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Open Chemical Data

Open Chemical Data

Feed of Open Chemical Data. Criterion: the data source must provide a (CML)RSS feed and the data must use an Open License (no 'public domain').
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Open Chemical Data
Data from: Molecular study of bacterial diversity within the trophosome of the vestimentiferan tubeworm Ridgeia piscesae - http://datadryad.org/resourc...
A large proportion of the faunal biomass in hydrothermal vent ecosystems relies on symbiotic relationships, with bacteria as a source of nutrition. Whereas multiple symbioses have been observed in diverse vent hosts, siboglinid tubeworms have been thought to harbour a single endosymbiont phylotype affiliated to the Gammaproteobacteria. In the case of the Northeast Pacific vestimentiferan Ridgeia piscesae, two previous studies suggested the presence of more than one symbiont. The possibility of multiple, and possibly habitat-specific, symbionts in R. piscesae provided a potential explanation for the tubeworm’s broad ecological niche, compared with other hydrothermal vent siboglinids. This study further explored the diversity of trophosome bacteria in R. piscesae using two methodological approaches not yet applied to this symbiosis. We carried out 454-pyrosequencing on trophosome samples from 46 individual worms and used catalyzed reporter deposition-fluorescence in situ hybridization...
Open Chemical Data
Data from: The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria - http://datadryad.org/resourc...
C4 photosynthesis represents a most remarkable case of convergent evolution of a complex trait, which includes the reprogramming of the expression patterns of thousands of genes. Anatomical, physiological, and phylogenetic and analyses as well as computational modeling indicate that the establishment of a photorespiratory carbon pump (termed C2 photosynthesis) is a prerequisite for the evolution of C4. However, a mechanistic model explaining the tight connection between the evolution of C4 and C2 photosynthesis is currently lacking. Here we address this question through comparative transcriptomic and biochemical analyses of closely related C3, C3-C4, and C4 species, combined with Flux Balance Analysis constrained through a mechanistic model of carbon fixation. We show that C2 photosynthesis creates a misbalance in nitrogen metabolism between bundle sheath and mesophyll cells. Rebalancing nitrogen metabolism requires anaplerotic reactions that resemble at least parts of a basic C4...
Open Chemical Data
Open Chemical Data
Data from: Predatory fish sounds can alter crab foraging behavior and influence bivalve abundance - http://datadryad.org/resourc...
The risk of predation can have large effects on ecological communities via changes in prey behaviour, morphology and reproduction. Although prey can use a variety of sensory signals to detect predation risk, relatively little is known regarding the effects of predator acoustic cues on prey foraging behaviour. Here we show that an ecologically important marine crab species can detect sound across a range of frequencies, probably in response to particle acceleration. Further, crabs suppress their resource consumption in the presence of experimental acoustic stimuli from multiple predatory fish species, and the sign and strength of this response is similar to that elicited by water-borne chemical cues. When acoustic and chemical cues were combined, consumption differed from expectations based on independent cue effects, suggesting redundancies among cue types. These results highlight that predator acoustic cues may influence prey behaviour across a range of vertebrate and invertebrate...
Open Chemical Data
Open Chemical Data
Data from: Natural enemy ecology: comparing the effects of predation risk, infection risk and disease on host behavior - http://datadryad.org/resourc...
1. Growing interest in unifying the field of natural enemy ecology has revealed similarities between predation and parasitism. In parallel with predation, parasite infection – and even the threat of infection – can alter host traits and indirectly affect community interactions. Nonetheless, few studies have considered multiple mechanisms of natural enemy-induced behavioural alteration in parallel (e.g. effects before and after enemy contact) or the factors that drive variation in behavioural responses. 2. We first evaluated how the threat of infection by a virulent trematode (Ribeiroia ondatrae) compared to the well studied risk of predation in triggering inducible defences in amphibian hosts, prior to direct contact with either enemy. We then evaluated five separate factors that influenced the magnitude of parasite-induced behavioural changes after successful transmission. 3. In both the laboratory and an outdoor mesocosm experiment, we found no evidence that tadpoles of two species...
