Design of bioinformatic tools for integrative analysis of microRNA-mRNA interactome applied to digestive cancers

[spa] En esta tesis se han desarrollado e implementado distintas herramientas bioinformáticas que permiten el estudio de las interacciones miRNA-mRNA en contextos celulares específicos. oncretamente se ha creado un paquete de R (miRComb) que calcula las interacciones miRNA-mRNA partiendo de expresión de miRNAs y mRNAs, y predicciones bloinformáticas de bases de datos preexistentes. Las interacciones miRNA-mRNA finales son aquellas que muestran una correlación negativa y han estado predichas por al meno una base de datos. Como valor añadido, el paquete miRComb realiza un resumen en pdf con los resultados básicos del análisis (número de interacciones, número de mRNAs target por miRNA, análisis funcional, etc.), que permite comparar los datos de distintos estudios. Hemos aplicado esta metodología en el contexto de cánceres digestivos. En un primer estudio hemos utilizado datos públicos de 5 cánceres digestivos (colon, recto, esófago, stómago e hígado) y hemos determinado las interacciones miRNA-mRNA comunes entre ellos y específicas de cada uno. En un segundo estudio, hemos utilizado la misma metodología para analizar datos de IRNA-mRNA en biopsias de pacientes del Hospital Clínic de Barcelona con cáncer de páncreas. En este estudio hemos descrito interacciones miRNA-mRNA en el contexto de cáncer pancreático y hemos podido validar dos de ellas a nivel experimental. En resumen, podemos concluir que el paquete miRComb es una herramienta útil para el estudio del interactoma de miRNA-mRNA, y que ha servido para establecer hipótesis biológicas que luego se han podido comprobar en el laboratori

Using Soil Moisture Sensors for Automated Irrigation Scheduling in a Plum Crop

The growing scarcity and competition for water resources requires the urgent implementation of measures to ensure their rational use. Farmers need affordable irrigation tools that allow them to take advantage of scientific know-how to improve water use efficiency in their common irrigation practices. The aim of this study is to test under field conditions, and adjust where required, an automated irrigation system that allows the establishment of regulated deficit irrigation (RDI) strategies in a stone fruit orchard. For this, an automated device with an algorithm which combines water-balance-based irrigation scheduling with a feedback adjustment mechanism using 15 capacitive sensors for continuous soil moisture measurement was used. The tests were carried out in 2016 and 2017 in Vegas Bajas del Guadiana (Extremadura, Spain) on an experimental plot of ‘Red Beaut’, an early-maturing Japanese plum cultivar. Three irrigation treatments were established: control, RDI and automatic. The control treatment was scheduled to cover crop water needs, a postharvest deficit irrigation (40% crop evapotranspiration (ETc)) strategy was applied in the RDI treatment, while the Automatic treatment simulated the RDI but without human intervention. After two years of testing, the automated system was able to “simulate” the irrigation scheduling programmed by a human expert without the need for human intervention.info:eu-repo/semantics/publishedVersio

Automatic Irrigation Scheduling on a Hedgerow Olive Orchard Using an Algorithm of Water Balance Readjusted with Soil Moisture Sensors

Recent technological advances have made possible automated irrigation scheduling using decision-support tools. These tools help farmers to make better decisions in the management of their irrigation system, thus increasing yields while preserving water resources. The aim of this study is to evaluate in a commercial plot an automated irrigation system combined with remote-sensing techniques and soil mapping that allows the establishment of regulated deficit irrigation (RDI) strategies. The study was carried out over 3 years (2015–2017) in a commercial hedgerow olive orchard of the variety ‘Arbequina’ located in Alvarado (Extremadura, Spain). An apparent electrical conductivity (ECa) map and a normalized difference vegetation index (NDVI) map were generated to characterize the spatial variability of the plot and classify the zones in homogeneous areas. Then, reference points were selected to monitor the different irrigation sectors. In 2015, the plot was irrigated according to the farmer’s technical criteria throughout the plot. In 2016 and 2017, two different areas of the plot were irrigated applying an RDI strategy, one under expert supervision and the other automatically. The results show that in a heterogeneous plot the use of new technologies can be useful to establish the ideal location for an automatic irrigation system. Furthermore, automatic irrigation scheduling made it possible to establish an RDI strategy recommended by an expert, resulting in the homogenization of production throughout the plot without the need for human intervention.info:eu-repo/semantics/publishedVersio

