Two-dimensional (2D) materials have properties that are often different from their three-dimensional (3D) bulk form. Many of these materials are stable at ambient conditions, which allows them to be integrated with other 2D- or 3D-materials to form heterostructures. Integration of various dimensional materials attains unique electrical and optical properties that aid in developing novel electronic devices. The interface of the heterogeneous integration of these films can exhibit a weak van der Waals-like bonding. In this thesis, an advanced characterization (from atomic to millimeter resolution) of various dimensional materials with weakly bonded interfaces is developed and employed to understand their behavior at scale. First, a large-area single-crystal cadmium telluride thin film is grown incommensurately and strain-free to a sapphire substrate despite a significant 3.7% lattice mismatch. The film remarkably delaminates as a bulk single crystal film due to an atomically thin tellurium that spontaneously forms at the interface. Aberration-corrected electron microscopy and spectroscopy reveal both the van der Waals-like structure and bonding at the film/substrate interface. Second, a large-area atomically thin gallium is intercalated at the interface of epitaxial graphene. Correlative microscopy workflows are applied to understand the thickness uniformity and area coverage of the 2D–gallium over few millimeters of the sample. Utilizing multiple correlative methods, SEM image contrast is found to be directly related to the presence of the intercalated gallium. The origin of the SEM contrast is investigated as a function of the surface potential. Then, the heterostructure characterization is scaled up over a few square millimeter areas by segmenting SEM images, each acquired with nanometer-scale resolution. Additionally, transmission electron microscopy is applied to investigate the interface of gallium–SiC, the gallium air–stability, and the role of the substrate on the heteroepitaxial growth of 2D–gallium, which charts a path for further development of these materials. / Thesis / Doctor of Philosophy (PhD)

Geometallurgy describes a holistic approach to mining (integrating geological, metallurgical, geotechnical, environmental, and more parameters) with the goal to improve the efficiency and sustainability of a mining operation. The potential of systematic optical petrography in a geometallurgical context was investigated in this study, as well as how petrography may be useful across disciplines in several blocks of the mining value chain. In a case study, twelve boulder samples (non-mineralized and mineralized) from the Rajapalot exploration property in Finland were characterized by detailed optical microscopy and scanning electron microscopy (SEM) with the aim to delineate the origin of the respective boulders. This allowed to demonstrate some benefits and challenges of systematic optical petrography in the mining value chain and geometallurgical programs. The study was performed through the geology department at Mitta AB in Luleå, Sweden, using rock samples supplied by Mawson Gold Ltd, Finland. The Rajapalot Au-Co property lies a few km east of the Rompas Au-U property, both owned by Mawson Gold Ltd and located in the Paleoproterozoic Peräpohja belt in northwest Finland. When determining the boulders’ origin, geochemical gradients of the Peräpohja belt lithostratigraphy; oxidized sodic rocks in the Kivalo group and reduced potassic rocks in the Paakkola group were crucial factors. The mineralization style of the Rompas Au-U association and the Rajapalot Au-Co association (including the “Palokas” Fe-Mg type and the “Rumajärvi” K-Fe type) were further crucial to classify the mineralized boulders. Results show that the rock types (and suggested origin) vary between boulder samples. Most samples are presumed to originate from the Paakkola group, one sample from the Kivalo group, and a few samples are inconclusive. Furthermore, the samples impact on the mining value chain was discussed based on the results of the petrographic analysis. A method description for a more systematic way of examining rock material is presented, including for example quantitative parameters such asmodal mineralogy and grain size distribution. However, the applicability of this method description needs further study.

