The Study Of Hydrophobic Biomolecules With Matrix Assisted Laser Desorption Ionization Mass Spectrometry And Atomic Force Microscopy, Brandy L. Perkins

LSU Doctoral Dissertations

Abstract

Matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) can be used to obtain localization and chemical information of hydrophobic biomolecules on tissue samples.  A technique has been developed to modify a standard MALDI matrix that improves the selectivity for hydrophobic biomolecules on the tissue sample. The modification involves the use of a Group of Uniform Materials Based on Organic Salts (GUMBOS). GUMBOS are ionic liquids (IL) that are bulky organic ions with a counter ion that can be changed for tuning.  They are more stable than traditional matrices under vacuum.  Unlike traditional IL’s, the GUMBOS melting point ranges …

Infrared Laser Ablation Of Biomolecules From Formalin-Fixed Tissue, Blessing Chisom Egbejiogu

LSU Doctoral Dissertations

In the research described in this dissertation, a high-precision infrared laser ablation microsampling method was utilized for spatially resolved proteomic and lipidomic analyses of formalin fixed paraffin embedded (FFPE) tissue, a widely used archival sample in biomedical research. Despite its extensive use, FFPE tissue presents challenges for proteomic analysis due to protein cross-linking and modifications introduced during fixation, which can hinder extraction and identification. Developing a streamlined high-resolution method to recover biomolecules from FFPE samples is critical for advancing biomarker discovery, retrospective studies, and multi-omics research. To address these challenges, this study employs an infrared (IR) laser ablation microdissection system …

Nanofabrication Of Tetraphenyl Porphyrin Surface Assemblies Linked With Tin Tetrachloride: A Scanning Probe Microscopy Investigation, Quynh Do

LSU Doctoral Dissertations

Scanning probe microscopy (SPM) and colloidal lithography methods were used to study the covalent coupling of porphyrins to surfaces. In this dissertation, experimental methods for SPM operation, techniques, and applications are described. Measurement of tip-sample interactions between a sharp tip and surface is translated into digital image data maps with x-, y-, and z-data. Colloidal lithography can be used to fabricate test platforms for AFM studies. The periodicity and arrangement of the designed nanostructures is determined by the size of the colloidal particles used for surface masks. Data processing is required to obtain images and topography information from raw AFM …

Effect Of Electronegativity On Environmentally Persistent Free Radical (Epfr) Formation, Persistence, And Toxicity On Transition Metal Oxides, Syed Monjur Ahmed

LSU Doctoral Dissertations

Environmentally persistent free radicals (EPFRs) are a group of emerging environmental pollutants. Owing to their resonance structures, EPFRs have significantly higher lifetimes than typical free radicals, and can induce the formation of reactive oxygen species (ROS) known to cause pulmonary and cardiovascular dysfunction. EPFRs form by the adsorption of organic precursors on a transition metal oxide (TMO) surface and exhibit enough stability to cause negative health and environmental effects. While aromatic and substituted aromatic precursors form EPFRs on TMO surface at elevated temperatures and numerous substituted organics are ubiquitous in various industrial processes and household products, studies have largely overlooked …

Molecular-Level Studies Of Nanopatterned Biomolecules With Atomic Force Microscopy, Ashley R. Walker

LSU Doctoral Dissertations

Atomic force microscopy (AFM) is an analytical technique in which a tipped probe is gently scanned across the surface in a raster pattern to generate digital images of a sample at the nanoscale. The AFM instrument has three general operational modes, which are contact, non-contact and tapping-mode, that can be used to examine materials at the atomic level. Single-molecular details of biological molecules and other soft organic materials can be captured with minimal denaturation in either ambient or liquid environments when using tapping-mode AFM. In tapping-mode, the probe is driven to oscillate vertically while the tip is scanned across the …

Synthesis And Characterization Of Porphyrin-Encapsulated Nanoparticles: Investigations With Scanning Probe Microscopy, Olajumoke Helen Olubowale

LSU Doctoral Dissertations

Scanning probe microscopy (SPM) encompasses a family of surface measurements that use a sharp probe to “feel” a surface. The tip is scanned point-by-point to build a map of the sample topography, which can be correlated with local measurements of surface properties. This dissertation outlines the history of SPM and describes techniques, operational modes, and applications. A review of force volume mapping (FVM), a 3D characterization mode of SPM used to map material properties detailed. Force volume mapping can be achieved by measuring multiple force measurements point-by-point in a grid pattern. Local properties such as chemical forces, dielectric properties, nanomechanical …

Design, Synthesis, And Characterization Of Nqo1-Activatable Luminescent Probes, Ovini Vionika Weeratung Kankanamge

