Microviruses (canonical members: øX174, G4, and alpha3) are T=1 icosahedral virions with a two scaffolding protein-mediated assembly pathway. The external scaffolding protein D mainly mediates the assembly of coat protein pentamers into procapsids. The results of previous genetic studies suggest that helix 1 of D protein may act as a substrate specificity domain, mediating the initial coat-scaffolding protein recognition in a species-specific manner. In an effort to elucidate a more mechanistic model, chimeric external scaffolding proteins were initially constructed in a plasmid, which over-expresses the protein, between the closely related phages G4 and øX174. The results of biochemical and genetic analyses identify coat-scaffolding domains needed to initiate procapsid formation and provide more evidence, albeit indirect, that the pores are the site of DNA entry during the packaging reaction.However, protein concentrations higher than those found in typical infections could drive reactions that may not occur under physiological conditions. In order to elucidate a more detailed mechanistic model, the same chimeric external scaffolding gene was placed directly in the øX174 genome, and the chimeric virus was characterized. The results of the genetic and biochemical analyses indicate that helix 1 most likely mediates the nucleation reaction for the formation of the first assembly intermediate containing the external scaffolding protein. Mutants that can more efficiently use the chimeric scaffolding protein were isolated. These second-site mutations appear to act on a kinetic level, shortening the lag phase before virion production.Finally, by using improved protocols, two novel early assembly intermediates, the 9S* and 12S* particles, have been isolated and characterized. The 9S* particle consists of a coat protein pentamer associated with the internal scaffolding protein. The 12S* intermediate is a complex of a 9S* particle with the major spike protein, and the DNA pilot protein. The existence of internal scaffolding and DNA pilot proteins that were absent in previously characterized intermediates suggest that 9S* and 12S* particles are biologically active intermediates. Moreover, preliminary in vitro assembly experiments performed with the 12S* particle and exogenous external scaffolding protein yield empty capsids-like particle, strongly suggesting that these are the physiologically relevant intermediates.

A number of compounds were synthesized with the ultimate goal being the synthesis of C₂ symmetric molecules which displayed thermotropic liquid crystalline behaviour. The compounds prepared were 4-alkoxy benzophenones, 3,4-bis-alkoxy benzophenones, 4- alkoxy dibenzylidene acetones, 3,4-bis-alkoxy dibenzylidene acetones and 4-alkoxy- 1, 9-diphenyl-nona-l,3,6,8-tetraen-5-ones. The length of the linear alkoxy side chain was varied from C₆H₁₃ to C₁₂H₂₅. All compounds were characterized by FTIR, ¹H, and ¹³C NMR spectroscopy. Mesophase behaviour of the synthesized compounds was investigated using differential scanning calorimetry and polarizing optical microscopy. It was determined that both the alkoxy side chain length, as well as the number of alkoxy side chains have an effect on the ability of this class of C₂ symmetric compounds to selfassemble into liquid crystalline phases. In addition, the overall core size and extent of conjugation also affected mesophase formation. The mono-alkoxy benzophenones and dibenzylidene acetones were non-mesogenic, while all four of the mono-alkoxy 1,9- diphenyl-nona-l,3,6,8-tetraen-5-ones (alkoxy side chain of lengths C₆H₁₃, C₈H₁₇, C₁₀H₂₁ and C₁₂H₂₅)self-assembled into nematic liquid crystalline phases. Increasing the number of alkoxy side chains from one to two per aromatic moiety helped induce liquid crystalline formation: the corresponding bis-C₆H₁₃ benzophenone and bis-C ₆H₁₃, bis C₈H₁₇, and bis-C₁₀H₂₁ dibenzylidene acetones were mesogenic, displaying smectic A (benzophenone) and nematic (dibenzylidene acetone) mesophases respectively.

I aimed to expand our understanding of community assembly and species co-existence by examining the implications of phylogenetic robustness on metrics describing phylogenetic community structure, as well as the phylogenetic patterns of co-occurring insect species in Churchill, MB. Using a variety of tree reconstruction methods, I found that cytochrome c oxidase subunit I (COI) was able to accurately estimate phylogenetic community structure metrics calculated from a multi-gene phylogeny when using more biologically realistic approaches. This included incorporating known phylogenetic relationships among families, and methods that employ best-fit models of molecular evolution (i.e. Bayesian inference). My second study examined the phylogenetic community patterns of freshwater insects. Overall communities were phylogenetically clustered suggesting environmental filtering, but community structure varied with time, habitat, taxonomic group, and water chemistry (particularly pH and turbidity). My thesis has suggested more robust techniques for calculating phylogenetic community structure, and described patterns of phylogenetic community composition in subarctic freshwater insects. / Natural Sciences and Engineering Research Council of Canada (NSERC), International Barcode of Life (iBOL), Genome Canada, Ontario Genomics Institute, Canadian Foundation for Innovation, Ontario Ministry of Research and Innovation, Churchill Northern Studies Centre, and Aboriginal Affairs and Northern Development Canada.

