Resultados de investigación

In 2014, the continental shelf and submarine canyon off Cap de Creus (NW Mediterranean) were included in the Site of Community Importance (SCI) “South-West Gulf of Lions canyons system” of the Natura 2000 Network of protected areas. Before the declaration of the SCI (2007-2103), 60 underwater video transects were performed in the area by means of ROVs and a manned submersible, covering more than 30 km of seafloor. Based on the annotation of the video images, we identified the main invertebrate megabenthic communities dwelling from the shelf (70 m depth) down to the bottom of the canyon head (400 m depth). The results of the multivariate analyses indicated that this marine area hosted several benthic communities dominated by suspension- and filter-feeding species, including octocoral gardens, soft-coral assemblages, crinoid fields, sponge grounds and cold-water corals. This dataset includes (1) the geographical location of the benthic communities identified in the video footage, as determined by the clustering analysis, (2) the intra-community diversity associated to the benthic communities, provided as the number of megafauna species identified in each sampling unit and the exponential of Shannon, and (3) the spatial distribution of the benthic communities mapped by means of the Random Forest classification algorithm. This dataset is related to the article “Diversity, structure and spatial distribution of megabenthic communities in Cap de Creus continental shelf and submarine canyon (NW Mediterranean)” submitted to Progress in Oceanography by Dominguez-Carrió et al., which contains further information on how the data were obtained and processed., This dataset was obtained in the framework of the European projects HERMES (Goce-CT-2005-511234-I) and Life+ INDEMARES (LIFE07/NAT/E/000732), and the Spanish projects DEEP CORAL (CTM2005-07756-C02-02/MAR) and the Acciones Complementarias (CTM2005-24174-E, CTM2006-27063-E/MAR, CTM2007-28758-E/MAR). [...] CD-C acknowledges the financial support received by the EU funded projects Life+ INDEMARES (LIFE07/NAT/E/000732) and ENPI ECOSAFIMED (ENPI CBC MED 2007-2013) and by the FCT-IP Project UIDP/05634/2020, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

Note the higher mutational load in comparison with the molecular NOS cases. B Summary of Variant classification in DLBCL NOS of the molecular NOS/other subtype (49%, 37 case. S2 Fig. A complete representation of genetic subtype associated Lymphgen features found on each case of DLBCL. Genetic subtype prediction, FISH results for MYC, BCL2 and BCL6, Histopathological subtype and cell of origin phenotype are shown. S3 Fig. Oncogenic signaling pathway analysis focusing on the RTK/RAS pathway in molecular NOS/Other DLBCL cases. Somatic mutations in genes such as ROS1 (7 cases) were prevalent in these cases. Mutations in MAPK/ERK pathway were absent with isolated cases showing NF1 (4 cases), BRAF (1 case) and NRAs (1 case) somatic mutations. B. Detail of gene locations for mutations in ROS1, NF1 and ALK. S4 Fig. TP53 somatic mutations in DLBCL cases. Detailed protein location of TP53 gene mutations are shown. Note the presence of hotspot mutations such as (p.Arg175His COSV52661038 and p.Gly245Ser, COSV52661877). S5 Fig. Detailed protein location of recurrent mutations in MAPK/ERK pathway genes, EGFR and ROS1 in plasmablastic lymphoma. S6 Fig. druggable categories in plasmablastic lymphoma according to mutational landscape. S1 Table. Summary of pathological features of the cohort of cases. Data regarding histopathological diagnosis according to current WHO classification, phenotype based on immunohistochemistry and/or gene expression profiling (LymphC2x), MYD88 L265P mutation status by allele-specific PCR and/or NGS in the tumor biopsy, FISH results, TP53 CNAs prediction, Lymphgen 2.0 genetic subtype predictions, EBV-EBER by in situ hybridization in tumor biopsy and HIV status are shown. S2 Table. MYD88L265P mutation status detected by AS-PCR in an independent series of 112 DLBCL samples, including seventy-one extranodal DLBCL. The prevalence of MYD88L265P mutation in extranodal samples was 45%, in contrast with <10% of nodal Lymphoma cases. S3 Table. Summary genetic subtype associated Lymphgen features found on each case of DLBCL. S4 Table. Summary of Lymphgen features found on each case of Plasmablastic Lymphoma. S5 Table. List of somatic variants identified in 108 cases. This list includes all type of variants (synonymous, intronic, missense, nonsense, splice site, frame-shift deletions, frame-shift insertions, in frame deletions, in-frame insertions, translation start site, non-stop mutations) with a DP superior or equal to 50 reads. For evaluation of complete raw data for each case, including germline DNA sequencing when available, please consider to log in the EGA repository (https://ega-archive.org/studies/EGAS50000000371). Request for data access may be referred directly to the Data Access Committee: https://ega-archive.org/dacs/EGAC50000000261, Peer reviewed