LSU Doctoral Dissertations

Being among the top ten causes of death, cancer has constantly been able to grab the attention of researchers all around the world. While several treatment methods prevail to cure cancer, the seriousness of this medical condition requires continuous work in the development of novel treatments as well as scientific advancements in order to achieve early detection of the disease. Luminescence imaging is an emerging field in both diagnosis of diseases, as well as a means to provide guidance in clinical surgeries. While there exist only a few contrasting agents approved by the Food and Drug Administration, the need for …

Determining The 3d Structure And Dynamics Of Mouse Notch1 Epidermal Growth Factor-Like Repeat 26 Using Nuclear Magnetic Resonance Spectroscopy, Kendra D. Jenkins

LSU Doctoral Dissertations

NOTCH is a transmembrane protein that transmits signals between cells in direct contact and alters gene expression. The signaling pathway is important because it is involved in cell fate determination. The NOTCH1 extracellular domain has 36 epidermal growth factor-like (EGF) repeats that are responsible for ligand binding. Mutations in the EGF-like repeats cause various neurological and developmental disorders. NOTCH1 signaling initiates when DSL ligands bind to EGF11-12, the minimum Ligand Binding Domain (LBD). The Abruptex region of the NOTCH1 protein (EGF24-29) is a highly glycosylated, flexible region with calcium binding sites that regulates NOTCH1 signaling and binding by interacting with …

3-Dimensional Structural Determination Of Epidermal Growth Factor-Like Repeat 27 From Mouse Notch1 Using Nuclear Magnetic Resonance Spectroscopy, Justin Grennell

LSU Doctoral Dissertations

NOTCH1 has been associated with a variety of human ailments, such as cancer and heart disease. NOTCH1 is a transmembrane protein that contains 36 epidermal growth factor-like (EGF) repeats, which facilitate cell signaling by binding proteins on neighboring cells. Each repeat contains about 40 amino acids and has to be folded in a specific manner to function properly. The amino acid sequence, carbohydrate pattern, and calcium-binding sites of EGF-like repeats vary, but the pattern along the 36-repeat chain is conserved. The Abruptex region (EGF24-29) of NOTCH1 is a highly glycosylated (having undergone sugar addition) and flexible region, which gained its …

Indicators Of Senescence And Their Relationship With The Antioxidant Response Element In Ovarian Cancer Cells—Toward A More Encompassing View Of Enzyme Activity Levels In Cells, Shaniqua Analycia Hayes

LSU Doctoral Dissertations

Enzymes and other related proteins are promising targets as biomarkers for cancer diagnostics, and it is therefore important to be able to quantify intracellular enzyme activity levels, not just presence of enzyme. Thus, there is a great need for the development of methods that offer spatiotemporal quantification of intracellular enzyme activity levels in respiring 2- and 3-dimensional cultures or their sample-processed variants. Previous studies have demonstrated that ß-gal is upregulated in senescence and in select ovarian cancers, and its expression/activity is upregulated when cells are under oxidative stress conditions. To that end, the primary goal of this work was to …

A Systematic Multiscale Investigation Of Nanoparticle-Assisted Co2 Enhanced Oil Recovery (Eor) Process For Shale Oil Reservoirs, Dayo A. Afekare

LSU Doctoral Dissertations

Shale oil reservoirs are prolific on the short term due to hydraulic fracturing and horizontal drilling but experience significant production decline, leading to poor ultimate recovery and leaving billions of barrels of oil buried in the ground. In this study, a systematic multi-scale investigation of an enhanced oil recovery (EOR) process using relatively inexpensive silicon dioxide nanoparticles and carbon dioxide for shale oil reservoirs was conducted. Using the Tuscaloosa Marine Shale (TMS) as a case study, aqueous dispersions of nanosilica in conjunction with CO₂ were investigated at nano-to-core scales. At the nanoscale, atomic force microscope was used to investigate …

Investigations Of The Structure And Protein-Protein Interactions Of Chlamydia Trachomatis Scc4, Thilini Oshadhi Senarath Ukwaththage

LSU Doctoral Dissertations

Chlamydia trachomatis (CT) is the most common, sexually transmitted bacterial disease (STD) in the world. In the developmental cycle of CT, specific chlamydia chaperone 4 (Scc4) is a unique protein with essential and multiple roles. Hence, Scc4 is significant as a virulence target for therapeutic approaches to treat chlamydial infections. A novel approach was discovered to purify tag free Scc4 by utilizing a 6X-histidine-tag on Scc1 in the co-expressed Scc4:Scc1 complex by capturing the complex on nickel-charged immobilized metal affinity chromatography resin, followed by dissociation of Scc4 with sarkosyl. Using triple resonance NMR experiments, backbone and sidechain resonances …

