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Isothermal Environmental Heat Energy Utilization By Transmembrane Electrostatically Localized Protons At The Liquid-Membrane Interface, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

This study employing the latest theory on transmembrane electrostatic proton localization has now, for the first time, consistently elucidated a decades-longstanding bioenergetic conundrum in alkalophilic bacteria and more importantly discovered an entirely new feature: isothermal environmental heat utilization by electrostatically localized protons at the liquid-membrane interface. It was surprisingly revealed that the protonic motive force (equivalent to Gibbs free energy) from the isothermal environmental heat energy utilization through the electrostatically localized protons is not constrained by the overall energetics of the redox-driven proton pump system because of the following: (a) the transmembrane electrostatically localized protons are not free to move …

Fluvial Sediment Organic Matter Degradation Identified With Elemental And Isotopic Fate During Laboratory Incubation, Brenden Riddle

Theses and Dissertations--Civil Engineering

Fluvial sediment is well recognized as a critical factor in both carbon and nutrient budgets within stream systems. However, we find very few studies of reactivity and isotope enrichment for stream water from agricultural and urban streams and the class of substrate known as fluvial sediment organic matter. This study investigated the hypothesis that fluvial sediment is subject to degradation even though many previous studies have considered this class of substrate generally inert. Therefore we qualify that elemental and isotopic signatures of fluvial sediment organic matter should be considered potentially non-conservative when used in tracer studies. Methods applied to this …

Physicochemical Characterization, Structural Determination, And Molecular Dynamic Modeling Of Proso Millet Proteins For Enhanced Food Functionality, Felix Akharume

Theses and Dissertations--Biosystems and Agricultural Engineering

More than one-third of Americans today incorporate plant-based protein into their diet and about 40% believed that plant-based protein is healthier than animal protein, especially Millennials. The increasing global demand for plant-based proteins driven by the high cost of animal proteins, consumers’ desire for lean protein, vegetarianism, and the need for more sustainable green protein products have necessitated research into alternate emerging and underutilized sources of protein to complement or supplement the major plant protein in the market- soy, pea, and gluten. Therefore, this dissertation is focused on the valorization of the proteins in proso millet. Specifically, this work focused …

Epigenetic Regulation Of Hormone Action In The Red Flour Beetle, Tribolium Castaneum (Herbst), Smitha George

Theses and Dissertations--Entomology

Hormones are the chemical communication signaling molecules released into the body fluid to stimulate target cells of multicellular organisms. Two major hormones, ecdysteroids (20-hydroxyecdysone, 20E) and juvenile hormones (JH), regulate a wide variety of physiological and developmental processes in insects. Therefore, hormones have been extensively studied and are attractive targets for the development of target-specific insect control methods. Recent studies suggest that epigenetics adds another layer of regulation to explain multiple functions of the same circulating hormone in different tissues and at various time points. In my dissertation, I focused on a major post-translational modification, ‘acetylation,’ to elucidate the epigenetic …

Impact Of Cold Plasma Processing On Major Peanut Allergens, Harshitha Venkataratnam, Orla Cahill, Chaitanya Sarangapani, Patrick J. Cullen, Catherine Barry-Ryan

Articles

Cold plasma is emerging as a novel food processing technology, with demonstrated efficacies for microbial inactivation and residual chemical dissipation of food products. Given the technology’s multimodal action it has the potential to reduce allergens in foods, however data on the efficacy and mechanisms of action are sparse. This study investigates the efficacy of cold plasma on major peanut allergens (Ara h 1 and Ara h 2). For this purpose, dry, whole peanut (WP) and defatted peanut flour (DPF) were subjected to an atmospheric air discharge using a pin to plate cold plasma reactor for different treatment durations. With increases …

