Probably no group of organisms has been as important as bacteriophages when it comes to the understanding of fundamental biological processes like transcriptional control, DNA replication, site-specific recombination, e.t.c. The work presented in this thesis is a contribution towards the complete understanding of these organisms. Two proteins, integrase, and Cox, which are important for the choice of the life mode of bacteriophage P2, are investigated. P2 is a temperate phage, i.e. it can either insert its DNA into the host chromosome (by site-specific recombination) and wait (lysogeny), or it can produce new progeny with the help of the host protein machinery and thereafter lyse the cell (lytic cycle). The integrase protein is necessary for the integration and excision of the phage genome. The Cox protein is involved as a directional factor in the site-specific recombination, where it stimulates excision and inhibits integration. It has been shown that the Cox protein also is important for the choice of the lytic cycle. The choice of life mode is regulated on a transcriptional level, where two mutually exclusive promoters direct whether the lytic cycle (Pe) or lysogeny (Pc) is chosen. The Cox pro-tein has been shown to repress the Pc promoter and thereby making tran-scription from the Pe promoter possible, leading to the lytic cycle. Further, the Cox protein can function as a transcriptional activator on the parasite phage, P4. P4 has gained the ability to adopt the P2 protein machinery to its own purposes. In this work the importance of the native size for biologically active integrase and Cox proteins has been determined. Further, structure-function analyses of the two proteins have been performed with focus on the protein-protein interfaces. In addition it is shown that P2 Cox and the P2 relative Wphi Cox changes the DNA topology upon specific binding. From the obtained results a mechanism for P2 Cox-DNA interaction is discussed. The results from this thesis can be used in the development of a gene delivery system based on the P2 site-specific recombination system.

P2-like bacteriophages integrate their genome into the E. coli host cell by a site-specific recombination event upon lysogenization. The integrative recombination occurs between a specific sequence in the phage genome, attP, and a specific sequence in the host genome, attB, generating the host-phage junctions attL and attR. The integration is mediated by the phage enzyme integrase (Int) and the host factor IHF. The excisive recombination takes place between attL and attR, and is mediated by Int, IHF and phage encoded protein Cox. For safe integration of foreign genes into eukaryotic chromosome a recombinases is necessary which can perform the integration site-specifically. P2-like phage integrases have the potential to become tools for safe gene therapy. Their target is simple but specific, and once integration has occurred it is very stable in the absence of the Cox protein. The site-specific recombination mechanism has to be understood at the molecular level. Therefore, I have initiated the characterization of the site-specific recombination system of the P2-like phage ΦD145. In this work, Int and IHF are shown to bind to the different attachment sites cooperatively. One of two possible inverted repeats in attP is shown to be the Int core recognition site. The attP core of this phage has high identity with a site on human chromosome, denoted as ΨattB. In this study we have shown that in in vivo recombination ΦD145 Int can accept ΨattB in both bacteria and in eukaryotic cells. Also shown that Int consists of an intrinsic nuclear localization signal. A study also reveled that ΦD145 Int activity was affected by the Tyr-phosphorylation. Attempts have been made to change the specificity of the other P2-like phage P2 and WΦ integrases and also structural and functional analysis was done. A study on comparative analysis of Cox proteins and Cox binding sites gave us the basic information about the recombination mechanism. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.

Until recently, multiple SPME fibres could not be automatically evaluated in a single sequence without manual intervention. This drawback had been a critical issue until recently, particularly during the analysis of numerous on-site samples. Recently, GERSTEL® has developed and commercialized a Multi-Fibre Exchanger (MFX) system designed to overcome this drawback. In this research, a critical evaluation of the MFX performance in terms of storage stability and long term operation is presented. It was established in the course of our research that the MFX can operate continuously and precisely for over 200 extraction/injection cycles. However, when the effect of residence time of commercial fibres on the MFX tray was evaluated, the results have shown that amongst the evaluated fibre coatings, carboxen/polydimethylsiloxane (CAR/PDMS) was the only coating capable of efficient storage on the MFX tray for up to 24 hours after field sampling without suffering significant loss of analytes. Additionally, the MFX system capability for high-throughput analysis was demonstrated by the unattended desorption of multiple fibres after on-site sampling of two different systems, indoor air and biogenic emissions. Subsequently, a protocol based on a new, fast, reproducible, reusable and completely automated method that enables quick assessment of SPME coatings was developed. The protocol consists of an innovative in-vial standard generator containing vacuum pump oil doped with McReynolds probes and subsequently mixed with a polystyrene-divinylbenzene resin. According to our results, the protocol has proven to be a useful tool for the quick assessment of inter-fibre reproducibility prior to their application in on-site analysis. The implications of such protocols include, but are not limited to: time-saving, assurance of reliable and reproducible data, and a dependable guide for novice users of the technique. Finally, an innovative, reusable and readily deployable pen-like diffusive sampler for needle traps (PDS-NT) is proposed. Results have shown that the new PDS-NT is effective for air analysis of benzene, toluene, and o-xylene (BTX). In addition, no statistically significant effects of pen geometry on the uptake of analytes were found.

