Tesis Doctorals - Facultat - Farmàcia i Ciències de l'Alimentació

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Computational Design and Redesign of Hydrolases for Biotechnological Applications
(Universitat de Barcelona, 2026-02-06) Robles Martín, Ana; Guallar i Tasies, Víctor; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Hydrolases, a versatile class of enzymes, play a pivotal role in numerous biotechnological applications, including waste recycling and improved laundry efficiency in the detergent industry. Recent advances in computational approaches have revolutionized the design and optimization of these enzymes, enabling precise tuning of their activity, and substrate specificity. This thesis highlights the impact of molecular modeling and structure-guided strategies in engineering hydrolases, focusing on both the fine-tuning of natural scaffolds and the creation of de novo catalytic architectures. A metagenomic lipase, LipMRD9, was identified as a dual lipase/PETase and shown to rely on a key residue for productive PET hydrolysis. Guided by physics-based simulations and energy landscape exploration, LipMRD9 was redesigned to yield variants with up to threefold higher PET activity while retaining lipase function. To transcend the limitations of soluble enzymes, pore-forming proteins were engineered into “porezymes” by embedding artificial Ser–His–Asp/Glu catalytic triads within their lumens. These catalytic nanopores displayed hydrolytic activity against PET nanoparticles surpassing benchmark hydrolases under mesophilic conditions, establishing them as a novel class of catalytic pores. Automated computational pipelines extended this principle to large pore scaffolds such as pneumolysin and 𝛼-hemolysin, demonstrating scalability and potential for multisite catalysis. By integrating structural biology, pluriZyme engineering methodologies, and advanced computational design, this work provides complementary solutions for PET degradation and sets the stage for sustainable, cost-effective applications in industrial biotechnology. Future directions emphasize the convergence of computational design with experimental validation to fully unlock the potential of hydrolases in addressing global environmental and industrial challenges.
Potencial bioestimulante de nuevas cepas del género Pararhizobium que promueven la tolerancia al estrés abiótico en plantas
(Universitat de Barcelona, 2025-01-15) Díaz Narváez, Lucía Candelaria; Alcázar Hernández, Rubén; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[spa] [spa] La agricultura moderna enfrenta desafíos crecientes debido a la incidencia de factores abióticos, como sequía y temperaturas extremas, que afectan la productividad y la seguridad alimentaria global. En este contexto, las rizobacterias promotoras del crecimiento vegetal (PGPR) se presentan como una estrategia sostenible para mejorar la resiliencia de los cultivos mediante la síntesis de fitohormonas, la movilización de nutrientes y la inducción de mecanismos de tolerancia al estrés. Esta tesis doctoral aporta un enfoque integral que combina una caracterización taxonómica, genómica, bioquímica, fisiológica y molecular de dos cepas de Pararhizobium sp., 44 y 128, y su capacidad para promover crecimiento y tolerancia a estrés abiótico en tomate (Solanum lycopersicum L.), un cultivo de alto interés económico y modelo experimental. Los resultados representan un avance significativo en el conocimiento de PGPR poco explorados y su aplicación en la agricultura resiliente al cambio climático. Los resultados demostraron que ambas cepas constituyen una nueva especie dentro del género Pararhizobium, diferenciada claramente de otras especies afines mediante análisis morfofisiológicos y genómicos. Su genoma revela un repertorio funcional asociado a colonización, producción de fitohormonas, metabolismo de poliaminas y tolerancia al estrés oxidativo, mientras que ensayos in vitro confirmaron su capacidad para promover el crecimiento vegetal y mitigar el daño por estrés osmótico, incluyendo modificaciones adaptativas en la arquitectura radicular. Se han identificado genes clave relacionados con la producción de enzimas como fosfatasas y glucosidasas, que contribuyen a la disponibilidad de nutrientes y adaptación al estrés, fortaleciendo el potencial bioestimulante de estas cepas. La inoculación con estas cepas induce tolerancia al frío y a la sequía en plantas de tomate, mediante un mecanismo integral de bioestimulación que combina señales hormonales, regulación del metabolismo de poliaminas y activación de sistemas antioxidantes. Las plantas inoculadas presentaron mayor supervivencia, mejor retención hídrica, reducción del daño celular y activación de enzimas antioxidantes como superóxido dismutasa (SOD), catalasa (CAT) y ascorbato peroxidasa (APX). A nivel molecular, se observó la activación de rutas transcripcionales clave, como la constituida por la cascada de señalización ICE1–CBF–COR, y la modulación de genes de biosíntesis y catabolismo de poliaminas, así como genes reguladores del estrés, lo que evidencia un estado de priming que prepara a la planta para responder de una manera eficiente a condiciones climáticas adversas. Estos hallazgos proporcionan una evidencia robusta de la integración de las respuestas fisiológicas, bioquímicas y genéticas mediadas por los PGPR, lo que representa un aporte novedoso sobre los estudios de la interacción planta-microorganismo. Además, las cepas promovieron ajustes estomáticos y metabólicos que permitieron conservar la eficiencia fotosintética y optimizaron la respuesta al déficit hídrico, sugiriendo un efecto preventivo frente a la sequía. Estos hallazgos respaldan la potencial aplicación de las cepas Pararhizobium sp. 44 y 128 como bioinoculantes específicos, contribuyendo a estrategias de agricultura sostenible y resiliente al cambio climático. En resumen, los resultados obtenidos en esta investigación presentan un alto potencial de transferencia hacia el desarrollo de nuevos productos bioestimulantes, orientados a la protección de cultivos frente a distintos tipos de estrés abiótico y a la mejora tanto de la producción como de la calidad del fruto en plantas de tomate.
Study of metabolic adaptations in neurological disease in the search of new therapeutical strategies
(Universitat de Barcelona, 2025-12-15) Sai Prashanth, Santhapuri; Cascante i Serratosa, Marta; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Neurodegenerative diseases, such as Huntington’s disease (HD) and Alzheimer’s disease (AD), are characterized by progressive neuronal dysfunction and complex molecular alterations, among which metabolic dysregulation plays a central role in their pathogenesis. Although HD is a monogenic disorder caused by CAG trinucleotide repeat expansion in exon 1 of the huntingtin (HTT) gene, its downstream metabolic consequences remain unclear. In contrast, AD has a multifactorial etiology, and metabolic alterations are increasingly recognized as key contributors to its progression. Despite advances in metabolomics, there is a critical need for deeper mechanistic insights and improved analytical strategies to identify robust metabolic signatures and potential therapeutic targets for both diseases. This thesis addresses the challenging metabolic framework through two complementary objectives. First, it aims to identify and visualize metabolomic signatures in Alzheimer’s disease using machine learning, applying Generative Topographic Mapping (GTM) to large-scale targeted metabolomic datasets from human biofluids and brain tissue. The goal of this study was to discover robust biomarkers and gain insights into disease-associated metabolic disruptions. Second, it seeks to characterize metabolic alterations in a cellular model of Huntington’s disease by integrating targeted metabolomics, transcriptomics, and functional bioenergetic profiling to identify genotype-specific metabolic vulnerabilities and reconstruct a genome-scale metabolic model (GSMM) of HD. In the first chapter, a novel multidimensional metabolomics analysis was performed using data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the AD Knowledge Portal. GTM, an unsupervised fuzzy logic-based dimensionality reduction technique, was applied to visualize the metabolomic landscape of AD. The dataset included the concentration levels of 182 metabolites per patient, and a metabolite selection procedure was implemented to identify the minimal set of relevant compounds capable of capturing AD-specific signatures. The resulting GTM maps revealed a relatively clear separation between patients with AD and cognitively normal (CN) individuals, comparable to the performance of supervised machine learning models, such as Support Vector Machines (SVM), but with enhanced interpretability. The key metabolites identified were glutamate, glutamine, arginine, ornithine, putrescine, spermidine, histidine, histamine, asparagine, aspartate, lysine, valine, phenylalanine, tryptophan, and serotonin. These compounds are involved in neurotransmitter cycling, energy metabolism, and polyamine regulation, suggesting that dysregulation contributes to the pathophysiology of AD. This study also highlighted significant inter-individual variability, known as the “singleton problem”, which limits the generalizability of the biomarker findings. The differences between the cross-validation and full dataset performance further underscore the need for larger, longitudinal, and multi-ethnic cohorts to validate metabolomic biomarkers. Nonetheless, the results support the potential of metabolomics and machine learning for the early diagnosis and patient stratification of AD. The second chapter focuses on Huntington’s disease and presents a comprehensive multi-omics investigation of striatal-derived neuronal progenitor cells expressing mutant huntingtin (STHdh-Q111/Q111) compared to wild-type control (STHdh-Q7/Q7) cells. This approach integrates extracellular flux measurements (OCR and ECAR), targeted metabolomics, transcriptomic analysis, and GSMM reconstruction to define the metabolic phenotype associated with mutant huntingtin expression. This study revealed marked metabolic reprogramming in mutant cells, characterized by impaired mitochondrial respiratory function, enhanced glycolytic flux, and activation of the hexosamine biosynthetic pathway. These changes indicate altered carbon flux and stress adaptation mechanisms. Disruptions in amino acid, polyamine, and lipid metabolism were also observed, with altered levels of glutamine, arginine, ornithine, putrescine, and spermidine. Transcriptomic data confirmed the dysregulation of genes involved in redox balance, lipid biosynthesis, and energy homeostasis. GSMM analysis identified subsystem-specific vulnerabilities, supporting a model in which mutant huntingtin triggers metabolic perturbations that compromise the cellular homeostasis. These findings provide a detailed cellular metabolic landscape of HD and identify key metabolic vulnerabilities that may inform future therapeutic strategies targeting energy homeostasis and metabolic resilience in HD. The conclusions of this thesis reinforce the central role of metabolism in neurodegenerative diseases and demonstrate the value of combining experimental and computational approaches to study metabolism. In AD, GTM-based analysis has enabled the identification of robust metabolic signatures and provided a framework for biomarker discovery, while highlighting the need for methodological rigor and cohort diversity. In HD, multi-omics integration has revealed coordinated metabolic reprogramming underlying bioenergetic deficits and identified actionable metabolic nodes for therapeutic intervention. Together, these findings contribute to a deeper mechanistic understanding of neurodegeneration and support the development of metabolism-based diagnostic and therapeutic strategies for neurodegenerative diseases. The integration of machine learning with metabolomics and systems biology offers promising avenues for future research and clinical translation in the field of neurodegenerative diseases.
