BUSCADOR RECOLECTA

The dataset consists of the prediction of transcription factor binding sites (ChIP-seq data) and transcription factor binding motifs (Position weight matrices and Transcription factor flexible models) in Drosophila melanogaster and humans., Although transposable elements (TEs) are an important source of regulatory variation, their genome-wide contribution to the transcriptional regulation of stress response genes has not been studied yet. Stress is a major aspect of natural selection in the wild, leading to changes in the transcriptional regulation of a variety of genes that are often triggered by one or a few transcription factors. In this work, we take advantage of the wealth of information available for Drosophila melanogaster and humans to analyze the role of TEs in stress regulatory networks. We used in silico predictions and chromatin immunoprecipitation sequencing (ChIP-seq) data to localize transcription factor binding sites (TFBS) for several stress-response transcription factors involved in six stress regulatory networks: immune, hypoxia, oxidative, xenobiotic, heat shock, and heavymetal stress responses. The predictions at the DNA level were complemented with the analysis of biochemical and genomic features, such as chromatin characteristics and location regarding nearby genes. In addition, we also used population level information to identify a subset of TEs that were more likely to contain functional TFBS. For a representative subset of the most likely candidate TEs, we performed in vivo transgenic reporter assays in different stress conditions. Overall, our results showed that TEs are relevant contributors to the transcriptional regulation of stress response genes., This work was funded by the Ministerio de Economia y Competitividad BFU2014-57779-P, Ministerio de Ciencia, Innovación y Universidades/AEI (BFU2017-82937-P) and the European Commission (H2020-ERC-2014-CoG-647900)., Peer reviewed

Invasive species cause major ecosystem impacts. To prioritise management, it is first necessary to recognise which invaders have the highest impact, as outlined by the Convention on Biological Diversity’s Strategic Plan 2020. We show for the first time that chemical compounds previously shown to be used in ant defence against other ant species can also be used to prey upon vertebrates of relatively greater size. We estimate the number of amphibian species whose ranges overlap with those of the Argentine ant across the globe and examine the likely global threat to terrestrial amphibians, an already endangered taxonomic group., Peer reviewed

WC4PopStr_26112018.vcf.gz: Contains SNP calligs for the 83 genomes (26 Swedish, 16 Italian, 24 North American, and 17 African) after filtering SNPs at regions of known cosmopolitan admixture in the African strains (3749072 SNPs).-- EUPopStr_26112018.vcf.gz: Contains SNP callings for the new 42 genomes (26 Swedish, 16 Italian) sequenced in this work. (extracted from WC4PopStr_26112018.vcf.gz)., Peer reviewed

The different datasets are divided in folders as follows: 1. In situ experiments. The article is based on 7 different in situ experiments: a. 400C_5mLmin_fr10; b. 400C_10mLmin_fr23; c. 400C_20mLmin_fr6; d. 400C_30mLmin_fr12; e. 300C_10mLmin_fr4; f. 350C_10mLmin_fr18; g. 500C_10mLmin_fr9. (Due to space limitations, only the data corresponding to the experiment c were uploaded to this repository. The remaining data are accessible through private communication with Cecilia Granados-Miralles, c.granados.miralles@icv.csic.es). The folder “c_400C_20mLmin_fr6” contains in situ PXRD data (time resolution=5 s) collected during reduction at the temperature and gas flow indicated in the folder name (i.e. 400C_20mLmin stands for 400 °C and 20 mL/min). The temperature indicated in the file names is the set temperature but the sample temperature is the indicated in the folder name (i.e. Tset430 led to a sample temperature of 400 °C). Heating started on the frame indicated in the folder name (i.e. fr6 stands for frame 6). This folder contains 2D-diffraction images in *.tif format, which may be opened with the Python-based program for on-the-fly data processing and exploration of two-dimensional X-ray diffraction area detector data, available for free download at http://www.clemensprescher.com/programs/dioptas., 2. Ex situ experiments: a. PXRD_Cu 1D-diffraction patterns in *.dat format. 3 space-/tab-separated columns: 2theta angle (degree), Diffracted Intensity (arbitrary units), σ (arbitrary units); b. PXRD_Co Same as previous; c. NPD_DMC 1D-diffraction patterns in *.dat format. The first line indicates: narrowest 2theta angle measured, measurement step, widest 2theta angle. The following values are the diffracted intensities recorded for each 2theta step; d. NPD_HRPT; Same as previous e. VSMHysteresis loops: Magnetic moment as a function of a variable applied field in *.dat format. Several comma-separated columns of which the relevant are the 4th, 5th, and 6th columns, which contain: Magnetic Field (Oe), Moment (emu), M. Std. Err. (emu)., During the past decade, CoFe2O4 (hard)/Co–Fe alloy (soft) magnetic nanocomposites have been routinely prepared by partial reduction of CoFe2O4 nanoparticles. Monoxide (i.e., FeO or CoO) has often been detected as a byproduct of the reduction, although it remains unclear whether the formation of this phase occurs during the reduction itself or at a later stage. Here, a novel reaction cell was designed to monitor the reduction in situ using synchrotron powder X-ray diffraction (PXRD). Sequential Rietveld refinements of the in situ data yielded time-resolved information on the sample composition and confirmed that the monoxide is generated as an intermediate phase. The macroscopic magnetic properties of samples at different reduction stages were measured by means of vibrating sample magnetometry (VSM), revealing a magnetic softening with increasing soft phase content, which was too pronounced to be exclusively explained by the introduction of soft material in the system. The elemental compositions of the constituent phases were obtained from joint Rietveld refinements of ex situ high-resolution PXRD and neutron powder diffraction (NPD) data. It was found that the alloy has a tendency to emerge in a Co-rich form, inducing a Co deficiency on the remaining spinel phase, which can explain the early softening of the magnetic material., European Comission through FP7 program, NANOPYME project, grant agreement no. 310516. European Comission through H2020 program, AMPHIBIAN Project, grant agreement no. 720853. Danish National Research Foundation through Center for Materials Crystallography, DNRF-93. Danish Center for Synchrotron and Neutron Science through DanScatt. European Comission through FP7 program, NMI3-II project, grant agreement no. 283883., Peer reviewed

