Matching Items (18)

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Light-induced CO2 Reduction By Cobalt-cytochrome b562: Rational Design and Directed Evolution Approaches

Description

The successful reduction of CO2 and protons by a light-induced cobalt porphyrin/cytb562 hybrid metalloenzyme in water is reported. Incorporation of the porphyrin into a protein scaffold results in increases in

The successful reduction of CO2 and protons by a light-induced cobalt porphyrin/cytb562 hybrid metalloenzyme in water is reported. Incorporation of the porphyrin into a protein scaffold results in increases in CO and H2 production over naked porphyrin. Rational point mutations to the CoPPIX binding site of cytb562 modulate production, indicating possible further improvements in catalytic activity.

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Date Created
  • 2020-05

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Proxy Assessment of Biospecimen Exposure to Thawed Conditions via Direct Fluorescence Visualization

Description

In the development of personalized medicine and many other clinical studies, biospecimen integrity serves as the prerequisite for not only the accurate derivation of patient- and disease-specific molecular data from

In the development of personalized medicine and many other clinical studies, biospecimen integrity serves as the prerequisite for not only the accurate derivation of patient- and disease-specific molecular data from biological specimens but the meaningful downstream validation of biomarkers. However, a large number of preanalytical variables may influence the quality of biospecimens in an undesired way and ultimately render the samples unsuitable for molecular analysis. The limited ability to directly reduce discrepancies caused by preanalytical variables gives rise to the need for development and retrospective application of appropriate tests for assessment of biospecimen integrity. Nevertheless, the most standard approaches to assessing biospecimen integrity involve nontrivial procedures. Thus, the need for quality control tools or tests that are readily applicable and can produce results in a straightforward way becomes critical. As one of the major ex vivo biomolecular degradation mechanisms, oxidation that occurs when blood plasma and serum samples are exposed to thawed states during storage and processing is hard to forestall and detect. In an attempt to easily detect and monitor the degree of oxidation, the technique of Fluorescence Resonance Energy Transfer (FRET) was examined to determine whether this concept could be employed to monitor exposure of samples to thawed conditions when controlled by spontaneous oxidative disulfide bonding. The intended mode of usage was envisioned as a fluorescence liquid being stored in a separate compartment but within the same test tube as archived plasma and serum samples. This would allow the assessment of sample integrity by direct visualization of fluorescence under a hand-held black light. The fluorescent dynamic range as well as kinetic control of the reaction were studied. While the addition of Cu(II) proved to facilitate excellent dynamic range with regard to fluorescence quenching, the kinetics of the reaction were too rapid for practical use. Further investigation revealed that the fluorescence quenching mechanism might have actually occurred via Intramolecular Charge Transfer (ICT) rather than FRET mediated by oxidative disulfide bond formation. Introduction of Cu(II) via copper metal slowed fluorescence quenching to the point of practical utility; facilitating demonstration that storing at room temperature, refrigerating or freezing the samples delayed fluorescence quenching to different extents. To establish better kinetic control, future works will focus on establishing controlled, thoroughly understood kinetic release of Cu(II) from copper metal.

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Date Created
  • 2018-12

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Numerical Modeling of Hydrodynamic Flow Focusing in a Microfluidic Device for Time-Resolved Serial Crystallography

Description

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser (XFEL) has enabled the determination of protein structures and protein reaction intermediates in millisecond to microsecond time resolutions. Mix-and-Inject crystallography (MISC)

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser (XFEL) has enabled the determination of protein structures and protein reaction intermediates in millisecond to microsecond time resolutions. Mix-and-Inject crystallography (MISC) at XFELs enables fast mixing in the magnitude of milliseconds in order to achieve desired reaction time points. For these experiments, numerical simulations of a hydrodynamic flow mixer capable of fast mixing by diffusion has been developed using both COMSOL Multiphysics 5.6 and QuickerSims Computational Fluid Dynamics (CFD) Toolbox for MATLAB. These simulation programs were compared by calculations of mixing times and concentration flow profiles. Mixing times in the range of 1-10 ms were calculated in COMSOL under certain flow rate conditions whereas mixing times in the range of 6-15 ms were calculated with QuickerSims. From these mixing times, reaction intermediates can be varied from sub-millisecond to several hundred millisecond time points for a MISC experiment. Explanations for the discrepancies between the two models were attributed to variations in parameter definitions and meshing. Further analysis on the mixing characteristics were investigated by calculating an analytical solution to the convection-diffusion equation for fluid flow in a two-dimensional rectangular channel. The concentration profile along the width of the channel for the analytical solution was compared with the numerical solution obtained with COMSOL and QuickerSims. Upon comparison, it was determined that the diffusion coefficient may not be a significant factor for the disagreement between the two hydrodynamic flow models.

