<p>Renewable fibers produced by forest trees provide excellentraw material of high economic value for industrialapplications. Despite this, the genes and corresponding enzymesinvolved in wood fiber biosynthesis in trees are poorlycharacterized. This thesis describes a functional genomicsapproach for the identification of carbohydrate-active enzymesinvolved in secondary cell wall (wood) formation in hybridaspen.</p><p>First, a 3' target amplification method was developed toenable microarray-based gene expression analysis on minuteamounts of RNA. The amplification method was evaluated usingboth a smaller microarray containing 192 cDNA clones and alarger microarray containing 2995 cDNA clones that werehybridized with targets isolated from xylem and phloem.Moreover, a gene expression study of phloem differentiation wasperformed to show the usefulness of the amplificationmethod.</p><p>A microarray containing 2995 cDNA clones representing aunigene set of a cambial region EST library was used to studygene expression during wood formation. Transcript populationsfrom thin tissue sections representing different stages ofxylem development were hybridized onto the microarrays. It wasdemonstrated that genes encoding lignin and cellulosebiosynthetic enzymes, as well as a number of genes withoutassigned function, were differentially expressed across thedevelopmental gradient.</p><p>Microarrays were also used to track changes in geneexpression in the developing xylem of transgenic, GA-20 oxidaseoverexpressing hybrid aspens that had increased secondarygrowth. The study revealed that a number of genes encoding cellwall related enzymes were upregulated in the transgenic trees.Moreover, most genes with high transcript changes could beassigned a role in the early events of xylogenesis.</p><p>Ten genes encoding putative cellulose synthases (CesAs) wereidentified in our own<i>Populus</i>ESTdatabase. Full length cDNA sequences wereobtained for five of them. Expression analyses performed withreal-time PCR and microarrays in normal wood undergoingxylogenesis and in tension wood revealed xylem specificexpression of four putative CesA isoenzymes.</p><p>Finally, an approach combining expressionprofiling,bioinformatics as well as EST and full length sequencing wasadopted to identify secondary cell wall related genes encodingcarbohydrate-active enzymes, such as glycosyltransferases andglycoside hydrolases. As expected, glycosyltransferasesinvolved in the carbohydrate biosynthesis dominated thecollection of the secondary cell wall related enzymes that wereidentified.</p><p><b>Key words:</b>Populus, xylogenesis, secondary cell wall,cellulose, hemicellulose, microarrays, transcript profiling,carbohydrate-active enzyme, glycosyltransferase, glycosidehydrolase</p>

<p>Forest biotechnology is a fast emerging field of research. The application of biotechnological tools will enhance the quality of the forest products. The resultant value added and environmentally sustainable products are an absolute necessity in the future. The study of wood biosynthesis and degradation will result in enormous knowledge resources, which can be used for exploiting wood properties. This thesis addresses questions representing both wood degradation and biosynthesis.</p><p>The wood degrading fungus <i>Phanerochaete chrysosporium</i> is expression profiled with the microarray technology. The objective is to understand the expression pattern of the extracellular carbohydrate active enzymes (CAZymes) secreted by the organism. The data obtained increases our understanding of gene expression upon growth on cellulose.</p><p>Wood biosynthesis is studied with the model wood forming tree species, <i>Populus</i>. The plentiful data resources from the expression profiling during wood formation in Populus are used as the platform of this work. One of the wood specific genes, <i>PttMAP20</i>, previously with an unknown function is studied in this thesis. The immunolocalisation of PttMAP20 with specific antibodies is demonstrated. The putative microtubule-targeting domain of the protein is demonstrated microscopically and by using a biochemical binding assay. </p>

<p>Phase-contrast magnetic resonance imaging (PC-MRI) is a powerful tool for measuring blood flow and has a wide range of cardiovascular applications. Simulation of PC-MRI from numerical flow data would be useful for addressing the data quality of PC-MRI measurements and to study and understand different artifacts. It would also make it possible to optimize imaging parameters prior to the PC-MRI measurements and to evaluate different methods for measuring wall shear stress.</p><p>Based on previous studies a PC-MRI simulation tool was developed. An Eulerian-Lagrangian approach was used to solve the problem. Computational fluid dynamics (CFD) data calculated on a fix structured mesh (Eulerian point of view) were used as input. From the CFD data spin particle trajectories were computed. The magnetization of the spin particle is then evaluated as the particle travels along its trajectory (Lagrangian point of view).</p><p>The simulated PC-MRI data were evaluated by comparison with PC-MRI measurements on an in vitro phantom. Results indicate that the PC-MRI simulation tool functions well. However, further development is required to include some of the artifacts. Decreasing the computation time will make more accurate and powerful simulations possible. Several suggestions for improvements are presented in this report.</p>

