Publications

High-solids biological deconstruction and microbiomes


Yu C, Harrold DR, Claypool JT, Simmons BA, Singer SW, Simmons CW, VanderGheynst JS. 2017. Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition. Process Biochemistry. 52: 214-222

Rezaei F, Simmons CW, Lee CM, Labavitch J, VanderGheynst JS. 2016. Dynamics in Carbohydrate Active Enzymes and Microbial Communities during Ensilage of Food Processing Residues. Applied Engineering in Agriculture. 32(3):439-447.

Wu Y-W, Higgins B, Yu C, Reddy AP, Ceballos S, Joh LD, Simmons BA, Singer SW, VanderGheynst JS. 2016. Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis. mSystems 1(6).

Yu C, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS. 2016. Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts. Applied Microbiology and Biotechnology 100(24):10237-10249.

Pace S, Ceballos SJ, Harrold D, Stannard W, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS. 2016. Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate. Applied Microbiology and Biotechnology:1-14.

Yu C, Reddy AP, Simmons CW, Simmons BA, Singer SW, VanderGheynst JS. 2015. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions. Biotechnology for Biofuels 8(206):1-13.

Simmons C, Reddy A, D’Haeseleer P, Khudyakov J, Billis K, Pati A, Simmons B, Singer S, Thelen M, VanderGheynst J. 2014. Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnology for Biofuels 7(1):495.

Simmons CW, Reddy AP, Simmons BA, Singer SW, VanderGheynst JS. 2014. Effect of inoculum source on the enrichment of microbial communities on lignocellulosic biofuel feedstocks under thermophilic and high-solids conditions. Journal of Applied Microbiology 117(4):1025-1034.

Simmons CW, Reddy AP, Simmons BA, Singer SW, VanderGheynst JS. 2014. Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture. Biotechnology Progress 30(2):311-316.

Zheng Y, Yu C, Cheng Y-S, Lee C, Simmons CW, Dooley TM, Zhang R, Jenkins BM, VanderGheynst JS. 2012. Integrating sugar beet pulp storage, hydrolysis and fermentation for fuel ethanol production. Applied Energy 93(0):168-175.

Zheng Y, Lee C, Yu C, Cheng Y-S, Simmons CW, Zhang R, Jenkins BM, VanderGheynst JS. 2012. Ensilage and Bioconversion of Grape Pomace into Fuel Ethanol. Journal of Agricultural and Food Chemistry 60(44):11128-11134.

Zheng Y, Cheng Y-S, Yu C, Zhang R, Jenkins B, VanderGheynst J. 2012. Improving the efficiency of enzyme utilization for sugar beet pulp hydrolysis. Bioprocess and Biosystems Engineering 35(9):1531-1539.

Reddy AP, Simmons CW, Claypool J, Jabusch L, Burd H, Hadi MZ, Simmons BA, Singer SW, VanderGheynst JS. 2012. Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Journal of Applied Microbiology 113(6):1362-1370.

Zheng Y, Yu C, Cheng Y-S, Zhang R, Jenkins B, VanderGheynst JS. 2011. Effects of ensilage on storage and enzymatic degradability of sugar beet pulp. Bioresource Technology 102(2):1489-1495.

Zheng Y, Yates M, Aung H, Cheng Y-S, Yu C, Guo H, Zhang R, VanderGheynst JS, Jenkins BM. 2011. Influence of moisture content on microbial activity and silage quality during ensilage of food processing residues. Bioprocess and Biosystems Engineering 34(8):987-995.

Singer SW, Reddy AP, Gladden JM, Guo H, Hazen TC, Simmons BA, VanderGheynst JS. 2011. Enrichment, isolation and characterization of fungi tolerant to 1-ethyl-3-methylimidazolium acetate. Journal of Applied Microbiology 110(4):1023-1031.

Rezaei F, Joh LD, Kashima H, Reddy AP, VanderGheynst JS. 2011. Selection of conditions for cellulase and xylanase extraction from switchgrass colonized by Acidothermus cellulolyticus. Applied Biochemistry and Biotechnology 164:793-803.

