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The intention with this thesis is to investigate a dimer in a spin chain. Inorder to do that, a model from Z2-gauge theory is taken as the theoretical motivation to construct a discrete lattice with Ising spin properties. A dimer is then allowed to exist indirectly in the empty space between sites. We choose to tackle the problem through a quantum mechanical approach in 1+1-dimensions, distancing ourselves from the original description in quantum field theory. The exposition begins by reviewing the spatial construction of the entire chain as well as its components, and ends with a discussion of time development where the main concern is dispersion in addition to reflection against a static charge.

Objective: Abnormal elevation of D-dimer levels is an important indicator of disseminated intravascular clotting. Therefore, we hypothesized that high D-dimer levels were associated with the risk of stroke and adverse clinical outcomes of patients with acute ischemic stroke (AIS) or transient ischemic attack (TIA). Methods: The present meta-analysis aimed to systematically analyze the associations between D-dimer and the risk of stroke as well as the clinical outcomes of patients with post-stroke or TIA. Meanwhile, dose–response analyses were conducted when there were sufficient data available. Three electronic databases including Pubmed, the Embase database, and the Cochrane Library were searched by two investigators independently. All the pooled results were expressed as risk ratios (RRs). Results: Finally, 22 prospective cohort studies were included into this meta-analysis. The results suggested that high D-dimer levels were associated with increased risks of total stroke (RR 1.4, 95%CI 1.20–1.63), hemorrhagic stroke (RR 1.25, 95%CI 0.69–2.25), and ischemic Stroke (RR 1.55, 95%CI 1.22–1.98), and the dose-dependent relationship was not found upon dose–response analyses. Besides, the high D-dimer levels on admission were correlated with increased risks of all-cause mortality [RR 1.77, 95% confidence interval (CI) 1.26–2.49], 5-day recurrence (RR 2.28, 95%CI 1.32–3.95), and poor functional outcomes (RR 2.01, 95%CI 1.71–2.36) in patients with AIS or TIA. Conclusions: On the whole, high D-dimer levels may be associated with the risks of total stroke and ischemic stroke, but not with hemorrhagic stroke. However, dose–response analyses do not reveal distinct evidence for a dose-dependent association of D-dimer levels with the risk of stroke. Besides, high D-dimer levels on admission may predict adverse clinical outcomes, including all-cause mortality, 5-day recurrence, and 90-day poor functional outcomes, of patients with AIS or TIA. More studies are warranted to quantify the effect of D-dimer levels on the risk of stroke or TIA, so as to verify and substantiate this conclusion in the future.

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<p> Under 248 nm laser flash photolysis, the photodecomposition of 1,3,4-trimethyl-1-phenyl-1-germacyclopent-3-ene (28) in dry, deoxygenated hexane solution at 23 °C leads to the prompt formation of two transient species: phenylmethylgermylene (29) and its Ge=Ge doubly bonded dimer, 1,2-dimethyl-1 ,2-diphenyldigemene (30). The formation of 29 proceeds in high chemical yield as shown by the results of steady state trapping experiments with methanol and isoprene. The transient assigned to 29 exhibits λmax = 490 nm and decays with second-order kinetics (τ ~ 2 μs). The second transient, which is formed from the latter, is assigned to digermene 30 and exhibits λmax = 420 nm and a lifetime, τ ~ 8 μs. The assignments are based on comparisons to the spectra of other simple germylenes, such as dimethyl-, diphenyl and dimesitylgermylene as well as on the pattern of reactivity with trapping reagents in solution at room temperature.</p> <p> Reactions studied include N-H, O-H and Sn-H insertion reactions, the [1+2] addition to isoprene and t-butylacetylene, and halogen atom abstraction from carbon tetrachloride.</p> <p> Absolute rate constants for quenching of 29 with the above mentioned scavengers were obtained by direct measurement of the germylene decay kinetics, over the concentration range where the formation of the digermene was more than 70% quenched. This ensures that the decay of 29 was dominated by the reaction with the trapping reagent.</p> <p> Absolute rate constants for reaction of the same reagents with 30 have also been determined for most of the scavengers studied. However, the digermene was found to be considerably less reactive than phenylmethylgermylene in all cases.</p> <p> The trends in spectroscopic properties and reactivity of simple germylenes in solution are discussed.</p> / Thesis / Master of Science (MSc)

