Source: PENNSYLVANIA STATE UNIVERSITY submitted to
THE SCIENCE AND ENGINEERING FOR A BIOBASED INDUSTRY AND ECONOMY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1002249
Grant No.
(N/A)
Project No.
PEN04561
Proposal No.
(N/A)
Multistate No.
S-1041
Program Code
(N/A)
Project Start Date
Jan 14, 2014
Project End Date
Sep 30, 2018
Grant Year
(N/A)
Project Director
Demirci, AL.
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802
Performing Department
Agri & Biological Engineering
Non Technical Summary
Use of increased renewable resources will require deliberate development of technologies for efficient use of resources due to three converging issues: (1) decrease in productive agricultural land areas under urbanization pressures; (2) clearing of land areas using unsustainable methods; and (3) increasing world population with an increased standard of living including a clean environment. One billion hectares of land will be cleared by 2050, resulting in the release of three Gt/year of greenhouse gases (Tilman et al., 2011). Global population will reach nine billion by 2050, resulting in increases in global food demand from 2005 to 2050 (Tilman et al., 2011). Breadth of these intersecting problems are so vast that constructive solutions can be designed and implemented only through collaborations crossing traditional disciplinary boundaries.The objectives of this project are to address research relating directly to SAAESD Goal 1 F (biobased products) and H (processing agricultural coproducts); research will influence Goal 5 B (rural community development and revitalizing rural economies) indirectly. Because renewable energy systems occupy large land expanses, they are typically not located in urban areas, promoting economic development of rural US communities. Transitioning from sequestered-carbon sources such as oil, natural gas and coal, to more renewable energy systems requires research and development work. Without this productive research, the technical capacity to switch from a sequestered-carbon economy to a diverse bioresource-based economy will be severely hampered with unanswered questions, undeveloped technologies, and under-delivered capacity in production and utilization of bioresources. Research proposed herein is designed to help address these limitations as conducted by professional scientists and engineers either directly with or strongly associated with the Land Grant University system.This project is written at a time when US natural gas has increased in productivity and decreased in costs. The natural gas production was 22.1 trillion cubic feet in the first nine months of 2012 compared to 21.0 for the same period in 2011. Although, natural gas may be considered the energy panacea for the next decade, natural gas combustion is a net emitter of greenhouse gases. Natural gas can certainly play a major role in assisting in the transition from sequestered-carbon based energy systems to renewable ones. However, due to continual increases in atmospheric carbon dioxide concentrations economically viable renewable energy systems must be developed and implemented. The Land Grant University system can partner with important policy-setting agencies including United States Departments of Agriculture (USDA), Energy (US DOE), Defense (US DOD), and the National Science Foundation (NSF) for doing the research that will allow us to meet our renewable energy production goals.
Animal Health Component
0%
Research Effort Categories
Basic
50%
Applied
40%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1310199310015%
4024099202075%
1121631107010%
Knowledge Area
112 - Watershed Protection and Management; 131 - Alternative Uses of Land; 402 - Engineering Systems and Equipment;

Subject Of Investigation
4099 - Microorganisms, general/other; 0199 - Soil and land, general; 1631 - Winter annual grasses;

Field Of Science
2020 - Engineering; 1070 - Ecology; 3100 - Management;
Goals / Objectives
Develop deployable biomass feedstock supply knowledge, processes and logistics systems that economically deliver timely and sufficient quantities of biomass with predictable specifications to meet conversion process-dictated feedstock tolerances. Investigate and develop sustainable technologies to convert biomass resources into chemicals, energy, materials and other value added products. Develop modeling and systems approaches to support development of sustainable biomass production and conversion to bioenergy and bioproducts. Identify and develop needed educational resources, expand distance-based delivery methods, and grow a trained work force for the biobased economy
Project Methods
A1. Identify biomass feedstock type and availability for selected geographic regions based on agronomic and climate conditions.A2. Characterize physical and chemical properties of feedstock along the logistics supply for different geographic regions.A3. Develop and evaluate harvest, pre-process, handling, densification, storage, and transport methods for specific biomass feedstock end-users.B1. Develop pretreatment methods for biological conversion processes.B2. Develop conversion processes.B3. Develop value-added, bio-based products from fractionated biomass.C1. Develop system models and data to represent integrated feedstock supply systems, including discrete processes and entire supply logistics.C2. Develop system models and data to assess sustainability of integrated conversion platforms.C3. Develop integrated system models to configure, analyze and optimize bioenergy and biofuel production systems.D1. Serve as a knowledge resource base for bio-based economy.D2. Develop and market educational programs.D3. Develop and disseminate educational materials in high-priority topic areas.

Progress 01/14/14 to 09/30/18

Outputs
Target Audience:The target audiences for this research include a) the science and engineering research community, b) biomass processing companies ranging from small start-ups to large multi-national companies, c) policy analysts and decision makers, and d) potential biomass producers and the general public. Stakeholders include state and national organizations, state and federal agencies, companies and industry consultants. There is also strong public interest in understanding the environmental impacts of the biomass production and processing technologies as well as comparisons to conventional petroleum-derived products. These various stakeholders are being engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension, and NEWBio.psu.edu), scientific journal articles and extension publications. The project results will be benefit biomass producers, the bioprocessing/fermentation industry and the rural public in general as a result of production of value-added products and bioenergy from raw agricultural products or by-products. The target audiences for this research also include algae, and bio-diesel biorefineries, aviation fuel supply chain stakeholders, airlines, airport management, biofuel policymakers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These project has provided substantial hands-on experiential training opportunities for both graduate and undergraduate students in in biomass feedstock supply knowledge, processes and logistics systems and logistics systems; sustainable technologies to convert biomass resources into chemicals, energy, materials and other value added products; policies impacting the U.S. biofuels industry; assessing issues for the adoption of sustainable jet fuel in the U.S.; lignin valorization from biorefinery waste streams. Graduate and undergraduate students become proficient in a full range of advanced molecular cloning and characterization techniques for engineering micro-organisms. Students present their research at the SEED, SIMB, SynBERC, and AIChE annual meetings & retreats, where a significant component of the meeting includes professional development, such as networking and career fairs. Researchers present their work during poster and oral presentations at the regional and national meetings. How have the results been disseminated to communities of interest?Stakeholders have been engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension, and NEWBio.psu.edu), scientific journal articles and extension publications. Outcomes of the projects have been presented to the interested audiences at national and regional conferences. Results have been disseminated through peer reviewed journals, USDA AFRI-CAP and FAA presentations and reports and presented at the 2nd NARA Biofuels and Co-Products Conference in Seattle, WA. Our peer-reviewed publications appear in high-impact journals relevant to the intended audience, such as the Journal of the American Chemical Society, Metabolic Engineering, and Nucleic Acids Research. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Following projects have been studied for objectives 1, 2, and 4 by Tom Richard: 1) Modeling feedstock production and harvesting strategies that spatially identify and efficiently manage economically marginal subfield areas. We are also characterizing feedstock characteristics along the value chain; 2) Investigating microbial conversion of biomass into methane and carboxylic acids through various modes of anaerobic mixed culture fermentation, with a strong emphasis on mechanical cotreatment (milling during fermentation, mimicking the rumination and cud-chewing of a cow); 3) Continued experimental and modeling efforts to understand and enhance system-level opportunities to find synergies between profitable on-farm biomass production, advanced conversion technologies, and innovative market products. We have intensified academic and private sector collaborations on the ecosystem service valuation of perennial energy grasses and energy winter crops for water quality in the Chesapeake Bay region as well as the Upper Mississippi Basin watersheds in Iowa. We continue our work to quantify carbon offset benefits in forest and cropland bioenergy systems, including opportunities for Biomass Energy Carbon Capture and Storage. A range of papers were published on these topics as indicated below. Following projects have been studied for objective 2 by Ali Demirci: 4) Simultaneous saccharification and fermentation of ethanol from industrial potato waste by co-culturing A. niger and S. cerevisiae in biofilm reactor was completed without needing added hydrolyzing enzymes; 5) Continued to work on Vitamin K production by using bioreactors; 6) Continued to work on the project to produce hydrolytic enzymes production from distillers dried grains with solubles (DDGS) for cellulosic biomass hydrolysis for biofuels and other uses. Following projects have been studied for objectives 2 and 3 by Howard Salis: The Salis lab's research focuses on the development of predictive models and optimization algorithms that enable rational engineering of micro-organisms for metabolic engineering applications; 7) Developed a new approach to simultaneously regulating many genes within an organism by co-expressing up to 20 single-guide RNAs within "Extra Long sgRNA Arrays" (ELSAs). ELSAs utilize the CRISPR/Cas9 system to target genes for transcriptional regulation. ELSAs can be used to redirect metabolic flows inside organisms by knocking down or knocking up the expression of many targeted genes / enzymes. 8) Carried out many experiments to validate our approach at several levels. For example, as a demonstration, we designed, built, and tested a 20-sgRNA ELSA that simultaneously knocks down 5 enzyme expression levels by 65 to 650-fold to over-produce succinic acid. Furthermore, following projects have been studied for objective 2 by Paul Smith: 9) Reviewed opportunities and challenges of the U.S. biofuels industry, 10) Examined major barriers and potential solutions to the scale-up of the U.S. integrated cellulosic biorefinery, 11) Explored lignin valorization from biorefinery waste streams and 12) Explored the drivers and barriers to E15 adoption for U.S. branded and unbranded retail fuel companies. Additionally, following project has been continued for objective 4 by Ali Demirci and Tom Richard: 13) Enhancement of the bioenergy online courses, which have been developed for "Master of Professional Studies in Renewable Energy and Sustainability Systems (MPS-RESS)" and "Online Graduate Certificate Program in Bioenergy" at Pennsylvania State University. The project aimed to create innovative tools for the hands-on practical/laboratory educational experiences associated with distance learning of technical subjects.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wolfe, M.L. and T.L. Richard. 2017. 21st century engineering for on-farm food-energy-water systems. Current Opinion in Chemical Engineering 18:69-76. DOI:10.1016/j.coche.2017.10.005
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Hoffman, E., Cavigelli, M.A., Camargo, G., Ryan, M., Ackroyd, V.J., Richard, T.L. and S. Mirsky. 2018. Energy use and greenhouse gas emissions in organic and conventional grain crop production: Accounting for nutrient inflows. Agricultural Systems. 162:89-96. DOI:10.1016/j.agsy.2018.01.021
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Malone, R.W., J.F. Obrycki, D.L. Karlen, L.Ma, T.C. Kaspar, D.B. Jaynes, T.B. Parkin, S.H. Lence, G.W. Feyereisen, Q.X. Fang, T.L. Richard, and K. Gillette. 2018. Harvesting fertilized rye cover crop: Simulated revenue, net energy, and drainage nitrogen loss. Agricultural and Environmental Letters 3:170041, doi:10.2134/ael2017.11.0041
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Ligaba-Osena, A., B. Hankoua, K. DiMarco, R. Pace, M. Crocker, J. McAtee, N. Nagachar, M. Tien and T.L. Richard. 2017. Reducing biomass recalicitrance by heterologous expression of a bacterial peroxidase in tobacco (Nicotiana benthamiana). Scientific Reports 7:17104, DOI:10.1038/s41598-017-16909-x
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Essien, D. and T.L. Richard. 2018. Wet ensiled storage enhances pretreatment and bioconversion of corn stover. Frontiers in Bioengineering and Biotechnology. In press.