Uppsatsen syftar till att ta reda på vad ungdomar uppmärksammar som offentlig konst och vad är det som gör att vissa konstverk får mer uppmärksamhet. Jag har genomfört intervjuer med personer som befinner sig på campus i Växjö eller runt Växjösjön som sedan analyseras. Den här uppsatsen har främst fokuserat på ungdomar. För att ungdomar i min studie ska uppfatta något som offentlig så måste den stå utomhus. Den ska finnas i en miljö där man lätt kan se den, även på långt håll ska man kunna urskilja att där står ett konstverk. Verket måste vara stort. Färgen på verket bör bryta mot miljön för att den ska vara mer utstickande. Om ett konstverk har en funktion blir detta ungdomars referens till föremålet, det vill säga att det inte ses som ett konstverk. Om meningen som konstnären har kring verket visas tydligt så kommer intresset att öka

Understanding the transport and retention of radionuclides in the environment is important for protecting freshwater supplies and minimizing impact to biologic systems. Technetium-99 (Tc⁹⁹) is a radionuclide of interest due to its long half-life (2.13 x 10⁵ years) and toxicity. In the form of pertechnetate (TcO₄⁻), Tc is expected to move nearly unretarded in the subsurface. Under reducing conditions Tc can precipitate in low solubility Tc oxide (TcO₂·nH₂O) and/or Tc sulfide (Tc₂S[subscript x]) phases. The studies presented in this dissertation investigate the physiochemical mechanisms for the transport and retention of Tc. Transport studies determined that TcO₄⁻ would move at pore water velocity in unsaturated sediments. Geochemical studies of contaminated sediments determined that nearly ~ 25 % of the total Tc was retained in phases associated with iron oxide and aluminosilicate minerals, thus reducing the mobility of Tc. Studies of Tc₂S[subscript x] mineral phases, generated using nano Zero Valent Iron (nZVI) and sulfide (HS-) in sediments, determined that Tc could be stabilized in mineral phases as Tc₂S[subscript x] that were slower to reoxidize than TcO₂·nH₂O phases. / Graduation date: 2013 / Access restricted to the OSU Community at author's request from Feb. 14, 2013 - Feb. 14, 2014

<p><i>Lactococcus lactis,</i> prolidase (<i>Lla</i>prol) hydrolyzes Xaa-Pro dipeptides. Since Xaa-Pro is known as bitter peptides, <i>Lla</i>prol is potentially applicable to reduce bitterness of fermented foods. <i>Lla</i>prol shows allosteric behaviour and substrate inhibition, which are not reported in other prolidases. Computer models of <i>Lla</i>prol based on an X-ray structure of non-allosteric <i>Pyrococcus furiosus</i> prolidase showed that a loop structure (Loop^32-43) is located at the interface of the protomers of this homodimeric metallodipeptidase. This study investigated roles of four charged residues (Asp³⁶, His³⁸, Glu³⁹, and Arg⁴⁰) of Loop^32-43 in <i>Lla</i>prol using a combination of kinetic examinations of ten mutant enzymes and their molecular models. Deletion of the loop structure by Î36-40 mutant resulted in a loss of activity, indicating Loop^32-43 is crucial for the activity of <i>Lla</i>prol. D36S and H38S exhibited 96.2 % and 10.3 % activity of WT, whereas little activities (less than 1.0 % of WT activity) were observed for mutants E39S, D36S/E39S, R40S, R40E, R40K and H38S/R40S. These results implied that Glu³⁹ and/or Arg⁴⁰ play critical role(s) in maintaining the catalytic activity of <i>Lla</i>prol. These observations suggested that the loop structure is flexible and this attribute, relying on charge-charge interactions contributed by Arg⁴⁰, Glu³⁹ and Lys¹⁰⁸, is important in maintaining the activity of <i>Lla</i>prol. When the loop takes a conformation close to the active site (closed state), Asp³⁶ and His³⁸ at the tip of the loop can be involved in the catalytic reaction of <i>Lla</i>prol. The two active mutant prolidases (D36S and H38S) resulted in modifications of the unique characteristics; the allosteric behaviour was not observed for D36S, and H38S <i>Lla</i>prol showed no substrate inhibition. D36E/R293K, maintaining the negative charge of position 36 and positive charge of position 293, still possessed the allosteric behaviour, whereas the loss of the charges at these positions (D36S of this study and R293S of a previous study (Zhang et al., 2009 BBA-Proteins Proteom 1794, 968-975) eliminated the allosteric behaviour. These results indicated the charge-charge attraction between Asp³⁶ and Arg²⁹³ is important for the allostery of <i>Lla</i>prol. In the presence of either zinc or manganese divalent cations as the metal catalytic centre, D36S and H38S enzymes also showed different substrate preferences from WT <i>Lla</i>prol, implying the influence of Asp³⁶ and His³⁸ on the substrate binding. D36S and H38S also showed higher activities at pH 5.0 to 6.0, in which range WT <i>Lla</i>prol steeply decreased its activity, indicating Asp³⁶ and His³⁸ are involved in the active centre and influence the microenvironment of catalytic His²⁹⁶. The above observations are attributed to modifications of their local structure in the active centre since the temperature dependency and thermal denaturing temperature indicated little effects on the overall structure of the <i>Lla</i>prol mutants.</p> <p>From these results, we concluded that the unique behaviours of <i>Lla</i>prol are correlated to Loop^32-43 and Asp³⁶ and His³⁸ on it. When Loop^32-43 takes a closed conformation, Asp³⁶ interacts with Arg²⁹³ via charge-charge attraction to form an allosteric subsite. The saturation of the allosteric site with substrates further allowed the communications of His³⁸ with S₁ site residues to complete the active site. When the substrate concentration becomes higher than it is required to saturated productive S₁' site, His³⁸, Phe¹⁹⁰ and Arg²⁹³ would resemble the residue arrangement of S₁' site residues (His²⁹², Tyr³²⁹, and Arg³³⁷) and bind to the proline residue of substrates. This non-productive binding would prevent the conformational change of Loop^32-43, which further results in the substrate inhibition. For further confirmation of this mechanism, crystallographic studies will be conducted. In this thesis, we have indentified the conditions to produce crystals of <i>Lla</i>prol proteins.</p>

