RNA-seq transcriptome analysis provides candidate genes for resistance to Tomato leaf cur New Delhi virus in melon

[EN] Tomato leaf curl New Delhi virus (ToLCNDV) emerged in the Mediterranean Basin in 2012 as the first DNA bipartite begomovirus (Geminiviridae family), causing severe yield and economic losses in cucurbit crops. A major resistance locus was identified in the wild melon accession WM-7 (Cucumis melo kachri group), but the mechanisms involved in the resistant response remained unknown. In this work, we used RNA-sequencing to identify disease-associated genes that are differentially expressed in the course of ToLCNDV infection and could contribute to resistance. Transcriptomes of the resistant WM-7 genotype and the susceptible cultivar Piñonet Piel de Sapo (PS)(C. melo ibericus group) in ToLCNDV and mock inoculated plants were compared at four time points during infection (0, 3, 6, and 12 days post inoculation). Different gene expression patterns were observed over time in the resistant and susceptible genotypes in comparison to their respective controls. Differentially expressed genes (DEGs) in ToLCNDV-infected plants were classified using gene ontology (GO) terms, and genes of the categories transcription, DNA replication, and helicase activity were downregulated in WM-7 but upregulated in PS, suggesting that reduced activity of these functions reduces ToLCNDV replication and intercellular spread and thereby contributes to resistance. DEGs involved in the jasmonic acid signaling pathway, photosynthesis, RNA silencing, transmembrane, and sugar transporters entail adverse consequences for systemic infection in the resistant genotype, and lead to susceptibility in PS. The expression levels of selected candidate genes were validated by qRT-PCR to corroborate their differential expression upon ToLCNDV infection in resistant and susceptible melon. Furthermore, single nucleotide polymorphism (SNPs) with an effect on structural functionality of DEGs linked to the main QTLs for ToLCNDV resistance have been identified. The obtained results pinpoint cellular functions and candidate genes that are differentially expressed in a resistant and susceptible melon line in response to ToLCNDV, an information of great relevance for breeding ToLCNDV-resistant melon cultivars.This work was supported by grants AGL201785563-C2-1-R and RTA2017-00061-C03-03 funded by MCIN/AEI/10.13039/501100011033 and by "ERDF A way of making Europe," by grant PID2020-116055RB-C21 funded by MCIN/AEI/10.13039/501100011033; and by PROMETEO projects 2017/078 and 2021/072 (to promote excellence groups) by the Conselleria d'Educacio, Investigacio, Cultura i Esports (Generalitat Valenciana).Sáez-Sánchez, C.; Flores-León, A.; Montero-Pau, J.; Sifres, A.; Dhillon N.P.S:; López, C.; Picó, B. (2022). RNA-seq transcriptome analysis provides candidate genes for resistance to Tomato leaf cur New Delhi virus in melon. Frontiers in Plant Science. 12:1-26. https://doi.org/10.3389/fpls.2021.7988581261

First record of the alien pest Rhaponticum repens (Compositae) in the Iberian Peninsula

First record of the alien pest Rhaponticum repens (Compositae) in the Iberian Peninsula.- Rhaponticum repens is reported for the first time for the flora of the Iberian Peninsula. The species is native from Central Asia and has become invasive in Argentina, Canada, Europe and the USA. It was detected for the first time in abandoned fields from Vilablareix, near the city of Girona (Catalonia, Spain) and in the valley of the Vinalopó in Alicante (Valencia, Spain), where it was collected as early as in 1959 but misdentified. Molecular data, based on nrDNA region ITS, suggest that the reported populations may be closely related to plants from the United States. Due to the extremely noxious character of the species and the possible relationship of Spanish plants with the invasive American populations, some kind of monitoring is recommended.Rhaponticum repens (Compositae), una nueva planta alóctona para la Península Ibérica.- Se cita por primera vez la especie Rhaponticum repens para la flora de la Península Ibérica. Rhaponticum repens es una especie nativa de Asia central que actúa como invasora en diversos países como Argentina, Canadá o los Estados Unidos. Se ha encontrado por primera vez en campos de cultivo abandonados en el pueblo de Vilablareix, cerca de la ciudad de Girona (Cataluña, España) y en el valle del Vinalopó (Valencia, España), donde fue recolectada y mal identificada en 1959. Los datos moleculares, obtenidos a partir de la región ITS del nrDNA, sugieren que estas poblaciones podrían estar relacionadas con plantas invasoras de Estados Unidos. Debido al carácter extremadamente invasor de la especie, y a su posible origen secundario a partir de las poblaciones norteamericanas, se recomienda el seguimiento de estas poblacione

Los Poyos del Molinillo (Frigiliana): new site of the Bronze Age in the East Axarquía (Málaga, Andalucía)

