Matching Items (79)
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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

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
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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

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.
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
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Description
Sn-based group IV materials such as Ge1-xSnx and Ge1-x-ySixSny alloys have great potential for developing Complementary Metal Oxide Semiconductor (CMOS) compatible devices on Si because of their tunable band structure and lattice constants by controlling Si and/or Sn contents. Growth of Ge1-xSnx binaries through Molecular Beam Epitaxy (MBE) started in

Sn-based group IV materials such as Ge1-xSnx and Ge1-x-ySixSny alloys have great potential for developing Complementary Metal Oxide Semiconductor (CMOS) compatible devices on Si because of their tunable band structure and lattice constants by controlling Si and/or Sn contents. Growth of Ge1-xSnx binaries through Molecular Beam Epitaxy (MBE) started in the early 1980s, producing Ge1-xSnx epilayers with Sn concentrations varying from 0 to 100%. A Chemical Vapor Deposition (CVD) method was developed in the early 2000s for growing Ge1-xSnx alloys of device quality, by utilizing various chemical precursors. This method dominated the growth of Ge1-xSnx alloys rapidly because of the great crystal quality of Ge1-xSnx achieved. As the first practical ternary alloy completely based on group IV elements, Ge1-x-ySixSny decouples bandgap and lattice constant, becoming a prospective CMOS compatible alloy. At the same time, Ge1-x-ySixSny ternary system could serve as a thermally robust alternative to Ge1-ySny binaries given that it becomes a direct semiconductor at a Sn concentration of 6%-10%. Ge1-x-ySixSny growths by CVD is summarized in this thesis. With the Si/Sn ratio kept at ~3.7, the ternary alloy system is lattice matched to Ge, resulting a tunable direct bandgap of 0.8-1.2 eV. With Sn content higher than Si content, the ternary alloy system could have an indirect-to-direct transition, as observed for Ge1-xSnx binaries. This thesis summarizes the development of Ge1-xSnx and Ge1-x-ySixSny alloys through MBE and CVD in recent decades and introduces an innovative direct injection method for synthesizing Ge1-x-ySixSny ternary alloys with Sn contents varying from 5% to 12% and Si contents kept at 1%-2%. Grown directly on Si (100) substrates in a Gas-phase Molecular Epitaxy (GSME) reactor, both intrinsic and n-type doped Ge1-x-ySixSny with P with thicknesses of 250-760 nm have been achieved by deploying gas precursors Ge4H10, Si4H10, SnD4 and P(SiH3)3 at the unprecedented low growth temperatures of 190-220 °C. Compressive strain is reduced and crystallinity of the Ge1-x-ySixSny epilayer is improved after rapid thermal annealing (RTA) treatments. High Resolution X-ray Diffraction (HR-XRD), Rutherford Backscattering Spectrometry (RBS), cross-sectional Transmission Electron Microscope (XTEM) and Atomic Force Microscope (AFM) have been combined to characterize the structural properties of the Ge1-x-ySixSny samples, indicating good crystallinity and flat surfaces.
ContributorsHu, Ding (Author) / Kouvetakis, John (Thesis advisor) / Menéndez, Jose (Committee member) / Trovitch, Ryan (Committee member) / Arizona State University (Publisher)
Created2019
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Description

Photoluminescence spectroscopy has been used to determine the direct gap E0 of Ge1-ySny alloys over a broad compositional range from pure Ge to Sn concentrations exceeding 10%. A fit of the compositional dependence of E0 using a standard quadratic expression is not fully satisfactory, revealing that the bowing parameter (quadratic

Photoluminescence spectroscopy has been used to determine the direct gap E0 of Ge1-ySny alloys over a broad compositional range from pure Ge to Sn concentrations exceeding 10%. A fit of the compositional dependence of E0 using a standard quadratic expression is not fully satisfactory, revealing that the bowing parameter (quadratic coefficient) b0 is compositionally dependent. Excellent agreement with the data is obtained with b0(y) = (2.66 ± 0.09) eV − (5.4 ± 1.1)y eV. A theoretical model of the bowing is presented, which explains the strong compositional dependence of the bowing parameter and suggest a similar behavior for the indirect gap. Combining the model predictions with experimental data for samples with y ≤ 0.06, it is proposed that the bowing parameter for the indirect gap is bind(y) = (1.11 ± 0.07) eV − (0.78 ± 0.05)y eV. The compositional dependence of the bowing parameters shifts the crossover concentration from indirect to direct gap behavior to yc  = 0.087, significantly higher than the value predicted earlier based on strictly quadratic fits.

