Bioanalytical applications of multicolour bioluminescence imaging: new tools for drug discovery and development

The subject of this thesis is multicolour bioluminescence analysis and how it can provide new tools for drug discovery and development.The mechanism of color tuning in bioluminescent reactions is not fully understood yet but it is object of intense research and several hypothesis have been generated. In the past decade key residues of the active site of the enzyme or in the surface surrounding the active site have been identified as responsible of different color emission. Anyway since bioluminescence reaction is strictly dependent from the interaction between the enzyme and its substrate D-luciferin, modification of the substrate can lead to a different emission spectrum too. In the recent years firefly luciferase and other luciferases underwent mutagenesis in order to obtain mutants with different emission characteristics. Thanks to these new discoveries in the bioluminescence field multicolour luciferases can be nowadays employed in bioanalysis for assay developments and imaging purposes. The use of multicolor bioluminescent enzymes expanded the potential of a range of application in vitro and in vivo. Multiple analysis and more information can be obtained from the same analytical session saving cost and time. This thesis focuses on several application of multicolour bioluminescence for high-throughput screening and in vivo imaging. Multicolor luciferases can be employed as new tools for drug discovery and developments and some examples are provided in the different chapters. New red codon optimized luciferase have been demonstrated to be improved tools for bioluminescence imaging in small animal and the possibility to combine red and green luciferases for BLI has been achieved even if some aspects of the methodology remain challenging and need further improvement. In vivo Bioluminescence imaging has known a rapid progress since its first application no more than 15 years ago. It is becoming an indispensable tool in pharmacological research. At the same time the development of more sensitive and implemented microscopes and low-light imager for a better visualization and quantification of multicolor signals would boost the research and the discoveries in life sciences in general and in drug discovery and development in particular.

New proton conducting membranes for fuel cell applications

In order to synthesize proton-conducting materials which retain acids in the membrane during fuel cell operating conditions, the synthesis of poly(vinylphosphonic acid) grafted polybenzimidazole (PVPA grafted PBI) and the fabrication of multilayer membranes are mainly focussed in this dissertation. Synthesis of PVPA grafted PBI membrane can be done according to "grafting through" method. In "grafting through" method (or macromonomer method), monomer (e.g., vinylphosphonic acid) is radically copolymerized with olefin group attached macromonomer (e.g., allyl grafted PBI and vinylbenzyl grafted PBI). This approach is inherently limited to synthesize graft-copolymer with well-defined architectural and structural parameters. The incorporation of poly(vinylphosphonic acid) into PBI lead to improvements in proton conductivity up to 10-2 S/cm. Regarding multilayer membranes, the proton conducting layer-by-layer (LBL) assembly of polymers by various strong acids such as poly(vinylphosphonic acid), poly(vinylsulfonic acid) and poly(styrenesulfonic acid) paired with basic polymers such as poly(4-vinylimidazole) and poly(benzimidazole), which are appropriate for ‘Proton Exchange Membranes for Fuel Cell’ applications have been described. Proton conductivity increases with increasing smoothness of the film and the maximum measured conductivity was 10-4 S/cm at 25°C. Recently, anhydrous proton-conducting membranes with flexible structural backbones, which show proton-conducting properties comparable to Nafion have been focus of current research. The flexible backbone of polymer chains allow for a high segmental mobility and thus, a sufficiently low glass transition temperature (Tg), which is an essential factor to reach highly conductive systems. Among the polymers with a flexible chain backbone, poly(vinylphosphonic acid), poly(vinylbenzylphosphonic acid), poly(2-vinylbenzimidazole), poly(4-styrenesulfonic acid), poly(4-vinylimidazole), poly(4-vinylimidazole-co-vinylphosphonic acid) and poly(4-vinylimidazole-co-4-styrenesulfonic acid) are interesting materials for fuel cell applications. Synthesis of polybenzimidazole with anthracene structural unit was carried out in order to avoid modification reaction in the imidazole ring, because anthracene would encourage the modification reaction with an olefin by Diels-Alder reaction.