Open Chemical Data
Open Chemical Data
InChI=1S/C102H172N36O32S7/c1-50(2)34-63-91(161)127-62(26-33-171-5)90(160)129-64(35-53-22-24-54(143)25-23-53)92(162)130-65(36-78(148)149)93(163)135-72-48-175-173-45-69(80(108)150)133-86(156)58(18-8-12-29-105)121-76(146)39-11 - http://cb.openmolecules.net/inchi...
Open Chemical Data
Open Chemical Data
Open Chemical Data
Open Chemical Data
Open Chemical Data
Data from: Two new sterile species of Loxospora (Sarrameanaceae: lichenized ascomycetes) from the mid-Atlantic coastal plain - http://datadryad.org/resourc...
Molecular phylogenetic analyses of mtSSU and nrITS sequence data show that two new crustose species belong to the genus Loxospora. Both species are sterile asexually reproducing crustose lichens from the Mid-Atlantic Coastal Plain of eastern North America, and are chemically similar to L. lecanoriformis in producing 2-0-methylperlatolic acid. Loxosopora assateaguensis is a sorediate species that is described from a single locality on Assateague Island in Maryland. Loxospora confusa is a granulose-isidiate species that is widespread in the Mid-Atlantic with a disjunct population in the Joccassee Gorges of the southern Appalachian Mountains.
Open Chemical Data
Data from: A locus in Drosophila sechellia affecting tolerance of a host plant toxin - http://datadryad.org/resourc...
Many insects feed on only one or a few types of host. These host specialists often evolve a preference for chemical cues emanting from their host and develop mechanisms for circumventing their host’s defenses. Adaptations like these are central to evolutionary biology, yet our understanding of their genetics remains incomplete. Drosophila sechellia, an emerging model for the genetics of host specialization, is an island endemic that has adapted to chemical toxins present in the fruit of its host plant, Morinda citrifolia. Its sibling species, D. simulans, and many other Drosophila species do not tolerate these toxins and avoid the fruit. Earlier work showed that a region with a strong effect on tolerance to the major toxin, octanoic acid, was on chromosome arm 3R. Using a novel assay we narrowed this region to a small span near the centromere containing 18 genes, including three odorant binding proteins. It has been hypothesized that the evolution of host specialization is facilitated...
Open Chemical Data
Open Chemical Data
Open Chemical Data
Data from: Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time - http://datadryad.org/resourc...
Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the stable core of the genome. Surprisingly, such lateral transfer events were readily identified and quantifiable, occurring only a relatively small number of times in the archaeal domain of life. By placing gene acquisition events into a temporal framework, the rates by which new metabolic genes were acquired can be quantified. The highest lateral transfer rates were among cytochrome oxidase genes that use oxygen as a terminal electron acceptor (with a total of 12-14 lateral...
Open Chemical Data
InChI=1S/C39H57NO12/c1-18-11-22-5-7-25-19(2)12-24(44-25)9-10-39-16-30-35(51-39)36-37(49-30)38(52-39)33-26(48-36)8-6-23(46-33)14-31(42)50-34-29(15-27(45-22)20(18)3)47-28(32(34)43-4)13-21(41)17-40/h18,21-30,32-38,41H,2-3,5-17 - http://cb.openmolecules.net/inchi...
Open Chemical Data
Open Chemical Data
Open Chemical Data
Data from: Hydrocarbon divergence and reproductive isolation in Timema stick insects - http://datadryad.org/resourc...
Background: Individuals commonly prefer certain trait values over others when choosing their mates. If such preferences diverge between populations, they can generate behavioral reproductive isolation and thereby contribute to speciation. Reproductive isolation in insects often involves chemical communication, and cuticular hydrocarbons, in particular, serve as mate recognition signals in many species. We combined data on female cuticular hydrocarbons, interspecific mating propensity, and phylogenetics to evaluate the role of cuticular hydrocarbons in diversification of Timema walking-sticks. Results: Hydrocarbon profiles differed substantially among the nine analyzed species, as well as between partially reproductively-isolated T. cristinae populations adapted to different host plants. In no-choice trials, mating was more likely between species with similar than divergent hydrocarbon profiles, even after correcting for genetic divergences. The macroevolution of hydrocarbon profiles,...
