Les répétitions en tandem sont constituées de successions de motifs d'ADN. Ces structures présentes dans tous les organismes, procaryotes comme eucaryotes, ont des applications dans de nombreux domaines. Depuis quelques années seulement, les répétitions en tandem sont étudiées chez les bactéries. Le polymorphisme associé à ces séquences peut être utilisé pour le génotypage de bactéries pathogènes, permettant une identification précise au niveau de la souche. Le polymorphisme des séquences répétées est de deux types : polymorphisme de longueur et mutations internes aux motifs. Les génomes des deux bactéries pathogènes responsables d'infections nosocomiales, Staphylococcus aureus et Pseudomonas aeruginosa, ont été étudiés dans le but d'identifier des séquences répétées polymorphes. Un ensemble de marqueurs polymorphes a été validé expérimentalement pour ces deux espèces permettant un typage dit MLVA (pour « Multiple Locus VNTR Analysis »). Le travail plus classique de typage par la taille de la répétition a été complété par un travail de séquençage de certains allèles. Les résultats obtenus montrent comment le typage « MLVA » complété si nécessaire par le séquençage d'allèles, pourraient constituer de nouvelles méthodes peu coûteuses participant au contrôle des infections bactériennes.

Les travaux effectués au cours de cette thèse au sein du groupe de structure nucléaire de l'IPN d'Orsay s'articulent autour de la production, en vue d'une étude par spectroscopie gamma, de noyaux exotiques riches en neutron de la couche fp. Dans ce cadre, nous avons mis en place, auprès de l'accélérateur Tandem d'Orsay, un multi-détecteur au germanium baptisé ORGAM, destiné à la spectroscopie gamma à haute résolution. Au cours de l'année 2008-2009, les détecteurs amenés à composer ORGAM ont été testés, ainsi que le dispositif annexe de réjection-Compton, en coopération avec la division instrumentation du laboratoire. Parallèlement, le système d'alimentation automatique en azote liquide, destiné au maintien des détecteurs à basse température, a été amélioré et fiabilisé. L'ensemble du dispositif a été mis en place sur une ligne de faisceau de l'accélérateur tandem avec le concours du personnel technique de l'accélérateur. La première expérience utilisant le dispositif ORGAM a été réalisée en juillet 2009. Cette expérience, dont les données ont été analysées dans le cadre de ce travail, visait à étudier les collisions profondément inélastiques entre un faisceau de 36S accéléré à 154 MeV, et une cible de 70Zn. Un dispositif permettant la détection des particules chargées émises à grand angle a été utilisé afin d'identifier les fragments de ces collisions. Il n'a pas été possible, du fait du fond important induit par la diffusion élastique du faisceau dans la cible, d'identifier directement ces fragments. L'étude des coïncidences gamma-gamma avec le détecteur ORGAM a cependant permis de mettre en évidence un certain nombre de cascades de photons désexcitant des noyaux potentiellement produits par le mécanisme de réaction d'intérêt. Les données recueillies au cours d'une autre expérience, réalisée auprès du tandem d'Orsay en 2005, ont également été analysées dans le cadre de ce travail. Cette expérience, visant à produire par fusion évaporation entre un faisceau de 14C à 25 MeV et une cible de 48Ca, les noyaux de 59Mn et de 57Cr, a permis d'établir une partie du spectre en énergie d'excitation de ces noyaux, jusqu'à une énergie d'excitation supérieure à 3 MeV. Une étude théorique des noyaux de chrome impairs de la couche fp a été tentée à l'aide d'un modèle phénoménologique de couplage intermédiaire. Ce modèle reproduit de manière satisfaisante le spectre en énergie d'excitation du 53Cr, qui possède un cœur semi-magique + 1 neutron. Les prédictions du modèle, qui ne prend pas en compte l'interaction entre nucléons de valence, s'avèrent en revanche moins bonnes dans le cas des noyaux de 55Cr et 57Cr.