En este trabajo damos a conocer un nuevo yacimiento descubierto recientemente en el municipio de Frigiliana. La delimitación del área denominada Los Poyos del Molinillo permitió definir la existencia de un poblado y una covacha con restos de una inhumación. El estudio de los materiales arqueológicos, que incluye cerámica, piezas metálicas o elementos de molturación, o la datación AMS obtenida, permiten adscribir el yacimiento a la Edad del Bronce y ampliar el conocimiento de esta etapa en la Axarquía oriental (Málaga, Andalucía).In this work we present a new site recently discovered in the Frigiliana municipality (Málaga). The spatial delimitation of the so called Los Poyos del Molinillo area let us define a Bronze age settlement and an inhumation burial cave. The archaeological record includes ceramic, metallic items or grinding elements, all of them belonging to the Bronze Age, as well as an AMS Radiocarbon data. This site extends the knowledge about this period in the Eastern Axarquía (Málaga, Andalucía)

Higher education segregation in Spain: Gender constructs and social background

The waning influence of ascriptive factors on occupational status has been related to the expansion of higher education systems and economic modernisation. The theory of Effectively Maintained Inequality observes that the horizontal stratification of university degrees is a strategy of social differentiation used mainly by the most advantaged social class to access the occupations that are better valued in the labour market. This article verifies the effectively maintained inequality theory by means of a statistical analysis of selected degrees, differentiated by gender and social class, carried out in a Spanish university during the period of expansion and consolidation of the higher education system. The results confirm the theory, but they are partially conditioned by the vertical stratification that alters the composition by gender of the contingent of students of less advantaged social class, in which women present a greater tendency to choose degrees that are less valued by the market

Revealing the last 13,500 years of environmental history from the multiproxy record of a mountain lake (Lago Enol, northern Iberian Peninsula)

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10933-009-9387-7.We present the Holocene sequence from Lago Enol (43°16′N, 4°59′W, 1,070 m a.s.l.), Cantabrian Mountains, northern Spain. A multiproxy analysis provided comprehensive information about regional humidity and temperature changes. The analysis included sedimentological descriptions, physical properties, organic carbon and carbonate content, mineralogy and geochemical composition together with biological proxies including diatom and ostracod assemblages. A detailed pollen study enabled reconstruction of variations in vegetation cover, which were interpreted in the context of climate changes and human impact. Four distinct stages were recognized for the last 13,500 years: (1) a cold and dry episode that includes the Younger Dryas event (13,500–11,600 cal. year BP); (2) a humid and warmer period characterizing the onset of the Holocene (11,600–8,700 cal. year BP); (3) a tendency toward a drier climate during the middle Holocene (8,700–4,650 cal. year BP); and (4) a return to humid conditions following landscape modification by human activity (pastoral activities, deforestation) in the late Holocene (4,650–2,200 cal. year BP). Superimposed on relatively stable landscape conditions (e.g. maintenance of well established forests), the typical environmental variability of the southern European region is observed at this site.The Spanish Inter-Ministry Commission of Science and Technology (CICYT), the Spanish National Parks agency, the European Commission, the Spanish Ministry of Science, and the European Social Fund

Revealing the last 13,500 years of environmental history from the multiproxy record of a mountain lake (Lago Enol, northern Iberian Peninsula)

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10933-009-9387-7.We present the Holocene sequence from Lago Enol (43°16′N, 4°59′W, 1,070 m a.s.l.), Cantabrian Mountains, northern Spain. A multiproxy analysis provided comprehensive information about regional humidity and temperature changes. The analysis included sedimentological descriptions, physical properties, organic carbon and carbonate content, mineralogy and geochemical composition together with biological proxies including diatom and ostracod assemblages. A detailed pollen study enabled reconstruction of variations in vegetation cover, which were interpreted in the context of climate changes and human impact. Four distinct stages were recognized for the last 13,500 years: (1) a cold and dry episode that includes the Younger Dryas event (13,500–11,600 cal. year BP); (2) a humid and warmer period characterizing the onset of the Holocene (11,600–8,700 cal. year BP); (3) a tendency toward a drier climate during the middle Holocene (8,700–4,650 cal. year BP); and (4) a return to humid conditions following landscape modification by human activity (pastoral activities, deforestation) in the late Holocene (4,650–2,200 cal. year BP). Superimposed on relatively stable landscape conditions (e.g. maintenance of well established forests), the typical environmental variability of the southern European region is observed at this site.The Spanish Inter-Ministry Commission of Science and Technology (CICYT), the Spanish National Parks agency, the European Commission, the Spanish Ministry of Science, and the European Social Fund

Carbapenem-resistant Citrobacter spp. isolated in Spain from 2013 to 2015 produced a variety of carbapenemases including VIM-1, OXA-48, KPC-2, NDM-1 and VIM-2

