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Biochemical and Biomolecular Engineering Commons

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Shaping A Functional And Sustainable Biofuels Industry Through Bridging Industrial Needs With Farmer Production Capabilities, Richard M. Cruse, James Richardson, Carl Herndl, Mack C. Shelley II, Elena Yu Polush, Brent H. Shanks, Carl Roberts 2010 Iowa State University

Shaping A Functional And Sustainable Biofuels Industry Through Bridging Industrial Needs With Farmer Production Capabilities, Richard M. Cruse, James Richardson, Carl Herndl, Mack C. Shelley Ii, Elena Yu Polush, Brent H. Shanks, Carl Roberts

Leopold Center Completed Grant Reports

In order for the biofuels industry to survive and succeed, it will need the cooperation of Iowa farmers to supply biomass. Farmers have concerns about production that need to be addressed in order to create a sustainable industry.


Synthetic Peptide Design For Functionalized Hydrogels: Development Of Cellularly Responsive Drug Delivery Platforms And Cyclic, Multivalent Peptide Derivatives Using Radical-Mediated Thiol-Ene/Thiol-Yne Chemistries, Alex Arthur Aimetti 2010 University of Colorado, Boulder

Synthetic Peptide Design For Functionalized Hydrogels: Development Of Cellularly Responsive Drug Delivery Platforms And Cyclic, Multivalent Peptide Derivatives Using Radical-Mediated Thiol-Ene/Thiol-Yne Chemistries, Alex Arthur Aimetti

Chemical & Biological Engineering Graduate Theses & Dissertations

Poly(ethylene glycol) (PEG)-based hydrogels represent a class of biomaterials with a growing interest for their application in numerous fields, such as drug delivery and regenerative medicine. PEG is commonly used in these applications due to its hydrophilic and bioinert properties. Additionally, peptides have been successfully incorporated within PEG hydrogels to serve as biological functionalities within a synthetic polymer platform. Peptide-functionalized PEG hydrogels have been shown to act as extracellular matrix (ECM)-mimics capable of enhancing cell survival, function, and differentiation. Alternatively, peptides can be designed to degrade in recognition of highly specific, cell-secreted proteases. This phenomenon has been ...


Self-Assembly Of Cdte Tetrapods Into Network Monolayers At The Air/Water Interface, Matthew Dave Goodman, Lei Zhao, Karen A. DeRocher, Jun Wang, Surya K. Mallapragada, Zhiqun Lin 2010 Iowa State University

Self-Assembly Of Cdte Tetrapods Into Network Monolayers At The Air/Water Interface, Matthew Dave Goodman, Lei Zhao, Karen A. Derocher, Jun Wang, Surya K. Mallapragada, Zhiqun Lin

Chemical and Biological Engineering Publications

Cadmium telluride (CdTe) tetrapods are synthesized with varying aspect ratios through multiple injections of the Te precursor, which provides an excellent means of controlling and tailoring the optical properties of the tetrapods. The self-assembly of CdTe tetrapods at the air/water interface is explored using the Langmuir-Blodgett (LB) technique due to potential use in solar cells arising from the intriguing tetrapod shape that improves charge transport and the optimum band gap energy of CdTe that enhances light absorption. Interestingly, the Langmuir isotherm shows two pressure plateau regions: one at ∼10 mN/m with the other at the high surface pressure ...


Reversible Addition - Fragmentation Chain Transfer In Microemulsions: Effect Of Chain Transfer Agent Aqueous Solubility, Jennifer M. O'Donnell, Eric W. Kaler 2010 University of Delaware

Reversible Addition - Fragmentation Chain Transfer In Microemulsions: Effect Of Chain Transfer Agent Aqueous Solubility, Jennifer M. O'Donnell, Eric W. Kaler

Jennifer M. Heinen

Microemulsion polymerizations are attractive for investigating compartmentalization effects in heterogeneous reversible addition - fragmentation chain transfer (RAFT) polymerizations because the propagating radicals are segregated into surfactant stabilized polymer particles, which drastically reduces the effects of biradical termination, Also, microemulsion polymerizations do not involve the large monomer droplets that are present in emulsion and miniemulsion polymerizations. RAFT microemulsion polymerizations of butyl aery late with a high water solubility chain transfer agent, methyl-2-(O-ethylxanthyl)propionate (MOEP), and a low water solubility chain transfer agent, methyl-2-(O-dodecylxanthyl)propionate (MODP), were investigated to determine the effect of chain transfer agent compartmentalization on the control of ...


