Digital Commons Network^™

Method Development Toward The Analysis Of The Functionalization Of Proteins, Victoria Calcote

Honors Theses

Calmodulin is a ubiquitous small intracellular protein that functions as a receptor for regulatory calcium signals and thus regulates a multitude of physiological processes in organisms as diverse as yeast, fruit flies, and mammals. Since its structure and function have been extensively studied, our goal is to create a calmodulin biomaterial, with the ultimate goal of in situ drug delivery or as a scaffold for stem cell growth and differentiation. We plan to create this biomaterial by using Click Chemistry, the rapid creation of new heteroatom bonds through a copper-catalyzed azide-alkyne cycloaddition. The bonds are created by treating calmodulin as …

Comparing The Regio- And Enantioselectivity Of Inverting Versus Retaining Epoxide Hydrolases, Mark A. Aliwalas

Theses and Dissertations (Comprehensive)

Epoxide hydrolases (EHs) are enzymes that catalyze the ring opening of an epoxide, yielding a vicinal diol. This exciting class of enzymes is often associated with natural product and small molecule biosynthesis. One interesting class of natural products that epoxide hydrolases are involved in the biosynthesis of is the enediynes. Previously, 5 enediyne-associated epoxide hydrolases have been characterized, revealing an inverting-versus-retaining paradigm for enediyne epoxide hydrolases. The work described herein sets the table for future studies involving the probing of the α/β-epoxide hydrolase mechanism for styrene oxide. Kinetic and regioselectivity characterization of the enediyne-associated CynF and SghF has determined that …

Computational And Experimental Evaluation Of Α-(N-2-Quinolonyl)Ketones: A New Class Of Nonbiaryl Atropisomers, Andrea N. Bootsma, Carolyn E. Anderson

University Faculty Publications and Creative Works

Given the usefulness of atropisomers within both asymmetric catalysis and pharmaceuticals, a thorough computational study of substituted α-(N-2-quinolonyl)ketones has been conducted. This class of tertiary amides is unique, as the amide is embedded within an aromatic construct, and the nitrogen bears an aliphatic substituent. Using a computational approach, 8′-substituted quinolones were identified as potential class 2 and 3 atropisomeric targets with calculated C–N rotational barriers of greater than 20 kcal/mol. These results, along with experimental efforts toward the synthesis of these targets, are reported.

Effect Of 5-Hydroxymethylcytosine Modifications On Stability Of Vegf I-Motifs, Bethany Summerford

Honors Theses

DNA i-motifs are a secondary structure of DNA formed at low pH by internal folding of strands rich in cytosine. This study focuses on trying to determine if the DNA from the vascular endothelial growth factor (VEGF) promoter, which can form an i-motif, can be stabilized with the epigenetic modification to 5- hydroxymethylcytosine in four separate locations on the DNA strand, and to what extent the degree of stabilization depends on the location of the modification. Stability of the i-motif was determined by measuring pKa and melting point (Tm) of each VEGF modification using circular dichroism spectroscopy. The modified samples …

Mutagenesis-Based Active-Site Characterization Of The Diabetes Drug Target Mitoneet, Lisa Mickley

Williams Honors College, Honors Research Projects

This project investigates the cluster stability of an outer mitochondrial membrane protein mitoNEET under mutational stress and drug binding analysis. MitoNEET is a part of a class of proteins that coordinate an Fe-S molecule into its tertiary structure. This protein is believed to facilitate the oxidative capacity of the electron transport chain by reversible loss of its coordinated Fe-S molecule. The research of this paper uses site directed protein mutagenesis to selectively alter the three cysteine, one histidine cluster coordination into more common coordination patterns such as two cysteine, two histidine or four cysteine. The ultimate goal is to optimize …

The Synthesis Of Poly(Propylene Fumarate), Brian N. Fitch

Williams Honors College, Honors Research Projects

Poly(propylene fumarate) is a promising material in the field of bone tissue engineering. A recently described chain growth polymerization was developed for the synthesis of poly(propylene fumarate). This pathway uses the ring-opening polymerization of maleic anhydride and propylene oxide with magnesium ethoxide as an initiator to yield poly(propylene maleate). The poly(propylene maleate) was then isomerized to poly(propylene fumarate) using diethyl amine. In order to scale up the reaction to a 20L reactor, several optimizations of the purification schemes was required. The main optimizations were done to the purification of poly(propylene maleate). Several methods were tested including replacing the water washes …

