Canola (Brassica napus) contributes $19.3 billion dollars to the Canadian economy each year as a result of its oil- and protein-rich seeds. These economically important seed products are produced in highest concentration in the embryo. Embryo development is supported nutritionally and structurally by the maternal subregions, which include the inner (ISC) and outer distal seed coat (OSC), the chalazal seed coat (CZSC), and the chalazal proliferating tissue (CPT). Research on the maternal seed subregions is limited to the SC as a result of its accessibility; the embedded CZSC and CPT subregions have yet to be characterized in canola. Using light and transmission electron microscopy, I found the CZSC and CPT to be anatomically distinct and experience profound changes throughout seed development. To understand these changes at the RNA level, laser microdissection and RNA sequencing were used to profile these subregions spatially and temporally from the ovule to mature green stage of seed development. Employing vigorous bioinformatics analyses, I found that the maternal subregions are transcriptomically distinct and possess unique RNA populations. From here I began to elucidate the biological processes operating within the maternal subregions. As a whole, the maternal subregions appear to have a critical role in transporting nutrients to the filial subregions as well as in coping with oxidative stress produced during these energy-rich processes. Additionally, using CanEnrich, I was able to generate predictive transcriptional circuits regulating the biological processes occurring within the maternal seed. This research has produced the most comprehensive dataset on the canola seed to date and will provide a valuable resource for research on seed development as well as seed improvement. / October 2016

"The adhesion of bacteria to surfaces has been analyzed in terms of surface charge, surface energy, and the characteristics of polymers on bacteria, to understand the factors that control bacterial adhesion. Pseudomonas aeruginosa has received a great deal of interest because it is responsible for a variety of chronic bacterial infections such as airway infections in cystic fibrosis patients and ulcerative bacterial keratitis in soft contact lens users. Over the past few years, force measurement techniques such as atomic force microscopy (AFM) have made it possible to examine interactions between colloidal particles and surfaces. In the present study, the AFM was used to study the interactions between each of two Pseudomonas aeruginosa strains with proteins. Topographical images and force cycles of bacterial cells and proteins were analyzed. Bovine serum albumin (BSA) and concanavalin A (Con A) were the model proteins chosen to represent protein molecules that might affect bacterial adhesion. In addition, the role of LPS structure in bacterial adhesion was investigated. The magnitude of adhesive forces for two P. aeruginosa stains was not statistically significant when they interact with silicon. Although it is not clear if the pull-off distances are accurate representatives of the absolute length of bacterial surface molecules, the trend indicates that the surface molecules of strain AK1401 are shorter than those of strain PAO1. The semi-rough strain AK1401 was more hydrophobic than the smooth strain PAO1, according to the water contact angle measurements. However, surface free energy components and zeta potential values were not significantly different for both strains. Zeta potential of bacterial cells decreased when they were suspended in HEPES/DTT buffer instead of ultrapure water. The AFM results demonstrate the importance of nano-scale interactions between proteins and bacterial cells. Our results show that the lipid A and core oligosaccharides are the most important molecules influencing the interactions of P. aeruginosa with protein molecules. The interactions of P. aeruginosa with model proteins in our study were weak. Therefore, the role of protein molecules may be inadequate for the purpose of enhancing subsurface delivery for bioremediation. Our results suggest that the semi-rough mutant, AK1401, can adhere to the protein receptors of the epithelial cells or protein coated implants stronger than the smooth strain, PAO1, and therefore can cause serious infections."

