All Publications

 

 

Published in 2014

 

BIOMASS DEPOLYMERIZATION

 

 

Rapid Determination of Cellulose, Stefan Bauer, Ana Ibanez, Biotechnology and Bioengineering, doi: 10.1002/bit.25276, 2014.

 

Molecular Dynamics Study of Enhanced Man5b Enzymatic Activity, Rafael Bernardi, Isaac Cann, Klaus Schulten, Biotechnology for Biofuels, 7: 83. doi: 10.1186/1754-6834-7-83, 2014.

 

Engineering Clostridium Acetobutylicum for Production of Kerosene and Diesel Blendstock Precursors, S. Bormann, Z. C. Baer, S. Sreekumar, J. M. Kuchenreuther, F. Dean Toste, H. W. Blanch, D. S. Clark, Metabolic Engineering, 25: 124-130. doi: 10.1016/j.ymben.2014.07.003, July 22, 2014.

 

Chemocatalytic Upgrading of Tailored Fermentation Products toward Biodiesel, S. Sreekumar, Z. C. Baer,E. Gross, S. Padmanaban, K. Goulas, G. Gunbas, S. Alayoglu, H. W. Blanch, D. S. Clark, F. D. Toste, ChemSusChem, doi: 10.1002/cssc.201402244, July 22, 2014. 

 

Rapid Small-Scale Determination of Extractives in Biomass, Christina Kuchelmeister, Stefan Bauer, BioEnergy Research, doi: 10.1007/s12155-014-9493-x, July 2014.

 

Downscaled Method Using Glass Microfiber Filters for the Determination of Klason Lignin and Structural Carbohydrates, Ana B. Ibanez, Stefan Bauer, Biomass and Bioenergy, 68: 75-81. doi: 10.1016/j.biombioe.2014.06.013, July 2014.

 

Overcoming Inefficient Cellobiose Fermentation by Cellobiose Phosphorylase in the Presence of Xylose, Kulika Chomvong, Vesna Kordic, Xin Li, Stefan Bauer, Abigail Gillespie, Suk-Jin Ha, Eun Joong Oh, Jonathan Galazka, Yong-Su Jin, Jamie Cate, Biotechnology for Biofuels, 7: 85. doi: 10.1186/1754-6834-7-85, June 7, 2014.

 

The Proteome and Phosphoproteome of Neurospora Crassa in Response to Cellulose, Sucrose and Carbon Starvation, Y. Xiong, S. T. Coradetti, X. Li, M. A. Gritsenko, T. Clauss, V. Petyuk, D. Camp, R. Smith, J. H. Cate, F. Yang, N. Louise Glass, Fungal genetics and biology, doi: 10.1016/j.fgb.2014.05.005, June 3, 2014.

 

The Roles of Small Laccases from Streptomyces in Lignin Degradation, S. Majumdar,T. Lukk, J. O. Solbiati, S. Bauer, S. K. Nair,J. E. Cronan, J. A. Gerlt, Biochemistry, doi: 10.1021/bi500285t, May 30, 2014.

 

Effects of NIPAm Polymer Additives on the Enzymatic Hydrolysis of Avicel and Pretreated Miscanthus, Katherine J. Mackenzie, Matthew B. Francis, Biotechnology and Bioengineering, 111(9): 1792-1800. doi: 10.1002/bit.25252, April 12, 2014.

 

Lignol Cleavage by Pd/C under Mild Conditions and without Hydrogen: A Role for Benzylic C-H Activation?, Xiaoyuan Zhou, Joyee Mitra, Thomas B. Rauchfuss, ChemSusChem, 7(6): 1623-6. doi: 10.1002/cssc.201301253, April 1, 2014.

 

Identification of Novel Biomass-Degrading Enzymes from Genomic Dark Matter: Populating Genomic Sequence Space with Functional Annotation, Hailan Piao, Jeff Froula, Changbin Du, Tae-Wan Kim, Erik Hawley, Stefan Bauer, Chong Wang, Nathalia Ivanova, Douglas A. Clark, Hans-Peter Klenk, Matthias Hess, Biotechnology and Bioengineering, 111(8): 1550-1565. doi: 10.1002/bit.25250, April 2014.

 

Syntheses of Biodiesel Precursors: Sulfonic Acid Catalysts for Condensation of Biomass-Derived Platform Molecules, Madhesan Balakrishnan, Eric R. Sacia, Alexis T. Bell, ChemSusChem, 7(4): 1078-1085. doi: 10.1002/cssc.201300931, March 5, 2014.

 

Evidence of a Critical Role for Cellodextrin Transporte 2 (Cdt-2) in Both Cellulose and Hemicellulose Degradation and Utilization in Neurospora crassa, P. Cai, R. Gu,B. Wang, J. Li, L. Wan,C. Tian, Y. Ma, Plos One, 9(2): e89330. doi: 10.1371/journal.pone.0089330, March 4, 2014.

 

Determining Optimal Size Reduction and Densification for Biomass Feedstock Using the Biofeed Optimization Model, Yogendra Shastri, Zewei Miao, Luis Rodriguez, Tony Grift, Alan Hansen, K.C. Ting, Biofuels Bioproducts & Biorefining, 8(3): 423-437. doi: 10.1002/bbb.1476, February 24, 2014.
 

Engineering and Science of Biomass Feedstock Production and Provision. Editors: Yogendra Shastri, Alan Hansen, Luis Rodriguez, K.C. Ting, Springer New York, 2014.

 

Switchgrass and Giant Miscanthus Agronomy,  Engineering and Science of Biomass Feedstock  Production and Provision, pp. 37-59, D. K. Lee, Allen S. Parrish, Thomas B. Voigt, Springer,  New York, 2014.

 

Systems Informatics and Analysis,  Engineering and Science of Biomass Feedstock Production and Provision, pp. 195-232, Yogendra Shastri, Alan Hansen, Luis Rodriguez, K.C. Ting,  Springer,  New York, 2014.

 

Preharvest Monitoring of Biomass ProductionEngineering and Science of Biomass Feedstock Production and Provision, pp. 61-83, Liujun Li, Lei Tian, Tofael Ahamed, Springer, New York, 2014.

 

Transportation,  Engineering and Science of Biomass Feedstock Production and Provision, pp. 141-164, Tony E. Grift, Zewei Miao, Alan C. Hansen, and K.C. Ting, Springer, New York, 2014.

 

ENVIRONMENTAL, SOCIAL, & ECONOMIC IMPACTS

 

Effect of Nitrogen Addition on Miscanthus X Giganteus Yield, Nitrogen Losses, and Soil Organic Matter across Five Sites, Morgan P. Davis, Mark B. David, Thomas B. Voigt, Corey A. Mitchell, Global Change Biology Bioenergy, doi: 10.1111/gcbb.12217, August 2014.

 

The Impacts of Biofuels on the Economy, Environment, and Poverty, Govinda R. Timilsina, David Zilberman, doi: 10.1007/978-1-4939-0518-8_1, 2014.

 

Production of Ethanol from Sugarcane in Brazil, M. Azanha, F. D.  de Moraes, D. Zilberman, doi: 10.1007/978-3-319-03140-8, 2014. 

 

How Big Is the Bioenergy Piece of the Energy Pie? Who Cares-It's Pie!, C. Somerville, H. Youngs, Biotechnology and Bioengineering, 111(9): 1717-1718. doi: 10.1002/bit.25312, 2014/07/26.

 

Role of Lignin in Reducing Life-Cycle Carbon Emissions, Water Use, and Cost for United States Cellulosic Biofuels, C. D. Scown, A. A. Gokhale, P. A. Willems, A. Horvath, T. E. Mckone, Environmental Science & Technology, 48(15): 8446-8455. doi: 10.1021/es5012753, July 6, 2014.

 

Take a Closer Look: Biofuels Can Support Environmental, Economic and Social Goals, Bruce Dale, James Anderson, Robert Brown, Steven Csonka, Virginia Dale, Gary Herwick, Randall Jackson, Nicholas Jordan, Stephen Kaffka, Keith Kline, Lee Lynd, Carolyn Malmstrom, Rebecca Ong, Tom Richard, Caroline Taylor, Michael Wang, Environmental Science and Technology Letters - Perspective, 48(13): 7200-7203. doi: 10.1021/es502433, June 17, 2014.

 

Optimizing Fermentation Process Miscanthus-to-Ethanol Biorefinery Scale under Uncertain Conditions, Matthew Bomberg, Daniel Sanchez, Timothy Lipman, Environmental Research Letters, 9(6): 064018.  doi: 10.1088/1748-9326/9/6/064018, June 13, 2014.

 

Abatement Cost of Wood-Based Energy Products at the Production Level on Afforested and Reforested Lands, Puneet Dwivedi, Madhu Khanna, Global Change Biology Bioenergy, doi: 10.1111/gcbb.12199, June 2, 2014.

 

Cattle Ranching Intensification in Brazil Can Reduce Global Greenhouse Gas Emissions by Sparing Land from Deforestation, A. S. Cohn, A. Mosnier, P. Havlik, H. Valin, M. Herrero, E. Schmid, M. O'hare, M. Obersteiner, Proceedings of the National Academy of Sciences of the United States of America, doi: 10.1073/pnas.1307163111, April 30, 2014.

 

Accountable Accounting: Carbon-Based Management on Marginal Lands, Tara L. Dirocco, Benjamin S. Ramage, Samuel G. Evans, Matthew D. Potts, Forests, 5(4): 847-861. doi: 10.3990/f5040847, April 23, 2014.

 

Bioenergy Crop Greenhouse Gas Mitigation Potential under a Range of Management Practices, Tara D. Hudiburg, Sarah C. Davis, William Parton, Evan H. Delucia, Glob Change Biology Bioenergy, doi: 10.1111/gcbb.12152, March 7, 2014.

 

Sustainability Issues in Biomass Feedstock Production: A Public Policy Perspective, Engineering and Science of Biomass Feedstock Production and Provision, pp. 233-259, Jody Endres, Springer, New York, 2014.

 

FEEDSTOCK DEVELOPMENT

 

Bioenergy Feedstocks at Low Risk for Invasion in the USA: A "White List" Approach, Lauren D. Quinn, Doria R. Gordon, Aviva Glaser, Deah Lieurance, S. Luke Flory, Bioenergy Res., doi: 10.1007/s12155-014-9503-z, July 2014.

 

Transcriptional Responses Indicate Maintenance of Photosynthetic Proteins as Key to the Exceptional Chilling Tolerance of C4 Photosynthesis in Miscanthus X Giganteus, Ashley Spence, Jay Boddu, Dafu Wang, Brandon James, Kankshita Swaminathan, Stephen Moose, Stephen Long, Journal of Experimental Botany, 65(13): 3737-47. doi: 10.1093/jxb/eru209, June 22, 2014.

 

Natural Variation in Miscanthus Sinensis Seed Germination under Low Temperatures, Maria S. Dwiyanti, J. Ryan Stewart, Aya Nishiwaki, Toshihiko Yamada, Grassland Science, doi: 10.1111/grs.12051, May 10, 2014.

 

A Comparative Life-Table Analysis of Sipha Flava (Hemiptera: Aphididae) on Two Biofuel Hosts, Miscanthus X Giganteus and Saccharum Spp., G. R. Pallipparambil, G. Cha, M. E. Gray, Journal of Economic Entomology, 107(3): 1069-75. doi: 10.1603/EC13263, May 6, 2014.

 

Mapping the Genome of Miscanthus Sinensis for Qtl Associated with Biomass Productivity, Justin M. Gifford, Won Byoung Chae, Kankshita Swaminathan, Stephen P. Moose, John A. Juvik, Global Change Biology Bioenergy, doi: 10.1111/gcbb.12201, May 2014.

 

Sensing Miscanthus Swath Volume for Maximizing Baler Throughput Rate, S.K. Mathanker, J.D. Maughan, A.C. Hansen, T.E. Grift, K.C. Ting, Trans (ASABE), 57(2): 335-362. doi: 10.13031/trans.57.10167, May 2014.

 

Light to Liquid Fuel: Theoretical and Realized Energy Conversion Efficiency of Plants Using Crassulacean Acid Metabolism (Cam) in Arid Conditions, S. C. Davis, D. S. Lebauer, S. P. Long, Journal of Experimental Botany, doi: 10.1093/jxb/eru163, April 20, 2014.

 

Agronomic Factors in the Establishment of Tetraploid Seeded Miscanthus X giganteus, Eric K. Anderson, D.K. Lee, Damian J. Allen, Thomas B. Voigt, Global Change Biology Bioenergy, doi: 10.1111/gcbb.12192, April 7, 2014.

 

Polygalacturonase Involved in Expansion1 Funtions in Cell Elongation and Flower Development in Arabidopsis, Chaowen Xiao, Chris Somerville, Charles T. Anderson, Plant Cell, 26(3): 1018-35. doi: 10.1105/tpc.114.123968, March 28, 2014.

 

The Implications of Lignocellulosic Biomass Chemical Composition for the Production of Advanced Biofuels, Nadav Sorek, Trevor Yeats, Heidi Szemenyei, Heather Youngs, Chris Somerville, BioScience, 64(3): 192. doi: 10.1093/biosci/bit037, February 2014.

 

Natural History Survey of the Ornamental Grass Miscanthus Sinensis in the Introduced Range, Ryan F. Dougherty, Lauren D. Quinn, A. Bryan Endres, Thomas B. Voigt, Jacob N. Barney, Invasive Plant Science and Management, 7(1): 113-120. doi: 10.1614/IPSM-D-13-00037.1, January 2014.

 

Plant Morphology, Genome Size, and Ssr Markers Differentiate Five Distinct Taxonomic Groups among Accessions in the Genus Miscanthus, Won Byoung Chae, Sae Jin Hong, Justin M. Gifford, A. Lane Rayburn, Erik J. Sacks, John A. Juvik, Global Change Biology Bioenergy, doi: 10.1111/gcbb.12101, January 3, 2014

 

 

BIOFUEL PRODUCTION

 

Fermentation of Hydrolysate Detoxified by Pervaporation through Block Copolymer Membranes, Douglas R. Greer,Thalita P. Basso, Ana B. Ibanez, Stefan Bauer, Jeffrey M. Skerker, A Evren Ozcam, Dacia Leon, Chaeyoung Shin, Adam P. Arkin, Nitash P. Balsara, Green Chemistry, doi: 10.1039/C4GC00756E, July 2014.

 

Reversal of the B-Oxidation Cycle in Saccharomyces Cerevisiae for Production O Fuels and Chemicals, Jiazhang Lian, Huimin Zhao, ACS Synthetic Biology, doi: 10.1021/sb500243c, June 24, 2014.

 

Synthesis of Well-Defined Polyethylene-Polydimethylsiloxane-Polyethylene Triblock Copolymers by Diimide-Based Hydrogenation of Polybutadiene Blocks, Nikos Petzetakis, Gregory Stone, Nitash Balsara, Macromolecules, 47(13): 4151-4159. doi: 10.1021/ma500686k, June 19, 2014.

 

Employing a Combinatorial Expression Approach to Characterize Xylose Utilization in Saccharomyces Cerevisiae, Luke Latimer, Michael Lee, Daniel Medina-Cleghorn, Rebecca Kohnz, Daniel Nomura, John Dueber, Metabolic Engineering, 25C: 20-29. doi: 10.1016/j.ymben.2014.06.002, June 12, 2014.

 

Expression of a Xylose-Specific Transporter Improves Ethanol Production by Metabolically Engineered Zymomonas Mobilis, K. L. Dunn, C. V. Rao, Applied Microbiology and Biotechnology, 98(15): 6897-905. doi: 10.1007/s00253-014-5812-6, May 20, 2014.
 
Avoidance of Truncated Proteins from Unintended Ribosome Binding Sites within Heterologous Protein Coding Sequences, Weston R. Whitaker, Hanson Lee, Adam P. Arkin, John E. Dueber, ACS synthetic biology, doi: 10.1021/sb500003x, April 30, 2014.

 

Indirect and Suboptimal Control of Gene Expression Is Widespread in Bacteria, M. N. Price, A. M. Deutschbauer, J. M. Skerker, K. M. Wetmore, T. Ruths, J. S. Mar, J. V. Kuehl, W. J. Shao, A. P. Arkin, Molecular Systems Biology, 9: 660. doi: 10.1038/Msb.2013.16, April 2013.

 

2,3-Butanediol Production from Cellobiose by Engineered Saccharomyces Cerevisiae, Hong Nan, Seung-Oh Seo, Eun Joong Oh, Jin-Ho Seo, Jamie H.D. Cate, Yong-Su Jin, Applied Microbiology and Biotechnology, 98(12): 5757-64. doi: 10.1007/s00253-014-5683-x, April 2014.

 

Metabolic Engineering of a Saccharomyces Cerevisiae Strain Capable of Simultaneously Utilizing Glucose and Galactose to Produce Enantiopure (2r,3r)-Butadeniol, Jiazhang Lian, Ran Chao, Huimin Zhao, Metabolic Engineering, 23: 92-9. doi: 10.1016/j.ymben.2014.02.003, February 2014.
 

Directed Evolution of a Cellodextrin Transporter for Improved Biofuel Production under Anaerobic Conditions in Saccharomyces Cerevisiae, Jiazhang Lian, Yanglin Li, Mohammad Hamedi Rad, Huimin Zhao, Biotechnology and Bioengineering, 111(8): 1521-1531. doi: 10.1002/bit.25214, February 2014.

 

 

FOSSIL FUEL BIOPROCESSING

 

Temperature and Injection Water Source Influence Microbial Community Structure in Four Alaskan North Slope Hydrocarbon Reservoirs, Yvette Marisa Piceno, Francine C. Reid, Leuren M. Tom, Mark E. Conrad, Markus Bill, Christopher George Hubbard, Bruce William Fouke, Craig J. Graff, Jiabin Han, William T. Stringfellow, Jeremy S. Hanlon, Ping Hu, Terry C. Hazen, Gary L. Andersen, Microbial Physiology and Metabolism, doi: 10.3389/fmicb.2014.00409, July 2014.

 

Inhibition of Microbial Sulfate Reduction in a Flow-through Column System by (Per)Chlorate Treatment, Anna Engelbrektson, Christopher Hubbard, Lauren Tom, Aaron Boussina,Yong Jin, Hayden Wong, Yvette Piceno,Hans Carlson, Mark Conrad, Gary Anderson, John Coates, Frontiers in Microbiology, 5: 315. doi: 10.3389/fmicb.2014.00315, June 26, 2014.

 

 

Published in 2013

BIOMASS DEPOLYMERIZATION

 

 

Exploring Bacterial Lignin Degradation, Margaret E. Brown, Michelle C.Y. Chang, Current Opinion in Chemical Biology, 4: 1-7. doi: 10.1016/j.cbpa.2013.11.015, December 2013.

 

The Importance of Pyroglutamate in Cellulase Cel7a, Craig M. Dana, Alexandra Dotson-Fagerstrom, Christine M. Roche, Sarala M. Kal, Harshal A. Chokhawala, Harvey W. Blanch, Douglas S. Clark, Biotechnology and Bioengineering, 111: 842-847. doi: 10.1002/bit.25178, December 30, 2013.

 

Evidence for Transceptor Function of Cellodextrin Transporters in Neurospora crassa, Elizabeth A. Znameroski, Xin Li, Jordan Tsai, Jonathon M. Galazka, N. Louise Glass, Jamie H.D. Cate, Journal of Biological Chemistry, 289(5): 2610-9. doi: 10.1074/jbc.M113.533273, December 16, 2013.

 

Molecular and Biochemical Analyses of Cbcel9a/Cel48a, a Highly Secreted Multi-Modular Cellulase by Caldicellulosiruptor bescii During Growth on Crystalline Cellulose, Zhoulin Yi, Xiaoyun Su, Vanessa Revindran, Roderick I. Mackie, Isaac Cann, PLoS One, 8(12): e84172. doi: 10.1371/journal.pone.0084172, December 2013.

 

Comprehensive Analysis of Monomeric Phenolics in Dilute Acid Plant Hydrolysates, Valerie D. Mitchell, Caroline M. Taylor, Stefan Bauer, BioEnergy Research, doi: 10.1007/s12155-013-9392-6, November 2013.

 

Expanding the Scope of Biomass-Derived Chemicals through Tandem Reactions Based on Oxorhenium-Catalyzed Deoxydehydration, Mika Shiramizu, F. Dean Toste, Angewandte Chemie, 52: 12905-12909. doi: 10.1002/anie.201307564, November 14, 2013.

 

Two-Step Delignification of Miscanthus to Enhance Enzymatic Hydrolysis: Aqueous Ammonia Followed by Sodium Hydroxide and Oxidants, Zhongguo Liu, Sasisanker Padmanabhan, Kun Cheng, Hongxue Xie, Amit A. Gokhale, Waheed Afzal, Hui Na, Markus Pauly, Alexis T. Bell, John M. Prausnitz, Energy & Fuels, 28(1): 542-548. doi: 10.1021/ef401317z, October 9, 2013.

 

Continuous Co-Fermentation of Cellobiose and Xylose by Engineered Saccharomyces cerevisiae, Suk-Jin Ha, Soo Rin Kim, Heejin Kim, Jing Du, Jamie H.D. Cate, Yong-Su Jin, Bioresource Technology, 149: 525-531. doi: 10.1016/j.biortech.2013.09.082, September 27, 2013.

 

Draft Genome Sequence of the Cellulolytic Bacterium Clostridium papyrosolvens C7 (Atcc 700395), V. Zepeda, B. Dassa, I. Borovok, R. Lamed, E. A. Bayer, J. H. Cate, Genome Announcements, 1(5): e00698-13. doi: 10.1128/genomeA.00698-13, September 14, 2013.

 

Pretreatment of Miscanthus X giganteus Using Aqueous Ammonia with Hydrogen Peroxide to Increase Enzymatic Hydrolysis to Sugars, Guangren Yu, Waheed Afzal, Fuxin Yang, Sasisanker Padmanabhan, Zhongguo Liu, Hongxue Xie, Mahmoud Abdel Shafy, Alexis T. Bell, J. M. Prausnitz, Journal of Chemical Technology and Biotechnology, doi: 10.1002/jctb.4172, August 14, 2013.

 

Physiological Role of Acyl-Coa Synthetase Homologs in Lipid Metabolism in Neurospora crassa, C. M. Roche, H. W. Blanch, D. S. Clark, N. L. Glass, Eukaryotic Cell, 12(9): 1244-57. doi: 10.1128/EC.00079-13, July 23, 2013.

 

Plant Cell Wall Deconstruction by Ascomycete Fungi, N. L. Glass,M. Schmoll,J. H. Cate, S. Coradetti, Annual Review of Microbiology, 67: 477-98. doi: 10.1146/annurev-micro-092611-150044, July 3, 2013.

