Browsing by Author "Pantano, Paul"
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Item Acute and Chronic Toxicity of Metal Oxide Nanoparticles in Chemical Mechanical Planarization Slurries with Daphnia Magna(Royal Society of Chemistry) Karimi, Sarah; Troeung, Meiline; Wang, Ruhung; Draper, Rockford K.; Pantano, Paul; 0000-0001-5535-8358 (Pantano, P); Karimi, Sarah; Troeung, Meiline; Wang, Ruhung; Draper, Rockford K.; Pantano, PaulThe semiconductor manufacturing industry uses metal oxide nanoparticles (NPs), including colloidal silica (c-SiO₂), fumed silica (f-SiO₂), ceria (CeO₂), and alumina (Al₂O₃), as abrasives in chemical mechanical planarization (CMP) processes. Assessing the toxicity of NPs used in commercial CMP slurries is difficult because these mixtures may contain undefined toxic constituents. Herein, the fresh water flea Daphnia magna (D. magna) was used to assess the effects of four model CMP slurries that did not contain known toxic additives. In the acute toxicity assessments, the key findings were that c-SiO₂ slurry caused a modest increase in body size indicative of a hormetic stress response, that the Al₂O₃ slurry was toxic to D. magna with a calculated 96 h LC-50 of 1.1 mg mL-1, that the CeO₂ and Al₂O₃ slurries caused significant dose-dependent decreases in body size, and that NP dissolution was not responsible for these responses. In the chronic toxicity assessments, the key findings were that the c-SiO₂ slurry caused a modest increase in reproduction indicative of a hormetic stress response, that the Al₂O₃ slurry lead to a modest increase in morbidity and a significant decrease in body size, and that the CeO₂ and Al₂O₃ slurries caused dose-dependent decreases in reproductive output. The acute and chronic toxicity results demonstrate that different model CMP slurries exert distinct and unpredictable effects on D. magna morbidity, growth, and reproductive output. Especially important is that the CeO₂ and Al₂O₃ slurries reduced D. magna reproduction upon chronic exposure at low applied doses, which could have adverse consequences to aquatic ecosystems.Item Acute and Chronic Toxicity to Daphnia Magna of Colloidal Silica Nanoparticles in a Chemical Mechanical Planarization Slurry after Polishing a Gallium Arsenide Wafer(Elsevier Science BV, 2018-12-29) Karimi, Sarah; Troeung, Meiline; Wang, Ruhung; Draper, Rockford K.; Pantano, Paul; Crawford, Steven; Aravamudhan, Shyam; 0000-0001-5535-8358 (Pantano, P); Karimi, Sarah; Troeung, Meiline; Wang, Ruhung; Draper, Rockford K.; Pantano, PaulSemiconductor chip manufacturers use slurries of metal oxide nanoparticles (NPs) as abrasives in chemical mechanical planarization (CMP) processes on wafers containing films of III/V semiconducting materials. Assessing the toxicity of these specialized NPs is challenging not only because commercial slurries may contain undefined toxic constituents, but because CMP processes can change the physical and chemical properties of the NPs. Herein, the fresh water flea Daphnia magna (D. magna) was used to assess the effects of Ultra-Sol (R) 200S CMP slurry containing similar to 30-nm colloidal silica (c-SiO₂) NPs before (pristine) and after (spent) a GaAs wafer was polished with an extreme arm-pressure of 5 psi. In the acute 96-hour toxicity assessments, both the pristine and spent slurries at 4.0 mg/mL c-SiO₂ NPs had little effect on D. magna morbidity and body sizes. In the chronic 21-day toxicity assessments, neither slurry at 0.10 mg/mL c-SiO₂ NPs was toxic, but both slurries lead to a modest (9-10%) increase in D. magna body sizes and a significant (similar to 2-fold) increase in reproductive output, indicative of a positive hormetic response. Identical increases in D. magna body sizes and reproductive output were observed with a supernatant of the pristine slurry, in the absence of the c-SiO₂ NPs, indicating that soluble material in the pristine supernatant contributed to the hormetic response, which suggests that the soluble material may also contribute to the hormetic response of the spent material.Item Biochemical and Biophysical Characterization of Bacterial Transition Metal Transporters by Functional Reconstitution in Artificial Lipid Bilayers(2022-05-01T05:00:00.000Z) Abeyrathna, Nisansala Sandamali; Meloni, Gabriele; Williams, Nathan; Nielsen, Steven O; Zheng, Jie; Pantano, PaulTransition metals play a vital role in all living organisms due to their key structural and functional properties central to diverse metabolic processes. However, because of their high reactivity organisms have evolved sophisticated biomolecular protein networks to control intercellular metal ion homeostasis, without reaching toxic intracellular levels. Transmembrane transporter proteins play a gate-keeper role in maintaining the dynamic flux of these transition metal ions across biological membranes, thereby finely tuning metal delivery and availability in cells and subcellular organelles. P-type ATPases are a superfamily of transmembrane primary active transporters involved in translocating substrates against an electrochemical gradient which play a key role in maintaining homeostasis of cellular concentrations of essential ions. They are classified into 5 classes (P1, P2, P3, P4 and P5) based on their substrate selectivity. This dissertation is focused on studying the substrate selectivity and mechanism of translocation in the P1B class of P-type ATPases which are involved in transition metal transport for both essential and