BUSCADOR RECOLECTA

[Description of methods used for collection/generation of data] Sequencing was performed using PE150 sequencing (150 bp paired-end sequencing on each strand) on the Illumina NovaSeq X Plus platform (Illumina, San Diego, CA, USA) from Novogene. Files are row data., Los datos depositados contienen los resultados de la secuenciación masiva del ARN total aislado a partir de 63 schwannomas vestibulares, 4 schwannomas de nervios distintos al nervio vestibular (VS11, VS33, VS34 y VS74) y 7 fragmentos de diferentes nervios sanos (VS56, VS58, VS65, VS66, VS67, VS68, VS99). Los fragmentos de VS conservados en RNAlater® a -80°C se trataron con el reactivo de lisis Qiazol para la extracción de ARN utilizando el mini kit RNeasy (Qiagen, 50974106) siguiendo las instrucciones recomendadas por el fabricante en el servicio de Génomica del Instituto de Investigaciones Biomédicas Sols-Morreale de Madrid. Se utilizó ARN con un RIN (índice de integridad del ARN) superior a 7 para la secuenciación. La secuenciación se llevó a cabo utilizando la secuenciación PE150 (secuenciación “paired-end” de 150 pb en cada hebra) en la plataforma Illumina NovaSeq X Plus (Illumina, San Diego, CA, EE.UU.) de la empresa Novogene. Los datos de secuenciación depositados se presentan en formato fastq., This research was funded by Spanish MCIN PID2020-115274RB-I00 (THEARPY), PID2023-147347OB-I00 (PROHEAR), and CSIC #2024AEP115 grants to Isabel Varela-Nieto and Silvia Murillo-Cuesta, ## FICHERO X204SC24075390-Z01-F003_1.tar ##MD5-manual.pdfMD5.txtcheckSize.xlsMD5-win.exe03.Result_X204SC24075390-Z01-F002_Homo_sapiens.zipReadme.html## FICHERO X204SC24075390-Z01-F003_2.tar 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FICHERO X204SC24075390-Z01-F003_3.tar 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FICHERO X204SC24075390-Z01-F003_4.tar ##04.Ref/genome.gtf.gz04.Ref/genome_gene.fa.gz04.Ref/genome.fa.gz, Peer reviewed

Endocrine-disrupting compounds (EDCs) constitute a wide variety of chemistries with diverse properties that may/can pose risks to both humans and the environment. Herein, a total of 26 compounds, including steroids, flame retardants, and plasticizers, were monitored in three major and heavily urbanized river catchments: the R. Liffey (Ireland), the R. Thames (UK), and the R. Ter (Spain), by using a single solid-phase extraction liquid chromatography-mass spectrometry (SPE-LC-MS/MS) method. Occurrence and frequency rates were investigated across all locations over a 10-week period, with the highest concentration obtained for the flame retardant tris(2-chloroethyl) phosphate (TCEP) at 4767 ng∙L-1 in the R. Thames in Central London. Geographical variations were observed between sites and were partially explained using principal component analysis (PCA) and hierarchical cluster analysis (HCA). In particular, discrimination between the R. Ter and the R. Thames was observed based on the presence and concentration of flame retardants, benzotriazole, and steroids. Environmental risk assessment (ERA) across sites showed that caffeine, a chemical marker, and bisphenol A (BPA), a plasticizer, were classified as high-risk for the R. Liffey and R. Thames, based on relative risk quotients (rRQs), and that caffeine was classified as high-risk for the R. Ter, based on RQs. The total risks at each location, namely ΣRQriver, and ΣrRQriver, were: 361, 455, and 723 for the rivers Liffey, Thames, and Ter, respectively. Caffeine, as expected, was ubiquitous in all 3 urban areas, though with the highest RQ observed in the R. Ter. High contributions of BPA were also observed across the three matrices. Therefore, these two compounds should be prioritized independently of location. This study represents a comprehensive EDC monitoring comparison between different European cities based on a single analytical method, which allowed for a geographically independent ERA prioritization to be performed., Peer reviewed

Volcanism can cause major impacts, including climate change and mass extinctions. However, the impact of monogenetic volcanism is often considered as limited in volcanological research. This work provides for the first time an interdisciplinary approach to the socio-ecological impact of monogenetic volcanism in a key region, the La Garrotxa Volcanic Field (GVF, Girona, NE Iberia), where intense monogenetic volcanic activity occurred in the past. The analyses of a sedimentary sequence from the GVF enabled identifying previously unknown volcanic eruptions in the time interval 14-8.4 ka cal BP, constrain their volcanic stratigraphy and age, and unfold the effects of environmental change on geomorphology, vegetation, aquatic organisms and humans. Moreover, we reconstruct the major palaeoenvironmental changes caused by the eruptions in terms of fire episodes and subsequent disturbance on vegetation, hydrology and limnological conditions. When put in context with the archaeological record, it appears that the last hunter-gatherer communities were resilient at an extra-local scale, facing episodes of vulnerability due to volcanic activity, suggesting that their flexible nomadic patterns and foraging economies were an efficient source of risk management against the volcanic eruptions and their ecological impacts., Peer reviewed

