Dichapetalum cymosum (poison leaf) is a very common problem plant in southern Africa. Fluoroacetic acid, believed to be the poisonous entity in the plant, is produced by the plant, but the micro-organisms associated with this plant may also play a role in the production thereof. A previous study on Burolderia cepacia, an endophyte of D. cymosum showed active metabolism of fluoroacetate by this endophyte. The isolated endophytes from D. cymosum were studied to determine whether they synthesise any fluorinated compounds. It seemed from preliminary results that symbionts might play a role in the synthesis of the poisonous entities in D. cymosum, but further investigation is required. The detection of glandular lesions on the abaxial side of the leaf led to closer examination and the cross sections revealed unusually deformed epidermis cells with adjacent cells containing vacuoles filled with phenolic-like crystals. Transmission electron microscopy (TEM) of the spongy parenchyma cells directly above the glandular lesions indicated the presence of clusters of small, virus-like particles (VLPs) in the chloroplasts. Observations by TEM showed that these VLPs have analogous structures to phytoferritin. Tapura fischeri (leafberry tree) is a tree member of the same family, and it was found to also contain a fluorinated compound. Endophytes were also found in the plant and similar glandular lesions with analogous VLPs were observed at these sites. This might indicate that endophytes have a share in the biosynthesis of the fluorinated compounds found in Dichapetalaceae. Numerous factors ought to be considered in order to fully understand the chemical ecology of the intricate system regarding the endophytes and the possible toxicity of the family Dichapetalaceae. / Dissertation (MSc)--University of Pretoria, 2012. / Plant Science / unrestricted

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Les puits quantiques InGaN/GaN montrent la plus grande efficacité connue dans le bleu-UV et le défi actuel dans ce type de matériau est de pousser leur émission vers les grandes longueurs d’ondes. Ceci serait possible en augmentant la composition en indium, mais il faut alors gérer les contraintes résultantes. Ce travail a mis en œuvre la microscopie électronique en transmission et la diffraction des rayons X pour déterminer la composition chimique à l’intérieur des couches InGaN, le taux de relaxation et le type de défauts présents. Les résultats montrent qu’il n’y a pas de fluctuations de composition en indium dans les couches d’InGaN étudiées avec des taux d’indium de l’ordre de 20%. Ainsi, la différence d’émission des échantillons pourrait s’expliquer par la variation d’épaisseur des puits quantiques InGaN et laprésence de défauts. En effet, plusieurs types de défauts ont été observés et caractérisés tels que les pinholes ou des domaines de défauts plans selon leur origine. Dans les multicouches InGaN/GaN avec couches AlGaN compensatrices de contrainte,la diffraction des rayons X a montré que lorsque l’épaisseur des couches d’AlGaN augmente en gardant constante l’épaisseur entre les couches actives d’InGaN (avec une valeur d’environ 16-17 nm), les puits quantiques sont totalement contraints dans le plan de croissance et en dehors. Par microscopie électronique, nous montrons queleur relaxation se fait par formation aussi bien de défauts en domaines plans que de dislocation de type a. Ces dislocations se propagent des pits quantiques vers la surface, et la densité des défauts augmente avec l’épaisseur des couches d’AlGaN. / InGaN/GaN quantum wells show the highest known emission efficiency in UV-blue and the current challenge is to push to longer wavelengths. This would be possible by increasing the indium composition but the challenge becomes how to handle the resulting strains. This work has combined transmission electron microscopy and Xray diffraction in order to determine the relaxation rates, the local chemical composition and defects formation in these systems. The results show that there are no composition fluctuations in these InGaN layers where the indium content was around 20%. Therefore, the differences in emission may be explained by the changes in quantum wells thicknesses and/or the presence of defects. Indeed, several types of defects have been observed and characterized, such as pinholes or planar defect domains. For InGaN/GaN quantum wells with strain compensating AlGaN layers, Xray diffraction showed that, when the AlGaN layer thickness increases, keeping constant the spacing between InGaN layers (around 16-17 nm), the quantum wellsare totally strained in and out the growth plan. Using transmission electron microscopy, it is shown that the relaxation occurs through the formation of domains as well as a type dislocations. The dislocations propagate from the quantum well tothe surface and the density of the defects increases with the thickness of the AlGaN layers.

