Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley

Heading time is a complex trait, and natural variation in photoperiod responses is a major factor controlling time to heading, adaptation and grain yield. In barley, previous heading time studies have been mainly conducted under field conditions to measure total days to heading. We followed a novel approach and studied the natural variation of time to heading in a world-wide spring barley collection (218 accessions), comprising of 95 photoperiod-sensitive (Ppd-H1) and 123 accessions with reduced photoperiod sensitivity (ppd-H1) to long-day (LD) through dissecting pre-anthesis development into four major stages and sub-phases. The study was conducted under greenhouse (GH) conditions (LD; 16/8 h; ∼20/∼16°C day/night). Genotyping was performed using a genome-wide high density 9K single nucleotide polymorphisms (SNPs) chip which assayed 7842 SNPs. We used the barley physical map to identify candidate genes underlying genome-wide association scans (GWAS). GWAS for pre-anthesis stages/sub-phases in each photoperiod group provided great power for partitioning genetic effects on floral initiation and heading time. In addition to major genes known to regulate heading time under field conditions, several novel QTL with medium to high effects, including new QTL having major effects on developmental stages/sub-phases were found to be associated in this study. For example, highly associated SNPs tagged the physical regions around HvCO1 (barley CONSTANS1) and BFL (BARLEY FLORICAULA/LEAFY) genes. Based upon our GWAS analysis, we propose a new genetic network model for each photoperiod group, which includes several newly identified genes, such as several HvCO-like genes, belonging to different heading time pathways in barley

Land use classification from Sentinel-2 imagery

[EN] Sentinel-2 (S2), a new ESA satellite for Earth observation, accounts with 13 bands which provide high-quality radiometric images with an excellent spatial resolution (10 and 20 m) ideal for classification purposes. In this paper, two objectives have been addressed: to determine the best classification method for S2, and to quantify its improve-ment with respect to the SPOT operational mission. To do so, four classifiers (LDA, RF, Decision Trees, K-NN) have been selected and applied to two different agricultural areas located in Valencia (Spain) and Buenos Aires (Argentina). All classifiers were tested using, on the one hand, all the S2 bands and, on the other hand, only selecting those bands from S2 closer to the four bands from SPOT. In all the cases, between 10%-50% of samples were used to train the classifier while remaining the rest for validation. As a result, a land use map was generated from the best classifier, according to the Kappa index, providing scientifically relevant information such as the area of each land use class.[ES] Sentinel-2 (S2) es un nuevo satélite de la ESA que cuenta con 13 bandas proporcionando imágenes de alta calidad radiométrica y excelente resolución espacial (10 y 20 m) ideal para trabajos de clasificación. En este trabajo se han abordado dos objetivos: determinar el mejor método de clasificación con S2, y cuantificar su mejora respecto a otras misiones operativas, como SPOT. Para ello se han seleccionado cuatro clasificadores (LDA, RF, Árboles de decisión, K-NN) que se han aplicado en dos zonas agrarias: una en la huerta de Valencia (España) y otra en la región de Buenos Aires (Argentina). Se han probado todos los clasificadores usando, por una parte, todas las bandas de S2, y por otra usando sólo las cuatro que coinciden con SPOT. En todos los casos se han aplicando porcentajes entre el 10 y el 50% de datos de entrenamiento y usado el resto de datos como validación. Como resultado se ha generado un mapa de usos del suelo a partir del mejor clasificador, basándose en el índice Kappa, proporcionando información científicamente relevante como es el área ocupada por cada una de las clases.Borràs, J.; Delegido, J.; Pezzola, A.; Pereira, M.; Morassi, G.; Camps-Valls, G. (2017). Clasificación de usos del suelo a partir de imágenes Sentinel-2. Revista de Teledetección. (48):55-66. doi:10.4995/raet.2017.7133.SWORD556648Breiman, L. (2001). Machine Learning, 45(1), 5-32. doi:10.1023/a:1010933404324Cohen, J. (1960). A Coefficient of Agreement for Nominal Scales. Educational and Psychological Measurement, 20(1), 37-46. doi:10.1177/001316446002000104Comber, A., Fisher, P., & Wadsworth, R. (2005). You know what land cover is but does anyone else?…an investigation into semantic and ontological confusion. International Journal of Remote Sensing, 26(1), 223-228. doi:10.1080/0143116042000274032Delegido, J., Verrelst, J., Alonso, L., & Moreno, J. (2011). Evaluation of Sentinel-2 Red-Edge Bands for Empirical Estimation of Green LAI and Chlorophyll Content. Sensors, 11(7), 7063-7081. doi:10.3390/s110707063Gislason, P. O., Benediktsson, J. A., & Sveinsson, J. R. (2006). Random Forests for land cover classification. Pattern Recognition Letters, 27(4), 294-300. doi:10.1016/j.patrec.2005.08.011Hastie, T., Tibshirani, R., & Friedman, J. (2009). The Elements of Statistical Learning. Springer Series in Statistics. doi:10.1007/978-0-387-84858-7Immitzer, M., Atzberger, C., & Koukal, T. (2012). Tree Species Classification with Random Forest Using Very High Spatial Resolution 8-Band WorldView-2 Satellite Data. Remote Sensing, 4(9), 2661-2693. doi:10.3390/rs4092661Landis, J. R., & Koch, G. G. (1977). The Measurement of Observer Agreement for Categorical Data. Biometrics, 33(1), 159. doi:10.2307/2529310Mena, A.J. 2014. Procesamiento de imágenes satelitales multiespectrales. Proyecto final de carrera, Facultad de Informática, Universidad del País Vasco.Quinlan, J.R. 1993. Programs for Machine Learning. 1st ed. San Mateo, CA, Morgan.Rees, G. 2005. The Remote Sensing Data Book. Cambridge University Press, 262 pp.Rodríguez-Galiano, V., Chica-Rivas, M. 2012. Clasificación de imágenes de satélite mediante software libre: Nuevas tendencias en algoritmos de Inteligencia artificial. Departamento de Geodinámica, Universidad de Granada