 

Insights into Lignin Degradation and its Potential Industrial Applications,  Abdel-Hamid AM, Solbiati JO, Cann IK, Advances in Applied Microbiology 82: 1-28, doi: 10.1016/B978-0-12-407679-2.00001-6, 2013.

 

Analysis of Conserved Cellulase Transcriptional Regulator Reveals Inducer-Independent Production of Cellulolytic Enzymes in Neurospora crassa, Samuel T. Coradetti, Yi Xiong, N. Louise Glass, MicrobiologyOpen, 2(4): 595-609. doi: 10.1002/mbo3.94, May 2013.

 

Compositional Analysis of Miscanthus giganteus by Near Infrared Spectroscopy, Haffner, FBM, Mitchell, VD, Arundale, R. Bauer S, Cellulose, 20(4): 1629-1637. doi:10.1007/s10570-013-9935-1, April 24, 2013.

 

Comparative Metagenomic and Metatranscriptomic Analysis of Hindgut Paunch Microbiota in Wood- and Dung-Feeding Higher Termites,  Shaomei He, Natalia Ivanova, Edward Kirton, Martin Allgaier, Claudia Bergin, Rudolf H. Scheffrahn, Nikos C. Kyrpides, Falk Warnecke, Susannah G. Tringe, Philip Hugenholtz, PLoS One 8(4): e61126. doi: 10.1371/journal.pone.0061126, April 12, 2013.

 

A Single-Molecule Analysis Reveals Morphological Targets for Cellulase Synergy, Fox JM, Jess P, Jambusaria RB, Moo GM, Liphardt J, Clark DS, Blanch HW., Nature Chemical Biology, 9: 356-361. doi: 10.1038/nchembio,1227, April 7, 2013.

 

Preferential Interactions between Lithium Chloride and Glucan Chains in N,N-Dimethylacetamide Drive Cellulose Dissolution, A. S. Gross, A. T. Bell, J. W. Chu, Journal of Physical Chemistry B, 117(12): 3280-6. doi: 10.1021/Jp311770u, March 28, 2013.

 

Single Amino Acid Substitutions in HXT2.4 from Scheffersomyces Stipitis Lead to Improved Cellobiose Fermentation by Engineered Saccharomyces Cerevisae, Ha SJ, Kim H, Lin Y, Jang MU, Galazka JM, Kim TJ, Cate JH, Jin YS, Metabolic Applied and Environmental Microbiology, 79(5): 1500-1507.doi: 10.1128/AEM.03253-12, March 2013.

 

Switchable Butadiene Sulfone Pretreatment of Miscanthus in the Presence of Water, J. Atilio de Frias, Hao Feng, Green Chemistry, 15: 1067-1078. doi: 10.1039/C3GC37099B, February 5, 2013.

 

Energetic Benefits and Rapid Cellobiose Fermentation by Saccharomyces cerevisiae Expressing Cellobiose Phosphorylase and Mutant Cellodextrin Transporters, Suk-Jin Ha, Jonathan Galazka, Eun Joong Oh, Vesna Kordic, Heejin Kim, Yong-Su Jin, Jamie Cate, Metabolic Engineering, 15: 134-143. doi: 10.1016/j.ymben.2012.11.005, January 2013.

 

Using a Model Filamentous Fungus to Unravel Mechanisms of Lignocellulose Deconstruction, E. A. Znameroski, N. L. Glass, Biotechnology for Biofuels, 6(1): 6. doi: 10.1186/1754-6834-6-6, January 22, 2013.

 

Recyclable Thermoresponsive Polymer-Cellulase Bioconjugates for Biomass Depolymerization, K. J. Mackenzie, M. B. Francis, Journal of the American Chemical Society, 135(1): 293-300. doi: 10.1021/Ja309277v, January 9, 2013.

 

 

 

ENVIRONMENTAL, SOCIAL, & ECONOMIC IMPACTS

 

Barking up the Wrong Tree? Forest Sustainability in the Wake of Emerging Bioenergy Policies, Jody M. Endres, Vermont Law Review, 37(3): 763. 2013.

 

Carbon Abatement in the Fuel Market with Biofuels: Implications for Second Best Policies, Christine Lasco Crago, Madhu Khanna, Journal of Environmental Economics and Management, 67(2): 89-103. doi: 10.1016/j.jeem.2013.11.001, November 2013.

 

Continents Divided: Understanding Differences between Europe and North America in Acceptance of GM Crops, David Zilberman,Scott Kaplan,Eunice Kim,Gal Hochman, Gregory Graff, GM Crops and Food: Biotechnology in Agriculture and the Food Chain, 4(3): 202-8. doi: 10.4161/gmcr.26981, November 21, 2013

 

To Learn or to Change: Optimal R&D Investments under Uncertainty in the Case of Climate Change, Ruiqing Miao, David Hennessy, Natural Resource Modeling, doi: 10.1111/nrm.12032, November 6, 2013.

 

Reducing the Impact of Model Scale on Simulated Gridded Switchgrass Yields, Alan V. Di Vittorio, Norman L. Miller, Environmental Modelling and Software, 51: 70-83. doi: 10.1016/j.envsoft.2013.09.016, 2013.

 

Ecological Correlates of Stress for a Habitat Generalist in a Biofuels Landscape, S.L. Fredebaugh-Siller,C.D. Suski,Z.C. Zuckerman, R.L. Schooley, Canadian Journal of Zoology, 91(12): 853-858. doi: 10.1139/cjz-2013-0157, October 15, 2013.

 

Biofuel-Related Price Transmission Literature: A Review, T. Serra, D. Zilberman, Energy Economics, 37: 141-151. doi: 10.1016/J.Eneco.2013.02.014, 2013.

 

On Market-Mediated Emissions and Regulations on Life Cycle Emissions, D. Rajagopal, D. Zilberman, Ecological Economics, 90: 77-84. doi: 10.1016/J.Ecolecon.2013.03.006, 2013.

 

Implications of Market-Mediated Emissions and Uncertainty for Biofuel Policies, D. Rajagopal, R. J. Plevin, Energy Policy, 56: 75-82. doi: 10.1016/J.Enpol.2012.09.076, 2013.

 

Energy Intensity, Life-Cycle Greenhouse Gas Emissions, and Economic Assessment of Liquid Biofuel Pipelines, Bret Strogen, Arpad Horvath, David Zilberman, Bioresource Technology, 150: 476-485. doi: 10.1016/j.biortech.2013.08.150, 2013.

 

Predicting Greenhouse Gas Emissions and Soil Carbon from Changing Pasture to an Energy Crop, Benjamin D Duval, Kristina J. Anderson-Texeira, Sarah C. Davis, Cindy Koegh, Stephen Long, William J. Parton, Evan H. Delucia, PLoS One, 8(8): e72019. doi: 10.1371/journal.pone.0072019, August 21, 2013. 

 

Is Use of Both Pulpwood and Logging Residues Instead of Only Logging Residues for Bioenergy Development a Viable Mitigation Strategy?, Puneet Dwivedi, Robert Bailis, Madhu Khanna, Bioenergy Res., 7: 217-231. doi: 10.1007/s12155-013-9362-z, August 14, 2013.

 

Stocks-to-Use Ratios and Prices as Indicators of Vulnerability to Spikes in Global Cereal Markets, E. Bobenrieth, B. Wright, D. Zeng, Agricultural Economics, 44: 43-52. doi: 10.1111/Agec.12049, June 28, 2013.

 

Economic, Energy Security, and Greenhouse Gas Effects of Biofuels: Implications for Policy, M. Khanna, Xiaoguang Chen, American Journal of Agricultural Economics, 95(5): 1325-1331. doi: 10.1093/ajae/aat037, June 27, 2013.

 

Gap-Filling Strategies and Error in Estimating Annual Soil Respiration,  Nuria Gomez-Casanovas, Kristina Anderson-Teixeira, Marcelo Zeri, Carl J Bernacchi, Evan H Delucia, Global Change Biology, 19: 1941-1952. doi: 10.1111/gcb.12127, June 2013.

 

Stacking Low-Carbon Policies on the Renewable Fuels Standard: Economic and Greenhouse Gas ImplicationsHaixiao Huang, Madhu Khanna, Hayri Önal, Xiaoguang Chen, Energy Policy, 56: 5-15. doi: 10.2139/ssrn.1998887, June 2013.

 

California's Energy Future: The Potential for Biofuels, Heather Youngs and Chris Somerville, California Council on Science and Technology, May 31, 2013.

 

Water Use Efficiency of Perennial and Annual Bioenergy Crops in Central Illinois, Marcelo Zeri, Mir Zaman Hussain, Kristina J Anderson-Teixeira, Evan Delucia, Carl J Bernacchi, Journal of Geophysical Research: Biogeosciences, 118(2): 581-589. doi: 10.1002/jgrg.20052, April 25, 2013.

 

Altered Dynamics of Forest Recovery Under a Changing Climate, Anderson-Teixeira KJ, Miller AD, Mohan JE, Hudiburg TW, Duval BD, Delucia EH, Global Change Biology, 19(7): 2001-21. doi: 10.1111/gcb.12194, March 25, 2013.

 

Bioenergy, Resource Scarcity and the Rising Importance of Land Use Definitions, Jody Endres, North Dakota Law Review, Vol. 88: 559, 2013.

 

Legitimacy, Innovation, and Harmonization: Precursors to Operationalizing Biofuels Sustainability Standards, Jody Endres, Southern Illinois University Law Journal, 37(1):1, 2013.

 

Frayed Seams in the 'Patchwork Quilt' of American Federalism: An Empirical Analysis of Invasive Plant Species Regulation, James McCubbins, A. Bryan Endres, Lauren Quinn, and Jacob Barney, Environmental Law, 43: 35-81, 2013.

 

The Legal Profession's Critical Role in Systems-Level Bioenergy Decision-MakingJody M Endres, Daniel Szewczyk, Pace Environmental Law Review, 30(2): 652, April 23, 2013.

 

Necessity is the Mother, but Protection May Not be the Father of Invention: The Limited Effect of Intellectual Property Regimes on Agricultural InnovationA. Bryan Endres, Carly Griffin, Columbia Science and Technology Law Review, 14: 203-253, 2012-2013.

 

Non-Linear Price Transmission Between Biofuels, Fuels, and Food CommoditiesLadistav Kristoufek, Karel Janda, David Zilberman, CERGE EI Working Paper Series No. 481, doi: 10.2139/ssrn.2257390, February 2013.

 

Navigating the 'Noxious' and 'Invasive' Regulatory Landscape: Suggestions for Improved RegulationLauren Quinn, Jacob Barney, James McCubbins, and A. Bryan Endres, Bioscience, 63(2): 124-131. doi: 10.1525/bio.2013.63.2.8, February 13, 2013.

 

Regime-Dependent Topological Properties of Biofuels Networks, Ladislav Kristoufek, Karel Janda, David Zilberman, The European Physical Journal  B, 86(2): 40. doi: 10.1140/epjb/e2012-30871-9, February 6, 2013.

 

Reduced Nitrogen Losses After Conversion of Row Crop Agriculture to Perennial Biofuel Crops, Candice M Smith, Mark B David, Corey A Mitchell, Michael D Masters, Kristina J Anderson-Teixeira, Carl J Bernacchi, Journal of Environmental Quality, 42: 219-228. doi: 10.2134/jeq2012.0210, January–February 2013.

 

Altered Belowground Carbon Cycling Following Land-Use Change to Perennial Bioenergy Crops,  Kristina J Anderson-Teixeira, Michael D Masters, Christopher K Black, Marcelo Zeri, Mir Zaman Hussain, Carl J Bernacchi, Evan H Delucia, Ecosystems, 16(3): 508-520. doi: 10.1007/s10021-012-9628-x, January 5, 2013.


Building Bio-based Supply Chains: Theoretical Perspectives on Innovative Contracts, Jody Endres et al., 31 UCLA Journal or Environmental Law and Policy, 2013 (in press).

 

 

FEEDSTOCK DEVELOPMENT

 

 

 

Genetic Variation in Miscanthus X Giganteus and the Importance of Estimating Genetic Distance Thresholds for Differentiating Clones, Katarzyna Glowacka, Lindsay V. Clark, Shivani Adhikari, Junhua Peng, J. Ryan Stewart, Aya Nishiwaki, Toshihiko Yamada, Uffe Jorgensen, Trevor R. Hodkinson, Justin Gifford, John A. Juvik, Erik J. Sacks, Global Change Biology Bioenergy, doi: 10.1111/gcbb.12166, December 2013.

 

A Detailed Gene Expression Study of the Miscanthus Genus Reveals Changes in the Transcriptome Associated with the Rejuvenation of Spring Rhizomes, Adam Barling, Kankshita Swaminathan, Therese Mitros, Brandon T. James, Juliette Morris, Ornella Ngamboma, Megan C. Hall, Jessica Kirkpatrick, Magdy Alabady, Ashley K. Spence, Matthew E. Hudson, Daniel S. Rokhsar, Stephen P. Moose, BMC Genomics, 14: 864. doi: http://dx.doi.org/10.4236/jsbs.2013.34038, December 9, 2013.

 

The Potential Impact of Second-Generation Biofuel Landscapes on at-Risk Species in the US, Samuel G. Evans, Lisa C. Kelley, Matthew D. Potts, Global Change Biology Bioenergy, doi: 10.1111/gcbb.12131, December 7, 2013.

 

Modeling Price-Driven Interactions between Wood Bioenergy and Global Wood Product Markets, Sijia Zhang, J. Keith Gilless, William Stewart, Biomass and Bioenergy, 60: 68-78. doi: 10.1016/j.biombioe.2013.10.027, 25 November 2013.

 

A Comparative Systems Analysis of Polysaccharide-Elicited Responses in Neurospora Crassa Reveals Carbon Source-Specific Cellular Adaptations, J. P. Benz, B. H. Chau, D. Zheng, S. Bauer, N. L. Glass, C. R. Somerville, Molecular Microbiology, 91(2): 275-99. doi: 10.1111/mmi.12459, November 15, 2013.

 

Nitrogen Fertilization Does Significantly Increase Yields of Stands of Miscanthus X Giganteus and Panicum Virgatum in Multiyear Trials in Illinois, Rebecca A. Arundale, Frank G. Dohleman, Thomas B. Voigt, Stephen P. Long, BioEnergy Research, 7(1): 408-416. doi: 10.1007/s12155-013-9385-5, October 2013.

 

Dynamics of the Bacterial Community Structure in the Rhizosphere of a Maize Cultivar, Xiangzhen Li, Junpeng Rui, Yuejian Mao, Anthony Yannarell, Roderick Mackie, Soil Biology and Biochemistry, 68: 392-401. doi: 10.1016/j.soilbio.2013.10.017, October 25, 2013.

 

A b-Glucuronosyltransferase from Arabidopsis Thaliana Involved in Biosynthesis of Type II Arabinogalactan Has a Role in Cell Elongation During Seedling Growth, Eva Knoch, Adiphol Dilokpimon, Theodora Tryfona, Christian P. Poulsen, Guangyan Xiong, Jesper Harholt, Bent L. Petersen, Peter Ulvskov, Masood Z. Hadi, Toshihisa Kotake, Yoichi Tsumaraya, Markus Pauly, Paul Dupree, Naomi Geshi, The Plant Journal, 76: 1016-1029. doi: 10.1111/tpj.12353, 2013.

 

E-Photosynthesis: a Comprehensive Dynamic Mechanistic Model of C3 Photosynthesis from Light Capture to Sucrose Synthesis, X. G. Zhu, Y. Wang, D. R. Ort, S. P. Long, Plant Cell and Environment, 36(9):1711-1727. doi: 10.1111/pce.12025, September 2013.

 

Transient Expression of the Arabidopsis Thaliana Callose Synthase Pmr4 Increases Penetration Resistance to Powdery Mildew in Barley, Antje Blumke, Shauna C. Somerville, Christian A. Voigt, Advances in Bioscience and Biotechnology, 4(8): 810-813. doi: 10.4236/abb.2013.48106, August 2013.

 

Scale Dependence in the Effects of Leaf Ecophysiological Traits on Photosynthesis: Bayesian Parameterization of Photosynthesis Models, X. Feng, M. Dietze, The New Phytologist, 200(4): 1132-44. doi: 10.1111/nph.12454, August 21, 2013.

 

Nitrogen Fertility and Harvest Management of Switchgrass for Sustainable Bioenergy Feedstock Production in Illinois,  Eric K. Anderson, Allen S. Parrish, Thomas B. Voigt, Vance N. Owens, Chang-Ho Hong, D.K. Lee, Industrial Crop and Products, 48: 19-27. doi: 10.1016/j.indcrop.2013.03.029, July 2013.

 

Retrospective Genomic Analysis of Sorghum Adaptation to Temperate-Zone Grain Production, C. S. Thurber, J. M. Ma, R. H. Higgins, P. J. Brown, Genome Biology, 14(6): R68. doi: 10.1186/gb-2013-14-6-r68, June 28, 2013.

 

Hemicellulose Biosynthesis, Markus Pauly, Sascha Gille, Lifeng Liu, Nasim Mansoori, Amancio De Souza, Alex Schultink, Planta, 238(4): 627-42. doi: 10.1007/s00425-013-1921-1, June 14, 2013.

 

Translating Probability Density Functions: From R to BUGS and Back Again, D. S. LeBauer, M. C. Dietze, B. M. Bolker, The R Journal, 5(1):207-209, June 2013.

 

Applicability of Phosphorus Site Indices to Wastewater Effluent-Irrigated Cropland D. Jaiswal and H.A. ElliottJournal of Soil and Water Conservation, 68(3): 228-237, May-June 2013.

 

Arabinosylation of a Yariv-Precipitable Cell Wall Polymer Impacts Plant Growth as Exemplified by the Arabidopsis Glycosyltransferase Mutant ray 1Dwiyanti, Gille, S, Sharma V, Baidoo EE, Keasling JD, Scheller HV, Pauly M, Molecular Plant, 6(4): 1369-72. doi: 10.1093/mp/sst029, May 17, 2013.

 

Germplasm Resources of Miscanthus and Their Application and Breeding, Chapter 4, M. Saha, H. Bhandari, J. Bouton, M. Dwiyanti, J. Ryan Stewart, T. Yamada, Bioenergy Feedstocks: Breeding and Genetics, doi:10.1002/9781118609477, April 25, 2013.

 

Toward Cool C Crops, S. P. Long and A. K. Spence, Annual Review of Plant Biology, 64: 701-22. doi:10.1146/annurev-arplant-050312-120033, April 13, 2013.

 

GIS-Enabled Biomass-Ethanol Supply Chain Optimization: Model Development and Miscanthus Application, Tao Lin, Luis F Rodríguez, Yogendra N Shastri, Alan C Hansen, KC TingBiofuels, Bioproducts, and Biorefining, 7(3): 314-333. doi: 10.1002/bbb.1394, April 2013.

 

Adult Activity and Oviposition of Corn Rootworms, Diabrotica spp (Coleoptera: Chrysomeliae) in Miscanthus, Corn, and Switchgrass,  J. R. Prasifka, J. L. Spencer, N. A. Tinsley, R. E. Estes, M. E. Gray, Journal of Applied Entomology, 137(7): 481-487. doi: 10.1111/jen.12050, March 15, 2013.

 

Solution-State 2D NMR Spectroscopy of Plant Cell Walls Enabled by a Dimethylsulfoxide-d6/1-Ethyl-3-methylimidazolium Acetate Solvent, Kun Cheng, Hagit Sorek, Herbert Zimmerman, David E. Wemmer, and Markus Pauley, Analytical Chemistry, 85(6): 3213-3221. doi: 10.1021/ac303529v, February 17, 2013.

 

Predicting Yields of Short-Rotation Hybrid Poplar (Populus spp.) for the Contiguous US Through Model-Data Synthesis, Dan Wang, David LeBauer, Michael C. Dietze, Ecological Applications, 23: 944-958. doi: 10.1890/12-0854.1, February 1, 2013.

 

On Improving the Communication Between Models and Data, Dietze, M.C., D.S. LeBauer, R. Kooper, Plant, Cell, and the Environment, 36(9): 1575-1585. doi: 10.1111/pce.12043, January 3, 2013. 

 

 

BIOFUEL PRODUCTION

 

 

Determinants of Regioselective Hydroxylation in the Fungal Polysaccharide Monooxygenases, Van V. Vu, William T. Beeson, Christopher M. Phillips, Jamie H.D. Cate, Michael A. Marletta, Journal of the American Chemical Society, 136(2): 562-565. doi: 10.1021/ja409384b, December 18, 2013.

 

Investigating Xylose Metabolism in Recombinant Saccharomyces Cerevisiae Via C-13 Metabolic Flux Analysis, X. Y. Feng, H. M. Zhao, Microbial Cell Factories, 12: 114. doi: 10.1186/1475-2859-12-114, November 18, 2013. 

 

Analysis of Cellodextrin Transporters from Neurospora Crassa in Saccharomyces Cerevisiae for Cellobiose Fermentation, H. Kim, W. H. Lee, J. M. Galazka, J. H. Cate, Y. S. Jin, Applied Microbiology and Biotechnology, doi: 10.1007/s00253-013-5339-2, November 6, 2013.

 

DNA Assembly Techniques for Next-Generation Combinatorial Biosynthesis of Natural Products, Ryan E. Cobb, Jonathon C. Ning, Huimin Zhao, J Ind Microbiol Biotechnol, 41(2): 469-77. doi: 10.1007/s10295-013-1358-3, October 15, 2013.

 

Enhanced Biofuel Production through Coupled Acetic Acid and Xylose Consumption by Engineered Yeast, N. Wei, J. Quarterman, S. R. Kim, J. H. Cate, Y. S. Jin, Nature communications, 4: 2580. doi: 10.1038/ncomms3580, October 10, 2013.

 

Expression-Level Optimization of a Multi-Enzyme Pathway in the Absence of a High-Throughput Assay, M. E. Lee, A. Aswani, A. S. Han, C. J. Tomlin, J. E. Dueber, Nucleic Acids Research, 41(22): 10668-78. doi: 10.1093/nar/gkt809, September 17, 2013.

 

The Bacterial Carbon-Fixing Organelle Is Formed by Shell Envelopment of Preassembled Cargo, A. H. Chen, A. Robinson-Mosher, D. F. Savage, P. A. Silver, J. K. Polka, PLoS One, 8(9): e76127. doi: 10.1371/journal.pone.0076127, September 4, 2013.

