Digitized by Kansas Correctional Industries

Call number: LD2668 .T4 1956 D45 / Master of Science

This essay focuses on developing non-destructive methods to investigate the relationship between elemental distribution and bone porosity in archaeological bone. The skeletal material, which was analyzed, came from the archaeological sites of Skara (county of Västergötland), Varnhem (county of Västergötland), Sigtuna (county of Uppland) and Kopparsvik (county of Gotland). The essay is based on the results of a previous project, Osteoporosis och osteoarthritis, då och nu (Sten 2012). That project aimed at establishing whether medieval people, buried on the above mentioned archaeological sites, were suffersing from osteoporosis and/or osteoarthritis. This knowledge might help the medical research of today to solve the problem of possibly preventing those bone diseases. The method used was DXA-scanning, which was developed for examine osteoporosis in bone from living people. The result showed that the skeletons from the Skara site had an increased bone mineral density (BMD) compared to the skeletons from the other three sites. This essay investigates why these skeletal remains have a higher BMD and how this affects the results of methods like DXA. In this bachelor project various X-ray instruments were used to analyze the BMD of the skeletal remains. The X-ray pictures were then modified to exhibit high and low density areas in the bone. The elemental distribution of the surface area of the neck of the femur was examined with a μXRF-spectrometer. As a complement to the μXRF-spectrometer a SEM (scanning electron microscope) was used to analyze the elemental distribution of a cross section of the femur neck. Soil samples were collected from Skara and Varnhem and analyzed by using μXRF-spectrometry to find out if there was a correlation between the elemental content of the bone and surrounding soil. The skeletal remains from Skara exhibited increased values of iron and manganese combined with higher bone density. The soil from Skara showed a high level of particularly iron. This could be the reason for the increased BMD of the individuals from Skara when using the DXA-analysis. It is likely that, in each archaeological site, iron and manganese ions have diffused from both ground water and soil into the bones and thus increased the BMD. This is especially notified of the skeletal remains of Skara.

Developing a greater understanding of multiferroic materials, particularly those in which a strong coupling is exhibited between magnetic and electrical orderings, is of great importance if potential applications are to be realised. This thesis reports new experimental findings on several multiferroics using the techniques of X-ray and neutron diffraction together with nonlinear optical experiments. Spherical neutron polarimetry measurements on RbFe(MoO<sub<4</sub>)₂ show how this system's chiral magnetic structure can be controlled by an external electric field. Consideration is given to the axial distortion that the crystal structure makes, and the effect that this has on the stabilised magnetic structures. A ferroaxial coupling is invoked to explain, from a symmetry point of view, the spin driven multiferroicity in this proper screw system. The charge ordering in YbFe₂O₄ is examined by a detailed imaging of reciprocal space measured by elastic X-ray diffraction. Continuous helices of scattering are observed above the three-dimensional ordering transition temperature, whereas the intensity is concentrated onto separated maxima below this. The low temperature data are modelled using a simple oxygen displacement pattern, generalised to an incommensurate structure. The observed incommensurability implies that YbFe₂O₄ cannot be truly ferroelectric. The low field magnetic structures of a Y-type hexaferrite Ba_0.5Sr_1.5Zn₂Fe₁₂O₂₂ are observed in a resonant soft X-ray diffraction study. In zero field the system is helimagnetic, and with small applied fields peaks corresponding to a new phase appear. Energy calculations are used to suggest a suitable magnetic structure for the new phase and to show how this relates to the known commensurate phases that are present in low fields. Finally, an experimental setup designed to measure second harmonic generation from non-centrosymmetric crystals is presented, along with static measurements on the multiferroic system MnWO₄. An optical pump / second harmonic probe study is then undertaken, with the result that a pump induced enhancement in the efficiency of the second harmonic generation is observed.