Rezaei F, Joh LD, Berry AM, VanderGheynst JS. 2011. Xylanase and cellulase production by Acidothermus cellulolyticus grown on switchgrass in solid-state fermentation. Biofuels 2(1):21-32.

Reddy AP, Allgaier M, Singer SW, Hazen TC, Simmons BA, Hugenholtz P, VanderGheynst JS. 2011. Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnology and Bioengineering 108(9):2088-2098.

Joh LD, Rezaei F, Barabote RD, Parales JV, Parales RE, Berry AM, VanderGheynst JS. 2011. Effects of Phenolic Monomers on Growth of Acidothermus cellulolyticus Biotechnology Progress 27(1):23-31.

VanderGheynst JS, Rezaei F, Dooley TM, Berry AM. 2010. Switchgrass leaching requirements for solid-state fermentation by Acidothermus cellulolyticus. Biotechnology Progress 26(3):622-626.

Allgaier M, Reddy AP, Park JI, Ivanova N, D’haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P. 2010. Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community. PLoS One 5(1):e8812.

Biofuels production from microalgae and analytical techniques


Higgins BT, Gennity I, Samra S, Kind T, Fiehn O, VanderGheynst JS. 2016. Cofactor symbiosis for enhanced algal growth, biofuel production, and wastewater treatment. Algal Research 17:308-315.

Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, M A. 2015. MS-DIAL: Data independent MS/MS deconvolution for comprehensive metabolome analysis. Nature Methods 12:523-526.

Higgins BT, Nobles D, Ma Y, Wikoff W, Kind T, Fiehn O, Brand J, VanderGheynst JS. 2015. Informatics for improved algal taxonomic classification and research: A case study of UTEX 2341. Algal Research 12:545-549.

Higgins B, Labavitch JM, VanderGheynst JS. 2015. Co-culturing Chlorella minutissima with Escherichia coli can increase neutral lipid production and improve biodiesel quality. Biotechnology and Bioengineering 112(9):1801-1809.

Cheng Y-S, Labavitch J, VanderGheynst JS. 2015. Organic and inorganic nitrogen impact Chlorella variabilis productivity and host quality for viral production and cell lysis. Applied Biochemistry and Biotechnology 176(2):467-479.

Cheng Y-S, Labavitch J, VanderGheynst JS. 2015. Elevated CO2 concentration impacts cell wall polysaccharide composition of green microalgae of the Genus Chlorella Letters in Applied Microbiology 60(1):1-7.

Higgins BT, Dunwoody A, Labavitch JM, VanderGheynst JS. 2014. Microplate assay for quantitation of neutral lipids in extracts from microalgae. Analytical Biochemistry 465:81-89.

Higgins BT, VanderGheynst JS. 2014. Effects of Escherichia coli on Mixotrophic Growth of Chlorella minutissima and Production of Biofuel Precursors. PLoS ONE 9(5):e96807.

Tanadul O-u-m, VanderGheynst JS, Beckles DM, Powell ALT, Labavitch JM. 2014. The impact of elevated CO2 concentration on the quality of algal starch as a potential biofuel feedstock. Biotechnology and Bioengineering 111(7):1323-1331.Cheng Y-S, Zheng Y, Labavitch JM, VanderGheynst JS. 2013. Virus infection of Chlorella variabilis and enzymatic saccharification of algal biomass for bioethanol production. Bioresource Technology 137:326-331.

Kind T, Meissen JK, Yang D, Nocito F, Vaniya A, Cheng Y-S, VanderGheynst JS, Fiehn O. 2012. Qualitative analysis of algal secretions with multiple mass spectrometric platforms. Journal of Chromatography A 1244(0):139-147.

Cheng Y-S, Labavitch J, VanderGheynst JS. 2011. The impact of cell wall carbohydrate composition on the chitosan flocculation of Chlorella. Process Biochemistry 46(10):1927-1933.

Cheng Y-S, Labavitch J, VanderGheynst J. 2011. High-throughput analysis of hexosamine using a colorimetric method Analytical Biochemistry 408:160-162.