toxic transition metals. P1B-type ATPases are classified into 7 sub families (P1B-1 - P1B-7 types) based on conserved amino acid motifs in their transmembrane helices that appear to control each sub-family’s substrate selectivity, resulting in the existence of pumps that can selectively translocate 1st, 2nd and 3rd row transition metals across the lipid bilayer. Considering their central role in controlling cellular metal levels and extrusion in cells they are also acting as virulence factors in pathogenic bacteria. Studies towards their characterization could therefore help in establishing them as new potential therapeutic targets to develop novel antibiotics to overcome the bacterial resistance observed with traditional antibiotics. However, the substrate transport across lipid bilayers, the overall mechanism for cargo translocation, and kinetics of these transporters remain elusive to a significant extent, due to lack of molecular tools to study putative metal substrate transport across membranes in real-time in a native-like environment. In light of this, metal-stimulated ATPase activity assays were coupled with an experimental platform based on multiple fluorescence sensor probes, to study substrate selectivity, transport mechanism, including counterion transport and electrogenicity, and translocation kinetics in realtime with recombinantly expressed proteins belonging to P1B-1 (CopA from E. coli) and P1B-5 (Nia from S. meliloti) classes reconstituted in artificial lipid bilayer vesicles known as proteoliposomes. The proteoliposomes were used as an in-vitro tool to determine metal selectivity and the kinetic parameters for metal transport by encapsulating fluorescent detector probes featuring turn-on florescence signal upon substrate ion binding and translocation. However, the use of the proteoliposomes is challenging due to their intrinsic structural instability and susceptibility to stressors like temperature, aging, and chemicals, which limits their shelf life. Therefore, an experimental approach was developed to stabilize membrane proteins and proteoliposomes by encapsulating them in a sheddable metal organic framework, which reduces their susceptibility to external stressors. This platform sheds light on developing methods to utilize proteoliposomes in biochemical and biophysical investigation of transmembrane proteins and in drug delivery applications. In addition, this approach would help to overcome the challenges of cold-chain therapeutic transport of liposomal vaccine formulations.Item A Carbon Nanotube-based Raman-imaging Immunoassay For Evaluating Tumor Targeting Ligands(Royal Society of Chemistry, 2014-04-16) Bajaj, Pooja; Mikoryak, Carole; Wang, Ruhung; Bushdiecker II, David K.; Memon, Pauras; Draper, Rockford K.; Dieckmann, Gregg R.; Pantano, Paul; Musselman, Inga H.; Pantano, Paul; Musselman, Inga H.Herein, we describe a versatile immunoassay that uses biotinylated single-walled carbon nanotubes (SWNTs) as a Raman label, avidin-biotin chemistry to link targeting ligands to the label, and confocal Raman microscopy to image whole cells. Using a breast tumor cell model, we demonstrate the usefulness of the method to assess membrane receptor/ligand systems by evaluating a monoclonal antibody, Her-66, known to target the Her2 receptors that are overexpressed on these cells. We present two-dimensional Raman images of the cellular distribution of the SWNT labels corresponding to the distribution of the Her2 receptors in different focal planes through the cell with validation of the method using immunofluorescence microscopy, demonstrating that the Her-66-SWNT complexes were targeted to Her2 cell receptors.;Item Characterizing the Role of Heme in Alzheimer’s Disease Pathogenesis(2021-05-01T05:00:00.000Z) Vidal, Chantal; Zhang, Li; Pantano, Paul; Burr, John G.; Ploski, Jonathan E.; Delk, NikkiIn humans, heme accounts for 97% of functional iron. With a porphyrin ring and an iron ion, heme possesses structural and chemical features fitting for electron transfer, oxidation/reduction, and interaction with oxygen. Three oxidative phosphorylation (OXPHOS) complexes, II, III, and IV, require heme for proper functioning. Cells that require high levels of adenosine triphosphate (ATP) and OXPHOS require elevated levels of heme. Heme also serves as a powerful antioxidant for cells because it can be degraded to biliverdin and reduced to bilirubin. The reduction of biliverdin to bilirubin helps relieve reactive oxygen species (ROS) in cells. Neuronal cells are known to be high-energy demanding cells that depend on mitochondrial respiration to function. Specifically, in neurodegenerative diseases such as Alzheimer’s Disease (AD), mitochondrial dysfunction is one of the key characteristics associated with the progression of this disease. Oxidative stress has also been implicated in the pathogenesis of AD. Due to the role of heme in both of these cellular functions, it is important to understand how heme contributes to neuronal function and how it may play a pivotal role in developing this neurodegenerative disease. The objective of this research is to dissect the role of heme in the pathogenesis of AD. Utilizing immunocytochemistry and Western blot techniques, I have depicted the importance of heme in neuronal development. Heme uptake, synthesis, and degradation are significantly increased in developing and differentiating neurons. This increase in heme flux coincides with an increase in mitochondrial proteins. Using