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- Strategies based on blocking the fibronectin synergy site for the treatment of solid malignant tumors(Universitat de València, 2026) Guerrero-Barberà, Gemma; Burday, Natalia; Costell, Mercedes; Departament de Bioquímica i Biologia Molecular; Institut de Biotecnologia i Biomedicina; Costell, Mercedes; Costell, MercedesThe extracellular matrices (ECM) are molecular networks that serve not only as the scaffold upon which cells are organized to form tissues but also provide essential biochemical and biomechanical cues that direct cell behavior. The malignant transformation of cancer cells is determined by both cell intrinsic properties, such as mutations, and extrinsic variables, such as the mixture of other cells in the tumor microenvironment and the ECM that they assemble. ECMs surrounding malignant solid tumors are fibrotic with abnormally increased stiffness. This feature was considered a mere consequence of the highly proliferative activity of the tumor, but abundant experimental evidence has changed the paradigm and now is well accepted that the high tumor rigidity potentiates de-differentiation, proliferation and invasion of tumor cells. Cancer-associated fibroblasts (CAFs) and infiltrating hematopoietic cells are major inducers of cancer stiffening. FN is a cell-adhesive protein and one of the firsts and more abundantly present in the stroma of primary tumors and metastatic foci. FN forms fibrillar and elastic networks that nucleate collagens and proteoglycans. Cells sense mechanical signals from their microenvironment through integrin receptors. FN contains two motifs, the RGD site and the synergy site, present in two adjacent modules (FNIII10 and FNIII9, respectively) that work in tandem to specifically regulate integrin-mediated cell adhesion, FN fibrils assembly and mechanosignaling. Upon a5b1 integrin binding to the RGD region and the nearby FN-synergy site, adhesions form and assemble large molecular signaling hubs that transduce information on ECM rigidity into the cell interior. Our project aims to explore a novel approach to prevent/reduce tumor growth by diminishing tumor cell mechanosensing alone or in combination with strategies impairing cell adhesion. The FN-synergy site is not critical for mesenchymal cell adhesion when tissue stiffness and av-class integrin expression are not perturbed. However, the synergy site becomes crucial to maintain cell adhesion when tensional forces increase above the physiological threshold, or when av-class integrin expression is lacking. Based on these findings, we are testing the hypothesis whether impairing the a5b1 adhesion reinforcement by blocking the synergy site in breast cancer prone mice represents a powerful strategy to curb tumor growth and metastasis, and whether concomitant application of Cilengitide, an av-class integrin inhibitor, increase its beneficial effect on tumorigenesis. To obtain a comprehensive picture of how FN-mediated mechano-sensing interferes with cancer, we will investigate an a5-synergy site blocking peptide-mimetic for in vivo use.
- Breast cancer cells with decreased fibronectin-integrin adhesion strength attenuate the malignancy of its microenvironment(Universitat de València, 2026) Burday, Natalia; Guerrero-Barberà, Gemma; Jayo, Assier; Sánchez del Pino, Manuel M; Ortiz-Zapater, Elena; Costell, Mercedes; Departament de Bioquímica i Biologia Molecular; Institut de Biotecnologia i Biomedicina; Costell, Mercedes; Costell, Mercedes; GIUV2016-309 ProMaExFibronectin (FN), a key component of many solid tumors microenvironment, increases their mechanical stiffening and promotes cancer progression and metastasis. We studied Fn1syn/syn;PyMT mice carrying the breast cancer-inducing PyMT oncogene and a Fn1 gene with a nonfunctional synergy site (FNsyn), which impairs the reinforcement of the a5b1 integrin adhesion to the FN-RGD motif. Here, we show that Fn1syn/syn;PyMT mice exhibit delayed tumor onset in the mammary glands and reduced lung metastasis associated with decreased tumor vascularization, reduced cancer cell proliferation and lower abundance of ECM fibrillar proteins within the tumor stroma. Isolated cancer-associated fibroblasts (CAFs) and tumor cells reveal that FNsyn makes them unresponsive to changes in substrate stiffness. Consequently, Fn1syn/syn CAFs cannot be activated, express low a-SMA and reduced Lysyl-2 and -3 oxidases leading to the assembly of loose fibrotic ECMs. Moreover, luminal beast cancer cells grown as organoids failed to acquire invasive traits on stiff FNsyn substrates. Importantly, these key alterations were strongly correlated with the phenotypic changes observed in the stroma of Fn1syn/syn;PyMT tumors, contributing to the establishment of a microenvironment characterized by a reduced abundance of immunosuppressive cytokines and an increased infiltration of immune cells. Therapeutic targeting of FNsyn is sufficient to reprogram the tumor microenvironment toward a less fibrotic and immunoactive state.
