BUSCADOR RECOLECTA

Ellis van Creveld syndrome and Weyers acrofacial dysostosis are two rare genetic diseases affecting skeletal development. They are both ciliopathies, as they are due to malfunction of primary cilia, microtubule-based plasma membrane protrusions that function as cellular antennae and are required for Hedgehog signaling, a key pathway during skeletal morphogenesis. These ciliopathies are caused by mutations affecting the EVC-EVC2 complex, a transmembrane protein heterodimer that regulates Hedgehog signaling from inside primary cilia. Despite the importance of this complex, the mechanisms underlying its stability, targeting and function are poorly understood. To address this, we characterized the endogenous EVC protein interactome in control and Evc-null cells. This proteomic screen confirmed EVC’s main known interactors (EVC2, IQCE, EFCAB7), while revealing new ones, including USP7, a deubiquitinating enzyme involved in Hedgehog signaling. We therefore looked at EVC-EVC2 complex ubiquitination. Such ubiquitination exists but is independent of USP7 (and of USP48, also involved in Hh signaling). We did find, however, that monoubiquitination of EVC-EVC2 cytosolic tails greatly reduces their protein levels. On the other hand, modification of EVC-EVC2 cytosolic tails with the small ubiquitin-related modifier SUMO3 has a different effect, enhancing complex accumulation at the EvC zone, immediately distal to the ciliary transition zone, possibly via increased binding to the EFCAB7-IQCE complex. Lastly, we find that EvC zone targeting of EVC-EVC2 depends on two separate EFCAB7-binding motifs within EVC2’s Weyers-deleted peptide. Only one of these motifs had been characterized previously, so we have mapped the second herein. Altogether, our data shed light on EVC-EVC2 complex regulatory mechanisms, with implications for ciliopathies., Peer reviewed

Ellis van Creveld syndrome and Weyers acrofacial dysostosis are two rare genetic diseases affecting skeletal development. They are both ciliopathies, as they are due to malfunction of primary cilia, microtubule-based plasma membrane protrusions that function as cellular antennae and are required for Hedgehog signaling, a key pathway during skeletal morphogenesis. These ciliopathies are caused by mutations affecting the EVC-EVC2 complex, a transmembrane protein heterodimer that regulates Hedgehog signaling from inside primary cilia. Despite the importance of this complex, the mechanisms underlying its stability, targeting and function are poorly understood. To address this, we characterized the endogenous EVC protein interactome in control and Evc-null cells. This proteomic screen confirmed EVC’s main known interactors (EVC2, IQCE, EFCAB7), while revealing new ones, including USP7, a deubiquitinating enzyme involved in Hedgehog signaling. We therefore looked at EVC-EVC2 complex ubiquitination. Such ubiquitination exists but is independent of USP7 (and of USP48, also involved in Hh signaling). We did find, however, that monoubiquitination of EVC-EVC2 cytosolic tails greatly reduces their protein levels. On the other hand, modification of EVC-EVC2 cytosolic tails with the small ubiquitin-related modifier SUMO3 has a different effect, enhancing complex accumulation at the EvC zone, immediately distal to the ciliary transition zone, possibly via increased binding to the EFCAB7-IQCE complex. Lastly, we find that EvC zone targeting of EVC-EVC2 depends on two separate EFCAB7-binding motifs within EVC2’s Weyers-deleted peptide. Only one of these motifs had been characterized previously, so we have mapped the second herein. Altogether, our data shed light on EVC-EVC2 complex regulatory mechanisms, with implications for ciliopathies., Peer reviewed

Data supporting the findings of the study "Constrained trait variation by water availability modulates radial growth in two coexisting Mediterranean oaks", Peer reviewed

29 figures, 7 tables., 1. Stability of the G−N4−TM structures.-- 2. O2 Interaction with the Fe–N4 Center.-- 3. Calculation methods of evaluating ORR, OER and HER activity.-- 4. Density of states calculations.-- Supplementary Figures and Tables, Peer reviewed

