Cyclodipeptides and their derivatives, the diketopiperazines (DKPs), constitute a large class of secondary metabolites with noteworthy biological activities that are mainly synthesized by microorganisms. The biosynthetic pathways of some DKPs contain cyclodipeptide synthases (CDPSs), a newly defined family of enzymes. CDPSs hijack aminoacyl-tRNAs from their essential role in ribosomal protein synthesis to catalyze the formation of the two peptide bonds of various cyclodipeptides. The aim of the work presented in this thesis manuscript is to characterize the CDPS family. At first, the structural and mechanistic characterization of the first identified CDPS, AlbC of Streptomyces noursei, is presented. Then, the results obtained with three other CDPSs, each of which having suitable properties to increase our understanding of the CDPS family, are described. The CDPS Ndas_1148 of Nocardiopsis dassonvillei extends our knowledge of the molecular bases of the CDPS specificity. The CDPS AlbC-IMI of S. sp. IMI 351155 is a good model to analyze the interaction of each of the two substrates required for the formation of a cyclodipeptide. Finally, the characterization of the CDPS Nvec-CDPS2 from Nematostella vectensis provides the first example of enzymes of animal origin involved in nonribosomal peptide synthesis.

The current understanding of lactate metabolism in fish is based almost entirely on interpretation of concentration measurements that cannot be used to infer changes in flux. Moreover, the transporters regulating these fluxes have never been characterized in rainbow trout. My goals were: (1) to quantify lactate fluxes in rainbow trout under normoxic resting conditions, during acute hypoxia, and exercise by continuous infusion of [U-14C] lactate; (2) to determine lactate uptake capacity of trout tissues by infusing exogenous lactate in fish rest and during graded exercise, and (3) to clone monocarboxylate transporters (MCTs) and determine the effects of exhausting exercise on their expression. Such information could prove important to understand the mechanisms underlying the classic “lactate retention” seen in trout white muscle after intense exercise. In normoxic resting fish, the rates of appearance (Ra) and disappearance (Rd) of lactate were always matched (~18 to 13 µmol kg-1 min-1), thereby maintaining a low baseline blood lactate concentration (~0.8 mM). In hypoxic fish, Ra lactate increased from baseline to 36.5 µmol kg-1 min-1, and was accompanied by an unexpected 52% increase in Rd reaching 30.3 µmol kg-1 min-1, accounting for a rise in blood lactate to 8.9 mM. In exercising fish, lactate flux was stimulated > 2.4 body lengths per second (BL s-1). As the fish reached critical swimming speed (Ucrit), Ra lactate was more stimulated (+67% to 40.4 μmol kg-1 min-1) than Rd (+41% to 34.7 μmol kg-1 min-1), causing an increase in blood lactate to 5.1mM. Fish infused with exogenous lactate stimulated Rd lactate by 300% (14 to 56 μmol kg-1 min-1) during graded exercise, whereas the Rd in resting fish increased by only 90% (21 to 40 µmol kg-1 min-1). Four MCT isoforms were partially cloned and characterized in rainbow trout: MCT1b was the most abundant in heart, and red muscle, but poorly expressed in gill and brain where MCT1a and MCT2 were prevalent. MCT4 was more expressed in the heart. Transcript levels of MCT2 (+260%; brain), MCT1a (+90%; heart) and MCT1b (+50%; heart) were stimulated by exhausting exercise. This study shows that: (i) the increase in Rd lactate plays a strategic role in reducing the lactate load imposed on the circulation. Without this response, blood lactate accumulation would double; (ii) a high capacity for lactate disposal in rainbow trout tissues is elicited by the increased blood-to-tissue lactate gradient when extra lactate is administered; and (iii) rainbow trout may be unable to release large lactate loads rapidly from white muscle after exhausting exercise (lactate retention) because they poorly express MCT4 in white muscle and fail to upregulate its expression during exercise.

