ALBERT

Description: The invasion of host cells by the intracellular protozoan Trypanosoma cruzi requires interactions with host cell molecules, and the replication of the parasite requires escape from a parasitophorous vacuole into the host cell cytosol. Galectin-3, a member of β-galactosidase-binding lectin family, has numerous extracellular and intracellular functions. In this study, we investigated the role of galectin-3 during the invasion and intracellular trafficking of T. cruzi extracellular amastigotes (EAs). Endogenous galectin-3 from mouse peritoneal macrophages accumulated around the pathogen during cell invasion by EAs. In addition, galectin-3 accumulated around parasites after their escape from the parasitophorous vacuole. Thus, galectin-3 behaved as a novel marker of phagolysosome lysis during the infection of host cells by T. cruzi .

Description: It is well established that artificial night lighting can influence animal orientation, but there is less information about its effects on other behaviors. Previous work suggested that light pollution can affect both seasonal and daily patterns of behavior. The aim of our study was to investigate the effects of artificial night lighting and daytime traffic noise on the timing of dawn and dusk singing in 6 common songbirds. We recorded singing behavior in 11 nonurban plots: 2 plots with light, but no noise, 3 with light and noise pollution, 3 with noise, but no light, and 3 undisturbed forests. Our results show that artificial night lighting, but not noise, leads to an earlier start of dawn singing in 5 out of 6 species, ranging on average from 10min for the song thrush to 20min for the robin and the great tit. This effect was strongest at higher light intensities. We further show that dusk song is also affected: 3 species continued dusk singing for longer in lighted areas, but the effect was smaller than that observed for dawn song (from about 8min for the blackbird to 14min for the great tit). For all species, onset and cessation of singing changed relative to sunrise and sunset with the progress of the season. Rain delayed the onset of singing at dawn and advanced the cessation at dusk. We discuss the implications of our findings in the context of sexual selection.

Description: Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third ‘Quest for Orthologs’ meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. Availability and implementation: All such materials are available at http://questfororthologs.org . Contact: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk

Description: Generalized linear models were applied to identify factors affecting the capture rates (catch per unit effort, cpue) of Xiphopenaeus kroyeri and to estimate time-series data with standardized abundance indices. The adjusted models revealed that the most powerful vessels (with greater HP) were up to 3.5 times more efficient than vessels with less powerful engines. The seasonal variation of the resource changed from year to year, most likely due to variations in the recruitment season and the timing of temporary fishing bans. The variation of cpue was similar between the northern and southern sectors of the study area. In these, X. kroyeri abundances increased in the years 1996, 1997, 2001 and 2002, while in the central sector, the cpue fluctuated with a period duration of approximately two years. During the period, the relative abundance of the species displayed neither a decreasing nor an increasing trend, indicating that this has been harvested at stable levels. However, X. kroyeri stock was reduced by overfishing during the 1980s and exhibits variations in abundance that may occur in response to environmental fluctuations; thus, the harvesting of this species should be managed with extreme caution.

Description: Motivation: The 1000 Genomes Project (1KGP) and thousands of Genome-Wide Association Studies (GWAS) performed during the last years have generated an enormous amount of information that needs to be integrated to better understand the genetic architecture of complex diseases in different populations. This integration is important in areas such as genetics, epidemiology, anthropology, as well as admixture mapping design and GWAS-replications. Network-based approaches that explore the genetic bases of human diseases and traits have not yet incorporated information on genetic diversity among human populations. Results: We propose Disease-ANCEstry networks (DANCE), a graph-based web tool that allows to integrate and visualize information on human complex phenotypes and their GWAS-hits, as well as their risk allele frequencies in different populations. DANCE provides an interactive way to explore the human SNP–Disease Network and its projection, a Disease–Disease Network. With these functionalities, DANCE fills a gap in our ability to handle and understand the knowledge generated by GWAS and 1KGP. We provide a number of case studies that show how DANCE can be used to explore the relationships between human complex diseases, their genetic bases and variability in different human populations. Availability and implementation: DANCE is freely available at http://ldgh.com.br/dance/ . We recommend using DANCE with Mozilla Firefox, Safari, Chrome or Internet Explorer (v9 or v10). Contact : gilderlanio@gmail.com or maira.r.rodrigues@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: We investigate the nature of extremely red galaxies (ERGs), objects whose colours are redder than those found in the red sequence present in colour–magnitude diagrams of galaxies. We selected from the Sloan Digital Sky Survey Data Release 7 a volume-limited sample of such galaxies in the redshift interval 0.010 〈 z  〈 0.030, brighter than M r  = –17.8 (magnitudes dereddened, corrected for the Milky Way extinction) and with ( g – r ) colours larger than those of galaxies in the red sequence. This sample contains 416 ERGs, which were classified visually. Our classification was cross-checked with other classifications available in the literature. We found from our visual classification that the majority of objects in our sample are edge-on spirals (73 per cent). Other spirals correspond to 13 per cent, whereas elliptical galaxies comprise only 11 per cent of the objects. After comparing the morphological mix and the distributions of Hα/Hβ and axial ratios of ERGs and objects in the red sequence, we suggest that dust, more than stellar population effects, is the driver of the red colours found in these extremely red galaxies.