This thesis studies the prolyl-hydroxylase family of 2-oxoglutarate dependent oxygenases from structural, functional and evolutionary perspectives. The role of prolyl-hydroxylation was first identified in collagen, wherein hydroxyproline was found to stabilise the collagen triple helix. In the 1960s, the presence of hydroxyproline in collagen was found to be a result of enzyme catalysed protein modification. An enzyme, now known as collagen prolyl-4-hydroxylase (CP4H), was found to be completely dependent on Fe(II), 2-oxoglutarate (2OG) and molecular oxygen for catalysis, and was the inaugural member of enzyme family known as the Fe(II) and 2OG-dependent oxygenases (2OG oxygenases), the members of which have since expanded dramatically – more than 60 2OG oxygenases are predicted to exist in humans alone. It was not until the 21st century that hydroxyproline was found to play roles in human biology beyond its well-characterised role in collagen stabilisation. In animals, cells adapt to low oxygen conditions (hypoxia) via the upregulation of hundreds of target genes as governed by the hypoxia-inducible transcription factor (HIF). The mammalian hypoxic sensing system was discovered to be regulated by a conserved family of hypoxia-inducible factor prolyl-hydroxylases (PHDs or EGLNs), which catalyse the prolyl-4-hydroxylation of a conserved proline residue in HIF-α under normoxic conditions, so targeting HIF-α for proteasomal degradation via the von Hippel-Lindau (pVHL) E3 ubiquitin ligase pathway. As a result, the PHDs are current therapeutic targets for the treatment of anemia and ischemia-related diseases. Thus, hydroxyproline also plays a critical role in mammalian oxygen sensing. However, the discovery also raised the question of the evolutionary origin of these enzymes and what roles, if any, they may play in other organisms. This thesis begins by describing the identification and biochemical characterisation of the first homologue of the human PHDs in prokaryotes, specifically, in Pseudomonas species, which contains pathogens such as P. aeruginosa. Pseudomonas PHD (PPHD) was discovered to catalyse the prolyl-hydroxylation of a conserved region of elongation factor Tu (EF-Tu), a translational GTPase universally conserved in prokaryotes and known for its critical role in bacterial translation. A crystal structure of PPHD, the first of a prokaryotic prolyl-hydroxylase, was then determined, revealing a striking structural homology of PPHD to the human PHDs. The further determination of crystal structures of Pseudomonas EF-Tu and a PPHD:EF-Tu protein-protein complex, the first of any 2OG oxygenase in complex with its full-length protein substrate, provides important insights into the substrate recognition mechanisms of both the CP4Hs and the PHDs and reveals an evolutionarily conserved pathway of substrate recognition that extends to prokaryotes and will be useful in the design of selective inhibitors of the PHDs. Differences were investigated between the PHDs and a recently discovered subfamily of eukaryotic prolyl-3-hydroxylases, which catalyse the hydroxylation of a conserved proline residue in the small ribosomal subunit S23 (RPS23) and have been implicated in translation accuracy and the stress response. Crystal structures of the RPS23 hydroxylases human OGFOD1 and yeast Tpa1 in complex with 2OG-mimetic inhibitors provide insight into their evolutionary origins. Analyses of the structures will be useful for targeting either OGFOD1 or the PHDs for human therapy. The thesis then describes work on human CP4H, a 240 kDa α2β2 heterotetramer. A novel expression and purification protocol is described for the CP4H complex in addition to the first known reports of its crystallisation and diffraction. Further, the foundations of a high-throughput inhibition assay of the human CP4Hs is presented and will be of immediate interest for assaying inhibitors of the human PHDs in clinical trials, some of which are also predicted to inhibit the CP4Hs. In closing, the thesis attempts to synthesise the results presented in order to provide further insight into the question of the ancestral origins of the prolyl-hydroxylases, a family of enzymes whose range of functions and biological roles likely will continue to expand.

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Physics / Master / Master of Philosophy

Liquid crystalline materials forming columnar mesophases are of importance for both the fundamental research and technological applications due to their supramolecular architecture allowing for one-dimensional charge transport. The potential applications of these materials include light emitting diodes, solar cells, field effect transistors and photovoltaic cells. However, to design a LC material suitable for a particular application, a fundamental understanding of the structure-property relationships is needed. In the present thesis, a variety of systems forming columnar mesophases have been explored. They include small molecular weight compounds (triphenylene, phthalocyanine derivatives and star-shaped mesogens) and polymer materials. The research was focused on the study of the influence of the molecular architecture and specific interactions such as hydrogen bonding on the supramolecular organization in the mesophase, as well as on the influence of columnar mesophase on crystal growth. The main results of the thesis are summarized below. The influence of hydrogen bonding on the structure and charge carrier mobility was investigated for a triphenylene derivative, hexaazatriphenylene, having lateral alkyl chains linked to the core via amide groups. These linking groups provide the possibility to form inter- and intra-molecular hydrogen bonds. Acting as “clamps”, the inter-molecular hydrogen bonds are found to enforce the attractive interactions between the molecules in the column. Thus, the columnar mesophase formed by this system is characterized by the smallest inter-disk distance ever found in columnar mesophases (3.18 Å). The improved intra-columnar order brings about a higher charge carrier mobility (0.02 cm2/Vs) as compared to other triphenylene derivatives without hydrogen bonds. Phthalocyanine derivatives, which are liquid crystalline at ambient temperature, could be suitable for opto-electronic applications due to their improved processibility and self-healing of structural defects. Our interest in these systems was inspired by the fact that, in spite of numerous studies performed to date, only very a few phthalocyanine derivatives were found to exhibit columnar mesophases at ambient temperature. We observed that by introducing branches in alkyl chains close to the core, we were able to render the material LC at ambient temperature. Analysis of X-ray diffraction patterns measured on oriented samples showed that these systems form hexagonal and rectangular ordered columnar mesophases. This finding is in contradiction with the general view stating that non-hexagonal mesophases can be only disordered. Since the absolute majority of applications require fabrication of films, it was very important to achieve the visualization of the organization of the phthalocyanine derivatives at the nanometer scale. AFM images on thick spin-coated films with columnar resolution are presented for the first time. They allowed the examination of columnar curvatures and breaks at the boundaries between different single crystal-like domains. The possibility of templating columnar crystal growth was studied for a star-shaped mesogen using a combination of direct- and reciprocal-space techniques. AFM images with columnar resolution showed that the crystal growth initiated in the monotropic columnar mesophase occurs almost in register with the mesomorphic template. In the final crystalline structure, the placement of the crystalline columns is controlled by the mesomorphic tracks at the scale of an individual column, i.e. at the scale of approximately 3.5 nm. The mesophase-assisted crystallization was also studied for the case of a polymer material forming columnar mesophase, poly(di-n-propylsiloxane). X-ray diffraction on oriented fibers allowed us to correct the previous indexation and solve the structure of the unit cell. The crystallization process was studied on samples crystallized in different conditions. It was found that, depending on crystallization conditions, both folded-chain and extended-chain crystals can be obtained. Thus, crystallization of the material from the mesophase results in the formation of 100-150nm thick crystals, which corresponds to a nearly extended-chain conformation. By contrast, when crystallized from a dilute solution, folded-chain crystals result. The mechanisms of chain unfolding was studied by variable temperature atomic force microscopy on PDPS single crystals. It was found that crystals rapidly thicken above the initial melting point, up to 80 nm.

No description available.

No description available.