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Parallel Synthesis And High Throughput Dissolution Testing Of Biodegradable Polyanhydride Copolymers, Brandon M. Vogel, Joao T. Cabral, Naomi Eidelman, Balaji Narasimhan, Surya K. Mallapragada 2018 National Institute of Standards and Technology

Parallel Synthesis And High Throughput Dissolution Testing Of Biodegradable Polyanhydride Copolymers, Brandon M. Vogel, Joao T. Cabral, Naomi Eidelman, Balaji Narasimhan, Surya K. Mallapragada

Brandon M Vogel

We have demonstrated that polycondensation reactions can be carried out in a combinatorial fashion and that the polymer library can be screened at high throughput using a rapid prototyping technique to fabricate multiwell substrates. A linearly varying compositional library of 100 different biodegradable polyanhydride random copolymers that are promising carriers for controlled drug delivery was designed, fabricated, and characterized by IR microscopy within a few hours. The polyanhydride copolymer library was based on 1,6-bis(p-carboxyphenoxy)hexane (CPH) and sebacic anhydride (SA) and was characterized with infrared microspectroscopy to determine the composition within each well. Since degradation and release rates ...


Combining Metabolic Engineering And Electrocatalysis: Application To The Production Of Polyamides From Sugar, Miguel Suastegui, John E. Matthiesen, Jack M. Carraher, Nacú Hernández, Natalia Rodriguez Quiroz, Adam Okerlund, Eric W. Cochran, Zengyi Shao, Jean-Philippe Tessonnier 2018 Iowa State University

Combining Metabolic Engineering And Electrocatalysis: Application To The Production Of Polyamides From Sugar, Miguel Suastegui, John E. Matthiesen, Jack M. Carraher, Nacú Hernández, Natalia Rodriguez Quiroz, Adam Okerlund, Eric W. Cochran, Zengyi Shao, Jean-Philippe Tessonnier

Eric W. Cochran

Biorefineries aim to convert biomass to a spectrum of products ranging from biofuels to specialty chemicals. To achieve economically sustainable conversion it is crucial to streamline the catalytic and downstream processing steps. Here we report a route that integrates bio- and chemical catalysis to convert glucose into bio-based unsaturated nylon 6,6. An engineered strain of Saccharomyces cerevisiae, with the highest reported muconic acid titer of 559.5 mg L-1 in yeast, was used as the initial biocatalyst to convert glucose into muconic acid. Without any separation, muconic acid was further electrocatalytically hydrogenated to 3-hexenedioic acid with 94% yield, despite ...


Responsive Pentablock Copolymers For Sirna Delivery, Surya K. Mallapragada, Metin Uz, Sacide Alsoy Altinkaya 2017 Iowa State University

Responsive Pentablock Copolymers For Sirna Delivery, Surya K. Mallapragada, Metin Uz, Sacide Alsoy Altinkaya

Surya K. Mallapragada

In this study, temperature and pH responsive cationic and amphiphilic pentablock copolymers, which consist of the temperature responsive triblock Pluronic F127 sandwiched between pH responsive PDEAEM (poly(2-diethylaminoethyl methacrylate)) end blocks, were used for the first time in the development of polyplex and gold nanoparticle (AuNP) based multicomponent siRNA delivery systems (MCSs). Copolymers in both systems protected siRNA from external effects, provided cell entry and endosomal escape. The thermoreversible micellization of the hydrophobic PPO block facilitated the cellular entry while the PDEAEM blocks enhanced the endosomal escape through protonated tertiary amine groups by pH buffering. The synergistic advantages of the ...


