Matching Items (86)
Description
The advent of new high throughput technology allows for increasingly detailed characterization of the immune system in healthy, disease, and age states. The immune system is composed of two main branches: the innate and adaptive immune system, though the border between these two states is appearing less distinct. The adaptive immune system is further split into two main categories: humoral and cellular immunity. The humoral immune response produces antibodies against specific targets, and these antibodies can be used to learn about disease and normal states. In this document, I use antibodies to characterize the immune system in two ways: 1. I determine the Antibody Status (AbStat) from the data collected from applying sera to an array of non-natural sequence peptides, and demonstrate that this AbStat measure can distinguish between disease, normal, and aged samples as well as produce a single AbStat number for each sample; 2. I search for antigens for use in a cancer vaccine, and this search results in several candidates as well as a new hypothesis. Antibodies provide us with a powerful tool for characterizing the immune system, and this natural tool combined with emerging technologies allows us to learn more about healthy and disease states.
ContributorsWhittemore, Kurt (Author) / Sykes, Kathryn (Thesis advisor) / Johnston, Stephen A. (Committee member) / Jacobs, Bertram (Committee member) / Stafford, Phillip (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2014
Description
Peptide microarrays are to proteomics as sequencing is to genomics. As microarrays become more content-rich, higher resolution proteomic studies will parallel deep sequencing of nucleic acids. Antigen-antibody interactions can be studied at a much higher resolution using microarrays than was possible only a decade ago. My dissertation focuses on testing the feasibility of using either the Immunosignature platform, based on non-natural peptide sequences, or a pathogen peptide microarray, which uses bioinformatically-selected peptides from pathogens for creating sensitive diagnostics. Both diagnostic applications use relatively little serum from infected individuals, but each approaches diagnosis of disease differently. The first project compares pathogen epitope peptide (life-space) and non-natural (random-space) peptide microarrays while using them for the early detection of Coccidioidomycosis (Valley Fever). The second project uses NIAID category A, B and C priority pathogen epitope peptides in a multiplexed microarray platform to assess the feasibility of using epitope peptides to simultaneously diagnose multiple exposures using a single assay. Cross-reactivity is a consistent feature of several antigen-antibody based immunodiagnostics. This work utilizes microarray optimization and bioinformatic approaches to distill the underlying disease specific antibody signature pattern. Circumventing inherent cross-reactivity observed in antibody binding to peptides was crucial to achieve the goal of this work to accurately distinguishing multiple exposures simultaneously.
ContributorsNavalkar, Krupa Arun (Author) / Johnston, Stephen A. (Thesis advisor) / Stafford, Phillip (Thesis advisor) / Sykes, Kathryn (Committee member) / Jacobs, Bertram (Committee member) / Arizona State University (Publisher)
Created2014
Description
Microplastics are emerging to be major problem when it comes to water pollution and they pose a great threat to marine life. These materials have the potential to affect a wide range of human population since humans are the major consumers of marine organisms. Microplastics are less than 5 mm in diameter, and can escape from traditional wastewater treatment plant (WWTP) processes and end up in our water sources. Due to their small size, they have a large surface area and can react with chlorine, which it encounters in the final stages of WWTP. After the microplastics accumulate in various bodies of water, they are exposed to sunlight, which contains oxidative ultraviolet (UV) light. Since the microplastics are exposed to oxidants during and after the treatment, there is a strong chance that they will undergo chemical and/or physical changes. The WWTP conditions were replicated in the lab by varying the concentrations of chlorine from 70 to 100 mg/L in increments of 10 mg/L and incubating the samples in chlorine baths for 1–9 days. The chlorinated samples were tested for any structural changes using Raman spectroscopy. High density polyethylene (HDPE), polystyrene (PS), and polypropylene (PP) were treated in chlorine baths and observed for Raman intensity variations, Raman peak shifts, and the formation of new peaks over different exposure times. HDPE responded with a lot of oxidation peaks and shifts of peaks after just one day. For the degradation of semi-crystalline polymers, there was a reduction in crystallinity, as verified by thermal analysis. There was a decrease in the enthalpy of melting as well as the melting temperature with an increase in the exposure time or chlorine concentration, which pointed at the degradation of plastics and bond cleavages. To test the plastic response to
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UV, the samples were exposed to sunlight for up to 210 days and analyzed under Raman spectroscopy. Overall the physical and chemical changes with the polymers are evident and makes a way for the wastewater treatment plant to take necessary steps to capture the microplastics to avoid the release of any kind of degraded microplastics that could affect marine life and the environment.
