Melt convection and solid phase movement play an important role in solidification processes, which significantly influence the formation of grain structures and solute segregations. In general, the melt convection and grain movement are a result of buoyancy forces. The densities within melt are different due to the variation of temperature and concentration, leading to thermally and solutally driven melt convection. Similarly, the density differences between the grains and the bulk melt cause the grain movement, leading to solid sedimentation or grain floating, as the case may be. Free, unattached solid grains are produced by partial remelting and fragmentation of dendrites, by mechanical disturbances such as stirring or vibration and by heterogeneous nucleation of grains in solidification of grain-refined alloys. In this way, movement of solid crystals during solidification can be ascertained in the following two cases. In the first case, during columnar solidification of non-grain-refined alloys, solid movement is possible in the form of dendrite fragments detached from the columnar stalks by the process of remelting and fragmentation. Movement of grains during columnar solidification gives rise to altogether different microstructure from columnar to equiaxed. In the second case, during equiaxed solidification of grain-refined alloys, the movement of solid crystals is possible in the form of equiaxed dendrite crystals nucleated due to presence of grain refiners. The rate and manner by which the free solids settle (or float) will influence macrosegregation in metal castings. Control of the solidification process is possible through an understanding of the solid movement and its effect on macrosegregation and microstructure. With this viewpoint, the overall objective of the present thesis is to study, experimentally and numerically, the phenomenon of solid phase movement during solidification. Through this study, deeper insights of the role of solid phase movement in solidification are developed which can be used for possible control of quality in castings. Both columnar and equiaxed solidification are considered. Models for transport phenomena associated with columnar solidification with solid phase movement are rarely found in the literature, because of inherent difficulty associated with consideration of microscopic features such as remelting and fragmentation. To tackle this problem, solidification modules for remelting and fragmentation are developed first, followed by integration of these molecules in a macroscopic solidification model. A Rayleigh number based fragmentation criterion is developed for detachment of dendrite fragments from the developing mushy zone, which determines the conditions favorable for fragmentation of dendrites. The criterion developed is a function of net concentration difference, liquid fraction, permeability, growth rate of mushy layer, and thermophysical properties of the material. The effect of various solidification parameters on fragmentation is highlighted. The integrated continuum model developed is applied to stimulate the solidification of aqua-ammonia system in a side-cooled rectangular cavity. The numerical results are in good qualitative agreement with those of experiments reported in literature. A gentle ramp of the mushy zone due to settling of solid crystals, as also noticed in experimental literature, is observed towards the bottom of the cavity. The influence of various modeling parameters on solid phase movement and resulting macrosegregation is investigated through a parametric study. Movement of grains during columnar solidification gives rise to altogether different microstructure and sometimes may initiate a morphological transition of the microstructure from columnar to equiaxed if the number and size of equiaxed grains ahead of the columnar front become sufficient to arrest the columnar growth. The generalised model developed, considering solid phase movement during columnar solidification is used to predict columnar-to-equiaxed transition (CET) based on a prescribed cooling rate criterion. It is found that presence of convection significantly affects the solidification behaviour. Moreover, the movement of dendrite fragments and their accumulation at the columnar front further trigger the occurrence of CET. Cooling configuration, too significantly affects the nature of CET. In unidirectional solidification cases, the locations of CET are found to be in a plane parallel to the chill face. However, for the case of the non-unidirectional solidification (as in side-cooled cavity), the locations of CET need not be in a plane parallel to the chill face. In contrast to fixed columnar solidification, equiaxed solidification is poorly understood; in particular, the phenomena associated with solid crystal movement. Movement of unattached solid crystals, formed due to heterogeneous nucleation on grain-refiners, is induced by the convective currents as well as by buoyancy effects, causing the solid to sediment or to float, depending on density of solid compared to that of the bulk melt. While moving in the bulk melt these crystals can also remelt or grow. A series of casting experiments with AI-based alloys are performed to investigate the role and influence of movement of solid crystals on macrosegregation and microstructure evolution during equiaxed solidification. Controlled experiments are designed for studying, separately, settling and floatation of equiaxed crystals for different cooling conditions and configurations. Further, these experiments are carried out in convective and non-convective cases to