Additional structural (XRD and STEM) and chemical x-ray microanalysis, a detailed description of the STEM image analysis and calculation of polarization images, including the LSAT substrate, and further details on the experimental conditions are provided in the supplementary material., Peer reviewed

pdf file contains: Table S1. Parameter values of the model fitted to empirical glucocorticoid data from the Jimeno et al. (2018; Zebra finch), Zimmer et al. (2021; House sparrow), and Zimmer et al. (2023; Tree swallow)., Glucocorticoid hormones (GCs) modulate acute ‘stress’ responses in vertebrates, exerting their actions across many physiological systems to help the organism face and overcome challenges. These actions take place via binding to the glucocorticoid receptor (GR), which determines not only the magnitude of the GC-mediated physiological response but also the negative feedback that downregulates GCs to restore homeostasis. Although GR function is assumed to determine GC regulation capacity, the associations between GR abundance and individuals' coping abilities remain cryptic. We developed a dynamic model fitted to empirical data to predict the effects of GR abundance on both plasma GC response patterns and the magnitude of GC-mediated physiological response. Individuals with higher GRs showed lower GC exposure, stronger physiological responses and greater capacity to adjust this response to stressor intensity, which may be translated into more resilient and flexible GC phenotypes. Our results also show that among-individual variability in GR abundance challenges the detectability of the association between plasma GC measurements and physiological responses. Our approach provides mechanistic insights into the role of GR on plasma GC measurements and function, which point at GR abundance fundamentally driving complex features of the GC regulation system in the face of environmental change.This article is part of the theme issue ‘Endocrine responses to environmental variation: conceptual approaches and recent developments’., Peer reviewed

Geochemical data of the Variscan gneisses derived from pre-Variscan intrusives and late-Variscan granitoids in the Pyrenees and the Catalan Coastal Ranges were obtained from two main sources: (1) individually mined from published articles and unpublished PhD theses (Autran et al., 1970; Guitard, 1970; Enrique, 1989; Soler and Enrique, 1989; Enrique, 1990; Soler, 1990; Gleizes, 1992; Debon et al., 1996; Arranz, 1997; Guitard et al., 1998b, 1998b; Roberts et al., 2000; Vilà et al., 2005; Casas et al., 2010; Navidad et al., 2010; Druguet et al., 2014; Laumonier et al., 2015; Navidad et al., 2018; Lemirre et al., 2019; Álvaro et al., 2021; Liesa et al., 2021; Casas et al., 2024), and (2) the GEOROC Database (Geochemistry of Rocks of the Oceans and Continents, Göttingen University, https://georoc.eu/; last access: 03/2024; Lehnert et al., 2000). Other Findable, Accessible, Interoperable, and Reusable (FAIR; Wilkinson et al., 2016) databases were searched using geographic and lithogeochemical constrains, yielding no results. The mined data were curated and classified based on the analysed rock types, ages, regional tectonic setting, and mode of occurrence in outcrop, resulting in more than 600 entries that are associated with up to 66 data fields. Associated with each entry are generic, descriptive and informative fields (Sample ID, Unit/Massif, Rock category, Rock details, Outcrop description, and References), major element oxide abundances (SiO2, Al2O3, FeOT, Fe2O3T, MnO, MgO, CaO, Na2O, K2O, TiO2, P2O5, and LOI), and trace element concentrations (Ag, As, Ba, Be, Bi, Co, Cr, Cs, Cu, Ga, Ge, Hf, In, Mo, Nb, Ni, Pb, Rb, Sb, Sc, Sn, Sr, Ta, Th, Tl, U, V, W, Y, Zn, Zr, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu). The resulting database, named NEIGRA (North-East Iberian GRAnitoids), represents the first Open-Access compilation of granite and orthogneiss geochemical data in the Pyrenees and the Catalan Coastal Ranges., This work was funded by DGICYT Projects PID2021-122467NB-C22 and PID2021-125585NB-I00 (MCIN/AEI/FEDER-UE/10.13039/501100011033) and PID2020-118999GB-I00 (MCIN/AEI/10.13039/501100011033), and by the Sedimentary Geology Research Group (2021 SGR 00349). EGE acknowledges the funding provided by the Geological Society of London (GSL) Student Research Grants and the PhD grants funded by Generalitat de Catalunya and the European Social Fund (2021 FI_B 00165 and 2022 FI_B1 00043). CPT acknowledges the PhD grant 2021 FISDU 00347 funded by Generalitat de Catalunya. EGR acknowledges funding provided by the Spanish Ministry of Science, Innovation and Universities (“Ramón y Cajal” fellowship RYC2018-026335-I). CA is grateful to the GEOXis Reseach Group (2021 SGR 00262) and the projects PID2020-117332GB-C21 (USAL) and PID2020-117332GB-C22 (UCM) funded by MCIN/AEI/10.13039/501100011033., 00_NEIGRA_Readme; NEIGRA_North-East Iberian GRAnitoids Database, Peer reviewed