  • Type: Theses/Dissertations Status: Published Year Published: 2018 Citation: Sciaudone, K.T. (2018). Impacts of Vegetative Buffers and Winter Crops on Water Quality and Profitability of Small to Midsize Farms in Pennsylvania. M.Sc. Thesis. The Pennsylvania State University, University Park, PA.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mahdinia, E., A. Demirci, and A. Berenjian. 2018. Utilization of glucose-based medium and optimization of Bacillus subtilis natto growth parameters for vitamin K (menaquinone-7) production in biofilm reactors. Biocatalysis and Agricultural Biotechnology. 13:219-224. DOI 10.1016/j.bcab.2017.12.009
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mahdinia, E., A. Demirci, and A. Berenjian. 2018. Optimization of Bacillus subtilis natto growth parameters in glycerol-based medium for vitamin K (Menaquinone-7) production in biofilm reactors. Bioprocess and Biosystems Engineering. 41(2):195204. DOI 10.1007/s00449-017-1857-0
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Germec, M., M. Karhan, K.L. Bialka, A. Demirci, and I. Turhan. 2018. Mathematical modeling of lactic acid fermentation in bioreactor with carob extract. Biocatalysis and Agricultural Biotechnology. 14: 254263. DOI: 10.1016/j.bcab.2018.03.018
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Cekmecelioglu, D. and A. Demirci. 2018. A statistical optimization study on dilute sulfuric acid pretreatment of distillers dried grains with solubles (DDGS) as a potential feedstock for fermentation applications. Waste and Biomass Valorization. Published online. https://doi.org/10.1007/s12649-018-0376-9
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Germec, M., M. Karhan, K.L. Bialka, A. Demirci, and I. Turhan. 2018. Ethanol production in biofilm reactor with non-sterile carob extract media and its modeling. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects. 40:22, 2726-2734, DOI: 10.1080/15567036.2018.1511643
  • Type: Theses/Dissertations Status: Published Year Published: 2018 Citation: Mahdinia, Ehsan. 2017. Vitamin K2 (Menaquinone-7) production by Bacillus subtilis natto in a biofilm reactor. Ph.D. Dissertation. Pennsylvania State University. University Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mahdinia, E., and A. Demirci. 2017. Optimization of growth parameters for menaquinone-7 (vitamin K2) production by Bacillus subilis natto in biofilm reactors. Allegheny Branch of the American Society for Microbiology. Huntingdon, PA. Abstract # G-7. (The paper won first place in graduate poster presentation)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mahdinia, E., A. Demirci, and A. Berenjian. 2017. Menaquinone-7 (vitamin K2) production by Bacillus subtilis natto in a biofilm reactor. Allegheny Branch of the American Society for Microbiology. Huntingdon, PA. Abstract # GT-4.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mahdinia, E., A. Demirci, and A. Berenjian. 2017. Menauinone-7 production using biofilm reactor. Waikato Young Engineers Symposium (WYRES), Hamilton, New Zealand.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Demirci, A. and D. Ciolkosz. 2018. Towards innovative online bioenergy education. Conference of Food Engineering. Minneapolis, MN. Abstract # 101.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Cekmecelioglu, D. and A. Demirci. 2018. Evaluating fungal co-production of cellulase and xylanase enzymes at shake-flask scale using distillers dried grain with solubles (DDGS) and its validation in benchtop fermenters. Minneapolis, MN. Abstract # 102.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Leistra, A.N., G. Gelderman, S.W. Sowa, A. Moon-Walker, H.M. Salis, and L.M. Contreras. 2018. A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions. Scientific reports, 8 (1), p9892.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Reis, A.C., and H.M. Salis. 2017. An automated model test system for systematic development and improvement of gene expression models, bioRxiv, 193367.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Halper, S.M., I. Farasat, and H.M. Salis. 2017. Automated Parameterization of Predictive Kinetic Metabolic Models from Sparse Datasets for Efficient Optimization of Many-Enzyme Heterologous Pathways. bioRxiv, 161372.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Harbaugh, S., Y. Chushak, J. Martin, H.M. Salis, M. Goodson, J. Chavez, and N. Kelley-Loughnane. 2018. In silico design and in vivo selection of riboswitches for cell-based detection of explosive compounds. Abstracts of Papers of the American Chemical Society. v255.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Halper S.M., D Cetnar, and H.M. Salis. 2018.Pathway engineering pipeline for efficiently engineering many-enzyme pathways. Abstracts of Papers of the American Chemical Society. v253.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Salis, H.M. 2017. Building a Synthetic Biology Discipline: Automated Design of Cellular Sensors, Circuits, and Pathways. Division Seminar, Pacific Northwest National Laboratory, Richland, WA. December.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Alex Reis, Sean Halper, Dan Cetnar, Grace Vezeau, Ayaan Hossain, Salis, H.M. 2018. Simultaneous Regulation of Many Genes using Highly Non-repetitive Extra Long sgRNA Arrays. Engineering Biology Research Center Retreat. Fort Collins, CA. September.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Salis, H.M. 2018. Building a Synthetic Biology Discipline: Automated Design of Cellular Sensors, Circuits, and Pathways. Du Pont Biosciences research seminar. Wilmington, DE. June.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Salis, H.M. 2018. Simultaneous Regulation of Many Genes using Highly Non-repetitive Extra Long sgRNA Arrays. Synthetic Biology Congress, Oxford Global. Boston, MA. May.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Salis, H.M. 2018. Toolboxes of Highly Non-repetitive CRISPR Parts for Highly Multiplexed Applications. DARPA Safe Genes Program Review. Tuscon, AZ. April.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Salis, H.M. 2018. System-wide Predictions using Biophysical Models and Machine Learning. DARPA Synergistic Design & Discovery Program Review. Austin, TX. January.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Hossain A., Reis, A., Cetnar, D., and Salis, H.M. 2018. The Non-Repetitive Parts Calculator: Thousands of Highly Non-repetitive Promoters for Synthetic Biology Applications. Engineering Biology Research Center Retreat. Seattle, WA. March.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Chen, M., P.M. Smith and E. Thomchick. 2017. Qualitative insights into supplier-supplier relationship attributes in the U.S. biofuels industry. Renewable Energy Focus. Vol.22, No. 00; pp, 1-9. DOI: 10.1016/j.ref.2017.09.001
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Chen, M. and P.M. Smith. 2018. Mixed methods research of integrated cellulosic biorefinery (ICBR) scale-up barriers in the United States: A case study. BioProducts Business 3(5):51-62. ISSN 2378-1394.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Smith, P.M., M.J. Gaffney, W. Shi, S. Hoard, I. Ibarrola Armendariz and D.W. Mueller. 2017. Drivers and barriers to the adoption and diffusion of sustainable jet fuel (SJF) in the U.S. Pacific Northwest. Journal of Air Transport Management, Vol. 58, January 2017:113-124. DOI: 10.1016/j.jairtraman.2016.10.004


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:The target audiences for this research include a) the science and engineering research community, b) biomass processing companies ranging from small start-ups to large multi-national companies, c) policy analysts and decision makers, and d) potential biomass producers and the general public. Stakeholders include state and national organizations, state and federal agencies, companies and industry consultants. There is also strong public interest in understanding the environmental impacts of the biomass production and processing technologies as well as comparisons to conventional petroleum-derived products. These various stakeholders are being engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension, and NEWBio.psu.edu), scientific journal articles and extension publications. The project results will be benefit biomass producers, the bioprocessing/fermentation industry and the rural public in general as a result of production of value-added products and bioenergy from raw agricultural products or by-products. The target audiences for this research also include algae, and bio-diesel biorefineries, aviation fuel supply chain stakeholders, airlines, airport management, biofuel policymakers. Changes/Problems:This research program is mostly funded by external grants, so adapts to the needs and interests of the current group of sponsoring agencies and organizations. What opportunities for training and professional development has the project provided?These project has provided substantial hands-on experiential training opportunities for both graduate and undergraduate students in in biomass feedstock supply knowledge, processes and logistics systems and logistics systems; sustainable technologies to convert biomass resources into chemicals, energy, materials and other value added products; policies impacting the U.S. biofuels industry; assessing issues for the adoption of sustainable jet fuel in the U.S.; lignin valorization from biorefinery waste streams; metabolic engineering and a full range of advanced molecular cloning and characterization techniques for engineering microorganisms. Graduate and undergraduate students become proficient in a full range of advanced molecular cloning and characterization techniques for engineering micro-organisms. Researchers present their work during poster and oral presentations at the regional and national meetings. How have the results been disseminated to communities of interest?Stakeholders have been engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension, and NEWBio.psu.edu), scientific journal articles and extension publications. Outcomes of the projects have been presented to the interested audiences at national and regional conferences. Results have been disseminated through peer reviewed journals, USDA AFRI-CAP and FAA presentations and reports and presented at the 2nd NARA Biofuels and Co-Products Conference in Seattle, WA. Our peer-reviewed publications appear in high-impact journals relevant to the intended audience, such as the Journal of the American Chemical Society, Metabolic Engineering, and Nucleic Acids Research. What do you plan to do during the next reporting period to accomplish the goals?Our experimental foci this year will be on 1) mixed culture fermentation to carboxylic acids and methane, including impacts of mechanical size reduction and in-situ separation on microbiome function and productivity, and 2) greenhouse gas emissions during high solids manure storage. System level simulation modeling efforts will include 3) biomass harvest supply chain logistics, 4) ecosystem service valuation, and 5) carbon offset benefits through winter energy crops and biomass carbon capture and storage. We have largely completed our plant biology research on biomass storage and also on lignin formation, deposition, and interactions with other components within plant cell walls, although additional papers are in preparation. 6) The project for Vitamin K production by using bioreactors will be completed; 7) Hydrolytic enzymes production from DDGS for cellulosic biomass hydrolysis for biofuels and other uses will be continued; 10) Continue to investigate biorefinery value-stream outputs, including chemicals, energy, materials and other value added products. 11) We will complete experimental validation of our Pathway Map Calculator algorithm. For experimental validation, we are engineering a 5-enzyme synthetic Entner-Doudoroff pathway to rapidly regenerate NADPH as well as 2-enzyme pathway to rapidly import and phosphorylate glucose. Together, by mapping these pathways' expression-flux relationships, we will have greater control over carbon and redox fluxes inside bacterial central metabolism. 12) Complete the project on enhancement of the bioenergy online courses.

