Tesis Doctorals - Departament - Genètica, Microbiologia i Estadística

Permanent URI for this collectionhttps://hdl.handle.net/2445/110547

Statistics

Browse

Now showing 1 - 20 of 137

Tailing Free: The Evolution of Tail Muscle in Oikopleura dioica Sheds Light on the Transition to a Fully Free-Swimming Lifestyle in Appendicularian Tunicates
(2025-11-13) Fabregà Torrus, Marc; Cañestro García, Cristian; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Tunicates constitute a large and diverse group of marine invertebrates encompassing a wide range of life strategies, from the fully free-swimming lifestyle of appendicularians to the biphasic lifestyle of ascidians, which are characterized by motile larvae and sessile adults. However, whether the ancestral tunicate resembled a biphasic, ascidian-like form or a fully free-swimming appendicularian remains an open evolutionary question. The free-swimming appendicularian lifestyle is tightly associated with the evolutionary innovation of the filtering house and the retention and specialization of a functional tail, which is maintained throughout the entire life cycle. This tail enables complex swimming behaviours, in contrast to the simpler dispersal function of the ascidian larval tail, which is lost during metamorphosis. To better understand how the evolution of the tail facilitated the emergence of the appendicularian lifestyle, in this PhD project, we investigate tail muscle development in the appendicularian Oikopleura dioica through embryonic lineage tracing, gene expression analysis, and comparative genomic surveys of the myofibrillar gene catalogue. Our findings reveal a profound remodelling of tail muscle lineages compared to ascidians, along with a massive expansion and diversification of cardioparaxial sarcomeric Myh genes (Myh-Scp), which exhibit temporally and spatially specific expression patterns. This diversification of myofibrillar genes suggest and increased diversity of muscle cell identities with distinct contractile properties along the anteroposterior axis of the tail, enabling the complex repertoire of movements observed in appendicularians. Finally, our results allow us to propose a new evolutionary model for the transition in lifestyle among tunicates, based on the evolution of the tail. This model, named “tailing free”, emphasizes the central role of the tail in enabling a transition from a biphasic ascidian-like ancestor to a fully free-swimming appendicularian lifestyle. Furthermore, it supports evidence of our previous work suggesting that the ancestral tunicate exhibited a biphasic lifestyle with a sessile, post-metamorphic adult stage, similar to ascidians. Metaphorically, appendicularians “break free” from their ancestral ties to a sessile, substrate-attached life and adapt to a free open-water existence, ultimately becoming one of the most abundant and ecologically important components of the mesozooplankton in marine ecosystems.
Aneuploidy in neural stem cells: linking proteostasis failure and mitochondrial dysfunction to microcephaly
(Universitat de Barcelona, 2025-10-03) González Blanco, Amanda; Milán, Marco; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] The precise acquisition of chromosome number is fundamental for proper brain development and function. Alterations in this process result in aneuploidy, defined as an abnormal chromosome number. Aneuploidy has profound detrimental effects at both the cellular and organismal levels. Several human conditions, such as Down syndrome and Mosaic Variegated Aneuploidy (MVA), are caused by aneuploidy and are associated with severe health problems, such as cognitive impairment, developmental delay and microcephaly. Unfortunately, therapeutic strategies for aneuploidy-related conditions are still lacking, highlighting the need for further investigation into the molecular mechanisms underlying these disorders. In this thesis, we investigated the cellular and molecular consequences of aneuploidy in the context of brain development. We used Drosophila neural stem cells (neuroblasts, NBs) as a robust model system to study both simple aneuploidies (trisomies) and chromosomal instability (CIN)-induced aneuploidy. We determined that just by downregulating one spindle assembly checkpoint gene, as observed in MVA human patients, we were able to recapitulate the microcephaly phenotype. Our findings revealed that CIN-induced aneuploidy caused a progressive decrease in the number of NBs and their proliferative capacity, as well as in the number of progeny cells, consequently resulting in smaller brains compared to controls. We explored the underlying mechanisms contributing to this impairment, distinguishing between the consequences of DNA damage and aneuploidy in the cells. We dissected the differences between complex (CIN) and simple aneuploidies (trisomies) and demonstrated that increasing the degree and complexity of aneuploidy correlates with a more detrimental outcome for NBs. Furthermore, we deeply characterized the cellular process by which NBs are lost from the tissue upon CIN. We assessed a mild contribution of apoptosis to the resulting microcephaly and discarded other types of cell death. Conversely, we propose that NBs undergo a novel mechanism of loss of stem cell identity, becoming cells that are neither stem cells nor fully differentiated. These cells lose typical NB markers, making them undetectable in the tissue, become non-functional, and no longer contribute to the generation of nervous system cells, ultimately leading to microcephaly. Finally, we detected several cellular stresses in the NBs that arise as a consequence of CIN, such as protein accumulation, proteasome saturation, autophagy activation and saturation, and mitochondrial dysfunction. Importantly, we demonstrated that alleviating these cellular stresses in CIN NBs improves brain health, thereby opening promising avenues for the development of targeted therapeutic strategies aimed at enhancing the well-being of patients affected by aneuploidies.
Development of Experimental Methodologies for Modeling Bacterial Infections
(Universitat de Barcelona, 2025-10-03) Admella Pedrico, Joana; Torrents Serra, Eduard; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] The rise of antimicrobial resistance has made bacterial infections a global and signiﬁcant health threat. Additionally, infections associated with bioﬁlms are typically persistent and hinder the penetration and eﬃcacy of traditional antibiotics. Therefore, the development of new antimicrobial therapies relies on a comprehensive understanding of bacterial pathogenesis, supported by reliable laboratory models and methodologies. First, various in vitro lung cell models were developed and optimized to recreate bacterial lung infections. Within these systems, Pseudomonas aeruginosa pathogenesis, bioﬁlm formation, virulence, host-pathogen interactions, and the eﬃcacy of diﬀerent antibiotics were investigated. Given that respiratory infections are usually polymicrobial, coinfections involving P. aeruginosa and other clinically relevant species, such as Staphylococcus aureus and Candida albicans were also modeled. This research explored how microbial interactions shape both virulence and antibiotic susceptibility. On the other hand, several methodologies were optimized and established in the Galleria mellonella in vivo model. Among its many advantages, this insect shares signiﬁcant similarities with the human innate immune system, being widely employed in both infection and toxicity studies. In vivo bacterial pathogenesis was investigated by analyzing pathogen dissemination and monitoring the expression of key bacterial genes using a simple bioluminescence-based system. Furthermore, novel protocols, such as the primary culture of hemocytes, were developed for nanotoxicology evaluation. Both nanomedicine and phage therapy represent promising alternative therapeutic approaches and can be easily assessed in G. mellonella. In summary, this thesis presents the optimization of various in vitro and in vivo methodologies for modeling bacterial infections caused by clinically relevant pathogens, while providing diverse tools for the evaluation of novel antimicrobial therapies.