Sequencing data from various tissues of European seabass (Dicentrarchus labrax).-- Accession: PRJNA1103406. Data Type:Raw sequence reads, Los programas tradicionales de cría se centran en la genética y suelen ignorar la influencia ambiental y epigenética en la variabilidad fenotípica. En este estudio con peces, se analizaron ~500 000 loci CpG de 60 familias para desarrollar biomarcadores epigenéticos (EBs) que ayuden a seleccionar reproductores. Mediante selección cuidadosa de muestras, filtrado estadístico y algoritmos de machine learning, se identificaron tres loci CpG heredables asociados con biomasa, crecimiento rápido de hembras y resistencia a efectos de masculinización por alta temperatura. Con estos EBs se construyó un modelo capaz de predecir los mejores reproductores, validado en tres ensayos independientes y en una cohorte externa, mostrando robustez. Incorporar la selección epigenética aumentó la producción hasta 1,4 veces respecto a la selección genética sola. Esta estrategia ofrece un enfoque económico para integrar selección genética y epigenética, aplicable también a estudios de enfermedades raras y conservación biológica. El conjunto de datos incluye 20 librerias de RRBS con las cuales se desarrollo el método inicial y librerías de MBS hechas para su validación, Este estudio fue financiado por el “Centro para el Desarrollo Tecnológico e Industrial” (CDTI) y el Fondo Europeo Marítimo y de Pesca (FEMP) a través del Proyecto IDI-20220244 para ML, y por los proyectos del Ministerio de Ciencia de España PID2019-108888RB-I00 y PID2022-139096OB-I00 para FP, con financiación del gobierno español mediante la acreditación de “Centro de Excelencia Severo Ochoa” (CEX2019-000928-S). NS contó con una beca predoctoral del Ministerio de Ciencia e Innovación de España (BES-2017-079744), 28 RRBS libraries with pools of 4 individuals per family and sex and 70 individual MBS libraries, Peer reviewed

This dataset contains annual series of coral growth rates (1912-2020) and environmental variables used to generate the results of the following research article: Cardoso, G. O., Kersting, D. K., Brachert, T. C. , Heiss, G. A., Leinfelder, R., Maréchal, J.P., D’Olivo, J.P. (2025). Emerging skeletal growth responses of Siderastrea sidereacorals to multidecadal anthropogenic impacts in Martinique, Caribbean Sea. Scientific Reports, Anthropogenic stressors on Caribbean reefs have shifted coral dominance toward stress-tolerant species such as Siderastrea siderea, increasing their importance for reef construction. However, the sublethal responses of these corals to past stressors remain understudied, limiting our understanding of their long-term acclimatization capacity. Here, we reconstructed the annual skeletal growth rates (1912 to 2020) of twelve S. siderea coral colonies from Martinique (Caribbean Sea) and examined their relationships with changes in human population, sea surface temperature (SST), precipitation, river discharge, and agricultural indicators between 1950 and 2020. Long-term growth rate declines observed since the 1950s were initially associated with human population, a proxy for local stress. Warming SST enhanced coral skeletal growth between 1950 and 1985, suggesting optimal temperatures for calcification during this interval. However, skeletal density exhibited a multidecadal (1950 to 2020) parabolic response, indicating a surpassing of this thermal optimum in recent decades. This parabolic response included persistent skeletal density declines from 2010 to 2020, possibly related to cumulative thermal stress or the interaction with ocean acidification effects. Our findings suggest a limited acclimatization capacity of long-lived S. siderea corals to cumulative pressures in Martinique and highlight their vulnerability to the compounding effects of local stressors and climate change., European Union’s Horizon 2020 Research and Innovation Programme (EU-MaCoBioS)Grant no. 869710; Ministerio de Ciencia, Innovación y Universidades Ramon y Cajalgrant no. RYC2021-033576-I; Deutsche Forschungsgemeinschaft grant no. 468545550; Deutsche Forschungsgemeinschaft SPP 2299 “Tropical Climate Variability & Coral Reefs”Project no. 441832482, Peer reviewed

