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Español: El herbario general de fanerogamia está formado por un 75 % de plantas ibéricas frente al 25 % de plantas de otro origen. Este herbario es el instrumento principal del proyecto "Flora Iberica" y también sostiene otras investigaciones como las prospecciones en áreas tropicales poco conocidas. En los últimos años las prospecciones realizadas en Guinea Ecuatorial y en la isla de Coiba (Panamá) son notables. El herbario general de fanerogamia está organizado por orden alfabético de especies, géneros y familias. Se divide en cuatro grupos: helechos, gimnospermas, dicotiledóneas y monocotiledóneas. Como guía básica se utiliza el trabajo de BRUMMITT, 1992 (Vascular Plant Families and Genera), con las modificaciones reflejadas en Flora Iberica. Para los helechos se utiliza el criterio de PICHI SERMOLLI (1977). Para gimnospermas, el de MELCHIOR y WERDERMANN (1954) y para monocotiledóneas el de DAHLGREN, CLIFFORD & YEO (1985). Existe un archivo informatizado con familias y géneros reconocidos en nuestro herbario. En cada especie, las hojas se agrupan en carteras de colores según el continente del que proceden. Los pliegos identificados solo como género o familia se colocan al final del herbario, separados en camisas con los colores de sus respectivos continentes. English: The Real Jardín Botánico de Madrid Vascular Plant Herbarium (Spain) is the largest herbarium in Spain and one of the most representative in Europe. The herbarium houses over a million specimens. It represents all plant groups and has a particularly important collection of specimens from the Iberian Peninsula, together with type specimens of South American plants gathered during historical expeditions. It is a restricted-use public collection. Under the regulations governing the management of the CSIC's collections, the Real Jardín Botánico de Madrid Herbarium is the property of the CSIC and is considered a national asset.

The monitoring of the macroinvertebrates community in Doñana wetlands was initiated in 2004 as part of the Monitoring Program of Natural Resources and Processes. The aim was to obtain a temporal and continuous series of data in the abundance and distribution of macroinvertebrates species to analyze the evolution of their numbers and estimates biodiversity values. Data were recorded annually between 2004-2019 by more than 2 members of the monitoring team which performed samplings in different locations twice per year in winter-spring and summer seasons when the study sites are flooded.The macroinvertebrates were sampled at the 139 stations classified according to their location (oneither aeolian sands or marshland). Funnel traps were used as a sampling method. Between 5-9 funnel traps were randomly distributed (until 50 cm of depth) in each location, depending of the flooded area and depth. The traps were left for 24 hours and emptied the content into white sorting pans. Individuals were counted and identified until the maximun taxonomic level in the field and realease. During samplings, it was identified 65 families. The most abundances were Notonectidae and Corixidae. Data recorded during the surveys included species identification, number of individuals, sex and life stage (pupa, larvae, juvenile, adult) of the organisms when possible, as well as the time and georreferenced data of the observation. Between 2004-2007 data was registered in Excel file and since 2008 data was recorded in CyberTracker sequence). The protocol used has been supervised by researchers and the data have been validated by the members who performed the sampling., The aim of this project is to provide information about the evolution of the conservation status of Doñana. To do that, it has been designed a monitoring program of the dynamic of natural processes and the distribution and abundance of species and communities. This monitoring is generating time series of data which is being used to analyzed long-term trends.

