Matching Items (12)

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Optimization of Human Neural Tissue Clearing for Immunohistochemical Imaging

Description

The combination of immunohistochemical (IHC) stainings and optical microscopy has allowed for the visualization of specific microscopic structures within tissue; however, limitations in light and antibody penetration mitigate the scale

The combination of immunohistochemical (IHC) stainings and optical microscopy has allowed for the visualization of specific microscopic structures within tissue; however, limitations in light and antibody penetration mitigate the scale on which these images can be taken (Alshammari et al, 2016; Marx, 2014). Tissue clearing, specifically the removal of lipids to improve sample transparency, solves the former weakness well, but does not improve antibody penetration significantly (Chung et al, 2013; Treweek et al, 2015). Therefore, there is a need to equalize the maximum depth that light can pass through a section with the depth at which there is recognizable fluorescence. This is particularly important when staining blood vessels as traditional size limitations exclusively allows for cross sectional visualization. Passive CLARITY Technique (PACT) has been at the forefront of tissue clearing protocols, utilizing an acrylamide hydrogel solution to maintain structure and sodium dodecyl sulfate to wash out lipids (Tomer et al, 2014). PACT is limited in its ability to clear larger sections and is not conducive to IHC antibody diffusion (Treweek et al, 2015). In order to circumvent these drawbacks, CUBIC was developed as an alternative passive protocol, aimed at being scalable to any tissue size (Richardson, 2015; Susaki et al, 2015). This study compared the effectiveness of both protocols in high and low lipid tissues in the context of blood vessel staining efficacy. Upon initial comparison, it became apparent that there was a statistically significant difference in mean DAPI intensity at all depths, up to 200 micrometers, between CUBIC and PACT \u2014 the former showcasing brighter stainings. Moreover, it was found that PACT does not remove erythrocytes from the tissue meaning that their auto-fluorescence is seen during imaging. Therefore, for blood vessel stainings, only CUBIC was optimized and quantitatively analyzed. In both tissue conditions as well as for two stainings, DAPI and fibronectin (FNCT), optimized CUBIC demonstrated a statistically significant difference from standard CUBIC with regards to mean fluorescent intensity.

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Date Created
  • 2018-05

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Ultra High Density Single Cell Metabolic Measurements

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In vitro measurements of cellular respiration have proven to be key biomarkers for the early onset of tumor formation in certain pathological mechanisms.1 The examination of isolated single cells has

In vitro measurements of cellular respiration have proven to be key biomarkers for the early onset of tumor formation in certain pathological mechanisms.1 The examination of isolated single cells has shown promise in predicting the onset of cancerous growth much earlier than current methods allow.2 Specifically, measurements of the oxygen consumption rates of precancerous cells have elucidated outliers which predict the early onset of esophageal cancer.2 Single cell profiling can fit in to current pathology studies and can serve as a step along the way, much like PCR or gel assays, in detecting biomarkers earlier than current clinical methods.3 Measurement of these single cell metabolic rates is currently limited to 25 cells per experiment. It is the aim of this project to increase throughput from 25 cells to 225 cells per experiment via the implementation of new hardware and software which fit with current methods to allow the same experimental structure. Successful implementation of such methods will allow for more rapid and efficient data collection, facilitating quantitative results and nine times the yield from the same experimental manpower and funding. This document focuses on the implementation ultra high density (UHD) hardware consisting of a pneumatic molar design, angular adjustment features and a mechanical Z-stage. These components have produced the most encouraging results thus far and are the key changes in transitioning to higher throughput experiments.

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Date Created
  • 2013-05

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Phenotypic Plasticity and Early Life Cycle Development of the Chytrid Fungus Batrachochytrium dendrobatidis

Description

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has captured human attention because it is a pathogen that has contributed to global amphibian declines. Despite increased research, much is still unknown

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has captured human attention because it is a pathogen that has contributed to global amphibian declines. Despite increased research, much is still unknown about how it develops. For example, the fact that Bd exhibits phenotypic plasticity during development was only recently identified. In this thesis, the causes of phenotypic plasticity in Bd are tested by exposing the fungus to different substrates, including powdered frog skin and keratin, which seems to play an important role in the fungus's colonization of amphibian epidermis. A novel swelling structure emerging from Bd germlings developed when exposed to keratin and frog skin. This swelling has not been observed in Bd grown in laboratory cultures before, and it is possible that it is analogous to the germ tube Bd develops in vivo. Growth of the swelling suggests that keratin plays a role in the phenotypic plasticity expressed by Bd.