Metaheuristics for Search Problems in Genomics - New Algorithms and Applications

In this thesis we made the first steps towards the systematic application of a methodology for automatically building formal models of complex biological systems. Such a methodology could be useful also to design artificial systems possessing desirable properties such as robustness and evolvability. The approach we follow in this thesis is to manipulate formal models by means of adaptive search methods called metaheuristics. In the first part of the thesis we develop state-of-the-art hybrid metaheuristic algorithms to tackle two important problems in genomics, namely, the Haplotype Inference by parsimony and the Founder Sequence Reconstruction Problem. We compare our algorithms with other effective techniques in the literature, we show strength and limitations of our approaches to various problem formulations and, finally, we propose further enhancements that could possibly improve the performance of our algorithms and widen their applicability. In the second part, we concentrate on Boolean network (BN) models of gene regulatory networks (GRNs). We detail our automatic design methodology and apply it to four use cases which correspond to different design criteria and address some limitations of GRN modeling by BNs. Finally, we tackle the Density Classification Problem with the aim of showing the learning capabilities of BNs. Experimental evaluation of this methodology shows its efficacy in producing network that meet our design criteria. Our results, coherently to what has been found in other works, also suggest that networks manipulated by a search process exhibit a mixture of characteristics typical of different dynamical regimes.

New functionalized ligands for luminescent metal complexes: from design to applications

The synthesis of luminescent metal complexes is a very challenging task since they can be regarded as the starting point for a lot of different areas. Luminescent complexes, in fact, can be used for technological, industrial, medical and biological applications. During my PhD I worked with different metals having distinguishing intrinsic properties that make them different from each other and, in particular, more or less suitable for the different possible uses. Iridium complexes show the best photophysical properties: they have high quantum yields, very long lifetimes and possess easily tunable emissions throughout the visible range. On the other hand, Iridium is very expensive and scarcely available. The aim of my work concerning this metal was, therefore, to synthesize ligands able not only to form luminescent complexes, but also able to add functionalities to the final complex, increasing its properties, and therefore its possible practical uses. Since Re(I) derivatives have been reported to be suitable as probes in biological system, and the use of Re(I) reduces the costs, the synthesized bifunctional ligands containing a pyridine-triazole and a biotin unit were employed to obtain new Re(I) luminescent probes. Part of my work involved the design and synthesis of new ligands able to form stable complexes with Eu(III) and Ce(III) salts, in order to obtain an emission in the range of visible light: these two metals are quite cheap and relatively non-toxic compared to other heavy metals. Finally, I plan to synthesize organic derivatives that already possessed an emission thanks to the presence of other many chromophoric groups and can be able to link the Zinc (II), a low cost and especially non-toxic “green” metal. Zinc has not its own emission, but when it sticks to ligands, it increases their photophysical properties.