Cancer diagnosis in Catalonia (Spain) after two years of COVID-19 pandemic: an incomplete recovery

Background: This study aimed to estimate potential undetected cancers over the first 2 years of the COVID-19 pandemic in Catalonia. Methods: Cancer incidence was compared between pre-pandemic (2019) and pandemic (March 2020-January 2022) periods in the Catalan Pathology Registry (CPR) according to sex, age, and tumor site. The correlation between cancer diagnosis and COVID-19 health care workload was also evaluated by means of the Pearson's correlation coefficient (R). The expected incident cancers (E) during the pandemic were estimated by applying 2019 CPR cancer incidence specific rates by sex and 5-year age groups to the 2020 and 2021 Catalan population pyramids. CPR incident cancers were considered observed (O). Standardized incidence ratios (SIR) and 95% confidence intervals (as) were calculated using the 0/E ratio. Results: After two pandemic years, cancer diagnosis decreased by 12% (SIR 0.88, 95% a 0.87-0.89), or similar to 7700 undetected cancers (13 000 with nonmelanoma skin cancer). Without nonmelanoma skin cancer, 72% of the cancer underdiagnosis was generated in 2020. Diagnoses decreased more in men (whole pandemic -14%; 2020 -21%; 2021 8%) than in women (---9%, 19%, 3%, respectively), dropping significantly overall in all pandemic waves but the fifth (first -37%, second -16%, third -8%, fourth -6%, fifth -2%, sixth -6%), and across all adult age groups. In the first wave, CPR cancer diagnosis was inversely correlated with COVID-19 caseload in primary care (R -0.91, 95% CI -0.97 to -0.75) and occupancy in conventional hospital wards (R -0.91, 95% a -0.99 to -0.48) and intensive care (R 0.91, 95% a 95% 0.98 to 0.70). Conclusions: Our study evaluated the overall pandemic impact on cancer diagnosis on a large scale and with minimal selection bias, showing that as of February 2022, cancer detection in Catalonia had not yet recovered to pre-pandemic levels. Pending cancer incidence data from population-based cancer registries, early CPR data could inform the development of Spanish cancer control plans

L'avaluació continuada i la millora en el rendiment acadèmic: el cas de de la Farmacologia i Toxicologia en R+D+i del Grau de Farmàcia

Podeu consultar la Vuitena trobada de professorat de Ciències de la Salut completa a: http://hdl.handle.net/2445/66524Des de la implantació de Espai Europeu d’Educació Superior i l’adopció per part de les universitats de l’avaluació continuada (AC) com a sistema d’acreditació del aprenentatges, existeix la preocupació tant per part dels estudiants com dels professors, que l’AC, entesa com la suma de proves i/o evidències parcials d’avaluació, ens porta a una disminució de notes en la franja alta de qualificació..

