Analytical Chemistry Commons^™

Structural Dynamics Of A Single-Stranded Rna–Helix Junction Using Nmr, Catherine D. Eichhorn, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, ¹³C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A₆-tract and forms an acute pivot point for …

New Carbohydrate-Based Anti-Cancer And Anti-Bacterial Vaccines, Zhifang Zhou

Wayne State University Dissertations

The unique carbohydrates expressed on the surface of cancer, bacterial, viral and fungal cells are excellent target antigens for the design of therapeutic or preventive vaccines. However, as antigens carbohydrates have problems. First, carbohydrates usually have low immunogenicity. Second, even if immunogenic, carbohydrates typically elicit T cell-independent immune responses. To overcome these problems and design useful vaccines based on carbohydrate antigens, they are usually coupled with carrier proteins to form conjugates to enhance the immunogenicity of the antigens. However, there are still some issues existing in glycoprotein vaccines, such as poor reproducibility of the conjugates, difficulties in quality control and …

Spontaneous Formation Of One-Dimensional Hydrogen Gas Hydrate In Carbon Nanotubes, Wenhui Zhao, Lu Wang, Jaeil Bai, Joseph S. Francisco, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We present molecular dynamics simulation evidence of spontaneous formation of quasi-one-dimensional (Q1D) hydrogen gas hydrates within single-walled carbon nanotubes (SW-CNTs) of nanometer-sized diameter (1−1.3 nm) near ambient temperature. Contrary to conventional 3D gas hydrates in which the guest molecules are typically contained in individual and isolated cages in the host lattice, the guest H₂ molecules in the Q1D gas hydrates are contained within a 1D nanochannel in which the H₂ molecules form a molecule wire. In particular, we show that in the (15,0) zigzag SW-CNT, the hexagonal H₂ hydrate tends to form, with one H₂ molecule …

A Photoelectron Spectroscopy And Ab Initio Study Of The Structures And Chemical Bonding Of The B25 − Cluster, Zachary A Piazza, Ivan H. Popov, Wei-Li Li, Rhitankar Pal, Xiao Cheng Zeng, Alexander I. Boldyrev, Lai-Sheng Wang

Xiao Cheng Zeng Publications

Photoelectron spectroscopy and ab initio calculations are used to investigate the structures and chemical bonding of the B₂₅ − cluster. Global minimum searches reveal a dense potential energy landscape with 13 quasi-planar structures within 10 kcal/mol at the CCSD(T)/6-311+G(d) level of theory. Three quasi-planar isomers (I, II, and III) are lowest in energy and nearly degenerate at the CCSD(T) level of theory, with II and III being 0.8 and 0.9 kcal/mol higher, respectively, whereas at two density functional levels of theory isomer III is the lowest in energy (8.4 kcal/mol more stable than I at PBE0/6-311+G(2df) level). Comparison with …

Investigation Of Pyrrolizidine Alkaloids In Foods Using Liquid Chromatography Mass Spectrometry, Caroline Griffin

PhDs

Pyrrolizidine Alkaloids (PAs) are known plant toxins which can cause hepatic veno-occlusive disease (HVOD) in both humans and livestock when ingested. Although PAs are primarily known for their hepatotoxicity they also induce genotoxicity, carcinogenicity and pneumotoxicity. PAs are consumed through plants as food, for medicinal purposes, or as contaminants of agricultural crops. Aside from ingesting the plants directly PA exposure may occur through the consumption of honey produced by bees that visit PA-containing plants or by drinking milk produced by animals that have consumed PA-containing plants. Possible PA contamination in our food chain is a potential health risk.

To assess …

The Development Of Liquid Chromatography Mass Spectrometry Methods For The Analysis Of Cyanobacterial Toxins In Environmental Freshwaters, Brian Anthony Dineen

Theses

Cyanobacteria, also known as blue-green algae, are a common component of many freshwater and marine ecosystems and have a potential to produce several different classes of biotoxins. The most common class of cyanobacterial toxins are the microcystins (MCs) and cylindrospermopsins (CYLs). MCs are cyclic heptapeptides that display potent hepatotoxicity and are tumour promoters. CYLs are alkaloids that are cytotoxic and can cause illness and display hepatotoxic effects in animals and humans. Worldwide, these toxins have caused fatal poisonings to animals, birds and fish. Several incidents of human intoxications have been reported and the presence of these toxins in environmental waters …

Investigation Of Pyrrolizidine Alkaloids In Foods Using Liquid Chromatography Mass Spectrometry, Caroline Griffin

Theses

Pyrrolizidine Alkaloids (PAs) are known plant toxins which can cause hepatic veno-occlusive disease (HVOD) in both humans and livestock when ingested. Although PAs are primarily known for their hepatotoxicity they also induce genotoxicity, carcinogenicity and pneumotoxicity. PAs are consumed through plants as food, for medicinal purposes, or as contaminants of agricultural crops. Aside from ingesting the plants directly PA exposure may occur through the consumption of honey produced by bees that visit PA-containing plants or by drinking milk produced by animals that have consumed PA-containing plants. Possible PA contamination in our food chain is a potential health risk.

