Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

The importance of micro-habitat in the breeding of Barn Owls Tyto alba

Capsule Habitat parameters associated with 706 Barn Owl (Tyto alba) nesting boxes in Israel were analysed. Pairs bred in 259 of the boxes. The intensity of agricultural practices at nestbox sites were shown to have only a weak effect on aspects of Barn Owl breeding in this region.

Defining the genomic signature of the parous breast.

ABSTRACT: BACKGROUND: It is accepted that a woman's lifetime risk of developing breast cancer after menopause is reduced by early full term pregnancy and multiparity. This phenomenon is thought to be associated with the development and differentiation of the breast during pregnancy. METHODS: In order to understand the underlying molecular mechanisms of pregnancy induced breast cancer protection, we profiled and compared the transcriptomes of normal breast tissue biopsies from 71 parous (P) and 42 nulliparous (NP) healthy postmenopausal women using Affymetrix Human Genome U133 Plus 2.0 arrays. To validate the results, we performed real time PCR and immunohistochemistry. RESULTS: We identified 305 differentially expressed probesets (208 distinct genes). Of these, 267 probesets were up- and 38 down-regulated in parous breast samples; bioinformatics analysis using gene ontology enrichment revealed that up-regulated genes in the parous breast represented biological processes involving differentiation and development, anchoring of epithelial cells to the basement membrane, hemidesmosome and cell-substrate junction assembly, mRNA and RNA metabolic processes and RNA splicing machinery. The down-regulated genes represented biological processes that comprised cell proliferation, regulation of IGF-like growth factor receptor signaling, somatic stem cell maintenance, muscle cell differentiation and apoptosis. CONCLUSIONS: This study suggests that the differentiation of the breast imprints a genomic signature that is centered in the mRNA processing reactome. These findings indicate that pregnancy may induce a safeguard mechanism at post-transcriptional level that maintains the fidelity of the transcriptional process.

Sleep and vigilance linked to melanism in wild barn owls.

Understanding the function of variation in sleep requires studies in the natural ecological conditions in which sleep evolved. Sleep has an impact on individual performance and hence may integrate the costs and benefits of investing in processes that are sensitive to sleep, such as immunity or coping with stress. Because dark and pale melanic animals differentially regulate energy homeostasis, immunity and stress hormone levels, the amount and/or organization of sleep may covary with melanin-based colour. We show here that wild, cross-fostered nestling barn owls (Tyto alba) born from mothers displaying more black spots had shorter non-REM (rapid eye movement) sleep bouts, a shorter latency until the occurrence of REM sleep after a bout of wakefulness and more wakefulness bouts. In male nestlings, the same sleep traits also correlated with their own level of spotting. Because heavily spotted male nestlings and the offspring of heavily spotted biological mothers switched sleep-wakefulness states more frequently, we propose the hypothesis that they could be also behaviourally more vigilant. Accordingly, nestlings from mothers displaying many black spots looked more often towards the nest entrance where their parents bring food and towards their sibling against whom they compete. Owlets from heavily spotted mothers might invest more in vigilance, thereby possibly increasing associated costs due to sleep fragmentation. We conclude that different strategies of the regulation of brain activity have evolved and are correlated with melanin-based coloration.

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any combination, data on the following features: predicted protein properties such as mass, pI, cellular location and transmembrane domains; SWISS-PROT annotations; Interpro domains; Gene Ontology records; verified transcription; BLAST matches to the proteomes of A.thaliana, Oryza sativa (rice), Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. The tool lends itself particularly well to the rapid analysis of contigs or of tens or hundreds of genes identified by high-throughput gene expression experiments. In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode. AVAILABILITY: http://centrifuge.unil.ch/ CONTACT: edward.farmer@unil.ch.

SNP2GO: functional analysis of genome-wide association studies.

Genome-wide association studies (GWAS) are designed to identify the portion of single-nucleotide polymorphisms (SNPs) in genome sequences associated with a complex trait. Strategies based on the gene list enrichment concept are currently applied for the functional analysis of GWAS, according to which a significant overrepresentation of candidate genes associated with a biological pathway is used as a proxy to infer overrepresentation of candidate SNPs in the pathway. Here we show that such inference is not always valid and introduce the program SNP2GO, which implements a new method to properly test for the overrepresentation of candidate SNPs in biological pathways.

Paikkatiedon perustukset puntarissa

Kokouksen esitysten verkko-osoite: http://www.geoinfo.tuwien.ac.at/events/Euresco2000/gdgis.htm

Darker eumelanic barn owls better withstand food depletion through resistance to food deprivation and lower appetite.