Part I: Signaling Role of the Sensor Kinase RetS in Biofilm formation Regulation of Pseudomonas aeruginosa-<br />The opportunistic human pathogen Pseudomonas aeruginosa causes both acute and chronic infections in predisposed individuals. Acute infections require a functional Type Three Secretion System (TTSS), which mediates the translocation of select cytotoxins into host cells. Chronic infections, the leading cause of death among cystic fibrosis patients, are characterized by drug-resistant biofilms formation. To regulate gene expression, Pseudomonas aeruginosa utilizes two-component regulatory systems (TCS). Specifically, we focus on the TCS signaling kinase RetS, which is a critical repressor of biofilm formation. The signaling mechanism of RetS is unusual. According to recent findings and one hypothesis, RetS employs a novel signaling mechanism involving direct binding to the signaling kinase GacS, thereby repressing the GacS-induced biofilm formation. RetS is believed to be regulated by the interaction of its periplasmic sensory domain (RetSperi) with an unknown ligand. As such, RetSperi is a potential drug target. We hypothesized that ligand-binding shifts the equilibrium between the formation of a RetS homo-dimer and the RetS-GacS complex by tuning the homo-dimerization of the RetSperi. While the molecular signal that regulates RetS is unknown, our structural studies of the sensory domain suggest that this ligand is a carbohydrate-based moiety. Unchanged biofilm-EPS production phenotype of RetSperi ligand binding site mutants indicates that the natural ligand is not from Pseudomonas aeruginosa.<br />Additional experiments unambiguously determined that the sensory domain forms a stable homodimer. Adding to the complexity of the system, we have identified<br />two possible dimer interfaces in our in vitro assays. However, inconsistent with the current model, elimination of RetSperi results in a slightly increased biofilm EPS production phenotype. Therefore, with the previous demonstration that RetS is able to dephosphorylate GacS, we propose an alternative hypothesis: the RetS kinase domain serves as a phosphatase for phosphorylated GacS; this phosphatase activity is tuned by signaling sensing on RetSperi. Finally, to provide an important piece of information for understanding the molecular basis of RetS-GacS signaling, we have developed a crystallization-based structure determination strategy in order to reveal the precise RetS-GacS interaction pattern.<br /><br />PartII: The catalytic domain of the germination-specific lytic transglycosylase SleB from Bacillus anthracis displays a unique active site topology-<br />germination-specific lytic enzymes (GSLEs) that degrade the unique cortex peptidoglycan to permit resumption of metabolic activity and outgrowth. We report the first crystal structure of the catalytic domain of a GSLE, SleB. The structure revealed a transglycosylase fold with unique active site topology and permitted identification of the catalytic glutamate residue. Moreover, the structure provided insights into the molecular basis for the specificity of the enzyme for muramic-"?lactam-containing cortex peptidoglycan. The protein also contains a metal-binding site that is positioned directly at the entrance of the substrate-binding cleft. / Ph. D.

No / Epidermal DNA damage, especially to the basal layer, is an established cause of keratinocyte cancers (KCs). Large differences in KC incidence (20- to 60-fold) between white and black populations are largely attributable to epidermal melanin photoprotection in the latter. The cyclobutane pyrimidine dimer (CPD) is the most mutagenic DNA photolesion; however, most studies suggest that melanin photoprotection against CPD is modest and cannot explain the considerable skin color-based differences in KC incidence. Along with melanin quantity, solar-simulated radiation-induced CPD assessed immediately postexposure in the overall epidermis and within 3 epidermal zones was compared in black West Africans and fair Europeans. Melanin in black skin protected against CPD by 8.0-fold in the overall epidermis and by 59.0-, 16.5-, and 5.0-fold in the basal, middle, and upper epidermis, respectively. Protection was related to the distribution of melanin, which was most concentrated in the basal layer of black skin. These results may explain, at least in part, the considerable skin color differences in KC incidence. These data suggest that a DNA protection factor of at least 60 is necessary in sunscreens to reduce white skin KC incidence to a level that is comparable with that of black skin.

