De Novo Design of Foldamers for Preparation of Nanostructured Materials

This thesis deals with the synthesis and the conformation analysis of hybrid foldamers containing the 4-carboxyoxazolidin-2-one unit or related molecules, in which an imido-type function is obtained by coupling the nitrogen of the heterocycle with the carboxylic acid moiety of the next unit. The imide group is characterized by a nitrogen atom connected to an endocyclic and an exocyclic carbonyl, which tend always to adopt the trans conformation. As a consequence of this locally constrained disposition effect, these imide-type oligomers are forced to fold in ordered conformations. The synthetic approach is highly tuneable with endless variations, so, simply by changing the design and the synthesis, a wide variety of foldamers with the required properties may be prepared “on demand”. Thus a wide variety of unusual secondary structures and interesting supramolecular materials may be obtained with hybrid foldamers. The behaviour in the solid state of some of these compounds has been analyzed in detail, thus showing the formation of different kinds of supramolecular materials that may be used for several applications. A winning example is the production of a bolaamphiphilic gelators that may also be doped with small amounts of dansyl containing compounds, needed to show the cellular uptake into IGROV-1 cells, by confocal laser scanning microscopy. These gels are readily internalized by cells and are biologically inactive, making them very good candidates in the promising field of drug delivery. In the last part of the thesis, a particular attention was directed to the search of new scaffolds that behave as constrained amino acid mimetics, showing that tetramic acids derivatives could be good candidates for the synthesis and applications of molecules having an ordered secondary structure.

Machine-learning methods for structure prediction of β-barrel membrane proteins

Different types of proteins exist with diverse functions that are essential for living organisms. An important class of proteins is represented by transmembrane proteins which are specifically designed to be inserted into biological membranes and devised to perform very important functions in the cell such as cell communication and active transport across the membrane. Transmembrane β-barrels (TMBBs) are a sub-class of membrane proteins largely under-represented in structure databases because of the extreme difficulty in experimental structure determination. For this reason, computational tools that are able to predict the structure of TMBBs are needed. In this thesis, two computational problems related to TMBBs were addressed: the detection of TMBBs in large datasets of proteins and the prediction of the topology of TMBB proteins. Firstly, a method for TMBB detection was presented based on a novel neural network framework for variable-length sequence classification. The proposed approach was validated on a non-redundant dataset of proteins. Furthermore, we carried-out genome-wide detection using the entire Escherichia coli proteome. In both experiments, the method significantly outperformed other existing state-of-the-art approaches, reaching very high PPV (92%) and MCC (0.82). Secondly, a method was also introduced for TMBB topology prediction. The proposed approach is based on grammatical modelling and probabilistic discriminative models for sequence data labeling. The method was evaluated using a newly generated dataset of 38 TMBB proteins obtained from high-resolution data in the PDB. Results have shown that the model is able to correctly predict topologies of 25 out of 38 protein chains in the dataset. When tested on previously released datasets, the performances of the proposed approach were measured as comparable or superior to the current state-of-the-art of TMBB topology prediction.

Mechanical behaviour of composite spandrels in unreinforced masonry buildings

La presente tesi tratta il comportamento meccanico delle fasce di piano in muratura composite. Con tale termine ci si riferisce alle fasce di piano che hanno al di sotto un elemento portante in conglomerato cementizio armato, come ad esempio cordoli o solai. Assieme ai maschi murari, le fasce di piano costituiscono gli elementi portanti di una parete in muratura. Tuttavia, in caso di analisi sismica di un edificio in muratura, l’effetto fornito da tali elementi è trascurato e si considera solamente il contributo dei maschi murari. Ciò è dovuto anche alla scarsa conoscenza che ancora oggi si possiede sul loro comportamento meccanico. Per questo motivo diversi gruppi di ricerca tutt’ora sono impegnati in tale studio. In particolare, il lavoro di questa tesi, s’inserisce nel più ampio progetto di ricerca condotto dalla professoressa Katrin Beyer, direttrice del Laboratorio di Ingegneria Sismica e Dinamica Strutturale del Politecnico di Losanna (Svizzera).

