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Self-Assembled Monolayers And Methods For Using The Same In Biosensing Applications, Patrick H. Dussault, Rebecca Lai, Thomas J. Fisher, Anita J. Zaitouna

Patrick Dussault Publications

Cross-linked amphiphile constructs that form self-assembled monolayers (SAMs) on metal Surfaces such as gold Surfaces are disclosed. These new SAMs generate well packed and highly oriented monolayer films on gold Surfaces. A method for using the SAMs in the fabrication of biomolecule sensors is also disclosed.

An Approach To An Agave Problem: The Bioremediation Of Agricultural Waste By Yeast Fermentations, Joshua Michael Jarodsky

Theses and Dissertations

The agricultural waste products created by industries, such as the Tequila manufacturing industry, create thousands of tons of waste material every year. This agricultural waste often becomes an environmental and ecological problem for fields and surrounding areas. The purpose of this study is to determine the potential of using the yeast Kluyveromyces marxianus 7-1 and Kluyveromyces marxianus 8-1 to ferment the leaf waste from the harvesting of the Agave tequilana as a form of bioremediation. Fermentations (anaerobic, under constant shaking, and at room temperature) were monitored for colony forming units, pH of fermentation broth, concentration of reducing sugars, and protein …

Fast And Sensitive Genome-Hashing Software And Its Application In Using Ngs As A Detection Agent For Bacterial Presence In Oral Metagenomic Samples, Paul Michael Gontarz

Dissertations

Next generation sequencing has increased the throughput of sequenced DNA into the range of billions of nucleotides sequenced per day. With the increased speed of DNA sequencing and the short length of reads produced by next generation sequencers, a significant challenge has been created in quickly and accurately assembling the hundreds of millions of short reads created by modern sequencing instruments into their full genomic sequences. With the increase in throughput in next generation sequencing and the decrease in time and cost to perform DNA sequencing, novel applications for DNA sequencing are being considered. Among them is a methodology by …

Mechanism Analysis Of Copper (Ii) Ions Interacting With Dimethylaminocyanostilbene, Eui Bin You, Ryan T. Hayes Ph.D.

Posters, Presentations, and Papers

Previous research has suggested that the fluorescence of dimethylaminocyanostilbene (DCS) is selectively quenched by copper(II) ions.¹ This study aimed to elucidate the fluorescence quenching mechanism and to explore its potential application to screen for copper ions in water samples. A spectroscopic Job Plot analysis was used to determine the stoichiometric ratio of DCS–copper(II) ion binding.² Additionally, DCS was mixed with various buffered metal ion solutions and tested in different pH environments to reveal any ion-dependent and/or pH-dependent fluorescence response. Nuclear magnetic resonance spectroscopy (NMR) analysis of DCS mixed with various amounts of buffered copper(II) solution was also performed …

Crossed Mcmurry Coupling Reactions For Porphycenic Macrocycles: Non-Statistical Selectivity And Rationalisation, Thomas Y. Cowie, Lorna Kennedy, Justyna M. Zurek, Martin J. Paterson, Magnus Bebbington

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Crossed McMurry reactions of bifuran- or bithiophenedicarbaldehydes with bipyrroledicarbaldehydes have been studied for the first time. Only those porphycenic macrocycles derived from homocoupled McMurry products were formed. The results are explained by using both density functional theory and electron propagator computations to model the electron affinity of the dialdehyde starting materials. It was predicted that bifuran\bithiophene cross-coupling would indeed occur, and this was demonstrated by the first synthesis of a novel dioxa,dithio hetero-porphycenoid annulene. This approach will allow the prior identification of viable substrates for related crossed McMurry reactions. In the first study of its type, experimental and computational studies …

Crystal Structure Of Catena-Poly[[Chlorido(4,4'-Dimethyl-2,2'-Bipyridine-Κ2n,N')Copper(Ii)]-Μ-Chlorido], Rafaela Nita, Jeffrey R. Deschamps, Scott A. Trammell, D. Andrew Knight

