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- Member of: ASU Electronic Theses and Dissertations
Description
Surface plasmon resonance (SPR) has emerged as a popular technique for elucidating subtle signals from biological events in a label-free, high throughput environment. The efficacy of conventional SPR sensors, whose signals are mass-sensitive, diminishes rapidly with the size of the observed target molecules. The following work advances the current SPR sensor paradigm for the purpose of small molecule detection. The detection limits of two orthogonal components of SPR measurement are targeted: speed and sensitivity. In the context of this report, speed refers to the dynamic range of measured kinetic rate constants, while sensitivity refers to the target molecule mass limitation of conventional SPR measurement. A simple device for high-speed microfluidic delivery of liquid samples to a sensor surface is presented to address the temporal limitations of conventional SPR measurement. The time scale of buffer/sample switching is on the order of milliseconds, thereby minimizing the opportunity for sample plug dispersion. The high rates of mass transport to and from the central microfluidic sensing region allow for SPR-based kinetic analysis of binding events with dissociation rate constants (kd) up to 130 s-1. The required sample volume is only 1 μL, allowing for minimal sample consumption during high-speed kinetic binding measurement. Charge-based detection of small molecules is demonstrated by plasmonic-based electrochemical impedance microscopy (P-EIM). The dependence of surface plasmon resonance (SPR) on surface charge density is used to detect small molecules (60-120 Da) printed on a dextran-modified sensor surface. The SPR response to an applied ac potential is a function of the surface charge density. This optical signal is comprised of a dc and an ac component, and is measured with high spatial resolution. The amplitude and phase of local surface impedance is provided by the ac component. The phase signal of the small molecules is a function of their charge status, which is manipulated by the pH of a solution. This technique is used to detect and distinguish small molecules based on their charge status, thereby circumventing the mass limitation (~100 Da) of conventional SPR measurement.
ContributorsMacGriff, Christopher Assiff (Author) / Tao, Nongjian (Thesis advisor) / Wang, Shaopeng (Committee member) / LaBaer, Joshua (Committee member) / Chae, Junseok (Committee member) / Arizona State University (Publisher)
Created2013
Description
Fluctuation Electron Microscopy (FEM) has become an effective materials' structure characterization technique, capable of probing medium-range order (MRO) that may be present in amorphous materials. Although its sensitivity to MRO has been exercised in numerous studies, FEM is not yet a quantitative technique. The holdup has been the discrepancy between the computed kinematical variance and the experimental variance, which previously was attributed to source incoherence. Although high-brightness, high coherence, electron guns are now routinely available in modern electron microscopes, they have not eliminated this discrepancy between theory and experiment. The main objective of this thesis was to explore, and to reveal, the reasons behind this conundrum.
The study was started with an analysis of the speckle statistics of tilted dark-field TEM images obtained from an amorphous carbon sample, which confirmed that the structural ordering is sensitively detected by FEM. This analysis also revealed the inconsistency between predictions of the source incoherence model and the experimentally observed variance.
FEM of amorphous carbon, amorphous silicon and ultra nanocrystalline diamond samples was carried out in an attempt to explore the conundrum. Electron probe and sample parameters were varied to observe the scattering intensity variance behavior. Results were compared to models of probe incoherence, diffuse scattering, atom displacement damage, energy loss events and multiple scattering. Models of displacement decoherence matched the experimental results best.
Decoherence was also explored by an interferometric diffraction method using bilayer amorphous samples, and results are consistent with strong displacement decoherence in addition to temporal decoherence arising from the electron source energy spread and energy loss events in thick samples.
It is clear that decoherence plays an important role in the long-standing discrepancy between experimental FEM and its theoretical predictions.
The study was started with an analysis of the speckle statistics of tilted dark-field TEM images obtained from an amorphous carbon sample, which confirmed that the structural ordering is sensitively detected by FEM. This analysis also revealed the inconsistency between predictions of the source incoherence model and the experimentally observed variance.
FEM of amorphous carbon, amorphous silicon and ultra nanocrystalline diamond samples was carried out in an attempt to explore the conundrum. Electron probe and sample parameters were varied to observe the scattering intensity variance behavior. Results were compared to models of probe incoherence, diffuse scattering, atom displacement damage, energy loss events and multiple scattering. Models of displacement decoherence matched the experimental results best.
Decoherence was also explored by an interferometric diffraction method using bilayer amorphous samples, and results are consistent with strong displacement decoherence in addition to temporal decoherence arising from the electron source energy spread and energy loss events in thick samples.
It is clear that decoherence plays an important role in the long-standing discrepancy between experimental FEM and its theoretical predictions.