This dataset compiles the code for the research article "Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses". Both the raw and processed transcriptomic data experimentally generated and analysed here in order to identify transcriptional indicators of plant immune cell death are available at GEO (currently under embargo). In addition, supplementary data published with the article, some of which was generated using this code, is available (currently under embargo until manuscript publication) in a linked dataset (https://doi.org/10.34810/data136). Code mainly created by Víctor González and José Salguero Linares. Additional code and analysis suport by David Rengel and Martí Bernardo-Faura., Code and analysis results for "Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses. The repository contains code folders for RNASeq analysis and Figure preparation as well as data folders for GO, annotation, qPCR and microscopy data and others., Peer reviewed

This repository contains experimental data, scripts used for the data analysis, scripts used for the numerical calculation and the microscopy analysis for the following paper: "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks"., Peer reviewed

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cancers14030670/s1, Figure S1. Sanger sequencing results of the CYBA (upper panel) and TRPM4 (lower panel) wild type and mutant sequences; Figure S2. Splicing functional assays of TRPM4 variant c.25-1G>T. (A) Fluorescent fragment analysis by capillary electrophoresis of RT-PCR products generated by the wild type and mutant minigenes. The canonical and the aberrant ∆(E2p2) transcripts are shown as blue and red peaks, respectively, while the LIZ500 size standard is displayed as orange peaks. (B) Schematic representation of the canonical (above) and anomalous (below) transcripts. Variant c.25-1G>T is shown in red; acceptor sites are underlined; splicing events are shown as broken arrows; Figure S3. SiRNA knockdown of CYBA or TRPM4 lead to reduced mRNA and protein of the respective genes: mRNA (A) and protein (B) levels of CYBA and TRPM4 decreased after siRNA knockdown of CYBA or TRPM4 in LS174T cells; mRNA (C) and protein (D) levels of CYBA and TRPM4, decreased after siRNA knockdown of CYBA or TRPM4 in HT-29 cells. For real-time PCR assays, three independent experiments in triplicate were performed and means and standard errors of the means are presented on the graphs. For western blot two independent experiments were performed;Table S1. Summary of the sequencing coverage and quality statistics for each sample; Table S2. Loss-of-function variants segregated with the disease in 15 colorectal cancer families., Peer reviewed

CiberAMP is an R package that uses differential expression analyses to stablish accurate correlations between specific SCNVs and changes in expression in the genes affected by them. The algorithm has been designed to be an easy-to-access tool for the TCGA, the largest database in the world with genomic and transcriptomic data ofr more than 10,000 samples of 33 different human cancers. Unlike other methods, CiberAMP can yield information on: (i) SCNV-DEGs (somatic copy number variations associated differentially expressed genes) in a cohort of TCGA tumor samples (ii) The type of copy number variation associated with each SCNV-DEG in terms of expression pattern and genomic context (iii) Insights on the potential functional relevance of each identified SCNV-DEG, Peer reviewed

The Integrated and Open Butterfly Database provide a massive dataset of curated COI sequences for West Palearctic butterflies and an updated checklist. Functions to manage the dataset are also provided., The IOdatabase is intended as a project integrating several datasets of butterflies from Western Palaearctic harmonised with a shared taxonomy. IOdatabase now includes a revised version of the species checklist from West Palerarctic (Wiemers et al. 2016 and Middleton Welling et al. 2020) and more than 30000 COI sequences for 532 species. COI sequences belong to three main sources: 1) De novo sequencing mostly for Maghreb and Macaronesia 2) Published DNA-barcode libraries and public BOLD projects compiled at regional level 3) Studies providing COI of single species or genera. In the latter case, we checked whether haplotypes, instead of specimens, were included in repositories (Paz‐Vinas et al. 2021). If the number of specimens sharing a given haplotype in a particular location was reported, we replicated the haplotype sequences to obtain data at the specimen level, otherwise the sequences were excluded. We verified species identifications by building neighbor-joining trees for each genus. When morphology could not be verified, we removed sequences not clustering within the species to which they were attributed if the mismatch did not involve one of the 74 species showing DNA-barcode sharing. Metadata are also available: coordinates in WGS84 (degrees) and Lambert projections (meters), BOLD and Genbank codes, Continental areas and country obtained by an autmatic attribution using the rworldextra R package. Using these data we also calculated some basic indexes of genetic diversity (number of haplotypes observed and predicted based on rarefaction curves, GST, DST, haplotype diversity and nucleotide diversity)., Peer reviewed