Sampling was conducted over a period of 14 yr (2000 to 2014) at the Blanes Bay Microbial Observatory (BBMO) station, located in the Bay of Blanes, in the Northwestern Mediterranean Coast (Fig. 1), approximately 60 km north of Barcelona. The BBMO station is a shallow site (~20 m depth) approximately 800 m offshore from the town of Blanes (41° 40' N, 2° 48' E). A total of 162 surface water samples were considered for analysis. The first one was taken in September 2000; from 2001 to 2014, samples were in general collected monthly, with some exceptions. A volume of water varying from 0.7 l to 1 l (depending on the sampling season) was filtered onto Whatman GF/F (nominal pore size 0.7 μm; 25 mm diameter) glass fiber filters with low vacuum (0.4 bars) to prevent cells from breaking. Subsequently, the filters were folded, dried, wrapped in aluminum foil and stored frozen at −80°C until analysis. For pigment extraction, the filters were placed in tubes with 2.5 ml of 90% acetone submerged in ice, and the pigments were extracted by sonication for 30 s. Subsequently, the filters were stored at −20°C. After 24 h, the samples were vortexed and filtered through Whatman GF/F glass fiber filters. Prior to 2008, the samples were analyzed at the Institut de Ciències del Mar (CSIC) in Barcelona according to the method of Zapata et al. (2000), using a ThermoQuest chromatograph (hereafter System 1), which included a P2000 solvent module, an A/S 3000 autosampler, a UV-3000 absorbance detector (440 nm), a FL2000 fluorescence detector (excitation = 430 nm, emission = 662 nm), and an SN 4000 controller. After 2008, analyses were carried out at the Centro Oceanográfico de Gijón/Xixón (IEO-CSIC) following the procedure (hereafter System 2) of Latasa (2014), which increased the sensitivity and lowered the detection limit, using an Agilent series 1200 chromatographic system consisting of a G1311A quaternary pump, a G1367C autosampler with a 100 μl capillary loop, a G1316B column thermostat, and a G1315C diode array detector. A significant change added to the System 2 analyses was the use of trans-β-apo-8'-carotenal, as an internal standard, dissolved in the acetone used for sample extraction. In total, 28 pigments were detected at 440 and 665 nm (System 1) or 474 and 664 nm (System 2) and identified by retention time and online diode array detector, - Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR), grant/award no. SGR/1179 - Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR), grant/award no. SGR/761 - Comissió Interdepartamental de Recerca i Innovació Tecnològica, Generalitat de Catalunya, grant/award no. 2005SGR/00872 - Comissió Interdepartamental de Recerca i Innovació Tecnològica, Generalitat de Catalunya, grant/award no. 2009SGR/1177 - Comissió Interdepartamental de Recerca i Innovació Tecnològica, Generalitat de Catalunya, grant/award no. 2014SGR/1179 - Comissió Interdepartamental de Recerca i Innovació Tecnològica, Generalitat de Catalunya, grant/award no. 2017SGR/1568 - Spanish Ministry of Science, Innovation and Universities (MICINN), grant/award no. CTM2015-70340-R, This work contributes to the Institut de Ciències del Mar "Severo Ochoa Centre of Excellence" accreditation CEX2024-001494-S funded by AEI 10.13039/501100011033 of the Spanish Ministry of Science and Innovation, Peer reviewed