Cold Atmospheric Plasma Stimulates Clathrin-Dependent Endocytosis To Repair Oxidised Membrane And Enhance Uptake Of Nanomaterial In Glioblastoma Multiforme Cells, Zhonglei He, Kangze Li, Laurence Scally, Eline Manaloto, Sebnem Gunes, Sing Wei Ng, Marcus Maher, Brijesh Tiwari, Hugh Byrne, Paula Bourke, Furong Tian, Patrick J. Cullen, James Curtin

Articles

Cold atmospheric plasma (CAP) is increasingly studied in a growing number of clinical trials for cancer treat-ment1,2 and research is ongoing to explore the combination of CAP with other therapies, including nanoparticles, radiotherapy and chemotherapy3–5.Gold nanoparticles (AuNPs) are known to be weakly-toxic to human cells and be readily manufactured and designed for targeting delivery of various therapeutic compounds into cells. Citrate-capped cationic AuNPs may adsorb serum proteins onto their surface and thereby stimulate receptor-mediated endocytosis6. Without special surface functionalisation, AuNPs enter cells and become trapped in vesicles6–8 or enter the nucleus, depending on their size/shape9,10. Meanwhile, AuNPs with functionalised surface …

Characterization Of An Aryl Piperazine/2-Hydroxypropyl-Β-Cyclodextrin Association, A Complex With Antidiabetic Potential, R. Devine, D.S.D. Martin, Gemma Kinsella, J.B.C. Findlay, J.C. Stephens

Articles

This study explores the molecular association between 4-(thiophen-2-yl)-1-(4-(4-(trifluoromethyl)phenyl)piperazin-1-yl)butan-1-one (RTC1), an antidiabetic compound recently reported by our research group with challenging aqueous solubility, and 2-hydroxypropyl-β-cyclodextrin (HPBCD). The formation of a RTC1/HPBCD complex resulted in improved solubility. A phase-solubility diagram was used to determine the complex stability constant and stoichiometric ratio. 2D ¹H NMR spectroscopy was utilized to study the molecular interaction between RTC1 and HPBCD in the complex. Differential scanning calorimetry and scanning electron microscopy was also employed to confirm complex formation. In vitro biological evaluation, using a glucose uptake assay, showed that the homogeneous RTC1/HPBCD complex solution showed the …

Gravity-Drawing Flexible Silicone Filaments As Fiber Optics And Model Foldamers, Katherine Snell

CMC Senior Theses

Here, we present a method of gravity-drawing polydimethylsiloxane (PDMS) silicone fibers with application as fiber optics and as model foldamers. Beginning as a viscous liquid, PDMS is cured using heat until its measured viscosity reaches 4000 mPa•s. The semi-cured elastomer is then extruded through a tube furnace to produce thin (diameters on the order of hundred micrometers) filaments with scalable lengths. PDMS is biocompatible, gas-permeable, flexible, and hydrophobic. Additionally, the PDMS surface hydrophobicity can be modified via UV exposure, O2 plasma, and corona discharge. We demonstrate the patternibility (i.e patterns of hydrophobicity) of PDMS fibers, adding complexity to potential foldamer …

Characterization And Enzyme Engineering Of Laccases Towards Lignin Valorization In Aqueous Ionic Liquids, Joseph Stevens

Theses and Dissertations--Biosystems and Agricultural Engineering

Lignin is one of the most abundant polymers found in nature, making up 15 – 40% of the weight of terrestrial biomass. Due to the structural and monomeric heterogeneity of lignin, it is recalcitrant thermochemical and biological valorization methods. Converting lignin to value-added products via sustainable and cost-effective pathways will reduce waste and add value to future cellulosic biorefineries. Biological methods for lignin valorization (e.g. lignin degrading enzymes or microbes) is limited by low lignin solubility in biocompatible solvents, resulting in low product yield. Recent reports on biocatalysts for lignin valorization have focused on the lignolytic multicopper oxidase laccase, …

Investigation Of The Phenotypic Effect Of Mutating A Highly-Conserved Cysteine Residue In The Rna Polymerase Beta Prime Subunit Of E. Coli Rna Polymerase, Meg Dillingham