ContributorsGallagher, J. D. (Author) / Senaratne, Charutha Lasitha (Author) / Kouvetakis, John (Author) / Menéndez, Jose (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-10-06
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Description

Novel hydride chemistries are employed to deposit light-emitting Ge1-y Snyalloys with y ≤ 0.1 by Ultra-High Vacuum Chemical Vapor Deposition (UHV-CVD) on Ge-buffered Si wafers. The properties of the resultant materials are systematically compared with similar alloys grown directly on Si wafers. The fundamental difference between the two systems is a fivefold

Novel hydride chemistries are employed to deposit light-emitting Ge1-y Snyalloys with y ≤ 0.1 by Ultra-High Vacuum Chemical Vapor Deposition (UHV-CVD) on Ge-buffered Si wafers. The properties of the resultant materials are systematically compared with similar alloys grown directly on Si wafers. The fundamental difference between the two systems is a fivefold (and higher) decrease in lattice mismatch between film and virtual substrate, allowing direct integration of bulk-like crystals with planar surfaces and relatively low dislocation densities. For y ≤ 0.06, the CVD precursors used were digermane Ge2H6 and deuterated stannane SnD4. For y ≥ 0.06, the Ge precursor was changed to trigermane Ge3H8, whose higher reactivity enabled the fabrication of supersaturated samples with the target film parameters. In all cases, the Ge wafers were produced using tetragermane Ge4H10 as the Ge source. The photoluminescence intensity from Ge1-y Sny /Ge films is expected to increase relative to Ge1-y Sny /Si due to the less defected interface with the virtual substrate. However, while Ge1-y Sny /Si films are largely relaxed, a significant amount of compressive strain may be present in the Ge1-y Sny /Ge case. This compressive strain can reduce the emission intensity by increasing the separation between the direct and indirect edges. In this context, it is shown here that the proposed CVD approach to Ge1-y Sny /Ge makes it possible to approach film thicknesses of about 1  μm, for which the strain is mostly relaxed and the photoluminescence intensity increases by one order of magnitude relative to Ge1-y Sny /Si films. The observed strain relaxation is shown to be consistent with predictions from strain-relaxation models first developed for the Si1-x Gex /Si system. The defect structure and atomic distributions in the films are studied in detail using advanced electron-microscopy techniques, including aberration corrected STEM imaging and EELS mapping of the average diamond–cubic lattice.

ContributorsSenaratne, Charutha Lasitha (Author) / Gallagher, J. D. (Author) / Jiang, Liying (Author) / Aoki, Toshihiro (Author) / Smith, David (Author) / Menéndez, Jose (Author) / Kouvetakis, John (Author) / Department of Chemistry and Biochemistry (Contributor)
Created2014-10-07
Description

Background: Cancer diagnosis in both dogs and humans is complicated by the lack of a non-invasive diagnostic test. To meet this clinical need, we apply the recently developed immunosignature assay to spontaneous canine lymphoma as clinical proof-of-concept. Here we evaluate the immunosignature as a diagnostic for spontaneous canine lymphoma at both

Background: Cancer diagnosis in both dogs and humans is complicated by the lack of a non-invasive diagnostic test. To meet this clinical need, we apply the recently developed immunosignature assay to spontaneous canine lymphoma as clinical proof-of-concept. Here we evaluate the immunosignature as a diagnostic for spontaneous canine lymphoma at both at initial diagnosis and evaluating the disease free interval following treatment.