Theoretical Estimation Of PkA'S Of Pyrimidines And Related Heterocycles, Rachael Ann Wessner

Browse all Theses and Dissertations

Pyrimidines and related heterocycles are an important class of compounds with a wide variety of applications. As a result, there is great interest in the chemical properties of these compounds, specifically their pKa's. Despite the importance of these compounds their reported pKa's are often only approximations or are completely absent from literature. Experimentally measuring pKa's can be challenging, especially if the pKa is below zero. Alternatively, pKa's can be estimated computationally using a Quantitative Structure-Activity Relationship (QSAR). However, most of the compounds included in this study exist as two or more forms that arise from tautomerism. Tautomerism complicates the estimation …

Implementation And Evaluation Of An Analytical Method For A Novel Derivatizing Agent To Measure 4,4'-Methylene Diphenyl Diisocyanate Atmospheres, Silvia Puscasu, Simon Aubin, Mark Spence, Sébastien Gagné

Études primaires

Accurate measurement of 4,4'-methylene diphenyl diisocyanate (MDI) atmospheres is a challenge since the molecule is both chemically reactive and likely to be present in aerosol form when heated and sprayed because of its low vapor pressure. Meeting this challenge requires optimizing both the sampling device used and the derivatization agent employed to stabilize the isocyanate functional group. This study describes the use of a novel derivatization reagent for isocyanate sampling to address the challenge of MDI aerosol exposure sampling. Like most conventional derivatizing agents for isocyanates, 1,8-diaminonapthalene (DAN) reacts with isocyanate functional groups to form a urea. However, unlike other …

Mass Spectrometric Analysis Of Biologically Relevant Compounds Hyphenated By Gas And High Performance Liquid Chromatography, Zach Laswell

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Analyzing Urine In Mice With Tyrosinemia Type 1 Using Nmr Spectroscopy, Emily Olsen

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Awareness Of Clinical Laboratory Sciences And Shortage Of Clinical Laboratory Scientists In The 21st Century, Cynthia Funnye Doby

Walden Dissertations and Doctoral Studies

Retiring baby boomers and the lack of interest and awareness among college students to enroll in an accredited Clinical Laboratory Science (CLS) program have created a shortage of CLS professionals in the 21st century. The U.S. Bureau of Labor Statistics predicts 18,000 CLS vacancies by 2018. However, only about 5,000 students graduate from accredited CLS programs each year. The purpose of this study was to explore students' perceptions of allied health professions and factors that influenced students and CLS professionals to select CLS as a profession. Bandura's social cognitive career theory served as the theoretical framework for this phenomenological study. …

Non-Conventional Approaches To Syntheses Of Ferromagnetic Nanomaterials, Dustin M. Clifford

Theses and Dissertations

The work of this dissertation is centered on two non-conventional synthetic approaches to ferromagnetic nanomaterials: high-throughput experimentation (HTE) (polyol process) and continuous flow (CF) synthesis (aqueous reduction and the polyol process). HTE was performed to investigate phase control between Fe_xCo_1-x and Co_3-xFe_xO_y. Exploration of synthesis limitations based on magnetic properties was achieved by reproducing M_s=210 emu/g. Morphological control of Fe_xCo_1-x alloy was achieved by formation of linear chains using an H_ext. The final study of the Fe_xCo_1-x chains used DoE to …

Sol-Gel Assembly Of Metal Nanostructures Into Metallic Gel Frameworks And Their Applications, Xiaonan Gao

Theses and Dissertations

The advent of nanoscience and nanotechnology has sparked many research forefronts in the creation of materials with control over size, shape, composition, and surface properties.^1,2 However, for most of the applications, nanoscale materials need to be assembled into functional nanostructures that exhibit useful and controllable physical properties. Therefore, numerous efforts on the assembly of nanoparticles (NPs) using organic ligands, polymers and polyelectrolytes have been reported.^3,4 However, the interactions between NPs are mediated by intervening ligands, which are detrimental to charge transport and limit the thermal stability. Hence, developing a new method to produce solid …