Mahurin Honors College Capstone Experience/Thesis Projects

All bacteria contain a multi-subunit RNA polymerase (RNAPs) that is essential for gene expression. Because of the centrality of these enzymes in cellular life, the structure and function of the various subunits is intensely studied. The primary sequence of the RNAP β’ subunit contains five cysteine residues that are highly conserved. Four of the cysteines coordinate a zinc atom and form the beta prime subunit zinc binding domain (ZBD). Mutation of any one of the ZBD cysteines is lethal to the cell. However, the role of the fifth residue (C58), which is located upstream of the ZBD cysteines, has not …

Therapeutic Efficacy Of Umbilical Cordderived Stem Cells For Diabetes Mellitus: A Meta-Analysis Study, Dina H. Kassem, Mohamed M. Kamal

Pharmacy

Background: Stem cell therapy provides great hope for patients with diabetes mellitus (DM). DM is a seriously alarming metabolic disease characterized by hyperglycemia and β cell dysfunction. Efficient novel therapeutic modalities to treat DM are indeed warranted. Stem cells (SC) derived from the umbilical cord specifically provide several advantages and unique characteristics being a readily available non-invasive source, with an additional credit for their banking potential. This meta-analysis study aims to provide a focused assessment for therapeutic efficacy of umbilical cord (UC)-derived SC-transplantation, namely Wharton’s jelly mesenchymal stem cells (WJMSCs) and umbilical cord blood (UCB) for DM. Methods: The clinical …

Functional Characterization Of Proteins From A Putative Chondroitin Sulfate A Degrading Operon And The Crystal Structure Of An Exo-N-Acetylgalactosamine-4-Sulfatase From Tannerella Forsythia, Peter Nguyen

Theses and Dissertations (Comprehensive)

Advanced periodontitis has been shown to have strong associations with the residence of a bacterial triad of Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola also known as the red complex. These bacteria were previously thought to be asaccharolytic, making them better suited to survive in deep in periodontal pockets where access to carbohydrates from food is limited. Information gathered from genomic analysis suggested that upregulation of an operon (BFO2285-BFO2295, BFO3043) could confer the capacity for T. forsythia to degrade chondroitin-4-sulfate, the principle glycosaminoglycan of alveolar bone tissue. Bioinformatics analysis suggested the operon was similar to an operon found in Bacteroidetes …

Life In A Rural Emergency Department: Patients Speak To Underlying, Fundamental Disparities In Physician And Resource Allocation, Jessica Gustad

Honors Projects

In the Journal of Health Services Research and Policy, access to health care was defined as, “The availability of an adequate supply of health care services and the individual’s opportunity to obtain health care when it is wanted or needed” (MacKinney, 2014). Current trends in rural emergency departments are trying to communicate a critical message about the fundamental problems with the distribution of health care services in America today and the inability to properly meet the definition above. In rural communities, patient complaints and behaviors demonstrate the pressing concerns of inadequate access to primary care, limited specialty care, insufficient mental …

Quantifying The Heterogeneity Of The Immunoglobulin G N-Glycome In An Ageing Australian Population: The Busselton Healthy Ageing Study, Alyce Russell

Theses: Doctorates and Masters

The use of immunoglobulin G N-glycomics to study chronic non-communicable disorders and other complex phenotypes emerged following the Human Genome Project. The consortium discovered that most phenotypes were too complex to be explained by genetics alone. Thus, the biological importance of epigenetics was recognised; heritable modifications to gene expression rather than the genome itself. Nglycosylation is a form of epigenetic regulation known as a post-translational modification. It stabilises the immunoglobulin G structure and alters downstream responses elicited by the antibody and is extensively studied as a candidate biomarker in the post-genomic era.