57 Fe and 119 Sn Mössbauer studies on new Heusler compounds for spintronic applications

Seit der Entwicklung einer großen Vielfalt von Anwendungsmöglichkeiten der Spintronik auf Basis von Heusler Verbindungen innerhalb der letzten Dekade kann der Forschungsfortschritt an dieser Material Klasse in einer Vielzahl von Publikationen verfolgt werden. Eine typische Heusler Verbindung X2YZ besteht aus zwei Übergangsmetallen (X, Y) und einem Hauptgruppenelement (Z). Diese Arbeit berichtet von Heusler Verbindungen mit besonderem Augenmerk auf deren potentielle halbmetallische Eigenschaften und davon insbesondere solche, die eine richtungsabhängige magnetische Anisotropie (perpendicular magnetic anisotropy- PMA) zeigen könnten. PMA ist insbesondere für Spin transfer Torque (STT) Bauelemente von großem Interesse und tritt in tetragonalrnverzerrten Heusler Verbindungen auf. Bei STT-Elementen werden mittels spinpolarisierter Ströme die magnetische Orientierung von magnetischen Schichten beeinflusst.rnDie signifikantesten Ergebnisse dieser Arbeit sind: die Synthese neuer kubischen Heusler Phasen Fe2YZ, die theoretisch als tetragonal vorausgesagt wurden (Kapitel 1), die Synthese von Mn2FeGa, das in der tetragonal verzerrten Struktur kristallisiert und Potential für STT Anwendungen zeigt (Kapitel 2); die Synthese von Fe2MnGa, das einen magnetischen Phasenübergang mit exchange-bias (EB) Effekt zeigt, der auf einer Koexistenz von ferromagnetischen (FM) und antiferromagnetischen (AFM) Phasen beruht (Kapitel 3); Schlussendlich wird in Kapitel 4 die Synthese von Mn3−xRhxSn diskutiert, in welcher insbesondere tetragonales Mn2RhSn als potentielles Material für Anwendungen in derrnSpintronik vorgestellt wird.rnIn dieser Arbeit wurden hauptsächlich Heusler Verbindungen mit mößbaueraktiven Elementen 57Fe und 119Sn, synthetisiert und untersucht. Im Falle der hier untersuchten Heusler Verbindungen spielt die Charakterisierung durch Mößbauer Spektroskopie eine entscheidende Rolle, da Heusler Verbindungen meistens ein gewisses Maß an Fehlordnung aufweisen, welche deren magnetischen und strukturellen Eigenschaften beeinflussen kann. Die Art der Fehlordnung jedoch kann nur schwer durch standard Pulver-Röntgendiffraktion bestimmt werden, weshalb wir die Vorteile der Mößbauer Spektroskopie als lokale Methode nutzen, um den Typ und den Grad der Fehlordnung aufzuklären. rnDiese Arbeit ist wie folgt gegliedert:rnIn Kapitel 1 wurden die neuen, kubisch-weichferromagnetischen Heuslerphasen Fe2NiGe, Fe2CuGa und Fe2CuAl synthetisiert und charakterisiert. In vorangegangenen theoretischen Studien wurde für deren Existenz in tetragonaler Heuslerstruktur vorhergesagt.rnUngeachtet dessen belegten unsere experimentellen Untersuchungen, dass diese Verbindungen hauptsächlich in der kubischen invers Heusler(X-) struktur mit unterschiedlichen Anteilen an atomarer Fehlordnung kristallisieren. Alle Verbindungen sind weiche Ferromagneten mit hoher Curietemperatur bis zu 900K, weswegen alle als potentielle Materialien für magnetische Anwendungen geeignet sind. In Kapitel 2 wurde Mn2FeGa synthetisiert. Es zeigte sich, dass Mn2FeGa nach Temperatur Nachbehandlung bei 400°C die invers tetragonale Struktur (I4m2) annimmt. Theoretisch wurde die Existenz in der inversen kubischen Heuslerstruktur vorausgesagt. Abhängig von den Synthesebedingungen ändern sich die magnetischen und strukturellen Eigenschaften von Mn2FeGa eklatant. Deshalb ändert sich die Kristallstruktur von M2FeGa bei Temperung bei 800 °C zu einer pseudokubischen Cu3Au-artigen Struktur, in welcher Fe- und Mn-Atome statistisch verteilt vorliegen. Dieser Übergang der Kristallstrukturen wurde durch Mößbauer Spektroskopie anhand des Vorliegens oder Fehlens der Quadrupolaufspaltung im Falle der invers tetragonalen bzw. pseudokubischen Modifikation nachgewiesen. In Kapitel 3 wurde Fe2MnGa ebenfalls erfolgreich synthetisiert und durch verschiedene Methoden charakterisiert. Der Zusammenhang von Kristallstruktur und magnetischen Eigenschaften wurde durch verschiedene Temperungskonditionen und mechanischer Behandlung untersucht. Der Schwerpunkt lag auf einer geschmolzenen Probe ohne weitere Temperung, die einen FM-AFM Phasenübergang zeigte. Diese magnetische Phasenumwandlung führt zu einem starken EB-Verhalten, welches seinen Ursprung hauptsächlich in der Koexistenz von FM- und AFM-Phasen unterhalb der FMAFM- Übergangstemperatur hat. Kapitel 4 ist den neuen Mn-basierten Heusler-Verbindungen Mn3−xRhxSn gewidmet, bei denen wir versuchten, durch den Austausch von Mn durch das größere Rh eine Umwandlung zu einer tetragonalen Struktur von den hexagonalen Mn3Sn-Struktur zu erreichen. Als interessant stellten sich Mn2RhSn und Mn2.1Rh0.9Sn heraus, da sie aus nur einer Phase vorzuliegen scheinen, wohingegen die anderen Verbindungen aus gemischten Phasen mit gleichzeitiger starken Fehlordnung bestehen. Im abschließenden Anhang wurden die Fehlordnung und gelegentliche Mischphasen einer großen Auswahl von Mn3−xFexGa Materialien mit 1≤x≤3, dokumentiert.rn

Diffusion-weighted MRI in head and neck radiology: applications in oncology

Extracranial application of diffusion-weighted magnetic resonance imaging (MRI) has gained increasing importance in recent years. As a result of technical advances, this new non-invasive functional technique has also been applied in head and neck radiology for several clinical indications. In cancer imaging, diffusion-weighted MRI can be performed for tumour detection and characterization, monitoring of treatment response as well as the differentiation of recurrence and post-therapeutic changes after radiotherapy. Even for lymph node staging promising results have been reported recently. This review article provides overview of potential applications of diffusion-weighted MRI in head and neck with the main focus on its applications in oncology.

