Nachweis von DNA-Doppelstrangbrüchen über gamma-H2AX: Immunhistochemie nach Einwirkung gentoxischer Agenzien auf Säugerzellen

Wie im Rahmen dieser Arbeit bestätigt werden konnte, eignet sich die Quantifizierung von γ-H2AX-Foci mittels Immunfluoreszenz zur Quantifizierung von DNA-Doppelstrangbrüchen, welche durch ionisierende Strahlung erzeugt werden. Dabei erzeugt ein Gy Strahlung der verwendeten 60Co-Quelle 33,8 ± 2,1 DNA-Doppelstrangbrüche. Durch UV-Strahlung sowie alkylierende Substanzen wie MMS und MNNG werden in CHO-Zellen γ-H2AX-Foci induziert. Die Anzahl der induzierten γ-H2AX-Foci ist Dosis- und replikationsabhängig. Die im Rahmen dieser Arbeit erhobenen Daten sprechen für eine Phosphorylierung von H2AX an Läsionen, welche die DNA-Replikation beeinträchtigen und insbesondere aktive Replikationsgabeln blockieren. Diese Läsionen können zu DNA-Doppelstrangbrüchen an blockierten Replikationsgabeln führen H2AX wird in der unmittelbaren Umgebung von DNA-Doppelstrangbrüchen zu γ-H2AX phosphoryliert und eignet sich damit zur Quantifizierung dieser Läsionen. Ob γ-H2AX ausschließlich an DNA-Doppelstrangbrüchen phosphoryliert wird, oder auch an anderen Läsionen ist in der Literatur umstritten. Die bis dato publizierte Literatur geht mehrheitlich davon aus, dass γ-H2AX einen ausschließlichen Marker von DNA-Doppelstrangbrüchen darstellt (Burma et al., 2001; Fernandez-Capetillo et al., 2004; Foster und Downs, 2005; Furuta et al., 2003; Halicka et al., 2005; Huang et al., 2005; Paull et al., 2000; Redon et al., 2002; Stucki und Jackson, 2006; Takahashi und Ohnishi, 2005; Ward und Chen, 2001). Neuere Arbeiten postulieren jedoch, dass H2AX auch durch andere, bisher nicht genau klassifizierte, Störungen der Chromatinstruktur phosphoryliert wird (Marti et al., 2006; Stojic et al., 2004). Die im Rahmen dieser Arbeit dargestellten Ergebnisse mit UV-Strahlung und den Alkylantien MMS und MNNG lassen sich gut durch die teils direkte, größtenteils jedoch replikationsabhängige Bildung von DNA-Doppelstrangbrüchen an blockierten Replikationsgabeln erklären. Ausschließen lässt sich die Hypothese, dass die beobachteten γ-H2AX-Foci auch aufgrund anderer Läsionen entstehen, auf Grundlage der erhaltenen Daten nicht. Die Quantifizierung von γ-H2AX eignet sich zur Darstellung von durch ionisierende Strahlung, UV-Strahlung sowie Alkylantien erzeugten Effekten. Eine abschließende Klärung, ob durch die hier angewandte Methode selektiv DNA-Doppelstrangbrüche detektiert werden, steht aber weiterhin aus.

