Physical Sciences and Mathematics Commons^™

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

Mass Spectrometry Based Proteomics And Lipidomics Studies, Huan Kang

Theses and Dissertations

Mass spectrometry has emerged as having a vital role in various applications to biochemical fields. In this thesis, we have utilized a variety of mass spectrometry techniques for both bacteriophage proteomics and colostrum and milk lipidomics studies. Our first study was the proteome characterization of Great Salt Lake bacteriophage NS01 with SDS-PAGE GEL to separate the viral proteins and high performance liquid chromatography (HPLC) coupled with an LTQ Orbitrap to identify the proteins after in-gel digestion. In this project, we have successfully identified 11 proteins with high confidence, p-values < 0.01, including coat protein gp88 with a coverage of 91% and tail protein gp86 with a coverage of 40.96%, which facilitated the classification of NS01 as a T7-like phage. Our second study was the discovery of colostrum and milk biomarkers that can be used to predict the likelihood of development of production-related metabolic diseases (PRMDs) in dairy cows through a lipidomics approach. In this study, an electrospray ionization, time-of-flight mass spectrometer was applied to lipid profiling, quantification and significant biomolecule selection. A Q-Star quadrupole, orthogonal time-of-flight mass spectrometer and an Agilent 6530 accurate-mass quadrupole/time-of flight mass spectrometer were both used for lipid biomarker fragmentation and identification. According to linear discriminative statistical modeling, three panels of biomarkers were defined. A combination of 2 milk lipid predictors, including DG18:0/18:0 and TG 18:0/18:0/18:1, provided PRMD predictions with 75.0% sensitivity at 90.0% specificity. A combination of 3 colostrum lipid predictors, including TG16:0/18:1/18:3, DG16:0/16:0 and C₄₀H₆₀NO, provided PRMD prediction with 90.0% sensitivity at …

Mass Spectrometric Analyses Of Surface Proteins From Candida Albicans After Treatment With Histatin 5, Shirley Fan

Electronic Thesis and Dissertation Repository

Current drug therapies have lost their effectiveness in controlling the fungal species known as C. albicans; therefore, the need for newer drugs becomes crucial. Histatin 5 (Hst 5), a naturally occurring peptide found in the oral cavity, has demonstrated strong effects on controlling candidiasis. Here, we have proposed that the adhesion of cells through surface proteins is an important process. To allow the analysis of surface proteins, the concept of on-whole cell tryptic digestions were developed. This on-target approach allows for isolation of the peptides of interest, while greatly reducing digestion times.

To study the effects of Histatin 5 …

Transferrin-Based Therapeutics And Analytical Methods To Characterize Them, Son N. Nguyen

Doctoral Dissertations

Modern development of medicine requires detailed characterization by state-of-the art analytical techniques that can be used to analyze covalent structure, conformations and protein-receptor interaction to quantitatively measure biodistribution of protein therapeutics. Mass spectrometry has already become an indispensable tool facilitating all stages of protein drug development. Particularly, this work has demonstrated the tremendous potential of electrospray ionization (ESI) mass spectrometry (MS) in this arena by providing invaluable information beyond mass measurement that can be used to optimize protein drug conjugate structures during early stages of development, and to further catalyze drug design efforts. Additionally, a new sensitive and selective method …

Ribosome Component Turnover Kinetics Describes A Two-Pool Kinetic Model In Dietary Restriction That Suggests Rpl10 Is Exchanged During Ribosome Lifespan, Andrew David Mathis

Theses and Dissertations

The eukaryotic ribosome is a large molecular machine consisting of ~80 ribosomal proteins and 4 rRNAs. The 40S and 60S ribosomal subunits are assembled in the nucleolus by ~200 helper proteins then shipped into the cytoplasm or to the endoplasmic reticulum where protein translation takes place. Eventually ribosomes are removed from the cytoplasm and recycled through ribophagy, however, very is little is known about ribosomal protein exchange after assembly but before ribophagy. Using kinetic turnover measurements of ribosomal proteins and rRNA in vivo we determined ribosomal protein replacement rates are diverse suggesting ribosomal components may be replaced without destruction of …

Hydrogen Exchange Mass Spectrometry For Studying Protein-Ligand Interactions, Modupeola A. Sowole

Electronic Thesis and Dissertation Repository

Hydrogen deuterium exchange (HDX) coupled with mass spectrometry is widely used for probing protein structure and dynamics. Protein-ligand interactions usually induce a reduction in the measured HDX rates an effect that may be ascribed to stabilization of the protein structure. This work aims to improve the general understanding of the changes in HDX patterns associated with ligand binding.

We initially applied HDX for studying differences between oxy-hemoglobin (Oxy-Hb) and aquomet-hemoglobin (Chapter 2). The results show that the α and β subunits respond differently to the oxy to aquomet transition with the heme binding pocket being destabilized in both cases. The …

Using Ion Mobility Spectrometry To Study Protein Conformations In The Gas Phase, Yu Sun

Electronic Thesis and Dissertation Repository

The question whether electrosprayed protein ions retain solution-like conformations remains a matter of debate. One way to address this issue involves comparisons of collision cross sections measured by travelling wave ion mobility spectrometry (TWIMS) with the values calculated for model structures. It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on four different proteins we demonstrated that collision cross section values and collisional unfolding profiles are virtually indistinguishable under both conditions. Calibration can be challenging because differences in the extent of collisional activation for TWIMS and drift tube calibrant data …

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

Arts & Sciences Electronic 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 …

Analysis Of Anacardic Acid On The Surface Of Pelargonium × Hortorum Using Matrix Assisted Laser Desorptoin Ionization Mass Spectrometry Imaging., Bryan Edward Wessel 1989-