<p>A new method for analysis of acidic herbicides, mostly phenoxy acids and their esters, in cereals with liquid chromatography-tandem quadrupole mass spectrometry (LS-MS/MS) has been developed. Samples were hydrolyzed with sodium hydroxide in order to release covalently bound compounds followed by neutralization and finally extraction with acidified ethyl acetate. The extraction efficiency for both ester formulations and acids were studied. Acceptable results (70-120 %) were obtained for 2,4-D, dichlorprop, MCPA and mecoprop for both esters and acids. However, low recoveries were observed for ester formulations of dicamba, fluroxypyr, fluazifop and haloxyfop, possibly due to the complex structure of the compounds in combination with the matrix and/or incomplete hydrolysis step. The limit of quantification (LOQ) for targeted pesticides was 0.01 mg/kg. The method has been tested in the EU Proficiency Test for cereals with good results.</p>

<p>The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. </p><p>Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. </p><p>Fragment ion abundances are a quantifiable tool providing chiral recognition (R_Chiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. </p><p>The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding.</p><p>The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.</p>

A computer program, WINPOST-MULT, is developed for the dynamic analysis of a multiple-body floating system coupled with mooring lines and risers in the presence of waves, winds and currents. The coupled dynamics program for a single platform is extended for analyzing multiple-body systems by including all the platforms, mooring lines and risers in a combined matrix equation in the time domain. Compared to the iteration method between multiple bodies, the combined matrix method can include the full hydrodynamic interactions among bodies. The floating platform is modeled as a rigid body with six degrees of freedom. The first- and second-order wave forces, added mass coefficients, and radiation damping coefficients are calculated from the hydrodynamics program WAMIT for multiple bodies. Then, the time series of wave forces are generated in the time domain based on the two-term Volterra model. The wind forces are separately generated from the input wind spectrum and wind force formula. The current is included in Morison's drag force formula. In case of FPSO, the wind and current forces are generated using the respective coefficients given in the OCIMF data sheet. A finite element method is derived for the long elastic element of an arbitrary shape and material. This newly developed computer program is first applied to the system of a turret-moored FPSO and a shuttle tanker in tandem mooring. The dynamics of the turret-moored FPSO in waves, winds and currents are verified against independent computation and OTRC experiment. Then, the simulations for the FPSO-shuttle system with a hawser connection are carried out and the results are compared with the simplified methods without considering or partially including hydrodynamic interactions.

<p>The objective of the study was to conduct an internal validation on miniSTR systems and apply it to cases received from the South African Missing Persons Task Team (SAMPTT). This was prompted by the fact that miniSTR systems have been shown to out perform some of the commercial kits available in the time of the study and provide an alternative to mtDNA when analysing degraded DNA from skeletal remains and that the DNA extracted from skeletal remains received from the SAMPTT would be degraded due to the remains generally being fragmented or charred and buried for many years. The miniSTR loci chosen for validation comprised the Combined DNA Index System (CODIS) thirteen core loci and were arranged into four triplexes and one uniplex.</p>

The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. Fragment ion abundances are a quantifiable tool providing chiral recognition (RChiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding. The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.

Bioinformatic methods were developed for improved identification of endogenous peptides using mass spectrometry. As a framework for these methods, a database for endogenous peptides, SwePep, was created. It was designed for storing information about endogenous peptides including tandem mass spectra. SwePep can be used for identification and validation of endogenous peptides by comparing experimentally derived masses of peptides and their fragments with information in the database. To improve automatic peptide identification of neuropeptides, targeted sequence collections that better mimic the peptidomic sample was derived from the SwePep database. Three sequence collections were created: SwePep precursors, SwePep peptides, and SwePep predicted. The searches for neuropeptides performed against these three sequence collections were compared with searches performed against the entire mouse proteome, and it was observed that three times as many peptides were identified with the targeted SwePep sequence collections. Applying the targeted SwePep sequence collections to identification of previously uncharacterized peptides yielded 27 novel potentially bioactive neuropeptides. Two fragmentations studies were performed using high mass accuracy tandem mass spectra of tryptic peptides. For this purpose, two databases were created: SwedCAD and SwedECD for CID and ECD tandem mass spectra, respectively. In the first study, fragmentation pattern of peptides with missed cleaved sites was studied using SwedCAD. It was observed that peptides with two arginines positioned next to each other have the same ability to immobilize two protons as peptides with two distant arginines. In the second study, SwedECD was used for studying small neutral losses from the reduced species in ECD fragmentation. The neutral losses were characterized with regard to their specificity and sensitivity to function as reporter ions for revealing the presence of specific amino acids in the peptide sequence. The results from these two studies can be used to improve identification of both tryptic and endogenous peptides. In summary, a collection of methods was developed that greatly improved the sensitivity of mass spectrometry peptide identification.