understand the effect of convection on solid phase movement. Temperature measurements are performed at various locations in the mould during the experiments. After the cavity is solidified, microstructural and chemical analyses of the experimental samples are carried out, several notable features are observed in temperature histories, macrosegregation pattern, and microstructures due to settling/flotation phenomenon of solid crystals. It is found that the flow behavior of solid grains has a profound influence on the progress of solidification (in terms of grain size distribution and fraction eutectic) and macrosegregation distribution. In some cases, the induced flow due to solid phase movement can cause a flow reversal. The observations and quantitative data obtained from experiments, with the help of detailed solidification conditions provided, can be used for future validations of models for equiaxed solidification. Subsequently, numerical studies are carried out, using a modified version of the macroscopic model developed for columnar solidification with motion of solid crystals, to predict the transport phenomena during equiaxed solidification. The model is applied to simulate the solidification processes corresponding to each of the experimental cases performed in this study. For a better understanding of the phenomenon of movement of solid crystals, the following two special cases of solidification are also presented: 1) without movement of solid crystals and 2) movement of solid crystals without any relative velocity between solid and liquid phases. The numerical predictions showing nature of flow field and progress of solidification are substantiated by the experimental data for the thermal analysis, qualitative microstructural Images and quantitative microstructural analysis. It is concluded, with the help of various experiments and simulations, that movement of solid crystals influences the casting quality appreciably, in terms of macrosegregation and microstructures. It is expected that the improved understanding of the role and influence of solid phase movement during solidification processes (both columnar and equiaxed) obtained through this thesis will be useful for possible control of quality of as-cast products.

<p>The successful genomic era has resulted in a great demand for efficient production and purification of proteins. The main objective of the work described in this thesis was to develop methods to facilitate recovery of target proteins after recombinant production in Escherichia coli.</p><p>A positively charged purification tag, Z_basic, has previously been constructed by protein design of a compact three-helix bundle domain, Z. The charged domain was investigated for general use as a fusion partner. All target proteins investigated could be selectively captured by ion-exchange chromatography under conditions excluding adsorption of the majority of Escherichia coli host proteins. A single cation-exchange chromatography step at physiological pH was sufficient to provide Z_basic fusion proteins of high purity close to homogeneity. Moreover, efficient isolation directly from unclarified <i>Escherichia coli</i> homogenates could also be accomplished using an expanded bed mode. Since the intended use of a recombinant protein sometimes requires removal of the purification tag, a strategy for efficient release of the Z_basic moiety using an immobilised protease was developed. The protease columns were reusable without any measurable decrease in activity. Moreover, subsequent removal of the released tag, Z_basic, was effected by adsorption to a second cation-exchanger. </p><p>Using a similar strategy, a purification tag with a negatively charged surface, denoted Z_acid, was constructed and thoroughly characterised. Contrary to Z_basic, the negatively charged Z_acid was highly unstructured in a low conductivity environment. Despite this, all Z_acid fusion proteins investigated could be efficiently purified from whole cell lysates using anion-exchange chromatography</p><p>Synthesis of polypeptides occurs readily in Escherichia coli providing large amounts of protein in cells of this type, albeit often one finds the recombinant proteins sequestered in inclusion bodies. Therefore, a high throughput method for screening of protein expression was developed. Levels of both soluble and precipitated protein could simultaneously be assessed <i>in vivo</i> by the use of a flow cytometer. </p><p>The positively charged domain, Z_basic, was shown also to be selective under denaturing conditions, providing the possibility to purify proteins solubilised from inclusion bodies. Finally, a flexible process for solid-phase refolding was developed, using Z_basic as a reversible linker to the cation-exchanger resin.</p>

Mass spectrometry (MS) is a power analytical tool which is capable of analyzing biomolecules in great detail, both structurally and quantitatively. With regards to glycans, special considerations regarding sample preparation are necessary in order to achieve reproducible identification and relative quantification of these analytes. A workflow for isolation at the glycopeptide level and subsequent detection at the glycan level with phenylhydrazine, demonstrated that monoclonal antibodies (mAbs) containing a specific amino acid mutation were able to express approximately an additional 50% of the α2,6 disialylated glycan compared to their non-mutant analogues. In a second experiment using mAbs, an azide modified glycan (Ac4ManAz) was introduced both metabolically and enzymatically during mAb production. This glycan is a precursor in the sialic