 

Investigation of the Functional Role of Aldose 1-Epimerase in Engineered Cellobiose Utilization, Sijin Li, Suk-Jin Ha, Hee Jin Kim, Jonathan M. Galazka, Jamie H.D. Cate, Yong-Su Jin, Huimin Zhao, Journal of Biotechnology, 168(1): 1-6. doi: 10.1016/j.biotec.2013.08.003, August 14, 2013.

 

Enhancing Tolerance to Short-Chain Alcohols by Engineering the Escherichia Coli Acrb Efflux Pump to Secrete the Non-Native Substrate N-Butanol, M. A. Fisher, S. Boyarskiy, M. R. Yamada, N. Kong,S. Bauer, D. Tullman-Ercek, ACS Synthetic Biology, 3(1): 30-40. doi: 10.1021/sb400065q, September 3, 2013.

 

Simultaneous Saccharification and Fermentation by Engineered Saccharomyces Cerevisiae without Supplementing Extracellular Beta-Glucosidase, W. H. Lee, H. Nan, H. J. Kim, Y. S. Jin, Journal of Biotechnology, 167(3): 316-322. doi: 10.1016/j.jbiotec.2013.06.016, July 10, 2013.

 

Investigating Host Dependence of Xylose Utilization in Recombinant Saccharomyces Cerevisiae Strains Using Rna-Seq Analysis, X. Y. Feng, H. M. Zhao, Biotechnology for Biofuels, 6: 96. doi: 10.1186/1754-6834-6-96, July 6, 2013.

 

Directed Evolution of a Cellobiose Utilization Pathway in Saccharomyces Cerevisiae by Simultaneously Engineering Multiple Proteins, D. T. Eriksen, P. C. Hsieh, P. Lynn, H. Zhao, Microbial cell factories, 12: 61. doi: 10.1186/1475-2859-12-61, June 28, 2013.

 

Investigating Glucose and Xylose Metabolism in Saccharomyces Cerevisiae and Scheffersomyces Stipitis Via 13c Metabolic Flux Analysis, Xueyang Feng, Huimin Zhao, AIChE Journal, 59: 3195-3202. doi: 10.1002/aic.14182, June 17, 2013.

 

Dissecting a Complex Chemical Stress: Chemogenomic Profiling of Plant Hydrolysates, Jeffrey M Skerker, Dacia Leon, Morgan N Price, Jordan S Mar, Daniel R Tarjan, Kelly M Wetmore, Adam M Deutschbauer, Jason K Baumohl, Stefan Bauer, Ana B Ibáñez, Valerie D Mitchell, Cindy H Wu, Ping Hu, Terry Hazen, and Adam P ArkinMolecular Systems Biology, 9: 674. doi: 10.1038/msb.2013.30, June 18, 2013.

 

Production of Advanced Biofuels in Engineered E. coli, Wen M, Bond-Watts BB, Chang MCCurrent Opinion in Chemical Biology, 17(3): 472-479. doi: 10.1016/j.cbpa.2013.03.034, May 6, 2013.

 

Directed Evolution of a Highly Efficient Cellobiose Utilizing Pathway in an Industrial Saccharomyces cerevisiae Strain, Yuan Y, Eriksen DT, Zhao HBiotechnology and Bioengineering, 110(11): 2874-81. doi: 10.1002/bit.24946, April 25, 2013.

 

Compartmentalizing Metabolic Pathways in Organelles, Deloache, W.C. and J.E. Dueber, Nature Biotechnology, 31(4): 320-321. doi: 10.1038/nbt.2549, April 5, 2013.

 

Combinatorial Genetic Perturbation to Refine Metabolic Circuits for Producing Biofuels and Biochemicals, Kim HJ, Turner TL, Jin YS, Biotechnology Advances, 31(6): 976-985. doi: 10.1016/j.biotechadv.2013.03.010, April 5, 2013.

 

Protein Design for Pathway Engineering, Eriksen, D.T., J. Lian, H. Zhao, Journal of Structural Biology, 185(2): 234-42. doi: 10.1016/j.jsb.2013.03.01, April 1, 2013.

 

Pathway Engineering as an Enabling Synthetic Biology Tool (book chapter), Eriksen, D.T., Jiazhang. L., H. Zhao, Synthetic Biology: Tools and Applications (edited by Huimin Zhao), 2013.

 

Change, Exchange, and Rearrange: Protein Engineering for the Biotechnological Production of Fuels, Pharmaceuticals, and Other Chemicals, Fisher, MA, Tullman-Ercek D, Current Opinions in Biotechnology, 24(6): 1010-6. doi: 10.1016/j.copbio.2013.02.027, March 202013.

 

Strain Engineering of Saccharomyces cerevisiae for Enhanced Xylose Metabolism,  Kim SR, Park YC, Jin YS, Seo JH, Biotechnology Advances, 31(6): 851-861. doi: 10.1016/j.biotechadv.2013.03.004, March 21, 2013.

 

Directed Evolution as a Powerful Synthetic Biology Tool,  Cobb R.E., Sun N., Zhao H., Methods, 60(1):81-90. doi: 10.1016/j.ymeth.2012.03.009, March 13, 2013.

 

Deletion of FPS1, Encoding Aquaglyceroporin Fps1p, Improves Xylose Fermentation by Engineered Saccharomyces cerevisiae, Wei N, Xu H, Kim SR, Jin YS, Applied and Environmental Microbiology, 79(10): 3193-3201. doi: 10.1128/AEM.00490-13, March 8, 2013.

 

Rational and Evolutionary Engineering Approaches Uncover a Small Set of Genetic Changes Efficient for Rapid Xylose Fermentation in Saccaromyces cerevisae, Soo Rin Kim, Jeffrey M. Skerker, Wei Kang, Anastashia Lesmana, Na Wei, Adam P. Arkin, Yong-Su Jin, PLoS One, 8(2): e57048. doi: 10.1371/journal.pone.0057048, February 262013.

 

Genomically and Biochemically Accurate Metabolic Reconstruction of Methanosarcina Barkeri Fusaro, iMG746, Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND, Biotechnology Journal, 8(9): 1070-9. doi: 10.1002/biot.201200266, February 19, 2013.

 

 

FOSSIL FUEL BIOPROCESSING

 

 

Halomonas Sulfidaeris-Dominated Microbial Community Inhabits a 1.8 Km-Deep Subsurface Cambrian Sandstone Reservoir, Yiran Dong, Charu Gupta Kumar, Nicholas Chia, Pan-Jun Kim, Philip A. Miller, Nathan D. Price, Isaac K.O. Cann, Theodore M. Flynn, Robert A. Sanford, Ivan G. Krapac, Randall A. Locke Ii, Pei-Ying Hong, Hideyuki Tamaki, Wen-Tso Liu, Roderick I. Mackie, Alvaro G. Hernandez, Chris L. Wright, Mark A. Mikel, Jared L. Walker, Mayandi Sivaguru, Glenn Fried, Anthony C. Yannarell, Bruce W. Fouke, Environmental Microbiology, doi: 10.1111/1462-2920.12325, December 2013.

 

Succession of Hydrocarbon-Degrading Bacteria in the Aftermath of the Deepwater Horizon Oil Spill in the Gulf of Mexico, E. A. Dubinsky, M. E. Conrad,R. Chakraborty,M. Bill, S. E. Borglin, J. T. Hollibaugh, O. U. Mason, M. Piceno Y, F. C. Reid, W. T. Stringfellow, L. M. Tom, T. C. Hazen, G. L. Andersen, Environmental Science & Technology, 47(19): 10860-10867. doi: 10.1021/es401676y, August 14, 2013.

 

Structure and Evolution of Chlorate Reduction Composite Transposons, I. C. Clark, R. A. Melnyk, A. Engelbrektson, J. D. Coates, mBio, 4(4): e00379-13. doi: 10.1128/mBio.00379-13, August 6, 2013.

 

Applicability of Anaerobic Nitrate-Dependent Fe(II) Oxidation to Microbial Enhanced Oil Recovery (MEOR), H. Zhu, H. K. Carlson, J. D. Coates, Environmental Science & Technology, 47(15): 8970-7. doi: 10.1021/es401838b, June 27, 2013.

 

Physiological and Genetic Description of Dissimilatory Perchlorate Reduction by the Novel Marine Bacterium Arcobacter Sp. Strain Cab,  C. I. Carlstrom, O. Wang, R. A. Melnyk, S. Bauer, J. Lee, A. Engelbrektson, J. D. Coates, mBio, 4(3): e00217-13. doi: 10.1128/mBio.00217-13, 2013/05/23 2013, May 21, 2013.

 

Surfaceomics and Surface-Enhanced Raman Spectroscopy of Environmental Microbes: Matching Cofactors With Redox-Active Surface Proteins,  Carlson HK, Lavarone AT, Coates JD, Proteomics, 13(18-19): 2761-5. doi: 10.1002/pmic.201300010, April 25, 2013 online.

 

Reactive Transport Modeling of Induced Selective Plugging by Leuconostoc mesenteroidesin Carbonate Formations, Javier Vilcaez, Li Li, Dinghao Wu, and Susan S. Hubbard, Geomicrobiology Journal, 30(9): 813-828. doi: 10.1080/01490451.2013.774074, 2013, February 21, 2013.

 

 

Published in 2012

BIOFUELS PRODUCTION

 

Marine Macroalgae: An Untapped Resource for Producing Fuels and Chemicals, Na Wei, Josh Quarterman, Yong-Su Jin, Trends in Biotechnology, http://dx.doi.org/10/1016/j.tibtech.2012.10.009, December 12, 2012.

 

Combinatorial Design of a Highly Efficient Xylose Utilizing Pathway for Cellulosic Biofuels Production in Saccharomyces cerevisiae, Byoungjin Kim, Jing Du, Dawn Eriksen, Huimin Zhao, Applied and Environmental Microbiology, doi: 10.1128/AEM.02736-12, November 2012.

 

Strain Improvement Via Evolutionary Engineering, Byoungjin Kim, Jing Du, and Huimin Zhao, Engineering Complex Phenotypes in Industrial Strains, Editor(s): Ranjan Patnaik, John Wiley & Sons, Inc, pp. 111-131, doi: 10.1002/9781118433034, October 24, 2012.

 

Engineering Robust Control of Two-Component System Phosphotransfer Using Modular Scaffolds, Weston R. Whitaker, Stephanie A. Davis, Adam P. Arkin, and John E. Dueber, Proceedings of the National Academy of Sciences, doi: : 10.1073/pnas.1209230109, October 15, 2012 online.
 

Elucidation of the Multiple Roles of CheD in Bacillus subtilis Chemotaxis , George Glekas, Matthew J. Plutz, Hanna Walukiewicz, George Allen, Christopher V. Rao, George Ordal, Molecular Microbiology, doi: 10.1111/mmi.12015, August 31, 2012.
 

Identification and Analysis of the Putative Pentose Sugar Efflux Transporters in Escherichia coli, Khushnuma Koita, Christopher V. Rao, PLoS One, 7(8): e43700. doi:10.1371/journal.pone.0043700, August 28, 2012.
 

Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering, Jing Du, Yongbo Yuan, Tang Si, Jiazhang Lian, Huimin Zhao, Nucleic Acids Research, doi: 10.1093/nar/gks549, June 19, 2012.
 

Challenges and Opportunities in Synthetic Biology for Chemical Engineers, Yunzi Luo, Jung-Kul Lee, Huimin Zhao, Chemical Engineering Science, http://dx.doi.org/10.1016/j.ces.2012.06.013, June 15, 2012.
 

Directed Evolution: An Evolving and Enabling Synthetic Biology Tool, Ryan Cobb, Tong Si, Huimin Zhao, Current Opinion in Chemical Biology, http://dx.doi.org/10.1016/j.cbpa.2012.05.186, June 4, 2012.
 

High Expression of XYL2 Coding for Xylitol Dehydrogenase Is Necessary for Efficient Xylose Fementation by Engineered Saccharomyces cerevisiae, Soo Rin Kim, Suk-Jin Ha, In Iok Kong, Yong-Su Jin, Metabolic Engineering, doi: 10.1016/j.ymben.2012.04.001, April 13, 2012.
 

Directed Evolution As a Powerful Synthetic Biology Tool, Ryan Cobb, Ning Sun, Huimin Zhao, Methods, http://dx.doi.org/j.ymethod.2012.03.009, March 23, 2012. 
 

An Evaluation of Cellulose Saccharification and Fermentation with an Engineered Saccharomyces cerevisiae Capable of Cellulose and Xylose Utilization, Jerome Fox, Seth Levine, Harvey Blanch, Douglas Clark, Biotechnology Journal, doi: 10.1002/biot.201100209, March 2, 2012.
 

Extractive Fermentation with Non-Ionic Surfactants to Enhance Butanol Production, Pradip Dhamole, Zhilong Wang, Yuanqin Liu, Bin Wang, Hao Feng, Biomass and Bioenergy, http://dx.doi.org/10.1016/j.biombioe.2012.02.007, February 25, 2012.
 

Simultaneous Co-Fermentation of Mixed Sugars: A Promising Strategy for Producing Cellulosic Ethanol, Soo Rin Kim, Suk-Jin Ha, Na Wei, Eun Joong Oh, Yong-Jin, Trends in Biotechnology, http://dx.doi.org/10.1016/j.tibntech.2012.01.005, February 20, 2012.
 

Master Curve Captures the Effect of Domain Morphology on Ethanol Pervaporation Through Block Copolymer Membranes, Ashish Jha, So Ling Tsang, Ali Evren Ozcam, Richard Offeman, Nitash Balsara, Journal of Membrane Science, http://dx.doi.org/10.1016/j.memsci.2012.01.037, February 6, 2012.

 

BIOMASS DEPOLYMERIZATION

 

Cellulose Microfibril Crystallinity Is Reduced By Mutating C-Terminal Transmembrane Region Residues CESA1and CESA3, Darby Harris, Kendall Corbin, Tuo Wang, Ryan Gutierrez, Anna Bertolo, Carloalberto Petti, Detlef Smilgies, Jose Estevez, Dario Bonetta, Breeanna Urbanowicz, David Ehrhardt, Chris Somerville, Jocelyn Rose, Mel Hong, and Seth DeBolt, Proceedings of the National Academy of Sciences 109, 4098-4103.

 

Energy Requirement for Lignocellulosic Feedstock Densifications in Relation to Particle Physical Properties, Preheating, and Binding Agents, Z. W. Miao,T. E. Grift,A. C. Hansen, K. C. Ting, Energy & Fuels, doi: Doi 10.1021/Ef301562k, December 23, 2013.

 

Production of Hybrid Diesel Fuel Precursors from Carbohydrates and Petrochemicals Using Formic Acid as a Reactive Solvent, Xiaoyuan Zhou, Thomas Rauchfuss, ChemSusChem, DOI: 10.1002/cssc.201200718, published online Dec. 23, 2012.

 

Reconstitution of a Thermostable Xylan-Degrading Enzyme Mixture from the Bacterium Caldicellulosiruptor bescii, X. Y. Su,Y. J. Han,D. Dodd,Y. H. Moon,S. Yoshida,R. I. Mackie, I. K. O. Cann, Applied and Environmental Microbiology, doi: Doi 10.1128/Aem.03265-12, 2013, published online Dec. 21, 2012.

 

Energetic Benefits and Rapid Cellobiose Fermentation by Saccharomyces Cerevisiae Expressing Cellobiose Phosphorylase and Mutant Cellodextrin Transporters, Suk-Jin Ha, Jonathan Galazka, Eun Joong Oh, Vesna Kordic, Heejin Kim, Yong-Su Jin, and Jamie H.D. Cate, Metabolic Engineering, http://dx.doi.org/10.1016/j.ymben.2012.11.005, Nov. 22, 2012.

 

A Heterogeneous Nickel Catalyst for the Hydrogenolysis of Aryl Ethers Without Arene Hydrogenation, A.G. Sergeev, J.D. webb, J.F. Hartwig, Journal of the American Chemical Society, doi/full/10.1021/ja3085912, November 19, 2012.

 

Integration of Chemical Catalysis with Extractive Fermentation to Produce Fuels, Pazhamalai Anbarasan, Zachary C. Baer, Sanil Sreekumar, Elad Gross, Joseph B. Binder, Harvey W. Blanch, Douglas S. Clark, and F. Dean Toste, Nature, doi: 10.1038/nature11594, November 8, 2012.

 

Identification and Characterization of a Multifunctional Dye Peroxidase from a Lignin-Reactive Bacterium, Margaret Brown, Tiago Barros, and Michelle C. Y. Chang, ACS Chemical Biology, , doi: 10.1012/cb300383y, October 10, 2012.

 

Automatic Sementation and Quantification of Filamentous Structures in Electron Tomagraphy,  Leandro Loss, Hang Chang, Purbasha Sarkar, George Bebis, Mandred Auer, Bahram Parvin, Accepted Papers, ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2012, doipdf/10.1890/12-0854.1, October 7, 2012.

 

Biased Clique Shuffling Reveals Stabilizing Mutations in Cellulase Cel7A, Craig Dana, Poonam Saija, Sarala Kal, Mara Bryan, Harvey W. Blanch, Douglas S. Clark, Biotechnology and Bioengineering, 109(11), pps. 2710-2719, doi: 10.1002/bit.24708, September 14, 2012.

 

Glucan Adsorption on Mesoporous Carbon Nanoparticles: Effect of Chain Length and Internal Surface, Po-Wen Chung, Alexandre Charmot, Oz M. Gazit, and Alexander Katz,  Langmuir : the ACS journal of surfaces and colloids, 109(11), pps. 2710-2719, doi:  10.1021/La3030364, September 12, 2012.

 

Heterologous Gene Expression in Filamentous Fungi, Xiaoyun Su, George E. Schmitz, Meiling Zhang, Roderick I. Mackie, and Isaac K. O. Cann, Advances in Applied Microbiology, http://dx.doi.org/10.1016/B978-0-12-394382-8.00001-0, Sept. 11, 2012.

 

Supplementing with Non-Glycoside Hydrolase Proteins Enhances Enzymatic Deconstruction of Plant Biomass, Xiaoyun Su, Jing Zhang, Roderick I. Mackie, and Isaac K. O. Cann, PLos One, http://dx.doi.org/10.1371/journal.pone.0043828, Sept. 7, 2012.

 

Competitive Sorption Kinetics of Inhibited Endo- and Exo-glucanases on a Model Cellulose Substrate, Sam Maurer, Clayton J. Radke, Claire N. Bedbrook, Langmuir, doi: 10.1021/la3024524, September 11, 2012.

 

Complexes with Mixed Primary and Secondary Cellulose Synthases are Functional in Arabidopsis thaliana Plants, Andrew Carroll, Nasim Mansoori, Shundai Li, Lei Lei, Samantha Vernhettes, Richard Visser, Chris Somerville, Yong Gu, Luisa Trindade, Plant Physiology, 160, 726-737, http://dx. doi.org/10.1104/pp.112.199208, August 26, 2012.

 

Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus, Yejun Han, Vinayak Agarwal, Dylan Dodd, Jason Kim, Brian Bae, Roderick I. Mackie, Satish K. Nair, and Isaac K.O. Cann,  Journal of Biological Chemistry, http://dx.doi.org/10.1074/jbc.M112.391532, August 25, 2012.

 

A Model for Optimizing the Enzymatic Hydrolysis of Ionic Liquid-Pretreated Lignocellulose, Kiersten Shill, Konrad Miller, Douglas S. Clark, Harvey W. Blanch, Bioresource Technology, http://dx.doi.org/10.1016/j.biortec.2012.08.062, August 23, 2012.

 

Escherichia coli for Biofuel Production: Bridging the Gap from Promise to Practice, Sarah Huffer, Christine Roche, Douglas S. Clark, Harvey W. Blanch, Trends in Biotechnology, http://dx.doi.org/10.1016/j.tibtech.2012.07.002, August 22, 2012.

 

Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus,Yejun Han, Vinayak Agarwal, Dylan Dodd, Jason Kim, Brian Bae, Roderick I. Mackie, Satish K. Nair, Issac K. O. Cann, the Journal of Biological Chemistry, doi: 10.1074/jbc.M112.391532, August 22, 2012.

 

The Kinetics of Bronsted Acid-Catalyzed Hydrolysis of Hemicellulose Dissolved in 1-Ethyl-3-Methylimidazolium Chloride, K. R. Enslow, A. T. Bell, Rsc Advances, doi: Doi 10.1039/C2ra21650g, August 2, 2012.

 

Deciphering the Parts List for the Mechanical Plant,  Chris Somerville, Daedalus, 141 (3), 89-977,doi/pdf/10.1162/DAED_a_00164, Summer 2012.

 

Cellulase Absorption and Reactivity on a Cellulose Surface from Flow Ellipsometry, Sam Maurer, C. N. Bedbrook, Clayton Radke, Industrial and Engineering Chemistry Research, 51(35), pp. 11389-11400, doi: 10.1021/ie3008538, July 31, 2012.

 

Molecular and Biochemical Analyses of the GH44 Module from CbMan5B/Cel44A, a Bifunctional Enzyme from the Hyperthermophylic Bacterium Caldicellulosiruptor bescii, Libin Ye, Xiaoyun Su, George Schmitz, Young Hwan Moon, Jing Zhang, Roderick I. Mackie, Isaac K. O. Cann, Applied and Environmental Microbiology, doi: 10.1128/AEM.02009-12, July 27, 2012.

 

Characterization of Miscanthus giganteus Lignin Isolated by Ethanol Organosolv Process under Reflux Condition, Stefan Bauer, Hagit Sorek, Ana B. Ibanez, David E. Wemmer, Valerie D. Mitchell, Journal of Agricultural and Food Chemistry, http://dx.doi.org/10.1021/jf302409d, July 23, 2012.

 

Dexoygenation of Biomass-Derived Feedstocks: Oxorhenium-Catalyzed Deoxydeydration of Sugars and Sugar Alcohols, Mika Shiramizu, F. Dean Toste, Angewandte Chemie, doi: 10.1002/anie.201203877, July 4, 2012.

 

Degree of Polymerization of Glucan Chains Shapes the Structure Fluctuations and Melting Thermodynamics of a Cellulose Microfibril, Rakwoo Chang, Adam Gross, Jhih-Wei Chu, The Journal of Physical Chemistry B, doi: 10.1021/jp302974x, June 22, 2012.

 

Solubility Parameters for Nine Ionic Liquids, Brian Woo, Waheed Afzal, John M. Prausnitz, Industrial and Engineering Chemistry Research, doi: 10.1021/ie300588s, June 18, 2012.

 

Illuminating the Wall: Using Click Chemistry to Image Pectins in Arabidopsis Cell Walls, Charles Anderson, Ian Wallace, Plant Signaling & Behavior, 7(6), http://dx. doi.org/10.4161/psb.19939, June 2012.

