Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii

Abstract Background Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C. Results We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. Conclusion We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

Synthesis and properties of substituted Hg-based superconductors

This thesis is focused on studies of substituted Hg-based superconducting copper oxides ((Hg1-xMx)Ba2Can-1CunO2n+2+δ). These compounds are promising objects of investigation, not only from a fundamental point of view but also because of their high values of superconducting transition temperature (Tc) and irreversibility field (Hirr). The first part of the thesis is devoted to optimization of the synthesis procedure for Hg-based cuprates. The influence of different parameters (T, t, p(Hg), p(O2)) on the synthesis of these compounds in sealed silica tubes was studied. Optimal conditions yielded samples containing up to 95% of HgBa2Ca2Cu3O8+δ (Hg-1223). The formation of solid solutions with the formula (Hg1-xCux)Ba2Ca2Cu3O8+δ (where x <= 0.5) was also established. Another technique was developed, using LiF as a flux, for synthesis of samples containing up to 90% of the HgBa2CaCu2O6+δ (Hg-1212) phase. The second part concerns synthesis and studies of oxyfluorides using Hg-1212 and Hg-1223 as starting materials together with XeF2 as a fluorinating agent. It was found that oxyfluorides of both phases have a parabolic dependence of Tc vs. a parameter as well as enhanced Tc values (ΔT ≈ 3-4 K) in comparison with optimally doped non-fluorinated analogues. The crystal structure of Hg-1223 oxyfluoride was studied by X-ray powder and neutron diffraction methods. It is suggested that chemical modification of the crystal structure leads to a decrease in Cu-O distance without noticeable change in Cu-O-Cu angle (in the (CuO2) layers), which may be the significant factors influencing this Tc increase. Hg-1223 oxyfluoride was also studied under high pressure for first time. It was found that this compound has a record-high Tc value (≈ 166 K) at P ≈ 23 GPa. The last part describes the investigation of substituted Hg-based superconductors in the series (Hg0.9M0.1)Ba2CuO4+δ {(Hg,M)-1201}, where M = Tl, Pb, W, Mo, Nb and V. A comprehensive study of these compounds by various methods (X-ray powder diffraction, EDX, IR-, EXAFS- and XANES -spectroscopy) indicated that the change of charge carrier doping level is a crucial factor determining the irreversibility line. (Hg0.9Mo0.1)Ba2CuO4+δ showed the most improved irreversibility line position among the (Hg,M)-1201 compounds studied in this series.

Meta-models, environment and layers: agent-oriented engineering of complex systems

Traditional software engineering approaches and metaphors fall short when applied to areas of growing relevance such as electronic commerce, enterprise resource planning, and mobile computing: such areas, in fact, generally call for open architectures that may evolve dynamically over time so as to accommodate new components and meet new requirements. This is probably one of the main reasons that the agent metaphor and the agent-oriented paradigm are gaining momentum in these areas. This thesis deals with the engineering of complex software systems in terms of the agent paradigm. This paradigm is based on the notions of agent and systems of interacting agents as fundamental abstractions for designing, developing and managing at runtime typically distributed software systems. However, today the engineer often works with technologies that do not support the abstractions used in the design of the systems. For this reason the research on methodologies becomes the basic point in the scientific activity. Currently most agent-oriented methodologies are supported by small teams of academic researchers, and as a result, most of them are in an early stage and still in the first context of mostly \academic" approaches for agent-oriented systems development. Moreover, such methodologies are not well documented and very often defined and presented only by focusing on specific aspects of the methodology. The role played by meta- models becomes fundamental for comparing and evaluating the methodologies. In fact a meta-model specifies the concepts, rules and relationships used to define methodologies. Although it is possible to describe a methodology without an explicit meta-model, formalising the underpinning ideas of the methodology in question is valuable when checking its consistency or planning extensions or modifications. A good meta-model must address all the different aspects of a methodology, i.e. the process to be followed, the work products to be generated and those responsible for making all this happen. In turn, specifying the work products that must be developed implies dening the basic modelling building blocks from which they are built. As a building block, the agent abstraction alone is not enough to fully model all the aspects related to multi-agent systems in a natural way. In particular, different perspectives exist on the role that environment plays within agent systems: however, it is clear at least that all non-agent elements of a multi-agent system are typically considered to be part of the multi-agent system environment. The key role of environment as a first-class abstraction in the engineering of multi-agent system is today generally acknowledged in the multi-agent system community, so environment should be explicitly accounted for in the engineering of multi-agent system, working as a new design dimension for agent-oriented methodologies. At least two main ingredients shape the environment: environment abstractions - entities of the environment encapsulating some functions -, and topology abstractions - entities of environment that represent the (either logical or physical) spatial structure. In addition, the engineering of non-trivial multi-agent systems requires principles and mechanisms for supporting the management of the system representation complexity. These principles lead to the adoption of a multi-layered description, which could be used by designers to provide different levels of abstraction over multi-agent systems. The research in these fields has lead to the formulation of a new version of the SODA methodology where environment abstractions and layering principles are exploited for en- gineering multi-agent systems.