The N-glycosylation of immunoglobulin G itself is complex, …

The Effects Of Induced Polycystic Ovary Syndrome In Nag-1 Transgenic Mice, Nicholas Werner

All Master's Theses

Polycystic ovary syndrome (PCOS) is the leading cause of infertility among women in the US and the most common endocrine disorder among women. PCOS is characterized by cystic ovaries, hyperandrogenism (heightened levels of male sex hormones), altered menstrual cycles and various metabolic dysfunctions. The metabolic symptoms associated with PCOS are difficult to treat, as they are a result of hormonal imbalances, rather than diet. The human Non-Steroidal Anti-Inflammatory Drug Activated Gene (NAG-1) been shown to prevent diet-induced metabolic disorders and weight gain in mice. We hypothesized that the expression of NAG-1 may also prevent hormonal-induced metabolic disorders. To test this …

Acoustic Analysis Of Nomascus Gibbon Songs As A Potential Measure Of Current Health Status, Caroline Rowley

All Master's Theses

Post-release monitoring is vital to the rehabilitation process. Gibbons offer a unique challenge, as they are notoriously difficult to follow through the forest, but their duets offer a non-invasive window into their lives. The aim of this project is to create a method that will evaluate the health of rehabilitated and released gibbons through acoustic analyses. Gibbon duets are in part genetically determined, but learning may play a role in song development. Additionally, songs may indicate resource holding potential, and are vital to acquiring mates and producing offspring. Captive-raised gibbons are often denied the experience of co-singing with their parents, …

Evaluating A Culprit: A Review Of The Biochemical Mechanisms Of Non-Celiac Gluten Intolerance, Callie Cinque

Honors Theses

Non-Celiac Gluten Intolerance (NCGI) has evaded biological and chemical mechanisms since it was first reported in 1978. Celiac Disease, a multi-system immune mediated disorder has long served as the most similar counterpart to NCGI. Less cases of celiac disease are going undiagnosed reflecting an improvement on sensitive and decisive diagnostic tools. However, NCGI has been significantly growing as a diagnosis over the past decade with little match or similarity to the markers found in celiac disease patients. Critical evaluation of NCGI theories, experimentation, and existing hypotheses is necessary. This review seeks to synthesize multiple disciplines of gluten research and enhance …

Application Of Β-Chloroenals: One-Pot Syntheses To Create Highly Variable, Functional, And Biologically Interesting Molecules, Julia Powell Siewert

Honors Theses

Pyrroles and pyrazoles are privileged structures which provide a molecular framework found in many different classes of bioactive compounds, thus rendering their syntheses useful in pharmaceutical drug development. Additionally, being able to selectively create these molecules with interesting substituents allows for different pharmacological and biological activities, such as antitumor and antibiotic effects. Our group has used β-chloroenals in the application of many different unique synthetic strategies in the past, and here I show that chloroenals can be used to synthesize novel 1,2,5 trisubstituted pyrroles as well as 1,5 di- and 1,4,5 trisubstituted pyrazoles in fewer steps and with milder conditions …

The Effects Of Signaling Molecules To Agrobacterium Tumefaciens Tumorigenesis At Plant Wound Sites, Nicole Walker

Honors Theses

Agrobacterium tumefaciens can live independently within soil before infecting its host (McCullen and Binns, 2006). The bacterium infects the plant through the rhizosphere, an area of soil along the plant root surface which contains microorganisms, making up the “external metabolome” (Bais et al. 2006). As these bacteria live in the rhizosphere, they are exposed to a multitude of chemical signals. These chemical signals include several conditions that must be met before the virulence machinery is expressed. These conditions include signaling from phenols and sugars as well as low PO4 levels and low pH. Upon wounding, sugars and phenols are released …

Genomic-Based Identification Of Environmental And Clinical Listeria Monocytogenes Strains Associated With An Abortion Outbreak In Beef Heifers, Katherine J. Whitman, James L. Bono, Michael L. Clawson, John D. Loy, Joseph M. Bosilevac, Terrance M. Arthur, Jeff D. Ondrak