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UV, the samples were exposed to sunlight for up to 210 days and analyzed under Raman spectroscopy. Overall the physical and chemical changes with the polymers are evident and makes a way for the wastewater treatment plant to take necessary steps to capture the microplastics to avoid the release of any kind of degraded microplastics that could affect marine life and the environment.
ContributorsKelkar, Varun (Author) / Green, Matthew D (Thesis advisor) / Tongay, Sefaattin (Committee member) / Halden, Rolf U. (Committee member) / Arizona State University (Publisher)
Created2017
Description
A new class of layered materials called the transition metal trichalcogenides (TMTCs) exhibit strong anisotropic properties due to their quasi-1D nature. These 2D materials are composed of chain-like structures which are weakly bound to form planar sheets with highly directional properties. The vibrational properties of three materials from the TMTC family, specifically TiS3, ZrS3, and HfS3, are relatively unknown and studies performed in this work elucidates the origin of their Raman characteristics. The crystals were synthesized through chemical vapor transport prior to mechanical exfoliation onto Si/SiO¬2 substrates. XRD, AFM, and Raman spectroscopy were used to determine the crystallinity, thickness, and chemical signature of the exfoliated crystals. Vibrational modes and anisotropic polarization are investigated through density functional theory calculations and angle-resolved Raman spectroscopy. Particular Raman modes are explored in order to correlate select peaks to the b-axis crystalline direction. Mode III vibrations for TiS3, ZrS3, and HfS3 are shared between each material and serves as a unique identifier of the crystalline orientation in MX3 materials. Similar angle-resolved Raman studies were conducted on the novel Nb0.5Ti0.5S3 alloy material grown through chemical vapor transport. Results show that the anisotropy direction is more difficult to determine due to the randomization of quasi-1D chains caused by defects that are common in 2D alloys. This work provides a fundamental understanding of the vibrational properties of various TMTC materials which is needed to realize applications in direction dependent polarization and linear dichroism.
ContributorsKong, Wilson (Author) / Tongay, Sefaattin (Thesis advisor) / Wang, Liping (Committee member) / Green, Matthew (Committee member) / Arizona State University (Publisher)
Created2017
Description
Immunosignature is a technology that retrieves information from the immune system. The technology is based on microarrays with peptides chosen from random sequence space. My thesis focuses on improving the Immunosignature platform and using Immunosignatures to improve diagnosis for diseases. I first contributed to the optimization of the immunosignature platform by introducing scoring metrics to select optimal parameters, considering performance as well as practicality. Next, I primarily worked on identifying a signature shared across various pathogens that can distinguish them from the healthy population. I further retrieved consensus epitopes from the disease common signature and proposed that most pathogens could share the signature by studying the enrichment of the common signature in the pathogen proteomes. Following this, I worked on studying cancer samples from different stages and correlated the immune response with whether the epitope presented by tumor is similar to the pathogen proteome. An effective immune response is defined as an antibody titer increasing followed by decrease, suggesting elimination of the epitope. I found that an effective immune response usually correlates with epitopes that are more similar to pathogens. This suggests that the immune system might occupy a limited space and can be effective against only certain epitopes that have similarity with pathogens. I then participated in the attempt to solve the antibiotic resistance problem by developing a classification algorithm that can distinguish bacterial versus viral infection. This algorithm outperforms other currently available classification methods. Finally, I worked on the concept of deriving a single number to represent all the data on the immunosignature platform. This is in resemblance to the concept of temperature, which is an approximate measurement of whether an individual is healthy. The measure of Immune Entropy was found to work best as a single measurement to describe the immune system information derived from the immunosignature. Entropy is relatively invariant in healthy population, but shows significant differences when comparing healthy donors with patients either infected with a pathogen or have cancer.