Routes To 1,3,4 - Oxadiazol-2(3h)-Ones, Karunakar Reddy Madaram

Browse all Theses and Dissertations

Various 1,3,4-oxadiazol-2(3H)-ones were synthesized by reaction of the bromocarbonylhydrazine salt(35) obtained from treatment of 4-bromo-3-phenylsydnone(34) with HCl with the corresponding acid chlorides in DME. The structures were confirmed by their physical, analytical and spectral data (IR, GC/MS, 1H and 13C NMR and CHN analysis). In general these compounds were synthesized in good to excellent yields and it is planned to continue exploration of their chemical behavior as a guide to their potential antimicrobial activity. As an initial approach to the synthesis of the desired 1,3,4-oxadiazol-2(3H)-ones, the starting material, 3-phenylsydnone, was prepared in 2 steps from commercially available N-phenylglycine in good …

Virus Particles Provide Nanotopographical Cues For Osteogenic Differentiation Of Mesenchymal Stem Cells, Kamolrat Metavarayuth

Theses and Dissertations

One key aspect of tissue engineering is to develop biomimetic scaffolding materials that can modulate the proliferation, self-renewal and differentiation of multipotent stem cells into different lineages. Bone marrow derived mesenchymal stem cells (BMSCs) can differentiate into several target cells such as osteoblasts, chondrocytes, adipocytes, and smooth muscle cells. BMSCs are commonly used for in vitro osteogenesis studies in bone tissue engineering field. However the mechanisms and signaling pathways that these cells use to recognize and response to biomaterial surface are still unclear. This dissertation focuses on investigating the effect of chemical and physical cues introduced by virus nanoparticles on …

The Role Of Ferric Oxide Particles As Sources And Sinks Of Reactive Oxygen Species During The Autoxidation Of Ferrous Iron, Shengnan Meng

Theses and Dissertations

The oxic portion of the biosphere is a metastable mixture of different oxidation states of carbon, sulfur and oxygen energetically poised from equilibrium by the net rate differentials between photosynthetic carbon fixation and its metabolic or abiotic oxidation. The direct reaction of dioxygen with reduced carbon or sulfur is spin forbidden and therefore kinetically slow, but ferric and ferrous iron species serve as catalysts for enabling their oxidation and therefore play critical roles in the environment. This thesis reports exploratory and hypothesis driven research that seeks a better understanding of the physical and chemical limitations on the effectiveness of iron …

Characterization Of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) From Vibrio Vulnificus, Nikita K. Ussin

Theses and Dissertations

Vibrio vulnificus, a gram-negative bacterium, is the leading cause of seafood-borne illnesses and mortality in the United States. Previous studies of bacterial pathogens have identified a metabolite essential to V. vulnificus growth and function. 1-deoxy-D-xylulose 5-phosphate reductoisomerase (Dxr) is an essential enzyme in the viability of many bacteria and catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (Dxp) to 2-C-methylerythritol 4-phosphate (MEP) within the MEP pathway found in plants and bacteria. Previous studies have been conducted to characterize Dxr homologs from other pathogens including E. coli, M. tuberculosis, and P. falciparum. Information on the structural and enzymatic characteristics of Dxr from Vibrio …

The Development Of Bicyclic Peptide Library Scaffolds And The Discovery Of Biostable Ligands Using Mrna Display, David E. Hacker

Theses and Dissertations

Peptides are a promising class of therapeutic candidates due to their high specificity and affinity for cellular protein targets. However, peptides are susceptible to protease degradation and are typically not cell-permeable. In efforts to design more effective peptide drug discovery systems, investigators have discovered that incorporation of non-canonical amino acids (ncAAs) and macrocyclization overcome these limitations, making peptides more drug-like.