Microbial infections of medical implants occur in more than 2 million surgical cases each year in the United States alone. These increase patient morbidity and mortality, as well as patient cost and recovery time. Many treatments are available, but none are guaranteed to remove the infection. The purpose of this work is to examine the initial events in microbial adhesion by simulating the approach and contact between a planktonic cell, immobilized on an Atomic Force Microscope (AFM) cantilever, and a biomaterial or biofilm substrate. Distinct adhesive interactions exist between Candida parapsilosis and both unmodified silicone rubber and Pseudomonas aeruginosa biofilms. Using C. parapsilosis cells immobilized on AFM cantilevers with a silicone substrate, we have measured attractive interactions with magnitude of 2.3 ± 0.5 nN (SD) in the approach portion of the force cycle. On P. aeruginosa biofilms, the magnitude of the attractive force increases to 3.5 ± 0.75 nN (SD), and is preceded by a 2.5 nN repulsion at approximately 175 nm from the cell surface. This repulsion may be attributed to steric and electrostatic interactions between the two microbial polymer brushes. Young's moduli for microbes and biofilms were calculated using Hertzian contact models. These produced values of 0.21 ± 0.003 MPa (SD) for the C. parapsilosis-silicone rubber system, and 0.84 ± 0.015 MPa (SD) for the C. parapsilosis-biofilm system. This technique may be extended to calculate the work per unit contact area involved in the attractions in experimental data. For example, the work of adhesion using a spore probe is an order of magnitude greater for unmodified silicone rubber than for a P. aeruginosa biofilm. This indicates a high affinity for silicone rubber, and suggests that this material is vulnerable to infection by C. parapsilosis in vivo. We have also demonstrated that AFM force curve analysis using established qualitative and quantitative models fails to accurately represent the physical interactions taking place between the probe and sample for the case where a polymer brush exists on the substrate, the probe, or both. As such, an approximate method defining the sample surface as the actual surface plus some vertical dimension associated with the maximum compressible thickness of the polymer brush is discussed. Characterization of cell-biomaterial and cell-cell interactions allows for a quantitative evaluation of the materials used for medical implantation. It also provides a link between the physicochemical and physicomechanical properties of these materials and the nanoscale interactions leading to microbial colonization and infection. The goal of this research is to study this link and determine how best to exploit it to prevent microbial infections of medical implant materials.

This thesis reflects two advances in atomic force microscopy. The first half is a new lateral force calibration procedure, which, in contrast to existing procedures, is independent of sample and cantilever shape, simple, direct, and quick. The second half is a high-throughput method for processing, fitting, and analyzing force curves taken on Pseudomonas aeruginosa bacteria in an effort to inspire better care for statistics and increase measurement precision.

This dissertation presents a quantitative phase imaging microscopy technique that combines phase-shifting interferometry with multi-wavelength optical phase unwrapping. The technique consists of a Michelson-type interferometer illuminated with any of three types of light sources; light emitting diodes, laser diodes and a ring dye laser. Interference images are obtained by using a 4-frame phase shifting method, and are combined to calculate the phase of the object surface. The 2π ambiguities are removed by repeating the experiment combining two and three different wavelengths, which yields phase images of effective wavelength much longer than the original. The resulting image is a profile of the object surface with a height resolution of several nanometers and range of several microns. To our knowledge, this is the first time that a three wavelength optical phase unwrapping method with no amplified phase noise has been presented for fullframe phase images. The results presented here are divided into three main categories based on the source of illumination; light emitting diodes, laser diodes and a ring dye laser. Results for both two-wavelength optical unwrapping and three-wavelength optical unwrapping techniques are demonstrated. The interferographic images using broadband sources such as light emitting diodes are significantly less affected by coherent noise compared to images obtained using lasers. Our results show that the three wavelength optical phase unwrapping can also be effectively applied to unwrap phase images obtained using coherent light sources such as lasers and laser diodes, without amplifying phase noise in the final phase image. We have successfully shown that our multi-wavelength phase-shifting technique extends the range free of 2π ambiguities in the phase map without using conventional computation intensive phase unwrapping methods. This phase imaging technique can be used to measure physical thickness or height of both biological and other microscopic samples, with nanometer axial resolution. An added advantage of the multi-wavelength optical phase unwrapping technique is that the beat wavelength can be tailored to match height variations of specific samples.