 

Detection of 3D Filamentous Networks from Tomographic Electron Microscopy, Hang Chang, Purbasha Sarkar, Manfred Auer, Bahram Parvin, Leandro A. Loss, Biomedical Imaging, 2012 9th IEEE International Symposium, pp. 1385-1388, May 2-5, 2012.

 

Structural Basis for Substrate Targeting and Catalysis by Fungal Polysaccharide Monooxygenases, Xin Li, William Beeson, Christopher Phillips, Michael A. Marletta, Jamie H. D. Cate, Structure, doi: 10.1016, j. str.2012.04.002, May 10, 2012.

 

Conserved and Essential Transcription Factors for Cellulase Gene Expression in Ascomycete Fungi, Samuel Coradetti, James Craig, Yi Xiong, Teresa Shock, Chaoguang Tian, N. Louise Glass, Proceedings of the National Academy of Sciences, 109(19), pp. 7397-7402, doi: 10.1073/pnas.1200785109, May 8, 2012.
 

Dialkylimidazolium Ionic Liquids Hydrolyze Cellulose Under Mild Conditions, Oz Gazit, Alexander Katz, ChemSUSChem, doi: 10.1002/cssc.201100803, April 30, 2012.


Induction of Lignocellulose-Degrading Enzymes in Neurospora crassa By Cellodextrins, Elizabeth Znameroski, Samuel Coradetti, Christine Roche, Jordan Tsai, Anthony Iavarone, Jamie H. D. Cate, N. Louise Glass, Proceedings of the National Academy of Sciences, 109(16), pp. 6012-6017, doi: 10.1073/pnas.1118440109, April 17, 2012.
 

Entropy of Cellulose Dissolution in Water and in the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride, Adam Gross, Alexis T. Bell, Jhih-Wei Chu, Physical Chemistry Chemical Physics, doi: 10.1039/C2CP40417F, March 27, 2012.
 

Inert-Gas-Stripping Method for Measuring Solubilities of Sparingly Soluble Gases in Liquids; Solubilities of Some Gases in Protic Ionic Liquid 1-Butyl, 3-Hydrogen-Imidazolium Acetate, Waheed Afzal, Brian Yoo, John H. Prausnitz, Industrial and Engineering Chemistry Research, 51(11), pp. 4433-4439, doi: 10.1021/ie20228-y, March 21, 2012.
 

Etherification and Reductive Etherification of 5-(hydroxymethyl) Furfural: 5-(alkoxymethyl) Furfurals and 2, 5-bis (alkoxymethyl) Furans as Potential Biodiesel Candidates, Madhesan Balakrishnan, Eric Sacia, Alexis T. Bell, Green Chemistry, doi: 10.1039/C2GC35102A, March 19, 2012.

 

Mass Spectrometry for Characterizing Plant Cell Wall Polysaccharides, Stefan Bauer, Frontiers in Plant Science, http://dx.doi.org/10.3389/fpls.2012.00045, March 12, 2012.
 

Model-Guided Strain Improvement: Simultaneous Hydrolysis and Co-Fermentation of Cellulose Sugars , Yong-Su Jin, Jamie Cate, Biotechnology Journal, 7(3), pp. 328-329, doi: 10.1002/biot.2011004489, March 2, 2012.

 

An Evaluation of Cellulose Saccharification and Fermentation with an Engineered Saccharomices cerevisiae Capable of Cellulose and Zylose Utilization, Jerome Fox, Seth Levine, Harvey Blanch, Douglas Clark, Biotechnology Journal, doi: 10.1002/biot.201100209, March 2, 2012.

 

Deciphering Transcriptional Regulatory Mechanisms Associated With Hemicellulose Degradation in Neurospora crassa, Jianping Sun, Chaoguang Tian, Spencer Diamond, N. Louise Glass, Eukaryotic Cell, doi: 10.1128/EC.05327-11, February 2012.

 

Extractive Fermentation with Non-Ionic Surfactants to Enhance Butanol Production, Pradip Dhamole, Zhilong Wang, Yuanqin Liu, Bin Wang, Hao Feng, Biomass and Bioenergy, http://dx.doi.org/10.1016/j.biombioe.2012.02.007, February 25, 2012.
 

Chemisorption and Dehydration of Ethanol on Silica: Effect of Temperature on Selectivity, Tatiana Luts, Alexander Katz, Topics in Catalysis, doi: 10.1007/s11244-012-9771-9, February 14, 2012.
 

CHITINASE-LIKE1/POM-POM1 and its Homolog CTL2 Are Glucan-Interacting Proteins Important for Cellulose Biosynthesis in Arabidopsis, Clara Sanchez-Rodriguez, Stefan Bauer, Kian Hematy, Friederike Saxe, Ana Belen Ibanez, Vera Vodermaier, Cornelia Konlechner, Arun Sampathkumar, Markus Ruggeberg, Ernst Aichinger, Lutz Neumetzler, Ingo Burgert, Chris Somerville, Marie-Theres Hauser, Staffan Persson, The Plant Cell, doi: http://dx.doi.org/10.1105/tpc.111.094672, February 2012.
 

Metabolic Click-Labeling with a Fucose Analog Reveals Pectin Delivery, Architecture, and Dynamics of Arabidopsis Cell Walls, Charles Anderson, Ian Wallace, Chris Somerville, Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1120429109, January 9, 2012.
 

Biochemical and Mutational Analyses of a Multi-Domain Cellulase/Mannanase from Caldicellulosiruptor bescii, Xiaoyun Su, Roderick Mackie, Isaac Cann, Applied and Environmental Microbiology, doi: 10.1128/AEM.06814-11, January 2012.

 

 

ENVIRONMENTAL, SOCIAL, & ECONOMIC IMPACTS

 

Adoption Versus Adaptation, with Emphasis on Climate Change, David Zilberman, Jinhua Zhao, Amir Heiman, Annual Review of Resource Economics, Vol. 4, doi:10.1146/annurev-resource-083110-115954, 2012.

 

Legitimacy, Innovation, and Harmonization: Precursors to Operationalizing Biofuels Sustainability Standards, Jody Endres, Southern Illinois University Law Journal, Vol. 37, 2012 online.

 

How the Roundtable on Sustainable Biofuels Has Addressed GMOs,  Sebastien Haye and A. Bryan Endres,  Agricultural Law News, December 2012.

 

Projecting an Energy Future: Biofuels, Bioenergy, and the Importance of Regionality in Scenarios and Potentials, Caroline Taylor, Perspectives on Biofuels: Potential Benefits and Possible Pitfalls, doi: 10.1021/bk-2012-1116.ch002, published online December 18, 2012.

 

Stimulating Learning-By-Doing in Advanced Biofuels: Effectiveness of Alternative Policies,  Xiaoguang Chen, Madhu Khanna, and Sonia Yeh,  Environmental Research Letters, doi:10.10888/1748-9326/7/4/045907, December 13, 2012.

 

Operationalizing Biofuels Sustainability Standards: Legitimacy, Technological and Institutional Innovation, and Harmonization, Jody Endres, 38 Southern Illinois University Law Review, Fall 2012.

 

Multi-Criteria Comparison of Fuel Policies: Renewable Fuel Mandate, Fuel Emission Standards, and Fuel Carbon Tax, Deepak Rajagopal, Gal Hochman, David Zilberman, UCLA Institute of the Environment and Sustainability (working paper), November 26, 2012.

 

Biofuel and Food-Commodity Prices, Gal Hochman, Scott Kaplan, Deepak Rajagopal, and David Zilberman, Agriculture, 2(3), 272-281; doi: 10:3390/agriculture2030272, 2012.

 

Grand Missions of Agricultural Innovation, Wright, Brian D, Research Policy, http://dx.doi.org/10.1016/j/respol.2012.04.021, October 22, 2012 online.

 

Intake Fractions of Primary Conserved Air Pollutants Emitted From On-Road Vehicles in  the United States, Agnes B. Lobscheid, William W. Nazaroff, Michael Spears, Arpad Horvath, and Thomas E. McKone, Atmospheric Environment, http://dx.doi.org/10/1016/j.atmosenv.2012.09.027, September 2012 online.

 

Greenhouse Gas Emissions from the Construction, Manufacturing, Operation and Maintenance of US Distribution Infrastructure for Petroleum and Biofuels, Bret Strogen, Arpad Horvath, Journal of Infrastructure Systems, Il  doi:10.1061/(ASCE)15.1943-555X.0000130, September 28, 2012.

 

The Renewable Fuel Standard 3.0?: Moving Forward With the Federal Biofuel Mandate, Timothy Slating, Jay Kesan, Social Sciences Research Network, Illinois Program in Law, Behavior and Social Science Paper No. LBSS13-06, September 11, 2012.

 

Time-Frequency Dynamics of Biofuels-Fuels-Food System, Lukas Vacha, Karel Janda, Ladislav Kristoufek, David Zilberman, Statistical Finance, arXiv:1209.0900, September 5, 2012.

 

Evaluating a Modified Point-Based Method to Downscale Cell-Based Climate Variable Data to High-Resolution Grids, Alan DiVittorio, Norman L. Miller, Theoretical and Applied Climatology, doi: 10.1007/s00704-012-0740-9, August 29, 2012.

 

Biofuels: Policies and Impacts, Karel Janda, Ladislav Kristoufek, David Zilberman, Agricultural Economics-Czech, 58(2012), pp. 372-386, 2012.

 

Miscanthus Biomass Productivity Within U.S. Croplands and its Potential Impact on Soil Organic Carbon, Umakant Mishra, Margaret Torn, Kevin Fingerman, Global Change Biology-Bioenergy, doi: 10.1111j.1757-1707.2012.01201.x, August 10, 2012.

 

Impact of Different Bioenergy Crops on N-Cycling Bacterial and Archaeal Communities in Soil, Yuejian Mao, Anthony Yannarell, Sarah Davis, Roderick I. Mackie, Environmental Microbiology, doi: 10.1111j.1462-2920.2012.02844.x, August 2012.

 

Role of Arthropod Communities in Bioenergy Crop Litter Decomposition, Arthur Zangerl, Saber Miresmailli, Paul Nabity, Allen Lawrence, Alan Yanahan, Corey Mitchell, Kristina Anderson-Teixeira, Mark David, May Berenbaum, Evan H. Delucia, Insect Science, doi: 10.1111/j.1744-7917.2012.01532.x, August 2, 2012.

 

Producer Perceptions and Information Needs Regarding Their Adoption of Bioenergy Crops, Maria Villamil, Myles Alexander, Anne Heinze Silvis, Michael E. Gray, Renewable and Sustainable Energy Reviews, 16(6), pp. 3604-3612, doi: 10.1016/j.rser.2012.03.033, August 2012.

 

Impacts of Herbaceous Bioenergy Crops on Atmospheric Volatile Organic Composition and Potential Consequences for Global Climate Change, Saber Miresmailli, Marcelo Zeri, Arthur Zangerl, Carl Bernacchi, May Berenbaum, Evan H. DeLucia, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2012.01189.x, July 9, 2012.

 

A Regional Comparison of Water Use Efficiency for Miscanthus, Switchgrass and Maize, Andy VanLoocke, Tracy Twine, Marcelo Zeri, Carl J. Bernacchi, Agricultural and Forest Metrology, 164, pp. 82-95, http://doi:dx.doi.org/10.1016j.agrformet.2012.05.016, June 16, 2012.

 

An Economic Analysis of the Future U.S. Biofuel Industry, Facility Location, and Supply Chain Network, Xiaoguang Chen, Hayri Onal, Social Science Research Network, June 14, 2012.

 

Mandatory Demand as a Policy Instrument: The Case of the Renewable Fuel Standard (RFS) Biofuel Program, Jay Kesan, Timothy Slating, Hsiao-Shan Yang, Illinois Program in Law, Behavior and Social Science Paper No. LBSS12-16, June 13, 2012.

 

Silica and Nitrogen Modulate Physical Defense Against Chewing Insect Herbivores in Bioenergy Crops Miscanthus x giganteus and Panicum virgatum (Poaceae), Paul Nabity, Robert Orpet, Saber Miresmailli, May Berenbaum, Evan H. Delucia, Journal of Economic Entomology, 105(3), pp. 878-883, doi: http://dx.doi.org/10.1603/EC11424, June 2012.

 

The Impact of Biofuels on Commodity Food Prices: Assessment of Findings, David Zilberman, Gal Hochman, Deepak Rajagopal, Steve Sexton, Govinda Timilsina, American Journal of Agricultural Economics, 95(2): 275-281. doi: 10.1093/ajae/aas037, June 7, 2012.

 

Carbon Sequestration in Soil in a Semi-Natural Miscanthus sinensis Grassland and Cryptomeria japonica Forest Plantation in Aso, Kuymamoto, Japan, Yo Toma, J. Ryan Stewart, Toshihiko Yamada, Aya Nishiwaki, Fabian Fernandez, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2012.01160.x, February 27, 2012.

 

Can India Meet Biofuel Policy Targets: Implications for Food and Fuel Prices, Madhu Khanna, Hayri Onal, Christine Crago, Kivoshi Mino, American Journal of Agricultural Economics, doi: 10.1093/ajae/aas040, May 18, 2012.
 

Food vs. Fuel: The Effect of Biofuel Policies, Xiaoguang Chen, Madhu Khanna, American Journal of Agricultural Economics, doi: 10.1093/ajae/aas039, May 11, 2012.
 

Definitional Debates and Uncertainty for Would-Be Biofuel Producers, James McCubbins, Lauren Quinn, A.Bryan Endres, Farmdoc Daily, Department of Agriculture and Consumer Economics, University of Illinois, May 2, 2012. 
 

The Market-Mediated Effects of Low Carbon Fuel Policies, Xiaoguang Chen, Madhu Khanna, AgBioForum, 15(1), pp. 89-105, May 2012.
 

Fuel Miles and the Blend Wall: Costs and Emissions from Ethanol Distribution in the United States, Bret Strogen, Arpad Horvath, Thomas E. McKone, Environmental Science and Technology, doi: 10.1021/es204547s, April 16, 2012.

 

GMO Bioenergy: Potential Risks and Liabilities, Jennifer Coleman, Jacob Barney and A. Bryan Endres, American Bar Association Agricultural Management Committee Newsletter, Vol. 16, No. 2, 9-11, April 2012.

 

New Hope for Dedicated Genetically Engineered Bioenergy Feedstocks?, A. Bryan Endres, Global Change Biology-Bioenergy 4, 127-129, DOI: 10.1111/j.1757-1707.2011.01134.x, March 2012.

 

Measuring Indirect Land Use Change with Biofuels: Implications for Policy, Madhu Khanna, Christine L. Crago, Annual Review of Resource Economics, doi: March 15, 2012.

 

Mass Spectrometry for Characterizing Plant Cell Wall Polysaccharides, Stefan Bauer, Frontiers in Plant Science, http://dx.doi.org/10.3389/fpls.2012.00045, March 12, 2012.

 

Determinants of U.S. Corn and Soybean Yields: Climate  Change and Crop Prices, H. Huang and M. Khanna, Social Science Research Network , March 2012.
 

Global Intraurban Intake Fractions for Primary Air Pollutants from Vehicles and Other Distributed Sources, Joshua Apte, Emilie Bombrun, Julian Marshall, William Nazaroff, Environmental Science & Technology, doi: 10.1021/es204021h, February 14, 2012.
 

Bioenergy Potential of the United States Constrained by Satellite Observations of Existing Productivity, William Kolby Smith, Cory Cleveland, Sasha Reed, Steven Running, Norman Miller, Environmental Science and Technology, doi: 10.1021/es203935d, February 9, 2012.
 

Explaining the Reductions in U.S. Corn Ethanol Processing Costs: Testing Competing Hypotheses, Xiaoguang Chen, Madhu Khanna, Energy Policy, http://dx.doi.org/10.1016/j.enpol.2012.01.032, February 9, 2012.
 

Land Use and Greenhouse Gas Implications of Biofuels: Role of Technology and Policy, Xiaoguang Chen, Haixiao Huang, Madhu Khanna, Social Science Research Network, February 8, 2012. 
 

Maize-Based Biofuels: Legal and Regulatory Issues in the US, Timothy Slating, Jay Kesan, doi: 10.2139/ssrn.2002143, February 2012.
 

Modeling Agricultural Supply Response Using Mathematical Programming and Crop Mixes, Xiaoguang Chen, Hayri Onal, American Journal of Agricultural Economics, doi: 10.1093/ajae/aar143, Feb. 2, 2012.

 

An Evolutionary Approach to Agricultural Biotechnology: Litigation Challenges to the Regulatory and Common Law Regimes for Genetically Engineered Plants, A. Bryan Endres, Northeastern University Law Journal 4, 59-87, doi: 10.1093/ajae/aar143, Feb. 2, 2012.
 

Farm Acreage Shocks and Food Prices: An SVAR Approach to Understanding the Impacts of Biofuels, Catherine Hausman, Maximilian Auffhammer, Peter Berck, Social Science Research Network Working Paper Series, doi: 10.2139/ssrn.1605507, January 24, 2012.
 

Life-Cycle Greenhouse Gas Implications of U.S. National Scenarios for Cellulosic Ethanol Production, Corinne Scown, William Nazaroff, Umakant Mishra, Bret Strogen, Agnes Lobscheid, Eric Masanet, Nicholas Santero, Arpad Horvath, Thomas McKone, Environmental Research Letters, 7(1), doi: 10.1088/1748-9326/7/1/014011, January 24, 2012.
 

A Legal Analysis of the Effects of the Renewable Fuel Standard (RFS2) and Clean Air Act on the Commercialization of Biobutanol as a Transportation Fuel in the United States, Timothy A. Slating & Jay P. Kesan, Global Change Biology-Bioenergy, 4(1), doi: 10.1111/j.1757-1707.2011.01146.x, January 9, 2012.
 

Climate-Regulation Services of Natural and Agricultural Ecoregions of the Americas, Kristina Anderson-Teixeira, Peter Snyder, Tracy Twine, Santiago Cuadra, Marcos Costa, Evan DeLucia, Nature Climate Change, doi:10.1038/nclimate1346, January 8, 2012.

 

 

FEEDSTOCK DEVELOPMENT

 

Population Genomic and Genome-Wide Association Studies of Agroclimatic Traits in Sorghum,  Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S.T,  Proceedings of the National Academy of Sciences,doi: 10.1073/pnas.1215985110, December 24, 2012 online.

 

Biofuels on the Landscape: Is Land Sharing Preferable to Land Sparing?  Kristina J Anderson-Teixeira,Benjamin D Duval,Stephen P Long, Evan H Delucia,  Ecological Applications, Vol. 22, Issue 8, doi: 10.1890/12-0711.1, December 2012.

 

Switchgrass:  Practical  Issues in Developing a Fuel Crop,  Y. Shastri, A.D. Hansen, L.F. Ropdriguez, K.C. Tin,  CAB Reviews,
doi: 10.1079/PAVSNNR20127037, 7 No. 037, 2012.

 

Soil Carbon and Accumulation over 12,000 years in a Semi-Natural Miscanthus Sinensis Grassland in Southern Japan,  David Howlett, Yo Toma, Hong Wang, Shinji Sugiyama, Toshiko Yamada, Aya Nishiwaki, Fabian Fernandez, J. Ryan Stewart,  CATENA, http://dx.doi.org/10.1016/catena.2012.11.002, December 8, 2012 online.

 

Biomechanical Properties of Miscanthus Stems, Q. Liu, S.K. Mathanker, Q. Zhang, A.C. Hansen,  Transactions of the ASABE, 55 (4): 1125-1131, 2012.

 

Detection of Switchgrass Mosaic Virus in Miscanthus and Other Grasses,  Bright Agindotan, Michael Gray, Rosemarie Hammond, and Carl Bradley, Archives of Virology, doi/abs/10.1080/07060661.2012.752763, November 28, 2012.

 

On Improving the Communication Between Models and Data, Michael Dietze, David LeBauer, Rob Kooper, Plant, Cell & Environment, doi: 10.1111/pce.12043, November 26, 2012.

 

Seed Set in Prairie Cordgrass (Spartina pectinata Link), Arvid Boe, Vance Owens, Jose Gonzalez-Hernandez, and D.K. Lee, Crop Science 53: 1-8, doi: 10.2135/cropsci2012.04.0250, November 14, 2012.

 

Aqueous-Ammonia Delignification of Miscanthus Followed by Enzymatic Hydrolysis to Sugars, Zhongguo Liu, Sasisanker Padmanabhan, Kun Cheng, Philippe Schwyter, Markus Pauly, Alexis T. Bell, John M. Prausnitz, Biosource Technology, http://dx.doi.org/10.1016/j.biotech.2012.10.133, November 5, 2012.

 

Enhanced Xylitol Production Through Simultaneous Co-Utilization of Cellobiose and Xylose by Engineered Saccharomyces cerevisae,  Eun Joong Oh, Suk-Jin Ha, Soo Rin Kim, Won-Heong Lee, Jonathan M. Galazka, Jamie H.D. Cate, Yong Su-Jin, Metabolic Engineering, http:/dx.doi.org/PDF/10.1016/j.ymben.2012.09.003, November 2, 2012.

 

Facilitating Feedbacks Between Field Measurements and Ecosystem Models, David LeBauer, D Wang, K Richter, C Davidson, Michael Dietze, http://www.esajournals.org/doi/pdf/10.1890/12-0137.1, Ecological Monographs, October 2012.

 

Cytogeographic Distribution and Genome Size Variation in Prairie Cordgrass (Spartina pectinata Bosc ex Link), Sumin M. Kim, A. L. Rayburn, Allen Parrish, and D.K. Lee, Plant Molecular Biology Reporter 7:1-13,  doi: 10.1007/511105-012-0414-x, October 2012.

 

Complete Genome Sequence of Switchgrass Mosaic Virus, a Member of the Proposed New Species in the Genus Marafivirus, Bright Agindotan, Michael E. Gray, Rosemarie Hammond, Carl A. Bradley, Archives of Virology, 157(9), pp. 1825-1830, doi: 10.1007/s00705-012-1354-3, September 2012.

 

Synthetic Polyploid Production of Miscanthus sacchariflorus, Miscanthus sinensis, and Miscanthus x giganteus, Won Byoung Chae, Sae Hong, Justin Gifford, Albert Lane Rayburn, Jack M. Widholm, John A. Juvik, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2012.01206.x, September 7, 2012.

 

Light Response of Native and Introduced Miscanthus sinensis Seedlings, David Matlaga, Lauren Quinn, Adam Davis, J. Ryan Stewart, Invasive Plant Science and Management, 5(3), pp.363-374, doi: http://dx.doi.org/10.1614/IPSM-D-11-00056.1, July-September 2012.