Numerical investigation of turbulent/non-turbulent interface

The subject of this work is the diffusion of turbulence in a non-turbulent flow. Such phenomenon can be found in almost every practical case of turbulent flow: all types of shear flows (wakes, jet, boundary layers) present some boundary between turbulence and the non-turbulent surround; all transients from a laminar flow to turbulence must account for turbulent diffusion; mixing of flows often involve the injection of a turbulent solution in a non-turbulent fluid. The mechanism of what Phillips defined as “the erosion by turbulence of the underlying non-turbulent flow”, is called entrainment. It is usually considered to operate on two scales with different mechanics. The small scale nibbling, which is the entrainment of fluid by viscous diffusion of turbulence, and the large scale engulfment, which entraps large volume of flow to be “digested” subsequently by viscous diffusion. The exact role of each of them in the overall entrainment rate is still not well understood, as it is the interplay between these two mechanics of diffusion. It is anyway accepted that the entrainment rate scales with large properties of the flow, while is not understood how the large scale inertial behavior can affect an intrinsically viscous phenomenon as diffusion of vorticity. In the present work we will address then the problem of turbulent diffusion through pseudo-spectral DNS simulations of the interface between a volume of decaying turbulence and quiescent flow. Such simulations will give us first hand measures of velocity, vorticity and strains fields at the interface; moreover the framework of unforced decaying turbulence will permit to study both spatial and temporal evolution of such fields. The analysis will evidence that for this kind of flows the overall production of enstrophy , i.e. the square of vorticity omega^2 , is dominated near the interface by the local inertial transport of “fresh vorticity” coming from the turbulent flow. Viscous diffusion instead plays a major role in enstrophy production in the outbound of the interface, where the nibbling process is dominant. The data from our simulation seems to confirm the theory of an inertially stirred viscous phenomenon proposed by others authors before and provides new data about the inertial diffusion of turbulence across the interface.

Controllo del flusso termico in convezione mista tramite fluidi visco-elastici

L'obiettivo del lavoro è stato quello di valutare l'influenza di fluidi viscoelastici sullo scambio termico in flussi in convezione mista, tramite l'analisi di simulazioni numeriche dirette del campo. Si è osservato che il numero di Nusselt aumenta se il numero di Deborah della soluzione cresce, ma l'incremento della componente di convezione forzata inibisce tale effetto positivo.

Effects of metal-induced oxidative stress on endothelial cells in vitro

Aseptic loosening of metal implants is mainly attributed to the formation of metal degradation products. These include particulate debris and corrosion products, such as metal ions (anodic half-reaction) and ROS (cathodic half-reaction). While numerous clinical studies describe various adverse effects of metal degradation products, detailed knowledge of metal-induced cellular reactions, which might be important for possible therapeutic intervention, is not comprehensive. Since endothelial cells are involved in inflammation and angiogenesis, two processes which are critical for wound healing and integration of metal implants, the effects of different metal alloys and their degradation products on these cells were investigated. Endothelial cells on Ti6Al4V alloy showed signs of oxidative stress, which was similar to the response of endothelial cells to cathodic partial reaction of corrosion induced directly on Ti6Al4V surfaces. Furthermore, oxidative stress on Ti6Al4V alloy reduced the pro-inflammatory stimulation of endothelial cells by TNF-α and LPS. Oxidative stress and other stress-related responses were observed in endothelial cells in contact with Co28Cr6Mo alloy. Importantly, these features could be reduced by coating Co28Cr6Mo with a TiO2 layer, thus favouring the use of such surface modification in the development of medical devices for orthopaedic surgery. The reaction of endothelial cells to Co28Cr6Mo alloy was partially similar to the effects exerted by Co2+, which is known to be released from metal implants. Co2+ also induced ROS formation and DNA damage in endothelial cells. This correlated with p53 and p21 up-regulation, indicating the possibility of cell cycle arrest. Since CoCl2 is used as an hypoxia-mimicking agent, HIF-1α-dependence of cellular responses to Co2+ was studied in comparison to anoxia-induced effects. Although important HIF-1α-dependent genes were identified, a more detailed analysis of microarray data will be required to provide additional information about the mechanisms of Co2+ action. All these reactions of endothelial cells to metal degradation products might play their role in the complex processes taking place in the body following metal device implantation. In the worst case this can lead to aseptic loosening of the implant and requirement for revision surgery. Knowledge of molecular mechanisms of metal-induced responses will hopefully provide the possibility to interfere with undesirable processes at the implant/tissue interface, thus extending the life-time of the implant and the overall success of metal implant applications.

