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Sample records for reveals widespread occurrence

  1. Widespread Natural Occurrence of Hydroxyurea in Animals

    PubMed Central

    Fraser, David I.; Liu, Kyle T.; Reid, Bryan J.; Hawkins, Emily; Sevier, Andrew; Pyle, Michelle; Robinson, Jacob W.; Ouellette, Pierre H. R.; Ballantyne, James S.

    2015-01-01

    Here we report the widespread natural occurrence of a known antibiotic and antineoplastic compound, hydroxyurea in animals from many taxonomic groups. Hydroxyurea occurs in all the organisms we have examined including invertebrates (molluscs and crustaceans), fishes from several major groups, amphibians and mammals. The species with highest concentrations was an elasmobranch (sharks, skates and rays), the little skate Leucoraja erinacea with levels up to 250 μM, high enough to have antiviral, antimicrobial and antineoplastic effects based on in vitro studies. Embryos of L. erinacea showed increasing levels of hydroxyurea with development, indicating the capacity for hydroxyurea synthesis. Certain tissues of other organisms (e.g. skin of the frog (64 μM), intestine of lobster (138 μM) gills of the surf clam (100 μM)) had levels high enough to have antiviral effects based on in vitro studies. Hydroxyurea is widely used clinically in the treatment of certain human cancers, sickle cell anemia, psoriasis, myeloproliferative diseases, and has been investigated as a potential treatment of HIV infection and its presence at high levels in tissues of elasmobranchs and other organisms suggests a novel mechanism for fighting disease that may explain the disease resistance of some groups. In light of the known production of nitric oxide from exogenously applied hydroxyurea, endogenous hydoxyurea may play a hitherto unknown role in nitric oxide dynamics. PMID:26600157

  2. Widespread occurrence of (per)chlorate in the Solar System

    NASA Astrophysics Data System (ADS)

    Jackson, W. Andrew; Davila, Alfonso F.; Sears, Derek W. G.; Coates, John D.; McKay, Christopher P.; Brundrett, Maeghan; Estrada, Nubia; Böhlke, J. K.

    2015-11-01

    Perchlorate (ClO4-) and chlorate (ClO3-) are ubiquitous on Earth and ClO4- has also been found on Mars. These species can play important roles in geochemical processes such as oxidation of organic matter and as biological electron acceptors, and are also indicators of important photochemical reactions involving oxyanions; on Mars they could be relevant for human habitability both in terms of in situ resource utilization and potential human health effects. For the first time, we extracted, detected and quantified ClO4- and ClO3- in extraterrestrial, non-planetary samples: regolith and rock samples from the Moon, and two chondrite meteorites (Murchison and Fayetteville). Lunar samples were collected by astronauts during the Apollo program, and meteorite samples were recovered immediately after their fall. This fact, together with the heterogeneous distribution of ClO4- and ClO3- within some of the samples, and their relative abundance with respect to other soluble species (e.g., NO3-) are consistent with an extraterrestrial origin of the oxychlorine species. Our results, combined with the previously reported widespread occurrence on Earth and Mars, indicate that ClO4- and ClO3- could be present throughout the Solar System.

  3. Widespread Occurrence of Bd in French Guiana, South America

    PubMed Central

    Courtois, Elodie A.; Gaucher, Philippe; Chave, Jérôme; Schmeller, Dirk S.

    2015-01-01

    The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is a purported agent of decline and extinction of many amphibian populations worldwide. Its occurrence remains poorly documented in many tropical regions, including the Guiana Shield, despite the area’s high amphibian diversity. We conducted a comprehensive assessment of Bd in French Guiana in order to (1) determine its geographical distribution, (2) test variation of Bd prevalence among species in French Guiana and compare it to earlier reported values in other South American anuran species (http://www.bd-maps.net; 123 species from 15 genera) to define sentinel species for future work, (3) track changes in prevalence through time and (4) determine if Bd presence had a negative effect on one selected species. We tested the presence of Bd in 14 species at 11 sites for a total of 1053 samples (306 in 2009 and 747 in 2012). At least one Bd-positive individual was found at eight out of 11 sites, suggesting a wide distribution of Bd in French Guiana. The pathogen was not uniformly distributed among the studied amphibian hosts, with Dendrobatidae species displaying the highest prevalence (12.4%) as compared to Bufonidae (2.6 %) and Hylidae (1.5%). In contrast to earlier reported values, we found highest prevalence for three Dendrobatidae species and two of them displayed an increase in Bd prevalence from 2009 to 2012. Those three species might be the sentinel species of choice for French Guiana. For Dendrobates tinctorius, of key conservation value in the Guiana Shield, smaller female individuals were more likely to be infected, suggesting either that frogs can outgrow their chytrid infections or that the disease induces developmental stress limiting growth. Generally, our study supports the idea that Bd is more widespread than previously thought and occurs at remote places in the lowland forest of the Guiana shield. PMID:25902035

  4. Widespread occurrence of the tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1 and p712.

    PubMed

    Kim, Dong-Uk; Kim, Min-Sun; Lim, Jong-Sung; Ka, Jong-Ok

    2013-05-01

    Variovorax sp. strain DB1 and Pseudomonas pickettii strain 712 are 2,4-dicholorophenoxy-acetic acid (2,4-D)-degrading bacteria, which were isolated from agricultural soils in Republic of Korea and USA, respectively. Each strain harbors a 2,4-D degradative plasmid and is able to utilize 2,4-D as the sole source of carbon for its growth. The 2,4-D degradative plasmid pDB1 of strain DB1 consisted of a 65,269-bp circular molecule with a G+C content of 66.23% and had 68 ORFs. The 2,4-D degradative plasmid p712 of strain 712 was composed of a 62,798-bp circular molecule with a 62.11% G+C content and had 62 ORFs. The plasmids pDB1 and p712 share significantly homologous 2,4-D degradative genes with high similarity to the tfdR, tfdB-II, tfdC-II, tfdD-II, tfdE-II, tfdF-II, tfdK and tfdA genes of plasmid pJP4 of Alcaligenes eutrophus isolated from Australia. In a phylogenetic analysis with trfA, traL, and trbA genes, pDB1 belonged to IncP-1β with pJP4, while p712 belonged to IncP-1ε with pKJK5 and pEMT3. The results indicated that, in spite of the differences in their backbone regions, the 2,4-D catabolic genes of the two plasmids were closely related and also related to the well-known 2,4-D degradative plasmid pJP4 even though all were isolated from different geographic regions. Other similarities in the genetic organization and the presence of IS1071 suggested that these catabolic genes may be on a transposable element, leading to widespread occurrence in soil bacteria.

  5. Widespread occurrence of expressed fungal secretory peroxidases in forest soils.

    PubMed

    Kellner, Harald; Luis, Patricia; Pecyna, Marek J; Barbi, Florian; Kapturska, Danuta; Krüger, Dirk; Zak, Donald R; Marmeisse, Roland; Vandenbol, Micheline; Hofrichter, Martin

    2014-01-01

    Fungal secretory peroxidases mediate fundamental ecological functions in the conversion and degradation of plant biomass. Many of these enzymes have strong oxidizing activities towards aromatic compounds and are involved in the degradation of plant cell wall (lignin) and humus. They comprise three major groups: class II peroxidases (including lignin peroxidase, manganese peroxidase, versatile peroxidase and generic peroxidase), dye-decolorizing peroxidases, and heme-thiolate peroxidases (e.g. unspecific/aromatic peroxygenase, chloroperoxidase). Here, we have repeatedly observed a widespread expression of all major peroxidase groups in leaf and needle litter across a range of forest ecosystems (e.g. Fagus, Picea, Acer, Quercus, and Populus spp.), which are widespread in Europe and North America. Manganese peroxidases and unspecific peroxygenases were found expressed in all nine investigated forest sites, and dye-decolorizing peroxidases were observed in five of the nine sites, thereby indicating biological significance of these enzymes for fungal physiology and ecosystem processes. Transcripts of selected secretory peroxidase genes were also analyzed in pure cultures of several litter-decomposing species and other fungi. Using this information, we were able to match, in environmental litter samples, two manganese peroxidase sequences to Mycena galopus and Mycena epipterygia and one unspecific peroxygenase transcript to Mycena galopus, suggesting an important role of this litter- and coarse woody debris-dwelling genus in the disintegration and transformation of litter aromatics and organic matter formation.

  6. Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages

    PubMed Central

    Shulse, Christine N.; Allen, Eric E.

    2011-01-01

    Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. The genes responsible for de novo bacterial PUFA biosynthesis, designated pfaEABCD, encode large, multi-domain protein complexes akin to type I iterative fatty acid and polyketide synthases, herein referred to as “Pfa synthases”. In addition to the archetypal Pfa synthase gene products from marine bacteria, we have identified homologous type I FAS/PKS gene clusters in diverse microbial lineages spanning 45 genera representing 10 phyla, presumed to be involved in long-chain fatty acid biosynthesis. In total, 20 distinct types of gene clusters were identified. Collectively, we propose the designation of “secondary lipids” to describe these biosynthetic pathways and products, a proposition consistent with the “secondary metabolite” vernacular. Phylogenomic analysis reveals a high degree of functional conservation within distinct biosynthetic pathways. Incongruence between secondary lipid synthase functional clades and taxonomic group membership combined with the lack of orthologous gene clusters in closely related strains suggests horizontal gene transfer has contributed to the dissemination of specialized lipid biosynthetic activities across disparate microbial lineages. PMID:21629834

  7. Historic Mining and Agriculture as Indicators of Occurrence and Abundance of Widespread Invasive Plant Species.

    PubMed

    Calinger, Kellen; Calhoon, Elisabeth; Chang, Hsiao-Chi; Whitacre, James; Wenzel, John; Comita, Liza; Queenborough, Simon

    2015-01-01

    Anthropogenic disturbances often change ecological communities and provide opportunities for non-native species invasion. Understanding the impacts of disturbances on species invasion is therefore crucial for invasive species management. We used generalized linear mixed effects models to explore the influence of land-use history and distance to roads on the occurrence and abundance of two invasive plant species (Rosa multiflora and Berberis thunbergii) in a 900-ha deciduous forest in the eastern U.S.A., the Powdermill Nature Reserve. Although much of the reserve has been continuously forested since at least 1939, aerial photos revealed a variety of land-uses since then including agriculture, mining, logging, and development. By 2008, both R. multiflora and B. thunbergii were widespread throughout the reserve (occurring in 24% and 13% of 4417 10-m diameter regularly-placed vegetation plots, respectively) with occurrence and abundance of each varying significantly with land-use history. Rosa multiflora was more likely to occur in historically farmed, mined, logged or developed plots than in plots that remained forested, (log odds of 1.8 to 3.0); Berberis thunbergii was more likely to occur in plots with agricultural, mining, or logging history than in plots without disturbance (log odds of 1.4 to 2.1). Mining, logging, and agriculture increased the probability that R. multiflora had >10% cover while only past agriculture was related to cover of B. thunbergii. Proximity to roads was positively correlated with the occurrence of R. multiflora (a 0.26 increase in the log odds for every 1-m closer) but not B. thunbergii, and roads had no impact on the abundance of either species. Our results indicated that a wide variety of disturbances may aid the introduction of invasive species into new habitats, while high-impact disturbances such as agriculture and mining increase the likelihood of high abundance post-introduction.

  8. Widespread Occurrence of Benzotriazoles and Benzothiazoles in Tap Water: Influencing Factors and Contribution to Human Exposure.

    PubMed

    Wang, Lei; Zhang, Junjie; Sun, Hongwen; Zhou, Qixing

    2016-03-01

    Despite the frequent detection of benzotriazoles (BTRs) and benzothiazoles (BTHs) in groundwater and surface-water environments, knowledge on their occurrence and profile in tap water is still scarce. This study demonstrates widespread occurrence of these compounds in tap water from 51 major cities in China, which have ranges of

  9. Hybridization in the Cetacea: widespread occurrence and associated morphological, behavioral, and ecological factors.

    PubMed

    Crossman, Carla A; Taylor, Eric B; Barrett-Lennard, Lance G

    2016-03-01

    Hybridization has been documented in a many different pairs of cetacean species both in captivity and in the wild. The widespread occurrence of hybridization indicates that postmating barriers to interbreeding are incomplete within the order Cetacea, and therefore raises questions about how species integrity is maintained in the face of interspecific (and often intergeneric) gene flow. We examined hybridization across the order Cetacea (oceanic species included: N = 78; species with 44 chromosomes included: N = 52) to test for associations between the occurrence of hybridization and similarity across 13 ecological, morphological and behavioral traits in hybridizing vs. non-hybridizing species pairs. We found that species pairs that share a greater number of traits had a higher propensity to hybridize than pairs of species that did not. This trend was driven by behavioral and morphological traits such as vocalization frequency and body size. Together our findings suggest the importance of divergent selection on morphological and behavioral traits within sympatric species in constraining opportunities for hybridization and preventing the collapse of parental species.

  10. Widespread distribution of encapsulin nanocompartments reveals functional diversity.

    PubMed

    Giessen, Tobias W; Silver, Pamela A

    2017-03-06

    Cells organize and regulate their metabolism via membrane- or protein-bound organelles. In this way, incompatible processes can be spatially separated and controlled. In prokaryotes, protein-based compartments are used to sequester harmful reactions and store useful compounds. These protein compartments play key roles in various metabolic and ecological processes, ranging from iron homeostasis to carbon fixation. One of the newest types of protein organelle are encapsulin nanocompartments. They are able to encapsulate specific protein cargo and are proposed to be involved in redox-related processes. We identified more than 900 putative encapsulin systems in bacterial and archaeal genomes. Encapsulins can be found in fifteen bacterial and two archaeal phyla. Our analysis reveals one new capsid type and nine previously unknown cargo proteins targeted to the interior of encapsulins. We experimentally characterize three newly identified encapsulin systems and illustrate their probable involvement in iron mineralization, oxidative and nitrosative stress resistance and anaerobic ammonium oxidation, a process responsible for 30% of the nitrogen lost from the oceans.

  11. Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria.

    PubMed

    Wang, Hao; Fewer, David P; Sivonen, Kaarina

    2011-01-01

    Cyanobacteria are a rich source of natural products with interesting biological activities. Many of these are peptides and the end products of a non-ribosomal pathway. However, several cyanobacterial peptide classes were recently shown to be produced through the proteolytic cleavage and post-translational modification of short precursor peptides. A new class of bacteriocins produced through the proteolytic cleavage and heterocyclization of precursor proteins was recently identified from marine cyanobacteria. Here we show the widespread occurrence of bacteriocin gene clusters in cyanobacteria through comparative analysis of 58 cyanobacterial genomes. A total of 145 bacteriocin gene clusters were discovered through genome mining. These clusters encoded 290 putative bacteriocin precursors. They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide. The gene clusters could be classified into seven groups according to their gene organization and domain composition. This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups. Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.

  12. Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages

    PubMed Central

    Kaur, Inderjeet; Zeeshan, Mohammad; Saini, Ekta; Kaushik, Abhinav; Mohmmed, Asif; Gupta, Dinesh; Malhotra, Pawan

    2016-01-01

    Post-transcriptional and post-translational modifications play a major role in Plasmodium life cycle regulation. Lysine methylation of histone proteins is well documented in several organisms, however in recent years lysine methylation of proteins outside histone code is emerging out as an important post-translational modification (PTM). In the present study we have performed global analysis of lysine methylation of proteins in asexual blood stages of Plasmodium falciparum development. We immunoprecipitated stage specific Plasmodium lysates using anti-methyl lysine specific antibodies that immunostained the asexual blood stage parasites. Using liquid chromatography and tandem mass spectrometry analysis, 570 lysine methylated proteins at three different blood stages were identified. Analysis of the peptide sequences identified 605 methylated sites within 422 proteins. Functional classification of the methylated proteins revealed that the proteins are mainly involved in nucleotide metabolic processes, chromatin organization, transport, homeostatic processes and protein folding. The motif analysis of the methylated lysine peptides reveals novel motifs. Many of the identified lysine methylated proteins are also interacting partners/substrates of PfSET domain proteins as revealed by STRING database analysis. Our findings suggest that the protein methylation at lysine residues is widespread in Plasmodium and plays an important regulatory role in diverse set of the parasite pathways. PMID:27762281

  13. Widespread occurrence of small inversions in the chloroplast genomes of land plants.

    PubMed

    Kim, Ki-Joong; Lee, Hae-Lim

    2005-02-28

    Large inversions are well characterized in the chloroplast genomes of land plants. In contrast, reports of small inversions are rare and involve limited plant groups. In this study, we report the widespread occurrence of small inversions ranging from 5 to 50 bp in fully and partially sequenced chloroplast genomes of both monocots and dicots. We found that small inversions were much more common than large inversions. The small inversions were scattered over the chloroplast genome including the IR, SSC, and LSC regions. Several small inversions were uncovered in chloroplast genomes even though they shared the same overall gene order. The majority of these small inversions were located within 100 bp downstream of the 3' ends of genes. All had inverted repeat sequences, ranging from 11 to 24 bp, at their ends. Such small inversions form stem-loop hairpin structures that usually have the function of stabilizing the corresponding mRNA molecules. Intra-molecular recombination between the inverted sequences in the stem-forming regions are responsible for generating flip-flop orientations of the loops. The presence of two different orientations of the stem-loop in the trnL-F noncoding region of a single species of Jasminum elegans suggests that a short inversion can be generated within a short period of time. Small inversions of non-coding sequences may influence sequence alignment and character interpretation in phylogeny reconstructions, as shown in nine species of Jasminum. Many small inversions may have been generated by parallel or back mutation events during chloroplast genome evolution. Our data indicate that caution is needed when using chloroplast non-coding sequences for phylogenetic analysis.

  14. Widespread occurrence of neonicotinoid insecticides in streams in a high corn and soybean producing region, USA

    USGS Publications Warehouse

    Hladik, Michelle; Kolpin, Dana W.; Kuivila, Kathryn

    2014-01-01

    Neonicotinoid insecticides are of environmental concern, but little is known about their occurrence in surface water. An area of intense corn and soybean production in the Midwestern United States was chosen to study this issue because of the high agricultural use of neonicotinoids via both seed treatments and other forms of application. Water samples were collected from nine stream sites during the 2013 growing season. The results for the 79 water samples documented similar patterns among sites for both frequency of detection and concentration (maximum:median) with clothianidin (75%, 257 ng/L:8.2 ng/L) > thiamethoxam (47%, 185 ng/L: imidacloprid (23%, 42.7 ng/L: <2 ng/L). Neonicotinoids were detected at all nine sites sampled even though the basin areas spanned four orders of magnitude. Temporal patterns in concentrations reveal pulses of neonicotinoids associated with rainfall events during crop planting, suggesting seed treatments as their likely source.

  15. Widespread occurrence of a domestic dog mitochondrial DNA haplotype in southeastern US coyotes.

    PubMed

    Adams, J R; Leonard, J A; Waits, L P

    2003-02-01

    Sequence analysis of the mitochondrial DNA control region from 112 southeastern US coyotes (Canis latrans) revealed 12 individuals with a haplotype closely related to those in domestic dogs. Phylogenetic analyses grouped this new haplotype in the dog/grey wolf (Canis familiaris/Canis lupus) clade with 98% bootstrap support. These results demonstrate that a male coyote hybridized with a female dog, and female hybrid offspring successfully integrated into the coyote population. The widespread distribution of this haplotype from Florida to West Virginia suggests that the hybridization event occurred long ago before the southeastern USA was colonized by coyotes. However, it could have occurred in the southeastern USA before the main front of coyotes arrived in the area between male coyotes released for sport and a local domestic dog. The introgression of domestic dog genes into the southeastern coyote population does not appear to have substantially affected the coyote's genetic, morphological, or behavioural integrity. However, our results suggest that, contrary to previous reports, hybridization can occur between domestic and wild canids, even when the latter is relatively abundant. Therefore, hybridization may be a greater threat to the persistence of wild canid populations than previously thought.

  16. Widespread occurrence of neuro-active pharmaceuticals and metabolites in 24 Minnesota rivers and wastewaters

    USGS Publications Warehouse

    Writer, Jeffrey; Ferrer, Imma; Barber, Larry B.; Thurman, E. Michael

    2013-01-01

    Concentrations of 17 neuro-active pharmaceuticals and their major metabolites (bupropion, hydroxy-bupropion, erythro-hydrobupropion, threo-hydrobupropion, carbamazepine, 10,11,-dihydro-10,11,-dihydroxycarbamazepine, 10-hydroxy-carbamazepine, citalopram, N-desmethyl-citalopram, fluoxetine, norfluoxetine, gabapentin, lamotrigine, 2-N-glucuronide-lamotrigine, oxcarbazepine, venlafaxine and O-desmethyl-venlafaxine), were measured in treated wastewater and receiving surface waters from 24 locations across Minnesota, USA. The analysis of upstream and downstream sampling sites indicated that the wastewater treatment plants were the major source of the neuro-active pharmaceuticals and associated metabolites in surface waters of Minnesota. Concentrations of parent compound and the associated metabolite varied substantially between treatment plants (concentrations ± standard deviation of the parent compound relative to its major metabolite) as illustrated by the following examples; bupropion and hydrobupropion 700 ± 1000 ng L−1, 2100 ± 1700 ng L−1, carbamazepine and 10-hydroxy-carbamazepine 480 ± 380 ng L−1, 360 ± 400 ng L−1, venlafaxine and O-desmethyl-venlafaxine 1400 ± 1300 ng L−1, 1800 ± 2300 ng L−1. Metabolites of the neuro-active compounds were commonly found at higher or comparable concentrations to the parent compounds in wastewater effluent and the receiving surface water. Neuro-active pharmaceuticals and associated metabolites were detected only sporadically in samples upstream from the effluent outfall. Metabolite to parent ratios were used to evaluate transformation, and we determined that ratios in wastewater were much lower than those reported in urine, indicating that the metabolites are relatively more labile than the parent compounds in the treatment plants and in receiving waters. The widespread occurrence of neuro-active pharmaceuticals and metabolites in Minnesota effluents and surface waters indicate that

  17. Widespread occurrence of neonicotinoid insecticides in streams in a high corn and soybean producing region, USA.

    PubMed

    Hladik, Michelle L; Kolpin, Dana W; Kuivila, Kathryn M

    2014-10-01

    Neonicotinoid insecticides are of environmental concern, but little is known about their occurrence in surface water. An area of intense corn and soybean production in the Midwestern United States was chosen to study this issue because of the high agricultural use of neonicotinoids via both seed treatments and other forms of application. Water samples were collected from nine stream sites during the 2013 growing season. The results for the 79 water samples documented similar patterns among sites for both frequency of detection and concentration (maximum:median) with clothianidin (75%, 257 ng/L:8.2 ng/L) > thiamethoxam (47%, 185 ng/L:<2 ng/L) > imidacloprid (23%, 42.7 ng/L: <2 ng/L). Neonicotinoids were detected at all nine sites sampled even though the basin areas spanned four orders of magnitude. Temporal patterns in concentrations reveal pulses of neonicotinoids associated with rainfall events during crop planting, suggesting seed treatments as their likely source.

  18. Widespread Occurrence of Chemical Residues in Beehive Matrices from Apiaries Located in Different Landscapes of Western France

    PubMed Central

    Lambert, Olivier; Piroux, Mélanie; Puyo, Sophie; Thorin, Chantal; L'Hostis, Monique; Wiest, Laure; Buleté, Audrey; Delbac, Frédéric; Pouliquen, Hervé

    2013-01-01

    Background The honey bee, Apis mellifera, is frequently used as a sentinel to monitor environmental pollution. In parallel, general weakening and unprecedented colony losses have been reported in Europe and the USA, and many factors are suspected to play a central role in these problems, including infection by pathogens, nutritional stress and pesticide poisoning. Honey bee, honey and pollen samples collected from eighteen apiaries of western France from four different landscape contexts during four different periods in 2008 and in 2009 were analyzed to evaluate the presence of pesticides and veterinary drug residues. Methodology/Findings A multi-residue analysis of 80 compounds was performed using a modified QuEChERS method, followed by GC-ToF and LC−MS/MS. The analysis revealed that 95.7%, 72.3% and 58.6% of the honey, honey bee and pollen samples, respectively, were contaminated by at least one compound. The frequency of detection was higher in the honey samples (n = 28) than in the pollen (n = 23) or honey bee (n = 20) samples, but the highest concentrations were found in pollen. Although most compounds were rarely found, some of the contaminants reached high concentrations that might lead to adverse effects on bee health. The three most frequent residues were the widely used fungicide carbendazim and two acaricides, amitraz and coumaphos, that are used by beekeepers to control Varroa destructor. Apiaries in rural-cultivated landscapes were more contaminated than those in other landscape contexts, but the differences were not significant. The contamination of the different matrices was shown to be higher in early spring than in all other periods. Conclusions/Significance Honey bees, honeys and pollens are appropriate sentinels for monitoring pesticide and veterinary drug environmental pollution. This study revealed the widespread occurrence of multiple residues in beehive matrices and suggests a potential issue with the effects of these residues

  19. On the occurrence of a widespread contamination by herbicides of coral reef biota in French Polynesia.

    PubMed

    Salvat, Bernard; Roche, Hélène; Ramade, François

    2016-01-01

    Research has been conducted within the framework of the French Initiative for Coral Reefs (IFRECOR) to assess pesticide pollution levels in the coral reef trophic webs in French Polynesia. Unexpected widespread contamination by herbicides was found in algae, fishes and macro-invertebrates located at various levels of the reef trophic web. Concentrations in organisms investigated were for the majority below the lowest observable effect level and do not pose a dietary risk to native population who subsist on these fish. However, the widespread contamination may affect the reef ecosystem in the future as coral symbiotic algae, Symbidinium sp. (Dinophyta) are particularly sensitive to photosystem II herbicides, particularly the substituted urea and triazine derivatives.

  20. Widespread occurrence of bacterial thiol methyltransferases and the biogenic emission of methylated sulfur gases

    SciTech Connect

    Drotar, A.; Burton, G.A. Jr.; Tavernier, J.E.; Fall, R.

    1987-07-01

    A majority of heterotrophic bacteria isolated from soil, water, sediment, vegetation, and marine algae cultures methylated sulfide, producing methanethiol. This was demonstrated (i) with intact cells by measuring the emission of methanethiol with a sulfur-selective chemiluminescence detector, and (ii) in cell extracts by detection of sulfide-dependent thiol methyltransferase activity. Extracts of two Pseudomonas isolates were fractionated by gel-filtration and ion-exchange chromatography, and with sulfide as the substrate a single peak of thiol methyltransferase activity was seen in each case. Extracts of several bacterial strains also contained thiol methyltransferase activity with organic thiols as substrates. Thus, S-adenosylmethionine-dependent thiol methyltransferase activities are widespread in bacteria and may contribute to biogenic emissions of methylated sulfur gases and to the production of methyl thioethers.

  1. Widespread occurrence of bacterial thiol methyltransferases and the biogenic emission of methylated sulfur gases.

    PubMed Central

    Drotar, A; Burton, G A; Tavernier, J E; Fall, R

    1987-01-01

    A majority of heterotrophic bacteria isolated from soil, water, sediment, vegetation, and marine algae cultures methylated sulfide, producing methanethiol. This was demonstrated with intact cells by measuring the emission of methanethiol with a sulfur-selective chemiluminescence detector, and in cell extracts by detection of sulfide-dependent thiol methyltransferase activity. Extracts of two Pseudomonas isolates were fractionated by gel-filtration and ion-exchange chromatography, and with sulfide as the substrate a single peak of thiol methyltransferase activity was seen in each case. Extracts of several bacterial strains also contained thiol methyltransferase activity with organic thiols as substrates. Thus, S-adenosylmethionine-dependent thiol methyltransferase activities are widespread in bacteria and may contribute to biogenic emissions of methylated sulfur gases and to the production of methyl thioethers. PMID:3662509

  2. Widespread occurrence of the chytrid fungus batrachochytrium dendrobatidis on oregon spotted frogs (rana pretiosa)

    USGS Publications Warehouse

    Pearl, C.A.; Bowerman, J.; Adams, M.J.; Chelgren, N.D.

    2009-01-01

    The pathogen Batrachochytrium dendrobatidis (Bd) has been associated with amphibian declines in multiple continents, including western North America. We investigated Bd prevalence in Oregon spotted frog (Rana pretiosa), a species that has declined across its range in the Pacific Northwest. Polymerase chain reaction analysis of skin swabs indicated that Bd was prevalent within populations (420 of 617 juvenile and adults) and widespread among populations (36 of 36 sites) where we sampled R. pretiosa in Oregon and Washington. We rarely detected Bd in R. pretiosa larvae (2 of 72). Prevalence of Bd in postmetamorphic R. pretiosa was inversely related to frog size. We found support for an interactive effect of elevation and sampling date on Bd: prevalence of Bd generally increased with date, but this effect was more pronounced at lower elevations. We also found evidence that the body condition of juvenile R. pretiosa with Bd decreased after their first winter. Our data indicate that some Oregon spotted frog populations are currently persisting with relatively high Bd prevalence, but the risk posed by Bd is unknown. ?? 2010 International Association for Ecology and Health.

  3. Widespread occurrence of an intranuclear bacterial parasite in vent and seep bathymodiolin mussels.

    PubMed

    Zielinski, Frank U; Pernthaler, Annelie; Duperron, Sébastien; Raggi, Luciana; Giere, Olav; Borowski, Christian; Dubilier, Nicole

    2009-05-01

    originated from intranuclear bacteria, and that these are widespread in marine invertebrates.

  4. Widespread Magnetofossil Occurrences in Deep-sea Sediments and Implications for Paleo- and Environmental Magnetism (Invited)

    NASA Astrophysics Data System (ADS)

    Yamazaki, T.; Roberts, A. P.

    2013-12-01

    Recent progress in rock magnetism has enabled quantitative estimation of magnetizations carried by magnetofossils. Using FORC diagrams, IRM component analyses, ferromagnetic resonance spectroscopy, low-temperature magnetometry, and transmission electron microscopy, it has been found that magnetofossils are widespread in deep-sea sediments and are often a dominant constituent of magnetic mineral assemblages. Some studies have documented a relationship between increased magnetofossil abundances and enhanced oceanic productivity induced by iron fertilization via eolian dust. The morphology of magnetosomes, which is species specific, may reflect a preference of magnetotactic bacteria for particular redox conditions. Dominant magnetofossil morphologies in sediments (cubo-octahedral vs. elongated) can be detected with rock magnetic techniques. Thus, magnetofossil abundance and morphology have considerable potential as paleoenvironmental indicators. It is widely held that magnetotactic bacteria live at or below the oxic-anoxic transition zone (OATZ) in chemically stratified aquatic environments. If so, it is expected that sediments that contain magnetofossils would have acquired their remanent magnetization at around the OATZ, and that the magnetization carried by magnetofossils will be delayed with respect to a pDRM carried by detrital magnetic minerals if the OATZ lies below the surface mixed layer and the pDRM acquisition zone. However, magnetofossils often dominate the magnetic mineral assemblage even in marine red clays that lack an OATZ. Changes in the relative abundance of biogenic and detrital magnetic components can be estimated from the ratio of ARM susceptibility to SIRM; a smaller average magnetic grain size and weaker magnetostatic interactions in the biogenic component causes higher ARM susceptibility. In relative paleointensity estimations, the kARM/SIRM ratio sometimes anti-correlates with normalized intensity regardless of the choice of normalizer (ARM or

  5. Widespread occurrence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in the southeastern USA

    USGS Publications Warehouse

    Rothermel, B.B.; Walls, S.C.; Mitchell, J.C.; Dodd, C.K.; Irwin, L.K.; Green, D.E.; Vazquez, Victoria M.; Petranka, James W.; Stevenson, Dirk J.

    2008-01-01

    From 1999 to 2006, we sampled >1200 amphibians for the fungal pathogen Batrachochytnum dendrobatidis (Bd) at 30 sites in the southeastern USA. Using histological techniques or PCR assays, we detected chytrid infection in 10 species of aquatic-breeding amphibians in 6 states. The prevalence of chytrid infection was 17.8% for samples of postmetamorphic amphibians examined using skin swab-PCR assays (n = 202 samples from 12 species at 4 sites). In this subset of samples, anurans had a much higher prevalence of infection than caudates (39.2% vs. 5.5%, respectively). Mean prevalence in ranid frogs was 40.7 %. The only infected salamanders were Notophthalmus viridescens at 3 sites. We found infected amphibians from late winter through late spring and in 1 autumn sample. Although we encountered moribund or dead amphibians at 9 sites, most mortality events were not attributed to Bd. Chytridiomycosis was established as the probable cause of illness or death in fewer than 10 individuals. Our observations suggest a pattern of widespread and subclinical infections. However, because most of the sites in our study were visited only once, we cannot dismiss the possibility that chytridiomycosis is adversely affecting some populations. Furthermore, although there is no evidence of chytrid-associated declines in our region, the presence of this pathogen is cause for concern given global climate change and other stressors. Although presence-absence surveys may still be needed for some taxa, such as bufonids, we recommend that future researchers focus on potential population-level effects at sites where Bd is now known to occur. ?? Inter-Research 2008.

  6. Widespread occurrence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in the southeastern USA

    USGS Publications Warehouse

    Rothermel, Betsie B.; Walls, Susan C.; Mitchell, Joseph C.; Dodd, C. Kenneth; Irwin, Lisa K.; Green, David E.; Vazquez, Victoria M.; Petranka, James W.; Stevenson, Dirk J.

    2008-01-01

     From 1999 to 2006, we sampled >1200 amphibians for the fungal pathogen Batrachochytrium dendrobatidis(Bd) at 30 sites in the southeastern USA. Using histological techniques or PCR assays, we detected chytrid infection in 10 species of aquatic-breeding amphibians in 6 states. The prevalence of chytrid infection was 17.8% for samples of postmetamorphic amphibians examined using skin swab-PCR assays (n = 202 samples from 12 species at 4 sites). In this subset of samples, anurans had a much higher prevalence of infection than caudates (39.2% vs. 5.5%, respectively). Mean prevalence in ranid frogs was 40.7%. The only infected salamanders were Notophthalmus viridescens at 3 sites. We found infected amphibians from late winter through late spring and in 1 autumn sample. Although we encountered moribund or dead amphibians at 9 sites, most mortality events were not attributed to Bd. Chytridiomycosis was established as the probable cause of illness or death in fewer than 10 individuals. Our observations suggest a pattern of widespread and subclinical infections. However, because most of the sites in our study were visited only once, we cannot dismiss the possibility that chytridiomycosis is adversely affecting some populations. Furthermore, although there is no evidence of chytrid-associated declines in our region, the presence of this pathogen is cause for concern given global climate change and other stressors. Although presence-absence surveys may still be needed for some taxa, such as bufonids, we recommend that future researchers focus on potential population-level effects at sites where Bd is now known to occur.

  7. Widespread, routine occurrence of pharmaceuticals in sewage effluent, combined sewer overflows and receiving waters.

    PubMed

    Kay, Paul; Hughes, Stephen R; Ault, James R; Ashcroft, Alison E; Brown, Lee E

    2017-01-01

    Research addressing the occurrence, fate and effects of pharmaceuticals in the aquatic environment has expanded rapidly over the past two decades, primarily due to the development of improved chemical analysis methods. Significant research gaps still remain, however, including a lack of longer term, repeated monitoring of rivers, determination of temporal and spatial changes in pharmaceutical concentrations, and inputs from sources other than wastewater treatment plants (WWTPs), such as combined sewer overflows (CSOs). In addressing these gaps it was found that the five pharmaceuticals studied were routinely (51-94% of the time) present in effluents and receiving waters at concentrations ranging from single ng to μg L(-1). Mean concentrations were in the tens to hundreds ng L(-1) range and CSOs appear to be a significant source of pharmaceuticals to water courses in addition to WWTPs. Receiving water concentrations varied throughout the day although there were no pronounced peaks at particular times. Similarly, concentrations varied throughout the year although no consistent patterns were observed. No dissipation of the study compounds was found over a 5 km length of river despite no other known inputs to the river. In conclusion, pharmaceuticals are routinely present in semi-rural and urban rivers and require management alongside more traditional pollutants.