Lake ecosystems are essential for human well-being. Due to its transboundary nature, connecting terrestrial and aquatic habitats, its environmental processes and functions support a wide array of ecosystem services (ES). Hence, despite its importance in supporting socio-ecologic systems, these freshwater ecosystems are highly impacted due to anthropogenic influence. ES may shed light on the importance of maintaining and restoring lake ecosystems. Hence, despite the increased effort in the last decades to provide robust spatial information, most scientific studies still follow a qualitative approach that carries a great deal of uncertainty and is not uptake by decision-makers. It is necessary to develop quantitative and robust methodologies for mapping ES, especially in the aquatic realm. This study develops several frameworks to map ES in lake ecosystems. Important to highlight is that this study.•develops a quantitative multi-method (biophysical and statistical) toolbox for lake ES multi-temporal mapping.•covers five ES from Provisioning, Regulating & Maintenance, and Cultural sections, namely: (1) Fibres and other materials for construction; (2) Water used for non-drinking purposes; (3) Maintenance of nursery populations; (4) nutrient regulation; and (5) recreation.•addresses three dimensions of ES: supply, flow; and demand., Peer reviewed

These files allow the estimation of equivalent Biot and Skempton coefficients for a fractured rock mass. The folder is organized into: validation: this folder contains the files used for the comparison of theoretical expressions with numerical results. In detail, it contains input scripts and results of the numerical HM simulation in 3DEC, input scripts and results for the DFN generation and analytical estimation of the coefficients, scripts for the comparison of numerical and theoretical estimations sensitivity: this folder contains the files used for the sensitivity analysis. In particular, it contains scripts for the direct estimation of coefficients and for the estimations from the generated DFNs, for the case of parallel fractures and for randomly oriented fractures., A quantitative and analytical approach is adopted to estimate two important parameters for coupled hydro-mechanical analysis at the scale of a fractured rock mass, namely the equivalent Biot effective stress coefficient α¯ and Skempton pore pressure coefficient B¯ . We derive formal expressions that estimate the two equivalent poroelastic coefficients from the properties of both the porous intact rock and the discrete fracture network, which includes fractures with different orientation, size, and mechanical properties. The coefficients are equivalent in the sense that they allow effectively predicting the volumetric deformation of the fluid-saturated fractured rock under an applied load in drained and undrained conditions. The formal expressions are validated against results from fully coupled hydro-mechanical simulations on systems with explicit representation of deformable fractures and rock blocks. We find that the coefficients are highly anisotropic as they largely vary with fracture orientations with respect to the applied stress tensor. For a given set of fracture and rock properties, B¯ increases with the ratio of normal to average stress undergone by the fractures, while the opposite occurs for α¯ . Additionally, both α¯ and B¯ increase with fracture density, which directly impacts the deformation caused by a load in undrained conditions. Because the effective stress variation is proportional to the applied load by (1 - α¯ B¯) , a factor that partly compensates for the decrease in equivalent rock stiffness caused by the fractures, a fully saturated fractured rock may deform less than an intact rock in undrained conditions, while the opposite occurs in dry conditions., Peer reviewed

Dataset and R code for the manuscript entitled 'Plastic debris in lakes and reservoirs' by Nava et al. (www.nature.com/articles/s4186-023-06168-4) - Article DOI: 10.1038/s41586-023-06168-4, Plastic debris is thought to be widespread in freshwater ecosystems globally1. However, a lack of comprehensive and comparable data makes rigorous assessment of its distribution challenging2,3. Here we present a standardized cross-national survey that assesses the abundance and type of plastic debris (>250 μm) in freshwater ecosystems. We sample surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes, with the aim to identify factors associated with an increased observation of plastics. We find plastic debris in all studied lakes and reservoirs, suggesting that these ecosystems play a key role in the plastic-pollution cycle. Our results indicate that two types of lakes are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas and large lakes and reservoirs with elevated deposition areas, long water-retention times and high levels of anthropogenic influence. Plastic concentrations vary widely among lakes; in the most polluted, concentrations reach or even exceed those reported in the subtropical oceanic gyres, marine areas collecting large amounts of debris4. Our findings highlight the importance of including lakes and reservoirs when addressing plastic pollution, in the context of pollution management and for the continued provision of lake ecosystem services., Peer reviewed

