Coronary atherosclerotic plaque rupture is a critical event during atherosclerosis disease progression. Clinical consequences of atherosclerotic plaque rupture vary from asymptomatic to acute arterial thrombosis, yet the mechanisms underpinning such divergent biological response remain poorly understood. Novel biological signatures of plaque rupture will confer further insights into the dynamic responses triggered by plaque rupture event(s), and may provide alternative strategies for modulation of this prevalent disease. This thesis aims to investigate the events that accompany coronary plaque rupture and their relations to subsequent, downstream systemic effects. In a prospective clinical study of patients undergoing non-emergency percutaneous coronary intervention (PCI), stenting induced plaque disruption was used as a model of plaque rupture in vivo. Optical coherence tomography (OCT) imaging of the plaque lesion was performed prior to stenting, followed by serial blood sampling from targeted anatomical sites in reference to the plaque disruption event. Coronary plaque debris were also retrieved in a controlled manner. Analysis of candidate markers demonstrated a role of matrix metalloproteinase 9 (MMP9) in the systemic response to plaque disruption. Local and systemic elevations of MMP9 were observed promptly after plaque disruption. The systemic release of MMP9 was independent to the myocardial injury and systemic inflammation as a result of PCI. OCT analysis further suggested that plaque morphology may be a determining factor in the subsequent MMP9 release, as the disruption of lipid rich plaque(s) resulted in more acute elevation 'of ~1'MP9 when compared to disruption of non-lipid lesions. Changes of systemic MMP9 served as an index of response to the stent induced plaque disruption. Subjects with divergent MMP9 responses to the plaque disruption event were put forward for further comprehensive investigation during the discovery phase, using mass spectrometry techniques to investigate the lipidomic, metabolomics, and proteomic signatures of plaque disruption. Coronary atherosclerotic plaque disruption was associated with immediate changes in the plasma lipidomics and metabolomics profiles, which had distinct relations to the subsequent systemic MMP9 release. Coronary plaque debris provided a "catalogue" of proteins which could be acutely liberated into systemic circulation. Several such novel proteins were detected in circulation after plaque disruption, which triggered disparate responses in known canonical pathways. Evidence from this thesis implicates the role of liver X receptor / retinoic acid receptor pathway (LXR/RXR) as a key mediator to the divergent systemic responses after plaque disruption, and pinpoints a direction for future investigations.

Travelling wave ion mobility spectrometry (TWIMS) in combination with ultra-high performance liquid chromatography (UHPLC) and mass spectrometry (MS) has been applied successfully for the untargeted, global metabolic profiling of biofluids such as mouse plasma and saliva. Methods based on UHPLC-MS alone and in combination with ion mobility spectrometry (UHPLC-IM-MS) have been developed and validated for the untargeted metabolite profiling of saliva, obtained non-invasively by passive drool. Three separate metabolic profiling studies have been carried out in conjunction with bioinformatics strategies to identify potential metabolomic biomarker ions that are associated with efficacy of rice bran in colorectal cancer, physiological stress and that have the potential for the diagnosis of asthma. The advantages offered by the utility of ion mobility in UHPLC-MS based metabolic profiling studies, including the increased analytical space, mass spectral clean-up of contaminants such as PEG post-UHPLC-IM-MS analysis, enhancement of the selectivity of targeted metabolites as well as the potential for the identification of metabolites by comparison of ion mobility drift times have been highlighted. Ten potential metabolic biomarker ions of asthma have been identified from the moderate asthmatics from untargeted metabolite profiling of saliva by UHPLC-MS. A predictive model based on partial least squares discriminant analysis (PLS-DA) has been constructed using these ten discriminant ions, which demonstrates good predictive capability for moderate asthmatics and controls. Potential metabolic biomarker ions of physiological stress have been identified through untargeted metabolite profiling analysis of saliva samples collected before and after exercise by UHPLC-IM-MS. Valerolactam has been identified as a potential biomarker of physiological stress from saliva by comparison of retention time, ion mobility drift time and MS/MS spectra with a standard of δ-valerolactam.