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Common Secondary And Tertiary Structural Features Of Aptamer–Ligand Interaction Shared By Rna Aptamers With Different Primary Sequences, Muslum Ilgu, Shuting Yan, Ryan M. Khounlo, Monica H. Lamm, Marit Nilsen-Hamilton 2019 Iowa State University, Aptalogic Inc., and Middle East Technical University

Common Secondary And Tertiary Structural Features Of Aptamer–Ligand Interaction Shared By Rna Aptamers With Different Primary Sequences, Muslum Ilgu, Shuting Yan, Ryan M. Khounlo, Monica H. Lamm, Marit Nilsen-Hamilton

Chemical and Biological Engineering Publications

Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target molecule. Here, we have combined computational and experimental approaches to understand if aptamers with different sequences but the same molecular target share structural and dynamical features. NEO1A, with a known NMR-solved structure, displays a flexible loop that interacts differently with individual aminoglycosides, its ligand affinities and specificities are responsive to ionic strength, and it possesses an adenosine in the loop that is critical for high-affinity ligand binding. NEO2A was obtained from the same selection and, although they are only 43% identical in overall sequence, NEO1A and ...


Cdse Quantum Dots Synthesis Laboratory Course For High School Students, Danlin Zuo, Gyuseok Kim, David Jones 2019 Singh Center for Nanotechnology

Cdse Quantum Dots Synthesis Laboratory Course For High School Students, Danlin Zuo, Gyuseok Kim, David Jones

Protocols and Reports

Cadmium selenide quantum dot is a fascinating subject for leading high school students to the quantum world. An 8-hour laboratory course for up to 12 high school students is proposed. The 8-hour course consist of two 4-hours sections. This laboratory course includes the quantum dot syntheses, absorption and emission characterization, and data analysis. The proposes process runs at relatively lower temperature which means safe and easy, and shows apparent experimental results.


Development Of A Comsol Microdialysis Model, Towards Creation Of Microdialysis On A Chip With Improved Geometries And Recovery, Patrick Pysz 2019 University of Arkansas, Fayetteville

Development Of A Comsol Microdialysis Model, Towards Creation Of Microdialysis On A Chip With Improved Geometries And Recovery, Patrick Pysz

Theses and Dissertations

Microdialysis (µD) sampling is a diffusion-limited sampling method that has been widely used in different biomedical fields for greater than 35 years. Device calibration for in vivo studies is difficult for current non-steady state analytes of interest correlated with both inflammatory response and microbial signaling molecules (QS); which exist in low ng/mL to pg/mL with molecular weights over a wide range of 170 Da to 70 kDa. The primary performance metric, relative recovery (RR), relating the collected sample to the extracellular space concentration varies from 10% to 60% per analyte even under controlled bench-top conditions. Innovations in microdialysis ...


Bioluminescence Resonance Energy Transfer (Bret) - Based Nanostructured Biosensor For Detection Of Glucose, Eugene Hwang 2019 The University of Western Ontario

Bioluminescence Resonance Energy Transfer (Bret) - Based Nanostructured Biosensor For Detection Of Glucose, Eugene Hwang

Electronic Thesis and Dissertation Repository

Bioluminescence resonance energy transfer (BRET) is a distance dependent, non-radiative energy transfer, which uses a bioluminescent protein to excite an acceptor through resonance energy transfer. In this thesis, BRET technology is incorporated into a sensor comprised of a recombinant protein and quantum dots. The recombinant protein, which includes the bioluminescent protein, Renilla luciferase (Rluc), is used as the donor molecule and cadmium tellurium quantum dots as the acceptor molecules. Separating the donor-acceptor pair is a recombinant protein, glucose binding protein, which changes conformation upon binding glucose and brings the pair closer together, thus allowing BRET to occur. Optimization of the ...