Hyperverzweigte Lacton-Copolymere: enzymatische Synthese, Charakterisierung und Darstellung strukturierter Polymernetzwerke = (Hyperbranched lactone copolymers by enzyme catalysis: synthesis, characterization and preparation of structured polymer networks)

Hyperverzweigte Polymere erfuhren in den letzten Jahren immer mehr Beachtung, da sie im Vergleich zu ihren linearen Analoga besondere Eigenschaften besitzen. Im Jahre 2002 wurde die erste enzymkatalysierte Darstellung hyperverzweigter Poly(epsilon-caprolacton)e (hb-PCL) beschrieben. Hier ermöglichte das Konzept der konkurrierenden ringöffnenden Polymerisation und Polykondensation die Kontrolle der Eigenschaften des dargestellten Polymers. Detaillierte Untersuchungen in Hinblick auf Grenzen und Möglichkeiten, aber auch die Synthese im Technikumsmaßstab sind wesentliche Aspekte dieser Arbeit. Außerdem wird ein neues Konzept eingeführt, das Reknitting genannt wurde. Ziel desselben ist das Recycling kommerziellen, linearen PCLs mittels Umesterung zu hb-PCL durch Enzymkatalyse. Diese hb-PCLs zeigen vergleichbare Eigenschaften zu den aus den Comonomeren dargestellten. Ausgehend von hb-PCL sollte eine geeignete Route zu methacrylierten Vernetzerverbindungen entwickelt werden. Aus Mischungen derselben mit 2-Hydroxyethylmethacrylat wurden komplexe Netzwerkarchitekturen durch Copolymerisation erhalten. Diese Netzwerke wurden in Hinblick auf ihre mechanisch physikalischen Eigenschaften untersucht. Zuletzt wurden Screeningexperimente an anderen zyklischen Estern durchgeführt, da ein Transfer des oben vorgestellten Konzepts angestrebt wurde. Zwei neue hyperverzweigte Polymerklassen, hb-Poly(delta-valerolacton) und hb-Polytrimethylencarbonat wurden detaillierter untersucht und in Ihren Eigenschaften mit hb-PCL verglichen.

Alkylidene malonates and acetoacetates as intermediates for the preparation of bioactive molecules

In this thesis we investigated the versatility and the potential applications of different kinds of alkylidene malonates, acetoacetates, malonamides and acetoacetoamides. Our research group devoted great attention to this kind of compounds since alkylidenes can be considered important intermediates in the synthesis of several scaffolds, to be inserted into molecules of potential biological and pharmaceutical interest. The increasing use of alkylidenes is due to their ability to react as unsaturated electrophiles and to the possibility to exploit them as intermediates for the introduction of different kind of functionalities.The preparation of alkylidene malonates, acetoacetates, malonamides and acetoacetoamides is presented in chapter 1. This section deals with different preparation methods of alkylidenes that we developed during the last few years and to the technologies involved for each synthetic protocol. The reactivity that allowed to use the alkylidenes as intermediates in the synthesis of scaffolds for biologically active compounds is shown in chapter 2. In particular, we will discuss the most important reactions used to obtain the desired molecules, and we will focus on the most interesting aspects of these latter ones. Finally, chapter 3 will illustrate the potential applications and the related syntheses of potential bioactive compounds. The synthesized molecules find application in several fields and for this reason we considered each class of compounds in its related branch of interest.

