The adaptative function of melanin-based colour variants

Résumé : Les mécanismes de contrôle des couleurs mélaniques chez les vertébrés sont encore discutés parmi les biologistes de l'évolution. Une hypothèse récente affirme que les effets pléiotropies du système des mélanocortines expliquent l'association fréquente entre la coloration eumélanique noire (due à la déposition d'eumélanine) et de nombreux traits physiologiques et comportementaux. De nombreuses études suggèrent, en effet, que des niveaux plus élevés des mélanocortines induisent l'assombrissement des téguments eumélaniques et affectent d'autres traits phénotypiques simultanément. Cependant, il n'est pas encore établi si ce mécanisme de pléiotropie peut s'appliquer aux colorations dues à la déposition de phaeomélanine, une autre forme commune de mélanine. Les antagonistes des mélanocortines déclenchent le phaeomélanogenèse et bloquent l'effet des mélanocortines ou ont un effet pharmacologique opposé. Nous nous proposons donc d'évaluer l'hypothèse que les effets pléiotropes des antagonistes des mélanocortines génèrent des covariations entre la coloration phaeomélanique et des aspects de la qualité individuelle. Comme prédit par cette hypothèse, nous constatons chez la chouette effraie (Tyto alba) que les traits phénotypiques (résistance au stress oxydatif et aux parasites) corrèlent positivement au degré d'expression d'une couleur eumélanique mais négativement au degré d'expression d'une coloration phaeomélanique. Puis, nous montrons chez la chouette hulotte (Strix aluco) que les associations génétiques entre la coloration phaeomélanique et la physiologie (immunité et la régulation de l'homéostasie) confèrent des avantages aux individus de différentes couleurs dans différents environnements caractérisés par l'abondance de nourriture et le niveau d'exposition aux parasites. Ainsi, nos études soutiennent l'hypothèse que les effets pléiotropes des antagonistes des mélanocortines génèrent des covariations entre les traits mélaniques et divers aspects de la qualité individuelle. Finalement, nous montrons chez le faucon crécerelle (Falco Tinnunculus) que l'expression des ornements mélaniques est sensible à la qualité de l'environnement dans lequel les individus grandissent. Ceci suggère que les gènes codant pour les mélanocortines et leurs antagonistes pourraient induire une expression des traits mélaniques dépendante de la condition de l'individu, un pattern d'expression rarement observé pour des traits généralement sous fort contrôle génétique. Summary : The information content and control mechanisms of melanin-based colour signals in vertebrates are still debated among evolutionary biologists. A recent hypothesis contends that pleiotropic effects of the melanocortin system accounts for the frequent association between black eumelanic coloration and physiological and behavioural traits. Accordingly, empirical evidence suggests that higher levels of melanocortins concurrently promote darker eumelanic integuments and affect other phenotypic traits. However, whether this mechanism may apply to signals relying on phaeomelanin, another common form of melanin pigments, remains to be established. Melanocortin antagonists trigger phaeomelanogenesis and block the effect of melanocortins or result in the opposite pharmacological effect. Therefore, we tested the hypothesis that pleiotropic effects of melanocortin antagonists and inverse agonists account for covariations between phaeomelanin-based coloration and aspects of individual quality. As predicted, we found that phenotypic traits (resistance to oxidative stress and parasites) correlated positively with a eumelanic trait and negatively with a phaeomelanic trait in the barn owl (Tyto alba). Then, we showed in the tawny owl (Strix aluco) that genetic associations between phaeomelanin-based coloration and physiology (immunity and regulation of energy homeostasis) confer benefits to differently coloured individuals under different levels of food abundance and parasite exposure. Altogether, our studies support the hypothesis that pleiotropic effects of melanocortins antagonists can indeed account for covariations between phaeomelanin-based traits and aspects of individual quality. Eventually, we show in the Eurasian kestrel (Falco Tinnunculus) that expression of melanin-based ornaments is sensitive to the environment in which individuals grow. This suggests that genes coding for melanocortins and their antagonists can mediate the condition-dependent component of melanin-based traits.

The InterPro protein families database: the classification resource after 15 years.

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012.