Estudis estructurals i funcionals d’un factor repressor nuclear amb un rol diferenciat al mitocondri
(Universitat de Barcelona, 2025-12-16) Oliver Turro, Nord; Solà Vilarrubias, Maria; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[cat] La funció mitocondrial depèn d’una importació proteica eficient: la majoria de les proteïnes mitocondrials es sintetitzen al citosol i s’han d’importar de manera ordenada per garantir l’activitat respiratòria, la integritat genòmica i la supervivència cel·lular. Quan aquesta importació falla, s’activen mecanismes d’adaptació per preservar l’homeòstasi mitocondrial. A Saccharomyces cerevisiae, s’ha descobert que el factor de transcripció ROX1 participa en una d’aquestes respostes primerenques a l’estrès mitocondrial. En condicions normals, ROX1 actua al nucli com a repressor de gens hipòxics, a través de la seva unió a promotors específics i la interacció amb el complexe corepressor Ssn6-Tup1. Tanmateix, quan s’inhibeix l’activitat de la proteasa mitocondrial MPP (Mitochondrial Processing Peptidase) i s’acumulen precursors no processats al mitocondri, ROX1 canvia de localització: abandona el nucli i es redirigeix cap a la matriu mitocondrial, on contribueix a estabilitzar el DNA mitocondrial (mtDNA) i a mantenir la funció oxidativa. El treball recent de la nostra colaboradora (Poveda-Huertes et al., 2020) ha demostrat que és possible modular tèrmicament l’activitat de MPP per induir un estat previ a la resposta mitocondrial a proteines desplegades (Unfolded Protein Response mitocondrial, UPRmt). En aquest context, ROX1 ja exerceix una funció activa en aquest estat primerenc i reversible d’estrès mitocondrial, suggerint l’existència d’una fase d’alerta cel·lular abans de l’activació de respostes més costoses com la UPRmt. Aquesta hipòtesi obre la possibilitat que el llevat pugui oferir un model útil per estudiar mecanismes de detecció precoç d’estrès mitocondrial conservats evolutivament en altres organismes. Aquesta tesi se centra en desxifrar com l’arquitectura estructural de ROX1 permet la seva transició entre compartiments cel·lulars i funcions diferents. Mitjançant tècniques de bioquímica, biofísica i biologia estructural, s’analitzen les propietats conformacionals de ROX1, la seva capacitat d’unió a DNA, i els elements estructurals que podrien explicar la seva localització mitocondrial en condicions d’estrès. El capítol introductori ofereix el marc cel·lular i molecular que contextualitza aquest estudi: en primer lloc, es revisa la fisiologia mitocondrial i la importància del processament proteic; tot seguit, es descriu el paper conegut de ROX1 i les seves característiques estructurals. Finalment, es formulen la hipòtesi i els objectius específics del treball.
Mechanobiology and ovarian functionalism: Pathophysiological and therapeutic implications in patients with low ovarian reserve and premature ovarian failure
(Universitat de Barcelona, 2025-12-18) Méndez Justo, Marta; Fabregues Gasol, Francisco; Cívico Vallejos, Maria Salvadora; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] The present doctoral thesis falls within the emerging field of mechanobiology, a discipline focused on studying the mechanisms by which cells detect and process information related to the physical properties of their environment, as well as on characterizing the biological responses that these conditions trigger. Although recent publications have highlighted the relevance of this area in fields such as oncology or cardiology, its potential application in the study of the female reproductive system—and, in particular, of the ovary, its functionality, and follicular depletion throughout the female reproductive lifespan—remains only minimally explored. Based on recent scientific evidence pointing to a close relationship between the biomechanical properties of the ovary, folliculogenesis, and the structural modifications associated with both specific pathologies and physiological aging, this work aims primarily to characterize the biomechanics of the ovarian cortex in various clinically relevant scenarios. In a first study, the biomechanical properties of the ovarian cortex are evaluated in patients with premature ovarian insufficiency undergoing the Drug-Free IVA (In Vitro Activation) procedure. The second study, developed in the context of fertility preservation, examines the impact of current human ovarian cortex cryopreservation protocols on tissue stiffness. Finally, the third study analyzes the effect of two innovative techniques for ovarian follicular reactivation: surgical activation through WOLI (Whole Ovary Laparoscopic Incision) and intraovarian administration of platelet-rich plasma—on follicular activation and ovarian biomechanics, using an experimental sheep model. All studies have been carried out using atomic force microscopy, considered the reference technique for the biomechanical characterization of tissues and extracellular matrix. The results obtained aim to provide new data contributing to the advancement of knowledge in reproductive mechanobiology and to facilitate its clinical translation.
Regulación de la homeostasis del hierro durante infección por Magnaporthe oryzae y función de OsNramp6 (Natural resistance-associated macrophage protein 6) en la inmunidad innata y tolerancia a salinidad en arroz
(Universitat de Barcelona, 2025-12-01) Mateluna Cuadra, Roberto Andrés; San Segundo, Blanca; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[spa] El hierro (Fe) es un nutriente esencial para el crecimiento y desarrollo de las plantas. Sin embargo, el exceso de Fe en las plantas puede causar toxicidad. La acumulación de Fe favorece la producción de especies reactivas de oxígeno (ROS) a través de reacciones redox entre Fe+3 y Fe+2 (reacciones de Haber-Weiss y Fenton). En presencia de H2O2, el Fe+2 se oxida a Fe+3, formando radicales altamente reactivos. Las especies ROS se producen como un producto normal del metabolismo en plantas y también son cruciales en la respuesta a estreses de tipo abiótico y biótico. En la resistencia de las plantas a enfermedades, las ROS funcionan como un compuesto antimicrobiano, así como moléculas de señalización para la inducción de respuestas inmunitarias. Si bien una producción controlada de ROS puede ser beneficiosa para la planta, su acumulación puede causar daños irreversibles en la célula vegetal a través de la oxidación de biomoléculas, incluyendo los lípidos de membrana, lo que puede conducir a muerte celular. En este trabajo, se ha demostrado que las plantas de arroz tratadas con una concentración alta de Fe son más resistentes a la infección por el hongo Magnaporthe oryzae, patógeno responsable del tizón del arroz (también conocida como piricularia; blast, en inglés), una de las enfermedades fúngicas más devastadoras del arroz cultivado a nivel mundial. Se investigaron los mecanismos por los cuales el Fe regula la resistencia a la infección por M. oryzae en arroz, centrándose en el estrés oxidativo. Estos estudios revelaron una mayor acumulación de peróxido de hidrógeno (H2O2) en plantas tratadas con una concentración alta de Fe durante la infección con M. oryzae. El aumento en H2O2 va acompañado de una mayor acumulación del radical superóxido (O₂-). El tratamiento con alto Fe también resulta en mayor peroxidación de lípidos. Estos resultados, en combinación con los obtenidos mediante el uso del inhibidor de ferroptosis Fer-1, sugieren que mayor resistencia a la infección por M. oryzae en plantas tratadas con Fe viene determinada por un proceso de ferroptosis. Por otro lado, confirmando resultados previamente reportados en el laboratorio, se ha comprobado que el gen OsNramp6 (Os01g31870) que codifica para un transportador de hierro tiene una función importante en la resistencia a M. oryzae en plantas de arroz. La caracterización funcional del promotor de OsNramp6 mostró actividad de este promotor en células del mesófilo en hojas de plántulas de arroz, y su actividad aumenta en respuesta al tratamiento con alta concentración de Fe. El gen OsNramp6 produce múltiples variantes de su ARN mensajero a través de procesamiento alternativo (ocho isoformas de tránscritos). El tránscrito primario da lugar a la proteína completa (l-NRAMP6; long-NRAMP6), mientras que la isoforma más corta genera una proteína truncada en su extremo C-terminal (s-NRAMP6 short-NRAMP6). Ambas proteínas, l-NRAMP6 y s-NRAMP6, son funcionales. En plantas transgénicas de arroz que expresan un gen fusión Nramp6-GFP, la proteína NRAMP6 se localizó en la membrana plasmática de células de arroz, tanto l-NRAMP6 como s-NRAMP6. Además, se ha comprobado que la mutación del gen OsNramp6 mediante la tecnología CRISPR/Cas9 confiere resistencia a la infección por M. oryzae. La resistencia a infección va acompañada de una mayor inducción en la expresión de genes que codifican para proteínas relacionadas con patogénesis (genes PR, Pathogenesis-Related) durante la infección. Las plantas editadas para OsNramp6 también presentan mayor tolerancia a salinidad en comparación con las plantas silvestres. El fenotipo de tolerancia a salinidad va acompañado de una menor acumulación de Na+ en las raíces. En resumen, estos resultados indican que la mutación sobre OsNramp6 mejora la resistencia a la infección por M. oryzae y la tolerancia a salinidad en plantas de arroz. En su conjunto, los resultados obtenidos en este estudio demuestran la relevancia que tiene el estado nutricional de la planta (particularmente Fe) en la resistencia a infección por patógenos y tolerancia a estrés salino en arroz.