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Date Created
  • 2021-05

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Capacitive Sensor for the Detection of Microdroplets in Serial Femtosecond Crystallography

Description

Microfluidic devices represent a growing technology in the world of analytical chemistry. Serial femtosecond crystallography (SFX) utilizes microfluidic devices to generate droplets of an aqueous buffer containing protein crystals, which

Microfluidic devices represent a growing technology in the world of analytical chemistry. Serial femtosecond crystallography (SFX) utilizes microfluidic devices to generate droplets of an aqueous buffer containing protein crystals, which are then fired out as a jet in the beam of an X-ray free electron laser (XFEL). A crucial part of the device is its method of droplet detection. This project presents a design for a capacitive sensor that uses a unique electrode configuration to detect the difference in capacitance between the aqueous and oil phases. This design was developed using MATLAB and COMSOL Multiphysics simulations and printed using high-resolution 3D printing. Results show that this design can successfully distinguish between the two immiscible liquids, confirming it as a possible detection method in future SFX experiments.

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Date Created
  • 2021-05

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Microanalysis for Oxygen Fugacity by Secondary Ion Mass Spectrometry

Description

Oxygen fugacity (ƒO2) is a thermodynamic variable used to represent the redox state of a material or a system. It is equivalent to the partial pressure of oxygen in a

Oxygen fugacity (ƒO2) is a thermodynamic variable used to represent the redox state of a material or a system. It is equivalent to the partial pressure of oxygen in a particular environment corrected for the non-ideal behavior of the gas. ƒO2 is often used to indicate the potential for iron to occur in a more oxidized or reduced state at a particular temperature and pressure in a natural system. Secondary ion mass spectrometry (SIMS) is a powerful analytical instrument that can be used to analyze elemental and isotopic compositional information about microscopic features within solid materials. SIMS analyses of the secondary ion energy distribution of semi-pure metals demonstrate that the energy spectrum of individual mass lines can provide information about alterations in its surface environment.

The application of high-resolution (see Appendix C) energy spectrum calibrations to natural ilmenite led to the investigation of zirconium (90Zr+) and niobium (93Nb+) as potential indicators of sample ƒO2. Energy spectrum measurements were performed on an array of ilmenite crystals from the earth’s upper mantle retrieved from kimberlites and from a reduced meteorite. In all studied materials, variability in the peak shape and width of the energy spectra has been correlated with inferred sample ƒO2. The best descriptor of this relationship is the full-width at half-maximum (FWHM; see Appendix C) of the energy spectra for each sample. It has been estimated that a 1eV change in the FWHM of 93Nb+ energy spectra is roughly equivalent to 1 log unit ƒO2. Simple estimates of precision suggest the FWHM values can be trusted to  1eV and sample ƒO2 can be predicted to ±1 log unit, assuming the temperature of formation is known.

The work of this thesis also explores the applicability of this technique beyond analysis of semi-pure metals and ilmenite crystals from kimberlites. This technique was applied to titanium oxides experimentally formed at known ƒO2 as well as an ilmenite crystal that showed compositional variations across the grain (i.e., core to rim chemical variations). Analyses of titanium oxides formed at known ƒO2 agree with the estimation that 1 eV change in the FWHM of 93Nb+ is equivalent to ~1 log unit ƒO2 (in all cases but one); this is also true for analyses of a natural ilmenite crystal with compositional variations across the grain.

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Date Created
  • 2019

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Synthesis, Characterization, and Optimization of Superconductor-Dielectric Interfaces

Description

The chemical, structural, and electrical properties of niobium-silicon, niobium-germanium, and YBCO-dielectric interfaces are characterized. Reduction in the concentration of interfacial defects in these structures can improve the performance of (i)

The chemical, structural, and electrical properties of niobium-silicon, niobium-germanium, and YBCO-dielectric interfaces are characterized. Reduction in the concentration of interfacial defects in these structures can improve the performance of (i) many devices including low-loss coplanar, microstrip, and stripline microwave resonators used in next-generation cryogenic communication, sensor, and quantum information technologies and (ii) layers used in device isolation, inter-wiring dielectrics, and passivation in microwave and Josephson junction circuit fabrication.

Methods were developed to synthesize amorphous-Ge (a-Ge) and homoepitaxial-Si dielectric thin-films with loss tangents of 1–2×10 -6 and 0.6–2×10 -5 at near single-photon powers and sub-Kelvin temperatures (≈40 mK), making them potentially a better choice over undoped silicon and sapphire substrates used in quantum devices. The Nb/Ge interface has 20 nm of chemical intermixing, which is reduced by a factor of four using 10 nm Ta diffusion layers. Niobium coplanar resonators using this structure exhibit reduced microwave losses.

