BUSCADOR RECOLECTA

Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reduction of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated, respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are regulated independently of the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling., Peer reviewed

Supplementary Table 8. Top 3 Gene Ontology (GO) terms enriched for each candidate transcription factor (TF) summarized from previously published GO enrichment analysis for GENIE3 network genes in Ramírez-González et al., 2018. The black boxes indicate that this is an enriched GO for this TF gene., Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reduction of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated, respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are regulated independently of the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling., Peer reviewed

Supplementary Table 9. Complete results of Gene Ontology (GO) enrichment analysis of genes in module 13 of co-expression network WGCNA published in Ramírez-González et al. (2018). GO:MF, Molecular Function domain; GO:BP, Biological Process domain; GO:CC, Cellular Component domain., Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reduction of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated, respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are regulated independently of the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling., Peer reviewed

Suppl. File 1. List of wild Helianthus accessions used in this study and associated phenotyping assays. Seventy one accessions were phenotyped in 6 L pots: 36 wild H. annuus accessions and 35 wild Helianthus accessions from other species than annuus, including 21 annual accessions from 8 species (12 taxa) and 14 perennial accessions from 7 species. Eighteen of these accessions were phenotyped for the exudate activity on broomrape seed germination and in rhizotrons. Suppl. File 2. Timeline of the culture and phenotyping in rhizotrons. Phenotyping in rhizotrons of the wild Helianthus species and the control cultivated H. annuus was performed at the attachment stage (14 days after inoculation-dai), tubercle stage (21 dai) and necrotic tubercle stage (28 dai). At 14 dai, samples (fragments of roots with compatible or incompatible attachments) were prepared for cytological studies. D0: Day 0 is the day of inoculation. Suppl. File 3. Numbers of rhizotrons and independent experiments/ accessions. Rhizotrons were inoculated with the race E-BOU (2017). At least 2 independent experiments were performed for each accession. The numbers of Non-Treated (NT) and Treated (T) rhizotrons (with GR24 + DCL) were variable depending on the germinating ability of the accession. At 14 dai and 21 dai, the number of attachments and tubercles were counted respectively. As one rhizotron/ experiment was used for cytological sampling at 14 dai, the number of rhizotrons differed between 14 and 21 dai. Suppl. File 4. Raw data of the number of attachments (at 14 dai), tubercles (at 21 dai) and necrotic tubercles (at 28 dai) / rhizotron for each accession. Raw data are detailed in the specific joined file. NA: data Not Available. Wild Helianthus plantlets were inoculated with conditioned Orobanche seeds (race E-BOU), following 15 days of culture in soil and 6 days in rhizotrons (see Materials and Methods and Suppl. File 2) except for the following experiments: I15: 17 days of culture in soil, and inoculation the day of transfer in rhizotron; I16 and I18: inoculation the day of transfer in rhizotron; I19: plantlets were grown 27 days in soil and 6 days in rhizotron before inoculation. Suppl. File 5. Germination dose-response curves of various O. cumana populations to various germination stimulants. Germination dose-response curves were modelled after normalization of the germination activity (bar : ± SD) thanks to the germination percentage of each populations obtained with 1 μM GR24 (Fig. 1a) using a four parameter logistic curve. For each compound, (±)-GR24; DCL and costunolide, and equimolar mixtures, a range of concentrations from 1 μM to 0.1 pM were applied to conditioned seeds of five O. cumana populations. Suppl. File 6. Half-maximal effective concentration (EC50) of various germination stimulants on various O. cumana populations. EC50 was determined for every compounds and mixtures, and for the five O. cumana populations thanks to the generated dose-response curves presented in the Suppl. File 5. Bar : ± SE. Different letters indicate significant differences at p < 0.05 (Student-Newman-Keuls Methodtest) between germination stimulants for a population (corresponding colored letters) or between population for a germination stimulant (black letters). Due to poor germination in response to DCL and costunolide, the EC50 of the G-RO population could not be determined. Suppl. File 7. Kinetic of GS activity exuded by a set of Helianthus accessions. Germination activities were normalized thanks to the germination percentage of both population obtained with GR24:DCL (equimolar, 1μM). For each accessions (except #774a and #826a), root exudates collected 3, 4, 5 and 6 weeks after sowing were applied to conditioned seeds of the two populations, E-BOU and G-RO. For #774a and #826a root exudates were collected at 3 and 4 weeks of culture only. Bar : ± SE. Suppl. File 8. Quantitative analysis of the phenotyping data at early stages (attachments and tubercles) in rhizotrons inoculated with the race E-BOU. Data were analysed taking into account only GS-treated rhizotrons, except for the cultivated susceptible controls XRQ and 2603. 