Bio-based strategies on golf course construction and management: unravelling microbiota relevance in turf soil management
(Universitat de Barcelona, 2025-12-19) Giol Casanova, Xavier; Romanyà i Socoró, Joan; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Turfgrass represents a managed ecosystem where complex biological relationships between soil matrices, microbial populations, and plant communities create functioning ecological networks. A balanced integrative approach is required to reconcile demands for high quality turf play surfaces with long-term sustainable practices under Mediterranean conditions. At Golf de Pals, we combined field assessments on mature greens with a newly built USGA-style trial plot to: (i) identify environmental drivers of microbial diversity in mature greens; (ii) test a peat-replacement strategy (sand + biochar–compost) under reduced water and fertilizer inputs; (iii) adapt an integrative soil quality multifunctional index to compare management options; and (iv) evaluate biostimulants across contrasting rootzones structures. We integrated Bacterial (16S rRNA) and Fungal (ITS) metabarcoding, soil physic-chemical parameters, environmental monitoring and bioinformatics including multivariate statistical analysis. Hierarchical partitioning indicated that soil temperature and the availability of nitrogen and phosphorus were the dominant drivers of microbial diversity in mature greens. Agrostis stolonifera-dominant greens showed higher foliar N, P, K and enrichment in nitrifiers and Trichoderma, whereas Poa annua-dominant greens accumulated more nutrients in soil with saprotroph-rich fungi and stable-state bacterial assemblages. All mature greens had lower fungal (ITS)/ bacteria (16S) ratios versus natural soils. In the pilot trial, a sand + biochar–compost rootzone maintained turf quality comparable to sand–peat while reducing water irrigation and fertilization about 20% and 50% respectively over two years, improving water retention, CEC, and nutrient availability and yielding more modular microbial networks. A multidimensional soil quality index was adapted (Turf Soil Global Multifunctionality Index – TSGMI), integrating soil physical-chemical indicators, turf quality metrics, and microbial descriptors (abundance, diversity, and network structure). As a new composite index, its weighting sensitivity and broader applicability require testing across sites and seasons. Collectively, these findings support compost and biochar as effective peat alternatives in USGA sand-based putting-green rootzones, sustaining turf quality while reducing input demands and enhancing soil ecological resilience. Biostimulant responses were substrate-dependent and emerged only under a multidimensional index TSGMI. In sand–peat rootzones, biostimulant treatments produced statistically significant increases in turf–soil multifunctionality relative to the control; in sand–biochar–compost rootzones, where baseline multifunctionality was higher, responses were smaller and only one formulation (B2) achieved a significant gain. Turf Soil Global Multifunctionality Index provided a practical framework to benchmark greens, track seasonal programs, and identify inputs that add value versus redundancy. Overall, these results highlight the utility of integrative, driver-focused, and site-specific approaches for sustainable turf management in Mediterranean environments.
Evaluación nutricional en población pediátrica con Fenilcetonuria y otros Errores Innatos del Metabolismo de los Aminoácidos
(Universitat de Barcelona, 2025-12-19) García Arenas, Dolores; Urpí Sardà, Mireia; Ormazabal Herrero, Aida; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[spa] El primer estudio de esta tesis tuvo como objetivo analizar la composición nutricional de 250 productos especiales bajos en proteínas disponibles en España, comparándolos con sus equivalentes convencionales, y evaluar su impacto en la dieta y en el perfil bioquímico de 59 pacientes con distintos EIM. Se observó que los grupos de lácteos, carnes, pescados y huevos bajos en proteínas presentan mayores diferencias nutricionales, especialmente en el contenido de hidratos de carbono y grasas. Los pacientes con una ingesta elevada de lácteos bajos en proteínas (>5%) mostraron un mayor consumo de azúcares simples, grasas totales y saturadas, así como niveles plasmáticos más altos de colesterol total y lipoproteínas de baja densidad (LDL-C), lo que sugiere un posible impacto negativo sobre el perfil lipídico. El segundo estudio se centró en 62 pacientes con fenilcetonuria (PKU) de distintos fenotipos, comparados con 20 controles sanos, con el objetivo de evaluar el patrón dietético, el estado nutricional, la adherencia a la dieta mediterránea y la práctica de actividad física. Los pacientes con PKU clásica (cPKU), que requieren una mayor restricción proteica, presentaron una ingesta significativamente más alta de carbohidratos y azúcares, con mayor frecuencia en el consumo de dulces y son menos activos físicamente. Aunque el 90% de los pacientes mantenía un buen control metabólico, se observó una tendencia entre la ingesta de hidratos de carbono y el índice HOMA-IR (p=0.08), lo que podría indicar un futuro riesgo potencial de resistencia a la insulina. Además, los pacientes con dietas bajas en proteínas naturales mostraron niveles plasmáticos más altos de vitamina B12, ácido linoleico, ácido α-linolénico, ácido eicosapentaenoico y ácido docosahexaenoico, que estarían ligados al consumo de suplementos proteicos y, bajos de colesterol total y lipoproteínas de alta densidad (HDL-C), posiblemente relacionados con patrones dietéticos más vegetarianos y una posible interferencia de la fenilalanina en los mecanismos de síntesis de colesterol. Los resultados de esta tesis permiten identificar áreas clave en el abordaje nutricional de los errores innatos del metabolismo (EIM) de los aminoácidos. Si bien la dieta restringida en proteínas naturales y el uso de alimentos especiales bajos en proteínas son pilares fundamentales del tratamiento dietético, su impacto metabólico no debe subestimarse, debido a la asociación mostrada con un perfil lipídico alterado, caracterizado por niveles elevados de colesterol total y LDL-C. Sin embargo, en nuestra población con fenilcetonuria (PKU), donde la restricción proteica es más estricta, se observaron niveles más bajos de colesterol total y HDL-C. Esta aparente contradicción sugiere que, además de la dieta, deben considerarse otros factores inherentes a la enfermedad, como las alteraciones metabólicas inducidas por los niveles elevados de fenilalanina, que podrían influir en el metabolismo lipídico, Asimismo el alto consumo de carbohidratos y azúcares junto con una menor práctica de actividad física observada podría contribuir a un mayor riesgo de resistencia a la insulina, aunque los datos actuales solo muestran una tendencia. Por otro lado, los perfiles bioquímicos observados sugieren que el uso de los sustitutos proteicos en PKU , puede tener efectos beneficiosos en la ingesta de micronutrientes, lo que subraya su valor nutricional, aunque también podrían influir en parámetros lipídicos que requieren seguimiento clínico. Los hallazgos de esta investigación refuerzan la necesidad de un enfoque nutricional individualizado en los EIM, que contemple no solo la dieta, sino también el estilo de vida, el contexto clínico y los mecanismos fisiopatológicos propios de cada enfermedad. Este enfoque integral es esencial para optimizar el manejo metabólico y prevenir complicaciones asociadas.