Glover's rule in North American barn owls

Studying the geographic variation of phenotypic traits can provide key information about the potential adaptive function of alternative phenotypes. Gloger's rule posits that animals should be dark-vs. light-colored in warm and humid vs. cold and dry habitats, respectively. The rule is based on the assumption that melanin pigments and/or dark coloration confer selective advantages in warm and humid regions. This rule may not apply, however, if genes for color are acting on other traits conferring fitness benefits in specific climes. Covariation between coloration and climate will therefore depend on the relative importance of coloration or melanin pigments and the genetically correlated physiological and behavioral processes that enable an animal to deal with climatic factors. The Barn Owl (Tyto alba) displays three melanin-based plumage traits, and we tested whether geographic variation in these traits at the scale of the North American continent supported Gloger's rule. An analysis of variation of pheomelanin-based reddish coloration and of the number and size of black feather spots in 1,369 museum skin specimens showed that geographic variation was correlated with ambient temperature and precipitation. Owls were darker red in color and displayed larger but fewer black feather spots in colder regions. Owls also exhibited more and larger black spots in regions where the climate was dry in winter. We propose that the associations between pigmentation and ambient temperature are of opposite sign for reddish coloration and spot size vs. the number of spots because selection exerted by climate (or a correlated variable) is plumage trait-specific or because plumage traits are genetically correlated with different adaptations.

Nestling barn owls beg more intensely in the presence of their mother than in the presence of their father

Nestling begging behaviour may be an honest signal of need used by parents to adjust optimally both feeding rate and within-brood food allocation. Although several studies showed that mothers and fathers can be differentially responsive to nestling begging behaviour with one parent showing a stronger tendency to feed the offspring that beg the most, little information is yet available on whether offspring beg for food at different intensities from the mother than father. In the present study, we investigated in nestling barn owls whether the intensity of vocal begging behaviour in the presence of the mother and in the presence of the father is different. A difference is expected because reproductive tasks are divided between the sexes with fathers bringing more food items to the nest than mothers. The results show that although mothers transfer their prey item to one of the offspring more rapidly than fathers once in their nestbox, nestlings begged more intensely in the presence of their mother than in the presence of their father. To our knowledge, this is the first empirical evidence that offspring vocalize to different levels in the presence of their mother than in the presence of their father.

The Microbe browser for comparative genomics.

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/api.

Organização e Publicação dos Termos do Website da ANACOM sob uma Perspetiva Linked Open Data

O propósito da Web Semântica é conseguir uma Web de dados totalmente ligada, isto é, numa perspetiva Linked Open Data. A Web Semântica deve garantir (estabelecendo padrões tecnológicos, vocabulários, linguagens lógicas, etc.) que os conteúdos publicados na Websejam inteligíveis quer por agentes humanos, quer por agentes máquina. Esta dissertação tem como objetivo responder à um problema delimitado, propondo uma solução no quadro da Web Semântica e suas tecnologias. Partindo-se de uma lista de termos em linguagem natural utilizados no Website da ANACOM (Autoridade Nacional de Comunicações), propomos uma organização de acordo com metodologias de construção de ontologias e vocabulários. Inspirámo-nos em duas metodologias, o Ontology Development 101 e o Process and Methodology for Core Vocabularies. O vocabulário controlado resultante, tem como base tecnológica o modelo de organização de conhecimento, recomendado pelo W3C (World Wide Web Consortium), o SKOS (Simple Knowledge Organization System). Trata-sede uma tecnologia standard da W3C desde 2009, utilizada na criação de tesauros,esquemas de classificação, taxonomias, glossários e outros tipos de vocabulários controlados. Como resultado da nossa intervenção, conseguimos organizar e codificar em SKOS, cerca de cinco centenas de termos identificados no Website da ANACOM. Para além da proposta do vocabulário controlado, passámos em revista às tecnologias e teorias que sustentam a temática da Web Semântica.

Experimental support for the make-up hypothesis in nestling tawny owls (Strix aluco)

Body condition can affect coloration of traits used in sexual selection and parent-offspring communication by inducing rapid internal changes in pigment concentration or aggregation, thickness of collagen arrays, or blood flux. The recent "makeup hypothesis" proposes an alternative honesty-reinforcing mechanism, with behaviorally mediated deposition of substances on body surfaces ("cosmetics") generating covariation between body condition and coloration. In birds, the uropygial gland wax is actively spread on feathers using the bill and changes in its deposition rate may cause rapid changes in bill and plumage coloration. Using tawny owl nestlings, we tested 3 predictions of the makeup hypothesis, namely that 1) quantity of preen wax deposited accounts for variation in bill coloration, 2) an immune stimulation (induced by injection of a lipopolysaccharide [LPS]) impairs uropygial gland wax production, and 3) different intensities of immune stimulations (strong vs. weak stimulations induced by injections of either LPS or phytohemagglutinin [PHA], respectively) and high versus low food availabilities result in different bill colorations. We found that 1) preen wax reduced bill brightness, 2) a challenge with LPS impaired uropygial gland development, and 3) nestlings challenged with LPS had a brighter bill than PHA-injected nestlings, whereas diet manipulation had no significant effect. Altogether, these results suggest that a strong immune challenge may decrease preen wax deposition rate on the bill of nestling birds, at least by impairing gland wax production, which causes a change in bill coloration. Our study therefore highlights that cosmetic colors might signal short-term variation in immunological status.