Preparation of cold Mg + ion clouds for sympathetic cooling of highly charged ions at SPECTRAP

Die Elektronen in wasserstoff- und lithium-ähnlichen schweren Ionen sind den extrem starken elektrischen und magnetischen Feldern in der Umgebung des Kerns ausgesetzt. Die Laserspektroskopie der Hyperfeinaufspaltung im Grundzustand des Ions erlaubt daher einen sensitiven Test der Quantenelektrodynamik in starken Feldern insbesondere im magnetischen Sektor. Frühere Messungen an wasserstoffähnlichen Systemen die an einer Elektronenstrahl-Ionenfalle (EBIT) und am Experimentierspeicherring (ESR) der GSI Darmstadt durchgeführt wurden, waren in ihrer Genauigkeit durch zu geringe Statistik, einer starken Dopplerverbreiterung und der großen Unsicherheit in der Ionenenergie limitiert. Das ganze Potential des QED-Tests kann nur dann ausgeschöpft werden, wenn es gelingt sowohl wasserstoff- als auch lithium-ähnliche schwere Ionen mit einer um 2-3 Größenordnung gesteigerten Genauigkeit zu spektroskopieren. Um dies zu erreichen, wird gegenwärtig das neue Penningfallensystem SPECTRAP an der GSI aufgebaut und in Betrieb genommen. Es ist speziell für die Laserspektroskopie an gespeicherten hochgeladenen Ionen optimiert und wird in Zukunft von HITRAP mit nierderenergetischen hochgeladenen Ionen versorgt werden.rnrnSPECTRAP ist eine zylindrische Penningfalle mit axialem Zugang für die Injektion von Ionen und die Einkopplung eines Laserstrahls sowie einem radialen optischen Zugang für die Detektion der Fluoreszenz. Um letzteres zu realisieren ist der supraleitende Magnet als Helmholtz-Spulenpaar ausgelegt. Um die gewünschte Genauigkeit bei der Laserspektroskopie zu erreichen, muss ein effizienter und schneller Kühlprozess für die injizierten hochegeladenen Ionen realisiert werden. Dies kann mittels sympathetischer Kühlung in einer lasergekühlten Wolke leichter Ionen realisiert werden. Im Rahmen dieser Arbeit wurde ein Lasersystem und eine Ionenquelle für die Produktion einer solchen 24Mg+ Ionenwolke aufgebaut und erfolgreich an SPECTRAP in Betrieb genommen. Dazu wurde ein Festkörperlasersystem für die Erzeugung von Licht bei 279.6 nm entworfen und aufgebaut. Es besteht aus einem Faserlaser bei 1118 nm der in zwei aufeinanderfolgenden Frequenzverdopplungsstufen frequenzvervierfacht wird. Die Verdopplerstufen sind als aktiv stabilisierte Resonantoren mit nichtlinearen Kristallen ausgelegt. Das Lasersystem liefert unter optimalen Bedingeungen bis zu 15 mW bei der ultravioletten Wellenlänge und erwies sich während der Teststrahlzeiten an SPECTRAP als ausgesprochen zuverlässig. Desweiteren wurde eine Ionequelle für die gepulste Injektion von Mg+ Ionen in die SPECTRAP Falle entwickelt. Diese basiert auf der Elektronenstoßionisation eines thermischen Mg-Atomstrahls und liefert in der gepulsten Extraktion Ionenbündel mit einer kleinen Impuls- und Energieverteilung. Unter Nutzung des Lasersystems konnten damit an SPECTRAP erstmals Ionenwolken mit bis zu 2600 lasergekühlten Mg Ionen erzeugt werden. Der Nachweis erfolgte sowohl mittels Fluoreszenz als auch mit der FFT-ICR Technik. Aus der Analyse des Fluoreszenz-Linienprofils lässt sich sowohl die Sensitivität auf einzelne gespeicherte Ionen als auch eine erreichte Endtemperatur in der Größenordnung von ≈ 100 mK nach wenigen Sekunden Kühlzeit belegen.