Methods: Sera from dogs with confirmed lymphoma (B cell n = 38, T cell n = 11) and clinically normal dogs (n = 39) were analyzed. Serum antibody responses were characterized by analyzing the binding pattern, or immunosignature, of serum antibodies on a non-natural sequence peptide microarray. Peptides were selected and tested for the ability to distinguish healthy dogs from those with lymphoma and to distinguish lymphoma subtypes based on immunophenotype. The immunosignature of dogs with lymphoma were evaluated for individual signatures. Changes in the immunosignatures were evaluated following treatment and eventual relapse.

Results: Despite being a clonal disease, both an individual immunosignature and a generalized lymphoma immunosignature were observed in each dog. The general lymphoma immunosignature identified in the initial set of dogs (n = 32) was able to predict disease status in an independent set of dogs (n = 42, 97% accuracy). A separate immunosignature was able to distinguish the lymphoma based on immunophenotype (n = 25, 88% accuracy). The individual immunosignature was capable of confirming remission three months following diagnosis. Immunosignature at diagnosis was able to predict which dogs with B cell lymphoma would relapse in less than 120 days (n = 33, 97% accuracy).

Conclusion: We conclude that the immunosignature can serve as a multilevel diagnostic for canine, and potentially human, lymphoma.

ContributorsJohnston, Stephen (Author) / Thamm, Douglas H. (Author) / Legutki, Joseph Barten (Author) / Biodesign Institute (Contributor)
Created2014-09-08
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Description

The emission properties of GeSn heterostructure pin diodes have been investigated. The devices contain thick (400–600 nm) Ge1-y Sny i-layers spanning a broad compositional range below and above the crossover Sn concentration yc where the Ge1-y Sny alloy becomes a direct-gap material. These results are made possible by an optimized device

The emission properties of GeSn heterostructure pin diodes have been investigated. The devices contain thick (400–600 nm) Ge1-y Sny i-layers spanning a broad compositional range below and above the crossover Sn concentration yc where the Ge1-y Sny alloy becomes a direct-gap material. These results are made possible by an optimized device architecture containing a single defected interface thereby mitigating the deleterious effects of mismatch-induced defects. The observed emission intensities as a function of composition show the contributions from two separate trends: an increase in direct gap emission as the Sn concentration is increased, as expected from the reduction and eventual reversal of the separation between the direct and indirect edges, and a parallel increase in non-radiative recombination when the mismatch strains between the structure components is partially relaxed by the generation of misfit dislocations. An estimation of recombination times based on the observed electroluminescence intensities is found to be strongly correlated with the reverse-bias dark current measured in the same devices.

ContributorsGallagher, J. D. (Author) / Senaratne, Charutha Lasitha (Author) / Sims, Patrick (Author) / Aoki, Toshihiro (Author) / Menéndez, Jose (Author) / Kouvetakis, John (Author) / College of Liberal Arts and Sciences (Contributor)
Created2015-03-02
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Description

The development of non-volatile logic through direct coupling of spontaneous ferroelectric polarization with semiconductor charge carriers is nontrivial, with many issues, including epitaxial ferroelectric growth, demonstration of ferroelectric switching and measurable semiconductor modulation. Here we report a true ferroelectric field effect—carrier density modulation in an underlying Ge(001) substrate by switching

The development of non-volatile logic through direct coupling of spontaneous ferroelectric polarization with semiconductor charge carriers is nontrivial, with many issues, including epitaxial ferroelectric growth, demonstration of ferroelectric switching and measurable semiconductor modulation. Here we report a true ferroelectric field effect—carrier density modulation in an underlying Ge(001) substrate by switching of the ferroelectric polarization in epitaxial c-axis-oriented BaTiO3 grown by molecular beam epitaxy. Using the density functional theory, we demonstrate that switching of BaTiO3 polarization results in a large electric potential change in Ge. Aberration-corrected electron microscopy confirms BaTiO3 tetragonality and the absence of any low-permittivity interlayer at the interface with Ge. The non-volatile, switchable nature of the single-domain out-of-plane ferroelectric polarization of BaTiO3 is confirmed using piezoelectric force microscopy. The effect of the polarization switching on the conductivity of the underlying Ge is measured using microwave impedance microscopy, clearly demonstrating a ferroelectric field effect.