Chemistry and Chemical Engineering Faculty Publications

The title compound, [CuCl2(C12H12N2)]n, was obtained via a DMSO-mediated dehydration of Cu(4,4'-dimethyl-2,2'-bipyridine)copper(II)·0.25H2O. The central CuII atom is coordinated in a distorted trigonal-bipyramidal geometry by two N atoms of a chelating 4,4'-dimethyl-2,2'-bipyridine ligand [average Cu-N = 2.03 (3) Å] and three Cl atoms, one terminal with a short Cu-Cl bond of 2.2506 (10) Å, and two symmetry-equivalent and bridging bonds. The bridging Cl atom links the CuII ions into chains parallel to [001] via one medium and one long Cu-Cl bond [2.3320 (10) and 2.5623 (9) Å]. The structure displays both inter- and intramolecular C-H⋯Cl hydrogen bonding.

The Best Of Both Worlds: Building On The Copus And Rtop Observation Protocols To Easily And Reliably Measure Various Levels Of Reformed Instructional Practice, Travis J. Lund, Matthew Pilarz, Jonathan B. Velasco, Devasmita Chakraverty, Kaitlyn Rosploch, Molly Undersander, Marilyne Stains

Department of Chemistry: Faculty Publications

Researchers, university administrators, and faculty members are increasingly interested in measuring and describing instructional practices provided in science, technology, engineering, and mathematics (STEM) courses at the college level. Specifically, there is keen interest in comparing instructional practices between courses, monitoring changes over time, and mapping observed practices to research-based teaching. While increasingly common observation protocols (Reformed Teaching Observation Protocol [RTOP] and Classroom Observation Protocol in Undergraduate STEM [COPUS]) at the postsecondary level help achieve some of these goals, they also suffer from weaknesses that limit their applicability. In this study, we leverage the strengths of these protocols to provide an …

Discovery Of Bisamide-Heterocycles As Inhibitors Of Scavenger Receptor Bi (Sr-Bi)-Mediated Lipid Uptake, Chris Dockendorff, Patrick W. Faloon, Andrew Germain, Miao Yu, Willmen Youngsaye, Partha P. Nag, Melissa Bennion, Marsha Penman, Thomas J.F. Nieland, Sivaraman Dandapani, José R. Perez, Benito Munoz, Michelle A. Palmer, Stuart L. Schreiber, Monty Krieger

Chemistry Faculty Research and Publications

A new series of potent inhibitors of cellular lipid uptake from HDL particles mediated by scavenger receptor, class B, type I (SR-BI) was identified. The series was identified via a high-throughput screen of the National Institutes of Health Molecular Libraries Small Molecule Repository (NIH MLSMR) that measured the transfer of the fluorescent lipid DiI from HDL particles to CHO cells overexpressing SR-BI. The series is characterized by a linear peptidomimetic scaffold with two adjacent amide groups, as well as an aryl-substituted heterocycle. Analogs of the initial hit were rapidly prepared via Ugi 4-component reaction, and select enantiopure compounds were prepared …

Advances In Understanding Carboxysome Assembly In Prochlorococcus And Synechococcus Implicate Csos2 As A Critical Component, Fei Cai, Zhicheng Dou, Susan L. Bernstein, Ryan Leverenz, Eric B. Williams, Sabine Heinhorst, Jessup M. Shively, Gordon C. Cannon, Cheryl A. Kerfeld

Faculty Publications

The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO₂-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in …

Synthesis, Rna Binding And Antibacterial Studies Of 2-Dos Mimetics And Development Of Polymer Supported Nanoparticle Catalysts For Nitroarene And Azide Reduction, Venkata Reddy Udumula

Theses and Dissertations

Project I 2-Deoxystreptamine (2-DOS), the most conserved central scaffold of aminoglycosides, is known to specifically recognize the 5'-GU-'3 sequence step through highly conserved hydrogen bonds and electrostatic interactions within and without the context of aminoglycosides (Figure 1a). We proposed that a novel monomeric unnatural amino acid building block using 2-DOS as a template would allow us to develop RNA binding molecules with higher affinity and selectivity than those currently available. Conjugating two or more of the monomeric building blocks by an amide bond would introduce extra hydrogen bonding donors and acceptors that are absent in natural aminoglycosides and increase specificity …