We present the development of a far-field magneto-optical Kerr effect microscope. An inverted optical microscope was constructed to accommodate Kerr imaging and atomic force microscopy. In Kerr microscopy, magnetic structure is investigated by measuring the polarization rotation of light reflected from a sample in the presence of a magnetic field. Atomic force microscopy makes use of a probe which is scanned over a sample surface to map the topography. The design was created virtually in SolidWorks, a three-dimensional computer-aided drafting environment, to ensure compatibility and function of the various components, both commercial and custom-machined, required for the operation of this instrument. The various aspects of the microscope are controlled by custom circuitry and a field programmable gate array data acquisition card at the direction of the control code written in National Instrument LabVIEW. The microscope has proven effective for both Kerr and atomic force microscopy. Kerr images are presented which reveal the bit structure of magneto-optical disks, as are atomic force micrographs of an AFM calibration grid. Also discussed is the future direction of this project, which entails improving the resolution of the instrument beyond the diffraction limit through near-field optical techniques. Preliminary work on fiber probe designs is presented along with probe fabrication work and the system modifications necessary to utilize such probes.

Thin film arrays of molecules or supramolecules are active subjects of investigation because of their potential value in electronics, chemical sensing, catalysis, and other areas. Scanning probe microscopes (SPMs), including scanning tunneling microscopes (STMs) and atomic force microscopes (AFMs) are commonly used for the characterization and metrology of thin film arrays. As opposed to transmission electron microscopy (TEM), SPMs have the advantage that they can often make observations of thin films in air or liquid, while TEM requires highly specialized techniques if the sample is to be in anything but vacuum. SPM is a surface imaging technique, while TEM typically images a 2D projection of a thin 3D sample. Additionally, variants of SPM can make observations of more than just topography; for instance, magnetic force microscopy measures nanoscale magnetic properties. Thin film arrays are typically two-dimensionally periodic. A perfect, infinite two-dimensionally periodic array is mathematically constrained to belong to one of only 17 possible 2D plane symmetry groups. Any real image is both finite and imperfect. Crystallographic Image Processing (CIP) is an algorithm that Fourier transforms a real image into a 2D array of complex numbers, the Fourier coefficients of the image intensity, and then uses the relationship between those coefficients to first ascertain the 2D plane symmetry group that the imperfect, finite image is most likely to possess, and then adjust those coefficients that are symmetry-related so as to perfect the symmetry. A Fourier synthesis of the symmetrized coefficients leads to a perfectly symmetric image in direct space (when accumulated rounding and calculation errors are ignored). The technique is, thus, an averaging technique over the direct space experimental data that were selected from the thin film array. The image must have periodicity in two dimensions in order for this technique to be applicable. CIP has been developed over the past 40 years by the electron crystallography community, which works with 2D projections from 3D samples. Any periodic sample, whether it is 2D or 3D has an "ideal structure" which is the structure absent any crystal defects. The ideal structure can be considered one average unit cell, propagated by translation into the whole sample. The "real structure" is an actual sample containing vacancies, dislocations, and other defects. Typically the goal of electron and other types of microscopy is examination of the real structure, as the ideal structure of a crystal is already known from X-ray crystallography. High resolution transmission electron microscope image based electron crystallography, on the other hand, reveals the ideal crystal structure by crystallographic averaging. The ideal structure of a 2D thin film cannot be easily in a spatially selective fashion examined by grazing incidence X-ray or low energy electron diffraction based crystallography. SPMs straightforwardly observe thin films in direct space, but SPM accuracy is hampered by blunt or multiple tips and other unavoidable instrument errors. Especially since the film is often of a supramolecular system whose molecules are weakly bonded (via pi bonds, hydrogen bonds, etc.) both to the substrate and to each other, it is relatively easy for a molecule from the film to adhere to the scanning tip during the scan and become part of the tip during subsequent observation. If the thin film array has two-dimensional periodicity, CIP is a unique and effective tool both for image enhancement (determination of ideal structure) and for the quantification of overall instrument error. In addition, if a sample of known 2D periodicity is scanned, CIP can return information about the contribution of the instrument itself to the image. In this thesis we show how the technique is applied to images of two dimensionally periodic samples taken by SPMs. To the best of our knowledge, this has never been done before. Since 2D periodic thin film arrays have an ideal structure that is mathematically constrained to belong to one of the 17 plane symmetry groups, we can use CIP to determine that group and use it for a particularly effective averaging algorithm. We demonstrate that the use of this averaging algorithm removes noise and random error from images more effectively than translational averaging, also known as "lattice averaging" or "Fourier filtering". We also demonstrate the ability to correct systematic errors caused by hysteresis in the scanning process. These results have the effect of obtaining the ideal structure of the sample, averaging out the defects crystallographically, by providing an average unit cell which, when translated, represents the ideal structure. In addition, if one has recorded a scanning probe image of a 2D periodic sample of known symmetry, we demonstrate that it is possible to use the Fourier coefficients of the image transform to solve the inverse problem and calculate the point spread function (PSF) of the instrument. Any real scanning probe instrument departs from the ideal PSF of a Dirac delta function, and CIP allows us to quantify this departure as far as point symmetries are concerned. The result is a deconvolution of the "effective tip", which includes any blunt or multiple tip effects, as well as the effects caused by adhesion of a sample molecule to the scanning tip, or scanning irregularities unrelated to the physical tip. We also demonstrate that the PSF, once known, can be used on a second image taken by the same instrument under approximately the same experimental conditions to remove errors introduced during that second imaging process. The preponderance of two-dimensionally periodic samples as subjects of SPM observation makes the application of CIP to SPM images a valuable technique to extract a maximum amount of information from these images. The improved resolution of current SPMs creates images with more higher-order Fourier coefficients than earlier, "softer" images; these higher-order coefficients are especially amenable to CIP, which can then effectively magnify the resolution improvement created by better hardware. The improved resolution combined with the current interest in supramolecular structures (which although 3D usually start building on a 2D periodic surface) appears to provide an opportunity for CIP to significantly contribute to SPM image processing.

