Abstract The properties of starch nanoparticles (SNPs) labeled with the fluorescent dye pyrene (Py-SNPs) were probed by using fluorescence quenching, pyrene excimer formation, and transmission electron microscopy (TEM). Pyrene labeling of the SNPs was achieved by reacting 1-pyrenebutyric acid with the hydroxyl groups of the SNPs under basic conditions and in the presence of diisopropylcarbodiimide. This procedure did not degrade the SNPs as confirmed by dynamic light scattering (DLS) and afforded a means to generate a pyrene labeling level ranging from 0.5 to 5.0 mol% of the glucose units making up the SNPs. A polymeric quencher was also synthesized to probe the accessibility of the interior of the Py-SNPs by using fluorescence quenching measurements. The polymeric quencher was a 2K poly(ethylene glycol) terminated at one end with a methyl group and a nitropropane group at the other. Unfortunately these quenching experiments were abandoned when it was found that the polymeric quencher synthesized for these experiments absorbed too strongly where pyrene absorbs. Intramolecular pyrene excimer formation in the Py-SNPs was investigated by steady-state and time-resolved fluorescence. These experiments demonstrated that the Py-SNPs contract but do not overlap like linear polymers do in the semi-dilute regime. They also showed that despite the inherent rigidity of starch, the Py-SNPs deformed in water to allow their hydrophobic pyrene labels to cluster toward the center of the SNPs to minimize pyrene-solvent contacts. This segregation of the hydrophobic pyrene labels led to a distinct core-shell structure for the Py-SNPs which was illustrated in TEM images acquired on films prepared with the Py-SNPs. In summary, this thesis has uncovered some unexpected properties of the SNPs. Their branched structure makes their interpenetration difficult in the semi-dilute regime which forces them to contract. SNPs are thus deformable and their deformation can be probed quantitatively by using fluorescence and TEM.

Neocortical circuits can adapt to changes in sensory input by modifying the strength or number of synapses. These changes have been well-characterized electrophysiologically in primary somatosensory (barrel) cortex of rodents across different ages and with different patterns of whisker stimulation. Previous work from our lab has identified layer-specific critical periods for synaptic potentiation after selective whisker experience (SWE), where all but one row of facial whiskers has been removed. Although whole-cell patch-clamp recording methods enable a mechanistic understanding of how synaptic plasticity can occur in vivo, they are painstakingly slow, typically focus on a small number of observed events, and are focused on a single pathway or restricted anatomical area. For example, most studies of plasticity in barrel cortex have focused on analyses of experience-dependent synaptic changes in layer 4 and layer 2/3, at a single time point, but it is unclear whether such changes are limited to these layers, or whether they persist over long time periods. Here we employ an established electron-microscopic technique that selectively intensifies synaptic contacts, in combination with unbiased, automated synapse detection, to broadly explore experience-dependent changes in synaptic size and density across many neocortical layers, regions, and time periods in a high-throughput fashion. To validate the method, we focused on imaging synaptic contacts at time points surrounding the critical period for strengthening of excitatory synapses in mouse barrel cortex, and compared these to electrophysiological analyses that show a doubling of synaptic events targeting layer 2/3 pyramidal neurons following SWE. We found that the pattern of occurrence of synapses across the cortical layers is significantly different following SWE. Also, an increase in length was observed specifically in layer 3 synapses. Furthermore, we uncovered potential bidirectional plasticity in L6 synapses depending on the developmental state of circuit and a potential critical period onset for L5A synapse at PND 18. The high resolution imaging and unbiased synapse detection has enabled us to potentially tease apart synaptic changes that occur in a laminar specific fashion. This high-throughput method will facilitate analysis of experience-dependent changes in synaptic density by age, sensory experience, genotype, pharmacological treatments or behavioral training, and will enable classification of synaptic structure to identify key parameters that can be changed by these variables.

Over the last few years, TEM has become a powerful technique to study cracks and specially crack tips. However, the number of publications including TEM results has not grown as it was expected. The main reason for this might be difficulties in the sample preparation. In this work we present a novel FIB sample preparation technique which has proved to be an ideal tool for preparing cross sectional samples containing crack tips. The morphology of intergranular stress corrosion cracking (IGSCC) has been investigated in Alloy 600 subjected to constant load and slow strain rate tests in simulated primary circuit pressurized water reactor conditions. Cracks were observed to nucleate at high-angle grain boundaries and propagate to depths of a few tens of micrometer along such boundaries, still in the initiation stage. Electron diffraction, energy dispersive x-ray (EDX) and electron energy loss spectroscopy (EELS) have been used to identify the different corrosion products and precipitates. Elemental mapping was employed to reveal changes in composition in the crack tip area. Major observations at cracks and grain boundaries include: the presence of different oxides in different locations, differences in grain boundary oxides and open crack/free surface oxides. These observations suggest that IGSCC involves oxygen diffusion through a porous oxide region along grain boundaries to the bare metal. This is a novel concept that offers an alternative to previous mechanisms proposed in the literature e.g. H embrittlement, slip-dissolution, etc., for which no supporting evidence has been found.