Development Of Engineered Soil Surrogates For Modeling Natural Soil Sorption Behavior, Ghada Yehia Abdalla

LSU Doctoral Dissertations

The land produces more than 95% of the global food supply, and with a continuously growing population, we need to optimize the use of the available agricultural land. Soil organic matter (SOM) is an essential component of soils, especially concerning their fertility and sorption behavior. The chemical composition of the SOM consists of lipids, lignin, and cellulose. However, the heterogeneous and complex nature of SOM, and real soils, makes their study challenging and introduces uncontrollable factors.

Therefore, structural mimics of natural soils with increasing complexity representing the real soil functionality were synthesized and evaluated for bulk properties related to their …

Deep-Ultraviolet Laser Ablation For Biomolecular Analysis, Oluwaremilekun Omowunmi Lawal

LSU Doctoral Dissertations

New sampling and ionization techniques were developed using a deep-ultraviolet (DUV) laser at 193 nm wavelength for analysis of large biomolecules. A micrometer spatial resolution DUV laser ablation and capture system was constructed to sample tissue biomolecules. The spot size measurements of the focused beam showed that subcellular spots with ca. 2 μm diameter can be readily achieved with this wavelength. To demonstrate the extraction of tissue biomolecules with the DUV laser, regions of tissue sections were ablated and captured for offline proteomic and genomic analysis. The proteomic studies revealed that the tissue proteins were ejected without fragmentation and that …

Structure And Dynamics Of Phospholipid Vesicles And The Dependence On Nanoscale Interactions With Molecules Of Varying Complexity, Lakshapathy Widanelage Judith Upeka De Mel

LSU Doctoral Dissertations

In this dissertation, molecular interactions and changes imposed by nano-scale structures on phospholipid vesicles were investigated. 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) large unilamellar vesicles (LUVs) were used as the model system. Understanding changes of the bilayer structure, interfacial properties, lipid dynamics, and self-assembly, allows bridging relationships between biological cell membrane structure and dynamics to cellular functionalities. For example, membrane curvature changes are linked to membrane protein functions, although the exact mechanisms of control are not yet understood. Moreover, the knowledge gained from vesicle models allows exploring novel strategies for drug delivery applications. To achieve this, DOPC LUVs were synthesized and characterized by a …

Antimicrobial Strategies For Topical Applications, Kelsey Marie Lopez

LSU Doctoral Dissertations

Bacteria can thrive in diverse environments and are often harmless or beneficial. Bacteria in digestive tracts is one example of beneficial bacteria; however, bacteria can be harmful and when this type proliferates, it can cause infections within hosts. Bacterial infections are easily treated with antibiotics in most cases. However, bacteria are also capable of developing mutations which could cause them to become multi-drug resistant and eventually, “superbugs.” Therefore, the development of novel antimicrobial agents and materials capable of combating drug-resistant bacteria is necessary. Research presented in this dissertation focuses on different strategies for minimizing and preventing topical bacterial infections using …

Synthesis, Characterization, And Investigation Of Metal Ion Quenching In Fluorescent Carbon Dot Surrogates For Particulate Matter Black Carbon And Evaluation Of Cellular Health Effects Due To The Surrogate Materials, Christopher Lee Sumner Jr

LSU Doctoral Dissertations

Black carbon (BC) is an environmental pollutant of particular concern to many international organizations for both its health effects and environmental effects. Probing health effects of BC as produced in the environment is difficult due to the complex nature of environmental pollutants found in their naturally occurring state. Fluorescent carbon dots (FCDs) were chosen to be used as a surrogate for BC. In the process of examining FCDs and their behavior as surrogates, information was gained on the health effects and behavior of FCDs as a class of nanomaterials for cell and tissue studies, which is outlined in this dissertation. …

Assessment Of Soil Protein And Refractory Soil Organic Matter Across Two Chronosequences Of Newly Developing Marshes In Coastal Louisiana, Usa, Stuart Alexander Mcclellan

LSU Doctoral Dissertations

The impacts of sea-level rise and hydrologic manipulation are threatening the stability of coastal marshes throughout the world, thereby increasing the potential for re-mineralization of soil organic matter (SOM) in these systems. Such threats have prompted marsh restoration efforts, particularly in coastal Louisiana, yet it is unclear how the slowly decomposing (refractory) and quickly decomposing (labile) fractions of SOM may be differentially affected by different approaches to marsh restoration. Additionally, otherwise labile compounds may accumulate in the soil via a range of protective mechanisms, including rapid burial and association with organic compounds that are thought to enhance soil aggregation, such …

