Projects

Genomics and Engineering of Stress-Tolerant Microbes for Lower Cost Production of Biofuels and Bioproducts Appropriated (D)   Accession Number: 408957

Discovery and Application of Microbial Production and Formulation Biotechnologies to Enhance Biocontrol of Fungal Plant Diseases Appropriated (D)   Accession Number: 410257

Genomic Mechanisms of in Situ Detoxification of Biomass Conversion Inhibitors for Ethanologenic Yeast Saccharomyces Cerevisiae Grant (G)   Accession Number: 411588

Genomic Mechanisms of in Situ Detoxification of Biomass Conversion Inhibitors for Ethanologenic Yeast Saccharomyces Cerevisiae Reimbursable (R)   Accession Number: 411400

Publications

Profiling of the peripheral leukocyte transcriptome of dairy cattle reveals gene expression patterns associated with genetic potential for milk production - (Abstract) - (14-Jan-09)

Tolerant ethanologenic yeast for low-cost lignocellulosic biomass conversion to ethanol - (Abstract) - (28-Nov-08)

Mechanisms of tolerance and in situ detoxification of biomass conversion inhibitors by Saccharomyces cerevisiae - (Abstract) - (24-Oct-08)

Discrete dynamic system modeling for gene regulatory networks of HMF tolerance for ethanologenic yeast - (Peer Reviewed Journal) - (21-Oct-08)

Genomic mechanisms of inhibitor-detoxification for low-cost lignocellulosic bioethanol conversion - (Abstract)

Liu, Z., Moon, J., Mingzhou, S.J. 2008. Genomic mechanisms of inhibitor-detoxification for low-cost lignocellulosic bioethanol conversion [abstract]. Journal of Biotechnology 136S:S218.

Multiple gene mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and HMF by Saccharomyces cerevisiae - (Peer Reviewed Journal)

Liu, Z., Moon, J., Andersh, B.J., Slininger, P.J., Weber, S.A. 2008. Multiple gene mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and HMF by Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. 81:743-753.

Change your conventional practice of qRT-PCR: A simple robust quality control standard for yeast mRNA quantification analysis - (Abstract)

Liu, Z. 2008. Change your conventional practice of qRT-PCR: A simple robust quality control standard for yeast mRNA quantification analysis [abstract]. 12th International Conference on Yeasts. p. 140.

Culture nutrition and physiology impact the inhibitor tolerance of the yeast Pichia stipitis NRRL Y-7124 - (Peer Reviewed Journal)

Slininger, P.J., Gorsich, S.W., Liu, Z. 2009. Culture nutrition and physiology impact the inhibitor tolerance of the yeast Pichia stipitis NRRL Y-7124. Biotechnology and Bioengineering. 102(3):788-790.

Functional genomic studies lead in situ detoxification of fermentation inhibitors for low-cost cellulosic ethanol production - (Abstract) - (21-May-08)

Impact of inoculum production conditions on stress tolerance and fermentation efficiency of natural xylose-fermenting yeasts presented xylose and glucose - (Abstract)

Slininger, P.J., Liu, Z. 2008. Impact of inoculum production conditions on stress tolerance and fermentation efficiency of natural xylose-fermenting yeasts presented xylose and glucose [abstract]. Biotechnology for Fuels and Chemicals Symposium Proceedings. Abstract No. 5734

Validation and standardization of gene expression data for microarray and real time quantitative PCR using universal external RNA controls - (Abstract)

Liu, Z. 2007. Validation and standardization of gene expression data for microarray and real time quantitative PCR using universal external RNA controls [abstract]. Cambridge Healthtech Institute Conference on Quantitative PCR, Microarrays, and Biological Validation.

Enhanced L-(+)-lactic acid production by an adapted strain of Rhizopus oryzae using corncob hydrolysate - (Peer Reviewed Journal)

Bai, D., Li, S., Liu, Z., Cui, Z. 2007. Enhanced L-(+)-lactic acid production by an adapted strain of Rhizopus oryzae using corncob hydrolysate. Applied Biochemistry and Biotechnology. 144:79-85.

Absolute mRNA quantification of Pseudomonas fluorescens Pf-5 by qRT-PCR using universal RNA controls - (Abstract)

Liu, Z., Slininger, P.J. 2007. Absolute mRNA quantification of Pseudomonas fluorescens Pf-5 by qRT-PCR using universal RNA controls [abstract]. American Society for Microbiology.