Traditional light microscopy suffers from the diffraction limit, which limits the spatial resolution to λ/2. The current trend in optical microscopy is the development of techniques to bypass the diffraction limit. Resolutions below 40 nm will make it possible to probe biological systems by imaging the interactions between single molecules and cell membranes. These resolutions will allow for the development of improved drug delivery mechanisms by increasing our understanding of how chemical communication within a cell occurs. The materials sciences would also benefit from these high resolutions. Nanomaterials can be analyzed with Raman spectroscopy for molecular and atomic bond information, or with fluorescence response to determine bulk optical properties with tens of nanometer resolution. Near-field optical microscopy is one of the current techniques, which allows for imaging at resolutions beyond the diffraction limit. Using a combination of a shear force microscope (SFM) and an inverted optical microscope, spectroscopic resolutions below 20 nm have been demonstrated. One technique, in particular, has been named tip enhanced near-field optical microscopy (TENOM). The key to this technique is the use of solid metal probes, which are illuminated in the far field by the excitation wavelength of interest. These probes are custom-designed using finite difference time domain (FDTD) modeling techniques, then fabricated with the use of a focused ion beam (FIB) microscope. The measure of the quality of probe design is based directly on the field enhancement obtainable. The greater the field enhancement of the probe, the more the ratio of near-field to far-field background contribution will increase. The elimination of the far-field signal by a decrease of illumination power will provide the best signal-to-noise ratio in the near-field images. Furthermore, a design that facilitates the delocalization of the near-field imaging from the far-field will be beneficial. Developed is a novel microscope design that employs two-photon non-linear excitation to allow the imaging of the fluorescence from almost any visible fluorophore at resolutions below 30 nm without changing filters or excitation wavelength. The ability of the microscope to image samples at atmospheric pressure, room temperature, and in solution makes it a very promising tool for the biological and materials science communities. The microscope demonstrates the ability to image topographical, optical, and electronic state information for single-molecule identification. A single computer, simple custom control circuits, field programmable gate array (FPGA) data acquisition, and a simplified custom optical system controls the microscope are thoroughly outlined and documented. This versatility enables the end user to custom-design experiments from confocal far-field single molecule imaging to high resolution scanning probe microscopy imaging. Presented are the current capabilities of the microscope, most importantly, high-resolution near-field images of J-aggregates with PIC dye. Single molecules of Rhodamine 6G dye and quantum dots imaged in the far-field are presented to demonstrate the sensitivity of the microscope. A comparison is made with the use of a mode-locked 50 fs pulsed laser source verses a continuous wave laser source on single molecules and J-aggregates in the near-field and far-field. Integration of an intensified CCD camera with a high-resolution monochromator allows for spectral information about the sample. The system will be disseminated as an open system design.