The urinary bladder is especially subject to infection by virtue of its direct connection to the external urethral opening, and it is natural to anticipate the presence of a well-developed immunological mechanism to respond to this potential threat. The present study describes small, very highly vascular lymph nodes located in the wall of the rabbit bladder, which may be involved in a local response to foreign antigens. The vasculature and structure of these lymph nodes was described using a combination of vascular corrosion casting, ink injection, and light and electron microscopy. The distal abdominal aorta was cannulated, and after clearing the bladder vasculature with buffered saline, one of the following procedures was used: 1) the bladder was perfuse-fixed in preparation for light and electron microscopy; 2) the bladder vasculature was filled with India ink for vessel tracing; or 3) vascular corrosion casts of the vasculature were prepared by infusing resin comprised of a mixture of Mercox, methyl methacrylate monomer, and catalyst. The resulting casts were cleaned with KOH, formic acid, and water in preparation for scanning electron microscopy. Vascular casts and India ink injections revealed the presence of a number of isolated capillary tufts consisting of clusters of one to five 'glomeruli,' closely associated with the major vesicular vessels along the lateral walls of the bladder, and supplied by tertiary branches of these vessels. Light and electron microscopy showed that the capillary tufts represented the blood supply to small, ovoid lymph nodes located near the serosal surface of the bladder wall and usually restricted to the basal half of the bladder. These nodes were encapsulated and exhibited subcapsular sinuses, numerous small blood vessels, a limited number of high endothelial cells, and, occasionally, nerves and a follicular substructure. The nodes contained abundant lymphocytes, stellate stromal cells, macrophages, and eosinophils, but lacked the obvious cortical and medullary organization and germinal centers often seen in larger lymph nodes. Vascular corrosion casts, vascular ink injections, and microscopic examination confirmed the presence of small, highly vascular lymph nodes closely associated with the main vesicular vessels along the lateral walls of the rabbit bladder. A follicular substructure of the nodes appears to correspond with the 'glomerular' capillary arrangement within the nodes as seen with corrosion casts. The rich blood supply may be indicative of the high metabolic demand of lymphatic tissue, and may be altered in response to the level of activity of the node. The close association between the lymphatic tissue and the rich blood supply to the nodes may allow a rapid mobilization of lymphocytes during a local immune response to foreign agents.

Background: The success of kidney transplant surgery and ureteral reconstruction requires the preservation of the ureteral blood supply. Because of its potential vulnerability to surgical trauma during trans plant and reconstructive surgery, the ureteral vasculature merits a full anatomical description. Methods: The microvascular anatomy of the ureter was studied in male New Zealand white rabbits by light microscopy and transmission electron microscopy and scanning electron microscopy of vascular corrosion casts and alkali digested tissue. Results: The rabbit ureter is supplied predominantly by a branch of the renal artery proximally (cranial ureteral artery) and by a branch of the vesicular artery distally (caudal ureteral artery). Minor vascular continuities are also present between the capillary beds of the ureter and those of the renal pelvis cranially and the bladder wall caudally. There are no external vascular connections to the middle ureter with the exception of a single, small vein which drains into the inferior vena cava. A single group of longitudinal arteries and veins runs the full length of the ureter within the adventitia. Branches of these longitudinal vessels pass tangentially through the muscularis to supply a vascular complex within the lamina propria. This complex in turn supports a rich, mucosal capillary plexus located at the junction between the transitional epithelium and the lamina propria. In the fixed ureter the capillary plexus lies in grooves formed by displacement of the basal layers of the overlying transitional epithelium. The capillaries are continuous or fenestrated, are often invested with pericytes, and are distributed uniformly around the entire circumference of the ureter. Conclusions: The ureteral vasculature exhibits several unique features related to its function in urine conduction and its ability to accommodate expansion and contraction. The combination of techniques used provides a clear three‐dimensional view of this vasculature. Our findings also confirm that, because of its limited blood supply, the ureter may be very susceptible to injury during renal transplantation or other abdominal surgery.

Background: The urinary bladder requires a rich blood supply to maintain its functions, the storage and release of urine. Specialized properties of the bladder vasculature might be anticipated to ensure the integrity of this blood supply, because it is known that blood flow is reduced by distension during bladder filling. However, the bladder vasculature has been described in detail only at the gross level. A comprehensive, threedimensional view of the blood supply to the bladder wall is presented here. Methods: The microvasculature of the bladder of male New Zealand white rabbits was described using the combination of vascular corrosion casting, alkali digestion, light microscopy, and scanning and transmission electron microscopy. Following administration of an anticoagulant and an overdose of anesthetic, the abdominal aorta was cannulated just above the inferior mesenteric artery to permit flushing of the distal vasculature. The bladder vasculature was cleared of blood with buffered saline and then either perfuse‐fixed with buffered 2% glutaraldehyde and sectioned, or filled with “Mercox” resin to prepare vascular corrosion casts. Casts were cleaned with NaOH, formic acid, and water. In some cases fixed bladders were partially digested with NaOH to expose the mucosal capillary plexus. Results: The bladder is supplied with blood by single, left and right vesicular branches of the internal or external iliac arteries. The serpentine vesicular arteries extend along the lateral borders of the bladder from base to apex just deep to the serosal surface and send dorsal and ventral branches to supply the dorsal and ventral bladder walls. Veins accompany the arteries and exhibit numerous valves. A very dense complex of vessels at the apex of the bladder apparently serves to accommodate bladder distension. The muscularis and submucosa contains few vessels, but the mucosa is well vascularized. An especially dense capillary plexus is present in the lamina propria at its junction with the transitional epithelium. In the relaxed bladder these capillaries lie in grooves formed by the basal layers of the epithelium. The endothelial cells of these capillaries display few cytoplasmic vesicles and are continuous or fenestrated. These capillaries are often invested with pericytes. The mucosal capillary plexus may be associated with an epithelial transport function or may be necessary for urothelial metabolism or maintenance of the barrier function of the urothelium. Unusual capillary tufts, possibly associated with vascular lymphatic tissue, are found associated with the main vessels on the lateral walls in the basal half of the bladder. Conclusions: These methods present a clear, comprehensive, three‐dimensional view of the microvasculature of the bladder wall. They also identify several unique features of this vasculature and provide a basis for studies of the response of this vasculature to pathologic states and experimental manipulation.

