CarGene: Characterisation of sets of genes based on metabolic pathways analysis

The great amount of biological information provides scientists with an incomparable framework for testing the results of new algorithms. Several tools have been developed for analysing gene-enrichment and most of them are Gene Ontology-based tools. We developed a Kyoto Encyclopedia of Genes and Genomes (Kegg)-based tool that provides a friendly graphical environment for analysing gene-enrichment. The tool integrates two statistical corrections and simultaneously analysing the information about many groups of genes in both visual and textual manner. We tested the usefulness of our approach on a previous analysis (Huttenshower et al.). Furthermore, our tool is freely available (http://www.upo.es/eps/bigs/cargene.html).Ministerio de Ciencia y Tecnología TIN2007-68084-C02-00Ministerio de Ciencia e Innovación PCI2006-A7-0575Junta de Andalucía P07-TIC-02611Junta de Andalucía TIC-20

Neighborhood-Based Clustering of Gene-Gene Interactions

n this work, we propose a new greedy clustering algorithm to identify groups of related genes. Clustering algorithms analyze genes in order to group those with similar behavior. Instead, our approach groups pairs of genes that present similar positive and/or negative interactions. Our approach presents some interesting properties. For instance, the user can specify how the range of each gene is going to be segmented (labels). Some of these will mean expressed or inhibited (depending on the gradation). From all the label combinations a function transforms each pair of labels into another one, that identifies the type of interaction. From these pairs of genes and their interactions we build clusters in a greedy, iterative fashion, as two pairs of genes will be similar if they have the same amount of relevant interactions. Initial two–genes clusters grow iteratively based on their neighborhood until the set of clusters does not change. The algorithm allows the researcher to modify all the criteria: discretization mapping function, gene–gene mapping function and filtering function, and provides much flexibility to obtain clusters based on the level of precision needed. The performance of our approach is experimentally tested on the yeast dataset. The final number of clusters is low and genes within show a significant level of cohesion, as it is shown graphically in the experiments

Role of prey and intraspecific density dependence on the population growth of an avian top predator

Exploring predator-prey systems in diverse ecosystems increases our knowledge about ecological processes. Predator population growth may be positive when conspecific density is low but predators also need areas with prey availability, associated with competition, which increases the risk of suffering losses but stabilises populations. We studied relationships between European rabbits Oryctolagus cuniculus (prey) and adult eagle owls Bubo bubo (predators) in south-western Europe. We assessed models explaining the predator population growth and stability. We estimated the abundance of rabbits and adult eagle owls during three years in eight localities of central-southern Spain. We explored models including rabbit and adult eagle owl abundance, accounting for yearly variations and including the locality as a random variable. We found that population growth of adult eagle owls was positive in situations with low conspecific abundance and tended to be negative but approaching equilibrium in situations of higher conspecific abundance. Population growth was also positively related to previous summer rabbit density when taking into account eagle owl conspecific abundance, possibly indicating that rabbits may support recruitment. Furthermore, abundance stability of adult eagle owls was positively related to previous winter-spring rabbit density, which could suggest predator population stabilisation through quick territory occupation in high-quality areas. These results exemplify the trade-off between prey availability and abundance of adult predators related to population growth and abundance stability in the eagle owl-rabbit system in south-western Europe. Despite rabbits have greatly declined during the last decades and eagle owls locally specialise on them, eagle owls currently have a favourable conservation status. As eagle owls are the only nocturnal raptor with such dependence on rabbits, this could point out that predators may overcome prey decreases in areas with favourable climate and prey in the absence of superior competitors with similar foraging mode.This study is a partial result from the I + D National Plan Projects CGL2005-02340 and CGL2009-10741, funded by the Spanish Ministry of Science and Innovation and EU-FEDER funds. J. Fernandez-de-Simon benefitted from an FPI scholarship (BES-2006-12562) funded by the Spanish Ministry of Science and Innovation and the European Social Fund.Peer Reviewe

Evaluación de diferentes técnicas para efectuar el diagnóstico precoz de gestación en bovinos productores de leche.

Se evaluaron tres métodos para efectuar el diagnóstico precoz: de gestación, con objeto de determinar cuál es el que menos pérdidas embrionarias produce. Las técnicas estudiadas fueron: Palpaciones de a) membranas fatales, b) vesícula amniótica y c) cotiledones y feto. El estudio fue realizado en 250 vacas de la raza Holstein, las cuales fueron distribuidas al azar en 3 grupos experimentales. En los dos primeros la exploración rectal se hizo entre los 30-39 y 40-49 días de no retorno al estro después del último servicio. En ambos lotes el criterio para diagnosticar gestación fue la palpación de las membranas fetales y la vesícula amniótica. En el tercer grupo el examen rectal se hizo entre los 60-69 días de no retorno al estro, determinándose la gestación mediante la palpación de los cotiledones y feto. No se encontró diferencia significativa (P>0.05), cuando se compararon individualmente y en conjunto las palpaciones de 30-39 y 40-49 días de membranas fetales y vesícula amniótica, respectivamente. Tampoco hubo diferencia significativa cuando se compararon los datos de las palpaciones de membranas de vesícula contra las palpaciones de cotiledones y feto

DIAGNÓSTICO DE LA FERTILIDAD QUÍMICA DE LA CAMADA SUPERFICIAL DEL RECURSO SUELO EN LA MICROCUENCA DEL ARROYO ATYRÁ EN EL DISTRITO DE ATYRÁ