Allele-Specific Expression of APC in Adenomatous Polyposis Families

BACKGROUND & AIMS: Germline mutations in the APC gene cause of most cases of familial adenomatous polyposis (FAP) and a lesser proportion of attenuated FAP (AFAP). Systematic analysis of APC at the RNA level could provide insight into the pathogenicity of identified mutations and the molecular basis of FAP/AFAP in families without identifiable mutations. Here, we analyzed the prevalence of imbalances in the allelic expression of APC in polyposis families with germline mutations in the gene and without detectable mutations in APC and/or MUTYH. METHODS: Allele-specific expression (ASE) was determined by single nucleotide primer extension using an exon 11 polymorphism as an allele-specific marker. In total, 52 APC-mutation-positive (36 families) and 24 APC/MUTYH-mutation-negative (23 families) informative patients were analyzed. Seventy-six controls also were included. RESULTS: Of the APC-mutation-positive families, most of those in whom the mutation was located before the last exon of the gene (12 of 14) had ASE imbalance, which is consistent with a mechanism of nonsense-mediated decay. Of the APC/MUTYH-mutation-negative Families, 2 (9%) had ASE imbalance, which might cause the disease. Normal allele expression was restored shortly after lymphocytes were cultured with puromycin, supporting a 'nonsense-mediated' hypothesis. CONCLUSIONS: ASE analysis might be used to determine the pathogenesis of some cases of FAP and AFAP in which APC mutations are not found. ASE also might be used to prioritize the order in which different areas of APC are tested. RNA-level studies are important for the molecular diagnosis of FAP

A taste sensor device for unmasking admixing of rancid or winey-vinegary olive oil to extra virgin olive oil

Electrochemical sensor devices have gathered great attention in food analysis namely for olive oil evaluation. The adulteration of extra-virgin olive oil with lower-grade olive oil is a common worldwide fraudulent practice, which detection is a challenging task. The potentiometric fingerprints recorded by lipid polymeric sensor membranes of an electronic tongue, together with linear discriminant analysis and simulated annealing meta-heuristic algorithm, enabled the detection of extra-virgin olive oil adulterated with olive oil for which an intense sensory defect could be perceived, specifically rancid or winey-vinegary negative sensations. The homemade designed taste device allowed the identification of admixing of extra-virgin olive oil with more than 2.5% or 5% of rancid or winey-vinegary olive oil, respectively. Predictive mean sensitivities of 84±4% or 92±4% and specificities of 79±6% or 93±3% were obtained for rancid or winey-vinegary adulterations, respectively, regarding an internal-validation procedure based on a repeated K-fold cross-validation variant (4 folds×10 repeats, ensuring that the dataset was forty times randomly split into 4 folds, leaving 25% of the data for validation purposes). This performance was satisfactory since, according to the legal physicochemical and sensory analysis, the intentionally adulterated olive oil with percentages of 2.510%, could still be commercialized as virgin olive oil. It could also be concluded that at a 5% significance level, the trained panelists could not distinguish extra-virgin olive oil samples from those adulterated with 2.5% of rancid olive oil or up to 5% of winey-vinegary olive oil. Thus, the electronic tongue proposed in this study can be foreseen as a practical and powerful tool to detect this kind of worldwide common fraudulent practice of high quality olive oil.This work was financially supported by Project POCI-01–0145FEDER-006984 – Associate Laboratory LSRE-LCM, Project UID/QUI/ 00616/2013 – CQ-VR, Project UID/BIO/04469/2013 – CEB and strategic project PEst-OE/AGR/UI0690/2014 – CIMO all funded by FEDER - Fundo Europeu de Desenvolvimento Regional through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) – and by national funds through FCT - Fundação para a Ciência e a Tecnologia, Portugal. Nuno Rodrigues thanks FCT, POPH-QREN and FSE for the Ph.D. Grant (SFRH/BD/104038/2014). Souheib Oueslati is also grateful for the support of the Tunisian Ministry of Agriculture.info:eu-repo/semantics/publishedVersio

Mesenchymal stromal cells induced regulatory B cells are enriched in extracellular matrix genes and IL-10 independent modulators

Regulatory B cells (Breg) are essential players in tolerance and immune homeostasis. However, lack of specific Breg markers limit their potential in clinical settings. Mesenchymal stromal cells (MSC) modulate B cell responses and are described to induce Breg in vitro. The aim of this work was to characterize MSC induced Breg (iBreg) and identify specific Breg biomarkers by RNAseq. After 7-day coculture with adipose tissue-derived MSC, B cells were enriched in transitional B cell populations, with increased expression and secretion of IL-10 and no TNFα. In addition, iBreg showed potential to modulate T cell proliferation at 2 to 1 cell ratios and their phenotype remained stable for 72h. RNAseq analysis of sorted IL-10 positive and negative iBreg populations identified over 1500 differentially expressed genes (DEG) among both populations. Analysis of biological processes of DEG highlighted an enrichment of immune regulation and extracellular matrix genes in IL-10 - iBreg populations, while IL-10 + iBreg DEG were mostly associated with cell activation. This was supported by T cells modulation assays performed in the presence of anti-IL-10 neutralizing antibodies showing the non-essential role of IL-10 in the immunomodulatory capacity of iBregs on T cells. However, based on RNAseq results we explored the role of TGF-β and found out that it plays a major role on iBreg induction and iBreg immunomodulatory properties. Therefore, we report that MSC induce B cell populations characterized by the generation of extracellular matrix and immune modulation independently of IL-10