En spectroscopie de résonance magnétique (SRM) in vivo, les principales méthodes utilisées permettent la quantification des concentrations de métabolites en utilisant des signaux à une dimension spectrale. Les travaux réalisés dans le cadre de cette thèse portent sur le développement de méthodes de SRM à deux dimensions spectrales (SRM 2D) de corrélation localisée afin d’accroître le pouvoir de résolution spectrale et la précision de la quantification de la SRM in vivo. Le premier axe de cette thèse concerne le développement d’une méthode fondée sur la spectroscopie 2D de corrélation localisée pour l’exploration des métabolites cérébraux. La séquence L-COSY (spectroscopie de corrélation localisée) est implantée sur imageur petit animal et étudiée. Une procédure de quantification dédiée aux signaux de corrélation acquis est développée. Cette dernière opère dans le domaine d’acquisition du signal, et s’appuie sur : 1) une connaissance a priori forte obtenue par simulation de l’effet quantique des séquences sur les spins des composés présents dans le spectre 2) un modèle de pondération lié aux effets de relaxation agissant sur le signal de SRM 2D. 3) une contrainte sur la relaxation liée aux effets d’inhomogénéités supposés toucher tous les spins de la même manière. Les résultats présentés s’attachent à étudier les performances quantitatives de la SRM 2D de corrélation, en comparaison à la SRM 2D dite J-résolue (avec la séquence JPRESS), de manière expérimentale, sur fantômes de métabolites mais aussi à travers la théorie des bornes de Cramér-Rao (CRBs). La quantification des signaux L-COSY, bien que défavorisée par une perte théorique du rapport signal sur bruit par unité de temps, présente des CRBs théoriques relatives du même ordre de grandeurs voire, pour certains métabolites couplés (e.g la glutamine, le GABA) plus petites que celles correspondantes à la spectroscopie J-résolue pour un même temps d’acquisition. Le second axe de cette thèse porte sur l’adaptation la SRM 2D de corrélation pour l’étude in vivo du métabolisme lipidique du foie et des tissus adipeux sous-cutanés sur un modèle de souris obèse à 7T. Cette application inédite montre la faisabilité de la SRM 2D de corrélation à être acquise sur un tel organe mouvant et sa capacité à être quantitative pour l’étude et la caractérisation des triglycérides hépatiques et sous-cutanées. / In in vivo Magnetic Resonance Spectroscopy (MRS), the main methods used allow metabolite concentration quantification using signals having one spectral dimension. This work focuses on the development of in vivo two dimensional correlated MRS in order to increase spectral resolution and quantification precision. The first axis is about the development of a method based on a 2D localized correlation MRS (L-COSY) for brain metabolite exploration. The L-COSY is implemented and studied on a small animal scanner. A dedicated quantification procedure operating in the acquisition domain is described. This latter is based on 1) a strong prior knowledge obtained by quantum mechanically simulate the effect of sequence on metabolite spin systems 2) a model function taking into account the relaxation weighting 3) constraints on the relaxation term linked to the field inhomogeneity effects which are assumed to act the same way on all the spins. Results are given experimentally using metabolites phantoms and through a comparison to other existing 2D MRS method, namely the J-resolved MRS (with the JPRESS sequence) using the Cramer Rao Lower Bounds (CRBs) theory. Although its inherent loss of signal to noise ratio is a disadvantage compared to J-PRESS, L-COSY quantification shows theoretically competitive relative CRBs, and even smaller CRBs for some coupled metabolites (e.g Glutamine or GABA), for an acquisition time similar to JPRESS. Second axis is about the adaptation of the 2D correlation MRS for the in vivo lipid metabolism study in the liver and subcutaneous adipose tissues of obese mice at 7T. This application shows the feasibility of 2D correlated MRS to be acquired on a moving organ and its quantitative relevance for triglyceride quantification and characterization in fatty liver and subcutaneous tissue.