Characterization and prognostic value of nutritional status, body composition, and smoking in patients with oropharyngeal cancer according to human papillomavirus (HPV) status
(Universitat de Barcelona, 2025-12-16) Choulli Amgait, Maryam; Mesía Nin, Ricard; Arribas Hortigüela, Lorena; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[cat] Antecedents: L’augment de la incidència del carcinoma escatós d’orofaringe (COF) relacionat amb el virus del papil·loma humà (VPH), juntament amb el seu pronòstic favorable, ha generat un interès creixent en la desescalada terapèutica. No obstant això, hi ha un subgrup important de pacients amb pitjor pronòstic que està poc caracteritzat, cosa que comporta la necessitat de nous biomarcadors que orientin la classificació i la gestió d’aquests pacients. Fins ara, la composició corporal i l’estat nutricional no s’han avaluat conjuntament com a marcadors pronòstics i/o predictius segons l’estat del VPH. Objectius: Els principals objectius d’aquesta tesi van ser: 1) explorar les característiques nutricionals i de composició corporal tant en estat basal com post-tractament en pacients amb COF positius i negatius per VPH, i 2) avaluar el valor pronòstic i predictiu del consum tabàquic, estat nutricional, composició corporal i biomarcadors inflamatoris segons la seva associació amb el VPH. Mètodes: La tesi comprèn un total de tres estudis. Dos d’ells, amb un disseny retrospectiu, exploren els canvis temporals (article 1) i les diferències geogràfiques (article 2) dels paràmetres nutricionals i de composició corporal en pacients amb COF. El tercer estudi conforma una cohort prospectiva multicèntrica (manuscrit 3) on s’identifiquen els predictors de resposta primerenca al tractament. La resposta es va classificar com a remissió completa (RC) o no completa (RNC) >3 mesos post-tractament. Les avaluacions basals van incloure antropometria, composició corporal mitjançant TC a nivell de L3, proves de rendiment funcional, biomarcadors inflamatoris sistèmics i diagnòstic nutricional amb el Patient-Generated Subjective Global Assessment (PG-SGA). Els arbres de classificació es van elaborar estratificats per estatus de VPH, incloent set predictors predefinits: edat, sexe, estatus tabàquic, Eastern Cooperative Oncology Group Performance Status (ECOG-PS), PG-SGA, modified Glasgow Prognostic Score (mGPS) i sarcopènia. Resultats: En l’article 1, de 70 pacients inclosos; els pacients VPH positius van presentar un índex de massa corporal (IMC) basal més alt (27,3 versus 21,9 kg/m²; p < 0,001) i un millor estat nutricional inicial (p = 0,023), però no es van observar diferències en l’índex de massa muscular esquelètica (SMI; p = 0,103) en comparació amb els pacients VPH negatius. Als 3 i 6 mesos post-tractament, ambdós grups van mostrar reduccions similars en SMI i en l’índex total de teixit adipós (TATI) (p > 0,05). L’estat del VPH no es va associar de manera independent amb els canvis en la composició corporal al llarg del temps (p = 0,624). En l’article 2, es van analitzar dades d’una cohort internacional agrupada de 442 pacients. Entre els VPH positius (n = 317), el 72,8% tenia sobrepès i/o obesitat, el 59,6% va presentar una pèrdua de pes mínima (WLG 0/1) i el 83,4% mostrava un SMI elevat. En canvi, el 61,5% dels pacients VPH negatius tenia un índex de massa corporal (IMC) normal i/o baix, el 50,8% va patir un grau de pèrdua de pes sever (WLG 3/4) i el 46,9% va presentar una disminució moderada o severa del SMI (p< 0,003). Cal destacar que es va observar una heterogeneïtat substancial dins de cada grup: el 35% dels VPH positius mostrava un WLG elevat i/o una depleció muscular moderada o severa, mentre que el 29% dels VPH negatius tenia perfils nutricionals favorables. L’estat VPH negatiu es va associar de manera independent amb una mortalitat més alta després d’ajustar per WLG, SMI, edat, estadiatge de la malaltia i tractament planificat (hazard ratio, HR 3,30; IC 95%, 2,17–5,02; p < 0,001). En el manuscrit 3, entre 97 pacients que van completar l’avaluació post-tractament, la desnutrició va ser el determinant més important de la resposta primerenca entre els pacients VPH positius. La RC es va aconseguir en el 74% dels pacients amb puntuacions <6 enfront del 33% amb ≥6 (AUC 0,683; sensibilitat 84%, especificitat 53%). En els VPH negatius, la RC es va associar principalment amb l’ECOG-PS i l’edat: tots els pacients amb ECOG-PS <1 van assolir RC, mentre que les taxes van disminuir al 73% en ECOG-PS 1 i ≥61 anys, al 43% en ECOG-PS 1 i <61 anys, i al 30% en ECOG-PS 2 (AUC 0,803; sensibilitat 69%, especificitat 83%). Conclusions: Els pacients amb COF presenten de manera consistent perfils clínics, nutricionals i de composició corporal diferents segons l’estat del VPH. Tot i que els pacients VPH positius estaven millor nodrits en el moment del diagnòstic, tant els grups VPH positius com els VPH negatius van experimentar un deteriorament nutricional similar al final del tractament. La desnutrició va emergir com el principal factor pronòstic, especialment en els pacients VPH positius, mentre que en els VPH negatius va predominar l’estat funcional. Aquests resultats posen de manifest la importància d’integrar l’avaluació nutricional en el maneig clínic dels pacients amb COF.
Physicochemical and biopharmaceutical properties of cryosprayed particulate lipid systems for oral liraglutide delivery
(Universitat de Barcelona, 2025-12-12) Carrie, Caroline; Prohens López, Rafael; Esposito, Pierandrea; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Oral delivery of peptides is an important challenge in the development of drug delivery systems as many peptides described as great therapeutic solutions exhibit poor absorption and permeability leading to low bioavailability. Liraglutide, a GLP-1 analog indicated in the treatment of type 2 diabetes, exists on the market as subcutaneous injection, causing issues in patient compliance and accessibility to the treatment. This thesis aimed to develop, using CryoXpand® technology, solid lipid liraglutide microparticles for oral administration with enhanced bioavailability. Liraglutide physicochemical characteristics were studied by studying its stability in solution at different pH and temperature conditions. Lipid formulations were developed using structuring agents, functional excipients and liraglutide solution, mixed into fine emulsions that resulted in solid lipid microparticles after cryospraying. Microparticles were characterized using optical microscopy, X-ray photoelectron spectroscopy and HPLC analysis and interactions between liraglutide and excipients were studied using tensiometer and fluorescence spectroscopy. In vitro performance of liraglutide microparticles was studied generating release profiles at gastric and intestinal pHs, liraglutide protection from enzymatic degradation and permeability across Caco-2 cells. Finally, in vivo studies were conducted on induced diabetes rats for pharmacodynamics and Wistar rats for pharmacokinetics information. Liraglutide solutions were shown to be stable under 37°C at pH range from 6.5 to 9 and were stable in the range of 37 to 58°C over short time periods corresponding to processing times. Cryosprayed formulations with CryoXpand® technology resulted in fine liraglutide microparticles, however some formulations showed homogeneity issues leading to lower drug loading in microparticles. Surface analysis showed a different liraglutide proportion in the surface layer of microparticles depending on the formulation. In vitro release studied showed an overall faster release of the peptide from microparticles at intestinal pH compared to acidic gastric pH and a different release profile among different formulations. Enzymatic degradation occurred on the liraglutide fraction released in the medium, while the lipid excipients seemed to protect a fraction of the peptide released and the fraction in the solid microparticle over the 5 to 10 minutes of release. Permeability studies on Caco-2 cells exhibited permeability enhancement in the presence of several excipients. Finally, in vivo studies demonstrated that liraglutide lipid microparticles have a positive effect on blood glucose levels and on the animal weight after oral and subcutaneous injection on one hand and sustained blood concentrations over 24 hours after oral administration of liraglutide cryosprayed microparticles. CryoXpand® technology allowed the production of lipid composite liraglutide microparticles with enhanced permeability and protection from enzymatic degradation. In vivo studies on optimized formulations showed promising biological activity on diabetic animals and although low, interesting bioavailability. However, manufacturing process lacks optimization to obtain consistent peptide loading and in vitro data must be completed to achieve bioavailability prediction. This work provides a base for the development of lipid-based GLP-1 microparticles for oral administration applying CryoXpand® technology. Continuous improvement of the early development of the latter is the key to achieve satisfying preclinical performance and further develop liraglutide microparticles for human use.