DNA hybrid materials consisting of oligonucleotides and organic molecules: synthesis, characterization and applications

The goal of this thesis was to increase the functionality of pristine DNA scaffolds by functionalizing them with fluorescent dyes and hydrophobic moieties. Two important steps were necessary to realize this aim successfully. First, nucleic acids needed to be synthesized making use of multidisciplinary toolbox for the generation and manipulation of polynucleic acids. The most important techniques were the solid phase synthesis involving the incorporation of standard and modified phosphoramidite building blocks as well as molecular biology procedures like the polymerase chain reaction, the bacterial amplification of plasmids and the enzymatic digestion of circular vectors. Second, and evenly important, was the characterization of the novel bioorganic hybrid structures by a multitude of techniques, especially optical measurements. For studying DNA-dye conjugates methods like UV/Vis and photoluminescence spectroscopy as well as time resolved luminescence spectroscopy were utilized. While these measurements characterized the bulk behavior of an ensemble of DNA-dye hybrids it was necessary for a complete understanding of the systems to look at single structures. This was done by single-molecule fluorescence spectroscopy and fluorescence correlation spectroscopy. For complete analysis the optical experiments were complemented by direct visualization techniques, i.e. high resolution transmission electron microscopy and scanning force microscopy.

Numerical and experimental investigation of turbulent dissipation

Turbulent energy dissipation is presented in the theoretical context of the famous Kolmogorov theory, formulated in 1941. Some remarks and comments about this theory help the reader understand the approach to turbulence study, as well as give some basic insights to the problem. A clear distinction is made amongst dissipation, pseudo-dissipation and dissipation surrogates. Dissipation regulates how turbulent kinetic energy in a flow gets transformed into internal energy, which makes this quantity a fundamental characteristic to investigate in order to enhance our understanding of turbulence. The dissertation focuses on experimental investigation of the pseudo-dissipation. Indeed this quantity is difficult to measure as it requires the knowledge of all the possible derivatives of the three dimensional velocity field. Once considering an hot-wire technique to measure dissipation we need to deal with surrogates of dissipation, since not all the terms can be measured. The analysis of surrogates is the main topic of this work. In particular two flows, the turbulent channel and the turbulent jet, are considered. These canonic flows, introduced in a brief fashion, are often used as a benchmark for CFD solvers and experimental equipment due to their simple structure. Observations made in the canonic flows are often transferable to more complicated and interesting cases, with many industrial applications. The main tools of investigation are DNS simulations and experimental measures. DNS data are used as a benchmark for the experimental results since all the components of dissipation are known within the numerical simulation. The results of some DNS were already available at the start of this thesis, so the main work consisted in reading and processing the data. Experiments were carried out by means of hot-wire anemometry, described in detail on a theoretical and practical level. The study of DNS data of a turbulent channel at Re=298 reveals that the traditional surrogate can be improved Consequently two new surrogates are proposed and analysed, based on terms of the velocity gradient that are easy to measure experimentally. We manage to find a formulation that improves the accuracy of surrogates by an order of magnitude. For the jet flow results from a DNS at Re=1600 of a temporal jet, and results from our experimental facility CAT at Re=70000, are compared to validate the experiment. It is found that the ratio between components of the dissipation differs between DNS and experimental data. Possible errors in both sets of data are discussed, and some ways to improve the data are proposed.