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Salvia africana lutea is one of 26 Sage species indigenous to Southern Africa from a total of 900 worldwide. The genus Salvia belongs to the Lamiaceae family. Labeled a ‘broad spectrum remedy’ S. africana lutea amongst other sage species is medicinally important. Reports are many highlighting its benefits, which include from alleviating coughs and colds to gynaecological complaints. Studies have revealed in vitro antimicrobial, anti-cancer and antioxidant activity. Plant secondary metabolites fundamentally have a strong bearing on the phytochemical activities a plant may possess. Consequently the environment indirectly affects the phytochemical properties as it influences the variation in the plant metabolome via plant-environment interactions. Five S. africana lutea plant populations, within the Western Cape province of South Africa were sampled and chemotypes and bioactivity tested. Four populations were wild growing in protected areas namely; Brackenfell, Koeberg, Silwerstroomstrand and Yzerfontein, while the fifth was a garden growing population from Stellenbosch. Using gas chromatography hyphenated with mass spectrometry (GC-MS), compounds such as monosaccharides, carboxylic acids and fatty acids were detected. Variation of compounds identified with 80% certainty was compared across all populations. Stellenbosch population showed some compounds that were not present in the other four sites. These compounds were namely; propanoic acid, rythronic acid, 2-keto-1-gluconic acid and 1,3-dibromobicyclon, while this population also did not have xylitol that was detected in all the other four populations. To consolidate the GC-MS findings, analysis on the metabolite profiles (utilizing liquid chromatography linked with mass spectrometry (LC-MS) and nuclear magnetic resonance (1H NMR)) was done. Principal component analysis (PCA) was applied to the NMR data. The partial least squaresdiscriminant analysis (PLS-DA) was used to integrate LC-MS and NMR data sets. All statistics were performed with the SIMCA-P+ 12.0 software. By integrating LC-MS and 1H NMR analyses, large chemotype differences leading to samples grouping by site, suggested strong plant-environment interactions as factors influencing metabolite composition. Signals distinguishing the Stellenbosch profile were in the aromatic part of the 1H NMR spectra. Antimicrobial activity was tested against two Fusarium species. Fusarium is a plant pathogenic species that causes large agricultural losses particularly in the maize crop, one of the staple foods in the African continent. Some species also produce mycotoxins in infected crop and lead to a significant increase in the risk factor of cancers when contaminated foods are consumed. Four high-mycotoxin producing strains from two species F. verticillioides (MRC 826 and MRC 8267); F. proliferatum (MRC 7140 and MRC 6809) were utilized in all in vitro antifungal assays in this study. A preliminary assay using dichloromethane: methanol (1:1 v/v) crude plant extracts of the five populations; Stellenbosch, Brackenfell, Koeberg, Silwerstoomstrand and Yzerfontein, from 2009 and 2011. All test samples exhibited good activity as the minimum inhibitory concentrations (MIC) values ranged from 0.031 mg ml-1 to 0.5 mg ml-1, values below the latter are regarded as strong inhibitors. The Stellenbosch extracts were the most active for both 2009 and 2011 collections, with the best activity against F. verticillioides MRC 8267 and MRC 826 at 0.031 mg ml-1. While the least activity, albeit still a strong inhibitor, was observed from the Yzerfontein extracts with an MIC value of 0.5 mg ml-1. Generally comparison between the two years revealed that samples collected in 2011 were more potent than those in 2009, possibly due to prolonged storage that may have resulted in chemical decomposition. As the Stellenbosch population had shown the best activity as well as a relatively different chemical profile, leaves from these plants were then introduced into tissue culture conditions. Leaf explants were placed on solid plant growth regulator (PGR)-free Murashige and Skoog media and that supplemented with hormones in various combinations. (two concentrations of benzyl adenine (BA) utilized individually and in combination with naphthalene acetic acid (NAA) 4.4 and 8.8, while for NAA 0.27, 2.7 and 5.4.) Namely: 4.4 BA, 8.8 BA, 0.27 NAA: 4.4 BA, 2.7 NAA: 4.4 BA, 5.4 NAA: 4.4 BA, 2.7 NAA: 8.8 BA and 5.4 NAA: 8.8 BA. The PGR combinations did not induce shooting nor rooting, only callus on PGR-free MS media. Antifungal activity of the callus extract was in the same range as the whole plant extracts from which the leaf explants were harvested from, showing no ‘loss’ of activity after introduction to tissue culture conditions. Metabolite profiles using LC-MS, however, did reveal qualitative and quantitative differences, though they appear to not have any bearing on the activity. A bioassay-guided fractionation was then conducted on samples collected from Stellenbosch. This led to the identification of carnosol and carnosic acid being involved in the anti-Fusarium activity of S africana-lutea. A combinational study revealed no synergistic activity of the two compounds against four Fusarium test strains, with fractional inhibitory concentration (FIC) values of 1.5 and 3.0. Antifungal activity of carnosol and carnosic acid was observed