Ageing, metabolism and telomere modulation: the impact of physiological and nutritional factors
(Universitat de Barcelona, 2025-11-21) Torres Oteros, Daniel; Lamuela Raventós, Rosa Ma.; Relat Pardo, Joana; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Ageing is an intrinsic, cumulative, multifactorial and irreversible process influenced by both genetic and environmental factors. Telomere length (TL) emerges as a molecular marker associated with ageing and stands out for its relationship with cellular senescence and organismal health. This doctoral thesis explores how physiological and nutritional interventions can modulate metabolism and telomere maintenance, using both animal and human models. Specifically, it focuses on the role of hepatic fibroblast growth factor 21 (FGF21), the impact of maqui supplementation and the effects of peanut consumption on TL dynamics and metabolic health. The first study examined the long-term metabolic and telomeric effects of hepatic FGF21 depletion in 12-month-old female mice. Female knockout (FKO) mice lacking hepatic FGF21 exhibited lower body weight, enhanced glucose tolerance and longer telomeres in both the liver and subcutaneous adipose tissue compared to control mice. In the liver, the expression of genes involved to de novo lipogenesis were reduced in the FKO mice, while an upregulation of genes associated with fatty acid uptake and oxidation were seen in these animals. Hepatic transcriptomic analysis revealed a downregulation of genes associated with cytoskeletal organization and immune system, including a significant decrease in Chrna4 expression, which have seen to play a protective role against metabolic-associated steatohepatitis (MASH). These effects were sex-specific, as male FKO mice displayed a different metabolic profile. These results suggest a possible protective role of hepatic FGF21 depletion in females, although the underlying mechanisms are yet to be fully understood. In the second study, we assessed the effects of a 17-week supplementation with maqui berry, an anthocyanin-rich berry, in male mice fed either a standard chow or a high-fat diet (HFD). Maqui supplementation preserved liver telomere length regardless of diet and enhanced glucose tolerance. In animals subjected to HFD, maqui restored the expression of several liver cytokines and growth factors related to the senescence-associated secretory phenotype (SASP), indicating a regulatory effect. These findings support the potential of dietary anthocyanins to influence telomere biology and metabolic health, even under non-obesogenic conditions. The third study examined a sub-cohort of young, healthy participants from the ARISTOTLE clinical trial who consumed either skin-roasted peanuts (SRP), peanut butter, or a control based in peanut oil cream for six months. Only the SRP group showed a significant increase in salivary telomere length, along with positive correlations with intake of monounsaturated fatty acids (MUFA) and m-coumaric acid. The results suggest that whole peanut consumption may support telomere maintenance through bioactive compounds and fibre content, potentially mediated by gut microbiota activity and the production of short-chain fatty acids. Globally, this thesis demonstrates that both physiological and nutritional strategies have the capacity to influence telomere dynamics and metabolic homeostasis. The observed sex-specific effects, the importance of bioactive dietary components and the emerging role of the microbiota suggest that ageing research should adopt a multidimensional approach. These findings provide novel insights into the intricate relationship between metabolism and telomere biology, thus paving the way for the development of potential strategies that could promote healthy ageing.
Optimization of therapeutic options against multidrug resistant microorganisms
(Universitat de Barcelona, 2025-10-10) Puig Collderram, Berta; Prim Bosch, Núria; González Ruiz, Juan Ramón; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Antibiotic resistance has become a public health concern. Combining antibiotics is a strategy to overcome the limited therapeutic options against multidrug-resistant bacteria, including extensively-drug resistant (XDR) Pseudomonas aeruginosa and carbapenemase-producing Klebsiella pneumoniae (CP-KP). Time-kill curves (TK) are used to study antibiotic combinations, but the colony count method to obtain the results is time-consuming. A bioluminescent ATP assay to analyze the results of TKs would allow the implementation of studies of antibiotic combination in clinical microbiology laboratories. The combination of meropenem and amikacin is commonly used to empirically treat infections caused by Gram-negative bacilli, but the time of amikacin administration is not well stablished. Simultaneous and staggered schedules of this combination may have different clinical impacts. The main aims of this study were 1) to standardize and evaluate an ATP assay as an alternative to the conventional colony count method in TK studies of antibiotic combinations, and 2) to determine the optimal dosing schedule of meropenem plus amikacin against XDR P. aeruginosa and CP-KP by means of TK experiments. The ATP assay was performed using the GloMax®96 Microplate Luminometer (Promega) that measures bioluminescence in relative light units (RLU). Background, linearity and detection limit were determined to standardize this assay. Twenty-four-hour TKs were performed, and results were analyzed in parallel using the conventional cell count method and the ATP assay. The conventional method was used as gold standard to establish the breakpoints in the ATP method. Standardization was performed with P. aeruginosa, K. pneumoniae and Enterococcus faecium. Different dosing schedules of meropenem (MEM) and amikacin (AK) were tested against seven XDR P. aeruginosa and five CP-KP clinical isolates by 24-hour TKs. The antibiotic concentrations AK8 (8.17 mg/L) and MEM17 (17.71 mg/L) were assessed against all isolates. A higher dose of MEM32 (32 mg/L) was also assessed on all CP-KP isolates and four selected P. aeruginosa isolates with different mechanisms of resistance. A higher concentration of AK40 (40 mg/L) was evaluated against four P. aeruginosa with different amikacin minimum inhibitory concentrations (MIC), and against the two high-level amikacin-resistant CP-KP. Simultaneous schedules included both antibiotics at the start of the curve. In staggered schedules the second antibiotic was added two hours after the first antibiotic: AK after meropenem or conversely. Viable cell count (log CFU/ mL) was analysed at different times. The initial bacterial load reduction was evaluated for each dosing schedule. Neutral saline solution (NSS) showed wider linearity and a lower detection limit than Cation-adjusted Mueller Hinton (CA-MH) in the ATP assay. Therefore, NSS was established as washing/dilution medium. Relative light forming units (RLU) signal correlated with colony forming units (CFU) when the assay was performed within the linear range. Categorization of the pharmacodynamic parameters using the ATP assay was equivalent to the colony-count method in the TKs. The bactericidal effect and synergy breakpoints were 1.348 (sensitivity 93%, specificity 78.5%) and 0.9 (98% sensitivity, 88% specificity) log RLU/ml for P. aeruginosa, and 0.764 (sensitivity 100%, specificity 76%) and 2.95 (78.6% sensitivity, 100% specificity) log RLU/ml for K. pneumoniae, respectively. Simultaneous schedules of amikacin and meropenem caused an initial bacterial load reduction in most of the XDR P. aeruginosa and CP-KP isolates. Staggered schedules caused an initial bacterial load reduction when the concentration of the first antibiotic was above the MIC, regardless of the mechanism of resistance. Summing up, the ATP assay was useful to determine the effectiveness of antibiotic combinations in TKs. This method, less laborious and faster than the colony count method, could be more easily performed in clinical microbiology laboratories. According to our results, simultaneous dosing schedules of amikacin and meropenem should be of choice in empirical treatments when the antibiotic susceptibility results of the infectious agent are unknown.
Computational Strategies for Improving PET-Degrading Enzymes: From Atomistic Simulations to AI Stability Prediction
(Universitat de Barcelona, 2025-10-31) Di Pede, Stefania; ColizzI, Francesco; Bouvier, Guillaume; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Plastic pollution remains a critical environmental challenge, with polyethylene terephthalate (PET) being one of the most widely used and persistent plastics. Enzymatic PET recycling offers a promising route toward a circular economy, leveraging biocatalysts to depolymerize PET under mild conditions. However, key barriers remain, including enzyme instability at process-relevant temperatures, low depolymerization activity towards post-consumer PET and the resistance of crystalline PET regions to enzymatic attack. This thesis addresses these challenges through an integrated computational strategy combining atomistic molecular simulations and AI-guided protein stability design. First, extensive molecular dynamics simulations were employed to investigate PETase-PET interactions at atomic detail. We developed realistic PET oligomer models representing amorphous and crystalline states, capturing experimentally informed torsional preferences. By applying enhanced sampling techniques such as Hamiltonian Replica Exchange and well-tempered metadynamics, we quantified the energetic barriers associated with binding and catalysis on crystalline PET, revealing a ~50 kJ/mol penalty relative to amorphous PET. Additionally, simulations of different PETase variants highlighted the relationship between thermostability, active site integrity, and catalytic competence, offering atomistic explanations for experimental observations. Second, we developed PANDORA, an AI-based framework for predicting protein stability from sequence alone. Leveraging the Megascale dataset of folding free energies, PANDORA evolved through successive architectures, from one-hot encoded CNNs to graph neural networks and transformer-based embeddings, culminating in a hybrid model that integrates both sequence and structural information. Applied to PETase variants, PANDORA offered accurate ΔG predictions to complement stabilising mutation design. Together, these complementary approaches deliver mechanistic insights into the molecular determinants of PETase function and provide generalizable computational tools for enzyme engineering. By bridging molecular simulations and AI-based predictions, this work contributes to advancing biocatalytic PET recycling toward industrial feasibility, while also offering frameworks applicable to broader challenges in sustainable materials science and protein engineering.
