The soil-borne filamentous fungus Trichoderma virens is a biocontrol agent with a well known ability to produce antibiotics, parasitize pathogenic fungi and induce systemic resistance in plants. Here we report the identification, purification and characterization of an elicitor secreted by T. virens; a small protein designated Sm1 (small protein 1). Confrontation and disk assays demonstrated that Sm1 lacks toxic activity against plants and microbes. Native, purified Sm1 triggers production of reactive oxygen species in rice (Oryza sativa) and cotton (Gossypium hirsutum), and induces the expression of defense related genes both locally and systemically in cotton. Gene expression analysis revealed that SM1 is expressed throughout fungal development and is transcriptionally regulated by nutrient conditions and the presence of a host plant. When T. virens was co-cultured with cotton in an axenic hydroponic system, SM1 expression and secretion of the protein was significantly higher than when the fungus was grown alone. These results indicate that Sm1 is involved in plant-Trichoderma recognition and the induction of resistance by activation of plant defense mechanisms. Following the cloning of SM1, strains disrupted in or over-expressing SM1 were generated. Targeted gene disruption revealed that SM1 was not involved in fungal development. Expression of defense related genes in cotton and maize (Zea mays) was induced locally and systemically following colonization by T. virens in the hydroponic system. Low levels of expression of cotton or maize defense genes were found when seedlings were grown with a T. virens strain disrupted in SM1, ssupporting the Sm1-elicitor hypothesis. Additionally, unique proteins in T.virens-cotton/maize interaction were identified. Thus, the induction of defense responses in two agriculturally important crops appears to be microbially mediated. Functional analysis of a cell wall degrading enzyme, beta-1,6-glucananse (Tv-bgn3) from T. virens, demonstrated involvement of this enzyme indirectly in mycoparasitic activity of T. virens. Protein extracts from the strain disrupted in TV-BGN3 displayed reduced capability to inhibit growth of Pythium ultimum as compared to the wild-type. Additionally, protein extracts from the strains co-expressed with TV-BGN2 (beta-1,3-glucananse) from T. virens showed a significantly increased capability to inhibit growth of P. ultimum and Rhizoctonia solani hyphae.

Cellulose is the most abundant biopolymer on earth and the main load-bearing structure in plant cell walls. Cellulose microfibrils are laid down in a tight parallel array, surrounding plant cells like a corset. Orientation of microfibrils determines the direction of growth by directing turgor pressure to points of expansion (Somerville et al., 2004). Hence, cellulose deficient mutants usually show cell and organ swelling due to disturbed anisotropic cell expansion (reviewed in Endler and Persson, 2011). How do cellulose microfibrils gain their parallel orientation? First experiments in the 1960s suggested, that cortical microtubules aid the cellulose synthases on their way around the cell (Green, 1962; Ledbetter and Porter, 1963). This was proofed in 2006 through life cell imaging (Paredez et al., 2006). However, how this guidance was facilitated, remained unknown. Through a combinatory approach, including forward and reverse genetics together with advanced co-expression analysis, we identified pom2 as a cellulose deficient mutant. Map- based cloning revealed that the gene locus of POM2 corresponded to CELLULOSE SYNTHASE INTERACTING 1 (CSI1). Intriguingly, we previously found the CSI1 protein to interact with the putative cytosolic part of the primary cellulose synthases in a yeast-two-hybrid screen (Gu et al., 2010). Exhaustive cell biological analysis of the POM2/CSI1 protein allowed to determine its cellular function. Using spinning disc confocal microscopy, we could show that in the absence of POM2/CSI1, cellulose synthase complexes lose their microtubule-dependent trajectories in the plasma membrane. The loss of POM2/CSI1, however does not influence microtubule- dependent delivery of cellulose synthases (Bringmann et al., 2012). Consequently, POM2/CSI1 acts as a bridging protein between active cellulose synthases and cortical microtubules. This thesis summarizes three publications of the author, regarding the identification of proteins that connect cellulose synthases to the cytoskeleton. This involves the development of bioinformatics tools allowing candidate gene prediction through co-expression studies (Mutwil et al., 2009), identification of candidate genes through interaction studies (Gu et al., 2010), and determination of the cellular function of the candidate gene (Bringmann et al., 2012). / Zellulose ist das abundanteste Biopolymer der Erde und verleiht pflanzlichen Zellwänden ihre enorme Tragkraft. Mit der Reißfestigkeit von Stahl umwickeln Zellulosefibrillen pflanzliche Zellwände wie ein Korsett. Die Orientierung der Zellulosefibrillen bestimmt zugleich die Wachstumsrichtung, indem sie den Zellinnendruck (Turgor) in die entsprechende Ausdehnungsrichtung dirigiert (Somerville et al.,2004).Folglich zeigen Mutanten mit gestörter Zellulosesynthese oft geschwollene Organe und Zellen, die sich nicht mehr gerichtet ausdehnen können (zusammengefasst von Endler und Persson,2011). Wie aber erhalten die Zellulosefibrillen ihre parallele Orientierung? Erste Experimente aus den1960ern führten zur Vermutung, kortikale Mikrotubuli leiten die Zellulosesynthasen auf ringförmigen Bahnen um die Zellen herum (Green, 1962; Ledbetter and Porter, 1963). Diese Theorie wurde 2006 mit Hilfe moderner mikroskopischer Methoden bestätigt (Paredez et al., 2006). Wie jedoch dieser Leitmechanismus funktioniert, blieb bisher unentdeckt. Durch die Kombination verschiedener genetischer und bioinformatischer Methoden, konnten wir pom2 als Zellulose defiziente Mutante identifizieren. Die Ermittlung des Genlocus durch Map-based cloning zeigte, dass es sich bei POM2 um CELLULOSE SYNTHASE INTERACTING 1 (CSI1) handelt, ein Gen, dessen korrespondierendes Protein, wie vorher von uns gezeigt, mit dem zytosolischen Teil der primären Zellulosesynthasen interagiert (Gu et al., 2010). Durch ausführliche zellbiologische Charakterisierung von POM2/CSI1 konnten wir seine zelluläre Funktion entschlüsseln. Mit Hilfe konfokaler Spinning- Disc-Mikroskopie konnten wir zeigen, dass in Abwesenheit von POM2/CSI1, Zellulosesynthasen von den Mikrotubuli- Bahnen abweichen. Der ebenfalls von den Mikrotubuli abhängige Transport der Zellulosesynthasen zur Zellmembran hingegen, war nicht beeinflusst (Bringmann et al., 2012). Demzufolge ist POM2/CSI1 das gesuchte Bindeglied zwischen aktiven Zellulosesynthasen und Mikrotubuli. In dieser Dissertationsschrift werden drei Publikationen des Autors zusammengefasst, die wa ̈hrend der Arbeit an der Dissertiation entstanden sind. Sie beinhalten die Entwicklung bioinformatischer Methoden zur Ko- Expressionsanalyse, um Kandidatengene zu ermitteln (Mutwil et al., 2009), die Identifikaton des Kandidatengens POM2/CSI1 in einer Interaktionsstudie (Gu et al., 2010), sowie die Bestimmung der zellula ̈ren Funktion des korrespondieren- den Proteins POM2/CSI1 (Bringmann et al., 2012).

