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    Characterisation of the filamentous bacteriophages end-caps : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry at Massey University, Manawatu, New Zealand
    (Massey University, 2021) León Quezada, Rayén
    Ff (f1, fd, and M13) filamentous phage of Escherichia coli have collectively been the workhorse of phage display technology over the past few decades. Their use has expanded in the recent years into nanotechnology, where they serve as filament-like templates (≥ 880 nm x 6 nm) for assembly of nanostructures such as nanowires, nanorings, and more complex assemblies including nano-scale batteries, among others. The filament end-caps are the key to improving phage display applications and design of novel Ff-built nanostructures. Furthermore, proteins pIII and pVI, that form the distal end-cap, are of key importance for understanding the Ff biology. They mediate the Ff assembly-release and entry, two opposing processes that involve, respectively, excision and insertion of the virion out of and into the inner membrane of E. coli. The mechanisms of these two processes are a mystery, and the only path towards understanding is to determine the structures of the pIII-pVI complex. While the atomic resolution structure of the Ff filament shaft made of the major coat protein pVIII has been determined, the structure of the phage end-caps remains unresolved, as they constitute only 2% of the virion mass. To enable the end-cap structural analyses we developed methodology for high-efficiency production and purification of short Ff-derived nanorods, where the end-caps are highly enriched, accounting for up to 38% of the total virion mass. Furthermore, methods for Ff-derived nanorod production have been majorly improved in this thesis by engineering a novel system, resulting in at least 200-fold increase relative to the systems described previously. The nanorod purification was also improved by including an anion exchange chromatography step. Highly pure and concentrated 50 nm and 80 nm nanorods were analysed structurally and biochemically to characterise the pIII-pVI complex. Intact nanorods were structurally characterised by cryo-EM single-particle analysis (cryo-EM SPA) that resulted in 2D classes of the filament end-caps. Furthermore, a preliminary 3D model of the pIII-pVI cap was generated at a resolution of 5 Å. Further refinement of the 3D model is under way. Besides the intact particles, analysis was expanded to purified pIII-pVI complex obtained from the DOC-chloroform-disassembled nanorods by size exclusion chromatography. Under native conditions, protein pIII could be detected in a complex larger than 720 kDa, indicating that multiple copies of pVI and pIII form a multimer-dimer that includes a substantial amount of the shaft protein, pVIII. Applications of nanorods benefit from precise control of the nanorod lengths, which is very difficult to achieve when it comes to non-biological materials. In this thesis, Ff-derived nanorods of novel sizes were designed by eliminating specific DNA regions from the nanorod replication cassettes that controls the length of the nanorod ssDNA backbone. This work showed that the DNA segment between the packaging signal and (-) ori is not essential for replication and resulted in production of 40 nm nanorods, shortest ever constructed to date. Two novel lengths, 40 and 70 nm, were added to the of sub-100-nm nanorod collection produced using this system.
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    Edge functionalisation of graphene nanoribbons with a boron dipyrrin complex : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Nanoscience at Massey University, Manawatū, New Zealand
    (Massey University, 2017) Way, Ashley Jacqulyne
    Chemical modification can be used to tune the properties of graphene and graphene nanoribbons, making them promising candidates for carbon-based electronics. The control of edge chemistry provides a route to controlling the properties of graphene nanoribbons, and their self-assembly into larger structures. Mechanically fractured graphene nanoribbons are assumed to contain oxygen functionalities, which enable chemical modification at the nanoribbon edge. The development of graphene nanoribbon edge chemistry is difficult using traditional techniques due to limitations on the characterisation of graphene materials. Through the use of a chromophore with well-defined chemistry, the reactivity of the edges has been investigated. Small aromatic systems were used to understand the reactivity of the boron dipyrrin Cl-BODIPY, and with the aid of spectroscopic and computational methods, the substitution mechanism and properties of the compounds have been investigated. The synthetic procedure was then applied to graphene nanoribbons. Results from infrared and Raman spectroscopy studies show that edge-functionalisation of graphene nanoribbons with BODIPY was successful, and no modifications to the basal plane have been observed.