Organic materials, such as conjugated polymers, have emerged as a promising alternative for the production of inexpensive and flexible photovoltaic cells. As conjugated polymers are soluble, liquid based printing techniques enable production on large scale to a price much lower than that for inorganic based solar cells. Present day state of the art conjugated polymer photovoltaic cells are comprised by blends of a semiconducting polymer and a soluble derivative of fullerene molecules. Such bulk heterojunction solar cells now show power conversion efficiencies of up to 4-6%. The quantum efficiency of thin film organic solar cells is however still limited by several processes, of which the most prominent limitations are the comparatively low mobility and the high level of charge recombination. Hence organic cells do not yet perform as well as their more expensive inorganic counterparts. In order to overcome this present drawback of conjugated polymer photovoltaics, efforts are continuously devoted to developing materials or devices with increased absorption or with better charge carrier transporting properties. The latter can be facilitated by increasing the mobility of the pure material or by introducing beneficial morphology to prevent carrier recombination. Minimizing the active layer film thickness is an alternative route to collect more of the generated free charge carriers. However, a minimum film thickness is always required for sufficient photon absorption. A further limitation for low cost large scale production has been the dependence on expensive transparent electrodes such as indium tin oxide. The development of cheaper electrodes compatible with fast processing is therefore of high importance. The primary aim of this work has been to increase the absorption in solar cells made from thin films of organic materials. Device construction, deploying new geometries, and evaluation of different methods to provide for light trapping and photon recycling have been strived for. Different routes to construct and incorporate light trapping structures that enable higher photon absorption in a thinner film are presented. By recycling the reflected photons and enhancing the optical path length within a thinner cell, the absorption rate, as well as the collection of more charge carriers, is provided for. Attempts have been performed by utilizing a range of different structures with feature sizes ranging from nanometers up to centimeters. Surface plasmons, Lambertian scatterers, micro lenses, tandem cells as well as larger folded cell structures have been evaluated. Naturally, some of these methods have turned out to be more successful than others. From this work it can nevertheless be concluded that proper light trapping, in thin films of organic materials for photovoltaic energy conversion, is a technique capable of improving the cell performance. In addition to the study of light trapping, two new alternative electrodes for polymer photovoltaic devices are suggested and evaluated.

<p>In this dissertation work, the aim was to garner better mechanistic understanding of how shock wave lithotripsy (SWL) breaks stones in order to guide design improvements to a modern electromagnetic (EM) shock wave lithotripter. To accomplish this goal, experimental studies were carefully designed to isolate mechanisms of fragmentation, and models for wave propagation, fragmentation, and stone motion were developed. In the initial study, a representative EM lithotripter was characterized and tested for in vitro stone comminution efficiency at a variety of field positions and doses using phantom kidney stones of variable hardness, and in different fluid mediums to isolate the contribution of cavitation. Through parametric analysis of the acoustic field measurements alongside comminution results, a logarithmic correlation was determined between average peak pressure incident on the stone surface and comminution efficiency. It was also noted that for a given stone type, the correlations converged to an average peak pressure threshold for fragmentation, independent of fluid medium in use. The correlation of average peak pressure to efficacy supports the rationale for the acoustic lens modifications, which were pursued to simultaneously enhance beam width and optimize the pulse profile of the lithotripter shock wave (LSW) via in situ pulse superposition for improved stone fragmentation by stress waves and cavitation, respectively. In parallel, a numerical model for wave propagation was used to investigate the variations of critical parameters with changes in lens geometry. A consensus was reached on a new lens design based on high-speed imaging and stone comminution experiments against the original lens at a fixed acoustic energy setting. The results have demonstrated that the new lens has improved efficacy away from the focus, where stones may move due to respiration, fragmentation, acoustic radiation forces, or voluntary patient movements. Using traditional theory of brittle fragmentation and newfound understanding of average peak pressure correlation to stone comminution, the entire set of stone comminution data for lens comparison was modeled using a Weibull-style distribution function. This model linked both the average peak pressure and shock wave dose to efficacy, including their respective threshold parameters, and demonstrated correlation of coefficients to cavitation activity. Subsequently, this model was used in prediction of stone comminution efficiency from mimicked respiratory motions in vitro, which compared favorably to actual simulated motion studies using both the new and original lenses. Under a variety of mimicked respiratory motions, the new lens produced statistically higher stone comminution efficiency than the original lens. These results were confirmed in vivo in a swine model, where the new lens produced statistically higher stone comminution after 1,000 and 2,000 shocks. Finally, a mechanistic investigation into the effects of cavitation with the original lens was conducted using an integrated, self-focusing annular ring transducer specially designed for tandem pulse lithotripsy. It was found that cavitation and stone comminution efficiency are progressively enhanced by tandem pulsing as source energies of both the primary LSW and trailing pressure pulse increase, which suggests cavitation and stress waves act synergistically enhance the efficacy in kidney stone fragmentation.</p> / Dissertation