A computational strategy for protein function assignment which addresses the multidomain problem

A method for assigning functions to unknown sequences based on finding correlations between short signals and functional annotations in a protein database is presented. This approach is based on keyword (KW) and feature (FT) information stored in the SWISS-PROT database. The former refers to particular protein characteristics and the latter locates these characteristics at a specific sequence position. In this way, a certain keyword is only assigned to a sequence if sequence similarity is found in the position described by the FT field. Exhaustive tests performed over sequences with homologues (cluster set) and without homologues (singleton set) in the database show that assigning functions is much 'cleaner' when information about domains (FT field) is used, than when only the keywords are used.     

Engene: the processing and exploratory analysis of gene expression data

Engene is a versatile, and platform-independent web tool for exploratory analysis of gene expression data that aims at storing, visualizing and processing large sets of gene expression patterns.     

Prokaryotic diversity across a pH gradient in the “El Chichón” crater-lake: a naturally thermo-acidic environment

Extremophiles - The research and education mine “Reiche Zeche” in Freiberg (Saxony, Germany) represents one of the most famous mining facilities reminiscent to the century-long history...     

Dioscorea howardiana,a new species in Dioscorea section Trigonobasis (Dioscoreaceae)

Dioscorea howardiana is proposed as a new species from Mexico and Central America as far south as Panama, and is described and illustrated. It most closely resemblesD. liebmannii. Relationships, distribution, and ecological preferences of the new species are discussed.

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Resumen   Dioscorea howardianase propone como una especie nueva de México y Centroamérica, es descrita e ilustrada. Es semejante aD. liebmannii. Se discuten sus relaciones, su distribución geográfica y preferencias ecológicas.

     

Tyrosol and tryptophol produced by <Emphasis Type="Italic">Ceratocystis adiposa</Emphasis>

Extracellular tyrosol and tryptophol were produced and isolated from the phytopathogen fungus Ceratocystis adiposa cultivated in a rich broth. These compounds have not been previously reported in this Ceratocystis species, as its identification was established through spectroscopic methods (¹H NMR, ¹³C NMR and MS). Productivity of tyrosol and tryptophol was 65.3 and 44 μg l⁻¹ day⁻¹, respectively, which were values higher than those reported to date. Tyrosol is a compound of pharmaceutical interest showing antioxidating activity, a property used in the treatment of atherosclerosis. Tryptophol is reported to have antibiotic and phytotoxic activity.     

Micropropagation of Isoplexis canariensis (l.) G. Don

Isoplexis canariensis is a source of compounds related to the Digitalis cardenolides and anthraquinones. It is a protected endemic plant, but even so, it is rapidly disappearing from nature. An optimal micropropagation procedure was achieved using nodal segments with two axillary buds as explants. A concentration of 0.5 μM kinetin in Murashige and Skoog liquid basal medium was found to be optimal for micropropagation. Rooting in vitro was unnecessary for ex vitro survival. This revised version was published online in June 2006 with corrections to the Cover Date.     

Abandonment of Dogs and Cats: Public Opinions as Population Management Indicators

This study involved characterizing public opinions on selected issues related to the abandonment of dogs and cats in Votorantim, São Paulo, Brazil. This goal was achieved by applying multiple correspondence analysis to answers recorded in questionnaires of a population-based survey. The results suggest that the tolerance of potentially problematic behaviors did not depend on the specific kind of behavior, at least among the behaviors evaluated. The opinions given for the most frequent fate of the companion animals did not depend on the species, and those who considered abandonment to be one of the most frequent fates tended to also consider abandonment as a solution to problematic behaviors. The provision of reasons for abandonment was more frequent among interviewees who considered abandonment as one of the more common fates of nonhuman animals and as a solution to problematic behaviors. Population management interventions should be reflected in public opinion, so the public opinion characteristics that were found can be used as indicators of changes generated by such interventions.     

Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea

Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full‐length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as Ecologically Significant Taxonomic Units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda‐related genera, and some depth‐associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi‐annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa‐related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans.     

Comprehensive Model of Jumbo Squid Dosidicus gigas Trophic Ecology in the Northern Humboldt Current System

The jumbo squid Dosidicus gigas plays an important role in marine food webs both as predator and prey. We investigated the ontogenetic and spatiotemporal variability of the diet composition of jumbo squid in the northern Humboldt Current system. For that purpose we applied several statistical methods to an extensive dataset of 3,618 jumbo squid non empty stomachs collected off Peru from 2004 to 2011. A total of 55 prey taxa was identified that we aggregated into eleven groups. Our results evidenced a large variability in prey composition as already observed in other systems. However, our data do not support the hypothesis that jumbo squids select the most abundant or energetic taxon in a prey assemblage, neglecting the other available prey. Indeed, multinomial model predictions showed that stomach fullness increased with the number of prey taxa, while most stomachs with low contents contained one or two prey taxa only. Our results therefore question the common hypothesis that predators seek locally dense aggregations of monospecific prey. In addition D. gigas consumes very few anchovy Engraulis ringens in Peru, whereas a tremendous biomass of anchovy is potentially available. It seems that D. gigas cannot reach the oxygen unsaturated waters very close to the coast, where the bulk of anchovy occurs. Indeed, even if jumbo squid can forage in hypoxic deep waters during the day, surface normoxic waters are then required to recover its maintenance respiration (or energy?). Oxygen concentration could thus limit the co-occurrence of both species and then preclude predator-prey interactions. Finally we propose a conceptual model illustrating the opportunistic foraging behaviour of jumbo squid impacted by ontogenetic migration and potentially constrained by oxygen saturation in surface waters.     

Chromosomal inversions promote genomic islands of concerted evolution of Hsp70 genes in the Drosophila subobscura species subgroup

Heat‐shock (HS) assays to understand the connection between standing inversion variation and evolutionary response to climate change in Drosophila subobscura found that “warm‐climate” inversion O₃₊₄ exhibits non‐HS levels of Hsp70 protein like those of “cold‐climate” O_ST after HS induction. This was unexpected, as overexpression of Hsp70 can incur multiple fitness costs. To understand the genetic basis of this finding, we have determined the genomic sequence organization of the Hsp70 family in four different inversions, including O_ST, O₃₊₄ , O₃₊₄₊₈ and O₃₊₄₊₁₆ , using as outgroups the remainder of the subobscura species subgroup, namely Drosophila madeirensis and Drosophila guanche. We found (i) in all the assayed lines, the Hsp70 family resides in cytological locus 94A and consists of only two genes, each with four HS elements (HSEs) and three GAGA sites on its promoter. Yet, in O_ST, the family is comparatively more compact; (ii) the two Hsp70 copies evolve in concert through gene conversion, except in D. guanche; (iii) within D. subobscura, the rate of concerted evolution is strongly structured by inversion, being higher in O_ST than in O₃₊₄ ; and (iv) in D. guanche, the two copies accumulated multiple differences, including a newly evolved “gap‐type” HSE2. The absence of concerted evolution in this species may be related to a long‐gone‐unnoticed observation that it lacks Hsp70 HS response, perhaps because it has evolved within a narrow thermal range in an oceanic island. Our results point to a previously unrealized link between inversions and concerted evolution, with potentially major implications for understanding genome evolution.