Desarrollo y aplicación de una terapia leucocitaria autóloga para la nefropatia isquémica: un enfoque prometedor hacia la recuperación renal mediante modulación fenotípica y el análisis de mecanismes moleculares asociados
(Universitat de Barcelona, 2025-11-20) Torrico Ponce, Selene Cinthia; Hotter Corripio, Georgina; Játiva Jiménez, Soraya; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[spa] La nefropatía isquémica constituye una causa significativa de lesión renal aguda, una condición caracterizada por una elevada morbilidad y riesgo de progresión a enfermedad renal crónica. Ante la ausencia de terapias regenerativas efectivas, se plantea la necesidad de enfoques innovadores que modulen el microambiente renal y promuevan la reparación tisular. En las últimas décadas, el uso de terapias celulares ha ganado terreno como una alternativa prometedora para contrarrestar los procesos inflamatorios y degenerativos asociados a la lesión renal aguda. En este contexto, la presente investigación doctoral propone y desarrolla una estrategia basada en la administración de una fracción leucocitaria autóloga, obtenida a partir de células mononucleares de sangre periférica (PBMC), con potencial terapéutico en un modelo experimental de nefropatía isquémica. Para ello se utilizó un modelo murino de isquemia renal bilateral con administración intravenosa de PBMC (A/R) tras la lesión. Se evaluaron parámetros funcionales (niveles de BUN y creatinina), histológicos (hematoxilina/eosina, tricrómico de Masson y rojo Sirius) y moleculares mediante la expresión de mRNA de marcadores de proliferación, inflamación, fibrosis, piroptosis y ferroptosis. Los resultados demostraron que la terapia PBMC (A/R) redujo significativamente los niveles séricos de BUN y creatinina y disminuyó la expresión de marcadores inflamatorios, al tiempo que aumentó la proliferación epitelial renal. Estos efectos estuvieron mediados por la liberación de NGAL por parte de los monocitos/macrófagos presentes en la terapia, cuya acción dependió de su interacción con sus receptores (LCN2-R y megalina) en células epiteliales. La vía PI3K/Akt también fue activada, contribuyendo a la regeneración tisular. La terapia también influyó en los procesos de muerte celular de monocitos/macrófagos, observándose diferencias significativas entre su administración en etapas tempranas frente a la administración en etapas tardías del daño renal. En conclusión, la terapia leucocitaria autóloga demuestra un efecto terapéutico beneficioso en la nefropatía isquémica. Su efecto se basa en una combinación de mecanismos regenerativos, antiinflamatorios y antifibróticos, cuya efectividad depende del momento de administración, abriendo un camino prometedor hacia terapias celulares personalizadas orientadas a la recuperación renal y la modulación de mecanismos moleculares asociados a la lesión.
Caracterització de la capacitat proangiogènica de les cèl·lules mare derivades del teixit adipós: Influència del microambient i dels factors reguladors
(Universitat de Barcelona, 2025-09-26) Civit Urgell, Anna; Arderiu i Marquès, Gemma; Badimón, Lina, 1953-; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[cat] Introducció: Les malalties cardiovasculars són una de les principals causes de morbimortalitat a nivell mundial. Dins d’aquest conjunt, la malaltia isquèmica és la més prevalent i es caracteritza per una reducció crítica del flux sanguini que compromet la viabilitat dels teixits afectats. En aquest context, l’angiogènesi terapèutica ha emergit com un enfocament innovador amb l’objectiu de promoure la formació controlada de nous vasos sanguinis en les zones isquèmiques. Una estratègia prometedora dins d'aquest camp és l'ús de cèl·lules mare mesenquimals adultes, especialment aquelles derivades del teixit adipós (ASCs). Aquestes cèl·lules han demostrat propietats proangiogèniques i immunoreguladores, així com una notable capacitat per secretar factors de creixement i diferenciar-se en diversos tipus cel·lulars. Gràcies a aquestes característiques, han mostrat un gran potencial per promoure la regeneració vascular tant en teixits perifèrics com en el cor. La recerca actual es centra en aprofundir en els mecanismes moleculars que regulen l’angiogènesi i optimitzar l’ús de teràpies cel·lulars per desenvolupar noves estratègies terapèutiques efectives pel tractament de les malalties isquèmiques. Hipòtesi: La hipòtesi de treball d’aquesta tesi és que el precondicionament de les ASCs amb molècules proangiogèniques regula el seu perfil transcriptòmic i augmenta la seva capacitat per formar nous vasos sanguinis. Objectius: Per poder donar resposta a aquesta hipòtesi, s’ha avaluat l’efecte de les diferents localitzacions del teixit adipós, l’obesitat i la diabetis en la capacitat proangiogènica de les ASCs. A més, s’ha analitzat la composició del seu perfil transcriptòmic i la seva relació amb l’angiogènesi. Mètodes: Aquest estudi s’ha realitzat amb ASCs humanes aïllades del teixit adipós subcutani i visceral d’individus amb normopès, obesitat mòrbida i/o diabetis mellitus. També s’han aïllat ASCs de teixit perivascular de l'artèria coronària descendent anterior esquerra dels cors extrets en trasplantaments cardíacs. Les ASCs s’han caracteritzat fenotípicament i s’ha avaluat la seva capacitat de proliferació, diferenciació i migració. La seva capacitat angiogènica s’ha estudiat mitjançant l’anàlisi del perfil de microARNs en resposta a estímuls proangiogènics. A més, s’ha investigat els efectes paracrins de les ASCs sobre les cèl·lules musculars llises vasculars mitjançant assajos de cicatrització de ferides, migració transwell i estudis de co-cultiu. Finalment, s’ha utilitzat un model de ratolí atímic per avaluar la capacitat de les ASCs de participar en la formació de noves estructures capil·lars. Resultats principals: Les ASCs dels diferents dipòsits de teixit adipós mostren una capacitat de proliferació, migració i potencial angiogènic, tot i que factors com l'obesitat i la diabetis mellitus redueixen aquestes propietats. No obstant això, el tractament de les ASCs amb molècules proangiogèniques, com el factor de creixement fibroblàstic (FGF), ha restaurat les seves capacitats angiogèniques. Aquest tractament ha augmentat la capacitat de proliferació i migració de les ASCs i ha modificat l'expressió de diferents microARNs implicats en la seva proliferació i capacitat angiogènica. En particular, s’han identificat tres microARNs (-29b-3p, -424-5p i -378a-3p) i els seus respectius gens diana (MAPK1, FGFR1, NRP2, i TGF-β2) com a inductors clau de les propietats angiogèniques de les ASCs. A més, el secretoma de les ASCs estimula la migració de les cèl·lules musculars llises vasculars i el seu co-cultiu afavoreix la formació d'estructures capil·lars. En el teixit perivascular, el factor tissular és un factor clau en la capacitat proangiogènica de les ASCs. L’expressió d’aquest factor en les ASCs obtingudes del teixit perivascular es modulada per les condicions isquèmiques del teixit, intervenint també en la seva capacitat de diferenciació a cèl·lula endotelial. A més, també s’ha observat que la seva localització subcel·lular determina la seva capacitat de migració. L’expressió del factor tissular en les ASCs perivasculars, regula la capacitat de secreció del lligand de quimiocines del motiu C-C 2 (CCL2, de l’anglès C-C Motif Chemokine Ligand 2) i indueix la formació d’estructures tubulars i la interacció amb les cèl·lules musculars llises vasculars, destacant la seva importància en l’angiogènesi. Conclusions: Aquestes troballes han demostrat que la localització del dipòsit adipós influeix en la capacitat de diferenciació de les ASCs mitjançant l'expressió de microARNs específics. El precondicionament de les ASCs amb el factor proangiogènic FGF modifica el seu perfil de microARNs i regula la seva capacitat de proliferació i remodelació vascular. A més, l'expressió del factor tissular en les ASCs residents en el teixit perivascular està regulada per les condicions isquèmiques, fet que regula la interacció amb les cèl·lules musculars llises vasculars. Així doncs, la regulació del perfil de microARNs i del factor tissular en les ASCs podria representar una estratègia terapèutica innovadora pel tractament de la malaltia isquèmica.
Manipulating levels of carotenoid-related enzymes and transcription factors in tomato (Solanum lycopersicum L.)