Utilizing Protein-Lean Coproducts From Corn Containing Recombinant Pharmaceutical Proteins For Ethanol Production, Ilankovan Paraman, Lorena Beatriz Moeller, M. Paul Scott, Kan Wang, Charles E. Glatz, Lawrence A. Johnson 2010 Iowa State University

Utilizing Protein-Lean Coproducts From Corn Containing Recombinant Pharmaceutical Proteins For Ethanol Production, Ilankovan Paraman, Lorena Beatriz Moeller, M. Paul Scott, Kan Wang, Charles E. Glatz, Lawrence A. Johnson

Chemical and Biological Engineering Publications

Protein-lean fractions of corn (maize) containing recombinant (r) pharmaceutical proteins were evaluated as a potential feedstock to produce fuel ethanol. The levels of residual r-proteins in the coproduct, distillers dry grains with solubles (DDGS), were determined. Transgenic corn lines containing recombinant green fluorescence protein (r-GFP) and a recombinant subunit vaccine of Escherichia coli enterotoxin (r-LTB), primarily expressed in endosperm, and another two corn lines containing recombinant human collagen (r-CIα1) andr-GFP, primarily expressed in germ, were used as model systems. The kernels were either ground and used for fermentation or dry fractionated to recover germ-rich ...


Data Fusion For The Problem Of Protein Sidechain Assignment, Yang Lei 2010 University of Massachusetts Amherst

Data Fusion For The Problem Of Protein Sidechain Assignment, Yang Lei

Masters Theses 1911 - February 2014

In this thesis, we study the problem of protein side chain assignment (SCA) given

multiple sources of experimental and modeling data. In particular, the mechanism

of X-ray crystallography (X-ray) is re-examined using Fourier analysis, and a novel

probabilistic model of X-ray is proposed for SCA's decision making. The relationship

between the measurements in X-ray and the desired structure is reformulated in terms

of Discrete Fourier Transform (DFT). The decision making is performed by developing

a new resolution-dependent electron density map (EDM) model and applying

Maximum Likelihood (ML) estimation, which simply reduces to the Least Squares

(LS) solution. Calculation of ...


Effects Of Preparative Parameters On The Structure And Performance Of Ca-La Metal Oxide Catalysts For Oil Transesterification, Shuli Yan, Manhoe Kim, Siddharth Mohan, Steven O. Salley, K.Y. Simon Ng 2010 Wayne State University

Effects Of Preparative Parameters On The Structure And Performance Of Ca-La Metal Oxide Catalysts For Oil Transesterification, Shuli Yan, Manhoe Kim, Siddharth Mohan, Steven O. Salley, K.Y. Simon Ng

National Biofuels Energy Laboratory

The effects of preparative parameters on the surface basicity, composition, and transesterification activities of several Ca-La metal oxide catalysts were investigated. Four different preparation methods: ammonia-ethanol-carbon dioxide precipitation, physical mixing, impregnation, and co-precipitation, were studied. It was found that the ammonia-ethanol-carbon dioxide precipitation method resulted in the highest BET specific surface area, base strength and base site concentration. Moreover, catalyst surface composition and basicity are a function of calcination temperature, precipitants, pH, and molar ratio of Ca to La in precursor solution, and storage conditions. XRD, XPS, basicity and BET tests revealed that catalyst structure and dispersion of Ca species ...


