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Chemical and Biological Process Development

David Culley

David Culley

Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352

Biography

Dave Culley has over 20 years laboratory research experience in the genetics, molecular biology and biochemistry of organisms ranging from archeal bacteria to higher plants. His research projects currently focus on the genetics and biochemistry of filamentous fungi as related to conversion of cellulosic biomass to advanced biofuels or commodity chemicals.

He has authored or co-authored more than 50 publications, including journal articles, review articles, book chapters, conference proceedings and technical reports. Dr. Culley originally joined PNNL in 2003 as part of the Environmental Microbiology group and transferred to the Fungal Biotechnology team in the Chemical & Biological Process Development Group in 2008.

Research Interests

  • Biochemical and biological conversion of cellulosic biomass to advanced biofuels.
  • Genome based investigations of the metabolic capabilities of filamentous fungi.
  • Biochemistry and bioenergetics of pentose sugar utilization in fungi
  • Genetics and biochemistry of secondary metabolite production.
  • Evolved associations between photosynthetic organisms and heterotrophic fungi.

Education and Credentials

  • Ph.D. Plant Physiology and Plant Breeding, University of Minnesota
  • B.A. Biology, University of California, Santa Cruz

PNNL Publications

2017

  • Dai Z, S Deng, DE Culley, KS Bruno, and JK Magnuson. 2017. "Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species." Applied Microbiology and Biotechnology 101(15):6099-6110.  doi:10.1007/s00253-017-8357-7
  • Mondo SJ, RO Dannebaum, RC Kuo, KB Louie, AJ Bewick, KM LaButti, S Haridas, A Kuo, A Salamov, S Ahrendt, R Lau, BP Bowen, A Lipzen, W Sullivan, WB Andreopoulos, A Clum, E Lindquist, C Daum, TR Northen, GK Ramamoorthy, RJ Schmitz, A Gryganskyi, DE Culley, JK Magnuson, T James, MA O'Malley, JE Stajich, J Spatafora, A Visel, and IV Grigoriev. 2017. "Widespread Adenine N6-methylation of Active Genes in Fungi." Nature Genetics 49(6):964-968.  doi:10.1038/ng.3859

2016

  • Goodwin S, CB McCorison, JR Cavaletto, DE Culley, KM LaButti, SE Baker, and IV Grigoriev. 2016. "The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete." Fungal Biology 120(8):961-974.  doi:10.1016/j.funbio.2016.05.003
  • Gunsalus R, LE Cook, BR Crable, L Rohlin, E McDonald, H Mouttaki, JR Sieber, N Poweleit, H Zhou, A Lapidus, HE Daligault, ML Land, P Gilna, N Ivanova, N Kyripides, DE Culley, and MJ McInerney. 2016. "Complete genome sequence of Methanospirillum hungatei type strain JF1." Standards in Genomic Sciences 11:Article No. 2.  doi:10.1186/s40793-015-0124-8

2013

  • Anderson LN, DE Culley, BA Hofstad, LM Chauvigne-Hines, EM Zink, SO Purvine, RD Smith, SJ Callister, JM Magnuson, and AT Wright. 2013. "Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30." Molecular Biosystems 9(12):2992-3000.  doi:10.1039/c3mb70333a
  • Piao H, LM Markillie, DE Culley, RI Mackie, and M Hess. 2013. "Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics." Advances in Microbiology 3(1):101-107.  doi:10.4236/aim.2013.31016
  • Tamano K, KS Bruno, SA Karagiosis, DE Culley, S Deng, JR Collett, M Umemura, H Koike, SE Baker, and M Machida. 2013. "Increased Production of Fatty Acids and Triglycerides in Aspergillus oryzae by Enhancing Expressions of Fatty Acid Synthesis-Related Genes." Applied Microbiology and Biotechnology 97(1):269-281.  doi:10.1007/s00253-012-4193-y

2012

  • Mitchell AC, L Peterson, CL Reardon, SB Reed, DE Culley, MF Romine, and GG Geesey. 2012. "Role of Outer Membrane C-Type Cytochromes MtrC and OmcA in Shewanella Oneidensis MR-1 Cell Production, Accumulation, and Detachment During Respiration on Hematite." Geobiology 10(4):355-370.  doi:10.1111/j.1472-4669.2012.00321.x
  • Sorensen A, BK Ahring, M Lubeck, W Ubhayasekera, KS Bruno, DE Culley, and PS Lubeck. 2012. "Identifying and characterizing the most significant -glucosidase of the novel species Aspergillus saccharolyticus." Canadian Journal of Microbiology 58(9):1035-1046.  doi:10.1139/w2012-076