Site quality, or the ability of land to grow trees, is an important component for identifying the most appropriate locations for establishing plantations of fast growing tree species to meet societys demands for timber and other environmental benefits. The goal of this thesis project was to predict site quality for poplars using soil and site information in Saskatchewan, Alberta and Quebec and to examine the effect of site quality on competition control in hybrid poplar plantations in Saskatchewan.<p>The first study examined factors affecting trembling aspen productivity in the boreal shield ecozone of Quebec on till and fluvial parent materials using general map data and measured soil and site information. Relationships with productivity were stronger using measured soil and site variables for individual parent materials (R2>0.6) than using general map data only (R2<0.25). Including biological variables, such as overstory species composition, had a major impact on site quality with conifer dominance negatively impacting the growth of trembling aspen.<p>The second study examined the factors affecting trembling aspen productivity in the boreal transition ecoregion of Saskatchewan on three different soil parent materials: fluvial, lacustrine and till. Relationships with productivity were stronger using soil and site variables for individual parent materials (R2 0.48-0.58) than using agricultural capability classes or other soil properties for all plots combined (R2<0.2). For fluvial and lacustrine sites, increasing clay content and nutrient availability (e.g. pH and total N) were positively related to productivity while tree productivity was negatively related to poor drainage for till sites. <p>The third study examined the factors affecting site quality for a single hybrid poplar clone in industrial plantations in Alberta at both the local scale (between plantations) and the microsite scale (within plantations). At the local scale, foliar P and Cu concentrations, soil water availability and drainage, and Ca and Mn in the C horizon were related to hybrid poplar productivity. There were also curved relationships with productivity and soil texture in the B horizon and pH of the A horizon, indicating an optimal range for poplar growth. At the microsite scale, soil texture was the best predictor of productivity with different relationships at each site depending on where the sites were in relation to the optimal soil texture.<p>The final study examined the response of hybrid poplar plantations in Saskatchewan to interspecific competition control on a range of site productivities. Competition control greatly increased tree growth with the greatest benefit being on the best quality sites. Both water and nutrients were highly competed for between trees and weeds. In the weed-free plots, tree growth was positively related to the amount of silt and clay in the soil and foliar P concentrations. This series of studies has demonstrated that it should be possible to predict poplar productivity reasonably well using only soil and site information within limited areas across Canada. However, the important drivers of productivity varied between the regions studied and between site groupings, such as by parent material, within local areas. This information can now be used to help land managers make better decisions regarding the establishment and management of plantations of fast growing tree species, notably hybrid poplar plantations.