Open Chemical Data
Data from: Expression of taste signal transduction molecules in the caecum of common marmosets - http://datadryad.org/resourc...
The extraoral presence of taste signal transduction proteins has recently been reported in rodents and humans. Here, we report for the first time the presence of these signal transduction proteins in the caecum of a non-human primate, the common marmoset. Quantitative RT-PCR data on the gene expression of taste signal transduction molecules (gustducin and TRPM5) in common marmosets suggested high expression in the caecum, which was not observed in other non-human primates. Immunohistochemical analysis confirmed the specific presence of gustducin and taste receptors in marmoset caecal cells. These results may relate to the specific feeding behaviour of marmosets, which consume plant exudates, primarily gums.
Open Chemical Data
Open Chemical Data
Open Chemical Data
Data from: When condition trumps location: seed consumption by fruit-eating birds removes pathogens and predator attractants - http://datadryad.org/resourc...
Seed ingestion by frugivorous vertebrates commonly benefits plants by moving seeds to locations with fewer predators and pathogens than under the parent. For plants with high local population densities, however, movement from the parent plant is unlikely to result in ‘escape’ from predators and pathogens. Changes to seed condition caused by gut passage may also provide benefits, yet are rarely evaluated as an alternative. Here, we use a common bird-dispersed chilli pepper (Capsicum chacoense) to conduct the first experimental comparison of escape-related benefits to condition-related benefits of animal-mediated seed dispersal. Within chilli populations, seeds dispersed far from parent plants gained no advantage from escape alone, but seed consumption by birds increased seed survival by 370% – regardless of dispersal distance – due to removal during gut passage of fungal pathogens and chemical attractants to granivores. These results call into question the pre-eminence of escape as the...
Open Chemical Data
Open Chemical Data
Data from: An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles - http://datadryad.org/resourc...
Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used...
Open Chemical Data
Open Chemical Data
Data from: Aquatic community structure across an Andes-to-Amazon fluvial gradient - http://datadryad.org/resourc...
Aim: Little is known about factors affecting the elevational and longitudinal zonation of tropical Andean stream communities. We investigated epilithon, macroinvertebrate and fish assemblages along a 4100-m elevational–longitudinal gradient in an Andean headwater of the Amazon Basin. We interpret our results within the context of environmental factors, emphasizing temperature, as well as ecological theory relating shifts in metazoan functional feeding groups to shifts in basal resources along the fluvial continuum. Location: Arazá-Inambari-Madre de Dios watershed, south-eastern Peru. Methods: We sampled water physicochemistry, epilithon and macroinvertebrate diversity and abundance, and fish diversity at 18 main-stem and 14 tributary sites from high puna grasslands (4300 m a.s.l.) to Amazon Basin lowlands (200 m a.s.l.). Results: Water physicochemical parameters and the taxonomic and ecological structure of invertebrate and fish assemblages displayed mostly nonlinear responses to...
Open Chemical Data
Data from: A radical shift in the taxonomy of Lepraria s.l.: molecular and morphological studies shed new light on the evolution of asexuality and lichen growth form diversification - http://datadryad.org/resourc...
A combination of molecular phylogenetic analyses of ITS and mtSSU sequences, morphological and chemical analyses were used to investigate the lineages nominally included in the sterile lichen genus Lepraria. A core group (Lepraria s.str.) was resolved as sister relationship to Stereocaulon. Species producing the secondary compounds argopsin, pannarin and usnic acid were found to belong to other lineages of lichen-forming ascomycetes. Study of Leprocaulon revealed that all species, except the type, likely represent members of the Lepraria s. str. that have evolved a fruticose growth form. The correct name for the type species of Leprocaulon is shown to be L. quisquiliare, not L. microscopicum, and the genus is redefined to include several species previously placed in Lepraria. Leprocaulon quisquiliare is also shown to comprise two morphologically convergent species. The name is lectotypified and epitypified on material from the type region (Germany) and its application restricted to...
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