Electronic Theses and Dissertations

The biosynthetic pathway leading to the production of anacardic acids (AnAcs) in glandular trichomes on the surface of geranium plants remains unclear. Anacardic acids are salicylic acid derivatives known to possess various medicinal benefits. Gene silencing techniques, such as RNA interference, could be useful in determining specific enzymes involved in the synthesis of AnAcs. However, it is first necessary to develop methodologies to image AnAcs. In this project, both fluorescence (FL) and mass spectral imaging (MSI) were tested. Our results indicate that cellular imaging of AnAcs, via FL, is not suitable because the spectral ranges of absorption and emission of …

Distinguishing Macrophage Activation States By Mass Spectrometry, Matthias Manfred Knust

Graduate Theses and Dissertations

Macrophages are versatile and highly adaptive cells that are involved in a wide range of physiological processes including host defense, homeostasis or regeneration, as well as pathogenesis. They react to their microenvironment, assuming various roles based on chemical and/or physical cues, and can reversibly shift between these so-called activation states. Concurrently, the technique of immunohistochemistry is used to gain spatial information on activated macrophages on tissue sections. The aim of this work was to find mass spectral biomarkers that allow the differentiation of activation states, and establish conditions that can be used in imaging mass spectrometry (IMS) experiments to investigate …

Investigation Of The Chemical Protection Capacity Of Common Shoe Materials In Undergraduate Laboratories, Sarah E. Lawson

Undergraduate Honors Theses

The objective of this study was to evaluate the chemical resistance of common shoe materials regularly worn in undergraduate chemistry laboratories by subjecting the materials to hydrochloric acid and sodium hydroxide. The materials tested were leather, canvas cotton, and polyester. Due to the lack of restriction on undergraduate laboratory footwear, the research discussed in this thesis is important to undergraduate universities. Currently, many universities across the nation only require undergraduate students to wear close-toed, close-heeled shoes in chemistry laboratories, and often the resistance of the shoe material to acids and bases may not be taken into careful consideration. Overall, the …

Investigation Into The Biological Importance And Function Of Proinsulin C-Peptide, Christina L. Newsome

Theses, Dissertations and Capstones

The C-peptide of insulin was thought to be biologically inactive, but recent studies have shown that the C-peptide causes multiple molecular and physiological effects. Evidence has shown that C-peptide binds to a cell surface receptor, probably a G-protein coupled receptor, and that the COOH-terminal pentapeptide is essential for binding and constitutes an active site. For a further understanding of the detailed nature of the physiological effects of C-peptide, the receptor structure needs to be determined. We designed an affinity column using C-peptide to try and gain a better understanding of the biological effects by examining what proteins the affinity column …

Synthesis, Characterization, And Rna Reactivity Of Amino-Acid-Linked Cisplatin Analogues, Xun Bao

Wayne State University Dissertations

The essential role of ribosomal RNA (rRNA) in the cell life cycle is highlighted by protein synthesis; therefore, the ribosome is considered to be an ideal drug target. Ribosomal RNAs exhibit a high level of structural diversity. The well-known anticancer drug cisplatin was previously applied as a chemical probe of rRNA structure to determine solvent accessible purines (guanosine) in vivo and in vitro. Cisplatin accumulates faster on RNA than DNA, with less chance of repair. As such, designing new RNA-targeting Pt compounds is not only a promising direction for chemical-probing applications, but also for the design of anticancer drugs that …

Development Of Inlet And Vacuum Ionization Methods For Characterization Of Biological Materials By Mass Spectrometry, Beixi Wang

Wayne State University Dissertations

Inlet ionization and vacuum ionization are novel ionization methods to produce electrospray ionization (ESI)-like ions from the solid or liquid states, operating from atmospheric pressure (AP) or vacuum, without the use of voltage or the necessity of high energy input such as a laser or particle beam. The fundamental aspects were probed for better understanding of the novel ionization processes. Initial applications were attempted to utilize the novel ionization methods for fast, robust, and quantitative analyses.

For inlet ionizations (laserspray ionization inlet, LSII; matrix assisted ionization inlet, MAII; and solvent assisted ionization inlet, SAII), small (e.g. drugs) to large (e.g. …

Characterization Of Noncovalent Complexes Of Polyelectrolytes By Mass Spectrometry, Anthony J. Marino

Williams Honors College, Honors Research Projects

Various ions of poly-L-lysine and polystyrene sulfonic acid were successfully observed first within a matrix-assisted laser desorption/ionization mass spectrometer and subsequently in an electrospray ionization mass spectrometer. The successful ionization of these polymers allowed for studies to be performed on the noncovalent interactions between the two. Noncovalent interactions were effectively studied on both instruments, but further quantified using tandem mass spectrometry found within the MALDI system and ion-mobility mass spectrometry found within the electrospray ionization system. As a result of employing the use of ion-mobility, various different stoichiometries and charges of polyelectrolyte complexes could be distinguished.

Mass Spectrometry-Based Rnomics : Global Surveys Of Ribonucleotide Modifications As Possible Indicators Of Cell Identity, Epigenetic, Metabolic And Pathological State, Rebecca Erin Rose

Legacy Theses & Dissertations (2009 - 2024)

Discovery of the regulatory roles of non-protein coding RNAs (ncRNAs), once considered “junk” or “transcriptional noise”, has prompted a reassessment of the significance of the multifaceted activities of RNA in cellular response, which can result in cell transformation and diseased states. This reassessment, however, can only be accomplished if techniques are developed to capture, characterize and quantify the more than 100 covalent post-transcriptional modifications (PTMs) that adorn natural RNAs. Undoubtedly, the creation of high-throughput platforms such as next-generation sequencing and RNA-seq have provided unparalleled accuracy and sensitivity, however, they rely on strand amplification procedures that are blind to the known …