To assess …

Quantitative Mass Spectrometric Investigations Of Protein Biomarkers: Serum Thymidine Kinase 1 And Human Osteopontin, Morse Faria

Theses and Dissertations

Mass spectrometry is being increasingly used in biomarker research mainly due to its ability to achieve high selectivity coupled with high sensitivity. This dissertation focuses on quantitative mass spectrometric investigations of two protein biomarkers i.e. serum thymidine kinase 1 (TK1) and human osteopontin (OPN).

First part of this research was focused on developing a liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method for measuring the activity of TK1 in serum by monitoring the conversion of a TK1 specific exogenous substrate, 3’-deoxy-3’-fluorothymidine (FLT), to its mono-phosphorylated form 3’-deoxy-3’-fluorothymidine monophosphate (FLT-MP). A method to quantify FLT-MP on LC-MS/MS was developed and …

Exploring The Asymmetric Environment Of Various Chiral Catalysts Using A Modified Ion-Trap Mass Spectrometer: Towards The Development Of A Rapid Chiral Catalyst Screening Method, Cary M. Davis

Theses and Dissertations

Since the tragedy of the drug Thalidomide® in the late 1950 to early 1960’s, chirality has been recognized as an important aspect that must be controlled in the drug development process in the pharmaceutical industry. Since then, there has been a considerable movement towards single enantiomer drugs. This demand has presented many challenges for the synthetic organic chemist. Chiral catalysts offer one solution to this problem, as they afford the unique ability to preferentially synthesize one enantiomer. Unfortunately, the design of new chiral catalysts is often empirical, with luck and trial and error necessary due to factors that govern enantioselectivity. …

Quantitative Structure-Activity Relationship (Qsar) Analysis Of Antileishmanial Natural Products, Jessica Ewald

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

No abstract provided.

Hiv-1 Rna Dimerization At Single Molecule Level, Hansini R. Mundigala

Wayne State University Dissertations

The Dimerization Initiation Sequence (DIS) is a conserved hairpin-loop motif on the 5' UTR of the HIV-1 genome. It plays an important role in genome dimerization through formation of a "kissing complex" intermediate between two homologous DIS sequences. This bimolecular kissing complex ultimately leads to the formation of an extended RNA duplex. Understanding the kinetics of this interaction is key to exploiting DIS as a possible drug target against HIV. We wish to report a novel study that makes an important contribution to understanding the dimerization mechanism of HIV-1 RNA in vitro. Our work has employed single-molecule fluorescence resonance energy …

Monitoring Ligand-Induced Nucleic Acid Conformational Changes Using Ion Mobility Spectrometry-Mass Spectrometry, Bill Kenneth Redick

Legacy Theses & Dissertations (2009 - 2024)

Three-dimensional structures of biopolymers frequently dictate the biological role those molecules play. As such, investigation into structure of nucleic acids can provide important information pertaining to how those nucleic acids work. Many nucleic acid species, especially single-stranded RNA, fold into unique structures that allow them to function properly. Metals, and other cationic species, are often bound to the nucleic acid to make folding into the proper structure more favorable by neutralizing the negative charge on the nucleic acid imparted by the phosphate group. This investigation explores tertiary structure of nucleic acids that have been folded in the presence of ligands …

Improving The Microbial Source Tracking Toolbox : Evaluating The Use Of Selective Enrichments And Artificial Sweeteners In A Multi-Tiered Approach, Stacey A. Helming

Legacy Theses & Dissertations (2009 - 2024)

Microbial contamination of surface waters is a public health concern world-wide, with non-point source fecal input contributing to millions of cases of waterborne illness annually. Numerous techniques have been proposed to monitor for non-point source fecal contamination, but few studies have explored the correlation of multiple chemical and microbial fecal source tracking markers in ambient waters. Therefore, the purpose of these studies was to evaluate the use of multiple "ideal" markers of fecal contamination and improve upon any analytical techniques required to identify species-specific fecal contamination in surface waters. The use of selective enrichments to improve the sensitivity of end-point …

Raman Spectroscopy Of Blood Serum And Cerebrospinal Fluid And Multivariate Data Analysis For Alzheimer's Disease Diagnostics, Elena Ryzhikova

Legacy Theses & Dissertations (2009 - 2024)

