Hidden Markov Models for Gene Sequence Classification: Classifying the VSG genes in the Trypanosoma brucei Genome

The article presents an application of Hidden Markov Models (HMMs) for pattern recognition on genome sequences. We apply HMM for identifying genes encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma brucei (T. brucei) and other African trypanosomes. These are parasitic protozoa causative agents of sleeping sickness and several diseases in domestic and wild animals. These parasites have a peculiar strategy to evade the host's immune system that consists in periodically changing their predominant cellular surface protein (VSG). The motivation for using patterns recognition methods to identify these genes, instead of traditional homology based ones, is that the levels of sequence identity (amino acid and DNA sequence) amongst these genes is often below of what is considered reliable in these methods. Among pattern recognition approaches, HMM are particularly suitable to tackle this problem because they can handle more naturally the determination of gene edges. We evaluate the performance of the model using different number of states in the Markov model, as well as several performance metrics. The model is applied using public genomic data. Our empirical results show that the VSG genes on T. brucei can be safely identified (high sensitivity and low rate of false positives) using HMM.Comment: Accepted article in July, 2015 in Pattern Analysis and Applications, Springer. The article contains 23 pages, 4 figures, 8 tables and 51 reference

How Fast Is the Sessile Ciona?

Genomewide analyses of distances between orthologous gene pairs from the ascidian species Ciona intestinalis and Ciona savignyi were compared with those of vertebrates. Combining this data with a detailed and careful use of vertebrate fossil records, we estimated the time of divergence between the two ascidians nearly 180 My. This estimation was obtained after correcting for the different substitution rates found comparing several groups of chordates; indeed we determine here that on average Ciona species evolve 50% faster than vertebrates

Biology of the <em>Trypanosoma cruzi</em> Genome

The genome of Trypanosoma cruzi was first made available in 2005, and the intrinsic genome complexity of this parasite has hindered high-quality genome assembly and annotation. Recent technological developments in long read sequencing allowed to circumvent this problem, showing very interesting features in the genome architecture of T. cruzi, allowing to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements), and the complexity of multigene families implied in host-parasite interactions. The genome of T. cruzi is composed of a “core compartment” and a “disruptive compartment” which exhibit opposite GC content and gene composition, with high differences on their regulatory regions. The novel tandem and dispersed repetitive sequences identified, in addition to recombination events, allows to conclude that genome plasticity is a key survival strategy during its complex life cycle

Bases de Datos Objeto-Relacionales y la Tecnología J2EE. Caso Práctico: Gestión del Macrosistema del Iberá. Experiencias durante el diseño y la implementación

En este trabajo se presenta el diseño de una aplicación web, teniendo como repositorio de datos una Base de Datos Objeto-Relacional. El objetivo es generar un sistema de información para gestionar la información de los reptiles y anfibios (herpetofauna) del macrosistema del Iberá en la provincia de Corrientes. El ORDBMS que se emplea es Oracle9i, debido a que en la actualidad es uno de los sistemas Objeto Relacional mas avanzado, que cumple en gran medida con los estándares de SQL:1999. Se emplea una Base de Datos Objeto-Relacional por la complejidad de los datos y de las relaciones entre lo mismos, que incluyen el manejo de tipos de datos complejos, colecciones, relaciones de herencia, composición y asociación. La aplicación se ejecutará en browsers estándar en un entorno web. Los módulos de la aplicación se desarrollan en Java sobre una plataforma J2EE. Se emplearon varias herramientas: Rational Rose (análisis en UML), Object Database Designer, JDeveloper 9i, Oracle Containers for Java, Struts, etc. En el trabajo se describen las partes más relevantes del modelo de datos, las experiencias recogidas en el desarrollo del mismo, las soluciones adoptadas en el diseño conceptual de la base de datos, el diseño de la arquitectura de la aplicación y cómo se relaciona la arquitectura con la base de datos.This work describes a web application design using an Object-Relational Database as data repository. The goal is to generate a computer system to manage the information of reptiles and amphibious (herpetofauna) of the Ibera macrosystem located in Corrientes, Argentina. The ORDBMS selected is Oracle9i, which is one of the most advanced ObjectRelational system existing today because it fulfils in a high percentage the SQL:1999 standards. The Object-Relational technology is selected due to the data complexity and the relationships between them including the handling of complex data types, collections, inheritance, composition and association. The application will be executed by standard web browsers. The modules of the application are developed in Java on a J2EE platform. Several tools are used for this system development: Rational Rose (analysis in UML ), Object Database Designer, JDeveloper 9i, Oracle Containers for Java, Struts, etc. The article also describes the most relevant parts of the data modeling, the experiences gathered in the development, the solutions adopted in the conceptual design of the database, the application architecture design and the links between this structure and the database.Fil: Golobisky, María Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Fiszman, Fernando Esteban. Universidad Tecnológica Nacional; ArgentinaFil: Hernandez, Federico. Universidad Tecnológica Nacional; ArgentinaFil: Rizzoni, Vanina. Universidad Tecnológica Nacional; ArgentinaFil: Valin, Maximiliano. Universidad Tecnológica Nacional; ArgentinaFil: Vecchietti, Aldo. Universidad Tecnológica Nacional; ArgentinaFil: Alvarez, Blanca. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas y Naturales y Agrimensura; Argentin