acid pathway and the azide moiety allows for specific chemistry post-production including the potential for highly specific enrichment. The results of this workflow demonstrated that [100 μM] of Ac4ManAz precursor added to the cell media was necessary for metabolic expression. More complex samples however, may contain multiple sites of glycosylation. To conserve the site of attachment, these molecules are often studied at the glycopeptide level, and require enrichment of glycopeptides to improve the lower signal intensity observed in the presence of co-eluting peptides. Carboxymethyl chitosan (CMCH) as well as amine-functionalized magnetic-nanoparticles (MNP) were developed as novel materials for this purpose. CMCH is naturally occurring, and therefore is cost-effective and readily available. In a 12 protein mixture CMCH demonstrated the bulk enrichment of glycopeptides yielding an approximately 20% higher enrichment of sialylated species as compared to a commercially available glycopeptide kit through the use of tandem mass tags for relative quantification. In the same approach, amine functionalized MNP were produced and used to enrich glycopeptides from tryptic digests. This approach was fast (about 10 mins) and quantitatively demonstrated improved retention for sialylated species. Examples of these techniques and their applications are reported in this work. / October 2015

The aim of this thesis was the investigation of the mitochondrial response mechanisms upon apoptotic stimuli. The specific objectives were the biophysical characterization of membrane dynamics and the specific roles of lipids in the context of apoptotic regulation occurring at the mitochondrion and its complex membrane systems. The BH4 domain is an anti-apoptotic specific domain of the Bcl-2 protein. Solid phase peptide synthesis was used to produce large amount of the peptide for biophysical studies. A protocol has been established and optimized, guarantying the required purity for biophysical studies. In detail the purification by high performance liquid chromatography and the characterisation via mass spectroscopy are described. The secondary structure of BH4 changes significantly in the presence of lipid vesicles as observed by infrared spectroscopy and circular dichroism. The BH4 peptide aggregates at the membrane surface and inserts slightly into the hydrophobic part of the membrane. Using nuclear magnetic resonance (NMR) and calorimetry techniques, it could even be shown that the BH4 domain modifies the dynamic and organization of the liposomes which mimic a mitochondrial surface. The second study was on the first helix of the pro-apoptotic protein Bax. This sequence called Bax-α1 has the function to address the cytosolic Bax protein to the mitochondrial membrane upon activation. Once again a protocol has been established for the synthesis and purification of this peptide. The aim was to elucidate the key role of cardiolipin, a mitochondria-specific phospholipid, in the interaction of Bax-α1 with the mitochondrial membrane system. The NMR and circular dichroism studies showed that Bax-α1 interacts with the membrane models only if they contain the cardiolipin, producing a strong electrostatic lock effect which is located at the membrane surface. Finally, a new NMR approach was developed which allows the investigation of the lipid response of isolated active mitochondria upon the presence of apoptotic stimuli. The goal was there to directly monitor lipid specific the occurring changes during these physiological activities.

Rheumatoid arthritis (RA) is an autoimmune disease affecting approximately 1% of the population in the western world. It is characterised by a tissue specific attack of cartilage in peripheral joints. Collagen induced arthritis (CIA) is one of the most commonly used animal models for (RA), with similar symptoms and histopathology. CIA is induced by immunisation of mice with type II collagen (CII), and the immunodominant part was previously found to be located between residues 256-270. This thesis describes the interaction between the MHC molecule, glycopeptide antigens from CII and the T cells that is essential in development of CIA. The glycopeptide properties for binding to the mouse MHC molecule Aq have been studied, as well as interaction points in the glycopeptide that are critical for stimulation of a T-cell response. The thesis is based on five studies. In the first paper the minimal glycopeptide core, that is required for binding to the Aq molecule while still giving a full T cell response was determined. The second paper studied the roles of amino acid side-chains and a backbone amide bond as T-cell contact points. In the third paper the hydrogen bond donor-acceptor characteristics of the 4-OH galactose hydroxyl group of the glycopeptide was studied in detail. In the fourth paper we established a structure activity relationship (QSAR model) for (glyco)peptide binding to the Aq molecule. Finally, the stereochemical requirements for glycopeptide binding to the Aq molecule and for T-cell recognition was studied in the fifth paper. The study was performed using collagen glycopeptide analogues, which were synthesised on solid phase. Amide bond and hydroxyl group isosteres were introduced for study of hydrogen bond donor-acceptor characteristics. Statistical methods were used to design a representative peptide test set and in establishing a QSAR model. The results give a deeper understanding of the interactions involved in the ternary MHC-glycopeptide-T cell complex. This information contributes to research directed towards finding new treatments for RA.