New method for quantification and statistical analysis of nociceptive reflex receptive fields in humans

A method for quantifying nociceptive withdrawal reflex receptive fields in human volunteers and patients is described. The reflex receptive field (RRF) for a specific muscle denotes the cutaneous area from which a muscle contraction can be evoked by a nociceptive stimulus. The method is based on random stimulations presented in a blinded sequence to 10 stimulation sites. The sensitivity map is derived by interpolating the reflex responses evoked from the 10 sites. A set of features describing the size and location of the RRF is presented based on statistical analysis of the sensitivity map within every subject. The features include RRF area, volume, peak location and center of gravity. The method was applied to 30 healthy volunteers. Electrical stimuli were applied to the sole of the foot evoking reflexes in the ankle flexor tibialis anterior. The RRF area covered a fraction of 0.57+/-0.06 (S.E.M.) of the foot and was located on the medial, distal part of the sole of the foot. An intramuscular injection into flexor digitorum brevis of capsaicin was performed in one spinal cord injured subject to attempt modulation of the reflex receptive field. The RRF area, RRF volume and location of the peak reflex response appear to be the most sensitive measures for detecting modulation of spinal nociceptive processing. This new method has important potential applications for exploring aspects of central plasticity in volunteers and patients. It may be utilized as a new diagnostic tool for central hypersensitivity and quantification of therapeutic interventions.

CompAS: A new approach to commonality and variability analysis with applications in computer assisted orthopaedic surgery

In rapidly evolving domains such as Computer Assisted Orthopaedic Surgery (CAOS) emphasis is often put first on innovation and new functionality, rather than in developing the common infrastructure needed to support integration and reuse of these innovations. In fact, developing such an infrastructure is often considered to be a high-risk venture given the volatility of such a domain. We present CompAS, a method that exploits the very evolution of innovations in the domain to carry out the necessary quantitative and qualitative commonality and variability analysis, especially in the case of scarce system documentation. We show how our technique applies to the CAOS domain by using conference proceedings as a key source of information about the evolution of features in CAOS systems over a period of several years. We detect and classify evolution patterns to determine functional commonality and variability. We also identify non-functional requirements to help capture domain variability. We have validated our approach by evaluating the degree to which representative test systems can be covered by the common and variable features produced by our analysis.

Social Work and a New Social Order - Challenging Neo-liberalism's Erosion of Solidarity

The world in which social work operates today is a very different world from that in which most of us took their social work training, and the changes we are facing are profound. This paper argues that these changes are not merely a regime change in social policy but that they are essentially about a re-ordering of social relationships and attempt to model them on neo-liberal ideas. In view of these pressures it is understandable that social workers often try to ignore those changes and withdraw into a private world of therapeutic relationships in which the methods they trained in are made to be still valid, or they simply go along with new service delivery designs without asking too many questions. Both reactions fail to question what the "social" can still mean in the light of these changes and how social workers can fulfil their mandate to be responsible for the social dimension of public life. Nothing less than a head-on challenge of the basic presuppositions of neo-liberalism (Willke 2003) and their manifold applications to social service delivery systems will thereby suffice.

Calving Giant Icebergs: Old Principles, New Applications

Earth-orbiting satellites can now monitor calving of large icebergs from ice shelves bordering the marine West Antarctic Ice Sheet, and recent calving events have stimulated interest in calving mechanisms. To advance this interest pioneering work in brittle and ductile fracture mechanics is reviewed, leading to a new application to calving of giant icebergs from Antarctic ice shelves. The aim is to view iceberg calving as more than terminal events for Antarctic ice when glaciologists lose interest. Instead calving launches Antarctic ice into the larger dynamic system of Earth's climate machine. This encourages a holistic approach to glaciology.

A New End-User Composition Model to Empower Knowledge Workers to Develop Rich Internet Applications

Enabling real end-user programming development is the next logical stage in the evolution of Internetwide service-based applications. Even so, the vision of end users programming their own web-based solutions has not yet materialized. This will continue to be so unless both industry and the research community rise to the ambitious challenge of devising an end-to-end compositional model for developing a new age of end-user web application development tools. This paper describes a new composition model designed to empower programming-illiterate end users to create and share their own off-the-shelf rich Internet applications in a fully visual fashion. This paper presents the main insights and outcomes of our research and development efforts as part of a number of successful European Union research projects. A framework implementing this model was developed as part of the European Seventh Framework Programme FAST Project and the Spanish EzWeb Project and allowed us to validate the rationale behind our approach.