- Repositorio de Enriquecimiento degenes y promotores por mCSEA de datos de arrays de metilación EPICv2(Universitat de València-INCLIVA, 2026) García-Gimenez, José Luis; Ferrando, Carolina; Carbonell Monleón, Nieves; Mena Mollá, Salvador; Departament de Fisiologia; García-Gimenez, José Luis; García-Gimenez, José Luis; Carbonell Monleón, NievesAnálisis funcional mediante el paquete clusterProfiler en R (249) por medio de un análisis de sobre-representación (over-representation analysis, ORA). Se aplicó el análisis tanto a las DMPs como a las DMRs asociadas a genes y promotores obtenidas con los paquetes lima y DMRcate. Estos conjuntos de DMPs y DMRs se enriquecieron con términos GO (Gene ontology) y vías KEGG (Kyoto enciclopedia of genes and genomes), lo que resultó en la identificación de procesos biológicos y vías metabólicas sobre-representadas. Se generaron mapas de calor con agrupación jerárquica de características significativas utilizando los paquetes gplots y stats, empleando las funciones heatmap.2 y hclust, respectivamente. Se realizaron análisis de componentes principales con la función plotMDS en el paquete ino. Se diseñaron gráficos de volcán utilizando el paquete EnhancedVolcano en R. Todos los pasos computacionales se llevaron a cabo utilizando scripts R diseñados específicamente para este propósito
- Phytoplankton and zooplankton, and ecological network in summer and winter in three lakes of the Lagunas de Ruidera Natural Park(Universitat de València, 2025) Armengol Díaz, Javier; Olmo Rodríguez, Carla; Puche, Eric; Muñoz, Manuel E.; Ramos-Jiliberto, Rodrigo; Rodrigo, Maria A.; Institut Cavanilles de Biodiversitat i Biologia Evolutiva; GIUV2013-135 LimnologiaThe database compiles phytoplankton and zooplankton sampling data from Lakes Colgada, Conceja, and Cueva Morenilla in the Lagunas de Ruidera Natural Park, collected during the winter and summer of 2022. It provides organism records with the highest possible taxonomic resolution. For phytoplankton, both density and biovolume data are included, while zooplankton records comprise density values. In addition, the database contains key parameters describing the structure of the planktonic ecological network of the studied sites.
- Raw data for publication in Limnology and Oceanography-DAMOLAKE Rodrigo et al(Universitat de València, 2025) Rodrigo, Maria A.; Puche, Eric; Muñoz-Colmenares, Manuel; Pascual, Carlos; Armengol Díaz, Javier; Sanchez-Carrillo, Salvador; Institut Cavanilles de Biodiversitat i Biologia Evolutiva; Ecologia Integrativa; MariaThis data set compiles the raw data of a mesocosm experiment performed in the framework of DAMOLAKE-2 project, funded by the Spanish Ministerio de Ciencia e Innovación (Agencia Estatal de Investigación). It show data about greenhouse gas production, isotopic values in different organisms, nutrients in water and sediment, charophyte and filamentous algae biomass and microprofiles of oxygen and redox in the water-sediment interphase and in the first centimeters of the sediment. The rest of data about plankton can be found in the Supplementary Material of the publication by Rodrigo et al.
- Phytoplankton and zooplankton communities in three lakes of Lagunas de Ruidera Natural Park(Universitat de València, 2025) Armengol Díaz, Javier; Olmo Rodríguez, Carla; Puche, Eric; Muñoz, Manuel E.; Ramos-Jiliberto, R.; Rodrigo, Maria A.; GIUV2013-135 LimnologiaThe database compiles phytoplankton and zooplankton sampling data from Lakes Colgada, Conceja, and Cueva Morenilla in the Lagunas de Ruidera Natural Park, collected during the winter and summer of 2022. It provides organism records with the highest possible taxonomic resolution. For phytoplankton, both density and biovolume data are included, while zooplankton records comprise density measurements. In addition, the database contains key parameters describing the structure of the planktonic ecological network.
- The influence of Chara hispida (freshwater macroalgae) on denitrifying anaerobic methane oxidation: a microcosm experiment(Universitat de València, 2025) Puche, Eric; Muñoz, Manuel E.; Sánchez-Carrillo, Salvador; Rodrigo, Maria A.; Institut Cavanilles de Biodiversitat i Biologia Evolutiva; GIUV2013-135 LimnologiaThis dataset compiles the raw experimental and analytical data obtained from short-term microcosm incubations designed to evaluate the effects of the charophyte Chara hispida L. and nitrate availability on denitrifying anaerobic methane oxidation (DAMO) and related processes in freshwater sediments. The experiment followed a fully factorial design combining trophic status (low vs. high nitrate concentrations), methanogenesis (allowed vs. inhibited), and denitrification (allowed vs. inhibited) in both vegetated and bare-sediment conditions. The database includes temporal measurements of greenhouse gas concentrations (CH₄, CO₂, and N₂O) in the incubation headspace, microprofiles of dissolved oxygen and redox potential at the sediment–water interface, and the taxonomic composition of bacterial and archaeal communities derived from 16S rRNA gene sequencing. Each spreadsheet provides data corresponding to specific experimental treatments and sampling times, together with metadata describing units, experimental conditions, and abbreviations.
