Expression of human protein S100A7 (psoriasin), preparation of antibody and application to human larynx squamous cell carcinoma

Background Up-regulation of S100A7 (Psoriasin), a small calcium-binding protein, is associated with the development of several types of carcinomas, but its function and possibility to serve as a diagnostic or prognostic marker have not been fully defined. In order to prepare antibodies to the protein for immunohistochemical studies we produced the recombinant S100A7 protein in E. coli. mRNA extracted from human tracheal tumor tissue which was amplified by RT-PCR to provide the region coding for the S100A7 gene. The amplified fragment was cloned in the vector pCR2.1-TOPO and sub-cloned in the expression vector pAE. The protein rS100A7 (His-tag) was expressed in E. coli BL21::DE3, purified by affinity chromatography on an Ni-NTA column, recovered in the 2.0 to 3.5 mg/mL range in culture medium, and used to produce a rabbit polyclonal antibody anti-rS100A7 protein. The profile of this polyclonal antibody was evaluated in a tissue microarray. Results The rS100A7 (His-tag) protein was homogeneous by SDS-PAGE and mass spectrometry and was used to produce an anti-recombinant S100A7 (His-tag) rabbit serum (polyclonal antibody anti-rS100A7). The molecular weight of rS100A7 (His-tag) protein determined by linear MALDI-TOF-MS was 12,655.91 Da. The theoretical mass calculated for the nonapeptide attached to the amino terminus is 12,653.26 Da (delta 2.65 Da). Immunostaining with the polyclonal anti-rS100A7 protein generated showed reactivity with little or no background staining in head and neck squamous cell carcinoma cells, detecting S100A7 both in nucleus and cytoplasm. Lower levels of S100A7 were detected in non-neoplastic tissue. Conclusions The polyclonal anti-rS100A7 antibody generated here yielded a good signal-to-noise contrast and should be useful for immunohistochemical detection of S100A7 protein. Its potential use for other epithelial lesions besides human larynx squamous cell carcinoma and non-neoplastic larynx should be explored in future.

Comparison of the n-alkanes and polycyclic aromatic hydrocarbons concentrations in the atmosphere during the preparation of warm and hot mixtures asphalt for pavements

O asfalto é utilizado na produção de misturas asfálticas a quente (HMA) para a pavimentação e, devido às altas temperaturas empregadas, gera fumos que contêm n-alcanos e hidrocarbonetos policíclicos aromáticos (HPAs). As misturas asfálticas preparadas em temperaturas mais baixas, como as misturas asfálticas mornas (WMA), podem contribuir na redução das emissões daqueles compostos e economizar energia. Este trabalho investiga os n-alcanos e os HPAs nas partículas totais em suspensão durante a preparação de uma WMA, em comparação com uma HMA, em laboratório. Os resultados mostraram que os n-alcanos da WMA e da HMA apresentaram Cmáx no n-C26 e n-C28, respectivamente, e o teor de n-alcanos total foi maior na HMA do que na WMA. Ademais, verificou-se que o benzo[b]fluoranteno e benzo[a]antraceno constituíam os maiores HPAs na WMA, enquanto as temperaturas mais altas da HMA volatilizaram todos seus grandes HPAs, demonstrando maior potencial de exposição por inalação.

Reactive sputter magnetron reactor for preparation of thin films and simultaneous in-situ structural study by X-ray diffraction.

Reactive Sputter Magnetron (RSM) is a widely used technique to thin films growing of compounds both, in research laboratories and in industrial processes. The nature of the deposited compound will depend then on the nature of the magnetron target and the nature of the ions generated in the plasma. One important aspect of the problem is the knowledge of the evolution of the film during the process of growing itself. In this work, we present the design, construction of a chamber to be installed in the Huber goniometer in the XRD2 line of LNLS in Campinas, which allows in situ growing kinetic studies of thin films.