Despite the significant progress in medicine, infectious diseases are life-threatening thanks to an increasing number of multiresistant strains of microorganisms and late detection of pathological agents. An opportunistic fungus Aspergillus fumigatus cause respiratory system diseases called aspergillosis. The invasive pulmonary aspergillosis affects immunocompromised patients after inhalation of ubiquitous conidia of A. fumigatus and results in 450,000 deaths per year. The biofilm formation in the infected tissue protects A. fumigatus against antimicrobial drugs. Late therapy may not be effective. Infection of immunocompromised patients and biofilm formation is characteristic also for gram negative bacteria Pseudomonas aeruginosa, which is due to the production of many factors of virulence and multiresistance a dreaded opportunistic pathogen. Scanning electron microscopy (SEM) provides detail information about morphology of microorganisms with the resolution in range of tens of nanometers that allows to observe microorganisms in the infected tissue and its pathological changes. Mass spectrometry allows to detect infection and its course based on identification of characteristic microbial molecules. The aim of this study was to optimize sample preparation of tissues infected with A. fumigatus or P....

In this work phase transformations in metastable β (primarily Ti-15Mo) alloys were studied utilizing electrical resistance, dilatometry, transmission electron microscopy and X-ray and neutron diffraction. The materials Ti-15Mo, Ti-6.8Mo-4.5Fe-1.5Al (LCB), Ti-5Al-5V-5Mo-3Cr (Ti-5553), Ti-29Nb-1Fe-0.5Si (TNFS), Ti-15Mo-3Nb-3Al-0.2Si (Timetal 21S) and Ti-13Cr-1Fe-3Al (TCFA) (in wt. %) - were subjected to a solution treatment at a temperature above β transus and quenched into water. In this condition, the microstructure of the investigated materials consists of β matrix and ω particles. Samples quenched from important temperatures determined from in-situ electrical resistance and dilatometry measurements were studied by post-mortem TEM. In-situ X-ray and neutron diffraction provided direct observations of microstructure of Ti-15Mo alloy during linear heating and confirmed statements based on results of indirect methods, such as: the decrease of volume fraction of ω phase during heating at low temperatures (up to 250 ◦ C), complete dissolution of ω phase at 560 ◦ C and precipitation of α phase without ω particles serving as its direct precursors. X-ray diffraction experiment allowed to determine relative evolution of the size of ω particles while phase fraction evolution was derived from neutron diffraction. The...

Tomographic electron holography combines tomography, the reconstruction of three-dimensionally resolved data from multiple measurements with different specimen orientations, with electron holography, an interferometrical method for measuring the complex wave function inside a transmission electron microscope (TEM). Due to multiple scattering and free wave propagation conventional, ray projection based, tomography does perform badly when approaching atomic resolution. This is remedied by incorporating propagation effects into the projection while maintaining linearity in the object potential. Using the Rytov approach an approximation is derived, where the logarithm of the complex wave is linear in the potential. The ray projection becomes a convolution with a Fresnel propagation kernel, which is considerably more computationally expensive. A framework for such calculations has been implemented in Python. So has a multislice electron scattering algorithm, optimised for large fields of view and high numbers of atoms for simulations of scattering at nanoparticles. The Rytov approximation gives a remarkable increase in resolution and signal quality over the conventional approach in the tested system of a tungsten disulfide nanotube. The response to noise seems to be similar as in conventional tomography, so rather benign. This comes at the downside of much longer calculation time per iteration. / Tomographische Elektronenholographie kombiniert Tomographie, die Rekonstruktion dreidimensional aufgelößter Daten aus einem Satz von mehreren Messungen bei verschiedenen Objektorientierungen, mit Elektronenholographie, eine interferrometrische Messung der komplexen Elektronenwelle im Transmissionselektronenmikroskop (TEM). Wegen Mehrfachstreuung und Propagationseffekten erzeugt konventionelle, auf einer Strahlprojektion basierende, Tomography ernste Probleme bei Hochauflösung hin zu atomarer Auflösung. Diese sollen durch ein Modell, welches Fresnel-Propagation beinhaltet, aber weiterhin linear im Potential des Objektes ist, vermindert werden. Mit dem Rytov-Ansatz wird eine Näherung abgeleitet, wobei der Logarithmus der komplexen Welle linear im Potential ist. Die Strahlen-Projektion ist dann eine Faltung mit dem Fresnel-Propagations-Faltungskernel welche rechentechnisch wesentlich aufwendiger ist. Ein Programm-Paket für solche Rechnungen wurde in Python implementiert. Weiterhin wurde ein Multislice Algorithmus für große Gesichtsfelder und Objekte mit vielen Atomen wie Nanopartikel optimiert. Die Rytov-Näherung verbessert sowohl die Auflösung als auch die Signalqualität immens gegenüber konventioneller Tomographie, zumindest in dem getesteten System eines Wolframdisulfid-Nanoröhrchens. Das Rauschverhalten scheint ähnlich der konventionallen Tomographie zu sein, also eher gutmütig. Im Gegenzug braucht die Tomographie basierend auf der Rytov-Näherung wesentlich mehr Rechenzeit pro Iteration.