The intensity of selection exerted on ornaments typically varies between environments. Reaction norms may help to identify the conditions under which ornamented individuals have a selective advantage over drab conspecifics. It has been recently hypothesized that in vertebrates eumelanin-based coloration reflects the ability to regulate the balance between energy intake and expenditure. We tested two predictions of this hypothesis in barn owl nestlings, namely that darker eumelanic individuals have a lower appetite and lose less weight when food-deprived. We found that individuals fed ad libitum during 24 h consumed less food when their plumage was marked with larger black spots. When food-deprived for 24 h nestlings displaying larger black spots lost less weight. Thus, in the barn owl the degree of eumelanin-based coloration reflects the ability to withstand periods of food depletion through lower appetite and resistance to food restriction. Eumelanic coloration may therefore be associated with adaptations to environments where the risk of food depletion is high.

Ontología y conocimiento en M. Merleau-Ponty

Se ofrece aquí una revisión de la filosofía de Merleau-Ponty atendiendo a la estructura básica desde la que se conforma tanto temporal como sistemáticamente: La coimplicación radical entre la vertiente metafísica y ontológica con la gnoseológica y crítica, en cuyo seno aparece una singular filosofía antropológica de la ambigüedad». El hilo conductor es el análisis del binomio conducta humana-existencia humana» del hombre-mundo como fenómeno unitario, lo que lleva a su autor a proyectar un monismo integrador que se desarrolla bajo el postulado de una síntesis inacabada de corte fluido y ambiguo.

La inversión ontológica de la crítica en Spinoza

El presente trabajo pretende poner de relieve los rasgos esenciales que configuran la sistematización spinozista del racionalismo heredado de Descartes, analizando las diferencias abismales que separan la actitud subjetual y antropológica de la crítica cartesiana, defensora de la categoría de "individualidad", frente a la de "totalidad" preconizada por Spinoza. La tarea se lleva a cabo, concretamente, contraponiendo las nociones de "método","razón" e "ideas", tal como se entienden en uno y otro sistema.

M.Merleau-Ponty: El hombre como unidad ontológica proyectiva

Este trabajo es un intento de retomar sistemáticamente el problema de la estructuraontológica unitaria del hombre, con su dinamicidad propia, partiendo de la temáticaexpuesta en la "Estructura del comportamiento ", con lo que se pone de relieve su unidad significativa para responder de forma nueva al clásico problema de las relaciones entre el alma y el cuerpo. La respuesta merleau-pontyana implica un monismo superador de exclusivismosreductivistas por los que se habían decantado soluciones históricas a las que hay que responder, sin recaer ni en el idealismo ni en el empirismo que desconocen el significado exacto del problema, y no ofrecen ninguna respuesta aceptable al problema de la percepción.En conclusión, lo que se pretende es llevar a cabo una reconstrucción de la antropologíafenomenológica del autor, con miras a mostrar la estructura ontológica que le sirve de fundamento.

EuroPhenome: a repository for high-throughput mouse phenotyping data.

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

Melanin-based colorations signal strategies to cope with poor and rich environments

One hypothesis for the maintenance of genetic variation states that alternative genotypes are adapted to different environmental conditions (i.e., genotype-by-environment interaction GxE) that vary in space and time. Although GxE has been demonstrated for morphological traits, little evidence has been given whether these GxE are associated with traits used as signal in mate choice. In three wild bird species, we investigated whether the degree of melanin-based coloration, a heritable trait, covaries with nestling growth rate in rich and poor environments. Variation in the degree of reddish-brown phaeomelanism is pronounced in the barn owl (Tyto alba) and tawny owl (Strix aluco), and variation in black eumelanism in the barn owl and Alpine swift (Apus melba). Melanin-based coloration has been shown to be a criterion in mate choice in the barn owl. We cross-fostered hatchlings to test whether nestlings sired by parents displaying melanin-based colorations to different extent exhibit alternative growth trajectories when raised by foster parents in poor (experimentally enlarged broods) and rich (experimentally reduced broods) environments. With respect to phaeomelanism, barn owl and tawny owl offspring sired by redder parents grew more rapidly in body mass only in experimentally reduced broods. With respect to eumelanism, Alpine swift offspring of darker fathers grew their wings more rapidly only in experimentally enlarged broods, a difference that was not detected in reduced broods. These interactions between parental melanism and offspring growth rate indicate that individuals display substantial plasticity in response to the rearing environment which is associated with the degree of melanism: at least with respect to nestling growth, phaeomelanic and eumelanic individuals are best adapted to rich and poor environments, respectively. It now remains to be investigated why eumelanism and phaeomelanism have a different signaling function and what the lifelong consequences of these melanism-dependent allocation strategies are. This is important to fully appraise the role played by environmental heterogeneity in maintaining variation in the degree of melanin-based coloration.

Comparativa entre dues BD semàntiques : OWLIM-Lite i Virtuoso

L'objectiu fonamental d'aquest treball és estudiar els conceptes bàsics de la web semàntica mitjançant l'estudi de dos sistemes de gestió de bases de dades (SGBD) utilitzats en el context de la web semàntica, OWLIM-Lite i Virtuoso, que ens permetran dissenyar i implementar una ontologia.