Redes Culturais nos Primórdios da Europa: 2400 Anos da Fundação da Academia de Platão

By celebrating the 2400th anniversary of the founding of Plato's Academy, this book gathers ten contributions concerning the founder of the Academy, his school and work, as well as the influence Plato exerted on later authors (from antiquity to the present), and the reception of his legacy throughout history.The themes explored in the five initial chapters focus on the analysis of various topics treated in individual Pla -tonic dialogues. To begin, the Phaedrusis considered for its significance regarding the philosophical conception of a “supra-heavenly place”. The next two chapters reflect upon Platonic paideia, first on the pedagogical princi-ples of The Statesman, and next on the analysis of sports activities in The Republic and inThe Laws. The dramatic and philosophical implications arising out of the multicultural origins of the characters in The Laws are brought into perspective alongside an insight drawn from the banquet, considered a model on which a philosophic com-munity can be constituted. The five remaining chapters have a general focus on Plato’s presence in later authors (from Neoplatonism to contemporary literature), as well the influence of the Academy

Carm1-arginine methylation of the transcription factor C/EBPα regulates transdifferentiation velocity

Developmental biology; Gene regulation; Transcription factorBiologia del desenvolupament; Regulació gènica; Factor de transcripcióBiología del desarrollo; Regulación génica; Factor de transcripciónHere, we describe how the speed of C/EBPα-induced B cell to macrophage transdifferentiation (BMT) can be regulated, using both mouse and human models. The identification of a mutant of C/EBPα (C/EBPαR35A) that greatly accelerates BMT helped to illuminate the mechanism. Thus, incoming C/EBPα binds to PU.1, an obligate partner expressed in B cells, leading to the release of PU.1 from B cell enhancers, chromatin closing and silencing of the B cell program. Released PU.1 redistributes to macrophage enhancers newly occupied by C/EBPα, causing chromatin opening and activation of macrophage genes. All these steps are accelerated by C/EBPαR35A, initiated by its increased affinity for PU.1. Wild-type C/EBPα is methylated by Carm1 at arginine 35 and the enzyme’s perturbations modulate BMT velocity as predicted from the observations with the mutant. Increasing the proportion of unmethylated C/EBPα in granulocyte/macrophage progenitors by inhibiting Carm1 biases the cell’s differentiation toward macrophages, suggesting that cell fate decision velocity and lineage directionality are closely linked processes.TG was supported by the Center for Genomic Regulation, Barcelona, the Spanish Ministry of Economy, Industry and Competitiveness, (Plan Estatal PID2019-109354GB-100), AGAUR (SGR 006713) and the 4D-Genome European Research Council Synergy grant. KSZ was supported by the NIH grant R01GM36477. We have used ChatGPT to improve parts of the text

Satisfacció envers els menjadors escolars: aspectes estructurals, funcionals i sensorials