the APPPS1 mouse model and microarray expression data of human patients, I detected specific heme-related enzymes that are downregulated in AD. These alterations can lead to a decrease in the availability of heme for cellular functions. The decrease in heme availability can lead to disturbed mitochondrial function and an increase in oxidative stress. Furthermore, to glean whether heme flux alterations are early and potentially initiating causes of AD, I utilized patient-derived neurons generated from human-induced pluripotent stem cells (iPSCs). These studies revealed a distinct role of heme in the development of familial (FAD) and sporadic AD (SAD). SAD neurons have downregulated heme synthetic and degradation enzymes, while FAD neurons only had a slight yet significant reduction in the biliverdin reductase B (BLVRB) enzyme involved in heme degradation. Moreover, analysis of the tricarboxylic acid (TCA) cycle enzymes and intermediates revealed a significant alteration in enzymes and intermediates within both SAD and FAD neurons relative to gender-matched controls. This study revealed that although heme flux alterations are likely an early event in SAD pathogenesis, perturbations in the TCA cycle are probably a common characteristic of both SAD and FAD.Item Electrochemical Performance of Polymer Derived Carbon Nanofibers and Tungsten Compound/Carbon Composites(2021-12-01T06:00:00.000Z) Garcia, Juan Alexandro; Ferraris, John P; Zhang, Li; Pantano, Paul; Balkus, Jr., Kenneth J; Yang, Duck JooCurrent energy demands and advancements in energy harvesting have driven research towards developing storage devices with high energy and power densities to better store and deliver charge. Battery devices fulfill many of these demands, but supercapacitor devices have garnered more favor due to their rapid charge rate capabilities and their vast cyclability. The different classifications of supercapcitors (electric double layer capacitors, pseudocapacitors, and hybrid supercapcitors) rely on either physical charge storage mechanisms which provide rapid delivery of charge, faradaic charge storage mechanisms which can be used to achieve how quantities of charge, or a combination of the two. While advancements in the field have been great, they are largely driven by trial-and-error approaches. To fully achieve the potential of supercapacitor devices, a better fundamental understanding of the aspects of the electrode materials and their influence over charge capabilities is needed. Chapter 1 introduces supercapacitor devices, and some of the materials that can be used to make them. It provides details on the production of activated carbon nanofibers (CNFs) derived from electrospun polyacrylonitrile (PAN) and tungsten compounds that were used in this work. Chapter 2 demonstrates the influence of miscibility in electrospun polymer blends on electrochemical performance on devices with ionic liquid electrolyte. In comparison to blends of PAN:polystyrene (PS) which have a miscibility parameter (MP) of 118, the studied blend of PAN:poly(styrene-co-acrylonitrile) has a miscibility parameter of 79. This resulted in a distinct morphology for phase separation of the blends, as well as a channel like morphology with interspersed domains. Devices from the PAN:SAN blend achieved a maximum power densities of approximately 17,500 W/kg when tested at 10 A/g in galvanostatic charge/discharge (GCD) and achieved a maximum energy density of 81 Wh/kg at 1750 W/kg when tested at 1 A/g. This device also boasted a capacitance retention of 82% after 3,500 cycles. Chapter 3 describes the preparation of hybrid electrode materials derived from polymer fibers with tungsten oxide nanoparticles and the influence of their degree of interaction on performance. A novel synthesis was described for the preparation of WO2.72, which normally is synthesized through a hydrothermal procedure in an autoclave, was prepared by in-situ synthesis of hybrid tungsten compound at CNFs with CO2 activation. This hybrid material (WO@CNF) was compared to pure WO2.72 and CNFs to determine the degree of interaction between the components in the hybrid and determine that interactions influence on the performance of the device. The WO@CNF material was found to have a low degree of interaction, but this still provided an improvement on the energy storage capabilities of the material over the physical mixture composite. Chapter 4 describes the modification of the synthesis used to make WO2.72 nanoparticles in carbon fibers to produce WN nanoparticles and the comparison of their electrochemical performance. Upon carbonization without activation, WN was found in the WO@CNF hybrid material. Metal nitrides possess favorable qualities for pseudocapacitors, and hybrid supercapacitors compared to metal oxides, and WN is not widely researched for these devices. Utilizing ammonia activation drove the synthesis towards WN to form WN@CNF hybrid materials. The WN@CNF produced carbons with a higher graphitic quality (Id:Ig ratio of 0.77 compared to 0.91 for WO@CNF), and achieved comparable power densities, but possessed lower energy densities.Item Incorporating Novel Functionality on In Vitro Microelectrode Arrays(2018-05) Hammack, Audrey Sue; 0000-0001-5620-1993 (Hammack, AS); Gnade, Bruce E.; Pantano, Paul; Sherry, A. Dean; Zheng, JieThe microelectrode array (MEA) is an inexpensive, high throughput platform for measuring and recording extracellular electrical potentials from a culture of