New laboratory measurements of hydrides have been carried out using terahertz direct absorption spectroscopy. Spin components of the N = 2 <- 1 transition of the free radical CrH (X (6)Sigma(+)) have been recorded in the range 730-734 GHz, as well as a new measurement of the J = 2 <- 1 line of AlH (X (1)Sigma(+)) near 755 GHz. Both species were created in an AC discharge of H-2, argon, and metal vapor. For CrH, the chromium source was Cr(CO)(6), while AlH was produced from Al(CH3)3. The J = 4.5 <- 3.5 and 3.5 <- 2.5 fine-structure components were recorded for CrH, each which consists of resolved proton hyperfine doublets. For AlH, the two main quadrupole components, F = 4.5 <- 3.5 and 3.5 <- 2.5, of the J = 2 <- 1 transition were observed as blended features. These data were analyzed with previous 1 <- 0 millimeter/submillimeter measurements with (6)Sigma and (1)Sigma Hamiltonians for chromium and aluminum hydrides, respectively, and rotational, fine-structure (CrH only), and hyperfine constants were derived. The new measurements have resulted in refined spectroscopic parameters for both species, as well as direct measurement of the respective 2 <- 1 rotational transitions. This work also resolves a 10 MHz discrepancy in the frequency of the AlH line. CrH and AlH have already been observed in the photospheres of stars via their electronic transitions. These data will facilitate their discovery at submillimeter/terahertz wavelengths in circumstellar envelopes and perhaps in diffuse clouds.

Master of Science / Department of Physics / Carlos Trallero / Over the past four decades, the single-electron ionization of atoms has been a subject of great interest within the ultra-fast community. While contemporary atomic ionization models tend to agree well with experiment across a wide range of intensities (10[superscript]13-10[superscript]15 W/cm[superscript]2), analogous models for the ionization of molecules are currently lacking in accuracy. The deficiencies present in molecular ionization models constitute a formidable barrier for experimentalists, who wish to model the single-electron ionization dynamics of molecules in intense laser fields. The primary motivation for the work presented in this thesis is to provide a comprehensive data set which can be used to improve existing models for the strong-field ionization of molecules. Our approach is to simultaneously measure the singly-charged ion yield of a diatomic molecule paired with a noble gas atom, both having commensurate ionization potentials. These measurements are taken as a function of the laser intensity, typically spanning two orders of magnitude (10[superscript]13-10[superscript]15 W/cm[superscript]2). By taking the ratio of the molecular to atomic yields as a function of laser intensity, it is possible to "cancel out" systematic errors which are common to both species, e.g. from laser instability, or temperature fluctuations. This technique is very powerful in our ionization studies, as it alludes to the distinct mechanisms leading to the ionization of both molecular and atomic species at the same intensity which are not a function of the experimental conditions. By using the accurate treatments of atomic ionization in tandem with existing molecular ionization models as a benchmark, we can use our experimental ratios to modify existing molecular ionization theories. We hope that the data procured in this thesis will be used in the development of more accurate treatments describing the strong-field ionization of molecules.