The Effects Of Temperature On The Yields Of Aliphatic And Aromatic Products From The Supercritical Pyrolysis Of 1-Octene, Elizabeth Anne Hurst

LSU Doctoral Dissertations

Prior to their combustion, fuels for future high-speed aircraft are expected to experience supercritical conditions, leading to the production of polycyclic aromatic hydrocarbons (PAH), precursors to solid carbonaceous deposits, via pyrolytic reactions. These solid deposits can clog fuel-transfer lines, causing unsafe aircraft operation. To prevent the formation of fuel-line deposits, it is critical to understand the reaction pathways that lead to PAH formation in the supercritical fuel pyrolysis environment.

To better understand the role of large 1-alkenes in PAH formation, supercritical pyrolysis experiments with model fuel 1-octene, a representative 1-alkene product from supercritical n-alkane pyrolysis, have been performed. The …

Electrification Ionization: Fundamentals And Applications, Bijay Kumar Banstola

LSU Doctoral Dissertations

Electrification ionization is a method to produce ions from solid samples by charge separation. This separation of charge can be enhanced by organic molecules known as matrix compounds to produce highly charged molecules. In this research, new methods were developed for the application of electrification ionization for surface analysis and the ionization mechanism was investigated. First, an electrification ionization matrix was used for tissue imaging using laser ablation. A two-component matrix of 2-nitrophloroglucinol and silica nanoparticles was found to increase the number of multiply charged ions from the tissue. Images of mouse brain with multiply charged ions were obtained. In …

Quartz Crystal Microbalance Based Sensors For Detection And Discrimination Of Volatile Organic Compounds Using Ionic Materials, Stephanie R. Vaughan

LSU Doctoral Dissertations

Volatile organic compounds (VOCs) are prevalent in everyday life, ranging from household chemicals, naturally occurring scents from common plants and animals, to industrial-scale chemicals. Many of these VOCs are known to cause adverse health and environmental effects and require regulation to prevent pollution. Detecting VOCs plays a critical role in food quality control, environmental quality control, medical diagnostics, and explosives detection. Thus, development of adequate sensing devices for detection and discrimination of VOCs is of great importance. In recent years, use of quartz crystal microbalance (QCM) based sensor arrays for analyses of VOCs has attracted significant interest. Detection of VOCs …

In Vitro Evaluation Of Ovarian Cancer Tumorigenesis As A Function Of Quinone Oxidoreducatse-1 And Cell Phenotype, Milcah S. Jackson

LSU Doctoral Dissertations

In vitro multicellular spheroids are attractive model systems for assessing genetic and epigenetic changes that occur in diseased tissues. Understanding how such alterations in gene and subsequent protein expression affect disease progression and metastasis, drug resistance, and recurrence is of great interest in cancer research. In this regard, examining expression and activity of proteins, such as those with cytoprotective ability that are overexpressed in cancer cells, in addition to cell phenotype (i.e., stem-like, epithelial, mesenchymal, or mixed), are two ways to evaluate genetic and epigenetic changes. Moreover, determining the impact that cytoprotective proteins and cell phenotype have on tumor formation …

Chemical Approaches For Nanofabrication Based On Colloidal Lithography With Organosilanes, Nanoparticles And Nickel Films: The Role Of Water In Directing Surface Self-Assembly, Neepa Malsi Kumari Kuruppu Arachchige

LSU Doctoral Dissertations

The capabilities for accomplishing fundamental surface studies with molecular systems are demonstrated in this dissertation using measurement and imaging modes of scanning probe microscopy. Model systems were chosen for investigations of surface self-assembly mechanisms, with an emphasis on understanding the role of interfacial water in surface reactivity. A key strategy for molecular level studies was to prepare nanostructures using protocols with colloidal lithography and scanning probe-based lithography (SPL). Nanofabricated samples were characterized ex situ with contact and tapping-mode atomic force microscopy (AFM) after key reaction steps, providing direct views of changes in surface morphology at the nanoscale. Magnetic sample modulation …

Photo-Physical Properties Of Novel Gumbos For Optoelectronic Applications, Thenahandi Prasanthi Deepthika De Silva

LSU Doctoral Dissertations

Organic Light Emitting Diodes (OLEDs) are predicted to revolutionize next generation consumer electronics by offering many advantageous device characteristics, including low power consumption, low heat dissipation, a tunable and wider color gamut, high resolution and contrast, light weight, flexibility, and semi-transparency. However, a major limiting factor for OLEDs to reach their full potential is that only a few known blue OLED emitters with substantial spectral purity and longevity are available to date. Therefore, focus of this research is on understanding and addressing limitations of OLED emitters, with an emphasis on improving the characteristics of blue emitters.