Characterization of alternative polyadenylation sites at single cell resolution and its impact on Alzheimer Disease
(Universitat de Barcelona, 2025-10-23) Ake, Franz Arnold; Plass Pórtulas, Mireya; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Alternative polyadenylation (APA) is a widespread mechanism of gene regulation that that affects more than 70% of human genes. mRNA isoforms generated though APA have distinct 3ʹ ends, which can affect mRNA regulation as well as the resulting proteins. APA is well known to be regulated during cell differentiation and it is a major source of gene regulation in the brain. Yet, it is not known till which extend APA contributes to the transcriptomic variability across individual cell populations. While bulk RNA sequencing has provided important insights into APA, it does not provide the resolution needed to resolve the cell-type-specific dynamics essential for understanding development and disease. The rapid development of 3’ tagged-based single-cell RNA sequencing (scRNA-seq) has enabled the study of gene expression and the implementation of methods for describing isoform usage at single cell resolution. However, challenges such as dropout effects or technical biases arising from the experimental setup have to be surmonted. In this thesis, we developed a novel computational approach to characterize isoform diversity at single-cell resolution using 3'-tagged scRNA-seq data, thereby enhancing the understanding of APA dynamics at single-cell resolution. First, I systematically evaluated the impact of various single-cell transcriptomics sample preservation methods on neural and glial cells derived from induced pluripotent stem cells. Secondly, I implemented and benchmarked SCALPEL, a novel computational Nextflow workflow designed for quantifying isoforms using standard 3′-tagged scRNA-seq data. Our results show that while DMSO provides the highest cell quality in terms of RNA molecules and genes detected per cell, it strongly affects the cellular composition and induces the expression of stress and apoptosis genes. In contrast, methanol fixed samples display a cellular composition similar to fresh samples and provide a good cell quality and little expression biases, indicating that methanol fixation is the method of choice for performing droplet-based single-cell transcriptomics experiments on neural cell populations. Furthermore, SCALPEL demonstrated high sensitivity and precision in quantifying isoforms, and the ability to detect differential isoform usage (DIU) in both synthetic and experimental datasets. In real datasets, SCALPEL predictions have a high agreement with other tools and can be experimentally validated. The use of SCALPEL on real datasets reveals novel cell populations undetectable using single-cell gene expression data, confirms known 3’ UTR length changes during cell differentiation, and identifies cell-type specific miRNA signatures regulating isoform expression. Additionally, we show that SCALPEL improves isoform quantification using paired long- and short-read scRNA-seq data. Overall, SCALPEL expands the current scRNA-seq toolkit to explore post-transcriptional gene regulation across species, tissues, and technologies, advancing our understanding of gene regulatory mechanisms at the single-cell level.
Fagos CrAssBcn: los nuevos virus crAssphage indicadores de contaminación fecal humana
(Universitat de Barcelona, 2025-10-31) Gómez Gómez, Clara; Muniesa Pérez, Ma. Teresa; García Aljaro, Cristina; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[spa] El estudio de la microbiota intestinal es esencial para comprender su impacto en la salud humana. Este ecosistema dinámico se estructura mediante complejas interacciones entre bacterias, bacteriófagos y otros microorganismos presentes en la microbiota. Los procesos evolutivos de las diferentes poblaciones y la acción de los fagos sobre las poblaciones bacterianas regulan su estabilidad y diversidad. En este contexto, el descubrimiento de crAssphage, posiblemente el fago más abundante en el intestino humano, ha revolucionado el conocimiento del viroma intestinal. El aislamiento de crAssphage mediante técnicas convencionales presenta desafíos significativos relacionados con su dificultad de propagación in vitro y la escasa visibilidad de las calvas de lisis que producen. A pesar de ello, disponer de crAssphage aislados es esencial para profundizar en su conocimiento. En la presente tesis doctoral, se ha logrado aislar 25 nuevos fagos tipo crAss en aguas residuales de Cataluña. Los fagos crAss aislados (crAssBcn) presentan una notable diversidad genética, posiblemente impulsada por la presión selectiva y la interacción con los sistemas de defensa de su hospedador bacteriano, Bacteroides intestinalis. La disponibilidad de viriones aislados ha permitido realizar ensayos experimentales más precisos sobre su ciclo de vida, superando así las limitaciones inherentes a los estudios realizados sólo con datos metagenómicos. Se observó la coexistencia de estos fagos virulentos con su hospedador bacteriano, cuyas poblaciones presentan fenotipos sensibles y resistentes a la infección. Los resultados sugieren que dicha resistencia, independiente del receptor del fago, está vinculada a una región genética en el hospedador B. intestinalis que está sujeta a variación de fase, la cual modula diferencialmente la expresión de polisacáridos capsulares (CPS) que, según se expresen o no, permiten la infección de los fagos. Los fagos del tipo crAss destacan como potenciales marcadores universales de contaminación fecal humana debido a su abundancia en heces, su ubicuidad y su resistencia a los tratamientos de desinfección. Sin embargo, buscando la selección de un candidato universal representativo de este grupo tan abundante y heterogéneo, los análisis de genomas completos, previamente anotados en bases de datos (tanto aislados como no), revelan la necesidad de considerar fagos tipo crAss específicos para ser aplicados en cada región geográfica. La ausencia de una relación filogenética entre ellos, su posible presencia en heces de origen animal y la inexistencia de un candidato con distribución global uniforme refuerzan la hipótesis de considerar variantes locales para su aplicación. Siguiendo esta premisa, se llevaron a cabo estudios experimentales más exhaustivos sobre la persistencia de los viriones crAssBcn autóctonos, siendo el primer estudio que ha evaluado la inactivación natural de fagos tipo crAss aislados. Los resultados confirman su mayor persistencia en comparación con otros indicadores microbiológicos e, incluso, con ciertos virus entéricos. En conjunto, los hallazgos obtenidos en esta tesis subrayan la necesidad de profundizar en la comprensión del papel ecológico de estos virus, con el propósito de desarrollar nuevas estrategias para el control ambiental, contribuyendo a mejorar la gestión de la calidad del agua, al tiempo que permitirá explorar nuevas aproximaciones diagnósticas y terapéuticas para abordar desequilibrios en la microbiota intestinal.
Evaluation of fecal pollution impact from a One Health perspective, in the southern region of Sétif (Algeria)
(Universitat de Barcelona, 2026-01-15) Boulainine, Dalal; García Aljaro, Cristina; Mezaache Aichour, Samia; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Water plays a fundamental role in sustaining life and supporting human social and economic development. However, its availability is unevenly distributed across the globe, and many regions are increasingly facing challenges related to water scarcity. These challenges are further exacerbated by rapid population growth, urbanization, and intensified agricultural and industrial activities. Among the regions most affected, the Mediterranean has seen a marked decline in water resources in recent years a trend expected to intensify due to the projected impacts of climate change. In this context, effective and sustainable water management has become a global priority, particularly through the lens of One Health and Global Health approaches, which recognize the interdependence of human, animal, and environmental health. A critical component of such management strategies is the monitoring of water quality, especially regarding microbial risks that pose threats to public health and ecosystem integrity. Within this framework, the primary objective of this doctoral thesis is to evaluate the impact of fecal pollution in aquatic environments, with the aim of identifying anthropogenic influences and associated public health risks. This research has been developed in various studies, resulting in three scientific articles. These studies have evaluated the dynamics and analysis of the main sources of fecal microbial contaminants, examining the presence of fecal indicators, antibiotic resistance genes (ARGs), and antibiotic-resistant bacteria (ARBs). They also examined the effectiveness of traditional and modern nature-based treatment techniques to reduce human fecal microbial contaminants, their impact on river community composition, and the natural deactivation processes of fecal indicator organisms. They also have examined environmental bacterial isolates from different environments including human and animal wastewaters, aquatic environments and vegetables, to understand the environmental reservoirs and transport pathways of antibiotic resistance genes ARGs and ARBs. The results obtained provide valuable information on the behavior of various fecal microbial indicators in the environment, and revealed that fecal pollution was widespread across the watershed, with higher concentrations primarily linked to urban wastewater discharges and animal sources. Changes in the structure and diversity of bacterial communities were also observed in this river. However, it was observed that the structure and diversity of bacterial communities can recover in the reservoir, demonstrating a high resilience to anthropogenic influences, as well as the persistence of ARGs and ARB in treated sewage, surface waters, and even fresh crops. Finally, the results of this research contribute to the evaluation of new water management tools in Algeria based on One Health and Global Health. It also highlights the urgent need for integrated monitoring, improved wastewater and agricultural practices, and a One Health approach to mitigate the public health risks associated with fecal contamination and antimicrobial resistance in Algerian watersheds.
