Integración de datos de expresión génica asociados a líneas celulares de cánceres: un enfoque utilizando la metodología STATIS-ACT, métodos biplot y minería de textos

Resumen - Lista de guras - Lista de tablas - Introducción - Objetivo general - Objetivos especícos - 1. Marco Teórico - 1.1 Nuevas perspectivas en la investigación sobre cáncer - 1.2 Análisis de datos económicos - 1.2.1 Normalización de datos - 1.3 Ontología de genes 1.4 Los métodos de k-tablas - 1.4.1 STATIS - 1.4.1.1 Interestructura - 1.4.1.2 Compromiso - 1.4.1.3 Intraestructura - 1.4.2 STATIS-Dual - 1.4.2.1 Interestructura - 1.4.2.2 Compromiso - 1.4.2.3 Intraestructura - 1.4.3 Análisis Parcial Triádico - 1.5 Medidas de calidad de representación - 1.5.1 Calidad de representación de las tablas - 1.5.2 Calidad de representación de los individuos - 1.5.3 Calidad de representación de las variables - 1.6 Variabilidad muestral - 1.7 Representación Biplot para medir interacción entre individuos y variables - 1.7.1 Formulación - 1.8 Redes y Grafos - 2. Ilustración de la metodología de análisis: integración de datos económicos provenientes de líneas celulares de cáncer del panel NCI60 - 2.1 Conjunto de Datos NCI60 - 2.2 Procesamiento de Datos - 2.2.1 Análisis de ontologías: integración de datos en una red - 2.3 Resultados - 2.3.1 Interestructura - 2.3.2 Configuración Compromiso - 2.3.3 Proyección de genes usando Biplot - 2.3.4 Selección de genes comunes a todas las tablas usando Biplot - 2.4 Análisis de ontologías: red de relaciones de genes seleccionados y genes activados ante la presencia de distintos tejidos - 2.5 Discusión - Conclusiones - Bibliografía - AnexoLos datos económicos, donde se analiza la expresión de miles de genes, proteínas, metabolitos en distintas muestras biológicas, comprenden una gran cantidad de áreas de aplicación y su estudio ha crecido de manera exponencial en los últimos a~nos. La integración de datos es uno de los principales objetivos actuales en bio-ciencias, dado que es común medir expresión simultánea de genes, proteínas y metabolitos o bien tener mediciones de la expresión genética de las mismas muestras en diferentes plataformas de análisis, generando, por lo tanto, distintas fuentes de información. La integración implica el meta-análisis de sus resultados o el análisis simultáneos de los datos originales. En el marco de este trabajo, se realiza una propuesta metodológica para abordar el problema de estudio y comparación de datos genéticos provenientes de distintas plataformas de microarreglos y el problema de selección de genes basada en los métodos estadísticos de k-tablas y Biplot. Se realiza una aplicación de la metodología propuesta a datos de expresión genética de 60 líneas celulares de 9 tipos diferentes de cáncer provenientes de cuatro plataformas de análisis del panel NCI-60.Fil: Zingaretti, María Laura. Universidad Nacional de Córdoba; Argentina

Estimating conformational traits in dairy cattle with deepAPS : A two-step deep learning automated phenotyping and segmentation approach

Assessing conformation features in an accurate and rapid manner remains a challenge in the dairy industry. While recent developments in computer vision has greatly improved automated background removal, these methods have not been fully translated to biological studies. Here, we present a composite method (DeepAPS) that combines two readily available algorithms in order to create a precise mask for an animal image. This method performs accurately when compared with manual classification of proportion of coat color with an adjusted R2 = 0.926. Using the output mask, we are able to automatically extract useful phenotypic information for 14 additional morphological features. Using pedigree and image information from a web catalog (www.semex.com), we estimated high heritabilities (ranging from h2 = 0.18-0.82), indicating that meaningful biological information has been extracted automatically from imaging data. This method can be applied to other datasets and requires only a minimal number of image annotations (50) to train this partially supervised machinelearning approach. DeepAPS allows for the rapid and accurate quantification of multiple phenotypic measurements while minimizing study cost. The pipeline is available at https://github.com/lauzingaretti/deepaps

SeqBreed : a python tool to evaluate genomic prediction in complex scenarios

Background: Genomic prediction (GP) is a method whereby DNA polymorphism information is used to predict breeding values for complex traits. Although GP can significantly enhance predictive accuracy, it can be expensive and difficult to implement. To help design optimum breeding programs and experiments, including genome-wide association studies and genomic selection experiments, we have developed SeqBreed, a generic and flexible forward simulator programmed in python3. Results: SeqBreed accommodates sex and mitochondrion chromosomes as well as autopolyploidy. It can simulate any number of complex phenotypes that are determined by any number of causal loci. SeqBreed implements several GP methods, including genomic best linear unbiased prediction (GBLUP), single-step GBLUP, pedigree-based BLUP, and mass selection. We illustrate its functionality with Drosophila genome reference panel (DGRP) sequence data and with tetraploid potato genotype data. Conclusions: SeqBreed is a flexible and easy to use tool that can be used to optimize GP or genome-wide association studies. It incorporates some of the most popular GP methods and includes several visualization tools. Code is open and can be freely modified. Software, documentation, and examples are available at https://github.com/miguelperezenciso/SeqBreed

Application of multivariate methods for the characterization of meteorological drought periods in Venezuela.