The microstructure, diffusion and phase transformations in aluminum-steel clad sheet were studied within the thesis by means of light optical microscopy, electron microscopy, resistometry and positron annihilation spectroscopy. Results of experimental methods were supplemented by finite element method employed for evaluation of electrical resistivity and simulation of diffusion between steel and aluminum. Several annealing experiments were carried out. The effective interdiffusion coefficient was evaluated by Boltzmann-Matano method from measured concentration profiles through the interface. Formation of an interfacial intermetallic phase was studied and orthorhombic phases Al13Fe4 and Al5Fe2 were identified present in the layer. Surprising results were obtained from the in-situ annealing in TEM (SEM) which go against the results found in a recent literature - the interfacial layer grows towards steel layer.

<div><div><div><p>Calcium-dependent protein kinase II alpha (CaMKIIα) is a highly abundant protein within the hippocampus, the region of the brain responsible for memory and learning. CaMKII has both structural and signaling roles in the regulation of the connective strength of synapses in excitatory neurons. It has a unique structure comprised of twelve subunits that form a dynamic assembly and is highly flexible. Its structural behavior has been shown to affect its activity, and a comprehensive mechanism of structure and function is still not fully understood. The determination of the quaternary structure of the CaMKII holoenzyme has been attempted for nearly 20 years by a variety of methods, with no one method giving a definitive structure. Problems in obtaining a structure originated with observation methods that estimated quaternary shape from low-resolution ensemble averages or required significant alteration of the protein to enforce a particular conformation. In this work, experiments were conducted to remove these limitations and provide a path towards the quaternary structure of CaMKIIα. Different expression and purification methods were evaluated to produce an optimal protocol for the generation of samples of concentrated, monodisperse, autoinhibited full-length wild-type CaMKIIα for study with cryo-electron microscopy. Strategies for microscopy sample preparation were investigated, including affinity girds, graphene-coated grids, and holey carbon grids. Lastly, experiments using negative stain electron microscopy, cryo-electron microscopy with single particle analysis, and cryo-electron tomography with subtomogram averaging were conducted to reveal the conditions required to produce an unambiguous three-dimensional structure. It was found that the assembly of the hexameric hub rings appeared to have flexible orientation, and superposition problems inherent in two-dimensional projection averaging requires the use of cryo-electron tomography to unravel the ambiguity in both hub orientation and catalytic module placement within the reconstructed volume. A subtomogram average of a limited number of particles revealed a hub domain that matched the morphology of prior reports, but the determination of catalytic module placement was not resolved. The cumulative result of this work establishes a strategy for the large-scale data collection needed to fully elucidate the structure of this challenging and fascinating protein.</p></div></div></div>