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. 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. 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. 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. Ten genes encoding putative cellulose synthases (CesAs) wereidentified in our ownPopulusESTdatabase. 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. 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. Key words:Populus, xylogenesis, secondary cell wall,cellulose, hemicellulose, microarrays, transcript profiling,carbohydrate-active enzyme, glycosyltransferase, glycosidehydrolase

This thesis deals with fibre orientation in wall-bounded shear flows. The primary application in mind is papermaking. The study is mainly experimental,but is complemented with theoretical considerations.The main part of the thesis concerns the orientation of slowly settlingfibres in a wall-bounded viscous shear flow. This is a flow case not dealt withpreviously even at small Reynolds numbers. Experiments were conducted usingdilute suspensions with fibres having aspect ratios of rp ≈ 7 and 30. It is foundthat the wall effect on the orientation is small for distances from the wall wherethe fibre centre is located farther than half a fibre length from the wall. Farfrom the wall most fibres were oriented close to the flow direction. Closer tothe wall than half a fibre length the orientation distribution first shifted to bemore isotropic and in the very proximity of the wall the fibres were orientedclose to perpendicular to the flow direction, nearly aligned with the vorticityaxis. This was most evident for the shorter fibres with rp ≈ 7.Due to the density difference between the fibres and the fluid there is anincreased concentration near the wall. Still, a physical mechanism is requiredin order for a fibre initially oriented close to the flow direction at about half afibre length from the wall to change its orientation to aligned with the vorticityaxis once it has settled down to the wall. A slender body approach is usedin order to estimate the effect of wall reflection and repeated wall contacts onthe fibre rotation. It is found that the both a wall reflection, due to settlingtowards the wall, and contact between the fibre end and the wall are expectedto rotate the fibre closer to the vorticity axis. A qualitative agreement withthe experimental results is found in a numerical study based on the theoreticalestimation.In addition an experimental study on fibre orientation in the boundarylayers of a headbox is reported. The orientation distribution in planes parallelto the wall is studied. The distribution is found to be more anisotropic closerto the wall, i.e. the fibres tend to be oriented closer to the flow direction nearthe wall. This trend is observed sufficiently far upstream in the headbox.Farther downstream no significant change in the orientation distribution couldbe detected for different distances from the wall. / QC 20100706