Studies On The Roles Of Translationally Recoded Proteins From Cyclooxygenase-1 And Nucleobindin Genes In Autophagy, Jonathan J. Lee

Theses and Dissertations

Advances in next-generation sequencing and ribosomal profiling methods highlight that the proteome is likely orders of magnitude larger than previously thought. This expansion potentially occurs through translational recoding, a process that results in the expression of multiple variations of a protein from a single messenger RNA. Our laboratory demonstrated that cyclooxygenase-3/1b (COX-3/1b), a frameshifted, intron-1-retaining, alternative splice variant from the COX-1 gene, is multiply recoded, which results in the translation of at least seven different COX-3 proteins. Two of the recoded COX-3 proteins that we identified are active prostaglandin synthases and are inhibited by non-steroidal anti-inflammatory drugs (NSAIDs). Here we …

A Study Of Allylic Aminations As Catalyzed By Heterobimetallic Pd-Ti Complexes, Diana Lauren Ellis

Theses and Dissertations

Heterobimetallic complexes present a unique approach to catalyzing challenging reactions. By having two metals in close proximity to each other, the metals are able to interact and alter their electronics in a way that simple organic ligands (carbon, nitrogen, sulfur etc.) cannot. Our studies of heterobimetallic complexes focus on a Pd–Ti complex. The complex features a dative interaction between the palladium and the titanium held together by a phosphonamide scaffold. This interaction increases the electrophilicity of the palladium and makes it a very suitable catalyst for allylic amination reactions. We have conducted extensive studies of this catalyst in allylic aminations, …

Development Of Flexible Batteries Using Nano-Carbons And Polymers, Zhiqian Wang

Dissertations

Flexible electronics such as wearable equipment, displays, cell phones and smart cards require flexible power sources like batteries. In this thesis, the development of flexible batteries and supercapacitors are presented. Different types of flexible batteries including zinc carbon batteries, primary alkaline batteries, secondary alkaline batteries and zinc air cells are presented, These were designed, fabricated and improved using polymers and nano-carbons like carbon nanotubes (CNTs). CNTs are found to be effective as conductive additives compared to the traditional graphite. Purification is important to remove impurities that lead to side reactions/ corrosions. However, further treatment like carboxylation lead to higher electric …

The Investigation Of The Low Temperature Combustion Of Mesitylene And Tert-Amyl Methyl Ether By Synchrotron Photoionization Mass Spectrometry, Martin Yu-Hin Ng

Master's Theses

This thesis describes the combustion experiments performed at the Chemical Dynamics Beamline of the Advanced Light Source (ALS) located at the Lawrence Berkeley National Laboratories (LBNL). The need for renewable fuel sources, the need for the study of their combustion in the contexts of homogenous charge combustion ignition (HCCI) engines can be found in Chapter 1. The components of the experimental set-up used throughout this thesis—time-of-flight mass spectrometer, Excimer laser, vacuum pumps and other components—and the components of ALS responsible in synchrotron radiation generation and processing—the linear accelerator, the booster ring, insertion devices, gas filters and monochromator are explained in …

Diol-Mediated Versus Water-Mediated Proton Transfer Reactions, Angela Moses

DePaul Discoveries

The triple-proton-transfer reactions of 8H-1,8-naphthyridin-2-one (8H-naph) have been investigated by employing different ab initio quantum mechanical methods. The proton transfer reactions studied were facilitated through an adjacent 1,3-propanediol molecule or two adjacent water molecules. Identical proton transfer reactions were studied using a model system of 8H-naph to investigate the validity of computational approaches that use model systems to study more complex systems. The solvent effects on the structures were investigated for comparison to the initial gas phase calculations. The potential energy, reaction force, and work profiles were studied along the intrinsic reaction coordinate to monitor the developing proton transfer reactions.