Impacts
What was accomplished under these goals? Following projects have been studied for objectives 1, 2, and 4 by Tom Richard: Accomplishments this year included progress on four major areas of research. 1) We continue investigating microbial conversion of biomass into methane and carboxylic acids through various modes of anaerobic mixed culture fermentation, with a new emphasis on mechanical cotreatment. 2) We also continued experiments to understand the factors that contribute to greenhouse gas and ammonia emissions during high solids manure storage and composting. 3) We have intensified academic and private sector collaborations on the ecosystem service valuation of perennial energy grasses and energy winter crops for water quality in the Chesapeake Bay region as well as the Upper Mississippi Basin watersheds in Iowa. And 4) We continue our work to quantify carbon offset benefits in forest and cropland bioenergy systems, including opportunities for Biomass Energy Carbon Capture and Storage. A range of papers were published on these topics as indicated below. Following projects have been studied for objective 2 by Ali Demirci: 1) Simultaneous saccharification and fermentation of ethanol from industrial potato waste by co-culturing A. niger and S. cerevisiae in biofilm reactor was completed without needing added hydrolyzing enzymes.3) Continued to work on Vitamin K production by using bioreactors. 6) Continued to work on the project to produce hydrolytic enzymes production from distillers dried grains with solubles (DDGS) for cellulosic biomass hydrolysis for biofuels and other uses. Furthermore, following projects have been studied for objective 2 by the new member of our team, Paul Dr. Smith: 1) Reviewed opportunities and challenges of the U.S. biofuels industry, 2) Summarized U.S. laws and policies impacting the U.S. biofuels industry, 3) Assessed drivers and barriers to the adoption and diffusion of sustainable jet fuel in the U.S. Pacific Northwest (PNW) region, 4) Explored lignin valorization from biorefinery waste streams and 5) Deployed a stepwise biogeophysical and social analysis approach to biorefinery site selection. Following projects have been studied for objectives 2 and 3 by Howard Salis: 1) Development of predictive models and optimization algorithms that enable rational engineering of micro-organisms for metabolic engineering applications. In the past year, we developed and experimentally validated two algorithms for controlling protein expression and maximizing the metabolic pathway's productivity: the Operon Calculator and the Pathway Map Calculator. The Operon Calculator designs bacterial operon sequences to express recombinant proteins at targeted expression levels, while ensuring the removal of cryptic or undesired genetic elements that can destabilize operon function or confound our control over all protein expression levels. The Pathway Map Calculator uses a small number of characterized pathway variants to determine the non-linear relationship between enzyme expression levels and pathway productivity. 2) Also, developed a genetically encoded biosensor that detects changes in a cell's growth rate, and utilized it together with a genetic circuit to regulate the expression of a terpenoid biosynthesis pathway. Together, the sensor-circuit-pathway autonomously finds the optimal trade-off between cellular growth rate and pathway productivity, which compete with one another for essential metabolites. Additionally, following project has been continued for objective 4 by Ali Demirci and Tom Richard: Enhancement of the bioenergy online courses, which have been developed for "Master of Professional Studies in Renewable Energy and Sustainability Systems (MPS-RESS)" and "Online Graduate Certificate Program in Bioenergy" at Pennsylvania State University. The project aimed to create innovative tools for the hands-on practical/laboratory educational experiences associated with distance learning of technical subjects.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liu, W., J. Wang, T.L. Richard, D. Hartley, S. Spatari, and T. Volk. 2017. Economic and Life Cycle Analyses of Biomass Utilization for Bioenergy Products in the Northeastern United States. Biofuels, Bioproducts and Biorefining 11(4):633-647. DOI: 10.1002/bbb1770.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Ramcharan, A.M, and T.L. Richard. 2017. Carbon and nitrogen environmental trade-offs of winter rye cellulosic biomass in the Chesapeake Watershed. Agricultural Systems 156:85-94. http://dx.doi.org/10.1016/j.agsy.2017.05.017.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bonifacio, H.L. C.A. Rotz and T.L. Richard. 2017. A process based model for cattle manure compost windrows: Part 2. Model performance and application. Transactions of the ASABE 60(3):893-913.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bonifacio, H.L. C.A. Rotz and T.L. Richard. 2017. A process based model for cattle manure compost windrows: Part 2. Model description. Transactions of the ASABE 60(3):877-892.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Eigenbrode, S. D., T. Martin, L. Wright Morton, J. Colletti, P. Goodwin, R. Gustafson, D. Hawthorne, A. Johnson, J. T. Klein, L. Mercado, S. Pearl, T.L. Richard, and M. Wolcott. 2017. Leading large transdisciplinary projects addressing social-ecological systems: A primer for project directors. 69 pp. Available at: https://nifa.usda.gov/leading-transdisciplinary-projects.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Bharadwaj, A. K. Dimarco, M. Campbell, S.D. Brown, X. Shao, L.R. Lynd and T.L. Richard. 2017. Effect of cotreatment (mechanical disruption) on microbial consortia involved in anaerobic digestion of lignocellulosic biomass. Presented at the 39th Symposium on Biotechnology for Fuels and Chemicals. May 1-4, 2017. San Francisco, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Vazhnik, V., J.K. Hansen and T.L. Richard. 2017. Multiattribute optimization of farm plans to improve economic, environmental and social conditions on the example of a farm in the Chesapeake Bay. ASABE Paper No. 1700562. ASABE, St. Joseph, MI.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Germec, M., I. Turhan, A. Demirci, and M. Karhan. 2016. Effect of media sterilization and enrichment on ethanol production from carob extract in biofilm reactor. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects, 38(21):3268-3272, DOI: 10.1080/15567036.2015.1138004.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Improved simultaneous saccharification and fermentation of bioethanol from industrial potato waste with co-cultures of Aspergillus niger and Saccharomyces cerevisiae by medium optimization. Fuel. 185:684691. DOI: 10.1016/j.fuel.2016.08.035.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ercan, D., and A. Demirci. 2016. Recent advances for production and recovery methods of lysozyme. Critical Reviews in Biotechnology. 36 (6):1078-1088. DOI: 10.3109/07388551.2015.1084263.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Mahdinia, E., A. Demirci, A. Berenjian. 2017. Production and application of Menaquinone-7 (Vitamin K2): A new perspective. World Journal of Microbiology and Biotechnology. 33:2. DOI: 10.1007/s11274-016-2169-2.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2017 Citation: Dale, V.W., K.L. Kline, T.L. Richard, D.L. Karlen and W.W. Belden. 2017. Bridging biofuel sustainability indicators and ecosystem services through stakeholder engagement. Biomass and Bioenergy (in press), https://doi.org/10.1016/j.biombioe.2017.09.016.
  • Type: Theses/Dissertations Status: Published Year Published: 2017 Citation: Ramcharan, A. 2017. Multidisciplinary applications of U.S. soil datasets: Machine learning models, data mining, and land use analyses. Ph.D. Dissertation. Pennsylvania State University. University Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Liang, X., X. Shao, E. Holwerda, D.G. Olson, S. Murphy, L. Tian, T.L. Richard, J.M. Whitham, D.M. Klingeman, J.G. Elkins, S.D. Brown and L.R. Lynd. 2017. Switchgrass fermentation by thermophilic microbiomes: Community characterization and comparison to pure cultures of Clostridium thermocellum. Presented at the 39th Symposium on Biotechnology for Fuels and Chemicals. May 1-4, 2017. San Francisco, CA.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Izmirlioglu, G. and A. Demirci. 2017. Simultaneous saccharification and fermentation of ethanol from potato waste by co-cultures of Aspergillus niger and Saccharomyces cerevisiae in biofilm reactors. Fuel. 202:260270. DOI: 10.1016/j.fuel.2017.04.047.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Mahdinia, E., A. Demirci, A. Berenjian. 2017. Strain and plastic composite support (PCS) selection for Vitamin K (Menaquinone-7) production in biofilm reactors. Bioprocess and Biosystems Engineering. 40:15071517. DOI 10.1007/s00449-017-1807-x.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Coban, H.B., and A. Demirci. 2017. An applied research perspectives of alpha-keto acids: From the production to applications. In Handbook of Food Bioengineering. Volume 1: Food Biosynthesis. A. M. Grumezescu and A. M. Holban, Eds. Elsevier Inc. Philadelphia, PA. June 1. pp 427-DOI: 447. /10.1016/B978-0-12-811372-1.00015-4. ISBN: 978-0128113721.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Coban, H.B., and A. Demirci. 2017. Phytase as a diet ingredient: From microbial production to its applications in food and feed industry. In Handbook of Food Bioengineering. Volume 5: Microbial Production of Food Ingredients and Additives. A. M. Grumezescu and A. M. Holban, Eds. Elsevier Inc. Philadelphia, PA. DOI: pp 33-55. June 1. 10.1016/B978-0-12-811520-6.00002-7. ISBN: 978-0128115206.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Izmirlioglu, Gulten. 2016. Simultaneous saccharification and fermentation for production of ethanol from waste mash potato in biofilm reactors. Ph.D. Dissertation. Pennsylvania State University. University Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Ciolkosz, D. and A. Demirci. 2017. The impact of hands-on activities on effective online learning of bioenergy. Northeast Agricultural and Biological Engineering Conference, Groton, CT. Abstract # 17-040.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Chen, M., P.M. Smith and M.P. Wolcott. 2016. U.S. Biofuels Industry: A Critical Review of Opportunities and Challenges. BioProducts Business 1(4), 2016, pp. 4259. http://biobus.swst.org/index.php/bpbj/article/view/18/6.