8a. There was no significant statistical difference in the number of attachments at 14 dai between the wild resistant accessions except for the wild H. annuus #826a. 8b. Ordering the accessions by the efficiency of the development of attachments into tubercles (% of tubercle/ attachment) revealed a significant difference between phenotyping classes I and III, compared to the classes II and IV. Suppl. File 9. Quantitative analysis of the percentage of necrotic tubercles at 28 dai in rhizotrons inoculated with the race E-BOU. Data were analysed taking into account only GS-treated rhizotrons, except for the cultivated susceptible controls XRQ and 2603 (non-treated rhizotrons). Accessions without tubercle development were not taken into account (Class I and Class III, except #833a which develop few tubercles). Statistical analysis was performed using the Kruskal-Wallis test (α = 0.05). Suppl. File 10. List of wild Helianthus accessions used for cytological studies and number of observed samples for each accession. A few accessions from each phenotyping class in rhizotrons were used, inoculated with the race E-BOU. Whole root segment with attachment were cleared with chloral hydrate, or sectioned, imbedded in technovit system and stained with toluidine blue O. Attachments of accessions from classes I and III were all Incompatible (IA). Attachments of accessions from class IV were all Compatible (CA). For the accessions from Class II there were a mixture of IA and CA. As accessions from Classes I and III did not induce seed germination, attachments were sampled only from GS-treated rhizotrons for these accessions. Suppl. File 11. Summary of the the cellular phenotypes observed by cytology on attachments (14 dai). Common cellular resistant mechanisms led to incompatible attachments (IA) independently of the phenotyping classes in rhizotrons. Rarely, some defence reactions were observed in compatible attachments (CA). Suppl. File 12. Defence reactions at proximity of compatible attachments revealed by cytological study of Class II accessions. At 14 dai, accessions from class II, such as H. praecox, developed a mixture of incompatible attachments and compatible attachments. In some cases, defence reactions at proximity of these compatible attachments were observed as green staining suggesting phenolic compounds (a. accession #677 H. preacox; arrowheads), or gumlike substance in xylem vessels (b. accesion #679 H. praecox; red asterisks). Bar = 100 μ. Suppl. File 13. Phenotyping in 6 L pots of wild Helianthus using the most virulent broomrape races G. Boxplots of 7 accessions phenotyped in pots following inoculation with 4 races G (assay No 3) The accessions #2601 H. exilis and #325 H. tuberosus were from class I, #584 H. bolanderi, #677 H. praecox, #761 H. petiolaris and #786 H. debilis tardiflorus from class II and #833 H. annuus from class III. The 4 races G were from Romania (G-RO), Russia (G-RU), Spain (G-GV) and Turkey (G-TK). Five to 8 pots were cultured for each accession/ race. In each pot, the number of broomrape emergences was counted at the time of sunflower flowering. For each accession, Kruskal-Wallis test was performed (α=0.05). The p values were respectively: #2601ex: p=0.29; #325t (no p value); #584b: p=0.52; #677pr: p=0.12; #761p: p=0.004; #786d: p=0.03; #833a: p=0.06; B117: p=0.29; LP2:p=0.008., Orobanche cumana Wall., sunflower broomrape, is one of the major pests for the sunflower crop. Breeding for resistant varieties in sunflower has been the most efficient method to control this parasitic weed. However, more virulent broomrape populations continuously emerge by overcoming genetic resistance. It is thus essential to identify new broomrape resistances acting at various stages of the interaction and combine them to improve resistance durability. In this study, 71 wild sunflowers and wild relatives accessions from 16 Helianthus species were screened in pots for their resistance to broomrape at the late emergence stage. From this initial screen, 18 accessions from 9 species showing resistance, were phenotyped at early stages of the interaction: the induction of broomrape seed germination by sunflower root exudates, the attachment to the host root and the development of tubercles in rhizotron assays. We showed that wild Helianthus accessions are an important source of resistance to the most virulent broomrape races, affecting various stages of the interaction: the inability to induce broomrape seed germination, the development of incompatible attachments or necrotic tubercles, and the arrest of emerged structure growth. Cytological studies of incompatible attachments showed that several cellular mechanisms were shared among resistant Helianthus species., Peer reviewed