This thesis describes bioanalytical methods for measuring melatonin and some anti-infective drugs in biological fluids. Solid-phase extraction (SPE) or protein precipitation was used for enrichment and purification of the analytes and Liquid Chromatography (LC) was used to analyze the samples. Developed methods were validated according to international guidelines. Melatonin is a hormone secreted by the pineal gland with a robust circadian rhythm. Bioanalytical methods for determination of melatonin in plasma and saliva have been developed which were used for monitoring melatonin levels in volunteers and patients suffering from sleep related diseases. Eflornithine (DFMO) is a chiral drug used for the treatment of human African trypanosomiasis. A bioanalytical method for determination of the DFMO enantiomers in plasma, after precolumn derivatization with o-phtalaldehyde and N-acetyl-L-cystein has been developed. The method has been used to study the L- and D-DFMO pharmacokinetics, in order to investigate the possible development of an oral treatment of DFMO. A method for simultaneous determination of three antiretroviral drugs i.e. Lamivudine (3TC), Zidovudine (AZT) and Nevirapine (NVP) in dried blood spots (DBS) was developed. The method was used for drug determination in two subjects after receiving standard antiretroviral treatment. The method seemed well suitable for the determination of 3TC and NVP and in some extent for AZT. Lumefantrine (LF) is one of the active components in a new fixed drug combination recommended by the WHO as a replacement to older drugs that has lost their effect. A method for the determination of LF in DBS was developed. The method is suitable for monitoring of drug treatment in rural settings. Tafenoquine is a new promising antimalarial drug under development. A method for the determination of Tafenoquine in plasma and in DBS is described. The method may be useful in future clinical studies in laboratory environment as well as in rural settings. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 703

Mannheimia haemolytica (M. haemolytica)-induced bovine respiratory disease causes millions of dollars in economic losses to Canadian cattle industry. Contemporary management strategies built around the use of antimicrobials are proving to be increasingly unavailing and lead to drug residues in meat which may contribute to the development of multi drug resistant bacteria. Many M. haemolytica vaccines are effective in stimulating antibody responses but studies of vaccina-tion in young calves and the cattle exposed to M. haemolytica (high-risk cattle) have shown poor vaccine efficacy. Antimicrobial peptides (AMPs) may help in the management of respiratory disease caused by M. haemolytica while minimizing the risk of drug residues in animal-derived food products. AMPs are positively charged molecules that can kill bacteria primarily through the electrostatic interactions with the anionic bacterial lipid bilayer. Since the primary target of AMPs is the bac-terial surface charge, which is evolutionarily conserved, the development of resistance towards AMPs seems less likely. These peptides hold potential to replace or reduce the use of antibiotics. Human β-Defensin 3 (HBD3) and Microcin J25 (MccJ25) are cationic peptides that have shown good activity against many Gram-negative bacteria. Five peptides, namely native HBD3, three synthetic HBD3 analogues (28 amino acid, 20AA, and 10AA), and MccJ25 were selected for microbicidal activity against M. haemolytica. Three C-terminal analogues of HBD3 with all cysteines replaced with valines were manually synthesized using solid phase peptide synthesis (SPPS). In all the three analogue, replacement of cysteine with valine rendered them linear and increased their antibacterial activity. Minimum Bactericidal concentration (MBC) assays were performed with the final inoculum size of 1-5x105 cells/ml, with the exception of the 10AA analogue which was incubated with 104 cells/ml final inoculum size. The antimicrobial assay showed that M. haemolytica was intermediately sensitive to HBD3, 28AA and 20AA analogue with an MBC of 50 µg/ml. MccJ25 had limited effect with an MBC greater than 100 µg/ml. The MBC value of 6.3 µg/ml achieved with the 10AA analogue is likely a result of lower final inoculum size. AMPs have several immunomodulatory functions, and these peptides can act as chemoattractant, induce cytokine release that in turn leads to chemotaxis of monocytes and neutrophils. Since neutrophils play an important role in the pathogenesis of BRD, the chemotactic effect of HBD3, 20AA and 28AA peptides on bovine neutrophils was studied using Boyden chamber. Peripheral blood neutrophils isolated from normal healthy cattle showed chemotaxis towards HBD3 and 20AA peptides (P<0.05) but not towards 28AA analogue. Co-incubation of neutrophils with any of the peptides did not affect their chemotaxis towards N-formyl-L-methionyl-L-leucyl-phenylalanine (fMLP). Based on these data, it can be concluded that HBD3 and its analogues showed antimicrobial ef-fects against M. haemolytica but MccJ25 had limited microbicidal activity against M. haemolytica. While HBD3 and 20AA analogue were chemotactic for bovine peripheral blood neutrophils, none of the peptides inhibited fMLP-induced migration of neutrophils. These peptides hold potential for further in vivo testing to develop them for use to manage M. haemolytica-induced respiratory disease in cattle.

