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Teoría de redes, educación y difusión del conocimiento

  • Contreras, Ruth S. (Ruth Sofhía)
Los lectores de este número encontrarán modelos teóricos que, basándose en simulaciones, auxilian en la explicación y predicción de procesos como la difusión de conocimiento en redes sociales, en las que la colaboración y la cooperación entre individuos toman lugar; también encontrarán modelos de redes relacionados con el entendimiento de discursos, ya sean como herramientas de apoyo o como método y técnica de análisis. Incluso, un trabajo que trata del mapeo de las redes de interacción entre los diversos actores que componen comunidades de práctica
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Investigación en el área de las Relaciones Públicas

  • Contreras, Ruth S. (Ruth Sofhía)
Las relaciones públicas han avanzado hacia el profesionalismo y ahora consideran la investigación, la medición y las normas éticas que se han desarrollado durante la última década. Las metodologías de investigación, tanto formal como informal y el análisis de los datos, establecen las razones de la investigación y evalúan los supuestos básicos que el investigador de relaciones públicas debe realizar en la práctica diaria.
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Development of a scoring function for finding differential expression - application to Lolium Perenne

  • Fradera Sola, Albert
RNA-sequencing for detecting changes between expression patterns has emerged as a frequent tool in life sciences stud- ies. However, it is an under-development tool which still lacks a standard procedure. This way, many software pack- ages and approaches could be used when designing an ex- periment. Here we develop and present an approach based on a scoring function. It allows using multiple packages and relies its e ciency on validated data. Thus, the function is adjusted using qPCR veri ed data. Then it is tested on experimental data obtained from a Lolium Perenne drought stress tolerance study yielding positive results with several potential uses in further studies.
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Comparative analysis of Microarray and RNAseq data from liver cancer samples

  • Gil Gálvez, Alejandro
Background: The field of transcriptomics has developed an exponential growth in the last years thanks to the advances in high throughput RNA sequencing (RNAseq), which is becoming more popular as the cost is decreasing. Traditional techniques to study transcriptomics like microarrays are trying to survive in this new scenario by developing new microarrays. New microarray chips like the Human Transcriptome Array 2.0 (HTA2.0, Affymetrix) are nowadays co-existing with RNAseq but the performance of these new arrays have not been compared yet to RNAseq. Results: Here we show a comparative analysis of RNAseq and HTA2.0 in terms of gene expression. We observe that there is a good concordance between the two techniques, but there are some differences that may be considered when choosing one. Using hepatoblastoma samples, we have worked at 3 levels. The first approach was to study different methods to normalize microarray data. We found that using SST-RMA normalization was the best method to examine HTA2.0 data. At a second level, we have studied different ways to analyze RNAseq data. We have worked with two splice aware aligners, HISAT2 and STAR, and we found that despite there are genes that have a significant difference in counts, this does not affect subsequent steps. Furthermore, we use 5 different tools to assess gene expression genes from count data. We have found that tweeDEseq gave us the best results when analyzing RNAseq data. Finally, we have compared microarray against RNAseq results, and we have found that despite having some differences, there is a good concordance between both techniques, in terms of finding differentially expressed genes and at functional level. Conclusions: Both RNAseq and microarrays are good options to study transcriptomics, as they give similar results at gene expression level. RNAseq has the advantage that more analysis can be performed, like variant calling, alternative splicing or finding new transcripts. On the other side, HTA2.0 compete with a more affordable cost, and an easier and standardized data analysis. Furthermore, HTA2.0 has probes to detect low expressed transcripts or short transcripts, which are lost in most RNAseq analyses. HTA2.0 can also be used to study alternative splicing, so is an interesting option if the researcher wants a relatively fast analysis of transcriptomics.
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The integration of transcriptome and epigenome in the association of mosaic loss of chromosome Y (mLOY) and cancer

  • Jené Cortada, Aina
It has been demonstrated that mosaic loss of chromosome Y (mLOY) is associated with aging and age-related disease such as cancer [1, 2] or Alzheimer's disease [3]. However, the integrate mechanisms of gene expression and methylation of mLOY have been poorly evaluated to date. In order to ll this gap, a total of 9.927 samples belonging to The Cancer Genome Atlas project were analyzed. LOY status was inferred from SNP-array data using our MADloy tool [4]. Association analysis revealed that the pooled odds ratio (OR) of association between mLOY and tumor samples was 8.04 (CI95% 4.60 { 14.06). Di erences in the magnitude of the OR were observed across cancer types, with no association with prostate cancer and high association with kidney tumor. Transcriptomic data analysis showed that only genes in chromosome Y were down-regulated having strong e ect in kidney, bladder and lung cancer. Epigenomic studies provided a large list of CpGs associated with LOY in Y chromosome as well as in autosomes. Gene enrichment analysis revealed a range of pathways involved in mLOY that vary across tumors. These include biosynthetic and metabolic processes, demethylation and immune response. In summary, we have established an unavoidable association between mosaic LOY events and cancer, adding the association of both, transcriptome and epigenome.
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Determinants of gut microbiota in 7-year old children from INMA birth cohort: a pilot study