Genome architecture and function in tissue regeneration
(Universitat de Barcelona, 2025-12-16) Llorens Giralt, Palmira; Corominas, Montserrat (Corominas Guiu); Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Regenerative capacity differs not only across species, but also between organs and developmental stages within the same organism. Understanding why this variability exists remains a major challenge in developmental biology. Studies in regenerative animals have shown that genes involved in development are often re-expressed during regeneration and tend to be evolutionary conserved. Therefore, differences in regenerative potential may depend on the ability of a given tissue to reactivate these programs in a context-dependent manner, rather than on the presence or absence of necessary genes. This transcriptional reactivation is orchestrated through multiple layers of regulation, including transcription factor activity, cis-regulatory DNA elements, chromatin remodeling, histone modifications, and the three-dimensional organization of the genome. In this work, we explore how chromatin organization and genome activity influence regenerative responses by studying two epithelial tissues that regenerate through compensatory proliferation. First, we use a highly regenerative mammalian model, the two-thirds partial hepatectomy in mouse liver, to study changes in chromatin structure during regeneration. By integrating chromatin accessibility and transcriptomic data, we show that transcriptional reprogramming is driven by a wide range of cis-regulatory elements, including regeneration-responsive regulatory elements (RREs). These RREs, which comprise both regeneration-specific and reactivated developmental enhancers, activate genes involved in hepatocyte priming and proliferation. In contrast, enhancers linked to energy-intensive functions of quiescent hepatocytes become repressed, leading to the downregulation of metabolic genes, particularly those involved in lipid metabolism. We further construct a gene regulatory network that uncovers a cascade of transcription factor activation, which modulates expression of repair genes in a time-specific manner. Altogether, we provide a genome-wide atlas of enhancer-gene interactions that offers new insights into the regulatory mechanisms driving liver regeneration. To investigate whether and how chromatin structure and genome folding influence regenerative potential, an area that remains largely unexplored, we use the wing imaginal disc of Drosophila melanogaster as a model. We find that the spatial organization of the genome in wing disc cells undergoes subtle but significant reorganization during regeneration, including reduced compartmentalization. Notably, we observe increased contact frequency across three long-range chromatin loops, termed meta-loops, whose anchors span over 3 megabases. Using chromosomal deficiencies and CRISPR/Cas9-mediated knockouts, we demonstrate that these loops are required for regeneration but are dispensable during development. Finally, we identify the architectural protein Cp190 as a key factor in the formation of these meta-loops. The results of this thesis reveal critical roles for chromatin states and higher-order genome architecture in regeneration, highlighting conserved regulatory principles underlying tissue repair.
Análisis transcripcional y epigenético de las interacciones de factores de transcripción ectópicos en nuevos entornos de cromatina
(2025-05-23) López Fernández, Maria José; Maeso, Ignacio; Almuedo Castillo, María; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[spa] Las entidades biológicas interactúan continuamente con otras estructuras, estableciendo redes complejas a través de las cuales se intercambia información biológica. Estas redes de interacción, como las complejas redes reguladoras de genes que controlan el desarrollo animal, se ensamblan y mantienen durante el curso de la evolución. Sin embargo, ¿qué ocurre cuando de repente se incorporan por primera vez nuevos elementos a estos sistemas? La hipótesis planteada es que las propiedades intrínsecas de los nuevos elementos y el entorno en el que se expresan por primera vez influyen en el resto de su proceso coevolutivo. Sin embargo, sólo se pueden investigar aquellos encuentros moleculares que tuvieron éxito y sobrevivieron. Para superar esto, en este trabajo utilizamos un enfoque sintético en el que ponemos en contacto estructuras moleculares que nunca antes habían interactuado, para generar encuentros reguladores de genes por primera vez. En primer lugar, expresamos factores de transcripción (FT) específicos de mamíferos y plantas en el entorno de cromatina completamente extraño de embriones de pez cebra y estudiamos estas interacciones mediante técnicas ómicas. Dos de ellos, LEUTX y WRKY40, detienen el desarrollo temprano del pez cebra durante la gastrulación. Además, mediante experimentos de RNA-seq de embriones inyectados con LEUTX demostramos que la activación del genoma cigótico se ve afectada, y los experimentos de ATAC-seq muestran que reconoce el mismo motivo de ADN en el pez cebra que en las células humanas. Por otra parte, el estudio de enriquecimiento de motivos de los picos diferencialmente accesibles de WRKY40 reveló el motivo característico de la familia de genes apoptóticos p53, p63 y p73. Finalmente, ARGFX está asociado con un motivo característico de la familia de factores de transcripción T-box. Estos resultados sugieren que tanto WRKY40 como ARGFX se podrían estar uniendo a la cromatina de forma indirecta, interaccionando con los genes de las familias p53 y Tbx, respectivamente. Por otro lado, estudiamos las interacciones desde la perspectiva del entorno de la cromatina, analizando el impacto del cambio en la accesibilidad de la cromatina a través de 2 estrategias diferentes, las líneas transgénicas Gal4 y UAS, y la administración de diferentes drogas. La primera estrategia revela que el silenciamiento de transgenes regulados por UAS es un desafío técnico para el campo del pez cebra y es necesario más esfuerzo de investigación en este campo. Con respecto a la administración de drogas, establecemos que SAHA y entinostato a las concentraciones de 50 ng/μL producen un aumento del nivel de acetilación en el pez cebra y, por tanto, son 2 buenos candidatos para estudiar sus efectos a nivel genómico y para aplicarlos en los embriones inyectados con los FT estudiados. En definitiva, estos resultados sugieren que las estructuras moleculares como los FT tienen capacidades inherentes para interpretar y leer la información contenida en otros sistemas biológicos, incluso cuando estos encuentros son completamente inesperados. Así, durante las primeras etapas del origen de nuevas interacciones biológicas, estas propiedades intrínsecas pueden tener un impacto fundamental en el desenlace evolutivo final de las novedades moleculares.
The role of RBFOX1 and its regulatory network in major depression and comorbid psychiatric phenotypes
(Universitat de Barcelona, 2025-05-29) Adel, Maja Rebecca; Fernàndez Castillo, Noèlia; Freudenberg, Florian; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] RBFOX1 is a master regulator of large transcriptomic networks with pleiotropic effects on numerous neurodevelopmental and psychiatric disorders, including major depressive disorder (MDD). MDD is a complex disorder characterized by symptoms such as anhedonia, hopelessness, feelings of emptiness and guilt. It frequently co-occurs with other psychiatric disorders, which can be partially explained by an overlapping genetic basis. Its aetiology involves complex interactions of biological predispositions, including a highly polygenic genetic basis, and environmental risk factors. In this doctoral thesis we aimed to study the role of RBFOX1 and its regulatory network on MDD and comorbid psychiatric phenotypes and characterize the underlying mechanisms through which this gene exerts its pleiotropic effects by using zebrafish models. To obtain a comprehensive overview, we followed a multi-faceted approach investigating the effects of RBFOX1 at the levels of genetics, transcriptomics, neurotransmission, brain activity, and behaviour. Our results show that RBFOX1 is an essential regulator of a large network of differentially spliced and expressed genes, which substantially contribute to the shared genetic basis of MDD, anxiety, irritability, and neuroticism. The RBFOX1-regulated genes associated with MDD and these comorbid traits show a substantial overlap and are mainly related to the neurodevelopment and neurotransmission. We furthermore identified enrichment of RBFOX1-regulated genes among genes causal for rare disorders with symptoms of depression, anxiety and irritability, suggesting that RBFOX1 contributes to these symptoms through shared pathways in psychiatric and rare disorders. Our integrative analyses highlighted 19 genes regulated by RBFOX1, including CADM2, CTSB, MAPT, NSF, PAX6, SCAI, SNCA, SP4, and TCF4, with a high pleiotropic effect on MDD and its comorbid traits. Experiments in two rbfox1 mutant zebrafish lines showed that the effects of rbfox1 on behavioural changes mirror various symptoms of different psychiatric disorders. We observed a range of consistent behavioural alterations in both lines, including hyperactivity, thigmotaxis, social impairments, and aggression in only one. The behavioural alterations in rbfox1 mutant zebrafish could be partially reversed through acute exposure to fluoxetine, a commonly prescribed antidepressant targeting the serotonergic system. In line with our findings of the involvement of RBFOX1-regulated genes in neurotransmission, we observed reduced levels of serotonin, dopamine, GABA, and glutamate in forebrain regions of adult rbfox1 mutant zebrafish. Interestingly, in vivo whole-brain imaging analyses showed increased neuronal activity in midbrain and hindbrain regions of rbfox1 mutant zebrafish larvae. Transcriptomic analyses of adult rbfox1 mutant zebrafish revealed numerous differentially spliced and expressed genes in all brain regions, and were enriched in cell development processes and DNA repair mechanisms. These transcriptomic changes likely explain the alterations in neurotransmission and neural activity.