  8. Widespread occurrence of diverse human pathogenic types of the fungus Fusarium detected in plumbing drains.

    PubMed

    Short, Dylan P G; O'Donnell, Kerry; Zhang, Ning; Juba, Jean H; Geiser, David M

    2011-12-01

    It has been proposed that plumbing systems might serve as a significant environmental reservoir of human-pathogenic isolates of Fusarium. We tested this hypothesis by performing the first extensive multilocus sequence typing (MLST) survey of plumbing drain-associated Fusarium isolates and comparing the diversity observed to the known diversity of clinical Fusarium isolates. We sampled 471 drains, mostly in bathroom sinks, from 131 buildings in the United States using a swabbing method. We found that 66% of sinks and 80% of buildings surveyed yielded at least one Fusarium culture. A total of 297 isolates of Fusarium collected were subjected to MLST to identify the phylogenetic species and sequence types (STs) of these isolates. Our survey revealed that the six most common STs in sinks were identical to the six most frequently associated with human infections. We speculate that the most prevalent STs, by virtue of their ability to form and grow in biofilms, are well adapted to plumbing systems. Six major Fusarium STs were frequently isolated from plumbing drains within a broad geographic area and were identical to STs frequently associated with human infections.

  9. Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules

    PubMed Central

    Valach, Matus; Burger, Gertraud; Gray, Michael W.; Lang, B. Franz

    2014-01-01

    5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator. PMID:25429974

  10. High resolution metabolomics technology reveals widespread pathway changes of alcoholic liver disease.

    PubMed

    Zhang, Aihua; Yan, Guangli; Zhou, Xiaohang; Wang, Yangyang; Han, Ying; Guan, Yu; Sun, Hui; Wang, Xijun

    2016-01-01

    Alcoholic liver disease (ALD) is a significant cause of death and morbidity. However little is known regarding the widespread pathway changes of ALD disorder. This study utilized metabolomic profiling to examine the pathogenic mechanisms of ALD based on a rat model. A total of 21 metabolites with significant changes were identified, involving several key metabolic pathways such as pentose and glucuronate interconversions, starch and sucrose metabolism, cysteine and methionine metabolism. Furthermore, the differential proteins corresponding to alterations in metabolism across the metabolic network were identified using iTRAQ-based quantitative proteomics analysis. The proteins appear to be involved in protein binding, metabolism, immune response, and signal conduction. Interestingly, integrated omics profiling firstly reveals that p53 and Fc epsilon RI signaling pathways were closely related to ALD. Our study indicates that most of these proteins were found to play a pivotal role in the regulation of multiple metabolism pathways. Collectively, the current study provides insights into the molecular mechanisms of ALD from widespread pathway changes.

  11. Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription

    PubMed Central

    Poole, Rebecca L; Barker, Gary LA; Werner, Kay; Biggi, Gaia F; Coghill, Jane; Gibbings, J George; Berry, Simon; Dunwell, Jim M; Edwards, Keith J

    2008-01-01

    gene expression. Conclusion Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development. PMID:18847483

  12. Widespread Occurrence of Batrachochytrium dendrobatidis in Contemporary and Historical Samples of the Endangered Bombina pachypus along the Italian Peninsula

    PubMed Central

    Canestrelli, Daniele; Zampiglia, Mauro; Nascetti, Giuseppe

    2013-01-01

    Batrachochytrium dendrobatidis is considered a main driver of the worldwide declines and extinctions of amphibian populations. Nonetheless, fundamental questions about its epidemiology, including whether it acts mainly as a “lone killer” or in conjunction with other factors, remain largely open. In this paper we analysed contemporary and historical samples of the endangered Apennine yellow-bellied toad (Bombina pachypus) along the Italian peninsula, in order to assess the presence of the pathogen and its spreading dynamics. Once common throughout its range, B. pachypus started to decline after the mid-1990s in the northern and central regions, whereas no declines have been observed so far in the southern region. We show that Batrachochytrium dendrobatidis is currently widespread along the entire peninsula, and that this was already so at least as early as the late 1970s, that is, well before the beginning of the observed declines. This temporal mismatch between pathogen occurrence and host decline, as well as the spatial pattern of the declines, suggests that the pathogen has not acted as a “lone killer”, but in conjunction with other factors. Among the potentially interacting factors, we identified two as the most probable, genetic diversity of host populations and recent climate changes. We discuss the plausibility of this scenario and its implications on the conservation of B. pachypus populations. PMID:23667603

  13. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting

    PubMed Central

    Court, Franck; Martin-Trujillo, Alex; Tayama, Chiharu; Kondova, Ivanela; Bontrop, Ronald; Poo-Llanillo, Maria Eugenia; Nakabayashi, Kazuhiko; Simón, Carlos; Monk, David

    2016-01-01

    Thousands of regions in gametes have opposing methylation profiles that are largely resolved during the post-fertilization epigenetic reprogramming. However some specific sequences associated with imprinted loci survive this demethylation process. Here we present the data describing the fate of germline-derived methylation in humans. With the exception of a few known paternally methylated germline differentially methylated regions (DMRs) associated with known imprinted domains, we demonstrate that sperm-derived methylation is reprogrammed by the blastocyst stage of development. In contrast a large number of oocyte-derived methylation differences survive to the blastocyst stage and uniquely persist as transiently methylated DMRs only in the placenta. Furthermore, we demonstrate that this phenomenon is exclusive to primates, since no placenta-specific maternal methylation was observed in mouse. Utilizing single cell RNA-seq datasets from human preimplantation embryos we show that following embryonic genome activation the maternally methylated transient DMRs can orchestrate imprinted expression. However despite showing widespread imprinted expression of genes in placenta, allele-specific transcriptional profiling revealed that not all placenta-specific DMRs coordinate imprinted expression and that this maternal methylation may be absent in a minority of samples, suggestive of polymorphic imprinted methylation. PMID:27835649

  14. Phylogeography of the widespread African puff adder (Bitis arietans) reveals multiple Pleistocene refugia in southern Africa.

    PubMed

    Barlow, Axel; Baker, Karis; Hendry, Catriona R; Peppin, Lindsay; Phelps, Tony; Tolley, Krystal A; Wüster, Catharine E; Wüster, Wolfgang

    2013-02-01

    Evidence from numerous Pan-African savannah mammals indicates that open-habitat refugia existed in Africa during the Pleistocene, isolated by expanding tropical forests during warm and humid interglacial periods. However, comparative data from other taxonomic groups are currently lacking. We present a phylogeographic investigation of the African puff adder (Bitis arietans), a snake that occurs in open-habitat formations throughout sub-Saharan Africa. Multiple parapatric mitochondrial clades occur across the current distribution of B. arietans, including a widespread southern African clade that is subdivided into four separate clades. We investigated the historical processes responsible for generating these phylogeographic patterns in southern Africa using species distribution modelling and genetic approaches. Our results show that interior regions of South Africa became largely inhospitable for B. arietans during glacial maxima, whereas coastal and more northerly areas remained habitable. This corresponds well with the locations of refugia inferred from mitochondrial data using a continuous phylogeographic diffusion model. Analysis of data from five anonymous nuclear loci revealed broadly similar patterns to mtDNA. Secondary admixture was detected between previously isolated refugial populations. In some cases, this is limited to individuals occurring near mitochondrial clade contact zones, but in other cases, more extensive admixture is evident. Overall, our study reveals a complex history of refugial isolation and secondary expansion for puff adders and a mosaic of isolated refugia in southern Africa. We also identify key differences between the processes that drove isolation in B. arietans and those hypothesized for sympatric savannah mammals.

  15. On the relation between fluvio-deltaic flood basin geomorphology and the wide-spread occurrence of arsenic pollution in shallow aquifers.

    PubMed

    Donselaar, Marinus E; Bhatt, Ajay G; Ghosh, Ashok K

    2017-01-01

    Pollution of groundwater with natural (geogenic) arsenic occurs on an enormous, world-wide scale, and causes wide-spread, serious health risks for an estimated more than hundred million people who depend on the use of shallow aquifers for drinking and irrigation water. A literature review of key studies on arsenic concentration levels yields that Holocene fluvial and deltaic flood basins are the hotspots of arsenic pollution, and that the dominant geomorphological setting of the arsenic-polluted areas consists of shallow-depth meandering-river deposits with sand-prone fluvial point-bar deposits surrounded by clay-filled (clay plug) abandoned meander bends (oxbow lakes). Analysis of the lithofacies distribution and related permeability contrasts of the geomorphological elements in two cored wells in a point bar and adjacent clay plug along the Ganges River, in combination with data of arsenic concentrations and organic matter content reveals that the low-permeable clay-plug deposits have a high organic matter content and the adjacent permeable point-bar sands show high but spatially very variable arsenic concentrations. On the basis of the geomorphological juxtaposition, the analysis of fluvial depositional processes and lithofacies characteristics, inherent permeability distribution and the omnipresence of the two geomorphological elements in Holocene flood basins around the world, a generic model is presented for the wide-spread arsenic occurrence. The anoxic deeper part (hypolimnion) of the oxbow lake, and the clay plugs are identified as the loci of reactive organic carbon and microbial respiration in an anoxic environment that triggers the reductive dissolution of iron oxy-hydroxides and the release of arsenic on the scale of entire fluvial floodplains and deltaic basins. The adjacent permeable point-bar sands are identified as the effective trap for the dissolved arsenic, and the internal permeability heterogeneity is the cause for aquifer compartmentalization

  16. Tracing the origins of rescued chimpanzees reveals widespread chimpanzee hunting in Cameroon

    PubMed Central

    2010-01-01

    Background While wild chimpanzees are experiencing drastic population declines, their numbers at African rescue and rehabilitation projects are growing rapidly. Chimpanzees follow complex routes to these refuges; and their geographic origins are often unclear. Identifying areas where hunting occurs can help law enforcement authorities focus scarce resources for wildlife protection planning. Efficiently focusing these resources is particularly important in Cameroon because this country is a key transportation waypoint for international wildlife crime syndicates. Furthermore, Cameroon is home to two chimpanzee subspecies, which makes ascertaining the origins of these chimpanzees important for reintroduction planning and for scientific investigations involving these chimpanzees. Results We estimated geographic origins of 46 chimpanzees from the Limbe Wildlife Centre (LWC) in Cameroon. Using Bayesian approximation methods, we determined their origins using mtDNA sequences and microsatellite (STRP) genotypes compared to a spatial map of georeferenced chimpanzee samples from 10 locations spanning Cameroon and Nigeria. The LWC chimpanzees come from multiple regions of Cameroon or forested areas straddling the Cameroon-Nigeria border. The LWC chimpanzees were partitioned further as originating from one of three biogeographically important zones occurring in Cameroon, but we were unable to refine these origin estimates to more specific areas within these three zones. Conclusions Our findings suggest that chimpanzee hunting is widespread across Cameroon. Live animal smuggling appears to occur locally within Cameroon, despite the existence of local wildlife cartels that operate internationally. This pattern varies from the illegal wildlife trade patterns observed in other commercially valuable species, such as elephants, where specific populations are targeted for exploitation. A broader sample of rescued chimpanzees compared against a more comprehensive grid of georeferenced

  17. Single-molecule analysis reveals widespread structural variation in multiple myeloma

    PubMed Central

    Gupta, Aditya; Place, Michael; Goldstein, Steven; Sarkar, Deepayan; Zhou, Shiguo; Potamousis, Konstantinos; Kim, Jaehyup; Flanagan, Claire; Li, Yang; Newton, Michael A.; Callander, Natalie S.; Hematti, Peiman; Bresnick, Emery H.; Ma, Jian; Asimakopoulos, Fotis; Schwartz, David C.

    2015-01-01

    Multiple myeloma (MM), a malignancy of plasma cells, is characterized by widespread genomic heterogeneity and, consequently, differences in disease progression and drug response. Although recent large-scale sequencing studies have greatly improved our understanding of MM genomes, our knowledge about genomic structural variation in MM is attenuated due to the limitations of commonly used sequencing approaches. In this study, we present the application of optical mapping, a single-molecule, whole-genome analysis system, to discover new structural variants in a primary MM genome. Through our analysis, we have identified and characterized widespread structural variation in this tumor genome. Additionally, we describe our efforts toward comprehensive characterization of genome structure and variation by integrating our findings from optical mapping with those from DNA sequencing-based genomic analysis. Finally, by studying this MM genome at two time points during tumor progression, we have demonstrated an increase in mutational burden with tumor progression at all length scales of variation. PMID:26056298

  18. Widespread dissemination of class 1 integron components in soils and related ecosystems as revealed by cultivation-independent analysis

    PubMed Central

    Jechalke, Sven; Schreiter, Susanne; Wolters, Birgit; Dealtry, Simone; Heuer, Holger; Smalla, Kornelia

    2014-01-01

    Class 1 integrons contribute to the emerging problem of antibiotic resistance in human medicine by acquisition, exchange, and expression of resistance genes embedded within gene cassettes. Besides the clinical setting they were recently reported from environmental habitats and often located on plasmids and transposons, facilitating their transfer and spread within bacterial communities. In this study we aimed to provide insights into the occurrence of genes typically associated with the class 1 integrons in previously not studied environments with or without human impact and their association with IncP-1 plasmids. Total community DNA was extracted from manure-treated and untreated soils, lettuce and potato rhizosphere, digestates, and an on-farm biopurification system and screened by PCR with subsequent Southern blot hybridization for the presence of the class 1 integrase gene intI1 as well as qacE and qacEΔ 1 resistance genes. The results revealed a widespread dissemination of class 1 integrons in the environments analyzed, mainly related to the presence of qacEΔ 1 genes. All 28 IncP-1ε plasmids carrying class 1 integrons, which were captured exogenously in a recent study from piggery manure and soils treated with manure, carried qacEΔ 1 genes. Based on the strong hybridization signals in the rhizosphere of lettuce compared to the potato rhizosphere, the abundances of intI1, qacE/qacEΔ 1, and sul1 genes were quantified relative to the 16S rRNA gene abundance by real-time PCR in the rhizosphere of lettuce planted in three different soils and in the corresponding bulk soil. A significant enrichment of intI1 and qacE/qacEΔ 1 genes was confirmed in the rhizosphere of lettuce compared to bulk soil. Additionally, the relative abundance of korB genes specific for IncP-1 plasmids was enriched in the rhizosphere and correlated to the intI1 gene abundance indicating that IncP-1 plasmids might have contributed to the spread of class 1 integrons in the analyzed soils

  19. Magnetoencephalography Reveals a Widespread Increase in Network Connectivity in Idiopathic/Genetic Generalized Epilepsy

    PubMed Central

    Elshahabi, Adham; Klamer, Silke; Sahib, Ashish Kaul; Lerche, Holger; Braun, Christoph; Focke, Niels K.

    2015-01-01

    Idiopathic/genetic generalized epilepsy (IGE/GGE) is characterized by seizures, which start and rapidly engage widely distributed networks, and result in symptoms such as absences, generalized myoclonic and primary generalized tonic-clonic seizures. Although routine magnetic resonance imaging is apparently normal, many studies have reported structural alterations in IGE/GGE patients using diffusion tensor imaging and voxel-based morphometry. Changes have also been reported in functional networks during generalized spike wave discharges. However, network function in the resting-state without epileptiforme discharges has been less well studied. We hypothesize that resting-state networks are more representative of the underlying pathophysiology and abnormal network synchrony. We studied functional network connectivity derived from whole-brain magnetoencephalography recordings in thirteen IGE/GGE and nineteen healthy controls. Using graph theoretical network analysis, we found a widespread increase in connectivity in patients compared to controls. These changes were most pronounced in the motor network, the mesio-frontal and temporal cortex. We did not, however, find any significant difference between the normalized clustering coefficients, indicating preserved gross network architecture. Our findings suggest that increased resting state connectivity could be an important factor for seizure spread and/or generation in IGE/GGE, and could serve as a biomarker for the disease. PMID:26368933

  20. Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing

    PubMed Central

    Chadani, Yuhei; Niwa, Tatsuya; Chiba, Shinobu; Taguchi, Hideki; Ito, Koreaki

    2016-01-01

    Although the importance of the nonuniform progression of elongation in translation is well recognized, there have been few attempts to explore this process by directly profiling nascent polypeptides, the relevant intermediates of translation. Such approaches will be essential to complement other approaches, including ribosome profiling, which is extremely powerful but indirect with respect to the actual translation processes. Here, we use the nascent polypeptide's chemical trait of having a covalently attached tRNA moiety to detect translation intermediates. In a case study, Escherichia coli SecA was shown to undergo nascent polypeptide-dependent translational pauses. We then carried out integrated in vivo and in vitro nascent chain profiling (iNP) to characterize 1,038 proteome members of E. coli that were encoded by the first quarter of the chromosome with respect to their propensities to accumulate polypeptidyl–tRNA intermediates. A majority of them indeed undergo single or multiple pauses, some occurring only in vitro, some occurring only in vivo, and some occurring both in vivo and in vitro. Thus, translational pausing can be intrinsically robust, subject to in vivo alleviation, or require in vivo reinforcement. Cytosolic and membrane proteins tend to experience different classes of pauses; membrane proteins often pause multiple times in vivo. We also note that the solubility of cytosolic proteins correlates with certain categories of pausing. Translational pausing is widespread and diverse in nature. PMID:26831095

  1. Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations

    PubMed Central

    Chateigner, Aurélien; Bézier, Annie; Labrousse, Carole; Jiolle, Davy; Barbe, Valérie; Herniou, Elisabeth A.

    2015-01-01

    Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%). K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs). Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential. PMID:26198241

  2. Metabolite mapping reveals severe widespread perturbation of multiple metabolic processes in Huntington's disease human brain.

    PubMed

    Patassini, Stefano; Begley, Paul; Xu, Jingshu; Church, Stephanie J; Reid, Suzanne J; Kim, Eric H; Curtis, Maurice A; Dragunow, Mike; Waldvogel, Henry J; Snell, Russell G; Unwin, Richard D; Faull, Richard L M; Cooper, Garth J S

    2016-09-01

    Huntington's disease (HD) is a genetically-mediated neurodegenerative disorder wherein the aetiological defect is a mutation in the Huntington's gene (HTT), which alters the structure of the huntingtin protein (Htt) through lengthening of its polyglutamine tract, thus initiating a cascade that ultimately leads to premature death. However, neurodegeneration typically manifests in HD only in middle age, and mechanisms linking the causative mutation to brain disease are poorly understood. Brain metabolism is severely perturbed in HD, and some studies have indicated a potential role for mutant Htt as a driver of these metabolic aberrations. Here, our objective was to determine the effects of HD on brain metabolism by measuring levels of polar metabolites in regions known to undergo varying degrees of damage. We performed gas-chromatography/mass spectrometry-based metabolomic analyses in a case-control study of eleven brain regions in short post-mortem-delay human tissue from nine well-characterized HD patients and nine matched controls. In each patient, we measured metabolite content in representative tissue-samples from eleven brain regions that display varying degrees of damage in HD, thus identifying the presence and abundance of 63 different metabolites from several molecular classes, including carbohydrates, amino acids, nucleosides, and neurotransmitters. Robust alterations in regional brain-metabolite abundances were observed in HD patients: these included changes in levels of small molecules that play important roles as intermediates in the tricarboxylic-acid and urea cycles, and amino-acid metabolism. Our findings point to widespread disruption of brain metabolism and indicate a complex phenotype beyond the gradient of neuropathologic damage observed in HD brain.

  3. Spinocerebellar ataxia type 4 (SCA4): Initial pathoanatomical study reveals widespread cerebellar and brainstem degeneration.

    PubMed

    Hellenbroich, Y; Gierga, K; Reusche, E; Schwinger, E; Deller, T; de Vos, R A I; Zühlke, C; Rüb, U

    2006-07-01

    Spinocerebellar ataxia type 4 (SCA4), also known as 'hereditary ataxia with sensory neuropathy', represents a very rare, progressive and untreatable form of an autosomal dominant inherited cerebellar ataxia (ADCA). Due to a lack of autopsy cases, no neuropathological or clinicopathological studies had yet been performed in SCA4. In the present study, the first available cerebellar and brainstem tissue of a clinically diagnosed and genetically-confirmed German SCA4 patient was pathoanatomically studied using serial thick sections. During this systematic postmortem investigation, along with an obvious demyelinization of cerebellar and brainstem fiber tracts we observed widespread cerebellar and brainstem neurodegeneration with marked neuronal loss in the substantia nigra and ventral tegmental area, central raphe and pontine nuclei, all auditory brainstem nuclei, in the abducens, principal trigeminal, spinal trigeminal, facial, superior vestibular, medial vestibular, interstitial vestibular, dorsal motor vagal, hypoglossal, and prepositus hypoglossal nuclei, as well as in the nucleus raphe interpositus, all dorsal column nuclei, and in the principal and medial subnuclei of the inferior olive. Severe neuronal loss was seen in the Purkinje cell layer of the cerebellum, in the cerebellar fastigial nucleus, in the red, trochlear, lateral vestibular, and lateral reticular nuclei, the reticulotegmental nucleus of the pons, and the nucleus of Roller. In addition, immunocytochemical analysis using the anti-polyglutamine antibody 1C2 failed to detect any polyglutamine-related immunoreactivity in the central nervous regions of this SCA4 patient studied. In view of the known functional role of affected nuclei and related fiber tracts, the present findings not only offer explanations for the well-known disease symptoms of SCA4 patients (i.e. ataxic symptoms, dysarthria and somatosensory deficits), but for the first time help to explain why diplopia, gaze-evoked nystagmus

  4. Stable carbon isotope analysis reveals widespread drought stress in boreal black spruce forests.

    PubMed

    Walker, Xanthe J; Mack, Michelle C; Johnstone, Jill F

    2015-08-01

    Unprecedented rates of climate warming over the past century have resulted in increased forest stress and mortality worldwide. Decreased tree growth in association with increasing temperatures is generally accepted as a signal of temperature-induced drought stress. However, variations in tree growth alone do not reveal the physiological mechanisms behind recent changes in tree growth. Examining stable carbon isotope composition of tree rings in addition to tree growth can provide a secondary line of evidence for physiological drought stress. In this study, we examined patterns of black spruce growth and carbon isotopic composition in tree rings in response to climate warming and drying in the boreal forest of interior Alaska. We examined trees at three nested scales: landscape, toposequence, and a subsample of trees within the toposequence. At each scale, we studied the potential effects of differences in microclimate and moisture availability by sampling on northern and southern aspects. We found that black spruce radial growth responded negatively to monthly metrics of temperature at all examined scales, and we examined ∆(13)C responses on a subsample of trees as representative of the wider region. The negative ∆(13)C responses to temperature reveal that black spruce trees are experiencing moisture stress on both northern and southern aspects. Contrary to our expectations, ∆(13)C from trees on the northern aspect exhibited the strongest drought signal. Our results highlight the prominence of drought stress in the boreal forest of interior Alaska. We conclude that if temperatures continue to warm, we can expect drought-induced productivity declines across large regions of the boreal forest, even for trees located in cool and moist landscape positions.

  5. An evolutionary analysis of flightin reveals a conserved motif unique and widespread in Pancrustacea.

    PubMed

    Soto-Adames, Felipe N; Alvarez-Ortiz, Pedro; Vigoreaux, Jim O

    2014-01-01

    Flightin is a thick filament protein that in Drosophila melanogaster is uniquely expressed in the asynchronous, indirect flight muscles (IFM). Flightin is required for the structure and function of the IFM and is indispensable for flight in Drosophila. Given the importance of flight acquisition in the evolutionary history of insects, here we study the phylogeny and distribution of flightin. Flightin was identified in 69 species of hexapods in classes Collembola (springtails), Protura, Diplura, and insect orders Thysanura (silverfish), Dictyoptera (roaches), Orthoptera (grasshoppers), Pthiraptera (lice), Hemiptera (true bugs), Coleoptera (beetles), Neuroptera (green lacewing), Hymenoptera (bees, ants, and wasps), Lepidoptera (moths), and Diptera (flies and mosquitoes). Flightin was also found in 14 species of crustaceans in orders Anostraca (water flea), Cladocera (brine shrimp), Isopoda (pill bugs), Amphipoda (scuds, sideswimmers), and Decapoda (lobsters, crabs, and shrimps). Flightin was not identified in representatives of chelicerates, myriapods, or any species outside Pancrustacea (Tetraconata, sensu Dohle). Alignment of amino acid sequences revealed a conserved region of 52 amino acids, referred herein as WYR, that is bound by strictly conserved tryptophan (W) and arginine (R) and an intervening sequence with a high content of tyrosines (Y). This motif has no homologs in GenBank or PROSITE and is unique to flightin and paraflightin, a putative flightin paralog identified in decapods. A third motif of unclear affinities to pancrustacean WYR was observed in chelicerates. Phylogenetic analysis of amino acid sequences of the conserved motif suggests that paraflightin originated before the divergence of amphipods, isopods, and decapods. We conclude that flightin originated de novo in the ancestor of Pancrustacea > 500 MYA, well before the divergence of insects (~400 MYA) and the origin of flight (~325 MYA), and that its IFM-specific function in Drosophila is a more

  6. Widespread occurrence of intersex in black basses (Micropterus spp.) from U.S. rivers, 1995-2004

    USGS Publications Warehouse

    Hinck, J.E.; Blazer, V.S.; Schmitt, C.J.; Papoulias, D.M.; Tillitt, D.E.

    2009-01-01

    Intersex occurrence in freshwater fishes was evaluated for nine river basins in the United States. Testicular oocytes (predominantly male testes containing female germ cells) were the most pervasive form of intersex observed, even though similar numbers of male (n = 1477) and female (n = 1633) fish were examined. Intersex was found in 3% of the fish collected. The intersex condition was observed in four of the 16 species examined (25%) and in fish from 34 of 111 sites (31%). Intersex was not found in multiple species from the same site but was most prevalent in largemouth bass (Micropterus salmoides; 18% of males) and smallmouth bass (M. dolomieu; 33% of males). The percentage of intersex fish per site was 8-91% for largemouth bass and 14-73% for smallmouth bass. The incidence of intersex was greatest in the southeastern United States, with intersex largemouth bass present at all sites in the Apalachicola, Savannah, and Pee Dee River Basins. Total mercury, trans-nonachlor, p,p???-DDE, p,p???-DDD, and total PCBs were the most commonly detected chemical contaminants at all sites, regardless of whether intersex was observed. Although the genotype of the intersex fish was not determined, the microscopic appearance of the gonads, the presence of mature sperm, and the concentrations of sex steroid hormones and vitellogenin indicate the intersex bass were males. Few reproductive endpoints differed significantly among male and intersex bass; plasma vitellogenin concentration in males was not a good indicator of intersex presence. Hierarchical linkages of the intersex condition to reproductive function will require a more quantitative measure of intersex (e.g. severity index) rather than presence or absence of the condition. The baseline incidence of intersex gonadal tissue in black basses and other freshwater fishes is unknown, but intersex prevalence may be related to collection season, age, and endocrine active compounds in the environment. Intersex was not found in

  7. Beaufort Sea deep-water gas hydrate recovery from a seafloor mound in a region of widespread BSR occurrence

    USGS Publications Warehouse

    Hart, Patrick E.; Pohlman, John W.; Lorenson, T.D.; Edwards, Brian D.

    2011-01-01

    Gas hydrate was recovered from the Alaskan Beaufort Sea slope north of Camden Bay in August 2010 during a U.S. Coast Guard Cutter Healy expedition (USCG cruise ID HLY1002) under the direction of the U.S. Geological Survey (USGS). Interpretation of multichannel seismic (MCS) reflection data collected in 1977 by the USGS across the Beaufort Sea continental margin identified a regional bottom simulating reflection (BSR), indicating that a large segment of the Beaufort Sea slope is underlain by gas hydrate. During HLY1002, gas hydrate was sampled by serendipity with a piston core targeting a steep-sided bathymetric high originally thought to be an outcrop of older, exposed strata. The feature cored is an approximately 1100m diameter, 130 m high conical mound, referred to here as the Canning Seafloor Mound (CSM), which overlies the crest of a buried anticline in a region of sub-parallel compressional folds beneath the eastern Beaufort outer slope. An MCS profile shows a prominent BSR upslope and downslope from the mound. The absence of a BSR beneath the CSM and occurrence of gas hydrate near the summit indicates that free gas has migrated via deep-rooted thrust faults or by structural focusing up the flanks of the anticline to the seafloor. Gas hydrate recovered from near the CSM summit at a subbottom depth of about 5.7 meters in a water depth of 2538 m was of nodular and vein-filling morphology. Although the hydrate was not preserved, residual gas from the core liner contained >95% methane by volume when corrected for atmospheric contamination. The presence of trace C4+hydrocarbons (<0.1% by volume) confirms at least a minor thermogenic component. Authigenic carbonates and mollusk shells found throughout the core indicate sustained methane-rich fluid advection and possible sediment extrusion contributing to the development of the mound. Blister-like inflation of the seafloor caused by formation and accumulation of shallow hydrate lenses is also a likely factor in CSM

  8. [Gene transfer agent--a novel and widespread occurrence mechanism of gene exchange in ocean-a review].

    PubMed

    Cai, Haiyuan

    2012-01-01

    Gene Transfer Agent (GTA) particles are released by bacteria and resemble small, tailed bacteriophages. GTA particles contain small, random pieces of host DNA rather than GTA structural genes or a phage genome. Gene transfer mediated by GTA is efficient and species specific based on knowledge of currently best studied GTAs produced by 4 anaerobes. Genome sequencing projects have revealed a remarkable distribution of GTA gene clusters in the genomes of marine bacterioplankton, implying GTA may be an important mechanism for horizontal gene transfer in ocean. On basis of characterization of the 4 best studied GTAs, this review described GTAs released by numerically dominant marine bacteria, discussed their properties that were important for horizontal gene transfer in ocean, and gave future perspectives to advance GTA research.

  9. Huntington's disease (HD): degeneration of select nuclei, widespread occurrence of neuronal nuclear and axonal inclusions in the brainstem.

    PubMed

    Rüb, Udo; Hentschel, Matthias; Stratmann, Katharina; Brunt, Ewout; Heinsen, Helmut; Seidel, Kay; Bouzrou, Mohamed; Auburger, Georg; Paulson, Henry; Vonsattel, Jean-Paul; Lange, Herwig; Korf, Horst-Werner; den Dunnen, Wilfred

    2014-04-01

    Huntington's disease (HD) is a progressive polyglutamine disease that leads to a severe striatal and layer-specific neuronal loss in the cerebral neo-and allocortex. As some of the clinical symptoms (eg, oculomotor dysfunctions) suggested a degeneration of select brainstem nuclei, we performed a systematic investigation of the brainstem of eight clinically diagnosed and genetically confirmed HD patients. This post-mortem investigation revealed a consistent neuronal loss in the substantia nigra, pontine nuclei, reticulotegmental nucleus of the pons, superior and inferior olives, in the area of the excitatory burst neurons for horizontal saccades, raphe interpositus nucleus and vestibular nuclei. Immunoreactive intranuclear neuronal inclusions were present in all degenerated and apparently spared brainstem nuclei and immunoreactive axonal inclusions were observed in all brainstem fiber tracts of the HD patients. Degeneration of brainstem nuclei can account for a number of less well-understood clinical HD symptoms (ie, cerebellar, oculomotor and vestibular symptoms), while the formation of axonal aggregates may represent a crucial event in the cascades of pathological events leading to neurodegeneration in HD.

  10. Widespread Occurrence of Two Carbon Fixation Pathways in Tubeworm Endosymbionts: Lessons from Hydrothermal Vent Associated Tubeworms from the Mediterranean Sea

    PubMed Central

    Thiel, Vera; Hügler, Michael; Blümel, Martina; Baumann, Heike I.; Gärtner, Andrea; Schmaljohann, Rolf; Strauss, Harald; Garbe-Schönberg, Dieter; Petersen, Sven; Cowart, Dominique A.; Fisher, Charles R.; Imhoff, Johannes F.

    2012-01-01

    Vestimentiferan tubeworms (siboglinid polychetes) of the genus Lamellibrachia are common members of cold seep faunal communities and have also been found at sedimented hydrothermal vent sites in the Pacific. As they lack a digestive system, they are nourished by chemoautotrophic bacterial endosymbionts growing in a specialized tissue called the trophosome. Here we present the results of investigations of tubeworms and endosymbionts from a shallow hydrothermal vent field in the Western Mediterranean Sea. The tubeworms, which are the first reported vent-associated tubeworms outside the Pacific, are identified as Lamellibrachia anaximandri using mitochondrial ribosomal and cytochrome oxidase I (COI) gene sequences. They harbor a single gammaproteobacterial endosymbiont. Carbon isotopic data, as well as the analysis of genes involved in carbon and sulfur metabolism indicate a sulfide-oxidizing chemoautotrophic endosymbiont. The detection of a hydrogenase gene fragment suggests the potential for hydrogen oxidation as alternative energy source. Surprisingly, the endosymbiont harbors genes for two different carbon fixation pathways, the Calvin-Benson-Bassham (CBB) cycle as well as the reductive tricarboxylic acid (rTCA) cycle, as has been reported for the endosymbiont of the vent tubeworm Riftia pachyptila. In addition to RubisCO genes we detected ATP citrate lyase (ACL – the key enzyme of the rTCA cycle) type II gene sequences using newly designed primer sets. Comparative investigations with additional tubeworm species (Lamellibrachia luymesi, Lamellibrachia sp. 1, Lamellibrachia sp. 2, Escarpia laminata, Seepiophila jonesi) from multiple cold seep sites in the Gulf of Mexico revealed the presence of acl genes in these species as well. Thus, our study suggests that the presence of two different carbon fixation pathways, the CBB cycle and the rTCA cycle, is not restricted to the Riftia endosymbiont, but rather might be common in vestimentiferan tubeworm endosymbionts

  11. Widespread Occurrence of Zircon in Slow- and Ultraslow Spreading Ocean Crust: A Tool for Studying Ocean Lithospheric Processes

    NASA Astrophysics Data System (ADS)

    Grimes, C. B.; John, B. E.; Cheadle, M. J.; Schwartz, J. J.

    2005-12-01

    zircon thermometry. Enrichment of U and Th (>100 ppm) is frequently observed, and allows for the application of isotopic dating techniques on rocks collected near ridge axes. SHRIMP-RG Pb/U age determinations reveal resolution on the order of 2% corresponding to 40,000 years in crust as young as 2 Ma, and errors of <2% for samples up to 13 Ma. Attempts to employ the (U-Th)/He dating method on oceanic zircon have also been successful. With a closure temperature (Tc) of 180±20°C, this technique can be used in conjunction with U/Pb dating (Tc = 900±50°C) to bracket magnetic ages (Tc = 450-580°C). By applying multi-temperature chronometers to zircon collected from boreholes we can measure cooling rates related to emplacement, denudation, and/or tectonic rotation. Finally, the relatively common presence of zircon in oceanic crust precludes the simple assumption that detrital zircons in Archean meta-sedimentary rocks demonstrate the existence of continental crust.

  12. Widespread Occurrence of Plant Perchlorate

    NASA Astrophysics Data System (ADS)

    Harvey, G.; Orris, G.; Jackson, W. A.; Rajagopalan, S.; Andraski, B.; Stonestrom, D.