 

Deciphering the Parts List for the Mechanical Plant, Chris Somerville, Daedalus, 141 (3), pp. 89-97, doi: 10.1162/DAED_a_00164, Summer 2012

 

Moth Diversity in Three Biofuel Crops and Native Prairie in Illinois, Terry Harrison, May R. Berenbaum, Insect Science, doi: 10.1111/j.1744-7917.2012.05130.x, July 13, 2012.

 

Neopolyploidy in Spartina pectinata Link: Morphological Analysis of Tetraploid and Hexaploid Plants in a Mixed Natural Population, Sumin Kim, A.L Rayburn, Arvid Boe, and D.K. Lee, Plant Systematics & Evolution, doi: 10.1007/s00606-012-0617-5, June 2012.

 

Harvesting Carbon from Eastern U.S. Forests: Opportunities and Impacts of an Expanding Bioenergy Industry, Sarah Davis, Michael Dietze, Evan DeLucia, Chris Field, Steven Hamburg, Scott Loarie, William Parton, Matthew Potts, Benjamin Ramage, Dan Wang, Heather Youngs, and Stephen P. Long, Forests, 3(2), pp. 370-397, doi: 10.3390/f3020370, June 19, 2012.

 

Envisioning the Transition to a Next-Generation Biofuels Industry in the U.S. Midwest, Ismail Dweikat, Clifford Well, Stephen Moose, Leon Kochian, Nathan Mosier, Klein Ileleji, Patrick Brown, Wendy Peer, Angus Murphy, Farzad Teheripour, Maureen McCann, Nicholas Carpita, Biofuels, Bioproducts and Biorefining, doi: 10.1002/bbb.1342, June 11, 2012.

 

Forage and Energy Sorghum Response to Nitrogen Fertilization in Central and Southern Illinois, Matt Maughan, Thomas Voigt, Allen Parish, German Bollero, William Rooney, D. K. Lee, Agronomy Journal, 104(4), pp. 1032-1040, June 2012.
 

Producer Perceptions and Information Needs Regarding Their Adoption of Bioenergy Crops, Maria Villamil, Myles Alexander, Anne Heinze Silvis, Michael E. Gray, Renewable and Sustainable Energy Reviews, 16(6), pp. 3604-3612, doi: 10.1016/j.rser.2012.03.033, August 2012.
 

Genetic Comparison of Introduced and Native Populations of Miscanthus sinensis (Poaceae), a Potential Bioenergy Crop, Lauren Quinn, Theresa Culley, J. Ryan Stewart, Grassland Science, doi: 10.1111/j.1744-697X.2012.00248.x, May 17, 2012.
 

Development of Feedstocks for Cellulosic Biofuels, Heather Youngs and Chris Somerville, F1000 Biology Reports, 4(10), doi: 10.3410/B4-10, May 2, 2012.
 

A Framework Genetic Map for Miscanthus sinensis from RNAseq-based Markers Shows Recent Tetraploidy, Kankshita Swaminathan, Won B Chae, Therese Mitros, Kranthi Varala, Liang Xie, Adam Barling, Katarzyna Glowacka, Megan Hall, Stanislaw Jezowski, Ray Ming, Matthew Hudson, John Juvik, Daniel Rokhsar, Stephen P. Moose, BMC Genomics, 13(142), doi: 10.1186/1471-2164-13-142, April 24, 2012.
 

Tower Remote-Sensing System for Monitoring Energy Crops; Image Acquisition and Geometric Corrections, Tofael Ahamed, Lei Tian, Yanshui Jiang, Bin Zhao, Hx Liu, Kuan Chong Ting, Biosystems Engineering, doi: 10.1016/j.biosystemseng.2012.03.003, April 18, 2012.
 

Greenhouse Gas Emissions, Nitrate Leaching, and Biomass Yields from Production of Miscanthus x giganteus in Illinois, USA, Gevan Behnke, Mark David, Thomas Voigt, BioEnergy Research, doi: 10.1007/s12155-012-9191-5, April 5, 2012.
 

Seed Reduction in Prairie Cordgrass, Spartina pectinata Link, By the Floret-Feeding Caterpillar Aethes spartina (Barnes and McDunnough), Jarrod R. Prasifka, D. K. Lee, J.D. Bradshaw, Allen S. Parrish, and Michael E. Gray, Bioenergy Research, doi: 10.1007/s12155-011-9120-z, March 2012.

 

Salinity Effects on Germination and Plant Growth of Prairie Cordgrass and Switchgrass, Sumin Kim, A. L. Rayburn, Thomas Voigt, Allen Parrish, and D. K. Lee, BioEnergy Research, 5 (1): 225-235, March 2012.

 

Impact of Probability of Working Day on Planning and Operation of Biomass Feedstock Production Systems, Yogendra Shastri, Alan Hansen, Luis Rodriguez, K.C. Ting, Biofuels, Bioproducts and Biorefining, doi: 10.1002/bbb.1329, March 2012.
 

Impact of Nitrogen Allocation on Growth and Photosynthesis of Miscanthus (Miscanthus x giganteus), Dan Wang, Mathew Maughan, Jindong Sun, Xiaohui Feng, Fernando Miguez, DoKyoung Lee, Michael Dietze, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2012.01167.x, March 13, 2012.
 

Cutting Energy Characteristics of Miscanthus x giganteus Stems With Varying Oblique Angle and Cutting Speed, Phillip Johnson, Clairmont Clementson, Sunil Mathanker, Tony Grift, Alan Hansen, PL0S ONE 7, http://doe:10.1371/journal.pone.0032253, February 28, 2012 online.

 

Development of High-Density Genetic Maps for Barley and Wheat Using Genotyping-by-Sequencing, J. Poland, P.J. Brown, M. Sorrels, J-L Jannink, Biosystems Engineering, http://dx.doi.org/10.1016/j.biosystemseng.2012.02.003, March 6, 2012.
 

Carbon Sequestration in Soil in a Semi-Natural Miscanthus sinensis Grassland and Cryptomeria japonica Forest Plantation in Aso, Kuymamoto, Japan, Yo Toma, J. Ryan Stewart, Toshihiko Yamada, Aya Nishiwaki, Fabian Fernandez, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2012.01160.x, February 27, 2012.
 

Lignocellulosic Biomass Feedstock Transportation Alternatives, Logistics, Equipment Configurations, and Modeling, Zewei Miao, Yogendra Shastri, Tony Grift, Alan Hansen, K.C. Ting, Biofuels, Bioproducts and Biorefining, doi: 10.1002/bbb.1322, February 17, 2012.

 

Growing Better Biofuel Crops, Heather Youngs and Chris Somerville, The Scientist 26, 46-52.

 

Impact of Distributed Storage and Pre-Processing on Miscanthus Production and Provision System, Y. Shastri, L.F. Rodriguez, A.C. Hansen, K.C. Ting, Biofuels, Biproducts, and Bioprocessing 26, 46-52, doi/10.1002/bbb.326/full, 2012.

 

Research Needs and Potential Effects of Biomass Crops on Pest Management , Jarrad Prasifka and Michael Gray, Journal of Integrated Pest Management, 3 (4), doi: http://dx.doi.org/10.1603/IPM12011, 2012.

 

Potential Biomass Reductions to Miscanthus x giganteus by Stem-Boring Caterpillars , Jarrad Prasifka, Jeffrey Bradshaw, and Michael Gray Environmental Entomology, Vol. 41, Issue 4, 2012.2012.

 

FOSSIL FUEL BIOPROCESSING

 

Microbial Response to the MC252 Oil and Corexit 9500 in the Gulf of Mexico, R. Chakraborty, S. E. Borglin, E. L. Dubinsky, G. L Andersen, T. C. Hazen, Frontiers in Microbiotechnology, Ecotoxicology, and Bioremediation, doi/10.3389/fmicb.2012.00357/full, Jul October 11, 2012.

 

Metagenome, Metatranscriptome and Single-Cell Sequencing Reveal Microbial Response to Deepwater Horizon Oil Spill, O. U. Mason, T.  C. Hazen, S. Borglin, P. S. Chain, E. A. Dubinsky, J. L. Fortney, J. Han, H. Y. Holman, J. Hultman, R. Lamendella, R. Mackelprang, S. Malfatti, L. M. Tom, S. G. Tringe, T. Woyke, J. Zhou, E. M. Rubin, J. K. Jansson, ISME Journal 6: 1715-1757,  doi:  10.1038/ismej.2012.59, September 2012.

 

Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill, M. J. Beazley, R. J. Martinez, S. Rajan, J. Powell, Y. M. Piceno, L. M. Tom, G. L. Andersen, T. C. Hazen, J. D. Van Nostrand, J. Zhou, B. Mortazavi, P. A. Sobecky, PLoS One,doi/10.1371/journal.pone.0041305, July 18, 2012.
 

Deep-Sea Bacteria Enriched by Oil and Dispersant from the Deepwater Horizon Spill, Jacob Baelum, Sharon Borglin, Romy Chakraborty, Julian Fortney, Regina Lamendella, Olivia Mason, Manfred Auer, Marcin Zemla, Markus Bill, Mark Conrad, Stephanie Malfatti, Susannah Tringe, Hoi-Ying Holman, Terry Hazen, Janet Jansson, Environmental Microbiology, doi: 10.1111/j.1462-2920.2012.02780, May 23, 2012.
 

Complete Genome Sequence of the Anaerobic Perchlorate-Reducing Bacterium Azospira Suillum Strain Ps, K. G. Byrne-Bailey, J. D. Coates, Journal of bacteriology, doi: 10.1128/JB.00124-12, 2012/04/27 2012.
 

Bioelectrical Redox Cycling of Anthraquinone-2,6-Disulfonate Coupled to Perchlorate Reduction, Iain Clark, Hans Carlson, Anthony Iavarone, John D. Coates, Energy & Environmental Science, doi: 10.1039/c0xx00000x, Accepted Manuscript, May 2012.
 

Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002 , Kathryne Byrne-Bailey, Karrie Weber, John D. Coates, Journal of Bacteriology, 194(9), pp. 2400-2401, doi: 10.1128/JB.00214-12, May 2012.
 

Pseudomonas syringae Coordinates Production of a Motility-Enabling Surfactant with Flagellar Assembly, Adrien Burch, Briana K. Shimada, Sean W. A. Mullin, Christopher Dunlap, Michael Bowman, Steven Lindow, Journal of Bacteriology194(4), doi: 10.1128/JB.06058-11, February 2012.
 

Towards a Mechanistic Understanding of Anaerobic Nitrate Dependent Iron Oxidation: Balancing Electron Uptake and Detoxification, Hans Karl Carlson, Iain Clark, Ryan Melnyk, John D. Coates, Frontiers in Microbiology, 3:57, doi: 10.3389/fmicb.2012.00057, February 20, 2012.
 

Microbial Gene Functions Enriched in the Deepwater Horizon Deep-Sea Plume, Z. Lu, Y. Deng, J. D. Van Nostrand,, Z. He, J. Voordeckers, A. Zhou, Y. J. Lee, O. U. Mason, E.  A. Dubinsky, K. L. Chavarria, L. M. Tom, J. L. Fortney, R. Lamendella, J. K. Jansson, P. D'haeseleer, T. C. Hazen, J. Zhou, ISME Journal 6: 451-460, doi:  10.1038/ismej.2011.91, February 2012.

 

Surface Multiheme C-Type Cytochromes from Thermincola potens and Implications for Dissimilatory Metal Reduction by Gram-Positive Bacteria, Hans Carlson, Anthony Iavarone, Amita Gorur, Boon Siang Yeo, Rosalie Tran, Ryan Melnyk, Richard Mathies, Manfred Auer, John D. Coates, Proceedings of the National Academy of Sciences, 109(5), pp. 1702-1707, doi: 10.1073/pnas.1112905109, January 31, 2012.

 

Microbial Response to the MC252 Oil and Corexit 9500 in the Gulf of Mexico, R. Chakraborty, S. E. Borglin, E. L. Dubinsky, G. L Andersen, T. C. Hazen, Frontiers in Microbiotechnology, Ecotoxicology, and Bioremediation, doi/10.3389/fmicb.2012.00357/full, Jul October 11, 2012.

 

 

Published in 2011

BIOFUELS PRODUCTION

 

 

Determination on Crystallinity of Ionic Liquids Pretreated Biomass, Hong Xue Xie, John Prausnitz, Xiu Ling Wu, Advanced Materials Research, Vols. 393-395, doi:10-4028/www.scientific.net/AMR393-395.668, pp. 668-671, November 22, 2011
 

Solubilities of Some Organic Solutes in 1-Ethyl-3-Methylimidazolium Acetate; Chromatographic Measurement and Predictions from COSMO-RS, Jan-Georg Rosenboom, Waheed Afzal, John Prausnitz, Journal of Chemical Thermodynamics, doi: 10.1016/j.jct.2011.11.005, November 15, 2011.
 

Genome-Scale Consequences of CoFactor Balancing in Engineering Pentose Utilization Pathways in Saccharomices cerevisiae, Amit Ghosh, Huimin Zhao, Nathan Price, PLoS One, 6(11), e27316; doi: 10.1371/journal.pone.0027316, November 4, 2011.
 

Spatial Organization of Enzymes for Metabolic Engineering, Hanson Lee, William DeLoache, John Dueber, Metabolic Engineering, doi: 10.1016/j.ymben.2011.09.003, September 17, 2011.
 

Cofermentation of Cellobiose and Galactose by an Engineered Saccharomyces cerevisiae Strain, Suk-Jin Ha, Qiaosi Wei, Soo Rin Kim, Jonathan Galazka, Jamie Cate, Yong-Su Jin, Applied and Environmental Microbiology, 77(16), pp. 5822-5825, doi:10.1128/AEM.05228-11, August 2011.
 

Solubility and Rate of Dissolution for Miscanthus in Hydrophylic Ionic Liquids, Sasisanker Padmanabhan, Michael Kim, Harvey Blanch, John Prausnitz, Fluid Phase Equilibria, doi: 10.1016/j.fluid.2011.06.034, July 5, 2011.
 

Tuning Structural Durability of Yeast-Encapsulating Alginate Gel Beads with Interpenetrating Networks for Sustained Bioethanol Production, Chaenyung Cha, Soo Rin Kim, Yong-Su Jin, Hyunjoon Kong, Biotechnology and Bioengineering, doi: 10.1002/bit.23258, July 5, 2011.
 

Xylitol Does Not Inhibit Fermentation by Engineered Saccharomyces cerevisiae Expressing xylA as Severely As It Inhibits Xylose Isomerase Reaction In Vitro, Suk-Jin Ha, Soo Rin Kim, Jin-Ho Choi, Myeong Soo Park, Yong-Su Jin, Applied Microbiology and Biotechnology, doi: 10.1007/s00253-011-3345-9, June 8, 2011.
 

Metabolic Pathway Flux Enhancement by Synthetic Protein Scaffolding, Weston Whitaker, John Dueber, Methods in Enzymology (Chapter 19), 497, pp. 447-468, doi: 10.1016/B978-0-12-385075-1.00019-6, May 19, 2011.
 

Engineering Microbial Factories for Synthesis of Value-Added Products, Jing Du, Zengyi Shao, Huimin Zhao, Journal of Industrial Microbiology and Biotechnology, doi:10.1007/s10295-011-0970-3, April 28, 2011. 
 

Effect of Nanoscale Morphology on Selective Ethanol Transport Through Block Copolymer Membranes, Ashish Jha, Liang Chen, Richard Offeman, Nitash Balsara, Journal of Membrane Science, doi:10.1016/j.memsci.2011.02.043, March 4, 2011.

 

 

BIOMASS DEPOLYMERIZATION

 

 

An Evaluation of Cellulose Saccharification and Fermentation with an Engineered Saccharomyces cerevisiae Capable of Cellobiose and Xylose Utilization, Jerome Fox, Seth Levine, Harvey Blanch, Douglas Clark, Biotechnology Journal, doi:10.1002/biot.201100209, December 29, 2011.
 

Oxidative Cleavage of Cellulose by Fungal Copper-Dependent Polysaccharide Monooxygenases, William Beeson, Christopher Phillips, Jamie Cate, Michael Marletta, Journal of the American Chemical Society, doi: 10.1021/ja210657t, December 20, 2011.
 

Structural Transformation of Miscanthus giganteus Lignin Fractionated Under Mild Formosolov, Basic Organoslov and Cellulolytic Enzyme Conditions, Kun Wang, Run-Cang Sun, Stefan Bauer, Journal of Agricultural and Food Chemistry, doi: 10.1021/jf2037399, November 30, 2011.
 

Initial- and Processive-cut Products from Cellobiohydrolase-catalyzed Hydrolysis of Cellulose Reveal Rate-limiting Steps and Role of Companion Enzymes, Jerome Fox, Seth Levine, Douglas Clark, Harvey Blanch, Biochemistry, doi: 10.1021/bi2011543, November 21, 2011. 
 

Grafted Poly(14-β-glucan) Strands on Silica: A Comparative Study of Surface Reactivity as a Function of Grafting Density, Oz Gazit, Alexander Katz, Langmuir (ACS), doi: 10.1021/la2036482, November 14, 2011.
 

Raman-Spectroscopy-Based Noninvasive Microanalysis of Native Lignin Structure, Pradeep Perera, Martin Schmidt, Vincent Chiang, James Schuck, Paul Adams, Analytical and Bioanalytical Chemistry, doi: 10.1007/s00216-011-5518-x, November 10, 2011.
 

Delignification of Miscanthus by Extraction, Sasisanker Padmanabhan, Edmond Zaia, Katherine Wu, Harvey Blanch, Douglas Clark, Alexis Bell, John Prausnitz, Separation Science and Technology, doi:10.1080/01496395.2011.629639, November 4, 2011.
 

A Mechanistic Model for Rational Design of Optimal Cellulase Mixtures, Seth Levine, Jerome Fox, Douglas Clark, Harvey Blanch, Biotechnology and Bioengineering, 108(11), pp. 2561-2570, doi: 10.1002/bit.23249, November 2011.
 

Extraction of Lignins from Aqueous-Ionic Liquid Mixtures by Organic Solvents, Qin Xin, Katie Pfeiffer, John Prausnitz, Doug Clark, Harvey Blanch, Biotechnology and Bioengineering, doi:10.1002/bit.24337, October 19, 2011.
 

Cellobiose Dehydrogenase and a Copper-Dependent Polysaccharide Monooxygenase Potentiate Cellulose Degradation by Neurospora crassa, Christopher Phillips, William Beeson, Jamie Cate, Michael Marletta, ACS Chemical Biology, 6(12), pp. 1399-1406, doi:10.1021/cb200351y, October 17, 2011.
 

Green Fluorescent Protein as a Screen for Enzymatic Activity in Ionic Liquid-aqueous Systems for in situ Hydrolysis of Lignocellulose, Paul Wolski, Douglas Clark, Harvey Blanch, Green Chemistry, doi:10.1039/C1GC15691H, October 5, 2011.
 

Blind Image Analysis for the Compositional and Structural Characterization of Plant Cell Walls, Pradeep Perera, Martin Schmidt, James Schuck, Paul Adams, Analytica Chimica Acta, 702(2), pp. 172-177, doi:10.1016/j.aca.2011.06.021, September 30, 2011. 
 

Identification of the CRE-1 Cellulolytic Regulon in Neurospora crassa, Jianping Sun, N. Louise Glass, PLoS ONE 6(9): e25654.doi:10.1371/journal/pone.0025654, September 29, 2011.
 

The Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride, Adam Gross, Alexis Bell, Jhih-Wei Chu, Journal of Physical Chemistry, doi: 10.1021/jp202415v, September 28, 2011.
 

On the Diels-Alder Approach to Solely Biomass-Derived Polyethylene Terephthalate (PET): Conversion of 2,5-Dimenthylfuran and Acrolein into p-Xylene, Mika Shiramizu, Dean Toste, Chemistry -- A European Journal, doi: 10.1002/chem.201101580, September 16, 2011.
 

High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery, Dae-Wan Kim, Harshal Chokhawala, Matthias Hess, Craig Dana, Zachary Baer, Alexander Sczyrba, Edward Rubin, Harvey Blanch, Douglas Clark, Angewandte Chemie, doi: 10.1002/anie.201104685, September 16, 2011.
 

Changes in N-Transforming Archaea and Bacteria in Soil During the Establishment of Bioenergy Crops, Yuegian Mao, Anthony Yannarell, Roderick Mackie, PLoS ONE 6(9): e24750.doi:10.1371/journal.pone.0024750, September 14, 2011.
 

Functional Analyses of Multiple Lichenin Degrading Enzymes from the Rumen Bacterium Ruminococcus, Michael Iakiviak, Roderick Mackie, Isaac Cann, Applied and Environmental Microbiology, doi:10.1128/AEM.06088-11, September 2, 2011.
 

A Study of Acid-Catalyzed Hydrolysis of Cellulose Dissolved in Ionic Liquids and the Factors Influencing the Dehydration of Glucose and the Formation of Humins, Sean Dee, Alex Bell, Chemistry and Sustainability Energy and Materials, doi: 10.1002/cssc.201000426, August 2, 2011.
 

Quantifying Bio-Engineering: the Importance of Biophysics in Biofuel Research, Patanjali Varanasi, Lan Sun, Bernhard Knierim, Elena Bosneaga, Purbasha Sarkar, Seema Singh, Manfred Auer, Biofuel's Engineering Process Technology (Chapter), Marco Aurélio dos Santos Bernardes (Ed.), ISBN: 978-953-307-480-1, InTech, August 2011. 
 

Improving the Bioconversion of Plant Biomass to Biofuels: A Multidisciplinary Approach, John Galazka and Jamie Cate, Energy and Environmental Science, 4, pp. 3329-3333, doi:10:1039/CIEE01569A, July 29, 2011.
 

Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance, Hyung Min Cho, Adam Gross, Jhih-Wei Chu, Journal of the American Chemical Society, doi: 10.1021/ja2046155, July 28, 2011.
 

The Role of Alcohols in Growth, Lipid Composition, and Membrane Fluidity of Yeast, Sarah Huffer, Melinda Clark, Jonathan Ning, Harvey Blanch, Douglas Clark, Applied Environmental Microbiology, doi:10.1128/AEM.00694-11, July 22, 2011. 
 

A Quantitative Proteomic Approach for Cellulosic Degradation by Neurospora crassa, Chris Phillips, Anthony Iavarone, Michael Marletta, Journal of Proteome Research, doi: 10.1021/pr200329b, July 11, 2011.
 