Effect Of Annealing On The Contact Resistance Of Aluminum On A P-Type Substrate, Shrey Shah, George Patrick Watson 2019 Singh Center for Nanotechnology

Effect Of Annealing On The Contact Resistance Of Aluminum On A P-Type Substrate, Shrey Shah, George Patrick Watson

Protocols and Reports

Aluminum contacts are widely used to form both ohmic and rectifying contacts. The process to form these contacts involves annealing, thus it is important to study the effect of annealing on the electrical properties of the contacts. Here, we present a way to measure the contact resistance of aluminum contacts formed on a p-type silicon substrate. It was found the contact resistivity decreased by an average of 18%. It was thus found that annealing at 400°C in a forming gas environment improves the electrical properties of aluminum contacts.


In-Situ Extraction And Impregnation Of Black Walnut Husk Into Polyethylene Film Using Supercritical Carbon Dioxide With An Ethanol Modifier, Johnathon Wenzel, Veronica Moorman, Lihua Wang, Cheryl S. Samaniego, Michelle Ammerman, Isaiah Spencer-Williams, Mitchell Hall 2019 Kettering University

In-Situ Extraction And Impregnation Of Black Walnut Husk Into Polyethylene Film Using Supercritical Carbon Dioxide With An Ethanol Modifier, Johnathon Wenzel, Veronica Moorman, Lihua Wang, Cheryl S. Samaniego, Michelle Ammerman, Isaiah Spencer-Williams, Mitchell Hall

Chemical Engineering Publications

Walnuts are commonly cultivated for their kernel, which is a rich source of antioxidant phenolic compounds. The husk likewise contains antioxidant and antimicrobial compounds, but is typically discarded without further processing. Antioxidant compounds are useful in creating active packaging films, but typically decompose at melt extrusion temperatures in polymer processing. Due to carbon dioxide's low critical point and ability to swell polymer films, supercritical carbon dioxide may be used to impregnate phenolic compounds into polymers. For this study, a novel technique is used to simultaneously produce walnut husk extracts and impregnate the extract into polymer films in the same ...


Gradient Precipitation Of Recombinant Proteins Contained In Silkworm Larvae (Bombyx Mori) With Ammonium Sulphate, Abdurhakhmanov Jaloliddin, Sasmakov Sobirdjan, Khasanov Shuhrat, Ashirov Оybek 2019 Institute of the Chemistry of Plant Substances, Tashkent, Uzbekistan

Gradient Precipitation Of Recombinant Proteins Contained In Silkworm Larvae (Bombyx Mori) With Ammonium Sulphate, Abdurhakhmanov Jaloliddin, Sasmakov Sobirdjan, Khasanov Shuhrat, Ashirov Оybek

CHEMISTRY AND CHEMICAL ENGINEERING

We investigated the protein extract of silkworm larvae. For the first time, an extract containing proteins from silkworm larvae, obtained by fractional precipitation using ammonium sulfate, was studied. As a result of experiment is established, that solutions of ammonium sulfate with a concentration from 20% to 65% are optimal for the sedimentation of protein molecules with a mass in the range of 25 and 45 kDa. Optimal results of the study proposed to use in the process of purification of recombinant proteins.


Development And Characterisation Of High Surface Energy Microstructured Sol-Gel Coatings For Sensing Applications, Emma MacHugh 2019 Technological University Dublin

Development And Characterisation Of High Surface Energy Microstructured Sol-Gel Coatings For Sensing Applications, Emma Machugh

Doctoral

This study investigates the development of high surface energy photoreactive organic inorganic hybrid sol-gel coatings for the microstructuration of high-resolution microfluidic platforms and optofluidic biosensor platforms by standard photolithography processes. To achieve this, the first step of our work consisted of identifying the fundamental physico chemical processes governing the structuration and surface properties of hybrid organic inorganic sol-gel coatings. For this purpose, a reference material based on the combination of an organosilane (3-Methacryloxypropytrimethoxysilane, MAPTMS) and a transition metal (zirconium propoxide, ZPO), was firstly developed and characterised. It was highlighted that chemical, physical and combined physical and chemical processes can be ...


