Sign in or Join FriendFeed
FriendFeed is the easiest way to share online. Learn more »
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').
Custom RSS/AtomCustom RSS/AtomCustom RSS/AtomCustom RSS/Atom
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...
Open Chemical Data
Data from: Review on the effects of toxicants on freshwater ecosystem functions - http://datadryad.org/resourc...
We reviewed 122 peer-reviewed studies on the effects of organic toxicants and heavy metals on three fundamental ecosystem functions in freshwater ecosystems, i.e. leaf litter breakdown, primary production and community respiration. From each study meeting the inclusion criteria, the concentration resulting in a reduction of at least 20% in an ecosystem function was standardized based on median effect concentrations of standard test organisms (i.e. algae and daphnids). For pesticides, more than one third of observations indicated reductions in ecosystem functions at concentrations that are assumed being protective in regulation. Moreover, the reduction in leaf litter breakdown was more pronounced in the presence of invertebrate decomposers compared to studies where only microorganisms were involved in this function. High variability within and between studies hampered the derivation of a concentration–effect relationship. Hence, if ecosystem functions are to be included as protection...
Open Chemical Data
Data from: Diversification of the monoterpene synthase gene family (TPSb) in Protium, a highly diverse genus of tropical trees - http://datadryad.org/resourc...
Plant monoterpenes are a diverse class of secondary metabolites mediating biotic and abiotic interactions with direct effects on plant fitness. To evaluate the hypothesis that monoterpene diversity is related to functional diversification after gene duplication, we reconstructed the evolutionary history of monoterpene synthases (TPSb) – the genes underlying monoterpene synthesis – in Protium, a taxonomically and chemically diverse genus of tropical trees. We isolated multiple copies of TPSb genes from chemically divergent Protium species, reconstructed the phylogeny of this gene family, used maximum-likelihood estimation of selection coefficients, and inferred residues evolving under positive selection. We found evidence for one ancient and multiple more recent duplication events giving rise to three, and potentially five, copies of TPSb genes currently present in Protium. There was evidence for adaptive evolution in one copy with a positively selected residue likely involved in...
Open Chemical Data
Data from: Variation in plastic responses of a globally distributed picoplankton species to ocean acidification - http://datadryad.org/resourc...
Phytoplankton are the basis of marine food webs, and affect biogeochemical cycles. As CO2 levels increase, shifts in the frequencies and physiology of ecotypes within phytoplankton groups will affect their nutritional value and biogeochemical function. However, studies so far are based on a few representative genotypes from key species. Here, we measure changes in cellular function and growth rate at atmospheric CO2 concentrations predicted for the year 2100 in 16 ecotypes of the marine picoplankton Ostreococcus. We find that variation in plastic responses among ecotypes is on par with published between-genera variation, so the responses of one or a few ecotypes cannot estimate changes to the physiology or composition of a species under CO2 enrichment. We show that ecotypes best at taking advantage of CO2 enrichment by changing their photosynthesis rates most should increase in relative fitness, and so in frequency in a high-CO2 environment. Finally, information on sampling location,...
Open Chemical Data
Data from: Stress hormones mediate predator-induced phenotypic plasticity in amphibian tadpoles - http://datadryad.org/resourc...
Amphibian tadpoles display extensive anti-predator phenotypic plasticity, reducing locomotory activity and, with chronic predator exposure, developing relatively smaller trunks and larger tails. In many vertebrates, predator exposure alters activity of the neuroendocrine stress axis. We investigated predator-induced effects on stress hormone production and the mechanistic link to anti-predator defences in Rana sylvatica tadpoles. Whole-body corticosterone (CORT) content was positively correlated with predator biomass in natural ponds. Exposure to caged predators in mesocosms caused a reduction in CORT by 4 hours, but increased CORT after 4 days. Tadpoles chronically exposed to exogenous CORT developed larger tails relative to their trunks, matching morphological changes induced by predator chemical cue; this predator effect was blocked by the corticosteroid biosynthesis inhibitor metyrapone. Tadpole tail explants treated in vitro with CORT increased tissue weight, suggesting that CORT...
Open Chemical Data
Data from: Generalist insects behave in a jasmonate-dependent manner on their host plants, leaving induced areas quickly and staying longer on distant parts - http://datadryad.org/resourc...
Plants are sessile so have evolved sensitive ways to detect attacking herbivores, and sophisticated strategies to effectively defend themselves. Insect herbivory induces synthesis of the phytohormone jasmonic acid which activates downstream metabolic pathways for various chemical defences such as toxins and digestion inhibitors. Insects are also sophisticated animals, and many have co-evolved physiological adaptations that negate this induced plant defence. Insect behaviour has rarely been studied in the context of induced plant defence, although behavioural adaptation to induced plant chemistry may allow insects to bypass the host’s defence system. By visualizing jasmonate-responsive gene expression within whole plants, we uncovered spatial and temporal limits to the systemic spread of plant chemical defence following herbivory. By carefully tracking insect movement, we found induced changes in plant chemistry were detected by generalist Helicoverpa armigera insects which then...
Open Chemical Data
Open Chemical Data
Data from: Hypogonadism and low bone mineral density in patients on long-term intrathecal opioid delivery therapy - http://datadryad.org/resourc...
Objectives This study aimed to investigate the hypothalamic-pituitary-gonadal axis in a sample of male patients undertaking intrathecal opioid delivery for the management of chronic non-malignant pain and the presence of osteopenia and/or osteoporosis in those diagnosed with hypogonadism. Design Observational study using health data routinely collected for non-research purposes. Setting Department of Pain Management, Russells Hall Hospital, Dudley, United Kingdom. Patients Twenty consecutive male patients attending follow-up clinics for intrathecal opioid therapy had the gonadal axis evaluated by measuring their serum luteinising hormone, follicle stimulating hormone, total testosterone, sex hormone binding globulin and calculation of free testosterone. Bone mineral density was measured by DEXA scanning in those patients diagnosed with hypogonadism. Results Based on calculated free testosterone concentrations, 17 (85%) patients had biochemical hypogonadism with 15 patients (75%)...
Open Chemical Data
Data from: Information content is more important than sensory system or physical distance in guiding the long-term evolutionary relationships between signaling modalities in Sceloporus lizards - http://datadryad.org/resourc...
Long-term signal evolution is shaped by a variety of selective pressures including the need to convey additional information or to improve message transfer to specific receivers or through multiple environments. Here, we test the relative importance of information and sensory modality in shaping the long-term evolution of multimodal signals in Sceloporus lizards. To broadcast identity at territorial boundaries, male Sceloporus use both visual motion (headbob) and chemical signals, whereas they use color (blue belly patches) to signal aggression. Using modern phylogenetic comparative methods, we found a negative correlation between evolutionary changes in visual motion (headbobs) and chemical (femoral pore) signals, but only indirect ties between the evolution of color and motion signals (both of which are perceived visually) through viviparity, and no evidence of an evolutionary link between color and chemical signals. We also find a negative correlation between arboreality and...
Open Chemical Data
Data from: Cross-biome metagenomic analyses of soil microbial communities and their functional attributes - http://datadryad.org/resourc...
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the...
Open Chemical Data
Other ways to read this feed:Feed readerFacebook