to be in the same range (strong inhibitor) as was the callus and whole plant extracts. The study showed variation in population chemotypes and identified two compounds that are involved in S. africana-lutea activity against Fusarium species. It also provided a tissue culture system onto which mass production of the two bioactives may be achieved from, in the development of new fungicides. / AFRIKAANSE OPSOMMING: Salvia Africana lutea is een van die 26 Salie spesies wat inheems aan Suid-Afrika is uit ‘n totaal van 900 spesies wêreldwyd. Die genus Salvia hoort tot die Lamiaceae familie. S. africana lutea word geklassifiseer as ‘n “breë spektrum geneesmiddel”, en medisinaal as belangrik geag tussen die ander salie spesies, want volgens verslag word dit gebruik vir die verligting van hoes en verkoues tot selfs ginekologiese ongesteldhede. Definitiewe biologiese aktiwiteit eksperimente het anti-mikrobiese, antikanker en anti-oksidant aktiwiteite aan die lig gebring. Plant sekondêre metaboliete het fundamenteel ‘n baie sterk verband met die fitochemiese aktiwiteite van ‘n plant. Gevolglik affekteer die omgewing indirek die fitochemiese eienskappe, want dit beïnvloed die variasie in die plant metaboloom deur die interaksies van die plant met die omgewing. In vyf streke binne die Wes-Kaap van Suid-Afrika waar S. africana lutea bevolkings voorkom, is steekproewe gedoen en chemotipes en bioaktiwiteit getoets. Vier bevolkings was wild-groeiende bevolkings in beskermde areas, naamlik; Brackenfell, Koeberg, Silwerstroomstrand en Yzerfontein, terwyl die vyfde uit ‘n tuingroeiende bevolking in Stellenbosch geneem is. Deur gas chromatografie gekoppel met massa spektrometrie te gebruik, is primêre samestellings soos monosakkariede, karboksielsure en vetsure gevind. Variasies van samestellings wat met 80% sekerheid geïdentifiseer is, is oorkruis met al die bevolkings vergelyk. Die Stellenbosch bevolking het ‘n paar samestellings geopenbaar wat nie aanwesig was in die ander vier terreine nie. Hierdie samestellings was: propanoësuur, erythroniese suur, 2-keto-1-glukoniese suur en 1,3-dibromobicyclon. Verder het hierdie bevolking geen xylitol gehad nie en dit is in al vier die ander bevolkings gevind. Verdere studies was gedoen met die gebruik van vloeibare chromatografie gekoppel met massa spektrometrie (LC-MS) sowel as kern magnetiese resonansie (1H NMR). Chemiese profiele het hoë variasies getoon, en dus deur te fokus op die aromatiese samestelling streke, het die Stellenbosch terrein duidelik merkbare verskille en punte op die PLS-DA aangetoon. Met die koppeling van NMR data met LC-MS data, is daar gevind dat onderskeidende punte van die NMR PLS-DA wat gegroepeer is met retensie tye die skeiding van die Stellenbosch terrein van ander terreine gedryf het. Dit het onweerlegbaar bewys dat daar variasie binne die vyf bevolkings voorkom en dat Stellenbosch die mees noemenswaardige chemotipe variasie het. Dit blyk uit die anti-mikrobiese eksperimente dat aktiwiteit teen Fusarium heel nuwe belangstelling wek. Fusarium is ‘n plant-patogeniese spesie wat groot landbou verliese veroorsaak veral in die mielie gewasse, een van die stapelvoedsels van die Afrika kontinent. Dit produseer ook mikotoksiene in aangetaste gewasse en hierdie kan lei tot die ontstaan van kankers wanneer besmette voedsel op groot skaal verbruik word. Vier hoë-mikotoksien produserende swamlyne van twee spesies, naamlik F. verticillioides (MRC 826 en MRC 8267) en F. proliferatum (MRC 7140 en MRC 6809) is gebruik in alle in vitro anti-swam ondersoeke in hierdie studie. Die eerste analise het dichloromethan: methanol (1:1 v/v) ongesuiwerde plant ekstrakte bevat van die vyf bevolkings: Stellenbosch, Brackenfell, Koeberg, Silwerstroomstrand en Yzerfontein, geneem gedurende 2009 en 2011. Al hierdie toets monsters het goeie aktiwiteit getoon waar die minimum beperkende konsentrasie (MIC) waardes van 0.031 mg ml-1 tot 0.5 mg ml-1 gevarieer het. Waardes laer as laasgenoemde word beskou as sterk inhibeerders. Die Stellenbosch ekstrakte was die mees aktief vir albei jare hierbo genoem, met die beste aktiwiteit teen F. verticillioides MRC 8267 en MCR 826 by 0.031 mg ml-1. Die minste aktiwiteit (hoewel nog ‘n sterk inhibeerder) waargeneem was van die Yzerfontein ekstrakte, met ‘n MIC waarde van 0.5 mg ml-1. Oor die algemeen het ‘n vergelyking tussen die twee jare aangetoon dat die monsters wat in 2011 versamel is veel sterker was dan dié van 2009, moontlik te wyte aan ‘n verlengde bewaringstyd wat moontlik ‘n chemiese dekomposisie ten gevolge gehad het. Omdat die Stellenbosch bevolking die beste aktiwiteit getoon het sowel as ‘n relatief afwykende chemiese profiel, is blare van hierdie plante toe bekendgestel aan weefselkultuur kondisies. Blaar eksplante is op soliede hormoonvrye Murashige en Skoog media geplaas en dit is aangevul met sintetiese auksien Naftaleen asynsuur (NAA) en sitokien Bensiel adenien (BA) individueel en in verskillende kombinasies. Geen wortels of uitloopsels is waargeneem in al die hormoon kombinasies nie maar in die hormoonvrye media het daar egter Kallus in twintig persent