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“Za Hranetsiu” – “Beyond the Border”: Constructions of Identities in Ukrainian-Canadian Literature
(2010)
Grounded in the literary and cultural studies, the dissertation “Za Hranetsiu” – “Beyond the Border”: Constructions of Identities in Ukrainian-Canadian Literature answers the question how identities of different Ukrainian immigrants and their offspring have been constructed, continuously developed and transformed in contemporary Canadian literature. The study simultaneously presents a discussion of postmodern identities, a concise historical survey of Ukrainian immigration to Canada in the nineteenth and twentieth centuries, and an overall picture of the exceptionally substantial body of Ukrainian-Canadian literature. Detailed literary analyses focus on seven Ukrainian-Canadian works: Sons of the Soil (1939-45/1959) by Illia Kiriak, Yellow Boots (1954) by Vera Lysenko, A Letter to My Son (1981) by George Ryga, The Green Library (1996) by Janice Kulyk Keefer, The Doomed Bridegroom: A Memoir (1998) by Myrna Kostash, Kalyna’s Song (2003) by Lisa Grekul, and The Ladies’ Lending Library (2007) by Janice Kulyk Keefer.
Pyrrolobenzodiazepines (PBDs) are a group of antitumor antibiotics that exert their biological activity by alkylation of guanine bases within the minor groove of double-stranded DNA through nucleophilic attack of the guanine amino group on the PBD imine functionality. In trying to increase both the binding strength and sequence selectivity for further enhancing their biological activity, PBDs were linked to additional DNA binding moieties. Preliminary DNA melting experiments partly also performed in our lab with a series of closely related PBD-naphthalimide and benzimidazole conjugates revealed extraordinary DNA-binding capability of hybrids PBD-NIM and PBD-BIMZ. These studies also indicated the favorable contribution of the piperazine structure on drug binding to the DNA duplex. Previously, in vitro cytotoxicity studies also showed promising antitumor activity of both compounds with PBD-BIMZ having the largest cytotoxic potential among various examined conjugates. In the present work, the kinetics, thermodynamics and structural details of the drug-DNA interactions have been determined employing a variety of spectroscopic, calorimetric and computational methods. Thus, a high thermal duplex stabilization upon DNA binding could be ascertained for both drugs and attributed to their covalent attachment to the DNA guanine bases. The 1:1 binding stoichiometry as well as the exclusive minor groove binding for the benzimidazole and the mixed minor grove - intercalative type of binding for the naphthalimide hybrid could be verified by several spectroscopic methods including NMR spectroscopy. Furthermore, by using a combination of solution NMR and some of the most recent molecular modeling techniques, the first high-resolution structures of DNA-drug complexes with PBD hybrid drugs could be obtained giving detailed insight into the specific drug-DNA interactions. Thus, details on van der Waals and hydrogen bond contacts within the complex and the tight fit of the benzimidazole hybrid into the DNA minor groove could be revealed. By using recent data analysis techniques like clustering algorithms, the high flexibility of the piperazine moiety within the PBD-BIMZ-DNA complex could be nicely captured and visualized. Additionally, a thermodynamic analysis for the non-covalent drug binding by UV and fluorescence spectroscopy as well as by direct calorimetric methods revealed a 1:1 binding mode driven by enthalpy changes and counteracted by unfavorable entropic contributions to result in moderately strong association constants. Analysis of the solvent-accessible surface area confirmed the importance of hydrophobic effects on drug binding and the combination of these data with ITC measurements allowed for an extensive thermodynamic characterization of the drug binding process. With respect to the influence of the individual drug moieties on DNA binding, the importance of the piperazine ring for drug-DNA interactions and the basis for its capability to enhance drug binding were addressed. Furthermore, it could be shown that the naphthalimide and benzimidazole moieties also impart additional sequence selectivity to the alkylating PBD structural unit and these distinct differences in the sequence selectivity could be linked to the three-dimensional structures of the DNA-drug complexes. Clearly, the combination of detailed structural and thermodynamic data of complex formation allows for a better understanding of the binding mechanism and structure-activity relationship when it comes to drug-DNA interactions. Therefore, the information gathered can assist in the design of more efficient derivatives of this type of alkylating DNA binding drugs in particular and of DNA recognition by ligands composed of several motifs in general.