Dynamics And Kinetics Of Singlet Oxygen Mediated Oxidation Of Methionine In The Gas Phase, Hydrated Clusters And Solution, Fangwei Liu

Dissertations, Theses, and Capstone Projects

The reaction between methionine (Met) and electronically excited singlet molecular oxygen (O₂[a¹Δ_g]) has been investigated in a systematic fashion, using a home-built electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer (MS). The study started from probing the reaction dynamics between the isolated protonated/deprotonated methionine ions with ¹O₂ in the gas phase, transited through the same systems micro-solvated with explicit water molecules in gaseous hydrated clusters, and concluded with real-time methionine oxidation kinetics determination in aqueous solution. The reaction products, cross sections, and collision energy dependence were measured by ESI-MS. Density functional theory (DFT) …

Evaluation Of The Feasibility Of Struvite Precipitation From Domestic Wastewater As An Alternative Phosphorus Fertilizer Resource, Amanda R. Bird

Master's Projects and Capstones

Finite phosphate rock ore reserves are estimated to be exhausted in 100 to 150 years. Phosphate rock ore is the single global source material for phosphorus fertilizer production. Once these reserves are gone, agricultural production will be negatively impacted. There are currently no alternative phosphorus resources. However, phosphorus concentrations present in human excrement traveling through domestic wastewater treatment facilities is being disposed of directly to the environment, often resulting in pollution problems. Recovering phosphorus from wastewater with struvite precipitation systems at wastewater treatment plants can alleviate future phosphorus scarcities. Evaluation of phosphorus recovery through struvite precipitation at wastewater treatment plants …

Investigations Of Thioether Generation For S-D-Ribosyl-L-Homocysteine Synthesis, Brendan Corcoran

Master's Theses

Creation of the thioether linkage is a fundamental step for the chemical preparation of the bacterial quorum sensing molecule S-D-ribosyl-L-homocysteine (SRH). Although previous preparations of SRH and its analogues have been reported in the literature, they employ assorted methods with varied results. Therefore, a reassessment of the methodology used for synthetic preparation of the thioether bond in SRH-like molecules is here considered. This work examines four methods of thioether generation following two mechanisms, bimolecular nucleophilic substitution (S_N2) and radical-initiated thiol-ene coupling, in an attempt to generate SRH in a more efficient and reproducible manner. Both mechanisms address …

Electrolyte Effects On The Kinetics Of Comproportionation Electron-Transfer Reactions And On Intervalence Charge-Transfer Band Energies Of Binuclear Ruthenium Ammine Complexes, Zhiji Han

Master's Theses

Chapter 1 describes an overview of electron-transfer reactions. The kinetic equations for ET reactions have also been described in detail.

Chapter 2 describes a series of novel kinetic accelerations which deviate strongly from the predictions of the classical Debye-Huckle theory with a range of different added “inert” electrolytes. The greater catalytic effects seen with the heavier halides and other catalytic electrolytes (especially certain dicarboxylates) indicate an important role for hole-transfer superexchange in the ET transition state. The hypothesis of a catalytic ternary association complex, [RuII--X--RuIII] has also been explored by kinetic modeling of the reaction. An increasing ratio of anion-catalyzed …

Investigation Of Oxidopyrylium-Alkene [ 5 +2 ] Cycloaddition Conjugate Addition Cascades And Extension To Chiral Auxiliary-Based Variants, Chunyin Marshall Law

Theses and Dissertations

Oxidopyrylium-based [5+2] cycloadditions have been extensively utilized to construct oxabridged seven-membered ring systems that often serve as the core structures in numerous biologically active natural products. By investigating these processes, we hope to reveal the highest potentials of [5+2] cycloaddition as a synthetic tool.

A novel oxidopyrylium-alkene [5+2] cycloaddition conjugate addition cascade (C3) sequence, which allows rapid build-up of molecular complexity with excellent diastereocontrol, was investigated. The scope and limitation of this process were explored as mixed results were shown for various acetoxypyranone-alkene substrates. In addition, oxidopyrylium [5+2] cycloadditions of ï?¢-silyloxy-ï?§-pyrones were investigated which revealed the accelerating role of carbonyl …

Monitoring Dissolution Of Nonsteroidal Anti-Inflammatory Drugs Using Infrared Spectroscopy, Julianne Berger

Seton Hall University Dissertations and Theses (ETDs)