Genomic engineering of Saccharomyces cerevisiae for biomass conversion to ethanol - (Abstract) - (03-Aug-07)

Multiple gene mediated aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae - (Abstract)

Liu, Z., Moon, J., Andersh, B.J., Slininger, P.J., Weber, S.A. 2007. Multiple gene mediated aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae [abstract]. Yeasts International Symposium. Abstract No. S-134.

A robust standard for absolute mRNA quantification of Saccharomyces cerevisiae by qRT-PCR using the universal RNA controls - (Abstract)

Liu, Z., Palmquist, D.E. 2007. A robust standard for absolute mRNA quantification of Saccharomyces cerevisiae by qRT-PCR using the universal RNA controls [abstract]. Yeasts International Symposium. Abstract No. S-84.

Lignocellulosic biomass conversion to ethanol by Saccharomyces - (Book/Chapter)

Liu, Z., Saha, B.C., Slininger, P.J. 2008. Lignocellulosic biomass conversion to ethanol by Saccharomyces. In: Wall, J., Harwood, C., Demain, A., editors. Bioenergy. Chapter 4. Washington, DC: ASM Press. p. 17-36.

Mechanisms of in situ detoxification of furfural and HMF by ethanologenic yeast Saccharomyces cerevisiae - (Abstract)

Liu, Z., Andersh, B.J., Slininger, P.J. 2007. Mechanisms of in situ detoxification of furfural and HMF by ethanologenic yeast Saccharomyces cerevisiae [abstract]. Biotechnology for Fuels and Chemicals Symposium Proceedings. Abstract No. 1B-28, p. 85.

Impact of culture nutrition on inhibitor tolerance and the conversion of high xylose concentrations to ethanol by Pichia stipitis NRRL Y-7124 - (Abstract)

Slininger, P.J., Liu, Z., Gorsich, S.W. 2007. Impact of culture nutrition on inhibitor tolerance and the conversion of high xylose concentrations to ethanol by Pichia stipitis NRRL Y-7124 [abstract]. Biotechnology for Fuels and Chemicals Symposium Proceedings. p. 88. Paper No. 1B-38.

Enhanced L(+)-lactic acid production from corncob hydrolysate by an adapted strain of Rhizopus oryzae - (Abstract)

Bai, D., Li, S., Liu, Z., Cui, Z. 2007. Enhanced L(+)-lactic acid production from corncob hydrolysate by an adapted strain of Rhizopus oryzae [abstract]. Biotechnology for Fuels and Chemicals Symposium Proceedings. Abstract No. 1B-44, p. 90.

Gene expression profiling for genetic merit in dairy cattle - (Abstract)

Rabel, C., Everts-Vam Der Womd, A., Everts, R., Band, M.R., Wallace, R.L., Liu, Z., Rodriguez-Zas, S., Lewin, H.A. 2007. Gene expression profiling for genetic merit in dairy cattle [abstract]. Plant and Animal Genome VX Conference Abstracts.

A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast - (Abstract) - (03-Dec-06)

Impact of culture nutrition on tolerance of furan inhibitors and the conversion of high xylose concentrations to ethanol by Pichia stipitis NRRL Y-7124 - (Abstract)

Slininger, P.J., Liu, Z., Gorsich, S.W. 2006. Impact of culture nutrition on tolerance of furan inhibitors and the conversion of high xylose concentrations to ethanol by Pichia stipitis NRRL Y-7124 [abstract]. American Institute of Chemical Engineers Annual Meeting. Paper No. 531d.

A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast - (Peer Reviewed Journal)

Song, M., Liu, Z. 2007. A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast. Lecture Notes in Bioinformatics. 4532:77-95.

Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR - (Peer Reviewed Journal)

Liu, Z., Slininger, P.J. 2007. Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR. Journal of Microbiological Methods. 68:486-496.

Transcriptional regulatory analysis reveals PDR3 and GCR1 as regulators of significantly induced genes by 5-hydroxymethylfurfural stress involved in bioethanol conversion for ethanologenic yeast Saccharomyces cerevisiae - (Abstract)

Liu, Z., Sinha, S. 2007. Transcriptional regulatory analysis reveals PDR3 and GCR1 as regulators of significantly induced genes by 5-hydroxymethylfurfural stress involved in bioethanol conversion for ethanologenic yeast saccharomyces cerevisiae [abstract]. Microarray Gene Expression Data Society (MGED 9) Meeting.

Gene Expression Response Impacting Desiccation Stress Tolerance for Cryptococcus Nodaensis (Nomen Nudem) Oh 182.9 Using Cross-Species Microarray Analysis - (Abstract)

Liu, Z., Schisler, D.A., Zhang, S. 2006. Gene expression response impacting desiccation stress tolerance for Cryptococcus nodaensis (nomen nudem) OH 182.9 using cross-species microarray analysis [abstract]. Yeast Genetics and Molecular Biology Meeting. Abstract No. 561C.

Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors - (Review Article)

Liu, Z. 2006. Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors. Applied Microbiology and Biotechnology. 73(1):27-36.

In Situ Detoxification of Fermentation Inhibitors by Stress Tolerant Ethanologenic Yeast for Low-Cost Biomass Conversion to Ethanol - (Abstract)

Liu, Z., Slininger, P.J. 2006. In situ detoxification of fermentation inhibitors by stress tolerant ethanologenic yeast for low-cost biomass conversion to ethanol [abstract]. World Bio-Energy 2006 Proceedings. p. 121.

Nitrogen Source and Mineral Optimization Enhance D-Xylose Conversion to Ethanol by the Yeast Pichia Stipitis Nrrl Y-7124 - (Peer Reviewed Journal)

Slininger, P.J., Dien, B.S., Gorsich, S.W., Liu, Z. 2006. Nitrogen source and mineral optimization enhance D-xylose conversion to ethanol by the yeast Pichia stipitis NRRL Y-7124. Applied Microbiology and Biotechnology. 72(6):1285-1296.

Engineering Stress-Tolerant Microbes for Lower Cost Production of Biofuels and Bioproducts - (Abstract)

Slininger, P.J., Liu, Z., Gorsich, S.W. 2005. Engineering stress-tolerant microbes for lower cost production of biofuels and bioproducts [abstract]. American Institute of Chemical Engineers Annual Meeting. Paper No. 303a.

Proposed Methods for Testing and Selecting the Ercc External Rna Controls - (Peer Reviewed Journal)

Liu, Z., Members of ERCC. 2005. Proposed methods for testing and selecting the ERCC external RNA controls. Biomed Central (BMC) Genomics. 6:150.

The External Rna Controls Consortium: a Progress Report - (Peer Reviewed Journal)

Liu, Z.L., External RNA Control Consortium. 2005. The external RNA controls consortium: A progress report. Nature Methods. 2(10):731-734.

Universal External Rna Quality Controls for Mrna Expression Analysis Using Microbial DNA Oligo Microarray and Real Time Quantitative Rt-Pcr - (Abstract)

Liu, Z., Slininger, P.J. 2005. Universal external RNA quality controls for mRNA expression analysis using microbial DNA oligo microarray and real time quantitative RT-PCR [abstract]. Eighth International Meeting of the Microarray Gene Expression Data Society. Poster #P161, p. 45-46.

Genomic Adaptive Response of Yeast to Biofuel Fermentation Inhibitors - (Abstract)

Liu, Z. 2005. Genomic adaptive response of yeast to biofuel fermentation inhibitors [abstract]. Society of Industrial Microbiology Annual Meeting. Abstract No. S37.

Mineral and Nitrogen Source Optimization Enhance D-Xylose Conversion to Ethanol by the Yeast Pichia Stipitis - (Abstract)

Slininger, P.J., Dien, B.S., Gorsich, S.W., Liu, Z. 2005. Mineral and nitrogen source optimization enhance d-xylose conversion to ethanol by the yeast Pichia stipitis [abstract]. Society of Industrial Microbiology Annual Meeting. Paper No. P07.

Physiological Responses to Furfural and Hmf and the Link to Other Stress Pathways - (Abstract)

Gorsich, S.W., Slininger, P.J., Liu, Z. 2005. Physiological responses to furfural and HMF and the link to other stress pathways [abstract]. European Congress on Biotechnology. Paper No. G.4.4.

A 7872 Cdna Microarray and Its Use in Bovine Functional Genomics - (Peer Reviewed Journal)

Everts, R.E., Band, M.R., Liu, Z., Kumar, C.G., Liu, L., Loor, J.J., Oliveria, R., Lewin, H.A. 2005. A 7872 cNDA microarray and its use in bovine functional genomics. Veterinary Immunology and Immunopathology. 105:235-245

Tolerance to Furfural-Induced Stress Is Associated with Pentose Phosphate Pathway Genes Zwf1, Gnd1, Rpe1,and Tkl1 in Saccharomyces Cerevisiae - (Peer Reviewed Journal)

Gorsich, S.W., Dien, B.S., Nichols, N.N., Slininger, P.J., Liu, Z., Skory, C.D. 2005. Tolerance to furfural-induced stress is associated with pentose phosphate pathway genes ZWF1, GND1, RPEL, and TKL1 in Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. 71(3):339-349.