Bases de datos Objeto-Relacionales y la tecnología J2EE. Caso práctico: gestión del macrosistema del Iberá. Experiencias durante el diseño y la implementación

En este trabajo se presenta el diseño de una aplicación web, teniendo como repositorio de datos una Base de Datos Objeto-Relacional. El objetivo es generar un sistema de información para gestionar la información de los reptiles y anfibios (herpetofauna) del macrosistema del Iberá en la provincia de Corrientes. El ORDBMS que se emplea es Oracle9i, debido a que en la actualidad es uno de los sistemas Objeto Relacional mas avanzado, que cumple en gran medida con los estándares de SQL:1999. Se emplea una Base de Datos Objeto Relacional por la complejidad de los datos y de las relaciones entre lo mismos, que incluyen el manejo de tipos de datos complejos, colecciones, relaciones de herencia, composición y asociación. La aplicación se ejecutará en browsers estándar en un entorno web. Los módulos de la aplicación se desarrollan en Java sobre una plataforma J2EE. Se emplearon varias herramientas: Rational Rose (análisis en UML), Object Database Designer, JDeveloper 9i, Oracle Containers for Java, Struts, etc. En el trabajo se describen las partes más relevantes del modelo de datos, las experiencias recogidas en el desarrollo del mismo, las soluciones adoptadas en el diseño conceptual de la Base de Datos, el diseño de la arquitectura de la aplicación y cómo se relaciona la arquitectura con la base de datos

Evolutionary and comparative genomics of leptospira - DOI: 10.3395/reciis.v1i2.Sup.103en

The availability of complete genome sequences has allowed the study of genic and nucleotide content changes during the evolution of pathogenic and symbiont bacterial lineages. Here we present the comparative genomics between four strains belonging to two species, Leptospira interrogans (L.interrogans Lai str. 56601 and L. interrogans Copenhageni str. Fiocruz L1-130) and L. borgpetersenii (L. borgpetersenii serovar Hardjo-bovis str. JB197 and L. borgpetersenii serovar Hardjo-bovis str. L550). Strains from the latter species have reduced their host range being restricted to a host-to-host transmission cycle while the former species could survive for long periods in fresh water. A detailed compositional and substitutional analysis of 2416 tetrads of orthologs indicates that this change in environmental condition is accompanied by changes in genomic GC content that affected the entire genome. Moreover, this analysis reveals that the interspecies divergence is surprisingly large, with a synonymous/amino acid distances ratio equal to 7.17, a ratio much larger than in other groups. We show that this increased ratio is an indication of acceleration in substitutions rates that especially affected synonymous positions and is in connection with the change in base composition already described. We hypothesize that this process specifically took place in the branch that leads to L. borgpetersenii