ContributorsWang, Lu (Author) / Johnston, Stephen (Thesis advisor) / Stafford, Phillip (Committee member) / Buetow, Kenneth (Committee member) / McFadden, Grant (Committee member) / Arizona State University (Publisher)
Created2018
Description
Since the discovery of graphene, two dimensional materials (2D materials) have become a focus of interest for material research due to their many unique physical properties embedded in their 2D structure. While they host many exciting potential applications, some of these 2D materials are subject to environmental instability issues induced by interaction between material and gas molecules in air, which poses a barrier to further application and manufacture. To overcome this, it is necessary to understand the origin of material instability and interaction with molecules commonly found in air, as well as developing a reproducible and manufacturing compatible method to post-process these materials to extend their lifetime. In this work, the very first investigation on environmental stability on Te containing anisotropic 2D materials such as GaTe and ZrTe3 is reported. Experimental results have demonstrated that freshly exfoliated GaTe quickly deteriorate in air, during which the Raman spectrum, surface morphology, and surface chemistry undergo drastic changes. Environmental Raman spectroscopy and XPS measurements demonstrate that H2O molecules in air interact strongly on the surface while O2, N2, and inert gases don't show any detrimental effects on GaTe surface. Moreover, the anisotropic properties of GaTe slowly disappear during the aging process. To prevent this gas/material interaction based surface transformation, diazonium based surface functionalization is adopted on these Te based 2D materials. Environmental Raman spectroscopy results demonstrate that the stability of functionalized Te based 2D materials exhibit much higher stability both in ambient and extreme conditions. Meanwhile, PL spectroscopy, angle resolved Raman spectroscopy, atomic force microscopy measurements confirm that many attractive physical properties of the material are not affected by surface functionalization. Overall, these findings unveil the degradation mechanism of Te based 2D materials as well as provide a way to significantly enhance their environmental stability through an inexpensive and reproducible surface chemical functionalization route.
ContributorsYang, Sijie (Author) / Tongay, Sefaattin (Thesis advisor) / Gould, Ian (Thesis advisor) / Trovitch, Ryan (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2017
Description
Photocatalytic activity of titanium dioxide (titania or TiO2) offers enormous potential in solving energy and environmental problems. Immobilization of titania nanoparticles on inert substrates is an effective way of utilizing its photocatalytic activity since nanoparticles enable high mass-transport, and immobilization avoids post-treatment separation. For competitive photocatalytic performance, the morphology of the substrate can be engineered to enhance mass-transport and light accessibility. In this work, two types of fiber architectures (i.e., dispersed polymer/titania phase or D-phase, and multi-phase polymer-core/composite-shell fibers or M-phase) were explored as effective substrate solutions for anchoring titania. These fibers were fabricated using a low-cost and scalable fiber spinning technique. Polymethyl methacrylate (PMMA) was selected as the substrate material due to its ultraviolet (UV) transparency and stability against oxidative radicals. The work systematically investigates the influence of the fiber porosity on mass-transport and UV light scattering. The properties of the fabricated fiber systems were characterized by scanning electron microscopy (SEM), Brunauer–Emmett–Teller (BET), UV-vis spectrophotometry (UV-vis), and mechanical analysis. The photocatalytic performance was characterized by monitoring the decomposition of methylene blue (MB) under UV (i.e., 365 nm) light. Fabrication of photocatalytic support structures was observed to be an optimization problem where porosity improved mass transport but reduced UV accessibility. The D-phase fibers demonstrated the highest MB degradation rate (i.e., 0.116 min-1) due to high porosity (i.e., 33.2 m2/g). The M-phase fibers reported a better degradation rate compared to a D-phase fibers due to higher UV accessibility efficiency.
ContributorsKanth, Namrata (Author) / Song, Kenan (Thesis advisor) / Tongay, Sefaattin (Thesis advisor) / Kannan, Arunachala Mada (Committee member) / Arizona State University (Publisher)
Created2020
Description
Metal-organic frameworks have made a feature in the cutting-edge technology with a wide variety of applications because they are the new material candidate as adsorbent or membrane with high surface area, various pore sizes, and highly tunable framework functionality properties. The emergence of two-dimensional (2D) metal-organic frameworks has surged an outburst of intense research to understand the feasible synthesis and exciting material properties of these class of materials. Despite their potential, studies to date show that it is extremely challenging to synthesize and manufacture 2D MOF at large scales with ultimate control over crystallinity and thickness.
The field of research to date has produced various synthesis routes which can further be used to design 2D materials with a range of organic ligands and metal linkers. This thesis seeks to extend these design rules to demonstrate the competitive growth of two- dimensional (2D) metal-organic frameworks(MOF) and their alloys to predict which ligands and metals can be combined, study the intercalation of Bromine in these frameworks and their alloys which leads to the discovery of reduced band gap in the layered MOF alloy.
