Tesis por compendio / [ES] Los ácidos grasos de cadena muy larga (VLC-FA; >C24), aunque presentes en pequeñas cantidades, juegan un importante papel para el correcto desarrollo y funcionalidad de los tejidos neurales en vertebrados, especialmente durante su desarrollo temprano. Sin embargo, a pesar de su aparente importancia, los estudios sobre estos compuestos en peces son escasos. La biosíntesis de los VLC-FA se lleva a cabo mediante las denominadas proteínas de elongación de los ácidos grasos de cadena muy larga 4 (Elovl4) y, en consecuencia, la dotación y la función de estas enzimas determinan la capacidad endógena que una determinada especie tiene para satisfacer las demandas fisiológicas de VLC-FA, especialmente durante su desarrollo temprano. Además, esta producción endógena de los ácidos grasos poliinsaturados de cadena muy larga (VLC-PUFA) es dependiente de los sustratos. Así, para su biosíntesis se requiere de ácidos grasos más cortos, es decir ácidos grasos poliinsaturados de cadena larga (LC-PUFA; C20-24) que actúen como precursores, los cuales son incorporados principalmente a través de la dieta. Teniendo esto en mente, el presente trabajo de investigación tuvo como objetivos caracterizar los genes elovl4 en dorada (Sparus aurata) y en lenguado senegalés (Solea senegalensis), determinar la función de sus correspondientes proteínas codificadas, así como analizar el patrón de expresión tisular de elovl4. Además, se ha investigado la regulación nutricional de los genes implicados en la biosíntesis de VLC-PUFA (elovl4a, elovl4b) y LC-PUFA (fads2, elovl5) durante las primeras etapas del ciclo de vida de ambas especies (larvas y poslarvas), mediante el uso de dietas adaptadas a cada etapa del desarrollo. Los resultados confirmaron que ambas especies de peces poseen dos genes elovl4 distintos, denominados elovl4a y elovl4b según su homología con sus ortólogos de pez cebra. Asimismo, los ensayos funcionales de sus correspondientes proteínas, llevados a cabo en levaduras, indicaron que tanto Elovl4a como Elovl4b tienen la capacidad de elongar los ácidos grasos precursores (C20-24) hasta VLC-FA en ambas especies. Sin embargo, Elovl4b mostró mayor actividad que Elovl4a para elongar todos los ácidos grasos poliinsaturados a productos de cadena más larga, especialmente de la serie n-3. Además, los resultados de expresión génica indicaron que, aunque fueron detectados transcritos de elovl4 en la mayoría de los tejidos analizados, ambos genes elovl4 se expresaron más intensamente en los tejidos neurales de ambas especies, como el cerebro y los ojos, que mostraron los niveles de expresión más altos de elovl4a y elovl4b, respectivamente. Además, los resultados procedentes de los ensayos de regulación nutricional indicaron que los genes fads2, elovl5, elovl4a y elovl4b pueden ser regulados a través del contenido en LC-PUFA presente en la dieta. Es importante destacar que elovl4a y elovl4b fueron regulados de manera distinta según las hipotéticas necesidades de VLC-PUFA asociadas, de manera específica, con cada etapa del desarrollo temprano y dependiendo de disponibilidad dietaria de LC-PUFA. Estos hallazgos pueden contribuir a alcanzar una mejor comprensión de la vía biosintética de los VLC-FA en los teleósteos marinos, resaltando así el papel crucial que los productos de Elovl4 desempeñan para el correcto desarrollo y mantenimiento de las funciones neurofisiológicas durante las primeras etapas del desarrollo de los peces. Asimismo, estos resultados pueden ayudar a esclarecer el mecanismo molecular que controla la biosíntesis de VLC-PUFA, así como a establecer sus requerimientos específicos a lo largo del desarrollo de los teleosteos marinos en función de la especie. De esta manera, se abre la posibilidad de incorporar con éxito fuentes lipídicas alternativas a través de una programación nutricional temprana que estimule la biosíntesis de los VLC-PUFA durante las primeras etapas de alimentación exógena. / [CA] Els àcids grassos de cadena molt llarga (VLC-FA; >C24), encara que presents en petites quantitats, juguen un important paper per al correcte desenvolupament i funcionalitat dels teixits neurals en vertebrats, especialment durant el seu desenvolupament inicial. No obstant, malgrat la seua aparent importància, els estudis sobre aquests compostos en peixos son escassos. La biosíntesi dels VLC-FA es porta a terme mitjançant les denominades proteïnes d'elongació dels àcids grassos de cadena molt llarga 4 (Elovl4) i, en conseqüència, la dotació i la funció d'aquests enzims determinen la capacitat endògena que una determinada espècie té per a satisfer les demandes fisiològiques de VLC-FA, especialment durant el seu desenvolupament inicial. A més, aquesta producció endògena dels àcids grassos poliinsaturats de cadena molt llarga (VLC-PUFA) és depenent dels substrats. Així, per a la seua biosíntesi es requereix d'àcids grassos més curts, és a dir àcids grassos poliinsaturats de cadena llarga (LC-PUFA; C20-24) que actuen com a precursors, els quals són incorporats principalment a través de la dieta. Tenint això en compte, el present treball de recerca va tindre com a objectius caracteritzar els gens elovl4 en orada (Sparus aurata) i llenguado (Solea senegalensis), determinar la funció de les seues corresponents proteïnes codificades, així com analitzar el patró d'expressió tissular de elovl4. A més, es va investigar la regulació nutricional dels gens implicats en la biosíntesi de VLC-PUFA (elovl4a, elovl4b) i LC-PUFA (fads2, elovl5), durant les primeres etapes del cicle de vida d'ambdues espècies (larves i poslarves), mitjançant l'ús de dietes adaptades a cada etapa del desenvolupament. Els resultats van confirmar que totes dues espècies de peixos posseeixen dos gens elovl4 diferents, denominats elovl4a i elovl4b segons la seua homologia amb els seus ortòlegs en peix zebra. Així mateix, els assajos funcionals de les corresponents proteïnes, duts a terme en llevats, van indicar que tant Elovl4a com Elovl4b tenen la capacitat d'elongar els àcids grassos precursors (C20-24) fins a VLC-FA en totes dues espècies. No obstant això, Elovl4b va mostrar major activitat que Elovl4a per a elongar tots els àcids grassos poliinsaturats (substrats) fins a productes de cadena més llarga, especialment de la sèrie n-3. A més, els resultats d'expressió gènica van indicar que, encara que van ser detectats trànscrits de elovl4 en la majoria dels teixits analitzats, tots dos gens elovl4 es van expressar més en teixits neurals de