This work is a compilation of ideas intended as a framework for an alternative approach to engaging ‘site’ in the design process, an approach that maintains and explores the complexities and subtleties of a landscape, of a place. Through two parallel explorations - one that considers an expanded and inclusive interpretation of landscape as the frame through which we engage with, and design, our surroundings, and one that examines the specific nature of this engagement as exchange between the self and the milieu - such an approach has been developed. This approach is called RECONNAISSANCE. Through encouragement of explicit, conscious consideration of how we perceive and experience a landscape, how this contributes to an understanding of a particular place and how this relates to and informs the practice of landscape architecture (both the process and the outcome), RECONNAISSANCE contributes to a strengthening of our abilities and actions as landscape architects. / February 2008

Le développement d'applications s'appuyant sur le Web a connu ces dernières années une très forte croissance. Dans le secteur public, les sites Web sont devenus l'épine dorsale du système informatique du gouvernement car leur importance est vitale à cause des services essentiels qu'ils offrent aux citoyens et aux entreprises. Le besoin de mettre au point des principes et méthodes spécifiques au développement de ce type d'applications d'une manière générale, et à l'évaluation de leur qualité se fait de plus en plus ressentir dans l'industrie du génie logiciel. En effet, l'évaluation quantitative de la qualité des applications Web (critères et métriques) est très récente. Dans ce mémoire, nous présentons d'abord les deux principales méthodes traditionnelles d'évaluation de la qualité des sites Web du gouvernement du Canada, à savoir l'analyse de la conformité à des normes et directives gouvernementales du Canada et la méthode de calcul de l'indice de maturité des services publics en ligne puis par la suite les principales composantes d'une méthode nouvelle, WebQEM (Web Quality Evaluation Method), à savoir l'arbre de qualité basé sur la norme ISO 9126 et la structure mathématique du modèle WebQEM. Finalement, nous proposons une adaptation de la méthode WebQEM pour son application à l'environnement spécifique du ministère RHDSC, ce qui conduira à une évaluation du niveau de satisfactions de 10 facteurs de qualité du site Web de ce ministère. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Évaluation quantitative, Qualité, Arbre de qualité, WebQEM, ISO 9126.

Le secteur des aliments fonctionnels, nutraceutiques et produits de santé naturels est un secteur émergent très présent au Québec par le nombre d'entreprises qui s'y trouvent (Saives et Cloutier, 2003, 2006; Demol, 2001). Ces entreprises sont très hétérogènes et comprendre les modalités de leur développement au Québec à long terme est source de questionnement avec l'entrée en vigueur d'une nouvelle réglementation des produits de santé naturels en 2004. Aussi, dans une perspective territoriale, la présente recherche tente de comprendre pourquoi et comment les entreprises de ce secteur s'ancrent au Québec. Dans ce travail, l'ancrage correspond à une dynamique de co-création de ressources entre l'entreprise et le territoire où elle est localisée, par la co-construction de ressources et compétences dans des espaces partagés dits « Ba ». En effet, les entreprises possèdent des ressources qui peuvent être stratégiques, c'est-à-dire sources d'avantage concurrentiel durable (Wernerfelt, 1984; Barney, 1991). Parmi les différentes ressources de l'entreprise, les connaissances s'avèrent les plus stratégiques. En effet, « Aujourd'hui, les connaissances et la capacité à créer et utiliser les connaissances sont considérées comme la plus importance source d'avantage concurrentiel soutenu de la firme » (Nonaka et Toyama, 2003, p. 2). La gestion des connaissances devient donc par le fait même une compétence importante pour les entreprises. Emprunté au modèle de Nonaka et Takeushi (1997), le concept de Ba est utilisé dans la littérature récente en économie régionale (Gilly et Lung, 2004) et rapproché de la notion de proximité afin d'expliquer la création et l'exploitation de ressources plus ou moins ancrées. Simultanément, à partir d'une littérature classique sur le sujet (Nekka et Dokou, 2004), les facteurs du choix de la localisation des entreprises sont identifiés pour comprendre l'essence de leur ancrage. Pour répondre à la question de recherche dans le cadre théorique choisi, une étude multi-cas a été menée par le biais d'entrevues de type semi dirigé auprès de cinq entreprises du secteur au Québec. Les données textuelles recueillies ont par la suite été analysées par catégorisation à la fois manuelle et statistique. Une interprétation selon laquelle il existe différents modèles de choix de localisation des entreprises et que celles-ci évoluent dans deux sortes de Ba reliés à leur environnement est proposée. Le croisement entre les Ba et les modèles de choix de localisation a permis de faire ressortir des modèles d'ancrage territorial différents selon les entreprises et leurs stratégies respectives. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Nutraceutique, aliment fonctionnel, produit de santé naturel, territoire, facteurs de localisation.