In the present work, a time- and radial-dependent fluid model has been developed to describe the glow-to-arc transition of the positive column in the course of constriction. The self-consistent model comprises the particle balance equations for the relevant species, the balance equation of the mean electron energy and the heavy particle temperature in the plasma, the Poisson equation for the space-charge potential, and a current balance determining the axial electric field. The model adopts the nonlocal moment method, i.e., the system of the balance equations resulting from the moments of the radially dependent Boltzmann equation is solved. The electron transport and rate coefficients are adapted as functions of the mean energy of the electrons, the gas temperature and the ionization degree. The model is applied to a description of the constriction of the dc positive column in argon, for a wide range of pressures and applied currents. Pronounced nonlocal features of the mean electron energy balance are found and their influence on the constricted argon positive column is analyzed. Different assumptions concerning the electron velocity distribution function (EVDF) have been considered in the present model. The assumption of a Maxwellian distribution for the electrons was found to be inappropriate, while the assumption of a Druyvesteyn distribution for the electrons was found to be suitable for describing qualitatively the glow-to-arc transition. However, the standard model using the EVDF obtained from the solution of the steady-state, spatially homogeneous electron Boltzmann equation including electron-electron collisions allows to describe the constriction effect and provides best agreement with experimental data and other available modelling results. The fluid model has also been used to study a medium-pressure pulsed positive column in xenon at conditions of the contracted discharge. The simulation results provide a detailed insight in the physical mechanisms of xenon discharges in pulsed mode. The stepwise ionization of the excited atoms, the conversion of the atomic ions into molecular ions as well as the dissociative recombination of the molecular ions are found to be the most important processes for the pulsed positive column in xenon plasmas at conditions of the contracted discharge. The comparison of the model predictions with experimental results generally shows good agreement. In particular, the model predictions are suitable for qualitative reproduction of the significant increase of low-lying atomic levels densities as well as of the higher and of the relaxed lowest vibrational states of the Xe2* excimers in the afterglow phase of the pulse.
This dissertation evaluates the effects of site conditions and livestock grazing on the vegetation of Azerbaijan’s winter pastures. We improved methods to estimate grazing intensity in vast rangelands and enhanced an approach to detect discontinuities in vegetation changes along environmental gradients. All analyses use field data from the semi-arid rangelands of Gobustan and Jeiranchel, at the foothills of the Greater Caucasus mountains. The data set comprises 313 vegetation relevés, each sized 100 m², based on a pre-stratification using topographical parameters. Additionally, we included data from farm transects and exclosure experiments. For each plot, selected site and soil variables were determined. VEGETATION AND SITE CONDITIONS: By means of cluster analysis, we derived 16 vegetation types with a total of 272 vascular plant species. Our vegetation classification, which is closely linked to site conditions, is an important groundwork for adapted rangeland management and monitoring. The study areas are dominated by semi-deserts with a high coverage of dwarf shrubs, and the mean number of vascular plant species was found to be about 28 per 100 m². According to ordination analysis (NMDS), species composition changes primarily along the altitudinal gradient, gradually proceeding from the Salsola nodulosa semi-deserts of the lowest parts (below 300 m a.s.l.) to the Salsola ericoides and Artemisia