    2007-12-01

    Perchlorate is a water soluble oxyanion containing four oxygens bonded to a single chlorine atom. High concentration of perchlorate can competitively block the uptake of iodide by the sodium iodide symporter and disrupt thyroid function. Due to this ability to potentially impair thyroid function, perchlorate in environmental exposure pathways has been of concern for more than a decade. Our knowledge of the spatial and temporal aspects of environmental perchlorate has increased dramatically in the past few years. To date, perchlorate has been found in numerous different environmental media, including water, soils and sediments, and plants, from many parts of the world. Perchlorate can be found in marine alage, food and plant samples from Asia, Africa, Europe, North and South America. It is becoming increasingly apparent that perchlorate in low levels is ubiquitous. Perchlorate has been found in several different carbon age-dated water and midden samples that pre-date the industrial age and agricultural use of Chilean nitrate fertilizers by thousands of years. While anthropogenic sources of perchlorate exist, the accumulating spatial and temporal evidence suggests that perchlorate must have a significant natural source. This natural source of perchlorate under the appropriate geochemical and climatic conditions is contributing a natural background level of perchlorate. Concentrations of perchlorate in soils appears to be influenced by soil geochemistry. Soils with low organic content usually have higher levels of perchlorate then soils with abundant organic matter. High levels of perchlorate have been found in remotely located xerophytes growing in aridosols and in deciduous phreatophytes growing in humid densely populated areas. Often the amount of perchlorate in a plant cannot be explained by the amount of perchlorate in either the soil or precipitation. Investigations into the relative source contribution of lithogenic, atmospheric and other sources and mechanisms that lead to plant perchlorate accumulation need to be conducted.

  13. High-Throughput Analysis of Human Cytomegalovirus Genome Diversity Highlights the Widespread Occurrence of Gene-Disrupting Mutations and Pervasive Recombination

    PubMed Central

    Thys, Kim; Mbong Ngwese, Mirabeau; Van Damme, Ellen; Dvorak, Jan; Van Loock, Marnix; Li, Guangdi; Tachezy, Ruth; Busson, Laurent; Aerssens, Jeroen; Van Ranst, Marc

    2015-01-01

    ABSTRACT Human cytomegalovirus is a widespread pathogen of major medical importance. It causes significant morbidity and mortality in immunocompromised individuals, and congenital infections can result in severe disabilities or stillbirth. Development of a vaccine is prioritized, but no candidate is close to release. Although correlations of viral genetic variability with pathogenicity are suspected, knowledge about the strain diversity of the 235-kb genome is still limited. In this study, 96 full-length human cytomegalovirus genomes from clinical isolates were characterized, quadrupling the amount of information available for full-genome analysis. These data provide the first high-resolution map of human cytomegalovirus interhost diversity and evolution. We show that cytomegalovirus is significantly more divergent than all other human herpesviruses and highlight hot spots of diversity in the genome. Importantly, 75% of strains are not genetically intact but contain disruptive mutations in a diverse set of 26 genes, including the immunomodulatory genes UL40 and UL111A. These mutants are independent of culture passage artifacts and circulate in natural populations. Pervasive recombination, which is linked to the widespread occurrence of multiple infections, was found throughout the genome. The recombination density was significantly higher than those of other human herpesviruses and correlated with strain diversity. While the overall effects of strong purifying selection on virus evolution are apparent, evidence of diversifying selection was found in several genes encoding proteins that interact with the host immune system, including UL18, UL40, UL142, and UL147. These residues may present phylogenetic signatures of past and ongoing virus-host interactions. IMPORTANCE Human cytomegalovirus has the largest genome of all viruses that infect humans. Currently, there is a great interest in establishing associations between genetic variants and strain pathogenicity of

  14. Genetic characterisation of Toxoplasma gondii in wildlife from North America revealed widespread and high prevalence of the fourth clonal type

    USGS Publications Warehouse

    Dubey, J.P.; Velmurugan, G.V.; Ragendran, C.; Yabsley, M.J.; Thomas, N.J.; Beckmen, K.B.; Sinnett, D.; Ruid, D.; Hart, J.; Fair, P.A.; McFee, W.E.; Shearn-Bochsler, V.; Kwok, O.C.H.; Ferreira, L.R.; Choudhary, S.; Faria, E.B.; Zhou, H.; Felix, T.A.; Su, C.

    2011-01-01

    Little is known of the genetic diversity of Toxoplasma gondii circulating in wildlife. In the present study wild animals, from the USA were examined for T. gondii infection. Tissues of naturally exposed animals were bioassayed in mice for isolation of viable parasites. Viable T. gondii was isolated from 31 animals including, to our knowledge for the first time, from a bald eagle (Haliaeetus leucocephalus), five gray wolves (Canis lupus), a woodrat (Neotoma micropus), and five Arctic foxes (Alopex lagopus). Additionally, 66 T. gondii isolates obtained previously, but not genetically characterised, were revived in mice. Toxoplasma gondii DNA isolated from these 97 samples (31+66) was characterised using 11 PCR-restriction fragment length polymorphism (RFLP) markers (SAG1, 5'- and 3'-SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico). A total of 95 isolates were successfully genotyped. In addition to clonal Types II, and III, 12 different genotypes were found. These genotype data were combined with 74 T. gondii isolates previously characterised from wildlife from North America and a composite data set of 169 isolates comprised 22 genotypes, including clonal Types II, III and 20 atypical genotypes. Phylogenetic network analysis showed limited diversity with dominance of a recently designated fourth clonal type (Type 12) in North America, followed by the Type II and III lineages. These three major lineages together accounted for 85% of strains in North America. The Type 12 lineage includes previously identified Type A and X strains from sea otters. This study revealed that the Type 12 lineage accounts for 46.7% (79/169) of isolates and is dominant in wildlife of North America. No clonal Type I strain was identified among these wildlife isolates. These results suggest that T. gondii strains in wildlife from North America have limited diversity, with the occurrence of only a few major clonal types.

  15. Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes.

    PubMed

    Wang, Hao; Fewer, David P; Holm, Liisa; Rouhiainen, Leo; Sivonen, Kaarina

    2014-06-24

    Nonribosomal peptides and polyketides are a diverse group of natural products with complex chemical structures and enormous pharmaceutical potential. They are synthesized on modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzyme complexes by a conserved thiotemplate mechanism. Here, we report the widespread occurrence of NRPS and PKS genetic machinery across the three domains of life with the discovery of 3,339 gene clusters from 991 organisms, by examining a total of 2,699 genomes. These gene clusters display extraordinarily diverse organizations, and a total of 1,147 hybrid NRPS/PKS clusters were found. Surprisingly, 10% of bacterial gene clusters lacked modular organization, and instead catalytic domains were mostly encoded as separate proteins. The finding of common occurrence of nonmodular NRPS differs substantially from the current classification. Sequence analysis indicates that the evolution of NRPS machineries was driven by a combination of common descent and horizontal gene transfer. We identified related siderophore NRPS gene clusters that encoded modular and nonmodular NRPS enzymes organized in a gradient. A higher frequency of the NRPS and PKS gene clusters was detected from bacteria compared with archaea or eukarya. They commonly occurred in the phyla of Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria in bacteria and the phylum of Ascomycota in fungi. The majority of these NRPS and PKS gene clusters have unknown end products highlighting the power of genome mining in identifying novel genetic machinery for the biosynthesis of secondary metabolites.

  16. Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection.

    PubMed

    Li, Li-Guan; Xia, Yu; Zhang, Tong

    2017-03-01

    The high frequency of antibiotic resistance is a global public health concern. More seriously, widespread metal pressure in the environment may facilitate the proliferation of antibiotic resistance via coselection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Given the lack of comprehensive understanding of the ARG and MRG coselection, in this study both abundance relationship and genetic linkage between ARGs and MRGs were rigorously investigated by performing a genomic analysis of a large complete genome collection. Many more ARGs were enriched in human-associated bacteria compared with those subjected to less anthropogenic interference. The signatures of ARG and MRG co-occurrence were much more frequent and the distance linkages between ARGs and MRGs were much more intimate in human pathogens than those less human-associated bacteria. Moreover, the co-occurrence structures in the habitat divisions were significantly different, which could be attributed to their distinct gene transfer potentials. More exogenous ARGs and MRGs on the genomes of human pathogens indicated the importance of recent resistance acquisition in resistome development of human commensal flora. Overall, the study emphasizes the potential risk associated with ARG and MRG coselection of both environmental and medical relevance.

  17. Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

    PubMed

    Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

    2015-01-01

    In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems.

  18. An episode of widespread ocean anoxia during the latest Ediacaran Period revealed by light U isotope compositions in carbonates

    NASA Astrophysics Data System (ADS)

    Zhang, F.

    2015-12-01

    Reconstruction of ocean redox chemistry during the Ediacaran Period is important for understanding the causal relationship between environmental oxygen levels and early metazoan evolution. Geochemical data (e.g., high Mo and U concentrations and/or heavy Mo and U isotope compositions from sedimentary rocks) provide evidence of extensive ocean oxygenation shortly after the Marinoan glaciation at ca. 632 Ma [1], during the late Ediacaran Period at ca. 560-551 Ma [2], and multiple times during the early Cambrian Period [3, 4]. These episodes of oxygenation may have been separated by intervals of less oxygenated conditions [1, 2]. However, the global redox state of the ocean during the terminal Ediacaran period (ca. 551-541 Ma) is poorly constrained. We address this knowledge gap by measuring carbonate U isotope compositions (δ238U) - a novel global ocean redox proxy - of the Gaojiashan Member of the late Ediacaran Dengying Formation (ca. 551-541 Ma) in South China. An abrupt negative shift in δ238U from values scattering around -0.45‰ to values averaging -0.95‰ (±0.20‰, 2sd) was observed in the middle Gaojiashan Member, suggesting a globally widespread expansion of ocean anoxia during the terminal Ediacaran Period. The negative δ238U shift coincides with the onset of a pronounced positive carbon isotope excursion (from 0‰ to +6‰), suggesting that ocean anoxia is the major driving force behind enhanced organic carbon burial that led to the carbon isotope excursion. The widespread anoxia recorded by the Gaojiashan Member is bracketed by known intervals of extensive ocean oxygenation, thus indicating that the Precambrian-Phanerozoic transition was characterized by oscillating ocean redox conditions. The Ediacara biota (ca. 541 Ma) [5] disappeared shortly after the widespread ocean anoxia, suggesting that an expansion of ocean anoxia may have triggerred the onset of a mass extinction in the latest Ediacaran time. References: [1] Sahoo, et al. (2012), Nature

  19. Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum.

    PubMed

    Moura, Andre E; Janse van Rensburg, Charlene; Pilot, Malgorzata; Tehrani, Arman; Best, Peter B; Thornton, Meredith; Plön, Stephanie; de Bruyn, P J Nico; Worley, Kim C; Gibbs, Richard A; Dahlheim, Marilyn E; Hoelzel, Alan Rus

    2014-05-01

    Ecosystem function and resilience is determined by the interactions and independent contributions of individual species. Apex predators play a disproportionately determinant role through their influence and dependence on the dynamics of prey species. Their demographic fluctuations are thus likely to reflect changes in their respective ecological communities and habitat. Here, we investigate the historical population dynamics of the killer whale based on draft nuclear genome data for the Northern Hemisphere and mtDNA data worldwide. We infer a relatively stable population size throughout most of the Pleistocene, followed by an order of magnitude decline and bottleneck during the Weichselian glacial period. Global mtDNA data indicate that while most populations declined, at least one population retained diversity in a stable, productive ecosystem off southern Africa. We conclude that environmental changes during the last glacial period promoted the decline of a top ocean predator, that these events contributed to the pattern of diversity among extant populations, and that the relatively high diversity of a population currently in productive, stable habitat off South Africa suggests a role for ocean productivity in the widespread decline.

  20. CasExpress reveals widespread and diverse patterns of cell survival of caspase-3 activation during development in vivo

    PubMed Central

    Ding, Austin Xun; Sun, Gongping; Argaw, Yewubdar G; Wong, Jessica O; Easwaran, Sreesankar; Montell, Denise J

    2016-01-01

    Caspase-3 carries out the executioner phase of apoptosis, however under special circumstances, cells can survive its activity. To document systematically where and when cells survive caspase-3 activation in vivo, we designed a system, CasExpress, which drives fluorescent protein expression, transiently or permanently, in cells that survive caspase-3 activation in Drosophila. We discovered widespread survival of caspase-3 activity. Distinct spatial and temporal patterns emerged in different tissues. Some cells activated caspase-3 during their normal development in every cell and in every animal without evidence of apoptosis. In other tissues, such as the brain, expression was sporadic both temporally and spatially and overlapped with periods of apoptosis. In adults, reporter expression was evident in a large fraction of cells in most tissues of every animal; however the precise patterns varied. Inhibition of caspase activity in wing discs reduced wing size demonstrating functional significance. The implications of these patterns are discussed. DOI: http://dx.doi.org/10.7554/eLife.10936.001 PMID:27058168

  1. Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species

    PubMed Central

    Honorio Coronado, Eurídice N; Dexter, Kyle G; Poelchau, Monica F; Hollingsworth, Peter M; Phillips, Oliver L; Pennington, R Toby; Carine, Mark

    2014-01-01

    Aim To examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia. Location Neotropics. Methods Plastid DNA (trnH–psbA; 410 individuals from 54 populations) and nuclear ribosomal internal transcribed spacer (ITS; 85 individuals from 27 populations) sequences were sampled from Mexico to Bolivia, representing the full extent of the taxon's distribution. Divergence of plastid lineages was dated using a Bayesian coalescent approach. Genetic diversity was assessed with indices of haplotype and nucleotide diversities, and genetic structure was examined using spatial analysis of molecular variance (SAMOVA) and haplotype networks. Population expansion within Amazonia was tested using neutrality and mismatch distribution tests. Results trnH–psbA sequences yielded 19 haplotypes restricted to either Mesoamerica or Amazonia; six haplotypes were found among ITS sequences. Diversification of the plastid DNA haplotypes began c. 14.6 Ma. Haplotype diversity for trnH–psbA was higher in Amazonia. Seven genetically differentiated SAMOVA groups were described for trnH–psbA, of which two were also supported by the presence of unique ITS sequences. Population expansion was suggested for both markers for the SAMOVA group that contains most Amazonian populations. Main conclusions Our results show marked population genetic structure in F. insipida between Mesoamerica and Amazonia, implying that the Andes and seasonally dry areas of northern South America are eco-climatic barriers to its migration. This pattern is shared with other widespread pioneer species affiliated to wet habitats, indicating that the ecological characteristics of species may impact upon large-scale phylogeography. Ficus insipida also shows genetic structure in north-western Amazonia potentially related to pre-Pleistocene historical events. In contrast, evident population expansion elsewhere in Amazonia, in

  2. A Comprehensive Analysis of MicroProteins Reveals Their Potentially Widespread Mechanism of Transcriptional Regulation1[W

    PubMed Central

    Magnani, Enrico; de Klein, Niek; Nam, Hye-In; Kim, Jung-Gun; Pham, Kimberly; Fiume, Elisa; Mudgett, Mary Beth; Rhee, Seung Yon

    2014-01-01

    Truncated transcription factor-like proteins called microProteins (miPs) can modulate transcription factor activities, thereby increasing transcriptional regulatory complexity. To understand their prevalence, evolution, and function, we predicted over 400 genes that encode putative miPs from Arabidopsis (Arabidopsis thaliana) using a bioinformatics pipeline and validated two novel miPs involved in flowering time and response to abiotic and biotic stress. We provide an evolutionary perspective for a class of miPs targeting homeodomain transcription factors in plants and metazoans. We identify domain loss as one mechanism of miP evolution and suggest the possible roles of miPs on the evolution of their target transcription factors. Overall, we reveal a prominent layer of transcriptional regulation by miPs, show pervasiveness of such proteins both within and across genomes, and provide a framework for studying their function and evolution. PMID:24616380

  3. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins

    PubMed Central

    Fang, Pan; Wang, Xin-jian; Xue, Yu; Liu, Ming-qi; Zeng, Wen-feng; Zhang, Yang; Zhang, Lei; Gao, Xing; Yan, Guo-quan; Yao, Jun; Shen, Hua-li; Yang, Peng-yuan

    2016-01-01

    N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins. PMID:27259237

  4. SILAC-based quantitative proteomic analysis reveals widespread molecular alterations in human skin keratinocytes upon chronic arsenic exposure.

    PubMed

    Mir, Sartaj Ahmad; Pinto, Sneha M; Paul, Somnath; Raja, Remya; Nanjappa, Vishalakshi; Syed, Nazia; Advani, Jayshree; Renuse, Santosh; Sahasrabuddhe, Nandini A; Prasad, T S Keshava; Giri, Ashok K; Gowda, Harsha; Chatterjee, Aditi

    2017-03-01

    Chronic exposure to arsenic is associated with dermatological and nondermatological disorders. Consumption of arsenic-contaminated drinking water results in accumulation of arsenic in liver, spleen, kidneys, lungs, and gastrointestinal tract. Although arsenic is cleared from these sites, a substantial amount of residual arsenic is left in keratin-rich tissues including skin. Epidemiological studies suggest the association of skin cancer upon arsenic exposure, however, the mechanism of arsenic-induced carcinogenesis is not completely understood. We developed a cell line based model to understand the molecular mechanisms involved in arsenic-mediated toxicity and carcinogenicity. Human skin keratinocyte cell line, HaCaT, was chronically exposed to 100 nM sodium arsenite over a period of 6 months. We observed an increase in basal ROS levels in arsenic-exposed cells. SILAC-based quantitative proteomics approach resulted in identification of 2111 proteins of which 42 proteins were found to be overexpressed and 54 downregulated (twofold) upon chronic arsenic exposure. Our analysis revealed arsenic-induced overexpression of aldo-keto reductase family 1 member C2 (AKR1C2), aldo-keto reductase family 1 member C3 (AKR1C3), glutamate-cysteine ligase catalytic subunit (GCLC), and NAD(P)H dehydrogenase [quinone] 1 (NQO1) among others. We observed downregulation of several members of the plakin family including periplakin (PPL), envoplakin (EVPL), and involucrin (IVL) that are essential for terminal differentiation of keratinocytes. MRM and Western blot analysis confirmed differential expression of several candidate proteins. Our study provides insights into molecular alterations upon chronic arsenic exposure on skin.

  5. Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin.

    PubMed

    Lamer, James T; Ruebush, Blake C; Arbieva, Zarema H; McClelland, Michael A; Epifanio, John M; Sass, Greg G

    2015-08-01

    Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North America, however, introgressant hybrids have been reported throughout their expanded range within the Mississippi River Basin (MRB). The extent of introgression, both spatially and generationally, is largely unknown. Therefore, we examined mixed-species populations from across the MRB to characterize the extent of interspecific gene flow. We assayed 2798 individuals from nine locations with a suite of species-diagnostic SNPs (57 nuclear and one mitochondrial). Forty-four per cent (n = 1244) of individuals displayed hybrid genotypes. Moreover, the composition of hybrid genotypes varied among locations and represented complex hybrid swarms with multiple generations of gene flow. Introgressive hybrids were identified from all locations, were bidirectional and followed a bimodal distribution consisting primarily of parental or parental-like genotypes and phenotypes. All described hybrid categories were present among individuals from 1999 to 2008, with parents and later-generation backcrosses representing the largest proportion of individuals among years. Our mitochondrial SNP (COII), tested on a subset of 730 individuals, revealed a silver carp maternal bias in 13 of 21 (62%) F1 hybrids, in all silver carp backcrosses, and maintained throughout many of the bighead carp backcrosses. The application of this suite of diagnostic markers and the spatial coverage permits a deeper examination of the complexity in hybrid swarms between two invasive, introduced species.

  6. Multilocus phylogeography of a widespread savanna-woodland-adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region.

    PubMed

    McDonough, Molly M; Šumbera, Radim; Mazoch, Vladimír; Ferguson, Adam W; Phillips, Caleb D; Bryja, Josef

    2015-10-01

    Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during the Pleistocene. However, these studies were often biased by limited geographic sampling or exclusively focused on large-bodied taxa. We exploited the broad southern African distribution of a savanna-woodland-adapted African rodent, Gerbilliscus leucogaster (bushveld gerbil) and generated mitochondrial, autosomal and sex chromosome data to quantify regional signatures of climatic and vicariant biogeographic phenomena. Results indicate the most recent common ancestor for all G. leucogaster lineages occurred during the early Pleistocene. We documented six divergent mitochondrial lineages that diverged ~0.270-0.100 mya, each of which was geographically isolated during periods characterized by alterations to the course of the Zambezi River and its tributaries as well as regional 'megadroughts'. Results demonstrate the presence of a widespread lineage exhibiting demographic expansion ~0.065-0.035 mya, a time that coincides with savanna-woodland expansion across southern Africa. A multilocus autosomal perspective revealed the influence of the Kafue River as a current barrier to gene flow and regions of secondary contact among divergent mitochondrial lineages. Our results demonstrate the importance of both climatic fluctuations and physiographic vicariance in shaping the distribution of southern African biodiversity.

  7. Volunteer Conservation Action Data Reveals Large-Scale and Long-Term Negative Population Trends of a Widespread Amphibian, the Common Toad (Bufo bufo)

    PubMed Central

    Petrovan, Silviu O.

    2016-01-01

    Rare and threatened species are the most frequent focus of conservation science and action. With the ongoing shift from single-species conservation towards the preservation of ecosystem services, there is a greater need to understand abundance trends of common species because declines in common species can disproportionately impact ecosystems function. We used volunteer-collected data in two European countries, the United Kingdom (UK) and Switzerland, since the 1970s to assess national and regional trends for one of Europe’s most abundant amphibian species, the common toad (Bufo bufo). Millions of toads were moved by volunteers across roads during this period in an effort to protect them from road traffic. For Switzerland, we additionally estimated trends for the common frog (Rana temporaria), a similarly widespread and common amphibian species. We used state-space models to account for variability in detection and effort and included only populations with at least 5 years of data; 153 populations for the UK and 141 for Switzerland. Common toads declined continuously in each decade in both countries since the 1980s. Given the declines, this common species almost qualifies for International Union for the Conservation of Nature (IUCN) red-listing over this period despite volunteer conservation efforts. Reasons for the declines and wider impacts remain unknown. By contrast, common frog populations were stable or increasing in Switzerland, although there was evidence of declines after 2003. “Toads on Roads” schemes are vital citizen conservation action projects, and the data from such projects can be used for large scale trend estimations of widespread amphibians. We highlight the need for increased research into the status of common amphibian species in addition to conservation efforts focusing on rare and threatened species. PMID:27706154

  8. Volunteer Conservation Action Data Reveals Large-Scale and Long-Term Negative Population Trends of a Widespread Amphibian, the Common Toad (Bufo bufo).

    PubMed

    Petrovan, Silviu O; Schmidt, Benedikt R

    2016-01-01

    Rare and threatened species are the most frequent focus of conservation science and action. With the ongoing shift from single-species conservation towards the preservation of ecosystem services, there is a greater need to understand abundance trends of common species because declines in common species can disproportionately impact ecosystems function. We used volunteer-collected data in two European countries, the United Kingdom (UK) and Switzerland, since the 1970s to assess national and regional trends for one of Europe's most abundant amphibian species, the common toad (Bufo bufo). Millions of toads were moved by volunteers across roads during this period in an effort to protect them from road traffic. For Switzerland, we additionally estimated trends for the common frog (Rana temporaria), a similarly widespread and common amphibian species. We used state-space models to account for variability in detection and effort and included only populations with at least 5 years of data; 153 populations for the UK and 141 for Switzerland. Common toads declined continuously in each decade in both countries since the 1980s. Given the declines, this common species almost qualifies for International Union for the Conservation of Nature (IUCN) red-listing over this period despite volunteer conservation efforts. Reasons for the declines and wider impacts remain unknown. By contrast, common frog populations were stable or increasing in Switzerland, although there was evidence of declines after 2003. "Toads on Roads" schemes are vital citizen conservation action projects, and the data from such projects can be used for large scale trend estimations of widespread amphibians. We highlight the need for increased research into the status of common amphibian species in addition to conservation efforts focusing on rare and threatened species.

  9. Intravital and whole-organ imaging reveals capture of melanoma-derived antigen by lymph node subcapsular macrophages leading to widespread deposition on follicular dendritic cells.

    PubMed

    Moalli, Federica; Proulx, Steven T; Schwendener, Reto; Detmar, Michael; Schlapbach, Christoph; Stein, Jens V

    2015-01-01

    Aberrant antigens expressed by tumor cells, such as in melanoma, are often associated with humoral immune responses, which may in turn influence tumor progression. Despite recent data showing the central role of adaptive immune responses on cancer spread or control, it remains poorly understood where and how tumor-derived antigen (TDA) induces a humoral immune response in tumor-bearing hosts. Based on our observation of TDA accumulation in B cell areas of lymph nodes (LNs) from melanoma patients, we developed a pre-metastatic B16.F10 melanoma model expressing a fluorescent fusion protein, tandem dimer tomato, as a surrogate TDA. Using intravital two-photon microscopy (2PM) and whole-mount 3D LN imaging of tumor-draining LNs in immunocompetent mice, we report an unexpectedly widespread accumulation of TDA on follicular dendritic cells (FDCs), which were dynamically scanned by circulating B cells. Furthermore, 2PM imaging identified macrophages located in the subcapsular sinus of tumor-draining LNs to capture subcellular TDA-containing particles arriving in afferent lymph. As a consequence, depletion of macrophages or genetic ablation of B cells and FDCs resulted in dramatically reduced TDA capture in tumor-draining LNs. In sum, we identified a major pathway for the induction of humoral responses in a melanoma model, which may be exploitable to manipulate anti-TDA antibody production during cancer immunotherapy.

  10. Insights into riming and aggregation processes as revealed by aircraft, radar, and disdrometer observations for a 27 April 2011 widespread precipitation event: Insights into Riming and Aggregation

    SciTech Connect

    Giangrande, Scott E.; Toto, Tami; Bansemer, Aaron; Kumjian, Matthew R.; Mishra, Subhashree

    2016-05-19

    Our study presents aircraft spiral ascent and descent observations intercepting a transition to riming processes during widespread stratiform precipitation. The sequence is documented using collocated scanning and profiling radar, including longer-wavelength dual polarization measurements and shorter-wavelength Doppler spectra. Riming regions are supported using aircraft measurements recording elevated liquid water concentrations, spherical particle shapes, and saturation with respect to water. Profiling cloud radar observations indicate riming regions during the event as having increasing particle fall speeds, rapid time-height changes, and bimodalities in Doppler spectra. These particular riming signatures are coupled to scanning dual polarization radar observations of higher differential reflectivity (ZDR) aloft. Moreover, reduced melting layer enhancements and delayed radar bright-band signatures in the column are also observed during riming periods, most notably with the profiling radar observations. The bimodal cloud radar Doppler spectra captured near riming zones indicate two time-height spectral ice peaks, one rimed particle peak, and one peak associated with pristine ice needle generation and/or growth between -4°C and -7°C also sampled by aircraft probes. We observe this pristine needle population near the rimed particle region which gives a partial explanation for the enhanced ZDR. The riming signatures aloft and radar measurements within the melting level are weakly lag correlated (r~0.6) with smaller median drop sizes at the surface, as compared with later times when aggregation of larger particle sizes was believed dominant.

  11. Widespread receptivity to neuropeptide PDF throughout the neuronal circadian clock network of Drosophila revealed by real-time cyclic AMP imaging

    PubMed Central

    Shafer, Orie T.; Kim, Dong Jo; Dunbar-Yaffe, Richard; Nikolaev, Viacheslav O.; Lohse, Martin J.; Taghert, Paul H.

    2008-01-01

    Summary The neuropeptide PDF is released by sixteen clock neurons in Drosophila and helps maintain circadian activity rhythms by coordinating a network of ~150 neuronal clocks. Whether PDF acts directly on elements of this neural network remains unknown. We address this question by adapting Epac1-camps, a genetically encoded cAMP FRET sensor, for use in the living brain. We find that a subset of the PDF-expressing neurons respond to PDF with long-lasting cAMP increases, and confirm that such responses require the PDF receptor. In contrast, an unrelated Drosophila neuropeptide, DH 31, stimulates large cAMP increases in all PDF-expressing clock neurons. Thus the network of ~150 clock neurons displays widespread, though not uniform, PDF receptivity. This work introduces a sensitive means of measuring cAMP changes in a living brain with sub-cellular resolution. Specifically, it experimentally confirms the longstanding hypothesis that PDF is a direct modulator of most neurons in the Drosophila clock network. PMID:18439407

  12. Insights into riming and aggregation processes as revealed by aircraft, radar, and disdrometer observations for a 27 April 2011 widespread precipitation event: Insights into Riming and Aggregation

    DOE PAGES

    Giangrande, Scott E.; Toto, Tami; Bansemer, Aaron; ...

    2016-05-19

    Our study presents aircraft spiral ascent and descent observations intercepting a transition to riming processes during widespread stratiform precipitation. The sequence is documented using collocated scanning and profiling radar, including longer-wavelength dual polarization measurements and shorter-wavelength Doppler spectra. Riming regions are supported using aircraft measurements recording elevated liquid water concentrations, spherical particle shapes, and saturation with respect to water. Profiling cloud radar observations indicate riming regions during the event as having increasing particle fall speeds, rapid time-height changes, and bimodalities in Doppler spectra. These particular riming signatures are coupled to scanning dual polarization radar observations of higher differential reflectivity (ZDR)more » aloft. Moreover, reduced melting layer enhancements and delayed radar bright-band signatures in the column are also observed during riming periods, most notably with the profiling radar observations. The bimodal cloud radar Doppler spectra captured near riming zones indicate two time-height spectral ice peaks, one rimed particle peak, and one peak associated with pristine ice needle generation and/or growth between -4°C and -7°C also sampled by aircraft probes. We observe this pristine needle population near the rimed particle region which gives a partial explanation for the enhanced ZDR. The riming signatures aloft and radar measurements within the melting level are weakly lag correlated (r~0.6) with smaller median drop sizes at the surface, as compared with later times when aggregation of larger particle sizes was believed dominant.« less

  13. Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

    PubMed Central

    Tomazou, Eleni M.; Sheffield, Nathan C.; Schmidl, Christian; Schuster, Michael; Schönegger, Andreas; Datlinger, Paul; Kubicek, Stefan; Bock, Christoph; Kovar, Heinrich

    2015-01-01

    Summary Transcription factor fusion proteins can transform cells by inducing global changes of the transcriptome, often creating a state of oncogene addiction. Here, we investigate the role of epigenetic mechanisms in this process, focusing on Ewing sarcoma cells that are dependent on the EWS-FLI1 fusion protein. We established reference epigenome maps comprising DNA methylation, seven histone marks, open chromatin states, and RNA levels, and we analyzed the epigenome dynamics upon downregulation of the driving oncogene. Reduced EWS-FLI1 expression led to widespread epigenetic changes in promoters, enhancers, and super-enhancers, and we identified histone H3K27 acetylation as the most strongly affected mark. Clustering of epigenetic promoter signatures defined classes of EWS-FLI1-regulated genes that responded differently to low-dose treatment with histone deacetylase inhibitors. Furthermore, we observed strong and opposing enrichment patterns for E2F and AP-1 among EWS-FLI1-correlated and anticorrelated genes. Our data describe extensive genome-wide rewiring of epigenetic cell states driven by an oncogenic fusion protein. PMID:25704812

  14. Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes.

    PubMed

    Bertrand, Joris A M; Borsa, Philippe; Chen, Wei-Jen

    2017-02-03

    On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species.

  15. Characterization of Enteroviruses from non-human primates in cameroon revealed virus types widespread in humans along with candidate new types and species.

    PubMed

    Sadeuh-Mba, Serge Alain; Bessaud, Maël; Joffret, Marie-Line; Endegue Zanga, Marie-Claire; Balanant, Jean; Mpoudi Ngole, Eitel; Njouom, Richard; Reynes, Jean-Marc; Delpeyroux, Francis; Rousset, Dominique

    2014-01-01

    Enteroviruses (EVs) infecting African Non-Human Primates (NHP) are still poorly documented. This study was designed to characterize the genetic diversity of EVs among captive and wild NHP in Cameroon and to compare this diversity with that found in humans. Stool specimens were collected in April 2008 in NHP housed in sanctuaries in Yaounde and neighborhoods. Moreover, stool specimens collected from wild NHP from June 2006 to October 2008 in the southern rain forest of Cameroon were considered. RNAs purified directly from stool samples were screened for EVs using a sensitive RT-nested PCR targeting the VP1 capsid coding gene whose nucleotide sequence was used for molecular typing. Captive chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla) were primarily infected by EV types already reported in humans in Cameroon and elsewhere: Coxsackievirus A13 and A24, Echovirus 15 and 29, and EV-B82. Moreover EV-A119, a novel virus type recently described in humans in central and west Africa, was also found in a captive Chimpanzee. EV-A76, which is a widespread virus in humans, was identified in wild chimpanzees, thus suggesting its adaptation and parallel circulation in human and NHP populations in Cameroon. Interestingly, some EVs harbored by wild NHP were genetically distinct from all existing types and were thus assigned as new types. One chimpanzee-derived virus was tentatively assigned as EV-J121 in the EV-J species. In addition, two EVs from wild monkeys provisionally registered as EV-122 and EV-123 were found to belong to a candidate new species. Overall, this study indicates that the genetic diversity of EVs among NHP is more important than previously known and could be the source of future new emerging human viral diseases.

  16. Arterial spin labeling imaging reveals widespread and Aβ-independent reductions in cerebral blood flow in elderly apolipoprotein epsilon-4 carriers.

    PubMed

    Michels, Lars; Warnock, Geoffrey; Buck, Alfred; Macauda, Gianluca; Leh, Sandra E; Kaelin, Andrea M; Riese, Florian; Meyer, Rafael; O'Gorman, Ruth; Hock, Christoph; Kollias, Spyros; Gietl, Anton F

    2016-03-01

    Changes in cerebral blood flow are an essential feature of Alzheimer's disease and have been linked to apolipoprotein E-genotype and cerebral amyloid-deposition. These factors could be interdependent or influence cerebral blood flow via different mechanisms. We examined apolipoprotein E-genotype, amyloid beta-deposition, and cerebral blood flow in amnestic mild cognitive impairment using pseudo-continuous arterial spin labeling MRI in 27 cognitively normal elderly and 16 amnestic mild cognitive impairment participants. Subjects underwent Pittsburgh Compound B (PiB) positron emission tomography and apolipoprotein E-genotyping. Global cerebral blood flow was lower in apolipoprotein E ɛ4-allele carriers (apolipoprotein E4+) than in apolipoprotein E4- across all subjects (including cognitively normal participants) and within the group of cognitively normal elderly. Global cerebral blood flow was lower in subjects with mild cognitive impairment compared with cognitively normal. Subjects with elevated cerebral amyloid-deposition (PiB+) showed a trend for lower global cerebral blood flow. Apolipoprotein E-status exerted the strongest effect on global cerebral blood flow. Regional analysis indicated that local cerebral blood flow reductions were more widespread for the contrasts apolipoprotein E4+ versus apolipoprotein E4- compared with the contrasts PiB+ versus PiB- or mild cognitive impairment versus cognitively normal. These findings suggest that apolipoprotein E-genotype exerts its impact on cerebral blood flow at least partly independently from amyloid beta-deposition, suggesting that apolipoprotein E also contributes to cerebral blood flow changes outside the context of Alzheimer's disease.