Telomere length and genetic anticipation in lynch syndrome

Telomere length variation has been associated with increased risk of several types of tumors, and telomere shortening, with genetic anticipation in a number of genetic diseases including hereditary cancer syndromes. No conclusive studies have been performed for Lynch syndrome, a hereditary colorectal cancer syndrome caused by germline mutations in the DNA mismatch repair genes. Here we evaluate telomere length in Lynch syndrome, both as a cancer risk factor and as a mechanism associated with anticipation in the age of cancer onset observed in successive generations of Lynch syndrome families. Leukocyte telomere length was measured in 244 mismatch repair gene mutation carriers from 96 Lynch syndrome families and in 234 controls using a monochrome multiplex quantitative PCR method. Cancer-affected mutation carriers showed significantly shorter telomeres than cancer-free mutation carriers. In addition, cancer-affected carriers showed the most pronounced shortening of telomere length with age, compared with unaffected carriers. The anticipation in the age of cancer onset observed in successive generations was not associated with telomere shortening, although, interestingly, all mother-son pairs showed telomere shortening. In conclusion, cancer-affected mismatch repair gene mutation carriers have distinct telomere-length pattern and dynamics. However, anticipation in the age of onset is not explained by telomere shortening. Pending further study, our findings suggest that telomere attrition might explain the previously reported dependence of cancer risk on the parent-of-origin of mismatch repair gene mutations

Is rare cancer care organized at national health system level? Multiple case study in six EU countries

Background: As a system of European Reference Networks (ERNs) emerges, we aimed to shed light on the processes through which reference centres (RCs) for rare cancers are embedded in national health systems, and to formulate hypotheses about which national care models favour equitable access for patients. Methods We used a multiple-case-study design based on the experiences of Czechia, Finland, France, Italy, Lithuania and Spain. Using sarcoma as an example of rare cancer, 52 semi-structured interviews were conducted during six on-site visits. Results The comparative analysis showed substantial heterogeneity in the processes for formalising RCs status and in their levels of integration in the different health systems, but two models, namely, the centre-based and the network-based, can be envisaged at national level. RCs for rare cancers were legally established only in France and Spain. Expert clinicians cooperate in a structured way, using network mechanisms, in France and Italy, and these countries, plus Finland and Lithuania, had a referral system to facilitate patients' access from non-expert centres to RCs. Comparative analysis of the cases enabled the identification of key healthcare planning principles in instituting RCs at the national level, among them the need to stipulate the involvement of expert professionals in steering the rare cancer care system

N-Glycans in Immortalized Mesenchymal Stromal Cell-Derived Extracellular Vesicles Are Critical for EV-Cell Interaction and Functional Activation of Endothelial Cells

Mesenchymal stromal cell-derived extracellular vesicles (MSC-EV) are widely considered as a cell-free therapeutic alternative to MSC cell administration, due to their immunomodulatory and regenerative properties. However, the interaction mechanisms between EV and target cells are not fully understood. The surface glycans could be key players in EV-cell communication, being specific molecular recognition patterns that are still little explored. In this study, we focused on the role of N-glycosylation of MSC-EV as mediators of MSC-EV and endothelial cells' interaction for subsequent EV uptake and the induction of cell migration and angiogenesis. For that, EV from immortalized Wharton's Jelly MSC (iWJ-MSC-EV) were isolated by size exclusion chromatography (SEC) and treated with the glycosidase PNGase-F in order to remove wild-type N-glycans. Then, CFSE-labelled iWJ-MSC-EV were tested in the context of in vitro capture, agarose-spot migration and matrigel-based tube formation assays, using HUVEC. As a result, we found that the N-glycosylation in iWJ-MSC-EV is critical for interaction with HUVEC cells. iWJ-MSC-EV were captured by HUVEC, stimulating their tube-like formation ability and promoting their recruitment. Conversely, the removal of N-glycans through PNGase-F treatment reduced all of these functional activities induced by native iWJ-MSC-EV. Finally, comparative lectin arrays of iWJ-MSC-EV and PNGase-F-treated iWJ-MSC-EV found marked differences in the surface glycosylation pattern, particularly in N-acetylglucosamine, mannose, and fucose-binding lectins. Taken together, our results highlight the importance of N-glycans in MSC-EV to permit EV-cell interactions and associated functions