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    The investigation of the surface properties and conductivity distribution of TiOb4s nanocrystalline film using scanning tunneling microscopy : a thesis submitted in partial fulfilment of the requirements for the degree of Master of Technology at Massey University
    (Massey University, 2002) Widodo, Mohamad
    The use of solid-state materials for efficient conversion of sunlight into electricity has long been a goal of inorganic photochemistry. A molecular approach has been to sensitize wide-bandgap oxide semiconductors to visible light with organic and inorganic compounds exhibiting charge-transfer excited states Atomic force microscopy (AFM) and scanning tunneling microscopy (STM) have been demonstrated in this research as powerful tools for surface studies of nanocrystalline TiO2 films, and has been used to characterize the surface properties of TiO2 film used as semiconducting material in dye-sensitized solar cells. The characterization of both the surface morphology and surface electronic properties of the film have been carried out In addition to the usual qualitative analysis of the sample surface based on the topography images, fractal dimension analysis as a measure of surface roughness and fractality has also been applied during the characterization.
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    At the cutting edge : structural analysis and chemical modification of the edges of mechanically cleaved graphene nanoribbons : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Nanoscience at Massey University, Manawatū, New Zealand
    (Massey University, 2017) Dykstra, Haidee Michaela
    The first decade of the new carbon nanomaterial graphene has been a time of great discovery and excitement as the exceptional properties of this material were uncovered and its promise for numerous applications realised. The unique properties of graphene, including its exceptional electronic structure, are now well-established, and investigations into how these properties can be manipulated and exploited are rapidly taking off. This research contributes to the emerging field by exploring the structure and chemistry of the edges of mechanically cleaved graphene nanoribbons; groundwork for the future development of edge-modified nanoribbons that could be used to form selfassembled graphene nanoribbon composite structures with potential for devices in solar energy conversion. For this purpose, a Raman microscope was built that enabled for various aspects of the structure of graphene nanoribbons to be probed, in particular the geometry and smoothness of the edges, which have important implications for the specific reactivity of the edge carbon atoms. Chemical approaches for the specific functionalisation of the edges of the nanoribbons were developed, involving reactions tailored to the reactive groups present at the edges, and these were found to be highly successful and selective.
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    The effects of cross linking on collagen type 1 nanostructure and nanostructural response to uniaxial tension : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Engineering at Massey University, Manawatu, New Zealand
    (Massey University, 2016) Kayed, Hanan
    Collagen type I, is a fibrillar protein with a complex hierarchical structure, forming the extracellular matrices of an extensive range of organs and tissues. Applications for treated collagen materials vary vastly from commercial uses to the medical field for bioprosthetics and tissue grafts. Glycosaminoglycan (GAG), cross links naturally bridge fibrils, whilst glutaraldehyde is widely used as a synthetic linking agent in medical and other industries. No consensus has been reached regarding what contribution, if any, such cross links have on collagen structure and mechanical responses to applied stresses. This research investigated the role of GAG and glutaraldehyde cross links on the nanostructure and nanostructural response of type I collagen fibrils under uniaxial strain. Bovine pericardium was decellularised, producing native samples, or further treated with glutaraldehyde or chondroitinase ABC to produce glutaraldehyde cross linked or GAG-depleted collagen samples respectively. Synchrotron small angle X-ray scattering (SAXS), and atomic force and polarised light microscopy provided quantitative and qualitative information on collagen nanostructure. Uniaxial tensile experiments in conjunction with SAXS were performed to monitor structural changes with applied strain. Glutaraldehyde cross links constrained fibrils into more networked isotropic structures and demonstrated a mechanical function, recruiting 45% of fibrils into stretching which experienced strains of up to 6.4%. Comparison of native with chondroitinase ABC-treated samples showed GAGs do not constrain fibrils into alignment and have potential fibril lubricating effects; 12% of fibrils in native tissue experienced strains up to 4.1%, and 36% of fibrils experienced strains up to 4.6% in the GAG-depleted tissue. A higher degree of fibril sliding occurs in native tissue. Interestingly, whilst adult pericardia are more cross linked and fibrils of neonatal pericardia are more aligned, both tissues share similar propensities to form more isotropic structures with glutaraldehyde treatment. These findings build a comprehensive picture as to the function cross linking has in collagen structure and mechanical response at the nano-level, where such knowledge may prove useful for the preparation of collagen materials for specific applications.