  • Type: Book Chapters Status: Published Year Published: 2016 Citation: Dahmann, K.S., L.B. Fowler, P.M. Smith. 2016. United States Law and Policy and the Biofuel Industry, included in Volume One: The Law and Policy of Biofuels co-editors, Yves Le Bouthillier, Annette Cowie, Paul Martin and Heather McLeod-Kilmurray, IUCN Academy of Environmental Law Series. June, 400pp. Hardback. 978 1 78254 454 8. Edward Elgar Pub., Inc., Northampton, MA. Pp. 102-140.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Smith, P.M., M.J. Gaffney, W. Shi, S. Hoard, I. Ibarrola Armendariz and D.W. Mueller. 2017. Drivers and barriers to the adoption and diffusion of sustainable jet fuel (SJF) in the U.S. Pacific Northwest. Journal of Air Transport Management, Vol. 58, January 2017:113-124. doi: 10.1016/j.jairtraman.2016.10.004.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Izmirlioglu, G., and A. Demirci. 2017. Comparison of pure and co-culture ethanol fermentations in biofilm reactors. Northeast Agricultural and Biological Engineering Conference, Groton, CT. Paper # 17-002. 13 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Germec, M., K. Tarhan, E. Yatmaz, N. Tetik, M. Karhan, A. Demirci, and I. Turhan. 2017. Optimization of ultrasound-assisted dilute acid hydrolysis conditions of tea processing wastes. Northeast Agricultural and Biological Engineering Conference, Groton, CT. Paper # 17-009. 8 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Germec, M., I. Turhan, M. Karhan, and A. Demirci. 2017. Ethanol production from carob extract by using Saccharomyces cerevisiae in biofilm reactor. Northeast Agricultural and Biological Engineering Conference, Groton, CT. Paper # 17-010. 10 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mahdinia, E., A. Demirci, and A. Berenjian. 2017. Optimization of growth parameters and media for vitamin K (MK-7) production by Bacillus subtilis. Northeast Agricultural and Biological Engineering Conference, Groton, CT. Paper # 17-011. 10 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mahdinia, E., A. Demirci, and A. Berenjian. 2017. Strain and plastic composite support (pcs) selection for Vitamin K (MK-7) production in biofilm reactors. Northeast Agricultural and Biological Engineering Conference, Groton, CT. Paper # 17-012. 14 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Cekmecelioglu, D., and A. Demirci. 2017. Feasibility of DDGS for production of cellulase and xylanase enzymes cocktail. Northeast Agricultural and Biological Engineering Conference, Groton, CT. Paper # 17-013. 10 pp.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Rijkhoff, S., Hoard, S., Gaffney, M., & Smith, P. 2017. Communities ready for takeoff: Integrating social assets for biofuel site-selection modeling. Politics and the Life Sciences, 36(1), 14-26. doi:10.1017/pls.2017.6.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Martinkus, N., Rijkoff, S.A.M., Hoard, S.A., Shi, W., Smith, P., Gaffney, M. & Wolcott, M. 2017. Biorefinery site selection using a stepwise biogeophysical and social analysis approach. Biomass and Bioenergy, Vol. 97, 139-148. doi: 10.1016/j.biombioe.2016.12.022.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Chen, M. and Smith, P.M. 2017. The U.S. cellulosic biofuels industry: Expert views on commercialization drivers and barriers. Biomass and Bioenergy, Vol. 102, 52-61. Doi: http://dx.doi.org/10.1016/j.biombioe.2017.05.002.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Cline, S.P. and P.M. Smith. 2017. Opportunities for Lignin Valorization: An Exploratory Process. Energy, Sustainability and Society. 7:26. DOI: 10.1186/s13705-017-0129-9.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2017 Citation: Chen, M., P.M. Smith and E. Thomchick. 2017. Qualitative insights into supplier-supplier relationship attributes in the U.S. biofuels industry. Accepted in Renewable Energy Focus. In Press.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Espah Borujeni, Amin, Daniel Cetnar, Iman Farasat, Ashlee Smith, Natasha Lundgren, and Howard M. Salis. 2017. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic acids research 45(9): 5437-5448.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Halper, S., Cetnar, D., & Salis, H. M. 2017. An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Optimization. Methods in Molecular Biology. Synthetic Metabolic Pathways. Chapter 4.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis, H. M. 2016 (Invited). The Power of Prediction: Optimization of Many-enzyme Metabolic Pathways without High-throughput Screening," AIChE Annual Meeting, San Francisco, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis, H. M., & Reis, A. 2016. A Model Test System for Systematically Comparing the Accuracies of Gene Expression Models," AIChE Annual Meeting, San Francisco, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis, H. M., & Alper, S. 2016.An Automated Pipeline for Designing and Optimizing Many-Enzyme Pathways. AIChE Annual Meeting, San Francisco, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis, H. M. 2016. Automated Design and Optimization of Many-enzyme Pathways. Invited Seminar for Arzeda Inc.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis, H. M. 2016. Automated Design of Cellular Sensors, Circuits, and Pathways. Chemical & Biomolecular Engineering. Invited Seminar (Chemical & Biomolecular Engineering), University of Nebraska, Lincoln.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis, H. M. 2016. Automated Design of Cellular Sensors, Circuits, and Pathways. Chemical & Biomolecular Engineering. Invited Seminar (Bioengineering), University of California, Santa Barbara.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis, H. M., & Vezeau, G. 2016. The Effect of Nucleic Acid Structure on Nanopore DNA Sequencing. EBRC Bi-annual Retreat, Engineering Biology Research Center, Pasadena, CA.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:The target audiences for this research include a) the science and engineering research community, b) biomass processing companies ranging from small start-ups to large multi-national companies, c) policy analysts and decision makers, and d) potential biomass producers and the general public. Stakeholders include state and national organizations, state and federal agencies, companies and industry consultants. There is also strong public interest in understanding the environmental impacts of the biomass production and processing technologies as well as comparisons to conventional petroleum-derived products. These various stakeholders are being engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension, and NEWBio.psu.edu), scientific journal articles and extension publications. The project results will be benefit biomass producers, the bioprocessing/fermentation industry and the rural public in general as a result of production of value-added products and bioenergy from raw agricultural products or by-products. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These project has provided substantial hands-on experiential training opportunities for both graduate and undergraduate students in in biomass feedstock supply knowledge, processes and logistics systems and logistics systems; sustainable technologies to convert biomass resources into chemicals, energy, materials and other value added products; metabolic engineering and a full range of advanced molecular cloning and characterization techniques for engineering microorganisms. Researchers present their work during poster and oral presentations at the reginal and national meetings. How have the results been disseminated to communities of interest?Stakeholders have been engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension, and NEWBio.psu.edu), scientific journal articles and extension publications. Outcomes of the projects have been presented to the interested audiences at national and regional conferences. The Salis Lab also maintains a website that enables biotech researchers to rationally design DNA sequences using biophysical model predictions (https://salislab.net/software). In the past year alone, over 10000 DNA sequences were designed by researchers from around the world for a wide variety of biotech applications. What do you plan to do during the next reporting period to accomplish the goals?Our experimental foci this year will be on 1) mixed culture fermentation to carboxylic acids and methane, including impacts of size reduction and in-situ separation on microbiome function and productivity, and 2) greenhouse gas emissions during high solids manure storage. System level simulation modeling efforts will include 3) biomass supply chain logistics, 4) ecosystem service valuation, and 5) carbon offset benefits through winter energy crops and biomass carbon capture and storage. We have largely completed our plant biology research on biomass storage and also on lignin formation, deposition, and interactions with other components within plant cell walls, although additional papers are in preparation. 6) Enhanced bio-ethanol production from industrial potato waste by using bioreactors will be completed; 7) The project for Vitamin K production by using bioreactors will be continued; 8) Hydrolytic enzymes production from DDGS for cellulosic biomass hydrolysis for biofuels and other uses will be continued; 9) We will complete development and experimental validation of our Pathway Map Calculator algorithm, an optimization algorithm that learns the kinetic parameters of a multi-enzyme pathway, while requiring characterization of relatively few pathway variants. This algorithm predicts the optimal enzyme expression levels of multi-enzyme pathways, significantly increasing their metabolic flux. For experimental validation, we are engineering a 5-enzyme synthetic Entner-Doudoroff pathway to rapidly regenerate NADPH as well as 2-enzyme pathway to rapidly import and phosphorylate glucose. Together, by mapping these pathways' expression-flux relationships, we will have total control over carbon and redox fluxes inside bacterial central metabolism.