ContributorsPonath, Patrick (Author) / Fredrickson, Kurt (Author) / Posadas, Agham B. (Author) / Ren, Yuan (Author) / Wu, Xiaoyu (Author) / Vasudevan, Rama K. (Author) / Okatan, M. Baris (Author) / Jesse, S. (Author) / Aoki, Toshihiro (Author) / McCartney, Martha (Author) / Smith, David (Author) / Kalinin, Sergei V. (Author) / Lai, Keji (Author) / Demkov, Alexander A. (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2015-01-01
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Description

The compositional dependence of the lowest direct and indirect band gaps in Ge1-ySny alloys has been determined from room-temperature photoluminescence measurements. This technique is particularly attractive for a comparison of the two transitions because distinct features in the spectra can be associated with the direct and indirect gaps. However, detailed

The compositional dependence of the lowest direct and indirect band gaps in Ge1-ySny alloys has been determined from room-temperature photoluminescence measurements. This technique is particularly attractive for a comparison of the two transitions because distinct features in the spectra can be associated with the direct and indirect gaps. However, detailed modeling of these room temperature spectra is required to extract the band gap values with the high accuracy required to determine the Sn concentration yc at which the alloy becomes a direct gap semiconductor. For the direct gap, this is accomplished using a microscopic model that allows the determination of direct gap energies with meV accuracy. For the indirect gap, it is shown that current theoretical models are inadequate to describe the emission properties of systems with close indirect and direct transitions. Accordingly, an ad hoc procedure is used to extract the indirect gap energies from the data. For y < 0.1 the resulting direct gap compositional dependence is given by ΔE0 = −(3.57 ± 0.06)y (in eV). For the indirect gap, the corresponding expression is ΔEind = −(1.64 ± 0.10)y (in eV). If a quadratic function of composition is used to express the two transition energies over the entire compositional range 0 ≤ y ≤ 1, the quadratic (bowing) coefficients are found to be b0 = 2.46 ± 0.06 eV (for E0) and bind = 1.03 ± 0.11 eV (for Eind). These results imply a crossover concentration yc = $0.073 [+0.007 over -0.006], much lower than early theoretical predictions based on the virtual crystal approximation, but in better agreement with predictions based on large atomic supercells.

ContributorsJiang, L. (Author) / Gallagher, J. D. (Author) / Senaratne, Charutha Lasitha (Author) / Aoki, Toshihiro (Author) / Mathews, J. (Author) / Kouvetakis, John (Author) / Menéndez, Jose (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-11-01
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Description

The relationship between carrier concentration and donor atomic concentration has been determined in n-type Ge films doped with P. The samples were carefully engineered to minimize non-active dopant incorporation by using specially designed P(SiH3)3 and P(GeH3)3 hydride precursors. The in situ nature of the doping and the growth at low

The relationship between carrier concentration and donor atomic concentration has been determined in n-type Ge films doped with P. The samples were carefully engineered to minimize non-active dopant incorporation by using specially designed P(SiH3)3 and P(GeH3)3 hydride precursors. The in situ nature of the doping and the growth at low temperatures, facilitated by the Ge3H8 and Ge4H10 Ge sources, promote the creation of ultra-low resistivity films with flat doping profiles that help reduce the errors in the concentration measurements. The results show that Ge deviates strongly from the incomplete ionization expected when the donor atomic concentration exceeds Nd  = 1017 cm-3, at which the energy separation between the donor and Fermi levels ceases to be much larger than the thermal energy. Instead, essentially full ionization is seen even at the highest doping levels beyond the solubility limit of P in Ge. The results can be explained using a model developed for silicon by Altermatt and coworkers, provided the relevant model parameter is properly scaled. The findings confirm that donor solubility and/or defect formation, not incomplete ionization, are the major factors limiting the achievement of very high carrier concentrations in n-type Ge. The commercially viable chemistry approach applied here enables fabrication of supersaturated and fully ionized prototypes with potential for broad applications in group-IV semiconductor technologies.

ContributorsXu, Chi (Author) / Senaratne, Charutha Lasitha (Author) / Kouvetakis, John (Author) / Menéndez, Jose (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-12-08