Cellulose is a biopolymer of great relevance in the plant cell walls, where it constitutes the most important skeletal component. Cellulose is also an important raw material in the pulp- and paper, forest, and textile industries, among others. Cellulose biosynthesis in particular, and xylogenesis in general are processes which are currently poorly understood. Yet, research in cellulose synthesis is progressing and different applications of cellulose, mainly cellulose derivatives for e.g. pharmaceuticals and coatings, are constantly emerging. This thesis depicts how cellulose synthase (CesA) genes in Populus were identified and characterized by gene expression- and bioinformatics analyses. Within an EST database of more than 100,000 clones from wood forming tissues of three different Populus taxa, ten CesA genes were identified in Populus tremula x tremuloides. Subsequent gene expression analyses by using microarrays and real-time PCR experiments in woody tissues, revealed distinct regulation patterns among the genes of interest. This enabled proper classification and characterization of the secondary cell wall related CesA genes, in particular. Bioinformatic analyses of the genome sequence of Populus trichocarpa further provided a complete picture of the number of putative CesA genes retained after several duplication events during tree evolution. In contrast to the previously reported set of ten 'true' CesA genes in many other plant species, the genome of P. trichocarpa encodes 18 putative proteins, which could be assembled into nine groups according to their sequence similarities. Interestingly, studies in the EST database suggested that paralogs within at least two groups have corresponding orthologs in P. tremula x tremuloides, which are furthermore transcribed. This implies that at least some of the duplicated genes have remained functional, or may have acquired a modified function. By focusing on the CesA genes associated with secondary cell wall formation, cellulose synthesis was also studied in poplar cell suspension cultures. Selection of CesA enriched material was performed by determining expression intensities of the CesA genes using RT-PCR, whereupon membrane protein extraction was initiated. CesA proteins are part of large cellulose synthesizing complexes in the plasma membrane. Subsequent proteomic approaches comprised partial purification of these cellulose synthesizing complexes from protein enriched culture material and in vitro cellulose synthesis experiments. De novo synthesized material was successfully characterized and the acquired yields were as high as 50% cellulose (compared to previously reported yields of 30% in other plant systems) of the total in vitro synthesized product. Elevated CesA gene expression levels can thus be correlated to increased protein activity in poplar cell suspension cultures. In addition, antibodies raised against CesA antigens were used in Western blot analyses comprising samples along the protein extraction- and purification procedure. Proteins with corresponding molecular weight to the theoretical 120kDa of CesA proteins were recognized by a range of different specific antibodies. The study demonstrates that poplar cell suspension cultures can provide a valuable model system for studies of cellulose synthesis and different aspects of xylogenesis. / QC 20101005

Knowledge of the ultrastructural arrangement within wood fibres is important for understanding the mechanical properties of the fibres themselves, as well as for understanding and controlling the ultrastructural changes that occur during pulp processing. The object of this work was to explore the use of atomic force microscopy (AFM) in studies of the cell wall ultrastructure and to see how this structure is affected in the kraft pulp fibre line. This is done in order to eventually improve fibre properties for use in paper and other applications, such as composites. On the ultrastructural level of native spruce fibres (tracheids), it was found that cellulose fibril aggregates exist as agglomerates of individual cellulose microfibrils (with a width of 4 nm). Using AFM in combination with image processing, the average side length (assuming a square cross-section) for a cellulose fibril aggregate was found to be 15–16 nm although with a broad distribution. A concentric lamella structure (following the fibre curvature) within the secondary cell wall layer of native spruce fibres was confirmed. These concentric lamellae were formed of aligned cellulose fibril aggregates with a width of about 15 nm, i.e. of the order of a single cellulose fibril aggregate. It was further found that the cellulose fibril aggregates had a uniform size distribution across the fibre wall in the transverse direction. During the chemical processing of wood chips into kraft pulp fibres, a 25 % increase in cellulose fibril aggregate dimension was found, but no such cellulose fibril aggregate enlargement occurred during the low temperature delignification of wood into holocellulose fibres. The high temperature in the pulping process, over 100 ºC, was the most important factor for the cellulose fibril aggregate enlargement. Neither refining nor drying of kraft or holocellulose pulp changed the cellulose fibril aggregate dimensions. During kraft pulping, when lignin is removed, pores are formed in the fibre cell wall. These pores were uniformly distributed throughout the transverse direction of the wood cell wall. The lamellae consisting of both pores and matrix material (“pore and matrix lamella”) became wider and their numeral decreased after chemical pulping. In holocellulose pulp, no such changes were seen. Refining of kraft pulp increased the width of the pore and matrix lamellae in the outer parts of the fibre wall, but this was not seen in holocellulose. Upon drying of holocellulose, a small decrease in the width of the pore and matrix lamellae was seen, reflecting a probable hornification of the pulp. Refining of holocellulose pulp led to pore closure probably due to the enhanced mobility within the fibre wall. Enzymatic treatment using hemicellulases on xylan and glucomannan revealed that, during the hydrolysis of one type of hemicellulose, some of the other type was also dissolved, indicating that the two hemicelluloses were to some extent linked to each other in the structure. The enzymatic treatment also decreased the pore volume throughout the fibre wall in the transverse direction, indicating enzymatic accessibility to the entire fibre wall. The results presented in this thesis show that several changes in the fibre cell wall ultrastructure occur in the kraft pulp fibre line, although the effects of these ultrastructural changes on the fibre properties are not completely understood. / QC 20101012

