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Additional file 17: Supplementary Table S8. Correlation of differentially expressed mRNAs and newly synthesized proteins in WT and METTL1 KO PC3 cells., Consejo Superior de Investigaciones Científicas (España), Peer reviewed

Additional file 18. Graphical abstract., Consejo Superior de Investigaciones Científicas (España), Peer reviewed

Supplementary tables to the manuscript entitled Assessment of milk metabolites as biomarkers for predicting feed efficiency in dairy sheep, Supplemental Table 1: Grids used in the hyperparameter tuning stage for each machine learning (ML) model. Supplemental Table 2: Summary of milk production and FE phenotypes in the 39 Assaf ewes analyzed in this work. For each animal (Sample_ID), the type of lambing (single or twins), the means (±coefficient of variation in %) of the milk production traits: milk yield (MY), milk protein percentage (PP), milk fat percentage (FP) and milk lactose percentage (LC) are presented. The FE parameters recorded during the three-week evaluation period: Dry matter intake (DMI), feed efficiency indices RFI and FCR and the high, medium or low-efficiency group for each FE-index are also presented. Supplemental Table 3: m/z and LC retention time (RT, min) for the features identified in the raw milk metabolomic signature for the 39 Assaf ewes. The four sheets show the results of the reversed-phase liquid chromatography (C8) and hydrophilic interaction liquid chromatography (HILIC) for the positive and negative poles, respectively. Supplemental Table 4: Selected features for residual feed intake (RFI) and feed conversion ratio (FCR) based on the Variable Importance in the Projection (VIP) values obtained in the partial least squares discriminant analysis. Supplemental Table 5: Results of the hyperparameter tunning stage for the 100 iterations of random assignment of samples in the train and training population for all machine learning models applied for both feed efficiency (FE) metrics, residual feed intake (RFI) and feed conversion ratio (FCR). The different sheets show the results of the four ML methods used (multi-layer feedforward artificial neural network (Deep), Randon Forest (RF), extreme gradient boosting (xgboost) and Support Vector Machine (SVM) using all features (All) and those selected by VIP. Supplemental Table 6: Candidate compounds annotated for the 41 and 26 features selected for residual feed intake (RFI) and feed conversion ratio (FCR) during the partial least squares discriminant analysis for the discrimination of the feed efficiency (FE) groups. Supplemental Table 7: Results of metabolic pathways enrichment analysis obtained using IMPaLA software for the candidate compound matches obtained during the annotation process for the metabolites selected for residual feed intake (RFI) and feed conversion ratio (FCR)., SMARTER – SMAll RuminanTs breeding for Efficiency and Resilience 772787 European Commission, Peer reviewed, v02