Some issues concerning the dynamic response and damage of composite laminates subjected to low velocity impact

Abstract. This thesis presents a discussion on a few specific topics regarding the low velocity impact behaviour of laminated composites. These topics were chosen because of their significance as well as the relatively limited attention received so far by the scientific community. The first issue considered is the comparison between the effects induced by a low velocity impact and by a quasi-static indentation experimental test. An analysis of both test conditions is presented, based on the results of experiments carried out on carbon fibre laminates and on numerical computations by a finite element model. It is shown that both quasi-static and dynamic tests led to qualitatively similar failure patterns; three characteristic contact force thresholds, corresponding to the main steps of damage progression, were identified and found to be equal for impact and indentation. On the other hand, an equal energy absorption resulted in a larger delaminated area in quasi-static than in dynamic tests, while the maximum displacement of the impactor (or indentor) was higher in the case of impact, suggesting a probably more severe fibre damage than in indentation. Secondly, the effect of different specimen dimensions and boundary conditions on its impact response was examined. Experimental testing showed that the relationships of delaminated area with two significant impact parameters, the absorbed energy and the maximum contact force, did not depend on the in-plane dimensions and on the support condition of the coupons. The possibility of predicting, by means of a simplified numerical computation, the occurrence of delaminations during a specific impact event is also discussed. A study about the compressive behaviour of impact damaged laminates is also presented. Unlike most of the contributions available about this subject, the results of compression after impact tests on thin laminates are described in which the global specimen buckling was not prevented. Two different quasi-isotropic stacking sequences, as well as two specimen geometries, were considered. It is shown that in the case of rectangular coupons the lay-up can significantly affect the damage induced by impact. Different buckling shapes were observed in laminates with different stacking sequences, in agreement with the results of numerical analysis. In addition, the experiments showed that impact damage can alter the buckling mode of the laminates in certain situations, whereas it did not affect the compressive strength in every case, depending on the buckling shape. Some considerations about the significance of the test method employed are also proposed. Finally, a comprehensive study is presented regarding the influence of pre-existing in-plane loads on the impact response of laminates. Impact events in several conditions, including both tensile and compressive preloads, both uniaxial and biaxial, were analysed by means of numerical finite element simulations; the case of laminates impacted in postbuckling conditions was also considered. The study focused on how the effect of preload varies with the span-to-thickness ratio of the specimen, which was found to be a key parameter. It is shown that a tensile preload has the strongest effect on the peak stresses at low span-to-thickness ratios, leading to a reduction of the minimum impact energy required to initiate damage, whereas this effect tends to disappear as the span-to-thickness ratio increases. On the other hand, a compression preload exhibits the most detrimental effects at medium span-to-thickness ratios, at which the laminate compressive strength and the critical instability load are close to each other, while the influence of preload can be negligible for thin plates or even beneficial for very thick plates. The possibility to obtain a better explanation of the experimental results described in the literature, in view of the present findings, is highlighted. Throughout the thesis the capabilities and limitations of the finite element model, which was implemented in an in-house program, are discussed. The program did not include any damage model of the material. It is shown that, although this kind of analysis can yield accurate results as long as damage has little effect on the overall mechanical properties of a laminate, it can be helpful in explaining some phenomena and also in distinguishing between what can be modelled without taking into account the material degradation and what requires an appropriate simulation of damage. Sommario. Questa tesi presenta una discussione su alcune tematiche specifiche riguardanti il comportamento dei compositi laminati soggetti ad impatto a bassa velocità. Tali tematiche sono state scelte per la loro importanza, oltre che per l’attenzione relativamente limitata ricevuta finora