A system-level, molecular evolutionary analysis of mammalian phototransduction

Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system.This system has shown marked evolution during mammalian divergence in such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis of proteins involved in mammalianphototransduction in order to unravel how the action of natural selection has been distributed throughout thesystem to evolve such traits. We found selective pressures to be non-randomly distributed according to both a simple protein classification scheme and a protein-interaction network representation of the signaling pathway. Proteins which are topologically central in the signaling pathway, such as the G proteins, as well as retinoid cycle chaperones and proteins involved in photoreceptor cell-type determination, were found to be more constrained in their evolution. Proteins peripheral to the pathway, such as ion channels and exchangers, as well as the retinoid cycle enzymes, have experienced a relaxation of selective pressures. Furthermore, signals of positive selection were detected in two genes: the short-wave (blue) opsin (OPN1SW) in hominids and the rod-specific Na+/Ca2+,K+ ion exchanger (SLC24A1) in rodents. The functions of the proteins involved in phototransduction and the topology of the interactions between them have imposed non-random constraints on their evolution. Thus, in shaping or conserving system-level phototransduction traits, natural selection has targeted the underlying proteins in a concerted manner.

High available GNU/Linux systems

High availability goals and ways to reach them, from a GNU/Linux point of view.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Comparative transcriptomics of early dipteran development

BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.

eggNOG v4.0: nested orthology inference across 3686 organisms

With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

Gurruminos, petimetres, abates y currutacos en el teatro breve del siglo XVIII

El estudio de ciertos modelos negativos del teatro breve del siglo XVIII revela no sólo la continuidad cómica de los tipos, sino también su relación con los ideales de conducta coetáneos: la autoridad del marido, la discreción de la mujer, el cuidado de la economía familiar... Los sainetes se unen a otros géneros literarios (el periodismo, la poesía satírica y el ensayo de carácter moral) en la ridiculización de quienes practican el cortejo y aplauden nuevas formas de sociabilidad, las modas y los bailes extranjeros, etc. frente a la conducta y los gustos tradicionales. Ejemplos tomados de Antonio de Zamora, Agramont, Ramón de la Cruz, Vázquez y González del Castillo sirven para argumentar tales reticencias ante el cambio de mentalidades de una nueva cultura del ocio, así como para observarlo a contrario: su “afeminación”, su frivolidad y su inutilidad.

Alkaloids and acetogenins in Annonaceae development: biological considerations

Chemical studies of the plant family Annonaceae have intensified in the last several decades due to the discovery of annonaceous molecules with medicinal potential (e.g., benzylisoquinoline alkaloids and acetogenins). Approximately 500 alkaloids have been identified in 138 Annonaceae species in 43 genera. In addition, until 2004, 593 annonaceous acetogenins (ACGs) had been identified, from 51 species in 13 genera.This suggests that plants from this family allocate important resources to the biosynthesis of these compounds. Despite the diversity of these molecules, their biological roles, including their physiological and/or ecological functions, are not well understood. In this study, it was provided new data describing the variety and distribution of certain alkaloids and ACGs in annonaceous plants in distinct stages of development. The potential relationships among some of these compounds and the seasonally climatic changes occurring in the plant habitat are also discussed. These data will improve our understanding of the secondary metabolism of these pharmacologically important molecules and their expression patterns during development, which will help to determine the optimal growth conditions and harvest times for their production.

Water uptake by Annona diversifolia Saff. and A. purpurea Moc. & sessé ex dunal seeds (Annonaceae)

Annonaceae seeds are known by presenting dormancy mechanisms, whose reports ranging from coating impermeable to the physiological dormancy. By this way, the present study aimed to evaluate water uptake in Annona diversifolia Saff and Annona purpurea Moc & Sessé ex Dunal seeds. For this study, seeds were placed under immersion in distilled water, and used four replicates of 25 seeds of each species, which were weighed during the 480 hours that were immersed. To determine the place of purchase of water, Annona diversifolia seeds were sealed with paraffin at different locations. Based on the results, seeds from both species reached the phases I and II of water uptake, which indicates they are not hard; however, germination (Phase III) was not reached. Annona diversifolia seeds completed Phase I with, 50h and Annona purpurea with 70h from imbibitions begin, which shows that even slowly, water is acquire.

El emperador Juliano y su relacion con los juegos romanos

La relación del emperador Juliano con los espectáculos romanos fue siempre compleja. Su actitud filosófica le llevó, según sus palabras, a rechazarlos en todo momento. Esta moral estricta y su desdén por las diversiones populares, posturas ambas muy cercanas al cristianismo que combatía, provocaron en parte algunos conocidos incidentes, como es el caso del conflicto de Antioquía. Sin embargo, a partir del testimonio de otros autores, se observa que en ocasiones Juliano no supo sustraerse a la tentación de ofrecerlos como un medio de tener entretenido al pueblo y al ejército.

Supersticions i espectacles a l'antiga Roma

La passió que els espectacles del circ, del teatre i de l"amfiteatre van despertar entre els habitants de l"antiga Roma és ben coneguda, i no respon només a un tòpic dels nostres dies. Les al·lusions que trobem en les fonts escrites són molt abundants. Igualment, són molt nombroses les manifestacions artístiques que tenen per subjecte un tema relacionat amb el món lúdic.Aquesta passió va afectar tothom, fins i tot els cristians, als quals no els era lícit acudir a exhibicions d"aquesta mena

Life span and reproductive cost explain interspecific variation in the optimal onset of reproduction.

Fitness can be profoundly influenced by the age at first reproduction (AFR), but to date the AFR-fitness relationship only has been investigated intraspecifically. Here, we investigated the relationship between AFR and average lifetime reproductive success (LRS) across 34 bird species. We assessed differences in the deviation of the Optimal AFR (i.e., the species-specific AFR associated with the highest LRS) from the age at sexual maturity, considering potential effects of life history as well as social and ecological factors. Most individuals adopted the species-specific Optimal AFR and both the mean and Optimal AFR of species correlated positively with life span. Interspecific deviations of the Optimal AFR were associated with indices reflecting a change in LRS or survival as a function of AFR: a delayed AFR was beneficial in species where early AFR was associated with a decrease in subsequent survival or reproductive output. Overall, our results suggest that a delayed onset of reproduction beyond maturity is an optimal strategy explained by a long life span and costs of early reproduction. By providing the first empirical confirmations of key predictions of life-history theory across species, this study contributes to a better understanding of life-history evolution.

El conflicto de Gamonal

En la provincia de Burgos, España, un movimiento vecinal en contra de un proyecto urbanístico acabó derivando en Enero de 2014 en un acontecimiento político con gran seguimiento por parte de los medios de comunicación tradicionales y las redes sociales. La relevancia política de un conflicto en un primer momento local empezó a aumentar y a generar diferentes lecturas e interpretaciones, tanto desde dentro del movimiento como en el resto del Estado español. En este trabajo analizamos las redes de interacciones, los marcos interpretativos del movimiento de protesta y cómo éstos fueron modulándose con base a las distintas fases del conflicto. El análisis sistemático del contenido y las redes sociales de Twitter se ha combinado con siete entrevistas realizadas a participantes en el conflicto. A partir de los datos obtenidos y su análisis, se puede concluir que se dieron cambios importantes en los marcos del movimientohacia perspectivas nacionales y globales en relación con una expansión ydesbordamiento de las redes de interacción que sustentaban el movimiento.