Producing Glucose 6-Phosphate From Cellulosic Biomass Structural Insights Into Levoglucosan Bioconversion, John-Paul Bacik, Justin R. Klesmith, Timothy A. Whitehead, Laura R. Jarboe, Clifford J. Unkefer, Brian L. Mark, Ryszard Michalczyk 2017 Los Alamos National Laboratory

Producing Glucose 6-Phosphate From Cellulosic Biomass Structural Insights Into Levoglucosan Bioconversion, John-Paul Bacik, Justin R. Klesmith, Timothy A. Whitehead, Laura R. Jarboe, Clifford J. Unkefer, Brian L. Mark, Ryszard Michalczyk

Laura R. Jarboe

The most abundant carbohydrate product of cellulosic biomass pyrolysis is the anhydrosugar levoglucosan (1,6-anhydro-β-D-glucopyranose), which can be converted to glucose 6-phosphate by levoglucosan kinase (LGK). In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O6 atom. Using x-ray crystallography, we show that LGK binds two magnesium ions in the active site that are additionally coordinated with the nucleotide and water molecules to result in ideal octahedral coordination. To further verify the metal binding sites, we co-crystallized LGK in the presence of manganese instead of ...


Escherichia Coli Attachment To Model Particulates: The Effects Of Bacterial Cell Characteristics And Particulate Properties, Xiao Liang, Chunyu Liao, Michelle L. Soupir, Laura R. Jarboe, Michael L. Thompson, Philip M. Dixon 2017 Iowa State University

Escherichia Coli Attachment To Model Particulates: The Effects Of Bacterial Cell Characteristics And Particulate Properties, Xiao Liang, Chunyu Liao, Michelle L. Soupir, Laura R. Jarboe, Michael L. Thompson, Philip M. Dixon

Laura R. Jarboe

E. coli bacteria move in streams freely in a planktonic state or attached to suspended particulates. Attachment is a dynamic process, and the fraction of attached microorganisms is thought to be affected by both bacterial characteristics and particulate properties. In this study, we investigated how the properties of cell surfaces and stream particulates influence attachment. Attachment assays were conducted for 77 E. coli strains and three model particulates (ferrihydrite, Ca-montmorillonite, or corn stover) under environmentally relevant conditions. Surface area, particle size distribution, and total carbon content were determined for each type of particulate. Among the three particulates, attachment fractions to ...


Peptoid-Modified Bicelles As Surrogate Cell Membranes For Membrane Protein Sensors And Analytics, Helya Najafi 2017 University of Arkansas, Fayetteville

Peptoid-Modified Bicelles As Surrogate Cell Membranes For Membrane Protein Sensors And Analytics, Helya Najafi

Theses and Dissertations

Membrane-affiliated interactions are significant in understanding cell function, detecting biomarkers to diagnose disease, and in testing the efficiency of new therapeutic targets. Model membrane systems have been developed to study membrane proteins, allowing for stable protein structure and maintaining native activity. Bicelles, disc-shaped lipid bilayers created by combining long- and short-chain phospholipids, are the model membrane system of focus in this study. Bicelles are accessible from both sides and have a wide size range, which make them attractive for studying membrane proteins without affecting function. In this work, bicelles were functionalized with two peptoids to alter the edge and face ...


Multiscale Modeling For Host-Guest Chemistry Of Dendrimers In Solution, Seung Ha Kim, Monica H. Lamm 2017 Iowa State University

Multiscale Modeling For Host-Guest Chemistry Of Dendrimers In Solution, Seung Ha Kim, Monica H. Lamm

Monica H. Lamm

Dendrimers have been widely used as nanostructured carriers for guest species in a variety of applications in medicine, catalysis, and environmental remediation. Theory and simulation methods are an important complement to experimental approaches that are designed to develop a fundamental understanding about how dendrimers interact with guest molecules. This review focuses on computational studies aimed at providing a better understanding of the relevant physicochemical parameters at play in the binding and release mechanisms between polyamidoamine (PAMAM) dendrimers and guest species. We highlight recent contributions that model supramolecular dendrimer-guest complexes over the temporal and spatial scales spanned by simulation methods ranging ...


Reintroducing Explicit Solvent To A Solvent-Free Coarse-Grained Model, Seung Ha Kim, Monica H. Lamm 2017 Iowa State University

Reintroducing Explicit Solvent To A Solvent-Free Coarse-Grained Model, Seung Ha Kim, Monica H. Lamm

Monica H. Lamm

A unique coarse-grained modeling scheme that combines a systematic, solvent-free multiscale coarse-graining algorithm for a complex macromolecule with an existing coarse-grained solvent model is proposed. We show that this procedure efficiently and reliably describes the interactions for complex macromolecules, using the specific example of dendrimers binding phenanthrenes in water. The experimentally measured binding capacity is predicted by the unique coarse-grained modeling approach; the conditions for this simulation are beyond what could be reasonably simulated with an all-atom molecular dynamics simulation.