The current understanding of lactate metabolism in fish is based almost entirely on interpretation of concentration measurements that cannot be used to infer changes in flux. Moreover, the transporters regulating these fluxes have never been characterized in rainbow trout. My goals were: (1) to quantify lactate fluxes in rainbow trout under normoxic resting conditions, during acute hypoxia, and exercise by continuous infusion of [U-14C] lactate; (2) to determine lactate uptake capacity of trout tissues by infusing exogenous lactate in fish rest and during graded exercise, and (3) to clone monocarboxylate transporters (MCTs) and determine the effects of exhausting exercise on their expression. Such information could prove important to understand the mechanisms underlying the classic “lactate retention” seen in trout white muscle after intense exercise. In normoxic resting fish, the rates of appearance (Ra) and disappearance (Rd) of lactate were always matched (~18 to 13 µmol kg-1 min-1), thereby maintaining a low baseline blood lactate concentration (~0.8 mM). In hypoxic fish, Ra lactate increased from baseline to 36.5 µmol kg-1 min-1, and was accompanied by an unexpected 52% increase in Rd reaching 30.3 µmol kg-1 min-1, accounting for a rise in blood lactate to 8.9 mM. In exercising fish, lactate flux was stimulated > 2.4 body lengths per second (BL s-1). As the fish reached critical swimming speed (Ucrit), Ra lactate was more stimulated (+67% to 40.4 μmol kg-1 min-1) than Rd (+41% to 34.7 μmol kg-1 min-1), causing an increase in blood lactate to 5.1mM. Fish infused with exogenous lactate stimulated Rd lactate by 300% (14 to 56 μmol kg-1 min-1) during graded exercise, whereas the Rd in resting fish increased by only 90% (21 to 40 µmol kg-1 min-1). Four MCT isoforms were partially cloned and characterized in rainbow trout: MCT1b was the most abundant in heart, and red muscle, but poorly expressed in gill and brain where MCT1a and MCT2 were prevalent. MCT4 was more expressed in the heart. Transcript levels of MCT2 (+260%; brain), MCT1a (+90%; heart) and MCT1b (+50%; heart) were stimulated by exhausting exercise. This study shows that: (i) the increase in Rd lactate plays a strategic role in reducing the lactate load imposed on the circulation. Without this response, blood lactate accumulation would double; (ii) a high capacity for lactate disposal in rainbow trout tissues is elicited by the increased blood-to-tissue lactate gradient when extra lactate is administered; and (iii) rainbow trout may be unable to release large lactate loads rapidly from white muscle after exhausting exercise (lactate retention) because they poorly express MCT4 in white muscle and fail to upregulate its expression during exercise.

Les furanocoumarines (FCs) sont des métabolites secondaires principalement synthétisés chez quatre familles botaniques et dérivent de la voie de biosynthèse des phénylpropanoïdes. Ces phytoalexines interviennent dans les processus de défense de la plante et présentent un fort potentiel thérapeutique. Des travaux réalisés dans les années 1960 sur des cultures cellulaires en parallèle de l’utilisation de précurseurs radiomarqués ont permis de démontrer que de nombreuses enzymes impliquées dans cette voie appartenaient à la famille des cytochromes P450 (P450s). Seules deux d’entre elles avaient pu être identifiées d’un point de vue moléculaire au début de ce travail de thèse. Afin de générer des informations concernant le génome de plantes productrices de FCs, nous avons fait séquencer les ARNm extraits de feuilles de Pastinaca sativa, de Ruta graveolens et de Cullen cinereum. L’analyse in silico de ces trois banques de données a permis d’identifier près de 800 fragments d’ADNc codants pour des P450s. Des travaux antérieurs réalisés au laboratoire et l’analyse comparative des transcriptomes de ces 3 plantes nous ont amenés à nous focaliser sur la sous-famille CYP71AZ au travers d’une étude fine de CYP71AZ3 et CYP71AZ4. La caractérisation fonctionnelle de ces enzymes a été réalisée dans un système d’expression hétérologue eucaryote : Saccharomyces cerevisiae. Les résultats obtenus ont permis de montrer que CYP71AZ4 avait une spécificité de substrat assez large puisqu’elle pouvait métaboliser au moins une FC et 4 coumarines. L’analyse et la comparaison des constantes cinétiques pour chacun de ces substrats indiquent néanmoins que le psoralène est le substrat préférentiel. La caractérisation fonctionnelle de CYP71AZ3 a mis en évidence que cette enzyme pouvait hydroxyler l’esculétine, une coumarine, mais ne jouait aucun rôle dans la synthèse de FCs. Ces travaux mettent en évidence la diversité fonctionnelle au sein d’une même sous-famille enzymatique et permettent d’émettre des hypothèses nouvelles quant à l’apparition de cette voie de biosynthèse chez les Apiacées d’une part, et chez les autres familles botaniques d’autre part / Furanocoumarins (FCs) are secondary metabolites mainly synthetized in four botanical families deriving from the phenylpropanoid biosynthetic pathway. These phytoalexins are involved in plant defense mechanisms and present strong therapeutic potential. Early studies in the 1960s based on cell cultures and the use of radiolabeled precursors have shown that many enzymes involved in this pathway belong to the