The nature and concentration of defects near Nb-Si interfaces prepared with commonly-used Si surface treatments were characterized. All samples have H, C, O, F, and Cl in the Si within 50 nm of the interface, and electrically active defects with activation energies of 0.147, 0.194, 0.247, 0.339, and 0.556 eV above the valence band maximum (E vbm ), with concentrations dominated by a hole trap at E vbm +0.556 eV (presumably Nb Si ). The optimum surface treatment is an HF etch followed by an in-situ 100 eV Ar ion mill. RCA etches, and higher energy ion milling processes increase the concentration of electrically active defects.

A thin SrTiO 3 buffer layer used in YBa 2 Cu 3 O 7-δ superconductor/high-performance Ba(Zn 1/3 Ta 2/3 )O 3 and Ba(Cd 1/3 Ta 2/3 )O 3 microwave dielectric trilayers improves the structural quality of the layers and results in 90 K superconductor critical temperatures. This advance enables the production of more compact high-temperature superconductor capacitors, inductors, and microwave microstrip and stripline devices.

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Date Created
  • 2020

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Identifying and Characterizing Type 1 and Type 2 Eosinophil Subtypes

Description

Eosinophils are innate immune cells that are most commonly associated with parasite infection and allergic responses. Recent studies, though, have identified eosinophils as cells with diverse effector functions at baseline

Eosinophils are innate immune cells that are most commonly associated with parasite infection and allergic responses. Recent studies, though, have identified eosinophils as cells with diverse effector functions at baseline and in disease. Eosinophils in specific tissue immune environments are proposed to promote unique and specific effector functions, suggesting these cells have the capacity to differentiate into unique subtypes. The studies here focus on defining these subtypes using functional, molecular, and genetic analysis as well as using novel techniques to image these subtypes in situ.

To characterized these subtypes, an in vitro cytokine induced type 1 (E1) and type 2 (E2) eosinophil model was developed that display features and functions of eosinophils found in vivo. For example, E1 eosinophils secrete type 1 mediators (e.g., IL-12, CXCL9 and CXCL10), express iNOS and express increased levels of the surface molecules PDL1 and MHC-I. Conversely, E2 eosinophils release type 2 mediators (e.g., IL4, IL13, CCL17, and CCL22), degranulate and express increased surface molecules CD11b, ST2 and Siglec-F. Completion of differential expression analysis of RNAseq on these subtypes revealed 500 and 655 unique genes were upregulated in E1 and E2 eosinophils, respectively. Functional enrichment studies showed interferon regulatory factor (IRF) transcription factors were uniquely regulated in both mouse and human E1 and E2 eosinophils. These subtypes are sensitive to their environment, modulating their IRF and cell surface expression when stimulated with opposing cytokines, suggesting plasticity.

To identify and study these subtypes in situ, chromogenic and fluorescent eosinophil-specific immunostaining protocols were developed. Methods were created and optimized, here, to identify eosinophils by their granule proteins in formalin fixed mouse tissues. Yet, eosinophil-specific antibodies alone are not enough to identify and study the complex interactions eosinophil subtypes perform within a tissue. Therefore, as part of this thesis, a novel highly-multiplexed immunohistochemistry technique was developed utilizing cleavable linkers to address these concerns. This technique is capable of analyzing up to 22 markers within a single biopsy with single-cell resolution. With this approach, eosinophil subtypes can be studied in situ in routine patient biopsies.

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Date Created
  • 2020

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Targeted proteomics studies: design, development and translation of mass spectrometric immunoassays for diabetes and kidney disease

Description

In an effort to begin validating the large number of discovered candidate biomarkers, proteomics is beginning to shift from shotgun proteomic experiments towards targeted proteomic approaches that provide solutions to

In an effort to begin validating the large number of discovered candidate biomarkers, proteomics is beginning to shift from shotgun proteomic experiments towards targeted proteomic approaches that provide solutions to automation and economic concerns. Such approaches to validate biomarkers necessitate the mass spectrometric analysis of hundreds to thousands of human samples. As this takes place, a serendipitous opportunity has become evident. By the virtue that as one narrows the focus towards "single" protein targets (instead of entire proteomes) using pan-antibody-based enrichment techniques, a discovery science has emerged, so to speak. This is due to the largely unknown context in which "single" proteins exist in blood (i.e. polymorphisms, transcript variants, and posttranslational modifications) and hence, targeted proteomics has applications for established biomarkers. Furthermore, besides protein heterogeneity accounting for interferences with conventional immunometric platforms, it is becoming evident that this formerly hidden dimension of structural information also contains rich-pathobiological information. Consequently, targeted proteomics studies that aim to ascertain a protein's genuine presentation within disease- stratified populations and serve as a stepping-stone within a biomarker translational pipeline are of clinical interest. Roughly 128 million Americans are pre-diabetic, diabetic, and/or have kidney disease and public and private spending for treating these diseases is in the hundreds of billions of dollars. In an effort to create new solutions for the early detection and management of these conditions, described herein is the design, development, and translation of mass spectrometric immunoassays targeted towards diabetes and kidney disease. Population proteomics experiments were performed for the following clinically relevant proteins: insulin, C-peptide, RANTES, and parathyroid hormone. At least thirty-eight protein isoforms were detected. Besides the numerous disease correlations confronted within the disease-stratified cohorts, certain isoforms also appeared to be causally related to the underlying pathophysiology and/or have therapeutic implications. Technical advancements include multiplexed isoform quantification as well a "dual- extraction" methodology for eliminating non-specific proteins while simultaneously validating isoforms. Industrial efforts towards widespread clinical adoption are also described. Consequently, this work lays a foundation for the translation of mass spectrometric immunoassays into the clinical arena and simultaneously presents the most recent advancements concerning the mass spectrometric immunoassay approach.