Dataset of the scientific article "Phenotypic plasticity in breeding plumage signals in both sexes of a migratory bird: responses to breeding conditions"., Peer reviewed

A detailed description can be found in the attached “readme.pdf” file. Datasets are subjected to a Creative Commons Attribution 4.0 International License, This data provides the THD measurement of an analog integrated circuit (a buffer) together with some indirect test signatures. Three cases are considered: a MonteCarlo simulation of mismatch variations, a MonteCarlo simulation of process variations and a defect simulation, Peer reviewed

Soil fauna play a key role in nutrient cycling and decomposition, and in recent years researchers have become more and more interested in this compartment of terrestrial ecosystems. In addition, soil fauna can act as ecosystem engineers by creating, modifying and maintaining the habitat for other organisms. Ecologists usually utilize alive catches in pitfalls traps as a standard method to study the activity of epigeic fauna in addition to relative abundance. Counts in pitfall traps can be used as estimates of relative activity to compare among experimental treatments. This requires taking independent estimates of abundance (e.g.: by sifting soil litter, mark-recapture), which can then be used as covariates in linear models to compare the levels of fauna activity (trap catches) among treatments. However, many studies show that the use of pitfall traps is not the most adequate method to estimate soil fauna relative abundances, and these concerns may be extensible to estimating activity. Here, we present two new types of traps devised to study activity in litter fauna, and which we call “cul-de-sac” and “basket traps” respectively. We experimentally show that, at least for litter dwellers, these new traps are more appropriate to estimate fauna activity than pitfall traps because: 1) Pitfall traps contain 3.5x more humidity than the surrounding environment, potentially attracting animals towards them when environmental conditions are relatively dry, 2) cul-de-sac and basket traps catch ca. 4x more both meso- and macrofauna than pitfall traps, suggesting that pitfall traps are underestimating activity; and 3) pitfall traps show a bias towards collecting 1.5x higher amounts of predators, which suggests that predation rates are higher within pitfall traps. We end with a protocol and recommendations for how to use these new traps in ecological experiments and surveys aiming at estimating soil arthropod activity., This work was funded by grants CGL2010-18602 and CGL2015-66192-R from the Spanish Ministerio de Economía y Competitividad (European funds FEDER), 020/2008 Spanish Organismo Autónomo de Parques Nacionales and P12-RNM-1521 from Junta de Andalucía (European funds FEDER), Peer reviewed