cytochrome P450 family (P450s). Only two of them had been identified from a molecular point of view at the beginning of this thesis. In order to generate information regarding the genome of plants producing FCs, we sequenced the mRNA extracted from leaves of Pastinaca sativa, Ruta graveolens, and Cullen cinereum. In silico analysis of these three libraries identified nearly 800 cDNA fragments encoding for P450s. Previous studies in the laboratory and comparative transcriptome analysis of these three plants have led us to focus on the subfamily CYP71AZ through a detailed study of CYP71AZ3 and CYP71AZ4. Functional characterization of these enzymes was performed in an eukaryote heterologous expression system: Saccharomyces cerevisiae. The results showed that CYP71AZ4 had a broad substrate specificity enough as it could metabolize one FC and 4 coumarins. The analysis and comparison of the kinetic constants for each of these substrates indicate, however, that the preferred substrate is psoralen. The functional characterization of CYP71AZ3 showed that this enzyme could hydroxylate esculetin, a coumarin, but played no role in the synthesis of FCs. This study highlights the functional diversity within a single enzyme subfamily and allows to issue new hypotheses about the emergence of this biosynthetic pathway in Apiaceae on one hand, and among other botanical families on the other hand

MEnvSC / Department of Ecology and Environmental Science

La drépanocytose est une maladie causée par une seule mutation dans le gène de la bêta-globine. Les complications liées à la maladie se manifestent sur le plan génétique, épigénique, transcriptionnel, et métabolique. Les approches intégratives des technologies de séquençage à haut-débit permettent de comprendre le mécanisme pathologique et de découvrir des thérapies en lien avec la maladie. Dans cette thèse, j’intègre divers jeux de données omiques et j’applique des méthodes statistiques pour élaborer de nouvelles hypothèses et analyser les données. Dans les deux premières études, je combine les résultats des études d'association pangénomique d'hémoglobine fœtale (HbF) et des globules rouges denses déshydratés (DRBC) avec l'expression génique, l'interaction chromatinienne, les bases de données relatives aux maladies et les cibles médicamenteuses sélectionnées par des experts. Cette approche intégrative a révélé trois nouveaux loci sur le chromosome 10 (BICC1), le chromosome 19 (KLF1) et le chromosome 22 (CECR2) comme régulateurs de l'HbF. Pour l’étude sur la densité de globules rouges, quatre cibles médicamenteuses (BCL6, LRRC32, KNCJ14 et LETM1) ont été identifiées comme des modulateurs potentiels de la sévérité. Dans la troisième étude, j’intégre la métabolomique à la génomique pour établir une relation causale entre la L-glutamine et les crises douleurs en utilisant la randomisation mendélienne. En outre, nous avons identifié 66 biomarqueurs pour 6 complications liées à la drépanocytose et le débit de filtration glomérulaire estimé (DFGe). Enfin, dans la dernière étude j’ai appliqué une approche de clustering aux métabolites que j’ai ensuite combiné aux données de génotype. J’ai découvert des changements métabolomiques mettant en évidence des familles de métabolites impliqués dans les dysfonctionnements rénaux et hépatiques, en plus de confirmer le rôle d'une classe d'acides gras dans la formation en faucille des globules rouges. Ce travail met en évidence l'importance des approches multi-omiques pour découvrir de nouveaux mécanismes biologiques et étudier les maladies humaines. / Sickle cell disease is a monogenic disorder caused by a point mutation in the beta-globin gene. The complications related to the disease are characterized by a broad spectrum of distinct genetic, epigenetic, transcriptional, and metabolomic states. Integrative high-throughput technologies approaches to sickle cell disease pathophysiology are crucial to understanding complications mechanisms and uncovering therapeutic interventions. In this thesis, I integrate various omics datasets and apply statistical methods to derive new hypotheses and analyze data. I combine genome-wide association studies results of fetal hemoglobin (HbF) and dehydrated dense red blood cells (DRBC) with gene expression, chromatin interaction, disease-relevant databases, and expert-curated drug targets. This integrative approach revealed three novel loci on chromosome 10 (BICC1), chromosome 19 (KLF1) and chromosome 22 (CECR2) as key modulators of HbF. For DRBC, four drug targets (BCL6, LRRC32, KNCJ14, and LETM1) were identified as potential severity modifiers. Using mendelian randomization, I integrated metabolomics with genomics in the third study to establish a potential causal relationship between L-glutamine and painful crisis. Additionally, we identified 66 biomarkers for 6 SCD-related complications and estimated glomerular filtration rate (eGFR). Finally, the last study applied a clustering framework to metabolites which I then combined with genotypes. I found specific metabolomics changes highlighting families of metabolites involved in renal and liver dysfunction and confirming the role of a class of fatty acids in red blood cell sickling. This work highlights the importance of multi-omics approaches to unearth new biology and study human diseases.