Genes of the Tumor Necrosis Factor Superfamily (TNFSF) encode proteins with critical roles in cell signaling in animals, particularly in immunity and development. The evolution of the TNF superfamily remains poorly understood. This study demonstrates that tunicates possess a much more complex TNF superfamily than previously assumed. Some species have a large number of TNFSF genes, up to 14, due to frequent, independent tandem duplications. Significantly, this number exceeds that observed in many vertebrates (e.g., all characterized cyclostomes, as well as some birds and reptiles). As in vertebrates, the TNF superfamily of tunicates is capable of rapid evolutionary change. All 24 model tunicate species analyzed have different sets of TNFSF genes and even closely related species often have quite distinct TNF superfamilies. A comparison of tunicate and vertebrate data suggests that four TNFSF genes were present in the last common ancestor of both lineages. One of these genes was subsequently lost while the other three underwent independent duplications in early tunicate evolution. Six TNFSF genes were likely present in the common ancestor of all tunicates except perhaps appendicularians, for which data remain inconclusive. These results are consistent with the current model of how the TNFSF vertebrate genes emerged and evolved, except that whole-genome duplications played a significant role in expanding the family in vertebrates but not in tunicates. Transcription data obtained from Ciona intestinalis type A (C. robusta) indicate that several distantly related TNFSF genes share similar patterns of expression during development and in adults. Gene expression data are compatible with TNFSF genes having multiple roles, some of them in the innate immune system. Their involvement in immune defense may explain the rapid changes in TNFSF gene number observed in both tunicates and vertebrates., pone.0338039.s001.txt, Peer reviewed

Genes of the Tumor Necrosis Factor Superfamily (TNFSF) encode proteins with critical roles in cell signaling in animals, particularly in immunity and development. The evolution of the TNF superfamily remains poorly understood. This study demonstrates that tunicates possess a much more complex TNF superfamily than previously assumed. Some species have a large number of TNFSF genes, up to 14, due to frequent, independent tandem duplications. Significantly, this number exceeds that observed in many vertebrates (e.g., all characterized cyclostomes, as well as some birds and reptiles). As in vertebrates, the TNF superfamily of tunicates is capable of rapid evolutionary change. All 24 model tunicate species analyzed have different sets of TNFSF genes and even closely related species often have quite distinct TNF superfamilies. A comparison of tunicate and vertebrate data suggests that four TNFSF genes were present in the last common ancestor of both lineages. One of these genes was subsequently lost while the other three underwent independent duplications in early tunicate evolution. Six TNFSF genes were likely present in the common ancestor of all tunicates except perhaps appendicularians, for which data remain inconclusive. These results are consistent with the current model of how the TNFSF vertebrate genes emerged and evolved, except that whole-genome duplications played a significant role in expanding the family in vertebrates but not in tunicates. Transcription data obtained from Ciona intestinalis type A (C. robusta) indicate that several distantly related TNFSF genes share similar patterns of expression during development and in adults. Gene expression data are compatible with TNFSF genes having multiple roles, some of them in the innate immune system. Their involvement in immune defense may explain the rapid changes in TNFSF gene number observed in both tunicates and vertebrates., pone.0338039.s002.txt, Peer reviewed

Details of sample preparation and characterization; THz emission spectroscopy, THz emission signals and signal pump fluence dependence; THz reflectivity signals, DC sheet conductance and THz impedance; current-relaxation dynamics of reference samples, electron-phonon coupling parameters, electron and lattice heat capacities; electron-temperature dynamics; and response function of Co|TI stacks and interpretation., Peer reviewed