Supplementary Figure 1. Isolated EVs present typical size and topology. Supplementary Figure 2. Protein profiling from total cell lysates and their derived EVs from WT and KO-HDAC6 BMDCs. Supplementary Figure 3. Enrichment in acetylated and ubiquitinated DC proteins upon Lm infection. Supplementary Figure 4. Ubiquitination in K-48 and K-63 state in T lymphoblast total cell lysates and their derived EVs. Supplementary Figure 5. Pore filtration methods restrain Lm and do not induce strong antipathogenic responses. Supplementary Figure 6. IFN-β is detected following Lm infection. Table S1. List of antibodies used for Western-blot and Flow Cytometry and the used dilution. Table S2. List of primers, with their corresponding sequence, used for qPCR. Table S3: Protein quantification in total cell lysates Table S4: IPA analysis of total cell lysates: canonical pathways and diseases and functions category Table S5: Protein quantification in EVs Table S6: IPA analysis of EVs: diseases and functions category Table S7: Ubiquitinated and acetylated peptides in total cell lysates and EVs Table S8: Enrichment analysis of ubiquitinated and acetylated proteins, Peer reviewed

Supplementary Table 9. Gene ontology (GO) functional enrichment analysis of the differentially expressed genes (DEGs) for cellular component., Mouse models of cancer provide a powerful tool for investigating all aspects of cancer biology. In this study, we used our recently developed machine learning approach to identify the cellular morphometric biomarkers (CMB) from digital images of hematoxylin and eosin (H&E) micrographs of orthotopic Trp53-null mammary tumors (n = 154) and to discover the corresponding cellular morphometric subtypes (CMS). Of the two CMS identified, CMS-2 was significantly associated with shorter survival (p = 0.0084). We then evaluated the learned CMB and corresponding CMS model in MMTV-Erbb2 transgenic mouse mammary tumors (n = 53) in which CMS-2 was significantly correlated with the presence of metastasis (p = 0.004). We next evaluated the mouse CMB and CMS model on The Cancer Genome Atlas breast cancer (TCGA-BRCA) cohort (n = 1017). Kaplan–Meier analysis showed significantly shorter overall survival (OS) of CMS-2 patients compared to CMS-1 patients (p = 0.024) and added significant prognostic value in multi-variable analysis of clinical and molecular factors, namely, age, pathological stage, and PAM50 molecular subtype. Thus, application of CMS to digital images of routine workflow H&E preparations can provide unbiased biological stratification to inform patient care., Peer reviewed

Identification of genomic alterations that influence the immune response within the tumor microenvironment is mandatory in order to identify druggable vulnerabilities. In this article, by interrogating public genomic datasets we describe copy number variations (CNV) present in breast cancer (BC) tumors and corresponding subtypes, associated with different immune populations. We identified regulatory T-cells associated with the Basal-like subtype, and type 2 T-helper cells with HER2 positive and the luminal subtype. Using gene set enrichment analysis (GSEA) for the Type 2 T-helper cells, the most relevant processes included the ERBB2 signaling pathway and the Fibroblast Growth Factor Receptor (FGFR) signaling pathway, and for CD8+ T-cells, cellular response to growth hormone stimulus or the JAK-STAT signaling pathway. Amplification of ERBB2, GRB2, GRB7, and FGF receptor genes strongly correlated with the presence of type 2 T helper cells. Finally, only 8 genes were highly upregulated and present in the cellular membrane: MILR1, ACE, DCSTAMP, SLAMF8, CD160, IL2RA, ICAM2, and SLAMF6. In summary, we described immune populations associated with genomic alterations with different BC subtypes. We observed a clear presence of inhibitory cells, like Tregs or Th2 when specific chromosomic regions were amplified in basal-like or HER2 and luminal groups. Our data support further evaluation of specific therapeutic strategies in specific BC subtypes, like those targeting Tregs in the basal-like subtype., Peer reviewed