Orobanche cumana Wall., sunflower broomrape, is one of the major pests for the sunflower crop. Breeding for resistant varieties in sunflower has been the most efficient method to control this parasitic weed. However, more virulent broomrape populations continuously emerge by overcoming genetic resistance. It is thus essential to identify new broomrape resistances acting at various stages of the interaction and combine them to improve resistance durability. In this study, 71 wild sunflowers and wild relatives accessions from 16 Helianthus species were screened in pots for their resistance to broomrape at the late emergence stage. From this initial screen, 18 accessions from 9 species showing resistance, were phenotyped at early stages of the interaction: the induction of broomrape seed germination by sunflower root exudates, the attachment to the host root and the development of tubercles in rhizotron assays. We showed that wild Helianthus accessions are an important source of resistance to the most virulent broomrape races, affecting various stages of the interaction: the inability to induce broomrape seed germination, the development of incompatible attachments or necrotic tubercles, and the arrest of emerged structure growth. Cytological studies of incompatible attachments showed that several cellular mechanisms were shared among resistant Helianthus species., Peer reviewed

Descripción de los métodos utilizados para la recopilación/generación de datos: • UNIVERSO: Personas residentes en Andalucía con edades iguales o superiores a 18 años. • TAMAÑO DE LA MUESTRA TEÓRICA: 3.192 entrevistas. • TAMAÑO DE LA MUESTRA REAL: 3.190 entrevistas. • TIPO DE ENTREVISTA: Presencial mediante entrevistador, realizada en los domicilios. • TIPO DE MUESTREO: Estratificado con submuestreo por conglomerados, y elección de la unidad final por rutas aleatorias y cuotas de sexo y edad. • ESTRATIFICACIÓN: Se han utilizado dos variables para crear los estratos: la provincia, y una clasificación de secciones según criterios sociodemográficos basada en el Censo de 2001. El estrato final aparece con la combinación de ambas variables. La afijación por provincias es uniforme, con 399 entrevistas en cada una, con el objetivo de obtener un nivel de error inferior al 5% en cada una. La afijación por grupos sociodemográficos es proporcional a la población del universo dentro de cada provincia. • PROCESO MUESTRAL: Las 456 secciones se eligen a través de un muestro sistemático dentro de cada estrato (provincia). • CALIBRACIÓN: Dado que la muestra no es proporcional a la población de cada provincia, se calculan unos pesos que corrigen esta desproporción. • NIVELES DE ERROR: El nivel de error absoluto máximo esperado de los resultados de la encuesta, para las frecuencias de cada variable, es de ±1.9%, para un nivel de confianza del 95%. Para cada una de las provincias este nivel de error es del 5%. • TIEMPO MEDIO DE LA ENTREVISTA: 24,3 minutos., [ES] El objetivo del Ecobarómetro de Andalucía (EBA) es analizar la conciencia ambiental de los andaluces y cómo se relacionan con el medio ambiente. Para ello se elabora un sistema de indicadores a partir de los resultados proporcionados por una encuesta anual dirigida a la población andaluza mayor de 18 años. La encuesta tiene por finalidad medir las distintas dimensiones de la conciencia ambiental (afectiva, cognitiva, activa y conativa), analizando las percepciones, actitudes, conocimiento y comportamiento de los andaluces respecto a diversas cuestiones ambientales. Este dataset corresponde a los resultados obtenidos en la encuesta realizada a una muestra representativa de la población andaluza mayor de 18 años durante los meses de mayo y junio de 2011. El EBA presenta su undécima edición desde que se iniciara en el año 2001. La estabilidad del contenido del cuestionario, así como su comparabilidad con barómetros similares empleados en estudios de ámbito estatal o