In this work, we exploit the promiscuity of wild-type aminoacyl-tRNA synthetases (aaRSs) to ‘mischarge’ ncAAs onto tRNA and ribosomally incorporate them into peptides using a cell-free translation system. We have demonstrated the ability to incorporate five ncAAs into a single …

Vespucci: A Free, Cross-Platform Software Tool For Spectroscopic Data Analysis And Imaging, Daniel Patrick Foose

Browse all Theses and Dissertations

Vespucci is a software application developed for imaging and analysis of hyperspectral datasets. Vespucci offers several advantages over other software packages, including a simple user interface, no cost, and less restrictive licensing. Vespucci incorporates several analysis techniques including univariate imaging, principal components analysis, partial-least-squares regression, vertex components analysis and k- means clustering. Additionally, Vespucci can perform a number of useful data-processing operations, including filtering, normalization, baseline correction, and background subtraction. Datasets that consist of spatial or temporal data with a corresponding digital signal, including spectroscopic images, mass spectrometric images, and X-ray diffraction data can be processed in this software. The …

Correction: Surprising Impact Of Remote Groups On The Folding–Unfolding And Dimer-Chain Equilibria Of Bifunctional H-Bonding Unimers, Rui Liu, Shuang Chen, Erin S. Baker, Richard D. Smith, Xiao Cheng Zeng, Bing Gong

Xiao Cheng Zeng Publications

The authors regret that in the original article the spelling of one author’s surname is incorrect. The correct name of the author is ‘Shuang Chen’.

The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.

Surprising Impact Of Remote Groups On The Folding–Unfolding And Dimer-Chain Equilibria Of Bifunctional H-Bonding Unimers, Rui Liu, Shuang Cheng, Erin S. Baker, Richard D. Smith, Xiao Cheng Zeng, Bing Gong

Xiao Cheng Zeng Publications

Oligoamide 1, consisting of two H-bonding units linked by a trimethylene linker, was previously found to form a very stable, folded dimer. In this work, replacing the side chains and end groups of 1 led to derivatives that show the surprising impact of end groups on the folding and dimer-chain equilibria of the resultant molecules.

Engineering Escherichia Coli For High‑Yield Geraniol Production With Biotransformation Of Geranyl Acetate To Geraniol Under Fed‑Batch Culture, Wei Liu, Xin Xu, Rubing Zhang, Tao Cheng, Yujin Cao, Xiaoxiao Li, Jiantao Guo, Huizhou Liu, Mo Xian

Department of Chemistry: Faculty Publications

Background: Geraniol is an acyclic monoterpene alcohol, which exhibits good prospect as a gasoline alternative. Geraniol is naturally encountered in plants at low concentrations and an attractive target for microbial engineering. Geraniol has been heterologously produced in Escherichia coli, but the low titer hinders its industrial applications. Moreover, bioconversion of geraniol by E. coli remains largely unknown.

Results: Recombinant overexpression of Ocimum basilicum geraniol synthase, Abies grandis geranyl diphosphate synthase, and a heterotic mevalonate pathway in E. coli BL21 (DE3) enabled the production of up to 68.6 ± 3 mg/L geraniol in shake flasks. Initial fed-batch fermentation only increased geraniol …

Close Encounters With Creative Chemical Thinking: An Outreach Presentation Using Movie Clips About The Elemental Composition Of Aliens And Extraterrestrial Minerals, Mark A. Griep, Marjorie L. Mikasen

Department of Chemistry: Faculty Publications

To introduce more chemistry into a middle and high school bioengineering camp experience, we developed an educational and entertaining presentation that examines the chemistry in movies about aliens and minerals from outer space. Our goal was to help the campers to think creatively about the bioengineering projects they are doing and about its chemistry. After watching each movie clip, we explain whether the chemistry in the clip is real or fake, and then describe the real chemistry that inspired it. The chemical touchstone for the presentation is the periodic table. First, the campers learn that aliens in five movies are …

Enabling Method To Design Versatile Biomaterial Systems From Colloidal Building Blocks, Shalini Saxena, L. Andrew Lyon