Impacts
What was accomplished under these goals? Following projects have been studied for objectives 1, 2, and 4 by Tom Richard: Accomplishments this year included progress on seven major areas of research. 1) Analyzing data from previous experiments on aerobic and anaerobic storage of willow, switchgrass and miscanthus. 2) Investigate microbial conversion of biomass into carboxylic acids and are expanding that into a broader study of anaerobic mixed culture fermentation. 3) Completed additional experiments to understand the factors that contribute to greenhouse gas emissions during high solids manure storage. 4) Continue work with DOE labs to quantify and simulate wet storage impacts on biomass supply chain logistics. 5) Expanded our collaborations on the ecosystem service valuation of perennial energy grasses and energy winter crops for water quality in the Chesapeake Bay region to now also include Upper Mississippi Basin watersheds in Iowa. 6) Continue our work to quantify carbon offset benefits in forest and cropland bioenergy systems. 7) And finally, Analyzing and publishing articles from a suite of experiments to develop and test synthetic monolignols as tracers in plant cell walls to determine cell structure and function. Following projects have been studied for objective 2 by Ali Demirci: 1) Enhanced bio-ethanol production from industrial potato waste hydrolyzsate in biofilm reactors were studied; 2) Simultaneous saccharification and fermentation of ethanol from industrial potato waste by co-culturing A. niger and S. cerevisiae in biofilm reactor was performed without needing added hydrolyzing enzymes.3) Continued to work on Vitamin K production by using bioreactors. Collaborated with researchers in Turkey on two projects 4) ultrasound-assisted dilute acid hydrolysis of tea processing waste for production of fermentable sugar, and 5) effect of media sterilization and enrichment on ethanol production from carob extract in biofilm reactor. Finally, 6) A new project started to produce hydrolytic enzymes production from distillers dried grains with solubles (DDGS) for cellulosic biomass hydrolysis for biofuels and other uses. Following projects have been studied for objectives 2 and 3 by Howard Salis: 1) development of predictive models and optimization algorithms that enable rational engineering of micro-organisms for metabolic engineering applications. In the past year, we developed advanced optimization algorithms capable of mapping a multi-enzyme pathway's expression-flux relationship, while requiring characterization of only a small number of pathway variants. This algorithm is currently being used by several academic and industrial labs to optimize metabolic pathways for the over-production of therapeutics and specialty chemicals. 2) Also developed advanced, non-equilibrium models of translation that enable more precise control over protein expression levels in bacteria. We have applied our biophysical models to the automated design and engineering of synthetic riboswitch sensors, capable of directly coupling the binding of a small molecule to the activation of protein expression. In this work, we engineered 72 riboswitches capable of detecting six different chemicals, including fluoride (a water additive) and 2,4-dinitrotoluene (a pollutant). Finally, 3) Engaged in a collaboration to rationally engineer a new metabolic pathway that converts methane into acetate, a key metabolic precursor. Additionally, following project has been continued for objective 4 by Ali Demirci and Tom Richard: Enhancement of the bioenergy online courses, which have been developed for "Master of Professional Studies in Renewable Energy and Sustainability Systems (MPS-RESS)" and "Online Graduate Certificate Program in Bioenergy" at Pennsylvania State University. The project aimed to create innovative tools for the hands-on practical/laboratory educational experiences associated with distance learning of technical subjects. Please note that Dr. Paul Smith just joined the project. He will be reporting next year.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2016 Citation: Pandey, J.L., S. N. Kiemle, T.L. Richard, Y. Zhu, D.J. Cosgrove and C.T. Anderson. 2016. Investigating biochemical and developmental dependencies of lignification with a click-compatible monolignol analog in Arabidopsis thaliana stems. Frontiers in Plant Science Research. In press.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Carroll, S., J. W. Carey, D. Dzombak, N.J. Huerta, L.Li, T.L. Richard, W. Um, S.D.C. Walsh and L. Zhang. 2016. Review: Role of chemistry, mechanics, and transport on well integrity in CO2 storage environments. International Journal of Greenhouse Gas Control 49:149-160.
  • Type: Book Chapters Status: Published Year Published: 2016 Citation: Webber, D., S.K. Mickelson, T.L. Richard and H.K. Ahn. 2016. Vegetative buffer and fly ash pad surface material system for reducing runoff, sediment and nutrient losses from livestock manure windrow composting facilities. Chapter 3, pages 39-60 in: Advances in Environmental Research. J.A. Daniels (ed). Nova Publishers, New York.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Coban, H.B., and A. Demirci. 2015. Improved submerged Aspergillus ficuum phytase production in bench-top bioreactors by optimization of fermentation medium . Acta Alimentaria, An International Journal of Food Science. 44 (4):549560.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Izmirlioglu, G. and A. Demirci. 2015. Enhanced bio-ethanol production from industrial potato waste by statistical medium optimization. The International Journal of Molecular Sciences. 16 (10), 24490-24505.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ercan. D. and A. Demirci. 2015. Effects of fed-batch and continuous fermentations on human lysozyme production by Kluyveromyces lactis K7 in biofilm reactors. Journal of Bioprocess and Biosystems Engineering. 38(12): 2461-2468.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Coban, H.B., and A. Demirci. 2016. Enhancement and modeling of microparticle added Rhizopus oryzae lactic acid production. Journal of Bioprocess and Biosystems Engineering. 39(2):323-330.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Coban, H.B., A. Demirci, P. H. Patterson, and R. J. Elias. 2016. Enhanced phenylpyruvic acid production with proteus vulgaris by optimizing of the fermentation medium. Acta Alimentaria, An International Journal of Food Science. 45(1): 1-10.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2016 Citation: Recent advances for production and recovery methods of lysozyme. Critical Reviews in Biotechnology. In-Print.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Strain selection and optimization of medium for glucoamylase production from industrial potato waste by Aspergillus niger. Journal of the Science of Food and Agriculture. 96 (8): 2788-2795.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Ethanol production in biofilm reactors from potato waste hydrolysate and optimization of growth parameters for Saccharomyces cerevisiae. Fuel. 181: 643651.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Germec, M., I. Turhan, M. Karhan, and A. Demirci. 2015. Ethanol production via repeated-batch fermentation from carob pod extract by using Saccharomyces cerevisiae in biofilm reactor. Fuel. 161:304311.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Germec, M., K. Tarhana, E. Yatmaz, E. Karahalil, M. Karhan, A. Demirci, and I. Turhan. 2016. Ultrasound-assisted dilute acid hydrolysis of tea processing waste for production of fermentable sugar. Biotechnology Progress. 32:393-403.
  • Type: Book Chapters Status: Published Year Published: 2016 Citation: Cheng, K. C., K. I. Chen, C. T. Chen, A. Demirci. 2015. An applied research perspective of pullulan-from production to application. In Applied Researches in Polysaccharides. F. D. Alsewailem, Ed. Research Signpost, Trivandrum, Kerala, India.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Ethanol fermentation by Saccharomyces cerevisiae from potato waste hydrolysate in biofilm reactor. ASABE Annual International Meeting. Orlando, FL. Paper # 2456273. 11 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Simultaneous saccharification and ethanol fermentation by co-culture in biofilm reactor. ASABE Annual International Meeting. Orlando, FL. Paper # 2456278. 11 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Germec, M., K. Tarhan, E. Yatmaz, N. Tetik, M. Karhan, A. Demirci. I. Turhan. 2016. Optimization of ultrasound-assisted dilute acid hydrolysis conditions of tea processing wastes. ASABE Annual International Meeting. Orlando, FL. Paper # 2456243. 7 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Germec, M., I. Turhan, M. Karhan, A. Demirci. 2016. Optimization of ultrasound-assisted dilute acid hydrolysis conditions of tea processing wastes. ASABE Annual International Meeting. Orlando, FL. Paper # 2456236. 9 pp.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Ciolkosz, D. and A. Demirci. 2016. Renewable energy and sustainability systems: Student preferences for graduate online education. Penn State Energy Days. Penn State University, University Park, PA. Abstract # 85.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Ethanol fermentation by Saccharomyces cerevisiae from potato waste hydrolysate in biofilm reactors. 38th Symposium on Biotechnology for Fuels and Chemicals. Baltimore, MD. Abstract # 31932.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Demirci, A., M. Germec, I. Turhan, and M. Karhan. 2016. Ethanol production from carob extract by using Saccharomyces cerevisiae in biofilm reactor. 38th Symposium on Biotechnology for Fuels and Chemicals. Baltimore, MD. Abstract # 31905.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Simultaneous saccharification and ethanol fermentation by co-culture in biofilm reactors. Conference of Food Engineering. Columbus, OH. Abstract # 1.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Ercan, D. and A. Demirci. 2016. Enhanced human lysozyme production by Kluyveromyces lactis K7 in biofilm reactor. Conference of Food Engineering. Columbus, OH. Abstract # 50.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Izmirlioglu, G. and A. Demirci. 2016. Simultaneous saccharification and ethanol fermentation by co-culture in biofilm reactors. 38th Symposium on Biotechnology for Fuels and Chemicals. Baltimore, MD. Abstract # 31929.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Espah Borujeni A., and H. M. Salis. (2016) Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism. Journal of the American Chemical Society, v138(22), p70167023.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Espah Borujeni, A. , D. M. Mishler, J. Wang, W. Huso, and H. M. Salis. (2016). Breakthrough Article: Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Research, 44(1), p1-13.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Farasat, I., and H. M. Salis. (2016). A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. PLoS Comput Biol, 12(1), e1004724.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Soo, V. W. C., McAnulty, M. J., Tripathi, A., Zhu, F., Zhang, L., Hatzakis, E., Smith, P. B., Agrawal, S., Nazem-Bokaee, H., Gopalakrishnan, S., Salis, H. M., Ferry, J. G., Maranas, C. D., Patterson, A. D. & Wood, T. K. 2016 Reversing methanogenesis to capture methane for liquid biofuel precursors. Microbial Cell Factories 15, 1-14.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Amin Espah Borujeni. December 2015. Ph.D. Chemical Engineering. The Development of Equilibrium and Non-equilibrium Models of Translation and Riboswitch Regulation: Towards the Automated Design of Cellular Sensors. Pennsylvania State University, University Park, PA.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Tian Tian. 2016. Ph.D. Agricultural & Biological Engineering. Coordination of Protein Expression and Autonomous Control of Biosynthesis Pathways. Pennsylvania State University, University Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis H.M. 2016. Automated, Predictive, Scalable Design and Efficient Optimization of Many-enzyme Genetic Systems. The Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting. New Orleans, LA. July 25-28. (invited)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Tian T. and H.M. Salis. Model-based autonomous regulation of biosynthesis pathways using a sensor-circuit device. The Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting. New Orleans, LA. July 25-28.