Capillary electrophoresis mass spectrometry (CE-MS) is a versatile instrumental method for metabolomics, which allows for comprehensive metabolite profiling of volume-limited biological specimens in order to better understand the molecular mechanisms associated with chronic diseases, including an alarming epidemic of obesity worldwide. Multiplexed CE separations enable high-throughput metabolite screening with quality assurance to prevent false discoveries when combined with rigorous method validation, robust experimental designs, complementary statistical methods, and high-resolution tandem mass spectrometry (MS/MS) for unknown metabolite identification. In this thesis, multiplexed CE-MS technology is applied for both targeted and untargeted metabolite profiling of various biological fluids, including covalently bound thiol-protein conjugates, as well as free circulating metabolites in serum and plasma, and excreted/bio-transformed compounds in urine due to complex host-gut microflora co-metabolism. This work was applied to characterize aberrant metabolic responses of obese subjects in response to dietary challenges, and measure the benefits of dietary interventions that reduce adiposity without deleterious muscle loss. Chapter 2 presents, a simple, sensitive yet robust analytical protocol to expand metabolome coverage in CE-MS for the discovery of labile protein thiols in human plasma using a rapid chemical derivatization method based on N-tert-butylmaleimide (NTBM). Chapter 3 describes targeted metabolite profiling of serum and plasma to investigate the differential metabolic responses between healthy and unhealthy obese individuals before and after consumption of a standardized high-caloric meal, respectively. Chapter 4 of this thesis describes an untargeted metabolite profiling strategy for urine using multisegment-injection (MSI)-CE-MS for elucidating the effects of protein supplementation following a short-term dietary weight-loss intervention study. This work revealed six urinary metabolites that were classified as top-ranking treatment response biomarkers useful for discriminating between subjects consuming carbohydrate (control), soy, and whey supplemented diets. In summary, this thesis demonstrated the successful implementation of multiplexed CE-MS technology for biomarker discovery in nutritional-based metabolomic studies as required for more effective treatment and prevention of obesity for innovations in public health. / Thesis / Doctor of Philosophy (PhD)

Esta tesis se centra en la construcción y usos de los modelos metabólicos a escala genómica para obtener biocombustibles de manera eficiente, como etanol e hidrógeno. Como organismo objetivo, se ha elegido a la cianobacteria Synechocystis sp. PCC6803. Este organismo ha sido estudiado como una potencial plataforma de producción alimentada por fotones, dada su capacidad de crecer solamente a partir de dióxido de carbono y fotones. Esta tesis versa acerca de los métodos para modelar, analizar, estimar y predecir el comportamiento del metabolismo de las células. La principal meta es extraer conocimiento de los diferentes aspectos biológicos de un organismo con el fin de utilizarlo para un objetivo industrial pertinente. Esta tesis ha sido estructurada en capítulos organizados de acuerdo con las sucesivas tareas que terminan con la construcción de una célula in silico que se comporta, idealmente, como la que está basada en el carbono. Este proceso suele comenzar con los archivos de anotación del genoma y termina con un modelo metabólico a escala genómica capaz de integrar datos -ómicos. El primer objetivo de la presente tesis es la reconstrucción de un modelo del metabolismo de esta cianobacteria que tenga en cuenta todas las reacciones presentes en la misma. Esta reconstrucción tenía que ser lo suficientemente flexible como para permitir el crecimiento en las distintas condiciones ambientales bajo las cuales este organismo crece en la naturaleza, así como permitir la integración de diferentes niveles de información biológica. Una vez que se cumplió este requisito, se pudieron simular variaciones ambientales y estudiar sus efectos desde una perspectiva de sistema. Se han estudiado hasta cinco diferentes condiciones de crecimiento en este modelo metabólico y sus diferencias han sido evaluadas. La