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This thesis deals primarily with supramolecular chemistry based on cucurbit[n]uril (CB[n], n = 7 and 8) host molecules. The research has been focused on the synthesis and characterization of host-guest complexes CB[n] with aromatic guest molecules, and the study of the effects of the host-guest complexation on the chemical reactivity and spectroscopic properties of the included guests, such as their photoreactivity and their UV-visible absorption and emission properties, in aqueous solution. The [4+4] photodimerization of protonated 2-aminopyridine (APH+) occurs stereoselectively to give the anti-trans product as the result of a preferred orientation of two APH+ guests in the cavity of CB[7]. The CB[7] host inhibits photohydration in the course of the photoisomerizations of protonated trans-1,2-bis(4-pyridyl)ethylene and trans-1,2-bis(1-methyl-4-pyridinium)ethylene by including the (4-pyridyl)ethylene portion of the guest, while this is not observed with trans-1,2-bis(1-hexyl-4-pyridinium)ethylene, as preferential inclusion of the hexyl groups leaves the vinyl group vulnerable to photohydration. Very strong CB[7] complexation of (E)-1-ferrocenyl-2-(1-methyl-4-pyridinium)ethylene completely inhibits the (E)→(Z) photoisomerization process. The H/D exchange rates and acidities of the C(2)-proton of cationic imidazolium and thiazolium (including thiamine and thiamine phosphates) carbon acids are decreased upon their complexation with CB[7]. Inclusion of protonated aromatic amines (and aromatic alcohols) in the cavity CB[7] significantly decreases their ground and excited state acidities, such that the emission is switched from the neutral amine to the protonated amine excited state, resulting in changes in the color of fluorescence. The fluorescence of acridizinium cations can be switched off by the formation of 2:1 complexes with CB[8] and then switched back on again by the addition of CB[7] or a competing guest molecule. The stabilization of the deep blue color of the 4,4’-bis(dimethylamino)diphenyl carbonium ion, upon complexation of the corresponding carbinol with CB[7], results from a complexation-induced shift in the carbinol/carbonium ion equilibrium. A dramatic purple to blue color change in pinacyanol chloride upon addition of CB[7] is due to a partial breakup of dye aggregates, upon the interactions of the dye with the host molecule. The CB[n] complexation-induced emission and/or absorption color switch have the potential to be employed in molecular switches and in chemical sensing. / Thesis (Ph.D, Chemistry) -- Queen's University, 2007-08-07 09:21:06.553

In this thesis, three specific research contributions to the use of non-uniform electric field driven colloidal assembly are described. The first relates to experimental work using dielectrophoretic and electrohydrodynamic forces (electroosmosis) to shape three-dimensional colloidal structures. Formation and stabilization of close-packed three-dimensional structures from colloidal silica was demonstrated, using gelation of pluronic F-127 to preserve medium structure against suspension evaporation. Stabilization of ordered structures was shown to be a significant challenge, with many of the conventional techniques for immobilizing colloidal crystals being ineffective. Secondly, the significance of electrohydrodynamic flows resulting from electric and particle concentration (entropic) gradients during the assembly process was demonstrated using numerical simulations based on a thermodynamic framework. These simulations, as well as experimental validation of assembly and the presence of fluid flows, showed that assuming equilibrium behavior (stationary fluid flow), a common assumption for most modelling work to date in these systems, is inappropriate at all but the most dilute concentration cases. Finally, the relevance of multiparticle effects on electric-field induced phase transitions of dielectric colloids was demonstrated. The effect of multiparticle/multiscattering effects on the suspension permittivity were accounted for using semi-empirical continuum permittivity formulations which have been previously shown to describe a wide variety of solid packing structures, including face-centered cubic and other colloidal crystal structures. It was shown that multiparticle effects have a significant impact on both the coexistence (slow phase separation) and spinodal (fast phase separation) behavior of dielectric suspensions, which has not been demonstrated to date using a continuum framework. / Thesis (Ph.D, Chemical Engineering) -- Queen's University, 2012-01-30 14:17:23.747

Production downtime caused by machine faults presents a major area of concern for the manufacturing industry and can especially impact the productivity of assembly systems. Traditional fault detection systems use a variety of conventional sensors that measure operating variables such as pressure, force, speed, current and temperature. Faults are detected when a reading from one of these sensors exceeds a preset threshold or does not match the predicted value provided by a mathematical model of the system. The primary disadvantage of these methods is that the relationship between sensor reading and fault is often indirect (if one exists at all). This can lead to time delays between fault occurrence and ‘fault reading’ from a sensor, during which additional machine damage could accumulate. This thesis describes progress with a project whose goal is to examine the effectiveness and feasibility of using machine vision to detect ‘visually cued’ machine faults in automated assembly equipment. It is proposed that machine vision technology could complement traditional methods and improve existing detection systems. Two different vision-based fault detection methods were developed and tests were conducted using a laboratory-scale assembly machine that assembles a simple 3-part component Typical faults that occurred with this machine were targeted for inspection. The first method was developed using Automated Visual Inspection (AVI) techniques that have been used extensively for quality inspection of manufactured products. The LabVIEW 2010 software was used to develop the system. Test results showed that the Colour Inspection tool performed the best with 0% false negative and false positive fault detection rates. Despite some success, this approach was found to be limited as it was unable to detect faults that varied in physical appearance or those that had not been identified prior to testing. The second method was developed using a video event detection method (spatiotemporal volumes) that has previously been used for traffic and pedestrian monitoring. This system was developed with MATLAB software and demonstrated strong false negative and false positive fault detection rates. It also showed the ability to detect faults that had not previously been identified as well as those that varied in appearance. Recommendations were made for future work to further explore these methods. / Thesis (Master, Mechanical and Materials Engineering) -- Queen's University, 2012-07-13 16:04:57.829

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