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Development of materials with fine spatial control over topographical, mechanical, or chemical features has been investigated for a variety of applications. Here we present a method to fabricate an array of polyelectrolyte constructs including two-dimensionally and three-dimensionally patterned assemblies using both compressible and incompressible colloidal building blocks. This method eliminates prior constraints associated with specific chemistries, and can be used to develop modular, multi-component, patterned assemblies. In particular, development of constructs were investigated using microgels, which are colloidally stable hydrogel microparticles, polystyrene (PS) beads, and PS-microgel core-shell building blocks in conjunction with the polycation poly(ethyleneimine) (PEI). The topography, mechanical properties, …

Seasonal Evolution Of Active Layer Formation In Subarctic Peat Plateaux And Implications For Dissolved Organic Matter Composition And Transfer, Jennifer L. Hickman

Theses and Dissertations (Comprehensive)

Peat-accumulating wetlands are ecosystems whose rate of photosynthetic production of organic matter is greater than that of its decomposition, resulting in a build up of soil organic matter that may take centuries to fully decompose. Carbon (C) stocks within these ecosystems are a function of inputs from photosynthesis, and losses from heterotrophic decomposition. Due to the short growing season and overall cold climate of boreal and tundra regions, C has been accumulating within these landscapes, mostly in soil organic matter, since the last glaciation. Climate change, predicted to result in rising temperatures and increased precipitation, has begun to degrade the …

The Role Of Organic Matter In The Surface Chemistry Of Arsenic Compounds On Iron−(Oxyhydr)Oxides Studied By Atr-Ftir, Arthur Situm

Theses and Dissertations (Comprehensive)

The interaction of organic matter with the interfaces of active soil components such as iron oxides is ubiquitous within soil environments. The presence of organics at these interfaces may have implications for other soil constituents whose mobility is controlled by their ability to bind to active soil components. Most of the studies performed to date which look at these interactions are bulk/batch studies performed ex-situ. Attenuated total internal reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was utilized within this work to study interactions between select model organics (citrate, oxalate and pyrocatechol) and iron−(oxyhydr)oxides, as well as their effect on the surface …

Phosphorus Removal Using Titanium Dioxide Nanoparticles In Wastewater Treatment, Suyoung Choi Mr.

Theses and Dissertations (Comprehensive)

Due to eutrophication caused by nutrients such as phosphorus (P), local surface water near military garrisons and camps has been deteriorated for several years in the Republic of Korea. Thus, in order to remove excessive P in local fresh water, various size of titanium dioxide (TiO₂) were used.

In the first investigation, TiO₂ mixed bulk powder (particle size > 5µm) showed maximum P removal with pH dependence (higher pH shows lower P removal), that was approximately 27%. To determine adsorption isotherms, Langmuir and Freudlich models were used. The experimental data was better fit by a Langmuir model compared …

Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis

Theses and Dissertations--Plant and Soil Sciences

Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me …

The Owl Sensor: A Smart Nanostructure For Single Nucleotide Variation Analysis, Rebekah Karadeema

Electronic Theses and Dissertations

Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is extensively used in healthcare for detection of genetic mutations and analysis of drug resistant pathogens. Here we developed a nucleic acid sensor able to differentiate between a fully matched analyte and one with a SNV in a wide temperature range of 5°C-32°C. The sensor, dubbed here the 'Owl Sensor' due to the complex's resemblance to owl eyes, utilizes recent developments in DNA nanotechnology and synthetic biology to self-assemble a fluorescent DNA nanostructure called a Double Crossover, or DX Tile, capable of differentiating SNVs in a large temperature range, …

Adsorption Of Antibiotics By Vermiculite, Mosa J. Ferdous

Dissertations and Theses

The occurrence of residual antibiotics in the environment has been a worldwide issue and warrants the development of inexpensive yet effective methods for antibiotics removal from contaminated water. In this thesis work, the adsorption of four antibiotics, namely chlorotetracycline (CTC), oxytetracycline (OTC), ofloxacin (OFL), and enrofloxacin (ENR), onto natural vermiculite has been studied using batch (static) and column (dynamic) adsorption techniques. The Langmuir and Freundlich isotherm models were initially used to explain the adsorption processes. The separation factor (RL) values derived from the Langmuir model and the 1/n values derived from Freundlich model in the present investigation were less than …