dalla comunità scientifica. La prima delle problematiche considerate è il confronto fra gli effetti prodotti da una prova sperimentale di impatto a bassa velocità e da una prova di indentazione quasi statica. Viene presentata un’analisi di entrambe le condizioni di prova, basata sui risultati di esperimenti condotti su laminati in fibra di carbonio e su calcoli numerici svolti con un modello ad elementi finiti. È mostrato che sia le prove quasi statiche sia quelle dinamiche portano a un danneggiamento con caratteristiche qualitativamente simili; tre valori di soglia caratteristici della forza di contatto, corrispondenti alle fasi principali di progressione del danno, sono stati individuati e stimati uguali per impatto e indentazione. D’altro canto lo stesso assorbimento di energia ha portato ad un’area delaminata maggiore nelle prove statiche rispetto a quelle dinamiche, mentre il massimo spostamento dell’impattatore (o indentatore) è risultato maggiore nel caso dell’impatto, indicando la probabilità di un danneggiamento delle fibre più severo rispetto al caso dell’indentazione. In secondo luogo è stato esaminato l’effetto di diverse dimensioni del provino e diverse condizioni al contorno sulla sua risposta all’impatto. Le prove sperimentali hanno mostrato che le relazioni fra l’area delaminata e due parametri di impatto significativi, l’energia assorbita e la massima forza di contatto, non dipendono dalle dimensioni nel piano dei provini e dalle loro condizioni di supporto. Viene anche discussa la possibilità di prevedere, per mezzo di un calcolo numerico semplificato, il verificarsi di delaminazioni durante un determinato caso di impatto. È presentato anche uno studio sul comportamento a compressione di laminati danneggiati da impatto. Diversamente della maggior parte della letteratura disponibile su questo argomento, vengono qui descritti i risultati di prove di compressione dopo impatto su laminati sottili durante le quali l’instabilità elastica globale dei provini non è stata impedita. Sono state considerate due differenti sequenze di laminazione quasi isotrope, oltre a due geometrie per i provini. Viene mostrato come nel caso di provini rettangolari la sequenza di laminazione possa influenzare sensibilmente il danno prodotto dall’impatto. Due diversi tipi di deformate in condizioni di instabilità sono stati osservati per laminati con diversa laminazione, in accordo con i risultati dell’analisi numerica. Gli esperimenti hanno mostrato inoltre che in certe situazioni il danno da impatto può alterare la deformata che il laminato assume in seguito ad instabilità; d’altra parte tale danno non ha sempre influenzato la resistenza a compressione, a seconda della deformata. Vengono proposte anche alcune considerazioni sulla significatività del metodo di prova utilizzato. Infine viene presentato uno studio esaustivo riguardo all’influenza di carichi membranali preesistenti sulla risposta all’impatto dei laminati. Sono stati analizzati con simulazioni numeriche ad elementi finiti casi di impatto in diverse condizioni di precarico, sia di trazione sia di compressione, sia monoassiali sia biassiali; è stato preso in considerazione anche il caso di laminati impattati in condizioni di postbuckling. Lo studio si è concentrato in particolare sulla dipendenza degli effetti del precarico dal rapporto larghezza-spessore del provino, che si è rivelato un parametro fondamentale. Viene illustrato che un precarico di trazione ha l’effetto più marcato sulle massime tensioni per bassi rapporti larghezza-spessore, portando ad una riduzione della minima energia di impatto necessaria per innescare il danneggiamento, mentre questo effetto tende a scomparire all’aumentare di tale rapporto. Il precarico di compressione evidenzia invece gli effetti più deleteri a rapporti larghezza-spessore intermedi, ai quali la resistenza a compressione del laminato e il suo carico critico di instabilità sono paragonabili, mentre l’influenza del precarico può essere trascurabile per piastre sottili o addirittura benefica per piastre molto spesse. Viene evidenziata la possibilità di trovare una spiegazione più soddisfacente dei risultati sperimentali riportati in letteratura, alla luce del presente contributo. Nel corso della tesi vengono anche discussi le potenzialità ed i limiti del modello ad elementi finiti utilizzato, che è stato implementato in un programma scritto in proprio. Il programma non comprende alcuna modellazione del danneggiamento del materiale. Viene però spiegato come, nonostante questo tipo di analisi possa portare a risultati accurati soltanto finché il danno ha scarsi effetti sulle proprietà meccaniche d’insieme del laminato, esso possa essere utile per spiegare alcuni fenomeni, oltre che per distinguere fra ciò che si può riprodurre senza tenere conto del degrado del materiale e ciò che invece richiede una simulazione adeguata del danneggiamento.