electrogenic tissues. However, this technology is not without drawbacks, which this work seeks to address. On conventional MEAs, stimulation of a culture is achieved via electrical stimulation through the electrodes, which may introduce recording artifacts. Optogenetics is a molecular biology technique that can be used to decouple the recording and stimulation functions of the MEA electrode, but hardware required to utilize optogenetics in combination with an MEA is a barrier that prevents utilization of this technique. One project presented here seeks to integrate an MEA with an array of organic light-emitting diodes (OLEDs) driven by thin film transistors (TFTs), to create a multifunctional MEA with optical stimulating capabilities, in order to streamline the hardware required for an in vitro optogenetics recording experiment. Discreet functional components are demonstrated and a proof of concept integrated substrate is presented. Another project presented in this dissertation seeks to insulate the MEA electrodes with polystyrene. The vast set of organic and inorganic materials used to insulate MEA electrodes present challenges to users who must modify cell culture protocols for cell adhesion to the surface of the MEAs. An MEA that features a patterned film of polystyrene, a material that is far more common to cell culture work, as electrode insulation is presented. Viable cell culture on this MEA and recordings that are comparable to other MEA substrates are demonstrated.Item Investigating the Functional Impacts of Tetrel Bonding in the Reaction Mechanism of Methyltransferases and Screening of Peptidomimetic Inhibitors(May 2023) Douglas, Teri Arnelle 1995-; Stelling, Allison L.; Meloni, Gabriele; Ahn, Jung-Mo; Pantano, Paul; Nielsen, Steven O.While protein methyltransferases have important roles in many biological processes such as gene regulation and RNA processing, their dysregulation has been implicated in the progression of a number of diseases such as cancers and neurological conditions. These enzymes catalyze the methylation of lysine and arginine residues of target proteins using the cofactor and methyl donor, S-adenosyl methionine (SAM). A study of crystal structures of SAM-bound methyltransferases, along with computational studies using small molecule models, have revealed the presence of a type of non-covalent interaction termed a tetrel bond between the SAM methyl group and electron donating atoms of the target substrate. Since the tetrel-bonded complex in methyltransferase active site precedes the transition state in the SN2 methylation pathway, in this project it was hypothesized that methyltransferase active site promotes the formation of the tetrel-bonded complex, which is fundamental to the catalytic role of these enzymes. Using an optimized coupled fluorescent kinetic assay and site-directed mutagenesis to change a tyrosine residue to a phenylalanine in the active site of a model methyltransferase, SET7/9, a hydrogen bond which is believed to hold the tetrel- bonded complex in the correct orientation was removed, resulting in a 15-fold decrease in enzyme activity. Moreover, using this optimized fluorescence-based assay, ~80 peptidomimetic compounds were screened for inhibition of SET7/9, with the most potent compound, B21-2, having an IC50 value of 5.2 μM. Through understanding tetrel bonding and the use of lead compounds discovered, inhibitors may be designed to exploit unique interactions yielding potent and selective inhibitors for these enzymes.Item Magnetic and Catalytic Properties of Lanthanide Complexes(2021-05-01T05:00:00.000Z) Miller, Justin Todd; Stefan, Mihaela C.; Choudhary, Pankaj K.; Biewer, Michael C.; Nielsen, Steven O.; Pantano, PaulLanthanides are an intriguing family of elements possessing unique properties useful in many diverse applications. The first chapter of this work describes the origins of some of these properties and their catalytic and magnetic applications. The second chapter will highlight a highly unusual neodymium catalyst for diene polymerization. This coordination polymer catalyst contains no halides and makes use of no halide donor, yet produces desirable 96% 1,4- cis stereospecific material. The third chapter is concerned with the surprising formation and superparamagnetism of a neodymium-peroxide diimine cluster and the associated crystals. The cluster is formed by a rare example of anion-templated assembly in which the anion is derived from dissolved atmospheric oxygen. The resulting structural motif featured an array of tight three-metal clusters separated by a distance long enough to prevent long-range magnetic order, which resulted in superparamagnetic behavior in the solid state. This is believed to be the first report of superparamagnetism in a bulk crystal state. The fourth and final chapter is concerned with MRI contrast agents and presents an example of a new variety of potential next-generation agents composed of coordination polymers. The gadolinium diethylphosphate polymer features a far longer rotational coordination time than conventional small gadolinium complexes and thus offers dramatically improved T1 relaxation performance at low-fields common in clinical imaging applications. All of these lanthanide complexes are synthesized using an azeotropic distillation method. This method avoids the need for strict water-free techniques and also occasionally allows for novel structures to be obtained, as demonstrated in Chapter 3 in particular.Item