Research Project: Biochemical Technologies to Enable the Commercial Production of Biofuels from Lignocellulosic Biomass

Location: Bioenergy Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Pathway-based signature transcriptional profiles as tolerance phenotypes for the adapted industrial yeast Saccharomyces cerevisiae resistant to furfural and HMF - (Peer Reviewed Journal)
Liu, Z., Ma, M. 2020. Distinctive expressions of transposable element genes impact adaptation of the industrial yeast Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. 104: 3473-3492. https://doi.org/10.1007/s00253-020-10434-0.

Protein expression analysis revealed a fine-tuned mechanism of in situ detoxification pathway for the tolerant industrial yeast Saccharomyces cerevisiae - (Peer Reviewed Journal)
Liu, Z., Huang, X., Zhou, Q., Xu, J. 2019. Protein expression analysis revealed a fine-tuned mechanism of in situ detoxification pathway for the tolerant industrial yeast Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. 103:5781–5796. https://doi.org/10.1007/s00253-019-09906-9.

Adaptive laboratory evolution of nanocellulose-producing bacterium - (Peer Reviewed Journal)
Vasconcellos, V.M., Farinas, C.S., Ximenes, E., Slininger, P., Ladisch, M. 2019. Adaptive laboratory evolution of nanocellulose-producing bacterium. Biotechnology and Bioengineering. 116(8):1923-1933. https://doi.org/10.1002/bit.26997.

Genetic transformation of Coniochaeta sp. 2T2.1, key fungal member of a lignocellulose-degrading microbial consortium - (Peer Reviewed Journal)
Nichols, N.N., Hector, R.E., Frazer, S.E. 2019. Genetic transformation of Coniochaeta sp. 2T2.1, key fungal member of a lignocellulose-degrading microbial consortium. Biology Methods and Protocols. 4:1-5. https://doi.org/10.1093/biomethods/bpz001.

Improved cellulosic ethanol production from corn stover with a low cellulase input using a ß-glucosidase-producing yeast following a dry biorefining process - (Peer Reviewed Journal)
Geberekidan, M., Zhang, J., Liu, Z.L., Bao, J. 2018. Improved cellulosic ethanol production from corn stover with a low cellulase input using a ß-glucosidase producing yeast. Bioprocess and Biosystems Engineering. 42(2): 297-304. https://doi.org/10.1007/s00449-018-2034-9.

Engineering Candida phangngensis – an oleaginous yeast from the Yarrowia clade – for enhanced detoxification of lignocellulose-derived inhibitors and lipid overproduction - (Peer Reviewed Journal)
Quarterman, J.C., Slininger, P.J., Hector, R.E., Dien, B.S. 2018. Engineering Candida phangngensis – an oleaginous yeast from the Yarrowia clade – for enhanced detoxification of lignocellulose-derived inhibitors and lipid overproduction. Federation Of European Microbiological Societies Yeast Research. 18(8):foy102. https://doi.org/10.1093/femsyr/foy102.

Screening for oily yeasts able to convert hydrolyzates from biomass to biofuels while maintaining industrial process relevance - (Peer Reviewed Journal)
Slininger, P.J., Dien, B.S., Quarterman, J.C., Thompson, S.R., Kurtzman, C.P. 2019. Screening for oily yeasts able to convert hydrolyzates from biomass to biofuels while maintaining industrial process relevance. Methods in Molecular Biology. 1995:249-283. https://doi.org/10.1007/978-1-4939-9484-7_16.

Reprogrammed pathways of genetically engineered industrial yeast for xylose utilization - (Abstract Only)
Liu, Z.L. 2018. Reprogrammed pathways of genetically engineered industrial yeast for xylose utilization [abstract]. Biotechnology for Fuels and Chemicals Symposium Proceedings. M27.

Tolerant industrial yeast Saccharomyces cerevisiae posses a more robust cell wall integrity signaling pathway against 2-furaldehyde and 5-(hydroxymethyl)-2-furaldehyde - (Peer Reviewed Journal)
Liu, Z.L., Wang, X., Weber, S.A. 2018. Tolerant industrial yeast Saccharomyces cerevisiae posses a more robust cell wall integrity signaling pathway against 2-furaldehyde and 5-(hydroxymethyl)-2-furaldehyde. Journal of Biotechnology. 276-277:15-24. doi: 10.1016/j.jbiotec.2018.04.002.

Understanding the tolerance of the industrial yeast Saccharomyces cerevisiae against a major class of toxic aldehyde compounds - (Review Article)
Liu, Z.L. 2018. Understanding the tolerance of the industrial yeast Saccharomyces cerevisiae against a major class of toxic aldehyde compounds. Applied Microbiology and Biotechnology. 102(13):5369-5390. doi: 10.1007/s00253-018-8993-6.

Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae - (Peer Reviewed Journal)
Quanzhou, F., Liu, Z.L., Weber, S.A., Li, S. 2018. Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae. PLoS One. 13(4):e0195633. doi: 10.1371/journal.pone.0195633.

Use of green fluorescent protein to monitor fungal growth in biomass hydrolysate - (Peer Reviewed Journal)
Nichols, N.N., Quarterman, J.C., Frazer, S.E. 2018. Use of green fluorescent protein to monitor fungal growth in biomass hydrolysate. Biology Methods and Protocols. 3(1)bpx012. doi: 10.1093/biomethods/bpx012.

Draft genome sequence of the D-Xylose-Fermenting yeast Spathaspora xylofermentans UFMG-HMD23.3 - (Peer Reviewed Journal)
Lopes, D.D., Cibulski, S.P., Mayer, F.Q., Siqueira, F.M., Rosa, C.A., Hector, R.E., Ayub, M.A.Z. 2017. Draft genome sequence of the D-Xylose-Fermenting yeast Spathaspora xylofermentans UFMG-HMD23.3. Genome Announcements. 5(33):e00815-17.

Cellobiose fermenting yeast produces varied forms of native ß-glucosidase - (Abstract Only)
Wang, X., Liu, Z.L., Weber, S. 2017. Cellobiose fermenting yeast produces varied forms of native ß-glucosidase [abstract]. For Symposium of Biotechnology for Fuels and Chemicals, May 1-4, 2017, San Francisco, California. M25.

Techniques for the evolution of robust pentose-fermenting yeast for bioconversion of lignocellulose to ethanol - (Peer Reviewed Journal)
Slininger, P.J., Shea-Andersh, M.A., Thompson, S.R., Dien, B.S., Kurtzman, C.P., Sousa, L.D., Balan, V. 2016. Techniques for the evolution of robust pentose-fermenting yeast for bioconversion of lignocellulose to ethanol. Journal of Visualized Experiments. 116:1-15. doi: 10.3791/54227.

Process strategies for high titers of lipid production by oleaginous yeasts in undetoxified hydrolyzates of lignocellulosic biomass - (Abstract Only)
Patricia J. Slininger*, Bruce S. Dien, Cletus P. Kurtzman, Bryan R. Moser, Erica L. Bakota, Stephanie R.Thompson, Patricia J. O’Bryan, Michael A. Cotta, Venkatesh Balan, Mingjie Jin, Leonardo D. Sousa, Bruce E. Dale. Process Strategies for High Titers of Lipid Production by Oleaginous Yeasts in Undetoxified Hydrolyzates of Lignocellulosic Biomass. Proceedings of the 2016 AICHE Annual Meeting, Biochemical Conversion Processes in Forest/Plant Biomass Biorefineries Session, Paper # 567b, San Francisco, CA, November 13-18, 2016.

Comparative physiology of forty-five Yarrowia lipolytica strains grown on pretreated switchgrass hydrolysate - (Abstract Only)
Quarterman, J.C., Slininger, P.J., Kurtzman, C.P., Dien, B.S. 2016. Comparative physiology of forty-five Yarrowia lipolytica strains grown on pretreated switchgrass hydrolysate [abstract]. Biotechnology for Fuels and Chemicals. M79

A new source of resistance to 2-furaldehyde from Scheffersomyces (Pichia) stipitis for sustainable lignocellulose-to-biofuel conversion - (Peer Reviewed Journal)
Wang, X., Liu, Z.L., Ma, M., Zhang, X. 2017. A new source of resistance to 2-furaldehyde from Scheffersomyces (Pichia) stipitis for sustainable lignocellulose-to-biofuel conversion. Applied Microbiology and Biotechnology. 101:4981–4993. doi: 10.1007/s00253-017-8208-6.

GRE2 from Scheffersomyces stipitis as an aldehyde reductase contributes tolerance to aldehyde inhibitors derived from lignocellulosic biomass - (Peer Reviewed Journal)
Wang, X., Ma, M., Liu, Z.L., Xiang, Q., Li, X., Liu, N., Zhang, X. 2016. GRE2 from Scheffersomyces stipitis as an aldehyde reductase contributes tolerance to aldehyde inhibitors derived from lignocellulosic biomass. Applied Microbiology and Biotechnology. 100(15):6671-6682. doi: 10.1007/s00253-016-7445-4.

Genomic mechanisms of stress tolerance for the industrial yeast Saccharomyces cerevisiae against the major chemical classes of inhibitors derived from lignocellulosic biomass conversion - (Abstract Only)
Liu, Z.L. 2016. Genomic mechanisms of stress tolerance for the industrial yeast Saccharomyces cerevisiae against the major chemical classes of inhibitors derived from lignocellulosic biomass conversion [abstract]. International Conference on Yeasts. p. 388.