A comparison study was conducted to look at the formulation of three brands of naproxen sodium. These brands included Bayer Aleve ®, CVS All Day Pain Relief and Walgreens All Day Pain Relief. The active and inactive ingredients were the same yet the size and shape of the tablets differ among the three brands. S-naproxen was extracted from the tablets and evaluated by GC-MS to determine the purity of naproxen in the tablets. Dissolution was monitored by an IR probe for eight hours while using 0.1M phosphate buffer pH 7.4, 0.05M phosphate buffer pH 4.5 and simulated gastric fluid pH …

Quechers (Quick, Easy, Cheap, Effective, Rugged, And Safe) Extraction – Gas Chromatography For The Analysis Of Drugs, Michelle L. Schmidt

Seton Hall University Dissertations and Theses (ETDs)

QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) is an extraction technique developed by Anastassiades and co-workers initially for the extraction of veterinary drugs from animal tissue. Since its inception, it was discovered that this method is particularly adept for the extraction of polar and basic compounds, thus the majority of research previously performed using QuEChERS involves the extraction of pesticides from various matrices, especially fruits, vegetables, and other food products. Combining a liquid-liquid extraction (LLE) and a dispersive solid phase extraction (d-SPE) clean up, QuEChERS provides a clean sample for analysis by gas chromatography (GC) or liquid chromatography (LC) …

A Study Whether Humans Can Produce Free Fatty Acids For Tasting, Emily Bacher

Student Scholarship

A growing concern throughout the world, especially the United States, is the health of our population. According to the National Health and Nutrition Examination Survey (NHANES) performed in 2009-2010, approximately 35% of both men and women in the United States are obese (Flegal, 2012). In 2005, more than 300,000 deaths in the United States were attributed to obesity. However, the World Health Organization listed obesity as one of ten most preventable health risks (Wilborn, 2005).
Why, then, do we as a society struggle so much with our weight? Some, such as Swinburn, believe this trend of obesity can be attributed …

Surface-Engineered Magnetic Nanoparticles For Sample Preparation And Analysis Of Proteins And Peptides, Parisa Pirani

LSU New Orleans Theses and Dissertations

Sample preparation as an essential step in mass spectrometry-based analysis, plays a critical role in proteomics studies. Magnetic nanoparticles (MNPs) have been widely used in protein and peptide sample preparation due to their magnetic properties, biocompatibility, easy synthesis and surface functionalization. MNPs loaded with analyte or analyte modification reagent can be easily separated from the reaction medium by an externally applied magnetic field. The small size of MNPs provides high analyte loading and extraction capacity. Additionally, MNP can be decorated with different functional groups to achieve selective modification or extraction of analyte. In this study we have utilized silica coated …

Development And Application Of Mass Spectrometry-Based Biophysical Approaches, Ying Zhang

Arts & Sciences Graduate Student Theses and Dissertations

Mass spectrometry (MS)-based biophysical approaches are new "tools" for protein characterization owing to its capability to analyze proteins and protein complexes that range in molecular weight from kDa to MDa. Protein characterization requires more than identifying the primary structure. More importantly, protein high order structures (i.e., secondary, tertiary and quaternary structures) are needed for biological studies. MS has become the major tool in studies of protein primary structure and post translational modifications (PTMs) over the past two decades. Because MS has high sensitivity and fast turnaround, more and more biophysical approaches rely on MS to generate information for protein higher …

Mass Spectrometry-Based Strategies For Biomolecular Structure Analysis: Steroid Metabolites Structures And Protein-Protein Interactions, Yuetian Yan

Arts & Sciences Graduate Student Theses and Dissertations

Mass spectrometry is an important method for studying the structure of both small molecules and large biomolecules (e.g., proteins). The majority of the applications prior to 1970 were focused on small molecules, owing to the limited ionization methods which posed difficulties in producing gas-phase ions for large biomolecules then. Beginning in the 1980's, with the introduction of new ionization methods (ESI and MALDI), the applications have gradually switched to biological science measuring large bioorganic molecules. Today, with the developing interest in metabolomics and proteomics, and ongoing improvement in MS-based techniques, mass spectrometry is extensively applied in the study of both …