Thesis advisor: Seth C. Kruckenberg / Quantitatively describing the deformational behavior (i.e. the rheology) of lower crustal materials has proven challenging due to the highly variable nature of structural and compositional fabrics in the lower crust. Further, many flow laws describing the rheology of monophase aggregates are experimentally derived and do not necessarily apply to polyphase materials, such as gabbro, that dominate the lower crust. Here, we present the results of integrated microstructural analysis and electron backscatter diffraction (EBSD) textural analysis from exhumed lower crustal granulites in the Mount Hay block of central Australia. The preservation of heterogeneous mafic and felsic granulites containing monophase and/or polyphase mixtures of anorthite, pyroxene, and quartz (interlayered on the mm- to m-scale) make this region uniquely suited for advancing our knowledge of the processes that affect deformation and the rheology of the lower crust. Forty-two samples from distinct structural and compositional domains were chosen to compare the microstructural record of deformation, the development of crystallographic textures, and to provide estimates of lower crustal rheology and deformation conditions. Full thin-section maps of crystallographic texture were produced using EBSD methods. The resultant orientation maps were processed to characterize crystallographic textures in all constituent phases, and all other quantifiable aspects of the rock microstructure (e.g., grain size, grain shape, misorientation axes). The EBSD analysis reveals the presence of strong crystallographic preferred orientations (CPO) in nearly all constituent phases, suggesting deformation dominated by dislocation creep. Differential stresses during deformation are calculated using grain size piezometry for all major phases, and range between 34-54 MPa in quartz within monophase layers. Two-pyroxene geothermometry was used to constrain deformation temperatures to ca. 780-810 C. Based on the estimated CPO patterns, stress, and temperature, we quantify strain rates and effective viscosities of all major phases through application of monophase flow laws. Monophase strain rates range from 2.10 x 10-12 s-1 to 1.56 x 10-11 s-1 for quartz, 4.68 x 10-15 s-1 to 2.48 x 10-13 s-1 for plagioclase feldspar, 1.56 x 10-18 s-1 to 1.64 x 10-16 s-1 for enstatite, and 5.66 x 10-16 s-1 to 1.00 x 10-14 s-1 for diopside. The determined flow law variables used for monophase calculations were subsequently applied to two different models – the Minimized Power Geometric model of Huet et al. (2014) and the Asymptotic Expansion Homogenization (AEH) method of Cook (2006) – in order to calculate a bulk aggregate viscosity of the polyphase material. At a strain rate of 10-14 s-1, polyphase effective viscosities for our samples range from 3.07 x 1020 to 2.74 x 1021 Pa·s. We find that the bulk viscosity of heterogeneous, gabbroic lower crust in the Mount Hay region lies between that of monophase plagioclase and monophase quartz, and varies as a function of composition. These results are consistent with past modeling studies and geophysical estimates. / Thesis (MS) — Boston College, 2019. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Earth and Environmental Sciences.

Electric and hybrid vehicles uses regenerative braking, where application of the brake triggers the electric motor to work as a generator to produce electricity, which in turn charges the battery. This results in much less use of the friction brake, changing the corrosion and wear behavior of the rotor surface. There is a need for research on this topic, since fully electric or hybrid vehicles are replacing combustion engines due to concerns about global warming and climate change. Here the corrosion behavior of coated cast iron vehicle rotors in 3.5wt% NaCl is studied. The corrosion study has been performed using electrochemical methods such as cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). All the coated samples were provided by Pure Forge Rotors. Based on the results from SEM and EDX, the coating is atomic forge proprietary coating, and the base material is gray cast iron. Our primary objective is to study the corrosion behavior of coated, non-coated and friction-tested samples. CV experiments indicate a shift in the corrosion potential and corrosion current density due to changes in the nature of the exposed surface. Cross-sectional SEM showed the thickness of the coating to be 16-23 µm. After friction testing, the friction layer created by rubbing the brake pad over the rotor plays a role in corrosion resistance, but this depends on the type of brake pad material (i.e. semi-metallic, non-asbestos organic and low metallic). Results showed that friction film that forms after testing against non-asbestos organic pads provides the highest corrosion resistance amongst the three brake pad materials.