Vitamin A Deficiency Impairs The Immune Response To Intranasal Vaccination And Rsv Infection In Neonatal Calves, Jodi L. McGill, Sean M. Kelly, Mariana Guerra-Maupome, Emma Winkley, Jamie Henningson, Balaji Narasimhan, Randy E. Sacco 2019 Iowa State University

Vitamin A Deficiency Impairs The Immune Response To Intranasal Vaccination And Rsv Infection In Neonatal Calves, Jodi L. Mcgill, Sean M. Kelly, Mariana Guerra-Maupome, Emma Winkley, Jamie Henningson, Balaji Narasimhan, Randy E. Sacco

Chemical and Biological Engineering Publications

Respiratory syncytial virus (RSV) infection is a leading cause of severe acute lower respiratory tract infection in infants and children worldwide. Vitamin A deficiency (VAD) is one of the most prevalent nutrition-related health problems in the world and is a significant risk factor in the development of severe respiratory infections in infants and young children. Bovine RSV (BRSV) is a primary cause of lower respiratory tract disease in young cattle. The calf model of BRSV infection is useful to understand the immune response to human RSV infection. We have previously developed an amphiphilic polyanhydride nanoparticle (NP)-based vaccine (i.e ...


Bioremediation Of Refinery Desalter Effluent Using Debaryomyces Hansenii And Parachlorella Kessleri, Leila Azimian 2019 The University of Western Ontario

Bioremediation Of Refinery Desalter Effluent Using Debaryomyces Hansenii And Parachlorella Kessleri, Leila Azimian

Electronic Thesis and Dissertation Repository

Crude oil desalting operations produce an effluent stream which is challenging to treat due to its salt, heavy metal and hydrocarbon content. Consequently, desalter effluent (DE) is usually diluted into other effluent streams and sent to conventional wastewater treatment plants which may lead to upsets the plant operation.

In this study, a novel microbial approach was applied which investigated DE treatment using halotolerant yeast Debaryomyces hansenii (LAF-3 10 U) or the environmentally robust micro-algae Parachlorella kessleri strain CPCC 266. The effect of these two different approaches on both synthetic and actual DE was investigated in both batch and/or continuous ...


Influence Of Flow Rate, Nozzle Speed, Pitch And The Number Of Passes On The Thickness Of S1805 Photoresist In Suss Microtec As8 Spray Coater, Rohan Sanghvi, Gyuseok Kim 2019 Singh Center for Nanotechnology

Influence Of Flow Rate, Nozzle Speed, Pitch And The Number Of Passes On The Thickness Of S1805 Photoresist In Suss Microtec As8 Spray Coater, Rohan Sanghvi, Gyuseok Kim

Tool Data

S1805 positive photoresist has been deposited on single crystalline Si wafers using a Suss MicroTec Alta Spray. The influence of flow rate, nozzle speed, pitch and number of passes on the thickness of the photoresist was studied. Results show that the thickness of S1805 is linearly proportional to the flow rate and number of passes, and inversely proportional to the nozzle speed and pitch.


Immobilization Of The Influenza A M2 Transmembrane Peptide In Virus Envelope−Mimetic Lipid Membranes: A Solid-State Nmr Investigation, Wenbin Luo, Sarah D. Cady, Mei Hong 2019 Iowa State University

Immobilization Of The Influenza A M2 Transmembrane Peptide In Virus Envelope−Mimetic Lipid Membranes: A Solid-State Nmr Investigation, Wenbin Luo, Sarah D. Cady, Mei Hong

Sarah Cady

The dynamic and structural properties of membrane proteins are intimately affected by the lipid bilayer. One property of membrane proteins is uniaxial rotational diffusion, which depends on the membrane viscosity and thickness. This rotational diffusion is readily manifested in solid-state NMR spectra as characteristic line shapes and temperature-dependent line narrowing or broadening. We show here that this whole-body uniaxial diffusion is suppressed in lipid bilayers mimicking the composition of eukaryotic cell membranes, which are rich in cholesterol and sphingomyelin. We demonstrate this membrane-induced immobilization on the transmembrane peptide of the influenza A M2 (AM2-TM) proton channel protein. At physiological temperature ...