Specification and Verification of Declarative Open Interaction Models - A Logic-based framework

The advent of distributed and heterogeneous systems has laid the foundation for the birth of new architectural paradigms, in which many separated and autonomous entities collaborate and interact to the aim of achieving complex strategic goals, impossible to be accomplished on their own. A non exhaustive list of systems targeted by such paradigms includes Business Process Management, Clinical Guidelines and Careflow Protocols, Service-Oriented and Multi-Agent Systems. It is largely recognized that engineering these systems requires novel modeling techniques. In particular, many authors are claiming that an open, declarative perspective is needed to complement the closed, procedural nature of the state of the art specification languages. For example, the ConDec language has been recently proposed to target the declarative and open specification of Business Processes, overcoming the over-specification and over-constraining issues of classical procedural approaches. On the one hand, the success of such novel modeling languages strongly depends on their usability by non-IT savvy: they must provide an appealing, intuitive graphical front-end. On the other hand, they must be prone to verification, in order to guarantee the trustworthiness and reliability of the developed model, as well as to ensure that the actual executions of the system effectively comply with it. In this dissertation, we claim that Computational Logic is a suitable framework for dealing with the specification, verification, execution, monitoring and analysis of these systems. We propose to adopt an extended version of the ConDec language for specifying interaction models with a declarative, open flavor. We show how all the (extended) ConDec constructs can be automatically translated to the CLIMB Computational Logic-based language, and illustrate how its corresponding reasoning techniques can be successfully exploited to provide support and verification capabilities along the whole life cycle of the targeted systems.

Designing and Programming Organizational Infrastructures for Agents situated in Artifact-based Environments

Actual trends in software development are pushing the need to face a multiplicity of diverse activities and interaction styles characterizing complex and distributed application domains, in such a way that the resulting dynamics exhibits some grade of order, i.e. in terms of evolution of the system and desired equilibrium. Autonomous agents and Multiagent Systems are argued in literature as one of the most immediate approaches for describing such a kind of challenges. Actually, agent research seems to converge towards the definition of renewed abstraction tools aimed at better capturing the new demands of open systems. Besides agents, which are assumed as autonomous entities purposing a series of design objectives, Multiagent Systems account new notions as first-class entities, aimed, above all, at modeling institutional/organizational entities, placed for normative regulation, interaction and teamwork management, as well as environmental entities, placed as resources to further support and regulate agent work. The starting point of this thesis is recognizing that both organizations and environments can be rooted in a unifying perspective. Whereas recent research in agent systems seems to account a set of diverse approaches to specifically face with at least one aspect within the above mentioned, this work aims at proposing a unifying approach where both agents and their organizations can be straightforwardly situated in properly designed working environments. In this line, this work pursues reconciliation of environments with sociality, social interaction with environment based interaction, environmental resources with organizational functionalities with the aim to smoothly integrate the various aspects of complex and situated organizations in a coherent programming approach. Rooted in Agents and Artifacts (A&A) meta-model, which has been recently introduced both in the context of agent oriented software engineering and programming, the thesis promotes the notion of Embodied Organizations, characterized by computational infrastructures attaining a seamless integration between agents, organizations and environmental entities.