In this study it has been shown that the key factor in achieving layered 2D MOFs and it relies on the use of carefully engineered ligands to terminate the out-of-plane sites on metal clusters thereby eliminating strong interlayer hydrogen bond formation.
The major contribution of pyridine is to replace interlayer hydrogen bonding or other weak chemical bonds. Overall results establish an entirely new synthesis method for producing highly crystalline and scalable 2D MOFs and their alloys. Bromine intercalation merits future studies on band gap engineering in these layered materials.
The field of research to date has produced various synthesis routes which can further be used to design 2D materials with a range of organic ligands and metal linkers. This thesis seeks to extend these design rules to demonstrate the competitive growth of two- dimensional (2D) metal-organic frameworks(MOF) and their alloys to predict which ligands and metals can be combined, study the intercalation of Bromine in these frameworks and their alloys which leads to the discovery of reduced band gap in the layered MOF alloy.
In this study it has been shown that the key factor in achieving layered 2D MOFs and it relies on the use of carefully engineered ligands to terminate the out-of-plane sites on metal clusters thereby eliminating strong interlayer hydrogen bond formation.
The major contribution of pyridine is to replace interlayer hydrogen bonding or other weak chemical bonds. Overall results establish an entirely new synthesis method for producing highly crystalline and scalable 2D MOFs and their alloys. Bromine intercalation merits future studies on band gap engineering in these layered materials.
ContributorsVijay, Shiljashree (Author) / Tongay, Sefaattin (Thesis advisor) / Green, Matthew D (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2020
Description
This work advances structural and biophysical studies of three proteins important in disease. First protein of interest is the Francisella tularensis outer membrane protein A (FopA), which is a virulence determinant of tularemia. This work describes recombinant expression in Escherichia coli and successful purification of membrane translocated FopA. The purified protein was dimeric as shown by native polyacrylamide gel electrophoresis and small angle X-ray scattering (SAXS) analysis, with an abundance of β-strands based on circular dichroism spectroscopy. SAXS data supports the presence of a pore. Furthermore, protein crystals of membrane translocated FopA were obtained with preliminary X-ray diffraction data. The identified crystallization condition provides the means towards FopA structure determination; a valuable tool for structure-based design of anti-tularemia therapeutics.
Next, the nonstructural protein μNS of avian reoviruses was investigated using in vivo crystallization and serial femtosecond X-ray crystallography. Avian reoviruses infect poultry flocks causing significant economic losses. μNS is crucial in viral factory formation facilitating viral replication within host cells. Thus, structure-based targeting of μNS has the potential to disrupt intracellular viral propagation. Towards this goal, crystals of EGFP-tagged μNS (EGFP-μNS (448-605)) were produced in insect cells. The crystals diffracted to 4.5 Å at X-ray free electron lasers using viscous jets as crystal delivery methods and initial electron density maps were obtained. The resolution reported here is the highest described to date for μNS, which lays the foundation towards its structure determination.
Finally, structural, and functional studies of human Threonine aspartase 1 (Taspase1) were performed. Taspase1 is overexpressed in many liquid and solid malignancies. In the present study, using strategic circular permutations and X-ray crystallography, structure of catalytically active Taspase1 was resolved. The structure reveals the conformation of a 50 residues long fragment preceding the active side residue (Thr234), which has not been structurally characterized previously. This fragment adopted a straight helical conformation in contrast to previous predictions. Functional studies revealed that the long helix is essential for proteolytic activity in addition to the active site nucleophilic residue (Thr234) mediated proteolysis. Together, these findings enable a new approach for designing anti-cancer drugs by targeting the long helical fragment.
Next, the nonstructural protein μNS of avian reoviruses was investigated using in vivo crystallization and serial femtosecond X-ray crystallography. Avian reoviruses infect poultry flocks causing significant economic losses. μNS is crucial in viral factory formation facilitating viral replication within host cells. Thus, structure-based targeting of μNS has the potential to disrupt intracellular viral propagation. Towards this goal, crystals of EGFP-tagged μNS (EGFP-μNS (448-605)) were produced in insect cells. The crystals diffracted to 4.5 Å at X-ray free electron lasers using viscous jets as crystal delivery methods and initial electron density maps were obtained. The resolution reported here is the highest described to date for μNS, which lays the foundation towards its structure determination.