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Date Created
  • 2016-05

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A Modelling Approach to Determine Gas and Temperature Profiles during Catalytic Reactions in Environmental Transmission Electron Microscopy

Description

A scheme has been developed for finding the gas and temperature profiles in an environmental transmission electron microscope (ETEM), using COMSOL Multiphysics and the finite element method (FEM). This model

A scheme has been developed for finding the gas and temperature profiles in an environmental transmission electron microscope (ETEM), using COMSOL Multiphysics and the finite element method (FEM). This model should permit better correlation between catalyst structure and activity, by providing a more accurate understanding of gas composition than the assumption of homogeneity typically used. While more data is needed to complete the model, current progress has identified several details about the system and its ideal modeling approach.
It is found that at the low pressures and flowrates of catalysis in ETEM, natural and forced convection are negligible forms of heat transfer. Up to 250 °C, radiation is also negligible. Gas conduction, being enhanced at low pressures, dominates.
Similarly, mass transport is dominated by diffusion, which is most accurately described by the Maxwell-Stefan model. Bulk fluid flow is highly laminar, and in fact borders the line between continuum and molecular flow. The no-slip boundary condition does not apply here, and both viscous slip and thermal creep must be considered. In the porous catalyst pellet considered in this work, Knudsen diffusion dominates, with bulk flow being best described by the Darcy-Brinkman equation.
With these physics modelled, it appears as though the gas homogeneity assumption is not completely accurate, breaking down in the porous pellet where reactions occur. While these results are not yet quantitative, this trend is likely to remain in future model iterations. It is not yet clear how significant this deviation is, though methods are proposed to minimize it if necessary.
Some model-experiment mismatch has been found which must be further explored. Experimental data shows a pressure dependence on the furnace temperature at constant power, a trend as-yet unresolvable by the model. It is proposed that this relates to the breakdown of the assumption of fluid continuity at low pressures and small dimensions, though no compelling mathematical formulation has been found. This issue may have significant ramifications on ETEM and ETEM experiment design.

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Date Created
  • 2017-05

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Combined AFM and Fluorescence Measurements for the Investigation of Nanophotonic Effects on Single Fluorophores

Description

In this project, we introduce a type of microscopy which produces correlated topography and fluorescence lifetime images with nanometer resolution. This technique combines atomic force microscopy (AFM) and time resolved

In this project, we introduce a type of microscopy which produces correlated topography and fluorescence lifetime images with nanometer resolution. This technique combines atomic force microscopy (AFM) and time resolved confocal fluorescence microscopy to conduct biological and materials research. This method is used to investigate nanophotonic effects on single fluorophores, including quantum dots and fluorescent molecules. For single fluorescent molecules, we investigate the effects of quenching of fluorescence with the probe of an atomic force microscope which is combined and synchronized with a confocal fluorescence lifetime microscope. For quantum dots, we investigate the correlation between the topographic and fluorescence data. With this method of combining an atomic force microscope with a confocal microscope, it is anticipated that there will be applications in nanomaterial characterization and life sciences; such as the determination of the structure of small molecular systems on surfaces, molecular interactions, as well as the structure and properties of fluorescent nanomaterials.

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Date Created
  • 2013-05

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TB or Not TB: Methodologies and Clinical Validation of Tuberculosis Detection Using Nanoplasmon-Enhanced Scattering and Dark Field Microscopy

Description

Mycobacterium tuberculosis is the primary bacteria responsible for tuberculosis, one of the most dangerous diseases, and top causes of death worldwide, as identified by the World Health Organization in a

Mycobacterium tuberculosis is the primary bacteria responsible for tuberculosis, one of the most dangerous diseases, and top causes of death worldwide, as identified by the World Health Organization in a 2018 report. Diagnostic tools currently exist for identifying those who carry active or latent versions of the infection including chest radiographs, a Mantoux tuberculin skin test, or an acid-fast bacilli smear of sputum samples. These methods are standard in the medical community of high income countries, but pose challenges for lower-income regions of the world as well as vulnerable populations. The need for a rapid, inexpensive, and non-invasive method of tuberculosis detection is evident by the ten million that contracted and 1.6 million that died from TB in 2017 alone. In our study, we used a previously developed nanoplasmon-enhanced scattering technology combined with dark field microscopy in order to investigate the potential for a blood-based TB detection assay. Twenty-eight capture antibodies were screened using cell culture exosomes and human serum samples to identify candidates for a TB-derived exosome biomarker. Four antibodies demonstrated potential for distinguishing negative controls from positive controls in this study: anti-AG85, anti-AG85B, anti-SodA, anti-Ald. These capture antibodies displayed significant differences (p<0.05) for both cell culture exosomes and human serum samples on more than one occasion. The work is significant in its ability to distinguish potential capture antibody targets, and future experimentation may yield a technology ready for clinical settings to address the gap in current TB detection methods.

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Date Created
  • 2019-05

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Single cell force spectroscopy for quantification of cellular adhesion on surfaces

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

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.

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Date Created
  • 2016

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Fluctuation electron microscopy of amorphous and polycrystalline materials

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

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.

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Date Created
  • 2015

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Small molecule detection by surface plasmon resonance: improvements in sensitivity and kinetic measurement

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

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.

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Date Created
  • 2013

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Synthesis and in situ environmental transmission electron microscopy investigations of ceria-based oxides for solid oxide fuel cell anodes

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 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.

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Date Created
  • 2011