Meteorological, dust and saltation data used in González-Flórez et al., 2023. Data are based on measurements taken during an intensive dust field campaign conducted in the context of the FRontiers in dust minerAloGical coMposition and its Effects upoN climaTe (FRAGMENT) project. The campaign took place in September 2019 in a small ephemeral lake, locally named "L'Bour", located in the Lower Drâa Valley in Morocco. The description of the data is provided below: - t.nc: time series of temperature measured with four aspirated shield temperature sensors (Campbell Scientific 43502 fan-aspirated shield with 43347 RTD Temperature probe) placed at heights of 1m, 2m, 4m and 8m. - t005.nc time series of temperature measured with a temperature and relative humidity probe (Campbell Scientific HC2A-S3) at 0.5m height. - rh005.nc: time series relative humidity measured with a temperature and relative humidity probe (Campbell Scientific HC2A-S3) at 0.5m height. - wspd.nc: time series of wind speed measured with five 2-D sonic anemometers (Campbell Scientific WINDSONIC4-L) placed at heights of 0.4m, 0.8m, 2m, 5m and 10m. - sdir.nc: time series of wind direction measured with five 2-D sonic anemometers (Campbell Scientific WINDSONIC4-L) placed at heights of 0.4m, 0.8m, 2m, 5m and 10m. - radout.nc: time series of outgoing long wave radiation measured with a four-component net radiometer (Campbell Scientific NR01-L radiometer) placed at 1.5m height. - p015.nc: times series barometric pressure measured with a barometer (Campbell Scientific CS106) at around 1.5m height. - u_star_law.nc: time series friction velocity calculated through the law of the wall method. - z0_law.nc: time series of roughness length calculated through the law of the wall method. - zeta_law.nc: time series of dimensionless height, zref/L, where zref is the reference height (zref=2m) and L is the Obukhov length calculated through the law of the wall method. - psd_lower_15avg_20190904_000000_integrated_bins.nc: time series of 15-min average number concentrations in integrated size bin resolution measured with an optical particle counter (Fidas 200S, Palas GmbH) at ~1.8m height. - psd_upper_15avg_20190904_000000_integrated_bins.nc: time series of 15-min average number concentrations in integrated size bin resolution measured with an optical particle counter (Fidas 200S, Palas GmbH) at ~3.5m height and corrected for systematic bias based on an intercomparison between the two Fidas at the end of the campaign. - diff_flux_nb_15avg_20190904_000000_integrated_bins.nc: time series of 15-min average number diffusive flux calculated using the flux-gradient method. - q_15avg.nc: time series of 15-min average saltation flux calculated based on measurements with optical gate devices at heights of 0.05m, 0.15m and 0.3m as part of the Standalone AeoliaN Transport Real-time Instrument (SANTRI, Desert Research Institute). - geometric_diameters_integrated_size_bins.csv: containing the minimum, maximum and mean logarithmic optical diameter of the integrated size bins. - optical_diameters_integrated_size_bins: containing the minimum, maximum and mean logarithmic geometric diameter of the integrated size bins. SANTRI data were processed by Martina Klose (martina.klose@kit.edu) and the rest by Cristina González Flórez (cristina.gonzalez@bsc.es). Please, cite González-Flórez et al. (2023, ACP) if you use these data. If the data become the key main component of a paper then co-authorship may be offered. Contact Carlos Pérez García-Pando (carlos.perez@bsc.es) if more details are needed. This work has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 773051, FRAGMENT)., Peer reviewed

This study analyzed the variability of equivalent black carbon (eBC) mass concentrations and their sources in urban Europe to provide insights into the use of eBC as an advanced air quality (AQ) parameter for AQ standards. This study compiled eBC mass concentration datasets covering the period between 2006 to 2022 from 50 measurement stations, including 23 urban background (UB), 18 traffic (TR), 7 suburban (SUB), and 2 regional background (RB) sites. The results highlighted the need for the harmonization of eBC measurements to allow for direct comparisons between eBC mass concentrations measured across urban Europe. The eBC mass concentrations exhibited a decreasing trend as follows: TR > UB > SUB > RB. Furthermore, a clear decreasing trend in eBC concentrations was observed in the UB sites moving from Southern to Northern Europe. The eBC mass concentrations exhibited significant spatiotemporal heterogeneity, including marked differences in eBC mass concentration and variable contributions of pollution sources to bulk eBC between different cities. Seasonal patterns in eBC concentrations were also evident, with higher winter concentrations observed in a large proportion of cities, especially at UB and SUB sites. The contribution of eBC from liquid fossil fuel combustion, mostly traffic (eBCT) was higher than that of residential and commercial sources (eBCRC) in all European sites studied. Nevertheless, eBCRC still had a substantial contribution to total eBC mass concentrations at a majority of the sites. eBC trend analysis revealed decreasing trends for eBCT over the last decade, while eBCRC remained relatively constant or even increased slightly in some cities., Attention: Use of data may require contact with data provider. Please request acknowledgement details from data originators in compliance with data sharing and citation. Attribution to RI-URBANS is required from users to give appropriate credit. Information on this is included in the files. All scientific articles and reports using data need to acknowledge the project; "This study is using data that has received funding from the European Union's Horizon 2020 research and innovation programm under grant agreement No 101036245". Grants: Agencia Estatal de Investigación, Spanish Ministry of Science and Innovation, CAIAC project (PID2019-108990RB-I00); Spanish Ministry of Science and Innovation, FPI grant (PRE-2020-095498); Generalitat de Catalunya (AGAUR, SGR-447), Peer reviewed