ContributorsRezikyan, Aram (Author) / Treacy, Michael M.J. (Thesis advisor) / Smith, David J. (Committee member) / McCartney, Martha R. (Committee member) / Rez, Peter (Committee member) / Arizona State University (Publisher)
Created2015
Description
The behavior of a solid oxide fuel cell (SOFC) cermet (ceramic-metal composite) anode under reaction conditions depends significantly on the structure, morphology and atomic scale interactions between the metal and the ceramic components. In situ environmental transmission electron microscope (ETEM) is an important tool which not only allows us to perform the basic nanoscale characterization of the anode materials, but also to observe in real-time, the dynamic changes in the anode material under near-reaction conditions. The earlier part of this dissertation is focused on the synthesis and characterization of Pr- and Gd-doped cerium oxide anode materials. A novel spray drying set-up was designed and constructed for preparing nanoparticles of these mixed-oxides and nickel oxide for anode fabrication. X-ray powder diffraction was used to investigate the crystal structure and lattice parameters of the synthesized materials. Particle size distribution, morphology and chemical composition were investigated using transmission electron microscope (TEM). The nanoparticles were found to possess pit-like defects of average size 2 nm after subjecting the spray-dried material to heat treatment at 700 °C for 2 h in air. A novel electron energy-loss spectroscopy (EELS) quantification technique for determining the Pr and Gd concentrations in the mixed oxides was developed. Nano-scale compositional heterogeneity was observed in these materials. The later part of the dissertation focuses mainly on in situ investigations of the anode materials under a H2 environment in the ETEM. Nano-scale changes in the stand-alone ceramic components of the cermet anode were first investigated. Particle size and composition of the individual nanoparticles of Pr-doped ceria (PDC) were found to affect their reducibility in H2 gas. Upon reduction, amorphization of the nanoparticles was observed and was linked to the presence of pit-like defects in the spray-dried material. Investigation of metal-ceramic interactions in the Ni-loaded PDC nanoparticles indicated a localized reduction of Ce in the vicinity of the Ni/PDC interface at 420 °C. Formation of a reduction zone around the interface was attributed to H spillover which was observed directly in the ETEM. Preliminary results on the fabrication of model SOFCs and in situ behavior of Ni/Gd-doped ceria anodes have been presented.
ContributorsSharma, Vaneet (Author) / Crozier, Peter A. (Thesis advisor) / Sharma, Renu (Thesis advisor) / Adams, James B (Committee member) / Dey, Sandwip (Committee member) / Arizona State University (Publisher)
Created2011
Description
In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different illumination intensities or different local environments); and (3) inferring the camera gain. My general theoretical framework utilizes the Bayesian nonparametric Gaussian and beta-Bernoulli processes with a Markov chain Monte Carlo sampling scheme, which I further specify and implement for Total Internal Reflection Fluorescence (TIRF) microscopy data, benchmarking the method on synthetic data. These three frameworks are self-contained, and can be used concurrently so that the fluorescence profile and emitter locations are both considered unknown and, under some conditions, learned simultaneously. The framework I present is flexible and may be adapted to accommodate the inference of other parameters, such as emission photophysical kinetics and the trajectories of moving molecules. My TIRF-specific implementation may find use in the study of structures on cell membranes, or in studying local sample properties that affect fluorescent molecule photon emission rates.
ContributorsWallgren, Ross (Author) / Presse, Steve (Thesis advisor) / Armbruster, Hans (Thesis advisor) / McCulloch, Robert (Committee member) / Arizona State University (Publisher)
Created2019
Description
The distinguishing feature of the filamentous fungi is the hyphae - tube-like microscopic cells that exhibit polarized growth via apical extension and allow the fungus to interact with its environment. Fungi elongate at the hyphal apex, through the localized construction of new plasma membrane and cell wall through the exocytosis of secretory vesicles. One population of these vesicles have been identified as chitosomes, containing chitin synthase isoenzymes, which are responsible for the polymerization of N-acetylglucosamine from UDP N-acetylglucosamine into chitin, the primary fibrillar component of the fungal cell wall. The chitosomes, in addition to other vesicles, can be observed aggregating in the hyphal tip in most filamentous fungi. In the Ascomycota and Basidiomycota, this collection of vesicles exhibits discrete organization and has been termed a Spitzenkörper. Although accumulations of vesicles can be observed in the hyphal tip of many growing filamentous fungi, some debate continues as to what precisely defines a Spitzenkörper. This study reports the details of three separate projects: first, to document the effects of deleting a single chitin synthase, CHS-1 and CHS-6 in Neurospora crassa with regards to hyphal ultrastructure, cytoplasmic organization, and growth in comparison to the wild-type. Given the importance of chitin synthesis in fungal cell growth, deletion of a critical chitin synthase presumably impacts cell wall structure, fungal growth and cytoplasmic organization. Second, an examination of the ultrastructure of four zygomycetous fungi - Coemansia reversa, Mortierella verticillata, Mucor indicus, and Gilbertella persicaria has been conducted. Utilization of cryofixation and freeze-substitution techniques for electron microscopy has produced improved preservation of cytoplasmic ultrastructure, particularly at the hyphal apex, allowing detailed analysis of vesicle size, contents, and organization. Lastly, hyphal tip organization was reviewed in a broad range of fungi. Previous studies had either focused on a few select fungi or representative groups. Vesicle organization, composition and size do appear to vary among the classes of fungi, but some trends, like the vesicle crescent in the zygomycetous fungi have been documented.