totes dues espècies, com el cervell i els ulls, que van mostrar els nivells d'expressió més alts d'elovl4a i elovl4b, respectivament. A més, els resultats procedents dels assajos de regulació nutricional van indicar que els gens fads2, elovl5, elovl4a i elovl4b poden ser regulats a través del contingut en LC-PUFA present en la dieta. És important destacar que elovl4a i elovl4b van ser regulats de manera diferent segons les hipotètiques necessitats de VLC-PUFA associades, de manera específica, amb cada etapa del desenvolupament inicial i depenent de la disponibilitat dietaria de LC-PUFA. Aquestes troballes poden contribuir a tenir una millor comprensió de la via biosintètica dels VLC-FA en els teleostis marins, ressaltant així el paper crucial que els productes d'Elovl4 exerceixen en el correcte desenvolupament i manteniment de les funcions neurofisiològiques durant les primeres etapes del desenvolupament dels peixos. De la mateixa forma, aquests resultats poden ajudar a esclarir el mecanisme molecular que controla la síntesi endògena de VLC-PUFA, així com a establir els requisits específics de cada espècie al llarg del desenvolupament dels teleostis marins. D'aquesta manera, s'obri la possibilitat d'incorporar amb èxit fonts lipídiques alternatives a través d'una programació nutricional inicial que estimuli la biosíntesi de VLC-PUFA durant les primeres etapes d'alimentació exògena. / [EN] Very long-chain fatty acids (VLC-FA; >C24), although present in small amounts, play important roles for the correct development and functionality of neural tissues, especially during early development of vertebrates. However, despite their putative importance, their study in fish is scarce. Biosynthesis of VLC-FA is carried out by the so-called elongation of very long-chain fatty acid 4 (Elovl4) proteins and, consequently, the complement and function of these enzymes determine the endogenous capacity that a given species has for satisfying the physiological demands for VLC-FA, especially during its early development. Moreover, this endogenous production of very long-chain polyunsaturated fatty acid (VLC-PUFA) is substrate-dependent. Therefore, shorter fatty acid precursors, i.e. long-chain polyunsaturated fatty acids (LC-PUFA; C20-24), are required. These nutrients are mostly incorporated by the diet and their bioavailability can influence the capacity of Elovl4 for satisfying the physiological VLC-PUFA demands in marine fish. Thus, nutritional regulation of elovl4, as well as other elongase and desaturase genes involved in LC-PUFA biosynthesis (elovl5, fads2) has been proposed as a strategy to enhance endogenous production of LC-PUFA and VLC-PUFA in fish farming. The present thesis aimed to characterize elovl4 genes from the marine teleosts Sparus aurata and Solea senegalensis, to determine the function of the corresponding encoded proteins, and to analyze the tissue expression pattern of these genes. Moreover, we investigated the nutritional regulation of genes involved in the biosynthesis of the VLC-PUFA (elovl4a, elovl4b) and the LC-PUFA (fads2, elovl5) in early life-cycle stages (larvae and post-larvae) of both fish species fed diets adapted to each development stage. Live preys were supplied to larvae (early and late larvae) and microdiets for post-larvae, with a variable content in VLC-PUFA precursors, i.e. LC-PUFA. The results confirmed that both fish species possess two distinct elovl4 genes termed as elovl4a and elovl4b based on their homology to the zebrafish orthologs. Functional assays of the corresponding proteins in yeast denoted that Elovl4a and Elovl4b from both species have the capability to elongate C20-24 fatty acid precursors to VLC-FA products. However, Elovl4b appeared to have a higher activity than Elovl4a elongating all the polyunsaturated fatty acid substrates assayed to longer chain polyunsaturated products, especially those of the n-3 series. Moreover, gene expression results indicated that, although elovl4 transcripts were detected in most of the tissues analyzed, elovl4 genes were more strongly expressed in the neural tissues of both species, such as brain and eyes, which showed the highest expression levels of elovl4a and elovl4b, respectively. Furthermore, the results from nutritional regulation assays denoted that fads2, elovl5, elovl4a and elovl4b genes could be regulated by the dietary LC-PUFA content. It is important to highlight that elovl4a and elovl4b genes were differently regulated according to the species-specific VLC-PUFA putative needs, associated with each early life-stage and the LC-PUFA dietary availability. Importantly, these findings can contribute to a better understanding of the VLC-FA biosynthetic pathway in marine teleosts, highlighting the crucial role that the Elovl4 products carry out for the correct development and maintenance of neurophysiological functions during early stages of the fish development. Therefore, these results can help to elucidate the molecular mechanism controlling the VLC-PUFA biosynthesis and their species-specific requirements along the marine fish development, opening the possibility to incorporate successfully alternative lipid sources, through an early nutritional programming that stimulates the VLC-PUFA biosynthesis during the first exogenous feeding stages. / Para desarrollarel trabajo de investigación descrito en esta memoria, Miguel Torres Rodríguez recibió una beca predoctoral de la Excma. Diputación de Castellón. / Torres Rodríguez, M. (2021). Estudio de los patrones de expresión de genes implicados en la síntesis de ácidos grasos de cadena muy larga durante el desarrollo de la dorada y el lenguado, y su regulación nutricional [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/166619 / Compendio