Lesion detection and classification in breast cancer: evaluation of approaches based on morphological features, tracer kinetic modelling and semi-quantitative parameters in MR functional imaging (DCE-MRI)

The diagnosis, grading and classification of tumours has benefited considerably from the development of DCE-MRI which is now essential to the adequate clinical management of many tumour types due to its capability in detecting active angiogenesis. Several strategies have been proposed for DCE-MRI evaluation. Visual inspection of contrast agent concentration curves vs time is a very simple yet operator dependent procedure, therefore more objective approaches have been developed in order to facilitate comparison between studies. In so called model free approaches, descriptive or heuristic information extracted from time series raw data have been used for tissue classification. The main issue concerning these schemes is that they have not a direct interpretation in terms of physiological properties of the tissues. On the other hand, model based investigations typically involve compartmental tracer kinetic modelling and pixel-by-pixel estimation of kinetic parameters via non-linear regression applied on region of interests opportunely selected by the physician. This approach has the advantage to provide parameters directly related to the pathophysiological properties of the tissue such as vessel permeability, local regional blood flow, extraction fraction, concentration gradient between plasma and extravascular-extracellular space. Anyway, nonlinear modelling is computational demanding and the accuracy of the estimates can be affected by the signal-to-noise ratio and by the initial solutions. The principal aim of this thesis is investigate the use of semi-quantitative and quantitative parameters for segmentation and classification of breast lesion. The objectives can be subdivided as follow: describe the principal techniques to evaluate time intensity curve in DCE-MRI with focus on kinetic model proposed in literature; to evaluate the influence in parametrization choice for a classic bi-compartmental kinetic models; to evaluate the performance of a method for simultaneous tracer kinetic modelling and pixel classification; to evaluate performance of machine learning techniques training for segmentation and classification of breast lesion.

Alpha, Omega end group functionalization of RAFT polymers based on pentafluorophenyl esters and methane thiosulfonates

While polymers with different functional groups along the backbone have intensively been investigated, there is still a challenge in orthogonal functionalization of the end groups. Such well-defined systems are interesting for the preparation of multiblock (co) polymers or polymer networks, for bio-conjugation or as model systems for examining the end group separation of isolated polymer chains. rnHere, Reversible Addition Fragmentation Chain Transfer (RAFT) polymerization was employed as method to investigate improved techniques for an a, w end group functionalization. RAFT produces polymers terminated in an R group and a dithioester-Z group, where R and Z stem from a suitable chain transfer agent (CTA). rnFor alpha end group functionalization, a CTA with an activated pentafluorophenyl (PFP) ester R group was designed and used for the polymerization of various methacrylate monomers, N-isopropylacrylamide and styrene yielding polymers with a PFP ester as a end group. This allowed the introduction of inert propyl amides, of light responsive diazo compounds, of the dyes NBD, Texas Red, or Oregon Green, of the hormone thyroxin and allowed the formation of multiblocks or peptide conjugates. rnFor w end group functionalization, problems of other techniques were overcome through an aminolysis of the dithioester in the presence of a functional methane thiosulfonate (MTS), yielding functional disulfides. These disulfides were stable under ambient conditions and could be cleaved on demand. Using MTS chemistry, terminal methyl disulfides (enabling self-assembly on planar gold surfaces and ligand substitution on gold and semiconductor nanoparticles), butynyl disulfide end groups (allowing the “clicking” of the polymers onto azide functionalized surfaces and the selective removal through reduction), the bio-target biotin, and the fluorescent dye Texas Red were introduced into polymers. rnThe alpha PFP amidation could be performed under mild conditions, without substantial loss of DTE. This way, a step-wise synthesis produced polymers with two functional end groups in very high yields. rnAs examples, polymers with an anchor group for both gold nanoparticles (AuNP) and CdSe / ZnS semi-conductor nanoparticles (QD) and with a fluorescent dye end group were synthesized. They allowed a NP decoration and enabled an energy transfer from QD to dye or from dye to AuNP. Water-soluble polymers were prepared with two different bio-target end groups, each capable of selectively recognizing and binding a certain protein. The immobilization of protein-polymer-protein layers on planar gold surfaces was monitored by surface plasmon resonance.Introducing two different fluorescent dye end groups enabled an energy transfer between the end groups of isolated polymer chains and created the possibility to monitor the behavior of single polymer chains during a chain collapse. rnThe versatility of the synthetic technique is very promising for applications beyond this work.