The dataset includes two Excel spreadsheets with the soil and water characteristics from samples obtained during wet (April) and dry (September) seasons in 2019, and at the end of the experiment, July 2020. The sampling was designed to characterize the soil and water in the context of the study of soil redox conditions using IRIS (Indicators of Reducing of Soils) devices. The selected sampling locations represent a gradient of water within the playa-lake: bare soil very frequently flooded (SAL-1); bare soil often flooded (SAL-2); and the plot colonized by annual and perennial halophytes (SAL-3). Soil data includes the main description of the soil layers per date in the three sampling plots, and their chemical and physical analytical data determined in the field and in the lab. We analyzed water from three different origins: i) surface water when present, ii) shallow groundwater from piezometers up to 80 cm depth, iii) suction probes installed at 20 and 40 cm depth, and iv) saturated paste extracts of soil samples. Photograph P1170434.jpg shows a view of the field setting of the experiment in 2019, April 17., The data corresponds to the Spanish study area, the Salineta inland saline wetland (41°28'55.34"N, 0° 9'23.59"W) located 60 km far from Zaragoza city, in one of the most arid areas of the Central Ebro Basin, NE Spain. In this project we studied the redox conditions of the hypersaline soils in Salineta playa-lake, which are subjected to intermittent flooding, along a period of 17 months, in 2019 and 2020., These data belong to the research project AQUASALT, EraNET that in Spain has been supported by grant PCI2018-09299 funded by MCIN/AEI/10.13039/50110 0 011033 and co-funded by the European Union., Peer reviewed

[Introduction]: Secreted mucins are highly O-glycosylated glycoproteins produced by goblet cells in mucosal epithelia. They constitute the protective viscous gel layer overlying the epithelia and are involved in pathogen recognition, adhesion and expulsion. The gill polyopisthocotylidan ectoparasite Sparicotyle chrysophrii, feeds on gilthead seabream (Sparus aurata) blood eliciting severe anemia., [Methods]: Control unexposed and recipient (R) gill samples of gilthead seabream experimentally infected with S. chrysophrii were obtained at six consecutive times (0, 11, 20, 32, 41, and 61 days post-exposure (dpe)). In histological samples, goblet cell numbers and their intensity of lectin labelling was registered. Expression of nine mucin genes (muc2, muc2a, muc2b, muc5a/c, muc4, muc13, muc18, muc19, imuc) and three regulatory factors involved in goblet cell differentiation (hes1, elf3, agr2) was studied by qPCR. In addition, differential expression of glycosyltransferases and glycosidases was analyzed in silico from previously obtained RNAseq datasets of S. chrysophrii-infected gilthead seabream gills with two different infection intensities., [Results and Discussion]: Increased goblet cell differentiation (up-regulated elf3 and agr2) leading to neutral goblet cell hyperplasia on gill lamellae of R fish gills was found from 32 dpe on, when adult parasite stages were first detected. At this time point, acute increased expression of both secreted (muc2a, muc2b, muc5a/c) and membrane-bound mucins (imuc, muc4, muc18) occurred in R gills. Mucins did not acidify during the course of infection, but their glycosylation pattern varied towards more complex glycoconjugates with sialylated, fucosylated and branched structures, according to lectin labelling and the shift of glycosyltransferase expression patterns. Gilthead seabream gill mucosal response against S. chrysophrii involved neutral mucus hypersecretion, which could contribute to worm expulsion and facilitate gas exchange to counterbalance parasite-induced hypoxia. Stress induced by the sparicotylosis condition seems to lead to changes in glycosylation characteristic of more structurally complex mucins., Peer reviewed