Smooth Muscle Stiffness Sensitivity Is Driven By Soluble And Insoluble Ecm Chemistry, William G. Herrick, Shruti Rattan, Thuy V. Nguyen, Michael S. Grunwald, Christopher W. Barney, Alfred J. Crosby, Shelly Peyton 2017 University of Massachusetts - Amherst

Smooth Muscle Stiffness Sensitivity Is Driven By Soluble And Insoluble Ecm Chemistry, William G. Herrick, Shruti Rattan, Thuy V. Nguyen, Michael S. Grunwald, Christopher W. Barney, Alfred J. Crosby, Shelly Peyton

Shelly Peyton

Smooth muscle cell (SMC) invasion into plaques and subsequent proliferation is a major factor in the progression of atherosclerosis. During disease progression, SMCs experience major changes in their microenvironment, such as what integrin-binding sites are exposed, the portfolio of soluble factors available, and the elasticity and modulus of the surrounding vessel wall. We have developed a hydrogel biomaterial platform to examine the combined effect of these changes on SMC phenotype. We were particularly interested in how the chemical microenvironment affected the ability of SMCs to sense and respond to modulus. To our surprise, we observed that integrin binding and soluble ...


Escherichia Coli Attachment To Model Particulates: The Effects Of Bacterial Cell Characteristics And Particulate Properties, Xiao Liang, Chunyu Liao, Michelle L. Soupir, Laura R. Jarboe, Michael L. Thompson, Philip M. Dixon 2017 Iowa State University

Escherichia Coli Attachment To Model Particulates: The Effects Of Bacterial Cell Characteristics And Particulate Properties, Xiao Liang, Chunyu Liao, Michelle L. Soupir, Laura R. Jarboe, Michael L. Thompson, Philip M. Dixon

Chemical and Biological Engineering Publications

E. coli bacteria move in streams freely in a planktonic state or attached to suspended particulates. Attachment is a dynamic process, and the fraction of attached microorganisms is thought to be affected by both bacterial characteristics and particulate properties. In this study, we investigated how the properties of cell surfaces and stream particulates influence attachment. Attachment assays were conducted for 77 E. coli strains and three model particulates (ferrihydrite, Ca-montmorillonite, or corn stover) under environmentally relevant conditions. Surface area, particle size distribution, and total carbon content were determined for each type of particulate. Among the three particulates, attachment fractions to ...


Advancement Of Oxygen Biosensor In Escherichia Coli, Caitlyn Meiser 2017 Rose-Hulman Institute of Technology

Advancement Of Oxygen Biosensor In Escherichia Coli, Caitlyn Meiser

Rose-Hulman Undergraduate Research Publications

Microbial biosensors can be used to provide information about the cells’ environment in large-scale fermentations. In this project an oxygen sensitive biosensor is being developed in Escherichia coli to determine what kind of conditions cells are growing in: aerobic or anaerobic. This project specifically studies expression from the fumarate and nitrate reductase (FNR) promoter (PFNR) under aerobic and anaerobic conditions. In fluorescence experiments, the expression levels of green fluorescent protein (GFP) were used to quantify the effectiveness of the PFNR in the DH5α, MG1655 and BL21 strains of E. coli. The negative control of the experiments, which are ...