Although numerous studies support a dose-effect relationship between Endocrine disruptors (EDs) and the progression and malignancy of tumors, the impact of a chronic exposure to non-lethal concentrations of EDs in cancer remains unknown. More specifically, a number of studies have reported the impact of Aldrin on a variety of cancer types, including prostate cancer. In previous studies, we demonstrated the induction of the malignant phenotype in DU145 prostate cancer (PCa) cells after a chronic exposure to Aldrin (an ED). Proteins are pivotal in the regulation and control of a variety of cellular processes. However, the mechanisms responsible for the impact of ED on PCa and the role of proteins in this process are not yet well understood. Here, two complementary computational approaches have been employed to investigate the molecular processes underlying the acquisition of malignancy in prostate cancer. First, the metabolic reprogramming associated with the chronic exposure to Aldrin in DU145 cells was studied by integrating transcriptomics and metabolomics via constraint-based metabolic modeling. Second, gene set enrichment analysis was applied to determine (i) altered regulatory pathways and (ii) the correlation between changes in the transcriptomic profile of Aldrin-exposed cells and tumor progression in various types of cancer. Experimental validation confirmed predictions revealing a disruption in metabolic and regulatory pathways. This alteration results in the modification of protein levels crucial in regulating triacylglyceride/cholesterol, linked to the malignant phenotype observed in Aldrin-exposed cells., Peer reviewed

Wastewater Treatment Plant (WWTP) effluents are important sources of antibiotics, antibiotic resistance genes (ARGs) and resistant bacteria that threaten aquatic biota and human heath. Antibiotic effects on host-associated microbiomes, spread of ARGs and the consequences for host health are still poorly described. This study investigated changes of the Daphnia magna associated microbiome exposed to the recalcitrant antibiotic doxycycline under artificial reconstituted lab water media (lab water) and treated wastewater media. D. magna individual juveniles were exposed for 10 days to treated wastewater with and without doxycycline, and similarly in lab water. We analysed 16 S rRNA gene sequences to assess changes in community structure, monitored Daphnia offspring production and quantified ARGs abundances by qPCR from both Daphnia and water (before and after the exposure). Results showed that doxycycline and media (lab water or wastewater) had a significant effect modulating Daphnia-associated microbiome composition and one of the most discriminant taxa was Enterococcus spp. Moreover, in lab water, doxycycline reduced the presence of Limnohabitans sp., which are dominant bacteria of the D. magna-associated microbiome and impaired Daphnia reproduction. Contrarily, treated wastewater increased diversity and richness of Daphnia-associated microbiome and promoted fecundity. In addition, the detected ARG genes in both lab water and treated wastewater medium included the qnrS1, sul1, and blaTEM, and the integron-related intI1 gene. The treated wastewater contained about 10 times more ARGs than lab water alone. Furthermore, there was an increase of sul1 in Daphnia cultured in treated wastewater compared to lab water. In addition, there were signs of a higher biodegradation of doxycycline by microbiomes of treated wastewater in comparison to lab water. Thus, results suggest that Daphnia-associated microbiomes are influenced by their environment, and that bacterial communities present in treated wastewater are better suited to cope with the effects of antibiotics., File: Hegg_et _al-Microcystin_tolerance_assay.csv Description: Data used for the Microcystin tolerance assay. Columns: individual_ID = individual identity trial_number = trial number (0=week 0; 1 = week 4; 2 = week 8; 3 = week 12; 4 = week 16) clone_ID = clone identity treatment = experimental treatment (0 = non-toxic / no microcystin producing; 1 = toxic / microcystin producing) bucket_ID = identity of the bucket the individual comes from replicate_number = replication number (5 replications per trial per treatment) days_of_survival = days of survival since the start of the experiment (19 = until the end of the assay) number_of_broods = number of produced broods average_brood_size = average brood size total_number_of_offspring = total number of offspring (average_brood_size * number_of_broods) survival_till_end = survival until the end of the assay (0 = no; 1 = yes) File: Hegg_et_al-Microcystin_measurements.csv Description: Measurements of Microcystin concentrations with ELISA-kit. Columns: elisa_sample = sample number on well plate (samples were randomized on plate: this is not the location on the plate) elisa_number = identity of ELISA well plate date = date of sampling (year-month-day) enclosure = identity of enclosure type = either inside the enclosure or in the surrounding water column. Site = site identity (A or B) Microcystin = average microcystin concentration (in microgram/liter) microcystin_stddev = standard deviation of microcystin concentration (in microgram/liter) File: Hegg_et_al-Overview_microbiome_samples.csv Description: Overview of microbiome samples including data linked to these samples such as Microcystin concentrations and output of the tolerance assays. Columns: sample = sample file name sample_id = sample identity (not for the control samples) type = type of sample (gut = pooled gut samples; wf = water sample from the field; control = control samples) date = date of sampling (year,month,day) site = experimental site identity enclosure = enclosure identity clone = clone identity (only available for gut samples) sequence_run = sequence run identity (1 or 2) microcystin = Microcystin concentration (in microgram/liter) in enclosures. offspring_tox = average number of offspring produced per individual in the toxic treatment (from the tolerance assay) offspring_nontox = average number of offspring produced per individual in the non-toxic treatment (from the tolerance assay) totalnumber_tox = total number of replicates in the toxic treatment (tolerance assay) totalsurv_tox = number of replicates that survived until the end of the assay in the toxic treatment (tolerance assay) totalrep_tox = number of replicates that reproduced before end of the assay in the toxic treatment (tolerance assay) totalnumber_nontox = total number of replicates in the non-toxic treatment (tolerance assay) totalsurv_nontox = number of replicates that survived until the end of the assay in the non-toxic treatment (tolerance assay) totalrep_nontox = number of replicates that reproduced before end of the assay in the non-toxic treatment (tolerance assay) File: Hegg_et_al-Phylogenetic_tree.tree Description: Phylogenetic tree of all microbiome samples. This file is readable with the package “ape” in “R”. File: Hegg_et_al-Microbiome_taxa_table.csv Description: List of all taxa present in the dataset and their 16S amplicon sequences. Row names are 16S amplicon sequences. Columns indicate taxonomic ranks (Kingdom, Phylum, Class, Order,Family and Genus)., Peer reviewed