2011

  • Andersen MR, M Salazar, P Schaap, P van de Vondervoort, DE Culley, J Thykaer, JC Frisvad, KF Nielsen, R Albang, K Albermann, R Berka, G Braus, SA Braus-Stromeyer, L Corrochano, Z Dai, P van Dijck, G Hofmann, LL Lasure, JK Magnuson, H Menke, M Meijer, S Meijer, JB Nielsen, ML Nielsen, A van Ooyen, HJ Pel, L Poulsen, R Samson, H Stam, A Tsang, JM van den Brink, A ATkins, A Aerts, H Shapiro, J Pangilinan, A Salamov, Y Lou, E Lindquist, S Lucas, J Grimwood, IV Grigoriev, CP Kubicek, D Martinez, N van Peij, JA Roubos, JB Nielsen, and SE Baker. 2011. "Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88." Genome Research 21(6):885-897.  doi:10.1101/gr.112169.110

2010

  • Gao H, S Barua, Y Liang, L Wu, Y Dong, SB Reed, J Chen, DE Culley, DW Kennedy, Y Yang, Z He, KH Nealson, JK Fredrickson, JM Tiedje, MF Romine, and J Zhou. 2010. "Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration." Microbial Biotechnology 3(4):455-466.  doi:10.1111/j.1751-7915.2010.00181.x
  • Gupta N, KK Hixson, DE Culley, RD Smith, and PA Pevzner. 2010. "Analyzing Protease Specificity and Detecting in Vivo Proteolytic Events Using Tandem Mass Spectrometry." Proteomics 10(15):2833-2844. 
  • Kovacik WP, Jr, JC Scholten, DE Culley, R Hickey, W Zhang, and FJ Brockman. 2010. "Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed." Microbiology 156(Pt. 8):2418-2427.  doi:10.1099/mic.0.036715-0
  • Plugge CM, JC Scholten, DE Culley, L Nie, FJ Brockman, and W Zhang. 2010. "Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism." Microbiology 156(9):2746-2756. 
  • Sieber JR, DR Sims, CF Han, E Kim, A Lykidis, A Lapidus, E McDonald, L Rohlin, DE Culley, R Gunsalus, and MJ McInerney. 2010. "The Genome of Syntrophomonas Wolfei: New Insights into Syntrophic Metabolism and Biohydrogen Production." Environmental Microbiology 12(8):2289-2301. 

2009

  • Baker SE, KS Bruno, MG Butcher, JR Collett, DE Culley, Z Dai, JK Magnuson, and EA Panisko. 2009. PNNL Fungal Biotechnology Core DOE-OBP ProjectPNNL-18820, Pacific Northwest National Laboratory, Richland, WA. 
  • Le Crom S, W Schackwitz, L Pennacchiod, JK Magnuson, DE Culley, JR Collett, JX Martin, IS Druzhinina, H Mathis, F Monot, B Seiboth, B Cherry, M Rey, R Berka, CP Kubicek, SE Baker, and A Margeot. 2009. "Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing." Proceedings of the National Academy of Sciences of the United States of America 106(38):16151-16156. 

2008

  • Chivian D, E Brodie, E Alm, DE Culley, PS Dehal, T DeSantis, T Gihring, A Lapidus, LH Lin, SR Lowry, DP Moser, P Richardson, G Southam, G Wanger, L Pratt, G Andersen, TC Hazen, FJ Brockman, AP Arkin, and TC Onstott. 2008. "Environmental genomics reveals a single-species ecosystem deep within the earth." Science 322(5899):275-278.  doi:10.1126/science.1155495
  • Chivian D, EL Brodie, E Alm, DE Culley, PS Dehal, T DeSantis, TM Gihring, A Lapidus, LH Lin, SR Lowry, DP Moser, P Richardson, G Southam, G Wanger, LM Pratt, G Andersen, TC Hazen, FJ Brockman, AP Arkin, and TC Onstott. 2008. "Environmental genomics reveals a single-species ecosystem deep within earth." Science 322:275-278.  doi:10.1126/science.1155495
  • Pinchuk GE, CG Ammons, DE Culley, SM Li, JS McLean, MF Romine, KH Nealson, JK Fredrickson, and AS Beliaev. 2008. "Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction." Applied and Environmental Microbiology 74(4):1198-1208.  doi:10.1128/AEM.02026-07

2007

  • Bretschger O, A Obraztsova, CA Sturm, IS Chang, YA Gorby, SB Reed, DE Culley, CL Reardon, S Barua, MF Romine, J Zhou, AS Beliaev, R Bouhenni, D Saffarini, F Mansfeld, BH Kim, JK Fredrickson, and KH Nealson. 2007. "Current Production and Metal Oxide Reduction by Shewanella Oneidensis MR-1 Wild Type and Mutants." Applied and Environmental Microbiology 73(21):7003-7012.  doi:10.1128/AEM.01087-07
  • Coleman JR, DE Culley, WB Chrisler, and FJ Brockman. 2007. "mRNA-targeted Fluorescent in Situ Hybridization (FISH) of Gram-negative Bacteria Without Template Amplification or Tyramide Signal Amplification." Journal of Microbiological Methods 71(3):246-255.  doi:10.1016/j.mimet.2007.09.011
  • Nie L, G Wu, DE Culley, JC Scholten, and W Zhang. 2007. "Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications." Critical Reviews in Biotechnology 27(2):63-75.  doi:10.1080/07388550701334212
  • Scholten JC, DE Culley, FJ Brockman, G Wu, and W Zhang. 2007. "Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer." Biochemical and Biophysical Research Communications 352(1):48-54. 
  • Scholten JC, DE Culley, L Nie, KJ Munn, L Chow, FJ Brockman, and W Zhang. 2007. "Development and Assessment of Whole-Genome Oligonucleotide Microarrays to Analyze an Anaerobic Microbial Community and its Responses to Oxidative Stress." Biochemical and Biophysical Research Communications 358(2):571-577.  doi:10.1016/j.bbrc.2007.04.160
  • Zhang W, DE Culley, L Nie, and JC Scholten. 2007. "Comparative Transcriptome Analysis of Desulfovibrio Vulgaris Grown in Planktonic Culture and Mature Biofilm on a Steel Surface." Applied Microbiology and Biotechnology 76(2):447-457.  doi:10.1007/s00253-007-1014-9