Genòmica de la conservació aplicada a la baldriga balear (Puffinus mauretanicus)
(2025-05-09) Cuevas Caballé, Cristian; Riutort León, Marta; Rozas Liras, Julio A.; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[cat] La baldriga balear (Puffinus mauretanicus) és l’ocell més amenaçat d’Europa. Les poblacions de l’espècie decreixen a un ritme de 7-14% anual, principalment degut a la mortalitat causada per la captura accidental (bycatch) per part de la flota pesquera, principalment del palangre, i per la depredació per part de mamífers invasors. Diferents estudis han previst que es podria extingir en només 60 anys si no es prenen ràpidament accions de conservació. L’objectiu principal d’aquesta tesi és l’aplicació de la genòmica de poblacions a l’estudi de la baldriga balear per tal d’augmentar el nostre coneixement sobre l’espècie i les seves poblacions, sempre tenint en compte que el coneixement generat haurà de servir per tal de fonamentar les accions de recuperació i conservació de les poblacions. Al Capítol 1, hem assemblat i anotat per primera vegada un genoma de referència de P. mauretanicus. Mitjançant la combinació de llibreries de seqüenciació de reads llargs i curts, el genoma assemblat per a la baldriga balear és d’elevada qualitat i completesa, comparable als genomes d’ocells d’alta qualitat disponibles. Aquest genoma és la pedra angular de tota la tesi. Al Capítol 2, mitjançant una anàlisi de genòmica de poblacions, hem identificat 1.304.832 SNPs que han mostrat la baixa diferenciació al llarg de tot el genoma entre la baldriga balear (P. mauretanicus) i la baldriga mediterrània (P. yelkouan). No obstant això, hem sigut capaços de delimitar 5 Unitats Evolutivament Significatives (ESU, en anglès): Pitiüses, Mallorca i Cabrera (pertanyents al llinatge P. mauretanicus) i Menorca i Yelkouan (pertanyents al llinatge P. yelkouan). De manera sorprenent, els resultats mostren que els individus mostrejats a Menorca, que fins ara es pensava que eren híbrids entre P. mauretanicus i P. yelkouan, pertanyen a P. yelkouan. Via anàlisis demogràfiques i de modelització per a diferents hipòtesis d’estructura poblacional i flux gènic, hem inferit que la separació entre la baldriga balear i la baldriga mediterrània va ocórrer durant l’últim màxim glacial (LGM), però durant el període interglacials de l’holocè s’ha facilitat la hibridació entre aquests tàxons, conduint a una reversió de l’especiació. Aquests contactes secundaris han permès mitigar una eventual depressió endogàmica a P. mauretanicus i que podria experimentar degut al seu baix cens poblacional. Tot i això, hem estimat el grau d’endogàmia i heterozigositat i no suposa a curt termini un risc per a la viabilitat de l’espècie. D’altra banda, les anàlisis de selecció mostren una regió de 200 kb on s’hi troba l’empremta genòmica d’una escombrada selectiva. En aquesta zona trobaríem haplotips adaptatius que tindrien a veure amb les estratègies migratòries diferents que presenten P. mauretanicus i P. yelkouan, i que s’han introgressat repetidament entre aquests llinatges. Combinant els paràmetres demogràfics prèviament estudiats per a la baldriga balear amb el grau de diversitat genètica que hem caracteritzat en aquesta tesi , hem simulat diferents projeccions del cens poblacional de P. mauretanicus sota diferents combinacions de flux gènic i intensitat del bycatch. Aquestes simulacions suggereixen que si no es pren acció immediata per tal de mitigar el bycatch, la baldriga balear s’extingirà en només 60 anys. A més, posen de manifest que inclús en els escenaris on s’aconsegueix mitigar el bycatch, el flux gènic entre la baldriga balear i P. yelkouan és crucial per a garantir la diversitat genètica suficient per a la supervivència de l’espècie. En resum, l’aplicació de la genòmica de poblacions a la baldriga balear permet posar èmfasi en que és una necessitat màxima protegir també el flux gènic entre els llinatges mauretanicus – yelkouan, que té lloc principalment a les illes de Menorca i Cabrera. Al Capítol 3 hem aprofitat tota aquesta caracterització de la diversitat genètica a nivell genòmic per a dissenyar un panell d’SNPs capaç de determinar el sexe i la colònia de procedència dels cadàvers de bycatch. Tot i la baixa diferenciació genètica entre les diferents colònies mostrejades (FST mitjana = 0,006), el panel proposat, de només 61 SNPs, ha sigut capaç d’assignar correctament la colònia de tots els individus mostrejats en provar-ne la seva validesa. El genoma de la baldriga balear ha sigut la primera espècie seqüenciada sota el paraigua de la la Iniciativa Catalana per a l’Earth BioGenome Project (CBP). Aquest genoma ha contribuït a comprendre els processos demogràfics que han modelat l’evolució de P. mauretanicus i P. yelkouan. A més, ha proporcionat un coneixement molt valuós per tal de poder guiar la presa de decisions per la conservació de la baldriga balear, alhora que ha proporcionat una eina pràctica que permetrà la determinació de l’origen del seu bycatch.
“Tailing free”. The evolution of tail muscle in Oikopleura dioica sheds light on the transition to a fully free-swimming lifestyle in appendicularian tunicates
(Universitat de Barcelona, 2025-11-13) Fabregà Torrus, Marc; Cañestro García, Cristian; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Tunicates constitute a large and diverse group of marine invertebrates encompassing a wide range of life strategies, from the fully free-swimming lifestyle of appendicularians to the biphasic lifestyle of ascidians, which are characterized by motile larvae and sessile adults. However, whether the ancestral tunicate resembled a biphasic, ascidian-like form or a fully free-swimming appendicularian remains an open evolutionary question. The free-swimming appendicularian lifestyle is tightly associated with the evolutionary innovation of the filtering house and the retention and specialization of a functional tail, which is maintained throughout the entire life cycle. This tail enables complex swimming behaviours, in contrast to the simpler dispersal function of the ascidian larval tail, which is lost during metamorphosis. To better understand how the evolution of the tail facilitated the emergence of the appendicularian lifestyle, in this PhD project, we investigate tail muscle development in the appendicularian Oikopleura dioica through embryonic lineage tracing, gene expression analysis, and comparative genomic surveys of the myofibrillar gene catalogue. Our findings reveal a profound remodelling of tail muscle lineages compared to ascidians, along with a massive expansion and diversification of cardioparaxial sarcomeric Myh genes (Myh-Scp), which exhibit temporally and spatially specific expression patterns. This diversification of myofibrillar genes suggest and increased diversity of muscle cell identities with distinct contractile properties along the anteroposterior axis of the tail, enabling the complex repertoire of movements observed in appendicularians. Finally, our results allow us to propose a new evolutionary model for the transition in lifestyle among tunicates, based on the evolution of the tail. This model, named “tailing free”, emphasizes the central role of the tail in enabling a transition from a biphasic ascidian-like ancestor to a fully free-swimming appendicularian lifestyle. Furthermore, it supports evidence of our previous work suggesting that the ancestral tunicate exhibited a biphasic lifestyle with a sessile, post-metamorphic adult stage, similar to ascidians. Metaphorically, appendicularians “break free” from their ancestral ties to a sessile, substrate-attached life and adapt to a free open-water existence, ultimately becoming one of the most abundant and ecologically important components of the mesozooplankton in marine ecosystems.