  17. Arterial spin labeling imaging reveals widespread and Aβ-independent reductions in cerebral blood flow in elderly apolipoprotein epsilon-4 carriers

    PubMed Central

    Warnock, Geoffrey; Buck, Alfred; Macauda, Gianluca; Leh, Sandra E; Kaelin, Andrea M; Riese, Florian; Meyer, Rafael; O’Gorman, Ruth; Hock, Christoph; Kollias, Spyros; Gietl, Anton F

    2015-01-01

    Changes in cerebral blood flow are an essential feature of Alzheimer’s disease and have been linked to apolipoprotein E-genotype and cerebral amyloid-deposition. These factors could be interdependent or influence cerebral blood flow via different mechanisms. We examined apolipoprotein E-genotype, amyloid beta-deposition, and cerebral blood flow in amnestic mild cognitive impairment using pseudo-continuous arterial spin labeling MRI in 27 cognitively normal elderly and 16 amnestic mild cognitive impairment participants. Subjects underwent Pittsburgh Compound B (PiB) positron emission tomography and apolipoprotein E-genotyping. Global cerebral blood flow was lower in apolipoprotein E ɛ4-allele carriers (apolipoprotein E4+) than in apolipoprotein E4− across all subjects (including cognitively normal participants) and within the group of cognitively normal elderly. Global cerebral blood flow was lower in subjects with mild cognitive impairment compared with cognitively normal. Subjects with elevated cerebral amyloid-deposition (PiB+) showed a trend for lower global cerebral blood flow. Apolipoprotein E-status exerted the strongest effect on global cerebral blood flow. Regional analysis indicated that local cerebral blood flow reductions were more widespread for the contrasts apolipoprotein E4+ versus apolipoprotein E4− compared with the contrasts PiB+ versus PiB− or mild cognitive impairment versus cognitively normal. These findings suggest that apolipoprotein E-genotype exerts its impact on cerebral blood flow at least partly independently from amyloid beta-deposition, suggesting that apolipoprotein E also contributes to cerebral blood flow changes outside the context of Alzheimer’s disease. PMID:26661143

  18. Isolation and RFLP Genotyping of Toxoplasma gondii in Free-Range Chickens (Gallus domesticus) in Grenada, West Indies, Revealed Widespread and Dominance of Clonal Type III Parasites.

    PubMed

    Chikweto, Alfred; Sharma, Ravindra N; Tiwari, Keshaw P; Verma, Shiv K; Calero-Bernal, Rafael; Jiang, Tiantian; Su, Chunlei; Kwok, Oliver C; Dubey, Jitender P

    2017-02-01

    The objectives of the present cross-sectional study were to isolate and genotype Toxoplasma gondii in free-range chickens from Grenada, West Indies. Using the modified agglutination test, antibodies to T. gondii were found in 39 (26.9%) of 145 free-range chickens with titers of 25 in 7 chickens, 50 in 6 chickens, 100 in 2 chickens, and 200 or higher in 24 chickens. The hearts of the 39 seropositive chickens were bioassayed in mice; viable T. gondii was isolated from 20 and further propagated in cell culture. Genotyping of T. gondii DNA extracted from cell-cultured tachyzoites using the 10 PCR-restriction fragment length polymorphism (RFLP) markers SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico revealed 4 genotypes, including ToxoDB PCR-RFLP no. 2 (Type III), no. 7, no. 13, and no. 259 (new). These results indicated that T. gondii population genetics in free-range chickens seems to be moderately diverse with ToxoDB no. 2 (Type III) as the most frequent (15/20 = 75%) compared to other genotypes in Grenada.

  19. Widespread Low-Latitude Diurnal CO2 Frost on Mars

    NASA Astrophysics Data System (ADS)

    Piqueux, S.; Kleinböhl, A.; Hayne, P. O.; Heavens, N. G.; Kass, D. M.; McCleese, D. J.; Schofield, J. T.; Shirley, J. H.

    2016-09-01

    We map and characterize MCS nighttime surface temperature observations consistent with the occurrence of CO2 frost on Mars. Low-latitude nighttime CO2 frost is widespread, with potential implications for the physical nature of the surface layer.

  20. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton.

    PubMed

    Milici, Mathias; Deng, Zhi-Luo; Tomasch, Jürgen; Decelle, Johan; Wos-Oxley, Melissa L; Wang, Hui; Jáuregui, Ruy; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H; Wurst, Mascha; Pieper, Dietmar H; Simon, Meinhard; Wagner-Döbler, Irene

    2016-01-01

    We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S-47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone.

  1. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton

    PubMed Central

    Milici, Mathias; Deng, Zhi-Luo; Tomasch, Jürgen; Decelle, Johan; Wos-Oxley, Melissa L.; Wang, Hui; Jáuregui, Ruy; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H.; Wurst, Mascha; Pieper, Dietmar H.; Simon, Meinhard; Wagner-Döbler, Irene

    2016-01-01

    We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone. PMID:27199970

  2. Charcoal records reveal past occurrences of disturbances in the forests of the Kisangani region, Democratic Republic of the Congo

    NASA Astrophysics Data System (ADS)

    Tshibamba Mukendi, John; Hubau, Wannes; Ntahobavuka, Honorine; Boyemba Bosela, Faustin; De Cannière, Charles; Beeckman, Hans

    2014-05-01

    Past disturbances have modified local density, structure and floristic composition of Central African rainforests. As such, these perturbations represent a driving force for forest dynamics and they were presumably at the origin of present-day forest mosaics. One of the most prominent disturbances within the forest is fire, leaving behind charcoal as a witness of past forest dynamics. Quantification and identification of ancient charcoal fragments found in soil layers (= pedoanthracology) allows a detailed reconstruction of forest history, including the possible occurrence of past perturbations. The primary objective of this study is to present palaeoenvironmental evidence for the existence of past disturbances in the forests of the Kisangani region (Democratic Republic of the Congo) using a pedoanthracological approach. We quantified and identified charcoal fragments from pedoanthracological excavations in the Yangambi, Yoko, Masako and Kole forest regions. Charcoal sampling was conducted in pit intervals of 10 cm, whereby pottery fragments were also registered and quantified. Floristic identifications were conducted using former protocols based on wood anatomy, which is largely preserved after charcoalification. 14 excavations were conducted and charcoal was found in most pit intervals. Specifically, 52 out of 56 sampled intervals from the Yangambi forest contained charcoal, along with 47 pit intervals from the Yoko forest reserve, 34 pit intervals from the Masako forest and 16 from the Kole forest. Highest specific anthracomasses were recorded in Yoko (167 mg charcoal per kg soil), followed by Yangambi (133 mg/kg), Masako (71,89 mg/kg) and finally Kole (42,4 mg/kg). Charcoal identifications point at a manifest presence of the family of Fabaceae (Caesalpinioideae). This family is characteristic for the tropical humid rainforest. The presence of charcoal fragments from these taxa, associated with pottery sherds on different depths within the profiles, suggests

  3. Widespread occurrence of honey bee pathogens in solitary bees.

    PubMed

    Ravoet, Jorgen; De Smet, Lina; Meeus, Ivan; Smagghe, Guy; Wenseleers, Tom; de Graaf, Dirk C

    2014-10-01

    Solitary bees and honey bees from a neighbouring apiary were screened for a broad set of putative pathogens including protists, fungi, spiroplasmas and viruses. Most sampled bees appeared to be infected with multiple parasites. Interestingly, viruses exclusively known from honey bees such as Apis mellifera Filamentous Virus and Varroa destructor Macula-like Virus were also discovered in solitary bees. A microsporidium found in Andrena vaga showed most resemblance to Nosema thomsoni. Our results suggest that bee hives represent a putative source of pathogens for other pollinators. Similarly, solitary bees may act as a reservoir of honey bee pathogens.

  4. Widespread occurrence of polyhalogenated compounds in fat from kitchen hoods.

    PubMed

    Bendig, Paul; Hägele, Florian; Vetter, Walter

    2013-09-01

    Food and contaminated indoor environments are the most relevant sources of human exposure to polyhalogenated chemicals. This study analyzed for the first time fat residues in kitchen hoods for contaminations with polyhalogenated compounds. A wide range of contaminants was detected in all kitchen hoods (n = 15) and most of them could be quantified. Between 0.2 and 18 μg polyhalogenated chemicals/g fat were detected, with chlorinated paraffins being the most relevant contaminant group. Aside from the chlorinated paraffins, each kitchen hood fat sample showed a distinct fingerprint. A wide range of old and current-use brominated flame retardants were also detected in the samples. In addition to these contaminants originating from their use in indoor equipment, residues of organochlorine pesticides and semi-volatile halogenated natural products verified that cooking of food, accompanied with the release of contaminants from the heated food, was another relevant source of contamination. Re-analyses of two samples after 3 months only resulted in small variations in contaminant pattern and concentrations. Therefore, fat from kitchen hoods is proposed as an easily accessible matrix to assess contamination of these hazardous polyhalogenated chemicals.

  5. Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches.

    PubMed

    Ettoumi, Besma; Bouhajja, Emna; Borin, Sara; Daffonchio, Daniele; Boudabous, Abdellatif; Cherif, Ameur

    2010-06-01

    Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n=53) and to Halomonas aquamarina (n=14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora.

  6. Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

    PubMed

    Marcelletti, Simone; Scortichini, Marco

    2016-10-01

    A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results.

  7. Pyrosequencing characterization of the microbiota from Atlantic intertidal marine sponges reveals high microbial diversity and the lack of co-occurrence patterns.

    PubMed

    Alex, Anoop; Antunes, Agostinho

    2015-01-01

    Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.

  8. Recent fracture induced electromagnetic field measurements revealing an Earth system in second order phase transition before the occurrence of significant earthquakes

    NASA Astrophysics Data System (ADS)

    Potirakis, Stelios M.; Contoyiannis, Yiannis; Kopanas, John; Antonopoulos, George; Nomicos, Constantinos; Eftaxias, Konstantinos

    2015-04-01

    A crucial feature observed in the study of fracture induced electromagnetic emissions (EMEs) is the asynchronous appearance of MHz and kHz AE-EM precursors: the MHz EMEs precede the kHz ones: the strong avalanche-like kHz emissions are launched in the tail of pre-fracture emissions. Herein, we focus on the systematically observed precursory MHz EME. We show that both, the MHz EMEs recorded prior to recent significant earthquakes that occurred in Greece and the associated seismic activities came to critical condition a few days before the main shock occurrence. The analyses were performed my means of two independent statistical method, namely, the method of critical fluctuation and the natural time method, both revealing critical features. This results indicates the existence of a strong connection of the MHz EME with the corresponding earthquake preparation process. Accumulated laboratory, theoretical and numerical evidence supports the hypothesis that the MHz EME is emitted during the fracture of process of heterogeneous medium surrounding the family of strong entities (asperities) distributed along the fault sustaining the system. The kHz EME is attributed to the family of asperities themselves.

  9. Pyrosequencing Characterization of the Microbiota from Atlantic Intertidal Marine Sponges Reveals High Microbial Diversity and the Lack of Co-Occurrence Patterns

    PubMed Central

    Alex, Anoop; Antunes, Agostinho

    2015-01-01

    Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts. PMID:25992625

  10. Environmental occurrences

    SciTech Connect

    Black, D.G.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the onsite and offsite releases of radioactive and regulated materials. The specific agencies notified of the releases depended on the type, amount, and location of the individual occurrences. The more significant of these off-normal environmental occurrences are summarized in this section.

  11. Integrative conjugative elements are widespread in field isolates of Mycoplasma species pathogenic for ruminants.

    PubMed

    Tardy, Florence; Mick, Virginie; Dordet-Frisoni, Emilie; Marenda, Marc Serge; Sirand-Pugnet, Pascal; Blanchard, Alain; Citti, Christine

    2015-03-01

    Comparative genomics have revealed massive horizontal gene transfer (HGT) between Mycoplasma species sharing common ruminant hosts. Further results pointed toward an integrative conjugative element (ICE) as an important contributor of HGT in the small-ruminant-pathogen Mycoplasma agalactiae. To estimate the prevalence of ICEs in ruminant mycoplasmas, we surveyed their occurrence in a collection of 166 field strains representing 4 (sub)species that are recognized as major pathogens. Based on available sequenced genomes, we first defined the conserved, minimal ICE backbone as composed of 4 coding sequences (CDSs) that are evenly distributed and predicted to be essential for ICE chromosomal integration-excision and horizontal transfer. Screening of the strain collection revealed that these 4 CDSs are well represented in ruminant Mycoplasma species, suggesting widespread occurrence of ICEs. Yet their prevalence varies within and among species, with no correlation found with the individual strain history. Extrachromosomal ICE forms were also often detected, suggesting that ICEs are able to circularize in all species, a first and essential step in ICE horizontal transfer. Examination of the junction of the circular forms and comparative sequence analysis of conserved CDSs clearly pointed toward two types of ICE, the hominis and spiroplasma types, most likely differing in their mechanism of excision-integration. Overall, our data indicate the occurrence and maintenance of functional ICEs in a large number of field isolates of ruminant mycoplasmas. These may contribute to genome plasticity and gene exchanges and, presumably, to the emergence of diverse genotypes within pathogenic mycoplasmas of veterinary importance.

  12. Widespread Synchronous Volcanism Reveals a Broad Galapagos Hotspot Melting Anomaly

    NASA Astrophysics Data System (ADS)

    O'Connor, J. M.; Stoffers, P.; Wijbrans, J. R.; Worthington, T. J.

    2004-12-01

    The massive aseismic ridges and associated seamounts dominating the morphology of the Panama Basin, eastern Central Pacific, have long been attributed to a Galapagos hotspot melting anomaly linked to a deep-seated mantle plume. Although these structures can provide information about the origin of hotspots and existence, or otherwise, of mantle plumes very little is known about their volcanic histories due to a lack of direct age and geochemical information. We report here 74 whole rock and 2 plagioclase 40Ar/39Ar ages for rocks dredged from 53 locations during the first systematic sampling of the Cocos, Carnegie, Coiba and Malpelo aseismic ridges and associated seamounts (F.S. SONNE PAGANINI expedition). In addition we also report ages for DSDP drill sites on Cocos, Carnegie and Coiba ridges and 7 Cocos Island subaerial samples. The distribution of new, and published ages for the Galapagos Archipelago-platform and NE end of the Cocos Ridge, show a general trend of increasing age with distance from the Galapagos Archipelago. A more dominant trend however is one of aseismic ridge-seamount formation in a progression of broad zones of synchronous, often overlapping volcanism created at discrete intervals. Broad zones of coeval Cocos and Carnegie volcanism once formed much larger regions of synchronous volcanism that have been split apart by the complex history of seafloor spreading associated with the Cocos-Nazca spreading center. We link these broad regions of synchronous volcanism to a correspondingly large hotspot melting anomaly. The present day, as yet unfragmented, zone of synchronous volcanism associated with this proposed broad hotspot is marked by the extensive region of recent volcanism extending across the Nazca and Cocos plates encompassing the Galapagos Archipelago-Platform and the Cocos Ridge as far north as Cocos Island. The complex tectonic history of the Cocos-Nazca spreading-center has controlled how the broad zones of synchronous, often overlapping volcanism created by the broad Galapagos melting anomaly have been fragmented between the Cocos and Nazca plates. However, interplay between the broad Galapagos melting anomaly and the Cocos-Nazca spreading center is a second-order process compared to a fundamental underlying mantle process responsible for a broad Galapagos hotspot melting anomaly exhibiting long-lived characteristics (size, time-progression, episodicity) which, on a first-order, are independent of local tectonics and lithospheric architecture. Evidence for a broad Galapagos hotspot melting anomaly and the possibility of detecting long-lived underlying mantle processes has implications for how oceanic hotspot volcanism is sampled for purposes of rigorously testing the mantle plume paradigm. A major question posed by our results is whether individual Pacific seamount chains are in fact the product of tectonic plate drift over narrow hotspots? If not, then inferring the existence and behavior of a mantle plume on the basis of age progression of volcanism produced by a narrow seamount chain could well prove to be misleading. Thus, although great leaps are being made in the theory and numerical modeling - often on a global scale - of hypothesized deep plumes, significantly more high-quality age and geochemical data are needed for oceanic hotspot volcanism that gave birth to the mantle plume hypothesis in the first place.

  13. Widespread RNA 3'-end oligouridylation in mammals.

    PubMed

    Choi, Yun S; Patena, Weronika; Leavitt, Andrew D; McManus, Michael T

    2012-03-01

    Nontemplated 3'-end oligouridylation of RNA occurs in many species, including humans. Unlike the familiar phenomenon of polyadenylation, nontemplated addition of uridines to RNA is poorly characterized in higher eukaryotes. Recent studies have reported nontemplated 3'-end oligouridylation of small RNAs and mRNAs. Oligouridylation is involved in many aspects of microRNA biology from biogenesis to turnover of the mature species, and it may also mark long mRNAs for degradation by promoting decapping of the protective 5'-cap structure. To determine the prevalence of oligouridylation in higher eukaryotes, we used next-generation sequencing technology to deeply examine the population of small RNAs in human cells. Our data revealed widespread nontemplated nucleotide addition to the 3' ends of many classes of RNA, with short stretches of uridine being the most frequently added nucleotide.

  14. Widespread horizontal transfer of retrotransposons

    PubMed Central

    Walsh, Ali Morton; Kortschak, R. Daniel; Gardner, Michael G.; Bertozzi, Terry; Adelson, David L.

    2013-01-01

    In higher organisms such as vertebrates, it is generally believed that lateral transfer of genetic information does not readily occur, with the exception of retroviral infection. However, horizontal transfer (HT) of protein coding repetitive elements is the simplest way to explain the patchy distribution of BovB, a long interspersed element (LINE) about 3.2 kb long, that has been found in ruminants, marsupials, squamates, monotremes, and African mammals. BovB sequences are a major component of some of these genomes. Here we show that HT of BovB is significantly more widespread than believed, and we demonstrate the existence of two plausible arthropod vectors, specifically reptile ticks. A phylogenetic tree built from BovB sequences from species in all of these groups does not conform to expected evolutionary relationships of the species, and our analysis indicates that at least nine HT events are required to explain the observed topology. Our results provide compelling evidence for HT of genetic material that has transformed vertebrate genomes. PMID:23277587

  15. Phylogeography of a widespread North American migratory songbird (Setophaga ruticilla).

    PubMed

    Colbeck, Gabriel J; Gibbs, H Lisle; Marra, Peter P; Hobson, Keith; Webster, Michael S

    2008-01-01

    Genetic analyses for many widespread North American species have revealed significant east-west differentiation, indicating that many survived through the Pleistocene in 2 glacial refugia-1 in the eastern and 1 in the western part of the continent. It remains unclear, however, whether other areas may have served as important glacial refugia. Moreover, many such species exhibit widespread genetic similarity within eastern and western regions because of recent expansion from small refugial populations, making it difficult to evaluate current-day levels of gene flow. In this study, we used mitochondrial DNA (mtDNA) control region sequence and amplified fragment length polymorphism markers to survey genetic variation in a widespread migratory bird, the American redstart (Setophaga ruticilla). mtDNA analyses revealed a pattern that contrasts with that found for most other widespread species studied to date: most redstart populations across North America appear to have spread out from a single glacial refugium, possibly located in the southeastern United States, whereas populations in far-eastern Canada may have survived in a second glacial refugium located on the now-submerged Atlantic coastal shelf off the coast of Newfoundland. A pattern of isolation by distance in mtDNA suggested some constraints on current-day gene flow among extant redstart populations. This study thus reveals a recent evolutionary history for this species that differs from that of most other widespread North American passerines and provides evidence for limited gene flow in a species with potentially large dispersal distances.

  16. Occurrence of silicate melt, carbonate-rich melt and fluid during medium pressure anatexis of metapelitic gneisses (Oberpfalz, Bavaria) revealed by melt and fluid inclusions study

    NASA Astrophysics Data System (ADS)

    Ferrero, Silvio; O'Brien, Patrick; Hecht, Lutz; Wunder, Bernd

    2014-05-01

    In the last decades our understanding of partial melting processes in the lower crust profited from the investigation of fluid inclusions (Touret et al., 2009) and more recently of anatectic melt inclusions (Cesare et al., 2011) within enclaves and high-grade terranes. The latter finding allowed us to directly analyse the original anatectic melt (Ferrero et al., 2012; Bartoli et al., 2013) preserved within peritectic phases, i.e. mainly garnet, but also ilmenite and spinel, before fractionation, mixing and contamination processes took place. Furthermore, the occurrence of primary fluid inclusions (FI) and anatectic melt inclusions (MI) within enclaves allowed the characterization of the COH fluid present during anatexis under fluid+melt immiscibility conditions (Ferrero et al., 2014). Primary crystallized MI, or "nanogranites", and FI have been identified to occur as clusters in garnet from stromatic migmatites (Zeilengneise) from Oberpfalz, Eastern Bavaria (Moldanubian Zone). During the late Carboniferous, these Grt+Bt+Sill+Crd+Spl metapelitic gneisses underwent HT/MP metamorphism, followed by a HT/LP event (Tanner & Behrmann, 1995). Nanogranites, ≤20 µm in size, consist of Qtz+Bt+Wm+Ab±Ap, and show abundant nanoporosity, localized in the quartz. Fluid inclusions are smaller, generally ≤10 µm, and contain CO2+N2+CH4 plus siderite, pyrophillite and cristobalite, mineral phases not observed in the surrounding rock or as mineral inclusion in garnet. Polycrystalline inclusions containing Cc+Wm+Opx±Qz, commonly ≤10 µm in diameter, occur in the same cluster with MI and FI. Microstructural features, negative-crystal shape and the well-developed crystalline faces of calcite within inclusions suggest that they may result from the crystallization of a carbonate-rich melt. The lack of arrays of carbonate-bearing MI, verified by cathodoluminiscence investigation, supports their primary nature, i.e. they formed during garnet growth. This would suggest the occurrence

  17. Organohalogens in nature: More widespread than previously assumed

    SciTech Connect

    Asplund, G.; Grimvall, A. )

    1991-08-01

    Although the natural production of organohalogens has been observed in several studies, it is generally assumed to be much smaller than the industrial production of these compounds. Nevertheless, two important natural sources have been known since the 1970s: red algae in marine ecosystems produce large amounts of brominated compounds, and methyl halides of natural origin are present in the atmosphere. During the past few years it has been shown that organohalogens are so widespread in groundwater, surface water, and soil that all samples in the studies referred to contain measurable amounts of absorbable organohalogens (AOX). The authors document the widespread occurrence of organohalogens in unpolluted soil and water and discuss possible sources of these compounds. It has been suggested that these organohalogens originate from long-range atmospheric transport of industrially produced compounds. The authors review existing evidence of enzymatically mediated halogenation of organic matter in soil and show that, most probably, natural halogenation in the terrestrial environment is the largest source.

  18. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits.

    PubMed

    Marcelletti, Simone; Scortichini, Marco

    2015-01-01

    The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches.

  19. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits

    PubMed Central

    Marcelletti, Simone; Scortichini, Marco

    2015-01-01

    The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches. PMID:26147218

  20. DNA sequence analyses reveal co-occurrence of novel haplotypes of Fasciola gigantica with F. hepatica in South Africa and Zimbabwe.

    PubMed

    Mucheka, Vimbai T; Lamb, Jennifer M; Pfukenyi, Davies M; Mukaratirwa, Samson

    2015-11-30

    The aim of this study was to identify and determine the genetic diversity of Fasciola species in cattle from Zimbabwe, the KwaZulu-Natal and Mpumalanga provinces of South Africa and selected wildlife hosts from Zimbabwe. This was based on analysis of DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS1 and 2) and mitochondrial cytochrome oxidase 1 (CO1) regions. The sample of 120 flukes was collected from livers of 57 cattle at 4 abattoirs in Zimbabwe and 47 cattle at 6 abattoirs in South Africa; it also included three alcohol-preserved duiker, antelope and eland samples from Zimbabwe. Aligned sequences (ITS 506 base pairs and CO1 381 base pairs) were analyzed by neighbour-joining, maximum parsimony and Bayesian inference methods. Phylogenetic trees revealed the presence of Fasciola gigantica in cattle from Zimbabwe and F. gigantica and Fasciola hepatica in the samples from South Africa. F. hepatica was more prevalent (64%) in South Africa than F. gigantica. In Zimbabwe, F. gigantica was present in 99% of the samples; F. hepatica was found in only one cattle sample, an antelope (Hippotragus niger) and a duiker (Sylvicapra grimmia). This is the first molecular confirmation of the identity Fasciola species in Zimbabwe and South Africa. Knowledge on the identity and distribution of these liver flukes at molecular level will allow disease surveillance and control in the studied areas.

  1. Division of shape-standardized tobacco cells reveals a limit to the occurrence of single-criterion-based selection of the plane of symmetric division.

    PubMed

    Asada, Tetsuhiro

    2013-06-01

    The plane of symmetric plant cell division tends to be selected so that the new cross-wall halving the cell volume has the least possible area, and several cases of such selection are best represented by a recently formulated model which promotes the view that the strength of the least area tendency is the only criterion for selecting the plane. To test this model, the present study examined the divisions of two types of shape-standardized tobacco BY-2 cell, oblate-spheroidal (os) cells prepared from protoplasts and spheri-cylindrical (sc) cells with unusual double-wall structures prepared from plasmolyzed cells. Measurements of cell shape parameters and division angles revealed that both cell types most frequently divide nearly along their short axes. While os cells did not exhibit any other division angle bias, sc cell division was characterized by another bias which made the frequency of longitudinal divisions secondarily high. The geometry of sc cells barely allows the longitudinal cross-walls to have locally minimum areas. Nevertheless, a comparison of detected and hypothetical standard divisions indicates that the frequency of longitudinal sc cell division can be significantly higher than that predicted when the longitudinal cross-walls are assumed to have locally minimum areas smaller than their original areas. These results suggest that, even in isolated plant cell types, the strength of the least area tendency is not the only criterion for selecting the division plane. The possibility that there is another basic, though often hidden, criterion is discussed.

  2. Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats

    PubMed Central

    Dealtry, Simone; Ding, Guo-Chun; Weichelt, Viola; Dunon, Vincent; Schlüter, Andreas; Martini, María Carla; Papa, María Florencia Del; Lagares, Antonio; Amos, Gregory Charles Auton; Wellington, Elizabeth Margaret Helen; Gaze, William Hugo; Sipkema, Detmer; Sjöling, Sara; Springael, Dirk; Heuer, Holger; van Elsas, Jan Dirk; Thomas, Christopher; Smalla, Kornelia

    2014-01-01

    IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are “hot spots” of plasmids potentially carrying catabolic genes. PMID:24587126

  3. Using U-series and beryllium isotopes to reveal the occurrence and relative timing of crustal and mantle processes in the Southern Volcanic Zone of Chile

    NASA Astrophysics Data System (ADS)

    Cooper, L. B.; Reubi, O.; Dungan, M. A.; Bourdon, B.; Langmuir, C. H.; Turner, S. J.; Schaefer, J. M.

    2012-12-01

    Magmas erupted from subduction zone volcanoes represent the end products of multiple magmatic processes occurring in the asthenospheric mantle wedge and overlying lithosphere (i.e., fluid addition, melting, assimilation, and crystal fractionation). To resolve the contributions of diverse processes and components, and the relative timing of these events, we have determined U-series activities (U-Th-Ra-Pa) for 60 and 10Be compositions for 20 historic or very young lavas carefully chosen on the basis of major and trace element analyses of 625 samples from six volcanoes in the Andean Southern Volcanic Zone of Chile (37.6-41.1°S: Nevados de Chillán, Antuco, Llaima, Lonquimay, Villarrica, and Osorno). Our dataset demonstrates that each of these volcanoes reflects a unique combination and sequence of magmatic processes that are only revealed through analysis of multiple samples spanning the extent of intra-volcano and intra-eruption chemical variation. Sigmarsson et al. (1990; 2002) identified a regional trend using U-series and Be from mostly single samples, which they interpreted to represent along-strike variations in the flux of slab-derived fluids into the wedge [from 230Th-excess plus 226Ra-deficit plus low 10Be/9Be at Chillán towards progressively higher 238U- and Ra-excesses and 10Be/9Be at Villarrica and Osorno]. These data fall within the much broader array defined by our results, but we infer the operation of assimilation (e.g., Llaima; Reubi et al., 2011) and aging of subduction zone components of variable compositions and proportions in the mantle prior to partial melting as important factors in generating the highly individualized and complex U-series systematics observed at each of these six volcanoes. All of the volcanoes exhibit evidence of assimilation, with the exception of Lonquimay which has undergone mostly closed-system fractional crystallization. At Llaima and Chillán the assimilant is crustal. At Villarica, flux-related melts that dominate in

  4. Type 2 Diabetes Widespread in Adults

    MedlinePlus

    ... version of this page please turn Javascript on. Type 2 Diabetes Widespread in Adults Past Issues / Fall 2006 Table ... pre-diabetes have an increased risk for developing type 2 diabetes, the most common form of diabetes, and for ...

  5. Microwave Photonics: current challenges towards widespread application.

    PubMed

    Capmany, José; Li, Guifang; Lim, Christina; Yao, Jianping

    2013-09-23

    Microwave Photonics, a symbiotic field of research that brings together the worlds of optics and radio frequency is currently facing several challenges in its transition from a niche to a truly widespread technology essential to support the ever-increasing values for speed, bandwidth, processing capability and dynamic range that will be required in next generation hybrid access networks. We outline these challenges, which are the subject of the contributions to this focus issue.

  6. THE WIDESPREAD OCCURRENCE OF THE ENTEROHEMOLYSIN GENE EHLYA AMONG ENVIRONMENTAL STRAINS OF ESCHERICHIA COLI

    EPA Science Inventory

    The putative virulence factor enterohemolysin, encoded for by the ehlyA gene, has been closely associated with the pathogenic enterohemorrhagic Escherichia coli (EHEC) group. E. coli isolates from effluents from seven geographically dispersed municipal ...

  7. Wildlife contamination with fluoroquinolones from livestock: Widespread occurrence of enrofloxacin and marbofloxacin in vultures.

    PubMed

    Blanco, Guillermo; Junza, Alexandra; Segarra, David; Barbosa, José; Barrón, Dolores

    2016-02-01

    There is much recent interest in the presence and impact of veterinary pharmaceuticals in wildlife. Livestock carcasses are often disposed of in supplementary feeding stations for avian scavengers, as a management and conservation tool for these species worldwide. In feeding stations, vultures and other scavengers can consume carcasses almost immediately after disposal, which implies the potential ingestion of veterinary pharmaceuticals as a non-target consequence of supplementary feeding. Using UPLC-MS/MS and HPLC-TOF, we evaluated the presence and concentration of fluoroquinolone residues in plasma of nestling vultures feeding on domestic livestock carrion. Three different fluoroquinolones (marbofloxacin, enrofloxacin and its metabolite ciprofloxacin) and a non-targeted β-lactam (nafcillin) were detected in vulture plasma. The high proportion of individuals (92%) with fluoroquinolone residues at variable concentrations (up to ∼20 μg L(-1) of enrofloxacin and ∼150 μg L(-1) of marbofloxacin) sampled in several geographically distant colonies and on different dates suggests that these and other drugs were potentially ingested throughout nestling development. Contamination with veterinary fluoroquinolones and other pharmaceuticals should be considered as an unintended but alarming consequence of food management in threatened wildlife.

  8. Widespread occurrence of bisphenol A in paper and paper products: implications for human exposure.

    PubMed

    Liao, Chunyang; Kannan, Kurunthachalam

    2011-11-01

    Bisphenol A (BPA) is used in a variety of consumer products, including some paper products, particularly thermal receipt papers, for which it is used as a color developer. Nevertheless, little is known about the magnitude of BPA contamination or human exposure to BPA as a result of contact with paper and paper products. In this study, concentrations of BPA were determined in 15 types of paper products (n = 202), including thermal receipts, flyers, magazines, tickets, mailing envelopes, newspapers, food contact papers, food cartons, airplane boarding passes, luggage tags, printing papers, business cards, napkins, paper towels, and toilet paper, collected from several cities in the USA. Thermal receipt papers also were collected from Japan, Korea, and Vietnam. BPA was found in 94% of thermal receipt papers (n = 103) at concentrations ranging from below the limit of quantitation (LOQ, 1 ng/g) to 13.9 mg/g (geometric mean: 0.211 mg/g). The majority (81%) of other paper products (n = 99) contained BPA at concentrations ranging from below the LOQ to 14.4 μg/g (geometric mean: 0.016 μg/g). Whereas thermal receipt papers contained the highest concentrations of BPA (milligram-per-gram), some paper products, including napkins and toilet paper, made from recycled papers contained microgram-per-gram concentrations of BPA. Contamination during the paper recycling process is a source of BPA in paper products. Daily intake (DI) of BPA through dermal absorption was estimated based on the measured BPA concentrations and handling frequency of paper products. The daily intake of BPA (calculated from median concentrations) through dermal absorption from handling of papers was 17.5 and 1300 ng/day for the general population and occupationally exposed individuals, respectively; these values are minor compared with exposure through diet. Among paper products, thermal receipt papers contributed to the majority (>98%) of the exposures.

  9. Gliding motility and Por secretion system genes are widespread among members of the phylum bacteroidetes.

    PubMed

    McBride, Mark J; Zhu, Yongtao

    2013-01-01

    The phylum Bacteroidetes is large and diverse, with rapid gliding motility and the ability to digest macromolecules associated with many genera and species. Recently, a novel protein secretion system, the Por secretion system (PorSS), was identified in two members of the phylum, the gliding bacterium Flavobacterium johnsoniae and the nonmotile oral pathogen Porphyromonas gingivalis. The components of the PorSS are not similar in sequence to those of other well-studied bacterial secretion systems. The F. johnsoniae PorSS genes are a subset of the gliding motility genes, suggesting a role for the secretion system in motility. The F. johnsoniae PorSS is needed for assembly of the gliding motility apparatus and for secretion of a chitinase, and the P. gingivalis PorSS is involved in secretion of gingipain protease virulence factors. Comparative analysis of 37 genomes of members of the phylum Bacteroidetes revealed the widespread occurrence of gliding motility genes and PorSS genes. Genes associated with other bacterial protein secretion systems were less common. The results suggest that gliding motility is more common than previously reported. Microscopic observations confirmed that organisms previously described as nonmotile, including Croceibacter atlanticus, "Gramella forsetii," Paludibacter propionicigenes, Riemerella anatipestifer, and Robiginitalea biformata, exhibit gliding motility. Three genes (gldA, gldF, and gldG) that encode an apparent ATP-binding cassette transporter required for F. johnsoniae gliding were absent from two related gliding bacteria, suggesting that the transporter may not be central to gliding motility.

  10. Laser light scattering in diagnostics of widespread diseases

    NASA Astrophysics Data System (ADS)

    Petrova, Galina P.; Petrusevich, Yurii M.; Alexeev, Sergei G.; Ivanov, Andrei V.

    2002-08-01

    The multiparametric physical method for diagnosing of widespread diseases including oncological disease based on Rayleigh light scattering is proposed. There was studied simultaneously dynamic and static parameters of blood plasma proteins. This method is the product of extensive research conducted on a molecular level on the indicative fields of the human body such as blood serum or lymph. Comprehensive measurements at molecular level and determinations of parameters related to these fluids, especially blood serum, have revealed significant differences in the values of certain parameters in patients with oncological diseases and for healthy individuals.

  11. Pain and the brain: chronic widespread pain.

    PubMed

    Arnold, Lesley M

    2009-04-01

    Chronic widespread pain is associated with several medical and psychiatric disorders including, but not limited to, chronic fatigue syndrome, fibromyalgia, mood disorders, hepatitis, endocrine disorders such as hypothyroidism, and rheumatologic disorders such as rheumatoid arthritis. Careful and comprehensive differential diagnosis must be performed to ensure a correct diagnosis before an appropriate treatment can be selected. Fibromyalgia, in particular, is challenging to diagnose and treat because it shares many characteristics with other disorders and is commonly concurrent with major mood disorders. A comprehensive disease management strategy including patient education, pharmacotherapy, cognitive-behavioral therapy, and aerobic and other forms of exercise can be beneficial for many patients with fibromyalgia.