Finally, structural, and functional studies of human Threonine aspartase 1 (Taspase1) were performed. Taspase1 is overexpressed in many liquid and solid malignancies. In the present study, using strategic circular permutations and X-ray crystallography, structure of catalytically active Taspase1 was resolved. The structure reveals the conformation of a 50 residues long fragment preceding the active side residue (Thr234), which has not been structurally characterized previously. This fragment adopted a straight helical conformation in contrast to previous predictions. Functional studies revealed that the long helix is essential for proteolytic activity in addition to the active site nucleophilic residue (Thr234) mediated proteolysis. Together, these findings enable a new approach for designing anti-cancer drugs by targeting the long helical fragment.
ContributorsNagaratnam, Nirupa (Author) / Fromme, Petra (Thesis advisor) / Johnston, Stephen (Thesis advisor) / Van Horn, Wade (Committee member) / Liu, Wei (Committee member) / Arizona State University (Publisher)
Created2020
Description
Losses in commercial microwave dielectrics arise from spin excitations in paramagnetic transition metal dopants, at least at reduced temperatures. The magnitude of the loss tangent can be altered by orders of magnitude through the application of an external magnetic field. The goal of this thesis is to produce “smart” dielectrics that can be switched “on” or “off” at small magnetic fields while investigating the influence of transition metal dopants on the dielectric, magnetic, and structural properties.
A proof of principle demonstration of a resonator that can switch from a high-Q “on state” to a low-Q “off state” at reduced temperatures is demonstrated in (Al1-xFex)2O3 and La(Al1-xFex)O3. The Fe3+ ions are in a high spin state (S=5/2) and undergo electron paramagnetic resonance absorption transitions that increase the microwave loss of the system. Transitions occur between mJ states with a corresponding change in the angular momentum, J, by ±ħ (i.e., ΔmJ=±1) at small magnetic fields. The paramagnetic ions also have an influence on the dielectric and magnetic properties, which I explore in these systems along with another low loss complex perovskite material, Ca[(Al1-xFex)1/2Nb1/2]O3. I describe what constitutes an optimal microwave loss switchable material induced from EPR transitions and the mechanisms associated with the key properties.
As a first step to modeling the properties of high-performance microwave host lattices and ultimately their performance at microwave frequencies, a first-principles approach is used to determine the structural phase stability of various complex perovskites with a range of tolerance factors at 0 K and finite temperatures. By understanding the correct structural phases of these complex perovskites, the temperature coefficient of resonant frequency can be better predicted.
A strong understanding of these parameters is expected to open the possibility to produce new types of high-performance switchable filters, time domain MIMO’s, multiplexers, and demultiplexers.
A proof of principle demonstration of a resonator that can switch from a high-Q “on state” to a low-Q “off state” at reduced temperatures is demonstrated in (Al1-xFex)2O3 and La(Al1-xFex)O3. The Fe3+ ions are in a high spin state (S=5/2) and undergo electron paramagnetic resonance absorption transitions that increase the microwave loss of the system. Transitions occur between mJ states with a corresponding change in the angular momentum, J, by ±ħ (i.e., ΔmJ=±1) at small magnetic fields. The paramagnetic ions also have an influence on the dielectric and magnetic properties, which I explore in these systems along with another low loss complex perovskite material, Ca[(Al1-xFex)1/2Nb1/2]O3. I describe what constitutes an optimal microwave loss switchable material induced from EPR transitions and the mechanisms associated with the key properties.
As a first step to modeling the properties of high-performance microwave host lattices and ultimately their performance at microwave frequencies, a first-principles approach is used to determine the structural phase stability of various complex perovskites with a range of tolerance factors at 0 K and finite temperatures. By understanding the correct structural phases of these complex perovskites, the temperature coefficient of resonant frequency can be better predicted.
A strong understanding of these parameters is expected to open the possibility to produce new types of high-performance switchable filters, time domain MIMO’s, multiplexers, and demultiplexers.
ContributorsGonzales, Justin Michael (Author) / Newman, Nathan (Thesis advisor) / Muhich, Christopher (Committee member) / Tongay, Sefaattin (Committee member) / Arizona State University (Publisher)
Created2020