Expresión génica y regulación transcripcional de los genes "nrd" en bacterias
(Universitat de Barcelona, 2025-02-21) Marchan del Pino, Domingo; Torrents Serra, Eduard; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[spa] A lo largo de la historia, el ser humano ha estado en contacto con el mundo microbiano, y un claro ejemplo de ello son las bacterias, causantes de diversas enfermedades infecciosas, aunque en otras ocasiones beneficiosas para nuestro organismo. El descubrimiento de los antibióticos marcó un hito en el tratamiento de estas infecciones, constituyendo la primera revolución en el tratamiento de las mismas. Sin embargo, en la actualidad, se hace cada vez más imperativo el desarrollo de nuevas metodologías para abordar y estudiar diferentes microorganismos patógenos, dado que estos pueden generar resistencia a los antibióticos disponibles. Aunque las nuevas generaciones de antibióticos son más sofisticadas y efectivas, están surgiendo bacterias multirresistentes que pueden evadir casi cualquier tipo de tratamiento antibiótico, lo que representa un gran desafío para la salud pública y la medicina moderna. En este contexto, se buscan nuevas alternativas que actúen en dianas antimicrobianas diferentes a los antibióticos convencionales. Por lo tanto, se requiere una comprensión a nivel molecular de los patógenos bacterianos para diseñar terapias dirigidas a objetivos moleculares previamente desconocidos o distintos de los abordados por los antibióticos actuales. Pseudomonas aeruginosa es una bacteria Gram-negativa multirresistente que codifica en su genoma las ribonucleótido reductasas (RNRs), enzimas encargadas de suministrar los desoxirribonucleótidos (dNTPs) necesarios para la síntesis y reparación del ADN. Estas enzimas se han considerado como dianas antimicrobianas en estudios recientes. Aunque en eucariotas sólo se encuentra codificada la RNR de clase Ia, eubacterias como P. aeruginosa, presentan las tres clases de RNR (clase I, II y III), lo que le confiere una gran versatilidad para adaptarse a diferentes ambientes, ya que cada clase tiene unas características que favorecen su actividad en diversas condiciones ambientales. En las últimas décadas, se han identificado varios factores transcripcionales que regulan la expresión génica de las RNR. Uno de estos factores es NrdR, capaz de reprimir todas las clases de RNR, aunque su regulación es incierta. Además, P. aeruginosa tiene capacidad de formar biopelículas o biofilms, donde suele haber un gradiente en la concentración de oxígeno, por lo que es interesante ver cómo puede cambiar la expresión génica de múltiples genes de forma simultánea. En este estudio, nos proponemos profundizar en el conocimiento de la expresión génica y la regulación transcripcional de los genes nrd en bacterias. Por un lado, buscamos los factores transcripcionales asociados a la regulación de la expresión génica del gen regulador de las RNR, nrdR. Hemos demostrado que FleQ regula el gen nrdR al unirse a la caja de unión FleQ Box bajo diferentes condiciones oxigénicas (aeróbicas y anaeróbicas) y durante la formación de biofilm bacteriano. También evaluamos el papel de FleQ durante la infección en el modelo in vivo de Galleria mellonella. Además, hemos desarrollado un sistema que combina el uso de un casete sintético llamado GLOW, que codifica para proteínas fluorescentes como genes reporteros, con plásmidos que pueden permanecer en el citoplasma de la bacteria o insertarse cromosómicamente en el genoma bacteriano. Probamos este sistema en diferentes condiciones comúnmente descritas en la expresión génica en bacterias, utilizando para ello los promotores génicos de las distintas RNRs de P. aeruginosa estudiados en nuestro laboratorio, obteniendo resultados similares a los previamente obtenidos y corroborando la utilidad de nuestro sistema. En conclusión, el entendimiento de la regulación transcripcional del gen nrdR es fundamental y se encuentra un poco más completo gracias a al papel que efectúa el factor transcripcional FleQ. Además, demostramos que el sistema de plásmidos que contiene el casete GLOW es una herramienta efectiva y fácil para estudiar simultáneamente varios genes bacterianos mediante proteínas fluorescentes bajo condiciones ambientales dinámicas.
Deciphering the role of the Arabidopsis thaliana METACASPASE I (AtMC1) as a stress granule protein in proteotoxic stress responses
(Universitat de Barcelona, 2025-03-20) Ruiz i Solaní, Nerea; Valls i Matheu, Marc; Sánchez Coll, Núria; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Rising temperatures pose a significant challenge for plant growth, metabolism, and productivity worldwide. One of the most detrimental consequences of heat stress is the accumulation of misfolded proteins into aggregates, which disrupt cellular homeostasis and can ultimately result in cell death. To counteract this phenomenon, cells activate sophisticated proteostasis mechanisms that aid in maintaining protein quality and eliminating aggregates. A crucial component of this response is the formation of stress granules (SGs), which are biomolecular condensates that assemble in response to diverse environmental stresses, such as heat, oxidative stress, and infections. Although SGs are highly conserved across eukaryotic organisms including mammals, plants, yeast, and protozoa, their precise functions in plants remain poorly understood. However, emerging evidence suggests that SGs play a central role in coordinating plant stress responses. This thesis aims to expand our understanding of SGs in plants, focusing on the Arabidopsis thaliana type I metacaspase 1 (MC1). In Chapter 1, we characterized the function and activity of MC1, demonstrating that it localizes to SGs during proteotoxic stress. Using predictive software, we identified two intrinsically disordered regions (IDRs) in the amino acid sequence of MC1 that regulate its recruitment to SGs. This discovery enabled us to generate and purify a recombinant version of MC1 (rMC1), overcoming previous limitations in isolating type I metacaspases in vitro. Functional assays revealed that rMC1 exhibits a strong and evolutionary conserved capacity to clear protein aggregates, including those formed by pathological protein forms that cause a diversity of life-threatening diseases in humans. We further studied the role of MC1 in proteostasis in aging tissues. Notably, we showed that plant overexpressing MC1 present a delay in leaf aging. Based on this data and previous evidences, we infer that MC1 has an important pro-life function linked to its disaggregase activity and its ability to form SGs. In Chapter 2, we explored the role of MC1 in heat stress responses. Heat shock proteins (HSPs) are crucial for protecting cells from heat-induced damage by maintaining correct protein folding and unfolding, and promoting aggregate degradation. In Arabidopsis, HSP101 is a key component in thermotolerance that participates in aggregate clearance and localizes to SGs under heat stress. Given the similarities between MC1 and HSP101 in terms of their localization and function, we examined their interplay. Our findings demonstrate that MC1 and HSP101 colocalize in SGs under heat stress, and that MC1 is necessary to stabilize and maintain the structural properties of HSP101 SGs. Furthermore, we elucidated that MC1 facilitates HSP101 degradation via autophagy. As HSP101 is essential for seedling thermotolerance, we assessed whether MC1 influences this process. Indeed, MC1 overexpression significantly enhances seedling survival under heat stress, confirming the pro-life function of this metacaspase. In Chapter 3, we expanded our investigation to encompass all type I metacaspases in Arabidopsis and examined their potential functional redundancy. We observed that all three type I metacaspases were recruited to SGs under heat stress. Additionally, MC2, but not MC3, was capable of clearing Serpin1, a known substrate of MC1. However, genetic analyses revealed that the autoimmune phenotype observed in mc1 mutant plants is not exacerbated by additional mutations in MC2 or MC3, nor does the deletion of all three genes affect seedling thermotolerance. These results suggest that Arabidopsis type I metacaspases have diverged functionally over the course of evolution, acquiring specialized roles rather than exhibiting redundancy. In conclusion, this thesis provides novel insights into how SGs contribute to plant stress tolerance. Our findings underscore the significance of SGs in plant proteostasis and elucidate new avenues for research on plant stress biology. Moreover, the discovery that MC1 can disassemble human protein aggregates opens the door for potential therapeutic uses in human diseases.
