BUSCADOR RECOLECTA

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

1 file, Supplementary information for the article https://doi.org/10.1038/s41598-020-57501-0, Table S1. Primer sequences used for qPCR.-- Supplementary Figure S1. Antiviral activity of the CRP1-7-depleted supernatants.-- Supplementary Figure S2. Assessment of the ability of CRP-mix to induce the transcription of ifnphi1 and ifnphi2 in vitro.-- Supplementary Figure S3. Assessment of the ability of IL-6 to induce the expression of crp1-7 transcripts in vivo.-- Supplementary Figure S4. Transcriptional modulation of autophagy by SVCV in the ZF4 cells.-- Supplementary Figure S5. Effect of the addition of exogenous cholesterol on intracellular autophagosome levels and SVCV infection in vitro, Peer reviewed

Documents: Chesas_Thin_sections_scans.zip Chesas_Fig.captions1991-01.xlsx, We show data of soils developed on the outcropping gypseous nucleus of the Barbastro-Balaguer anticline, NE Spain. Chesas is the local name for the lands of this outcrop that stand out by their whitish tones. The data collected here come from soils of the municipalities —from West to East— of Peraltilla, Almunia de San Juan, Tamarite, Torá, and Iborra. The analytical methods plus details of the landscape and sampling sites can be found in: (i) the book entitled “Morfología y génesis de suelos sobre yesos” (http://hdl.handle.net/10261/84695), and (ii) the article entitled “Salada Farrachuela, a saline wetland in Tamarite de Litera, Spain” (DOI: 10.29077/bol.114.ce05.herrero). Here we present a compressed zip file with 302 TIFF images corresponding to 151 thin sections of these soils. Most of the sections —with the prevalent size of 13.5 × 5.7 cm— were manufactured by the first author in the Institut National Agronomique de Paris-Grignon under the technical supervision of Mr. P. Guilloré, in the context of a scholarship granted by the Government of France for working in the lab of Dr. N. Fédoroff. The surviving thin sections from chesas are archived and scanned at the EEAD-CSIC in Zaragoza, Spain. Their scans are compiled in the file “Chesas_Thin_sections_scans.zip”. Several dozen micrographs of the chesas thin sections appeared in the abovementioned book published in 1991 (http://hdl.handle.net/10261/84695). The file “Chesas_Fig.captions1991-01.xlsx” presents a tentative English translation of the 154 Figure captions for the micrographs and the other figures in the book., We acknowledge the grant PID2021-127170OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”, and the grant TED2021-130303B-I00 funded by MCIN/AEI/10.13039/501100011033 and by the “European Union NextGeneration EU/PRTR”., Peer reviewed

This dataset contains structural data of the southern sector of the Sierra de Reyes Antiform along the Andean front in the Neuquén Basin, Argentina. This structural data consist of bedding dips and their strike as well as Remote Sensing Mapping of the main units outcropping in the area. Location of calcite shells within the Vaca Muerta-Quintuco System and Mulichinco Formation for Sr isotopic dating is also included., This work was funded by a collaborative knowledge transfer project between the CSIC and Equinor Research Center in Bergen (Norway), MAPA project (PIE–CSIC–202430E005), and the Grup de Recerca Reconegut per la Generalitat de Catalunya “Modelització Geodinàmica de la Litosfera” (2021 SGR 00410), Neuquén Basin.KMZ, Peer reviewed

102 pages, Supplementary information for the article https://doi.org/10.1093/bioinformatics/bty736.-- Computational settings. Histograms and dispersion plots of the multi-starts of local searches (MS). Convergence curves of eSS and MS. Tables and figures. Appendix: adjoint vs forward sensitivities, Peer reviewed

3 files, Additional file 1. Remarks on the eSS optimisation solver and detailed results for the Goodwin Oscillator problem and additional ENSO contour plots. This file describes our modifications to the eSS global optimisation solver. It also contains tables and figures showing the detailed results for the Goodwin Oscillator problem, and additional contour plots for the ENSO example.-- Additional file 2. Critical comparison of optimisation solvers. In GEARS, the optimisation problems are solved using the hybrid metaheuristic eSS. A comparison of the eSS global optimisation solver used in GEARS with other competitive local and global optimisation solvers.-- Additional file 3. Detailed results for the Fitzhugh-Nagumo, Repressilator and Enzymatic Oscillator problems. This file contains tables and figures showing the detailed results for the Fitzhugh-Nagumo, Repressilator and Enzymatic Oscillator problems, Peer reviewed