Coating of surfaces of composite materials with enzymatically formed biosilica

Die Bildung kieselsäurehaltiger Spicula in marinen Schwämmen ist nur möglich durch die enzymatische Aktivität des Silicatein- in Verbindung mit der stöchiometrischen Selbstassemblierung des Enzyms mit anderen Schwammproteinen. Die vorliegende Arbeit basiert auf einem biomimetischen Ansatz mit dem Ziel, unterschiedliche Oberflächen für biotechnologische und biomedizinische Anwendungen mit Biosilica und Biotitania zu beschichten und zu funktionalisieren. Für biotechnologische Anwendungen ist dabei das Drucken von Cystein-getaggtem Silicatein auf Gold-Oberflächen von Bedeutung, denn es ermöglichte die Bildung definierter Biotitania-Strukturen (Anatas), welche als Photokatalysator den Abbau eines organischen Farbstoffs bewirkten. Des Weiteren zeigte sich die bio-inspirierte Modifikation von Tyrosin-Resten an rekombinantem Silicatein-(via Tyrosinase) als vielversprechendes Werkzeug zur Beschleunigung der Selbstassemblierung des Enzyms zu mesoskaligen Filamenten. Durch eine solche Modifikation konnte Silicatein auch auf der Oberfläche von anorganischen Partikeln immobilisiert werden, welches die Assemblierung von anorganisch-organischen Verbundwerkstoffen in wäßriger Umgebung förderte. Die resultierenden supramolekularen Strukturen könnten dabei in bio-inspirierten und biotechnologischen Anwendungen genutzt werden. Weiterhin wurde in der vorliegenden Arbeit die Sekundärstruktur von rekombinantem Silicatein- (Monomer und Oligomer) durch Raman Spektroskopie analysiert, nachdem das Protein gemäß einer neu etablierten Methode rückgefaltet worden war. Diese Spektraldaten zeigten insbesondere Änderungen der Proteinkonformation durch Solubilisierung und Oligomerisierung des Enzyms. Außerdem wurden die osteoinduzierenden und osteogenen Eigenschaften unterschiedlicher organischer Polymere, die herkömmlich als Knochenersatzmaterial genutzt werden, durch Oberflächenmodifikation mit Silicatein/Biosilica verbessert: Die bei der Kultivierung knochenbildender Zellen auf derart oberflächenbehandelten Materialien beobachtete verstärkte Biomineralisierung, Aktivierung der Alkalischen Phosphatase, und Ausbildung eines typischen zellulären Phänotyps verdeutlichen das Potential von Silicatein/Biosilica für der Herstellung neuartiger Implantat- und Knochenersatzmaterialien.

Long-term results after muscle-rib flap transfer for reconstruction of composite limb defects

The authors present the long-term results in a series of 44 cases with post-traumatic bone defects solved with muscle-rib flaps, between March 1997 and December 2007. In these cases, we performed 21 serratus anterior-rib flaps (SA-R), 10 latissimus dorsi-rib flaps (LD-R), and 13 LD-SA-R. The flaps were used in upper limb in 18 cases and in lower limb in 26 cases. With an overall immediate success rate of 95.4% (42 of 44 cases) and a primary bone union rate of 97.7% (43 of 44 cases), and despite the few partisans of this method, we consider that this procedure still remains very usefully for small and medium bone defects accompanied by large soft tissue defects.

Relevance of In-vitro Tests of Adhesive and Composite Dental Materials. A Review in 3 Parts. Part 2: Non-standardized tests of composite materials

Summary The first part of this review examined ISO approval requirements and in vitro testing. In the second part, non-standardized test methods for composite materials are presented and discussed. Physical tests are primarily described. Analyses of surface gloss and alterations, as well as aging simulations of dental materials are presented. Again, the importance of laboratory tests in determining clinical outcomes is evaluated. Differences in the measurement protocols of the various testing institutes and how these differences can in?uence the results are also discussed. Because there is no standardization of test protocols, the values determined by different institutes cannot be directly compared. However, the ranking of the tested materials should be the same if a valid protocol is applied by different institutes. The modulus of elasticity, the expansion after water sorption, and the polishability of the material are all clinically relevant, whereas factors measured by other test protocols may have no clinical correlation. The handling properties of the materials are highly dependent on operators' preferences. Therefore, no standard values can be given.

