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Biocompatible And Multifunctional Trityl Spin Probes For Electron Paramagnetic Resonance Spectroscopy, Teresa D. Gluth

Graduate Theses, Dissertations, and Problem Reports (ETD)

The primary objective of my thesis was to develop and utilize a biocompatible multifunctional trityl spin probe for concurrent measurement of pO₂, pH_e, and [P_i] in vivo by electron paramagnetic resonance (EPR) spectroscopy (Chapter 2). My first goal was to synthesize the proposed probe we are terming HOPE71. Secondly, HOPE71 was characterized by X-band and L-band EPR spectroscopy. Next, the biocompatibility of HOPE71 was assessed through an albumin binding test, cytotoxicity assays, and in vivo intravenous tolerance. Then, the use of HOPE71 to measure the target parameters was demonstrated in a breast cancer …

Sample Mislabeling Detection And Correction In Bioinformatics Experimental Data, Soon Jye Kho

Browse all Theses and Dissertations

Sample mislabeling or incorrect annotation has been a long-standing problem in biomedical research and contributes to irreproducible results and invalid conclusions. These problems are especially prevalent in multi-omics studies in which a large set of biological samples are characterized by multiple types of omics platforms at different times or different labs. While multi-omics studies have demonstrated tremendous value in understanding disease biology and improving patient outcomes, the complexity of these studies may increase opportunities for human error. Fortunately, the interrelated nature of the data collected in multi-omics studies can be exploited to facilitate the identification and, in some cases, correction …

Harnessing Acoustic Streaming For Bioanalysis In Microfluidics, Xiaojun Li

Graduate Theses, Dissertations, and Problem Reports (ETD)

In the past few decades, microfluidic technology has been developed rapidly in both fabrication methods and multifunctionality integrations, making it a powerful tool for a wider variety of biological applications. The device fabrication method has expanded from conventional polymer-based micro devices to 3D-printed micro devices, and allows multiple functions such as electric, optic, magnetic and acoustic to be integrated on a single platform. This dissertation focuses on method development of acoustic streaming-based microfluidics in bioanalysis such as immunoassay, enzyme kinetics and DNA fragmentation analysis. In this dissertation, a micromixer was developed based on acoustic streaming generated from sharp-edge structure vibration …

Rational Design Of Small Molecule Disruptors Of Protein-Protein Interactions: Pd-1/Pd-L1; C-Myc, Arid4b, Samuel Ofori

Theses and Dissertations--Chemistry

Protein-protein interactions (PPIs) are vital to many biological processes, including gene expression, and immune reactions to pathogens. There are approximately 650,000 PPIs in humans with pertinent physiological functions. Aberrant expression of PPIs lead to improper function and contribute to a plethora of disease conditions including cancer. Thus, PPIs represent an enormous target space for drug discovery and chemical probes. Direct targeting of clinically relevant PPIs with small molecules remains an unmet medical need. Development of small-molecule inhibitors of PPIs is a challenging enterprise and in most cases considered undruggable due to large protein surfaces, lack of deep binding pockets and …

Design, Synthesis, And Anticancer Properties Of Ru(Ii) Complexes With Organometallic, “Expanded” Bipyridine, And O,O’-Chelating Ligands, Raphael Ryan

Theses and Dissertations--Chemistry

Cancer is a worldwide public health crisis that requires new and improved drugs to be developed to extend survival rates and improve quality of life for the patient. Platinum-based drugs are used in approximately 50% of cancer treatment regimens. These drugs are highly effective in many kinds of cancer; however, cancers can develop platinum resistance and these drugs have troubling side effects that reduced their use and efficacy. To overcome these disadvantages, many other metals have been studied for their anticancer properties. Notably, the anticancer properties of ruthenium-based agents have drawn considerable attention with multiple ruthenium complexes entering clinical trials. …

Wildlife-Friendly Fence Policy On Federal Public Lands Managed By The U.S. Forest Service And Bureau Of Land Management, Joshua D. Elliott

Graduate Student Theses, Dissertations, & Professional Papers

Many wildlife species are negatively impacted by the presence of fences on the landscape. Climate change is only exacerbating the problem as home ranges shift and species face heightened levels of stress. In recent decades, wildlife biologists have studied these impacts and devised ways of constructing fences to increase habitat connectivity and significantly reduce fence-related injury and mortality rates. Conservationists attempting to address this issue on a landscape level face significant challenges resulting from complex land ownership patterns, specifically across the western United States.