The immunogenicity of breast cancer (BC) is quite heterogeneous among the clinical subtypes, with immune responses identified most frequently in triple negative (TNBC) and HER2-positive tumors. The extent, spatial localization, distribution patterns, organization and phenotype of the BC immune infiltrate are currently being widely investigated but require standardization before they can be used clinically. One highly relevant unmet clinical need is to understand how immune features are linked to prognosis and potential benefit from treatments, particularly immunotherapy. The present work investigated tumor-infiltrating lymphocytes (TIL), tertiary lymphoid structures (TLS), the expression of multiple targetable inhibitory immune checkpoint molecules (PD-1, PD-L1 and PD-L2, CTLA-4, LAG3 and TIM3) and their clinical relevance in primary BC. Different technical approaches were employed including: flow cytometry (FC) on fresh tissue homogenates; immunohistochemistry (IHC) and immunofluorescence (IF) on formalin-fixed paraffin embedded (FFPE) tissue blocks from untreated primary tumors; and gene expression on a large dataset of BC patients with available long-term survival data. Flow cytometric analysis of PD-1 expression and its principal ligands PD-L1 and PD-L2 together with CTLA-4, LAG3 and TIM3 on TIL in fresh untreated primary tumors revealed that PD-1 and CTLA-4 are most highly expressed on BC TIL and PD-L1 is the principal PD-1 ligand in BC. Immune checkpoint molecule expression parallels the extent of TIL infiltration and TLS presence and number, with the patterns detected similar to that observed in secondary lymphoid organs. Significantly improved disease-specific survival (DSS) has been associated with PD-1hi HER2-enriched and PD-L1hi, PD-L2hi and CTLA-4hi basal-like BC; however there is significant heterogeneity between individual tumors even within the same subtype. These observations suggest that determining expression levels of multiple targetable inhibitory immune checkpoint molecules in patients might help to successfully target them in BC patients most likely to respond.We examined the concordance between two experienced immuno-pathologists who read 800 IHC-stained slides from five independent series over a period of four years to determine the reproducibility of assessing multiple immune biomarkers. This included scoring TIL, TLS, PD-1 and PD-L1 together with detailed information on the spatial localization and cell types expressing these molecules in the tumor microenvironment (TME). The interobserver reproducibility for the assessment of TIL and TLS was consistently good to excellent overtime, while the concordance for PD-L1 evaluation ranged from fair to excellent when it was only expressed on tumor cells (TC); and the concordance for PD-1 evaluation was fair to excellent when it was expressed in TLS and evaluated in primary tumors. Neither PD-L1 expression by TC, nor PD-1 expression within a TLS was significantly associated with prognosis in our datasets.The extent of TIL, TLS and PD-1 and PD-L1 expression were studied in a cohort of TNBC patients who underwent genetic counseling for their personal/familial history of BC or ovarian cancer (OC). This study revealed a remarkable similarity in patterns of immune infiltration between the two cohorts. Interestingly, a higher prevalence of TIL intermediate cases (≥10% and <50% TIL) was detected in the BRCA-mutated cohort, suggesting that this group may be more immunogenic.We next investigated whether the extent and presence of these immune parameters were associated with prognosis in the most highly infiltrated, aggressive BC subtypes (TNBC and HER2-positive). We determined the ideal cut-off for each subtype (TNBC and HER2-positive) to use TIL as a categorical variable. This study found a consistent prognostic impact from TIL (in any tumor compartment including stromal, intratumoral and global areas) and a novel association between PD-L1 expression within TLS and better survival in TNBC. This last effect was driven by baseline stromal TIL, strengthening the importance of reliably quantifying the levels of TIL in BC. Overall, our analyses show that among the targetable inhibitory immune checkpoint molecules investigated in BC, PD-1 and CTLA-4 are most highly expressed by BC TIL and are associated with higher infiltration of TIL; PD-L1 is the principal ligand for PD-1; TIL and TLS are reproducibly scored on IHC-stained tissues; and TIL levels are associated with a better prognosis in TNBC independent of their location in the TME at optimal cut-offs. Our data also provide new insight on targetable inhibitory immune checkpoint molecule expression and location as well as showing a prognostic role for TIL assessed by IHC in primary BC, which identifies these biomarkers as ideal candidates for further investigation. / Doctorat en Sciences médicales (Médecine) / info:eu-repo/semantics/nonPublished

Abstract Background The South African Healthcare landscape has changed dramatically over the last two years with the implementation of mandatory substitution, single exit pricing and prescribed minimum benefits. The private market for medicines is becoming more competitive and commoditized. Between July 2004 and June 2005 there were 119 generic registrations at the Medicines Control Council. In the US and Canada research has been conducted on the change in prescribing behaviour induced through incentive based formularies and the impact of generic medicines on healthcare costs. This research protocol aims to build on this body of knowledge by analysing sales trends within a therapeutic class after the launch of a generic molecule in the same class. This research investigates how the introduction of generics may impact the growth of the innovator molecules and subsequent generics. The therapeutic class Acid Pump Inhibitors has been selected. Method Unit sales of Proton Pump Inhibitors are drawn monthly from sales in the total private market. They are then grouped by molecule and comparisons are drawn between the originator and it’s generic to determine association. This is also done at the aggregate level where the originators form one group and generics the second group. Each aggregate group’s average growth in the therapeutic class is then calculated to determine the aggregate group’s evolution index. Data Analysis Data is analysed through descriptive and interpretative statistics. The descriptive statistics establish a relationship between generisized molecules and the non generisized molecules. A t-test for two independent means is used to test the hypothesis that the non generisized molecules in the therapeutic class have a significant higher growth. Conclusion The results demonstrate that the number of units sold of the generisized molecules increase as they become more affordable, however contrary to intuition the number of iv units sold of the non generisized molecules also increase. The research shows that there is a statistically significant greater growth, albeit on a smaller base, of the non generisized molecules over generisized molecules.