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis H.M. 2016. Ribosome Drafting: Next-generation Biophysical Models & Algorithms for Engineering Genetic Systems. Synthetic Biology: Engineering, Evolution, and Design. Chicago, IL. July 18-20.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Cetnar D., A.E. Borujeni, and H.M. Salis. The Operon Calculator: multi-objective optimization for de novo design of bacterial operons. Synthetic Biology: Engineering, Evolution, and Design. Chicago, IL. July 18-20.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis H.M. 2016. Next-generation Sequence-to-Function Models for Engineering Genetic Systems. Bi-Annual Meeting of the Synthetic Biology Engineering Research Center (SynBERC). Berkeley, CA. March 23-25. (invited Keynote)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Alexander Reis and H.M. Salis. 2016. A Model Test System for Systematic Comparisons of Model Accuracy on Large Sequence Datasets. Bi-Annual Meeting of the Synthetic Biology Engineering Research Center (SynBERC). Berkeley, CA. March 23-25.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Grace Vezeau and H.M. Salis. 2016. Rational Engineering of Synthetic Riboswitch Sensors to Detect an Array of Relevant Chemicals. Bi-Annual Meeting of the Synthetic Biology Engineering Research Center (SynBERC). Berkeley, CA. March 23-25.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis H.M. 2016. An Automated Pipeline for Engineering Multi-Enzyme Pathways and Gene Clusters. Joint Genome Institute Workshop on Synthetic Biology. Walnut Creek, CA. March 21. (invited)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Salis H.M. 2016. Predictive Biophysical Models of Translation Initiation and Regulation. Workshop on Computational Modeling of Translation. Tel Aviv University. Tel Aviv, Israel. October 13-15. (invited)


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:The target audiences for this research include the science and engineering research community; biomass processing and the synthetic biology and metabolic engineering companies ranging from small start-ups to large multi-national companies, policy analysts and decision makers, and potential biomass producers and the general public. Stakeholders include state and national organizations, state and federal agencies, companies and industry consultants. There is also strong public interest in understanding the environmental impacts of the biomass production and processing technologies as well as comparisons to conventional petroleum-derived products. These various stakeholders are being engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension), scientific journal articles and extension publications. The project results will be benefit bioprocessing/fermentation industry in general as a result of production of value-added products and bioenergy from raw agricultural products or by-products. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students and other researchers were trained in biomass feedstock supply knowledge, processes and logistics systems and logistics systems; sustainable technologies to convert biomass resources into chemicals, energy, materials and other value added products; metabolic engineering and the application of several characterization techniques to measure RNA, protein, and metabolite levels inside cells metabolic; and develop modeling and systems approaches to support development of sustainable biomass production and conversion to bioenergy and bioproducts; How have the results been disseminated to communities of interest?Outcomes of the projects have been presented to the interested audiences at national and regional conferences. Stakeholders have been engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension, and NEWBio.psu.edu), scientific journal articles and extension publications. What do you plan to do during the next reporting period to accomplish the goals?Our experimental foci this year will be on 1) dry matter loss and compositional changes during biomass storage under anaerobic (ensiled) and aerobic (hay) conditions; 2) mixed culture fermentation to carboxylic acids and methane, including impacts of size reduction and in-situ separation on microbiome function and productivity; 3) greenhouse gas emissions during high solids manure storage. System level simulation modeling efforts will include 4) biomass supply chain logistics; 5) ecosystem service valuation, and 6) carbon offset benefits through winter energy crops and biomass carbon capture and storage. We have largely completed our plant biology research on lignin formation, deposition, and interactions with other components within plant cell walls, although additional papers using quantum mechanical calculations of lignin-protein interactions are in preparation; 7) Enhanced bio-ethanol production from industrial potato waste by using bioreactors will continue; 8) The project for Vitamin K production by using bioreactors will continue; 9) Develop the Pathway Map Calculator, an automated algorithm that designs optimally balanced heterologous metabolic pathways while requiring the characterization of only a small number of pathway variants with varying enzyme expression levels; 10) Design and characterize a toolbox of RNA-based sensors to detect a wide variety of chemicals (toxins, pollutants, metabolites) for applications in bioremediation and metabolic engineering.

Impacts
What was accomplished under these goals? Following projects have been studied for objectives 1, 2, and 4 by Tom Richard: i) Multiple experiments on aerobic and anaerobic storage of willow, switchgrass and miscanthus have been studied; ii) Microbial conversion of biomass into carboxylic acids was investigated, publishing a paper on the use of nanofiltration for integrated acid separation; iii) A new project to understand the factors that contribute to greenhouse gas emissions during high solids manure storage was initiated; iv) A work has been initiated with the Idaho National Laboratory to quantify and simulate wet storage impacts on biomass supply chain logistics; v) Another work initiated as a new collaboration with Cornell University and the Oak Ridge National Laboratory on the ecosystem service valuation of perennial energy grasses and energy winter crops for water quality in the Chesapeake Bay; vi) A project to quantify carbon offset benefits in forest and cropland bioenergy systems has been started; vii) A suite of experiments to develop and test synthetic monolignols as tracers in plant cell walls to determine cell structure and function was completed. Following projects have been studied for objective 2 by Ali Demirci: i) Strain selection and medium optimization for glucoamylase production from industrial potato waste by Aspergillus niger have been studied; ii) Enhanced bio-ethanol production from industrial potato waste by statistical medium optimization were performed; iii) Medium optimization for simultaneous saccharification and fermentation of ethanol from industrial potato waste by A. niger and S. cerevisiae was studied. iv) The project for production of human lysozyme by Kluyveromyces lactis K7 in biofilm reactors including fed-batch and continuous fermentations have been completed as well as online recovery of lysozyme; v) The project for production of alpha-keto acids by using microbial cell cultures have been completed including fed-batch and continuous fermentations; vi) The project for the production of lactic acid by Rhizopus oryzae microparticles additions has been completed which aimed to enhance lactic acid fermentation; vii) The cultivation conditions and medium composition a novel probiotic strain Bacillus pumilus STF26 have been studied; vi) A new project has been started to enhance Vitamin K production by using bioreactors. Following projects have been studied for objectives 2 and 3 by Howard Salis: i) A predictive biophysical model of translational coupling has been developed that enables the rational engineering of bacterial operons for metabolic engineering and synthetic biology applications; ii) A genetic circuit was engineered that uses mixed feedback loops to express similar amounts of T7 RNA polymerase in diverse host organisms, enabling the rational engineering of metabolic pathways without relying on host-specific promoters; iii) A 5-enzyme Entner-Doudoroff metabolic pathway was engineered that rapidly regenerates the cofactor NADPH in E. coli, and demonstrated that this modular pathway could be used to double the production titer of a terpenoid product; iv) A predictive biophysical model of translation-regulating riboswitches has been developed that was used to rationally engineer 62 RNA-based sensors that detect six different chemicals, including the environmental pollutant dinitrotoluene to engineer RNA-based sensors that can detect and respond to many types of environmental pollutants; v) A quantitative model of the CRISPR/Cas9 system was developed that explains how several factors collectively control Cas9's ability to precisely cut genomic DNA sites and regulate transcriptional activity; vi) A non-equilibrium biophysical model of translation initiation was developed that accounts for differences in a mRNA's folding kinetics. This model can be used to more accurately predict translation initiation rates of mRNA with several applications in Synthetic Biology and Metabolic Engineering. Following project has been studied for objective 4 by Ali Demirci and Tom Richard: i) A project is started to enhance the bioenergy online courses, which have been developed for " Master of Professional Studies in Renewable Energy and Sustainability Systems (MPS-RESS)" and "Online Graduate Certificate Program in Bioenergy". Special effort will be placed on the creation of innovative hands-on practical/laboratory educational experiences that utilize a variety of learning tools and counteract the difficulties associated with distance learning of technical subjects.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Xiong, X., T.L. Richard and M. Kumar. 2015. Integrated acidogenic digestion and carboxylic acid separation by nanofiltration membranes for the lignocellulosic carboxylate platform. Journal of Membrane Science 489:275-283.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kapp, N.E., W.J. Barnes, T.L. Richard and C.T. Anderson. 2015. Imaging with the fluorogenic dye Basic Fuchsin reveals subcellular patterning and ecotype variation of lignification in Brachypodium distachyon. Journal of Experimental Botany erv 158. DOI: 10.1093/jxb/erv158.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Shao, X., K.M DiMarco, T.L Richard and L.R Lynd. 2015. Winter rye as a bioenergy feedstock: impact of crop maturity on composition, biological solubilization and potential revenue. Biotechnology for Biofuels 8:35. DOI: 10.1186/s13068-015-0225-z.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Pandey, J.L., B. Wang, B.G. Diehl, T.L. Richard, G. Chen, and C.T. Anderson. 2015. A versatile click-compatible monolignol probe to study lignin deposition in plant cell walls. PLOS ONE 10(4) e0121334.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Malcolm, G.M., G.G.T. Camargo, V.A. Ishler; T.L. Richard and H.D. Karsten. 2015. Energy and greenhouse gas analysis of northeast U.S. dairy cropping systems. Agriculture, Ecosystems and Environment 199:407-417.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Bukowski, N., J.L. Pandey, L. Doyle, T.L. Richard, C.T. Anderson and Y. Zhu. 2014. Development of a clickable designer monolignol for interrogation of lignification in plant cell walls. Bioconjugate Chemistry. 25(12): 2189-2196.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Dale, B.E., J.E. Anderson, R.C. Brown, S. Csonka, V.H. Dale, G. Herwick, R.D. Jackson, N. Jordan, S. Kaffka, K.L. Kline, L.R. Lynd, C. Malmstrom, R.G. Ong, T.L. Richard, C. Taylor and M.Q. Wang. 2014. Take a closer look: Biofuels can support environmental, economic and social goals. Environmental Science and Technology 48(13):7200-7203. DOI: 10.1021/es5025433.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Davis, E.B. and T.L Richard. 2014. Biomass energy and the implications for climate and food: The U.S. response. Bulletin of the Atomic Scientists 70 (1): 16-20.