  12. Widespread Antarctic glaciation during the Late Eocene

    NASA Astrophysics Data System (ADS)

    Carter, Andrew; Riley, Teal R.; Hillenbrand, Claus-Dieter; Rittner, Martin

    2017-01-01

    Marine sedimentary rocks drilled on the southeastern margin of the South Orkney microcontinent in Antarctica (Ocean Drilling Program Leg 113 Site 696) were deposited between ∼36.5 Ma to 33.6 Ma, across the Eocene-Oligocene climate transition. The recovered rocks contain abundant grains exhibiting mechanical features diagnostic of iceberg-rafted debris. Sand provenance based on a multi-proxy approach that included petrographic analysis of over 275,000 grains, detrital zircon geochronology and apatite thermochronometry rule out local sources (Antarctic Peninsula or the South Orkney Islands) for the material. Instead the ice-transported grains show a clear provenance from the southern Weddell Sea region, extending from the Ellsworth-Whitmore Mountains of West Antarctica to the coastal region of Dronning Maud Land in East Antarctica. This study provides the first evidence for a continuity of widespread glacier calving along the coastline of the southern Weddell Sea embayment at least 2.5 million yrs before the prominent oxygen isotope event at 34-33.5 Ma that is considered to mark the onset of widespread glaciation of the Antarctic continent.

  13. Ultraviolet vision may be widespread in bats

    USGS Publications Warehouse

    Gorresen, P. Marcos; Cryan, Paul; Dalton, David C.; Wolf, Sandy; Bonaccorso, Frank

    2015-01-01

    Insectivorous bats are well known for their abilities to find and pursue flying insect prey at close range using echolocation, but they also rely heavily on vision. For example, at night bats use vision to orient across landscapes, avoid large obstacles, and locate roosts. Although lacking sharp visual acuity, the eyes of bats evolved to function at very low levels of illumination. Recent evidence based on genetics, immunohistochemistry, and laboratory behavioral trials indicated that many bats can see ultraviolet light (UV), at least at illumination levels similar to or brighter than those before twilight. Despite this growing evidence for potentially widespread UV vision in bats, the prevalence of UV vision among bats remains unknown and has not been studied outside of the laboratory. We used a Y-maze to test whether wild-caught bats could see reflected UV light and whether such UV vision functions at the dim lighting conditions typically experienced by night-flying bats. Seven insectivorous species of bats, representing five genera and three families, showed a statistically significant ‘escape-toward-the-light’ behavior when placed in the Y-maze. Our results provide compelling evidence of widespread dim-light UV vision in bats.

  14. Weird Weather: Large Abrupt Widespread Climate Changes

    SciTech Connect

    Alley, Richard B.

    2001-01-24

    Ice-core records and other paleoclimatic indicators show that large (up to 10 degrees C), abrupt (in about 10 years), widespread (hemispheric to global) climate changes have been common for much of the last 100,000 years and beyond, but rare during the most recent few millennia. Changes in the coupled ocean-atmosphere system with a center of activity in the north Atlantic probably have been important, but several hypotheses remain possible including solar influence and a stochastically resonant interaction with changing freshwater fluxes. Our current understanding does not allow us to exclude the possibility that human or natural processes could 'flip the switch' of another abrupt change in the future.

  15. International arrivals: widespread bioinvasions in European Seas

    PubMed Central

    Galil, B.S.; Marchini, A.; Occhipinti-Ambrogi, A.; Minchin, D.; Narščius, A.; Ojaveer, H.; Olenin, S.

    2014-01-01

    The European Union lacks a comprehensive framework to address the threats posed by the introduction and spread of marine non-indigenous species (NIS). Current efforts are fragmented and suffer substantial gaps in coverage. In this paper we identify and discuss issues relating to the assessment of spatial and temporal patterns of introductions in European Seas (ES), based on a scientifically validated information system of aquatic non-indigenous and cryptogenic species, AquaNIS. While recognizing the limitations of the existing data, we extract information that can be used to assess the relative risk of introductions for different taxonomic groups, geographic regions and likely vectors. The dataset comprises 879 multicellular NIS. We applied a country-based approach to assess patterns of NIS richness in ES, and identify the principal introduction routes and vectors, the most widespread NIS and their spatial and temporal spread patterns. Between 1970 and 2013, the number of recorded NIS has grown by 86, 173 and 204% in the Baltic, Western European margin and the Mediterranean, respectively; 52 of the 879 NIS were recorded in 10 or more countries, and 25 NIS first recorded in European seas since 1990 have since been reported in five or more countries. Our results highlight the ever-rising role of shipping (commercial and recreational) as a vector for the widespread and recently spread NIS. The Suez Canal, a corridor unique to the Mediterranean, is responsible for the increased introduction of new thermophilic NIS into this warming sea. The 2020 goal of the EU Biodiversity Strategy concerning marine Invasive Alien Species may not be fully attainable. The setting of a new target date should be accompanied by scientifically robust, sensible and pragmatic plans to minimize introductions of marine NIS and to study those present. PMID:24899770

  16. Ice Nucleation Activity in the Widespread Soil Fungus Mortierella alpina

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Hill, T. C. J.; Pummer, B. G.; Franc, G. D.; Pöschl, U.

    2014-08-01

    Biological residues in soil dust are a potentially strong source of atmospheric ice nuclei (IN). So far, however, the abundance, diversity, sources, seasonality, and role of biological - in particular, fungal - IN in soil dust have not been characterized. By analysis of the culturable fungi in topsoils, from a range of different land use and ecosystem types in south-east Wyoming, we found ice nucleation active (INA) fungi to be both widespread and abundant, particularly in soils with recent inputs of decomposable organic matter. Across all investigated soils, 8% of fungal isolates were INA. All INA isolates initiated freezing at -5 to -6 °C, and belonged to a single zygomycotic species, Mortierella alpina (Mortierellales, Mortierellomycotina). By contrast, the handful of fungal species so far reported as INA all belong within the Ascomycota or Basidiomycota phyla. M. alpina is known to be saprobic, widespread in soil and present in air and rain. Sequencing of the ITS region and the gene for γ-linolenic-elongase revealed four distinct clades, affiliated to different soil types. The IN produced by M. alpina seem to be proteinaceous, <300 kDa in size, and can be easily washed off the mycelium. Ice nucleating fungal mycelium will ramify topsoils and probably also release cell-free IN into it. If these IN survive decomposition or are adsorbed onto mineral surfaces, their contribution might accumulate over time, perhaps to be transported with soil dust and influencing its ice nucleating properties.

  17. Widespread Surface Weathering on Early Mars

    NASA Astrophysics Data System (ADS)

    Loizeau, Damien; Carter, John; Mangold, Nicolas; Poulet, François; Rossi, Angelo; Allemand, Pascal; Quantin, Cathy; Bibring, Jean-Pierre

    2014-05-01

    The recent discovery of widespread hydrous clays on Mars indicates that diverse and widespread aqueous environments existed on Mars, from the surface to kilometric depths [1,2]. The study of the past habitability and past climates of the planet requires assessing the importance of sustained surface water vs. subsurface water in its aqueous history. Using remote sensing data, we propose that surface weathering existed on Mars, suggesting that Mars experienced durable episodes of sustained liquid water on its surface. Weathering profiles are identified as vertical sequences of Al-rich clays and Fe/Mg-rich clays in the top tens of meters of the surface, similar to cases of pedogenesis on Earth (e.g. [3,4]). Such localized clay sequences have been reported by other works in 3 regions of Mars [5-8] and a similar origin was also proposed. Their frequency is however likely underestimated due to limitations of orbital investigations and re-surfacing processes. A large survey of the CRISM dataset leaded to a down-selection of ~100 deposits with clear vertical sequences, widely distributed over the southern highlands and grouped in regional clusters [9]. These putative weathering sequences are found either on inter-crater plateaus, on the floor of craters and large basins, or on crater ejectas. We investigated the thickness of the altered sequences, the age of the altered units and the different geological contexts to further understand the weathering process(es). Using few HiRISE DEMs where possible, and CTX DEMs, we find that the thickness of the exposed Al clays is on average of the order of several meters to few tens of meters. The clay sequences reported here are consistent with terrestrial weathering sequences which form under wet climates over geological timescales (>105-107 years). The combined age assessment of the altered unit and the unaltered capping (where present) provides constraints on the age of the weathering itself. All investigated cases point to an

  18. Widespread Surface Weathering on Early Mars

    NASA Astrophysics Data System (ADS)

    Loizeau, D.; Carter, J.; Mangold, N.; Poulet, F.; Rossi, A.; Allemand, P.; Quantin, C.; Bibring, J.

    2013-12-01

    The recent discovery of widespread hydrous clays on Mars indicates that diverse and widespread aqueous environments existed on Mars, from the surface to kilometric depths [1,2]. The study of the past habitability of the planet requires assessing the importance of sustained surface water vs. subsurface water in its aqueous history. Using remote sensing data, we propose that surface weathering existed on Mars, suggesting that Mars experienced durable episodes of sustained liquid water on its surface. Weathering profiles are identified as vertical sequences of Al-rich clays and Fe/Mg-rich clays in the top tens of meters of the surface, similar to cases of pedogenesis on Earth (e.g. [3,4]). Such localized clay sequences have been reported by other works in 3 regions of Mars [5-8] and a similar origin was also proposed. Their frequency is however likely underestimated due to limitations of orbital investigations and re-surfacing processes. A large survey of the CRISM dataset leaded to a down-selection of 104 deposits with clear vertical sequences, widely distributed over the southern highlands and grouped in regional clusters [9]. These putative weathering sequences are found either on inter-crater plateaus, on the floor of craters and large basins, or on crater ejectas. We investigated the thickness of the altered sequences, the age of the altered units and the different geological contexts to further understand the weathering process(es). Using few HiRISE DEMs where possible, and CTX DEMs, we find that the thickness of the exposed Al clays is on average of the order of several meters to few tens of meters. The clay sequences reported here are consistent with terrestrial weathering sequences which form under wet climates over geological timescales (> 105-107 years). The combined age assessment of the altered unit and the unaltered capping (where present) provides constraints on the age of the weathering itself. All investigated cases point to an active weathering

  19. Widespread RNA 3′-end oligouridylation in mammals

    PubMed Central

    Choi, Yun S.; Patena, Weronika; Leavitt, Andrew D.; McManus, Michael T.

    2012-01-01

    Nontemplated 3′-end oligouridylation of RNA occurs in many species, including humans. Unlike the familiar phenomenon of polyadenylation, nontemplated addition of uridines to RNA is poorly characterized in higher eukaryotes. Recent studies have reported nontemplated 3′-end oligouridylation of small RNAs and mRNAs. Oligouridylation is involved in many aspects of microRNA biology from biogenesis to turnover of the mature species, and it may also mark long mRNAs for degradation by promoting decapping of the protective 5′-cap structure. To determine the prevalence of oligouridylation in higher eukaryotes, we used next-generation sequencing technology to deeply examine the population of small RNAs in human cells. Our data revealed widespread nontemplated nucleotide addition to the 3′ ends of many classes of RNA, with short stretches of uridine being the most frequently added nucleotide. PMID:22291204

  20. The characterization of widespread fatigue damage in fuselage structure

    NASA Technical Reports Server (NTRS)

    Piascik, Robert S.; Willard, Scott A.; Miller, Matthew

    1994-01-01

    The characteristics of widespread fatigue damage (WSFD) in fuselage riveted structure were established by detailed nondestructive and destructive examinations of fatigue damage contained in a full size fuselage test article. The objectives of this were to establish an experimental data base for validating emerging WSFD analytical prediction methodology and to identify first order effects that contribute to fatigue crack initiation and growth. Detailed examinations were performed on a test panel containing four bays of a riveted lap splice joint. The panel was removed from a full scale fuselage test article after receiving 60,000 full pressurization cycles. The results of in situ examinations document the progression of fuselage skin fatigue crack growth through crack linkup. Detailed tear down examinations and fractography of the lap splice joint region revealed fatigue crack initiation sites, crack morphology, and crack linkup geometry. From this large data base, distributions of crack size and locations are presented and discussions of operative damage mechanisms are offered.

  1. Cryoprotective dehydration is widespread in Arctic springtails.

    PubMed

    Sørensen, Jesper Givskov; Holmstrup, Martin

    2011-08-01

    Cryoprotective dehydration (CPD) is a cold tolerance strategy employed by small invertebrates that readily lose water by evaporation when subjected to sub-zero temperatures in the presence of ice. Until now, relatively few species have been investigated using methods by which CPD can be shown. In the present study we investigated the cold tolerance strategy of seven soil arthropod species from the high Arctic Spitzbergen, and compared water content and water loss, body fluid melting points (MP) and survival under cold and desiccating conditions. We tested the hypothesis that CPD is a commonly occurring cold hardiness strategy among soil arthropods. We found that four springtail species (Hypogastrura viatica, Folsomia quadrioculata, Oligaphorura groenlandica and Megaphorura arctica; Collembola) went through severe dehydration and MP equilibration with ambient temperature, and thus overwinter by employing CPD, whereas a beetle (Atheta graminicola) and one of the springtails (Isotoma anglicana) were typical freeze avoiding species over-wintering by supercooling. Desiccation tolerance of the red velvet mite (Neomolgus littoralis) was also investigated; very low water loss rates of this species indicated that it does not survive winter by use of CPD. All in all, the results of the present study confirm the hypothesis that CPD is an effective over-wintering strategy which is widespread within soil arthropods.

  2. Ecosystem scale acoustic sensing reveals humpback whale behavior synchronous with herring spawning processes and re-evaluation finds no effect of sonar on humpback song occurrence in the Gulf of Maine in fall 2006.

    PubMed

    Gong, Zheng; Jain, Ankita D; Tran, Duong; Yi, Dong Hoon; Wu, Fan; Zorn, Alexander; Ratilal, Purnima; Makris, Nicholas C

    2014-01-01

    We show that humpback-whale vocalization behavior is synchronous with peak annual Atlantic herring spawning processes in the Gulf of Maine. With a passive, wide-aperture, densely-sampled, coherent hydrophone array towed north of Georges Bank in a Fall 2006 Ocean Acoustic Waveguide Remote Sensing (OAWRS) experiment, vocalizing whales could be instantaneously detected and localized over most of the Gulf of Maine ecosystem in a roughly 400-km diameter area by introducing array gain, of 18 dB, orders of magnitude higher than previously available in acoustic whale sensing. With humpback-whale vocalizations consistently recorded at roughly 2000/day, we show that vocalizing humpbacks (i) were overwhelmingly distributed along the northern flank of Georges Bank, coinciding with the peak spawning time and location of Atlantic herring, and (ii) their overall vocalization behavior was strongly diurnal, synchronous with the formation of large nocturnal herring shoals, with a call rate roughly ten-times higher at night than during the day. Humpback-whale vocalizations were comprised of (1) highly diurnal non-song calls, suited to hunting and feeding behavior, and (2) songs, which had constant occurrence rate over a diurnal cycle, invariant to diurnal herring shoaling. Before and during OAWRS survey transmissions: (a) no vocalizing whales were found at Stellwagen Bank, which had negligible herring populations, and (b) a constant humpback-whale song occurrence rate indicates the transmissions had no effect on humpback song. These measurements contradict the conclusions of Risch et al. Our analysis indicates that (a) the song occurrence variation reported in Risch et al. is consistent with natural causes other than sonar, (b) the reducing change in song reported in Risch et al. occurred days before the sonar survey began, and (c) the Risch et al. method lacks the statistical significance to draw the conclusions of Risch et al. because it has a 98-100% false-positive rate and lacks

  3. Ecosystem Scale Acoustic Sensing Reveals Humpback Whale Behavior Synchronous with Herring Spawning Processes and Re-Evaluation Finds No Effect of Sonar on Humpback Song Occurrence in the Gulf of Maine in Fall 2006

    PubMed Central

    Gong, Zheng; Jain, Ankita D.; Tran, Duong; Yi, Dong Hoon; Wu, Fan; Zorn, Alexander; Ratilal, Purnima; Makris, Nicholas C.

    2014-01-01

    We show that humpback-whale vocalization behavior is synchronous with peak annual Atlantic herring spawning processes in the Gulf of Maine. With a passive, wide-aperture, densely-sampled, coherent hydrophone array towed north of Georges Bank in a Fall 2006 Ocean Acoustic Waveguide Remote Sensing (OAWRS) experiment, vocalizing whales could be instantaneously detected and localized over most of the Gulf of Maine ecosystem in a roughly 400-km diameter area by introducing array gain, of 18 dB, orders of magnitude higher than previously available in acoustic whale sensing. With humpback-whale vocalizations consistently recorded at roughly 2000/day, we show that vocalizing humpbacks (i) were overwhelmingly distributed along the northern flank of Georges Bank, coinciding with the peak spawning time and location of Atlantic herring, and (ii) their overall vocalization behavior was strongly diurnal, synchronous with the formation of large nocturnal herring shoals, with a call rate roughly ten-times higher at night than during the day. Humpback-whale vocalizations were comprised of (1) highly diurnal non-song calls, suited to hunting and feeding behavior, and (2) songs, which had constant occurrence rate over a diurnal cycle, invariant to diurnal herring shoaling. Before and during OAWRS survey transmissions: (a) no vocalizing whales were found at Stellwagen Bank, which had negligible herring populations, and (b) a constant humpback-whale song occurrence rate indicates the transmissions had no effect on humpback song. These measurements contradict the conclusions of Risch et al. Our analysis indicates that (a) the song occurrence variation reported in Risch et al. is consistent with natural causes other than sonar, (b) the reducing change in song reported in Risch et al. occurred days before the sonar survey began, and (c) the Risch et al. method lacks the statistical significance to draw the conclusions of Risch et al. because it has a 98–100% false-positive rate and

  4. Cholinergic urethral brush cells are widespread throughout placental mammals.

    PubMed

    Deckmann, Klaus; Krasteva-Christ, Gabriela; Rafiq, Amir; Herden, Christine; Wichmann, Judy; Knauf, Sascha; Nassenstein, Christina; Grevelding, Christoph G; Dorresteijn, Adriaan; Chubanov, Vladimir; Gudermann, Thomas; Bschleipfer, Thomas; Kummer, Wolfgang

    2015-11-01

    We previously identified a population of cholinergic epithelial cells in murine, human and rat urethrae that exhibits a structural marker of brush cells (villin) and expresses components of the canonical taste transduction signaling cascade (α-gustducin, phospholipase Cβ2 (PLCβ2), transient receptor potential cation channel melanostatin 5 (TRPM5)). These cells serve as sentinels, monitoring the chemical composition of the luminal content for potentially hazardous compounds such as bacteria, and initiate protective reflexes counteracting further ingression. In order to elucidate cross-species conservation of the urethral chemosensory pathway we investigated the occurrence and molecular make-up of urethral brush cells in placental mammals. We screened 11 additional species, at least one in each of the five mammalian taxonomic units primates, carnivora, perissodactyla, artiodactyla and rodentia, for immunohistochemical labeling of the acetylcholine synthesizing enzyme, choline acetyltransferase (ChAT), villin, and taste cascade components (α-gustducin, PLCβ2, TRPM5). Corresponding to findings in previously investigated species, urethral epithelial cells with brush cell shape were immunolabeled in all 11 mammals. In 8 species, immunoreactivities against all marker proteins and ChAT were observed, and double-labeling immunofluorescence confirmed the cholinergic nature of villin-positive and chemosensory (TRPM5-positive) cells. In cat and horse, these cells were not labeled by the ChAT antiserum used in this study, and unspecific reactions of the secondary antiserum precluded conclusions about ChAT-expression in the bovine epithelium. These data indicate that urethral brush cells are widespread throughout the mammalian kingdom and evolved not later than about 64.5millionyears ago.

  5. Ice nucleation activity in the widespread soil fungus Mortierella alpina

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, Janine; Hill, Thomas C. J.; Pummer, Bernhard G.; Yordanova, Petya; Franc, Gary D.; Pöschl, Ulrich

    2015-04-01

    Biological residues in soil dust are a potentially strong source of atmospheric ice nucleators (IN). However, the sources and characteristics of biological - in particular, fungal - IN in soil dust have not been characterized. By analysis of the culturable fungi in topsoils, from a range of different land use and ecosystem types in south-east Wyoming, we found ice nucleation active (INA, i.e., inducing ice formation in the probed range of temperature and concentration) fungi to be both widespread and abundant, particularly in soils with recent inputs of decomposable organic matter. For example, in harvested and ploughed sugar beet and potato fields, and in the organic horizon beneath Lodgepole pine forest, their relative abundances and concentrations among the cultivable fungi were 25% (8 x 103 CFU g-1), 17% (4.8 x 103 CFU g-1) and 17% (4 x 103 CFU g-1), respectively. Across all investigated soils, 8% (2.9 x 103 CFU g-1) of fungal isolates were INA. All INA isolates initiated freezing at -5° C to -6° C and all belonged to a single zygomycotic species, Mortierella alpina (Mortierellales, Mortierellomycotina). By contrast, the handful of fungal species so far reported as INA all belong within the Ascomycota or Basidiomycota phyla. Mortierella alpina is known to be saprobic (utilizing non-living organic matter), widespread in soil and present in air and rain. Sequencing of the ITS region and the gene for γ-linolenic elongase revealed four distinct clades, affiliated to different soil types. The IN produced by M. alpina seem to be extracellular proteins of 100-300 kDa in size which are not anchored in the fungal cell wall. Ice nucleating fungal mycelium will ramify topsoils and probably also release cell-free IN into it. If these IN survive decomposition or are adsorbed onto mineral surfaces, these small cell-free IN might contribute to the as yet uncharacterized pool of atmospheric IN released by soils as dusts.

  6. Analysis of co-occurrence networks with clique occurrence information

    NASA Astrophysics Data System (ADS)

    Shen, Bin; Li, Yixiao

    2014-12-01

    Most of co-occurrence networks only record co-occurrence relationships between two entities, and ignore the weights of co-occurrence cliques whose size is bigger than two. However, this ignored information may help us to gain insight into the co-occurrence phenomena of systems. In this paper, we analyze co-occurrence networks with clique occurrence information (CNCI) thoroughly. First, we describe the components of CNCIs and discuss the generation of clique occurrence information. And then, to illustrate the importance and usefulness of clique occurrence information, several metrics, i.e. single occurrence rate, average size of maximal co-occurrence cliques and four types of co-occurrence coefficients etc., are given. Moreover, some applications, such as combining co-occurrence frequency with structure-oriented centrality measures, are also discussed.

  7. Becker muscular dystrophy with widespread muscle hypertrophy and a non-sense mutation of exon 2.

    PubMed

    Witting, N; Duno, M; Vissing, J

    2013-01-01

    Becker muscular dystrophy features progressive proximal weakness, wasting and often focal hypertrophy. We present a patient with pain and cramps from adolescence. Widespread muscle hypertrophy, preserved muscle strength and a 10-20-fold raised CPK were noted. Muscle biopsy was dystrophic, and Western blot showed a 95% reduction of dystrophin levels. Genetic analyses revealed a non-sense mutation in exon 2 of the dystrophin gene. This mutation is predicted to result in a Duchenne phenotype, but resulted in a mild Becker muscular dystrophy with widespread muscle hypertrophy. We suggest that this unusual phenotype is caused by translation re-initiation downstream from the mutation site.

  8. REVIEW: Widespread access to predictive models in the motor system: a short review

    NASA Astrophysics Data System (ADS)

    Davidson, Paul R.; Wolpert, Daniel M.

    2005-09-01

    Recent behavioural and computational studies suggest that access to internal predictive models of arm and object dynamics is widespread in the sensorimotor system. Several systems, including those responsible for oculomotor and skeletomotor control, perceptual processing, postural control and mental imagery, are able to access predictions of the motion of the arm. A capacity to make and use predictions of object dynamics is similarly widespread. Here, we review recent studies looking at the predictive capacity of the central nervous system which reveal pervasive access to forward models of the environment.

  9. 77 FR 55105 - Aging Airplane Program: Widespread Fatigue Damage; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-07

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION Federal Aviation Administration 14 CFR Parts 121 and 129 RIN 2120-AI05 Aging Airplane Program: Widespread... entitled ``Aging Airplane Program: Widespread Fatigue Damage'' (77 FR 30877), which corrected a final...

  10. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife

    PubMed Central

    Balk, Lennart; Hägerroth, Per-Åke; Gustavsson, Hanna; Sigg, Lisa; Åkerman, Gun; Ruiz Muñoz, Yolanda; Honeyfield, Dale C.; Tjärnlund, Ulla; Oliveira, Kenneth; Ström, Karin; McCormick, Stephen D.; Karlsson, Simon; Ström, Marika; van Manen, Mathijs; Berg, Anna-Lena; Halldórsson, Halldór P.; Strömquist, Jennie; Collier, Tracy K.; Börjeson, Hans; Mörner, Torsten; Hansson, Tomas

    2016-01-01

    Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiamine-dependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported. PMID:27958327

  11. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife.

    PubMed

    Balk, Lennart; Hägerroth, Per-Åke; Gustavsson, Hanna; Sigg, Lisa; Åkerman, Gun; Ruiz Muñoz, Yolanda; Honeyfield, Dale C; Tjärnlund, Ulla; Oliveira, Kenneth; Ström, Karin; McCormick, Stephen D; Karlsson, Simon; Ström, Marika; van Manen, Mathijs; Berg, Anna-Lena; Halldórsson, Halldór P; Strömquist, Jennie; Collier, Tracy K; Börjeson, Hans; Mörner, Torsten; Hansson, Tomas

    2016-12-13

    Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiamine-dependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported.

  12. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife

    USGS Publications Warehouse

    Balk, Lennart; Hägerroth, Per-Åke; Gustavsson, Hanna; Sigg, Lisa; Akerman, Gun; Ruiz Muñoz, Yolanda; Honeyfield, Dale C.; Tjarnlund, Ulla; Oliveira, Kenneth; Strom, Karin; McCormick, Stephen D.; Karlsson, Simon; Strom, Marika; van Manen, Mathijs; Berg, Anna-Lena; Halldórsson, Halldór P.; Stromquist, Jennie; Collier, Tracy K.; Borjeson, Hans; Morner, Torsten; Hansson, Tomas

    2016-01-01

    Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiamine-dependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported.

  13. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife

    NASA Astrophysics Data System (ADS)

    Balk, Lennart; Hägerroth, Per-Åke; Gustavsson, Hanna; Sigg, Lisa; Åkerman, Gun; Ruiz Muñoz, Yolanda; Honeyfield, Dale C.; Tjärnlund, Ulla; Oliveira, Kenneth; Ström, Karin; McCormick, Stephen D.; Karlsson, Simon; Ström, Marika; van Manen, Mathijs; Berg, Anna-Lena; Halldórsson, Halldór P.; Strömquist, Jennie; Collier, Tracy K.; Börjeson, Hans; Mörner, Torsten; Hansson, Tomas

    2016-12-01

    Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiamine-dependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported.

  14. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    NASA Astrophysics Data System (ADS)

    Comte, J.; Lovejoy, C.; Crevecoeur, S.; Vincent, W. F.

    2015-07-01

    Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North-South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

  15. Archaea were widespread in sediments of the Messinian Salinity Crisis

    NASA Astrophysics Data System (ADS)

    Birgel, Daniel; Peckmann, Jörn

    2015-04-01

    The Messinian salinity crisis (MSC) was among the most extreme and short-lived paleooceanographic events in Earth history and dramatically impacted the depositional environments of the Mediterranean. Many of the Messinian sedimentary sequences reflect environmental variability on extremely short time scales, typified by phenomena like evaporation and high salinities, anoxia, and desiccation. Only few organisms tolerate such severe conditions. Among those are archaea, many of which are especially well adapted to extreme conditions. We studied various MSC locations and deposits to shed light onto the role of archaea in the MSC, focusing on lipid biomarkers. These are (1) primary gypsum with abundant, yet problematic filamentous microfossils from various locations in the Mediterranean, (2) Calcare di Base, limestones from Sicily and Calabria, and (3) Calcare Solfifero, authigenic carbonates associated with native sulfur from Sicily. (1) Primary gypsum beds with abundant filamentous fossils are widespread in the Mediterranean. Archaea were found as important contributor of organic matter in these evaporites. The filaments, however, have previously been interpreted to represent cyanobacteria based on the extraction and amplification of cyanobacterial DNA. Cyanobacteria produce specific and long-lasting biomarkers, but no such compounds were found in the studied deposits, thus, the assignment of the filaments to cyanobacteria necessitates further verification. (2) The Calcare di Base are widespread, genetically heterogeneous Messinian limestones, which are particularly common in Sicily and Calabria. The environmental conditions during their deposition, as well as mechanisms and timing of formation are a matter of debate. The studied Calcare di Base samples were found to contain specific halophilic archaeal signatures and numerous pseudomorphs after halite. (3) The Calcare Solfifero, authigenic carbonates accompanied by elemental sulfur formed in the course of microbial

  16. High co-occurrence of anorectal chlamydia with urogenital chlamydia in women visiting an STI clinic revealed by routine universal testing in an observational study; a recommendation towards a better anorectal chlamydia control in women

    PubMed Central

    2014-01-01

    Background Symptom- and sexual history-based testing i.e., testing on indication, for anorectal sexually transmitted infections (STIs) in women is common. Yet, it is unknown whether this strategy is effective. Moreover, little is known about alternative transmission routes i.e. by fingers/toys. This study assesses anorectal STI prevalence and infections missed by current testing practice, thereby informing the optimal control strategy for anorectal STIs in women. Methods Women (n = 663) attending our STI-clinic between May 2012-July 2013 were offered routine testing for anorectal and urogenital Chlamydia trachomatis and Neisseria gonorrhoeae. Data were collected on demographics, sexual behaviour and symptoms. Women were assigned to one of the categories: indication (reported anal sex/symptoms), fingers/toys (only reported use of fingers/toys), or without indication. Results Of women, 92% (n = 654) participated. There were 203 reports (31.0%) of anal sex and/or symptoms (indication), 48 reports (7.3%) of only using fingers/toys (fingers/toys), and 403 reports (61.6%) of no anal symptoms, no anal sex and no anal use of fingers/toys (without indication). The overall prevalence was 11.2% (73/654) for urogenital chlamydia and 8.4% (55/654) for anorectal chlamydia. Gonorrhoea infections were not observed. Prevalence of anorectal chlamydia was 7.9% (16/203) for women with indication and 8.6% (39/451) for all other women (P = 0.74). Two-thirds (39/55) of anorectal infections were diagnosed in women without indication. Isolated anorectal chlamydia was rare (n = 3): of all women with an anorectal infection, 94.5% (52/55) also had co-occurrence of urogenital chlamydia. Of all women with urogenital chlamydia, 71.2% (52/73) also had anorectal chlamydia. Conclusions Current selective testing on indication of symptoms and sexual history is not an appropriate control strategy for anorectal chlamydia in women visiting an STI clinic. Routine universal anorectal

  17. Occurrence of non-hydrolysable amides in the macromolecular constituent of Scenedesmus quadricauda cell wall as revealed by [sup 15]N NMR: Origin of n-alkylnitriles in pyrolysates of ultralaminai-containing kerogens

    SciTech Connect

    Derenne, S.; Largeau, C. ); Taulelle, F. )

    1993-02-01

    New structures, termed ultralaminae, were recently shown to occur in kerogens from numerous oil shales and source rocks. Morphological and chemical studies revealed that ultralaminae originate from the selective preservation of the non-hydrolysable biomacromolecules (algaenans) building up the thin outer walls of several Chlorophyceae (green microalgae) including the cosmopolitan general Scenedesmus and Chlorella. The chemical correlation between such algaenans and fossil ultralaminae was mainly based on the production, on pyrolysis, of nitrogen compounds, n-alkylnitriles, with specific distributions depending on the lacustrine of marine origin of the considered samples. In addition, these bio-and geopolymers were characterized by quite high N levels.

  18. Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

    PubMed Central

    Erwin, Patrick M; Pineda, Mari Carmen; Webster, Nicole; Turon, Xavier; López-Legentil, Susanna

    2014-01-01

    Ascidians are ecologically important components of marine ecosystems yet the ascidian microbiota remains largely unexplored beyond a few model species. We used 16S rRNA gene tag pyrosequencing to provide a comprehensive characterization of microbial symbionts in the tunic of 42 Great Barrier Reef ascidian samples representing 25 species. Results revealed high bacterial biodiversity (3 217 unique operational taxonomic units (OTU0.03) from 19 described and 14 candidate phyla) and the widespread occurrence of ammonia-oxidizing Thaumarchaeota in coral reef ascidians (24 of 25 host species). The ascidian microbiota was clearly differentiated from seawater microbial communities and included symbiont lineages shared with other invertebrate hosts as well as unique, ascidian-specific phylotypes. Several rare seawater microbes were markedly enriched (200–700 fold) in the ascidian tunic, suggesting that the rare biosphere of seawater may act as a conduit for horizontal symbiont transfer. However, most OTUs (71%) were rare and specific to single hosts and a significant correlation between host relatedness and symbiont community similarity was detected, indicating a high degree of host-specificity and potential role of vertical transmission in structuring these communities. We hypothesize that the complex ascidian microbiota revealed herein is maintained by the dynamic microenvironments within the ascidian tunic, offering optimal conditions for different metabolic pathways such as ample chemical substrate (ammonia-rich host waste) and physical habitat (high oxygen, low irradiance) for nitrification. Thus, ascidian hosts provide unique and fertile niches for diverse microorganisms and may represent an important and previously unrecognized habitat for nitrite/nitrate regeneration in coral reef ecosystems. PMID:24152714

  19. High resolution mass spectrometry imaging reveals the occurrence of phenylphenalenone-type compounds in red paracytic stomata and red epidermis tissue of Musa acuminata ssp. zebrina cv. 'Rowe Red'.

    PubMed

    Hölscher, Dirk; Fuchser, Jens; Knop, Katrin; Menezes, Riya C; Buerkert, Andreas; Svatoš, Aleš; Schubert, Ulrich S; Schneider, Bernd

    2015-08-01

    The banana epidermis and in particular their stomata are conducive sites for the penetration of pathogenic fungi which can severely limit global banana production. The red pseudostem of the ornamental banana Musa acuminata ssp. zebrina cv. 'Rowe Red' was used to study the chemical constituents of the epidermal cell layer using matrix-free laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometric imaging (LDI-FT-ICR-MSI). The high resolution of this technique allowed phenylphenalenone-type compounds to be located in single plant cells. Some of these secondary metabolites were identified as constitutive compounds and found in specialized epidermal cells in banana pseudostem tissue. Especially the red paracytic stomata revealed higher signal intensities of certain phenylphenalenones than normal epidermis cells. The ease of detection of polycyclic aromatic compounds on the cellular level is discussed with regard to future investigations of plant-pathogen interactions.

  20. Worldwide Occurrence of Integrative Conjugative Element Encoding Multidrug Resistance Determinants in Epidemic Vibrio cholerae O1

    PubMed Central

    Marin, Michel A.; Fonseca, Erica L.; Andrade, Bruno N.; Cabral, Adriana C.; Vicente, Ana Carolina P.