Molecular Basis for Chaperone Control of Rtt109 Acetylation of Histone H3-H4(2021-08-01T05:00:00.000Z) Akhavantabib, Noushin; D'Arcy, Sheena; Cao, Yan; Meloni, Gabriele; Zheng, Jie; Pantano, PaulAcetylation is one of many protein post-translational modifications (PTMs) that frequently occurs in the cell. One type of acetylation is when the acetyl group from acetyl-coenzyme A (Ac-CoA) is transferred onto the ε-amino group of lysine sidechains. Histones are highly basic proteins that associate with genomic DNA and compact it into chromatin in the nucleus of the cell. They are often accompanied by a group of histone-binding proteins called histone chaperones in events such as nucleosome assembly/disassembly, histone transport and nuclear import. Being rich in lysine content, histones are frequently acetylated and therefore influence chromatin structure. Enzymes that carry out histone acetylation are termed histone acetyltransferases (HATs). Rtt109 is one such HAT that is found in fungal species, and requires association with histone chaperones to efficiently acetylate histones. Vps75 and Asf1 are the two known histone chaperones that when bound to Rtt109, enhance its enzymatic activity significantly. They also play a role determining Rtt109 selectivity and specificity towards different lysine residues in histones H3-H4. Cells deleted for Rtt109, Asf1 or both, are highly sensitive to genotoxic exposure; and it has been shown that Rtt109 acetylation of K56 is required for a cell to maintain its genomic integrity. This has made Rtt109 and its chaperone-containing complexes attractive anti-fungal therapeutic targets. The structure, dynamics and function of Rtt109 complexes are the focus of this dissertation. Utilizing comprehensive biophysical and biochemical analysis, we first investigate molecular interactions between Vps75 and H3-H4. We report the stoichiometry of binding in multiple ionic conditions and compare their interactions to a homologous complex containing Nap1. We identify the interface between Vps75 and H3-H4, and reveal how specific structural elements are tailored for Vps75 chaperoning activity with Rtt109. Next, we add Rtt109 to the Vps75-(H3-H4) complex and extensively characterize complex homogeneity and absolute stoichiometry. We define a detailed step-by-step Rtt109-Vps75 co-expression and purification protocol that maximizes yield and purity. We show the stoichiometry of binding is 1:2, with a second Rtt109 binding only at high concentration and readily replaced with H3-H4. We show that Rtt109-Vps75-(H3-H4) has a 1:2:1 unit that can self-associate to become a 2:4:2 complex through the H3-H3 contacts in a H3-H4 tetramer. Our large-scale reconstitution methods for various Rtt109 complexes paved the way for acquiring high-resolution structures via crystallography or cryo-electron microscopy. It also facilitated solution characterization via hydrogen-deuterium exchange mass spectrometry (HDXMS). Finally, we added Asf1, the last binding partner to reconstitute the double-chaperone complex − Rtt109-Vps75-(H3-H4)-Asf1. This allows for a comprehensive comparative HDX-MS experiment to uncover the mechanism behind chaperone activation of Rtt109. We purified and reconstituted eleven relevant protein complexes for analysis. We identify direct binding sites between each member of the complex and compare them to existing structures, and show different conformations upon addition of each chaperone. These results elucidate the acetylation mechanisms facilitated by cross-talk between two histone chaperones Vps75 and Asf1.Item Multifunctional Carbon Nanotube Yarns for Artificial Muscles and Energy Harvesters(2021-08-01T05:00:00.000Z) Wang, Zhong; Baughman, Ray H.; Da Silveira Rodrigues, Fabiano; Zakhidov, Anvar A.; Ferrairs, John P.; Pantano, PaulThe superb mechanical, physical, and chemical properties of carbon nanotube (CNT) yarns have promoted their application as function components that program actuation, sensing, and power management for soft robotics and smart systems. Success in making artificial muscles that are faster, more powerful, and that can provide larger strokes would expand their applications. Efficient conversion of ambient mechanical energy into electrical energy is needed for diverse applications, including self-powered wireless sensors, structural and human health monitoring systems, and the extraction of energy from ocean waves. Herein, the development of CNT yarn artificial muscles and mechanical energy harvesters are first discussed, and the obtained understanding of underlying mechanisms provide guidance for optimizing muscle and harvester performances. Next, unipolar stroke CNT yarn muscles are described, in which muscle stroke changes between extreme potentials are additive and muscle stroke remarkably increases with increasing potential scan rate. The normal decrease in stroke with increasing scan rate, because of decreased capacitance, is overwhelmed by a dramatic increase in effective ion size caused by electroosmotic pumping of solvent. These coiled carbon nanotube yarn muscles contain a yarn guest that shifts the yarn’s potential of zero charge (pzc) by over a volt, either positively or negatively. Such pzc shift agents include ion-exchange membrane polymers, oxidized graphene platelets, and surfactants. Record muscle strokes, contractile work-per-cycle, contractile power densities, and energy conversion efficiencies are obtained for unipolar muscles. Then, powerful CNT yarn