M.Sc. (Chemistry) / According to the International Union of Applied Chemistry (IUPAC) mesoporous silica materials are a class of materials which contain pore size with diameters ranging from 2 to 50 nm. Due to their attractive features such as large surface area along with tunable pore size, accessible silano groups and easy functionalization make them with special properties to be employed as stationary phases for different chromatographic applications such as clean up, preconcentration, purification and separation of analytical samples. Organic–inorganic mesoporous hybrid materials are a new class of materials obtained when an inorganic material, such as mesoporous silicas are surface modified using an organic material via silylation. The main advantage of these hybrid materials is that they are formed by combining dissimilar properties of inorganic and organic materials into one material. Whereas the inorganic materials provide rigidity and thermal stability, the organic components provide flexibility, dielectric, ductility, and processability. Therefore the advantages of these hybrid materials lead them to be used over a wide range of applications. The main objective of this study was to synthesize organic-inorganic hybrid mesoporous silica materials for use as stationary phases for solid phase extraction and high performance liquid chromatography columns. The materials were prepared under basic conditions using silica gel and tetraethyl orthosilicate used as a source of silica and modified by either surface polymerization or grafting methods using octadecyltrimethoxysilane followed endcapping with hexamethyldisilazane. The materials were characterized before and after surface modification using different analytical methods. Scanning electron microscopy (SEM) pictures showed that the morphology of the materials remained unchanged after surface modification.

L'arrivée des technologies de séquençage d’ADN à haut-débit a représenté une révolution dans le domaine de la génomique personnalisée, en raison de leur résolution et leur faible coût. Toutefois, ces nouvelles technologies présentent un taux d’erreur élevé, qui varie entre 0,1% et 1% pour les séquenceurs de seconde génération. Cette valeur est problématique dans le cadre de la recherche de variants de faible ratio allélique, comme ce qui est observé dans le cas des tumeurs hétérogènes. En effet, un tel taux d’erreur peut mener à des milliers de faux positifs. Chaque région de l’ADN étudié doit donc être séquencée plusieurs fois, et les variants sont alors filtrés en fonction de critères basés sur leur profondeur. Malgré ces filtres, le nombre d’artefacts reste important, montrant la limite des approches conventionnelles et indiquant que certains artefacts de séquençage ne sont pas aléatoires.Dans le cadre de cette thèse, nous avons développé un algorithme exact de recherche des motifs d’ADN dégénérés sur-représentés en amont des erreurs de séquençage non aléatoires et donc potentiellement liés à leur apparition. Cet algorithme a été mis en oeuvre dans un logiciel appelé DiNAMO, qui a été testé sur des données de séquençage issues des technologies IonTorrent et Illumina.Les résultats expérimentaux ont mis en évidence plusieurs motifs, spécifiques à chacune de ces deux technologies. Nous avons ensuite montré que la prise en compte de ces motifs dans l’analyse, réduisait considérablement le taux de faux positifs. DiNAMO peut donc être utilisé en aval de chaque analyse, comme un filtre supplémentaire permettant d’améliorer l’identification des variants, en particulier des variants à faible ratio allélique. / The advent of Next Generation DNA Sequencing technologies has revolutionized the field of personalized genomics through their resolution and low cost. However, these new technologies are associated with a relatively high error rate, which varies between 0.1% and 1% for second-generation sequencers. This value is problematic when searching for low allelic ratio variants, as observed in the case of heterogeneous tumors. Indeed, such error rate can lead to thousands of false positives. Each region of the studied DNA must therefore be sequenced several times, and the variants are then filtered according to criteria based on their depth. Despite these filters, the number of errors remains significant, showing the limit of conventional approaches and indicating that some sequencing errors are not random.In the context of this thesis, we have developed an exact algorithm for over-represented degenerate DNA motifs discovery on the upstream of non-random sequencing errors and thus potentially linked to their appearance. This algorithm was implemented in a software called DiNAMO, which was tested on sequencing data from IonTorrent and Illumina technologies.The experimental results revealed several motifs, specific to each of these two technologies. We then showed that taking these motifs into account in the analysis reduced significantly the false-positive rate. DiNAMO can therefore be used downstream of each analysis, as an additional filter to improve the identification of variants, especially, variants with low allelic ratio.

Yes / Alfred Werner was awarded the Nobel Prize in Chemistry just over 100 years ago. We recall briefly the era in which he was working, his co-workers, and the equipment he used in his laboratories. His ideas were ground breaking: not only does a metal ion have a primary valency (“hauptvalenz”, now the oxidation state), but also a secondary valency, the coordination number (“nebenvalenz”). At that time some refused to accept this idea, but he realised that his new thinking would open up new areas of research. Indeed it did. We illustrate this for the emerging field of medicinal metal coordination chemistry, the design of metal-based therapeutic and diagnostic agents. The biological activity of metal complexes depends intimately not only on the metal and its oxidation state, but also on the type and number of coordinated ligands, and the coordination geometry. This provides a rich platform in pharmacological space for structural and electronic diversity. It is necessary to control both the thermodynamics (strengths of metal-ligand bonds) and kinetics of ligand substitution reactions to provide complexes with defined mechanisms of action. Outer-sphere interactions can also play a major role in target recognition. Our current interest is focussed especially on relatively inert metal complexes which were very familiar to Werner (RuII, OsII, RhIII, IrIII, PtII, PtIV). / We thank the Leverhulme Trust (Early Career Fellowship No. ECF-2013-414 to NPEB), the University of Warwick (Grant No. RDF 2013-14 to NPEB) the ERC (Grant No. 247450 to PJS), EPSRC (Grant No. EP/F034210/1) and EC COST Action CM1105 for support.

Yes