Functional polymer based nanoparticles : development of defined complex structures as basis for in-vitro and in-vivo applications

In Rahmen der vorliegenden Arbeit wurde ein neuartiger Zugang zu einer Vielzahl von Polymerstrukturen auf Basis des klinisch zugelassenen Polymers Poly(N-(2-Hydroxypropyl)-methacrylamide) (PHPMA) entwickelt. Der synthetische Zugang beruht zum einen auf der Verwendung von Reaktivesterpolymeren und zum anderen auf der Reversible Addition Fragmentation Chain Transfer (RAFT) Polymerisationsmethode. Diese Form einer kontrollierten radikalischen Polymerisation ermöglichte es, neben der Synthese von besser definierten Homopolymeren auch statistische und Blockcopolymere herzustellen. Die Reaktivesterpolymere können durch einfache Aminolyse in HPMA-basierte Systeme überführt werden. Somit können sie als eine vielversprechende Basis zur Synthese von umfangreichen Polymerbibliotheken angesehen werden. Die hergestellten Polymere kombinieren verschiedene Funktionalitäten bei konstantem Polymerisationsgrad. Dies ermöglicht eine Optimierung auf eine gezielte Anwendung hin ohne den Parameter der Kettenlänge zu verändern.rnIm weiteren war es durch Verwendung der RAFT Polymerisation möglich partiell bioabbaubare Blockcopolymere auf Basis von Polylactiden und HPMA herzustellen, in dem ein Kettentransferreagenz (CTA) an ein wohl definiertes Polylactid Homopolymer gekoppelt wurde. Diese Strukturen wurden in ihrer Zusammensetzung variiert und mit Erkennungsstrukturen (Folaten) und markierenden Elementen (Fluoreszenzfarbstoffe und +-emittierenden Radionukleide) versehen und im weiteren in vitro und in vivo evaluiert.rnAuf Grund dieser Errungenschaften war es möglich den Einfluss der Polymermikrostruktur auf das Aggregationsverhalten hin mittel Lichtstreuung und Fluoreszenzkorrelationsspektroskopie zu untersuchen. Es konnte gezeigt werden, dass erst diese Informationen über die Überstrukturbildung die Kinetik der Zellaufnahme erklären können. Somit wurde die wichtige Rolle von Strukturwirkungsbeziehungen nachgewiesen.rnSomit konnte neben der Synthese, Charakterisierung und ersten biologischen Evaluierungen ein Beitrag zum besseres Verständnis zur Interaktion von polymeren Partikeln mit biologischen Systemen geleistet werden.

Saccharide based nanocapsules - From monomer building blocks to improved capsules properties