ContributorsFisher, Karen Elizabeth (Author) / Roberson, Robert W. (Thesis advisor) / Chandler, Douglas (Committee member) / Riquelme, Meritxell (Committee member) / Stutz, Jeam (Committee member) / Wojciechowski, Martin (Committee member) / Arizona State University (Publisher)
Created2015
Description
Cell adhesion is an important aspect of many biological processes. The atomic force microscope (AFM) has made it possible to quantify the forces involved in cellular adhesion using a technique called single cell force spectroscopy (SCFS). AFM based SCFS offers versatile control over experimental conditions for probing directly the interaction between specific cell types and specific proteins, surfaces, or other cells. Transmembrane integrins are the primary proteins involved in cellular adhesion to the extra cellular matix (ECM). One of the chief integrins involved in the adhesion of leukocyte cells is αMβ2 (Mac-1). The experiments in this dissertation quantify the adhesion of Mac-1 expressing human embryonic kidney (HEK Mac-1), platelets, and neutrophils cells on substrates with different concentrations of fibrinogen and on fibrin gels and multi-layered fibrinogen coated fibrin gels. It was shown that multi-layered fibrinogen reduces the adhesion force of these cells considerably. A novel method was developed as part of this research combining total internal reflection microscopy (TIRFM) with SCFS allowing for optical microscopy of HEK Mac-1 cells interacting with bovine serum albumin (BSA) coated glass after interacting with multi-layered fibrinogen. HEK Mac-1 cells are able to remove fibrinogen molecules from the multi-layered fibrinogen matrix. An analysis methodology for quantifying the kinetic parameters of integrin-ligand interactions from SCFS experiments is proposed, and the kinetic parameters of the Mac-1 fibrinogen bond are quantified. Additional SCFS experiments quantify the adhesion of macrophages and HEK Mac-1 cells on functionalized glass surfaces and normal glass surfaces. Both cell types show highest adhesion on a novel functionalized glass surface that was prepared to induce macrophage fusion. These experiments demonstrate the versatility of AFM based SCFS, and how it can be applied to address many questions in cellular biology offering quantitative insights.
ContributorsChristenson, Wayne B (Author) / Ros, Robert (Thesis advisor) / Beckstein, Oliver (Committee member) / Lindsay, Stuart (Committee member) / Ugarova, Tatiana (Committee member) / Arizona State University (Publisher)
Created2016
Label-free Biomolecule Characterization and Functional Study by Surface Sensitive Optical Microscopy
Description
Analysis of the characteristics of biomolecules, including size, charge and binding kinetics, is essential for biomedical and life science research and applications. State-of-the-art protein analysis methods rely on separate technologies to quantify these characteristics, and considerable time, cost and analytes are required. Lack of single molecule analysis capability in above methods also making them difficult to study heterogeneous processes and achieving precision diagnosis.To address these issues, several techniques based on surface sensitive optical imaging principles were developed. The first technique is evanescent scattering microscopy (ESM) with single molecule resolution, which is capable of imaging single immunoglobulin G with high signal-to-noise ratio. In addition, nano-oscillator was combined with the ESM to achieve the simultaneous size and charge detection of single proteins.
Based on the unique high axial sensitivity of the surface plasmon resonance (SPR), a 3D tracking technique to study the motion and interaction of biomolecules was introduced. With the additional dimension, more information in particle motions can be revealed compared to conventional 2D bright field tracking. By tracking the motion of nanoparticles, motion pattern of tethered nanoparticles and interaction between double-stranded DNA and an enzyme can be visualized.
The G protein-coupled receptors (GPCRs) expressed virion oscillator array for quantification of the binding kinetics of small molecule drugs and different GPCRs was attempted. Cross-talking signals between the array spots were discovered, and several control experiments were performed to explore the possible reason. As an alternative solution for multiplexing, DNA barcode technique was implemented with the GPCR virions and achieved with the ESM, which paved a way for multiplexed single molecule binding kinetics studies.
Circular RNAs has been found as an important class of regulators at the transcriptional and posttranscriptional level and could be potential biomarkers for many diseases. However, determination of its existence from the linear RNAs is challenging for the tradition molecular detection methods. Due to the no ending feature, by designing a unique complementary probe sequence, hybridization affinity difference between circular and linear RNA can be distinguished. Affinities with different hybridization nucleotides number were measured and verified.
ContributorsWan, Zijian (Author) / Wang, Shaopeng SW (Thesis advisor) / Wang, Chao CW (Committee member) / Forzani, Erica EF (Committee member) / Jing, Tianwei TJ (Committee member) / Arizona State University (Publisher)
Created2023