    2014-01-01

    In the last decades, there has been an increase of cholera epidemics caused by multidrug resistant strains. Particularly, the integrative and conjugative element (ICE) seems to play a major role in the emergence of multidrug resistant Vibrio cholerae. This study fully characterized, by whole genome sequencing, new ICEs carried by multidrug resistant V. cholerae O1 strains from Nigeria (2010) (ICEVchNig1) and Nepal (1994) (ICEVchNep1). The gene content and gene order of these two ICEs are the same, and identical to ICEVchInd5, ICEVchBan5 and ICEVchHai1 previously identified in multidrug resistant V. cholerae O1. This ICE is characterized by dfrA1, sul2, strAB and floR antimicrobial resistance genes, and by unique gene content in HS4 and HS5 ICE regions. Screening for ICEs, in publicly available V. cholerae genomes, revealed the occurrence and widespread distribution of this ICE among V. cholerae O1. Metagenomic analysis found segments of this ICE in marine environments far from the direct influence of the cholera epidemic. Therefore, this study revealed the epidemiology of a spatio-temporal prevalent ICE in V. cholerae O1. Its occurrence and dispersion in V. cholerae O1 strains from different continents throughout more than two decades can be indicative of its role in the fitness of the current pandemic lineage. PMID:25265418

  1. Widespread positive selection in the photosynthetic Rubisco enzyme

    PubMed Central

    Kapralov, Maxim V; Filatov, Dmitry A

    2007-01-01

    Background Rubisco enzyme catalyzes the first step in net photosynthetic CO2 assimilation and photorespiratory carbon oxidation and is responsible for almost all carbon fixation on Earth. The large subunit of Rubisco is encoded by the chloroplast rbcL gene, which is widely used for reconstruction of plant phylogenies due to its conservative nature. Plant systematicists have mainly used rbcL paying little attention to its function, and the question whether it evolves under Darwinian selection has received little attention. The purpose of our study was to evaluate how common is positive selection in Rubisco among the phototrophs and where in the Rubisco structure does positive selection occur. Results We searched for positive selection in rbcL sequences from over 3000 species representing all lineages of green plants and some lineages of other phototrophs, such as brown and red algae, diatoms, euglenids and cyanobacteria. Our molecular phylogenetic analysis found the presence of positive selection in rbcL of most analyzed land plants, but not in algae and cyanobacteria. The mapping of the positively selected residues on the Rubisco tertiary structure revealed that they are located in regions important for dimer-dimer, intradimer, large subunit-small subunit and Rubisco-Rubisco activase interactions, and that some of the positively selected residues are close to the active site. Conclusion Our results demonstrate that despite its conservative nature, Rubisco evolves under positive selection in most lineages of land plants, and after billions of years of evolution Darwinian selection still fine-tunes its performance. Widespread positive selection in rbcL has to be taken into account when this gene is used for phylogenetic reconstructions. PMID:17498284

  2. Direct chemical evidence for widespread dairying in prehistoric Britain

    PubMed Central

    Copley, M. S.; Berstan, R.; Dudd, S. N.; Docherty, G.; Mukherjee, A. J.; Straker, V.; Payne, S.; Evershed, R. P.

    2003-01-01

    Domesticated animals formed an important element of farming practices in prehistoric Britain, a fact revealed through the quantity and variety of animal bone typically found at archaeological sites. However, it is not known whether the ruminant animals were raised purely for their tissues (e.g., meat) or alternatively were exploited principally for their milk. Absorbed organic residues from pottery from 14 British prehistoric sites were investigated for evidence of the processing of dairy products. Our ability to detect dairy fats rests on the observation that the δ13C values of the C18:0 fatty acids in ruminant dairy fats are ≈2.3‰ lower than in ruminant adipose fats. This difference can be ascribed to (i) the inability of the mammary gland to biosynthesize C18:0; (ii) the biohydrogenation of dietary unsaturated fatty acids in the rumen; and (iii) differences (i.e., 8.1‰) in the δ13C values of the plant dietary fatty acids and carbohydrates. The lipids from a total of 958 archaeological pottery vessels were extracted, and the compound-specific δ13C values of preserved fatty acids (C16:0 and C18:0) were determined via gas chromatography-combustion-isotope ratio mass spectrometry. The results provide direct evidence for the exploitation of domesticated ruminant animals for dairy products at all Neolithic, Bronze Age, and Iron Age settlements in Britain. Most significantly, studies of pottery from a range of key early Neolithic sites confirmed that dairying was a widespread activity in this period and therefore probably well developed when farming was introduced into Britain in the fifth millennium B.C. PMID:12574520

  3. Widespread Miocene deep-sea hiatuses: coincidence with periods of global cooling.

    USGS Publications Warehouse

    Barron, J.A.; Keller, G.

    1982-01-01

    High-resolution biostratigraphic analyses of Miocene deep-sea cores reveal eight intervals of widespread hiatuses in the world ocean. In complete sections these hiatuses correspond to intervals of cool faunal and floral assemblages, rapid enrichment of delta 18O, and sea-level regressions. These factors suggest that Miocene deep-sea hiatuses result from an increased intensity of circulation and corrosiveness of bottom currents during periods of increased polar refrigeration.-Authors

  4. Significance of satellite DNA revealed by conservation of a widespread repeat DNA sequence among angiosperms.

    PubMed

    Mehrotra, Shweta; Goel, Shailendra; Raina, Soom Nath; Rajpal, Vijay Rani

    2014-08-01

    The analysis of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of plant nuclear DNA. In the present study, we analyzed the nature of pCtKpnI-I and pCtKpnI-II tandem repeated sequences, reported earlier in Carthamus tinctorius. Interestingly, homolog of pCtKpnI-I repeat sequence was also found to be present in widely divergent families of angiosperms. pCtKpnI-I showed high sequence similarity but low copy number among various taxa of different families of angiosperms analyzed. In comparison, pCtKpnI-II was specific to the genus Carthamus and was not present in any other taxa analyzed. The molecular structure of pCtKpnI-I was analyzed in various unrelated taxa of angiosperms to decipher the evolutionary conserved nature of the sequence and its possible functional role.

  5. Steroid profiling reveals widespread local regulation of glucocorticoid levels during mouse development.

    PubMed

    Taves, Matthew D; Plumb, Adam W; Sandkam, Benjamin A; Ma, Chunqi; Van Der Gugten, Jessica Grace; Holmes, Daniel T; Close, David A; Abraham, Ninan; Soma, Kiran K

    2015-02-01

    Glucocorticoids (GCs) are produced by the adrenal glands and circulate in the blood to coordinate organismal physiology. In addition, different tissues may independently regulate their local GC levels via local GC synthesis. Here, we find that in the mouse, endogenous GCs show tissue-specific developmental patterns, rather than mirroring GCs in the blood. Using solid-phase extraction, HPLC, and specific immunoassays, we quantified endogenous steroids and found that in tissues of female and male mice, (1) local GC levels can be much higher than systemic GC levels, (2) local GCs follow age-related patterns different from those of systemic GCs, and (3) local GCs have identities different from those of systemic GCs. For example, whereas corticosterone is the predominant circulating adrenal GC in mice, high concentrations of cortisol were measured in neonatal thymus, bone marrow, and heart. The presence of cortisol was confirmed with liquid chromatography-tandem mass spectrometry. In addition, gene expression of steroidogenic enzymes was detected across multiple tissues, consistent with local GC production. Our results demonstrate that local GCs can differ from GCs in circulating blood. This finding suggests that steroids are widely used as local (paracrine or autocrine) signals, in addition to their classic role as systemic (endocrine) signals. Local GC regulation may even be the norm, rather than the exception, especially during development.

  6. Widespread interspecies homologous recombination reveals reticulate evolution within the genus Streptomyces.

    PubMed

    Cheng, Kun; Rong, Xiaoying; Huang, Ying

    2016-09-01

    Homologous recombination is increasingly being recognized as a driving force in microbial evolution. However, recombination in streptomycetes, a rich source of diverse secondary metabolites, particularly among different species, remains minimally investigated. In this study, the largest sample of Streptomyces species to date, consisting of 142 type strains spanning the genus, with available sequences of 16S rRNA, atpD, gyrB, recA, rpoB and trpB genes, were collected and subjected to a comprehensive population genetic analysis to generate an overall estimate of the level of Streptomyces interspecies genetic exchange and its effect on the evolution of this genus. The results indicate frequent homologous recombination among Streptomyces species, which occurred three times more frequently and was nearly 14 times more important than point mutation in nucleotide sequence divergence (ρ/θw=3.10, r/m=13.74). As a result, a facilitating effect on the evolutionary process and confusion in phylogenetic relationships were observed, as well as a number of specific transfer events of the six gene fragments. A resultant phylogenetic network depicted extensive horizontal genetic exchange which decays clonality in streptomycetes. Moreover, seven evolutionary lineage groups were identified in the present sample in the Structure analysis, generally consistent with morphological and physiological data, and the contribution of recombination was detected to be varied among them. Our analyses demonstrated a reticulate evolution within Streptomyces due to the high level of interspecies gene exchange, which greatly challenges the traditional tree-shaped phylogeny in this genus and may advance our evolutionary understanding of a genuine Streptomyces species.

  7. Spatially integrated assessment reveals widespread changes in penguin populations on the Antarctic Peninsula.

    PubMed

    Lynch, Heather J; Naveen, Ron; Trathan, Philip N; Fagan, William F

    2012-06-01

    As important marine mesopredators and sensitive indicators of Antarctic ecosystem change, penguins have been a major focus of long-term biological research in the Antarctic. However, the vast majority of such studies have been constrained by logistics and relate mostly to the temporal dynamics of individual breeding populations from which regional trends have been inferred, often without regard for the complex spatial heterogeneity of population processes and the underlying environmental conditions. Integrating diverse census data from 70 breeding sites across 31 years in a robust, hierarchical analysis, we find that trends from intensely studied populations may poorly reflect regional dynamics and confuse interpretation of environmental drivers. Results from integrated analyses confirm that Pygoscelis adeliae (Adélie Penguins) are decreasing at almost all locations on the Antarctic Peninsula. Results also resolve previously contradictory studies and unambiguously establish that P. antarctica (Chinstrap Penguins), thought to benefit from decreasing sea ice, are instead declining regionally. In contrast, another open-water species, P. papua (Gentoo Penguin), is increasing in abundance and expanding southward. These disparate population trends accord with recent mechanistic hypotheses of biological change in the Southern Ocean and highlight limitations of the influential but oversimplified "sea ice" hypothesis. Aggregating population data at the regional scale also allows us to quantify rates of regional population change in a way not previously possible.

  8. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

    PubMed

    Core, Leighton J; Waterfall, Joshua J; Lis, John T

    2008-12-19

    RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on approximately 30% of human genes, transcription extends beyond pre-messenger RNA 3' cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene. This divergent polymerase is associated with active genes but does not elongate effectively beyond the promoter. These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.

  9. Phylogenetic relationships of rat lungworm, Angiostrongylus cantonensis, isolated from different geographical regions revealed widespread multiple lineages.

    PubMed

    Tokiwa, Toshihiro; Harunari, Tsunehito; Tanikawa, Tsutomu; Komatsu, Noriyuki; Koizumi, Nobuo; Tung, Kwong-Chung; Suzuki, Jun; Kadosaka, Teruki; Takada, Nobuhiro; Kumagai, Takashi; Akao, Nobuaki; Ohta, Nobuo

    2012-09-01

    We conducted a pilot survey of genetic variation of A. cantonensis using small subunit (SSU) ribosomal (r) RNA and mitochondrial cytochrome c oxidase subunit I (coxI) gene sequences. Two distinct SSU genotypes (G1 and G2) were identified among 17 individual A. cantonensis worms from 17 different geographical localities in Japan, Mainland China, Taiwan, and Thailand. The partial coxI sequences were determined for 83 worms from 18 different geographical localities from Japan, Mainland China, Taiwan, and Thailand. Phylogenetic analysis showed eight distinct coxI haplotypes (ac1 to ac8). In 16 out of 18 localities, only a single coxI haplotype was found. However, in two localities, two coxI haplotypes coexisted. The common haplotypes found were: haplotype ac1 (Tokyo, Chiba, Kanagawa, Amamioshima Island, and Taichung), haplotype ac2 (Ishikawa, Shenzhen, and Lianjiang), haplotype ac5 (the Okinawa and the Ogasawara Islands), and haplotype ac7 (Miyagi, Aichi, and Kanagawa). Each of these regions is separated from the others by high mountain ranges or oceans. In addition, the lower genetic variation and particular geographical distribution of A. cantonensis in each location could indicate a founder effect, which may have resulted from multiple independent origins, and suggests that haplotypes migrated from endemic areas via human-related transportation.

  10. A widespread self-cleaving ribozyme class is revealed by bioinformatics

    PubMed Central

    Roth, Adam; Weinberg, Zasha; Chen, Andy G. Y.; Kim, Peter B.; Ames, Tyler D.; Breaker, Ronald R.

    2013-01-01

    Ribozymes are noncoding RNAs that promote chemical transformations with rate enhancements approaching those of protein enzymes. Although ribozymes are likely to have been abundant during the RNA world era, only ten classes are known to exist among contemporary organisms. We report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. Nearly 2700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. Two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs. PMID:24240507

  11. Effects of Recreation on Animals Revealed as Widespread through a Global Systematic Review

    PubMed Central

    Reed, Sarah E.; Merenlender, Adina M.; Crooks, Kevin R.

    2016-01-01

    Outdoor recreation is typically assumed to be compatible with biodiversity conservation and is permitted in most protected areas worldwide. However, increasing numbers of studies are discovering negative effects of recreation on animals. We conducted a systematic review of the scientific literature and analyzed 274 articles on the effects of non-consumptive recreation on animals, across all geographic areas, taxonomic groups, and recreation activities. We quantified trends in publication rates and outlets, identified knowledge gaps, and assessed evidence for effects of recreation. Although publication rates are low and knowledge gaps remain, the evidence was clear with over 93% of reviewed articles documenting at least one effect of recreation on animals, the majority of which (59%) were classified as negative effects. Most articles focused on mammals (42% of articles) or birds (37%), locations in North America (37.7%) or Europe (26.6%), and individual-level responses (49%). Meanwhile, studies of amphibians, reptiles, and fish, locations in South America, Asia, and Africa, and responses at the population and community levels are lacking. Although responses are likely to be species-specific in many cases, some taxonomic groups (e.g., raptors, shorebirds, ungulates, and corals) had greater evidence for an effect of recreation. Counter to public perception, non-motorized activities had more evidence for a negative effect of recreation than motorized activities, with effects observed 1.2 times more frequently. Snow-based activities had more evidence for an effect than other types of recreation, with effects observed 1.3 times more frequently. Protecting biodiversity from potentially harmful effects of recreation is a primary concern for conservation planners and land managers who face increases in park visitation rates; accordingly, there is demand for science-based information to help solve these dilemmas. PMID:27930730

  12. Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.

    PubMed

    Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendón, María A; Calton, Christine M; Hernández, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene

    2010-07-28

    Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange.

  13. Widespread decadal-scale decrease of glacier speed revealed using repeat optical satellite images

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2012-04-01

    Matching of repeat optical satellite images to derive glacier velocities is an approach that is much used within glaciology. Lately, focus has been put into developing, improving, automating and comparing different image matching methods. This makes it now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have decreased their speeds over the last decades, Pamir by 43 % in average per decade, Caucasus by 8 % in average per decade, Penny Ice Cap by 25 % in average per decade, Alaska Range by 11 % in average per decade and Patagonia by 20 % in average per decade. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area.

  14. Repeat optical satellite images reveal widespread and long term decrease in land-terminating glacier speeds

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2012-04-01

    By matching of repeat optical satellite images it is now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have over the last decades decreased their velocity at an average rate per decade of: 43 % in the Pamir, 8 % in the Caucasus, 25 % on Penny Ice Cap, 11 % in the Alaska Range and 20 % in Patagonia. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area. Therefore the calculated average speed change is not representative for this area.

  15. Worldwide widespread decadal-scale decrease of glacier speed revealed using repeat optical satellite images

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2011-10-01

    Matching of repeat optical satellite images to derive glacier velocities is an approach that is much used within glaciology. Lately, focus has been put into developing, improving, automating and comparing different image matching methods. This makes it now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have decreased their speeds over the last decades, Pamir by 43 % in average per decade, Caucasus by 8 % in average per decade, Penny Ice Cap by 25 % in average per decade, Alaska Range by 11 % in average per decade and Patagonia by 20 % in average per decade. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area.

  16. Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

    PubMed Central

    Bonocora, Richard P.; Smith, Carol; Lapierre, Pascal; Wade, Joseph T.

    2015-01-01

    Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs. PMID:26425847

  17. Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species

    PubMed Central

    Marri, Pradeep Reddy; Paniscus, Mary; Hernández, Diana R.; Higashi, Dustin L.; Sodergren, Erica; Weinstock, George M.; Rounsley, Steven D.; So, Magdalene

    2010-01-01

    Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange. PMID:20676376

  18. Glycoproteins: Occurrence and Significance

    NASA Astrophysics Data System (ADS)

    Wittmann, Valentin

    Protein glycosylation is regarded as the most complex form of post-translational modification leading to a heterogeneous expression of glycoproteins as mixtures of glycoforms. This chapter describes the structure and occurrence of glycoproteins with respect to their glycan chains. Discussed are different carbohydrate-peptide linkages including GPI anchors, common structures of N- and O-glycans, and the structure of glycosaminoglycans contained in proteoglycans. Also covered are the bacterial cell wall polymer peptidoglycan and the glycopeptide antibiotics of the vancomycin group. Properties and functions of the glycans contained in glycoproteins are dealt with in the next chapter of this book.

  19. Widespread occurrence of perchlorate in water, foodstuffs and human urine collected from Kuwait and its contribution to human exposure.

    PubMed

    Alomirah, Husam F; Al-Zenki, Sameer F; Alaswad, Marivi C; Alruwaih, Noor A; Wu, Qian; Kannan, Kurunthachalam

    2016-06-01

    Perchlorate is a thyroid hormone-disrupting compound and is reported to occur widely in the environment. Little is known on human exposure to perchlorate in Kuwait. In this study, 218 water samples, 618 commonly consumed foodstuffs and 532 urine samples collected from Kuwait were analysed to assess the exposure of the Kuwaiti population to perchlorate. For the estimation of daily intake of perchlorate, food consumption rates were obtained from the National Nutrition Survey in the State of Kuwait (NNSSK). The results showed that leafy vegetables accounted for a major share of perchlorate exposure among the Kuwaiti population at 0.062 µg kg(-)(1) bw day(-)(1) (36.2%), followed by fruits at 0.026 µg kg(-)(1) bw day(-)(1) (15.3%) and non-leafy vegetables at 0.017 µg kg(-)(1) bw day(-)(1) (10.1%). The urinary perchlorate geometric mean (GM) concentrations ranged from 8.51 to 17.1 µg l(-)(1) for the five age groups, which were higher than those reported in other countries. The estimated urinary perchlorate exposure for the Kuwaiti general population was 0.42 µg kg(-)(1) bw day(-)(1), which was higher than that reported for the United States. The dietary intake of perchlorate for the Kuwaiti population ranged from 0.14 to 0.67 µg kg(-)(1) bw day(-)(1) for the five age groups, with a mean total daily intake of 0.17 µg kg(-)(1) bw day(-)(1) for the general population. The highest estimated dietary mean daily intake of perchlorate (0.67 µg kg(-)(1) bw day(-)(1)) was found for children at 3-5 years. The estimated dietary perchlorate exposure in Kuwait is higher than the recommended mean reference dose (RfD) but lower than that of provisional maximum tolerable daily intake (PMTDI) set by the Joint FAO/WHO Expert Committee on Food Additives (JECFA).

  20. Discovery and widespread occurrence of polyhalogenated 1,1'-dimethyl-2,2'-bipyrroles (PDBPs) in marine biota.

    PubMed

    Hauler, Carolin; Martin, René; Knölker, Hans-Joachim; Gaus, Caroline; Mueller, Jochen F; Vetter, Walter

    2013-07-01

    Polyhalogenated 1,1'-dimethyl-2,2'-bipyrroles (PDBPs) are halogenated natural products (HNPs) previously shown to bioaccumulate in marine mammals and birds. Since their discovery in 1999, six hexahalogenated and a few lesser halogenated congeners have been identified in diverse marine mammal samples. Here we report the identification of 17 additional hexahalogenated PDBPs in the blubber extract of a humpback dolphin (Sousa chinensis) from Queensland, Australia. Thirteen of these new PDBPs were also detected in an Australian sea cucumber (Holothuria sp.). Additional samples were also tested positive on several new PDBPs, including an Australian venus tuskfish (Choerodon venustus) as well as a white whale (Delphinapterus leucas) and a sperm whale (Physeter macrocephalus) from the Northern Hemisphere. GC/ECNI-MS-SIM quantification of the molecular ions was carried out with the help of synthesized standards. The sum concentration of PDBPs was 1.1 mg/kg lipid in the humpback dolphin and 0.48 mg/kg lipid in the sea cucumber.

  1. PERCHLORATE: Occurrence is Widespread but at Varying Levels; Federal Agencies Have Taken Some Actions to Respond to and Lessen Releases

    DTIC Science & Technology

    2010-08-01

    Compensation, and Liability Act of 1980 DOD Department of Defense DOE Department of Energy EPA Environmental Protection Agency FDA Food and...Hazard Assessment RCRA Resource Conservation and Recovery Act UCMR 1 Unregulated Contaminant Monitoring Rule 1 This is a work of the U.S...Drinking Water Act , as amended,3 when EPA decides to regulate a contaminant, its determination must be based on findings that (1) the contaminant may have

  2. Phthalates - widespread occurrence and the effect on male gametes. Part 1. General characteristics, sources and human exposure.

    PubMed

    Dobrzyńska, Małgorzata M

    2016-01-01

    Phthalates are widely present in human environment. Widespead exposure to those agents, which are compounds of numerous daily use products, is unavoidable. In the current paper following phthalates benzylbutyl phthalate (BBP), di- n-butyl phthalate (DBP), di(2-ethylhexyl)phthalate (DEHP), diethyl phthalate (DEP), di-isononyl phthalate (DINP) are described. Phthalates mainly enter to the composition of plastic goods, like boxes and containers for storage of foods, toys, medical devices, and also cosmetics, personal care products, as well as paints, vanishes, printing inks. This paper describes the occurence of individual phthalates in the environment (water, air) and in different products. During production, transportation, manufacturing of goods and improper disposal, phthalates released into soil, water and air. For example indoor air included 13 mg/m3 phthalates, where 72 % of all constitutes DEP (2.29 mg/m(3)), BBP (3.97 mg/m(3)) and DEHP (2.43 mg/m(3)). Exposure to phthalates take place mainly by ingestion or inhalation air or through the skin. Presence of phthalates were observed in numerous food products and is connected with migration of those compounds from food storage containers to preserved food. They could mirgate to salivia during sucking and chewing of toys and this way increased exposure to of children. The results of studies regarding to concentration of phthalates in human tissues and excretions are also described. The level of phthalates were measured in numerous of human biological samples. For example, DEHP, DEP and DBP were detected at levels of 5.71 mg/L in blood serum, of 0.30 mg/L in semen and of 0.72 mg/kg in fat samples.

  3. Widespread occurrence and seasonal variation of pharmaceuticals in surface waters and municipal wastewater treatment plants in central Finland.

    PubMed

    Lindholm-Lehto, Petra C; Ahkola, Heidi S J; Knuutinen, Juha S; Herve, Sirpa H

    2016-04-01

    The presence of five selected pharmaceuticals, consisting of four anti-inflammatory drugs, diclofenac, ibuprofen, ketoprofen, naproxen, and an antiepileptic drug carbamazepine, was determined at four municipal wastewater treatment plants (WWTPs) and in the receiving waterway in central Finland. The samples were taken from influents and effluents of the WWTPs and from surface water of six locations along the water way, including northern Lake Päijänne. In addition, seasonal variation in the area was determined by comparing the concentrations in the winter and summer. The samples were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in the multiple reaction monitoring mode. The concentrations in the influents and effluents ranged from hundreds of nanogram per liter to microgram per liter while ranged from tens of nanogram per liter in northern parts of the waterway to hundreds of nanogram per liter in northern Lake Päijänne near the city area. In addition, the concentrations were higher in the winter compared to summer time in surface water due to decreased temperature and solar irradiation. On the other hand, higher concentrations of ibuprofen, ketoprofen, and naproxen were found in summer at the WWTPs, possibly due to seasonal variations in consumption. In conclusion, there are considerable amounts of pharmaceuticals not only in influents and effluents of the WWTPs but also in lake water along the waterway and in northern Lake Päijänne.

  4. Anaerobic ammonium oxidation in traditional municipal wastewater treatment plants with low-strength ammonium loading: Widespread but overlooked.

    PubMed

    Wang, Shanyun; Peng, Yongzhen; Ma, Bin; Wang, Shuying; Zhu, Guibing

    2015-11-01

    Occurrence of anaerobic ammonium oxidation (anammox) in marine and freshwater systems has greatly changed our understanding of global nitrogen (N) cycle and promoted the investigation of the role and ecological features of anammox in anthropogenic ecosystems. This study focused on the spatio-temporal abundance, activity, and biodiversity of anammox bacteria in full-scale municipal wastewater treatment plants (WWTPs) via traditional nitrification/denitrification route with low-strength ammonium loading. The anammox bacteria were detected in all the treatment units at the five WWTPs tested, even in aerobic zones (dissolved oxygen >2 mg L(-1)) with abundance of 10(5)-10(7) hydrazine synthase (hzs) gene copies g(-1). The (15)N-isotope tracing technology revealed that the anammox rates in WWTPs ranged from 0.08 to 0.36 μmol N g(-1) h(-1) in winter and 0.12-1.20 μmol N g(-1) h(-1) in summer with contributions of 2.05-6.86% and 1.71-7.26% to N2 production, respectively. The diversity of anammox bacteria in WWTPs was distributed over only two genera, Brocadia and Kuenenia. Additionally, the exploration of potential interspecies relationships indicated that ammonia oxidation bacteria (AOB) was the major nitrite-substrate producer for anammox during nitrification, while Nitrospira, a nitrite oxidation bacteria (NOB), was the potential major competitor for nitrite. These results suggested the contribution of N-removal by the widespread of anammox has been overlooked in traditional municipal WWTPs, and the ecological habitats of anammox bacteria in anthropogenic ecosystems are much more abundant than previously assumed.

  5. Inspecting for widespread fatigue damage: Is partial debonding the key?

    NASA Technical Reports Server (NTRS)

    Brewer, John

    1994-01-01

    Experimental and analytical results indicate that cracks can initiate, grow, and coalesce more rapidly in fuselage lap joints that have experienced partial or complete debonding. Computational analysis in this paper shows that stress concentrations and stress intensity factors at the rivet holes are far less severe when the bond is intact. Debonding hastens the initiation of widespread fatigue cracks and significantly increases crack growth rate. Thus, debonded regions serve as "breeding grounds" for widespread fatigue damage. Therefore, the effectiveness of lap joint inspection programs may be enhanced if detailed inspections are focused on areas in which debonding has been detected.

  6. Inspecting for widespread fatigue damage: Is partial debonding the key?

    NASA Astrophysics Data System (ADS)

    Brewer, John

    1994-09-01

    Experimental and analytical results indicate that cracks can initiate, grow, and coalesce more rapidly in fuselage lap joints that have experienced partial or complete debonding. Computational analysis in this paper shows that stress concentrations and stress intensity factors at the rivet holes are far less severe when the bond is intact. Debonding hastens the initiation of widespread fatigue cracks and significantly increases crack growth rate. Thus, debonded regions serve as "breeding grounds" for widespread fatigue damage. Therefore, the effectiveness of lap joint inspection programs may be enhanced if detailed inspections are focused on areas in which debonding has been detected.

  7. Widespread microplastic ingestion by fish assemblages in tropical estuaries subjected to anthropogenic pressures.

    PubMed

    Vendel, A L; Bessa, F; Alves, V E N; Amorim, A L A; Patrício, J; Palma, A R T

    2017-04-15

    Our aim was to quantify microplastic ingestion by fish assemblages in two tropical Brazilian estuaries and to evaluate whether biological and ecological factors influence the ingestion of microplastics by fish species. Of 2233 fish from both estuaries (from 69 species) examined in this study, 9% of the individuals (24 species) had microplastics in their gut contents. Microplastic ingestion occurred irrespective of fish size and functional group. The diet of fish species was analyzed based on prey items identified in the fish's full stomach contents and five feeding guilds were defined. Microplastics were common throughout all feeding guilds. Low (average ingestion values 1.06±0.30 items/total fish) but widespread occurrence among estuaries also indicates proliferation of microplastic pollution. Our findings highlight the need to focus on assemblage level studies to understand the real magnitude of the problem and emphasize the urgency of mitigation measures directed at microplastic pollution in estuarine ecosystems.

  8. Widespread inhibition proportional to excitation controls the gain of a leech behavioral circuit

    PubMed Central

    Kristan, William B.

    2014-01-01

    SUMMARY Changing gain in a neuronal system has important functional consequences, but the underlying mechanisms have been elusive. Models have suggested a variety of neuronal and systems properties to accomplish gain control. Here, we show that the gain of the neuronal network underlying local bending behavior in leeches depends on widespread inhibition. Using behavioral analysis, intracellular recordings, and voltage-sensitive dye imaging, we compared the effects of blocking just the known lateral inhibition with blocking all GABAergic inhibition. This revealed an additional source of inhibition, which was widespread and increased in proportion to increasing stimulus intensity. In a model of the input/output functions of the three-layered local bending network, we showed that inhibiting all interneurons in proportion to the stimulus strength produces the experimentally observed change in gain. This relatively simple mechanism for controlling behavioral gain could be prevalent in vertebrate as well as invertebrate nervous systems. PMID:18215624

  9. 75 FR 69745 - Aging Airplane Program: Widespread Fatigue Damage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-15

    ...This final rule amends FAA regulations pertaining to certification and operation of transport category airplanes to prevent widespread fatigue damage in those airplanes. For certain existing airplanes, the rule requires design approval holders to evaluate their airplanes to establish a limit of validity of the engineering data that supports the structural maintenance program (LOV). For future......

  10. Fibromyalgia and chronic widespread pain in autoimmune thyroid disease.

    PubMed

    Ahmad, Jowairiyya; Tagoe, Clement E

    2014-07-01

    Fibromyalgia and chronic widespread pain syndromes are among the commonest diseases seen in rheumatology practice. Despite advances in the management of these conditions, they remain significant causes of morbidity and disability. Autoimmune thyroid disease is the most prevalent autoimmune disorder, affecting about 10 % of the population, and is a recognized cause of fibromyalgia and chronic widespread pain. Recent reports are shedding light on the mechanisms of pain generation in autoimmune thyroid disease-associated pain syndromes including the role of inflammatory mediators, small-fiber polyneuropathy, and central sensitization. The gradual elucidation of these pain pathways is allowing the rational use of pharmacotherapy in the management of chronic widespread pain in autoimmune thyroid disease. This review looks at the current understanding of the prevalence of pain syndromes in autoimmune thyroid disease, their likely causes, present appreciation of the pathogenesis of chronic widespread pain, and how our knowledge can be used to find lasting and effective treatments for the pain syndromes associated with autoimmune thyroid disease.

  11. Are neonicotinoid insecticides driving declines of widespread butterflies?

    PubMed Central

    Bunnefeld, Nils; Wilson, John McVean; Botham, Marc S.; Brereton, Tom M.; Fox, Richard; Goulson, Dave

    2015-01-01

    There has been widespread concern that neonicotinoid pesticides may be adversely impacting wild and managed bees for some years, but recently attention has shifted to examining broader effects they may be having on biodiversity. For example in the Netherlands, declines in insectivorous birds are positively associated with levels of neonicotinoid pollution in surface water. In England, the total abundance of widespread butterfly species declined by 58% on farmed land between 2000 and 2009 despite both a doubling in conservation spending in the UK, and predictions that climate change should benefit most species. Here we build models of the UK population indices from 1985 to 2012 for 17 widespread butterfly species that commonly occur at farmland sites. Of the factors we tested, three correlated significantly with butterfly populations. Summer temperature and the index for a species the previous year are both positively associated with butterfly indices. By contrast, the number of hectares of farmland where neonicotinoid pesticides are used is negatively associated with butterfly indices. Indices for 15 of the 17 species show negative associations with neonicotinoid usage. The declines in butterflies have largely occurred in England, where neonicotinoid usage is at its highest. In Scotland, where neonicotinoid usage is comparatively low, butterfly numbers are stable. Further research is needed urgently to show whether there is a causal link between neonicotinoid usage and the decline of widespread butterflies or whether it simply represents a proxy for other environmental factors associated with intensive agriculture. PMID:26623186

  12. Are neonicotinoid insecticides driving declines of widespread butterflies?

    PubMed

    Gilburn, Andre S; Bunnefeld, Nils; Wilson, John McVean; Botham, Marc S; Brereton, Tom M; Fox, Richard; Goulson, Dave

    2015-01-01

    There has been widespread concern that neonicotinoid pesticides may be adversely impacting wild and managed bees for some years, but recently attention has shifted to examining broader effects they may be having on biodiversity. For example in the Netherlands, declines in insectivorous birds are positively associated with levels of neonicotinoid pollution in surface water. In England, the total abundance of widespread butterfly species declined by 58% on farmed land between 2000 and 2009 despite both a doubling in conservation spending in the UK, and predictions that climate change should benefit most species. Here we build models of the UK population indices from 1985 to 2012 for 17 widespread butterfly species that commonly occur at farmland sites. Of the factors we tested, three correlated significantly with butterfly populations. Summer temperature and the index for a species the previous year are both positively associated with butterfly indices. By contrast, the number of hectares of farmland where neonicotinoid pesticides are used is negatively associated with butterfly indices. Indices for 15 of the 17 species show negative associations with neonicotinoid usage. The declines in butterflies have largely occurred in England, where neonicotinoid usage is at its highest. In Scotland, where neonicotinoid usage is comparatively low, butterfly numbers are stable. Further research is needed urgently to show whether there is a causal link between neonicotinoid usage and the decline of widespread butterflies or whether it simply represents a proxy for other environmental factors associated with intensive agriculture.

  13. Effects of Local and Widespread Muscle Fatigue on Movement Timing

    PubMed Central

    Cowley, Jeffrey C.; Dingwell, Jonathan B.; Gates, Deanna H.

    2014-01-01

    Repetitive movements can cause muscle fatigue, leading to motor reorganization, performance deficits, and/or possible injury. The effects of fatigue may depend on the type of fatigue task employed, however. The purpose of this study was to determine how local fatigue of a specific muscle group versus widespread fatigue of various muscle groups affected the control of movement timing. Twenty healthy subjects performed an upper-extremity low-load work task similar to sawing for 5 continuous minutes both before and after completing a protocol that either fatigued all the muscles used in the task (widespread fatigue) or a protocol that selectively fatigued the primary muscles used to execute the pushing stroke of the sawing task (localized fatigue). Subjects were instructed to time their movements with a metronome. Timing error, movement distance, and speed were calculated for each movement. Data were then analyzed using a goal-equivalent manifold (GEM) approach to quantify changes in goal-relevant and non-goal-relevant variability. We applied detrended fluctuation analysis to each time series to quantify changes in fluctuation dynamics that reflected changes in the control strategies used. After localized fatigue, subjects made shorter, slower movements and exerted greater control over non-goal-relevant variability. After widespread fatigue, subjects exerted less control over non-goal-relevant variability and did not change movement patterns. Thus, localized and widespread muscle fatigue affected movement differently. Local fatigue may reduce the available motor solutions and therefore cause greater movement reorganization than widespread muscle fatigue. Subjects altered their control strategies but continued to achieve the timing goal after both fatigue tasks. PMID:25183157

  14. Widespread evidences of hoarfrost formation at a rock glacier in the Seckauer Tauern, Austria

    NASA Astrophysics Data System (ADS)

    Kellerer-Pirklbauer, A.; Winkler, G.; Pauritsch, M.