For any crankcase scavenged two-stroke engine, the fuel dynamics is not easily predicted. This is due to the fact that the fuel has to pass the crankcase volume before it enters the combustion chamber. This thesis is about the development of a model for fuel dynamics in the crankcase of a small crankcase scavenged two-stroke engine that gives realistic dynamic behavior. The crankcase model developed in this thesis has two parts. One part is a model for wall wetting and the other part is a model for concentration of evaporated fuel in the crankcase. Wall wetting is a phenomenon where fuel is accumulated in fuel films on the crankcase walls. The wall wetting model has two parameters that have to be tuned. One is for the fraction of fuel from the carburetor that is not directly evaporated and one parameter is for the evaporation time of the fuel film. The thesis treats tuning of these parameters by running the model with input data from measurements. Since not all input data are possible to measure, models for these inputs are also needed. Hence, development of simple models for air flows, fuel flow, gas mixing in the exhaust and the behavior of the λ-probe used for measurements are also treated in this thesis. The parameter estimation for the crankcase model made in this thesis results in parameters that corresponds to constant fraction of fuel from the carburetor that evaporates directly and a wall wetting evaporation rate that increases with increasing engine speed. The parameter estimation is made with measurements at normal operation and three specific engine speeds. The validity of the model is limited to these speeds and does not apply during engine heat-up. The model is run and compared to validation data at some different operation conditions. The model predicts dynamic behavior well, but has a bias in terms of mean level of the output λ. Since this mean value depends on the relation between input air and fuel flow, this bias is probably an effect of inaccuracy in the simple models developed for these flows. / För alla tvåtaktsmotorer med bränslematning genom vevhuset är bränsledynamiken svårpredikterad. Detta beror på att bränslet måste passera vevhusvolymen innan det når förbränningskammaren. Denna uppsats handlar om utveckling av en modell som ger realistisk dynamik för bränslet i tvåtaktsmotorers vevhus. Vevhusmodellen i denna uppsats har två delar. Den ena delen är en modell för bränslefilm på motorväggar och den andra delen är en modell för koncentration av förångat bränsle i vevhusvolymen. Bränslefilmsmodellen har två parametrar som måste trimmas. Den ena är andelen bränsle från förgasaren som inte förångas direkt och den andra är tidsåtgången för förångning av bränslefilmen. Uppsatsen behandlar trimning av dessa parametrar genom körning av modellen med indata från mätningar. Eftersom inte all indata kan mätas behövs även modeller för dessa. Därför behandlar uppsatsen även utveckling av enkla modeller för luftflöde, bränsleflöde, gasblandning i avgasvolymen och beteende hos den för mätningar använda λ-sonden. Parameterestimeringen för vevhusmodellen som är gjord i denna uppsats resulterar i parametrar som svarar mot konstant andel av bränslet från förgasaren som förångas direkt och en förångningshastighet för bränslefilmen som ökar med ökande motorhastighet. Parameterestimeringen är gjord med mätdata från normal körning vid tre olika motorhastigheter. Giltigheten för modellen är begränsad till dessa hastigheter och kan inte appliceras på körning av motorn vid kallstart. Modellen är körd och jämförd med valideringsdata från olika körfall. Modellen förutser dynamiska beteenden väl, men har ett systematiskt fel gällande medelvärdet på λ. Eftersom detta medelvärde beror på förhållandet mellan luftflöde och bränsleflöde in i vevhuset är sannolikt detta systematiska fel en effekt av osäkerhet i de enkla modeller som utvecklats för dessa flöden.

Tilt-up construction basically involves job-site prefabrication of concrete building members under controlled and relatively economical conditions. This master’s report presents tilt-up design procedures, along with construction procedures and planning at the job-site, erection, finishing and architectural treatments. It is intended to bring together the five steps of design, planning, construction, erection, and finishing which are crucial to a successful tilt-up project. / text

The research described here is part of a multi-university project on “Performance-based Seismic Design Methods and Tools for Reinforced Masonry Shear-Wall Structures.” Within the context of that project, the objective of the research described in this dissertation was to develop and validate a specific displacement-based seismic design methodology for masonry structures. Experimental work consisted of reversed cyclic loading tests of reinforced masonry wall segments with different boundary conditions, aspect ratios, axial loads, and reinforcement detailing. Analytical work consisted of developing analytical models for in-plane concrete masonry shear wall segments; calibrating those models using reversed cyclic test data; and using those models to successfully predict the nonlinear seismic response of two full-scale, multi-story reinforced masonry specimens tested on the shake-table at the University of California at San Diego. Design work consisted of the force-based and displacement based design of those specimens. Based on the results, provisions for displacement-based seismic design are proposed for inclusion in United States design codes. / text