Ab Initio Study Of Molecular Interactions In Cellulose Iα, Ajitha Devarajan, Sergiy Markutsya, Monica H. Lamm, Xiaolin Cheng, Jeremy C. Smith, John Ysrael Baluyut, Yana Kholod, Mark S. Gordon, Theresa Lynn Windus 2017 Iowa State University

Ab Initio Study Of Molecular Interactions In Cellulose Iα, Ajitha Devarajan, Sergiy Markutsya, Monica H. Lamm, Xiaolin Cheng, Jeremy C. Smith, John Ysrael Baluyut, Yana Kholod, Mark S. Gordon, Theresa Lynn Windus

Monica H. Lamm

Biomass recalcitrance, the resistance of cellulosic biomass to degradation, is due in part to the stability of the hydrogen bond network and stacking forces between the polysaccharide chains in cellulose microfibers. The fragment molecular orbital (FMO) method at the correlated Møller–Plesset second order perturbation level of theory was used on a model of the crystalline cellulose Iα core with a total of 144 glucose units. These computations show that the intersheet chain interactions are stronger than the intrasheet chain interactions for the crystalline structure, while they are more similar to each other for a relaxed structure. An FMO chain ...


An Adaptable Pentaloop Defines A Robust Neomycin-B Rna Aptamer With Conditional Ligand-Bound Structures, Muslum Ilgu, D. Bruce Fulton, Ragothaman M. Yennamalli, Monica H. Lamm, Taner Z. Sen, Marit Nilsen-Hamilton 2017 Iowa State University

An Adaptable Pentaloop Defines A Robust Neomycin-B Rna Aptamer With Conditional Ligand-Bound Structures, Muslum Ilgu, D. Bruce Fulton, Ragothaman M. Yennamalli, Monica H. Lamm, Taner Z. Sen, Marit Nilsen-Hamilton

Monica H. Lamm

Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP ...


Computational And Experimental Analyses Converge To Reveal A Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity, Tianjiao Wang, Julie A. Hoy, Monica H. Lamm, Marit Nilsen-Hamilton 2017 Iowa State University

Computational And Experimental Analyses Converge To Reveal A Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity, Tianjiao Wang, Julie A. Hoy, Monica H. Lamm, Marit Nilsen-Hamilton

Monica H. Lamm

As short nucleic acids, aptamers in solution are believed to be structurally flexible. Consistent with this view, most aptamers examined for this property have been shown to bind their target molecules by mechanisms that can be described as “induced fit”. But, it is not known to what extent this structural flexibility affects the integrity of the target−aptamer interaction. Using the malachite green aptamer (MGA) as a model system, we show that the MGA can protect its bound target, malachite green (MG), from oxidation over several days. Protection is reversed by an oligonucleotide complementary to the MGA binding pocket. Computational ...


Bacterial Cellulose Nanocrystals: Production And Application, Isabela Reiniati 2017 The University of Western Ontario

Bacterial Cellulose Nanocrystals: Production And Application, Isabela Reiniati

Electronic Thesis and Dissertation Repository

The aims of this study were to investigate the effect of culture conditions on the production of bacterial cellulose (BC) by Komagataeibacter xylinus (K. xylinus), to assess the feasibility of tailoring the surface properties of bacterial cellulose nanocrystals (BCNs) through the culture conditions, and to use the BCNs in an aqueous system for drug adsorption application. BC fibers production improved with increased agitation rates in a stirred tank bioreactor resulting in yields of 0.54 and 1.13 g of BC per litre at agitation rates of 500 rpm and 700 rpm, respectively. Separation and purification of bacterial cellulose were ...


Identification Of Developmental Stage And Anatomical Fraction Contributions To Cell Wall Recalcitrance In Switchgrass, Jacob D. Crowe, Nicholas Feringa, Sivakumar Pattathil, Brian Merritt, Cliff Foster, Dayna Dines, Rebecca G. Ong, David B. Hodge 2017 Michigan State University

Identification Of Developmental Stage And Anatomical Fraction Contributions To Cell Wall Recalcitrance In Switchgrass, Jacob D. Crowe, Nicholas Feringa, Sivakumar Pattathil, Brian Merritt, Cliff Foster, Dayna Dines, Rebecca G. Ong, David B. Hodge

Rebecca Ong

Background

Heterogeneity within herbaceous biomass can present important challenges for processing feedstocks to cellulosic biofuels. Alterations to cell wall composition and organization during plant growth represent major contributions to heterogeneity within a single species or cultivar. To address this challenge, the focus of this study was to characterize the relationship between composition and properties of the plant cell wall and cell wall response to deconstruction by NaOH pretreatment and enzymatic hydrolysis for anatomical fractions (stem internodes, leaf sheaths, and leaf blades) within switchgrass at various tissue maturities as assessed by differing internode.