    2012-04-01

    The mechanism of deep reversible air circulation (the so called "chimney effect" or "wind tube") is known to be a process of ground overcooling in the lower and deeper parts of porous sediments and related landforms such as scree slopes or intact and relict rock glaciers. Warm air outflow emerging from relatively small voids within these mostly coarse-grained sediment bodies is sometimes noticeable. However, easier to identify are associated phenomena such as snowmelt windows, snow cover depressions and hoarfrost formations. Generally, these indications for warm air outflow are found at the upper part of scree slopes or the rooting zone of rock glaciers. Here we present widespread field evidences of hoarfrost from the pseudo-relict Schöneben Rock Glacier in the Seckauer Tauern Range, Austria located at E14°40'26'' and N47°22'31''. Herewith, a pseudo-relict rock glacier is defined as an intermediate rock glacier type between a relict and a climatic-inactive rock glacier, hence a relict rock glacier with locally isolated patches of permafrost. The rock glacier covers an area of about 0.11km2, ranges from ca. 1720 to 1905 m a.s.l., and consists predominantly of coarse-grained gneissic sediments with blocks up to a size of several cubic metres at the surface. In particular the lower part and some ridges in the central and upper part are covered by dwarf pines (pinus mugo) mirroring the flow structure of the previously active rock glacier. Isolated permafrost occurs presumably at the rooting zone of the rock glacier as indicated by evidences from a neighbouring rock glacier in a comparable setting. Field observations in November 2011 showed widespread occurrences of hoarfrost crystals growing around the funnel edge indicating the sublimation of vapour from warm funnels. Such hoarfrost sites were found at more than 50 single locations distributed over the entire rock glacier from the tongue to the rooting zone generally. The occurrence of hoarfrost can get classified

  15. Widespread inflammation in CLIPPERS syndrome indicated by autopsy and ultra-high-field 7T MRI

    PubMed Central

    Blaabjerg, Morten; Ruprecht, Klemens; Sinnecker, Tim; Kondziella, Daniel; Niendorf, Thoralf; Kerrn-Jespersen, Bjørg Morell; Lindelof, Mette; Lassmann, Hans; Kristensen, Bjarne Winther; Paul, Friedemann

    2016-01-01

    Objective: To examine if there is widespread inflammation in the brain of patients with chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS) syndrome by using histology and ultra-high-field MRI at 7.0T. Methods: We performed a detailed neuropathologic examination in 4 cases, including 1 autopsy case, and studied 2 additional patients by MRI at 7.0T to examine (1) extension of inflammation to areas appearing normal on 3.0T MRI, (2) potential advantages of 7.0T MRI compared to 3.0T MRI in reflecting widespread inflammation, perivascular pathology, and axonal damage, and (3) the possibility of lymphoma. Results: In the autopsy case, perivascular inflammation dominated by CD4+ T cells was not only detected in the brainstem and cerebellum but also in brain areas with normal appearance on 3.0T MRI, including supratentorial regions and cranial nerve roots. There was no evidence of lymphoma in any of the 4 patients. The 7.0T MRI in clinical remission also revealed supratentorial lesions and perivascular pathology in vivo with contrast-enhancing lesions centered around a small venous vessel. Ultra-high-field MRI at 7.0T disclosed prominent T1 hypointensities in the brainstem, which were not seen on 3.0T MRI. This corresponded to neuropathologic detection of axonal injury in the autopsy case. Conclusion: Our findings suggest more widespread perivascular inflammation and postinflammatory axonal injury in patients with CLIPPERS. PMID:27144217

  16. Bilateral widespread mechanical pain sensitivity in carpal tunnel syndrome: evidence of central processing in unilateral neuropathy.

    PubMed

    Fernández-de-las-Peñas, César; de la Llave-Rincón, Ana Isabel; Fernández-Carnero, Josué; Cuadrado, María Luz; Arendt-Nielsen, Lars; Pareja, Juan A

    2009-06-01

    The aim of this study was to investigate whether bilateral widespread pressure hypersensitivity exists in patients with unilateral carpal tunnel syndrome. A total of 20 females with carpal tunnel syndrome (aged 22-60 years), and 20 healthy matched females (aged 21-60 years old) were recruited. Pressure pain thresholds were assessed bilaterally over median, ulnar, and radial nerve trunks, the C5-C6 zygapophyseal joint, the carpal tunnel and the tibialis anterior muscle in a blinded design. The results showed that pressure pain threshold levels were significantly decreased bilaterally over the median, ulnar, and radial nerve trunks, the carpal tunnel, the C5-C6 zygapophyseal joint, and the tibialis anterior muscle in patients with unilateral carpal tunnel syndrome as compared to healthy controls (all, P < 0.001). Pressure pain threshold was negatively correlated to both hand pain intensity and duration of symptoms (all, P < 0.001). Our findings revealed bilateral widespread pressure hypersensitivity in subjects with carpal tunnel syndrome, which suggest that widespread central sensitization is involved in patients with unilateral carpal tunnel syndrome. The generalized decrease in pressure pain thresholds associated with pain intensity and duration of symptoms supports a role of the peripheral drive to initiate and maintain central sensitization. Nevertheless, both central and peripheral sensitization mechanisms are probably involved at the same time in carpal tunnel syndrome.

  17. Evidence of widespread axonal pathology in Wolfram syndrome.

    PubMed

    Shannon, P; Becker, L; Deck, J

    1999-09-01

    Wolfram syndrome, characterised by diabetes insipidus, diabetes mellitus, optic atrophy sensorineural deafness and acquired urinary tract abnormalities, is an hereditary neurodegenerative syndrome, the pathogenesis of which is unknown. We report the post-mortem findings on a patient with well-documented Wolfram syndrome. The brain showed severe degeneration of the optic nerves, chiasm and tracts as well as severe loss of neurons from the lateral geniculate nuclei, basis pontis, and the hypothalamic paraventricular and supraoptic nuclei. In addition, there was a widespread axonal dystrophy with axonal swellings in the pontocerebellar tracts, the optic radiations, the hippocampal fornices and the deep cerebral white matter. This widespread axonal pathology parallels the pattern of neurodegeneration and in many areas is more striking than neuronal loss.

  18. Non-pharmacological treatment of chronic widespread musculoskeletal pain.

    PubMed

    Hassett, Afton L; Williams, David A

    2011-04-01

    Individuals with chronic widespread pain, including those with fibromyalgia, pose a particular challenge to treatment, given the modest effectiveness of pharmacological agents for this condition. The growing consensus indicates that the best approach to treatment involves the combination of pharmacological and non-pharmacological interventions. Several non-pharmacological interventions, particularly exercise and cognitive-behavioural therapy (CBT), have garnered good evidence of effectiveness as stand-alone, adjunctive treatments for patients with chronic pain. In this article, evidenced-based, non-pharmacological management techniques for chronic widespread pain are described by using two broad categories, exercise and CBT. The evidence for decreasing pain, improving functioning and changing secondary symptoms is highlighted. Lastly, the methods by which exercise and CBT can be combined for a multi-component approach, which is consistent with the current evidence-based guidelines of several American and European medical societies, are addressed.

  19. Thermal Non-equilibrium Consistent with Widespread Cooling

    NASA Technical Reports Server (NTRS)

    Winebarger, A.; Lionello, R.; Mikic, Z.; Linker, J.; Mok, Y.

    2014-01-01

    Time correlation analysis has been used to show widespread cooling in the solar corona; this cooling has been interpreted as a result of impulsive (nanoflare) heating. In this work, we investigate wide-spread cooling using a 3D model for a solar active region which has been heated with highly stratified heating. This type of heating drives thermal non-equilibrium solutions, meaning that though the heating is effectively steady, the density and temperature in the solution are not. We simulate the expected observations in narrowband EUV images and apply the time correlation analysis. We find that the results of this analysis are qualitatively similar to the observed data. We discuss additional diagnostics that may be applied to differentiate between these two heating scenarios.

  20. Active Longitude and Coronal Mass Ejection Occurrences

    NASA Astrophysics Data System (ADS)

    Gyenge, N.; Singh, T.; Kiss, T. S.; Srivastava, A. K.; Erdélyi, R.

    2017-03-01

    The spatial inhomogeneity of the distribution of coronal mass ejection (CME) occurrences in the solar atmosphere could provide a tool to estimate the longitudinal position of the most probable CME-capable active regions in the Sun. The anomaly in the longitudinal distribution of active regions themselves is often referred to as active longitude (AL). In order to reveal the connection between the AL and CME spatial occurrences, here we investigate the morphological properties of active regions. The first morphological property studied is the separateness parameter, which is able to characterize the probability of the occurrence of an energetic event, such as a solar flare or CME. The second morphological property is the sunspot tilt angle. The tilt angle of sunspot groups allows us to estimate the helicity of active regions. The increased helicity leads to a more complex buildup of the magnetic structure and also can cause CME eruption. We found that the most complex active regions appear near the AL and that the AL itself is associated with the most tilted active regions. Therefore, the number of CME occurrences is higher within the AL. The origin of the fast CMEs is also found to be associated with this region. We concluded that the source of the most probably CME-capable active regions is at the AL. By applying this method, we can potentially forecast a flare and/or CME source several Carrington rotations in advance. This finding also provides new information for solar dynamo modeling.

  1. Geochemical evidence for widespread euxinia in the later Cambrian ocean.

    PubMed

    Gill, Benjamin C; Lyons, Timothy W; Young, Seth A; Kump, Lee R; Knoll, Andrew H; Saltzman, Matthew R

    2011-01-06

    Widespread anoxia in the ocean is frequently invoked as a primary driver of mass extinction as well as a long-term inhibitor of evolutionary radiation on early Earth. In recent biogeochemical studies it has been hypothesized that oxygen deficiency was widespread in subsurface water masses of later Cambrian oceans, possibly influencing evolutionary events during this time. Physical evidence of widespread anoxia in Cambrian oceans has remained elusive and thus its potential relationship to the palaeontological record remains largely unexplored. Here we present sulphur isotope records from six globally distributed stratigraphic sections of later Cambrian marine rocks (about 499 million years old). We find a positive sulphur isotope excursion in phase with the Steptoean Positive Carbon Isotope Excursion (SPICE), a large and rapid excursion in the marine carbon isotope record, which is thought to be indicative of a global carbon cycle perturbation. Numerical box modelling of the paired carbon sulphur isotope data indicates that these isotope shifts reflect transient increases in the burial of organic carbon and pyrite sulphur in sediments deposited under large-scale anoxic and sulphidic (euxinic) conditions. Independently, molybdenum abundances in a coeval black shale point convincingly to the transient spread of anoxia. These results identify the SPICE interval as the best characterized ocean anoxic event in the pre-Mesozoic ocean and an extreme example of oxygen deficiency in the later Cambrian ocean. Thus, a redox structure similar to those in Proterozoic oceans may have persisted or returned in the oceans of the early Phanerozoic eon. Indeed, the environmental challenges presented by widespread anoxia may have been a prevalent if not dominant influence on animal evolution in Cambrian oceans.

  2. Widespread Usutu virus outbreak in birds in the Netherlands, 2016.

    PubMed

    Rijks, J M; Kik, M L; Slaterus, R; Foppen, Rpb; Stroo, A; IJzer, J; Stahl, J; Gröne, A; Koopmans, Mgp; van der Jeugd, H P; Reusken, Cbem

    2016-11-10

    We report a widespread Usutu virus outbreak in birds in the Netherlands. Viral presence had been detected through targeted surveillance as early as April 2016 and increased mortality in common blackbirds and captive great grey owls was noticed from August 2016 onwards. Usutu virus infection was confirmed by post-mortem examination and RT-PCR. Extensive Usutu virus activity in the Netherlands in 2016 underlines the need to monitor mosquito activity and mosquito-borne infections in 2017 and beyond.

  3. Identifying patients with chronic widespread pain in primary care

    PubMed Central

    Mansfield, Kathryn E.; Sim, Julius; Croft, Peter; Jordan, Kelvin P.

    2016-01-01

    Abstract Chronic widespread pain (CWP) is common in the general population. It is unclear how people reporting this problem present in primary care; they may regularly consult for regional pains without being recognized as having a generalized condition. Our objectives were to determine the prevalence of people consulting in primary care for musculoskeletal conditions in different body regions on different occasions (recurrent regional pain consultation), the proportion with diagnosed generalized pain and survey-reported widespread pain, and if they have features characteristic of CWP. Phase 1 used electronic records from 12 general practices in North Staffordshire (Consultations in Primary Care Archive) from 2005 to 2009. Phase 2 used linked self-reported health and primary health care data from 8286 people aged >50 years in 8 general practices (North Staffordshire Osteoarthritis Project) between 2002 and 2005. In Phase 1, 11% of registered patients fulfilled criteria for recurrent regional pain consultation. Three-quarters had no recorded CWP-related generalized pain condition (eg, fibromyalgia). In Phase 2, 53% of recurrent regional pain consulters had survey-reported widespread pain and 88% had consulted for somatic symptoms. Self-reported general health was worse in recurrent regional pain consulters than in single-region consulters and poorest in those who also reported persistent widespread pain. Recurrent regional pain consulters are a heterogeneous group of frequent consulters sharing features with CWP (eg, somatic symptoms) but including those less severely affected. They lie on the spectrum of polysymptomatic distress characteristic of CWP and represent a group whose needs may be better met by earlier diagnosis of multisite pain. PMID:27749607

  4. Widespread Usutu virus outbreak in birds in the Netherlands, 2016

    PubMed Central

    Rijks, JM; Kik, ML; Slaterus, R; Foppen, RPB; Stroo, A; IJzer, J; Stahl, J; Gröne, A; Koopmans, MGP; van der Jeugd, HP; Reusken, CBEM

    2016-01-01

    We report a widespread Usutu virus outbreak in birds in the Netherlands. Viral presence had been detected through targeted surveillance as early as April 2016 and increased mortality in common blackbirds and captive great grey owls was noticed from August 2016 onwards. Usutu virus infection was confirmed by post-mortem examination and RT-PCR. Extensive Usutu virus activity in the Netherlands in 2016 underlines the need to monitor mosquito activity and mosquito-borne infections in 2017 and beyond. PMID:27918257

  5. Past Occurrences of Hypoxia in the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Zillen, L.; Conley, D. J.; Bjorck, S.

    2007-12-01

    The hypoxic zone in the Baltic Sea has increased in area by about four times since 1950. Widespread oxygen deficiency below the halocline has severely reduced macro benthic communities in the Baltic Proper and the Gulf of Finland over the past decades and negatively effected food chain dynamics, fish habitats and fisheries in the entire Baltic Sea. In addition, hypoxia alters nutrient biogeochemical cycles. The cause of the increased hypoxia is believed to be enhanced eutrophication through increased anthropogenic input of nutrients, such as phosphorous and nitrogen. Conditions prior to the 1950s are considered as the benchmark and some authors suggest that the earlier Baltic Sea was an oligothrophic, clear-water body with oxygenated deep waters. By contrast, studies of short sediment cores reveal that hypoxia has been present in some of the deepest basins for at least the last 100-200 years. In addition, long sediment cores suggest that hypoxia in the Baltic Sea has occurred intermittently in deep basins over the last c. 8500 years. Thus, the occurrence of present day hypoxia in the deeper basins need not necessarily be attributed to human activity but rather to natural oceanographic, geologic and climate conditions. We present a compilation of previous publications that reported the occurrence of laminated sediments (i.e. a palaeo-proxy for hypoxia) in the Baltic Sea. This review shows that the deeper parts of the Baltic Sea have experienced either intermittent or more regular hypoxia during most of the Holocene and that more continuous laminations started to form c. 7800-8500 cal. yr BP ago, in association with the establishment of a permanent halocline during the transition from the Ancylus Lake to the Littorina Sea. Laminated sediments were more common during the early and late Holocene and coincided with intervals of high organic productivity (high TOC content) and high salinity during the Holocene Thermal Maximum and the Medieval Climate Optimum. This study

  6. Widespread plant species: natives vs. aliens in our changing world

    USGS Publications Warehouse

    Stohlgren, Thomas J.; Pyšek, Petr; Kartesz, John; Nishino, Misako; Pauchard, Aníbal; Winter, Marten; Pino, Joan; Richardson, David M.; Wilson, John R.U.; Murray, Brad R.; Phillips, Megan L.; Ming-yang, Li; Celesti-Grapow, Laura; Font, Xavier

    2011-01-01

    Estimates of the level of invasion for a region are traditionally based on relative numbers of native and alien species. However, alien species differ dramatically in the size of their invasive ranges. Here we present the first study to quantify the level of invasion for several regions of the world in terms of the most widely distributed plant species (natives vs. aliens). Aliens accounted for 51.3% of the 120 most widely distributed plant species in North America, 43.3% in New South Wales (Australia), 34.2% in Chile, 29.7% in Argentina, and 22.5% in the Republic of South Africa. However, Europe had only 1% of alien species among the most widespread species of the flora. Across regions, alien species relative to native species were either as well-distributed (10 comparisons) or more widely distributed (5 comparisons). These striking patterns highlight the profound contribution that widespread invasive alien plants make to floristic dominance patterns across different regions. Many of the most widespread species are alien plants, and, in particular, Europe and Asia appear as major contributors to the homogenization of the floras in the Americas. We recommend that spatial extent of invasion should be explicitly incorporated in assessments of invasibility, globalization, and risk assessments.

  7. Widespread plant species: Natives versus aliens in our changing world

    USGS Publications Warehouse

    Stohlgren, T.J.; Pysek, P.; Kartesz, J.; Nishino, M.; Pauchard, A.; Winter, M.; Pino, J.; Richardson, D.M.; Wilson, J.R.U.; Murray, B.R.; Phillips, M.L.; Ming-yang, L.; Celesti-Grapow, L.; Font, X.

    2011-01-01

    Estimates of the level of invasion for a region are traditionally based on relative numbers of native and alien species. However, alien species differ dramatically in the size of their invasive ranges. Here we present the first study to quantify the level of invasion for several regions of the world in terms of the most widely distributed plant species (natives vs. aliens). Aliens accounted for 51.3% of the 120 most widely distributed plant species in North America, 43.3% in New South Wales (Australia), 34.2% in Chile, 29.7% in Argentina, and 22.5% in the Republic of South Africa. However, Europe had only 1% of alien species among the most widespread species of the flora. Across regions, alien species relative to native species were either as well-distributed (10 comparisons) or more widely distributed (5 comparisons). These striking patterns highlight the profound contribution that widespread invasive alien plants make to floristic dominance patterns across different regions. Many of the most widespread species are alien plants, and, in particular, Europe and Asia appear as major contributors to the homogenization of the floras in the Americas. We recommend that spatial extent of invasion should be explicitly incorporated in assessments of invasibility, globalization, and risk assessments. ?? 2011 Springer Science+Business Media B.V.

  8. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    NASA Astrophysics Data System (ADS)

    Comte, J.; Lovejoy, C.; Crevecoeur, S.; Vincent, W. F.

    2016-01-01

    Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north-south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial "keystone species". These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

  9. Occurrence of halogenated alkaloids.

    PubMed

    Gribble, Gordon W

    2012-01-01

    Once considered to be isolation artifacts or chemical "mistakes" of nature, the number of naturally occurring organohalogen compounds has grown from a dozen in 1954 to >5000 today. Of these, at least 25% are halogenated alkaloids. This is not surprising since nitrogen-containing pyrroles, indoles, carbolines, tryptamines, tyrosines, and tyramines are excellent platforms for biohalogenation, particularly in the marine environment where both chloride and bromide are plentiful for biooxidation and subsequent incorporation into these electron-rich substrates. This review presents the occurrence of all halogenated alkaloids, with the exception of marine bromotyrosines where coverage begins where it left off in volume 61 of The Alkaloids. Whereas the biological activity of these extraordinary compounds is briefly cited for some examples, a future volume of The Alkaloids will present full coverage of this topic and will also include selected syntheses of halogenated alkaloids. Natural organohalogens of all types, especially marine and terrestrial halogenated alkaloids, comprise a rapidly expanding class of natural products, in many cases expressing powerful biological activity. This enormous proliferation has several origins: (1) a revitalization of natural product research in a search for new drugs, (2) improved compound characterization methods (multidimensional NMR, high-resolution mass spectrometry), (3) specific enzyme-based and other biological assays, (4) sophisticated collection methods (SCUBA and remote submersibles for deep ocean marine collections), (5) new separation and purification techniques (HPLC and countercurrent separation), (6) a greater appreciation of traditional folk medicine and ethobotany, and (7) marine bacteria and fungi as novel sources of natural products. Halogenated alkaloids are truly omnipresent in the environment. Indeed, one compound, Q1 (234), is ubiquitous in the marine food web and is found in the Inuit from their diet of whale

  10. Widespread Weathered Glass on the Surface of Mars

    NASA Technical Reports Server (NTRS)

    Horgan, Briony; Bell, James F., III

    2012-01-01

    Low albedo sediments cover >10(exp 7) sq km in the northern lowlands of Mars, but the composition and origin of these widespread deposits have remained ambiguous despite many previous investigations. Here we use near-infrared spectra acquired by the Mars Express OMEGA (Observatoire pour la Mineralogie, l'Eau, les Glaces, et l'Activite') imaging spectrometer to show that these sediments exhibit spectral characteristics that are consistent with both high abundances of iron-bearing glass and silica-enriched leached rinds on glass. This interpretation is supported by observations of low-albedo soil grains with possible rinds at the Phoenix Mars Lander landing site in the northern lowlands. By comparison with the extensive glass-rich dune fields and sand sheets of Iceland, we propose an explosive volcanic origin for these glass-rich sediments. We also propose that the glassy remnant rinds on the sediments are the result of post-depositional alteration, as these rinds are commonly formed in arid terrestrial volcanic environments during water-limited, moderately acidic leaching. These weathered, glass-rich deposits in the northern lowlands are also colocated with the strongest concentrations of a major global compositional surface type previously identified in mid-infrared spectra, suggesting that they may be representative of global processes. Our results provide potential confirmation of models suggesting that explosive volcanism has been widespread on Mars, and also raise the possibilities that glass-rich volcaniclastics are a major source of eolian sand on Mars and that widespread surficial aqueous alteration has occurred under Amazonian climatic conditions.

  11. Insecure attachment style is associated with chronic widespread pain.

    PubMed

    Davies, K A; Macfarlane, G J; McBeth, J; Morriss, R; Dickens, C

    2009-06-01

    Individuals with "insecure" adult attachment styles have been shown to experience more pain than people with secure attachment, though results of previous studies have been inconsistent. We performed a cross-sectional study on a large population-based sample to investigate whether, compared to pain free individuals, subjects with chronic widespread pain were more likely to report insecure adult attachment style. Subjects in a population-based cross-sectional study completed a self-rated assessment of adult attachment style. Attachment style was categorised as secure (i.e., normal attachment style); or preoccupied, dismissing or fearful (insecure attachment styles). Subjects completed a pain questionnaire from which three groups were identified: pain free; chronic widespread pain; and other pain. Subjects rated their pain intensity and pain-related disability on an 11 point Likert scale. Subjects (2509) returned a completed questionnaire (median age 49.9 years (IQR 41.2-50.0); 59.2% female). Subjects with CWP were more likely to report a preoccupied (RRR 2.6; 95%CI 1.8-3.7), dismissing (RRR 1.9; 95%CI 1.2-3.1) or fearful attachment style (RRR 1.4; 95%CI 1.1-1.8) than those free of pain. Among CWP subjects, insecure attachment style was associated with number of pain sites (Dismissing: RRR 2.8; 95%CI 1.2-2.3, Preoccupied: RRR=1.8, 95%CI 0.98-3.5) and degree of pain-related disability (Preoccupied: RRR=2.1, 95%CI 1.0-4.1), but not pain intensity. These findings suggest that treatment strategies based on knowledge of attachment style, possibly using support and education, may alleviate distress and disability in people at risk of, or affected by, chronic widespread pain.

  12. Widespread 3′-end uridylation in eukaryotic RNA viruses

    PubMed Central

    Huo, Yayun; Shen, Jianguo; Wu, Huanian; Zhang, Chao; Guo, Lihua; Yang, Jinguang; Li, Weimin

    2016-01-01

    RNA 3′ uridylation occurs pervasively in eukaryotes, but is poorly characterized in viruses. In this study, we demonstrate that a broad array of RNA viruses, including mycoviruses, plant viruses and animal viruses, possess a novel population of RNA species bearing nontemplated oligo(U) or (U)-rich tails, suggesting widespread 3′ uridylation in eukaryotic viruses. Given the biological relevance of 3′ uridylation to eukaryotic RNA degradation, we propose a conserved but as-yet-unknown mechanism in virus-host interaction. PMID:27151171

  13. Ferroan anorthosite - A widespread and distinctive lunar rock type

    NASA Technical Reports Server (NTRS)

    Dowty, E.; Prinz, M.; Keil, K.

    1974-01-01

    Eight of eleven Apollo 16 rake-sample anorthosites are very similar to each other, to hand-specimen Apollo 16 anorthosites, and to Apollo 15 anorthosites. They have feldspar An-96.6, both high- and low-Ca pyroxene with a restricted range of (low-magnesium) composition, minor olivine, traces of ilmenite and chromite, and originally coarse-grained, but now cataclastic texture. Such ferroan anorthosite is evidently a coherent, distinctive and widespread lunar rock type of cumulate origin which may not necessarily be very closely related genetically to other highland rock types.

  14. Historic Late Blight Outbreaks Caused by a Widespread Dominant Lineage of Phytophthora infestans (Mont.) de Bary.

    PubMed

    Saville, Amanda C; Martin, Michael D; Ristaino, Jean B

    2016-01-01

    Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, was responsible for the Irish potato famine of the 1840s. Initial disease outbreaks occurred in the US in 1843, two years prior to European outbreaks. We examined the evolutionary relationships and source of the 19th-century outbreaks using herbarium specimens of P. infestans from historic (1846-1970) and more recent isolates (1992-2014) of the pathogen. The same unique SSR multilocus genotype, named here as FAM-1, caused widespread outbreaks in both US and Europe. The FAM-1 lineage shared allelic diversity and grouped with the oldest specimens collected in Colombia and Central America. The FAM-1 lineage of P. infestans formed a genetic group that was distinct from more recent aggressive lineages found in the US. The US-1 lineage formed a second, mid-20th century group. Recent modern US lineages and the oldest Mexican lineages formed a genetic group with recent Mexican lineages, suggesting a Mexican origin of recent US lineages. A survey of mitochondrial haplotypes in a larger set of global herbarium specimens documented the more frequent occurrence of the HERB-1 (type Ia) mitochondrial haplotype in archival collections from 1866-75 and 1906-1915 and the rise of the Ib mitochondrial lineage (US-1) between 1946-1955. The FAM-1 SSR lineage survived for almost 100 years in the US, was geographically widespread, and was displaced first in the mid-20th century by the US-1 lineage and then by distinct new aggressive lineages that migrated from Mexico.

  15. Historic Late Blight Outbreaks Caused by a Widespread Dominant Lineage of Phytophthora infestans (Mont.) de Bary

    PubMed Central

    Martin, Michael D.

    2016-01-01

    Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, was responsible for the Irish potato famine of the 1840s. Initial disease outbreaks occurred in the US in 1843, two years prior to European outbreaks. We examined the evolutionary relationships and source of the 19th-century outbreaks using herbarium specimens of P. infestans from historic (1846–1970) and more recent isolates (1992–2014) of the pathogen. The same unique SSR multilocus genotype, named here as FAM-1, caused widespread outbreaks in both US and Europe. The FAM-1 lineage shared allelic diversity and grouped with the oldest specimens collected in Colombia and Central America. The FAM-1 lineage of P. infestans formed a genetic group that was distinct from more recent aggressive lineages found in the US. The US-1 lineage formed a second, mid-20th century group. Recent modern US lineages and the oldest Mexican lineages formed a genetic group with recent Mexican lineages, suggesting a Mexican origin of recent US lineages. A survey of mitochondrial haplotypes in a larger set of global herbarium specimens documented the more frequent occurrence of the HERB-1 (type Ia) mitochondrial haplotype in archival collections from 1866–75 and 1906–1915 and the rise of the Ib mitochondrial lineage (US-1) between 1946–1955. The FAM-1 SSR lineage survived for almost 100 years in the US, was geographically widespread, and was displaced first in the mid-20th century by the US-1 lineage and then by distinct new aggressive lineages that migrated from Mexico. PMID:28030580

  16. Widespread methanotrophic primary production in lowland chalk rivers.

    PubMed

    Shelley, Felicity; Grey, Jonathan; Trimmer, Mark

    2014-05-22

    Methane is oversaturated relative to the atmosphere in many rivers, yet its cycling and fate is poorly understood. While photosynthesis is the dominant source of autotrophic carbon to rivers, chemosynthesis and particularly methane oxidation could provide alternative sources of primary production where the riverbed is heavily shaded or at depth beneath the sediment surface. Here, we highlight geographically widespread methanotrophic carbon fixation within the gravel riverbeds of over 30 chalk rivers. In 15 of these, the potential for methane oxidation (methanotrophy) was also compared with photosynthesis. In addition, we performed detailed concurrent measurements of photosynthesis and methanotrophy in one large chalk river over a complete annual cycle, where we found methanotrophy to be active to at least 15 cm into the riverbed and to be strongly substrate limited. The seasonal trend in methanotrophic activity reflected that of the riverine methane concentrations, and thus the highest rates were measured in mid-summer. At the sediment surface, photosynthesis was limited by light for most of the year with heavy shading induced by dense beds of aquatic macrophytes. Across 15 rivers, in late summer, we conservatively calculated that net methanotrophy was equivalent to between 1% and 46% of benthic net photosynthetic production within the gravel riverbed, with a median value of 4%. Hence, riverbed chemosynthesis, coupled to the oxidation of methane, is widespread and significant in English chalk rivers.

  17. Potential environmental functions of widespread, abundant, uncultured marine archaea

    NASA Astrophysics Data System (ADS)

    Lloyd, K. G.; Schreiber, L.; Petersen, D. G.; Schramm, A.; Jorgensen, B.

    2012-12-01

    The vast majority of marine subsurface microorganisms are uncultivated, and therefore have unknown metabolisms. Much of the prokaryotes present in the marine subsurface are archaea, and, in turn, much of the archaea fall into the Miscellaneous Crenarchaeotal Group. These organisms are widely distributed globally and are phylogenetically diverse, comprising 17 distinct subgroups, defined by 16S rRNA genes (Kubo et al. 2012). The subgroups do not seem to have any well-defined environmental distribution (i.e., they are all present in different types of marine and terrestrial environments). However, the abundance of sequences from a certain environment type differs among subgroups, and may provide clues to their role in these environments. We sequenced the genome of a single cell of MCG extracted directly from marine sediments. Although coverage was low (~30%), the data quality was high. Conserved genes show that MCG is deeply branching within the newly named "Thaumarchaeota", and contains a complete pathway for the degradation or extracellular proteins. A further search through metagenomic data shows that this process may be widespread in marine sediments. We hypothesize that MCG archaea may be important in anaerobic protein decomposition in marine sediments. Reference Kubo et al., 2012. Archaea of the Miscellaneous Crenarchaeotal Group (MCG) are abundant, diverse, and widespread in marine sediments. ISME Journal, in press, doi:10.1038/ismej.2012.37.

  18. Widespread effects of alcohol on white matter microstructure

    PubMed Central

    Fortier, Catherine Brawn; Leritz, Elizabeth C.; Salat, David H.; Lindemer, Emily; Maksimovskiy, Arkadiy L.; Shepel, Juli; Williams, Victoria; Venne, Jonathan R.; Milberg, William P.; McGlinchey, Regina E.

    2014-01-01

    Background Evidence suggests that chronic misuse of alcohol may preferentially affect the integrity of frontal white matter tracts, which can impact executive functions important to achieve and maintain abstinence. Methods Global and regional white matter (WM) microstructure was assessed using diffusion magnetic resonance (MR) measures of fractional anisotropy (FA) for 31 abstinent alcoholics with an average of 25 years of abuse and approximately 5 years of sobriety and 20 nonalcoholic control participants. Data processing was conducted with FreeSurfer and FSL processing streams. Voxelwise processing of the FA data was carried out using TBSS (Tract-Based Spatial Statistics). Clusters of significance were created to provide a quantitative summary of highly significant regions within the voxel wise analysis. Results Widespread, bilateral reductions in FA were observed in abstinent alcoholics as compared to nonalcoholic control participants in multiple frontal, temporal, parietal, and cerebellar WM tracts. FA in the left inferior frontal gyrus was associated with drinking severity. Conclusions The present study found widespread reductions in WM integrity in a group of abstinent alcoholics compared to nonalcoholic control participants, with most pronounced effects in frontal and superior tracts. Decreased FA throughout the frontostriatal circuits that mediate inhibitory control may result in impulsive behavior and inability to maintain sobriety. PMID:25406797

  19. Archaeological implications of a widespread 13th Century tephra marker across the central Indonesian Archipelago

    NASA Astrophysics Data System (ADS)

    Alloway, Brent V.; Andreastuti, Supriyati; Setiawan, Ruly; Miksic, John; Hua, Quan

    2017-01-01

    Despite the occurrence of exceptionally large eruptions in the Indonesian Archipelago in recent historic times (i.e. Krakatoa 1883, Tambora 1815), no historic tephra beds have been widely identified in the terrestrial realm that could facilitate the correlation of equivalent aged sequences and/or archaeological remains. This study has identified one such tephra bed of 13th Century age that can be correlated throughout central-east Java and now can be unequivocally correlated with the Samalas 1257 A.D. tephra recently described from Lombok. The occurrence of this historic tephra marker extending ≥650 km west from its eruptive source provides the first opportunity to effect inter-regional correlation over large swathes of central Indonesia. It remains entirely conceivable that in the aftermath of this exceptionally large eruptive event there was considerable westward disruption to subsistence agriculture and trade, food shortages and famine, dislocation of affected populations and socio-political unrest on a scale that equalled or exceeded the catastrophic effects documented from the more recent Tambora 1815 A.D. eruption. Indeed the effects of this mid-13th Century eruption can be registered globally in a variety of records from Antarctica, Europe, Middle East and the Americas. Unfortunately, archaeological evidence indicating such disruption in mid-13th Century Indonesia is yet to be deciphered from the so-far sparse accounts and inscriptions of that time. However, this paucity of evidence does not diminish the utility of this widespread tephra bed as a unique chronostratigraphic marker for archaeological studies across large areas of central Indonesia.

  20. Occurrence of hemocyanin in ostracod crustaceans.

    PubMed

    Marxen, Julia C; Pick, Christian; Oakley, Todd H; Burmester, Thorsten

    2014-08-01

    Hemocyanin is a copper-containing protein that transports O2 in the hemolymph of many arthropod species. Within the crustaceans, hemocyanin appeared to be restricted to Malacostraca but has recently been identified in Remipedia. Here, we report the occurrence of hemocyanin in ostracods, indicating that this respiratory protein is more widespread within crustaceans than previously thought. By analyses of expressed sequence tags and by RT-PCR, we obtained four full length and nine partial hemocyanin sequences from six of ten investigated ostracod species. Hemocyanin was identified in Myodocopida (Actinoseta jonesi, Cypridininae sp., Euphilomedes morini, Skogsbergia lerneri, Vargula tsujii) and Platycopida (Cytherelloidea californica) but not in Podocopida. We found no evidence for the presence of hemoglobin in any of these ostracod species. Like in other arthropods, we identified multiple hemocyanin subunits (up to six) to occur in a single ostracod species. Bayesian phylogenetic analyses showed that ostracod hemocyanin subunit diversity evolved independently from that of other crustaceans. Ostracod hemocyanin subunits were found paraphyletic, with myodocopid and platycopid subunits forming distinct clades within those of the crustaceans. This pattern suggests that ostracod hemocyanins originated from distinct subunits in the pancrustacean stemline.