The two largest landowners in the U.S. are the Bureau of Land Management (BLM) and the …

Searching For A Technology-Driven Acute Rheumatic Fever Test: The Start Study Protocol, Anna P. Ralph, Rachel Webb, Nicole J. Moreland, Reuben Mcgregor, Anthony Bosco, David Broadhurst, Timo Lassmann, Timothy C. Barnett, Rym Benothman, Jennifer Yan, Bo Remenyi, Julie Bennett, Nigel Wilson, Mark Mayo, Glenn Pearson, Tobias Kollmann, Jonathan R. Carapetis

Research outputs 2014 to 2021

Introduction:

The absence of a diagnostic test for acute rheumatic fever (ARF) is a major impediment in managing this serious childhood condition. ARF is an autoimmune condition triggered by infection with group A Streptococcus. It is the precursor to rheumatic heart disease (RHD), a leading cause of health inequity and premature mortality for Indigenous peoples of Australia, New Zealand and internationally.

Methods and analysis:

Searching for a Technology-Driven Acute Rheumatic Fever Test' (START) is a biomarker discovery study that aims to detect and test a biomarker signature that distinguishes ARF cases from non-ARF, and use systems biology and serology to …

Visual Arts Enhance Instruction In Observation And Analysis Of Microscopic Forms In Developmental And Cell Biology, Max Ezin, Christina Noravian, Amira Mahomed, Adam Lyle, Aveleen Gill, Tamira Elul

The Transdisciplinary STEAM+ Journal

Two important skills for scientists in developmental and cell biology, as well as in fields such as neurobiology, histology and pathology, are: 1) observation of features and details in microscopic images of cells, and 2) quantification of cellular features observed in microscopic images. However, current training in developmental and cell biology does not emphasize observation and quantitative analysis of microscopic images, and it is unclear how best to teach students these skills. Here, we describe our experiences applying visual artistic approaches to instruct undergraduate and graduate students in how to observe and analyze cellular forms in microscopic images. At Loyola …

The Application And Development Of Metabolomics Methodologies For The Profiling Of Food And Cellular Toxicity, Jade Woods

Department of Chemistry: Dissertations, Theses, and Student Research

Metabolomics is a rapidly growing field of study. Its growth reflects advancements in technology and an improved understanding of the impact of the environment on metabolism. As a result, metabolomics is now commonly employed to investigate and characterize human and plant metabolism. The first chapter of this thesis provides an introduction to metabolomics and an overview of the protocols for sample preparation, data collection and statistical analysis. The second thesis chapter describes in explicit detail the step-by-step process of extracting and analyzing metabolites collected from mammalian cells, specifically brain tissue with a focus on Parkinson’s disease. The chapter highlights important …

Development Of Computational To Ols To Target Microrna, Luo Song

Dissertations and Theses (Open Access)

MicroRNAs (a.k.a, miRNAs) play an important role in disease development. However, few of their structures have been determined and structure-based computational methods remain challenging in accurately predicting their interactions with small molecules. To address this issue, my thesis is to develop integrated approaches to screening for novel inhibitors by targeting specific structure motifs in miRNAs. The project starts with implementing a tool to find potential miRNA targets with desired motifs. I combined both sequence information of miRNAs and known RNA structure data from Protein Data Bank (PDB) to predict the miRNA structure and identify the motif to target, then I …

Triggerable, Targetable, And Trackable Flavonol-Based Carbon Monoxide-Releasing Molecules, Livia S. Lazarus