In dieser Arbeit wurde der vielfältige Nutzen von Kohlenhydraten in Nanokapsel Systemen untersucht. Drei verschiedene Nanokapsel-Typen wurden durch Reaktion an der Grenzfläche von inversen Miniemulsionen hergestellt. Es wurde gezeigt, dass die Kohlenhydrate nach Modifizierung als Monomer an der Kapselbildung teilnehmen können, oder zur Erhöhung der Sensitivität eines verkapselten Kontrastmittels beitragen können. Im Folgenden werden die Ergebnisse der einzelnen Projekte zusammengefasst. Eine neuartige Grenzflächen-Synthese zur Herstellung von Nanokapseln wurde entwickelt und untersucht. Bei der Reaktion handelt es sich um eine Ruthenium katalysierte Olefin-Kreuzmetathese, welche für die Reaktion an der Grenzfläche angepasst wurde. Als wasserlösliches Macromonomer wurde Dextranacrylat synthetisiert. Der Reaktionspartner war ein öl-löslichen Phosphoester (Phenyldi(undec-10-en-1-yl)phosphat). Anhand von NMR-Spektren wurde gezeigt, dass die Kapselbildung auf Olefin Kreuzmetathese beruht. Im Vergleich zu konventionellen Estern haben Phosphorester eine weitere Möglichkeit zur chemischen Funktionalisierung. Dies wurde exemplarisch durch die Verwendung von fluoreszenzmarkierten Phosphoestern gezeigt. Die Markierung wurde verwendet, um die pH-induzierte Abbaubarkeit der Nanokapseln mittels Fluoreszenz-Korrelations-Spektroskopie zu beobachten. Ziel des zweiten Projekts war es, Nanostrukturen zu entwickeln, um Infektionen mit Antibiotika-resistenten Bakterien lokal zu behandeln. Dazu wurden mit Dextranmethacrylat vernetzte Poly(acrylamid) basierte Nanogele synthetisiert und Zinknitrat zugesetzt. Die Synthese der Nanogele wurde erweitert, um durch Vernetzung freier Alkoholgruppen mit Toluoldiisocyanat eine Kapselschale zu erhalten. Die Schalenbildung spiegelte sich in einer geringeren Quellbarkeit der Gel- Schale-Hybride wieder. Die erhaltenen Gel-Schale-Hybride waren in der Lage das Wachstum von zwei Methicillin-resistenten Bakterienstämmen (S. aureus) zu unterdrücken und verzögern. Die synthetisierten Hybridstrukturen könnten in der Beschichtung von Wundauflagen Verwendung finden, um bakterielle Infektionen lokal und direkt nach Ausbruch zu behandeln. Ziel des dritten Projektes war es, die wichtigen Parameter in der Herstellung von Nanokapseln mit hoher Kontrastmittel Sensitivität zu identifizieren. Relaxivität/Signalsensitivität des Kontrastmittels ist von großer Bedeutung für die Bildgebung mittels MRI, dies kann durch die Begrenzung der Mobilität des Kontrastmittels erreicht werden. Aufgrund seiner hohen Komplexstabilität und seiner klinischen Bedeutung wurde das Kontrastmittel Gadobutrol für die Verkapselung verwendet. Das Kontrastmittel wurde in Polyharnstoff-Kapseln eingeschlossen, die durch einen inversen Miniemulsion-Prozess hergestellt wurden. Um die Viskosität im Inneren der Nanokapsel zu erhöhen, wurden zusätzlich Saccharose, Dextran und Polyacrylsäure verkapselt. In Gegenwart von Saccharose konnte die Relaxivität verdoppelt werden. Dies gründet sich vermutlich auf einem Second-sphere Effekt der Saccharose, einer auf Wasserstoffbrückenbindungen beruhende Interaktion von Kontrastmittel und Saccharose.

Synthesis, characterization and crystallization of bionanocomposites based on PLLA, PCL and nanocellulose

In recent years, environmental concerns and the expected shortage in the fossil reserves have increased further development of biomaterials. Among them, poly(lactide) PLA possess some potential properties such as good ability process, excellent tensile strength and stiffness equivalent to some commercial petroleum-based polymers (PP, PS, PET, etc.). This biobased polymer is also biodegradable and biocompatible However, one great disadvantage of commercial PLA is slow crystallization rate, which restricts its use in many fields. Using of nanofillers is viewed as an efficient strategy to overcome this problem. In this thesis, the effect of bionanofillers in neat PLA and in blends of poly (L-lactide)(PLA)/poly(ε-Caprolactone) (PCL) has been investigated. The used nanofillers are: poly(L-lactide-co-ε-caprolactone) and poly(L-lactide-b-ε-caprolactone) grafted on cellulose nanowhiskers and neat cellulose nanowhiskers (CNW). The grafting reaction of poly(L-lactide-co-caprolactone) and poly (L-lactide-b-caprolactone) on the nanocellulose has been performed by the grafting from technique. In this way the polymerization reaction it is directly initiated on the substrate surface. The condition of the reaction were chosen after a temperature and solvent screening. By non-isothermal an isothermal DSC analysis the effect of bionanofillers on PLA and 80/20 PLA/PCL was evaluated. Non-isothermal DSC scans show a nucleating effect of the bionanofillers on PLA. This effect is detectable during PLA crystallization from the glassy state. Cold crystallization temperature is reduced upon the addition of the poly(L-lactide-b-caprolactone) grafted on cellulose nanowhiskers that is most performing bionanofiller in acting as a nucleating agent. On the other hand, DSC isothermal analysis on the overall crystallization rate indicate that cellulose nanowhiskers are best nucleating agents during isothermal crystallization from the melt state. In conclusion, nanofillers have different behavior depending on the processing conditions. However, the efficiency of our nanofillers as nucleating agent was clearly demonstrated in both isothermal as in non-isothermal condition.