[Introduction]: Secreted mucins are highly O-glycosylated glycoproteins produced by goblet cells in mucosal epithelia. They constitute the protective viscous gel layer overlying the epithelia and are involved in pathogen recognition, adhesion and expulsion. The gill polyopisthocotylidan ectoparasite Sparicotyle chrysophrii, feeds on gilthead seabream (Sparus aurata) blood eliciting severe anemia., [Methods]: Control unexposed and recipient (R) gill samples of gilthead seabream experimentally infected with S. chrysophrii were obtained at six consecutive times (0, 11, 20, 32, 41, and 61 days post-exposure (dpe)). In histological samples, goblet cell numbers and their intensity of lectin labelling was registered. Expression of nine mucin genes (muc2, muc2a, muc2b, muc5a/c, muc4, muc13, muc18, muc19, imuc) and three regulatory factors involved in goblet cell differentiation (hes1, elf3, agr2) was studied by qPCR. In addition, differential expression of glycosyltransferases and glycosidases was analyzed in silico from previously obtained RNAseq datasets of S. chrysophrii-infected gilthead seabream gills with two different infection intensities., [Results and Discussion]: Increased goblet cell differentiation (up-regulated elf3 and agr2) leading to neutral goblet cell hyperplasia on gill lamellae of R fish gills was found from 32 dpe on, when adult parasite stages were first detected. At this time point, acute increased expression of both secreted (muc2a, muc2b, muc5a/c) and membrane-bound mucins (imuc, muc4, muc18) occurred in R gills. Mucins did not acidify during the course of infection, but their glycosylation pattern varied towards more complex glycoconjugates with sialylated, fucosylated and branched structures, according to lectin labelling and the shift of glycosyltransferase expression patterns. Gilthead seabream gill mucosal response against S. chrysophrii involved neutral mucus hypersecretion, which could contribute to worm expulsion and facilitate gas exchange to counterbalance parasite-induced hypoxia. Stress induced by the sparicotylosis condition seems to lead to changes in glycosylation characteristic of more structurally complex mucins., Peer reviewed

(A) CBK1 cbk1Δ cdc15-2 (YMF3869), (B) cbk1-6E cbk1Δ cdc15-2 (YMF3763), (C) cbk1-5E-E409S cbk1Δ cdc15-2 (YMF4279), (D) cbk1-5E-E574T cbk1Δ cdc15-2 (YMF4280), and (E) cbk1-9A cbk1Δ cdc15-2 (YMF3764) cells were grown in YPD and arrested in late anaphase by raising the temperature to 37 °C before rapamycin was added to half of the culture for 20 min. Subsequently, to allow progression through the cell cycle, cells were released in the absence (i) or presence (ii) of rapamycin. Samples were taken at the indicated times to study cell-cycle progression by flow cytometry. Schematic illustration of cbk1-9A mutant in which phosphosites containing serines or threonines followed by prolines were changed to alanine to block phosphorylations (iii). FACS graphs can be found in the supplementary FACS file (S1 File)., pbio.3002263.s006.pdf, Peer reviewed

(A) DSE4-6HA cdc15-2 (YMF4029) cells were grown in YPD and arrested in late anaphase by shifting the temperature to 37 °C before the addition of DMSO (−) or rapamycin (+) for 20 min. Subsequently, cells were released from the anaphase arrest in the absence (−) or presence (+) of rapamycin before protein extracts were prepared from shown time points and analysed by immunoblotting. Raw data for blot can be found in Supporting information (S6A Raw Images). (B) iHA-CTS1 cdc14-1 cells (YMF4088) were grown and processed as in A. Protein extracts were prepared from indicated time points and analysed by immunoblotting. Raw data for blot can be found in Supporting information (S6B Raw Images). (C) CTS1-GFPEnvy cdc14-1 cells (YMF4231) were grown as in C. Samples were taken at the indicated times to determine the proportion of cells with Cts1 at the division site in the presence (i) of rapamycin. Examples of cells are shown for the 60 min time point after the release at 24 °C in the presence (ii) of rapamycin. Scale bar indicates 5 μm. Underlying data for all the graphs can be found in S1 Data file., pbio.3002263.s007.pdf, Peer reviewed