Detecting differential usage of exons from RNA-Seq data

RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package

Metagenomic Analyses of the Human Gut Virome

The human gut harbors tens of trillions of microbes belonging to all three domains of life, Bacteria, Archaea, and Eukarya; most are members of Bacteria. These organisms collaborate and compete for functional niches and physical space: habitats), together forming a continuously functioning metabolic organ that influences many aspects of host biology. The factors that drive the assembly, determine the stability, and shape the adaptive responses of the gut microbiota to a variety of perturbations are the subject of intense study as greater appreciation is gained of the importance of this microbial community for human health. My thesis focused on the viral component of the microbiota that had been less characterized than its bacterial component. I first developed and applied a series of experimental and computational tools for metagenomic analyses of viruses purified from frozen fecal samples obtained from healthy adult monozygotic twin pairs and their mothers living in the USA, over the course of a year. The virome in this population was dominated by phages and exhibited high inter-personal variation and contrasting intrapersonal stability, suggesting a prevalent temperate lifestyle rather than a predator-prey relationship that is a feature of marine microbial communities. To further characterize the role of phage in shaping gut community structure, I colonized adult germ-free mice with a defined model human gut microbiota composed of 15 sequenced human gut symbionts, seven of which harbored 10 prophages, one of which: Bacteroides cellulosilyticusWH2) was represented by a library of \u3e25,000 isogenic transposon mutants covering 80% of genes in its genome. Once assembled, this model microbiota was subjected to a staged phage attack with a pool of virus-like particles: VLPs) purified from the fecal microbiota of five humans from the first study. Shotgun sequencing of DNA isolated from the input human VLP preparation, cecal and fecal samples collected over time from these gnotobiotic mice, and VLPs recovered from their fecal samples, revealed a ordered and reproducible sequence of phage attack, allowing me to associate novel phages present in the input VLP preparation with bacterial hosts, and to characterize the dynamics and identify genetic determinants of prophage induction. Finally, I used the tools I developed to characterize the phages and eukaryotic viruses present in the fecal microbiota of healthy and malnourished twins living in Malawi, sampled during their first two years of life. Together, this work provided new perspectives about viral diversity and viral-bacterial host dynamics associated with the human gut microbiota

Psychometric properties of the Brief-COPE for the evaluation of coping strategies in the Chilean population

The Brief-COPE is an abbreviated version of the COPE (Coping Orientation to Problems Experienced) Inventory, a self-report questionnaire developed to assess a broad range of coping responses. Currently, it is one of the best validated and most frequently used measures of coping strategies. The aim of this study was to validate a culturally appropriate Chilean version of the Brief-COPE, assess its psychometric properties and construct and congruent validity. The Spanish version of the Brief-COPE was administrated in a community sample of 1847 Chilean adult (60.4% women) exposed to a variety of stressful experiences. The factorial structure of the inventory was examined by comparing four different models found in previous studies in Latin American population. The results of confirmatory factor analyses revealed, as in the original studies, a 14-factor structure of the Brief-COPE. These dimensions showed adequate internal structure and consistency. The factorial invariance comparing women and men confirmed strict invariance. Additionally, the results showed significant correlation between some Brief-COPE scales, such as denial and substance use, with perceived stress and emotional support and active coping with subjective well-being. Overall, the present work offers a valid and reliable tool for assessing coping strategies in the Chilean population.This study was funded by CONICYT/FONDECYT (grant number 1180134) awarded to Felipe E. Garcia

Homecoming 2015

Photos of Homecoming 201

Object localization with RFID technology

In this work we analyse the approaching of a mobile robot using RFID (Radio Frequency Identification) Technology with the purpose of finding and navigating towards RFID tags without visual object detection. The aim is the evaluation of ROS to provide the means to allow a mobile robot to approach to RFID tags, using a radiofrequency antenna as a transmitter/receptor element of signals. As part of this system the robot emits radiofrequency signals searching for a particular RFID tag, and then it is approached towards the particular RFID tag until the signal strength was maximized, it means that the object was localized and captured. The approach has been tested using two different algorithms which work together: - Linear search. - Advanced search. All the code and tests of this project are based to work with one antenna. On one hand it means simplicity, but on the other hand it can mean a lack of precision.En este proyecto se pone en práctica la tecnología RFID (Radio Frequency Identification) con el propósito de localización y aproximación de un robot móvil hacia una etiqueta RFID fijada en un objeto sin utilizar detección visual. El objetivo es utilizar ROS (Robot Operating System) para lograr que un robot móvil se acerque a las etiquetas RFID, utilizando una antena RF como elemento TX/ RX. El robot emite señales RF en busca de una etiqueta RFID en particular. Tras hallar la etiqueta RFID deseada se comienza a realizar la maniobra de aproximación hasta superar cierto umbral de potencia de señal recibida, RSSI (Received Signal Strengh Indicator), especificado por parámetro. Este proyecto funciona con una sola antena. Esto significa simplicidad, pero por otro lado, cierta falta de precisión.Ingeniería de Telecomunicació

Differential expression of three galaxin-related genes during settlement and metamorphosis in the scleractinian coral Acropora millepora

BACKGROUND: The coral skeleton consists of CaCO3 deposited upon an organic matrix primarily as aragonite. Currently galaxin, from Galaxea fascicularis, is the only soluble protein component of the organic matrix that has been characterized from a coral. Three genes related to galaxin were identified in the coral Acropora millepora. RESULTS: One of the Acropora genes (Amgalaxin) encodes a clear galaxin ortholog, while the others (Amgalaxin-like 1 and Amgalaxin-like 2) encode larger and more divergent proteins. All three proteins are predicted to be extracellular and share common structural features, most notably the presence of repetitive motifs containing dicysteine residues. In situ hybridization reveals distinct, but partially overlapping, spatial expression of the genes in patterns consistent with distinct roles in calcification. Both of the Amgalaxin-like genes are expressed exclusively in the early stages of calcification, while Amgalaxin continues to be expressed in the adult, consistent with the situation in the coral Galaxea. CONCLUSION: Comparisons with molluscs suggest functional convergence in the two groups; lustrin A/pearlin proteins may be the mollusc counterparts of galaxin, whereas the galaxin-like proteins combine characteristics of two distinct proteins involved in mollusc calcification. Database searches indicate that, although sequences with high similarity to the galaxins are restricted to the Scleractinia, more divergent members of this protein family are present in other cnidarians and some other metazoans. We suggest that ancestral galaxins may have been secondarily recruited to roles in calcification in the Triassic, when the Scleractinia first appeared. Understanding the evolution of the broader galaxin family will require wider sampling and expression analysis in a range of cnidarians and other animals