No description available.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

The ochratoxins, metabolites of certain Aspergillus and Penicillium species are the first group of mycotoxins discovered subsequent to the epoch-making discovery of the aflatoxins. Ochratoxin A (OTA) is a very important mycotoxin owing to its frequent occurrence in nature, its established role in Danish porcine nephropathy and in poultry mycotoxicoses and its implicated role in Balkan endemic nephropathy and urinary system tumors among population groups in North Africa. Chapters 2 and 3 highlight the importance of OTA and the research currently being done on mycotoxins. These efforts are focused on the molecular genetics of toxinogenic fungi; the mechanism of their action; species differences in metabolism and pharmacokinetics; quantification of mycotoxins; risk assessments on the exposure of man and animals to mycotoxins and regulations for the control of mycotoxin contamination. Methods developed to analyse OTA in different matrices by using reversed phase high performance-liquid chromatography with fluorescence detection and tandem liquid chromatography-mass spectrometry techniques are described in Chapter 10. Amino propyl solid phase extraction columns were used for the first time in cleanup steps of ochratoxin analysis. These techniques and methods were applied to the first survey on the levels of OTA in coffee on the South African retail market (Chapter 5). The results suggest that the levels of OT A in the coffee on the South African market are somewhat higher than the levels of OTA in coffees on the European market. The possibility to biologically produce different halogen-ochratoxins by supplementing the growth medium of Aspergillus ochraceus with halogen salts was investigated. Bromoochratoxin A was produced for the first time in this way. Supplementation of inoculated wheat with potassium iodide and -fluoride resulted in the poisoning of the yeast and no iodoor fluoro-ochratoxin B was produced. It was found that Aspergillus ochraceus produced OTA in higher yields at elevated levels of potassium chloride. This finding has important commercial applications in the production ofOTA (Chapter 4). The ochratoxins are hydrolyzed in vivo by carboxypeptidase A. The hydrolysis of the ochratoxins and analogues by carboxypeptidase A was measured in vitro in a structurefunction relation study by employing mass spectrometric techniques. The kinetic data of the ochratoxins were compared to the values of a number of synthesized structural analogues. It was found that the halogen containing analogues had lower turnovers than their des-halo analogues. There were no substantial differences in the kinetic data between the different halogen containing analogues (Chapter 8). The toxicokinetics of OTA in vervet monkeys were determined for the first time. The clearance of OTA from the plasma suggested a two-compartment model and the elimination half-life was determined to be 19-21 days. The half-life of OTA in humans was determined by allometric calculations to be 46 days. We came to the conclusion that the long term consumption of OT A contaminated foods will lead to potentially hazardous levels of the toxin in the body (Chapter 9). This hypothesis can be substantiated by the incidence of OTA in the blood of various population groups. Possible ways to decontaminate OT A contaminated foods by degrading the compound biologically with yeast; moulds or lipases to non-toxic compounds were investigated. Eight moulds, 323 yeasts and 23 lipases were screened for ochratoxin degradation. A lipase from Aspergillus niger is the first lipase that was proven to degrade OTA (Chapter 7). Four yeasts were found to degrade OT A of which one, Trichosporon mucoides degraded OTA substantially within 48 hours in a growing culture (Chapter 6). In addition to this first report of yeasts which have the ability to degrade OTA, the fungi Cochliobolus sativus, Penicillium islandicum and Metarhizium anispoliae also proved to degrade OT A. OT A was degraded in all instances to the non-toxic ochratoxin a and the amino acid phenylalanine. / Thesis (PhD (Chemistry))--Potchefstroom University for Christian Higher Education, 2000