van die eksplante voorgekom. Kallus is toe as subkultuur van hormoonvrye MS media gekweek en saamgevoeg en dichloromethan: methanol (1:1v/v) ekstrakte is getoets teen die volgende Fusarium swamlyne MRC 826; MRC 8267; MRC 7140 en MRC 6809. MIC waardes het sterk inhiberende eienskappe getoon met die laagste waarde as 0.025 mg ml-1 teen drie swamlyne: MRC 1740, MRC 8267 en MRC 826, en die hoogste was 0.25 mg ml-1 na 48 uur. Die minimum inhiberende konsentrasie waardes het gestyg na 0.5mg ml-1 na 60 uur, wat ‘n fungistatiese aksie getoon het. Maar van 60 tot 92 uu het waardes egter ‘n swamdodende aksie aangetoon met geen verandering van 0.5mg ml-1 nie. In die identifisering van die bioaktiewe komponente, is die ekstraksie van Stellenbosch se bevolking in dichloromethan: methanol (1:1 v/v) uitgevoer, en met gebruik van vyftig gram van die ekstrak is bioanalise-geleide fraksionering gedoen deur gebruik van ‘n VersaFlash®. Die mees aktiewe fraksie is verder gefraksioneer deur die gebruik van ‘n konvensionele silikajel kolom. Aktiewe fraksies is getoets deur LC-MS te gebruik, en twee verbindings, carnosol en carnosic suur, is geïdentifiseer. Voorbereidende TLC is gebruik om identiteit te bevestig, want fraksies was naas die kommersiele standaarde van die twee verbindings getoets. Sinergistiese aktiwiteit van die twee samestellings is ondersoek deur ‘n antiswam ontleding teen die vier swamlyne uit te voer. Hierdie studie het dus die veronderstelde bestaan van verskillende chemotipes tussen die bevolkings waarvan voorbeelde geneem is, bekend gestel. Veral die Stellenbosch se bevolking het die meeste verskil, heel moontlik omrede die verlengde en hoër versteurings deur die nabyheid van mense. Plant– omgewing interaksies speel ‘n belangrike rol in die metaboloom van plante, wat dan indirek hul eienskappe verander, en in hierdie geval die antiswam aktiwiteit. Die tuingroeiende bevolking was die mees aktief, heel moontlik omrede hierdie aspek. Nietemin was geen bioaktiwiteit verloor waar die mees kragtige bevolking met weefsel kultuur kondisies in aanraking gebring is nie. Dus is dit ideaal vir kommersialisering. Een nuwe belangrike bevinding was die carnosol en carnosic suur wat twee welbekende samestellings is wat meesal geassosieer is met Rosmarinus officinalis en gedokumenteer is vir antioksidant aktiwiteit. Hier dui laasgenoemde samestellings ‘n antiswam aktiwiteit aan teen die getoetste Fusarium swamlyne. Met ‘n gevestigde weefsel kultuur sisteem alreeds in plek, voorsien dit ‘n beginpunt vir die bestudering van hoe hierdie bioaktiewe komponente in massa geproduseer kan word in die ontwikkeling van nuwe swamdodende produkte.

Clostridium thermocellum is a thermophilic bacterium that converts biomass to ethanol directly; however, high sensitivity of this bacterium toward ethanol limits its commercial utility. To elucidate the effect of ethanol on the growth of this bacterium a metabolite analysis of C. thermocellum was performed. The hypothesis of the project was that exogenous ethanol alters the metabolite profile of C. thermocellum. For metabolite analysis, capillary electrophoresis-electrospray ionization-mass spectrometry method (CE-ESI-MS) was developed due to highly polar and charged nature of metabolites. To increase the sensitivity of CE-ESI-MS, several parameters at the ESI interface were optimized. The application of 50% isopropanol as a sheath liquid increased sensitivity for metabolite analysis dramatically. Trimethylamine acetate (pH 10) was used as background electrolyte (BGE) due to its ability to separate the structural isomers of glucose phosphate. For metabolite sample preparation, novel methods for quenching and CE compatible metabolite extraction protocols were developed. Newly developed protocols were applied to metabolite analysis of wild type (WT) and ethanol adapted (EA) strains of C. thermocellum grown in batch cultures. Significant differences were found in key intracellular metabolites such as NAD+ and pyruvic acid. Intracellular concentrations of NAD+ were low in EA cells compared to WT cells and pyruvic acid was only detected in EA cells. To further understand the effect of ethanol on metabolite fluxes, WT and EA cells were grown in increasing concentrations of ethanol and the metabolite profile for each ethanol treatment was obtained. Significant changes were found in intracellular metabolite concentrations. Metabolic data showed that the glycolysis process in WT cells was obstructed due to exogenous ethanol which was evident from accumulation of G6P. On the other hand, no such accumulation of G6P was observed in the EA strain; however pyruvate began to accumulate in EA strain. These changes in intracellular metabolite concentrations due to perturbation of exogenous ethanol supported the hypothesis. Also, this investigation revealed a correlation between ethanol and metabolite profile changes and was able to explain a possible mechanism of growth inhibition of C. thermocellum which will certainly help genetic engineers to develop superior strains of C. thermocellum for commercial cellulosic ethanol production.