(Universitat de Barcelona, 2025-10-31) Burbano Erazo, Esteban; Rodríguez Concepción, Manuel; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Carotenoids are essential isoprenoids in plants, primarily required for photoprotection. However, their functions vary depending on the plant species and organ, serving as pigments in many flowers and fruits and as precursors of hormones such as abscisic acid (ABA) and strigolactones (SLs) in other tissues. In humans, dietary carotenoids serve as important sources of antioxidant compounds and vitamin A. Therefore, carotenoid biofortification is a key strategy to enhance food security and improve nutrition. Carotenoids are present at relatively high levels in the fruit of agriculturally important species such as tomato (Solanum lycopersicum L.). However, our knowledge of how isoprenoid precursors are channeled into the carotenoid pathway in fruits and other organs of this important crop is still very limited. Phytoene synthase (PSY) is a key enzyme that produces phytoene (the first intermediate in the carotenoid pathway) from geranylgeranyl pyrophosphate (GGPP). In the previous step, GGPP synthases (GGPPS) synthesize GGPP from the universal isoprenoid precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. Tomato has three genes encoding isoforms of GGPPS (here referred to as SlG1, SlG2, and SlG3) and PSY (PSY1, PSY2, and PSY3). In the first part of this thesis, we used previously generated tomato edited lines defective in individual GGPPS or PSY isoforms to generate double mutant combinations. The main objective was to understand what GGPPS-PSY pairs regulated the channeling of isoprenoid precursors into the carotenoid pathway in different organs of the tomato plant, including leaves, flowers and fruits (as the SlG1-PSY3 tandem had been previously shown to be involved in SL production in roots). The generation and analysis of double mutants revealed a major role for SlG3 in providing GGPP to PSY2 for carotenoid production in the leaf, while SlG2 and PSY1 appeared to be most relevant in flower and fruit tissues. In the second chapter of the thesis, we aimed at editing the tomato gene encoding HY5, a transcription factor shown to activate carotenoid biosynthesis in many plant systems. HY5 is accumulated in the light but degraded in the dark or in the shade via interaction with the E3 ubiquitin ligase COP1. To increase HY5 activity, we generated tomato lines with a truncated version of HY5 that is unable to interact with COP1. The resulting HY5 gain-of-function lines (referred to as slhy5-D lines) exhibited shorter hypocotyls, epicotyls and higher leaf anthocyanin content compared to their respective backgrounds, whereas Western blot analysis confirmed increased stability and abundance of the mutant HY5 protein in different light conditions. Strikingly, slhy5-D lines did not show substantially increased levels of carotenoids in leaves or fruits. We further investigated the phenotype of slhy5-D lines considering that increased HY5 activity might result in shade tolerance. The presence of neighboring plants results in a decreased ratio of red to far-red light (low R:FR) resulting from the preferential use of R for photosynthesis and the reflection or filtering of FR. Shade associated to vegetation proximity can be simulated in the lab by enriching white light (W, high R:FR) with FR (W+FR, low R:FR). All tomato accessions analyzed were found to elongate and reduce their photosynthetic pigment levels (including carotenoids) in response to W+FR illumination compared to W-exposed controls. When exposed to W+FR, slhy5-D lines displayed partial shade tolerance compared to their unedited parental lines, as deduced from attenuated plant elongation. However, no effects were observed in carotenoid levels. Finally, in the last chapter of the thesis, we investigated whether alterations in other molecular components resulting in shade tolerance could prevent the degradation of carotenoids associated to low R:FR signaling. Specifically, we carried out an untargeted approach to look for shade-tolerant mutants in collections of tomato landraces and introgression lines (ILs). As a result, we identified an introgression line (IL2-2) as tolerant to W+FR conditions in terms of elongation. In this line, photosynthetic carotenoid levels did not decrease under W+FR compared to W at the seedling stage, but the phenotype was not preserved in adult plants. This line exhibited altered auxin homeostasis and reduced expression of auxin-responsive genes under simulated proximity shade. Notably, IL2-2 also showed improved yield performance under high-density planting conditions in open-field trials.
Mechanistic understanding of amyloid nucleation at scale
(Universitat de Barcelona, 2025-11-28) Badia Graset, Marta; Bolognesi, Benedetta; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Proteins have evolved to remain soluble inside cells, yet nearly all proteins can aggregate, at least under certain conditions. Amyloids are a specific type of protein aggregates and typically present as highly ordered fibrils which are the hallmarks of at least 50 human diseases. Mutations can affect the process of aggregation into amyloids by altering not only the rate of the aggregation reaction, but also the final structures formed. Understanding the diverse mechanisms that can lead to aggregation offers more than a binary view of the effects of different variants. Systematic approaches to study amyloid aggregation at scale open the door to uncovering how variants impact this process, insights that are critical for understanding disease progression and guiding the development of mechanism-based therapies. At the moment, our understanding of these processes remains limited due to scarce detailed data and technical challenges in studying amyloid formation. To address these challenges, I apply multiplexed assays of variant effects (MAVE) to systematically investigate amyloid formation across three distinct systems: the islet amyloid polypeptide (IAPP), which aggregates in type 2 diabetes (T2D); amyloid beta (Aβ42), whose aggregation causes familial Alzheimer’s disease (AD); and the yeast prion protein Sup35. In IAPP, high-throughput profiling of over 1,600 variants reveals a structured amyloidogenic core, with the NNFGAIL segment being especially sensitive to mutation. This work constitutes the first in vivo mutational atlas of IAPP aggregation, uncovering over 300 variants that accelerate amyloid formation and providing new insights into T2D risk. Building on this framework, I apply intra-molecular genetic interaction profiling, a method that groups variants based on their molecular effects, to Aβ42. This reveals two distinct classes of aggregation-increasing mutations, which also differ in their morphological and structural features. Notably, all known familial Alzheimer’s disease (fAD) variants fall within one class, suggesting a shared pathogenic mechanism. These findings establish this approach as a powerful tool for uncovering mechanistic diversity and functionally classifying disease-linked variants, informing patient stratification and targeted therapeutic strategies. Additionally, I use MAVEs to dissect how mutations in the N-terminal domain of the yeast prion Sup35 control early amyloid formation and prion transmission. Focusing on cross-nucleation, the process where aggregates of one protein variant seed another, I show that the first 69 residues define the minimal segment required. Nucleation is primarily driven by the initial segment of Sup35 N-domain, where mutations strongly disrupt the process, while mutations in the following region are more tolerated. I also identify key “gatekeeper” residues that act as key players in maintaining a cross-nucleation barrier and demonstrate that sequence matching is essential for cross-nucleation but less so for self-seeding within the same sequence (cis-nucleation). Together, these studies provide a high-resolution, comparative view of amyloid nucleation across diverse systems. They showcase how MAVEs enable large-scale quantitative analysis of aggregation-prone proteins, revealing mutational effects and mechanisms missed by traditional methods. This integrative approach advances our understanding of amyloid biology, provides large datasets that can be used by the scientific community to train new models of amyloid formation and variant classification and, finally, can also serve to guide precise, mechanism-based therapies.
Computational exploration of protein-ligand interactions: substrate selectivity and small molecule inhibition
(Universitat de Barcelona, 2025-06-19) Valdivia, Aitor; Llabrés Prat, Salomé; Luque Garriga, F. Xavier; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] The continuous development of molecular modelling and computational methods is pivotal in addressing the challenges encountered in the fields of biomedicine and drug design. Among them, the lack of structural and mechanistic information underlying protein dysfunction and drug resistance stands out. In this context, the present doctoral thesis focuses on elucidating the molecular interactions behind the mechanism of action (MOA) of two druggable targets that are directly involved in major public health concerns highlighted by the World Health Organization (WHO), namely cardiovascular disease (CVD) and infectious diseases. In the first project, the mechanism and selectivity of the main cholesterol transporter in mammals, the Niemann-Pick C1-Like 1 transporter (NPC1L1) has been investigated. The imbalance of the correct blood lipid profile, caused by a dysregulation on cholesterol homeostasis, plays a key role in the development of CVD. Cholesterol is a fat-like substance endowed with a high physiological relevance in humans, and its homeostasis is tightly regulated by various cellular processes including the import in the small intestine and the reabsorption in the biliary ducts by the NPC1L1 importer. NPC1L1 can mediate the absorption of a variety of sterols but strikingly exhibits a large sensitivity to cholesterol epimerization. The existence of two distinct binding modes for cholesterol and epi-cholesterol to the N-terminal domain (NTD) of NPC1L1 provides the structural basis to rationalize the affinity difference between the two substrates. The configuration of the hydroxyl group of cholesterol and the presence of a structural water molecule are key features for the effective binding to NTD. In addition, the existence of a gating mechanism involved in the sterol binding to this protein domain was confirmed by the conformational rearrangements of the α8/β7 loop. Furthermore, distinct single-point mutations that impair cholesterol transport show a mild effect on the binding of cholesterol to the NTD, but a drastic influence on the conformational landscape of the α8/β7 loop in the apo species compared to the wild-type protein. Overall, these results support the functional role played by the α8/β7 loop in regulating the access of ligands to NPC1L1, and hence in assessing the impact of these mutations on diseases related to disruption of sterol absorption. In the second project, the MOA of an anti-viral inhibitor against the Hemagglutinin (HA) of Influenza A virus (IAV) has been investigated. We explored the putative binding site and the binding mode of the pinanamine-based inhibitor M090, able to block the HA-mediated membrane fusion mechanism in early stages of the infection and active against a wide range of HA variants. The predicted binding site is located at the interface defined by the α-helix L802-A962 and by the loops P3011-K3181 and M592-L732, i.e. in close proximity to the main stem region of the HA trimer. The results obtained from relative binding free energy (RBFE) calculations show close agreement with the differences in inhibitory potency determined in antiviral assays for M090 and its derivatives, providing in silico validation of the proposed binding mode. In addition, the E742 → D drug-resistant mutation weakens the optimal hydrogen bonding network established between the loops forming the M090 binding site. Altogether, a change in the overall packing against the stem region of HA leads to a disruption of the binding mode thus explaining the loss of activity. In the third project, we examined the binding site and the binding mode of the sulphonamide derivative VF-57a, synthesised by the group of Prof. Santiago Vázquez (Departament de Farmacologia, Toxicologia i Química Terapèutica, UB) and tested against IAV-infected MDKC cells by the group of Prof. Lieve Naesens (Department of Microbiology, Immunology and Transplantation, KUL). The compound shows sub-micromolar activities against A/H1N1 strains (EC50 = 0.31 µM and EC50 = 0.92 µM against A/Virginia/ATCC3/2009 and A/Puerto Rico/8/1934, respectively) and H5N1 strains (EC50 = 0.81 µM against A/bald eagle/Florida/W22-134-OP/2022). We predicted the binding site for VF-57a to be in close proximity to the binding site for the broad-spectrum inhibitor Arbidol (Umifenovir). In this pocket, the thiophene ring of VF-57a is stabilised by van der Waals contacts with V361, L491, P3081, F3091, V552 and L992 from one protomer and with L982 and L1022 from a second protomer. The ring containing the trifluoromethyl moiety is stabilised by π-stacking interactions with Y942 and F3091. In addition, RBFE predictions for VF-57a and some derivatives support the predicted MOA by showing a good correlation with the experimental activities. By combining state-of-the-art computational chemistry methods with experimental data, this doctoral thesis facilitates the understanding of certain cholesterol-related physiological disorders and contributes to the development of new small molecules as antivirals against IAV.