Identification and Characterization of a Multidomain Hyperthermophilic Cellulase from an Archaeal Enrichment, Joel Graham, Melinda Clark, Dana Nadler, Sarah Huffer, Harshal Chokhawala, Sara Rowland, Harvey Blanch, Douglas Clark, Frank Robb, Nature Communications, doi:10.1038/ncomms1373, July 5, 2011.
 

A New Diet for Yeast to Improve Biofuel Production, Jonathan Galazka, Jamie Cate, Bioengineered Bugs, 2(4), pp. 199-202, doi: 10:4161/bbug.2.4.15624, July 2011
 

Systematic Search for Cultivatable Fungi That Best Deconstruct Cell Walls of Miscanthus and Sugarcane in the Field, Prachand Shrestha, Timothy Szaro, Thomas Bruns, John Taylor, Journal of Applied Environmental Microbiology, doi: 10.1128/AEM.02996-10, June 17, 2011.
 

Discovery and Characterization of Heme Enzymes from Unsequenced Bacteria: Application to Microbial Lignin Degradation, Margaret Brown, Mark Walker, Toshiki Nakashige, Anthony Iararone, Michelle Chang, Journal of the American Chemical Society, doi: 10.1021/ja203972q, June 14, 2011.
 

Biochemical Analysis of Multiple Endoxylanases from the Rumen Bacterium Ruminococcus albus and their Synergistic Activities with Accessory Hemicellulose Degrading Enzymes, Young Hwan Moon, Michael Lakiviak, Stefan Bauer, Roderick Mackie, Isaac Cann, Applied and Environmental Microbiology, doi: 10.1128/AEM.00353-11, June 10, 2011.
 

Recovery of Glucose from an Aqueous Ionic Liquid by Adsorption onto a Zeolite-Based Solid, Maria Francisco, Anton Mlinar, Brian Yoo, Alexis Bell, John Prausnitz, Chemical Engineering Journal, doi:10.1016/j.cej.2011.05.087, May 31, 2011.
 

Effects of Reaction Conditions on the Acid-Catalyzed Hydrolysis of Miscanthus Dissolved in an Ionic Liquid, Sean Dee, Alexis Bell, Green Chemistry, doi:10.1039/CIGC15317J, May 27, 2011.
 

Construction of de Novo Biosynthetic Pathways for Chemical Synthesis Inside Living Cells, Amy Weeks, Michelle C. Y. Chang, Biochemistry, 50(24), pp. 5404-5418, doi: 10.1021/bi200416g, May 17, 2011.
 

Selective, Nickel-Catalyzed Hydrogenolysis of Aryl Ethers, Alexey Sergeev, John Hartwig, Science, Vol. 332(6028), pp. 439-443, April 22, 2011.
 

"Fluctuograms" Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution, Jordi Silvestre-Ryan, Yuchin Lin, Jhih-Wei Chu, PLOS Computational Biology, 7(3): e1002023. doi:10.1371/journal.pcbi.1002023, March 24, 2011.
 

Structural and Functional Analyses of a Glycoside Hydrolase Family 5 Enzyme with an Unexpected Beta-Fucosidase Activity, Shosuke Yoshida, David Park, Brian Bae, Roderick Mackie, Isaac Cann, Satish Nair, Biochemistry 50(16), pp. 3369-3375, doi: 10.1021/bi200222u, March 16, 2011.
 

Ionic Liquid Pretreatment of Cellulosic Biomass: Enzymatic Hydrolysis and Ionic Liquid Recycle, Kierston Shill, Sasisanker Padmanabhan, Qin Xin, John Prausnitz, Douglas Clark, Harvey Blanch, Biotechnology and Bioengineering, 108(3), pp. 511-520, doi: 10.1002/bit.23014, March 2011.
 

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen, Matthias Hess, Alexander Sczyrba, Rob Egan, Tae-Wan Kim, Harshal Chokhawala, Gary Schroth, Shujun Luo, Douglas S. Clark, Feng Chen, Tao Zhang, Roderick Mackie, Len Pennacchio, Susannah Tringe, Axel Visel, Tanja Woyke, Zhong Wang, Edward M. Rubin, Science, 331: (6016), pps. 463-467, January 28, 2011.
 

Engineered Saccharomyces cerevisiae Capable of Simultaneous Cellobiose and Xylose Fermentation, Suk-Jin Ha, Jonathan Galazka, Soo Rin Kim, Jin-Ho Choi, Xiaomin Yang, Jin-Ho Seo, N. Louise Glass, Jamie H. D. Cate, Yong-Su Jin, Proceedings of the National Academy of Sciences, DOI: 10.1073, January 11, 2011.
 

Xylan Degradation, a Metabolic Property Shared By Rumen and Human Colonic Bacteroidetes, Dylan Dodd, Robert Mackie, Isaac Cann, Molecular Microbiology, 79(2), pp. 1365-2958, doi:10.1111/j.1365-2958.2010.07473.x, January 2011. 
 

Viscosities of Acetate or Chloride-Based Ionic Liquids and Some of Their Mixtures with Water or Other Common Solvents, Sebastian Fendt, Sasisanker Padmanabhan, Harvey Blanch, John Prausnitz, Journal of Chemical and Engineering Data, 56(1), pp. 31-34, doi: 10.1021/je1007235, January 2011.

 

 

ENVIRONMENTAL, SOCIAL, & ECONOMIC IMPACTS

 

 

Alternative Transportation Fuel Standards: Economic Effects and Climate Benefits, X Chen, H Huang, M Khanna, H Önal, Association of Environmental and Resource Economists Summer Conference, doi: 2011.

 

The Lessons of Fermentation for the New Bio-Economy, David Zilberman, Eunice Kim, AgBioForum, 14(3), pp. 97-103, 2011.
 

Persistence of Cattle Ranching in the Brazilian Amazon: A Spatial Analysis of the Rationale for Beef Production, Maria Bowman, Britaldo Soares-Filho, Frank Merry, Daniel Nepstad, Hermann Rodrigues, Oriana Almeida, Land Use Policy, doi:10.1016/j.landusepol.2011.09.009, October 14, 2011. 
 

Carbon Exchange by Establishing Biofuel Crops in Central Illinois, Marcelo Zeri, Kristina Anderson-Teixeira, George Hickman, Michael Masters, Evan Delucia, Carl Bernacchi, Agriculture, Ecosystems & Environment, 144(1), pp, 319-329, doi:10.1016/j.agee.2011.09.006, October 14, 2011.
 

Are Local, State and Federal Government Bioenergy Efforts Synchronized?, Stephen Kaffka, Jody Endres, Book Chapter (20), Sustainable Alternative Fuel Feedstock Opportunities, Challenges and Roadmaps for Six U.S. Regions, Soil and Water Conservation Society, October 4, 2011. 
 

Biobutanol Blending Limits in the U.S.: An Explanation and Application of the 'Substantially Similar' Regulatory Framework, Timothy A. Slating, Biofuels International, Vol. 5, SSRN-id1932340, September 2011.
 

An Analysis of the Effects of the Renewable Fuel Standard (RFS2) and the Clean Air Act on the Commercialization of Biobutanol as a Transportation Fuel in the U.S., Timothy Slating, Jay Kesan, Social Science Research Network, Vol. 5, SSRN-id1932385, September 12, 2011.
 

Ethanol from Sugarcane in Brazil: A 'Midway' Strategy for Increasing Ethanol Production While Maximizing Environmental Benefits, Marcos Buckeridge, Amanda DeSouza, Rebecca Arudale, Kristina Anderson-Teixeira, Evan Delucia, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2011.01122.x, September 12, 2011.
 

Optimal Taxation of Externalities Interacting Through Markets: A Theoretical General Equilibrium Analysis, Xiaolin Ren, Don Fullerton, John Braden, Resource and Energy Economics, 33(3), pp. 496-514, doi: 10.1016/j.reseneeco.2010.10.002, September 2011. 
 

The Viability of Cattle Ranching Intensification in Brazil as a Strategy to Spare Land and Mitigate Greenhouse Gas Emissions, Avery Cohn, Maria Bowman, David Zilberman, Kate O'Neill, Climate Change Agriculture and Food Security, CCAFS Working Paper #11, CGIAR Research Program on Climate Change, September 2011.
 

No Free Pass: Putting the "Bio" in Biomass, Jody M. Endres, Natural Resources and Environment, 26 (1), Summer 2011.
 

Beyond the 'Food or Biofuel' Dilemma, Steve Sexton and David Zilberman, Biofuels, 2(4), pp. 361-363, doi: 10.4155/bfs.11.111, July 2011.
 

Multicriteria Comparison of Fuel Policies: Renewable Fuel Standards, Clean Fuel Standards, and Fuel GHG Tax, Deepak Rajagopal, Gal Hochman, David Zilberman, Working Paper Series, UC Center for Energy and Environmental Economics, WP-012, July 2011.
 

Impact of Second-Generation Biofuel Agriculture on Greenhouse-Gas Emissions in Corn-Growing Regions of the U.S., Sarah Davis, William Parton, Stephen Del Grosso, Cindy Keough, Ernest Marx, Paul Adler, Evan DeLucia, Frontiers in Ecology and the Environment, doi:10.1890/110003, July 1, 2011.
 

Meeting a Growing Demand for Food and Fuel in a Sustainable Manner, David Zilberman, Gal Hochman, ARE Update, 14(4), pp. 5-8, July 2011.
 

Making Regulatory Innovation Keep Pace with Technological Innovation, Timothy A. Slating and Jay P. Kesan, Wisconsin Law Review, Vol. 2011, 2011.
 

Do Biofuels Life Cycle Analyses Accurately Quantify the Climate Impacts of Biofuels-Related Land Use Change?, Kristina J. Anderson-Teixeira, Peter K. Snyder, Evan H. Delucia, Illinois Law Review 2011(2), pp. 589-622, April 2011.
 

Economics of Herbaceous Bioenergy Crops for Electricity Generation: Implications for Greenhouse Gas Mitigation, Madhu Khanna, Hayri Onal, Basanta Dhungana, Michelle Wander, Biomass and Bioenergy, 35(4), doi: 10.1016/j.biombioe.2010.11.031, April 2011.
 

Water Footprint of U.S. Transportation Fuels, Corinne Scown, Arpad Horvath, Thomas E. McKone, Environmental Science & Technology, 45 (7), pp. 2541-2553, doi: 10.1021/es102633h, March 15, 2011.
 

Land Use and Greenhouse Gas Mitigation Effects of Biofuel Policies, Madhu Khanna, Xiaoguang Chen, Haixiao Huang, Hayri Onal, University of Illinois Law Review, 2, pp. 549-588, March 14, 2011.
 

On the Inclusion of Indirect Land use in Biofuel Regulations, David Zilberman, Gal Hochman, Deepak Rajagopal, University of Illinois Law Review, Vol. 2011, pp. 413-434, March 4, 2011.
 

The Renewable Energy Policy Puzzle: Putting the Pieces Together, Jay P. Kesan, University of Illinois Law Review, Vol. 2011, pp. 333-339, March 3, 2011.
 

Geologic Carbon Sequestration: Balancing Efficiency Concerns and Public Interest in Property Rights Allocations, A. Bryan Endres, University of Illinois Law Review, Vol. 2011, pp. 625-650, March 2, 2011.
 

The Economics of Grain Price Volatility, Brian D. Wright, Applied Economic Perspectives and Policy, 33(1), pp. 32-58, Spring 2011.
 

Can Biofuels Be a Solution to Climate Change? The Implications of Land Use Change-Related Emissions for Policy, Madhu Khanna, Christine Crago, Mairi Black, Interface Focus (Royal Society Journal), 1, pp. 233-247, doi: 10.1098/rsfs.2010.0016, February 2, 2011.
 

Grand Challenges for Life-Cycle Assessment of Biofuels, Tom McKone, William Nazaroff, Peter Berck, Maximilian Auffhammer, Tim Lipman, Margaret Torn, Eric Masanet, Agnes Lobscheid, Nicholas Santero, Umakant Mishra, Audrey Barrett, Matt Bomberg, Kevin Fingerman, Corinne Scown, Bret Strogen, Arpad Horvath, Environmental Science and Technology, DOI: 10.1021/es103579c, January 11, 2011.
 

Meeting the Mandate for Biofuels: Implications for Land Use, Food and Fuel Prices, Xiaoguang Chen, Haixiao Huang, Madhu Khanna, Hayri Önal, NBER Working Paper 16697, National Bureau Of Economic Research, January 2011. 
 

The Greenhouse Gas Value of Ecosystems, Kristina Anderson-Teixeira, Evan DeLucia, Global Change Biology, 17(1), pp. 425-438, doi: 10.1111/j.1365-2486.2010.02220.x, January 2011.
 

Agricultural Expansion Induced By Biofuels: Comparing Predictions of Market-Equilibrium Models to Historical Trends, Deepak Rajagopal, David Zilberman, UCLA Institute of the Environment and Sustainability, Working Paper Series #5, January 2011. 
 

Indirect Fuel Use Change (IFUC) and the Lifecycle Environmental Impact of Biofuel Policies, Deepak Rajagopal, Gal Hochman, David Zilberman, Energy Policy, 39 (1), pps. 228-233, January 2011.
 

Land Availability for Biofuel Production, Ximing Cai, Xiao Zhang, Dingbao Wang, Environmental Science and Technology, 45(1), pps. 334-339, January 2011.
 

How Agricultural Biotechnology Boosts Food Supply and Accommodates Biofuels, Steve Sexton, David Zilberman, National Bureau of Economic Research, Working Paper #16699, January 2011.
 

Impacts of Second-Generation Biofuel Agriculture on Greenhouse-Gas Emissions in Corn-Growing Regions of the U.S. , Sarah Davis, William Parton, Stephen Del Grosso, Cindy Keough, Ernest Marx, Paul Adler, Evan DeLucia, Frontiers in Ecology and the Environment, doi:10.1890/110003, 2011.
 

Managing R&D Risk in Renewable Energy: Biofuels vs. Alternate Technologies, Gordon Rausser, Reid Stevens, Kiran Torani, AgBioForum, 13(4), pps. 375-381, 2011.
 

 

 

FEEDSTOCK DEVELOPMENT

 

Cytogeographic Distribution and Genome Size Variation in Prairie Cordgrass (Spartina pectinata Bosc ex Link), S.M. Kim, A.L. Rayburn, A. Parrish, and D.K. Lee, Plant Molecular Biology Reporter 7:1-13, doi: 10.1007/511105-012-0414-x, 2012.

 

Predicting yields of short-rotation hybrid poplar (Populus spp.) for the contiguous U.S. through model-data synthesis, Dan Wang, David LeBauer, Michael C. Dietze, Ecological Applications, http//dx. doi.org/10.1890/12-0854.1,  2011 (online version)

 

Cellulose Synthase Interactive Protein 1 (CSI1) Links Microtubules and Cellulose Synthase Complexes, Shundai Li, Lei Lei, Chris Somerville, Ying Gu, Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1118560109, December 21, 2011.
 

Modeling Spatial and Dynamic Variation in Growth, Yield, and Yield Stability of the Bioenergy Crops Miscanthus x giganteus and Panicum virgatum Across the Conterminous United States, Fernando Miguez, Matthew Maughan, German Bollero, Steve Long, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2011.01150.x, December 16, 2011. 
 

Miscanthus x giganteus Productivity: the Effects of Management in Different Environments, Matt Maughan, German Bollero, D. K. Lee, Robert Darmody, Stacy Bonos, Laura Cortese, James Murphy, Roch Gaussoin, Matthew Sousek, David Williams, Linda Williams, Fernando Miguez, Thomas Voigt, Global Change Biology-Bioenergy, doi: 10.1111/j.1757-1707.2011.01144.x, December 5, 2011.
 

Environmental Tolerances of Miscanthus sinensis in Invasive and Native Populations, Lauren Quinn, J. Ryan Stewart, Toshihiko Yamada, Yo Toma, Masanori Sato, Katsuhisa Shimoda, Fabian Fernandez, Bioenergy Research, doi: 10.1007/s12155-011-9163-1, November 25, 2011.
 

O-Acetylation of Arabidopsis Hemicellulose Xyloglucan Requires AXY4L, Proteins with a TBL and DUF231 Domain, Sascha Gille, Amancio de Souza, Guangyan Xiong, Monique Benz, Kun Cheng, Alex Schultink, Ida-Barbara Reca, Markus Pauly, The Plant Cell, doi: 10.1105/tpc.111.091728, November 15, 2011.
 

A Simple System for Promoting Flowering of Upland Switchgrass in the Greenhouse, Joseph Castro, Arvid Boe, D.K. Lee. Crop Science, 51(6), doi: 10.2135/cropsci2011.03.0142, pp. 2607-2614, November 2011.
 

Waste-to-Energy in California: Technology, Issues, and Context, Heather Youngs, California Council on Science and Technology, October 2011.
 

New Hope for Dedicated Genetically Engineered Bioenergy Feedstocks?, A. Bryan Endres, Global Change Biology-Bioenergy, DOI: 10.1111/j.1757-1707.2011.01134.x, October 17, 2011.
 

Development of Microsatellite Markers in Autopolyploid Sugarcane and Comparative Analysis of Conserved Microsatellites in Sorghum and Sugarcane, Brandon James, Cuixia Chen, Arthur Rudolph, Kankshita Swaminathan, Jan Murray, Jong-Kuk Na, Ashley Spence, Brandon Smith, Matthew Hudson, Stephen Moose, Ray Ming, Molecular Breeding, doi: 10.1007/s11032-011-9651-1, October 14, 2011. 
 

Overexpression of the Maize Corngrass1 MicroRNA Gene Prevents Flowering, Improves Digestability and Increases Starch Content of Switchgrass, George Chuck, Christian Tobias, Florian Kraemer, Chenlin Li, Dean Dibble, Rohit Arora, Jennifer Bragg, John Vogel, Seema Singh, Blake Simmons, Markus Pauly, Sarah Hake, Proceedings of the National Academy of Sciences, 108 (42), pp. 17550-17555,  doi: 10.1073/pnas.1113971108, October 10, 2011.
 

Arabidopsis Heterotrimeric G-protein Regulates Cell Wall Defense and Resistance to Necrotrophic Fungi, Magdalena Delgado-Cerezo, Clara Sánchez-Rodríguez, Viviana Escudero, Eva Miedes, Paula Virginia Fernandez, Lucia Jordá, Camilo Hernández-Blanco, Andrea Sánchez-Vallet, Pawel Bednarek, Paul Schulze-Lefert, Shauna Somerville, Jose Manuel Estevez, Staffan Persson, Antonio Molina, Molecular Plant, doi:10.1093/mp/ssr082, October 6, 2011.
 

Relative Feeding and Development of Armyworm on Switchgrass and Corn, and its Potential Effects on Switchgrass Grown for Biomass, Jarrad Prasifka, D. K. Lee, Jeffrey Bradshaw, Michael Gray, Journal of Economic Entomology, 104(5):pp. 1561-1567, doi: 10.1603/EC10304, October 2011.
 

Changes in N-transforming Archaea and Bacteria During the Establishment of Bioenergy Crops, Yuejian Mao, Anthony Yannarell, Roderick Mackie,. PloS One 6(9), doi:10.1371/journal.pone.0024750, September 14, 2011.
 

Prairie Yield, Moisture and Nitrogen Content Response to Harvest Time, Xiaohui Feng, Michael Dietze. Aspects of Applied Biology 112, Biomass and Energy Crops IV Conference, Association of Applied Biologists, pp. 271-277, September 2011.
 

Impacts of Canopy Position and Nitrogen on Nitrogen Allocation and Photosynthesis of Switchgrass (Panicum virgatum), Dan Wang, Mathew Maughan, Jindong Sun, Xiaohui Feng, Fernando Miguez, D.K. Lee, Michael Dietze, Aspects of Applied Biology 112, Biomass and Energy Crops IV Conference, pp. 341-351, September 2011.
 

Impact of Distributed Storage and Pre-Processing on Miscanthus Production and Provision Systems, Yogendra Shastri, Luis Rodriguez, Alan Hansen, K.C. Ting, Biofuels Bioproducts and Biorefining, DOI: 10.1002/bbb.326, August 25, 2011.
 

Agent-Based Analysis of Biomass Feedstock Production Dynamics, Yogendra Shastri, Luis Rodriguez, Alan Hansen, K.C. Ting, BioEnergy Research, doi: 10.1007/s12155-011-9139-1, August 3, 2011.
 

Influence of Feedstock Particle Size on Lignocellulose Conversion, Bernardo Vidal Jr., Bruce Dien, K.C. Ting, Vijay Singh, Applied Biochemistry and Biotechnology, 164(8): pp. 1405-1421, doi: 10.1007/s12010-011-9221-3, August 2011.
 

Distribution and Diversity of Root-Lesion Nematode (Pratylenchus spp.) Associated with Miscanthus x giganteus and Panicum virgatum Used for Biofuels, and Species Identification in a Multiplex Polymerase Chain Reaction, Tesfamariam Mekete, Kimberly Reynolds, Horatio D. Lopez-Nicora, Michael E. Gray and Terry L. Niblack. Nematology 13(6): pp. 673-686, July 1, 2011.
 

Miscanthus x giganteus Response to Tillage and Glyphosate, Eric Anderson, Thomas Voigt, German Bollero, Aaron Hager, Weed Technology, 25(3), pp. 356-362, doi: 10.1614/WT-D-10-00097.1, July 2011.
 

O-Glycosylated Cell Wall Proteins Are Essential in Root Hair Growth, Markus Pauly, Chris Somerville, Sascha Gille, Jose Estevez, et. al., Science, Vol. 332, pp. 1401-1403, June 17, 2011.
 

Deep Sequencing of Voodoo Lily (Amorphophallus konjac): an Approach to Identify Relevant Genes Involved in the Synthesis of the Hemicellulose Glucomannan, Sascha Gille, Kun Cheng, Mary E. Skinner, Aaron Liepman, Curtis Wilkerson, Markus Pauly, Planta, doi:10.1007/s00425-011-1422-z, May 3, 2011.
 

Stem-boring Caterpillars of Switchgrass in the Midwestern United States, Jarrad Prasifka, Jennifer Buhay, Thomas Sappington, Emily Heaton, Jeffrey Bradshaw, Michael E. Gray, Annals of the Entomological Society of America, 104(3): pp. 507-514, May 2011.
 

Development and Application of BioFeed Model for Optimization of Herbaceous Biomass Feedstock Production, Yogendra Shastri, Alan Hansen, Luis Rodriguez, KC Ting, Biomass and Bioenergy, doi:10.1016/j.biombioe.2011.03.035, April 12, 2011. 
 

A Review of Remote Sensing Methods for Biomass Feedstock Production, Tofael Ahamed, Lei Tian, Yuliang Zhang, K.C. Ting, Biomass and Bioenergy, doi:10.1016/j.biombioe.2011.02.028, April 8, 2011.
 