Dans le monde entier, les infections virales causent des problèmes de santé majeurs et récurrents, engendrant de sérieux problèmes socio-économiques. Notamment, les virus de la famille Flaviviridae qui représentent un fardeau considérable sur la santé mondiale et font partie des domaines prioritaires de la virologie médicale selon le rapport 2016 du ‘Global Virus Network’. Bien que le traitement actuel contre le virus de l’hépatite C (VHC) ait un taux de guérison dépassant 98%, d’autres comme le virus de la dengue (DENV) et le virus zika (ZIKV) n’ont pas encore de traitement spécifique autorisé. En prenant avantage de la grande expertise de notre laboratoire dans l’étude du VHC, nous avons utilisé des données d’une étude de biologie des systèmes visant à identifier l’interactome des différentes protéines virales. Les techniques utilisées ont combiné l’immunoprécipitation des protéines virales suivie de l’identification des protéines interacteurs humaines par spectrométrie de masse. Des études de génomique fonctionnelle par ARN interférent (ARNi) ont permis d’étudier l’effet de la diminution de l’expression des protéines identifiées sur la réplication du VHC. Cette étude a conduit à la découverte de l’interactant spécifique 17-bêta-hydroxystéroïde déshydrogénase de type 12 (HSD17B12 ou DHB12) de la protéine virale Core comme facteur cellulaire requis à la réplication du VHC. HSD17B12 est une enzyme cellulaire dont l’activité catalytique est requise pour l’élongation des acides gras à très longue chaîne (VLCFA) lors de la deuxième des quatre réactions du cycle d’élongation. Dans cette étude, nous avons déterminé que les cycles de réplication du VHC, ZIKV et DENV dépendent de l’expression et de l’activité métabolique du facteur cellulaire HSD17B12. Ainsi, nous avons étudié les effets de l’inhibition de l’expression génique par ARNi et de façon pharmacologique sur la réplication de plusieurs flavivirus dans une approche antivirale à large spectre. Nous avons démontré que le silençage de HSD17B12 diminue significativement la réplication virale, l’expression des protéines virales et la production de particules infectieuses de cellules Huh7.5 infectées par la souche JFH1 du VHC. L'analyse de la localisation cellulaire de HSD17B12 dans des ii cellules infectées suggère une colocalisation avec l'ARN double brin (ARNdb) aux sites de réplication virale, ainsi qu’avec la protéine Core (et les gouttelettes lipidiques) aux des sites d’assemblage du virus. Nous avons également observé que le silençage de HSD17B12 réduit considérablement le nombre et la taille des gouttelettes lipidiques. En accord avec ces données, la diminution de l’expression de HSD17B12 par ARNi réduit significativement l’acide oléique et les espèces lipidiques telles que triglycérides et phosphatidyl-éthanolamine dans l'extrait cellulaire total. Ces travaux suggèrent une contribution de la capacité métabolique de HSD17B12 lors de la réplication du VHC. De même, nous avons démontré que le silençage de HSD17B12 réduit significativement les particules infectieuses de cellules infectées par DENV et ZIKV. Ces études supportent le rôle de HSD17B12 dans l’efficacité des processus de la réplication de l'ARN viral et de l’assemblage de particules virales. De plus, l'inhibiteur spécifique de HSD17B12, INH-12, réduit la réplication du VHC à des concentrations pour lesquelles aucune cytotoxicité notable n'est observée. Le traitement avec 20 μM d'INH-12 réduit jusqu'à 1,000 fois les particules infectieuses produite par des cellules Huh-7.5 infectées par DENV et ZIKV lors de plusieurs cycles de réplication, et bloque complètement l'expression des protéines virales. En conclusion, ces travaux ont conduit à une meilleure compréhension du rôle de HSD17B12 lors de la synthèse de VLCFA et de lipides requise à la réplication du VHC, permettant d’explorer l’inhibition de HSD17B12 et de l’élongation d’acides gras à très longue chaîne comme nouvelle approche thérapeutique pour le traitement à large spectre des infections par les virus de la famille Flaviviridae. / Infections with viruses are major recurrent socio-economical and health problems worldwide. These include infections by viruses of the Flaviviridae family, which present a substantial global health burden and are among the priority areas of medical virology according to the Global Virus Network 2016 report. While the current treatment regimens for hepatitis C virus (HCV) infection have cure rates of more than 98%, other important members of Flaviviridae like dengue virus (DENV) and zika virus (ZIKV) have no specific licensed treatments. By taking advantage of the most-studied HCV, which our lab has developed a vast expertise in the last 20 years, we used proteomics data of an HCV interactome study, combining viral protein immunoprecipitation (IP) coupled to tandem mass spectrometry identification (IP-MS/MS) and functional genomics RNAi screening. The study uncovered the 17-beta-hydroxysteroid dehydrogenase type 12 (HSD17B12, also named DHB12), as a specific host interactor of core that promotes HCV replication. HSD17B12 catalytic activity is involved in the synthesis of very-long-chain fatty acids (VLCFA) upon the second step of the elongation cycle. In this study, taking HCV as a virus model, we elucidated the dependency of HCV, dengue virus (DENV) and zika virus (ZIKV) replication on expression and metabolic capacity of the host factor HSD17B12. We investigated the effects of the inhibition of gene expression by RNAi and of its pharmacological enzymatic inhibition on flavivirus replication in a broad-spectrum antiviral approach. We showed that silencing expression of HSD17B12 decreases viral replication, viral proteins and iv infectious particle production of the JFH1 strain of HCV in Huh7.5 cells. The cellular localization analysis of HSD17B12 showed a co-staining with double-stranded RNA (dsRNA) at viral replication sites and with core protein (and lipid droplets) at virus assembly sites. Furthermore, HSD17B12 gene silencing drastically reduced the number and size of lipid droplets. In association, the reduced expression of HSD17B12 by RNAi decreases oleic acid levels and lipids such as triglycerides (TG) and phosphatidylethanolamine (PE) in whole-cell extract. The data suggested the requirement of the metabolic capacity of HSD17B12 for HCV replication. Similarly, we provide evidence that HSD17B12 silencing significantly reduces DENV and ZIKV infectious particles. The studies support a role of HSD17B12 for effective viral RNA replication and particle assembly processes. Moreover, the specific HSD17B12 inhibitor, INH-12, reduces HCV replication at concentrations for which no appreciable cytotoxicity is observed. The treatment of DENV- and ZIKV-infected Huh- 7.5 cells with 20 μM of INH-12 dramatically reduces production of infectious particles by up to 3-log10 in infection assays, and completely block viral protein expression. In conclusion, these studies extends our understanding of the role of HSD17B12 in VLCFA synthesis required for the replication of HCV, allowing to explore the inhibition of HSD17B12 and elongation of VLCFA as a novel therapeutic approach for the treatment of a broad-spectrum of viruses of the Flaviviridae family.