lerchiana semi-deserts of the upper regions (300–650 m a.s.l.). Soil salinity and carbonate concentration decrease as altitude increases. A second gradient reflects grazing intensity. One plant community that is typically found on intensively grazed sites in the vicinity of farmyards stands apart from the rest, which are subject to lower grazing and trampling pressures. A third factor that differentiates plant communities is the sand concentration of the soils. Additionally, communities that occur on steep slopes differ from communities that occur on level terrain. EXCLOSURE EXPERIMENTS: Exclosure experiments revealed that short-time abandonment of grazing leads to an increase in the number of annual species, in vegetation coverage, and in the heights of forbs and grasses. Clipping experiments indicated that the herbaceous species show hardly any compensatory growth in response to grazing. ESTIMATING GRAZING INTENSITY: A recurrent theoretical problem in rangeland research is the spatial modelling of grazing intensity around grazing hotspots like farms or watering places, the so called piospheres. In a widely used approach, grazing intensity is assumed to decrease in direct proportion to the distance from a hotspot. The resulting response patterns, which relate characteristics of the vegetation or site conditions to grazing intensity, are often nonlinear, and have been interpreted as indicating threshold changes or diff erent state-and-transitions along grazing gradients. However, we show that these ‘thresholds’ are usually geometrical artefacts. Taking into account the concentric structure of grazing hotspots, we suggest a new approach that approximates grazing intensity as the ratio of the total number of livestock kept at the farm to the distance between a given plot and the hotspot centre. Our approach is a simple yet significant improvement over current approaches because it enables us to merge or compare data from different sampling sites and because the approximation is in direct proportion to other grazing indicators like dung density or soil salinity. SPECIES TURNOVER PATTERNS: Combining our new grazing pressure model with species presence/absence data, we modelled vascular plant species responses, patterns of species richness and species turnover along grazing gradients on farm transects in Gobustan. The derived typical species response pattern along the finite grazing gradient is a sigmoid decrease. Species richness declines monotonically with increasing grazing intensity and thus conforms to generally acknowledged assumptions on the relationship between species richness and grazing pressure in semi-arid rangelands. Species turnover along the gradient was calculated using the slopes of species response curves. At first sight, the resulting pattern gives evidence for a discontinuous change. However, it ranges within the 95 % confidence interval of a null model based on assumptions of the individualistic continuum concept. Thus, species composition seems to change continuously along grazing gradients in Gobustan. This new null model approach can probably be adapted and applied to all ecological gradients and is useful for the validation of individualcontinuum or community concepts.
Macrophages are cells of immune system and distributed throughout the body. They provide the first line of defense against microbial pathogen infections. Using bone marrow macrophages (BMMs) which derived from mice of strain BALB/c and strain C57BL/6, this study aimed to identify the changes in proteome of the macrophages due to IFN gamma stimulation and S. aureus infection. Two quantitative proteomic techniques, two-dimensional difference gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were applied in this study. The analysis results indicated that many proteins which play important roles in immunological functions of macrophages were changed due to IFN gamma stimulation and S. aureus infection. This study also identified the differences in proteome of macrophages derived from mice of strain BALB/c in comparing to macrophages of strain C57BL/6.