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Richard, T.L. and H. El-Lakany. 2015. Bioenergy and Food Security. Pages. 462-483 in: Bioenergy and Sustainability: Bridging the Gaps. G.M. Souza, R.L. Victoria, C.A Joly, and L.M. Verdade (eds.). Scientific Committee on Problems in the Environment (SCOPE)  FAPESP  BIOEN  BIOTA+10  FAPESP Climate Change, Sao Paulo, Brazil.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Diaz-Chavez, R., F.X. Johnson, T.L. Richard and H. Chanakya. 2015. Biomass Resources, Energy Access and Poverty Reduction. Pages 704-725 in: Bioenergy and Sustainability: Bridging the Gaps. G.M. Souza, R.L. Victoria, C.A Joly, and L.M. Verdade (eds.). Scientific Committee on Problems in the Environment (SCOPE)  FAPESP  BIOEN  BIOTA+10  FAPESP Climate Change, Sao Paulo, Brazil.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Foust, T.D., D. Arent, I. de Carvelho Macedo, J. Goldemberg, C. Hoysala, R.M. Filho, F.E.B. Nigro, T.L. Richard, J.N. Saddler, J. Samseth, and C.R. Somerville. 2015. Energy Security. Pages 58-87 in: Bioenergy and Sustainability: Bridging the Gaps. G.M. Souza, R.L. Victoria, C.A Joly, and L.M. Verdade (eds.). Scientific Committee on Problems in the Environment (SCOPE)  FAPESP  BIOEN  BIOTA+10  FAPESP Climate.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Malcolm, G.M., G.G.T. Camargo, V.A. Ishler, T.L. Richard, and H.D. Karsten. 2015. Corrigendum to Energy and greenhouse gas analysis of northeast U.S. dairy cropping systems. Agriculture, Ecosystems & Environment 204: 83-84.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Souza, G.M., R.L. Victoria, L.M. Verdade, C.A. Joly, P.E.A. Netto, C.H. de Brito Cruz, H. Cantarella, H.L. Chum, L.A.B. Cortez, R. Diaz-Chavez, E. Fernandes, G.B. Fincher, J. Goldemberg, L.A.H. Nogueira, B.J. Huntley, F.X. Johnson, S. Kaffka, A. Karp, M.R.L.V. Leal, S. P. Long, L.R. Lynd, I. de Carvelho Macedo, R.M. Filho, A.M. Nassar, F.E.B. Nigro, P. Osseweijer, T.L. Richard, J.N. Saddler, J. Samseth, V. Seebaluck, C.R. Somerville, L. van der Wielen, M.-A. Van Sluys, J. Woods, and H. Youngs. 2015. SCOPE Bioenergy and Sustainability. Pages 5-24 in: Bioenergy and Sustainability: Bridging the Gaps. G.M. Souza, R.L. Victoria, C.A Joly, and L.M. Verdade (eds.). Scientific Committee on Problems in the Environment (SCOPE)  FAPESP  BIOEN  BIOTA+10  FAPESP Climate Change, Sao Paulo, Brazil.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Souza, G.M., R.L. Victoria, L.M. Verdade, C.A. Joly, P.E.A. Netto, H. Cantarella, H.L. Chum, L.A.B. Cortez, R. Diaz-Chavez, E. Fernandes, G.B. Fincher, J. Goldemberg, L.A.H. Nogueira, B.J. Huntley, F.X. Johnson, A. Karp, M.R.L.V. Leal, L.R. Lynd, I. de Carvelho Macedo, R.M. Filho, M.P. Massafera, A.M. Nassar, F.E.B. Nigro, P. Osseweijer, T.L. Richard, J.N. Saddler, J. Samseth, V. Seebaluck, C.R. Somerville, L. van der Wielen, M.-A. Van Sluys, J. Woods, and H. Youngs. 2015. Bioenergy Numbers. Pages 26-54 in: Bioenergy and Sustainability: Bridging the Gaps. G.M. Souza, R.L. Victoria, C.A Joly, and L.M. Verdade (eds.). Scientific Committee on Problems in the Environment (SCOPE)  FAPESP  BIOEN  BIOTA+10  FAPESP Climate Change, Sao Paulo, Brazil.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Tanjore, D. and T.L. Richard. 2015. A Systems View of Lignocellulose Hydrolysis. In: Advances in Bioprocess Technology. R. Pogaku (ed.). Springer International Publishing, Zug, Switzerland.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Camargo, G. 2015. Water and Light Competition in Mixed Plant Communities. Ph.D. Dissertation, Agricultural and Biological Engineering, Pennsylvania State University, University Park, PA.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Pandey, J. 2015. Investigation of Lignin Interactions and Deposition in Plant Cell Walls. Ph.D. Dissertation, Agricultural and Biological Engineering, Pennsylvania State University, University Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Cangiano, M.L., A.R. Kemanian, F. Montes and T.L. Richard. 2014. Net ecosystem carbon exchange of maize and shrub willow for bioenergy. Presented at 138th ASA/CSSA/SSSA International Annual Meetings, Nov. 2-5, 2014. Long Beach, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ramcharan, A., A. Kemanian and T.L. Richard. 2014. Can winter rye be a carbon sink energy source? A biophysically-modeled case study Presented at 138th ASA/CSSA/SSSA International Annual Meetings, Nov. 2-5, 2014. Long Beach, CA.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Ercan, D., Demirci, A., and A. L. Pometto III. 2015. Applications of biofilm reactors for production of value-added products by microbial fermentation. In Biofilms in the Food Environment. 2nd edition. Pometto III. A. L. and Demirci, A., Eds. Wiley-Blackwell Publishing, Chichester, West Sussex, UK.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ercan. D. and A. Demirci. 2014. Enhanced Human Lysozyme Production in Biofilm Reactor by Kluyveromyces lactis K7. Biochemical Engineering Journal. 92: 28.
  • Type: Theses/Dissertations Status: Published Year Published: 2014 Citation: Kapp, N. 2014. Investigating Spatio-temporal Patterns of Lignification in Flowering-time Variants of the Model Grass Brachypodium distachyon. M.S. Thesis. Plant Biology, Pennsylvania State University, University Park, PA.
  • Type: Theses/Dissertations Status: Published Year Published: 2014 Citation: Xiong, B. 2014. The Development of Carboxylic Acid Separation by Nanofiltration Membrane for Carboxylate Platform Using Lignocellulosic Biomass. M.S. Thesis. Agricultural and Biological Engineering, Pennsylvania State University, University Park, PA.
  • Type: Theses/Dissertations Status: Published Year Published: 2014 Citation: Lewis, R. 2014. Effect of Storage Conditions on the Dry Matter, Composition, and Respiration Concentrations of Willow Chips. M.S. Thesis. Agricultural and Biological Engineering, Pennsylvania State University, University Park, PA.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Coban, H.B., and A. Demirci. 2014. Screening of phytase producers and optimization of culture conditions for submerged fermentation. Bioprocess and Biosystems Engineering. 37:609616.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Coban, H.B., and A. Demirci. 2014. Enhanced submerged Aspergillus ficuum phytase production by implementation of fed-batch fermentation. Bioprocess and Biosystems Engineering. 37:25792586.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Coban, H.B., A. Demirci, P. H. Patterson, and R. J. Elias. 2014. Screening of phenylpyruvic acid producers and optimization of culture conditions in bench scale bioreactors. Bioprocess and Biosystems Engineering. 37:23432352.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Han, D., N.O. San, P. Angun, O.C. Onarman Umu, A. Demirci, and T. Tekinay. 2014. Response surface optimization of the cultivation conditions and medium composition a novel probiotic strain Bacillus pumilus STF26. International Food Research Journal 21(4):1355-1361.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Richard, T.L. Making the Numbers Count: Toward a general framework for bioeconomy carbon accounting. University of Freiburg. June 8, 2015. Freiburg, Germany.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Zhu, Y., Bukowski, N., Doyle, L., Vergari, A., Pandey, J., Anderson, C., & T. L. Richard. 2014. Development of a lignin toolbox on one "negligible" auxiliary. Presented at the 248 National Meeting, American Chemical Society, August 10-14, 2014. San Francisco, CA. In: Abstracts of papers of the American Chemical Society (Vol. 248). American Chemical Soc., Washington, DC.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ercan. D., and A. Demirci. 2015. Enhanced human lysozyme produced by Kluyveromyces lactis K7 in biofilm reactor coupled with online recovery system. Biochemical Engineering Journal. 98:6874.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ercan, D. and A. Demirci. 2015. Current and future trends for biofilm reactors for fermentation processes. Critical Reviews in Biotechnology. 35 (1):1-14.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Coban, H.B., A. Demirci, and I. Turhan. 2015. Microparticle enhanced aspergillus ficuum phytase production in submerged fermentations. Bioprocess and Biosystems Engineering. 38(6):1075-1080.
  • Type: Theses/Dissertations Status: Published Year Published: 2014 Citation: Coban, H.B. 2014. Conversion of amino Acids to their specific alpha-keto acids by microbial fermentation. Ph.D. Dissertation, Agricultural and Biological Engineering, Pennsylvania State University, Univeristy Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Izmirlioglu, G. and A. Demirci. 2014. Optimization of fermentation parameters for production of ethanol from industrial potato waste by simultaneous saccharification and co-fermentation in biofilm reactors. Conference of Society for Industrial Microbiology and Biotechnology. St. Louis, MO. Abstract # 30524.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Ercan, D., A. Demirci, and V. M. Puri. 2015. Modeling of human lysozyme production by Kluyveromyces lactis K7 in biofilm reactor. Institute of Food Technologists Annual Meeting. New Orleans, LA. Abstract # 026.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Izmirlioglu, G. and A. Demirci. 2015. Ethanol fermentation from industrial potato waste in biofilm reactors. 37th Symposium on Biotechnology for Fuels and Chemicals. St. San Diego, CA. Abstract # 29592.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Izmirlioglu, G. and A. Demirci. 2015. Medium optimization of simultaneous starch saccharification and ethanol fermentation in biofilm reactors. 37th Symposium on Biotechnology for Fuels and Chemicals. St. San Diego, CA. Abstract # 29611.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Coban, H.B., A. Demirci, and I. Turhan. 2015. Microparticle-enhanced phytase production in fed-batch and continuous fermentations by Aspergillus ficuum. Bioprocess and Biosystems Engineering. 38:14311436.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Tian T. and H.M. Salis. 2015. A Predictive Biophysical Model of Translational Coupling to Coordinate and Control Protein Expression in Bacterial Operons. Nucleic Acid Research, 10.1093/nar/gkv635. 15 pages.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kushwaha M. and H.M. Salis. 2015. A Portable Expression Resource for Engineering Cross-species Genetic Circuits and Pathways. Nature Communications, v6. 11 pages.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ng C.Y., I. Farasat, C. Maranas, and H.M. Salis. 2015. Rational Design of a Synthetic Entner-Doudoroff pathway for Improved and Controllable NADPH Regeneration. Metabolic Engineering, v29. 11 pages.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Iman Farasat. 2015. Ph.D. Chemical Engineering. Systematic optimization of metabolic pathways and genetic circuits using next-generation biophysical models and design algorithms, Pennsylvania State University, Univeristy Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Salis H.M. 2015. The Pathway Map Calculator: an Automated Learning Algorithm to Determine a Pathway's Optimal Expression Levels. The Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting. Philadelphia, PA. July 3-7. (invited)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Farasat I. and H.M. Salis. 2015. Scalable System-wide Design of TF- and dCas9-Based Genetic Circuits. Synthetic Biology: Engineering, Evolution, and Design. Boston, MA. June 11-13.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Espah Borujeni A., D.M. Mishler, J. Wang, W. Huso, and H.M. Salis. 2015. Automated Design of Synthetic Riboswitches from Diverse RNA Aptamers. Bi-Annual Meeting of the Synthetic Biology Engineering Research Center (SynBERC). Berkeley, CA. April 2.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Espah Borujeni A., D.M. Mishler, J. Wang, W. Huso, and H.M. Salis. 2015. Automated Design of Synthetic Riboswitches from Diverse RNA Aptamers. International Conference on Biomolecular Engineering. Austin, TX. January 11.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ng C.Y., C. Maranas, and H.M. Salis. 2014. Design and Optimization of a Synthetic Pathway for Improved NADPH Regeneration. Bi-Annual Meeting of the Synthetic Biology Engineering Research Center (SynBERC). Cambridge, MA. September 14.