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Long known as a toxic gas, carbon monoxide (CO) has been recently redefined as a health beneficial molecule produced endogenously in humans. The biological activity of CO has been extensively examined in inflammatory conditions, vasoprotection, anti-apoptotic and anticancer studies, although the mechanisms of action are still not well defined. Because CO is a gaseous molecule, a straightforward administration would be inhalation. However, this delivery method is limited to use in hospital settings under professional supervision. For improved control over the amount and location of CO delivery, metal-free and light-triggered carbon monoxide-releasing molecules are of particular current interest. Our lab is …

Lysenin Channels As Sensors For Ions And Molecules, Andrew Bogard, Gamid Abatchev, Zoe Hutchinson, Jason Ward, Pangaea W. Finn, Fulton Mckinney, Daniel Fologea

Physics Faculty Publications and Presentations

Lysenin is a pore-forming protein extracted from the earthworm Eisenia fetida, which inserts large conductance pores in artificial and natural lipid membranes containing sphingomyelin. Its cytolytic and hemolytic activity is rather indicative of a pore-forming toxin; however, lysenin channels present intricate regulatory features manifested as a reduction in conductance upon exposure to multivalent ions. Lysenin pores also present a large unobstructed channel, which enables the translocation of analytes, such as short DNA and peptide molecules, driven by electrochemical gradients. These important features of lysenin channels provide opportunities for using them as sensors for a large variety of applications. In …

Determination Of Vitamin D Metabolites And Their Epimers In Obese Emirati Population, Bashar Hiatham Alzohily

Theses

Vitamin D deficiency is a global issue, and despite all-year-round sunshine, it is a big problem in the UAE. Obesity or overweight refers to an accumulation of excessive fat that may harm health so, it is considered a worldwide health concern. The accurate measurement of vitamin D active forms is a problematic issue. This study aimed to develop and validate a UHPLC-MS/MS method for the new method for determining vitamin D levels in the obese Emirati population. The vitamin D epimers and other metabolites were determined by UHPLC-MS/MS system, model 8060. The methods include the collection of blood samples from …

Chemical Synthesis Of Homogeneous Human E-Cadherin N-Linked Glycopeptides: Stereoselective Convergent Glycosylation And Chemoselective Solid-Phase Aspartylation, Chen Zeng, Bin Sun, Xuefeng Cao, Joshua Zhu, Olawale Micheal Oluwadahunsi, Ding Liu, He Zhu, Jiabin Zhang, Qing Zhang, Gaolan Zhang, Christopher Andrew Gibbons, Yunpeng Liu, Jun Zhou, Peng George Wang

Faculty Work Comprehensive List

We report herein an efficient chemical synthesis of homogeneous human E-cadherin N-linked glycopeptides consisting of a heptapeptide sequence adjacent to the Asn-633 N-glycosylation site with representative N-glycan structures, including a conserved trisaccharide, a core-fucosylated tetrasaccharide, and a complex-type biantennary octasaccharide. The key steps are a chemoselective on-resin aspartylation using a pseudoproline-containing peptide and stereoselective glycosylation using glycosyl fluororide as a donor. This synthetic strategy demonstrates potential utility in accessing a wide range of homogeneous N-linked glycopeptides for the examination of their biological function.

Machine Learning Applications For Drug Repurposing, Hansaim Lim

Dissertations, Theses, and Capstone Projects

The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected …

Highly Swelling Ph-Responsive Microgels For Dual Mode Near Infra-Red Fluorescence Reporting And Imaging, Mingning Zhu, Dongdong Lu, Qing Lian, Shanglin Wu, Wenkai Wang, L. Andrew Lyon, Weiguang Wan, Paulo Bártolo, Mark Dickinson, Brian R. Saunders