Cheng Y-S, Zheng Y, VanderGheynst JS. 2010. Rapid quantitative analysis of lipid using a colorimetric method in a microplate format. Lipids 46:95-103.

Microalgae storage and delivery


Fernández L, Higgins BT, Scher H, VanderGheynst JS. 2016. Spray application and release of microalgae from water-in-oil emulsions. Current Biotechnology(5):154-162.

Fernández L, Scher H, VanderGheynst JS. 2015. The role of silica nanoparticles on long-term room-temperature stabilization of water-in-oil emulsions containing microalgae. Letters in Applied Microbiology 61(6):568–572.

Fernández L, Scher H, Jeoh T, VanderGheynst J. 2015. Room-temperature storage of microalgae in water-in-oil emulsions: influence of solid particle type and concentration in the oil phase. Bioprocess and Biosystems Engineering 38(12):2451-2460.

Fernández LE, Cheng Y-S, Scher H, VanderGheynst JS. 2014. Managing the cultivation and processing of microalgae to prolong storage in water-in-oil emulsions. Applied Microbiology and Biotechnology 98(12):5427-5433.

VanderGheynst J, Guo H-Y, Cheng Y-S, Scher H. 2013. Microorganism viability influences internal phase droplet size changes during storage in water-in-oil emulsions. Bioprocess and Biosystems Engineering:1-8.

VanderGheynst JS, Dooley TM, Guo H, Scher H, Cheng Y. 2010. Storage and release of solutes and microalgae from water-in-oil emulsions stabilized by silica nanoparticles. Process Biochemistry 45(1):1-6.

VanderGheynst JS, Scher H; Regents of the University of California, assignee. 2009. US Patent 7,485,45. Storage Stable Compositions of Biological Materials. United States.

Soil solarization


Achmon Y, Fernández-Bayo JD, Hernandez K, McCurry DG, Harrold DR, Su J, Dahlquist-Willard RM, Stapleton JJ, VanderGheynst JS, Simmon CW. 2017. Weed seed inactivation in soil mesocosms via biosolarization with mature compost and tomato processing waste amendments Pest Management Science In press.

Oldfield TL, Achmon Y, Perano KM, Dahlquist-Willard RM, VanderGheynst JS, Stapleton JJ, Simmons CW, Holden NM. 2017. A life cycle assessment of biosolarization as a valorization pathway for tomato pomace utilization in California. Journal of Cleaner Production. 141: 146-156.

Achmon Y, Harrold DR, Claypool JT, Stapleton JJ, VanderGheynst JS, Simmons CW. 2016. Assessment of tomato and wine processing solid wastes as soil amendments for biosolarization. Waste Management 48:156-164.

Dahlquist-Willard RM, Marshall MN, Betts S, Tuell-Todd C, VanderGheynst J, Stapleton J. 2016. Development and validation of a Weibull-Arrhenius model to predict thermal inactivation of Black Mustard (Brassica nigra) seeds under fluctuating temperature regimens. Biosystems Engineering 151:350-360.

Simmons CW, Higgins B, Staley S, Joh LD, Simmons BA, Singer SW, Stapleton JJ, VanderGheynst JS. 2016. The role of organic matter amendment level on soil heating, organic acid accumulation, and development of bacterial communities in solarized soil. Applied Soil Ecology 106:37-46.

Simmons CW, Claypool JT, Marshall MN, Jabusch LK, Reddy AP, Simmons BA, Singer SW, Stapleton JJ, VanderGheynst JS. 2014. Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter. Applied Soil Ecology 73:97-104.

Simmons CW, Guo H, Claypool JT, Marshall MN, Perano KM, Stapleton JJ, VanderGheynst JS. 2013. Managing compost stability and amendment to soil to enhance soil heating during soil solarization. Waste Management 33(5):1090-1096.

Marshall MN, Rumsey TR, Stapleton JJ, VanderGheynst JS. 2013. A Predictive Model for Soil Temperature During Solarization and Its Validation at Two California Field Sites. Transactions of the ASABE 56(1):117-133.