La surface des vignobles mondiaux représente environ 7,9 millions ha, ce qui correspond à une production annuelle de 67 millions de tonnes de baies. La production mondiale annuelle de vins est de l’ordre de 300 millions hl/an. La surface du vignoble français est de 843 000 ha. La viticulture moderne doit affronter trois défis majeurs interdépendants : réduire l’utilisation des produits phytosanitaires, s'adapter au changement climatique, maîtriser la qualité et la typicité pour garder ou conquérir de nouveaux marchés.En 2007, la vigne est devenue la première espèce fruitière pérenne dont le génome a été séquencé. Cette avancée scientifique ouvre de nombreuses perspectives en termes de génomique fonctionnelle (ensemble de méthodes permettant de caractériser la fonction des gènes) et de biologie intégrative (ensemble de méthodes visant à appréhender le fonctionnement global de la plante et ses réponses à l’environnement). Ces perspectives dépendent pour une bonne part de la maîtrise de quantités importantes de données qu’il convient d’organiser et de corréler grâce à des outils informatiques adaptés.Des approches fonctionnelles concernant des gènes candidats et des approches transcriptomiques à haut débit ont permis d’identifier certains gènes ou certaines familles de gènes impliqués dans le développement et la maturation de la baie de raisin, mais au moment où cette thèse a débuté, aucun travail de biologie intégrative n’avait été entrepris.Le travail présenté ici, qui décrit l’obtention et l’analyse de métadonnées transcriptomiques et biochimiques portant sur la réponse de la baie à l’environnement radiatif, s’inscrit dans ce contexte. En procédant à un effeuillage partiel après la véraison, nous avons modulé l’exposition des baies au rayonnement solaire. Ceci a permis d’étudier l’influence du rayonnement (baie exposée, non exposée), de la position de la grappe (est, ouest) et de la position de la baie (à l’extérieur ou à l’intérieur de la grappe). Des baies ont été récoltées à 5 moments différents après l’effeuillage et utilisées pour des analyses métabolomiques et transcriptomiques. Leur contenu en sucres, acides organiques, acides aminés, anthocyanes et flavonols a été analysé par des dosages enzymatiques et par chromatographie liquide à haute performance). L’expression des gènes a été étudiée avec des microarrays représentatifs de l’ensemble du génome de la vigne (29600 gènes) pour les conditions présentant les différences métaboliques les plus marquées (baies exposées, situées à l’ouest et à l’extérieur de la grappe vs baies non exposées, situées à l’est et à l’intérieur de la grappe). Des analyses statistiques et corrélatives ont été conduites pour (a) déterminer les métabolites qui répondent au traitement et les facteurs qui les influencent (b) déterminer les gènes qui répondent aux traitements et ceux qui semblent co-régulés (c) préciser les réseaux de gènes et de métabolites qui semblent reliés. L’effeuillage n’affecte pas la teneur en sucres ou en acide tartrique des baies, il affecte peu les acides aminés, mais il augmente la teneur en flavonols et diminue la teneur en acide malique. Il affecte plus particulièrement les gènes associés au stress abiotique, au métabolisme secondaire, au transport et au métabolisme hormonal. Des expériences complémentaires ont permis d’identifier divers gènes spécifiquement associés à la composante thermique de l’exposition au soleil, parmi lequels des gènes codant pour des HSP, des transporteurs ABC, et des enzymes du métabolisme flavonoïdique. Des réseaux reliant des gènes et des métabolites ont pu être construits, qui associent des métabolites secondaires à des gènes de fonctions connues, ou à de nouveaux gènes candidats dont il conviendra d’étudier la fonction précise. / The total surface of vineyards worldwide is about 7.9 millions ha, which corresponds to an annual production of 67 millions tons berries. The annual world production of wines is about 300 millions hl/year. The French wineyard occupies 843 000 ha, among which 481 000 ha are dedicated to high quality wines (VQPRD) and 362 000 ha to table wines. Modern viticulture must deal with three major and related challenges : reduce the use of organic and inorganic phytochemicals, adapt the vineyard to climatic change and control the quality and the typicity in order to keep or gain new markets.In 2007, the grapevine became the first perennial fruit species whose genome was sequenced. This scientific breakthrough opens new pespectives in terms of functional genomics (set of methods allowing to characterize the function of genes) and integrative biology (set of methods allowing to study the global functioning of the plant and its response to the environment). These perspectives mainly depend on our ability to analyze large sets of data with adequate informatic tools.Functional approaches on candidate genes, and high throughput transcriptomic approaches have allowed to identify some genes or some gene families involved in the development and ripening of the grape berry, but when this Ph. D work started, no paper based on integrative biology was published on grapevine. The present work, which describes the collection and analysis of transcriptomic and metabolomic metadata related to the response of the berry to sun exposure. The exposure of the berries to the sun was controlled through a partial defoliation after veraison. This allowed to study the effects of sun exposure (exposed or shaded berries), of the position