Sensing Polymer/Dna Polyplex Dissociation Using Quantum Dot Fluorophores, Bingqi Zhang, Yanjie Zhang, Surya K. Mallapragada, Aaron R. Clapp 2010 Iowa State University

Sensing Polymer/Dna Polyplex Dissociation Using Quantum Dot Fluorophores, Bingqi Zhang, Yanjie Zhang, Surya K. Mallapragada, Aaron R. Clapp

Chemical and Biological Engineering Publications

We characterized the dissociation of polymer/DNA polyplexes designed for gene delivery using water-soluble quantum dots (QDs). A pH-responsive pentablock copolymer was designed to form stable complexes with plasmid DNA via tertiary amine segments. Dissociation of the polyplex was induced using chloroquine where the efficiency of this process was sensed through changes in QD fluorescence. We found that increasing concentrations of pentablock copolymer and DNA led to quenching of QD fluorescence, while chloroquine alone had no measurable effect. The mechanism of quenching was elucidated by modeling the process as the combination of static and dynamic quenching from the pentablock copolymer ...


Tertiary Structure And Characterization Of A Glycoside Hydrolase Family 44 Endoglucanase From Clostridium Acetobutylicum, Christopher D. Warner, Julie A. Hoy, Taran C. Shilling, Michael J. Linnen, Nathaniel D. Ginder, Clark Ford, Richard B. Honzatko, Peter J. Reilly 2010 Iowa State University

Tertiary Structure And Characterization Of A Glycoside Hydrolase Family 44 Endoglucanase From Clostridium Acetobutylicum, Christopher D. Warner, Julie A. Hoy, Taran C. Shilling, Michael J. Linnen, Nathaniel D. Ginder, Clark Ford, Richard B. Honzatko, Peter J. Reilly

Chemical and Biological Engineering Publications

A gene encoding a glycoside hydrolase family 44 (GH44) protein from Clostridium acetobutylicum ATCC 824 was synthesized and transformed into Escherichia coli.The previously uncharacterized protein was expressed with a C-terminal His tag and purified by nickel-nitrilotriacetic acid affinity chromatography. Crystallization and X-ray diffraction to a 2.2-Å resolution revealed a triose phosphate isomerase (TIM) barrel-like structure with additional Greek key and β-sandwich folds, similar to other GH44 crystal structures. The enzyme hydrolyzes cellotetraose and larger cellooligosaccharides, yielding an unbalanced product distribution, including some glucose. It attacks carboxymethylcellulose and xylan at approximately the same rates. Its activity on carboxymethylcellulose is ...


Numerical Simulation Of Turbulent Gas-Particle Flow In A Riser Using A Quadrature-Based Moment Method, Alberto Passalacqua, Rodney O. Fox 2010 Iowa State University

Numerical Simulation Of Turbulent Gas-Particle Flow In A Riser Using A Quadrature-Based Moment Method, Alberto Passalacqua, Rodney O. Fox

Chemical and Biological Engineering Conference Presentations and Proceedings

Gas-particle flows are used in many industrial applications in the energy, oil and gas fields, such as coal gasification, production of light hydrocarbons by fluid catalytic cracking, catalytic combustion and different treatments aiming to reduce or eliminate pollutants. The particle phase of a gas-particle flow is described by analogy to a granular gas, by finding an approximate solution of the kinetic equation in the velocity-based number density function. In the recent past, many studies have been published on the mathematical modeling of gas-particle flows using hydrodynamic models (e.g. Enwald et al. 1996), where Navier-Stokes-type equations are solved to describe ...


Metabolic Analysis Of Wild-Type Escherichia Coli And A Pyruvate Dehydrogenase Complex (Pdhc)-Deficient Derivative Reveals The Role Of Pdhc In The Fermentative Metabolism Of Glucose, Abhishek Murarka, James M. Clomburg, Sean Moran, Jacqueline V. Shanks, Ramon Gonzalez 2010 Rice University

Metabolic Analysis Of Wild-Type Escherichia Coli And A Pyruvate Dehydrogenase Complex (Pdhc)-Deficient Derivative Reveals The Role Of Pdhc In The Fermentative Metabolism Of Glucose, Abhishek Murarka, James M. Clomburg, Sean Moran, Jacqueline V. Shanks, Ramon Gonzalez