Uso de wikis semánticas

En el presente PFC vamos a estudiar a fondo las wikis semánticas, para tratar de plasmar primeramente el estado del arte de éstas, su aprovechamiento y uso real, más allá de su concepción teórica o prototípica. Posteriormente utilizaremos una de ellas para realizar un ejercicio práctico, cargando una ontología nueva desarrollada para ésta y probando la potencia de las consultas sobre ésta.

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

Corticosterone mediates the condition-dependent component of melanin-based coloration

The handicap principle of sexual selection theory states that colourful phenotypic traits signal aspects of individual quality because only individuals in prime condition can afford to produce and bear conspicuous traits. Melanin-based pigments participate in the elaboration of many secondary sexual characters and, given their role in sexual selection, melanin-based coloration may therefore honestly reject individual quality. Although the expression of melanism is usually under genetic control, in some species it is condition dependent. However, the underlying physiological mechanism is yet unknown. Based on the negative feedback link between corticosterone and melanogenesis ( melanocortins, tyrosinase) in response to stressful environmental factors, we hypothesize that corticosterone mediates the condition-dependent component of melanism. This hypothesis predicts that stressful factors induce a rise in circulating corticosterone which inhibits the secretion of melanocortins and tyrosinase and in turn melanin production. We tested this prediction by manipulating the level of corticosterone at the time of melanin production in nestling barn owls, Tyto alba, a species showing heritable variation in the degree of phaeomelanism from reddish-brown to white. The finding that corticosterone-implanted nestlings produced feathers with less phaeomelanic coloration than placebo-implanted nestlings is consistent with the hypothesis that the environment-mediated reduction in the degree of melanism is, at least in part, caused by a rise in corticosterone. In species in which the expression of melanin-based coloration is condition dependent, we now need a test showing that individuals with less corticosterone and more melanin-based signals are individuals in better condition.

Vocal sib-sib interactions: how siblings adjust signaling level to each other

Game theory states that iterative interactions between individuals are necessary to adjust behaviour optimally to one another. Although our understanding of the role of begging signals in the resolution of parent-offspring conflict over parental investment rests on game theory implying repeated interactions between family members, empiricists usually consider interactions at the exact moment when parents allocate food among the brood. Therefore, the mechanisms by which siblings adjust signalling level to one another remain unclear. We tackled this issue in the barn owl, Tyto alba. In the absence of parents, hungry nestlings signal vocally to siblings their intention to contest vigorously the next, indivisible, food item. Such behaviour deters siblings from competing and begging when parents return to the nest. In experimental two-chick broods, nestlings producing the longest calls in the absence of parents, a signal of hunger level, were more successful at monopolizing the food item at the first parental feeding visit of the night. Moreover, nestlings increased (versus decreased) call duration when their sibling produced longer (versus shorter) calls, and an individual was more likely to call again if its sibling began to vocalize before or just after it had ended its previous call. These results are in agreement with the hypothesis that siblings challenge each other vocally to reinforce the honesty of sib-sib communication and to resolve conflicts over which individual will have priority of access to the next delivered food item. Siblings challenge each other vocally to confirm that the level of signalling accurately reflects motivation.

Uso de wikis semánticas

En este trabajo se ha realizado una tarea de investigación con la finalidad de construir una ontología para cargarla en una wiki semántica y así analizar su funcionamiento.

Uso de wikis semánticas

Este es el producto obtenido del proyecto final de carrera sobre el uso de wikis semánticas en el que se describen lo que son ontologías, sus lenguajes, las wikis semánticas y un caso práctico.

Web semàntica aplicada a la gestió i caracterització de dades, sensors i accés a serveis per a vaixells d'investigació oceanogràfica

Amb el present projecte es proposa fer un estudi de la web semàntica aplicada a la descripció i modelització de la instrumentació marina operada en el context de campanyes d'investigació oceanogràfica.

Transformation rules form OntoProcED to OntoOKI

This file contains the transformtion rules in SWRL to translate formal specifications of two lower ontology levels (patterns and organization) to the upper level (implementation according to the OKI specification).