of the cluster (east, west) and of the anatomical position of the berry (outside or inside the berry). Berries were collected at 5 different time points after defoliation and used for metabolomic and transcriptomic analysis. Their content in sugars, amino acids, organic acids, anthocyanins and flavonols was analyzed by enzymatic assays and high performance liquid chromatography. For the berries whose metabolic content differed the most (exposed, west and outside berries vs shaded, east and inside berries), gene expression was studied with microarrays bearing a set of probes covering the whole genome of grapevine (29600 genes). Correlative and statistical analysis were conducted in order to (a) determine the metabolites that are the most responsive to the treatment, and the most important factors that control them (b) determine the genes that respond to the treatment and seem to be co-regulated (c) to precise the networks of genes and metabolites which seem related. Defoliation does not affect the sugar and tartaric acid contents, hardly affects amino acids, but it increases flavonol content and decreases malic acid content. It affects more specifically genes associated with abiotic stress, secondary metabolism, transport and hormonal metabolism. Additional experiments allowed us to identify genes that are specifically associated with the thermal component of sun exposure, among which genes encoding HSP, ABC transporters, and enzymes of flavonoid metabolism. Networks relating genes and metabolites could be constructed. These networks associate secondary metabolites with genes of known function and new candidate genes for which the function will have to be precised.

One main goal of ecological research is to understand nature´s complexity, in order to predict the potential impact of environmental perturbations. In this thesis, I investigate the ecological interactions between some of the most ancient organisms living on our planet: plants and insects. Focus of my research is the interaction between the wild brassicaceous plant black mustard (Brassica nigra L.) and its specialist insect herbivore, the large white cabbage butterfly (Pieris brassicae L). Both organisms are well characterized model species used in chemical ecology research. Using different analytical techniques, such as liquid and gas chromatography coupled to mass-spectrometry (LC- and GC-MS) and headspace collection of volatile organic compounds (VOCs), I apply the approach of metabolomics and systems biology to the field of ecology to explore the metabolic changes occurring inside the plants exposed to biotic and abiotic stresses. Particularly, I study the plant metabolic responses against P. brassicae chewing caterpillars during sequential treatment exposure to: abiotic stress by the oxidative air pollutant ozone (O3); dual herbivory with specialist Brevicoryne brassicae piercing-sucking aphids; and chemical induction of plant defences with the oxylipin phytohormone methyl-jasmonate (MeJA). Results show how during herbivore-induced responses, changes in defence- and growth-metabolic processes are tightly connected to stress protection mechanisms, indicating that plants actively reprogram their inner metabolic networks in order to adapt to consecutive changes in the environment. This thesis illustrates how evaluating the plant metabolome in its entirety rather than single metabolites, can help us understanding plant responses towards abiotic and biotic stresses, and improve our ability to predict how constant shifts in the environment affect plant physiology and ecology. / Ett huvudsyfte för ekologisk forskning är att förstå naturens komplexitet för att kunna förutse effekter av störningar i miljön. I min avhandling har jag fokuserat på ekologiska interaktioner mellan växter och insekter, två av de äldsta terrestra organismgrupperna på jorden. I mina studier har jag undersökt interaktioner mellan den korsblommiga växten svartsenap (Brassica nigra L.) och den specifika herbivoren kålfjäril (Pieris brassicae L.). Båda är väl karaktäriserade modellarter i kemisk-ekologisk forskning. De metaboliska förändringar som sker när växten utsätts för biotisk och abiotisk stress har analyserats hjälp av metabolomik, det vill säga analyser av metabolomet i sin helhet med hjälp av tekniker som vätske- och gaskromatografi kopplad till masspektrometri (LC- och GC-MS), och så kallad headspace-uppsamling av flyktiga organiska föreningar (VOCs). Jag har särskilt undersökt de metaboliska förändringar som sker när växten betas av kålfjärilslarver vid samtidig exponering för: abiotisk stress i form av ozon (O3), en oxidativ luftförorening; ytterligare betning i form av stickande och sugande bladlus (Brevicoryne brassicae); tillsats av oxylipinfytohormon metyl-jasmonat (MeJA), ett ämne som inducerar växtens försvar. Resultaten visar att de metaboliska förändringar som sker i växten vid herbivori med konsekvenser för dess försvar och tillväxt är nära kopplade till de metaboliska förändringar som sker vid stress, vilket visar att växten kan fortlöpande och aktivt omprogrammera sina metaboliska nätverk för att anpassa sig till förändringar i miljön. Avhandlingen visar att genom att utvärdera växtmetabolomet i sin helhet, snarare än att studera enskilda metaboliter, vi kan få bättre förståelse för hur växter reagerar på olika former av stress och därmed också bidra till att vi kan göra förutsägelser för hur förändringar i miljön kan påverka växters fysiologi och ekologi.