Relevance of in vitro tests of adhesive and composite dental materials, a review in 3 parts. Part 1: Approval requirements and standardized testing of composite materials according to ISO specifications

The first part of this three-part review on the relevance of laboratory testing of composites and adhesives deals with approval requirements for composite materials. We compare the in vivo and in vitro literature data and discuss the relevance of in vitro analyses. The standardized ISO protocols are presented, with a focus on the evaluation of physical parameters. These tests all have a standardized protocol that describes the entire test set-up. The tests analyse flexural strength, depth of cure, susceptibility to ambient light, color stability, water sorption and solubility, and radiopacity. Some tests have a clinical correlation. A high flexural strength, for instance, decreases the risk of fractures of the marginal ridge in posterior restorations and incisal edge build-ups of restored anterior teeth. Other tests do not have a clinical correlation or the threshold values are too low, which results in an approval of materials that show inferior clinical properties (e.g., radiopacity). It is advantageous to know the test set-ups and the ideal threshold values to correctly interpret the material data. Overall, however, laboratory assessment alone cannot ensure the clinical success of a product.

Preparation of intact bovine tail intervertebral discs for organ culture

The intervertebral disc (IVD) is the joint of the spine connecting vertebra to vertebra. It functions to transmit loading of the spine and give flexibility to the spine. It composes of three compartments: the innermost nucleus pulposus (NP) encompassing by the annulus fibrosus (AF), and two cartilaginous endplates connecting the NP and AF to the vertebral body on both sides. Discogenic pain possibly caused by degenerative intervertebral disc disease (DDD) and disc herniations has been identified as a major problem in our modern society. To study possible mechanisms of IVD degeneration, in vitro organ culture systems with live disc cells are highly appealing. The in vitro culture of intact bovine coccygeal IVDs has advanced to a relevant model system, which allows the study of mechano-biological aspects in a well-controlled physiological and mechanical environment. Bovine tail IVDs can be obtained relatively easy in higher numbers and are very similar to the human lumbar IVDs with respect to cell density, cell population and dimensions. However, previous bovine caudal IVD harvesting techniques retaining cartilaginous endplates and bony endplates failed after 1-2 days of culture since the nutrition pathways were obviously blocked by clotted blood. IVDs are the biggest avascular organs, thus, the nutrients to the cells in the NP are solely dependent on diffusion via the capillary buds from the adjacent vertebral body. Presence of bone debris and clotted blood on the endplate surfaces can hinder nutrient diffusion into the center of the disc and compromise cell viability. Our group established a relatively quick protocol to "crack"-out the IVDs from the tail with a low risk for contamination. We are able to permeabilize the freshly-cut bony endplate surfaces by using a surgical jet lavage system, which removes the blood clots and cutting debris and very efficiently reopens the nutrition diffusion pathway to the center of the IVD. The presence of growth plates on both sides of the vertebral bone has to be avoided and to be removed prior to culture. In this video, we outline the crucial steps during preparation and demonstrate the key to a successful organ culture maintaining high cell viability for 14 days under free swelling culture. The culture time could be extended when appropriate mechanical environment can be maintained by using mechanical loading bioreactor. The technique demonstrated here can be extended to other animal species such as porcine, ovine and leporine caudal and lumbar IVD isolation.

Measuring substrate binding and affinity of purified membrane transport proteins using the scintillation proximity assay

The scintillation proximity assay (SPA) is a rapid radioligand binding assay. Upon binding of radioactively labeled ligands (here L-[(3)H]arginine or D-[(3)H]glucose) to acceptor proteins immobilized on fluoromicrospheres (containing the scintillant), a light signal is stimulated and measured. The application of SPA to purified, detergent-solubilized membrane transport proteins allows substrate-binding properties to be assessed (e.g., substrate specificity and affinity), usually within 1 d. Notably, the SPA makes it possible to study specific transporters without interference from other cellular components, such as endogenous transporters. Reconstitution of the target transporter into proteoliposomes is not required. The SPA procedure allows high sample throughput and simple sample handling without the need for washing or separation steps: components are mixed in one well and the signal is measured directly after incubation. Therefore, the SPA is an excellent tool for high-throughput screening experiments, e.g., to search for substrates and inhibitors, and it has also recently become an attractive tool for drug discovery.