A comprehensive understanding of thioTEPA metabolism in the mouse using UPLC-ESI-QTOFMS-based metabolomics

ThioTEPA, an alkylating agent with anti-tumor activity, has been used as an effective anticancer drug since the 1950s. However, a complete understanding of how its alkylating activity relates to clinical efficacy has not been achieved, the total urinary excretion of thioTEPA and its metabolites is not resolved, and the mechanism of formation of the potentially toxic metabolites S-carboxymethylcysteine (SCMC) and thiodiglycolic acid (TDGA) remains unclear. In this study, the metabolism of thioTEPA in a mouse model was comprehensively investigated using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOFMS) based-metabolomics. The nine metabolites identified in mouse urine suggest that thioTEPA underwent ring-opening, N-dechloroethylation, and conjugation reactions in vivo. SCMC and TDGA, two downstream thioTEPA metabolites, were produced from thioTEPA from two novel metabolites 1,2,3-trichloroTEPA (VII) and dechloroethyltrichloroTEPA (VIII). SCMC and TDGA excretion were increased about 4-fold and 2-fold, respectively, in urine following the thioTEPA treatment. The main mouse metabolites of thioTEPA in vivo were TEPA (II), monochloroTEPA (III) and thioTEPA-mercapturate (IV). In addition, five thioTEPA metabolites were detected in serum and all shared similar disposition. Although thioTEPA has a unique chemical structure which is not maintained in the majority of its metabolites, metabolomic analysis of its biotransformation greatly contributed to the investigation of thioTEPA metabolism in vivo, and provides useful information to understand comprehensively the pharmacological activity and potential toxicity of thioTEPA in the clinic.

Spike-based decision learning of nash equilibria in two-player games

Humans and animals face decision tasks in an uncertain multi-agent environment where an agent's strategy may change in time due to the co-adaptation of others strategies. The neuronal substrate and the computational algorithms underlying such adaptive decision making, however, is largely unknown. We propose a population coding model of spiking neurons with a policy gradient procedure that successfully acquires optimal strategies for classical game-theoretical tasks. The suggested population reinforcement learning reproduces data from human behavioral experiments for the blackjack and the inspector game. It performs optimally according to a pure (deterministic) and mixed (stochastic) Nash equilibrium, respectively. In contrast, temporal-difference(TD)-learning, covariance-learning, and basic reinforcement learning fail to perform optimally for the stochastic strategy. Spike-based population reinforcement learning, shown to follow the stochastic reward gradient, is therefore a viable candidate to explain automated decision learning of a Nash equilibrium in two-player games.

Microarray based study on virulence-associated genes and resistance determinants of Staphylococcus aureus isolates from cattle

Staphylococcus aureus is a common pathogen which can colonise and infect not only man, but also domestic animals. Especially, infection of cattle is of high economic relevance as S. aureus is an important causal agent of bovine mastitis. In the present contribution, a DNA microarray was applied for the study of 144 different gene targets, including resistance genes and genes encoding exotoxins, in S. aureus isolated from cows. One hundred and twenty-eight isolates from Germany and Switzerland were tested. These isolates were assigned to 20 different strains and nine clonal complexes. The majority of isolates belonged either to apparently closely related clonal complexes 8, 25, and 97 (together 34.4%) or were related to the sequenced bovine strain RF122 (48.4%). Notable characteristics of S. aureus of bovine origin are the carriage of intact haemolysin beta (in 82% of isolates tested), the absence of staphylokinase (in 89.1%), the presence of allelic variants of several exotoxins such as toxic shock syndrome toxin and enterotoxin N, and the occurrence of the leukocidin lukF-P83/lukM (in 53.1%). Two isolates were methicillin-resistant S. aureus (MRSA). One of them was a clonal complex 8 MRSA related to the epidemic MRSA strain Irish 01. The other one belonged to ST398/spa-type 34 resembling a newly emerging MRSA strain which has been described to occur in humans as well as in domestic animals. The presence of these two strains highlights the possibility of transfers of S. aureus strains between different host species.