El trabajo tuvo por objeto estudiar y caracterizar el nivel de la fertilidad de la camada superficial del recurso suelo en sus diferentes categorías de uso en la microcuenca del arroyo Atyrá, distrito de Atyrá. La hipótesis formulada fue que el nivel de fertilidad de los suelos en los agroecosistemas de la microcuenca del arroyo Atyrá es considerablemente más bajo en relación a la fertilidad de los suelos de los ecosistemas forestales. En el área de estudio se obtuvieron 50 muestras compuestas de O- 20 cm de profundidad, distribuidas en diferentes categorías de uso (ecosistema forestal, ecosistema de praderas naturales, agroecosistemas, ecosistema de agua dulce y ecosistema urbano) y analizadas en el laboratorio; los resultados fueron introducidos en una planilla electrónica, en la cual se procesó y determinó el nivel de fertilidad del suelo. Los parámetros utilizados para la determinación del nivel de fertilidad fueron la materia orgánica, el fósforo disponible, la suma de bases intercambiables, pH (acidez activa) y la acidez intercambiable. Los resultados obtenidos permiten concluir que: en general el nivel de fertilidad de los suelos de la microcuenca es bajo, con 68% de todas las muestras analizadas en dicho nivel; en donde los ecosistemas de agua dulce y el ecosistema urbano presentan niveles medios de fertilidad, ambos con 67% de todas las muestras analizadas en dicho nivel, en comparación con los demás categorías de uso que poseen niveles bajos de fertilidad. En general los suelos de la microcuenca son ácidos, con baja suma de bases (calcio, magnesio, potasio y sodio), bajos en contenido de fósforo y materia orgánica a excepción del ecosistema de agua dulce y ecosistema urbano que presentan niveles altos en materia orgánica, 100 y 66,7% de todas las muestras analizadas respectivamente.

Dysfunction of Inflammatory Pathways and Their Relationship With Psychological Factors in Adult Female Patients With Eating Disorders.

The attempts to clarify the origin of eating disorders (ED) have not been completely successful and their etiopathogenesis remains unknown. Current research shows an activation of the immune response in neuropsychiatric diseases, including ED. We aimed to investigate immune response parameters in patients with ED and to identify psychological factors influencing the inflammatory response. The relationship between inflammation markers and impulsivity and affective symptomatology was explored as well. Thirty-four adult female patients with current diagnosis of ED, none of them under psychopharmacological treatment (excluding benzodiazepines), were included in this study. Patients were compared with a healthy control group of fifteen adult females. The levels of inflammatory markers and indicators of oxidative/nitrosative stress were evaluated in plasma and/or in peripheral blood mononuclear cells (PBMCs). Subjects were assessed by means of different ED evaluation tools. Additionally, the Barratt Impulsiveness Scale, the Montgomery-Asberg Depression Rating Scale and the Hamilton Anxiety Rating Scale were also employed. Patients with ED shown increased plasma levels of the pro-inflammatory nuclear factor kappa B (NFκB) and the cytokine tumor necrosis factor-alpha (TNF-α), among other factors and an increment in the oxidative/nitrosative stress as well as increased glucocorticoid receptor (GR) expression levels in their PBMCs. Moreover, the inflammatory prostaglandin E2 (PGE2) correlated with impulsiveness and the anti-inflammatory prostaglandin J2 (15d-PGJ2) correlated with depressive symptomatology. Our results point towards a relationship between the immune response and impulsiveness and between the immune response and depressive symptomatology in female adult patients with ED.post-print1075 K

Towards a standardized index of European rabbit abundance in Iberian Mediterranean habitats

European rabbits Oryctolagus cuniculus are a keystone species in Iberian Mediterranean ecosystems. However, the reliability of methods for estimating rabbit abundance, particularly when at low numbers, is not well understood. Further, better standardization of these methodologies would allow abundance estimates to be more reliably compared between areas and periods. Consequently, we compared several frequently used methods of estimating rabbit abundance and assessed their advantages and disadvantages. During the summers of 2008 and 2009, in 11 localities of central-southern Spain we undertook (a) driving transect counts of rabbits, either at dusk or at night, (b) linear transects on foot recording rabbit signs, (c) cleared-plot pellet counts at permanent plots, and (d) standing crop counts, both with and without habitat stratification. Density estimated at night from driving transects using the Distance Sampling method (the reference method against which all other indices were compared) varied from 0 to 2. 69 rabbits ha-1. Most pellet-count indices were significantly related to the reference method. In particular, cleared-plot pellet counts in permanent plots corrected for pellet persistence showed the best correlation with the reference method. In contrast, latrine counts were not related to the reference method index, and we recommend against their use. A standard methodology based on cleared-plot pellets counts could be used to monitor rabbit abundance on a large scale.This work is a partial result from the projects CGL2005-02340, CGL2009-10741, and CGL2009-11665 funded by the Spanish Ministry of Science and Innovation and EU-FEDER funds, and projects POII09-0099-2557 and 07/NAT/E/000742 funded by the Junta de Comunidades de Castilla-La Mancha with EU-FEDER and LIFE funds, respectively. Javier Fernandez-de-Simon benefits from a FPI scholarship and Miguel Delibes-Mateos is currently holding a Juan de la Cierva research contract, both funded by the Spanish Ministry of Science and Innovation and the European Social Fund.Peer Reviewe