GA, McKeown C, Wang W, Gu B, Mortensen NP, Allison DP, Joy DC, Brown SD et al: Engineered cerium oxide nanoparticles: Effects on bacterial growth and viability. Appl Environ Microbiol 2010, 76:7981-7989.
  18. Green SJ, Prakash O, Gihring TM, Akob DM, Jasrotia P, Jardine PM, Watson DB, Brown SD, Palumbo AV, Kostka JE: Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination. Appl Environ Microbiol 2010, 76:3244-3254.
  19. Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B et al: Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T. J Bacteriol 2010, 192:6099-6100.
  20. Bochner B, Gomez V, Ziman M, Yang SH, Brown SD: Phenotype MicroArray Profiling of Zymomonas mobilis ZM4. Appl Biochem Biotechnol 2010, 161:116-123.
  21. Yang SH, Tschaplinski TJ, Engle NL, Carroll SL, Martin SL, Davison BH, Palumbo AV, Rodriguez M, Brown SD: Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC Genomics 2009, 10:34.
  22. Yang SH, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB, Pan CL, Kouvelis VN, Typas MA, Pelletier DA et al: Improved genome annotation for Zymomonas mobilis. Nat Biotechnol 2009, 27:893-894.
  23. Learman DR, Yi H, Brown SD, Martin SL, Geesey GG, Stevens AM, Hochella MF: Involvement of Shewanella oneidensis MR-1 LuxS in Biofilm Development and Sulfur Metabolism. Appl Environ Microbiol 2009, 75:1301-1307.
  24. Learman DR, Bose S, Wigginton NS, Brown SD, Hochella MF: Reduction of hematite nanoparticles by Shewanella oneidensis MR-1. Geochim Cosmochim Acta 2007, 71:A551-A551.
  25. Brown SD, Raman B, McKeown CK, Kale SP, He ZL, Mielenz JR: Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray. Appl Biochem Biotechnol 2007, 137:663-674.
  26. Leaphart AB, Thompson DK, Huang K, Alm E, Wan XF, Arkin A, Brown SD, Wu LY, Yan TF, Liu XD et al: Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. J Bacteriol 2006, 188:1633-1642.
  27. Chourey K, Thompson MR, Morrell-Falvey J, VerBerkmoes NC, Brown SD, Shah M, Zhou JZ, Doktycz M, Hettich RL, Thompson DK: Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1. Appl Environ Microbiol 2006, 72:6331-6344.
  28. Brown SD, Thompson MR, VerBerkmoes NC, Chourey K, Shah M, Zhou JZ, Hettich RL, Thompson DK: Molecular dynamics of the Shewanella oneidensis response to chromate stress. Mol Cellular Proteomics 2006, 5:1054-1071.
  29. Brown SD, Martin M, Deshpande S, Seal S, Huang K, Alm E, Yang YF, Wu LY, Yan TF, Liu XD et al: Cellular response of Shewanella oneidensis to strontium stress. Appl Environ Microbiol 2006, 72:890-900.
  30. Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS et al: Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 2002, 184:3086-3095.
  31. Sullivan JT, Brown SD, Yocum RR, Ronson CW: The bio operon on the acquired symbiosis island of Mesorhizobium sp strain R7A includes a novel gene involved in pimeloyl-CoA synthesis. Microbiol 2001, 147:1315-1322.

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Curriculum Vitae