Individual, well structurally characterised dislocations present in n-type silicon have been studied using the electron beam induced current (EBIC) mode of an SEM.</p>An EBIC system has been designed and constructed which includes i) phase sensitive detection, ii) computerised control of the experimental equipment and data capture and iii) a variable temperature SEM specimen stage. With this system measurements have been made of the EBIC contrast of individual segments of deformation induced dislocations produced by two stage compressive deformation at 850°C and 420°C. An experimental and theoretical analysis of EBIC signal generation in the Schottky barrier specimens used in this work is presented. This shows that the EBIC contrast measurements made may be directly correlated to the dislocation recombination strength. Contrast measurements have been made at temperatures in the range 120K to 370K and for electron beam currents from 6 x 10^-12A to 2 x 10^-9A. Several new effects have been observed. Minority carrier diffusion length measurements have also been performed in silicon containing dislocations. These show that the value obtained may depend upon experimental parameters used in a hitherto undetected manner. A new theory describing recombination of carriers at charged dislocations has been developed and this has been extended to provide a description of the variation of the EBIC contrast of dislocations with temperature, electron beam current and also the transient response of the EBIC contrast. Comparison of the theoretical predictions with the results gained experimentally shows full agreement for low temperatures or large beam currents. At high temperatures and small beam currents the theory shows the EBIC contrast will behave differently depending on the density of dislocation states present. Interpretation of the experimental results in terms of this theory allows some new insight to be gained for recombination at dislocations, and values for some of the parameters controlling recombination have been obtained.

Most living eukaryotes are currently classified into one of five or six ‘supergroups’, which are in turn often divided between two assemblages: ‘unikonts’ and ‘bikonts’. This thesis explores the cytoskeletal morphology and phylogeny of three lineages that do not belong to any supergroup: ancyromonads, apusomonads, and breviates, likely relatives of supergroups Opisthokonta and Amoebozoa. It also investigates the phylogeny of malawimonads (basal members of supergroup Excavata) and collodictyonids (another unaffiliated lineage). Serial-section transmission electron microscopy was used to model the flagellar apparatus cytoskeletons of the ancyromonad Ancyromonas sigmoides, the breviate Breviata anathema, and the apusomonad Thecamonas trahens. Each has two main posterior microtubular roots and at least one anterior root (two in Ancyromonas). All three possess splitting posterior right microtubular roots and supernumerary singlets, features also characteristic of basal members of the supergroup Excavata (‘typical excavates’). One peripheral microtubule system in Ancyromonas, and the ‘right ribbon’ in Thecamonas, are likely homologous to dorsal fans in Breviata and ‘typical excavates’, and to the ‘r2’ root of myxogastrid Amoebozoa. One of the branches of the splitting root in Breviata and Thecamonas joins the right and intermediate roots, similarly to some myxogastrids. This implies that myxogastrids, and not the simpler pelobionts, represent the ancestral state for Amoebozoa. A phylogenomic analysis was performed focussing on apusomonads breviates, ancyromonads, and the problematic ‘typical excavate’ malawimonads, based on new transcriptomic data from Ancyromonas and an undescribed malawimonad. Rapid-site- removal analyses recover the ‘unikont’/‘bikont’ partition, and do not support the previously demonstrated affiliation between breviates and the ‘unikont’ supergroup Amoebozoa. Specifically, they group apusomonads with the ‘unikont’ supergroup Opisthokonta, and ancyromonads with breviates. Taxon-removal analyses group ancyromonads, breviates, and apusomonads together. Most analyses group malawimonads (perhaps with collodictyonids, another problematic group) between ‘unikonts’ and (other) ‘bikonts’, while other excavates are in a basal position amongst other ‘bikonts’. Combining these morphological and phylogenetic results suggests that splitting right roots, supernumerary intermediate singlets, and dorsal fans are found in multiple ‘basal’ lineages in both ‘unikont’ and ‘bikont’ portions of the eukaryotic tree, are likely characters of the last common ancestor of most or all living eukaryotes.