Engineering Faculty Articles and Research

Near infra-red (NIR) fluorescence is a desirable property for probe particles because such deeply penetrating light enables remote reporting of the local environment in complex surroundings and imaging. Here, two NIR non-radiative energy transfer (NRET) fluorophores (Cy5 and Cy5.5) are coupled to preformed pH-responsive poly(ethylacrylate-methacrylic acid-divinylbenzene) microgel particles (PEA-MAA-5/5.5 MGs) to obtain new NIR fluorescent probes that are cytocompatible and swell strongly. NIR ratiometric photoluminescence (PL) intensity analysis enables reporting of pH-triggered PEA-MAA-5/5.5 MG particle swelling ratios over a very wide range (from 1–90). The dispersions have greatly improved colloidal stability compared to a reference temperature-responsive NIR MG based on …

Synthesis, Characterization, And Biological Studies Of Novel Organoantimony(V) Cyanoximates, Kevin Anthony Pinks

Graduate Theses/Dissertations

The requirement of new antimicrobial treatments has become an urgent field recently. Multi-drug resistant (MDR) bacteria are now resistant to common antibiotics. To antagonize such bacteria 8 novel organoantimony(V) cyanoximates were synthesized to be characterized and submitted for biological activity studies. Eight organoantimony(V) cyanoximates were characterized by elemental analysis, thermal analysis, IR-, ¹³C{¹H} NMR, some with UV-visible spectroscopy, and single crystal X-ray analysis. Antimicrobial Disk studies indicated Sb(Ph)₄(ACO) and Sb(Ph)₄(ECO) had significant antimicrobial effect against all three strains: two gram-negative a) Escherichia coli strain S17 and b) Pseudomonas aeruginosa strain PAO1, alongside a …

Electrochemically-Modulated Surface Plasmon Waves At A Nano-Scale For Investigations And Applications Of Redox Assemblies., Aymen Hasan Qatamin

Electronic Theses and Dissertations

In this thesis, an electrochemically-modulated surface plasmon resonance (EC-SPR) technique was developed for challenging investigations and applications in different redox assemblies. The principle of the technique is based on the nano-scale confined and sensitive interplay between a surface plasmon wave and a redox-active probe featuring an optical transition when undergoing a faradaic redox process. Such faradaic process is electrochemically controlled by modulating the surface electric potential of the SPR platform to create an optical output signal that is substantially immune to the negative impacts of background environment and enabling the identification and quantification minute properties linked to a molecular event …

The Development Of A New Entry Point Into Enantiomerically Enriched Sulfinyl Derivatives, Jessica Shaw

Theses and Dissertations

Optical probes may be used as reliable tools for detecting and imagining the inside of cells for medical diagnostics. Among available options, the use of thiol probes is of interest as thiols are present in nearly all cells and their levels are tightly regulated, thus any variation is associated with disease. A proper thiol bioimaging probe must have a thiol cleavage group/reactive group and a fluorophore. It is found that novel sulfinate aryl ester (phenoxysulfinate esters) probes selectively cleave thiols at physiological pH and show much promise as effective tools for bioimaging.

In this context, the synthesis of the related …

1. Dft-Guided Discovery Of Hybrid Catalysts For C-C Bond Formation; 2. Synthesis Of A Reported Pdi Inhibitor, Eric Greve

Dissertations (1934 -)

1. Dual amine/pi Lewis acid catalyst systems have been reported for intramolecular direct additions of aldehydes/ketones to unactivated alkynes and occasionally alkenes, but related intermolecular reactions are rare. We reasoned that bulky metal ligands and bulky amine catalysts could minimize catalyst poisoning and could facilitate certain examples of direct intermolecular additions of unactivated aldehydes/ketones to alkenes/alkynes. Density Functional Theory (DFT) ground state calculations on putative catalytic intermediates for alkyne versus organocatalyst complexation to the -acid, and also the key carbon-carbon bond formation were used to prioritize ligand/organocatalyst combinations. Our calculations suggested that PyBOX-Pt(II) catalysts for alkene/alkyne activation could be combined …