Biofilms microbianos: Virulencia e interacciones hongo-bacteria
(Universitat de Barcelona, 2024-11-13) Arévalo Jaimes, Betsy Verónica; Torrents Serra, Eduard; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[spa] En la naturaleza la mayoría de los microorganismos viven en comunidades protegidas por una matriz extracelular. Estas agrupaciones, denominadas biofilms, generalmente albergan múltiples especies de microorganismos que interactúan entre sí. En el contexto biomédico, los biofilms se asocian con infecciones comunes, infecciones causantes de morbilidad severa e incluso infecciones causantes de mortalidad. Una vez adquiridas, estas infecciones son difíciles de erradicar, generando típicamente enfermedades recurrentes y/o crónicas. La consecuente prolongación en las hospitalizaciones genera una carga económica considerable e impacta negativamente en la calidad de vida de los pacientes. A pesar de esto, actualmente existen varias limitaciones que dificultan el manejo adecuado de las infecciones causadas por biofilms. La presente tesis estudió interacciones ambientales e inter-especies que influencian las características de los biofilms de hongos del género Candida y bacterias patógenas, siendo de particular interés aquellas relacionadas con la susceptibilidad y la virulencia. En primer lugar, se evaluó el impacto de cuatro medios de cultivo comúnmente usados en las principales características patogénicas de Candida parapsilosis. Las variaciones obtenidas en la tasa de crecimiento, morfología, susceptibilidad y virulencia asociadas al medio de cultivo resaltan el papel de las adaptaciones metabólicas en la patogenicidad de esta levadura y señalan la importancia de elegir adecuadamente las condiciones de los diseños experimentales. Luego, se estudiaron biofilms polimicrobianos de Candida albicans y Pseudomonas aeruginosa. Los resultados demuestran que el orden de colonización de las especies es un factor importante en el establecimiento de las interacciones entre estos microorganismos. En este escenario, los efectos de prioridad no sólo influencian la biomasa de las especies, sino también la estructura, susceptibilidad y virulencia del biofilm resultante. Por otra parte, el estudio de las interacciones no físicas entre C. albicans y Staphylococcus aureus permitió identificar que cambios ambientales relacionados con el pH y la disponibilidad de recursos resultan en nuevos fenotipos de S. aureus. Estas variantes presentan cambios en la expresión de factores de virulencia pertenecientes al sistema agr, que impactan negativamente la supervivencia de larvas de Galleria mellonella. I Finalmente, conscientes de la necesidad de contar con métodos y plataformas confiables para la realización de pruebas de susceptibilidad de biofilms, se evaluó el uso de diferentes tinciones en el estudio de los biofilms de C. parapsilosis. De esta manera, se encontró que las tinciones Syto 9, Naranja de tiazol y Diacetato de fluoresceína tenían un bajo rendimiento en el marcaje de C. parapsilopsis, a diferencia de la tinción FUN-1. Adicionalmente, se diseñó un dispositivo de microfluídica para el estudio de biofilms bacterianos en condiciones dinámicas. El BiofilmChip permite la formación de biofilms partir de cepas de laboratorio, aislamientos clínicos y muestras de pacientes, proporcionando condiciones que se asemejan a las encontradas en infecciones naturales. Además, posee un método de lectura rápido y sencillo basado en la impedancia, que permite monitorear el crecimiento y los cambios de biomasa asociados a la efectividad del tratamiento. En conclusión, el presente trabajo demuestra la importancia de caracterizar las respuestas de los microorganismos que crecen en biofilms frente a variaciones ambientales, para así definir mejores protocolos para su estudio. Además, resalta la necesidad de estudiar las coinfecciones hongo-bacteria como una comunidad, donde las interacciones físicas y químicas y los efectos de prioridad pueden aumentar el potencial patogénico de los microorganismos. Esto permitirá la formación de biofilms en condiciones más realistas, lo que se traducirá en avances de conocimiento en el campo. Por último, el desarrollo conjunto de métodos para la evaluación de susceptibilidad en biofilms, brindará las herramientas necesarias para ofrecer un tratamiento con mayor probabilidad de éxito en el manejo de las infecciones.
Population genomics of the nesting and foraging areas of the loggerhead turtle (Caretta caretta) facing climate change
(Universitat de Barcelona, 2024-11-18) Luna Ortiz, Patricia Astrid; Pascual Berniola, Marta; Carreras Huergo, Carlos; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Genomic techniques are increasingly being utilized in conservation biology, providing critical insights into the behavior, reproductive success, and various threats faced by vulnerable species. The loggerhead sea turtle (Caretta caretta) is particularly sensitive to climate change and presents a complex life cycle characterized by long migrations from nesting populations to foraging grounds. The threats and characteristics of the species highlight the importance of understanding its population dynamics for informed management decisions and effective conservation strategies. In this study, we focused on loggerhead turtles at different life stages. We first established a robust genomic baseline using the 2bRAD technique, analyzing 278 individuals from three regional management units (RMUs): the Mediterranean RMU (MED), represented by individuals from 11 nesting sites; the North West Atlantic RMU (NWA), represented by individuals from two nesting sites; and the North East Atlantic RMU (NEA), represented by individuals from one nesting site. We revealed significant genetic differentiation among the three RMUs and subsequently within the Mediterranean RMU identified three genetically differentiated SubRMUs: Greece (GRE), Levantine (LEV), and Sirte (SIR). Additionally, we tested our baseline assessing the natal origin of juvenile loggerhead turtles in foraging areas employing a hierarchical approach, moving from a global perspective that included all three RMUs to a regional level that considered the three SubRMUs within the Mediterranean. We genotyped 103 individuals from four Mediterranean foraging areas: the Catalan region (CAT), Lampedusa (LAM), Eastern Aegean Sea (EAS), and Western Aegean Sea (WAS). Only 3 individuals were assigned to NWA and 1 to NEA, thus indicating that these foraging areas are primarly used by Mediterranean individuals. Among the 99 individuals assigned to the Mediterranean RMU, the individuals assigned to the Lebantine SubRMU were predominant, with some exhibiting mixed assignments, indicating some admixture among subregions. Finally, to assess the rapid increase in the number of nesting events observed in Spain, we sampled 45 hatchlings from eight nests laid between 2016 and 2019. We found that nests were laid by different females, except for two nests attributed to the same female but within the same season. This suggests that the nesting activity is due to a surge of colonizing individuals rather than a return of females born in the region. We hypothesize that the rising number of colonizers results from successful conserva- tion efforts, a feminization of the originating populations, and earlier sexual maturation among individuals. Using our baseline, we identified in the emerging nesting area, one hybrid nest between an Atlantic female and a Mediterranean male assigned to the Sirte SubRMU, as well as several nests resulting from the genetic admixture among different Mediterranean SubRMUs. Thus, in response to climate change, the expansion into new nesting sites may be promoting genetic mixing between previously isolated populations, with potential implications for the species’ conservation. Our results not only clarify the current status of this colonization, but also highlight the need for ongoing efforts to monitor returning individuals to confirm the establishment of a stable resident population. In conclusion, the results obtained in this study provide critical information for understanding the ecological and evolutionary processes affecting loggerhead sea turtles. Our findings will contribute to enhancing conservation strategies in long lived species with high and complex dispersal behavior by identifying populations impacted by threats beyond nesting areas and facilitating the study of specific origins in mixed foraging habitats.