Cold Shock During Liquid Production Increases Storage Shelf-Life of Cryptococcus Nodaensis Oh 182.9 after Air Drying - (Peer Reviewed Journal)

Zhang, S., Schisler, D.A., Jackson, M.A., Boehm, M.J., Slininger, P.J., Liu, Z. 2006. Cold shock during liquid production increases storage shelf-life of Cryptococcus nodaensis OH 182.9 after air drying. Biocontrol Science and Technology. 16(3):281-293.

A New DNA Oligo Microarray for Complete Genome of Pseudomonas Fluorescens Pf-5 - (Abstract)

Liu, Z., Duboy, R.T., Press, C., Loper, J.E., Paulsen, I.T., Slininger, P.J. 2005. A new DNA oligo microarray for complete genome of Pseudomonas fluorescens pf-5 [abstract]. International Union of Microbiological Societies. Abstract No. B-1258, p. 63-64.

Induction of Pleiotropic Drug Resistance Gene Expression Indicates Important Roles of Pdr to Cope with Furfural and 5-Hydroxymethylfurfural Stress in Ethanologenic Yeast - (Abstract)

Liu, Z., Slininger, P.J. 2005. Induction of pleiotropic drug resistance gene expression indicates important roles of pdr to cope with furfural and 5-hydroxymethylfurfural stress in ethanologenic yeast [abstract]. Biotechnology for Fuels and Chemicals Symposium Proceedings. Abstract No. 169.

The Role of the Pentose Phosphate Pathway in Fermentation Inhibitor Tolerance - (Abstract)

Gorsich, S.W., Liu, Z., Slininger, P.J. 2005. The role of the pentose phosphate pathway in fermentation inhibitor tolerance. Biotechnology for Fuels and Chemicals Symposium Proceedings. Abstract No. 5-33.

Transcriptome Dynamics of Ethanologenic Yeast in Response to 5-Hydroxymethylfurfural Stress Related to Biomass Conversion to Ethanol - (Proceedings/Symposium)

Liu, Z., Slininger, P.J. 2005. Transcriptome dynamics of ethanologenic yeast in response to 5-hydroxymethylfurfural stress related to biomass conversion to ethanol [abstract]. Abstract Book. p. 991.

Transcriptome Dynamics of Ethanologenic Yeast in Response to 5-Hydroxymethylfurfural Stress Related to Biomass Conversion to Ethanol - (Abstract)

Liu, Z., Slininger, P.J. 2005. Transcriptome dynamics of ethanologenic yeast in response to 5-hydroxymethylfurfural stress related to biomass conversion to ethanol [abstract]. Paper No. 177C.

Functional Genomics of Microbial Stress Tolerance - (Abstract) - (02-Dec-04)

The Saccharomyces Cerevisiae Pentose Phosphate Pathway Gene, Rpe1, functions in Furfural Tolerance During Fermentation - (Proceedings/Symposium)

Gorsich, S.W., Dien, B.S., Nichols, N.N., Slininger, P.J., Liu, Z. 2004. The Saccharomyces cerevisiae pentose phosphate pathway gene, rpe1, functions in furfural tolerance during fermentation [abstract]. Proceedings of the 11th International Congress on Yeasts in Science and Biotechnology. Paper No. PM24.

Enhanced Biotransformation of Furfural and 5-Hydroxymethylfurfural by Newly Developed Ethanologenic Yeast Strains - (Peer Reviewed Journal)

Liu, Z., Slininger, P.J., Gorsich, S.W. 2005. Enhanced biotransformation of furfural and 5-hydroxymethylfurfural by newly developed ethanologenic yeast strains. Applied Biochemistry and Biotechnology. 121-124: 451-460.

Exogenous Nucleic Acid Controls for DNA Oligo Microarrays - (Abstract)

Liu, Z., Slininger, P.J. 2004. Exogenous nucleic acid controls for DNA oligo microarrays [abstract]. 7th International Meeting of the Microarray Gene Expression Data Society, Toronto, ON, Canada. Paper No. 908.

Identification of Saccharomyces Cerevisiae Genes Involved in Furfural Tolerance During Fermentation. - (Abstract)

Gorsich, S.W., Slininger, P.J., Liu, Z., Nichols, N.N., Dien, B.S. 2004. Identification of Saccharomyces cerevisiae genes involved in furfural tolerance during fermentation [abstract]. Proceedings of the Yeast Genetics and Molecular Biology. Abstract No. 166A, p. 104.