No description available.

Phosducin-like protein (PhLP), a G protein beta gamma subunit dimer binder and G protein signaling regulator, was suggested to regulate the activity of cytosolic chaperonin CCT by their high affinity interaction. In the present study, the three-dimensional structure of PhLP:CCT complex has been solved by cryoelectron microscopy. PhLP was found to bind only one of the chaperonin rings with both N- and C-terminal domains. It spans the central folding cavity of CCT and interacts with two opposite sides of the top apical region, inducing the constraining of the entry of the folding cavity. These findings support a putative role of PhLP as a co-chaperone similar to prefoldin. Docking studies with the atomic model of PhLP generated from several known structures of the homologous phosducin (Pdc) together with the immuno-EM studies have provided more details of the complex structure and predicted some regions of PhLP and the subunits of CCT involved in the interaction. Taking advantage of the fact that Pdc is highly homologous to PhLP but lack of binding to CCT, the regions of PhLP involved in the interaction with CCT were determined by testing various PhLP/Pdc chimeric proteins in the CCT binding assay. In the other part of this dissertation, the physiological role of PhLP in G protein signaling was investigated. Cellular expression of PhLP was blocked using RNA interference targeting PhLP. Together with overexpression of PhLP variants and kinetic studies of G protein beta gamma dimer formation, PhLP was determined to be a positive mediator of G protein signaling and essential for G protein beta gamma dimer expression and dimer formation. Phosphorylation of PhLP at serines 18—20 by protein kinase CK2 was required for G protein beta gamma dimer formation, while a high-affinity interaction of PhLP with CCT appeared unnecessary. Interestingly, G protein beta subunit was found to interact with CCT by co-immunoprecipitation and PhLP over-expression increased the binding of G protein beta subunit to CCT. These results suggest that PhLP and CCT act as co-chaperones in the folding and assembly of the G protein beta gamma subunit dimer by forming a ternary PhLP-Gbeta-CCT complex that is a necessary intermediate in the assembly process.

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal native to the Andean region of South America and a staple crop for subsistence farmers in the altiplano of Bolivia and Peru. Downy mildew is the most significant disease of quinoa caused by the pathogen Peronospora farinosa f.sp. chenopodii Byford. This disease greatly impacts quinoa crops with yield losses up to 99%. As fungicides are expensive for farmers, the development of resistant cultivars appears to be the most efficient means for controlling downy mildew. The quinoa germplasm bank contains high amounts of genetic diversity, some of which exhibit mildew resistance. Methods for evaluating mildew severity are important for finding resistant genotypes that are useful in breeding programs. The main objectives of this study were to evaluate and investigate downy mildew resistance in quinoa through several different methods. A simple inoculation method was developed for downy mildew disease assessment by placing a damp piece of cheesecloth on a leaf, pipetting a known spore solution onto the cloth, and subjecting the plants to specific humidity cycles in a growth chamber. After inoculation of five quinoa-breeding lines in a growth chamber, accession 0654 was found to be the most resistant, while genotypes NL6 and Sayana showed moderate resistance. Each of these genotypes displayed some potential for resistance breeding programs. Investigation of the growth and development of P. farinosa through resistant and susceptible quinoa genotypes revealed fewer sporangiophores, hyphal strands, and haustoria among leaf tissues of accession 0654 than in the susceptible Chucapaca cultivar. Peronospora farinosa growth was detected in leaf, petiole, and stem tissues with polymerase chain reaction (PCR) using ITSP primers designed from the internal transcribed spacer (ITS) region of the pathogen. Scanning electron microscopy (SEM) also revealed that P. farinosa penetrated stomata via appressoria, secreted extracellular matrices during sporangia germination, grew intercellularly in leaf and petiole tissues, and exited leaf tissue through stomata. Future research requiring knowledge of resistant quinoa genotypes, P. farinosa growth and development, or inoculation methods for large numbers of small quinoa plants would benefit from this report.