Results

Substantial differences in both cell wall composition ...


Fabrication And Characterization Of Hybrid Nanocomposites By Matrix Assisted Pulsed Laser Evaporation, Songlin Yang 2017 The University of Western Ontario

Fabrication And Characterization Of Hybrid Nanocomposites By Matrix Assisted Pulsed Laser Evaporation, Songlin Yang

Electronic Thesis and Dissertation Repository

Different methods have been applied to deposit hybrid nanocomposites which can be applied in various fields due to their light weight and multifunctional properties. Here, matrix assisted pulsed laser evaporation (MAPLE) equipment with 532 nm Nd:YAG laser is applied to fabricate three types of hybrid nanocomposites on different substrates.

Chemical synthesized FeCo nanoparticles were deposited on graphene sheets by MAPLE technique (laser fluence: 300 mJ/cm2). The effects of deposition time (t) on particle amount, shape and size have been investigated. Yttrium barium copper oxide (YBCO) materials are one type of high-temperature superconductive materials and could be applied ...


Nanostructured Biosensor For Tear Glucose Detection Based On Bioluminescence Resonance Energy Transfer (Bret) Mechanism., Denghuang Zhan 2017 The University of Western Ontario

Nanostructured Biosensor For Tear Glucose Detection Based On Bioluminescence Resonance Energy Transfer (Bret) Mechanism., Denghuang Zhan

Electronic Thesis and Dissertation Repository

Bioluminescence Resonance Energy Transfer (BRET), a sensitive, non-destructive and self-illuminated method, has been now commonly used to test protein interactions. Here, we describe a BRET sensor for non-invasively detecting glucose molecules. The sensor is made by the bioconjugation of quantum dots and recombinant protein. The recombinant protein contains the bacterial glucose binding protein (GBP) and a bioluminescent protein, Renilla luciferase (Rluc), used as the donor with the emission peak at 470 nm, which is able to excite the acceptor of BRET sensor made of cadmium tellurium quantum dots ( CdTe QDs) with the emission peak at 570 nm. The distance between ...


Peptoid-Based Microsphere Coatings For Use As Tunable Biocompatible Interfaces, German Raul Perez Bakovic 2017 University of Arkansas, Fayetteville

Peptoid-Based Microsphere Coatings For Use As Tunable Biocompatible Interfaces, German Raul Perez Bakovic

Theses and Dissertations

The pursuit of sensitive, non-invasive, and cost efficient diagnostic tools for early stage disease detection have led to the development of sophisticated biosensor technologies for proteomic studies. As these markers increase in complexity, the role of support substrates grows increasingly important. Limitations in existing support substrates include the potential for increased sensitivity, binding specificity, and bio-stability. Ideal support substrates need to provide biocompatible and bioresistant surfaces, that offer high surface areas for binding, and enables the incorporation of diverse chemistries. The use of peptoids as the basis for the deposition of uniform microsphere coatings offers a mean to the attainment ...


Effects Of Filtration Conditions On Clearance Of Bacteriophage, Rigen Te 2017 University of Arkansas, Fayetteville

Effects Of Filtration Conditions On Clearance Of Bacteriophage, Rigen Te

Theses and Dissertations

Virus Clearance is one of the major challenges in biopharmaceutical industry, especially in the manufacturing of drugs. U.S. Food and Drug Administration (FDA) recommends using several model bacteriophages as surrogates of pathogenic mammalian virus for process validation. In this work, two bacteriophages were tested against 30 kDa, 100 kDa, 300 kDa polyethersulfone (PES) membranes to investigate the effects of pore size on virus clearance. Virus particles were spiked into the protein feed solutions containing bovine serum albumin (BSA) or lysozyme at different concentrations. Besides protein concentration, the effects of feed pH on the filtration performance and virus rejection were ...


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