The recently developed Shear-Force Acoustic Near-Field Microscope (SANM) is used to investigate the viscoelastic properties of a mesoscopic fluid layer confined between two trapping boundaries, one being a stationary substrate and the other the apex of a laterally oscillating tapered probe. Hardware improvements and evaluation of the SANM-probe robustness will be a major focus of this thesis. The investigation first discusses characterization and recent developments made to the microscope, including: modifications to the sensor head, conditioning of the Nano positioners electrical drive signal, and the assessment of the probe against eventual plastic deformation or compliance against interactions with samples (the latter comprising a solid substrate and its adhered fluid layer which is typically a few monolayers thick). Furthermore, this study includes an analysis of the adsorbed mesoscopic fluid's viscoelastic properties. This inquiry aims to better understand probe-sample interactions with the mesoscopic fluid. This includes adhesion, wetting, and to inquire the nature of the hydrophobic interaction, which is relevant in many areas of study such a protein folding, and interfacial friction which has wide ranging applications including desalination. This analysis will be performed using a Sheer force microscopy (implemented with quartz tuning fork QTF), and another recently introduced technique Whispering Gallery Acoustic Sensor (WGAS). The latter allows more direct monitoring of the QTF's mechanical displacement. These measurements will be supplemented by simultaneously monitoring the acoustic emission from the mesoscopic fluid under confinement between the probe and the substrate, which will be monitored using the SANM sensor positioned beneath the substrate.

The deformation mechanisms operating in diamond-like carbon (DLC) coatings on (100) and (111) Si, has been investigated. The effect of coating thickness, indenter geometry, substrate orientation and deposition technique on the deformation of DLC coatings and the underlying substrate was studied by undertaking nanoindentation followed by subsurface microstructural characterization. Uncoated (111) Si was also investigated for comparison. The observed microstructural features were correlated to the indentation response of the coatings and compared with simulation studies, as well as observations on uncoated Si. In uncoated (111) Si, phase transformation was found to be responsible for the discontinuities in the load-displacement curves, similar to (100) Si. However, slip was activated on {311} planes instead of on {111} planes. Moreover, the density of defects was also significantly lower and their distribution asymmetric. The coatings were adherent, uniformly thick and completely amorphous. The load-displacement curves displayed several pop-ins and a pop-out, the indentation loads for the first pop-in and the pop-out depending primarily on the thickness of the coating. The coatings exhibited localized compressive deformation in the direction of loading without any through-thickness cracks. The extent of this localized deformation increased with indentation load. Hardness and thickness of the coatings and the geometry of the indenter influenced the magnitude of compressive strains. Harder and thinner coatings and a blunt indenter exhibited the minimum degree of deformation. Densification by rearrangement of molecules has been suggested as the mechanism responsible for plastic compression. At indentation loads corresponding to the first pop-in, (100) and (111) silicon substrates initially deformed by <111> and <311> slip respectively. Higher indentation loads caused phase transformation. Therefore, unlike in uncoated Si, dislocation nucleation in the Si substrate has been proposed as the mode responsible for the first pop-in. Subsequent pop-ins were attributed to further deformation by slip and twinning, phase transformation and extensive cracking (median and secondary cracks) of the substrate. The pop-out, however, was ascribed to phase transformation. Extensive deformation in the substrate, parallel to the interface, is attributed to the wider distribution of the stress brought about by the DLC coating. Good correlation was obtained between the nanoindentation response, microstructural features and simulation studies.