Radiochemical aspects of production and processing of radiometals for preparation of metalloradiopharmaceuticals

Radiometals play an important role in nuclear medicine as involved in diagnostic or therapeutic agents. In the present work the radiochemical aspects of production and processing of very promising radiometals of the third group of the periodic table, namely radiogallium and radiolanthanides are investigated. The 68Ge/68Ga generator (68Ge, T½ = 270.8 d) provides a cyclotron-independent source of positron-emitting 68Ga (T½ = 68 min), which can be used for coordinative labelling. However, for labelling of biomolecules via bifunctional chelators, particularly if legal aspects of production of radiopharmaceuticals are considered, 68Ga(III) as eluted initially needs to be pre-concentrated and purified. The first experimental chapter describes a system for simple and efficient handling of the 68Ge/68Ga generator eluates with a cation-exchange micro-chromatography column as the main component. Chemical purification and volume concentration of 68Ga(III) are carried out in hydrochloric acid – acetone media. Finally, generator produced 68Ga(III) is obtained with an excellent radiochemical and chemical purity in a minimised volume in a form applicable directly for the synthesis of 68Ga-labelled radiopharmaceuticals. For labelling with 68Ga(III), somatostatin analogue DOTA-octreotides (DOTATOC, DOTANOC) are used. 68Ga-DOTATOC and 68Ga-DOTANOC were successfully used to diagnose human somatostatin receptor-expressing tumours with PET/CT. Additionally, the proposed method was adapted for purification and medical utilisation of the cyclotron produced SPECT gallium radionuclide 67Ga(III). Second experimental chapter discusses a diagnostic radiolanthanide 140Nd, produced by irradiation of macro amounts of natural CeO2 and Pr2O3 in natCe(3He,xn)140Nd and 141Pr(p,2n)140Nd nuclear reactions, respectively. With this produced and processed 140Nd an efficient 140Nd/140Pr radionuclide generator system has been developed and evaluated. The principle of radiochemical separation of the mother and daughter radiolanthanides is based on physical-chemical transitions (hot-atom effects) of 140Pr following the electron capture process of 140Nd. The mother radionuclide 140Nd(III) is quantitatively absorbed on a solid phase matrix in the chemical form of 140Nd-DOTA-conjugated complexes, while daughter nuclide 140Pr is generated in an ionic species. With a very high elution yield and satisfactory chemical and radiolytical stability the system could able to provide the short-lived positron-emitting radiolanthanide 140Pr for PET investigations. In the third experimental chapter, analogously to physical-chemical transitions after the radioactive decay of 140Nd in 140Pr-DOTA, the rapture of the chemical bond between a radiolanthanide and the DOTA ligand, after the thermal neutron capture reaction (Szilard-Chalmers effect) was evaluated for production of the relevant radiolanthanides with high specific activity at TRIGA II Mainz nuclear reactor. The physical-chemical model was developed and first quantitative data are presented. As an example, 166Ho could be produced with a specific activity higher than its limiting value for TRIGA II Mainz, namely about 2 GBq/mg versus 0.9 GBq/mg. While free 166Ho(III) is produced in situ, it is not forming a 166Ho-DOTA complex and therefore can be separated from the inactive 165Ho-DOTA material. The analysis of the experimental data shows that radionuclides with half-life T½ < 64 h can be produced on TRIGA II Mainz nuclear reactor, with specific activity higher than any available at irradiation of simple targets e.g. oxides.