Evolución en Cataluña de la técnica óptica oftálmica para la mejora de la salud visual
(Universitat de Barcelona, 2025-07-16) Simón Castellví, Guillermo Luis; Carmona i Cornet, Anna M.; García Celma, Ma José; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[spa] Poco o nada se sabe realmente sobre la invención de los anteojos para el tratamiento de los errores de refracción. El objetivo de esta investigación es dar a conocer la evolución de la técnica óptica oftálmica para la corrección de los defectos de refracción y la mejora de la salud visual, “per se” explícita en lo referente a Cataluña, en un período de la historia muy falto de datos, desde la primera cita de las “ulleres” (anteojos) hasta finales del siglo XVIII. Aunque no podemos prescindir de ella, no se trata de una historia de la óptica, sino de evaluar la evolución de tratamiento de los errores de refracción en Cataluña en el período mencionado del que no hay apenas datos publicados. Hemos investigado en fuentes iconográficas y fuentes escritas de acuerdo con las normas de estudio de la cultura material (Amenós, 2017) para el período de nuestro estudio, tan escaso en fuentes fiables de información. Por desgracia no disponemos de los primeros ejemplares de anteojos de Cataluña en el período de nuestro estudio, por lo que hemos estudiado la representación de las “ulleres” en la iconografía (tapices, pintura, grabado y escultura) catalana y española en el período de nuestro interés, ampliándola en algunos casos a obras ya conocidas del resto de Europa por si aportaban algún dato interesante o diferencial. En cuanto a las fuentes escritas, la primera fuente de información de este tipo de investigación son los inventarios y los encantes notariales. En segundo lugar, como complemento indispensable de esta investigación hemos recurrido a los libros y archivos de aduanas, a fuentes documentales inéditas de archivos de Cataluña y las muy escasas fuentes bibliográficas y pictóricas o iconográficas. El análisis comparativo de los datos aportados por fuentes iconográficas y documentales nos permite reflexionar sobre su validez como documentos históricos. En la larga introducción, intentamos centrar el amplio tema de la evolución de los métodos terapéuticos para la corrección de los defectos de refracción, señalamos la evolución hasta el siglo XIX de la venta y fabricación de las lentes para la corrección de defectos de refracción en Cataluña, con sus características propias. Seguidamente, entramos en el propio tema de nuestra investigación, que no podría comprenderse sin la previa introducción, presentando y valorando los datos por nosotros obtenidos sobre anteojos. Damos a conocer en los resultados, y en la discusión, los aparatos visores, los estudios de óptica oftálmica y algunos aspectos legislativos relacionados con la salud visual. También comentamos el valor de los datos obtenidos, evaluando la evolución de la técnica óptica oftálmica y su impacto social y sanitario.
Nutraceutical Interventions and Lipoprotein Characterisation: Strategies for Cardiovascular Risk Management
(Universitat de Barcelona, 2025-05-15) Santisteban Villaplana, Victoria Marta de; Padró Capmany, M. Teresa; Badimón, Lina, 1953-; Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
[eng] Introduction: Cardiovascular diseases (CVDs) represent the leading cause of death globally (32%), with atherosclerosis as the main underlying pathology. Dyslipidemia is one of the most influential risk factors in the development of atherosclerotic cardiovascular disease (ACVD), with low-density lipoprotein cholesterol (LDLc) being the main target of lipid-lowering therapies. However, small and dense low-density lipoprotein particles (LDLp) increase cardiovascular risk even when LDLc levels are optimal. Although high-density lipoprotein cholesterol (HDLc) is considered protective, the quality and functionality of high-density lipoprotein (HDL) count as much as its quantity. This highlights that the composition, size, number, and functionality of lipoproteins are crucial in determining their atherogenicity or atheroprotection. In addition, factors such as sex, obesity, and lipid background are associated with differences in the pattern of lipoprotein subclasses, contributing to a more or less favorable cardiovascular status. Growing evidence associates hypercholesterolemia with dysbiosis of the gut microbiota. The gut microbiota acts as an endocrine organ and influences various metabolic processes, including lipid metabolism. Therefore, the administration of nutraceutical supplements that act at the intestinal level has been considered a useful tool to improve the metabolic profile and help in the control of conditions such as dyslipidemia, obesity, or diabetes. Objectives: In this doctoral thesis we aimed to: a) investigate the effects of regular and continuous intake of a probiotic based in Lactiplantibacillus plantarum on lipid metabolism, including lipoprotein profiles, pattern of bile acids (BAs), metabolic and inflammatory markers in overweight and obese individuals without a known history of CVDs; b) investigate the effects of regular and continuous intake of a polysaccharide containing β-glucan/chitin-chitosan (βGluCnCs) in overweight and obese individuals without a known history of CVDs; and, c) perform advanced lipoprotein characterization in samples of various human cohorts. Methods: Lipid profile and hepatic and renal variables were assessed by standardized biochemistry. Lipoprotein profile (composition, number, and size), glycoproteins, lipids, and low molecular weight metabolites were performed by proton nuclear magnetic resonance (1H-NMR). Lipoprotein functionality was evaluated by conjugated dienes, total radical trapping antioxidant potential [TRAP] (antioxidant potential of HDL), and HDL cholesterol efflux assays. BAs pattern was assessed by ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS). Markers of inflammation and glucose metabolism, adipokines, fibroblast growth factor (FGF)-19, and apolipoprotein (Apo)B48 and ApoB100 were measured by immunoassays [Enzyme linked immunosorbent assays (ELISAs) and Multilplex]. Serum levels of lipoprotein(a) [Lp(a)], ApoA-I and ApoB were determined by immunoturbidimetric assays. Results: Probiotic intake reduced conjugated BAs, FGF-19, ApoB100 and ApoB48 levels, small LDLp concentration, and low-density lipoprotein (LDL) susceptibility to oxidation, while enhancing HDL antioxidative activity. βGluCnCs supplementation increased HDLc levels and HDLc/total cholesterol (TC), HDLc/Non-HDLc ratios, and ApoA-1/ApoB, particularly in women, and in individuals with overweight and LDLc levels below 130 mg/dL. Moreover, βGluCnCs reduced the concentration of ApoB, particularly in men. Additionaly, βGluCnCs reduced non-HDLc and LDLc, and improved HDL antioxidant capacity in individuals with LDLc levels equal or above 130 mg/dL. Advanced lipoprotein characterization identified differential features and attributes in women and men and in overweight and obese individuals. Conclusions: In an apparently healthy overweight/obese population with no additional cardiovascular risk factors, our results showed that consumption of Lactiplantibacillus plantarum KABP011, KABP012, and KABP013 induced changes in the BAs and lipoprotein profile, reduced LDL susceptibility to oxidation, and increased HDL antioxidant capacity, suggesting a pattern of protection against atherosclerosis. Consumption of βGluCnCs leads to increased HDLc and reduced ApoB levels, with the response depending on sex and baseline LDLc levels. Finally, men and obese individuals have a higher-risk lipoprotein subclass profile compared to women and overweight individuals.

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