Evaluating Silicon Concentrations in Biofuel Feedstock Crops Miscanthus and Switchgrass, Krishna Woli, Mark David, Jenwei Tsai, Tom Voigt, Robert Darmody, Corey Mitchell, Biomass and Bioenergy, doi:10.1016/j.biombioe.2011.03.007, April 3, 2011.
 

Plant-Parasitic Nematodes Are Potential Pathogens of Miscanthus x giganteus and Panicum virgatum Used for Biofuels, Tesfamariam Mekete, Kimberly Reynolds, Horacio D. Lopez-Nicora, Michael Gray, Terry Niblack, Plant Disease, doi: 10.1094/PDIS-05-10-0335, 95(4),  April 2011.
 

Bioenergy Crops Miscanthus x giganteus and Panicum virgatum Reduce Growth and Survivorship of Spodoptera frugiperda (Lepidoptera: Noctuidae), Paul Nabity, Arthur Zangeri, May Berenbaum, Evan DeLucia, Journal of Economic Entomology, 104(2), pp. 459-464, April 2011.
 

Empirical Evidence of Long-Distance Dispersal in Miscanthus sinensis and Miscanthus x giganteus, Lauren Quinn, David Matlaga, J. Ryan Stewart, Adam Davis, Invasive Plant Science and Management, 4, pp. 142-150, January-March 2011. 
 

Rotating a Field of Mature Miscanthus x giganteus to Glyphosate-Resistant Crops, Eric Anderson, Thomas Voigt, German Bollero, Aaron Hager, Agronomy Journal, 103(5), pp. 1383-1388, doi: 10.2134/agronj2011.0091, March 25, 2011.
 

Seed Reduction in Prairie Cordgrass, Spartina pectinata Link., by the Floret-Feeding Caterpillar Aethes spartinana (Barnes and McDunnough), Jarrad Prasifka, D. K. Lee, Jeffrey Bradshaw, Allen Parrish, Michael Gray, Bioenergy Research, doi: 10.1007/s12155-011-9120-z, March 9, 2011. 
 

Loss-of-Function Mutation of Reduced Wall Acetylation 2 in Arabidopsis Leads to Reduced Cell Wall Acetylation and Increased Resistance to Botrytis cinerea, Yuzuki Manabe, Majse Nafisi, Yves Verhertbruggen, Caroline Orfila, Sascha Gille, Carsten Rautengarten, Candice Cherk, Susan Marcus, Shauna Somerville, Markus Pauly, J. Paul Knox, Yumiko Sakuragi, Henrik Scheller, Plant Physiology, 155 (3), 1068-1078, doi:10.1104/pp.110.168989, March 2011. 
 

Growth and Agronomy of Miscanthus x giganteus for Biomass Production, Eric Anderson, Rebecca Arundale, Matthew Maughan, Adebosola Oladeinde, Andrew Wycislo, Thomas Voigt, Biofuels 2(2), pp. 167-183, March 2011.
 

First Report of Basal Stem Rot and Foliar Blight Caused by Pythium sylvaticum on Miscanthus sinensis in Illinois, USA, Monday Obaigboruen Ahonsi, Bright Agindotan, Michael Gray, Carl Bradley, Plant Disease, DOI:10.1094/PDIS-08-10-0592, February 22, 2011.
 

A Novel Decomposition and Distributed Computing Approach for the Solution of the Large-Scale Optimization Models, Yogendra Shastri, Alan Hansen, Luis Rodriguez, K.C. Ting, Computers and Electronics in Agriculture, DOI:10.1016/j.compag.2011.01.006, February 16, 2011. 
 

Biomass Supply Chains for a Bioenergy Future, Heather Youngs, Caroline Taylor, Resource, 18(1), pp. 22, January-February 2011. 
 

The Evaluation of Feedstocks in GCBB Continues With a Special Issue on Agave for Bioenergy, Sarah Davis, Howard Griffiths, Joseph Holtum, Alfonso Larque Saavedra, Stephen P. Long, Global Change Biology-Bioenergy, 3(1), pps. 1-3, January 11, 2011.
 

  - The Global Potential of Agave as a Biofuel Feedstock, Sarah Davis, Frank Dohleman, Stephen P. Long, Global Change Biology-Bioenergy, 3(1), pps. 68-78.
 

  - Agave for Tequila and Biofuels: an Economic Assessment and Potential Opportunities, Hector Nunez, Luis Rodriguez, Madhu Khanna, Global Change Biology-Bioenergy, 3(1), pps. 43-57.
 

 

Development of Feedstocks for Cellulosic Biofuels, Heather Youngs and Chris Somerville, F1000 Biology Reports, 4(10), doi: 10.3410/B4-10, May 2, 2012.

 

Loss-of-Function Mutation of REDUCED WALL ACETYLATION2 in Arabidopsis Leads to Reduced Cell Wall Acetylation and Increased Resistance to Botrytis cinerea, Yuzuki Manabe, Majse Nafisi, Yves Verhertbruggen, Caroline Orfila, Sascha Gille, Carsten Rautengarten, Candice Cherk, Susan E. Marcus, Shauna Somerville, Markus Pauly, J. Paul Knox, Yumiko Sakuragi, Henrik Vibe Schelle, Plant Physiology, 155: pp. 1068-1078, doi:10.1104/pp.110.168989, January 6, 2011.
 

Energy Requirement for Comminution of Biomass in Relation to Particle Physical Properties, Zewei Maio, Tony Grift, Alan Hansen, K. C. Ting, Industrial Crops and Products, doi: 10.1016j.indcrop.2010.12.016, January 2011.
 

 

FOSSIL FUEL BIOPROCESSING

 

 

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill, Joel Kostka, Will Overholt, Stefan Green, Gina Freyer, Andy Canion, Jonathan Delgardio, Nikita Norton, Terry Hazen, Markus Huettel, Applied and Environmental Microbiology, 77(22), pp. 7962–7974. November, 2011. 
 

Microbial Gene Functions Enriched in the Deepwater Horizon Deep-Sea Oil Plume , Zhenmei Lu, Ye Deng, Joy Van Nostrand, Zhili He, James Voordeckers, Aifen Zhou, Yong-Jin Lee, Olivia Mason, Eric Dubinsky, Krystle Chavarria, Lauren Tom, Julian Fortney, Regina Lamendella, Janet Jansson, Patrik D’haeseleer, Terry Hazen, Jizhong Zhou, ISME Journal, doi: 10.1038/ismej.2011.91, August 4, 2011.
 

Identification of a Perchlorate Reduction Genomic Island with Novel Regulatory and Metabolic Genes, Ryan Melnyk, Anna Engelbrektson, Iain Clark, Hans Carlson, Kathy Byrne-Bailey, John D. Coates, Applied and Environmental Microbiology, doi: 10.1128/AEM.05758-11, August 2011.
 

Oil Degradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History, Ronald Atlas, Terry Hazen, Environmental Science & Technology, 45(16), pp. 6709-6715, doi: 10.1021/es2013227, June 23, 2011.
 

Seismic Monitoring of Permeability Reduction Due to Biopolymer Formation in Unconsolidated Materials, Tae-Hyuk Kwon, Jonathan Ajo-Franklin, 2011, SEG Expanded AbstractsVol. 30, pp. 2282, doi:10.1190/1.3627663, 2011.
 

 


 

Published in 2010

BIOFUELS PRODUCTION

 

 

Overcoming Glucose Repression in Mixed Sugar Fermentation by Co-Expressing a Cellobiose Transporter and a beta-Glucosidase in Saccharomyces Cerevisiae, Yanglin Li, Jing Du, Jie Sun, John Galazka, Louise Glass, Jamie Cate, Xiang Yang, Huimin Zhao, Molecular Biosystems, (publication ahead of print), September 27, 2010. 
 

Cellodextrin Transport in Yeast for Improved Biofuel Production, Jonathan Galazka, Chaoguang Tian, William Beeson, Bruno Martinez, N. Louise Glass, Jamie Cate, Science, DOI: 10.1126/science1192838, August 25, 2010.  
 

Discovery and Characterization of Novel d-xylose-specific Transporters from Neurospora crassa and Pichia stipitis, Jing Du, Sijin Li, Huimin Zhao, Molecular BioSystems, DOI: 10.1039/COMB00007H, August 11, 2010.
 

Efficient Production of the Liquid Fuel 2,5-Dimethylfuran from Fructose Using Formic Acid as a Reagent, Todsapon Thananatthanachon and Thomas Rauchfuss, Angewandte Chemie International Edition, DOI: 10.1002/anie.201002267, August 2, 2010. 
 

A Two-Step Approach for the Catalytic Conversion of Glucose to 2,5-dimethylfuran in Ionic Liquids, Mandan Chidambaram, Alexis T. Bell, Green Chemistry, 12: pp. 1253-1262, May 28, 2010.
 

Elucidating Mechanisms of Solvent Toxicity in Ethanologenic Escherichia coli, Cong Trinh, Sarah Huffer, Melinda Clark, Harvey Blanch, Douglas Clark, Biotechnology and Bioengineering, 106(5): pp. 721-730, March 26, 2010.  
 

Regulation of Arabinose and Xylose in Escherichia coli, Tasha Desai and Christopher Rao, Applied and Environmental Microbiology, 76(5): pp. 1524-1532, March 2010. 

 

 

BIOMASS DEPOLYMERIZATION

 

 

Fluid-Phase Equilibria in Binary Systems Containing an Ionic Liquid, Application of the Percus-Yevick-van der Waals Equation of State, Qin Xin, Geoffrey Poon, John Prausnitz, Journal of Supercritical Fluids, 55(2), pp. 817-824, DOI: 10.1016/j.supflu.2010.09.043, December 2010.  
 

Extracellular Aldonolactonase from Myceliophthora thermophilia, William Beeson, Anthony Iavarone, Corinne Hausmann, Jamie Cate, Michael Marletta, Applied and Environmental Microbiology, DOI: 10.1128/AEM.01922-10, November 12, 2010.
 

Label-free in situ Imaging of Lignification in Plant Cell Walls, Martin Schmidt, Pradeep Perera, Adam Schwartzberg, Paul Adams, James Schuck, Journal of Visual Experiments, Vol. 45, DOI: 10.3791/2064, November 1, 2010.
 

Chemical Profiling of the Plant Cell Wall Through Raman Microspectroscopy, Ju Han, Seema Singh, Lan Sun, Blake Simmons, Manfred Auer, Bahram Parvin, Information Bridge: DOE Scientific and Technical Information, Record 137, October 2010.
 

Sugaring Out: A New Method for Removal of Acetonitrile from Preparative RP-HPLC Eluent for Protein Purification, Pradip Dhamole, Prafulla Mahajan, Hao Feng, Process Biochemistry, 45(10), pp. 1672-1676, October 2010.
 

On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils, Adam Gross, Jhih-Wei Chu, The Journal of Physical Chemistry B, 114(42), pps. 13333-13341, Sept. 30, 2010.
 

Mutations of Cellulose Synthase (CESA1) Phosphorylation Sites Modulate Anisotropic Cell Expansion and Bidirectional Mobility of Cellulose Synthase, Shaolin Chen, David Eherhardt, Chris Somerville; Proceedings of the National Academy of Sciences, doi/10.1073/pnas.1012348107, September 22, 2010.
 

Validation of Two Ribosomal RNA Removal Methods for Microbial Metatranscriptomics, Shaomei He, Omri Wurtzel, Kanwar Singh, Jeff Froula, Susan Yilmaz, Susannah Tringe, Zhong Wang, Feng Chen, Erika Lundquist, Rotem Sorek and Phillip Hugenholtz, Nature Methods, 7: 807-812, September 19, 2010.
 

Unexpected Phosphate Salt-Catalyzed Hydrolysis of Glycosidic Bonds in Model Disaccharides: Cellobiase and Maltose, Alexandre Charmot and Alex Katz, Journal of Cataysis, DOI: 10.1016j.jcat2010.08.006, September 16, 2010.
 

Expression and Characterization of the Neurospora crassa endoglucanase GH5-1 , Jainping Sun, Christopher Phillips, Charles Anderson, William Beeson, Michael Marletta, Louise Glass, Protein Expression and Purification, 75(2), pp. 147-154, September 6, 2010.
 

Comparative Analyses of Two Thermophilic Enzymes Exhibiting both beta-1,4 Mannosidic and beta-1,4 Glucosidic Cleavage Activities from Caldanaerobius polysaccharolytus, Yujan Han, Dylan Dodd, Charles Hesen, Samuel Ohene-Adjei, Charles Schroeder, Roderick Mackie, Isaac Cann, Journal of Bacteriology, 192(16): pp. 4111-4121, August 2010.
 

Mutational Insights into the Roles of Amino Acid Residues in Ligand Binding for Two Closely Related Family 16 Carbohydrate Binding Modules, Xiaoyun Su, Vinayak Agarwal, Dylan Dodd, Brian Bae, Roderick Mackie, Satish Nair, Isaac Cann, Journal of Biological Chemistry, DOI: 10.1074/jbc.M110.168302, August 24, 2010. 
 

Catalytic C-O Bond Cleavage of 2-Aryloxy-1-arylethanols and Its Application to the Depolymerization of Lignin-Related Polymers, Jason Nichols, Lee Bishop, Robert Bergman, Jonathan Ellman, Journal of the American Chemical Society, 132(36), pp. 12554-12555, August 23, 2010.  
 

Domain Analysis of a Modular (alpha)-L-arabinofuranosidase with a unique carobhydrate Binding Strategy from the Fiber Degrading Bacterium Fibrobacter succinogenes S85, Shosuke Yoshida, Charles W. Hespen, Robert Beverly, Roderick Mackie, and Isaac Cann, Journal of Bacteriology, DOI: 10.1128/JB.00503-10, August 13, 2010.
 

Improved United-Atom Force Field for 1-Alkyl-methylimidazolium Chloride , Zhiping Liu, Ting Chen, Alexis Bell, Berend Smit, Journal of Physical Chemistry, 114(13): pp. 4572-4582, July 26, 2010. 
 

Synthetic Biology: Putting Synthesis into Biology, Jing Liang, Yunzi Luo, Huimin Zhao, Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 3(1), pp. 7-20, July 13, 2010.
 

Transcriptomic Analyses of Xylan Degradation by Prevotella bryantii and Insights into Energy Acquisition by Xylanolytic Bacteroidetes, Dylan Dodd, Young-Hwan Moon, Kankishita Swaminathan, Roderick Mackie, Isaac Cann, Journal of Biological Chemistry, DOI: 10.1074/jbcM110.14178, July 9, 2010.
 

Binding Modules Alter the Activity of Chimeric Cellulases: Effects of Biomass Pretreatment and Enzyme Source , Tae-Wan Kim, Harshal Chokhawala, Dana Nadler, Harvey Blanch, Douglas Clark, Biotechnology and Bioengineering, June 21, 2010.
 

Double Cloud Point of Ethylene Oxide-Propylene Osice Triblock CoPolymer in an Aqueous Solution, Zhilong Wang and Hao Feng, Colloids and Surfaces A: Physiochemical and Engineering Aspects, 362(1-3): pp. 110-116, June 5, 2010. 
 

Identification of a Cellulose Synthase-Associated Protein Required for Cellulose Biosynthesis , Ying Gu, Nick Kaplinsky, Martin Bringmann, Alex Cobb, Andrew Carroll, Arun Sampathkumar, Tobias Baskin, Staffan Persson, Chris Somerville, Proceedings of the National Academy of Sciences, 107(29): pp. 12866-12871, May 24, 2010. 
 

Phase Separation Conditions for Sugaring-Out in Acetonitrile-Water Systems, Pradip Dhamole, Prafulla Mahajan, Hao Feng, Journal of Chemical & Engineering Data, 55(9), pp. 3803-3806, May 19, 2010. 
 

A Mechanistic Model of the Enzymatic Hydrolysis of Cellulose, Seth Levine, Jerome Fox, Harvey Blanch, Douglas Clark, Biotechnology and Bioengineering, May 18, 2010. 
 

Non-Oxidative Vanadium-Catalyzed C-O Bond Cleavage: Application to Degradation of Lignin Model Compounds, Sunghee Son and F. Dean Toste, Angewandte Chemie, 49(22): pp. 3791-3794, May 2010.  
 

Functional Diversity of Four Glycoside Hydrolase Family 3 Enzymes from the Rumen Bacterium Prevotella bryantii B14, Dylan Dodd, Shinichi Kiyonari, Roderick I. Mackie, Isaac K. O. Cann, Journal of Bacteriology, 192(9): pp. 2335-2345, May 2010.
 

Cloning, Characterization, and Engineering of Fungal L-arabinitol Dehydrogenases , Byoungjin Kim, Ryan Sullivan, Huimin Zhao, Applied Microbiology and Biotechnology, 87(4): pp. 1407-1414, April 23, 2010.
 

Raman Imaging of Cell Wall Polymers in Arabidopsis thaliana , Martin Schmidt, Adam M. Schwartzberg, Andrew Carroll, Adisorn Chaibang, Paul D. Adams, P. James Schuck, Biochemical and Biopysical Research Communications, 395(4): 3, April 13, 2010.
 

Viscosities of the Mixtures of 1-Ethyl-3-Methylimidazolium Chloride with Water, Acetonitrile and Glucose: A Molecular Dynamics Simulation and Experimental Study, Ting Chen, Mandan Chidambaram, Zhiping Liu, Berend Smit, Alexis Bell, Journal of Physical Chemistry, 114(17): pp. 5790-5794, April 13, 2010.
 

Thermostable Enzymes as Biocatalysts in the Biofuel Industry, Carl J. Yeoman, Yejun Han, Dylan Dodd, Charles M. Schroeder, Roderick Mackie, Isaac Cann, Advances in Applied Microbiology, 70: pp. 1-55, March 6, 2010. 
 

Biochemical and Domain Analyses of FSUAxe6B, a Modular Acetyl Xylan Esterase, Identify a Unique Carbohydrate Binding Molecule in Fibrobacter succinogenes S85, Shosuke Yoshida, Roderick Mackie, Isaac Cann, Journal of Bacteriology, 192(2): pp. 483-493, January 9-13, 2010. 
 

Deconstructing Recalcitrant Miscanthus with Alkaline Peroxide and Electrolyzed Water, Bin Wang, Xiaojuan Wang, Hao Feng, Bioresource Technology, 101(2): pp. 752-760, January 2010. 
 

 

ENVIRONMENTAL, SOCIAL, & ECONOMIC IMPACTS

 

 

The Effect of Biofuels on Crude Oil Markets, Gal Hochman, Deepak Rajagopal, David Zilberman, AgBioForum, 13(2), pp. 112-118, 2010.
 

The Expansion of Sugarcane-Ethanol in Brazil and Controversies Surrounding Human Rights, Renata Marson Teixeira de Andrade, Andrew Miccolis, Part 4 chapter from the book Controversies in Science and Technology Volume 3: From Evolution to Energy, ISBN13 978-1-934854-20-4, 2010.
 

Land Use and Greenhouse Gas Mitigation Effects of Biofuel Policies, Madhu Khanna, Xiaoguang Chen, Haixiao Huang, Hayri Onal, University of Illinois Law Review, Record 148, October 23, 2010.
 

Supply of Cellulosic Biofuel Feedstocks and Regional Production Patterns, Madhu Khanna, Xiaoguang Chen, Haixiao Huang, Hayri Onal, American Journal of Agricultural Economics (forthcoming), October 23, 2010.
 

Carbon Budget and Methane and Nitrous Oxide Emissions Over the Growing Season in a Miscanthus sinensis Grassland in Tomakomai, Hokkaido, Japan, Yo Toma, Fabian Fernandez, Syohei Sato, Miki Izumi, Ryusuke Hatano, Toshihiko Yamada, Aya Nishiwaki, German Bollero, J. Ryan Stewart, Global Change Biology-Bioenergy, DOI: 10.1111/j.1757-1707.2010.01070.x, October 18, 2010.
 

A Realistic Technology and Engineering Assessment of Algae Biofuel Production, Tryg Lundquist, Ian Woertz, Nigel Quinn, John Benemann, Energy Biosciences Institute Report, October 2010; also, Digital Commons @ Cal Poly, October 1, 2010. 
 

Multi-Objective Fuel Policies: Renewable Fuel Standards versus Fuel Greenhouse Gas Intensity Standards, Deepak Rajagopal, Gal Hochman, David Zilberman, UCLA Institute of the Environment and Sustainability, Working Paper Series, October 2010.
 

The Expansion of Sugarcane-Ethanol in Brazil and Controversies Surrounding Human Rights, Teixeira de Andrade and Andrew Miccolis, Controversies in Science and Technology: From Evolution to Energy, 3, Fall 2010.
 

The Politics of Estimating the Greenhouse Gas Impacts of Biofuels, Alistair Iles, Controversies in Science and Technology: From Evolution to Energy, Vol. 3, Fall 2010.
 

The Climate Impacts of Bioenergy Systems Depend on Market and Regulatory Policy Contexts, Derek Lemoine, Richard Plevin, Avery Cohn, Andrew Jones, Adam Brandt, Sintana Vergara, Daniel Kammen, Environmental Science and Technology, 44(19): pp. 7347-7350, September 13, 2010.
 

Comparison of Canopy Evapotranspiration for Maize and Two Perennial Grasses Identified as Potential Bioienergy Crops, George Hickman, Andy VanLoocke, Frank Dohleman, Carl Bernacchi, Global Change Biology-Bioenergy, 2(4), pp. 157-168, August 2010.
 

Development and Optimization of an Agro-BGC Ecosystem Model for C4 Perennial Grasses, Alan DiVittorio, Ryan Anderson, Joseph White, Norman Miller, Steven Running, Ecological Modelling, 221(17): pp. 2038-2053, August 24, 2010. 
 

Competitiveness of Brazilian Sugarcane Ethanol Compared to U.S. Corn Ethanol, Christine Crago, Madhu Khanna, Jason Barton, Eduardo Giuliani, Weber Amaral, Social Science Research Network, August 17, 2010.
 

Modeling Miscanthus in the Soil and Water Assessment Tool (SWAT) to Simulate Its Water Quality Effects as a Bioenergy Crop, Tze Ling Ng, J. Wayland Eheart, Ximing Cai, Fernando Miguez, Environmental Science and Technology, 44(18), pps. 7138-7144, August 3, 2010.
 

Agriculture at a Crossroads: Energy Biomass Standards and a New Sustainability Paradigm? Jody Endres, Timothy Slating, Social Science Research Network, Working Paper Series, July 30, 2010.
 

Are Biofuels the Culprit? OPEC, Food and Fuel, Gal Hochman, Deepak Rajagopal, David Zilberman, American Economic Review, 100(2), pp. 183-187, May 2010.
 