Studio preliminare di flusso attorno ad un pantografo per treno ad alta velocità

In questo elaborato di tesi viene presentata la comparazione tra due codici CFD, rispettivamente Fluent e OpenFOAM, mediante simulazioni che sono alla base di uno studio numerico di flusso attorno ad un pantografo per treno ad alta velocità. Si è apprezzato quindi la facilità d’uso di un software venduto tramite licenza e la difficoltà di un software open source come OpenFOAM, il quale però ha vantaggi in termini di adattamento ai casi più specifici. Sono stati quindi studiati due casi, scambio termico in regime laminare attorno ad un cilindro bidimensionale e flusso turbolento completamente sviluppato in un canale. Tutte le simulazioni numeriche hanno raggiunto convergenza e sono state validate positivamente mediante confronto con dati sperimentali. Il primo caso prevede un cilindro investito da un flusso a temperatura minore rispetto alla temperatura della superficie del cilindro; per avere più riscontri, sono state condotte diverse prove a valori differenti del numero di Prandtl, e per ogni simulazione è stato ricavato il corrispettivo numero di Nusselt, successivamente comparato con i dati sperimentali per la validazione delle prove. A partire dalla creazione della griglia di calcolo, è stato effettuato uno studio del fenomeno in questione, creando così una griglia di calcolo sviluppata a valle del cilindro avente maggior densità di celle a ridosso della parte del cilindro. In aggiunta, svolgendo le prove con schemi numerici sia del primo che del secondo ordine, si è constatata la miglior sensibilità degli schemi numerici del secondo ordine rispetto a quelli del primo ordine. La seconda tipologia di simulazioni consiste in un flusso turbolento completamente sviluppato all’interno di un canale; sono state svolte simulazioni senza e con l’uso delle wall functions, e quindi usate griglie di calcolo differenti per i due tipi di simulazioni, già disponibili per entrambi i software. I dati ottenuti mostrano uno sforzo computazionale maggiore per le simulazioni che non prevedono l’uso delle wall functions, e quindi una maggiore praticità per le simulazioni con le wall functions. Inoltre, le simulazioni di questo secondo caso sono state svolte con diversi modelli di turbolenza; in Fluent sono stati utilizzati i modelli k-ε e RSM mentre in OpenFOAM è stato utilizzato solo il modello k-ε in quanto il modello RSM non è presente. La validazione dei risultati è affidata alla comparazione con i dati sperimentali ricavati da Moser et all mediante simulazioni DNS, mettendo in risalto la minor accuratezza delle equazioni RANS.

EPR spectroscopy as a tool for the elucidation of non-covalent structuring principles in complex soft matter

This thesis aims at connecting structural and functional changes of complex soft matter systems due to external stimuli with non-covalent molecular interaction profiles. It addresses the problem of elucidating non-covalent forces as structuring principle of mainly polymer-based systems in solution. The structuring principles of a wide variety of complex soft matter types are analyzed. In many cases this is done by exploring conformational changes upon the exertion of external stimuli. The central question throughout this thesis is how a certain non-covalent interaction profile leads to solution condition-dependent structuring of a polymeric system.rnTo answer this question, electron paramagnetic resonance (EPR) spectroscopy is chosen as the main experimental method for the investigation of the structure principles of polymers. With EPR one detects only the local surroundings or environments of molecules that carry an unpaired electron. Non-covalent forces are normally effective on length scales of a few nanometers and below. Thus, EPR is excellently suited for their investigations. It allows for detection of interactions on length scales ranging from approx. 0.1 nm up to 10 nm. However, restriction to only one experimental technique likely leads to only incomplete pictures of complex systems. Therefore, the presented studies are frequently augmented with further experimental and computational methods in order to yield more comprehensive descriptions of the systems chosen for investigation.rnElectrostatic correlation effects in non-covalent interaction profiles as structuring principles in colloid-like ionic clusters and DNA condensation are investigated first. Building on this it is shown how electrostatic structuring principles can be combined with hydrophobic ones, at the example of host-guest interactions in so-called dendronized polymers (denpols).rnSubsequently, the focus is shifted from electrostatics in dendronized polymers to thermoresponsive alkylene oxide-based materials, whose structuring principles are based on hydrogen bonds and counteracting hydrophobic interactions. The collapse mechanism in dependence of hydrophilic-hydrophobic balance and topology of these polymers is elucidated. Complementarily the temperature-dependent phase behavior of elastin-like polypeptides (ELPs) is investigated. ELPs are the first (and so far only) class of compounds that is shown to feature a first-order inverse phase transition on nanoscopic length scales.rnFinally, this thesis addresses complex biological systems, namely intrinsically disordered proteins (IDPs). It is shown that the conformational space of the IDPs Osteopontin (OPN), a cytokine involved in metastasis of several kinds of cancer, and BASP1 (brain acid soluble protein one), a protein associated with neurite outgrowth, is governed by a subtle interplay between electrostatic forces, hydrophobic interaction, system entropy and hydrogen bonds. Such, IDPs can even sample cooperatively folded structures, which have so far only been associated with globular proteins.