La bactérie phytopathogène E. amylovora, est l'agent responsable du Feu bactérien des Spiraeoideae (pommier, poirier, pyracantha), une maladie caractérisée par l'apparition de symptômes nécrotiques des tissus infectés. Le pouvoir pathogène d’E. amylovora repose entre autre sur un système de sécrétion de type III (SSTT) qui permet la sécrétion et l'injection d'effecteurs dans la cellule hôte végétale. Parmi les protéines injectées par le T3SS d'E. amylovora, DspA est essentielle au pouvoir pathogène de la bactérie puisqu’un mutant dspA est non pathogène sur plante (Gaudriault et al., 1997). Le rôle de DspA est dual, d’une part, l’expression de dspA est suffisante pour provoquer des symptômes nécrotiques sur plante et une toxicité chez la levure, d’autre part, DspA est impliquée dans la suppression des réactions de défense telles que la déposition de callose (Degrave et al., 2008; Boureau et al., 2006; Oh et al., 2007; DebRoy et al., 2004). DspA appartient à la famille des effecteurs AvrE qui sont répandus chez les bactéries phytopathogènes et semblent posséder une fonction similaire. Cependant, peu de connaissance existe sur la structure ainsi que la fonction de DspA. L'objectif de ce travail de thèse était de déterminer les domaines ou motifs importants pour la fonction de DspA. Pour cela nous avons choisi d'effectuer une analyse in silico et fonctionnelle de la protéine DspA. L'analyse in silico révèle la présence d'un domaine bêta-propeller au sein de la protéine DspA ainsi que de tous les homologues analysés. De plus, l'analyse fonctionnelle indique que ce domaine est important pour la structure et la fonction de DspA. Dans un second temps, j'ai étudié le mécanisme d'action de DspA dans la levure Saccharomyces cerevisiae. J'ai pu mettre en évidence que l'expression de dspA chez la levure induit un arrêt de croissance et une forte altération du trafic cellulaire. L'étude de mutants de levure suppresseurs de la toxicité de DspA, effectuée avant mon arrivée au laboratoire, montre que les suppresseurs les plus forts sont affectés dans la voie de biosynthèse des sphingolipides, je me suis donc plus particulièrement intéressée au rôle des sphingolipides dans la toxicité générée par DspA. Nos résultats montrent que DspA inhibe la biosynthèse des sphingolipides indirectement via les régulateurs négatifs de la voie, les protéines Orms. / Erwinia amylovora is the causative agent of fire blight of Spiraeoideae (apple, pear, pyracantha), a disease characterized by the apparition of necrotic symptoms on infected tissues. The pathogenicity of E. amylovora relies on a functional type III secretion system (T3SS) that allows secretion and injection of effector proteins into the host plant cell. Among these effector proteins injected by the T3SS of E. amylovora, DspA is essential to the bacteria disease process since a dspA mutant is nonpathogenic on plants (Gaudriault et al., 1997). DspA has a dual role; on the one hand dspA expression is sufficient to induce cell death on plants and toxicity on yeast, on the other hand, DspA is involved on suppression of defense reactions like callose deposition (Degrave et al., 2008; Boureau et al., 2006; Oh et al., 2007; DebRoy et al., 2004). DspA belongs to the AvrE familly of type III effectors which are widespread on phytopathogenic bacteria and likely possess a similar function. However, the structure and function of DspA remain unknown. In the first part of my thesis, I attempted to characterize domains or motifs important for the function of DspA. We performed an in silico and a functional analysis of the DspA protein. In silico analysis predicted a bêta-propeller domain in DspA and all the analysed effectors. In the second part of my thesis, I analysed the mechanism of function of DspA in the yeast Saccharomyces cerevisiae. Results showed that expression of dspA in yeast inhibits cell growth and alters the actin cytoskeleton and endocytosis. Screening of the Euroscarf library for mutants resistant to DspA induced toxicity revealed that mutants impaired in the sphingolipid biosynthetic pathway are the best suppressors. Based on this results, I attempted to determine the role of sphingolipids in the toxicity induced by DspA. Results showed that DspA inhibits indirectly the sphingolipid biosynthetic pathway via the negative regulators, Orm proteins.