Description: Montados are evergreen oak woodlands dominated by Quercus species, which are considered to be key to biodiversity conservation and ecosystem services. This ecosystem is often used for cattle breeding in most regions of the Iberian Peninsula, which causes plants to receive extra nitrogen as ammonia (NH 3 ) through the atmosphere. The effect of this atmospheric NH 3 (NH 3atm ) on ecosystems is still under discussion. This study aimed to evaluate the effects of an NH 3atm concentration gradient downwind of a cattle barn in a Montado area. Leaves from the selected Quercus suber L. trees along the gradient showed a clear influence of the NH 3 on 13 C, as a consequence of a strong limitation on the photosynthetic machinery by a reduction of both stomatal and mesophyll conductance. A detailed study of the impact of NH 3atm on the photosynthetic performance of Q. suber trees is presented, and new mechanisms by which NH 3 affects photosynthesis at the leaf level are suggested.

Description: Selectivity has traditionally been well estimated internally in stock assessment models when length or age composition data are available. However, in stock assessment, temporal or spatial variation in fishery or stock structure can lead to misspecification of the selectivity pattern, which can contribute substantially to the uncertainty in stock assessment results. Consequently, generating auxiliary information to help stock assessment scientists avoid unrealistic specifications of selectivity patterns should be encouraged. Here, we combine data from pop-up satellite archival tags (PSATs) deployed on blue sharks in the South Atlantic Ocean, and information on maximum pelagic longline fishing depths, to introduce an alternative approach for estimating selectivity of fishing gear. Further, we present how this externally estimated tag-based selectivity can be used to inform the most appropriate form of selectivity curves (e.g. asymptotic or dome-shaped) in a spatially structured stock assessment model for the South Atlantic blue shark population. The estimated tag-based selectivity showed substantially different selectivity patterns within the area of the assessed stock, in one area the depth range of the longline gear is inhabited mostly by adults, which is consistent with an asymptotic selectivity. In another area, the overlap shifts to younger ages, with older sharks located in deeper waters, consequently the expected selectivity is more dome-shaped. To account for this variability in the stock assessment model, we assigned fishing fleets with different selectivity patterns. The form of the selectivity curve assigned for each fleet was based on the tag-based selectivity estimates for the area of where that fleet operates. The assessment model demonstrated relatively good fit to the data and that the estimated management quantities were robust. This study provides additional evidence that externally derived estimates of selectivity using PSATs data can assist implementing stock assessments that capture some of the spatial variability of pelagic fish species.

Description: Disturbances in space weather can negatively affect several fields, including aviation and aerospace, satellites, oil and gas industries, and electrical systems, leading to economic and commercial losses. Solar flares are the most significant events that can affect the Earth’s atmosphere, thus leading researchers to drive efforts on their forecasting. The related literature is comprehensive and holds several systems proposed for flare forecasting. However, most techniques are tailor-made and designed for specific purposes, not allowing researchers to customize them in case of changes in data input or in the prediction algorithm. This paper proposes a framework to design, train, and evaluate flare prediction systems which present promising results. Our proposed framework involves model and feature selection, randomized hyperparameters optimization, data resampling, and evaluation under operational settings. Compared to baseline predictions, our framework generated some proof-of-concept models with positive recalls between 0.70 and 0.75 for forecasting ≥M class flares up to 96 h ahead while keeping the area under the ROC curve score at high levels.