Plant biotechnology


Simmons CS, Nitin N, VanderGheynst JS. 2014. Attachment of Agrobacterium tumefaciens to leaf tissue in response to infiltration conditions. Biotechnology Progress 30(5):1137-1144.

Simmons CW, Nitin N, VanderGheynst JS. 2012. Rapid, in situ detection of Agrobacterium tumefaciens attachment to leaf tissue. Biotechnology Progress 28(5):1321-1328.

Luo Z, Simmons CW, VanderGheynst JS, Nitin N. 2012. Quantitative real time measurements of bacteria–bacteriophages interactions in fresh lettuce leaves. Journal of Food Engineering 111(1):176-185.

Simmons CW, VanderGheynst JS, Upadhyaya SK. 2009. A Model of Agrobacterium tumefaciens Vacuum Infiltration Into Harvested Leaf Tissue and Subsequent In Planta Transgene Transient Expression. Biotechnology and Bioengineering 102(3):965-970.

VanderGheynst JS, Guo HY, Simmons CW. 2008. Response surface studies that elucidate the role of infiltration conditions on Agrobacterium tumefaciens-mediated transient transgene expression in harvested switchgrass (Panicum virgatum). Biomass & Bioenergy 32(4):372-379.

Simmons CW, VanderGheynst JS. 2007. Transient co-expression of post-transcriptional gene silencing suppressors and beta-glucuronidase in harvested lettuce leaf tissue does not improve recombinant protein accumulation in planta. Biotechnology Letters 29(4):641-645.

Joh LD, VanderGheynst JS. 2006. Agroinfiltration of plant tissues for production of high-value recombinant proteins: an alternative to production in transgenic crops. Journal of the Science of Food and Agriculture 86(13):2002-2004.

Joh LD, McDonald KA, VanderGheynst JS. 2006. Evaluating extraction and storage of a recombinant protein produced in agroinfiltrated lettuce. Biotechnology Progress 22(3):723-730.

Joh LD, Wroblewski T, Ewing NN, VanderGheynst JS. 2005. High-level transient expression of recombinant protein in lettuce. Biotechnology and Bioengineering 91(7):861-871.

Composting and Compost Stability Assessment


Yu C, Harrold DR, Claypool JT, Simmons BA, Singer SW, Simmons CW, VanderGheynst JS. 2017. Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition. Process Biochemistry. 52: 214-222

Aslam DN, VanderGheynst JS. 2009. Tools to evaluate compost phytotoxicity: employing stability measurements. Biocycle 50(12):28-31.

Aslam DN, VanderGheynst JS. 2009. Tools to evaluate compost phytotoxicity. Biocycle 50(12):28-31.

Aslam DN, VanderGheynst JS, Rumsey TR. 2008. Development of models for predicting carbon mineralization and associated phytotoxicity in compost-amended soil. Bioresource Technology 99(18):8735-8741.

Aslam DN, VanderGheynst JS. 2008. Predicting phytotoxicity of compost-amended soil from compost stability measurements. Environmental Engineering Science 25(1):72-81.

Aslam DN, Horwath W, VanderGheynst JS. 2008. Comparison of several maturity indicators for estimating phytotoxicity in compost-amended soil. Waste Management 28(11):2070-2076.

VanderGheynst JS, Lei F. 2003. Microbial community structure dynamics during aerated and mixed composting. Transactions of the ASAE 46(2):577-584.

Marshall MN, Cocolin L, Mills DA, VanderGheynst JS. 2003. Evaluation of PCR primers for denaturing gradient gel electrophoresis analysis of fungal communities in compost. Journal of Applied Microbiology 95(5):934-948.

VanderGheynst JS, Dooley TM, Marshall MN. The influence of process management and microbial community structure on the cultivation of a biological control agent in compost. In: Michel FC, Hoitink HAJ, Rynk R, editors; 2002. JG Press, Emmaus, PA.

Lei F, VanderGheynst JS. 2000. The effect of microbial inoculation and pH on microbial community structure changes during composting. Process Biochemistry 35(9):923-929.

 

 

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