2006

  • Culley DE, WP Kovacik, Jr, FJ Brockman, and W Zhang. 2006. "Optimization of RNA Isolation from the Archaebacterium Methanosarcina Barkeri and Validation for Oligonucleotide Microarray Analysis." Journal of Microbiological Methods 67(1):36-43.  doi:10.1016/j.mimet.2006.02.014
  • Gorby YA, S Yanina, JS Mclean, KM Rosso, DM Moyles, A Dohnalkova, TJ Beveridge, IS Chang, BH Kim, KS Kim, DE Culley, SB Reed, MF Romine, D Saffarini, EA Hill, L Shi, DA Elias, DW Kennedy, GE Pinchuk, K Watanabe, S Ishii, B Logan, KH Nealson, and JK Fredrickson. 2006. "Electrically Conductive Bacterial Nanowires Produced by Shewanella Oneidensis Strain MR-1 and Other Microorganisms ." Proceedings of the National Academy of Sciences of the United States of America 103(30):11358-11363. 
  • Marshall MJ, AS Beliaev, A Dohnalkova, DW Kennedy, L Shi, Z Wang, MI Boyanov, B Lai, KM Kemner, JS Mclean, SB Reed, DE Culley, VL Bailey, CJ Simonson, D Saffarini, MF Romine, JM Zachara, and JK Fredrickson. 2006. "c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis ." PloS Biology 4(8):1324-1333. 
  • Zhang W, DE Culley, G Wu, and FJ Brockman. 2006. "Two-Component Signal Transduction Systems of Desulfovibrio Vulgaris: Structural and Phylogenetic Analysis and Deduction of Putative Cognate Pairs." Journal of Molecular Evolution 62:473-487.  doi:10.1007/s00239-005-0116-1
  • Zhang W, DE Culley, JC Scholten, M Hogan, L Vitiritti, and FJ Brockman. 2006. "Global Transcriptomic Analysis of Desulfovibrio vulgaris Grown on Different Carbon Sources." Antonie Van Leeuwenhoek 89(2):221-237. 
  • Zhang W, DE Culley, L Nie, and FJ Brockman. 2006. "DNA Microarray Analysis of Anaerobic Methanosarcina Barkeri Reveals Responses to Heat Shock and Air Exposure." Journal of Industrial Microbiology and Biotechnology 33(9):784-790.  doi:10.1007/s10295-006-0114-3
  • Zhang W, DE Culley, M Hogan, L Vitiritti, and FJ Brockman. 2006. "Oxidative Stress and Heat-Shock Responses in Desulfovibrio vulgaris by Genome-Wide Transcriptomic Analysis." Antonie Van Leeuwenhoek 90:41-55.  doi:10.1007/s10482-006-9059-9
  • Zhang W, DE Culley, MA Gritsenko, RJ Moore, L Nie, JC Scholten, K Petritis, EF Strittmatter, DG Camp, II, RD Smith, and FJ Brockman. 2006. "LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris." Biochemical and Biophysical Research Communications 349(4):1412-1419.  doi:10.1016/j.bbrc.2006.09.019
  • Zhang W, DE Culley, MA Gritsenko, RJ Moore, L Nie, JC Scholten, K Petritis, EF Strittmatter, DG Camp, II, RD Smith, and FJ Brockman. 2006. "LC-MS/MS Based Proteomic Analysis and Functional Inference of Hypothetical Proteins in Desulfovibrio Vulgaris." Biochemical and Biophysical Research Communications 349(4):1412-1419.  doi:10.1016/j.bbrc.2006.09.019
  • Zhang W, MA Gritsenko, RJ Moore, DE Culley, L Nie, K Petritis, EF Strittmatter, DG Camp, II, RD Smith, and FJ Brockman. 2006. "A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry." Proteomics 6(15):4286-4299.  doi:10.1002/pmic.200500930

2005

  • Wu G, DE Culley, and W Zhang. 2005. "Predicted Highly Expressed Genes in the Genomes of Streptomyces Coelicolor and Streptomyces Avermitilis and the Implications for their Metabolism." Microbiology 151(7):2175-2187.  doi:10.1099/mic.0.27833-0

Chemical and Biological Process Development

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