Résumé : L’exposition aux rayons ultraviolets (UV) du soleil est le principal facteur menant au développement du cancer cutané. Les dimères cyclobutyliques de pyrimidines (DCP) résultant d’une exposition aux UV sont considérés comme les principaux dommages à l’ADN impliqués dans la cancérogenèse cutanée. La fréquence des DCP et leur distribution entre les quatre types de sites dipyrimidiniques ont souvent été étudiés in vitro ou en utilisant des UVC alors que nous ne sommes pas exposés à ce type d’UV. L’utilisation d’écrans solaires permet de prévenir la formation des DCP. Grâce à sa capacité à absorber les UVB, l’acide sulfonique 2-phénylbenzymidazole-5 (PBSA) est utilisé dans des écrans solaires mais des études in vitro ont montré qu’il peut oxyder les guanines lors d’une irradiation aux UVB. Face à ces problèmes, nous avons choisi d’étudier l’effet du PBSA, la fréquence et la distribution des DCP, de même que l’influence de la séquence nucléotidique sur la formation des DCP, dans des conditions plus représentatives de la réalité. Nous avons irradié des fibroblastes humains normaux (in cellulo) et de l’ADN purifié (in vitro) aux UVB et aux UVC. Nous avons comparé la formation des DCP in cellulo et in vitro. Suite à une exposition aux UVB, nous avons trouvé que la distribution des DCP in cellulo est similaire à la distribution des DCP in vitro. Nous avons ensuite comparé l’effet du type d’UV sur la formation des DCP et nous avons trouvé que les TT sont plus souvent endommagés après une irradiation aux UVC alors que les sites potentiellement mutés (contenant des cytosines) sont plus souvent endommagés après une exposition aux UVB, in cellulo. Concernant l’effet de la séquence d’ADN sur la formation des DCP, nous avons trouvé que certains sites dipyrimidiniques sont beaucoup plus fréquemment endommagés que les autres et que la position d’un site dipyrimidinique dans une série de pyrimidines adjacentes est un facteur influençant la formation des DCP. Nous avons étudié l’effet du PBSA in cellulo et in vitro suite à une irradiation aux UVA et aux UVB. Nous avons montré que le PBSA protège efficacement contre la formation de DCP, lors d’une irradiation UVB mais qu’il photosensibilise la formation de guanines oxydées lors d’une irradiation aux UVA et aux UVB. Le PBSA peut donc agir comme une épée à double tranchant et ceci questionne son utilisation dans les écrans solaires. Les travaux réalisés dans le cadre de cette thèse améliorent notre compréhension de la cancérogenèse cutanée, montrent l’importance du choix de modèles d’étude pertinents, de même que l’importance d’utiliser une protection solaire efficace contre tous les types de dommages causés par les UV. / Abstract : Exposure to the UV component of sunlight is the principal factor leading to skin cancer development. Cyclobutane pyrimidine dimers (CPD) are considered as the most important DNA damage involved in skin carcinogenesis. CPD frequencies and their distribution between the four types of dipyrimidine sites are mostly investigated in vitro or using UVC, even if we are not exposed to these wavelengths. On the other hand, sunscreens are used to protect against CPD formation. The 2-phenylbenzimidazole-5-sulfonic acid (PBSA) is a sunscreen agent used because it absorbs UVB. However, previous studies have shown that PBSA oxidizes guanines in vitro, during UVB exposure. To address these issues, we chose to study the effect of PBSA, the DCP frequencies and their distribution frequency and distribution of CPD, as well as the influence of DNA sequence on CPD formation, in conditions more representative of reality. We irradiated normal human fibroblasts (in cellulo) and purified DNA (in vitro) with UVB and UVC. We compared the CPD distribution in cellulo and in vitro. Our results show that CPD distribution in cellulo is different to CPD distribution in vitro after UVB exposure. Then, we compared the impact of UV type on CPD formation and we found that TT are more frequently damaged after UVC exposure while potentially mutated dipyrimidine sites (dipyrimidine sites containing cytosine) are more frequently damaged after UVB exposure. Concerning the influence of DNA sequence on CPD formation, we observed that some dipyrimidine sites are extremely frequently damaged compared to others and that the position of a dipyrimidine site within a dipyrimidine run is an important factor influencing the frequency of CPD formation. We studied the effect of PBSA, in cellulo and in vitro, during UVA and UVB exposure. We found that PBSA provides good protection against CPD formation during UVB exposure, in cellulo. However, PBSA photosensitized the formation of oxidized guanines during UVA and UVB exposure. This indicates that PBSA can act as a double-edged sword and question its suitability in sunscreens. The works presented in this thesis provide important elements to understand the skin carcinogenesis process and demonstrate the importance to use an effective protection against UV-induced DNA damage.