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: In a beef cattle facility an outbreak of abortions occurred over a 36-day period and included samples from two aborted (non-viable) fetuses and 21 post-abortion clinical cases. There are numerous etiologies, including clinical listeriosis. At the species level, Listeria monocytogenes is ubiquitous in cattle production environments, including soil, feed, and occasionally water sources, and is a common enteric resident of cattle and other mammals. There are four genetically distinct lineages of L. monocytogenes (I-IV), with most lineage III and IV isolates obtained from ruminants. Definitive diagnosis of L. monocytogenes as a causative agent in disease outbreaks relies upon case …

Correction: Visible-Light Photooxidation In Water By 1o2-Generating Supramolecular Hydrogels, Sankarsan Biswas, Mohit Kumar, Andrew Levine, Ian Jimenez, Rein V. Ulijn, Adam Braunschweig

Advanced Science Research Center

Correction for ‘Visible-light photooxidation in water by ¹O₂-generating supramolecular hydrogels’ by Sankarsan Biswas et al., Chem. Sci., 2020, 11, 4239–4245, DOI: 10.1039/C9SC06481H.

Targeting The Nt17 Of The Huntingtin Protein Via Natural And Chemical Modifications: Impact On Aggregation And Membrane Interactions, Faezeh Sedighi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington Disease (HD) is a fatal neurodegenerative disorder caused by an expanded polyglutamine domain (polyQ) in the first exon of the huntingtin protein (htt-exon1). The major hallmark of HD is the accumulation of aggregates into proteinaceous inclusion bodies. PolyQ expansion in huntingtin promotes self-assembly into a variety of toxic aggregates such as oligomers, fibrils, and amorphous aggregates. The resulting heterogeneous mixture of distinct species makes it difficult to assign a toxic function to specific aggregate structures. In addition, htt interacts with a variety of membranous surfaces. The first 17 amino acids (Nt17) of htt directly flanking the polyQ domain functions …

Virus Purification Framework And Enhancement In Aqueous Two-Phase System, Pratik Umesh Joshi

Dissertations, Master's Theses and Master's Reports

Viral infections regularly pose detrimental health risks to humans. Preventing viral infections through global immunization requires the production of large doses of vaccines. The increasing demand for vaccines, especially during pandemics such as COVID-19, has challenged current manufacturing strategy to develop advanced unit operations with high throughput capability. Over the decade, the upstream processing responsible for synthesizing viral products in cell cultures has shown significant success in yielding high titers of viruses and virus-like particles. The progress in the upstream stage has now shifted the bottleneck to the downstream processing (DSP). Overlooked for decades, the DSP responsible for viral product …

Archaeosine Modification Of Archaeal Trna - A Role In Structural Stabilization, Ben Turner, Brett W. Burkhart, Katrin Weidenbach, Robert Ross, Patrick A. Limbach, Ruth A. Schmitz, Valérie De Crécy-Lagard, Kenneth M. Stedman, Thomas J. Santangelo, Dirk Iwata-Reuyl

Biology Faculty Publications and Presentations

Archaeosine (G+) is a structurally complex modified nucleoside found quasi-universally in the tRNA of Archaea and located at position 15 in the dihydrouridine loop, a site not modified in any tRNA outside of the Archaea. G+ is characterized by an unusual 7-deazaguanosine core structure with a formamidine group at the 7-position. The location of G+ at position 15, coupled with its novel molecular structure, led to a hypothesis that G+ stabilizes tRNA tertiary structure through several distinct mechanisms. To test whether G+ contributes to tRNA stability and define the biological role of G+, we investigated the consequences of introducing targeted …

Complex Ciliary Flows Around Stentor Polymorphus In Solutions Of 2% Buttermilk And Chlamydomonas Reinhardtii, Eliana B. Smithstein

Scripps Senior Theses

Stentor are large, unicellular ciliates of the Heterotricha order. They live in both freshwater and marine habitats and are mostly found in ponds. I studied Stentor polymorphus, which is a species of Stentor only recently discovered to be lab culturable. They range from 0.5-1.5mm in length and are unusual because they live with endosymbiotic algae and are much more likely than other, more widely studied, species of Stentor to form aggregates while they are eating. There are three main components to this thesis: First, I established protocols for keeping a viable S. polymorphus culture, since no protocols had been …