siguiente tarea fue definir estrategias de producción para sopesar la viabilidad de este organismo como una plataforma de producción. Se simularon perturbaciones genéticas para e / This thesis is focused on the construction and uses of genome-scale metabolic models to efficiently obtain biofuels, such as ethanol and hydrogen. As a target organism, cyanobacterium Synechocystis sp. PCC6803 was chosen. This organism has been studied as a potential photon-fuelled production platform, for its ability to grow only from carbon dioxide, water and photons. This dissertation verses about methods to model, analyse, estimate and predict the metabolic behaviour of cells. Principal goal is to extract knowledge from the different biological aspects of an organism in order to use it for an industrial relevant objective. This dissertation has been structured in chapters accordingly organized as the successive tasks that end up building an in silico cell that behaves as the carbon-based one. This process usually starts with the genome annotation files and ends up with a genome-scale metabolic model able to integrate ¿omics data. First objective of present thesis is to reconstruct a model of this cyanobacteria¿s metabolism that accounts for all the reactions present in it. This reconstruction had to be flexible enough as to allow growth under the different environmental conditions under which this organism grows in nature as well as to allow the integration of different levels of biological information. Once this requisite was met, environmental variations could be simulated and their effect studied under a system-wide perspective. Up to five different growth conditions were simulated on this metabolic model and differences were evaluated. Following assignment was to define production strategies to weigh this organism¿s viability as a production platform. Genetic perturbations were simulated to design strains with an enhanced production of three industrially-relevant metabolites: succinate, ethanol and hydrogen. Resulting sets of genetic modifications for the overproduction of those metabolites are, thus, proposed. Moreover, functional reactions couplings were studied and weighted to their metabolite production importance. Finally, genome-scale metabolic models allow establishing integrative approaches to include different types of data that help to find regulatory hotspots that can be targets of genetic modification. Such regulatory hubs were identified upon light/dark shifts and general metabolism operational principles inferred. All along this process, blind spots in Synechocystis sp. PCC6803 metabolism, and more importantly, blind spots in our understanding of it, are revealed. Overall, the work presented in this thesis unveils the industrial capabilities of cyanobacterium Synechocystis sp. PCC6803 to evolve interesting metabolites as a clean production platform. / Esta tesis es centra en la construcció i els usos del models metabòlics a escala genòmica per a obtenir eficientment biocombustibles, com etanol i hidrogen. Com a organisme diana, s¿elegí el cianobacteri Synechocystis sp. PCC6803. Aquest organisme ha segut estudiat com una plataforma de producció nodrida per fotons, per la seva habilitat per créixer a partir únicament de diòxid de carboni, aigua i fotons. Aquesta tesi versa sobre mètodes per a modelitzar, analitzar, estimar i predir el comportament metabòlic de cèl¿lules. La principal meta és extreure coneixement del diferents aspectes biològics d¿un organisme de manera que s¿usen per a un objectiu industrial rellevant. La tesi ha segut estructurada en capítols organitzats d¿acord a les successives tasques que acaben construint una cèl¿lula in silico que es comporta, idealment, com la que està basada en carboni. Aquest procés generalment comença amb els arxius de l¿anotació del genoma i acaba amb un model metabòlic a escala genòmica capaç d¿integrar dades ¿òmiques. El primer objectiu de la present tesi és la reconstrucció d¿un model del metabolisme d¿aquest cianobacteri que tinga en compte totes les reaccions que hi estan presents. Esta reconstrucció havia de ser prou flexible com per permetre la simulació del creixement en les diferents condicions ambientals en les quals aquest cianobacteri creix en la natura, així com permetre la integració de diferents nivells