This thesis describes the synthesis, characterisation and application of artificial metalloenzymes as catalysts. The focus was on two mutants of SCP-2L (SCP-2L A100C and SCP-2L V83C) both of which possess a hydrophobic tunnel in which apolar substrates can accumulate. The crystal structure of SCP-2L A100C was determined and discussed with a special emphasis on its hydrophobic tunnel. The SCP-2L mutants were covalently modified at their unique cysteine with two different N-ligands (phenanthroline or dipicolylamine based) or three different phosphine ligands (all based on triphenylphosphine) in order to increase their binding capabilities towards metals. The metal binding capabilities of these artificial proteins towards different transition metals was determined. Phenanthroline modified SCP-2L was found to be a promising scaffold for Pd(II)-, Cu(II)-, Ni(II)- and Co(II)-enzymes while dipicolylamine-modified SCP-2L was found to be a promising scaffold for Pd(II)-enzymes. The rhodium binding capacity of two additional phosphine modified protein scaffolds was also investigated. Promising scaffolds for Rh(I)- and Ir(I)-enzymes were identified. Rh-enzymes of the phosphine modified proteins were tested in the aqueous-organic biphasic hydroformylation of linear long chain 1-alkenes and compared to the Rh/TPPTS reference system. Some Rh-enzymes were found to be several orders of magnitude more active than the model system while yielding comparable selectivities. The reason for this remarkable reactivity increase could not be fully elucidated but several potential modes of action could be excluded. Cu-, Co-, and Ni-enzymes of N-ligand modified SCP-2L A100C were tested in the asymmetric Diels-Alder reaction between cyclopentadiene and trans-azachalcone. A promising 29% ee for the exo-product was found for the phenanthroline modified protein in the presence of nickel. Further improvement of these catalyst systems by chemical means (e.g. optimisation of ligand structure) and bio-molecular tools (e.g. optimisation of protein environment) can lead to even more active and (enantio)selective catalysts in the future.

Au niveau du cerveau et dans le plasma de malades atteints de maladie d’Alzheimer (MA), l’accumulation de C22:0 et d’acides gras à très longue chaîne (C24:0 ; C26:0), la diminution d’acide docosahexaenoique (C22:6 n-3) et les modifications quantitatives et qualitatives de plasmalogènes suggèrent l’implication de dysfonctions peroxysomales. En fonction de ces constatations, les activités biologiques de C22:0, C24:0 et C26:0 ont été recherchées sur des cellules neuronales humaines SK-N-BE. La lipotoxicité des acides gras (C22:0, C24:0 et C26:0) induit divers effets au niveau des mitochondries (modifications topographiques, morphologiques et fonctionnelles), conduit à une rupture de l’équilibre RedOx (surproduction d’espèces radicalaires de l’oxygène, modification de l’activité des enzymes anti-oxydantes : catalase, SOD, GPx), à une peroxydation lipidique et à une désorganisation du cytosquelette (microfilaments d’actine, tubuline, neurofilaments). Ces acides affectent aussi l’amyloïdogenèse et la tauopathie. L’amyloïde béta favorise aussi l’accumulation intracellulaire de C22:0, C24:0 et C26:0. A fortes concentrations, ces acides gras induisent une mort cellulaire non apoptotique. Par ailleurs, les données immunohistochimiques en relation avec l’expression de marqueurs peroxysomaux (ABCD1, ABCD2, ABCD3, ACOX1 et catalase) au niveau du cerveau de souris transgéniques APP PS1 ΔE9 ainsi que les profil d’acide gras obtenus sur le cerveau et le sang de ces souris suggèrent qu’elles pourraient constituer un bon modèle pour l’étude des relations entre MA et métabolisme peroxysomal. L’étude clinique réalisée sur plasma et érythrocytes de malades déments (MA, démences vasculaires, autres démences) montre une forte accumulation de C22:0, C24:0 et C26:0. Le C26:0 pourrait constituer un excellent biomarqueur de la MA. Le C18:0 à est aussi augmenté ainsi que les acides gras n-6. De forts indices de stress oxydant sont aussi révélés. Dans son ensemble, le travail réalisé suggère que les acides gras (C22:0, C24:0 et C26:0) ainsi que le métabolisme des acides gras en relation avec le métabolisme peroxysomal pourraient contribuer à la neurodégénéréscence associée aux démences incluant la MA / In the brain and in the plasma of patients with Alzheimer’s disease (AD), marked accumulation of C22:0 and of very long chain fatty acids (C24:0 ; C26:0) have been reported. Important decreases of docosahexaenoic acid (DHA; C22:6 n-3) have also been described as well as quantitative and qualitative modifications of plasmalogens. Altogether, these lipid modifications suggest an implication of peroxisomal metabolism disorders in the physiopathology of AD. Therefore, the biological activities of C22:0, C24:0 and C26:0 have been studied on human neuronal cells SK-N-BE. On these cells, the lipotoxicity of fatty acids (C22:0, C24:0 and C26:0) leads to various cellular modifications: topographical, morphological and functional changes at the mitochondrial level, rupture of RedOx equilibrium (overproduction of reactive oxygen species, modification of the activity of enzymes involved in anti-oxidant defenses: catalase, SOD, GPx), lipid peroxidation, cytoskeleton disorganization (actin microfilaments, tubulin, neurofilaments). These fatty acids also favor amyloidogenesis and tauopathy. At elevated concentrations, these fatty acids trigger a non apoptotic mode of cell death. Moreover, data obtained by immunohistochemistry with antibodies raised against peroxisomal components (ABCD1, ABCD2, ABCD3, ACOX1 and catalase) on histological tissue sections of the brain of transgenic mice APP PS1 ΔE9 as well as lipidomic analysis performed on the blood and the brain of these mice suggest that they could constitute interesting model to study the relationships between AD and peroxisomal metabolism. The clinical study performed on the plasma and on the erythrocytes of patients with dementia (AD, vascular dementia, other dementia) revealed an important accumulation of C22:0, C24:0 and C26:0. Hexacosanoic acid (C26:0) might constitute an excellent biomarker of AD. The fatty acid C18:0 and (n-6) fatty acids have also been found at increased concentrations. A strong oxidative stress has also been revealed. Altogether, our data support that the fatty acids (C22:0, C24:0 and C26:0) as well as the fatty acid metabolism depending on the peroxisome might contribute to neurodegeneration leading to various types of dementia including AD