Leukocytes play a central role in protecting the body against infectious organisms and their research is essential for understanding the mechanisms of immunity. By studying leukocytes across a range of species, insights are provided into differing strategies employed to ensure resistance to disease. Surprisingly, the structure and function of marsupial leukocytes has received very limited study. Marsupials represent a major evolutionary pathway with distinct differences in reproduction and development from placental mammals. These differences in the life history of marsupials place unique challenges on the immune system, and differences in leukocyte structure and function could be reasonably expected. In this thesis, studies were undertaken to examine the cytochemical, ultrastructural and functional features of leukocytes from species of marsupials, belonging to the family Macropodidae (kangaroos and wallabies). The aim of these studies was to elucidate the characteristics of macropodid leukocytes and to compare and contrast these features with the known characteristics of other mammalian leukocytes. Leukocytes from two species of macropodid, the tammar wallaby (Macropus eugenii) and the western grey kangaroo (Macropus fuliginosis), formed the basis of this study with additional material provided from quokka (Setonix brachyurus), woylie (Bettongia pencillata) and red kangaroo (Macropus rufus). Staining characteristics of cells were examined following reaction with Sudan black B, peroxidase, chloroacetate esterase, naphthyl butyrate esterase, alkaline phosphatase and periodic acid-Schiff. Peroxidase and Sudan Black B reactions were similar to domestic animal species but chloroacetate esterase and naphthyl butyrate esterase were unreliable as markers for macropodid neutrophils and monocytes, respectively. Significant variation in staining for alkaline phosphatase was seen between species of macropodid. Tammar wallabies and quokka demonstrated strong neutrophil alkaline phosphatase activity whereas western grey kangaroos, red kangaroos and woylies contained no activity within their leukocytes. Peroxidase and alkaline phosphatase cytochemistry were also assessed at the ultrastructural level with transmission electron microscopy. This allowed the identification of distinct granule populations within macropodid neutrophils. Two subcellular compartments containing alkaline phosphatase activity were identified within tammar wallaby neutrophils. These were considered equivalent to secretory vesicles and a subpopulation of specific granules. Tubular vesicles containing alkaline phosphatase were also identified within the eosinophils of tammar wallabies. These structures were a novel finding having not been reported previously in the eosinophils of other animal species. In addition to cytochemistry, the general ultrastructure of leukocytes from tammar wallabies and western grey kangaroos were reported. Results were similar to previous reports for other marsupial species. The current body of knowledge was extended by the first detailed description of the ultrastructure of basophils in a marsupial. To assess functional aspects of macropdid neutrophils, flow cytometric assays were performed examining oxidative burst responses and phagocytosis. Reactive oxygen species were generated by neutrophils from tammar wallabies and western grey kangaroos in response to phorbol 12-myristate 13-acetate but not N-formyl-Met-Leu-Phe or opsonised bacteria. Phagocytosis of opsonised bacteria was also measured in neutrophils from tammar wallabies, which was poor in contrast to ovine neutrophils. However, flow cytometric studies were limited by sample preparation. Further optimisation of isolation methods for tammar wallaby leukocytes should be undertaken before dogmatic conclusions are drawn. Overall, the results of this thesis demonstrate that, in the areas examined, the general characteristics of leukocyte structure and function of mammals are present in macropodids. However differences were identified both within and outside of the macropodid group. These differences have important ramifications for the use of ‘model’ species in the study of leukocyte biology in marsupials. The results also provide potentially useful tools for the clinical diagnosis of haematological disease in macropodids and may be of interest to those studying comparative and evolutionary aspects of leukocyte structure and function.

Novel carbon materials such as carbon onions, nanotubes and amorphous carbon (a-C) are technologically important due to their useful properties. Normally synthesised using plasmas, their growth mechanisms are not yet fully understood. For example, the growth mechanism of the high density phase of a-C, tetrahedral amorphous carbon (ta-C), has been a subject of debate ever since its discovery. The growth mechanism of carbon nanostructures such as carbon onions and nanotubes is also not well known. The aim of this thesis is two-fold. Firstly, to provide insight into the growth of carbon films, in particular, the driving force behind the formation of diamond-like bonding in a-C which leads to ta-C. Secondly, to investigate the growth of carbon onions and other sp2 bonded carbon nanostructures such as nanotubes. To achieve the first aim, carbon thin films were deposited using cathodic arc deposition at a range of ion energies, substrate temperatures and Ar background gas pressures. These films were characterised using electron microscopy techniques to examine their microstructure, density and sp3 content. It was found that the formation of the ta-C is due to a stress-induced transition whereby a critical stress of 6.5±1.5 GPa is needed to change the phase of the film from highly sp2 to highly sp3. Within this region, a preferentially oriented phase with graphitic sheets aligned perpendicular to the substrate surface was found. By investigating the role of elevated temperatures, the ion energy-temperature

Typewritten copy / Includes bibliographical references (leaves 141-144) / [5], 144 leaves : ill. ; 27 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / An account of experimental investigations carried out from January 1952 to September 1954. / Thesis (Ph.D.)--University of Adelaide, Dept. of Physics, 1956

Thesis (Ph.D.) -- McMaster University, 1998. / Includes bibliographical references (leaves 186-196). Also available via World Wide Web.

Thesis (Ph. D.)--Missouri University of Science and Technology and University of Missouri--St. Louis, 2008. / Vita. The entire thesis text is included in file. Title from title screen of thesis/dissertation PDF file (viewed August 28, 2008) Thesis completed as part of a cooperative degree program with Missouri University of Science & Technology and the University of Missouri--St. Louis. Includes bibliographical references (p. 129-142).