The aim of this thesis was to validate a method called OSCARR for One-pot, Simple Cassette Randomization and Recombination for focused directed evolution, which had been developed by Dr. Hidalgo. It is based upon the megaprimer PCR method using outer primers differing in TM and including asymmetric cycles before the addition of the forward primer to generate more mutated megaprimer. As mutation-carrying primers, spiked oligonucleotides are employed. These spiked oligonucleotides are designed using an algorithm and have strictly defined composition of nucleotides at each position. An OSCARR library of the Pseudomonas fluorescens esterase I (PFE I) of approximately 8000 clones was generated and screened for altered chain-length selectivity. Two mutants with higher activity towards medium chain length p-nitrophenyl esters were identified, both carried the mutation F126I, which causes the substrate entrance tunnel to be widened, thus facilitating access of bulkier substrates to the active site. One mutant carried the additional mutation G120S which completes a catalytic tetrad which is observed mainly in proteases. F126I had a stronger influence on chain-length specificity, so the further amino acids which form the “bottleneck” to the active site were mutated to further widen the entrance, and mutants with improved activity were found. The bottleneck mutants which consist of single, double, triple and quadruple mutants which are mostly combinations of F126L, F144L, F159L and I225L were then assayed for altered enantioselectivity against chiral acids and secondary alcohols. For substrates 1-phenyl-1-propyl acetate (2), 1-phenyl-2-propyl acetate (3) and 1-phenyl ethyl acetate (4), mutants with increased enantioselectivity were found. I225L plays a crucial role, as it is vital for enantioselectivity against 3, but destroys selectivity against 2, both facts obvious from the comparison of the triple mutant without I225L (mutant T3) and the corresponding quadruple mutant including I225L (mutant Q). However, the single mutant I225L alone does not possess high selectivity against 3, so synergistic effects play an important role. The PFE I wild type already possesses a good enantioselectivity in the hydrolysis of 4, but all mutants which were analyzed in detail surpass the wild type. The program YASARA was then used to calculate docking solutions for both enantiomers of 2 and 3 into the wild type and the best mutant. The results revealed that the mutants’ widened bottleneck allows the phenyl moiety of the substrates to point towards the access tunnel, while only (R)-2 does so in the wild type. Residues 126 and 144 do not come very close to the substrate and are more likely to influence substrate diffusion. Another goal was to find a way to confer promiscuous amidase activity upon the PFE I. In the search for structural homologues, a close structural neighbour with amidase activity was found. The --lactamase from Aureobacterium sp. was named after its activity toward the Vince lactam 2-azabicyclo[2.2.1]hept-5-en-3-one. Biocatalysis experiments with the PFE I and its mutants revealed an excellent enantioselectivity against the ( )-lactam. Specific activities were determined for purified proteins, and the activity of some mutants was within the same order of magnitude as lactamase’s activity.
To uncover the genetic structure of Populus euphratica forests along the Tarim River in Xinjiang, China, a PCR set of eight microsatellite markers was established. 18 primer pairs originally developed for P. tremuloides and P. trichocarpa were screened for amplification in P. euphratica. The eight most variable loci were selected for further genotyping experiments. Subsequently, two multiplex PCR assays, each containing four loci, were set up and optimized. Three populations containing altogether 436 trees were used to characterize the selected loci. The set was found to be moderately polymorphic (mean expected heterozygosity = 0.57). The resolution was sufficient to discriminate even siblings with high confidence (PID = 1.81x10-5). Cumulative exclusion probabilities were 0.89 (single parent), 0.98 (paternity), and 1.00 (parent pair) and proved the set’s suitability for parentage analysis. Practical and theoretical analysis of consequences of genotyping errors in this semi-clonal plant showed that the vast majority of errors (62.1%) lead to division of identical genotypes. Merging of different genotypes was found to be a very rare case (0.4%). This always leads to an overestimation of genotypes. A similarity threshold of one allele difference between two genotypes to be regarded as being identical lead to an underestimation of clonal richness and genotype number of one per cent compared to an overestimation of more than 20 per cent without such a threshold. Allowing a certain amount of variation is therefore expected to reflect the clonal structure better than an analysis that considers exact matches only. Using a combination of morphological and molecular analyses, a first study demonstrated that root suckers are clearly distinguished from seedlings in their root architecture. Root suckering starts when trees are 10–15 years old and bridges distances of up to 40 m at a time. Root suckers depend on their parent tree for at least five years and are expected to have a higher mortality than generatively grown trees. Molecular analysis of old growth stands revealed a highly variable proportion of clonal growth between different stands. In the study area, the proportion of clonality decreases with distance to the main river bed (R = 0.31 at the site closest to the main river, R = 0.97 at the site farthest away from the river). An analysis of the history of river movements at different sites indicates a dependency of clonal growth on the frequency of ground water replenishment by the yearly floods. Genetic differentiation among the stands in the study area is low (FST = 0.055), and isolation by distance was not detectable (P = 0.058). Also, the river does not function as a vector for directed gene flow in downstream direction (P > 0.11). The forests are therefore considered to be one large panmictic metapopulation with unrestricted gene flow. Clonal growth does not lead to higher final stand densities (P = 0.99) and is obviously not of crucial importance for stand survival. Furthermore, analysis of vitality measures and size differences indicate that root suckers are in disadvantage both in vitality and in survival rate compared to seedlings. In this light, a possible function of clonal growth as a luxury strategy to enhance a genetic individual’s reproduction success under good site conditions can be discussed. The genetic structure of the (meta)population bears direct implications for management and conversation of the Tugai forest in Xinjiang. Due to the low degree of differentiation and the unhindered gene flow even small, fragmented, or isolated populations have conservational value, thereby clearly answering the SLOSS question (a single large or several small protected areas) in the latter sense. More than that, non-clonal stands with the highest amount of genotypic diversity can be easily identified on satellite and aerial images. Selection of such stands for conservation is therefore possible without expensive and time-consuming molecular analyses.