Cellulolytic organisms are being heavily studied for the production of biofuels, given that lignocellulosic biomass would be a cheap, abundant, and renewable starting material for chemical production. A challenge with cellulolytic microorganisms is that they are typically poorly characterized and often difficult to genetically manipulate. Our group focuses characterization and engineering of a thermophilic aerobic, cellulolytic actinobacterium, Thermobifida fusca. The wider range of optimal temperature and pH for the growth condition, besides the secretion of several group of cellulases, have made this microbe a potentially efficient host system for industrially application. After the development of first ever successful genetic manipulation protocol by for T. fusca in 2011 in our group the quest continues to better understand and further explore this microbe with such remarkable capabilities. Available genome annotation of the bacteria gives a preliminary clue towards the exploration of its biological system. Genome-scale metabolic reconstruction provides one such framework to populate all the available piece of information to mimic the biological systems to the closest functional state. Further, this skeletal base network can be made more realistic by applying the constraint that controls the flux through various reactions in the pathway network thereby providing the optimal solution space for operation. For the purpose of curation of this in silico model, we aim to integrate the experimental datasets (proteomic and metabolomics) and optimize the agreement between the in silico and in vivo conditions at a steady state condition. Once the model considerably imitates the original biological network, it will be used for the fundamental understanding of the microbial system for the application towards production biofuel and high yields of compound of pharmaceutical interest. The ultimate objective of this project is to design the candidate strain for the cellulolytic production of Natural products. Natural products play an important role in manufacturing of several active pharmaceutical ingredients (APIs). APIs or precursors of APIs can be produced in living organisms with the major challenge of designing and optimizing metabolic pathways to obtain the compounds of interest. In this capacity, living organisms can act as renewable catalysts with high product specificity to produce APIs with potential cost savings over purely synthetic chemistry synthesis routes. This is an effort to understand and design industrially usable microorganism T. fusca to act as a host system for the purpose of production of these compounds. The present project focuses on, in silico characterization and experimental validation of T. fusca, with particular focus on the terpenoids backbone biosynthesis (TBB) pathways using a genome-scale metabolic model, transcriptomics, proteomics and metabolite analysis. The DXP pathway leads to the production of terpenoids precursors that have applications in nutraceutics and pharmaceutics. This study generates the metabolic model, iTFU975 for T. fusca based on the proteomics dataset as the starting point. Further the model and the experimental dataset together helps to characterize the secondary metabolites pathways and compounds in the network associated with the production of terpenoids. In conclusion, this is an effort to characterize the natural products biosynthesis in T. fusca by establishing a bridge between the analytical methodologies and computational efficiencies on “-omics” knowledge to prove the diverse applicability of Systems Biology.

The World Health Organization has called stress-related illness “the health epidemic of the 21st century.” While the biochemical pathways associated with the acute stress response are well-characterized, many of the pathways behave differently under conditions of chronic stress. The purpose of this project is to apply high-sensitivity mass spectrometry (MS)-based targeted and untargeted metabolomics approaches to generate new insights into the biochemical processes and pathways associated with the chronic stress response, and potential mechanisms by which chronic stress produces adverse health effects. Chapter 1 describes the application of sets of targeted and untargeted metabolomics approaches to analyze serum samples from a human epigenetic model of chronic stress in order to identify potential targets for further analysis. To test the resulting hypothesis that oxidative stress is a key feature of chronic stress, a new targeted multiple reaction monitoring (MRM)-MS assay was developed for the accurate quantitation of aldehyde products of lipid peroxidation, as described in Chapter 2. In Chapter 3, the validated method for quantitation of malondialdehyde (MDA) was t applied to mouse plasma samples from a model of chronic social defeat stress to determine whether animals exposed to psychosocial stress show increases in oxidative stress. Mouse plasma samples from this model were also analyzed by untargeted metabolomics using Fourier-transform (FT)-MS to identify other important metabolite features, particularly those that overlap with metabolites identified in the human epigenetic model. Analysis of metabolomic data from two very different models of chronic stress supports the consistent detection of a metabolomic phenotype for chronic stress that is characterized by the dysregulation of energy metabolism associated with decreased concentrations of diacyl-phospholipids in blood. Increased blood concentrations of fatty acids, carnitines, acylcarnitines, and ether phospholipids were also observed. In addition to metabolites associated with energy metabolism, chronic stress also significantly influenced metabolites associated with amino acid metabolism and cell death. This characteristic pattern of differences in metabolite concentrations was observed in the plasma of mice exposed to chronic social defeat stress, irrespective of whether or not they displayed outward signs of a chronic stress response; In fact, mice that were “resilient” to the behavioural effects of chronic social defeat stress displayed an exaggerated phenotype over mice that showed depressive-like symptoms following chronic stress exposure. This may suggest that the observed changes in fatty acid composition are protective against stress. However, changes in fatty acid composition are also known to be associated with a wide variety of pathologies including heart disease, neurodegenerative diseases, and mood disorders, so the lipidomic changes associated with chronic stress may also contribute to its health impact. Overall, the results provide further evidence that changes in energy metabolism are a central part of allostatic adaptation to chronic stress. / Graduate / 0487 / csobsey@gmail.com