Dans cette thèse, nous présentons une approche algorithmique permettant la génération de guides de construction de cages moléculaires organiques. Il s'agit d'architectures semi-moléculaires possédant un espace interne défini capable de piéger une molécule cible appelée substrat. De nombreuses œuvres proposent de générer des cages organiques moléculaires obtenues à partir de structures symétriques, qui ont une bonne complexité, mais elles ne sont pas spécifiques car elles ne prennent pas en compte des cibles précises. L'approche proposée permet de générer des guides de construction de cages moléculaires organiques spécifiques à un substrat donné. Afin de garantir la spécificité de la cage moléculaire pour le substrat cible, une structure intermédiaire, qui est une expansion de l'enveloppe du substrat cible, est utilisée. Cette structure définie la forme de l'espace dans lequel est piégé le substrat. Des petits ensembles d'atomes, appelés motifs moléculaires liants, sont ensuite intégrés à cette structure intermédiaire. Ces motifs moléculaires sont les ensembles d'atomes nécessaires aux cages moléculaires pour leur permettre d’interagir avec le substrat afin de le capturer. / In this thesis, we present an algorithmic approach allowing the generation of construction guides of organic molecular cages. These semi-molecular architectures have a defined internal space capable of trapping a target molecule called substrate. Many works propose to generate molecular organic cages obtained from symmetrical structures, which have a good complexity, but they are not specific because they do not take into account precise targets. The proposed approach makes it possible to generate guides for the construction of organic molecular cages specific to a given substrate. In order to ensure the specificity of the molecular cage for the target substrate, an intermediate structure, which is an expansion of the envelope of the target substrate, is used. This structure defines the shape of the space in which the substrate is trapped. Small sets of atoms, called molecular binding patterns, are then integrated into this intermediate structure. These molecular patterns are the sets of atoms needed by molecular cages to allow them to interact with the substrate to capture it.