Folic acid derivatives for PET imaging and therapy addressing folate receptor positive tumors

Folic acid, also known as vitamin B9, is the oxidized form of 5,6,7,8-tetrahydrofolate, which serves as methyl- or methylene donor (C1-building blocks) during DNA synthesis. Under physiological conditions the required amount of 5,6,7,8-tetrahydrofolate for survival of the cell is accomplished through the reduced folate carrier (RFC). In contrast, the supply of 5,6,7,8-tetrahydrofolate is insufficient under pathophysiological conditions of tumors due to an increased proliferation rate. Consequently, many tumor cells exhibit an (over)expression of the folate receptor. This phenomenon has been applied to diagnostics (PET, SPECT, MR) to image FR-positive tumors and on the other hand to treat malignancies related to a FR (over)expression. Based on this concept, a new 18F-labeled folate for PET imaging has been developed and was evaluated in vivo using tumor-bearing mice. The incorporation of oligoethylene spacers into the molecular structure led to a significant enhancement of the pharmacokinetics in comparison to previously developed 18F-folates. The liver uptake could be reduced by one sixth by remaining a tumor uptake of 3%ID/g leading to better contrast ratios. Encouraged by these results, a clickable 18F-labeled serine-based prosthetic group has been synthesized, again with the idea to improve the metabolic and pharmacokinetic profile of hydrophilic radiotracers. Therefore, an alkyne-carrying azido-functionalized serine derivative for coupling to biomolecules was synthesized and a chlorine leaving group for 18F-labeling, which could be accomplished using a microwave-assisted synthesis, a [K⊂2.2.2]+/carbonate system in DMSO. Radiochemical yields of 77±6% could be achieved.rnThe promising results obtained from the FR-targeting concept in the diagnostic field have been transferred to the boron neutron capture therapy. Therefore, a folate derivative was coupled to different boron clusters and cell uptake studies were conducted. The synthesis of the folate-boron clusters was straightforward. At first, a linker molecule based on maleic acid was synthesized, which was coupled to the boron cluster via Michael Addition of a thiol and alkene and subsequently coupled to the targeting moiety using CuAAC. The new conjugates of folate and boron clusters led to a significant increase of boron concentration in the cell of about 5-times compared to currently used and approved boron pharmaceuticals. rnMoreover, azido-folate derivatives were coupled to macromolecular carrier systems (pHPMA), which showed an enhanced and specific accumulation at target sites (up to 2.5-times) during in vivo experiments. A specific blockade could be observed up to 30% indicating an efficient targeting effect. A new kind of nanoparticles consisting of a PDLLA core and p((HPMA)-b-LMA)) as surfactants were developed and successfully radiolabeled via 18F-click chemistry in good RCYs of 8±3%rnThe nanoparticles were obtained via the miniemulsion technique in combination with solvent evaporation. The 18F-labeled nanoparticles were applied to in vivo testing using a mouse model. PET imaging showed a “mixed” biodistribution of low molecular weight as well as high molecular weight systems, indicating a partial loss of the 18F-labeled surfactant.rnIn conclusion, the presented work successfully utilized the FR-targeting concept in both, the diagnostic field (PET imaging) and for therapeutic approaches (BNCT, drug delivery systems). As a result, the high potential of FR-targeting in oncological applications has been shown and was confirmed by small animal PET imaging.rn

Testing of subgrid scale (SGS) models for large-eddy simulation (LES) of turbulent channel flow