The aim of this study is the three-dimensional structural characterization of the genome packaging inside viral capsids via cryo-electron microscopy and three-dimensional reconstruction. The genome of some single-stranded viruses can be densely packaged within their capsid shells. Several stretches of the genome are known to adopt stable secondary structures, however, to date, little is known about the three-dimensional organization of the genome inside their capsid shells. Two techniques have been developed to facilitate the structural elucidation of genome packaging: the asymmetric random-model method, and the symmetry-mismatch, random model method. Both techniques were successfully tested with model and experimental data. The new algorithms were applied to study the genome structure of poliovirus and satellite tobacco mosaic virus. We have not yet found a consistent structure for the two genomes. Nevertheless, we have found that the genome of satellite tobacco mosaic genome is very stable, supporting a model where the RNA acts as a scaffold, with potential implications in capsid stability and assembly.

Vanadium dioxide (VO_2) is a material of particular interest due to its exhibited metal to insulator phase transition at 68°C that is accompanied by an abrupt and significant change in its electronic and optical properties. Since this material can exhibit a reversible drop in resistivity of up to five orders of magnitude and a reversible drop in infrared optical transmission of up to 80%, this material holds promise in several technological applications. Solid phase crystallization of VO_2 thin films was obtained by a post-deposition annealing process of a VO_{x,x approx 2} amorphous film sputtered on an amorphous silicon dioxide (SiO_2) layer. Scanning electron microscopy (SEM) and electron-backscattered diffraction (EBSD) were utilized to study the morphology of the solid phase crystallization that resulted from this post-deposition annealing process. The annealing parameters ranged in temperature from 300°C up to 1000°C and in time from 5 minutes up to 12 hours. Depending on the annealing parameters, EBSD showed that this process yielded polycrystalline vanadium dioxide thin films, semi-continuous thin films, and films of isolated single-crystal particles. In addition to these films on SiO_2, other VO_2 thin films were deposited onto a-, c-, and r-cuts of sapphire and on TiO_2(001) heated single-crystal substrates by pulsed-laser deposition (PLD). The temperature of the substrates was kept at ~500°C during deposition. EBSD maps and orientation imaging microscopy were used to study the epitaxy and orientation of the VO_2 grains deposited on the single crystal substrates, as well as on the amorphous SiO_2 layer. The EBSD/OIM results showed that: 1) For all the sapphire substrates analyzed, there is a predominant family of crystallographic relationships wherein the rutile VO_2{001} planes tend to lie parallel to the sapphire's {10-10} and the rutile VO_2{100} planes lie parallel to the sapphire's {1-210} and {0001}. Furthermore, while this family of relationships accounts for the majority of the VO_2 grains observed, due to the sapphire substrate's geometry there were variations within these rules that changed the orientation of VO_2 grains with respect to the substrate's normal direction. 2) For the TiO_2, a substrate with a lower lattice mismatch, we observe the expected relationship where the rutile VO_2 [100], [110], and [001] crystal directions lie parallel to the TiO_2 substrate's [100], [110], and [001] crystal directions respectively. 3) For the amorphous SiO_2 layer, all VO_2 crystals that were measurable (those that grew to the thickness of the deposited film) had a preferred orientation with the the rutile VO_2[001] crystal direction tending to lie parallel to the plane of the specimen. The use of transmission electron microscopy (TEM) is presented as a tool for further characterization studies of this material and its applications. In this work TEM diffraction patterns taken from cross-sections of particles of the a- and r-cut sapphire substrates not only solidified the predominant family mentioned, but also helped lift the ambiguity present in the rutile VO_2{100} axes. Finally, a focused-ion beam technique for preparation of cross-sectional TEM samples of metallic thin films deposited on polymer substrates is demonstrated.