We developed a kinetic model that reveals the key factors, including aerosol oxidants and atmospheric variables, that determine the multiphase formation of sulfate aerosols in the atmosphere. This dataset includes the output results discussed in an unpublished paper., Severe haze in Beijing is characterized by the rapid formation of sulfate via the multiphase oxidation of SO2. While many factors, including aerosol oxidants and atmospheric variables, were discovered and investigated, their relative importance remains unclear. Herein, based on the field observation data obtained in Beijing, China, we developed a kinetic model to explore the key factors that determine the multiphase formation of sulfate. Sensitivity tests give the kinetics of each oxidation pathway varying with pH and temperature, based on which the total sulfate formation rate at room temperature (298 K) is calculated to be generally greater than that at standard temperature (273 K), especially during nighttime. Interfacial oxidants are responsible for sulfate formation within a wide pH range, and transition metal ions become more efficient with increased temperature. The multiphase chemistry is additionally affected by aerosol liquid water content (ALWC), particle radius (Rp), and ionic strength (IS). Within the usual aerosol acidity, the kinetic discrepancy induced by different ALWC levels is more significant at the lower temperature, in contrast to the temperature dependence related to Rp, and the effect of IS depends highly on pH. Machine learning reveals the potential importance of temperature, acidity, and Rp. Temperature and acidity are impactful for the formation of both aqueous and interfacial sulfates, whereas Rp only affects the interfacial processes. The discrepancy between nighttime and daytime is considered throughout this study. Overall, this study reveals the key factors for multiphase sulfate formation and is recommended for kinetic evaluation in future laboratory research., Peer reviewed

Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. Atlantic cod (Gadus morhua) is an important fish species in the North Atlantic ecosystem and in human nutrition, with a highly fatty liver. Here we study the involvement of Atlantic cod Ppar a and b subtypes in systemic regulation of lipid metabolism using two model agonists after in vivo exposure. WY-14,643, a specific PPARA ligand in mammals, activated cod Ppara1 and Ppara2 in vitro. In vivo, WY-14,643 caused a shift in lipid transport both at transcriptional and translational level in cod. However, WY-14,643 induced fewer genes in the fatty acid beta-oxidation pathway compared to that observed in rodents. Although GW501516 serves as a specific PPARB/D ligand in mammals, this compound activated cod Ppara1 and Ppara2 as well as Pparb in vitro. In vivo, it further induced transcription of Ppar target genes and caused changes in lipid composition of liver and plasma. The integrative approach provide a foundation for understanding how Ppars are engaged in regulating lipid metabolism in Atlantic cod physiology. We have shown that WY-14,643 and GW501516 activate Atlantic cod Ppara and Pparb, affect genes in lipid metabolism pathways, and induce changes in the lipid composition in plasma and liver microsomal membranes. Particularly, the combined transcriptomic, proteomics and lipidomics analyses revealed that effects of WY-14,643 on lipid metabolism are similar to what is known in mammalian studies, suggesting conservation of Ppara functions in mediating lipid metabolic processes in fish. The alterations in the lipid profiles observed after Ppar agonist exposure suggest that other chemicals with similar Ppar receptor affinities may cause disturbances in the lipid regulation of fish. Model organism: Atlantic cod (Gadus morhua). LSID: urn:lsid:zoobank.org:act:389BE401-2718-4CF2-BBAE-2E13A97A5E7B. COL Identifier: 6K72F., Peer reviewed