This work proposes and experimentally evaluates a new method and the first prototypic design of an apparatus for the objective assessment of peripheral dynamic stereovision. Peripheral dynamic stereovision is understood as the ability to perceive, recognize and observe moving objects in the visual periphery without sacrificing foveal fixation, i.e. shifting the line of sight (e.g. moving the eyes or the head) and loosing attention to the scene of interest. The presence of stereopsis on top further enhances the perceptive quality by adding the third dimension with judgment of depth and estimation of relative spatial positions as central clues for orientation, coordinative interaction and navigation in space. Based on findings that moving stereoscopic contours can induce distinctive optokinetic reactions, a panoramic stimulus pattern was rotated round subjects’ heads. Designed after the Frisby Stereotest, solely the binocular parallax resulting from the plate thickness carries stereoscopic information, excluding all other depth clues. A specially fitted goggle frame assured correct binocular alignment of the subjects adding objectivity. In first experiments, voluntary reactions (pushing a buzzer button) and involuntarily triggered ocular responses have been registered. The Performance Level (PL) and Confidence Ratio (CR) were introduced as benchmarks for voluntary reactions. Despite larger spreads, the PL averaged at 60 % while an elevated CR confirmed a low error rate of 16 % and thus high overall credibility. Poor performance of available recording hard- and software, in many cases, rendered the analysis of involuntary ocular reactions less exhaustive. It was however observable that objects that appear in the periphery of the visual field triggered the onset of nystagmoid search and tracking mechanisms. Finally, mean peripheral locations of subjects’ active reactions have been established at 30 degrees. The outcome of this pilot study in principle confirmed basic feasibility, conceptual validity and practical applicability of this novel method. Prospective fields of application with raised demands on peripheral dynamic stereopsis have been identified and critically assessed. The applicative possibilities and exclusive advantages of this test combining the assessment of stereopsis and dynamic visual field testing have not been matched by solutions published so far. Before however commercialization should be aimed at, design-related issues, including the implementation of electrophysiological ocular measurements, need to be addressed first to lead the post-prototype development to higher diagnostic expressiveness and reliability.
Parsimonious Histograms
(2010)
The dissertation is concerned with the construction of data driven histograms. Histograms are the most elementary density estimators at all. However, they require the specification of the number and width of the bins. This thesis provides two new construction methods delivering adaptive histograms where the required parameters are determined automatically. Both methods follow the principle of parsimony, i.e. the histograms are solutions of predetermined optimization problems. In both cases, but under different aspects, the number of bins is minimized. The dissertation presents the algorithms that solve the optimization problems and illustrates them by a number of numerical experiments. Important properties of the estimators are shown. Finally, the new developed methods are compared with standard methods by an extensive simulation study. By means of synthetic samples of different size and distribution the histograms are evaluated by special performance criteria. As one main result, the proposed methods yield histograms with considerably fewer bins and with an excellent ability of peak detection.