The work presented in …

Improving Coupled Enzyme Assays With Capillary Electrophoresis, Thu Hoai Nguyen

LSU Doctoral Dissertations

The goal of this project is to address limitations of coupled enzyme assays using capillary electrophoresis (CE). In some enzyme assays, it is ineffective to directly detect products and substrates spectroscopically (absorption or fluorescence). Coupling the enzyme-catalyzed reaction of interest with another enzyme-catalyzed reaction allows for indirect detection of product formation or substrate depletion for the target enzyme. While conventional coupled enzyme assays are facile for kinetic measurements, they can be problematic for inhibition screening due to spectral and inhibitor interferences. To address these limitations of coupled assays, CE has been used to develop enzyme assays for acetyl-coenzyme A carboxylase …

Infrared Laser Ablation For Biomolecule Sampling, Kelin Wang

LSU Doctoral Dissertations

In this research, an infrared laser at a wavelength of 3 µm was used to ablate material from tissue sections for biomolecule analysis. Pulsed infrared (IR) irradiation of tissue with a focused laser beam efficiently removed biomolecules, such as proteins, enzymes, DNA, and RNA from tissue sections for further analysis. In a proteomics project, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was used to determine regions of interest (ROI) for laser ablation. The matrix was then washed off. By overlaying the MSI generated heat-map, the section was sampled using IR laser ablation and custom stage-control software. Two ROI were selected …

Atomic Force Microscopy Tip-Enhanced Laser Ablation, Fan Cao

LSU Doctoral Dissertations

In the present work, an apertureless atomic force microscope (AFM) tip-enhanced laser ablation (TELA) system was developed and investigated. An AFM was coupled to an optical parametric oscillator (OPO) wavelength tunable laser for sample ablation with a submicron sampling size. The AFM was used to image the surface and hold the AFM tip 10 nm above the sample surface. The AFM tip is coated with a layer of gold with a thickness of 35 nm. The incident laser wavelength was tuned in the visible and near-infrared (IR) region and focused on the AFM tip. With the tip-enhancement effect, ablation craters …

Toward The Impact Of Particulate Matter On Human Health: Evaluation Of Fluorescent Environmentally Persistent Free Radical (Epfr) Surrogates, Ansonia Badgett

LSU Doctoral Dissertations

Environmentally persistent free radicals (EPFRs)—a newly discovered pollutant associated with particulate matter (PM)—form during combustion and thermal processes, such as the incineration of hazardous waste. Various chlorine- and hydroxy-substituted benzenes chemisorb on the surface of metal oxides (e.g., NiO, CuO, and Fe₂O₃) and then form EPFRs, stabilized radical species, as the result of the transfer of electrons between the adsorbate and the metal ion of the metal oxide. Previous studies have shown direct correlations between ultra-fine (d < 0.1 mm) particulate matter (PM_0.1) exposure and adverse pulmonary health effects. PM_0.1 has the potential …

Molecular Level Interactions And Transformations Of Natural Organic Matter Within The Environment, Benjamin J. Haywood

LSU Doctoral Dissertations

This work was done in order to deepen the understanding of interactions occurring during sorption of anthropogenic organic compounds and dissolved organic matter (DOM) onto soil. As well as the transformation DOM undergoes during the sorption process and the overall transformation OM undergoes in the environment. This was achieved through the use of a “bottom-up” synthetic investigation, “top-down” natural system study, and a combination of these approaches.

The “bottom-up” approach, discussed in Chapter 2, involved the synthesis of a modular multi-tiered engineered soil surrogate (ESS) designed to mimic OM and general trends identified in the literature that impacts sorption behavior. …

Influence Of Salinity, Sunlight, And Sediment On The Toxicity Of Pesticides In Three Non-Target Organisms, Emily Noelle Vebrosky

LSU Doctoral Dissertations

Pesticides used in the United States must undergo registration by the United States Environmental Protection Agency (USEPA), after a multitude of analyses ranging from environmental fate to aquatic toxicological impacts to human risk exposure. Testing varies for each chemical, some requiring more testing than others. In many cases, environmental factors are restricted in the analysis of chemical behavior and organismal testing is limited to larvae. Many pesticides are formulated to breakdown in the environment by means of photolysis, hydrolysis, or oxidation, either to ensure low-persistence, limited transport, or to form the active ingredient (pro-pesticides). Environmental influences on chemical behaviors include …