- Raw data for short communication submitted to Wetlands(Universitat de València, 2025) Rodrigo, Maria A.; Puche, Eric; Muñoz-Colmenares, Manuel; Armengol Díaz, Javier ; Sanchez-Carrillo, Salvador; Institut Cavanilles de Biodiversitat i Biologia Evolutiva; Rodrigo, Maria A.; Rodrigo, Maria A.; Ecologia IntegrativaSe presentan los datos correspondientes a la publicación Advancing experimental tools for wetlands: testing limnocorrals for greenhouse gas emissions and food web studies
- Supporting data to: Fucose dependent rotavirus and norovirus require fucosidase activity for optimal replication(Universitat de Valencia, 2025) Rodríguez Díaz, JesúsSupporting data to: Fucose dependent rotavirus and norovirus require fucosidase activity for optimal replication
- Supporting Information(Universitat de València, 2025) Antón González, Laura; Pellicer Chenoll, María Teresa; Villarrasa Sapiña, Israel; Toca Herrera, José Luis; González Moreno, Luis Millán; Devís Devís, JoséSupporting Information "Trends in the discussion of cycling in urban environments: An X-based study"
- Seroepidemiología de rotavirus no A(Universitat de València, 2025-03-12) Buesa Gómez, JavierTítulos de anticuerpos séricos frente a rotavirus A (RVA), RVB, RVC, RVH
- Microcosm experiment results, main variables, bacteria and archaea values [Dataset](Universitat de Valencia, 2025) Muñoz Colmenares, Manuel Eduardo; Rodrigo Alacreu, María A.; Puche Franqueza, Eric; Sánchez Carrillo, SalvaThis dataset presents the results obtained from a microcosm-scale experiment. In this dataset, the first columns indicate the assigned microcosm number and the factorial design and levels (assigned treatment, plant type, and temperature). Then, it contains greenhouse gas (carbon dioxide and methane) data, including emissions (flux) and dissolved concentrations in water. It also includes physicochemical variables (temperature, pH, dissolved oxygen, dissolved inorganic carbon, etc.), nutrients and macrophyte biomass (Myriophyllum and Chara). Furthermore, the dataset includes relative abundance values of bacterial and archaeal phyla and families, derived from sequencing the sediment-associated community. Dataset of the research paper "Vascular macrophytes versus charophytes: how the macrophyte type and warming affect the sediment microbial community and the production of greenhouse gases" Publication under review.
- Phytoplankton and zooplankton at Tancat de la Pipa (Albufera de València Natural Park)(Universitat de València, 2024-10-04) Carabal, Nuria; Cardoso, Luciana S.; Padisák, Judit; Selmeczy, Géza B.; Puche, Eric; Rodrigo, María A.; Departament de Microbiologia i EcologiaPhytoplankton and zooplankton data (from 2009 to 2023) collected in the Tancat de la Pipa, within the Albufera de València Natural Park. In the dataset can be find the raw data of the biovolume or biomass of the plankton during these years of study.
- Dataset Ecological status and type of alteration determine the C-balance and climate change mitigation capacity of Mediterranean inland brackish and saline shallow lakes(Scientific Reports, 2024 ) Morant, Daniel; Rochera, Carlos; Picazo, Antonio; Miralles-Lorenzo, Javier; Camacho-Santamans, Alba; Camacho, AntonioUnderstanding the metabolic processes governing carbon biogeochemistry in inland brackish and saline shallow lakes is crucial for assessing their capacity to mitigate climate change. This study aimed to investigate the relationship between carbon biotic processes, metabolic carbon balances, and environmental factors such as salinity, hydroperiod, and ecological status, which can be affected by human activities. We analysed carbon metabolic rates and budgets in 19 sites in the Spanish Mediterranean region, representing diverse ecological conditions. Results revealed that alterations in natural salinity levels, often linked to changes in hydrological regimes and ecological degradation, decreased carbon retention capacity and increased greenhouse gas emissions. Well-preserved or restored lakes exhibited higher carbon retention and mitigation capacities, particularly those with lower salinity levels, indicating higher biological activity. However, higher salinity levels mitigated methane emissions, reducing warming potential risks. This is the dataset of the study, that emphasised the importance of proper wetlands management or restoration to enhance their climate regulation services.