A interação de várias substancias bioativas com monocamadas de fosfolipídios foi investigada usando isotermas de pressão e potencial de superfície, incluindo as drogas farmacológicas dipiridamol (DIP), clopromazina (CPZ) e trifluoperazina (TFP), além da melatonina (MEL) e o colesterol (COL). Os fosfolipídios empregados foram o zwiteriônico dipalmitoil fosfatidil colina (DPPC) e o aniônico dipalmitoil fosfatidil glicerol (DPPG) espalhados na superfície de água ultrapura, sendo que as monocamadas servem como modelo simples de membranas. A cooperatividade na interação entre fosfolipídios e moléculas com atividade biológica foi essencial para entender os acentuados efeitos na expansão (ou condensação) das monocamadas e as mudanças no momento de dipolo (até 10% de aumento na expansão em relação à monocamada do fosfolipídio puro para as misturas DIP/DPPC) que ocorreram a concentrações molares muito baixas entre 0,2-0,4% do DIP. Tais efeitos foram observados para todas as cinco substâncias investigadas, em todos os regimes de pressão. Nas altas concentrações, o comportamento da interação depende do tipo de mólecula e também de se a monocamada é de DPPC ou DPPG. Para o DPPC, as drogas farmacológicas foram expelidas da interface em vários graus a altas pressões, e existia um máximo de concentração da droga acima do qual ocorria a saturação, provavelmente porque as moléculas em excesso foram para a subfase. Essas concentrações críticas foram de 2% em mol para o DIP e a CPZ e de 5% em mol para a TFP. Para o DIP, em particular, os resultados das isotermas foram correlacionados com experimentos de espectroscopia de FTIR e microscopia de fluorescência \"in situ\", realizados por colaboradores, os quais permitiram a determinação de uma localização precisa da droga estudada. Não existe inserção do DIP na região da cauda hidrofóbica da monocamada do DPPC, com a interação ocorrendo com o grupo fosfato no zwiteríon, cujas pequenas mudanças na orientação induzidas pelo DIP levam a grandes mudanças no momento de dipolo. Como o DPPG está carregado negativamente sobre a superfície da água pura, não existe saturação nos efeitos de expansão com o aumento da concentração das drogas. O aumento do momento de dipolo efetivo na monocamada mista é atribuído a alterações na densidade de carga superficial pela adsorção da droga catiônica, que reduz a contribuição negativa do potencial da dupla camada, quando comparado com o da monocamada de DPPG puro. Os resultados do COL e a MEL devem ser considerados separadamente devido a sua natureza distinta, embora um comportamento cooperativo também tenha observado com grandes efeitos nas baixas concentrações. Tanto o COL como o MEL induzem mudanças na expansão das monocamadas de DPPC até a máxima concentração empregada, 20% molar. Para o COL foi observado um efeito de condensação a baixas concentrações, o qual foi seguido por uma expansão a altas concentrações, confirmando assim resultados prévios da literatura. Todas as monocamadas mistas COL/DPPG apresentavam-se expandidas, também confirmando alguns resultados da literatura para lipídios (diferentes do DPPC) quando misturados com o COL. A interação da MEL com o DPPC foi essencialmente similar à do COL, apesar do fato de a MEL pura não formar monocamadas estáveis. Sua interação com o DPPG foi peculiar já que o efeito que esta induz satura a 5% em mol. Isto também difere do comportamento das drogas farmacológicas. A MEL é neutra em todos os pHs, portanto, sua intenção com as membranas modelo de DPPG e DPPC só pode ocorrer via dipolo. O mesmo se aplica ao colesterol, o que justifica as diferenças no comportameto destas duas moléculas quando comparadas com as drogas (DIP, CPZ, TFP), que são carregadas sobre a água pura, nas misturas com os dois fosfolipídios (DPPG e DPPC). / The interaction of various bioactive substances with phospholipids monolayers has been investigated using surface pressure and surface potential isotherms, which include the pharmaceutical drugs dipyridamole (DIP), chlorpromazine (CPZ) and trifluoperazine (TFP), in addition to melatonin (MEL) and cholesterol (COL). The phospholipids employed were the zwitterionic dipalmitoyl phosphatidyl choline (DPPC) and the anionic dipalmitoyl phosphatidyl glycerol (DPPG) spread onto ultra pure water surfaces, where the monolayers served as simple model membrane systems. Cooperativity in the interaction between phospholipid and bioactive molecules was essential to account for the large effects of expansion (up to 10% increase in area in relation to the pure phospholipid monolayer for the DIP/DPPC mixture) of the monolayers and changes in dipole moment, which occurred at very low concentrations, e.g. 0.2 - 0.4 mol% of the substance. Such large effects were observed for all 5 substances investigated, at all surface pressure regimes. At higher concentrations, the interaction behavior depended on the type of molecule and also on whether the host monolayer was DPPC or DPPG. For DPPC, the pharmaceutical drugs were expelled at varying degrees from the interface at high surface pressures, and there was a maximum drug concentration above which the effects saturated, probably because the molecules in excess were lost to the subphase. These critical concentrations were 2mol% for DIP and CPZ and 5mol% for TFP. For DIP, in particular, the results from isotherm were correlated with in situ FTIR spectroscopy and fluorescent microscopy experiments, carried out by collaborators, which allowed the precise location of the drug to be determined. There is no insertion of DIP into the hydrophobic tail region of the DPPC monolayer, with interaction taking place with the phosphate group in the zwitterion, whose small changes in orientation induced by DIP lead to the large changes in dipole moment. Because DPPG is negatively charged on a pure water surface monolayer, there is no saturation of the expansion effects with the increase in drug concentration. The increase in the effective dipole moment of the mixed monolayers are attributed to alterations in the surface charge density by adsorption of the cationic drugs, which then reduces the negative contribution of the double-layer potential as compared to the pure DPPG monolayer. The results for COL and MEL must be considered separately owing to their distinct nature, even though a cooperative behavior was also observed with large effects at low concentrations. Both COL and MEL induce changes in the DPPC monolayers up to the highest concentration employed, viz. 20mol%. For COL, a condensation effect was observed at low concentrations, which was followed by monolayer expansion at high concentrations, thus confirming previous results in the literature. All COL/DPPG monolayers were more expanded than pure DPPG, also confirming previous results from the literature. While the interaction of MEL with DPPC was essentially similar to that of COL, in spite of the fact that MEL does not form stable monolayers on its own, its interaction with DPPG was somewhat peculiar in that the effects it induced saturate at 5mol%. This also differs from the behavior of the pharmaceutical drugs. MEL is neutral over a wide range of pHs, and therefore its interaction with DPPC and DPPG monolayers must occur via dipole interaction. The same applies to COL, and this explains why the behavior of these two substances is different from the drugs (DIP, CPZ and TFP) that are charged on the water surface, in the interaction with DPPC and DPPG.