mechanical energy harvesters (we call twistrons) are described, which are electrochemical artificial muscles run in reverse. Stretching a coiled CNT yarn can provide large, reversible changes in electrochemical capacitance, which enables conversion of mechanical energy to electrical energy. The performance of these twistron harvesters can be increased by diverse fabrication methods: optimizing the structure of the precursor CNT forest, using stretchinduced alignment, thermal annealing under tension, and incorporating reduced graphene oxide nanoplates. The peak output power at 1 Hz and at 30 Hz for a sinusoidal stretch were 0.73 and 3.19 kW/kg, which are 15- and 13-fold higher than for previous twistron harvesters at these respective frequencies. This performance at 30 Hz was over 12-fold that of other prior-art mechanical energy harvesters for frequencies between 1 Hz and 600 Hz. Last, the opportunities and challenges for future practical applications of CNT yarns are highlighted.Item Scavenger Receptor A1 Distinguishes Bovine Serum Albumin-Coated Pristine and Carboxylated Multi-Walled Carbon Nanotubes(2021-04-23) Huynh, Mai T.; Draper, Rockford K.; Pantano, PaulThis dissertation concerns the interactions of multi-walled carbon nanotubes (MWNTs) with mammalian macrophages, cells that are first responders to foreign invaders in the body. The production and use of MWNTs are rapidly increasing world-wide despite the possible adverse effects they may have on human health. For example, MWNTs pose a human respiratory hazard because they can cause pulmonary fibrosis, which may lead to mesothelioma. How MWNTs trigger such adverse effects is not well understood, especially whether MWNT binding to surface receptors on macrophages occurs. A complicating factor is what effects a protein corona, derived from serum proteins such as bovine serum albumin (BSA), may have on the interaction of MWNTs with cells. Achieving consensus in this research field is hampered by batch-to-batch inconsistencies with commercially synthesized MWNTs. This dissertation first presents a comprehensive physicochemical characterization of two lots of pristine MWNTs (pMWNTs) and carboxylated MWNTs (cMWNTs), which is important since the biological response of MWNTs is related to their physicochemical properties. There were many similarities between the physicochemical properties of the two commercial lots of cMWNTs and neither significantly diminished the 24-h proliferation of RAW 264.7 macrophages up to the highest concentration tested (200 μg cMWNTs/mL). Conversely, several physicochemical properties of the two lots of pMWNTs were different: notably, the newer lot of pMWNTs displayed less oxidative stability, a higher defect density, and a smaller amount of surface oxygen species relative to the original lot. Furthermore, a 72-h half maximal inhibitory concentration of ~90 µg pMWNTs/mL was determined for RAW 264.7 cells with the new lot of pMWNTs. These results demonstrate that subtle physicochemical differences can lead to significantly dissimilar cellular responses, and that production-lot consistency must be considered when assessing the toxicity or biomedical performance of MWNTs. Next, using the lots of well-characterized pMWNTs and cMWNTs, the interaction of MWNTs with class A-type 1 scavenger receptors (SR-A1s) was studied with a direct binding assay under conditions where the influence of nanotube functionalization and protein coronas could be carefully controlled. Both pMWNTs and cMWNTs coated with BSA bound to and were accumulated by RAW 264.7 macrophages, although the cells bound two times more BSA-coated cMWNT than pMWNTs. RAW 264.7 cells that were deleted for SR-A1 using CRISPR-Cas9 gene-editing technology had markedly reduced binding and accumulation of both BSA-coated cMWNTs and pMWNTs, suggesting that SR-A1 was responsible for the uptake of both MWNT types. Moreover, Chinese hamster ovary (CHO) cells that ectopically expressed SRA1 accumulated both MWNT types, whereas wild-type CHO cells did not. One model to explain these results is that SR-A1 can interact with two structural features of BSA-coated cMWNTs, one inherent to the carboxylated nanotubes and the other provided by the BSA corona, whereas SRA1 only interacts with the BSA corona of BSA-pMWNTs. A better understanding of the mechanisms by which MWNTs interact with macrophages should lead to the rational design of nanotoxicity remediation efforts and biomedical applications of carbon nanomaterials.Item Studies on the Toxicity, Bioaccumulation and Biopersistence of Model and Commercial Chemical Mechanical Planarization Slurries with Daphnia Magna(2018-08) Karimi, Sarah; Pantano, Paul; Draper, RockfordNanoparticle (NP) abrasives are components of chemical mechanical planarization (CMP) slurries used to polish wafers of semiconducting materials such as silicon. The semiconductor industry is interested in understanding the potential environmental toxicity associated with CMP NPs because the NPs may be discharged to aquatic ecosystems. However, assessing the toxicity of these specialized CMP NPs is challenging because commercial slurries may contain undefined toxic constituents. In response to this challenge, a manufacturer produced four model CMP slurries comprising colloidal or fumed silicon oxide (c-SiO₂ or f-SiO₈), cerium oxide (CeO₂), or aluminum oxide (Al₂O₃) NPs without known soluble toxicants to permit toxicity assessments of actual NPs used in commercial CMP slurries. This