Structure and properties of composite polyolefin materials

This thesis is based on three main studies, all dealing with structure-property investigation of semicrystalline polyolefin-based composites. Low density poly(ethylene) (LDPE) and isotactic poly(propylene) (iPP) were chosen as parts of the composites materials and they were investigated either separately (as homoploymers), either in blend systems with the composition LDPE/iPP 80/20 or as filled matrix with layered silicate (montmorillonite). The beneficial influence of adding ethylene-co-propylene polymer of amorphous nature, to low density poly(ethylene)/isotactic poly(propylene) (80/20) blend is demonstrated. This effect is expressed by the major improvement of mechanical properties of ternary blends as examined at a macroscopic size scale by means of tensile measurements. The structure investigation also reveals a clear dependence of the morphology on adding ethylene-copropylene polymer. Both the nature and the content of ethylene-co-propylene polymer affect structure and properties. It is further demonstrated that the extent of improvement in mechanical properties is to be related to the molecular details of the compatibilizer. Combination of high molecular weight and high ethylene content is appropriate for the studied system where the poly(ethylene) plays the role of matrix. A new way to characterize semicrystalline systems by means of Brillouin spectroscopy is presented in this study. By this method based on inelastic light scattering, we were able to measure the high frequency elastic constant (c11) of the two microphases in the case where the spherulites size is exhibit size larger than the size of the probing phonon wavelength. In this considered case, the sample film is inhomogeneous over the relevant length scales and there is an access to the transverse phonon in the crystalline phase yielding the elastic constant c44 as well. Isotactic poly(propylene) is well suited for this type of investigation since its morphology can be tailored through different thermal treatment from the melt. Two distinctly different types of films were used; quenched (low crystallinity) and annealed (high crystallinity). The Brillouin scattering data are discussed with respect to the spherulites size, lamellae thickness, long period, crystallinity degree and well documented by AFM images. The structure and the properties of isotactic poly(propylene) matrix modified by inorganic layered silicate, montmorillonite, are discussed with respect to the clay content. Isotactic poly(propylene)-graft-maleic anhydride was used as compatibilizer. It is clearly demonstrated that the property enhancement is largely due to the ability of layered silicate to exfoliate. The intimate dispersion of the nanometer-thick silicate result from a delicate balance of the content ratio between the isotactic poly(propylene)-graft-maleic anhydride compatibilizer and the inorganic clay.

Preparation of new crystal forms via photochemical, mechanochemical and sol-gel methods

This work of thesis involves various aspects of crystal engineering. Chapter 1 focuses on crystals containing crown ether complexes. Aspects such as the possibility of preparing these materials by non-solution methods, i.e. by direct reaction of the solid components, thermal behavior and also isomorphism and interconversion between hydrates are taken into account. In chapter 2 a study is presented aimed to understanding the relationship between hydrogen bonding capability and shape of the building blocks chosen to construct crystals. The focus is on the control exerted by shape on the organization of sandwich cations such as cobalticinium, decamethylcobalticinium and bisbenzenchromium(I) and on the aggregation of monoanions all containing carboxylic and carboxylate groups, into 0-D, 1-D, 2-D and 3-D networks. Reactions conducted in multi-component molecular assemblies or co-crystals have been recognized as a way to control reactivity in the solid state. The [2+2] photodimerization of olefins is a successful demonstration of how templated solid state synthesis can efficiently synthesize unique materials with remarkable stereoselectivity and under environment-friendly conditions. A demonstration of this synthetic strategy is given in chapter 3. The combination of various types of intermolecular linkages, leading to formation of high order aggregation and crystalline materials or to a random aggregation resulting in an amorphous precipitate, may not go to completeness. In such rare cases an aggregation process intermediate between crystalline and amorphous materials is observed, resulting in the formation of a gel, i.e. a viscoelastic solid-like or liquid-like material. In chapter 4 design of new Low Molecular Weight Gelators is presented. Aspects such as the relationships between molecular structure, crystal packing and gelation properties and the application of this kind of gels as a medium for crystal growth of organic molecules, such as APIs, are also discussed.