Myotonic dystrophy (DM) is one of the most common forms of muscular dystrophy, characterized by its hallmark symptom myotonia. DM is an autosomal dominant disease caused by a toxic gain of function RNA. The toxic RNA is produced from expanded non-coding CTG/CCTG repeats, and these CUG/CCUG repeats sequester a family of RNA binding proteins. The Muscleblind-like (MBNL) family of RNA binding proteins are sequestered to the expanded CUG/CCUG repeats. The MBNL proteins are regulators of alternative splicing, and their sequestration to the toxic RNA leads to mis-splicing events, which are believed to cause the symptoms observed in DM patients. A previously reported screen for small molecules used to identify compounds that could disrupt MBNL from binding the toxic CUG repeats found that pentamidine was able to rescue splicing defects associated with DM. Herein, we present a new class of molecules (phenolsulphonphthaleins) that inhibited MBNL1/CUG repeat complex formation in a competitive electrophoretic mobility shift assay (EMSA). Additionally, one of these molecules, bromophenol blue (BPB), acted in a synergistic manner with the previously described inhibitor pentamidine. We also demonstrated that the halogenation of the phenolsulphonphthalein dyes is an important factor for activity. Moreover, we presentant analysis of a series of methylene linker variants of pentamidine that revealed heptamidine (an analog of pentamidine) could reverse splicing defects in a DM1 tissue culture model and rescue myotonia in a DM1 mouse model. Finally, we report on a new crystal structure of CUG repeats, crystallized in the context of a GAAA tetraloop/receptor which facilitated ordered packing within the crystal. This structure was consistent with previous structures showing that the repeats are essentially A-form RNA, despite having a U-U mismatch every third base pair. We also identified six types of U-U mismatch in the context of the 5'CUG/3'GUC motif, suggesting that the interactions between the uridines are dynamic. This structure also contains the highest resolution GAAA tetraloop/receptor structure (1.95 Å) reported to date. This dissertation includes previously unpublished co-authored material.

The work described in this thesis is in three parts:. Part I deals with the metabolism of 5-p-aminobenzene-sulphonamide- 3-methylisothiazole (sulphasomizole), 5-amino-3--methylisothiazole, sulphanilamide, and some of the acetyl derivatives. A marked species difference has been found in the metabolism of sulphasomizole.

Integrin recycling has been generally assumed to be important for cell migration but the trafficking pathways and the molecules regulating integrin trafficking remain poorly characterized. Furthermore, little is known about the activation status of endocytosed integrins and how it affects the recycling of these receptors. It is likely that FA-engaged integrins will follow different trafficking pathways than bulk integrins and here I sought to study the endocytic fate of this particular integrin pool using the MT-induced FA disassembly assay. I found that integrins previously resident at FAs travel through different Rab compartments after FA disassembly and that their return to the plasma membrane is Rab11- and Src-dependent. Strikingly, I unveiled new functions for FAK and Src family kinases in this process by showing that these kinases are critical to keep integrins active during endocytic trafficking. This finding is unprecedented since it was not known whether endocytosed integrins were kept active during their trafficking. Interestingly, reassembly of FAs from endocytosed integrin occurred preferentially at the leading edge of migrating cells suggesting that integrins are trafficked in a polarized fashion. Furthermore, the recycling of integrins from the Rab11-positive compartment to the plasma membrane is a long-range transport implying the existence of a MT motor committed to this task. Consistently, I identified that a kinesin-II motor, Kif3AC, is engaged in this process. My work establishes a FAK- and Src family kinases-based mechanism for integrin "adhesion memory" during endocytic trafficking and identifies a direct link between FA disassembly and reassembly through an endocytic recycling pathway involving Rab5 and Rab11 and a kinesin-II family member.

Small molecules have played an important role in defining the functions and identities of numerous proteins involved in fundamental biological processes as well as pathways involved in disease. Chemical genetics represents the formalization of this process into a defined field desiring to achieve the breadth and specificity of classical genetics. In order to gain full advantage of a small molecule's ability to perturb the cell for novel or desired phenotypes, a complete understanding of the molecule's mechanism of action must be achieved. Identification of the biological targets of a molecule represents the most direct approach to attaining this knowledge. In our strategy to find novel mechanisms to target cancers with oncogenic RAS mutations, we have used small molecules to probe specific weaknesses of this cancerous network through synthetic lethal screening. One molecule identified in these screens, RSL3, attracted interest as a candidate for target identification studies because of its potent lethality and potentially unique mechanism of action. We used an affinity chromatography approach to directly isolate binding partners of RSL3 by modifying the molecules structure to incorporate various affinity tags. Through these experiments we ultimately identified a number of interesting candidate targets. Investigations validating these targets suggest that multi-targeted modulation of antioxidant and prostaglandin networks may be a mechanism for selectively killing cancers with oncogenic RAS. The identification of biological targets of small molecules poses a difficult challenge to the field of forward chemical genetics. Thus, we attempted to optimize a unique method for target identification, the yeast three-hybrid system (Y3H), which detects small molecule-protein interactions through a transcriptional assay in vivo. We created a version of our Y3H system that incorporated a covalent anchor and compared it with the existing state-of-the-art, which uses a high affinity non-covalent anchor. Transcriptional assays indicated our new system was functional, but surprisingly could not improve upon the original Y3H system. These results highlight the complexities of manipulating ligand-receptor interactions in vivo.