Nestlings of most avian species produce faecal sacs, which facilitate the removal of nestlings’ excrements by parents, thereby reducing proliferation of potentially pathogenic microorganisms and/or detectability by predators and parasites. The nest microbial environment that birds experience during early life might also affect their development and thus, faecal sacs facilitating parental removal may be a strategy to decrease bacterial contamination of nests that could harm developing nestlings. Here, we tested this hypothesis by experimentally broken faecal sacs and spreading them in nests of spotless starlings (Sturnus unicolor), thereby avoiding their removal by adults. In accordance with the hypothesis, experimental nests harboured higher bacterial density than control nests. Nestlings in experimental nests were of smaller size (tarsus length) and experienced lower probability of survival (predation) than those in control nests. Moreover, nestlings in experimental nests tended to suffer more from ectoparasites than those in control nests. We discuss the possible pivotal role of bacteria producing chemical volatiles that ectoparasites and predators might use to find avian nests, and that could explain our experimental results in starlings, Ministerio de Ciencia, Innovación y Universidades and European (FEDER) funds (CGL2013-48193-C3-1-P, CGL2017-83103-P), Peer reviewed

Data used in the study correspond to two datasets.-- Last update has been done in February 2019., [Flux_data.xls] Fluxes of PM in rain, throughfall and stemflow for two tree species (Quercus pubescens Willd. and Pinus sylvestris L.) from June 2015 to June 2016. In this file, no available data is indicated as “NA”. Data structure: • Date: Date of the sample collection • Rain flux: Particulate matter flux in rain (in mg m-2). • Th_Oak_flux: Particulate matter flux in throughfall for Quercus pubescens Willd. (in mg m-2). • Th_Pine_flux: Particulate matter flux in throughfall for Pinus sylvestris L. (in mg m-2). • Sf_Oak_flux: Particulate matter flux in stemflow for Quercus pubescens Willd. (in mg m-2). • Sf_Pine_flux: Particulate matter flux in stemflow for Pinus sylvestris L. (in mg m-2). • Rainfall: Accumulated rainfall between sampling days (in mm). • Origin: Air trajectory coming from: East, West or South. Calculated through 5-day backward trajectories using the HYSPLIT model (Rolph et al., 2017; Stein et al., 2015)., [Filters_data.xlsx] Results from the examination of filters of rainfall, throughfall and stemflow for both species and for 7 events. Data comes from a Zeiss LSM 510 Meta-5 Live Duo confocal microscope and a post processing made with ImageJ. The confocal microscopy analyses have been conducted at the BioImaging Centre at the University of Delaware. Data structure: Area: Area of particles (μm2). Perim.: Perimeter, length of the outside boundary of the particle (μm). Major: Primary axis of the best fitting ellipse (μm). Minor: Secondary axis of the best fitting ellipse (μm). Angle: Angle between the primary axis and a line parallel to the X-axis of the image (º). Circ.: Circularity 4π·([Area])/〖[Perimeter]〗^2 with a value of 1.0 indicating a perfect circle. As the value approaches 0.0, it indicates an increasingly elongated shape. Feret: Feret diameter, the longest distance between any two points along the selection boundary, also known as maximum caliper (μm). FeretAngle: The angle (0 - -180 degrees) of the Feret’s diameter (º). MinFeret: The minimum caliper diameter (μm). AR: Aspect ratio, the aspect ratio of the particle’s fitted ellipse, i.e., ([Major Axis])/([Minor Axis]) Round: Roundness, 4·([Area])/(π · 〖[Major axis]〗^2 ) or the inverse of Aspect Ratio. Solidity: ([Area])/([Convex Area]) Date: Date of the sampling. Type: Corresponding water flux. Rainfall (Rf), throughfall pines (Th_Pine), throughfall oaks (Th_Oak), stemflow pines (Sf_Pine) and stemflow oaks (Sf_Oak)., Particulate matter fluxes in a Mediterranean mountain forest: inter-specific differences between throughfall and stemflow in oak and pine stands. This project analyses the redistribution of water and particulate matter (PM) below forested areas in the Vallcebre research catchments during rainfall events. Data to analyse PM fluxes and diameter and shape distribution of PM has been produced by: Carles Cayuela, Delphis F. Levia, Jérôme Latron and Pilar Llorens., This research was supported by the projects TransHyMed (CGL2016-75957-R AEI/FEDER, UE) and MASCC-DYNAMITE (PCIN-2017-061/AEI) funded by the ‘‘Agencia Estatal de Investigación”. C. Cayuela was the beneficiary of a pre-doctoral FPI grant (BES-2014-070609) and a pre-doctoral mobility grant (EEBB-I-16-11510)., No

Genome assembly of the Anopheles fontenillei genome based on the high coverage sequencing of a single individual of this species. The raw reads for this assembly can be found in SRA under accession number SRX5100439., No