Newborn screening programs measure analyte levels in neonatal blood spots to identify individuals at high risk of disease. Carnitine and acylcarnitine levels are primary markers used in the detection of fatty acid oxidation disorders. These analytes may be influenced by certain pre/perinatal or newborn screening related factors. The primary objective of this study was to explore the association between these characteristics and levels of blood carnitines and acylcarnitines in the newborn population. The study was composed of two parts: a systematic review and a clinical database analysis of existing newborn screening data. The systematic review results suggested considerable variability across studies in the presence and directionality of associations between analyte levels and birth weight, gestational age, age at time of blood spot collection, type of sample, and storage time. Sex was not significantly associated with carnitine or acylcarnitine levels in neonatal blood. We identified a need to more fully investigate a potential interaction between gestational age and birth weight in regard to analyte levels. The secondary data analyses indicated a statistically significant relationship between analyte levels and all perinatal / infant and newborn screening related factors of interest, but effect sizes were generally small. The interaction between gestational age and birth weight was significant in all models; when further explored through graphical analysis with conditional means, extremely premature neonates stood out as having distinct analyte patterns in relation to birth weight. Variation in the ratio of total acylcarnitine to free carnitine was better accounted for by the perinatal and newborn factors than was variation in any individual carnitine or acylcarnitine, indicating that proportions of carnitine and acylcarnitines may be more important in understanding an individual’s metabolic functioning than individual analyte levels. A low proportion of variation was explained in all multivariate models, supporting the use of universal algorithms in newborn screening and suggesting the need for further large scale empirical research targeted at previously unaccounted for perinatal factors such as birth stress.

Newborn screening programs measure analyte levels in neonatal blood spots to identify individuals at high risk of disease. Carnitine and acylcarnitine levels are primary markers used in the detection of fatty acid oxidation disorders. These analytes may be influenced by certain pre/perinatal or newborn screening related factors. The primary objective of this study was to explore the association between these characteristics and levels of blood carnitines and acylcarnitines in the newborn population. The study was composed of two parts: a systematic review and a clinical database analysis of existing newborn screening data. The systematic review results suggested considerable variability across studies in the presence and directionality of associations between analyte levels and birth weight, gestational age, age at time of blood spot collection, type of sample, and storage time. Sex was not significantly associated with carnitine or acylcarnitine levels in neonatal blood. We identified a need to more fully investigate a potential interaction between gestational age and birth weight in regard to analyte levels. The secondary data analyses indicated a statistically significant relationship between analyte levels and all perinatal / infant and newborn screening related factors of interest, but effect sizes were generally small. The interaction between gestational age and birth weight was significant in all models; when further explored through graphical analysis with conditional means, extremely premature neonates stood out as having distinct analyte patterns in relation to birth weight. Variation in the ratio of total acylcarnitine to free carnitine was better accounted for by the perinatal and newborn factors than was variation in any individual carnitine or acylcarnitine, indicating that proportions of carnitine and acylcarnitines may be more important in understanding an individual’s metabolic functioning than individual analyte levels. A low proportion of variation was explained in all multivariate models, supporting the use of universal algorithms in newborn screening and suggesting the need for further large scale empirical research targeted at previously unaccounted for perinatal factors such as birth stress.

Newborn screening programs measure analyte levels in neonatal blood spots to identify individuals at high risk of disease. Carnitine and acylcarnitine levels are primary markers used in the detection of fatty acid oxidation disorders. These analytes may be influenced by certain pre/perinatal or newborn screening related factors. The primary objective of this study was to explore the association between these characteristics and levels of blood carnitines and acylcarnitines in the newborn population. The study was composed of two parts: a systematic review and a clinical database analysis of existing newborn screening data. The systematic review results suggested considerable variability across studies in the presence and directionality of associations between analyte levels and birth weight, gestational age, age at time of blood spot collection, type of sample, and storage time. Sex was not significantly associated with carnitine or acylcarnitine levels in neonatal blood. We identified a need to more fully investigate a potential interaction between gestational age and birth weight in regard to analyte levels. The secondary data analyses indicated a statistically significant relationship between analyte levels and all perinatal / infant and newborn screening related factors of interest, but effect sizes were generally small. The interaction between gestational age and birth weight was significant in all models; when further explored through graphical analysis with conditional means, extremely premature neonates stood out as having distinct analyte patterns in relation to birth weight. Variation in the ratio of total acylcarnitine to free carnitine was better accounted for by the perinatal and newborn factors than was variation in any individual carnitine or acylcarnitine, indicating that proportions of carnitine and acylcarnitines may be more important in understanding an individual’s metabolic functioning than individual analyte levels. A low proportion of variation was explained in all multivariate models, supporting the use of universal algorithms in newborn screening and suggesting the need for further large scale empirical research targeted at previously unaccounted for perinatal factors such as birth stress.