Previously our laboratory had identified a novel component of the Staphylococcus aureus regulatory network, an extracytoplasmic function ó factor, óS, involved in stress response and disease causation. Here we present additional characterization of óS, demonstrating a role for it in protection against DNA damage, cell wall disruption and interaction with components of the innate immune system. Promoter mapping reveals the existence of four unique sigS start sites, one of which appears to be subject to auto-regulation. Transcriptional profiling revealed that sigS expression remains low in a number of S. aureus wild-types, but is upregulated in the highly mutated strain RN4220. Further analysis demonstrates sigS expression is inducible upon exposure to a variety of chemical stressors that elicit DNA damage, including methyl methanesulfonate (MMS) and ciprofloxacin, as well as those that disrupt cell wall stability, such as ampicillin and oxacillin. Ex vivo transcriptional analysis reveals that significant expression of sigS can be induced upon phagocytosis by RAW 264.7 murine macrophage-like cells. Regulation of óS appears to be unique, as the downstream encoded protein, SACOL1828, seemingly acts as a positive activator, rather than as an expected anti-sigma factor. Using a global transposon screen we have elucidated additional genes implicated in the regulation of sigS, including those involved in cell wall stability, cellular detoxification, virulence and DNA base excision repair. Phenotypically, óS mutants display sensitivity to a broad range of DNA damaging agents, such as ultraviolet light, MMS and ethidium bromide. These effects are seemingly mediated via regulation of the purine biosynthesis pathway, as microarray, proteomic and qRT-PCR analysis of óS mutants reveal decreased transcription of all genes involved. Enzymatic profiling of PurA involved in adenine biosynthesis, demonstrates decreased activity in the óS mutant. Finally, we provide further evidence for the role of óS in S. aureus pathogenesis, revealing that sigS mutants display decreased ability to cause localized infections and are impaired in their interactions with components of the human innate immune system. Collectively, our data argues for the important, and perhaps novel, role of óS in the stress and virulence responses of S. aureus.

AEgIS is an experiment at CERN where the goal is to directly measure the gravitational force on antimatter by producing antihydrogen. The antihydrogen will be produced by a charge exchange reaction using laser excited positronium and cold antiprotons. Having a well-characterized positron plasma with at least 108 positrons and knowing how it can be controlled is essential for the positronium production. This thesis is based on the goals of AEgIS experiment and describes the positron plasma manipulations being used in AEgIS in order to achieve the required plasma properties for the experiment. The positron system is made up by a source, a Surko trap and a Penning-Malmberg trap. This system was first optimized to increase the number of positrons. The plasma was then moved to the main traps of the experiment where it was systematically characterized in terms of lifetime, cooling efficiency and compression. Positron plasma compression in time, trapping and cooling was tested for the first time in AEgIS using a buncher and Penning-Malmberg traps respectively. In this thesis, it is shown that a compression of more than 50 % in time of the positron cloud using a buncher can be achieved. It is also shown that trapping and cooling with an efficiency of nearly 100 % in the main traps using a “V” shaped potential trap was successful. On top of that, the lifetime inside this “V” shaped potential trap was observed to be longer than 30 minutes.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第18977号 / 工博第4019号 / 新制||工||1619 / 31928 / 京都大学大学院工学研究科建築学専攻 / (主査)教授 中島 正愛, 教授 金子 佳生, 教授 吹田 啓一郎 / 学位規則第4条第1項該当

We attack the question of BPS occupancy in a wide class of 4d N = 2 quantum field theories. We first review the Seiberg-Witten approach to finding the low energy Wilsonian effective action actions of such theories. In particular, we analyze the case of Gaiotto theories, which provide a large number of non-trivial examples in a unified framework. We then turn to understanding the massive BPS spectrum of such theories, and in particular their relation to BPS quivers. We present a purely 4d characterization of BPS quivers, and explain how a quiver's representation theory encodes the solution to the BPS occupancy problem. Next, we derive a so called mutation method, based on exploiting quiver dualities, to solve the quiver's representation theory. This method makes previously intractable calculations nearly trivial in many examples. As a particular highlight, we apply our methods to understand strongly coupled chambers in ADE SYM gauge theories with matter. Following this, we turn to the general story of quivers for theories of the Gaiotto class. We present a geometric approach to attaining quivers for the rank 2 theories, leading to a very elegant solution which includes a specification of quiver superpotentials. Finally, we solve these theories by an unrelated method based on gauging flavor symmetries in their various dual weakly coupled Lagrangian descriptions. After seeing that this method agrees in the rank 2 case, we will apply our new approach to the case of rank n. / Physics