Theoretical studies of fluid membrane mechanics

Biologische Membranen sind Fettmolekül-Doppelschichten, die sich wie zweidimensionale Flüssigkeiten verhalten. Die Energie einer solchen fluiden Oberfläche kann häufig mit Hilfe eines Hamiltonians beschrieben werden, der invariant unter Reparametrisierungen der Oberfläche ist und nur von ihrer Geometrie abhängt. Beiträge innerer Freiheitsgrade und der Umgebung können in den Formalismus mit einbezogen werden. Dieser Ansatz wird in der vorliegenden Arbeit dazu verwendet, die Mechanik fluider Membranen und ähnlicher Oberflächen zu untersuchen. Spannungen und Drehmomente in der Oberfläche lassen sich durch kovariante Tensoren ausdrücken. Diese können dann z. B. dazu verwendet werden, die Gleichgewichtsposition der Kontaktlinie zu bestimmen, an der sich zwei aneinander haftende Oberflächen voneinander trennen. Mit Ausnahme von Kapillarphänomenen ist die Oberflächenenergie nicht nur abhängig von Translationen der Kontaktlinie, sondern auch von Änderungen in der Steigung oder sogar Krümmung. Die sich ergebenden Randbedingungen entsprechen den Gleichgewichtsbedingungen an Kräfte und Drehmomente, falls sich die Kontaktlinie frei bewegen kann. Wenn eine der Oberflächen starr ist, muss die Variation lokal dieser Fläche folgen. Spannungen und Drehmomente tragen dann zu einer einzigen Gleichgewichtsbedingung bei; ihre Beiträge können nicht mehr einzeln identifiziert werden. Um quantitative Aussagen über das Verhalten einer fluiden Oberfläche zu machen, müssen ihre elastischen Eigenschaften bekannt sein. Der "Nanotrommel"-Versuchsaufbau ermöglicht es, Membraneigenschaften lokal zu untersuchen: Er besteht aus einer porenüberspannenden Membran, die während des Experiments durch die Spitze eines Rasterkraftmikroskops in die Pore gedrückt wird. Der lineare Verlauf der resultierenden Kraft-Abstands-Kurven kann mit Hilfe der in dieser Arbeit entwickelten Theorie reproduziert werden, wenn der Einfluss von Adhäsion zwischen Spitze und Membran vernachlässigt wird. Bezieht man diesen Effekt in die Rechnungen mit ein, ändert sich das Resultat erheblich: Kraft-Abstands-Kurven sind nicht länger linear, Hysterese und nichtverschwindende Trennkräfte treten auf. Die Voraussagen der Rechnungen könnten in zukünftigen Experimenten dazu verwendet werden, Parameter wie die Biegesteifigkeit der Membran mit einer Auflösung im Nanometerbereich zu bestimmen. Wenn die Materialeigenschaften bekannt sind, können Probleme der Membranmechanik genauer betrachtet werden. Oberflächenvermittelte Wechselwirkungen sind in diesem Zusammenhang ein interessantes Beispiel. Mit Hilfe des oben erwähnten Spannungstensors können analytische Ausdrücke für die krümmungsvermittelte Kraft zwischen zwei Teilchen, die z. B. Proteine repräsentieren, hergeleitet werden. Zusätzlich wird das Gleichgewicht der Kräfte und Drehmomente genutzt, um mehrere Bedingungen an die Geometrie der Membran abzuleiten. Für den Fall zweier unendlich langer Zylinder auf der Membran werden diese Bedingungen zusammen mit Profilberechnungen kombiniert, um quantitative Aussagen über die Wechselwirkung zu treffen. Theorie und Experiment stoßen an ihre Grenzen, wenn es darum geht, die Relevanz von krümmungsvermittelten Wechselwirkungen in der biologischen Zelle korrekt zu beurteilen. In einem solchen Fall bieten Computersimulationen einen alternativen Ansatz: Die hier präsentierten Simulationen sagen voraus, dass Proteine zusammenfinden und Membranbläschen (Vesikel) bilden können, sobald jedes der Proteine eine Mindestkrümmung in der Membran induziert. Der Radius der Vesikel hängt dabei stark von der lokal aufgeprägten Krümmung ab. Das Resultat der Simulationen wird in dieser Arbeit durch ein approximatives theoretisches Modell qualitativ bestätigt.

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.