Objectives: There is little information about carbapenemase-producing (CP) Citrobacter spp.We studied the molecular epidemiology and microbiological features of CP Citrobacter spp. isolates collected in Spain (2013-15). Methods: In total, 119 isolates suspected of being CP by the EUCAST screening cut-off values were analysed. Carbapenemases and ESBLs were characterized using PCR and sequencing. The genetic relationship among Citrobacter freundii isolates was studied by PFGE. Results: Of the 119 isolates, 63 (52.9%) produced carbapenemases, of which 37 (58.7%) produced VIM-1, 20 (31.7%) produced OXA-48, 12 (19%) produced KPC-2, 2 (3.2%) produced NDM-1 and 1 (1.6%) produced VIM- 2; 9 C. freundii isolates co-produced VIM-1 plus OXA-48. Fourteen isolates (22.2%) also carried ESBLs: 8 CTX-M-9 plus SHV-12, 2 CTX-M-9, 2 SHV-12 and 2 CTX-M-15. Fifty-seven isolates (90.5%) were C. freundii, 4 (6.3%) were Citrobacter koseri, 1 (1.6%) was Citrobacter amalonaticus and 1 (1.6%) was Citrobacter braakii. By EUCAST breakpoints, eight (12.7%) of the CP isolates were susceptible to the four carbapenems tested. In the 53 CP C. freundii analysed by PFGE, a total of 44 different band patterns were observed. Four PFGE clusters were identified: cluster 1 included eight isolates co-producing VIM-1 and OXA-48; blaVIM-1 was carried in a class 1 integron (intI-blaVIM-1 - aacA4-dfrB1-aadA1-catB2-qacE¿1/sul1) and blaOXA-48 was carried in a Tn1999.2 transposon. Conclusions: We observed the clonal and polyclonal spread of CP Citrobacter spp. across several Spanish geographical areas. Four species of Citrobacter spp. produced up to five carbapenemase types, including coproduction of VIM-1 plus OXA-48. Some CP Citrobacter spp. isolates were susceptible to the four carbapenems tested, a finding with potential clinical implications

‘They're not girly girls’: an exploration of quantitative and qualitative data on engineering and gender in higher education

This article was published in the journal, European Journal of Engineering Education [© Taylor & Francis] and the definitive version is available at: http://dx.doi.org/10.1080/03043797.2012.661702Despite sustained efforts to promote engineering careers to young women, it remains the most male-dominated academic discipline in Europe. This paper will provide an overview of UK data and research on women in engineering higher education, within the context of Europe. Comparisons between data from European countries representing various regions of Europe will highlight key differences and similarities between these nations in terms of women in engineering. Also, drawing on qualitative research the paper will explore UK students' experiences of gender, with a particular focus on the decision to study engineering and their experiences in higher education. © 2012 Copyright SEFI

The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease

Background\ud In order to identify novel loci associated with Alzheimer's disease (AD), we conducted a genome-wide association study (GWAS) in the Spanish population.\ud \ud Methods\ud We genotyped 1,128 individuals using the Affymetrix Nsp I 250K chip. A sample of 327 sporadic AD patients and 801 controls with unknown cognitive status from the Spanish general population were included in our initial study. To increase the power of the study, we combined our results with those of four other public GWAS datasets by applying identical quality control filters and the same imputation methods, which were then analyzed with a global meta-GWAS. A replication sample with 2,200 sporadic AD patients and 2,301 controls was genotyped to confirm our GWAS findings.\ud \ud Results\ud Meta-analysis of our data and independent replication datasets allowed us to confirm a novel genome-wide significant association of AD with the membrane-spanning 4-domains subfamily A (MS4A) gene cluster (rs1562990, P = 4.40E-11, odds ratio = 0.88, 95% confidence interval 0.85 to 0.91, n = 10,181 cases and 14,341 controls).\ud \ud Conclusions\ud Our results underscore the importance of international efforts combining GWAS datasets to isolate genetic loci for complex diseases

An insight into imbalanced Big Data classification: outcomes and challenges

Big Data applications are emerging during the last years, and researchers from many disciplines are aware of the high advantages related to the knowledge extraction from this type of problem. However, traditional learning approaches cannot be directly applied due to scalability issues. To overcome this issue, the MapReduce framework has arisen as a “de facto” solution. Basically, it carries out a “divide-and-conquer” distributed procedure in a fault-tolerant way to adapt for commodity hardware. Being still a recent discipline, few research has been conducted on imbalanced classification for Big Data. The reasons behind this are mainly the difficulties in adapting standard techniques to the MapReduce programming style. Additionally, inner problems of imbalanced data, namely lack of data and small disjuncts, are accentuated during the data partitioning to fit the MapReduce programming style. This paper is designed under three main pillars. First, to present the first outcomes for imbalanced classification in Big Data problems, introducing the current research state of this area. Second, to analyze the behavior of standard pre-processing techniques in this particular framework. Finally, taking into account the experimental results obtained throughout this work, we will carry out a discussion on the challenges and future directions for the topic.This work has been partially supported by the Spanish Ministry of Science and Technology under Projects TIN2014-57251-P and TIN2015-68454-R, the Andalusian Research Plan P11-TIC-7765, the Foundation BBVA Project 75/2016 BigDaPTOOLS, and the National Science Foundation (NSF) Grant IIS-1447795