The Greenhouse Gas Value of Ecosystems, Kristina Anderson-Teixeira, Evan DeLucia, Global Change Biology, DOI:10.1111/j.1365-2010.02220.x, May 19, 2010.
 

An Integrated Biogeochemical and Economic Analysis of Bioenergy Crops in the Midwestern United States, Atul Jain, Madhu Khanna, Matthew Erickson, Haixiao Huang, Global Change Biology - Bioenergy, May 13, 2010. 
 

Ecosystem Services: From Eye-Opening Metaphor to Complexity Blinder, Richard Norgaard, Ecological Economics, 69(6): pp. 1219-1227, April 2010.
 

Above-Ground Plant Biomass, Carbon, Nitrogen Dynamics Before and After Burning in a Seminatural Grassland of Miscanthus sinensis in Kumamoto, Japan, Yo Toma, Fabian Fernandez, Aya Nishiwaki, Toshihiko Yamada, German Bollero, J. Ryan Stewart, Global Change Biology - Bioenergy, 2(2): pp. 52-62, April 28, 2010. 
 

Indirect Land Use: One Consideration Too Many in Biofuel Regulation, David Zilberman, Gal Hochman, Deepak Rajagopal, Agriculture and Resource Economics Update, 13(4): 4, March/April 2010.
 

Effects of U.S. Maize Ethanol on Global Land Use and Greenhouse Gas Emissions: Estimating Market-Mediated Responses, Thomas Hertel, Alla Golub, Andrew Jones, Michael O'Hare, Richard Plevin, Daniel Kammen, BioScience, 60(3): pp. 223-231, March 2010.
 

Accounting for the Water Impacts of Ethanol Production, Kevin Fingerman, Margaret Torn, Michael O'Hare, Daniel Kammen, Environmental Research Letters, 5(1), January-March 2010.
 

Clearing the Air: The Meta-Standard Approach to Ensuring Biofuels' Environmental and Social Sustainability, Jody M. Endres, Virginia Environmental Law Journal, 28(1), February 2010.
 

Handbook of Bioenergy Economics and Policy, Madhu Khanna and David Zilberman editors, Springer Publications, Natural Resource Management and Policy, Vol. 33, 2010. Chapters in:

      - Introduction and Overview, Madhu Khanna, Jurgen Scheffran, David Zilberman
      - Optimizing the Biofuels Infrastucture: Transportation Networks and Biorefinery Locations in Illinois (Chapter), Seungmo Kang and Hayri Onal, Yanfeng Ouyang, Jurgen Scheffran, U. Deniz Tursun
      - A Simple Framework for Regulation of Biofuels, Gal Hochman, Deepak Rajagopal, David Zilberman
      - Food and Biofuel in a Global Environment, Gal Hochman, Deepak Rajagopal, David Zilberman
 

The Biomass Crop Assistance Program: Orchestrating the Government's First Significant Step to Incentivize Biomass Production for Renewable Energy, Jody Endres, Timothy Slating, Christopher Miller, Environmental Law Reporter, 40: 10066, 2010.
 

 

FEEDSTOCK DEVELOPMENT

 

 

Discovery of Natural Miscanthus (Poaceae) Triploid Plants in Sympatric Populations of Miscanthus sacchariflorus and Miscanthus sinensis in Southern Japan , Aya Nishiwaki, Aki Mizuguti, Shotaro Kuwabara, Yo Toma, Genki Ishigaki, Tomomi Miyashita, Toshihiko Yamada, Hiroya Matuura, Sachi Yamaguchi, A. Lane Rayburn, Ryo Akashi, J. Ryan Stewart, American Journal of Botany, Vol. 98: pp. 154-159, December 20, 2010.  
 

Visualizing Cellular Dynamics in Plant-Microbe Interactions Using Fluorescent-Tagged Proteins, William Underwood, Serry Koh, Shauna Somerville, Methods in Molecular Biology, 712: pp. 283-91 (Chapter 21), doi:10.1007/978-1-61737-998-7_21, 2011.
 

Modeling Tools and Strategies for Developing Sustainable Feedstock Supplies, Fernando Miguez, Michael Dietze, Armen Kemanian, Chapter 19, Sustainable Alternative Fuel Feedstock Opportunities, Challenges and Roadmaps for Six U.S. Regions, Soil and Water Conservation Society, pp. 319-338, 2011.
 

Genetic Support for Phenotype-based Racial Classification in Sorghum, Patrick Brown, Sean Myles, Stephen Kresovich, Crop Sciences 51(1), pp. 224-230, doi:10.2135/cropsci2010.03.0179, 2011.
 

The Global Potential for Agave as a Biofuel Feedstock, Sarah Davis, Frank Dohleman, Steve Long, Global Change Biology-Bioenergy, DOI: 10:1111/j.1757-1707.2010.01077.x, November 21, 2010. 
 

Invasiveness Potential of Miscanthus sinensis: Implications for Bioenergy Production in the United States, Lauren Quinn, Damian Allen, J. Ryan Stewart, Global Change Biology-Bioenergy, 2(6), pps. 310-320, November 10, 2010. 
 

Optimization of Miscanthus Harvesting and Handling as an Energy Crop: BioFeed Model Application, Yogandra Shastri, Alan Hansen, Luis Rodriguez, K.C. Ting, Biological Engineering, 3(1): pp. 37-69, November 2010.
 

Miscanthus x giganteus Response to Preemergence and Postemergence Herbicides, Erik Anderson, Thomas Voigt, German Bollero, Aaron Hager, Weed Technology, 24(4), pp. 453-460, October-December 2010.
 

Application of Sequence-Independent Amplification (SIA) for Identification of RNA Viruses in Bioenergy Crops, Bright Agindotan, Monday Ohonsi, Leslie Domier, Michael Gray, Carl Bradley, Journal of Virological Methods, 169(1): pp. 119-128, October 2010. 
 

Feedstocks for Lignocellulosic Biofuels, Chris Somerville, Heather Youngs, Caroline Taylor, Sarah Davis, Stephen Long, Science, 329(5993): pp. 790-792, August 13, 2010.
 

Miscanthus x giganteus Plant Regeneration: Effect of Callus Types, Ages and Culture Methods on Regeneration Competence, Hyoung Seok Kim, Guirong Zhang, John Juvik, Jack Widholm, Global Change Biology-Bioenergy, 2(4), pps. 192-200, July 2, 2010.
 

Development of an Application Programming Interface (API) for Biomass Feedstock Production Engineering, Konstantinos Domdouzis, Luis Rodriguez, Alan Hansen, KC Ting, presentation at the American Society of Agricultural and Biological Engineers International Meeting, June 2010. 
 

Spectral Sensing for Dry Matter Biomass Estimation of Energy Crops, Tofael Ahamed, Lei Tian, Casimiro Gadanha Junior, Francisco Pinto, Hx Liu, Bin Zhao, KC Ting, presentation at the American Society of Agricultural and Biological Engineers International Meeting, June 20-23, 2010.
 

Development of Stand-Alone Tower Remote Sensing for Energy Crops, Tofael Ahamed, Lei Tian, Yanshui Jiang, Hx Liu, KC Ting, presentation at the American Society of Agricultural and Biological Engineers International Meeting, June 20-23, 2010.
 

First Report of Pithomyces chartarum Causing a Leaf Blight of Miscanthus x giganteus in Kentucky, Monday Ahonsi, Bright Agindotan, D. W. Williams, Rebecca Arundale, Michael Gray, Tom Voigt, Carl Bradley, Plant Disease, 94(4), p. 480, April 2010.
 

Microcollinearity Between Autopolyploid Sugarcane and Diploid Sorghum Genomes, Jianping Wang,  Bruce Roe, Simone Macmil, Qingyi Yu, Jan Murray, Haibao Tang, Cuixia Chen, Fares Najar, Graham Wiley, John Bowers, Marie-Ane Van Sluys, Daniel Rokhsar, Matthew Hudson, Stephen Moose, Andrew Paterson, Ray Ming, BMC Genomics, 11(261), April 23, 2010. 
 

First Report of Field Populations of Two Potential Aphid Pests of the Bioenergy Crop Miscanthus x giganteus, Jeffrey Bradshaw, Jarrad Prasifka, Kevin Steffey, Michael Gray, Florida Entomologist, 93: pp. 135-137, March 2010. 
 

A Quantitative Review Comparing the Yield of Switchgrass in Monocultures and Mixtures in Relation to Climate and Management Factors, Dan Wang, David LeBauer, Michael Dietze, Global Change Biology - Bioenergy, 2(1): pp. 16-25, Feb. 28, 2010. 
 

Genomic and Small RNA Sequencing of Miscanthus x Giganteus Shows the Utility of Sorghum as a Reference Genome Sequence for Andropogoneae Grasses , Kankshita Swaminathan, Magdy Alabady, Kranthi Varala, Emanuele De Paoli, Isaac Ho, Dan Rokhsar, Aru Arumuganathan, Ray Ming, Pamela Green, Blake Meyers, Stephen Moose, Matthew Hudson, Genome Biology, 11(2), Feb. 3, 2010.
 

Surveying and Characterizing Genomic Repeats and Small RNA Production in Miscanthus x giganteus, Matthew Hudson, Kankshita Swaminathan, Magdy Alabady, Kranthi Valara, Ray Ming, Cuixia Chen, Daniel Rokhsar, Stephen Moose, Plant and Animal Genomes XVIII, San Diego, January 2010. 
 

 

FOSSIL FUEL BIOPROCESSING

 

 

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria, Terry Hazen, Eric  Dubinsky, et. al, Science, DOI: 10.1126/science1195979, August 25, 2010. 


 

Published in 2009

BIOFUELS PRODUCTION

 

 

Systems Analysis of Plant Cell Wall Degradation by the Model Filamentous Fungus Neurospora crassa, Chaoguong Tian, William T. Beeson, Anthony T. Iavarone, Jianping Sun, Michael A. Marletta, Jamie H. D. Cate, N. Louise Glass, Proceedings of the National Academy of Sciences, 106(52): pp. 22157-22162, Dec. 15, 2009. 
 

Industrial Biotechnology: Tools and Applications, Weng Lin Tang, Huimin Zhao, Biotechnology Journal, 4: pp. 1725-1739, Oct. 20, 2009. 

 

 

BIOMASS DEPOLYMERIZATION

 

 

Are Pressure Fluctuation-Based Equilibrium Methods Really Worse Than Nonequilibrium Methods for Calculating Viscosities?, Ting Chen, Berend Smit, Alexis Bell, Journal of Chemical Physics, 131, Dec. 30, 2009.
 

Real Time Visualization of Cellulose Reorientation During Cell Wall Expansion in Arabidopsis Roots, Charles T. Anderson, Andrew Carroll, Laila Akhmetova, Chris Somerville, Plant Physiology, 152: pp. 787-796, Dec. 4, 2009.
 

Deconstructing Recalcitrant Miscanthus with Alkaline Peroxide and Electrolyzed Water, Hao Feng, Bin Wang, Xiaojuan Wang, Bioresource Technology, 101(2): pp. 752-760, Sept. 16, 2009.
 

Protein Engineering in Designing Tailored Enzymes and Microorganisms for Biofuels Production, Fei Wen, Nakhil U Nair, Huiman Zhao, Current Opinion in Biotechnology, 20(4): pp. 412-419, August 2009. 
 

Plant Cell Walls Throughout Evolution: Towards a Molecular Understanding of Their Design Principles, Purbasha Sarkar, Elena Bosneaga, Manfred Auer, Journal of Experimental Botany, 60(13): pp. 3615-3635, Aug. 17, 2009.
 

Mutations in UDP-Glucose: Sterol Glucosyltransferase in Arabidopsis Cause Transparent Testa Phenotype and Suberization Defect in Seeds , Seth DeBolt, Wolf-Rudiger Scheible, Kathrin Schrick, Manfred Auer, Fred Beisson, Volker Bischoff, Pierrette Bouvier-Nave, Andrew Carroll, Kian Hematy, Yonghua Li, Jennifer Milne, Meera Nair, Hubert Schaller, Marcin Zemla, Chris Somerville, Plant Physiology, 151: pp. 78-87, July 29, 2009.
 

Label-Free in situ Imaging of Lignification in the Cell Wall of Low Lignin Transgenic Populus trichocarpa , M. Schmidt, A. M. Schwartzberg, P. N. Perera, A. Weber-Bargioni, A. Carroll, P. Sarkar, E. Bosneaga, J. J. Urban, J. Song, M. Y. Balakshin, E. A. Capanema, M. Auer, P. D. Adams, V. I. Chiang, P. James Schuck, Planta, 230(3): pp. 589-597, June 13, 2009.
 

Tying Up the Loose Ends: Circular Permutation Decreases the Proteolytic Susceptibility of Recombinant Proteins, Timothy Whitehead, Lisa Bergeron, Douglas Clark, Protein Engineering Design and Selection, 22(10): pp. 607-613, June 8, 2009.
 

Cellulosic Biofuels, Andrew Carroll and Chris Somerville, Annual Review of Plant Biology, pp. 165-182, June 2009.
 

Complexes of Lignols With Manganese and Ruthenium, Didier Morvan, Thomas Rauchfuss, Scott Wilson, Organometallics, 28(11): pp. 3161-3166, May 13, 2009.  
 

Enzymatic Deconstruction of Xylan for Biofuel Production, Dylan Dodd and Isaac Cann, Global Change Biology - Bioenergy, 1: pp. 2-17, February 18, 2009. 

 

 

ENVIRONMENTAL, SOCIAL, & ECONOMIC IMPACTS

 

 

Comparative Biogeochemical Cycles of Bioenergy Crops Reveal Nitrogen-Fixation and Low Greenhouse Gas Emissions in a Miscanthus x giganteus Agro-Ecosystem, Sarah Davis, William Parton, Frank Dohleman, Candice Smith, Stephen Del Grosso, Angela Kent, Evan DeLucia, Ecosystems, 13(1), Dec. 22, 2009. 
 

Model Estimates Food-Versus-Biofuel Trade-off, Deepak Rajagopal, Steven Sexton, Gal Hochman, David Roland-Holst, David Zilberman, California Agriculture, 63(4): pp. 199-201, Oct.-Dec. 2009.
 

Biofuels and Land Use Change: Sugarcane and Soybean Acreage Response in Brazil, Catherine Hausman Almirall, Social Science Research Network, Sept. 24, 2009.
 

Seasonal Nitrogen Dynamics of Miscanthus x giganteus and Panicum virgatum , Emily Heaton, Frank Dohleman and Steve Long, Global Change Biology - Bioenergy, 1, pp. 297-307, Aug. 24, 2009. 
 

An Economic Evaluation of the Renewable Fuel Standard (RFS) Biofuel Program: An Industrial Policy Approach, Jay Kesan and Atsushi Ohyama, Social Science Research Network, LE09-035, Aug. 19, 2010.
 

Beneficial Biofuels – The Food, Energy and Environment Trilemma, Chris Somerville, et. al., Science, 325(5938): 270-271, July 17, 2009.
 

Food or fuel? What European Farmers Can Contribute to Europe’s Transport Energy Requirements and the Doha Round, Jennifer Baka, David Roland-Holst, Energy Policy, 37: pp. 2505-2513, April 5, 2009.
 

Sustainability of Food, Energy and Environment with Biofuels, Madhu Khanna, Gal Hochman, Deepak Rajagopal, Steven Sexton, David Zilberman, CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, (Review) 4(028): pp. 1-10, April 3, 2009.
 

Ecosystem Services: From Eye-Opening Metaphor to Complexity Blinder, Richard Norgaard, Ecological Economics, 69(6): pp. 1219-1227, April 1, 2009.
 

Life-Cycle Analysis and the Ecology of Biofuels, Sarah Davis, Kristina Anderson-Teixeira, Evan DeLucia, Trends in Plant Science, 14(3): pp. 140-146, March 2009.
 

Patents vs. Patenting: Implications of Intellectual Property Protection for Biological Research, Zhen Lei, Brian Wright, Nature Biotechnology, pp. 36-40, January 2009
 

Changes in Soil Organic Carbon Under Biofuel Crops, Kristina Anderson-Teixeira, Sarah Davis, Michael Masters, Evan DeLucia, Global Change Biology-Bioenergy, 1: pp. 75-96, 2009.
 

Greener Pastures for Globalization: How European Farmers Can Help Save the Planet as well as the Doha Round, Jenn Baka, David Roland-Holst, Giannini Foundation of Agricultural Economics, 11(1), 2009.
 

Recent Developments in Renewable Technologies: R&D Investment in Advanced Biofuels, Deepak Rajagopal, Steve Sexton, Gal Hochman, David Zilberman, Annual Review of Resource Economics, 1: pp. 621-644, 2009.
 

The Role of Biotechnology in a Sustainable Biofuel Future, Steven Sexton, David Zilberman, Deepak Rajagopal, Gal Hochman, AgBioForum, 12(1): pp. 130-140, 2009.
 

The Political Economy of Agricultural Biotechnology Policies, Gregory D. Graff, Gal Hochman, David Zilberman, AgBioForum, 12(1): pp. 34-46, 2009.
 

 


FEEDSTOCK DEVELOPMENT

 

 

Symptoms, Distribution and Abundance of the Stem-Boring Caterpillar, Blastobasis repartella (Dietz) in Switchgrass, Jarrad Prasifka, Jeffrey Bradshaw, Arvid Boe, DoKyoung Lee, David Adamski, Michael Gray, Bioenergy Research, Dec. 10, 2009.
 

Biomass Feedstock Production and Provision: A System-Level Optimization Approach, Yogendra Shastri, Alan Hansen, Luis Rodriguez and K.C. Ting, presentation at the American Institute of Chemical Engineers (AIChE) Annual Meeting, November 2009.
 

Distribution, Morphological Description, and Molecular Characterization of Xiphinema and Longidorous spp. Associated with Plants (Miscanthus spp. And Panicum virgatum) Used for Biofuels, Tesfamariam Mekete, Michael Gray, Terry Niblack, Global Change Biology - Bioenergy, 1(4): pp. 257-266, Aug. 24, 2009.
 

A Semi-Mechanistic Model Predicting the Growth and Production of the Bioenergy Crop Miscanthus x giganteus: Description, Parameterization, and Validation, Fernando Miguez, Xinguang Zhu, Stephen Humphries, German Bollero, Stephen Long, Global Change Biology-Bioenergy, 1(4): pp. 282-296, July 23, 2009. 
 

Systems Level Analysis of Biomass Feedstock Production for Bioenergy Sector, Yogendra Shastri, Konstantinos Domdouzis, Ming-Che Hu, Luis Rodriguez, Alan Hansen, K. C. Ting, Meeting of the American Society of Agricultural and Biological Engineers, June 2009.
 

Systems Informatics Techniques in Biomass Feedstock Production Engineering, Konstantinos Domdouzis, Yogendra Shastri, Ming-Che Hu, Luis Rodriguez, Alan Hansen, K. C. Ting, Meeting of the American Society of Agricultural and Biological Engineers, June 2009.
 

Does Greater Leaf-Level Photosynthesis Explain the Larger Solar Energy Conversion Efficiency of Miscanthus Relative to Switchgrass? , Frank Dohleman, Emily Heaton, Andrew Leakey, Steve Long, Plant, Cell and Environment, 32, pp. 1525-1537, June 25, 2009.
 

More Productive Than Maize in the Midwest: How Does Miscanthus Do It? , Frank Dohleman and Steve Long, Plant Physiology, 150, pp. 2104-2115, June 17, 2009.
 

Development and Feeding of Fall Armyworm on Miscanthus x giganteus and Switchgrass, Jarrad Prasifka, Jeffrey Bradshaw, R. L. Meagher, R. N. Nagoshi, Kevin Steffey, Michael Gray, Journal of Economic Entomology, 102(6), June 13, 2009.
 

Engineering Solutions for Biomass Feedstock Production, K.C. Ting, Resource, pp. 12-13, April/May 2009.
 

The Ecology and Agronomy of Miscanthus sinensis, a Species Important to Bioenergy Crop Development, in its Native Range in Japan: a Review, J. Ryan Stewart, Yo Toma, Fabian G. Fernandez, Aya Nishiwaki, Toshihiko Yamada, and German Bollero, Global Change Biology - Bioenergy, 1(2): pp. 126-153, March 10, 2009. 
 


 

Published in 2008

BIOMASS DEPOLYMERIZATION

 

 

Prefoldin 6 Is Required for Normal Microtubule Dynamics and Organization in Arabidopsis, Ying Gu, Zhiping Deng, Alexander Paredez, Seth DeBolt, Zhi-Yong Wang, Chris Somerville, Proceedings of the National Academic of Sciences, 105(46): pp. 18064-18069, Sept. 14, 2008.

 

 

ENVIRONMENTAL, SOCIAL, & ECONOMIC IMPACTS

 

 

Transition to a Bioeconomy, Impacts on Rural Development and the Environment, Conference Proceedings, Madhu Khanna, Editor, Oct. 15-16, 2008. 
 

Quantifying the Impact of Current and Future Tropospheric Ozone on Tree Biomass, Growth, Physiology and Biochemistry: A Quantitative Meta-Analysis, Victoria Wittig, Elizabeth Ainsworth, Shawna Naidu, David Karnosky, Steve Long, Global Change Biology, 15, pp. 396-424, October 2008. 
 

Food Versus Fuel: How Biofuels Make Food More Costly and Gasoline Cheaper, Steve Sexton, Deepak Rajagopal, David Zilberman, Gal Hochman, Agriculture and Resource Economics, 12(1), Sept.-Oct. 2008.
 

Welfare Effects and Unintended Consequences of Ethanol Subsidies, Madhu Khanna, Amy W. Ando, Farzad Taheripour, Review of Agricultural Economics, 30(3): pp. 411-421, Fall 2008.
 

Cellulosic Biofuels: Are They Economically Viable and Environmentally Sustainable?, Madhu Khanna, Choices, 23(3). Fall 2008.
 

Interactions Between Water, Energy, Food and Environment: Evolving Perspectives and Policy Issues, Petra Hellegers, David Zilberman, Pasquale Steduto, Peter McCornick, Water Policy, 10 (Supplement 1): pp. 1-10, 2008.
 

Rising Energy Prices and the Economics of Water in Agriculture, David Zilberman, Thomas Sproul, Deepak Rajagopal, Steven Sexton, Petra Hellegers, Water Policy, 10 (Supplement 1): pp. 11-21, 2008.
 

The Economics of Biofuel Policy and Biotechnology, Gal Hochman, Steven Sexton, David Zilberman, Journal of Agricultural and Food Industrial Organization, 6, 2008.
 

 

 


 

 

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