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No / This study shows that prostaglandins in human FM55 melanoma cells and epidermal melanocytes are produced by COX-1. Prostaglandin production in FM55 melanoma cells was unrelated to that of melanin suggesting that the two processes can occur independently. ¿-Melanocyte stimulating hormone (¿-MSH), which had no effect on melanin production in FM55 cells, stimulated PGD2 production in these cells without affecting PGE2. While cAMP pathways may be involved in regulating PGD2 production, our results suggest that ¿-MSH acts independently of cAMP, possibly by regulating the activity of lipocalin-type PGD synthase. This ¿-MSH-mediated effect may be associated with its role as an immune modulator. / The Wellcome Trust

No / The Flinders Sensitive Line (FSL) rat is a genetic animal model of depression. Following recent findings that the brain fatty acid composition of FSL is characterised by increased arachidonic acid (AA), we used electrospray tandem mass spectrometry and 1H-NMR to examine lipid species in different brain areas. Cholesterol and sphingolipids were increased in the hypothalamus of the FSL rats. Furthermore, arachidonic acid-containing phosphatidylcholine species (AA-PC) were elevated with PC16:0/20:4, PC18:1/20:4 and PC18:0/20:4 (p<0.003) increased in the hypothalamus and striatum. In contrast, there was a decrease in some docosahexaenoic acid (DHA)-containing species, specifically PC18:1/22:6 (p<0.003) in the striatum and PE18:1/22:6 (p<0.004) in the prefrontal cortex. Since no significant differences were observed in the erythrocyte fatty acid concentrations, dietary or environmental causes for these observations are unlikely. The increase in AA-PC species which in this animal model may be associated with altered neuropathy target esterase activity, an enzyme involved in membrane PC homeostasis, may contribute to the depressive phenotype of the FSL rats.

No / Prostanoids modulate the activity of human pregnant myometrium and their functional role can be appreciated through characterisation of prostanoid receptors and tissue concentration of prostanoids. We have applied a lipidomic approach to elucidate the profile of prostanoids in human non-labouring and labouring myometrium. We have identified a total of nineteen prostanoids including prostacyclin, thromboxanes, prostaglandins and dihydro-prostaglandins. Prostacyclin was the predominant prostanoid in both non-labouring and labouring myometria, with PGD2 and PGF2¿ being the second most abundant. Although the total amount of prostanoids was increased in the labouring tissue, PGE2 and 13,14-dihydro-15-keto-PGE2 were the only prostanoids to increase significantly at early and late labour (p¿0.001). Our data suggest that PGF2¿ plays an important role in parturition, whilst the increase in PGE2 could occur to facilitate cervical dilation and relaxation of the lower myometrium during labour. Although the elevation in TXA2 was less marked than expected, in terms of translation to function even a relatively small increase in the level of this potent spasmogen may have significant effects.

No / Lipid mediators are produced from the oxidation of polyunsaturated fatty acids through enzymatic and free radical-mediated reactions. When subject to oxygenation via cyclooxygenases, lipoxygenases, and cytochrome P450 monooxygenases, polyunsaturated fatty acids give rise to an array of metabolites including eicosanoids, docosanoids, and octadecanoids. These potent bioactive lipids are involved in many biochemical and signaling pathways, with inflammation being of particular importance. Moreover, because they are produced by more than one pathway and substrate, and are present in a variety of biological milieus, their analysis is not always possible with conventional assays. Liquid chromatography coupled to electrospray mass spectrometry offers a versatile and sensitive approach for the analysis of bioactive lipids, allowing specific and accurate quantitation of multiple species present in the same sample. Here we explain the principles of this approach to mediator lipidomics and present detailed protocols for the assay of enzymatically produced oxygenated metabolites of polyunsaturated fatty acids that can be tailored to answer biological questions or facilitate assessment of nutritional and pharmacological interventions.