  • Llambrich Rodríguez, Maria
Introduction: Gut microbiota plays an important role in humans. Its composition changes from birth to adulthood. Type of delivery, antibiotics use, diet, obesity, and host genetics, among others have been associated with gut bacterial composition. However, associations are not conclusive and not many studies have evaluated these factors in childhood. Objective: To evaluate the association of several factors with gut microbiota composition in 7-year children from the INfancia y Medio Ambiente (INMA) project. Methods: 154 stool samples were collected at the age of 7-years and gut composition assessed with the 16S rDNA method. The association between 14 factors and alpha and beta diversity was evaluated. We also performed a differential analysis for each taxon in respect to each factor. Multiple testing was controlled with the False Discovery Method (FDR). Results: Gut microbiota was heterogeneous among children, being Bacteroidetes and Firmicutes the more prevalent phyla. Higher number of siblings, consistent with lower maternal education, was robustly associated with higher alpha diversity. Mode of delivery was associated with overall gut diversity (Bray-Curtis dissimilarity). Overweight/obese had higher evenness and higher levels of Firmicutes. Fucosyltransferase 2 (FUT2) non-secretor children (rs601338 sese genotype) had higher evenness and higher levels of Rhodospirillales, Lachnospiraceae and Roseburia. Conclusions: As in adults, gut microbiota in 7-year children was heterogeneous and dominated by Bacteroidetes and Firmicutes. Determinants explained a small proportion of the gut bacterial composition.
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Functional annotation pipeline for the analisys of microarray data with regards to subcellular protein localization

  • Noguera Vila-Masana, Maria
Subcellular protein localization prediction is a bioinformatics approach (faster and cheaper than experimental procedure) to determine the targeting location of proteins into the cell organelles. Therefore, many programs exist to address this issue, but TPpred is the most up-to-date option regarding mitochondria targeting prediction. On the other hand, the development of a Drosophila melanogaster transgenic model to study mitochondria-related diseases in humans has brought up many questions. Some mitochondria mechanisms are still not explored. The translation pathways present in mitochondria have similarities to the ones present in the cytosol. But they are older, essential in the origins of live and also in the eukaryote cell development from prokaryotes. A new paralog of the seryl tRNA synthetize enzyme that catalyses aminoacylation of tRNASer was found in insects. The SLIMP protein, which is not a Seryl tRNA synthetases(SRS) anymore, is now known to interact with SRS2 and LON protease, a fact that can lead to a modulation in both mitochondrial translation and replication, respectively. A microarray of the knock-down of SLIMP expression in S2 D.melanogaster cells was performed and their analyzed row data gives rise to the current pipeline reported. The functional annotation pipeline developed is a new analysis procedure to describe differences in transcriptome considering mitochondria targeting status in a microarray-wide approach. Proportions tests is performed, which in our data did not report a significative increase or depletion of mitochondria targeted transcript products under the SLIMP knockdown condition. Moreover, the GO enrichment analysis suggested an imbalance in serine metabolism that extends to the selenocysteine biosynthetic pathway. CG1427 protein is behind this enrichment result, taking into account its up-regulation status from microarray and its mitochondria status from the Ttpred prediction. However, since this and other proteins (5%) are theoretical (one analysis step deals with genes having proteins targeted to mitochondria as well as outside of it, due to differences in their sequence from alternative splicing process), experimental evidence should support this results.
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StP: a web server to predict pathogenesis of non-synonymous single nucleotide polymorphisms in membrane proteins

  • Reina Fuente, Iker
Next-generation sequencing has speed up the process of sequencing a complete human genome, while reducing the cost. Consequently its use is increasing in healthcare in order to identify genetic variations and its association with pathology. Single Nucleotide Variants are the most common form of DNA variation in human population and consists in a change in a single nucleotide. One of the current challenges is to be able to predict if a single nucleotide polymorphism can be associated to a single-genetic diseases. Thus, in order to identify the variant among hundreds of variants in a genome that is the cause of a single genetic disease, in silico mutation prediction tools have been developed these lasts years. These tools are based in mathematical, rule-based, and statistical learning methods relying on evolutionary, sequence, or structural information methods to characterize if a residue substitution in proteins is affecting its structure and function. These tools are mainly developed for globular proteins. In order to develop a mutation predictor server specific for membrane proteins, we have developed Single Nucleotide Polymorphisms Transmembrane Predictor (StP). This web server aims to predict if a missense mutation in a transmembrane region of a membrane protein is likely to affect the structure and/or function of a protein and consequently being damaging. The predictive algorithm is based on the entropy of the mutated position, the frequency of the non-mutated amino acid and the frequency of the mutated amino acid computed from Pfam multiple sequence alignments and also on the score associated to the amino acid change. Comparison to existing mutation server shows that StP improves the specificity, although loosing sensitivity in the prediction if a SNP is damaging or not in a membrane protein.
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Disseny i dimensionat d’una instal·lació industrial de vapor