internacional, lo configuran como un valioso instrumento para el estudio de la opinión pública andaluza en temas de medio ambiente, así como su evolución en el tiempo y sus peculiaridades en el contexto más amplio de las sociedades europeas., [EN] The objective of Andalusian Barometer (EBA) is to analyze the environmental awareness of Andalusians and how they relate to the environment. For this purpose, a system of indicators is elaborated from the results provide by an annual survey directed to the Andalusian population over 18 years of age. The survey aims to measure the different dimensions of environmental awareness (affective, cognitive, active and conative), analyzing the perceptions, attitudes, knowledge and behavior of Andalusians respect different environmental issues. This dataset corresponds to the results obtained in the survey carried out on a representative sample of the Andalusian population over 18 years of age during the months of May and June 2011. The EBA is in its eleventh edition since it began in the year 2001. The stability of the content of questionnaire, as well as its comparability with similar barometers used in national or international studies, make it a valuable instrument for the study of Andalusian public opinion on environmental issues, as well as its evolution over time and its peculiarities in the broader context of the European societies., Research carried out within the framework of a collaboration agreement signed between the Department of Environment of the Regional Government of Andalusia and the Institute for Advanced Social Studies of the Spanish National Research Council (IESA-CSIC)., BAROMETER2011_Datafile.csv BAROMETER2011_Datafile.sav BAROMETER2011_Codebook_EN.pdf BAROMETER2011_Codebook_SP.pdf BAROMETER2011_Readme_EN.pdf BAROMETER2011_Readme_SP.pdf BAROMETER2011_Survey.pdf, Peer reviewed

The dataset contains measurements of Chlorophyll-a (mg m-3), nitrate (μM) and suspended matter (“SM”, g m-3) concentrations, temperature (ºC) and mesozooplankton biovolume (mL 100m-3), collected between 2002 and 2007, in a network of sampling stations (“Station_ID”) distributed across the northeast continental shelf of the Gulf of Cádiz. The year and Julian day (number of days after 1 January) in which each sample was obtained are indicated, as well as their geolocation with latitude and longitude coordinates in degrees. Chlorophyll-a, suspended matter (SM), nitrate and temperature data were taken from the surface layer (<5m) of the water column. Oblique plankton hauls were conducted up to 100 meters using a Bongo net with a 40-cm mouth diameter and 200 mm mesh size, for mesozooplankton sampling., [General Notes] The dataset is provided (“Dataset.txt”) within a compressed folder that also includes a single file in text format (“Readme.txt”) containing a detailed description of the data structure. Dataset.txt file has column titles as the first line. One column is written for each measured variable. Missing data are filled with NaN. Data files are in UTF8 encoding, plain text format with [space] used as the delimiter. The data are provided under an Attribution-ShareAlike 4.0 International license. However, if you use the data, so as to support the authors, please consider citing the above mentioned article where data collection and analytical techniques are given in detail. Here we only give a brief details and a guide to the contents of the data files., [Geographical coordinates of the sampling area] Coordinates.txt file provides the geographical coordinates of the sampling area., This data set includes physical and biogeochemical data collected between 2002 and 2007 on the northeast continental shelf of the Gulf of Cádiz., Data adquisition was supported by projects “Recursos pesqueros del golfo de Cádiz” and “Fluctuaciones y potencialidad de especies pesqueras de plataforma en la región atlántica andaluza” (Junta de Andalucía)., Peer reviewed