Synthesis, Characterisation And Biological Evaluation Of Tyramine Derived Schiff Base Ligand And Its Transition Metal(Ii) Complexes, Abdul Khader Jailani, N.S.K. Gowthaman, Mookkandi Palsamy Kesavan

Karbala International Journal of Modern Science

In this study, a new tyramine derived Schiff base ligand (L) (L=1,3-phenylene-bis-4-aminoantipyrinyl-4-aminoethylphenol) and its derived transition metal(II) complexes [Cu(L)Cl₂](1), [Ni(L)Cl₂](2), [Co(L)Cl₂] (3) and [Zn(L)Cl₂] (4) have been synthesized and well characterized by the way of different spectroscopic and analytical techniques. Analytical and spectroscopic studies result suggests that metal(II) complexes more probably have octahedral geometry. DNA binding tendency of L and metal(II) complexes 1-4 have been assessed by probing their ability to bind with Calf Thymus DNA (CT-DNA) via electronic absorption and cyclic voltammetry titration methods. The results clearly reveal that the metal(II) …

Learning Transferable Deep Convolutional Neural Networks For The Classification Of Bacterial Virulence Factors, Dandan Zheng, Guansong Pang, Bo Liu, Lihong Chen, Jian Yang

Research Collection School Of Computing and Information Systems

Motivation: Identification of virulence factors (VFs) is critical to the elucidation of bacterial pathogenesis and prevention of related infectious diseases. Current computational methods for VF prediction focus on binary classification or involve only several class(es) of VFs with sufficient samples. However, thousands of VF classes are present in real-world scenarios, and many of them only have a very limited number of samples available.Results: We first construct a large VF dataset, covering 3446 VF classes with 160 495 sequences, and then propose deep convolutional neural network models for VF classification. We show that (i) for common VF classes with sufficient samples, …

The Weibull Topp-Leone Generated Family Of Distributions: Statistical Properties And Applications, Hamid Karamikabir, Mahmoud Afshari, Haitham M. Yousof, Morad Alizadeh, Gholamhossein G. Hamedani

Mathematical and Statistical Science Faculty Research and Publications

Statistical distributions are very useful in describing and predicting real world phenomena. Consequently, the choice of the most suitable statistical distribution for modeling given data is very important. In this paper, we propose a new class of lifetime distributions called the Weibull Topp-Leone Generated (WTLG) family. The proposed family is constructed via compounding the Weibull and the Topp-Leone distributions. It can provide better fits and is very flexible in comparison with the various known lifetime distributions. Several general statistical properties of the WTLG family are studied in details including density and hazard shapes, limit behavior, mixture representation, skewness and kurtosis, …

Icdp Workshop On The Lake Tanganyika Scientific Drilling Project: A Late Miocene–Present Record Of Climate, Rifting, And Ecosystem Evolution From The World's Oldest Tropical Lake, James M. Russell, Philip Barker, Andrew Cohen, Sarah Ivory, Ishmael Kimirei, Christine Lane, Melanie Leng, Neema Maganza, Michael M. Mcglue, Emma Msaky, Anders Noren, Lisa Park Boush, Walter Salzburger, Christopher Scholz, Ralph Tiedemann, Shaidu Nuru, Lake Tanganyika Scientific Drilling Project Consortium

Earth and Environmental Sciences Faculty Publications

The Neogene and Quaternary are characterized by enormous changes in global climate and environments, including global cooling and the establishment of northern high-latitude glaciers. These changes reshaped global ecosystems, including the emergence of tropical dry forests and savannahs that are found in Africa today, which in turn may have influenced the evolution of humans and their ancestors. However, despite decades of research we lack long, continuous, well-resolved records of tropical climate, ecosystem changes, and surface processes necessary to understand their interactions and influences on evolutionary processes. Lake Tanganyika, Africa, contains the most continuous, long continental climate record from the mid-Miocene …