Tesis por compendio / [ES] El rápido crecimiento de la acuicultura ha generado una serie de problemas relacionados con la disponibilidad de ingredientes marinos esenciales en la alimentación de peces, debido a su alto contenido en ácidos grasos poliinsaturados de cadena larga (LC-PUFAs) omega-3. Una estrategia altamente innovadora para la obtención de nuevos ingredientes ricos en LC-PUFAs, consiste en el cultivo intensivo de organismos que sean capaces de producirlos a partir de fuentes que carecen de éstos, como son los subproductos de industrias agroalimentarias. Este enfoque requiere entender la capacidad biosintética del organismo en cuestión, y cómo ésta se puede modular para aumentar la acumulación de estos compuestos. Esta Tesis Doctoral plantea una serie de estudios dirigidos a esclarecer el potencial de los gamáridos para aplicar esta estrategia. La biosíntesis de LC-PUFAs en animales requiere de la acción coordinada de enzimas elongasas y desaturasas, implicadas en la conversión de ácidos grasos relativamente cortos y poco insaturados, en LC-PUFAs de alto valor nutricional. Así pues, esta Tesis Doctoral ha investigado, por un lado, la presencia y la actividad de genes involucrados en la biosíntesis de LC-PUFAs en gamáridos tanto marinos como dulceacuícolas. Por otro lado, ha estudiado cómo diferentes dietas y temperaturas afectan al metabolismo de ácidos grasos, crecimiento y supervivencia, en el gamárido marino Gammarus locusta, tanto a nivel fisiológico y composicional, como a nivel molecular. Los resultados de la primera parte demuestran que los gamáridos tienen varias elongasas, pero carecen de desaturasas. Se identificaron tres tipos de elongasas (elovl4, elovl6, y elovl1/7-like) en el gamárido marino Echinogammarus marinus, siendo elovl4 y elovl1/7-like clave para la elongación de LC-PUFAs. Este mismo patrón de elongasas se repite también para los gamáridos dulceacuícolas. Sorprendentemente, se han encontrado desaturasas front-end (fed), methyl-end (wx-des), y una elongasa del tipo Elovl2/5 únicamente en transcriptomas de gamáridos dulceacuícolas. Posteriores análisis moleculares y filogenéticos han podido determinar que estas secuencias fed, wx-des, y elovl2/5 son propias de rotíferos bdeloideos, epibiontes de gamáridos dulceacuícolas. Estos hallazgos, más allá de apuntar el potencial biosintético de los rotíferos bdeloideos, revela una relación constante entre éstos y los gamáridos en ecosistemas dulceacuícolas. La segunda parte de la Tesis analiza cómo dieta y temperatura modulan el metabolismo de ácidos grasos, crecimiento y supervivencia en Gammarus locusta. Los resultados han mostrado que G. locusta experimenta un mayor crecimiento, aunque también mayores tasas de mortalidad, cuando se cultiva a temperaturas elevadas. La mortalidad en G. locusta también aumenta cuando este se alimenta con una dieta rica en ácidos grasos saturados (SFAs) y carente de LC-PUFAs. Los perfiles de ácidos grasos en gamáridos reflejan las dietas consumidas, independientemente de la temperatura; aunque cabe destacar que los gamáridos alimentados con dietas carentes de LC-PUFAs conservan niveles apreciables de estos compuestos en sus lípidos corporales. A nivel molecular, una dieta sin LC-PUFAs y rica en SFAs disminuye el catabolismo de ácidos grasos y favorece su acumulación modulando la expresión de genes involucrados en estos procesos. Además, estas mismas condiciones afectan negativamente el desarrollo y supervivencia al influir en genes relacionados con el ciclo de muda. Además, se ha observado que temperaturas altas aceleran el desarrollo e incrementan la mortalidad. Según estos resultados, puede concluirse que las temperaturas elevadas y dietas carentes de LC-PUFAs no son adecuadas para el cultivo de G. locusta cuando el objetivo final es la obtención de biomasa rica en estos compuestos, ya que dichas condiciones afectan negativamente al perfil nutricional del animal y a su supervivencia. / [CA] El ràpid creixement de l'aqüicultura ha generat una sèrie de problemes relacionats amb la disponibilitat d'ingredients marins essencials en l'alimentació de peixos, a causa del seu alt contingut en àcids grassos poliinsaturats de cadena llarga (LC-PUFAs) omega-3. Una estratègia altament innovadora per a l'obtenció de nous ingredients rics en LC-PUFAs, consistix en el cultiu intensiu d'organismes que siguen capaços de produir-los a partir de fonts que no els ténen, com són els subproductes d'indústries agroalimentàries. Aquesta estratègia requerix entendre la capacitat biosintètica de l'organisme en qüestió, i com aquesta es pot modular per a augmentar l'acumulació d'estos compostos. Esta Tesi Doctoral planteja una sèrie d'estudis dirigits a esclarir el potencial dels gammàrids per a aplicar esta estratègia. La biosíntesi de LC-PUFAs en animals requerix de l'acció coordinada d'enzims elongases i desaturases, implicats en la conversió d'àcids grassos relativament curts i poc insaturats, en LC-PUFAs d'alt valor nutricional. Així doncs, esta Tesi Doctoral ha investigat, d'una banda, la presència i l'activitat de gens involucrats en la biosíntesi de LC-PUFAs en gammàrids tant marins com dulciaqüícoles. D'altra banda, ha estudiat com diferents dietes i temperatures afecten el metabolisme d'àcids grassos, creixement i supervivència, en el gammàrid marí Gammarus locusta, tant a nivell fisiològic i composicional, com a nivell molecular. Els resultats de la primera part demostren que els gammàrids ténen diverses elongases, però manquen de desaturases. Es van identificar tres tipus d'elongases (elovl4, elovl6, i elovl1/7-like) en el gammàrid marí Echinogammarus marinus, sent elovl4 i elovl1/7-like clau per a l'elongació de LC-PUFAs. Este mateix patró d'elongases es repetix també per als gammàrids dulciaqüícoles. Sorprenentment, s'han trobat desaturases front-end (fed), methyl-end (wx-des), i una elongasa del tipus Elovl2/5 únicament en transcriptomes de gammàrids dulciaqüícoles. Posteriors anàlisis moleculars i filogenètics han pogut determinar que estes seqüències fed, wx-des, i elovl2/5 són pròpies de rotífers bdeloides, epibionts