Advances in micro/nano-fabrication, thin electron transparent materials, holder designs, and acquisition methods have made it possible to perform meaningful experiments using liquid electron microscopy (liquid EM). Liquid EM provides researchers with micro-to-nano scale tools to explore biomaterials in liquid environments capable of capturing dynamic in situ reactions, providing characterization means in mimetic conditions to the human body. However, these emerging techniques remain in their infancy; limited work presents best practice strategies, and several challenges remain for their effective implementation, particularly for beam-sensitive, soft biological materials. This thesis seeks to address these shortcomings by exploring strategies for liquid EM of biomaterials and real-time dynamic processes using two key methods: room temperature ionic liquid (RTIL) treatment for scanning EM (SEM) and liquid cell transmission EM (TEM). With these techniques, the research explores the characterization of hard-tissue systems relevant to bone and seeks to provide new methods of exploring structurally biological culprits behind diseases like COVID-19. Research in this thesis is presented by increasing complexity, touching on three themes: (i) exploring liquid EM for the first time using RTILs for SEM of biological samples notably bone (static, micro-scale), (ii) developing new methods for high-resolution liquid biological TEM of viruses (static, nano-scale), and (iii) applying novel liquid TEM to dynamic biomineralization systems (dynamic, nano-scale). After review articles serve as introductory material in Chapter 2, in Chapter 3, healthy and pathological bone was explored in hydrated conditions with liquid SEM using a new workflow involving RTIL treatment, demonstrated to be highly efficient for biological SEM. Moving to the nanoscale, Chapter 4 presents a commercial liquid TEM option and a new liquid TEM clipped enclosure developed for imaging biological specimens, specifically virus assemblies such as Rotavirus and SARS-CoV-2. Combined with automated acquisition tools and low-dose direct electron detection, enclosures resolved high-resolution structural features in the range of ~3.5 Å – 10 Å and were correlatively used for cryo TEM. Chapter 5 applies these liquid TEM methods to study collagen mineralization, revealing in high-resolution the presence of precursor calcium phosphate mineral phases, important transitional phases to mineral platelets found in mineralized tissues. But – dynamic reactions were not captured, attributed to confinement effects, lack of heating functionality, and cumulative beam damage experienced. Chapter 6 overcomes these challenges by optimizing collagen-liquid encapsulation within a commercial liquid TEM holder mimicking physiological conditions at 37°C. Dynamic nanoscale interactions were highlighted, where evidence of the coexistence of amorphous precursor phases involving polymer-induced liquid as well as particle attachment was presented within this model. Several liquid TEM challenges remain particularly beam sensitivity and distribution for biomaterials, providing many exciting avenues in future to explore. Taken together, this thesis is advancing characterization through the development and applied use of new liquid EM strategies for studying biomaterials and dynamic reactions. Insights on these reactions and structures anticipate leading to a better understanding of diseases and treatment pathways, the key to moving Canada’s health care system forward. / Thesis / Doctor of Philosophy (PhD) / In the electron microscopy (EM) community, there is a need for improved methodologies for high-resolution liquid imaging of biological materials and dynamic processes. Imaging biological structures and reactions in hydrated biomimetic environments improves our understanding of their true nature, thus providing better insight into how they behave in the human body. While liquid EM methods have surged in publications recently, the field is still in its infancy; limited works present best practice strategies, and several challenges remain for their effective implementation. To address these shortcomings, this thesis aims to strategically explore the improvement of liquid EM of biomaterials and real-time dynamic processes through two key methods: room temperature ionic liquid treatment for scanning EM and liquid cell transmission EM. Using these novel techniques, the research explores the characterization of hard-tissue systems relevant to bone and seeks to provide new means of exploring structurally biological culprits behind diseases like COVID-19.

Immunolocalization of proteins within the cell is a significant and powerful tool that improves understanding of cellular functions and processes, such as molecule secretion during immune responses. Immunogold electron microscopy (IEM) is an immunohistochemistry technique that uses gold-conjugated antibodies and electron microscopy (EM) to identify and localize antigens at the ultrastructural level. Here, we are trying to develop and optimize an IEM staining protocol that targets glomerular proteins of interest in Minimal Change Disease (MCD), and eliminates background staining, and preserves tissue morphology. Using this optimized protocol, we hope to learn more about the relationship between IgG and Nephrin in MCD. Kidney biopsies diagnosed with MCD, Membranous Nephropathy (MN), and Thin Basement Membrane Disease (TBMD) and previously embedded in paraffin blocks were retrieved from the tissue archive of the Renal Pathology Laboratory at Boston Medical Center. MN and TBMD were selected as positive controls for IgG and Nephrin staining protocols, respectively. Co-staining of IgG and Nephrin was performed after the protocols for each target were optimized. During protocol development, it was observed that section quality is significantly affected by the angle and sharpness of the knife, and the thickness of the section. Moreover, section quality highly impacted gold particle localization. Ultimately, co-staining of IgG and Nephrin was successful in MCD cases. However, further improvements are needed to optimize IgG and Nephrin staining, and in turn, our understanding of MCD.

The objective of the current study was to determine the efficacy of 3% acetic acid in reducing Salmonella in pork trimming and the effects of such treatment on meat quality. For 15-s dipping and 5-log CFU/pork cube inoculation, only 0.2- to 0.3-log reduction was observed (P ≤ 0.026). Acetic acid worked best at 75 s and 50°C, providing 1.4-log reduction (P < 0.001), damaging Salmonella cell membranes. When an inoculated pork cube was placed at the geometrical center of 2.3-kg pork trimming, dipping at 50°C for 75 s only reduced Salmonella by 0.2 log (P = 0.040). Although dipping slightly increased lightness (P < 0.001) and decreased redness (P ≤ 0.008) on the meat surface, no inside color change was detected (P = 0.120). Neither lipid oxidation (TBARS, P = 0.644), protein solubility (P = 0.187), nor water-holding capacity (P = 0.076) were affected by treatments.