Il tema del progetto di ricerca è lo studio della pittura romana nell’area della Cisalpina orientale, con particolare riferimento alle problematiche connesse alla definizione dei processi formativi e delle peculiarità delle maestranze. L’ambito geografico considerato è compreso tra Altino e Trieste: all’interno di questo comparto territoriale Aquileia e Altino hanno costituito i due ambiti privilegiati della ricerca, anche per la possibilità di condurre un’indagine rigorosa su tutto il materiale pittorico conservato presso i Musei Archeologici. L’esame autoptico condotto con un approccio metodologico volto a considerare il supporto e la superficie dipinta è stato incrociato con l’analisi delle fonti documentarie inedite, che nel caso di Aquileia hanno rappresentato un imprescindibile strumento per la restituzione dei contesti: sono stati riqualificate nel senso topografico alcune partizioni edite, che assieme a numerose altre inedite vanno a restituire una nuova immagine alle abitazioni scavate nel secolo scorso. Lo studio ha messo in evidenza un panorama ricco dal punto di vista quantitativo che ho offerto significativi spunti di analisi sui caratteri della produzione, soprattutto nell’ottica del riconoscimento delle peculiarità regionali elaborate dalle officine pittoriche operanti sul territorio. / The subject of this research project is the study of Roman wall-painting in eastern Cisalpine Gaul, more specifically dealing with the aspects of the creation and development of the local workshops and their peculiar characteristics. The area taken into consideration is set between Altino and Trieste: within this territory Aquileia and Altino have represented the two privileged research fields, given the possibility to analyse thoroughly all the wall-painting evidence preserved in the Archaeological Museums. Direct examination, conducted with a specific attention to the plaster bearer and the painted surface, has been combined with the analysis of unpublished documentation which, in the case of Aquileia, has represented an indispensable instrument for the reconstruction of the original contexts. In this way it has been possible to re-define topographically some well known examples of wall-paintings which, together with many yet unpublished examples, contribute to give a new image of the private houses excavated during the last century. This research has revealed an outline very rich in respect of the quantities and which has offered interesting starting points for the analysis of the different aspects of the production, specifically aimed to the recognition of local peculiarities developed by the workshops operating in this area.

名古屋大学年代測定総合研究センターシンポジウム報告

The risk of food insecurity in the form of higher food prices has prompted policymakers in the United States (US) and European Union (EU) to revise their approach to biofuel development. The US Renewable Fuel Standard (RFS) and EU Directive 2009/28/EC require long term use of renewable energy in transportation, subject to sustainability. This thesis examines the implications of the US RFS and EU Directive 2009/28/EC in a trade context using a partial equilibrium/comparative static framework. The focus is on the effect of the revised biofuels policies on opportunities for developing countries to supply the US and/or EU markets. For the US, the implications when the volume produced and/or required under the RFS is technologically infeasible with imports of ethanol as a potential policy alternative are explored. For the EU, the impact of the sustainability criteria on foreign biodiesel suppliers in terms of compliance cost is examined. In general, the US policy may enhance opportunities for trade while the EU policy will likely inhibit trade. A discussion of the implications of the mandates for developing countries and WTO is included.

The goal of this thesis was to produce an animal model that develops atherosclerotic plaque featuring plaque neovascularization leading to intraplaque hemorrhage and is suitable for noninvasive imaging studies. Several strategies were tested for their effectiveness in producing such plaques in the rabbit aorta, including: a high cholesterol diet, vascular endothelial growth factor injections, therapeutic contrast ultrasound, and balloon catheter injury. It was found that a combination of the high cholesterol diet and balloon injury was able to achieve plaque neovascularization in a manner dependent on circulating plasma cholesterol levels. In addition, a contrast-enhanced magnetic resonance imaging technique implemented in the animal model was able to detect plaque neovascularization and monitor its change over time in a single group of animals. In conclusion, an animal model was created where plaque neovascularization occurs in a predictable fashion and can be studied with non-invasive magnetic resonance imaging.