Progress 01/14/14 to 09/30/14

Outputs
Target Audience: The target audience for this research includes science discovery and biomass processing companies ranging from small start-ups. Agricultural stakeholders include state and national organizations, state and federal agencies. Communities are interested in these technologies from economic and community development perspectives. There is also strong public interest in understanding the environmental impacts of the biomass production and processing technologies as well as comparisons to conventional petroleum-derived products. These various stakeholders are being engaged through ongoing extension education programming that includes public presentations, short courses, websites (www.bioenergy.psu.edu, eXtension), scientific journal articles and extension publications. The project results will be benefit bioprocessing/fermentation industry in general as a result of production of value-added products and bioenergy from raw agricultural products or by-products. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Outcomes of the projects have been presented to the interested audiences at national and regional conferences. What do you plan to do during the next reporting period to accomplish the goals? All these projects mentioned above except bacterial cellulose production project will be continued and the results of these studies will continued to be published in peer-reviewed journals and/or presented at the professional meetings. Our first engineered version of the Entner-Doudoroff pathway improves NADPH regeneration rates, and we expect that continued optimization of its enzyme expression levels will result in further increases. We will also utilize dynamic regulation to activate this pathway once NADPH levels have reached critically low levels, enabling metabolic engineers to utilize this pathway as a "plug and play" module for improving the production rate of a desired biochemical.

Impacts
What was accomplished under these goals? Following projects have been studied for objecvtive 2 by Ali Demirci: Simultaneous saccharification and fermentation for production of ethanol from waste mash potato in biofilm reactors; Aspergillus niger and Saccharomyces cerevisiae has been evaluated in biofilm reactors.; xi) Production of human lysozyme by using biofilm reactors; Kluyveromyces lactis K7, fed-batch and continuous fermentations have been evaluated. Also, online recovery of lysozyme was studied to enhance the human lysozyme production further, xii) Production of alpha-keto acids by using microbial cell cultures; optimizations of fermentation conditions and media for Proteus vulgaris have been performed for alpha-keto acid production in bioreactors by using surface response methodology; xiii) production of phytase by using microbial cell cultures; optimization of fermentation conditions and media for Aspergiluus ficuum have been performed by using surface response methodology and fed-batch and continuous fermentations have been evaluated ix) production of microbial cellose production; semi-continuous bacterial cellulose production in a rotating disk biofilm bioreactor; x) production of lactic acid by Rhizopus oryzae; effect of microparticles have been studied to enhance lactic acid fermentation. Following projects have been studied for objecvtives 2 and 3 by Howard Salis: NADPH is a required cofactor for manufacturing biochemicals from biomass inside cells. The NADPH regeneration rate is often a rate-limiting step to increasing the production rate of biochemicals. We have engineered a synthetic version of the Entner-Doudoroff pathway in recombinant Escherichia coli cells that is capable of increasing the NADPH regeneration rate by 6-fold, compared to a wild-type strain. As an example application, we demonstrated that this synthetic pathway increases the production rate of a terpenoid product. This work has been submitted to the journal Metabolic Engineering. We have developed new approaches to systematically optimizing metabolic pathways using biophysical model predictions and flux control coefficients. This work has been published in Molecular Systems Biology. We have also developed predictive biophysical models of riboswitch biosensors and CRISPR/Cas9 regulators, which we utilize to rationally engineer biosensors and gene expression regulators to control the expression of metabolic pathways according to the presence of specific chemicals.

Publications

  • Type: Book Chapters Status: Published Year Published: 2014 Citation: Demirci, A., G. Izmirlioglu, and D. Ercan. 2014. Fermentation and enzyme technologies in food processing in food processing: In Food Processing: Principles and Applications, 2nd Edition, S. Clark, S. Jung, and B. Lamsal, Eds. Wiley-Blackwell, Hoboken, NJ.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Lin, S-P., S. C. Hsieh, K. I. Chen, A. Demirci, K. C. Cheng. 2014. Semi-continuous bacterial cellulose production in a rotating disk bioreactor and its materials properties analysis. Cellulose. 21:835844.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Coban, H. B., and A. Demirci. 2014. Screening of phytase producers and optimization of culture conditions for submerged fermentation. Bioprocess and Biosystems Engineering. 37:609616.
  • Type: Theses/Dissertations Status: Published Year Published: 2014 Citation: Ercan, D. 2014. Production of human by using biofilm reactors. Ph.D. Dissertation, Agricultural and Biological Engineering, Pennsylvania State University, Univeristy Park, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ercan, D., and A. Demirci. 2014. Comparison of Continuous Fermentations in Biofilm and Suspended-cell Bioreactors for Production of Human Lysozyme. Paper # 1895901. July 13-16, Montreal, Quebec, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Coban, H.B., and A. Demirci. 2014. Screening of Phytase Producer Microorganisms and Optimization of Growth Conditions in Submerged Fermentation. Paper # 1896452. July 13-16, Montreal, Quebec, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ercan, D., and A. Demirci. 2014. Simultaneous Online Recovery of Human Lysozyme Produced by Kluyveromyces lactis K7 in Biofilm Reactor. Paper # 1895913. July 13-16, Montreal, Quebec, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Coban, H.B., A. Demirci, P.H. Patterson, and R.J. Elias. 2014. Conversion of Phenylalanine to Phenylpyruvic Acid by Microbial Fermentation. Paper # 1895857. July 13-16, Montreal, Quebec, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Izmirlioglu, G., and A. Demirci. 2014. Strain Selection and Medium Optimization for Aspergillus niger and Saccharomyces cerevisea for Ethanol Fermentation. Paper # 1899729. July 13-16, Montreal, Quebec, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ercan, D., and A. Demirci. 2014. Simultaneous Online Recovery to Enhance Human Lysozyme Production by Kluyveromyces lactis K7 in Biofilm Reactor. Abstract # 27428. Conference of Society for Industrial Microbiology and Biotechnology. July 20-24, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ercan, D., and A. Demirci. 2014. Human Lysozyme Production by Kluyveromyces lactis K7 in Fed-Batch and Continuous Biofilm Reactors. Abstract # 27424. Conference of Society for Industrial Microbiology and Biotechnology. July 20-24, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Coban, H.B., and A. Demirci. 2014. Enhanced submerged phytase fermentation with Aspergillus ficuum by optimization of process conditions for batch and fed-batch fermentations. Abstract # 27351. Conference of Society for Industrial Microbiology and Biotechnology. July 20-24, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Coban, H.B., A. Demirci, P.H. Patterson, and R.J. Elias. 2014. Conversion of phenylalanine to phenylpyruvic acid by microbial Fermentation. Abstract # 27345. Conference of Society for Industrial Microbiology and Biotechnology. July 20-24, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Gulten Izmirlioglu and Ali Demirci. Ethanol Fermentation From Industrial Potato Waste in Biofilm. Reactors. Abstract # 27451. Conference of Society for Industrial Microbiology and Biotechnology. July 20-24, St. Louis, MO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ercan, D., and A. Demirci. 2014. Effects of different fermentation strategies to enhance human lysozyme production by Kluyveromyces lactis K7 in biofilm reactor. Conference of Food Engineering. April 7-9, Omaha, NE.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ercan, D., and A. Demirci. 2014. Simultaneous Online Recovery to enhance Human Lysozyme Production by Kluyveromyces lactis K7 in Biofilm Reactor. . Conference of Food Engineering. April 7-9, Omaha, NE.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Farasat, I., M. Kushwaha, J. Collens, M. Easterbrook, M. Guido, and H.M. Salis. 2014. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology, v10. 18 pages.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Salis, H.M. 2014. The Promises and Perils of Interpreting Ribosome Profiling Data. AIChE Annual Meeting. Atlanta, GA. November 14-17.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ng C.Y., C. Maranas, and H.M. Salis. 2014. Design and Optimization of a Synthetic Pathway for Improved NADPH Regeneration. AIChE Annual Meeting. Atlanta, GA. November 14-17.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Tian T., I. Farasat, and H.M. Salis. 2014. Autonomous control of metabolism with synthetic sensor-circuits. AIChE Annual Meeting. Atlanta, GA. November 14-17.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Salis, H.M. 2014. Predictive Biophysical Models for Engineering Synthetic Genetic Systems. Indo-US Program on Systems and Synthetic Biology. New Delhi, India. November 9-12.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ng C.Y., C. Maranas, and H.M. Salis. 2014. Design and Optimization of a Synthetic Pathway for Improved NADPH Regeneration. SynBERC Fall Retreat. September 27-29.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Farasat, I., A. Espah Borujeni, T. Tian, J. Collens, H.M. Salis. 2013. A DNA Compiler for Efficient Design and Optimization of Genetic Circuits and Metabolic Pathways. Synthetic Biology v6.0 International Conference. London, United Kingdom. July 9-11.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ng C.Y., C. Maranas, and H.M. Salis. 2014. Design and Optimization of a Synthetic Pathway for Improved NADPH Regeneration. SIMB Annual Meeting. St. Lious, MO. July 20-24.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Farasat I. and H.M. Salis. 2014. Genetic Circuit Modeling: Measured TF Binding Free Energies from Proportional Data. q-Bio Winter Meeting, Kona, HI. February 17-20.