de gammàrids dulciaqüícoles. Estes troballes, més enllà d'apuntar el potencial biosintètic dels rotífers bdeloides, revela una relació constant entre estos i els gammàrids en ecosistemes dulciaqüícoles. La segona part de la Tesi analitza com dieta i temperatura modulen el metabolisme d'àcids grassos, creixement i supervivència en Gammarus locusta. Els resultats han mostrat que G. locusta experimenta un major creixement, encara que també majors taxes de mortalitat, quan es cultiva a temperatures elevades. La mortalitat en G. locusta també augmenta quan este s'alimenta amb una dieta rica en àcids grassos saturats (SFAs) i sense LC-PUFAs. Els perfils d'àcids grassos en gammàrids reflectixen les dietes consumides, independentment de la temperatura; encara que cal destacar que els gamàrids alimentats amb dietes mancants de LC-PUFAs conserven nivells apreciables d'estos compostos en els seus lípids corporals. A nivell molecular, una dieta sense LC-PUFAs i rica en SFAs disminuïx el catabolisme d'àcids grassos i afavorix la seua acumulació modulant l'expressió de gens involucrats en estos processos. A més, estes mateixes condicions afecten negativament el desenvolupament i supervivència al influir en gens relacionats amb el cicle de muda. A més, s'ha observat que temperatures altes acceleren el desenvolupament i incrementen la mortalitat. Segons estos resultats, pot concloure's que les temperatures elevades i dietes mancants de LC-PUFAs no són adequades per al cultiu de G. locusta quan l'objectiu final és l'obtenció de biomassa rica en estos compostos, ja que estes condicions afecten negativament el perfil nutricional de l'animal i a la seua supervivència. / [EN] The rapid growth of aquaculture has generated a series of problems related to the availability of essential marine ingredients in fish feed, due to their high content of omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs). A highly innovative strategy for obtaining new ingredients rich in LC-PUFAs relies on the intensive culture of organisms that are capable of producing LC-PUFAs from sources that lack them, such as the by-products of agri-food industries. This approach requires understanding the biosynthetic capacity of the organism, and how this can be modulated to increase the accumulation of these compounds. This Doctoral Thesis proposes a series of studies aimed at clarifying the potential of gammarids to apply this strategy. LC-PUFA biosynthesis requires the coordinated action of elongase and desaturase enzymes, involved in the conversion of relatively short and poorly unsaturated fatty acids into LC-PUFAs of high nutritional value. Thus, this Doctoral Thesis has investigated, on one hand, the presence and activity of genes involved in the LC-PUFAs biosynthesis in both marine and freshwater gammarids. On the other hand, we have studied how different diets and temperatures affect fatty acid metabolism, growth and survival, in the marine gammarid Gammarus locusta, both at a physiological and compositional level, and at a molecular level. The results of the first part demonstrate that gammarids have several elongases, but lack desaturases. Three types of elongases (elovl4, elovl6, and elovl1/7-like) were identified in the marine gammarid Echinogammarus marinus, being elovl4 and elovl1/7-like key for LC-PUFA elongation. This same pattern of elongases is also present in their freshwater counterparts. Surprisingly, front-end desaturases (fed), methyl-end (wx-des), and an Elovl2/5-type elongase have been found only in transcriptomes built from freshwater gammarids. Subsequent molecular and phylogenetic analyses have been able to determine that these fed, wx-des, and elovl2/5 sequences are typical of bdelloid rotifers, which are epibionts of freshwater gammarids. These findings, beyond pointing out the biosynthetic potential of bdelloid rotifers, reveal a constant relationship between them and gammarids in freshwater ecosystems. The second part of the Thesis focuses on how diet and temperature modulate fatty acid metabolism, growth and survival in Gammarus locusta. The results have shown that G. locusta experiences greater growth, but also higher mortality rates, when grown at higher temperatures. Mortality in G. locusta also increases when it is fed with a diet rich in saturated fatty acids (SFAs) and lacking LC-PUFAs. Fatty acid profiles in gammarids reflect the diets consumed, regardless of temperature; although it is worth noting that gammarids fed with diets lacking LC-PUFAs still show levels of these compounds in their body lipids. At a molecular level, a diet lacking LC-PUFAs and rich in SFAs decreases the catabolism of fatty acids and enhances their accumulation by modulating the expression of genes involved in these processes. Furthermore, these same conditions negatively affect development and survival by influencing genes related to the molting cycle. In addition, it has been observed that higher temperatures accelerate development and increase mortality. According to these results, it can be concluded that higher temperatures and diets lacking LC-PUFAs are not suitable for the culture of G. locusta when the final outcome is to obtain a biomass rich in these compounds, since these conditions negatively affect the nutritional profile of the animal and its survival. / This research was supported by the ERA-NET BlueBio COFUND Project SIDESTREAM (Grant ID 68), co-funded through national funds provided by the Agencia Estatal de Investigación, Spain, grant no. PCI2020-111960/MCIN/AEI/10.13039/501100011033, the German Federal Ministry of Education and Research (BMBF), FKZ161B0950B, and the Fundação para a Ciência e a Tecnologia, Por- tugal (BLUEBIO/0005/2019). Additional funding was received through the project IMPROMEGA Agencia Española de Investigación, Spain, grant no. RTI2018-095119-B-100, MCIU/AEI/FEDER/UE/ MCIN/AEI/10.13039/501100011033/ and FEDER ‘A way to make Europe / Ribes Navarro, A. (2024). Biosíntesis de ácidos grasos poliinsaturados de cadena larga en gamáridos [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/207006 / Compendio