Influence Of Naoh Concentration On Transfer Process Of Graphene, Francisco Saldana, Chengyu Wen, George Patrick Watson 2019 Singh Center for Nanotechnology

Influence Of Naoh Concentration On Transfer Process Of Graphene, Francisco Saldana, Chengyu Wen, George Patrick Watson

Protocols and Reports

The process of transferring a monolayer of graphene using two different concentrations of sodium hydroxide (NaOH) solution unto a silicon dioxide (SiO2) coated Si chip using electrochemistry was performed. The transfer process is crucial for the delamination of a continuous graphene monolayer film from copper foil. After examining and inspecting the integrity of the graphene monolayer, it was observed that the lower concentration to NaOH led to slower rate of hydrogen bubble generation; this condition was found to be less destructive and yielded a graphene film with fewer visible tears.


Evaluation Of Biohydrogen Production From Co-Fermentation Of Carbohydrates And Proteins, Emmanuel Andrew Tepari Jr, 2019 The University of Western Ontario

Evaluation Of Biohydrogen Production From Co-Fermentation Of Carbohydrates And Proteins, Emmanuel Andrew Tepari Jr,

Electronic Thesis and Dissertation Repository

The aim of this study was to examine volatile fatty acid (VFA) production from a proteinaceous substrate, bovine serum albumin (BSA) for a pH range of 5 – 9, and to further assess its impact on hydrogen production in a co-fermentation process using starch and BSA at different ratios. The established optimum conditions for VFA production from BSA were an initial pH of 8, incubation time of 3 days and an operating temperature of 37 ℃. Using these fermentation conditions, the stoichiometric reactions that describe the anaerobic degradation of BSA were investigated. A methodology that describes organic acid production from BSA by ...


Renal Specific Rnai Delivery By Fibrillar Nanoparticle Excipients, Sam Wong 2019 The Graduate Center, City University of New York

Renal Specific Rnai Delivery By Fibrillar Nanoparticle Excipients, Sam Wong

Dissertations, Theses, and Capstone Projects

RNA interference (RNAi) is a powerful tool to manipulate the phenotype of an organism by silencing the expression of specific genes and is viewed as a highly promising platform for treating undruggable targets and disorders where small molecule drugs and antibodies would fail. However, development of RNAi based therapies has faced major barriers including cellular and tissue-specific uptake of the Small Interfering RNA (siRNA). Utilizing different nanoparticles as RNAi excipients, cellular uptake and gene silencing potency can be greatly improved. The research in Dr. McDevitt groups has fibrillar carbon nanotubes (CNT) as carriers for siRNA for gene silencing in vitro ...


Imaging Of Unstained Dna Origami Triangles With Electron Microscopy, Alejandra Londono‐Calderon, Md Mir Hossen, Pierre E. Palo, Lee Bendickson, Sandra Vergara, Marit Nilsen-Hamilton, Andrew C. Hillier, Tanya Prozorov 2019 Ames Laboratory

Imaging Of Unstained Dna Origami Triangles With Electron Microscopy, Alejandra Londono‐Calderon, Md Mir Hossen, Pierre E. Palo, Lee Bendickson, Sandra Vergara, Marit Nilsen-Hamilton, Andrew C. Hillier, Tanya Prozorov

Ames Laboratory Accepted Manuscripts

Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy of samples immobilized on bulk substrates. Less commonly used are electron microscopy techniques, typically carried out after negative staining of DNA structures or by using cryo‐transmission electron microscopy (TEM). Here, direct imaging of unstained DNA origami on common electron‐transparent substrates with utilizing high angular annular dark field scanning transmission electron microscopy (HAADF‐STEM) is reported. This approach establishes a method for depositing and imaging intact DNA triangles with mass‐thickness contrast sufficient to measure the scaffold‐to‐scaffold distances and the length of ...