Menjadors escolars; Avaluació; EstadístiquesSchool menus; Evaluation; StatisticsMenús escolares; Evaluación; EstadísticasEl menjador escolar és un espai on mengen habitualment molts infants i per saber el grau de satisfacció global, a més del compliment de les recomanacions per garantir la qualitat nutricional, és necessari conèixer la percepció organolèptica o sensorial dels menús per part dels alumnes, així com d’altres aspectes estructurals i funcionals del servei de menjador. Els objectius de l’estudi van ser determinar el grau de satisfacció dels alumnes i la seva associació amb aspectes estructurals i funcionals del menjador escolar i amb la qualitat sensorial dels menús així com conèixer els aspectes de millora proposats pels alumnes.El comedor escolar es un espacio donde comen habitualmente muchos niños y para saber el grado de satisfacción global, además del cumplimiento de las recomendaciones para garantizar la calidad nutricional, es necesario conocer la percepción organoléptica o sensorial de los menús por parte de los alumnos, así como otros aspectos estructurales y funcionales del servicio de comedor. Los objetivos del estudio fueron determinar el grado de satisfacción de los alumnos y su asociación con aspectos estructurales y funcionales del comedor escolar y con la calidad sensorial de los menús así como conocer los aspectos de mejora propuestos por los alumnos.The school dining room is a place where many children often eat and to know the degree of global satisfaction, in addition to complying with the recommendations to guarantee nutritional quality, it is necessary to know the organoleptic or sensory perception of the menus on the part of the students, as well as Other structural and functional aspects of the dining room service. The objectives of the study were to determine the degree of satisfaction of the students and their association with structural and functional aspects of the school dining room and with the sensory quality of the menus as well as know the aspects of improvement proposed by the students

Novel Circulating miRNA Signatures for Early Detection of Pancreatic Neoplasia

OBJECTIVES: Pancreatic ductal adenocarcinoma (PDAC) presents the lowest survival rate of all cancers because only 6% of patients reach five-year survival. Alterations in the expression of several microRNAs (miRNAs) occur in the tumor of PDAC and in preneoplastic lesions as the called intraductal papillary mucinous neoplasm (IPMN). Here, we aimed at identifying which miRNAs are significantly altered in liquid biopsies from patients with PDAC and IPMN to find new noninvasive biomarkers for early detection of PDAC. METHODS: We analyzed by real-time quantitative reverse transcription-PCR (qRT-PCR) the expression of 17 circulating miRNAs, previously found to be significantly overexpressed in tissue pancreatic neoplasms, in a set of 182 plasma samples (94 PDAC, 19 IPMN, 18 chronic pancreatitis, and 51 disease-free controls). Then, we analyzed CA19.9 levels in the same plasma set, and we assessed the diagnostic values of differentially expressed miRNAs, CA19.9, and all possible combinations. RESULTS: Of note, 16, 14, and 9 miRNAs were significantly increased in PDAC, IPMN, and chronic pancreatitis, respectively, compared with control plasmas. miR-21-5p, miR-33a-3p, miR-320a, and miR-93-5p showed the highest discriminating capacity for pancreatic neoplasia (PDAC or IPMN) with an area under the receiver operating characteristic curve (AUC) of 0.86, 0.85, 0.85, and 0.80, respectively. 2-miRNA combinations improved these performances reaching AUC = 0.90 for "miR-33a-3p+miR-320a." Addition of CA19.9 increased the diagnostic potential of miRNA signatures even further achieving an AUC of 0.95 (93% sensitivity and 85% specificity) for the combination of "miR-33a-3p+miR-320a+CA19.9." CONCLUSIONS: Novel signatures combining miRNAs and CA19.9 could be used as noninvasive biomarkers for early detection of PDAC

CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications.

Somatic copy number alterations (CNAs) are a hallmark of cancer, but their role in tumorigenesis and clinical relevance remain largely unclear. Here, we developed CNApp, a web-based tool that allows a comprehensive exploration of CNAs by using purity-corrected segmented data from multiple genomic platforms. CNApp generates genome-wide profiles, computes CNA scores for broad, focal and global CNA burdens, and uses machine learning-based predictions to classify samples. We applied CNApp to the TCGA pan-cancer dataset of 10,635 genomes showing that CNAs classify cancer types according to their tissue-of-origin, and that each cancer type shows specific ranges of broad and focal CNA scores. Moreover, CNApp reproduces recurrent CNAs in hepatocellular carcinoma and predicts colon cancer molecular subtypes and microsatellite instability based on broad CNA scores and discrete genomic imbalances. In summary, CNApp facilitates CNA-driven research by providing a unique framework to identify relevant clinical implications. CNApp is hosted at https://tools.idibaps.org/CNApp/