Following the discovery of graphene, 2D nanostructures have been noted for their potential in a range of high-impact applications, such as sensing, catalysis, and composite reinforcement. Liquid-phase exfoliation and chemical vapour deposition have been demonstrated and indicate the feasibility of mass-scale production. With the advent of mass-produced 2D nanostructures a key focus of research is to characterise these materials. This thesis is concerned with imaging and structural properties of the 2D nanomaterials, hexagonal boron nitride (h-BN), molybdenum disulfide (MoS₂), tungsten disulfide (WS₂), titanium disulfide (TiS₂) and hexabenzocoronene (HBC), produced via liquid phase exfoliation. HBC strictly speaking is not 2D nanomaterial, however, it can be viewed as transition molecule from benzene to graphene. The data used for characterisation is based primarily on electron diffraction and, in particular, aberration corrected annular dark field (ADF) scanning transmission electron microscopy (STEM). The incoherent nature of ADF STEM provides direct atomic imaging without the contrast reversals upon focus changes seen in conventional high-resolution transmission electron microscopy (HRTEM). The main structural feature investigated in this thesis was the stacking sequences in few-layers h-BN, MoS₂, WS₂ and TiS₂. Simple stacking (AAA) can be distinguished from Bernal (ABA) and rhombohedral (ABC) on the basis of intensity ratio, I_{10̅10}/I_{11̅20} , in diffraction patterns and indirectly in HRTEM images. Nonetheless acquisition of the diffraction patterns suitable for analysis can be challenging due to the sample issues. Non-bulk stacking sequences were reliably confirmed for all above 2D nanomaterials on the basis of atomically resolved ADF STEM. 20 h-BN, 28 MoS₂, 5 WS₂ and 6 TiS₂ nanoflakes were imaged and analysed. Amongst them 2 h-BN, 9 MoS2, 4 WS2 and 1 TiS2 nanoflakes displayed non-bulk stacking. Hence, it appears that 2D WS2 has the greatest affinity for non-bulk stacking. Finally, an interesting structural transformation was observed in HBC molecules. Under the influence of electron beam HBC agglomerates were transformed into crystalline phase with 90^o symmetry.

published_or_final_version / Dentistry / Doctoral / Doctor of Philosophy

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No description available.

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Inorganic and metal-organic framework materials possessing accessible and permanent pores are receiving tremendous attention. Among them, zeolites are the most famous class due to their wide applications on petrochemistry and gas separation. Besides zeolites, the other oxide framework materials are also intensively investigated because of their diverse structures and compositions. Metal-organic frameworks are built from metal clusters and organic linkers. By rational designing the reagent, the network with desired topology and functionality can be synthesized. For all of the framework materials mentioned above, to explore novel framework structures is important for improving properties and discovering new applications. This thesis includes the synthesis of zeolites and structure characterization for various types of inorganic framework materials. The zeolite synthesis conditions was exploited. With the optimized condition, the zeolite ITQ-33 was synthesized as single crystals. From the single crystal X-ray diffraction data, the disorder in the structure is discovered and explained. Following the topic of disorder and twinning, we proposed a novel method of solving structure of pseudo-merohedric twinning crystal by using an example of a metal-organic complex crystal. Then we also showed methods for solving structures of high complexity and nano-crystal by using mainly powder X-ray diffraction and transmission electron microscopy. Four examples were shown in chapter 4 including open-framework germanates and metal-organic frameworks. / <p>At the time of the doctoral defence the following paper was unpublished and a status as follows: Paper  4: Manuscript</p>

A series of investigations were conducted in order to evaluate the effect of MOS supplementation in finfish aquaculture. Fish with great potential in aquaculture industry were tested with regards to effect of dietary MOS supplementation on intestinal histology and microbiology as well as overall animal health and production. Two levels of MOS supplementation were applied 0.2% and 0.4%. Experimental fish were Atlantic salmon (Salmon salar), rainbow trout (Oncorhynchys mykiss), sole (Solea senegalensis) and gilthead sea bream (Sparus aurata). The results from the sea bream studies revealed that MOS supplementation may have a beneficial effect on growth performance of fish greater than 100 g. Additionally, there is a systemic improvement of the intestinal histology for all species investigated, especially when using 0.4% of MOS supplementation level. Both light and electron microscopy revealed increased intestinal surface and improved intestinal integrity of MOS fed fish. MOS alters the intestinal microbiota, in the case of gilthead sea bream modulation was evident even when fish were fed 0.2% dietary MOS for as little as 2 weeks. Blood immune parameters were also affected by the MOS inclusion and total leukocytes counts were increased and leukocytes relative abundance was also changed. MOS induced intestinal microbial modulation was more evident in fish are reared in outdoor conditions. Feed utilization and digestibility were improved with the addition of 0.4% MOS supplementation in the Atlantic salmon. The sole experiment revealed that MOS could reduce fish mortalities induced by pasteurelliosis. These investigations, suggest a potential role for application of MOS in aquaculture. Future research should be conducted in order to evaluate other parameters that MOS may influence and ascertain optimum dosage for each fish species and developmental stage.