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Chemical and Biological Process Development

Ziyu Dai

Ziyu Dai

Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352


Ziyu Dai concentrates his work in the area of the molecular biology and biotechnology of eukaryotic systems. He is currently applying his expertise to research on filamentous fungi to develop biobased technology and products, and is heading the fungal genetics component of the Lab's Bio-based Products Initiative. Dr. Dai's diverse experience includes the isolation, analysis, and manipulation of genes. He has isolated a series of eukaryotic genes and examined their functions and regulations in the eukaryotic systems. This work has resulted in two issued patents and five pending patents. Dr. Dai has also studied the transgenic expression of various proteins in green plants, including the expression of various microbial cellulase enzymes and human blood proteins in tobacco and potato plants. He has published extensively in the area of molecular biology, biochemistry, and physiology of green plants.

PNNL Patents

Education and Credentials

  • Ph.D., Botany, Washington State University, 1993
  • M.S., Agronomy, Southern China Agricultural University, 1986
  • B.S., Agronomy, Southern China Agricultural University, 1983

PNNL Publications


  • Bredeweg EL, KR Pomraning, Z Dai, JB Nielsen, EJ Kerkhoven, and SE Baker. 2017. "A Molecular Genetic Toolbox for Yarrowia lipolytica." Biotechnology for Biofuels 10:Article No. 2.  doi:10.1186/s13068-016-0687-7
  • 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


  • Liu J, M Arentshorst, D Nair, Z Dai, SE Baker, J Frisvad, KF Nielsen, PJ Punt, and AF Ram. 2016. "Identification of a classical mutant in the industrial host Aspergillus niger by systems genetics: LaeA is required for citric acid production and regulates the formation of some secondary metabolites." G3 Genes, Genomes, Genetics 6(1):193-204.  doi:10.1534/g3.115.024067
  • Mo KF, Z Dai, and DS Wunschel. 2016. "Production and Characterization of Desmalonichrome Relative Binding Affinity for Uranyl Ions in Relation to other Siderophores." Journal of Natural Products 79(6):1492-1499.  doi:10.1021/acs.jnatprod.5b00933


  • Dai Z, UK Aryal, AK Shukla, W Qian, RD Smith, JK Magnuson, WS Adney, GT Beckham, R Brunecky, ME Himmel, SR Decker, X Ju, X Zhang, and SE Baker. 2013. "Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger." Fungal Genetics and Biology : FG & B 61:120-132.  doi:10.1016/j.fgb.2013.09.004
  • Kim JS, Z Dai, UK Aryal, RJ Moore, DG Camp, II, SE Baker, RD Smith, and W Qian. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing." Analytical Chemistry 85(14):6826-6832.  doi:10.1021/ac401000q


  • Beckham GT, Z Dai, JF Mattews, M Momany, CM Payne, WS Adney, SE Baker, and ME Himmel. 2012. "Harnessing glycosylation to improve cellulase activity." Current Opinion in Biotechnology 23(3):338-345.  doi:10.1016/j.copbio.2011.11.030
  • Wang L, UK Aryal, Z Dai, AC Mason, ME Monroe, Z Tian, J Zhou, D Su, KK Weitz, T Liu, DG Camp, II, RD Smith, SE Baker, and W Qian. 2012. "Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry." Journal of Proteome Research 11(1):143-56.  doi:10.1021/pr200916k


  • 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
  • Chou HL, Z Dai, CW Hsieh, and MS Ku. 2011. "High level expression of Acidothermus cellulolyticus -1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid." Biotechnology for Biofuels 4:Article No. 58.  doi:10.1186/1754-6834-4-58
  • Yang B, Z Dai, SY Ding, and CE Wyman. 2011. "Enzymatic Hydrolysis of Cellulosic Biomass." Biofuels 2(4):421-450.  doi:10.4155/BFS.11.116
  • Yang B, Z Dai, SY Ding, and CE Wyman. 2011. "Review: Enzymatic Hydrolysis of Cellulosic Biomass." Biofuels 2(4):421-450.  doi:10.4155/bfs.11.116




  • Lee AC, Z Dai, B Chen, H Wu, J Wang, A Zhang, L Zhang, TM Lim, and Y Lin. 2008. "Electrochemical Branched-DNA Assay for Polymerase Chain Reaction-Free Detection and Quantification of Oncogenes in Messenger RNA." Analytical Chemistry 80(24):9402-9410.  doi:10.1021/ac801263r
  • Taylor LE, Z Dai, SR Decker, R Brunecky, WS Adney, SY Ding, and ME Himmel. 2008. "Heterologous Expression of Glycosyl Hydrolases in planta: A New Departure for Biofuels ." Trends in Biotechnology 26(8):413-424. 


  • Baker SE, CF Wend, AD Martinez, JK Magnuson, EA Panisko, Z Dai, KS Bruno, KK Anderson, ME Monroe, DS Daly, and LL Lasure. 2007. "Genome and Proteome Analysis of Industrial Fungi." Chapter 1 in Exploitation of Fungi, ed. GD Robson, P van West and G Gadd, pp. 3-9.  Cambridge University Press, New York, NY.  doi:10.1017/CBO9780511902451.002


  • Dai Z, BS Hooker, RD Quesenberry, and SR Thomas. 2005. "Optimization of Acidothermus Celluloyticus Endoglucanase (E1) Production in Transgenic Tobacco Plants by Transcriptional, Post-transcription and Post-Translational Modification." Transgenic Research 14(5):627-643.  doi:10.1007/s11248-005-5695-5


  • Dai Z, X Mao, JK Magnuson, and LL Lasure. 2004. "Identification of Genes Associated with Morphology in Aspergillus Niger by Using Suppression Subtractive Hybridization ." Applied and Environmental Microbiology 70(4):2474-2485. 


  • Hooker BS, Z Dai, DB Anderson, RD Quesenberry, MF Ruth, and SR Thomas. 2001. "Production of Microbial Cellulases in Transgenic Crop Plants." In Glycosyl Hydrolases in Biomass Conversion. ACS Symposium Series, vol. 769, ed. ME Himmel, JO Baker, JN Saddler, pp. 55-90.  American Chemical Society, Washington DC. 
  • Mauzey-Amato JM, and Z Dai. 2001. "Functional Analysis of Plant Promoter rpL34 Using the GUS Marker Gene in New Tr,tnsgene Expression Vector pZD428." Journal of Undergraduate Research 1:37. 


  • Dai Z, BS Hooker, DB Anderson, and SR Thomas. 2000. "Improved Plant-based Production of E1 endoglucanase Using Potato: Expression Optimization and Tissue Targeting." Molecular Breeding 6(3):277-285. 


  • Dai Z, BS Hooker, RD Quesenberry, and J Gao. 1999. "Expression of Trichoderma reesei exo-cellobiohydrolase I transgenic tobacco leaves and calli." Applied Biochemistry and Biotechnology 77(9):689-699 . 

Chemical and Biological Process Development

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