  • Benet Cáliz, Josep Maria
Aquest Treball de final de Grau està basat en el disseny i dimensionament d’una instal·lació industrial de vapor, destinada a proporciona l’energia calorífica necessària a una industria làctia per du a terme un procés tèrmic per tractar la llet de vaca crua, aquest procés és conegut com a ultra high temperature (UHT) i està marcat per un diagrama de flux i unes condicions de treball dels dos fluids. La base del projecte comença determinant, a partir de formules matemàtiques orientades a càlculs termodinàmics, aquestes necessitats calorífiques necessàries a subministrar per assolir els increments de temperatura del producte làctic en els diferents punts del procés. Paral·lelament i a partir d’una representació 3D es tracen les canalitzacions que formen la xarxa de distribució, dins d’uns emplaçaments físics que representen les zona de processos. A partir de les necessitats calorífiques i les condicions dimensionals de la instal·lació, es comença a determinar les seccions de les tuberies necessàries per el transport del vapor d’aigua, sempre complint les condicions de disseny de pressió i temperatura del vapor ja que la secció de les canalitzacions influeix. Com a càlculs tèrmics també es desenvolupa un estudi de les pèrdues de calor per superfície de les tuberies, utilitzant dos sistemes on el primer és a partir de càlculs matemàtics, i el segon a partir de simulacions tèrmiques per ordinador, i aquests resultats són sospesats i contrastats. A partir d’aquí, posteriorment es determina un aïllament tèrmic per reduir aquestes pèrdues i es repeteix l’operació anterior. I com a últim punt del disseny es modela un sistema PID per el control dels punts de consum i gestionar el cabal de vapor en funció de la necessitat de temperatura del producte. Els objectius han sigut la resolució de cadascun dels punts que marquen la pauta del disseny, i s’arriba a conclusions satisfactòries observant que els resultats obtinguts en tots els càlculs tenen coherència i es troben dins de valors raonables. Aquests resultats que son producte de la relació entre les pautes de procés UHT, les restriccions dimensionals de la instal·lació i les condicions dels fluids marcats en el disseny, estan estretament relacionades durant tot el desenvolupament, on la utilització de càlculs matemàtics i d’eines assistides per ordinador han donat lloc al dimensionat d’una instal·lació industrial de vapor que per la seva finalitat pot esdevenir adequada, i han atorgat una ampliació de coneixements de condicions de treball de diferents fluids, materials, components, sistemes de regulació i de capacitats de disseny que poden ser molt útils per un entorn professional futur. Un treball de fi de grau que s’espera que pugui ser una guia de procediment o font de consulta per la realització d’estudis relacionats en instal·lacions tèrmiques de fluids.
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Análisis del éxito de incubación de la tortuga lora (Lepidochelys olivacea) en función del manejo de los nidos. Península de Osa, Costa Rica

  • Malmierca Pérez, Atenea
En este trabajo de final de grado se expone un análisis del éxito de incubación (éxito de eclosión y éxito de emergencia) de la tortuga lora (Lepidochelys olivacea) en las playas Carate y La Leona (Península de Osa, Costa Rica), según los diferentes métodos de manejo de nidos realizados (nidos in situ, nidos reubicados en playa y nidos reubicados en el vivero). El objetivo principal de este trabajo es ver si tanto el manejo de los nidos, como la temperatura de la arena y el recubrimiento herbáceo, arbustivo y arbóreo que hay alrededor del nido, afectan a este éxito de incubación en nuestra zona de estudio. De esta manera, establecer qué tipo de manejo de los nidos es mejor utilizar, teniendo en cuenta las amenazas ambientales y antropológicas presentes en la zona. Para llevar a cabo estos objetivos, se han realizado exhumaciones de todos los tipos de nidos y se ha calculado el éxito de eclosión y de emergencia de cada nido. Posteriormente, se han analizado estadísticamente los resultados con el programa R. Los resultados obtenidos nos muestran que no hay diferencias significativas del éxito de eclosión y de emergencia entre los diferentes tipos de nidos, así como tampoco influye la diferente temperatura que hay entre las zonas donde hay nidos, ni el recubrimiento de la vegetación que hay alrededor. De todas maneras, nos encontramos que la depredación y el saqueo de huevos son constantes en las playas, por lo que se puede asegurar que la estrategia de reubicar nidos en el vivero permite garantizar la conservación de los nidos en nuestra zona de estudio.
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