dissertation presents, for the first time, studies on the acute and chronic toxicities, the bioaccumulation, and the biopersistence of model CMP NPs with Daphnia magna (D. magna) – a fresh-water organism used in ecotoxicity assessments. The major findings presented in chapter two are that different model CMP slurries exert distinct effects on D. magna morbidity, growth, and reproductive output, and that the CeO₂ and Al₂O₃ CMP slurries severely reduced D. magna reproduction upon chronic exposure at sub-lethal applied doses, which could have adverse consequences to aquatic ecosystems. The major findings presented in chapter two are that different model CMP slurries exert distinct effects on D. magna morbidity, growth, and reproductive output, and that the CeO₂ and Al₂O₃ CMP slurries severely reduced D. magna reproduction upon chronic exposure at sub-lethal applied doses, which could have adverse consequences to aquatic ecosystems. The major findings in chapter three are that CeO₂ and Al₂O₃ NPs were accumulated in different amounts by D. magna, and that after 48 h of depuration, D. magna exposed to 0.10 mg/mL CeO₂ eliminated 85% of the CeO₂ load, and D. magna exposed to 0.10 mg/mL of Al₂O₃ eliminated 78% of the Al₂O₃ load. The fourth and the final chapter of this dissertation addresses the question of whether polishing a gallium arsenide (GaAs) wafer can impart added toxicity to CMP NPs. Using a commercial c-SiO₂ CMP slurry (Ultra-Sol® 200S), the key findings were that neither the pristine or spent slurry at 0.10 mg/mL c-SiO₂ NPs was toxic after a 21-day exposure, but both slurries led to a slight increase in body size and a ~2-fold increase in reproduction, indicative of a hormetic response. Further testing revealed that the effector was a soluble component(s) in the pristine slurry, and not the pristine or spent NPs.Item Supercapacitor Electrode Materials Comprising Uniformly Dispersed Chromium Nitride/ Carbon Fiber Composite(2022-05-01T05:00:00.000Z) Rifat, Samia; Ferraris, John P.; Balkus Jr., Kenneth J.; Nielsen, Steven O.; Pantano, PaulNowadays, researchers and industrial designers are looking for an eco-friendly alternative energy source to fulfill the increasing need for energy and reduce environmental pollution. Electricity based on energy storage devices can be a way of solving the crisis. Among different energy storage devices, the faster charging and discharging speeds or higher power densities, working in a wider range of temperatures, and longer cycle life of supercapacitor make them attractive for several applications. The commercially available supercapacitors are mostly electric double-layer capacitors (EDLCs) and to a lesser degree of pseudocapacitors. Recently, researchers have been focusing on hybrid supercapacitors (HSCs) due to their ability to combine the properties of both EDLCs and pseudocapacitors to expand the applications. Engineered carbon nanofibers can be coupled with conductive metal nitrides to form composites and used as electrode materials for supercapacitor applications. In this work, a new hybrid nanocomposite of carbon fibers and chromium nitride (CFs/CrN) was fabricated as electrode materials, where polyacrylonitrile (PAN) was utilized as the carbonizing materials and polymethyl methacrylic acid (PMAA) as the sacrificial agents. Here, pore-forming agents, PMAA, assisted in improving the supercapacitor's performance by increasing the electrode materials' surface area. Also, growing CrN nanoparticles in the fiber contributed by the pseudocapacitance from proton adsorption. Furthermore, the chelation ability of the PMAA might be beneficial for the homogeneous distribution of CrN all over the CFs. Furthermore, the use of aqueous electrolytes and comparatively low-cost transition metal materials lowered the fabrication costs, and the utilization of the electrospinning technique makes CFs/metal nitrides composite electrodes freestanding and readily produced. Chapter 1 describes a detailed introduction to supercapacitors, including a brief description of the storage principle of EDLCs, pseudo capacitors, and hybrid supercapacitors and their advantages and disadvantages. It also describes the basics of the electrospinning process, thermal treatments, and aqueous electrolytes, all of which were applied to fabricate the supercapacitors using CFs and metal nitrides composite-based electrodes. Chapter 2 represents the fabrication of CFs and chromium nitrides composites using polymer blends containing PAN and PMAA and Cr precursor as a source of chromium. This chapter also describes the characterization of synthesized PAM-PMAA-CrN electrode materials and their electrochemical performance and analysis. The highest capacitance was obtained from PANPMAA-CrN based electrode 159 F/g at 5 mV/s. Also, the highest energy densities of 13.26 Wh/Kg at 1.2 V were obtained from the PAN-PMAA-CrN and CNFs based asymmetric device. Furthermore, the PAN-PMAA-CrN electrode showed higher stability with 80.4% capacitance retention after 10000 cycles.Item Synthesis of Functionalized Polycaprolactones for Drug Delivery Applications(2021-08-01T05:00:00.000Z) Calubaquib, Erika Joy; Stefan, Mihaela C.; Pereira, L. Felipe; Biewer, Michael C.; Meloni, Gabriele; Pantano, PaulPolycaprolactones (PCLs) have been used in various applications due to their biodegradability, biocompatibility, and favorable mechanical properties. The ability to attach multiple functionalities in the PCL backbone can provide many possibilities