Chemical and Biological Engineering Publications

Pyruvate is located at a metabolic junction of assimilatory and dissimilatory pathways and represents a switch point between respiratory and fermentative metabolism. In Escherichia coli, the pyruvate dehydrogenase complex (PDHC) and pyruvate formate-lyase are considered the primary routes of pyruvate conversion to acetyl-CoA for aerobic respiration and anaerobic fermentation, respectively. During glucose fermentation, the in vivo activity of PDHC has been reported as either very low or undetectable, and the role of this enzyme remains unknown. In this study, a comprehensive characterization of wild-type E. coli MG1655 and a PDHC-deficient derivative (Pdh) led to the identification of the role of ...


Metabolic Engineering For Production Of Biorenewable Fuels And Chemicals: Contributions Of Synthetic Biology, Laura R. Jarboe, Xueli Zhang, Xuan Wang, Jonathan C. Moore, K. T. Shanmugam, Lonnie O. Ingram 2010 Iowa State University

Metabolic Engineering For Production Of Biorenewable Fuels And Chemicals: Contributions Of Synthetic Biology, Laura R. Jarboe, Xueli Zhang, Xuan Wang, Jonathan C. Moore, K. T. Shanmugam, Lonnie O. Ingram

Chemical and Biological Engineering Publications

Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemicalbased production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use ...


Characterization Of Biochars Produced From Cornstovers For Soil Amendment, James W. Leeq, MIchelle Kidder, Barbara R. Evans, Sokwon Paik, A.C. Buchanan III, Charles T. Garten, Robert C. Brown 2010 Oak Ridge National Laboratory

Characterization Of Biochars Produced From Cornstovers For Soil Amendment, James W. Leeq, Michelle Kidder, Barbara R. Evans, Sokwon Paik, A.C. Buchanan Iii, Charles T. Garten, Robert C. Brown

Mechanical Engineering Publications

Through cation exchange capacity assay, nitrogen adsorption−desorption surface area measurements, scanning electron microscopic imaging, infrared spectra and elemental analyses, we characterized biochar materials produced from cornstover under two different pyrolysis conditions, fast pyrolysis at 450 °C and gasification at 700 °C. Our experimental results showed that the cation exchange capacity (CEC) of the fast-pyrolytic char is about twice as high as that of the gasification char as well as that of a standard soil sample. The CEC values correlate well with the increase in the ratios of the oxygen atoms to the carbon atoms (O:C ratios) in the ...


Elucidating Mechanisms Of Solvent Toxicity In Ethanologenic Escherichia Coli, Cong Trinh, Sarah Huffer, Melinda Clark, Harvey Blanch, Douglas Clark 2009 University of Tennessee - Knoxville

Elucidating Mechanisms Of Solvent Toxicity In Ethanologenic Escherichia Coli, Cong Trinh, Sarah Huffer, Melinda Clark, Harvey Blanch, Douglas Clark

Cong T Trinh

No abstract provided.


On Algebraic Properties Of Extreme Pathways In Metabolic Networks, Dimitrije Jevremovic, Cong Trinh, Daniel Boley 2009 University of Tennessee - Knoxville

On Algebraic Properties Of Extreme Pathways In Metabolic Networks, Dimitrije Jevremovic, Cong Trinh, Daniel Boley

Cong T Trinh

No abstract provided.


Cloning And Heterologous Expression Of The Spectinabilin Biosynthetic Gene Cluster From Streptomyces Spectabilis, Zengyi Shao 2009 Iowa State University

Cloning And Heterologous Expression Of The Spectinabilin Biosynthetic Gene Cluster From Streptomyces Spectabilis, Zengyi Shao

Zengyi Shao

Spectinabilin is a rare nitrophenyl-substituted polyketide metabolite. Here we report the cloning and heterologous expression of the spectinabilin gene cluster from Streptomyces spectabilis. Unexpectedly, this gene cluster is evolutionarily closer to the aureothin gene cluster than to the spectinabilin gene cluster from Streptomyces orinoci. Moreover, the two nearly identical spectinabilin gene clusters use a distinctly different regulation mechanism.


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