Sulfoxides as an intramolecular sulfenylating agent for indoles and diverse applications of the sulfide-sulfoxide redox cycle in organic chemistry

This dissertation involves study of various aspects of sulfoxide chemistry. Specifically designed t-butyl and propanenitrile sulfoxides tethered to indole-2-carboxamide were used as a source of intramolecular sulfenylating agents to synthesize novel indolo[3,2-b]-1-5-benzothiazepinones which are structurally analogous to the other biologically active benzothiazepinones. This study reveals that the intramolecular cyclization of sulfoxide follows an electrophilic sulfenylation (Sulfoxide Electrophilic Sulfenylation, SES) reaction pathway. Evidence of the absence of sulfenic acid as a transient reactive intermediate in such intramolecular cyclization is also provided. In another study, sulfoxide was used as a “protecting group” of thioether to synthesize 8-membered, indole substituted, thiazocine-2-acetic acid derivative via Ring Closing Metathesis (RCM). Protection (oxidation) of inert (to RCM) sulfide to sulfoxide followed by RCM produced cyclized product in good yields. Deprotection (reduction) of sulfoxide was achieved using Lawessons Reagent (L.R.). Application of the sulfide-sulfoxide redox cycle to solve the existing difficulties in using RCM methodology to thioethers is illustrated. A new design of a “molecular brake”, based on the sulfide-sulfoxide redox cycle is described. N-Ar rotation in simple isoindolines is controlled by the oxidation state of the proximate sulfur atom. Sulfide [S(II)] shows “free” [brake OFF] N-Ar rotation whereas sulfoxide displayed hindered [brake ON] N-Ar rotation. The semi-empirical molecular orbital (PM3) calculations revealed concerted pyramidalization of amidic nitrogen with N-Ar rotation.

Multimetallic complexes based on phosphine- and phosphine oxide- appended p-hydroquinones

Presented here, is the work done with a series of binucleating ligands based on phosphine and phosphine oxide appended p-hydroquinones and their reactions towards various metals sources. The long term goal of the project was to produce coordination polymers that would have novel electronic, magnetic, and optical properties which would be of use in the field of molecular electronics. Binucleating ligands contained a p-hydroquinone motif in which various phosphine- and phosphine oxide substituents have been placed in the ortho position relative to each of the hydroxy position were synthesized. A previously published synthetic method for such lugands utilized n-BuLi to form a phenyl lithium intermediate which was quenched with chlorodiphenylphosphine. This technique was also used to produce a ligand with diisopropylphosphine groups. Phosphine ligands, containing the same structural motif, were also generated using LDA as the lithiating agent. This technique was found to be higher yielding. Phosphine chalcogenide ligands were accessed by further oxidizing the low valent phosphorous centers with either hydrogen peroxide or with elemental sulfur. These ligands were characterized using multinuclear NMR, low and high resolution mass spectroscopy, FTIR, and single crystal X-ray diffraction. Their electrochemical properties were explored with cyclic voltammetry. The phosphine appended ligands were used in the synthesis of a several bimetallic complexes. It was found that the ligands readily reacted with NiCp2 and NiCp*2, displacing one of the cyclopentadiene (Cp) or pentamethylcyclopentadiene (Cp*) rings. A cyclopentadiene complexes, containing diisopropylphine, was readily oxidized by[FeCp2]PF6 to give a NMR silent mixed valence complex. Cyclic voltammetry of these complexes showed a number of reversible waves with a large potential separation. The mixed valence compounds also showed a large absorbance band in the NIR region which was assigned to be an intervalence charge transfer. The cyclic voltammetry and NIR spectroscopy suggest that these systems are very capable of efficient metal-to-metal charge transfer. These complexes were characterized by multinuclear NMR, single crystal X-ray diffraction, UV/VIS-NIR spectroscopy and elemental analysis. The phosphine oxide ligands were reacted with a variety of different metal sources but limited success was gained in obtaining single crystals, allowing structural characterization of these compounds. Single crystals were obtained from products generated by reacting the diphenylphosphine oxide ligand with (Bipy)Cu(NO3)2 and Cu(NO3)2. In all cases the ligand had been further oxidized to a 2,5-dihydroxy-1,4-benzoquinone motif. In the reaction between the diphenylphosphine oxide ligand and (Bipy)Cu(NO3)2 it was found that the phosphine oxide moiety was involved with intermolecular coordination leading to the formation of a one-dimensional polymer composed of a series of bimetallic complexes tethered together. When NaSbF6 was present in the reaction with (Bipy)Cu(NO3)2 a unique tetrametallic complex was formed. Here the phospine oxide moiety was oriented so that two bimetallic complexes were bound together. If only Cu(NO3)2 was present, a two-dimensional polymeric sheet was formed where the ligand was present in two different coordination modes. The electronic properties of these complexes remained to be assessed.