BACKGROUND:The widespread utilization of organic compounds in modern society and their dispersion through wastewater have resulted in extensive contamination of source and drinking waters. The vast majority of these compounds are not regulated in wastewater outfalls or in drinking water while trace amounts of certain compounds can impact aquatic wildlife. Hence it is prudent to monitor these contaminants in water sources until sufficient toxicological data relevant to humans becomes available. A method was developed for the analysis of 36 trace organic contaminants (TOrCs) including pharmaceuticals, pesticides, steroid hormones (androgens, progestins, and glucocorticoids), personal care products and polyfluorinated compounds (PFCs) using a single solid phase extraction (SPE) technique with ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS). The method was applied to a variety of water matrices to demonstrate method performance and reliability.RESULTS:UHPLC-MS/MS in both positive and negative electrospray ionization (ESI) modes was employed to achieve optimum sensitivity while reducing sample analysis time (<20min) compared with previously published methods. The detection limits for most compounds was lower than 1.0 picogram on the column while reporting limits in water ranged from 0.1 to 15ng/L based on the extraction of a 1L sample and concentration to 1mL. Recoveries in ultrapure water for most compounds were between 90-110%, while recoveries in surface water and wastewater were in the range of 39-121% and 38-141% respectively. The analytical method was successfully applied to analyze samples across several different water matrices including wastewater, groundwater, surface water and drinking water at different stages of the treatment. Among several compounds detected in wastewater, sucralose and TCPP showed the highest concentrations.CONCLUSION:The proposed method is sensitive, rapid and robust / hence it can be used to analyze a large variety of trace organic compounds in different water matrixes.

Formamide is a solvent of great interest to prebiotic chemists because it is liquid over a wide range, it is less volatile than either water or HCN, and it possesses a versatile reactivity. When formamide is heated in the presence of minerals or inorganic catalysts, a variety of products including purine nucleobases are generated. Irradiation of formamide reaction solutions with ultraviolet light increases the yield and diversity of products, and eliminates the need for a mineral catalyst. We have also performed formamide reactions in the presence of pyrite, a mineral which is likely to have been available on the primordial Earth, under a variety of atmospheric conditions. Our results indicate the greatest yield and diversity of products result from the combination of a pyrite mineral catalyst, heat, UV irradiation, and a carbon dioxide atmosphere. Purine nucleobases are simple to synthesize in model reactions and they stack well in aqueous solution; it has been hypothesized that the first nucleic acids were composed of only purine bases, and that water-soluble, cationic, aromatic molecules with large stacking surfaces (“”molecular midwives””) may have aided the assembly of the earliest nucleic acid analogs. We have characterized the interactions of various intercalators with a standard DNA duplex as well as with an antiparallel homopurine DNA duplex and have determined that molecules which possess four or more rings and a curved shape interact selectively with all-purine DNA; such molecules can serve as models for putative prebiotic midwives.

<p>Disease-specific compounds (biomarkers) are analyzed in clinical laboratories to assist with diagnosing diseases. This thesis describes development and validation of liquid chromatography tandem mass spectrometry (LC-MS/MS) based tests for diagnosing a diverse group of endocrine and metabolic diseases. The analytical methods used on-line and off-line sample extraction and analytical derivatization as means of enhancing the analytical sensitivity, specificity and clinical utility. All developed methods were extensively validated and reference intervals for the biomarker concentrations were established in blood samples of healthy adults and children. Advantages of the LC-MS/MS as an analytical technique include possibility of simultaneous measurement of multiple analytes and ability of confirming their identity. In this thesis we proposed and evaluated approaches for the assessment of the specificity of analysis in the methods that use tandem mass spectrometry detection. To enhance throughput of the LC-MS/MS tests for the biomarkers that have endogenous or exogenous isomers an approach was developed for quantitation of isomers from unresolved chromatographic peaks. Using methods developed in this thesis we performed a study of the steroidogenesis in ovarian follicles of healthy women and women with polycystic ovary syndrome (PCOS). Obtained data on the steroid concentrations and associations between the steroid metabolites in the pathway would be helpful for better understanding of the ovarian pathophysiology. Potential biomarkers of PCOS were identified in the thesis; further studies will be necessary to confirm their clinical utility.</p>

Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate and invertebrate blood clotting, barnacle cement polymerization was shown to involve proteolytic activation of enzymes and structural precursors, transglutaminase cross-linking and assembly of fibrous proteins. Proteolytic activation of structural proteins maximizes the potential for bonding interactions with other proteins and with the surface. Transglutaminase cross-linking reinforces cement integrity. Remarkably, epitopes and sequences homologous to bovine trypsin and human transglutaminase were identified in barnacle cement with tandem mass spectrometry and/or western blotting. Akin to blood clotting, the peptides generated during proteolytic activation functioned as signal molecules, linking a molecular level event (protein aggregation) to a behavioral response (barnacle larval settlement). Our results draw attention to a highly conserved protein polymerization mechanism and shed light on a long-standing biochemical puzzle. We suggest that barnacle cement polymerization is a specialized form of wound healing. The polymerization mechanism common between barnacle cement and blood may be a theme for many marine animal glues. / Dissertation

La protéogénomique consiste à affiner l'annotation du génome d'organismes modèles pour lesquels des données protéomiques sont générées à haut-débit. Des erreurs d'annotation structurale ou fonctionnelle sont encore fréquentes. Innover dans les méthodologies permettant de lever ces ambiguïtés est essentiel. L'étude spécifique du N-terminome permet de vérifier expérimentalement l'identification du codon d'initiation de la traduction et de certifier les données obtenues. Pour cela, deux stratégies innovantes ont été développées basées sur : i) le marquage sélectif du N-terminal des protéines, ii) une digestion multienzymatique en parallèle, et ii) l'enrichissement spécifique des peptides N-terminaux marqués par chromatographies liquides successives ou immunocapture dirigée contre le groupement N-terminal ajouté. L'efficacité de ces méthodologies a été démontrée à partir du modèle bactérien Roseobacter denitrificans. Après enrichissement par chromatographie, 480 protéines ont été validées et 46 ré-annotées. Plusieurs sites d'initiation de la traduction ont été décelés et l'annotation par similarité a été remise en cause dans certains cas. Après immunocapture, 269 protéines ont été caractérisées dont 40% ont été identifiées spécifiquement après enrichissement. Trois gènes ont également été annotés pour la première fois. Les résultats complémentaires obtenus après analyse par spectrométrie de masse en tandem facilitent l'interprétation des données pour révéler les sites d'initiation réels de la synthèse des protéines et identifier de nouveaux produits d'expression des gènes. La ré-annotation peut devenir automatique et systématique pour améliorer les bases de données protéiques. / Proteogenomics is a recent field at the junction of genomics and proteomics which consists of refining the annotation of the genome of model organisms with the help of high-throughput proteomic data. Structural and functional errors are still frequent and have been reported on several occasions. Innovative methodologies to prevent such errors are essential. N-terminomics enables experimental validation of initiation codons and certification of the annotation data. With this objective in mind, two innovative strategies have been developed combining: i) selective N-terminal labeling of proteins, ii) multienzymatic digestion in parallel, and iii) specific enrichment of most N-terminal labeled peptides using either successive liquid chromatography steps or immunocapture directed towards the N-terminal label. Efficiency of these methodologies has been demonstrated using Roseobacter denitrificans as bacterial model organism. After enrichment with chromatography, 480 proteins were validated and 46 re-annotated. Several start sites for translation initiation were detected and homology driven annotation was challenged in some cases. After immunocapture, 269 proteins were characterized of which 40% were identified specifically after enrichment. Three novel genes were also annotated for the first time. Complementary results obtained after tandem mass spectrometry analysis allows easier data interpretation to reveal real start sites of translation initiation of proteins and to identify novel expressed products. In this way, the re-annotation process may become automatic and systematic to improve protein databases.