d¿informació biològica. Una vegada que aquest requisit fou assolit, es pogueren simular variacions ambientals i estudiar els seus efectes amb una perspectiva de sistema. S¿han simulat fins a cinc condicions de creixement en este model metabòlic i les seves diferències han segut avaluades. La següent tasca fou definir estratègies de producció per a valorar la viabilitat d¿aquest organisme com a plataforma de producció. Es simularen pertorbacions genètiques per al disseny de soques amb producció millorada de metabòlits de rellevància industrial: succinat, etanol i hidrogen. Així, es proposen conjunts de modificacions genètiques per a la sobreproducció d¿aquests metabòlits. També s'han estudiat reaccions acoblades funcionalment i s¿ha ponderat la seva importància en la producció de metabòlits. Finalment, els models metabòlics a escala genòmica permeten establir criteris per integrar diferents tipus de dades que ens ajuden a trobar punts importants de regulació. Eixos centres reguladors, que poden ser objecte de modificacions genètiques, han segut investigats baix canvis dràstics d¿il¿luminació i s¿han inferit principis operacionals del metabolisme. Al llarg d'aquest procés, s¿han revelat punts cecs al metabolisme de Synechocystis sp. PCC6803 i, el més important, punts cecs en la nostra comprensió d'aquest metabolisme. En general, el treball presentat en aquesta tesi dona a conèixer les capacitats industrials del cianobacteri Synechocystis sp. PCC6803 per a produir metabòlits d'interès, tot sent una plataforma de producció neta i sostenible. / Montagud Aquino, A. (2012). Modelling and analysis of biological systems to obtain biofuels [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/17319

The discovery of antibiotics is considered as one of the most significant scientific achievements of the 20th century – lives of millions of people and animals have been saved. Thenceforth, substantial amounts of administered antibiotics and their metabo-lites have been excreted into waste stream via urine and faeces. In this dissertation, primary focus is the qualitative balance of 14 antibiotics and one metabolite in urban water management and in urban waters, respectively. In particular, antibiotics pre-scribed to human beings are drained in the urban sewer system and finally enter the environment: (i) Continuously via the effluent of the wastewater treatment plant after a partially effective removal or degradation or (ii) Intermittent via combined sewer overflow structures due to capacity limitations of the urban drainage system. The fate and the potential effects and risks of these substances on ecosystems and hu-man health are of major concern – their direct toxic effect to all trophic levels as well as the global spread of antibiotic resistance genes are challenging. Hence, an assessment of microbial community activity due to antibiotic exposure is presented. In particular, systematic work has been carried out to study the presence and character-istics of 14 antibiotics in urban waters. In detail, investigations were conducted to gain scientific knowledge with respect to adsorption, desorption, abiotic, biotic and photolyt-ic degradation as well as activity-inhibition of microorganism communities in sewage and of natural freshwater biofilm communities, respectively, due to inevitable urban drainage overflows. In order to provide information to assist potential management strategies, which miti-gate surface water pollution and minimize the adverse impacts of antibiotics on activity of microorganism communities, the following specific topics were addressed: ⑴ The occurrence of 14 antibiotics and one metabolite were determined in sewag-es at three sampling sites in the city of Dresden, Germany. ⑵ The adsorption affinities of 14 antibiotics and one metabolite to size dependent sewer sediments were determined in experimental investigations, three sam-pling campaigns and subsequently an antibiotic-specific adsorption coefficient, normalized to organic content, was quantified. ⑶ The desorption affinity and -dynamics of 14 antibiotics and one metabolite were quantified in size dependent sewer sediments in experimental investigation and with statistical analysis. ⑷ The abiotic, biotic and photolytic degradation affinity of 14 antibiotics and one metabolite were quantified based