Two new native ß-glucosidases from Clavispora NRRL Y-50464 confer its dual function as cellobiose fermenting ethanologenic yeast - (Peer Reviewed Journal)
Wang, X., Liu, Z.L., Weber, S.A., Zhang, X. 2016. Two new native ß-glucosidases from Clavispora NRRL Y-50464 confer its dual function as cellobiose fermenting ethanologenic yeast. PLoS One. 11(3):e0151293. doi: 10.1371/journal.pone.0151293.

Tolerant yeast in situ detoxifies major class of toxic chemicals while producing ethanol - (Abstract Only)
Liu, Z.L. 2016. Tolerant yeast in situ detoxifies major class of toxic chemicals while producing ethanol. In: TechConnect World Innovation Conference, May 22-25, 2016, National Harbor, Maryland. #705.

Systems biology and pathway engineering enable Saccharomyces cerevisiae to utilize C-5 and C-6 sugars simultaneously for cellulosic ethanol production - (Abstract Only)
Liu, Z.L., Moon, J. 2016. Systems biology and pathway engineering enable Saccharomyces cerevisiae to utilize C-5 and C-6 sugars simultaneously for cellulosic ethanol production. In: TechConnect World Innovation Conference, May 22-25, 2016, National Harbor, Maryland. #706.

Lower-cost cellulosic ethanol production using cellobiose fermenting yeast Clavispora NRRL Y-50464 - (Abstract Only)
Liu, Z.L., Weber, S.A. 2016. Lower-cost cellulosic ethanol production using cellobiose fermenting yeast Clavispora NRRL Y-50464. In: TechConnect World Innovation Conference, May 22-25, 2016, National Harbor, Maryland. p. 388.

Technical assessment of cellulosic ethanol production using ß-glucosidase producing yeast Clavispora NRRL Y-50464 - (Peer Reviewed Journal)
Liu, Z., Cotta, M.A. 2015. Technical assessment of cellulosic ethanol production using ß-glucosidase producing yeast Clavispora NRRL Y-50464. BioEnergy Research. DOI: 10.1007/s12155-014-9575-9.

A reference model systesm of industrial yeasts Saccharomyces cerevisiae is needed for development of the next-generation biocatalyst toward advanced biofuels production - (Other)
Liu, Z., Wang, X. 2015. A reference model systesm of industrial yeasts Saccharomyces cerevisiae is needed for development of the next-generation biocatalyst toward advanced biofuels production. Journal of Microbial and Biochemical Technology. 7:6. doi: 10.4172/1948-5948.1000e125

Cellulosic ethanol production from green solvent-pretreated rice straw - (Peer Reviewed Journal)
Kumar, A.K., Parikh, B.S., Shah, E., Liu, L.Z., Cotta, M.A. 2016. Cellulosic ethanol production from green solvent-pretreated rice straw. Biocatalysis and Agricultural Biotechnology. 7:14-23. doi: 10.1016/j.bcab.2016.04.008.

Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment - (Peer Reviewed Journal)
Yi, X., Gu, H., Gao, Q., Liu, Z.L., Bao, J. 2015. Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment. Biotechnology for Biofuels. 8(1):153. doi: 10.1186/s13068-015-0333-9.

Genomic mechanisms of stress tolerance for the industrial yeast Saccharomyces cerevisiae against major chemical classes of inhibitors - (Abstract Only)
Liu, Z. 2015. Genomic mechanisms of stress tolerance for the industrial yeast Saccharomyces cerevisiae against major chemical classes of inhibitors [abstract]. Meeting Abstract. p. 1.

Virulence structure of Blumeria graminis f.sp. tritici and its genetic diversity by ISSR and SRAP profiling analyses - (Peer Reviewed Journal)
Liu, N., Liu, Z., Guoshu, G., Zhang, M., Wang, X., Zhou, Y., Qi, X., Chen, H., Yang, J., Luo, P., Yang, C. 2015. Virulence structure of Blumeria graminis f.sp. tritici and its genetic diversity by ISSR and SRAP profiling analyses. PLoS One. DOI: 10.1371/journal.pone.0130881.

Process strategies to maximize lipid accumulations of novel yeast in acid and base treated hydrolyzates - (Abstract Only)
Slininger, P.J., Dien, B.S., Moser, B.R., Bakota, E.L., Evangelista, R.L., Thompson, S.R., O Bryan, P.J., Cotta, M.A., Balan, V., Xue, Y., Jin, M., Orjuela, A., De Costa Sousa, L., Dale, B. 2015. Process strategies to maximize lipid accumulations of novel yeast in acid and base treated hydrolyzates [abstract].

Signature gene expressions of cell wall integrity pathway concur with tolerance response of industrial yeast Saccharomyces cerevisiae against biomass pretreatment inhibitors - (Abstract Only)
Liu, Z.L. 2015. Signature gene expressions of cell wall integrity pathway concur with tolerance response of industrial yeast Saccharomyces cerevisiae against biomass pretreatment inhibitors [abstract]. Meeting Abstract. pp. 211-212..