to tune the polymer’s physicochemical properties. Among the applications, extensive efforts have been dedicated to developing PCLs as carriers of bioactive compounds; however, some limitations still encountered are low payload, instability, and uncontrolled release of the cargo. In this work, micellar drug delivery systems obtained from the self-assembly of amphiphilic block copolymers comprising of benzyloxy- and oligo(ethylene glycol)-substituted PCLs were designed to load the doxorubicin anticancer drug and a quercetin cardioprotective polyphenol. The co-loading approach provided a way to enhance the loading capacity of the micelle for both cargoes. The utilization of various lengths of oligo(ethylene glycol) side-chains permitted tuning of the polymer’s thermoresponsive behavior to modulate the release of the cargo. These micelles exhibited a low critical micelle concentration, which is necessary for tolerating severe dilutions. Many copolymers have been explored for drug delivery; however, amphiphilic homopolymers can also be an alternative due to their more straightforward synthesis. Most reported amphiphilic homopolymers have a nonbiodegradable backbone, exhibits pH-dependent assembly, and are charged. Herein, non-ionic amphiphilic PCL homopolymers readily self-assembled to form micelles. The potential of using these micelles as drug carriers were explored by loading a eugenol anti-inflammatory molecule.Item Testing Quasi-independence With Survival Tree Approaches(2022-08-01T05:00:00.000Z) Guo, Qi; Chiou, Sy Han; Pantano, Paul; Chen, Min; Choudhary, Pankaj K.; Shin, SunyoungThis dissertation aims to address two common issues in survival analysis. First, we develop a powerful quasi-independence test for survival and recruitment times. The proposed test extends existing permutation tests by incorporating cutting-edge survival tree algorithms to achieve high power in detecting various quasi-dependence scenarios. Second, we explore tools from frailty models, recurrent event models, and meta-analysis while considering the longitudinal information collected throughout the last decade to understand the risk of injury and re-injury. The dissertation is organized as follows. Chapter 2 develops the tree-based method to test the quasi-independence between left trun- cation time and survival time. Individuals who experienced the event prior to when the study began are left-truncated. Quasi-independence of truncation and event times refers to a factorization of their joint density in the observable region (the event time is no less than the left truncation time). Unlike the assumption of independence between censoring time and event time, the assumption of quasi-independence between truncation time and event time can be tested. Existing tools such as the conditional Kendall’s tau test are pow- erful in detecting monotonic dependencies. Extensions of existing quasi-independent tests have been proposed to detect non-monotonic alternatives. Thus, the two minimum p-value tests (minp1 and minp2 tests) are also proposed to test simple non-monotonic dependencies. In this paper, we develop a powerful and computationally fast tree-based p-value test for quasi-independence where the data has complicated non-monontonic dependencies. We also developed different permutation and bootstrap methods to approximate the null distribution of the tree-based test. Chapter 3 assesses the aggregated overall effect of different covariates on injury risk during the eight competitive seasons for soccer players in German Bundesliga. One of the standard approaches in modeling the risk in recurrent event data is to model the rate function. We start by stratifying the injury data by season where we assume that the eight Bundesliga seasons are mutually independent, and the seasons are not interacting with any of the co- variates. We then apply the Anderson-Gill (AG) model to find the regression coefficients of the covariates without accounting for overlapping players thus ignoring between seasons dependence. To solve this issue, we apply the AG model for each season and aggregate the results by meta-analysis. However, the common meta-analysis models such as the fixed effects model, and the random effects model assume that there are no overlapping subjects between studies. Since our data has overlapping players between seasons, we developed a novel meta-analysis model which can handle our injury data. This new model suggests that the presence of a pre-season injury, and additional game-time during a match might be associated with a lower risk of getting a regular season injury. As the number of previ- ous injuries increases, there might be a higher risk of getting a regular season injury. We found that the Goalkeeper position is less likely to get injured compared to the Defender position. In this chapter, we also take into account that the playing condition of a soccer player will go from “healthy” to “injured” multiple times (alternating gap times) within a season. The semiparametric estimation approach under the accelerated failure time (AFT) model was used to evaluate the covariate effects on the two alternating states. To get the aggregated overall effect, we applied a fixed effects model. From this analysis, we find that the presence of pre-season injuries and frequent injuries in the past imply shorter healthy times. Additionally, increased game-time during a season might be associated with longer healthy times and shorter injury times.