on batch experiments with three different sewages at 7°C and 22°C, with artificial irradiation and different dilution ratios of the sewage at 30°C and subsequently a model framework decrypted ranges of abiotic, biotic and photolytic degradation coefficients. ⑸ The occurrence of three antibiotics, namely ciprofloxacin, clarithromycin and doxycycline was determined in sewage sampled during dry weather conditions in a small catchment of Dresden, which spills intermittently combined sewage (a mixture of sewage and storm water) to an adjacent brook in the case of capacity limitations of the urban drainage system during periods of intense rainfall and subsequently the three antibiotics were determined in the adjacent brook water. ⑹ Then, the activity-inhibition of microorganism community in sewage of this small catchment was quantified due to an exposition with three different antibiotics and three different antibiotic concentrations. ⑺ Last but not least, the activity-inhibition of natural freshwater biofilm communities in the adjacent brook was quantified via exposure to three antibiotics, which were individually dosed in three different concentrations, and also in mixture. ⑻ Finally, a two-dimensional hierarchical cluster analysis with dendrogram and heat map based on before mentioned activity inhibition of natural freshwater biofilm communities were conducted to identify hot spots of antibiotic tolerant and resistant bacterial subpopulations due to inevitable urban drainage system overflows.:List of Figures IV List of Tables VIII Symbols and Abbreviations XII List of Publications on the Ph.D. topic XIX 1 General Introduction 2 1.1 Background 2 1.2 Aims and Objectives 3 1.3 Innovation and Contribution to the Knowledge 4 1.4 Outline of this Thesis 4 1.5 References 6 2 Adsorption and Desorption Affinity of 14 Antibiotics and One Metabolite for particulate components in urban drainage systems 10 2.1 Introduction 11 2.2 Materials and Methods 12 2.2.1 Study area 12 2.2.2 Sewer sediment and sewage sample collection 12 2.2.3 Sediment fractionation 13 2.2.4 Antibiotic determination in sewage and sediment 13 2.3 Results and Discussion 18 2.3.1 Antibiotics in composite sewage samples 18 2.3.2 Antibiotics adsorbed to sewer sediments 19 2.3.3 Organic-bound antibiotic load as a linear function of liquid concentration 20 2.3.4 Adsorption dynamics and adsorption coefficient determined by bath experiments 20 2.3.5 Mineral composition of sewer sediment SED#1B 23 2.3.6 Initial characteristics of sediment SED#1B 23 2.3.7 Desorption dynamics and desorption coefficient of SED#1B 24 2.4 Conclusions 25 2.5 References 26 3 Abiotic, Biotic and Photolytic Degradation Coefficients of 14 Antibiotics and One Metabolite 32 3.1 Introduction 34 3.2 Materials and Methods 35 3.2.1 Study area and sample collection 35 3.2.2 Experimental set up 35 3.2.3 Modelling framework 38 3.2.4 Procedure of model calibration 40 3.3 Results and Discussion 43 3.3.1 Primary metabolic parameter 43 3.3.2 Secondary metabolic parameter 44 3.4 Conclusions 50 3.5 References 50 4 Activity-Inhibition of Microorganisms due to an Exposition with different Antibiotics and Concentrations 56 4.1 Assessing Antibiotic Resistance of Microorganisms in Sanitary Sewage 56 4.1.1 Introduction 57 4.1.2 Material and Methods 58 4.1.2.1 Sampling Site and Antibiotic Agents 58 4.1.2.2 Analyzing Antibiotics 60 4.1.2.3 Respiration Rate 60 4.1.3 Results and Discussion 60 4.1.3.1 Concentration Range of Antibiotics and Typical Sewage Parameters 60 4.1.3.2 Oxygen Uptake Rate 62 4.1.4 Summary and Conclusions 63 4.1.5 References 64 4.2 Hot Spots of Antibiotic Tolerant and Resistant Bacterial Subpopulations in Natural Freshwater Biofilm Communities due to Inevitable Urban Drainage System Overflows 66 4.2.1 Introduction 68 4.2.2 Material and Methods 69 4.2.3 Results and Discussion 72 4.2.4 Conclusions 76 4.2.5 References 76 5 Summery and General Coclusions 82 5.1 Adsorption and Desorption Affinity 82 5.2 Abiotic, Biotic and Photolytic Degradation 83 5.3 Activity-Inhibition of Microorganism Communities due to Antibiotic Exposure 84 5.4 Enhancement of the Stockholm County Council (2014) assessment of antibiotics 84 5.5 References 87 6 Proposed Directions of Future Research 90 7 Appendixes 94 7.1 Chapters 94 7.2 Figures 95 7.3 Tables 115 7.4 References 139