This study aimed to evaluate two anaesthetic methods for the shrimp Penaeus vannamei: oregano oil immersion and cold seawater exposure (~11 °C), using a holistic approach combining behavioural, physiological, and neurophysiological indicators. Both methods showed expected behavioural anaesthesia stages, with different induction times. However, physiological responses differed. Oregano oil induced metabolic, immunological, and oxidative stress without major neurophysiological (visual evoked response and electroencephalogram) changes, suggesting immobility rather than anaesthesia. On the contrary, cold seawater induced immediate alterations in neurophysiological parameters, which returned to baseline shortly after recovery, indicating that timely hypothermia could act as an effective and reversible anaesthetic, Co-funded by UNAM through PAPIIT projects IN225225, IN202926, the European Union’s Horizon Europe Project 101136346 EUPAHW, CEREBAL project (CSIC-AECID) INTER23001, and the Spanish government through the ‘Severo Ochoa Center of Excellence’ accreditation (CEX2020-001494-S). RL received funding from the European Commission through the HORIZON-MSCA-2023-PF-01-01, grant no. 101151377, Behaviour; Physiology; Neurophysiology, Peer reviewed

8 Pags.- 2 Figs.- 4 Tabls. Data Availability: Gypsum from soils of chesas, NE Spain (Original data) (Mendeley Data: https://data.mendeley.com/datasets/r57drh58pm/4). © 2024 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license., The dataset [1] hosts pedological info and images of the lands —locally known as chesas— of the outcropping gypsiferous core of the Barbastro-Balaguer anticline (Fig. 1). It stands out in the landscape for the linear reliefs due to outcrops of dipping strata with differential resistance to erosion, and also because of its whitish color (Fig. 2) and gypsophilous vegetation. This gypsum outcrop was named in the 19th Century [2] as a gypseous belt, and has been further studied by other geologists like [3,4] and by civil engineers e.g. Hué and Llamas [5]. Traditionally chesas were rangeland, with sparse almond and olive trees and rainfed winter cereals confined at the flat —and often terraced— valley bottoms, or vales as known in NE Spain. The chesas have attracted the attention of botanists [[6], [7], [8]], foresters [9,10], and soil hydrophysical properties researchers [11]. Moreover, public interest is increasing as the administrations are establishing rules for nature protection in the gypseous lands, e.g., a demarcation of 137 km2 set within the chesas was declared a Special Conservation Area “ES2410074 Yesos de Barbastro”, and then protected by the Habitats Directive of European Union. Also, plant physiologists are focusing on the adaptations of plants to gypsum as reviewed by Escudero et al. [12]. No soil map is available, but according to [13,14] the Gypsic Haploxerepts [15] are dominant. In the absence of a soil map, our dataset can help in the decisions to be made by the authorities, as is the case for water allocation to irrigated estates both in operation and planned, or for authorizations for the spreading of pig slurry. The herein presented soil data were collected with the classical techniques of pedological prospection. The dataset [1] contains the scans in .TIFF format of 150 whole thin sections of the soils, under both plane polarized light (PPL) and cross polarized light (XPL). Moreover, this dataset directs to a freely downloadable book [16] with the corresponding pedological descriptions, chemical and physical analyses, hydrophysical data, and scanning electron microscope images of the soils, plus micrographs of relevant pedofeatures of thin sections seen under petrographic microscope. The dataset [1] also presents a .xlsx file with an English translation of all figure captions of [16], including those of micrographs, and two more .xlsx files with analytical data. All data can be reused directly by naturalists, engineers, technicians and public servants in charge of environmental law development and enforcement, as well as by people involved in citizen science activities. Thin sections remain stored at EEAD and can be examined at our premises upon request., This research was made possible by the grant PID2021-127170OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”, and the grant TED2021-130303B-I00 funded by MCIN/AEI/10.13039/501100011033 and by the “European Union NextGeneration EU/PRTR”., Peer reviewed