Synthesis, Characterization, And Biological Activity Of Imidazolium Salts, David Weader

Williams Honors College, Honors Research Projects

Nonmuscle invasive bladder cancer (NMIBC) inflicts thousands of Americans annually, and is typically treated with the immunotherapy BCG. However, due to a BCG shortage, there is a new need for novel treatments of NMIBC. Addressing this issue, several imidazolium salt derivatives were synthesized and characterized with the intent of treatment within the bladder. These imidazolium salts were tested against different human bladder cancer cell lines in vitro to determine their reactivity and cytotoxicity. Among these results are GI50 concentrations for each drug, which is the concentration of drug needed to see growth inhibition in 50% of treated cells. Previous published …

Molecular And Functional Characterization Of Α-Galactosyl Epitopes In Trypanosoma Cruzi, Uriel Ortega Rodriguez

Open Access Theses & Dissertations

Trypanosoma cruzi, the causative agent of Chagas disease (CD) currently affects 6-7 million people across the world. Currently, only two drugs, benznidazole and nifurtimox, are available for treatment of CD and they are highly toxic and less effective in the chronic stage of the disease. Specific biomarkers for diagnosis and follow-up of treatment do not exist in the clinical settings. following chemotherapy, patients take approximately 10-20 years to exhibit negative seroconversion with the conventional serology assays. Moreover, there is no vaccine available to prevent or treat CD. T. cruzi contains a complex cell surface consisting of several classes of glycoconjugates …

Expression, Purification, And Characterization Of Recombinant Human Npas2, Brenda Moreno

Open Access Theses & Dissertations

Many living organisms have biological clocks known as circadian rhythms that control various physiological and behavioral processes, tailored with the day and night. At the cellular level, the circadian clock drives daily rhythms with a transcriptional-translational feedback loop (TTFL) established by multiple transcription factors and genes under their regulation. Circadian Locomotor Output Cycles Kaput (CLOCK) and Brain and Muscle ARNT-like protein 1 (BMAL1) are two of those transcription factors, initiating the TTFL by forming a heterodimeric complex that bind to DNA promoters. Neuronal PAS domain protein 2 (NPAS2) is a functional analog to CLOCK. Less knowledge about NPAS2, in contrast …

Plant-Soil Interactions Dominate Soil Microbial Respiration And Soil Organic Carbon Sequestration In A Subtropical Moist Evergreen Broadleaved Forest In China, Zhijie Yang

Theses and Dissertations--Plant and Soil Sciences

Tropical forest soils contain one-third of global soil carbon (C). The warm and moist climate in tropical forests leads to rapid soil organic carbon (SOC) decomposition, with the highest soil microbial respiration rates in the world, so even a slight change in soil C and microbial respiration could affect atmospheric carbon dioxide concentration. However, there remains a lack of understanding of the mechanisms driving microbial respiration in tropical forests, due to different climate and biophysical drivers compared to temperate or boreal forests. Furthermore, forest conversions (from natural forests to plantations) are most widespread in tropical regions, leading to a loss …

In Planta Evaluation Of Gene Regulation By Soybean Auxin Response Factors, Pratiksha K C

Electronic Theses and Dissertations

Nitrogen (N) is an important plant nutrient but its abundance in the soil is not sufficient for profitable crop production. N input in the form of chemical fertilizers helps fill this need; however, an alternative for fertilizers is an immediate need due to the environmental pollution resulting from excessive use of fertilizers. Leguminous plants such as soybean (Glycine max) that form root nodules through symbiotic association with N-fixing rhizobia and therefore need little or no chemical N fertilizers. The plant hormone auxin plays a crucial role in determining the number of nodules and their rate of maturity in soybean. Auxin …