Building Microbial Factories For The Production Of Aromatic Amino Acid Pathway Derivatives: From Commodity Chemicals To Plant-Sourced Natural Products, Mingfeng Cao, Meirong Gao, Miguel Suastegui, Yanzhen Mei, Zengyi Shao 2019 Iowa State University

Building Microbial Factories For The Production Of Aromatic Amino Acid Pathway Derivatives: From Commodity Chemicals To Plant-Sourced Natural Products, Mingfeng Cao, Meirong Gao, Miguel Suastegui, Yanzhen Mei, Zengyi Shao

Chemical and Biological Engineering Publications

The aromatic amino acid biosynthesis pathway, together with its downstream branches, represents one of the most commercially valuable biosynthetic pathways, producing a diverse range of complex molecules with many useful bioactive properties. Aromatic compounds are crucial components for major commercial segments, from polymers to foods, nutraceuticals, and pharmaceuticals, and the demand for such products has been projected to continue to increase at national and global levels. Compared to direct plant extraction and chemical synthesis, microbial production holds promise not only for much shorter cultivation periods and robustly higher yields, but also for enabling further derivatization to improve compound efficacy by ...


Bioengineering Extracellular Matrix Scaffolds For Volumetric Muscle Loss, Kevin Roberts 2019 University of Arkansas, Fayetteville

Bioengineering Extracellular Matrix Scaffolds For Volumetric Muscle Loss, Kevin Roberts

Theses and Dissertations

Volumetric muscle loss overwhelms skeletal muscle’s ordinarily capable regenerative machinery, resulting in fibrosis and severe functional deficits which have defied clinical repair strategies. My work spans the design and preclinical evaluation of implants intended to drive the cell community of injured muscle toward a regenerative state, as well as the development of an understanding of the molecular responses of this cell community to biomaterial interventions. I demonstrate a new class of biomaterial by leveraging the productive capacity of sacrificial hollow fiber membrane cell culture; I show specifically that unique threads of whole extracellular matrix can be isolated by solvent ...


Characterization Of Tetrazolium Salts And Formazans Using Computational Chemistry For Radiochromic Dosimetry, Teshome G. Bedada 2019 The University of Western Ontario

Characterization Of Tetrazolium Salts And Formazans Using Computational Chemistry For Radiochromic Dosimetry, Teshome G. Bedada

Electronic Thesis and Dissertation Repository

Computational chemistry is a powerful tool to model different materials and predict their physical and chemical properties. The goal of this thesis was to apply different computational chemistry tools to model the properties of two classes of closely related organic compounds: formazans and tetrazolium salts for ionizing radiation dosimetry in water-based gels, whereby the absorbed dose is registered by optical detection of formazan formation from tetrazolium salts. The structural parameters of phenyl and benzothiazolyl-substituted tetrazolium salts and formazans were computed using the APFD density functional theory (DFT) model and 6-311+G(2d,p) basis set. Conformational searching of stereoisomers (TSCA ...


K-Fit: Parameterizing Kinetic Models Of Metabolism Using Multiple Fluxomic Datasets, Costa Maranas 2019 Penn State University, USA

K-Fit: Parameterizing Kinetic Models Of Metabolism Using Multiple Fluxomic Datasets, Costa Maranas

Biochemical and Molecular Engineering XXI

Kinetic models predict the metabolic flows by directly linking metabolite concentrations and enzyme levels to reaction fluxes. Robust parameterization of organism-level kinetic models that faithfully reproduce the effect of different genetic or environmental perturbations remains an open challenge due to the intractability of existing algorithms. This paper introduces K-FIT, an accelerated kinetic parameterization workflow that leverages a novel decomposition approach to identify steady-state fluxes in response to genetic perturbations followed by a gradient-based update of kinetic parameters until predictions simultaneously agree with the fluxomic data in all perturbed metabolic networks. The applicability of K-FIT to large-scale models is demonstrated by ...


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