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. …

Establishment Of High-Efficiency Agrobacterium-Mediated Transformation Of Callus Derived From Sehima Nervosum, An Important Range Grass Species, Krishna Kumar Dwivedi, Tanu Sonkar, R. Katiyar, Auji Radhakrishna, P. Kaushal

IGC Proceedings (1977-2023)

Sehima nervosum is one of the important rangeland grass in India, It is commonly known as Saen grass in India, white grass in Australia, and has also been reported from the Central East Africa and Sudan. It is a good forage grass and maybe utilized for grazing as well as for hay preparation. It is a perennial grass, prefers hot and dry climate and survive even in limited rainfalls. As this natural grass is found inherently rich in precursors for several industrially important biomolecules, fractionation of these precursors seems to be a promising endeavour. Production of nutraceuticals (prebiotic xylo-oligosaccharides) from …

Influence Of The Spatial Distribution Of Cationic Functional Groups At Nanoparticle Surfaces On Bacterial Viability And Membrane Interactions, Yongqian Zhang, Natalie V. Hudson-Smith, Seth D. Frand, Meghan S. Cahill, Larissa S. Davis, Vivian Feng, Christy L. Haynes, Robert J. Hamers

Faculty Authored Articles

While positively charged nanomaterials induce cytotoxicity in many organisms, much less is known about how the spatial distribution and presentation of molecular surface charge impact nanoparticle–biological interactions. We systematically functionalized diamond nanoparticle surfaces with five different cationic surface molecules having different molecular structures and conformations, including four small ligands and one polymer, and we then probed the molecular-level interaction between these nanoparticles and bacterial cells. Shewanella oneidensis MR-1 was used as a model bacterial cell system to investigate how the molecular length and conformation of cationic surface charges influence their interactions with the Gram-negative bacterial membranes. Nuclear magnetic resonance (NMR) …

Recombinant Expression Of Preptin Analogs For Alanine Scanning Mutagenesis Of Residues 27-29, Tehgan N. Anguilm

Theses and Dissertations

The novel peptide preptin consists of 34 amino acid residues corresponding to Asp⁶⁹-Leu¹⁰² of proinsulin-like growth factor E-peptide. Preptin has been isolated from pancreatic beta cells, and it has been found to exhibit both metabolic and mitogenic activities. This makes preptin an attractive candidate to treat insulin-independent diabetes and osteoporosis. Alanine scanning mutagenesis was utilized to substitute an alanine for residues Trp²⁷, Arg²⁸, and Gln²⁹ of preptin in order to ultimately study the structure-activity relationship of these residues to preptin’s metabolic activity.

Novel Bayesian Methodology For The Analysis Of Single-Cell Rna Sequencing Data., Michael Sekula

Electronic Theses and Dissertations

With single-cell RNA sequencing (scRNA-seq) technology, researchers are able to gain a better understanding of health and disease through the analysis of gene expression data at the cellular-level; however, scRNA-seq data tend to have high proportions of zero values, increased cell-to-cell variability, and overdispersion due to abnormally large expression counts, which create new statistical problems that need to be addressed. This dissertation includes three research projects that propose Bayesian methodology suitable for scRNA-seq analysis. In the first project, a hurdle model for identifying differentially expressed genes across cell types in scRNA-seq data is presented. This model incorporates a correlated random …

Non-Uniform Haar Wavelet Method For Solving Singularly Perturbed Differential Difference Equations Of Neuronal Variability, Akmal Raza, Arshad Khan

Applications and Applied Mathematics: An International Journal (AAM)

A non-uniform Haar wavelet method is proposed on specially designed non-uniform grid for the numerical treatment of singularly perturbed differential-difference equations arising in neuronal variability.We convert the delay and shift terms using Taylor series up to second order and then the problem with delay and shift is converted into a new problem without the delay and shift terms. Then it is solved by using non-uniform Haar wavelet. Two test examples have been demonstrated to show the accuracy of the non-uniform Haar wavelet method. The performance of the present method yield more accurate results on increasing the resolution level and converges …