Traditional water monitoring encounter limitations due to the large number of contaminants present in our waters possible giving raise to mixture effects. This thesis aimed to investigate how the emerging omics approaches (transcriptomics, proteomics and metabolomics) can be used as an effect-based monitoring approach to assess and predict adverse effects in the freshwater environment. Moreover, this thesis analysed challenges and barrier with omics. A systematic literature search was conducted using Scopus and Web of Science to find case-studies using omics in field studies and reviews regarding challenges and barriers. The results in this thesis suggest that the use of fish species (either collected in the wild or in situ set-ups), transcriptomics and investigations of WWTP recipient was the most common way to apply omics. In order to interpret omics-data multiple studies conducted chemical monitoring in conjunction, investigated additional traditional biomarkers and/or used omics to identify altered biological or functional pathways that possible could lead to adverse effects at higher levels. According to the challenges and barriers identified in this thesis, the future of omics in environmental monitoring rely on the possibility to characterise and quantify natural variability, define appropriate critical effect sizes (i.e. thresholds of critical effects) and define baseline data. Moreover, it is necessary to develop frameworks and standardisations for omics-approaches (e.g. study-designs) to promote the interpretation of the results. Future research is also needed to develop and increase the understanding of how the proteomics and metabolomics can be applied. By improving the use of omics a more holistic water monitoring can be achieved including screenings for biological responses and the ability to detect early warnings which will enhance the prioritisation and site management of polluted water bodies, including those with limited prior knowledge regarding potential contaminants.

L’étiologie des troubles du spectre autistique (TSA) est multifactorielle mettant en jeu une forte composante génétique ainsi que des facteurs environnementaux. A ce jour, il n’existe aucun biomarqueur facilitant un diagnostic précoce des TSA, ce qui permettrait une meilleure prise en charge des patients. De plus, les mécanismes physiopathologiques sont encore mal connus. La majorité des études sur les TSA ont été réalisées sur des populations occidentales. Ainsi, nous avons voulu étudier un groupe de patients libanais atteints de TSA. Nos objectifs s’articulent autour de trois volets : 1) L’identification de facteurs de risques environnementaux dans le but de mieux comprendre la pathologie. Les résultats de cette étude ont montré que plusieurs facteurs tels que la consanguinité, le stress au cours de la grossesse et la prématurité semblent être des facteurs de risques. 2) L’identification des variations structurales dans le génome des enfants atteints de TSA afin d'évaluer la contribution de CNV par l'approche de CGH array à haute résolution. Cette étude nous a permis d’identifier de nouveaux gènes dans les TSA ainsi de confirmer la présence des régions et des gènes déjà cités dans des études précédentes sur les TSA. 3) L’identification des métabolites urinaires et des voies métaboliques associés afin de proposer des biomarqueurs aidant à un diagnostic précoce et à une meilleure compréhension de la physiopathologie de la maladie. De nouveaux métabolites ont été identifiés, comme nous avons confirmé des variations anomalies déjà citées dans la littérature concernant certains métabolites qui pourraient représenter des marqueurs robustes de la maladie. / The etiology of autism spectrum disorders (ASD) is multifactorial involving a strong genetic component as well as environmental factors. To date, there is no biomarker facilitating early diagnosis of ASD to improve patient management and outcomes. In addition, the physiopathological mechanisms are still poorly understood. Most studies on ASD have been conducted in Western populations. Thus, we wanted to study a group of Lebanese patients with ASD. Our objectives focus around three aspects: 1) The identification of environmental risk factors in order to better understand the pathology. The results of this study showed that several factors such as consanguinity, stress during pregnancy and prematurity appear to be risk factors. 2) The identification of structural variations in the genome of children with ASD in order to evaluate the contribution of CNV by high resolution CGH array approach. This study allowed us to identify new genes in ASD as well as to confirm the presence of regions and genes already cited in previous ASD studies. 3) The identification of metabolites and associated metabolic pathways to provide biomarkers for early diagnosis and to better understanding of the pathophysiology of the disease. New metabolites have been identified and we have confirmed variations already mentioned in the literature concerning certain metabolites that could represent robust markers of the disease.