El análisis multivariado consiste en determinar si existen maneras más simples de representar un conjunto de datos complejo, además de explorar si las observaciones se concentran en grupos y si existe una interdependencia entre los elementos. Este tipo de técnicas se han utilizado ampliamente para analizar datos climatológicos. Es por ello que el objetivo de esta investigación fue caracterizar la ocurrencia de períodos de sequía por medio de series temporales del Índice Normalizado de Precipitación (SPI) para siete localidades agrícolas de Venezuela, mediante el uso de dos métodos multivariados. A través del SPI, se cuantificaron las condiciones de déficit o exceso de precipitación en las localidades agrícolas con una escala mensual del periodo 1980-2014. Para el análisis, se usó la combinación de dos métodos multivariados: el Análisis de Coordenadas Principales de las matrices de datos usando distancia Euclídea y el Análisis de Conglomerados. En las siete localidades se describieron dos o tres grupos de años de SPI. En el caso de las localidades que resultaron con tres grupos (CENIAP, El Cují y Yaritagua) estos se categorizaron en años húmedos, años intermedios y años con déficit hídrico significativo. En tanto que, en el caso de las localidades que resultaron con dos grupos (Turén, Quíbor, Mucuchíes y Bramón) se clasificaron en años húmedos y años asociados al déficit hídrico. La aplicación de estos métodos multivariados permitió identificar los patrones espaciales mensuales dominantes del SPI sobre las localidades estudiadas, además de estar relacionados con la ocurrencia de sequías locales de gran importancia desde el punto de vista agrícola.Multivariate analysis consists in determining if there are simpler ways to represent a complex set of data, besides exploring if the observations are concentrated in groups and if there is interdependence between the elements. These types of techniques have been widely used to analyze climatological data. That is why the objective of this research was to characterize the occurrence of drought periods by means of time series of the Standard Precipitation Index (SPI) for seven agricultural locations in Venezuela, by using two multivariate methods. The conditions of deficit or excess of precipitation in the agricultural localities were quantified through the SPI with a monthly scale of the period 1980-2014. The combination of two multivariate methods was used for the analysis: Principal Coordinate Analysis of the data matrices using Euclidean distance and Cluster Analysis. Two or three groups of years of SPI were described in the seven locations. In the case of the locations that resulted with three groups (CENIAP, El Cují and Yaritagua), these were categorized in wet years, intermediate years and years with significant water deficit. Meanwhile, in the case of the locations that resulted with two groups (Turén, Quíbor, Mucuchíes and Bramón), they were classified into wet years and years associated with the water deficit. The application of these multivariate methods made it possible to identify the dominant monthly spatial patterns of the SPI on the studied locations, besides being related to the occurrence of local droughts of great importance from the agricultural point of view

On the holobiont ‘predictome’ of immunocompetence in pigs

Background Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available. Methods We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only. Results Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy. Conclusions Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default.info:eu-repo/semantics/publishedVersio

On the holobiont 'predictome' of immunocompetence in pigs

Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available. We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only. Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy. Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default. The online version contains supplementary material available at 10.1186/s12711-023-00803-4

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Background The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. Results Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. Conclusions Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets’ body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.info:eu-repo/semantics/publishedVersio

The Anomalous Temperatures of Cu and Their Physical Significance. (II, 3)

The experimental evidences concerning anomalous changes of various properties of Cu, with temperature, were studied in literature, and it was found that four anomalous temperatures, including the melting point, exist, the values being 503°, 553°, 823° and 1356°K (mp), and that in these temperatures and the absolute zero, there exists a regurality as shown in the following table where the numbers in parentheses show the ratios of the intervals between the adjacent temperatures in each group. This regurality was understood by the writer to be identical ; in nature, with Lande\u27s interval rule in atomic spectra in the case of odd multiplicity, and, accordingly, it was inferred that the temperatures in each of the groups, II and I, would correspond to the components of the fine structures of the energy levels, E_1 and E_2 respectively. These levels, as well as E_3 and E_4 had been determined from experimental data, as those associated with the valence electron, their energy positions being in the order of E_1, E_2, E_3 and E_4. Further, it was considered that each of E_1 and E_2 is associated with two electrons and two atoms, hence, they may be denoted as, E_1 : (A_1, B_1) ^3D1, 2, 3 E_2 : (A_2, B_2) ^3D3, 2, 1 where A_1, B_1 and A_1, B_2 denote two pairs of atoms which associate respectively with the levels, E_1 and E_2, forming the diatomic molecules, (A_1, B_1) and (A_2, B_2). Concerning E_3 and E_4, it was assumed that, as in the case of Zn, there exist two groups of anomalies in low temperature range, which show the multiple structures of E_3 and E_4, respectively. Further it was assumed that the electrons associating with E_3 and E_4 are identical with those which associate to E_l and E_2, respectively, and they oscillate between E_1 and E_3, E_2 and E_4, respectively. Furthermore, that these oscillations take place, in resonance, in the group of the above molecules of the same kind, and, accordingly the molecules in the above group are bound mutually by the energy of the resonance exchange. On the other hand, it was proved previously that, when the electron is in E_3 or E_4, it plays the role of electric conduction, but, in E_1 or E_2, it binds the atoms firmly, and so, with the above idea the important properties of metals were explained consistently

Gut eukaryotic communities in pigs : diversity, composition and host genetics contribution

Background. The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. Results. Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. Conclusions. Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health