Less, but more: Massive gene losses and expansions in appendicularians stretch the evolutionary limits of the FGF signalling pathway within chordates
(Universitat de Barcelona, 2024-10-14) Sánchez Serna, Gaspar; Cañestro García, Cristian; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] The extensive diversity of forms in the animal kingdom arises from a limited set of evolutionarily conserved genes that coordinate during embryonic development to build complex bodies. Consequently, minor variations in this conserved set can lead to morphological innovations. The impact of gene loss on the evolution of developmental mechanisms has become an important topic in EvoDevo, especially since genomics revealed a high prevalence of gene loss across the tree of life. Over the past decade, the appendicularian Oikopleura dioica has emerged as a key model for studying this phenomenon in chordates. Despite a drastic reduction in its genome size and the loss of many developmental genes, O. dioica retains a typical chordate body plan, oﬀering a unique opportunity to investigate the organization of gene regulatory networks (GRNs) in a biological system heavily aﬀected by gene loss. Previous research has shown that O. dioica has experienced signiﬁcant losses in developmental signalling pathways, including the complete dismantling of the retinoic acid (RA) signalling machinery and a major reduction in the number of Wnt families. The extensive interactions between these pathways and the Fibroblast Growth Factor (FGF) signalling pathway in other chordates raise an interest in investigating the evolution of FGF signalling in this species. This study characterizes the FGF signalling pathway in O. dioica, revealing an unprecedented remodelling compared to other chordates. The species has lost six of the eight Fgf subfamilies present in the last common chordate ancestor, but the remaining two subfamilies have expanded along with the FgfR gene. Phylogenetic analyses, combined with comparative studies on gene structure and conserved protein motifs, provide robust evidence that the 10 Fgf genes identiﬁed in O. dioica belong exclusively to two subfamilies: Fgf9/16/20 and Fgf11/12/13/14. Analyses of gene structure, putative functional motifs, and developmental expression paherns indicate functional diversiﬁcation of these paralogs, as well as of the FgfR gene, following gene expansion. Additionally, examination of the three main intracellular transduction pathways associated with FgfR activation—MAPK, PLCγ/PKC, and PI3K/AKT—reveals that their main components are preserved and expressed throughout O. dioica development. However, structural rearrangements in FGF signal transduction have occurred, including the loss of classical Ras and Spred genes. Functional studies using the pharmacological inhibitor SU5402 demonstrate that the FGF signalling is crucial for embryonic development in O. dioica. Phenotypic analyses via whole-mount in situ hybridization of tissue-speciﬁc genes and omic approaches reveal that FGF signalling is involved in gastrulation and cellular lineage diﬀerentiation. Finally, by comparing the developmental expression domains of O. dioica Fgf genes with those in the ascidian Ciona robusta, an evolutionary scenario is proposed where the evolution of FGF signalling in O. dioica is related to the transition from an ascidian-like biphasic lifestyle to a fully free-living one. This scenario categorizes expression domain changes into three types: extinction of ancestral domains due to gene loss, functional shuﬄing among surviving paralogs, and innovation of novel expression domains in new paralogs. Overall, this doctoral thesis presents a comprehensive study of the FGF signalling pathway in a chordate with unprecedented levels of developmental gene loss. Our ﬁndings unveil the evolution of the Fgf family in appendicularians as a paradigmatic example of what we call “less, but more”, where massive gene losses, but also extensive duplications, result in the loss, conservation, and innovation of Fgf expression domains. This research provides new insights into the ﬂexibility and resilience of the FGF signalling pathway in chordates and raises questions about the evolutionary signiﬁcance of the Fgf9/16/20 and Fgf11/12/13/14 subfamilies. These ﬁndings contribute to a broader understanding of gene loss in EvoDevo, highlighting the complex interplay between genetic conservation and innovation.
Characterization of Hippo downstream effectors in the maintenance of planarian cellular identity
(Universitat de Barcelona, 2024-10-30) Font Martín, Daniel; Adell i Creixell, Teresa; González Estévez, Cristina; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] The study of tissue renewal in adult organisms has widely been viewed as a source to uncover the triggers for the disruption of cell lineages in pathologies such as cancer. One of pathways involved in this process is the Hippo pathway. The Hippo pathway acts as a mechanosensor of extracellular physical forces. These inputs lead to the control of organ growth through the regulation of cellular fate. However, the exact mechanisms and biological processes that underly this maintenance of cellular fate remain elusive and require further characterization. One of this biological processes is cellular senescence. Cellular senescence has been linked with the onset of tumoral transformation and other age-associated disorders similar to dysregulations of the Hippo pathway. Other processes that share similarities with Hippo in regards to tumorigenesis include the regulation of cell cycle progression, cytoskeleton maintenance and transcriptional regulation. Nonetheless, the connection between the Hippo pathway and these biological processes have been poorly characterized so far. To better understand these mechanisms we use planarians (Schmidtea mediterranea). These are ageless flatworms able to regenerate any body part and constantly resize according to food availability. The aim of this thesis revolves around highlighting the importance of cellular senescence, transcriptomic and cytoskeletal regulation and cell cycle progression downstream of the Hippo pathway to properly maintain cellular differentiation in vivo. In order to assess the role of these biological processes we use a RNAi screening approach by inhibiting putative effectors of the pathway representative of these biological functions. All in all, we found that cellular senescence predates and contributes to the loss of cellular differentiation. Moreover senescence rescues are able to prevent such phenotype. Furthermore we show that defects in maintenance of the cytoskeletal architecture impair proper metaphase progression of the cell cycle and induce dedifferentiation. We also detect that deregulation in transcription also impairs the progression of the cell cycle and is associated with loss of cellular identity. Finally we also correlate defects in the progression of the cell cycle with proliferation and alterations in growth and degrowth dynamics according to the nutrient status of the planarian. In conclusion we affirm that the biological processes of cellular senescence, cytoskeletal maintenance, transcriptional regulation and cell cycle progression are linked with the Hippo molecular pathway and their physiological regulation are key for maintaining the cellular fate.
Study of early signaling events governing epithelial regeneration
(Universitat de Barcelona, 2024-09-13) Esteban Collado, José; Serras Rigalt, Florenci; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] The mechanisms through which cells communicate to initiate a regenerative response remains unsolved. It is established that Reactive Oxygen Species (ROS) are early signals released from injured cells that propagates to stimulate the replacement of lost tissue. ROS triggers the activation of the stress activated protein kinases (SAPKs) p38 and JNK via phosphorylation. Prolonged or elevated activation of these kinases may induce apoptosis, while brief or minimal activation can foster regeneration. Nonetheless, the precise connection between ROS generation and the initiation of regenerative signaling pathways remains incompletely elucidated. To this aim, we used Drosophila wing imaginal discs as a model system due to its well-characterized regenerative ability aCer injury or genetic ablation. We found that The Apoptosis signal-regulating kinase 1 (Ask1) emerges as a pivotal factor for driving regenerative growth. It exhibits the remarkable ability to sense ROS both in dying and living cells. However, in living cells, its activation is intricately regulated by nutrient sensitivity through Akt, a core kinase of the insulin (PI3K/Akt) pathway. Akt phosphorylates Ask1 at Ser83, an indispensable event for Ask1 to catalyze the activation of p38, albeit not JNK. Moreover, nutrient restriction or mutations targeting Ser83 of the Drosophila Ask1 block regeneration. Impediments that can be rescued by the ectopic activation of p38, but not JNK. Besides, ROS plays a critical role in the ligand-independent TNF receptor (TNFR) Wengen (Wgn) activation in response to apoptosis. Wgn, but not Grindelwald (Grnd), exhibits a protective mechanism mediated by the signaling molecule TRAF1, ultimately leading to the activation of the Ask1-p38 axis. This stress-response mechanism could be evolutionary conserved as Wgn cysteine rich domain (CRD) shows greater similarity with TNFR families found in other deuterostomes. Our ﬁndings underscore a non-autonomous activation of a ROS sensing mechanism orchestrated by Ask1, Akt1 and Wgn that results in the activation of a p38-dependent regenerative response.