An Unprecedented Nadph Domain Conformation In Lysine Monooxygenase Nbtg Provides Insights Into Uncoupling Of Oxygen Consumption From Substrate Hydroxylation, Claudia Binda, Reeder M. Robinson, Julia S. Martin Del Campo, Nicholas D. Keul, Pedro J. Rodriguez, Howard H. Robinson, Andrea Mattevi, Pablo Sobrado

Chemistry Faculty Research & Creative Works

N-Hydroxylating monooxygenases are involved in the biosynthesis of iron-chelating hydroxamate-containing siderophores that play a role in microbial virulence. These flavoenzymes catalyze the NADPH-and oxygen-dependent hydroxylation of amines such as those found on the side chains of lysine and ornithine. In this work we report the biochemical and structural characterization of Nocardia farcinica Lys monooxygenase (NbtG), which has similar biochemical properties to mycobacterial homologs. NbtG is also active on D-Lys, although it binds L-Lys with a higher affinity. Differently from the ornithine monooxygenases PvdA, SidA, and KtzI, NbtG can use both NADH and NADPH and is highly uncoupled, producing more superoxide …

Benzo-Fused Lactams From A Diversity-Oriented Synthesis (Dos) Library As Inhibitors Of Scavenger Receptor Bi (Sr-Bi)-Mediated Lipid Uptake, Chris Dockendorff, Patrick W. Faloon, Jun Pu, Miao Yu, Stephen Johnston, Melissa Bennion, Marsha Penman, Thomas J.F. Nieland, Sivaraman Dandapani, José R. Perez, Benito Munoz, Michelle A. Palmer, Stuart L. Schreiber, Monty Krieger

Chemistry Faculty Research and Publications

We report a new series of 8-membered benzo-fused lactams that inhibit cellular lipid uptake from HDL particles mediated by Scavenger Receptor, Class B, Type I (SR-BI). The series was identified via a high-throughput screen of the National Institutes of Health Molecular Libraries Small Molecule Repository (NIH MLSMR), measuring the transfer of the fluorescent lipid DiI from HDL particles to CHO cells overexpressing SR-BI. The series is part of a previously reported diversity-oriented synthesis (DOS) library prepared via a build-couple-pair approach. Detailed structure–activity relationship (SAR) studies were performed with a selection of the original library, as well as additional analogs prepared …

Light-Harvesting, Redox Control, And Biomimicry Of The Photosynthetic Antennas Of Green Sulfur Bacteria, Gregory Scott Orf

Arts & Sciences Graduate Student Theses and Dissertations

The green sulfur bacteria (class Chlorobea) are obligately anaerobic photoautotrophic prokaryotes. Members of this bacterial class are found in anoxic, sulfur- or iron-rich environments such as hydrothermal vents and hot springs. These bacteria are champions of lowlight adaptation, with some species being able to thrive photosynthetically on less than eight photons hr-1 per pigment. We have studied the two photosynthetic antenna complexes from these organisms that are responsible for light capture: the chlorosome and the Fenna-Matthews-Olson (FMO) protein.In regards to the chlorosome, we studied, using steady-state and time-resolved spectroscopic methods, the effect of incorporation of an expected, but as-yet-undiscovered-in-nature, light-harvesting …

Biological Degradation Of Acetaldehyde In Southern California Coastal Waters, Mary Senstad, Sovanndara Hok, Ori Barashy, Catherine D. Clark, Warren J. De Bruyn

Student Scholar Symposium Abstracts and Posters

Oxygenated hydrocarbons are ubiquitous in the atmosphere with levels ranging from low ppt (acetaldehyde) to low ppb (methanol). As an OH sink and an atmospheric HOx and ozone source, oxygenated hydrocarbons have a direct impact on the oxidative capacity of the atmosphere. The oceans are one of the largest sources of uncertainty in current atmospheric budget estimates of these species. A better understanding of the processes that produce and destroy these species in seawater would improve our understanding of the role of the oceans in cycling these species into or out of the atmosphere. We have measured the degradation rate …