File 1 (.doc): 1Table - Mean (±SD) δ13C and δ15N values (‰) of the prey species used to analyze the diet of the common bottlenose dolphin in Madeiran waters, per season; 1 figure - Simulated mixing region calculated for each season (‘summer/autumn’- top; ‘winter/spring’- bottom) with the most likely prey (white crosses) based on bi-plot interpretation.-- File 2 (.xls), Supplementary material of the article Trophic ecology of common bottlenose dolphins in a pelagic insular environment inferred by stable isotopes, https://doi.org/10.1007/s10750-023-05294-4, Peer reviewed

This repository may be useful for further studies, for the development of new therapeutic treatments for food intoxication and for tracking microbial sources in foodstuffs, Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds, such as histamine, cadaverine, tyramine and putrescine, after foods spoil due to microorganisms. In the present work, we applied a shotgun proteomics approach to quickly and easily characterize 15 different foodborne strains of biogenic amine-producing bacteria. A total of 10673 peptide spectrum matches (PSMs) belonging to 4081 nonredundant peptides and corresponding to 1811 annotated proteins were identified. With the results, relevant functional pathways were determined and the strains were differentiated into different Euclidean hierarchical clusters. Moreover, a predicted protein‒protein interaction network of biogenic amine foodborne strains was created. The whole confidence network contains 260 nodes and 1973 interactions. Most of the identified proteins were related to pathways and networks of energy, putrescine metabolism and host‒virus interaction. In addition, a total of 556 nonredundant peptides were identified as virulence factors, and most of these peptides corresponded to functions such as toxins, antimicrobial compound production, antimicrobial resistance, additional resistances and tolerances, host colonization and immune evasion, ABC transporters, phage proteins, and alternative virulence factors and proteins involved in horizontal transfer. Potential species-specific peptide biomarkers were screened. Thus, 77 species-specific peptide biomarkers belonging to 64 different proteins were proposed to identify 10 species (Enterobacter aerogenes, Enterobacter cloacae, Hafnia alvei, Klebsiella oxytoca, Morganella morganii, Proteus mirabilis, Proteus penneri, Proteus vulgaris, Raoutella planticola, Stenotrophomonas maltophilia). All of these results constitute the first major dataset of peptides and proteins of seafood biogenic amine-producing strains, Peer reviewed

This dataset contains all data used in the analysis for the associated manuscript, as well as an R script which can be used to replicate the analysis.-- There are six files, including multispecies stable isotope data, cod sampling data, cod specific stable isotope data, cod meta data, cod positions and an R script for analysis, Foraging is a behavioural process and, therefore, individual behaviour and diet are theorized to covary. However, few comparisons of individual behaviour type and diet exist in the wild. We tested whether behaviour type and diet covary in a protected population of Atlantic cod, Gadus morhua. Working in a no-take marine reserve, we could collect data on natural behavioural variation and diet choice with minimal anthropogenic disturbance. We inferred behaviour using acoustic telemetry and diet from stable isotope compositions (expressed as δ13C and δ15N values). We further investigated whether behaviour and diet could have survival costs. We found cod with shorter diel vertical migration distances fed at higher trophic levels. Cod δ13C and δ15N values scaled positively with body size. Neither behaviour nor diet predicted survival, indicating phenotypic diversity is maintained without survival costs for cod in a protected ecosystem. The links between diet and diel vertical migration highlight that future work is needed to understand whether the shifts in this behaviour during environmental change (e.g. fishing or climate), could lead to trophic cascades, The Research Council of Norway, Award: CODSIZE 294926; Natural Sciences and Engineering Research Council; European Commission, Award: 793627; Spanish National Research Council, IF_ERC; Academy of Finland, Award: 317495; European Research Council, Award: 770884, file: cod_stable_isotopes.rdata; description: Cod specific stable isotopes data in the .rdata format.-- file: TVE2011Effort.csv; description: Sampling effort and locations in the Tvedestrand fjord.-- file: SI.rdata; description: stable isotope samples collected throughout the Tvedestrand foodweb.-- file: telem.rdata; description: Data collected during each cod sampling event, including recaptures.-- file: Allcodpositions.rdata; description: dataset "pos" contains a list of all cod positions used in the stable isotope anaylsis, Peer reviewed