Sub-grid scale (SGS) models are required in order to model the influence of the unresolved small scales on the resolved scales in large-eddy simulations (LES), the flow at the smallest scales of turbulence. In the following work two SGS models are presented and deeply analyzed in terms of accuracy through several LESs with different spatial resolutions, i.e. grid spacings. The first part of this thesis focuses on the basic theory of turbulence, the governing equations of fluid dynamics and their adaptation to LES. Furthermore, two important SGS models are presented: one is the Dynamic eddy-viscosity model (DEVM), developed by \cite{germano1991dynamic}, while the other is the Explicit Algebraic SGS model (EASSM), by \cite{marstorp2009explicit}. In addition, some details about the implementation of the EASSM in a Pseudo-Spectral Navier-Stokes code \cite{chevalier2007simson} are presented. The performance of the two aforementioned models will be investigated in the following chapters, by means of LES of a channel flow, with friction Reynolds numbers $Re_\tau=590$ up to $Re_\tau=5200$, with relatively coarse resolutions. Data from each simulation will be compared to baseline DNS data. Results have shown that, in contrast to the DEVM, the EASSM has promising potentials for flow predictions at high friction Reynolds numbers: the higher the friction Reynolds number is the better the EASSM will behave and the worse the performances of the DEVM will be. The better performance of the EASSM is contributed to the ability to capture flow anisotropy at the small scales through a correct formulation for the SGS stresses. Moreover, a considerable reduction in the required computational resources can be achieved using the EASSM compared to DEVM. Therefore, the EASSM combines accuracy and computational efficiency, implying that it has a clear potential for industrial CFD usage.

Studies of spatial clustering of inertial particles in turbulence

We present studies of the spatial clustering of inertial particles embedded in turbulent flow. A major part of the thesis is experimental, involving the technique of Phase Doppler Interferometry (PDI). The thesis also includes significant amount of simulation studies and some theoretical considerations. We describe the details of PDI and explain why it is suitable for study of particle clustering in turbulent flow with a strong mean velocity. We introduce the concept of the radial distribution function (RDF) as our chosen way of quantifying inertial particle clustering and present some original works on foundational and practical considerations related to it. These include methods of treating finite sampling size, interpretation of the magnitude of RDF and the possibility of isolating RDF signature of inertial clustering from that of large scale mixing. In experimental work, we used the PDI to observe clustering of water droplets in a turbulent wind tunnel. From that we present, in the form of a published paper, evidence of dynamical similarity (Stokes number similarity) of inertial particle clustering together with other results in qualitative agreement with available theoretical prediction and simulation results. We next show detailed quantitative comparisons of results from our experiments, direct-numerical-simulation (DNS) and theory. Very promising agreement was found for like-sized particles (mono-disperse). Theory is found to be incorrect regarding clustering of different-sized particles and we propose a empirical correction based on the DNS and experimental results. Besides this, we also discovered a few interesting characteristics of inertial clustering. Firstly, through observations, we found an intriguing possibility for modeling the RDF arising from inertial clustering that has only one (sensitive) parameter. We also found that clustering becomes saturated at high Reynolds number.

[Concurrent irradiation and DNA tumor vaccination in canine oral malignant melanoma: a pilot study].

Melanoma is the most common oral tumor in dogs, characterized by rapid growth, local invasion, and high metastatic rate. The goal of this study was to evaluate the combination of radiation therapy and DNA tumor vaccine. We hypothesized, that the concurrent use would not increase toxicity. Nine dogs with oral melanoma were treated with 4 fractions of 8 Gray at 7-day intervals. The vaccine was given 4 times every 14 days, beginning at the first radiation fraction. Local acute radiation toxicities were assessed according to the VRTOG toxicity scoring scheme over a time period of 7 weeks. In none of the evaluated dogs, mucositis, dermatitis and conjunctivitis exceeded grade 2. In 3 dogs mild fever, lethargy, and local swelling at the injection site were seen after vaccine application. In conclusion, the concurrent administration of radiation therapy and vaccine was well tolerated in all dogs.