Figure S1. Presence/absence of genes coding for potential PAMPs and CWDE across well-annotated genomes of Xylella species. The circles from in to out represent elf18, csp20, chiA, pglA, prtA, lesA and wzy. GBK and fasta files of both the amino acid and nucleotide sequences of the represented genomes were downloaded from the NCBI database. Blast searches were performed using the sequence of X. fastidiosa subsp. fastidiosa Temecula as a template. Blasts using Koala were performed to check for presence absence of the LPS, EPS, and PGN biosynthesis pathway, as well as secretion systems. Table S1. Gene expression to microbial stimuli in xylem tissues. For creating this list, two published datasets were crossed: Wendrich et al., 2020 (https://bioit3.irc.ugent.be/plant-sc-atlas/) and Fröscher et al., 2020. Table S2. Potential PRRs and NLRs in genomes of plants susceptible to X. fastidiosa based on annotation searches. GBK files from each of the host plants' genomes were downloaded from the NCBI database. Then, for retrieving the number of potential PRR and NLR genes we have searched for known protein keywords related to these two families of genes using python custom scripts to parse the GBK files using the Biopython library and specifically SeqIO function. Based on gene name or TAIR locustag (in the case of A. thaliana) we dropped the duplicate genes (splicing products)., Peer reviewed

TotalDat.fits.gz: A FITS table storing information for each of the quasars used in the sample. The names, formats, and contents of each of the columns in this table are described in Table 1. All time-series data (MJD_x, MAG_x, MAG_ERR_x), structure function data (DT_REST_x, SF_x, SF_ERR_x), and PSD data (REST_FREQ_x, CARMA_PSD_x, CARMA_PSD_ERR_L_x, CARMA_PSD_ERR_U_x) are stored as arrays., EnsDat.fits.gz: A FITS table storing information for the ensemble analysis conducted on different subsets of the total sample. The names, formats, and contents of each of the columns in this table are described in Table 2. Similar to the previous file, time-series, structure function, and PSD data are stored as arrays., It should be noted that for each quasar/ensemble, each array will be the same length to conform to the FITS file standards. Therefore, to force each array to be the same shape, arrays shorter than the largest array will be filled with either NaNs or empty strings until they reach this maximum array length. There will be three columns for many of the values, one for each bandpass (g,r,i), also described in Table 1., Peer reviewed

Muscle development is a multistep process that involves cell specification, myoblast fusion, myotube migration, and attachment to the tendons. In spite of great efforts trying to understand the basis of these events, little is known about the molecular mechanisms underlying myotube migration. Knowledge of the few molecular cues that guide this migration comes mainly from studies in Drosophila. The migratory process of Drosophila embryonic muscles involves a first phase of migration, where muscle progenitors migrate relative to each other, and a second phase, where myotubes migrate searching for their future attachment sites. During this phase, myotubes form extensive filopodia at their ends oriented preferentially toward their attachment sites. This myotube migration and the subsequent muscle attachment establishment are regulated by cell adhesion receptors, such as the conserved proteoglycan Kon-tiki/Perdido. Laminins have been shown to regulate the migratory behavior of many cell populations, but their role in myotube migration remains largely unexplored. Here, we show that laminins, previously implicated in muscle attachment, are indeed required for muscle migration to tendon cells. Furthermore, we find that laminins genetically interact with kon-tiki/perdido to control both myotube migration and attachment. All together, our results uncover a new role for the interaction between laminins and Kon-tiki/Perdido during Drosophila myogenesis. The identification of new players and molecular interactions underlying myotube migration broadens our understanding of muscle development and disease., Peer reviewed