L’exposició a virus presents en l’ambient: descripció del viroma i avaluació del risc
(Universitat de Barcelona, 2024-07-19) Itarte Sorolla, Marta; Bofill Mas, Silvia; Rusiñol Arantegui, Marta; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[cat] Existeix una gran diversitat de virus presents en l’ambient als quals els humans estem exposats, constituint l’exposoma víric. Les eines de vigilància ambiental, com ara l’epidemiologia basada en aigües residuals, han posat de manifest el seu potencial per monitoritzar la circulació vírica en una comunitat, sobretot amb la recent pandèmia de la COVID-19. Per aquest motiu, aquesta tesi s’ha centrat, primerament, en l’estudi de l’aigua residual com a font de contaminació i eina per a estudis epidemiològics. Concretament, s’han avaluat diferents mètodes de detecció i caracterització dels coronavirus presents en les aigües residuals en un context de pandèmia, principalment mitjançant tècniques de seqüenciació de nova generació (NGS). Els virus excretats a les aigües residuals poden ser resistents als tractaments de les estacions depuradores d’aigües residuals (EDARs) i acabar contaminant les fonts d’aigua que s’utilitzen per beure, per regar o per a ús recreatiu, suposant així potencials vies de transmissió d’aquests virus. En aquesta tesi, s’ha estudiat l’exposició a virus patògens presents en aigües i aliments mitjançant la detecció i caracterització vírica, especialment aplicant tècniques de NGS en aliments de producció orgànica i les seves fonts d’aigua de reg. A més, també s’ha avaluat la contaminació vírica i s’ha explorat la diversitat de virus presents en escorrenties i aigües subterrànies d’un entorn urbà, les quals, en l’actual context de sequera, són de gran interès per a diferents usos. Finalment, considerant que l’exposició ocupacional a patògens pot comportar riscos per a la salut dels treballadors, s’ha avaluat l’exposició vírica en entorns laborals. S’ha quantificat la contaminació vírica i s’han identificat virus presents en aerosols i superfícies d’una EDAR i una granja de porcs mitjançant tècniques de NGS. A més, s’han realitzat estimacions del risc ocupacional associat a l’exposició a virus amb l’avaluació quantitativa del risc microbiològic (QMRA), seleccionant l’adenovirus humà (HAdV) per a l’EDAR i un virus hipotèticament zoonòtic amb característiques similars a l’adenovirus porcí (PAdV) per a la granja de porcs com a patògens de referència. Les vies d’exposició considerades en els models són la inhalació d’aerosols i la ingestió oral a través de superfícies contaminades i el contacte mà-boca. Aquesta tesi ha permès la identificació de virus presents en diverses matrius ambientals, incloent-hi aigües residuals, aigües d’escorrentia, aigües subterrànies, mostres d’origen animal, aliments de producció orgànica i aigües de reg, així com superfícies i aerosols d’entorns de treball. S’ha avaluat el nivell de contaminació vírica mitjançant la quantificació de virus indicadors de contaminació fecal i altres virus patògens. S’han identificat virus humans i animals d’interès aplicant tècniques de NGS, com la seqüenciació massiva d’amplicons i la seqüenciació amb enriquiment de dianes, utilitzant panells específics dirigits a la captura de seqüències de virus de vertebrats o també de coronavirus. Finalment, els resultats de QMRA han revelat un potencial risc ocupacional associat a l’exposició a HAdV per als treballadors d’EDARs, si no es prenen mesures. La simulació de QMRA a la granja de porcs també suggereix un potencial risc en cas d’exposició a un virus potencialment zoonòtic. Els resultats d’aquesta tesi ofereixen una visió rellevant sobre la presència de virus en diverses matrius ambientals i els potencials riscos associats amb l’exposició a aquests, contribuint al desenvolupament de mesures que ajudin a reduir aquests riscos i destacant la importància del monitoratge i la vigilància ambiental per a la detecció de virus emergents i zoonòtics, així com per a entendre les seves rutes de transmissió i identificar possibles fonts de contaminació.
Of flatworms and genes: Systematics, hybridization and evolutionary history of the Corso-Sardinian Dugesia (Platyhelminthes, Tricladida)
(Universitat de Barcelona, 2024-07-19) Dols Serrate, Daniel; Riutort León, Marta; Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística
[eng] Planarian flatworms (Platyhelminthes, Tricladida), commonly referred to as triclads, constitute a diverse taxonomic group encompassing a wealth of species exhibiting a broad spectrum of phenotypic diversity. Triclads are present in all biogeographical realms and have colonized terrestrial, marine, and freshwater environments distributed all across the globe, bearing testament to their evolutionary success. Free-living freshwater planarians of the family Dugesiidae encompass some of the most well studied taxa in the group and stand out due to their outstanding regenerative capabilities and diversity of reproductive strategies. Among the 12 genera presently recognized in the family, Dugesia is possibly one of the most emblematic. This taxon constitutes the most speciose genus of Dugesiidae, probably even of Tricladida, and is a well-defined taxonomic group that has silently colonized freshwater environments spread across Africa, Europe, the Middle East and Australasia, in spite of the low vagility of its species. In recent years, numerous studies have placed European Dugesia in the limelight as rising model systems for phylogeography and, ultimately, evolutionary biology. Understanding the processes by which populations differentiate and evolve into new species is fundamental to the field of evolutionary biology and holds significant implications for the underpinning of novel conceptual frameworks and the generation of both local and global patterns of species-level biodiversity. This thesis aims to contribute to the pursual of this knowledge by gaining insights into the processes that have shaped the genetic diversification, speciation and evolutionary history of a seemingly small taxonomic group of the longstanding genus Dugesia, namely: the Corso-Sardinian clade. This particular group, which only comprises endemics from Corsica and Sardinia, caught my interest for several reasons: (i) no phylogenetic or phylogeographic studies dedicated to its taxa were ever carried out; (ii) its diversity had not been evaluated under the light of integrative taxonomy approaches; (iii) this group harbors the only species with a haploid chromosome complement of 7 chromosomes in the entire Western Palearctic region, posing a possible case of speciation by chromosomal re- arrangement; (iv) the only putative case of interspecific hybridization in Dugesiidae (and Tricladida) was reported in this group. To unravel the evolutionary history and processes that have shaped the diversification of this group, I employed an integrative approach, incorporating morphological, karyological and molecular data. This approach has enabled the reevaluation of the taxonomic status of several Dugesia populations, resulting in the description of 3 new species for the group and the uncovering of multiple species candidates whose status and pertinent taxonomic decisions will be addressed in a forthcoming paper. Furthermore, divergence time estimation analyses indicated that most species within this group diverged during the Pleistocene, probably due to population fragmentation, contraction, and extinction events caused by the glacial phases. While it cannot be claimed that the phylogenetic relationships within the Corso-Sardinian clade have been fully resolved, this thesis has significantly contributed to elucidating its hidden diversity and phylogeography, thus laying the foundations for future research on this group. Most notably, by using phylogenomic markers and combining phylogenetic, genetic clustering and introgression analyses, this thesis reports and characterizes the first case of interspecific hybridization in Dugesiidae, and likely Tricladida. Furthermore, I examine the potential origin of the hybrids, their status as a potential hybrid species, and their seemingly mixoploid chromosome set. In addition, I also debate on the established concepts of hybrid speciation and assess their suitability for the current case presented within this thesis. Finally, this thesis has contributed to the planarian research community by presenting the first chromosome-scale genome assemblies of Dugesia. The results obtained from the analysis of these genomes have elucidated the origin of Dugesia hepta’s unique karyotype, while shedding light on the evolution of genome size in the genus. These results highlighted a differential expansion of transposable elements (TEs) in Dugesia involving large DNA TEs as the likely cause for the increment of genome size in this genus with respect to Schmidtea, while discarding a whole-genome duplication event as the underlying cause. Most importantly, these new genome assemblies will benefit the planarian research community and contribute to improving the understanding of the structure, organization, and genome evolution in planarians.

Browse

Recent Submissions