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Date Created
  • 2011

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Structure activity studies of quinones and analogues

Description

Many natural and synthetic quinones have shown biological and pharmacological activity. Some of them have also shown anticancer activity. Ubiquinone (CoQ10) which is a natural quinone, is a component of

Many natural and synthetic quinones have shown biological and pharmacological activity. Some of them have also shown anticancer activity. Ubiquinone (CoQ10) which is a natural quinone, is a component of the electron transport chain and participates in generation of ATP (adenosine triphosphate). Cellular oxidative stress is key feature of many neurodegenerative diseases such as Friedreich's ataxia, Alzheimer's disease and Parkinson's disease. The increased generation of reactive oxygen species damages cell membranes and leads to cell death. Analogues of ubiquinone in the form of pyrimidinols and pyridinols, were effective in protecting Friedreich's ataxia lymphocytes from oxidative stress- induced cell death. There were some structural features which could be identified that should be useful for the design of the analogues for cellular protection against oxidative stress. There are quinones such as doxorubicin, daunomycin and topopyrones which have anticancer activity. Here I evaluated topopyrone analogues which poison both topoisomerases I and II. The topopyrone analogues were lethal to human breast cancer cells, but these analogues were not as potent as camptothecin.

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Date Created
  • 2011

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Solar wind sodium and potassium abundance analysis in Genesis diamond-on-silicon and silicon bulk solar wind collectors, and how hydration affects the microtexture of olivine phase transformation at 18 GPa

Description

The present work covers two distinct microanalytical studies that address issues in planetary materials: (1) Genesis Na and K solar wind (SW) measurements, and (2) the effect of water on

The present work covers two distinct microanalytical studies that address issues in planetary materials: (1) Genesis Na and K solar wind (SW) measurements, and (2) the effect of water on high-pressure olivine phase transformations.

NASA’s Genesis mission collected SW samples for terrestrial analysis to create a baseline of solar chemical abundances based on direct measurement of solar material. Traditionally, solar abundances are estimated using spectroscopic or meteoritic data. This study measured bulk SW Na and K in two different Genesis SW collector materials (diamond-like carbon (DlC) and silicon) for comparison with these other solar references. Novel techniques were developed for Genesis DlC analysis. Solar wind Na fluence measurements derived from backside depth profiling are generally lower in DlC than Si, despite the use of internal standards. Nevertheless, relative to Mg, the average SW Na and K abundances measured in Genesis wafers are in agreement with solar photospheric and CI chondrite abundances, and with other SW elements with low first ionization potential (within error). The average Genesis SW Na and K fluences are 1.01e11 (+9e09, -2e10) atoms/cm2 and 5.1e09 (+8e08, -8e08) atoms/cm2, respectively. The errors reflect average systematic errors. Results have implications for (1) SW formation models, (2) cosmochemistry based on solar material rather than photospheric measurements or meteorites, and (3) the accurate measurement of solar wind ion abundances in Genesis collectors, particularly DlC and Si.

Deep focus earthquakes have been attributed to rapid transformation of metastable olivine within the mantle transition zone (MTZ). However, the presence of H2O acts to overcome metastability, promoting phase transformation in olivine, so olivine must be relatively anhydrous (<75 ppmw) to remain metastable to depth. A microtextural analysis of olivine phase transformation products was conducted to test the feasibility for subducting olivine to persist metastably to the MTZ. Transformation (as intracrystalline or rim nucleation) shifts from ringwoodite to ringwoodite-wadsleyite nucleation with decreasing H2O content within olivine grains. To provide accurate predictions for olivine metastability at depth, olivine transformation models must reflect how changing H2O distributions lead to complex changes in strain and reaction rates within different parts of a transforming olivine grain.

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Date Created
  • 2015