The efficient and accurate diagnosis at the early stages of dementia is a key moment for effective treatment and productive research to find a new ways to combat the disease. It is especially true for Alzheimer's disease (AD) for which there is no effective cure, but several treatments are known to allow slowing down the degenerative processes. Alzheimer's disease (AD) displays only non-specific clinical symptoms of mental decline for decades after the initiation and is very challenging to differentiate even at the later stages when it becomes very aggressive. Despite the great need, current diagnostic tests are unable to diagnose …

Quantification Of Free Sialic Acid In Human Plasma Through A Robust Quinoxalinone Derivatization And Lc–Ms/Ms Using Isotope-Labeled Standard Calibration, Dan Wang, Xiang Zhou, Lin Wang, Sihe Wang, Xue-Long Sun

Chemistry Faculty Publications

We report an accurate quantification of free sialic acid (SA) in human plasma using LC–MS/MS method with isotope-labeled standard calibration (ILSC) and robust derivatization. Specifically, derivatization of SA with a stable and inexpensive 3,4-diaminotoluene (DAT) provides a stable product of SA with high MS response, proving a convenient and cost-effective LC–MS/MS analysis of free SA. In addition, the use of ¹³C₃-SA as calibration standard ensured the accuracy for the measurement. This assay used ultra high performance liquid chromatography (UHPLC) for separation of native/labeled SA and IS from matrix interference, and employed mass spectrometry in multiple reaction monitoring …

Structural Analysis Of Bulky Thiolate-Protected Gold Nanomolecules, David Walton Crasto

Electronic Theses and Dissertations

Routine preparation of thiolate-protected gold nanomolecules involves, most commonly, straight-chain organic thiolate ligands for which the sulfhydryl `head' group is bound to a primary carbon atom. The primary connectivity of these sulfur atoms, such as for the case of n-hexanethiol and phenylethanethiol, allows for even packing, and the relative ease of formation of gold-thiolate oligomers about the surface monolayer in the formation of Au-SR bonds. Moreover, these straight-chain ligands routinely support the formation of an icosahedron-based series of core-size gold nanomolecules. Within this series of nanoparticles, Au25(SR)18 and Au38(SR)24 are among the most commonly studied core-sizes; Au25(SR)18 is situated upon …

Application Of Stir Bar Sorptive Extraction Thermal Desorption Gas Chromatography Mass Spectrometry For The Study Of Water Accommodated Fractions Of Fossil Fuels And Biodiesel, Ricardo Mccreary

Open Access Theses & Dissertations

Even though measures are taken to decrease accidental release of crude oil and refined fuels into the aquatic environment, continued demand of such fuels--particularly in the transportation sector--pose a continued threat to the aquatic environment throughout their handling, processing, and consumption. Even though measures can be taken to remove the visible layers of fuel in water, it has been shown that constituents of these fuels--that partition into water--can have adverse health effects on the aquatic organisms at low concentrations that are not necessarily predictable through the study of the actual fuel's original composition. Consequently, this renders the need for an …

Science Classics, Mark Masthay

Chemistry Faculty Publications

An essay on the impact of the works in the Imprints and Impressions: Milestones in Human Progress, an exhibition of rare books from the collection of Stuart Rose. Exhibition was held Sept. 29-Nov. 9, 2014, at the University of Dayton.

Environmental Assessment Of Used Motor Oil In The Ciudad Juarez-El Paso Area, Alma Leticia Figueroa

Open Access Theses & Dissertations

As a hazardous waste generated in large amounts worldwide, used motor oil (UMO) is an important issue for environmental science. UMO contains the carcinogenic and mutagenic compounds Polycyclic Aromatic Hydrocarbons (PAHs). Unless properly managed and disposed of PAHs remain in the environment, principally in sediments and soil. From such environmental sinks, PAHs can migrate to watersheds contaminate drinking water, and damage ecosystems and human health.

Generators of used oil include "businesses that handle used oil through commercial or industrial operations or from the maintenance of vehicles and equipment," (United States Environmental Protection Agency (USEPA), 2013). An example of such a …

Impact Of Zinc Oxide Nanoparticles On Green Pea Plant & Seed Quality And Effects On Physiological Traits Of Green Peas, Corn, And Zucchini By Silver Nanoparticles, Arnab Mukherjee

Open Access Theses & Dissertations

The production and use of numerous engineered nanomaterials (ENMs) have increased exponentially over the past decade. Nanoparticles (NPs), ENMs possessing diameter between 1-100 nm, (NPs), are widely used in many applications. Worldwide consumption of NPs has increased their possible release into the environment. This, in turn, has elevated the extent of the potential impacts of NP exposure to living and non-living organisms. This is why the assessment of the impact of NPs on different environmental components, especially on plants, the producer in the food web, has become a very important aspect of nano-ecotoxicology. However, studies focusing on phytotoxicity and effects …