- Biochemical characterization of three heterologous lactic acid bacteria laccases from Pediococcus, Lactobacillus and Lacto-coccus genus and their potential to degrade biogenic amines using ABTS and epicatechin as mediators- DATASET(2024) Monroy, Isaac; Olmeda, Isidoro; Ferrer, Sergi; Pardo Cubillos, IsabelEn este trabajo se clonaron y caracterizaron tres lacasas bacterianas de las especies Pediococcus parvulus, Lacticaseibacillus paracasei y Lactococcus lactis, aisladas de vino y queso, y se evaluó su habilidad degradadora de aminas biógenas en presencia y ausencia de los mediadores ABTS (artificial) y epicatequina (natural).
- Dataset of benthic diatom taxa identified in Serranía de Cuenca (central Spain) waters during summer of 2017(2020) Alvarez Cobelas, Miguel; Rojo García-Morato, CarmenLos datos aqui presentados comprenden la ocurrencia y abundancia relativa de las diatomeas bentónicas identificadas en sistemas acuáticos de la Serranía de Cuenca (centro de España) durante el verano de 2017. Los taxones se ordenan en la matriz alfabéticamente y se les asigna un código. Las muestras se caracterizan tambien por un código y por información sobre su cuenca de origen (rio Tajo o Júcar), sustrato (mineral o planta) y hábitat (ambientes lénticos o lóticos). Toda esta información contenida en varias página de un documento excel.
- Central Iberian Mediterranean as refugium (MIS 5–3). Data and script(2020) Real Margalef, Cristina; Martínez Varea, Carmen María; Carrión Marco, Yolanda; Badal, Ernestina; Sanchis Serra, Alfred; Martínez Valle, Rafael; Guillem Calatayud, Pere MiquelSe aporta por un lado los datos base de los restos arqueobotánicos y arqueozoológicos identificados en yacimientos del Paleolítico medio y superior de la región central del Mediterráneo ibérico (Cova Negra, Abrigo de la Quebrada, Cova de les Malladetes y Cova de les Cendres). Y por otro, el script generado en el software R (con el paquete "Vegan") para calcular diferentes índices de diversidad. Todo ello utilizado en el artículo "Could the central Iberian Mediterranean region be defined as a refugium? Fauna and flora in MIS 5–3 and their implications for Palaeolithic human behaviour".
- Database of nodes' topological indices from experimental aquatic communities(2020) Puche Franqueza, Eric; Jordán, Ferenc; Rodrigo Alacreu, María A.; Rojo García-Morato, CarmenEsta base de datos contiene los valores de diversos índices topológicos calculados a partir de los nodos funcionales de las comunidades acuáticas plánctónicas-bentónicas de un experimento a escala de mesocosmos. Mediante un diseño experimental que constaba de tres escenarios ambientales con cuatro réplicas cada uno (con la temperatura y la radiación ultravioleta como factores experimentales), se agruparon los organismos presentes en cada réplica (mesocosmos) en nodos funcionales. Con estos nodos se construyeron redes ecológicas tróficas (solo considerando relaciones tróficas entre ellos) y redes multi-interacción (considerando relaciones tróficas y no-tróficas). A cada uno de los nodos en cada versión de la red ecológica se le calcularon diversos índices (topological importance index, toplogical overlap index, closeness centrality y betweenness centrality) que muestran su importancia topológica en la red. Las abreviaciones y explicaciones sobre los escenarios experimentales, las replicas de cada escenario y los detalles sobre los índices y los nodos de las redes están detallados en la primera hoja de esta base de datos.
- Carbon biomass planktonic-periphytic organisms of a mesocosm experiment [Dataset](2020) Puche Franqueza, Eric; Rojo García-Morato, Carmen; Rodrigo Alacreu, María A.Este documento presenta los datos de biomasa en carbono (mgC m-2) de taxones planctónicos y perifíticos de un experimento a escala de mesocosmos. La comunidad planctónica-perifítica fue sometida a tres escenarios de cambio global, con la temperatura y la radiación ultravioleta como factores experimentales testados independientemente. Cada elemento de la comunidad fue identificado a la máxima resolución taxonómica posible. Las abreviaciones y explicaciones sobre los escenarios experimentales, las replicas de cada escenario y los detalles de los compartimentos considerados en cada mesocosmos se muestran en la primera página de este documento.
- Database of an ecological multi-interaction network of a macrophyte-dominated lake(2019) Puche, EricThis database presents the community matrix of an ecological multi-interaction network (considering both trophic and non-trophic relationships) among planktonic and benthic organisms of a macrophyte-dominated freshwater system. This dataset comes from an experimental recreation, at a mesocosm scale, of this type of system. Furthermore, values of global- and node-metrics are provided as well as the results of the alteration of these metrics after the removal of each node of the network.