Functional Genomic Studies of in Situ Detoxification of Bioethanol Fermentation Inhibitors Using Ethanologenic Yeast - (Abstract)

Liu, Z., Slininger, P.J. 2004. Functional genomic studies of in situ detoxification of bioethanol fermentation inhibitors using ethanologenic yeast [abstract]. Society of Industrial Microbiology Annual Meeting. Abstract No. S146.

Development of Genetically Engineered Stress Tolerant Ethanologenic Yeasts Using Integrated Functional Genomics for Effective Biomass Conversion to Ethanol - (Book/Chapter)

Liu, Z., Slininger, P.J. 2005. Development of genetically engineered stress tolerant ethanologenic yeasts using integrated functional genomics for effective biomass conversion to ethanol. In: Collins, K., Duffield, J., Outlaw, J., editors. Agriculture as a Producer and Consumer of Energy. Wallingford, UK: CAB International, p. 283-294.

Enhanced Biotransformation of Furfural and 5-Hydroxymethylfurfural by Newly Developed Ethanologenic Yeast Strains - (Abstract)

Liu, Z., Slininger, P.J., Gorsich, S.W. 2004. Enhanced biotransformation of furfural and 5-hydroxymethylfurfural by newly developed ethanologenic yeast strains [abstract]. 26th Symposium on Biotechnology for Fuels and Chemicals. Abstract No. 2-40. p. 153.

Identification of Saccharomyces Cerevisiae Genes Involved in Furfural Tolerance During Fermentation. - (Abstract)

Gorsich, S.W., Slininger, P.J., Liu, Z. 2004. Identification of Saccharomyces cerevisiae genes involved in furfural tolerance during fermentation. Biotechnology for Fuels and Chemicals Symposium Proceedings. May 9-12, 2004. Chattanooga, TN. Poster No. 2-42. p. 155.

Adaptive Response of Yeasts to Furfural and 5-Hydroxymethylfurfural and New Chemical Evidence for Hmf Conversion to 2,5-Bis-Hydroxymethylfuran - (Peer Reviewed Journal)

Liu, Z., Slininger, P.J., Dien, B.S., Berhow, M.A., Kurtzman, C.P., Gorsich, S.W. 2004. Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for hmf conversion to 2,5-bis-hydroxymethylfuran. Journal of Industrial Microbiology and Biotechnology. 31:345-352. Available http://dx.doi.org/10.1007/s10295-004-0148-3.

Global Gene Expression Analysis of Ethanologenic Yeasts in Adaptation to Bioethanol Fermentation Inhibitory Stress - (Abstract)

Liu, Z., Slininger, P.J. 2004. Global gene expression analysis of ethanologenic yeasts in adaptation to bioethanol fermentation inhibitory stress [abstract]. International Conference on Microbial Genomes. Genomes 2004. p. 61.

27-Hydroxycholesterol Inhibits Neutral Sphingomyelinase in Cultured Human Endothelial Cells - (Peer Reviewed Journal)

Zhou, Q., Band, M.R., Hernandez, A., Liu, Z., Kummerow, F.A. 2004. 27-Hydroxycholesterol inhibits neutral sphingomyelinase in cultured human endothelial cells. Life Sciences. 75:1567-1577.

Development of Genetically Engineered Stress Tolerant Ethanologenic Yeasts Using Integrated Functional Genomics for Effective Biomass Conversion to Ethanol - (Abstract)

Liu, Z., Slininger, P.J. 2004. Development of genetically engineered stress tolerant ethanologenic yeasts using integrated functional genomics for effective biomass conversion to ethanol [abstract]. Proceedings of the Conference of Agriculture as a Producer and Consumer of Energy. Selected Paper Abstracts, Session D, Paper No. 7.

Comparative Tolerance Studies Reveal Dose-Dependent Inhibition of Ethanologenic Yeasts by Furfural and 5-Hydroxymethylfurfural - (Abstract)

Liu, Z., Slininger, P.J., Dien, B.S., Kurtzman, C.P., Gorsich, S.W. 2004. Comparative tolerance studies reveal dose-dependent inhibition of ethanologenic yeasts by furfural and 5-hydroxymethylfurfural [abstract]. Society of Industrial Microbiology. Paper No. 40.

Identification of Saccharomyces Cerevisiae Genes Involved in Tolerance of Fermentation Inhibitors - (Abstract)

Gorsich, S.W., Slininger, P.J., Liu, Z. 2003. Identification of saccharomyces cerevisiae genes involved in tolerance of fermentation inhibitors. Society of Industrial Microbiology Annual Meeting.