  1. Ichthyosis associated with widespread tinea corporis: report of three cases.

    PubMed

    Freitas, Camila Fernanda Novak Pinheiro de; Mulinari-Brenner, Fabiane; Fontana, Hanae Rafaela; Gentili, Arthur Conelian; Hammerschmidt, Mariana

    2013-01-01

    Ichthyoses are a common group of keratinization disorders. A non-inflammatory generalized persistent skin desquamation is observed. It is characterized by increased cell turnover, thickening of the stratum corneum and functional changes of sebaceous and sweat glands. All of these favor fungal proliferation. Dermatophytes may infect skin, hair and nails causing ringworm or tinea. They have the ability to obtain nutrients from keratinized material. One of its most prevalent genera is Trichophyton rubrum. Although tineas and ichthyoses are quite common, the association of the two entities is rarely reported in the literature. Three cases of ichthyosis associated with widespread infection by T. rubrum are presented. Resistance to several antifungal treatments was responsible for worsening of ichthyosis signs and symptoms.

  2. A widespread family of bacterial cell wall assembly proteins

    PubMed Central

    Kawai, Yoshikazu; Marles-Wright, Jon; Cleverley, Robert M; Emmins, Robyn; Ishikawa, Shu; Kuwano, Masayoshi; Heinz, Nadja; Bui, Nhat Khai; Hoyland, Christopher N; Ogasawara, Naotake; Lewis, Richard J; Vollmer, Waldemar; Daniel, Richard A; Errington, Jeff

    2011-01-01

    Teichoic acids and acidic capsular polysaccharides are major anionic cell wall polymers (APs) in many bacteria, with various critical cell functions, including maintenance of cell shape and structural integrity, charge and cation homeostasis, and multiple aspects of pathogenesis. We have identified the widespread LytR–Cps2A–Psr (LCP) protein family, of previously unknown function, as novel enzymes required for AP synthesis. Structural and biochemical analysis of several LCP proteins suggest that they carry out the final step of transferring APs from their lipid-linked precursor to cell wall peptidoglycan (PG). In Bacillus subtilis, LCP proteins are found in association with the MreB cytoskeleton, suggesting that MreB proteins coordinate the insertion of the major polymers, PG and AP, into the cell wall. PMID:21964069

  3. Repeated and Widespread Evolution of Bioluminescence in Marine Fishes

    PubMed Central

    Davis, Matthew P.; Sparks, John S.; Smith, W. Leo

    2016-01-01

    Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world’s oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication. PMID:27276229

  4. The widespread threat of calcium decline in fresh waters.

    PubMed

    Jeziorski, Adam; Yan, Norman D; Paterson, Andrew M; Desellas, Anna M; Turner, Michael A; Jeffries, Dean S; Keller, Bill; Weeber, Russ C; McNicol, Don K; Palmer, Michelle E; McIver, Kyle; Arseneau, Kristina; Ginn, Brian K; Cumming, Brian F; Smol, John P

    2008-11-28

    Calcium concentrations are now commonly declining in softwater boreal lakes. Although the mechanisms leading to these declines are generally well known, the consequences for the aquatic biota have not yet been reported. By examining crustacean zooplankton remains preserved in lake sediment cores, we document near extirpations of calcium-rich Daphnia species, which are keystone herbivores in pelagic food webs, concurrent with declining lake-water calcium. A large proportion (62%, 47 to 81% by region) of the Canadian Shield lakes we examined has a calcium concentration approaching or below the threshold at which laboratory Daphnia populations suffer reduced survival and fecundity. The ecological impacts of environmental calcium loss are likely to be both widespread and pronounced.

  5. Widespread Losses of Vomeronasal Signal Transduction in Bats

    PubMed Central

    Zhao, Huabin; Xu, Dong; Zhang, Shuyi; Zhang, Jianzhi

    2011-01-01

    The vertebrate vomeronasal system (VNS) detects intraspecific pheromones and environmental odorants. We sequenced segments of the gene encoding Trpc2, an ion channel crucial for vomeronasal signal transduction, in 11 species that represent all main basal lineages of Yinpterochiroptera, one of the two suborders of the order Chiroptera (bats). Our sequences show that Trpc2 is a pseudogene in each of the 11 bats, suggesting that all yinpterochiropterans lack vomeronasal sensitivity. The Trpc2 sequences from four species of Yangochiroptera, the other suborder of bats, suggest vomeronasal insensitivity in some but not all yangochiropterans. These results, together with the available morphological data from the bat VNS, strongly suggest multiple and widespread losses of vomeronasal signal transduction and sensitivity in bats. Future scrutiny of the specific functions of the VNS in the few bats that still retain the VNS may help explain why it is dispensable in most bats. PMID:20693241

  6. Repeated and Widespread Evolution of Bioluminescence in Marine Fishes.

    PubMed

    Davis, Matthew P; Sparks, John S; Smith, W Leo

    2016-01-01

    Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world's oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication.

  7. Widespread transcription of a Qa region gene in adult mice

    PubMed Central

    1987-01-01

    The mouse MHC class I family includes genes encoded in four regions: H- 2K, H-2D, Qa and Tla. While K/D genes are well characterized, relatively little is known about Qa or Tla genes. We have studied the transcription of a B10.P Qa region gene. DNA sequence comparisons of the transmembrane region, supported by Southern blot analysis of cosmid and genomic DNAs from BALB/c and C57BL/10, demonstrate the lambda 3a gene corresponds to Q4p. In both Northern blots and RNA protection experiments using probes derived from the 3' noncoding region, we found that Q4, like the H-2K and H-2D genes, is widely transcribed in B10.P tissues. These data demonstrate for the first time widespread transcription of a Qa gene. PMID:2439640

  8. Developing a Scenario for widespread use: Best practices, lessons learned

    USGS Publications Warehouse

    Perry, S.; Jones, L.; Cox, D.

    2011-01-01

    The ShakeOut Scenario is probably the most widely known and used earthquake scenario created to date. Much of the credit for its widespread dissemination and application lies with scenario development criteria that focused on the needs and involvement of end users and with a suite of products that tailored communication of the results to varied end users, who ranged from emergency managers to the general public, from corporations to grassroots organizations. Products were most effective when they were highly visual, when they emphasized the findings of social scientists, and when they communicated the experience of living through the earthquake. This paper summarizes the development criteria and the products that made the ShakeOut Scenario so widely known and used, and it provides some suggestions for future improvements. ?? 2011, Earthquake Engineering Research Institute.

  9. Are Epigenetic Factors Implicated in Chronic Widespread Pain?

    PubMed Central

    Burri, Andrea; Marinova, Zoya; Robinson, Mark D.; Kühnel, Brigitte; Waldenberger, Melanie; Wahl, Simone; Kunze, Sonja; Gieger, Christian; Livshits, Gregory; Williams, Frances

    2016-01-01

    Background Chronic widespread musculoskeletal pain (CWP) is the cardinal symptom of fibromyalgia and affects about 12% of the general population. Familial aggregation of CWP has been repeatedly demonstrated with estimated heritabilities of around 50%, indicating a genetic susceptibility. The objective of the study was to explore genome-wide disease-differentially methylated positions (DMPs) for chronic widespread pain (CWP) in a sample of unrelated individuals and a subsample of discordant monozygotic (MZ) twins. Methodology/Principle Findings A total of N = 281 twin individuals from the TwinsUK registry, including N = 33 MZ twins discordant for self-reported CWP, were part of the discovery sample. The replication sample included 729 men and 756 women from a subsample of the KORA S4 survey–an independent population-based cohort from Southern Germany. Epigenome-wide analysis of DNA methylation was conducted using the Illumina Infinium HumanMethylation 450 DNA BeadChip in both the discovery and replication sample. Of our 40 main loci that were carried forward for replication, three CPGs reached significant p-values in the replication sample, including malate dehydrogenase 2 (MDH2; p-value 0.017), tetranectin (CLEC3B; p-value 0.039), and heat shock protein beta-6 (HSPB6; p-value 0.016). The associations between the collagen type I, alpha 2 chain (COL1A2) and monoamine oxidase B (MAOB) observed in the discovery sample–both of which have been previously reported to be biological candidates for pain–could not be replicated. Conclusion/Significance Our results may serve as a starting point to encourage further investigation in large and independent population-based cohorts of DNA methylation and other epigenetic changes as possible disease mechanisms in CWP. Ultimately, understanding the key mechanisms underlying CWP may lead to new treatments and inform clinical practice. PMID:27832094

  10. Widespread homologous recombination within and between Streptomyces species.

    PubMed

    Doroghazi, James R; Buckley, Daniel H

    2010-09-01

    Horizontal gene transfer (HGT) is widespread in the microbial world, but its impact on the origin and persistence of microbial species remains poorly defined. HGT can result in either acquisition of new genetic material or homologous replacement of existing genes. The evolutionary significance of homologous recombination in a population can be quantified by examining the relative rates at which polymorphisms are introduced from recombination (rho) and mutation (theta(w)). We used multilocus sequence analysis (MLSA) to quantify both intraspecies and interspecies homologous recombination among streptomycetes, multicellular Gram-positive bacteria ubiquitous in soil, which are an important source of antibiotics and bioactive compounds. Intraspecies recombination was examined using strains of Streptomyces flavogriseus isolated from soils at five locations spanning 1000 km. The strains had >99.8% nucleotide identity across the loci examined. We found remarkable levels of gene exchange within S. flavogriseus (rho/theta(w)=27.9), and found that the population was in linkage equilibrium (standardized index of association=0.0018), providing evidence for a freely recombining sexual population structure. We also examined interspecies homologous recombination among different Streptomyces species in an MLSA data set and found that 40% of the species had housekeeping genes acquired through HGT. The recombination rate between these named species (rho/theta(w)=0.21) exceeds that observed within many species of bacteria. Despite widespread gene exchange in the genus, the intraspecies recombination rate exceeded the interspecies rate by two orders of magnitude suggesting that patterns of gene exchange and recombination may shape the evolution of streptomycetes.

  11. Spatial Assessment of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) in South Africa Confirms Endemic and Widespread Infection

    PubMed Central

    Tarrant, Jeanne; Cilliers, Dirk; du Preez, Louis H.; Weldon, Ché

    2013-01-01

    Chytridiomycosis has been identified as a major cause of global amphibian declines. Despite widespread evidence of Batrachochytrium dendrobatidis infection in South African frogs, sampling for this disease has not focused on threatened species, or whether this pathogen poses a disease risk to these species. This study assessed the occurrence of Bd-infection in South African Red List species. In addition, all known records of infection from South Africa were used to model the ecological niche of Bd to provide a better understanding of spatial patterns and associated disease risk. Presence and prevalence of Bd was determined through quantitative real-time PCR of 360 skin swab samples from 17 threatened species from 38 sites across the country. Average prevalence was 14.8% for threatened species, with pathogen load varying considerably between species. MaxEnt was used to model the predicted distribution of Bd based on 683 positive records for South Africa. The resultant probability threshold map indicated that Bd is largely restricted to the wet eastern and coastal regions of South Africa. A lack of observed adverse impacts on wild threatened populations supports the endemic pathogen hypothesis for southern Africa. However, all threatened species occur within the limits of the predicted distribution for Bd, exposing them to potential Bd-associated risk factors. Predicting pathogen distribution patterns and potential impact is increasingly important for prioritising research and guiding management decisions. PMID:23894506

  12. Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage

    PubMed Central

    Garnica, Sigisfredo; Riess, Kai; Schön, Max E.; Oberwinkler, Franz; Setaro, Sabrina D.

    2016-01-01

    Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales. PMID:26938104

  13. On the relationship between tropospheric conditions and widespread hot days in Iran

    NASA Astrophysics Data System (ADS)

    Asakereh, Hossein; Shadman, Hassan

    2016-12-01

    The present study investigated how the tropospheric conditions relate to the occurrence of widespread hot days (WHD) in Iran using the data of maximum daily temperature and other tropospheric variables. To better understand the tropospheric conditions during WHD, different patterns of tropospheric circulation were examined systematically. Four tropospheric types were identified based on sea level pressure (SLP). SLP, 500 hPa height, anomaly patterns, and warm advection maps were constructed for typical days of each group. The tropospheric conditions associated with hot days occurred simultaneously with a low-pressure system at sea level, a ridge at middle troposphere over Iran, and a pronounced trough over the Mediterranean Sea at 500 hPa. These conditions caused air mass from subtropical regions toward Iran. That is, northward, northeastward, and even eastward winds injected heat with warm origins toward the country. Hot days compounded by drought conditions have affected many parts of the country in different ways such as decrease in the agricultural products in numerous areas and significant discharge reduction in many rivers. The society is also very likely to face considerable challenges to cope with hot days. The findings of the study can be utilized in climate modeling and climate prediction of hot days in the country. Accordingly, water and electricity consumption can be planned with further precision and water consumption can be managed in crises.

  14. Parasite species of the endangered Iberian wolf (Canis lupus signatus) and a sympatric widespread carnivore.

    PubMed

    Figueiredo, Ana; Oliveira, Lucia; Madeira de Carvalho, Luís; Fonseca, Carlos; Torres, Rita Tinoco

    2016-08-01

    Parasites have a profound impact on wildlife population dynamics. However, until some years ago, studies on the occurrence and prevalence of wildlife parasites were neglected comparatively with the studies on humans and domestic animals. In this study, we determined the parasite prevalence of two sympatric wild canids: the endangered Iberian wolf (Canis lupus signatus) and the widespread red fox (Vulpes vulpes), in central Portugal. From November 2014 to July 2015, fresh fecal samples from both species were collected monthly in several transects distributed throughout the study area. All samples were submitted to several coprological techniques. In total, 6 helminth parasites (Crenosoma vulpis, Angiostrongylus vasorum, Toxocara canis, Trichuris vulpis, Ancylostomatidae, Toxascaris leonina), and a protozoa (Balantidium coli) were identified based on size and morphology. The red fox was infected by seven different parasites while the Iberian wolf was infected by four. All parasites present in wolf were also present in the red fox. C. vulpis had the higher prevalence in red fox, while Ancylostomatidae were the most prevalent parasites in wolf. To our knowledge, this is the first study in this isolated subpopulation of the Iberian wolf. Our results show that both carnivores carry parasites that are of concern as they are pathogenic to humans and other wild and domestic animals. We suggest that surveillance programs must also include monitoring protocols of wildlife; particularly endangered species.

  15. Discovery of a widespread low-latitude diurnal CO2 frost cycle on Mars

    NASA Astrophysics Data System (ADS)

    Piqueux, Sylvain; Kleinböhl, Armin; Hayne, Paul O.; Heavens, Nicholas G.; Kass, David M.; McCleese, Daniel J.; Schofield, John T.; Shirley, James H.

    2016-07-01

    While the detection of CO2 ice has only been reported outside the Martian polar regions at very high elevation (i.e., Elysium, Olympus Mons, and the Tharsis Montes), nighttime surface observations by the Mars Climate Sounder on board the Mars Reconnaissance Orbiter document the widespread occurrence of atmospherically corrected ground temperatures consistent with the presence of extensive carbon dioxide frost deposits in the dusty low thermal inertia units at middle/low latitudes. Thermal infrared emissivities, interpreted in conjunction with mass balance modeling, suggest micrometer size CO2 ice crystals forming optically thin layers never exceeding a few hundreds of microns in thickness (i.e., 10-2 kg m-2) locally, which is insufficient to generate a measurable diurnal pressure cycle (<<0.1% of the Martian atmosphere). Atmospheric temperatures at middle/low latitudes are not consistent with precipitation of CO2 ice, suggesting that condensation occurs on the surface. The recurring growth and sublimation of CO2 ice on Martian dusty terrains may be an important process preventing soil induration and promoting dynamic phenomena (soil avalanching and fluidization and regolith gardening), maintaining a reservoir of micrometer size dust particles that are mobile and available for lifting. The discovery of this diurnal CO2 cycle represents an important step forward in our understanding of the way the Martian atmosphere interacts with the surface.

  16. Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change.

    PubMed

    Thorpe, Roger S; Barlow, Axel; Malhotra, Anita; Surget-Groba, Yann

    2015-03-01

    Global warming will impact species in a number of ways, and it is important to know the extent to which natural populations can adapt to anthropogenic climate change by natural selection. Parallel microevolution within separate species can demonstrate natural selection, but several studies of homoplasy have not yet revealed examples of widespread parallel evolution in a generic radiation. Taking into account primary phylogeographic divisions, we investigate numerous quantitative traits (size, shape, scalation, colour pattern and hue) in anole radiations from the mountainous Lesser Antillean islands. Adaptation to climatic differences can lead to very pronounced differences between spatially close populations with all studied traits showing some evidence of parallel evolution. Traits from shape, scalation, pattern and hue (particularly the latter) show widespread evolutionary parallels within these species in response to altitudinal climate variation greater than extreme anthropogenic climate change predicted for 2080. This gives strong evidence of the ability to adapt to climate variation by natural selection throughout this radiation. As anoles can evolve very rapidly, it suggests anthropogenic climate change is likely to be less of a conservation threat than other factors, such as habitat loss and invasive species, in this, Lesser Antillean, biodiversity hot spot.

  17. Lessons learned from occurrences involving procedures at Los Alamos National Laboratory in 1994

    SciTech Connect

    Frostenson, C.K.

    1995-07-01

    This study used the Department of Energy (DOE) Occurrence Reporting and Processing System (ORPS) data to investigate occurrences reported during one year at Los Alamos National Laboratory (LANL). ORPS provides a centralized database and computerized support for the Collection, distribution, updating, analysis, and validation of information in occurrence reports about abnormal events related to facility operation. Human factors causes for occurrences are not always defined in ORPS. Content analysis of narrative data revealed that 33% of all LANL 1994 adverse operational events have human factors causes related to procedures. Procedure-caused occurrences that resulted in injury to workers, damage to facilities or equipment, or a near-miss are analyzed.

  18. Glycolipids: Occurrence, Significance, and Properties

    NASA Astrophysics Data System (ADS)

    Holst, Otto

    This chapter focuses on the occurrence and the physicochemical properties of glycolipids in Nature. Owing to space limitations, the presented overview must be incomplete, and, thus, mainly publications of the past 15 years are included. However, all review articles cited herein inform the interested reader about earlier work. Although lipopolysaccharides (LPS), lipoarabinomannan (LAM), lipomannan, lipoglycans, and lipoteichoic acids are not understood as glycolipids per definition, their occurrence and properties are also described in this chapter. GPI-anchored lipids is a main topic of Chap. 7.4.

  19. A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment

    PubMed Central

    van der Heijden, Marcel GA; Bruin, Susanne de; Luckerhoff, Ludo; van Logtestijn, Richard SP; Schlaeppi, Klaus

    2016-01-01

    Highly diverse microbial assemblages colonize plant roots. It is still poorly understood whether different members of this root microbiome act synergistically by supplying different services (for example, different limiting nutrients) to plants and plant communities. In order to test this, we manipulated the presence of two widespread plant root symbionts, arbuscular mycorrhizal fungi and nitrogen-fixing rhizobia bacteria in model grassland communities established in axenic microcosms. Here, we demonstrate that both symbionts complement each other resulting in increased plant diversity, enhanced seedling recruitment and improved nutrient acquisition compared with a single symbiont situation. Legume seedlings obtained up to 15-fold higher productivity if they formed an association with both symbionts, opposed to productivity they reached with only one symbiont. Our results reveal the importance of functional diversity of symbionts and demonstrate that different members of the root microbiome can complement each other in acquiring different limiting nutrients and in driving important ecosystem functions. PMID:26172208

  20. Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria.

    PubMed

    Cai, Fei; Axen, Seth D; Kerfeld, Cheryl A

    2013-05-01

    Members of the phylum Cyanobacteria inhabit ecologically diverse environments. However, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR associated genes), an extremely adaptable defense system, has not been surveyed in this phylum. We analyzed 126 cyanobacterial genomes and, surprisingly, found CRISPR-Cas in the majority except the marine subclade (Synechococcus and Prochlorococcus), in which cyanophages are a known force shaping their evolution. Multiple observations of CRISPR loci in the absence of cas1/cas2 genes may represent an early stage of losing a CRISPR-Cas locus. Our findings reveal the widespread distribution of their role in the phylum Cyanobacteria and provide a first step to systematically understanding CRISPR-Cas systems in cyanobacteria.

  1. Evidence for strong, widespread chlorine radical chemistry associated with pollution outflow from continental Asia

    NASA Astrophysics Data System (ADS)

    Baker, Angela K.; Sauvage, Carina; Thorenz, Ute R.; van Velthoven, Peter; Oram, David E.; Zahn, Andreas; Brenninkmeijer, Carl A. M.; Williams, Jonathan

    2016-11-01

    The chlorine radical is a potent atmospheric oxidant, capable of perturbing tropospheric oxidative cycles normally controlled by the hydroxyl radical. Significantly faster reaction rates allow chlorine radicals to expedite oxidation of hydrocarbons, including methane, and in polluted environments, to enhance ozone production. Here we present evidence, from the CARIBIC airborne dataset, for extensive chlorine radical chemistry associated with Asian pollution outflow, from airborne observations made over the Malaysian Peninsula in winter. This region is known for persistent convection that regularly delivers surface air to higher altitudes and serves as a major transport pathway into the stratosphere. Oxidant ratios inferred from hydrocarbon relationships show that chlorine radicals were regionally more important than hydroxyl radicals for alkane oxidation and were also important for methane and alkene oxidation (>10%). Our observations reveal pollution-related chlorine chemistry that is both widespread and recurrent, and has implications for tropospheric oxidizing capacity, stratospheric composition and ozone chemistry.

  2. Soil-type influences human selenium status and underlies widespread selenium deficiency risks in Malawi.

    PubMed

    Hurst, Rachel; Siyame, Edwin W P; Young, Scott D; Chilimba, Allan D C; Joy, Edward J M; Black, Colin R; Ander, E Louise; Watts, Michael J; Chilima, Benson; Gondwe, Jellita; Kang'ombe, Dalitso; Stein, Alexander J; Fairweather-Tait, Susan J; Gibson, Rosalind S; Kalimbira, Alexander A; Broadley, Martin R

    2013-01-01

    Selenium (Se) is an essential human micronutrient with critical roles in immune functioning and antioxidant defence. Estimates of dietary Se intakes and status are scarce for Africa although crop surveys indicate deficiency is probably widespread in Malawi. Here we show that Se deficiency is likely endemic in Malawi based on the Se status of adults consuming food from contrasting soil types. These data are consistent with food balance sheets and composition tables revealing that >80% of the Malawi population is at risk of dietary Se inadequacy. Risk of dietary Se inadequacy is >60% in seven other countries in Southern Africa, and 22% across Africa as a whole. Given that most Malawi soils cannot supply sufficient Se to crops for adequate human nutrition, the cost and benefits of interventions to alleviate Se deficiency should be determined; for example, Se-enriched nitrogen fertilisers could be adopted as in Finland.

  3. Evidence for strong, widespread chlorine radical chemistry associated with pollution outflow from continental Asia

    PubMed Central

    Baker, Angela K.; Sauvage, Carina; Thorenz, Ute R.; van Velthoven, Peter; Oram, David E.; Zahn, Andreas; Brenninkmeijer, Carl A. M.; Williams, Jonathan

    2016-01-01

    The chlorine radical is a potent atmospheric oxidant, capable of perturbing tropospheric oxidative cycles normally controlled by the hydroxyl radical. Significantly faster reaction rates allow chlorine radicals to expedite oxidation of hydrocarbons, including methane, and in polluted environments, to enhance ozone production. Here we present evidence, from the CARIBIC airborne dataset, for extensive chlorine radical chemistry associated with Asian pollution outflow, from airborne observations made over the Malaysian Peninsula in winter. This region is known for persistent convection that regularly delivers surface air to higher altitudes and serves as a major transport pathway into the stratosphere. Oxidant ratios inferred from hydrocarbon relationships show that chlorine radicals were regionally more important than hydroxyl radicals for alkane oxidation and were also important for methane and alkene oxidation (>10%). Our observations reveal pollution-related chlorine chemistry that is both widespread and recurrent, and has implications for tropospheric oxidizing capacity, stratospheric composition and ozone chemistry. PMID:27845366

  4. Soil-type influences human selenium status and underlies widespread selenium deficiency risks in Malawi

    PubMed Central

    Hurst, Rachel; Siyame, Edwin W. P.; Young, Scott D.; Chilimba, Allan D. C.; Joy, Edward J. M.; Black, Colin R.; Ander, E. Louise; Watts, Michael J.; Chilima, Benson; Gondwe, Jellita; Kang'ombe, Dalitso; Stein, Alexander J.; Fairweather-Tait, Susan J.; Gibson, Rosalind S.; Kalimbira, Alexander A.; Broadley, Martin R.

    2013-01-01

    Selenium (Se) is an essential human micronutrient with critical roles in immune functioning and antioxidant defence. Estimates of dietary Se intakes and status are scarce for Africa although crop surveys indicate deficiency is probably widespread in Malawi. Here we show that Se deficiency is likely endemic in Malawi based on the Se status of adults consuming food from contrasting soil types. These data are consistent with food balance sheets and composition tables revealing that >80% of the Malawi population is at risk of dietary Se inadequacy. Risk of dietary Se inadequacy is >60% in seven other countries in Southern Africa, and 22% across Africa as a whole. Given that most Malawi soils cannot supply sufficient Se to crops for adequate human nutrition, the cost and benefits of interventions to alleviate Se deficiency should be determined; for example, Se-enriched nitrogen fertilisers could be adopted as in Finland. PMID:23478344

  5. Occurrences and Effects of Drought across Africa

    NASA Astrophysics Data System (ADS)

    Mwangi, M. N.

    2009-12-01

    Drought is a common occurrence in Africa and its effects vary temporally and spatially across the continent. The objective of this paper is to synthesize available information on droughts in Africa in order to discern emerging trends vis-à-vis spatiotemporal occurrences, impacts and adaptation. Drought forcings in the Sahelian region and southern Africa are predominately related to the passage of mid-latitude air masses while in locations near the equator is strongly linked to the position of ITCZ, except perhaps in the deserts where albedo may predominate. The review shows that drought occurrences have increased both temporally and spatially; its effects on the society vary across scales, and are influenced by political, economic, social, cultural, and ecological factors. The drought occurrence and its impacts varied spatially and temporally. The effect of drought also varied with socioeconomic sector; agriculture and pastoralism were the widely reported. The greater horn of Africa, specifically Kenya, has the most continuous record of droughts. The synthesis also reveals that a suite of drought adaptation strategies exists at the local scale; in contrasts, at the aggregate scale, coping strategies are scarce. Drought management tailored for specific livelihood system or societies are non-existent. The study found that occurrence of drought alongside issues related to the multiscale political economy affect the viability of most adaptation strategies used by societies across Africa. Drought management has been silent on the social, political, and economic dimensions that reasonably aggravate the vulnerability of lives and livelihood systems to this climatic hazard. The effect of drought and social pressures is relational and simultaneous to such a degree that differential vulnerability among communities across Africa is to be expected. Although scenarios about rainfall and drought vis-à-vis Africa are largely contested there is a general indication that most

  6. Heavy metal resistant strains are widespread along Streptomyces phylogeny.

    PubMed

    Alvarez, Analía; Catalano, Santiago A; Amoroso, María Julia

    2013-03-01

    The genus Streptomyces comprises a group of bacteria species with high economic importance. Several of these species are employed at industrial scale for the production of useful compounds. Other characteristic found in different strains within this genus is their capability to tolerate high level of substances toxic for humans, heavy metals among them. Although several studies have been conducted in different species of the genus in order to disentangle the mechanisms associated to heavy metal resistance, little is known about how they have evolved along Streptomyces phylogeny. In this study we built the largest Streptomyces phylogeny generated up to date comprising six genes, 113 species of Streptomyces and 27 outgroups. The parsimony-based phylogenetic analysis indicated that (i) Streptomyces is monophyletic and (ii) it appears as sister clade of a group formed by Kitasatospora and Streptacidiphilus species, both genera also monophyletic. Streptomyces strains resistant to heavy metals are not confined to a single lineage but widespread along Streptomyces phylogeny. Our result in combination with genomic, physiological and biochemical data suggest that the resistance to heavy metals originated several times and by different mechanisms in Streptomyces history.

  7. Recent Arctic tundra fire initiates widespread thermokarst development

    DOE PAGES

    Jones, Benjamin M.; Grosse, Guido; Arp, Christopher D.; ...

    2015-10-29

    Fire-induced permafrost degradation is well documented in boreal forests, but the role of fires in initiating thermokarst development in Arctic tundra is less well understood. Here we show that Arctic tundra fires may induce widespread thaw subsidence of permafrost terrain in the first seven years following the disturbance. Quantitative analysis of airborne LiDAR data acquired two and seven years post-fire, detected permafrost thaw subsidence across 34% of the burned tundra area studied, compared to less than 1% in similar undisturbed, ice-rich tundra terrain units. The variability in thermokarst development appears to be influenced by the interaction of tundra fire burnmore » severity and near-surface, ground-ice content. Subsidence was greatest in severely burned, ice-rich upland terrain (yedoma), accounting for -50% of the detected subsidence, despite representing only 30% of the fire disturbed study area. Microtopography increased by 340% in this terrain unit as a result of ice wedge degradation. Increases in the frequency, magnitude, and severity of tundra fires will contribute to future thermokarst development and associated landscape change in Arctic tundra regions.« less

  8. Recent Arctic tundra fire initiates widespread thermokarst development

    SciTech Connect

    Jones, Benjamin M.; Grosse, Guido; Arp, Christopher D.; Miller, Eric; Liu, Lin; Hayes, Daniel J.; Larsen, Christopher F.

    2015-10-29

    Fire-induced permafrost degradation is well documented in boreal forests, but the role of fires in initiating thermokarst development in Arctic tundra is less well understood. Here we show that Arctic tundra fires may induce widespread thaw subsidence of permafrost terrain in the first seven years following the disturbance. Quantitative analysis of airborne LiDAR data acquired two and seven years post-fire, detected permafrost thaw subsidence across 34% of the burned tundra area studied, compared to less than 1% in similar undisturbed, ice-rich tundra terrain units. The variability in thermokarst development appears to be influenced by the interaction of tundra fire burn severity and near-surface, ground-ice content. Subsidence was greatest in severely burned, ice-rich upland terrain (yedoma), accounting for -50% of the detected subsidence, despite representing only 30% of the fire disturbed study area. Microtopography increased by 340% in this terrain unit as a result of ice wedge degradation. Increases in the frequency, magnitude, and severity of tundra fires will contribute to future thermokarst development and associated landscape change in Arctic tundra regions.

  9. [Widespread gastrointestinal CMV infection as the presenting manifestation of AIDS].

    PubMed

    Dayan, K; Neufeld, D M; Lang, R; Novis, B; Bernheim, J; Freund, U

    1993-02-01

    A 53-year-old man is reported who developed a widespread gastrointestinal infection due to cytomegalic (CMV) virus and was found to be suffering from AIDS. He died of overwhelming pulmonary infection. There is need for awareness of the rapid increase of AIDS in our local population, particularly in groups not regarded as at high risk. It is imperative to keep this diagnosis in mind when dealing with patients with gastroenterocolitis not responding to standard treatments. CMV has a broad spectrum of clinical manifestations, from carrier state to life-threatening infection. In the gastrointestinal system it causes inflammation and ulcers in the mucosa that may bleed or perforate. There are increasing numbers of reports of CMV ileocolitis in homosexuals with AIDS. The rate of sero-positive CMV in healthy homosexual populations is 94-100% and in 14% there is active infection. CMV is the main infective agent in patients suffering from AIDS; 90% will develop an infection with this virus and in most cases it will be fatal.

  10. Widespread Rickettsia spp. Infections in Ticks (Acari: Ixodoidea) in Taiwan.

    PubMed

    Kuo, Chi-Chien; Shu, Pei-Yun; Mu, Jung-Jung; Lee, Pei-Lung; Wu, Yin-Wen; Chung, Chien-Kung; Wang, Hsi-Chieh

    2015-09-01

    Ticks are second to mosquitoes as the most important disease vectors, and recent decades have witnessed the emergence of many novel tick-borne rickettsial diseases, but systematic surveys of ticks and tick-borne rickettsioses are generally lacking in Asia. We collected and identified ticks from small mammal hosts between 2006 and 2010 in different parts of Taiwan. Rickettsia spp. infections in ticks were identified by targeting ompB and gltA genes with nested polymerase chain reaction. In total, 2,732 ticks were collected from 1,356 small mammals. Rhipicephalus haemaphysaloides Supino (51.8% of total ticks), Haemaphysalis bandicota Hoogstraal & Kohls (28.0%), and Ixodes granulatus Supino (20.0%) were the most common tick species, and Rattus losea Swinhoe (44.7% of total ticks) and Bandicota indica Bechstein (39.9%) were the primary hosts. The average Rickettsia infective rate in 329 assayed ticks was 31.9% and eight Rickettsia spp. or closely related species were identified. This study shows that rickettsiae-infected ticks are widespread in Taiwan, with a high diversity of Rickettsia spp. circulating in the ticks. Because notifiable rickettsial diseases in Taiwan only include mite-borne scrub typhus and flea-borne murine typhus, more studies are warranted for a better understanding of the real extent of human risks to rickettsioses in Taiwan.

  11. Recent Arctic tundra fire initiates widespread thermokarst development

    NASA Astrophysics Data System (ADS)

    Jones, Benjamin M.; Grosse, Guido; Arp, Christopher D.; Miller, Eric; Liu, Lin; Hayes, Daniel J.; Larsen, Christopher F.

    2015-10-01

    Fire-induced permafrost degradation is well documented in boreal forests, but the role of fires in initiating thermokarst development in Arctic tundra is less well understood. Here we show that Arctic tundra fires may induce widespread thaw subsidence of permafrost terrain in the first seven years following the disturbance. Quantitative analysis of airborne LiDAR data acquired two and seven years post-fire, detected permafrost thaw subsidence across 34% of the burned tundra area studied, compared to less than 1% in similar undisturbed, ice-rich tundra terrain units. The variability in thermokarst development appears to be influenced by the interaction of tundra fire burn severity and near-surface, ground-ice content. Subsidence was greatest in severely burned, ice-rich upland terrain (yedoma), accounting for ~50% of the detected subsidence, despite representing only 30% of the fire disturbed study area. Microtopography increased by 340% in this terrain unit as a result of ice wedge degradation. Increases in the frequency, magnitude, and severity of tundra fires will contribute to future thermokarst development and associated landscape change in Arctic tundra regions.

  12. Recent Arctic tundra fire initiates widespread thermokarst development.

    PubMed

    Jones, Benjamin M; Grosse, Guido; Arp, Christopher D; Miller, Eric; Liu, Lin; Hayes, Daniel J; Larsen, Christopher F

    2015-10-29

    Fire-induced permafrost degradation is well documented in boreal forests, but the role of fires in initiating thermokarst development in Arctic tundra is less well understood. Here we show that Arctic tundra fires may induce widespread thaw subsidence of permafrost terrain in the first seven years following the disturbance. Quantitative analysis of airborne LiDAR data acquired two and seven years post-fire, detected permafrost thaw subsidence across 34% of the burned tundra area studied, compared to less than 1% in similar undisturbed, ice-rich tundra terrain units. The variability in thermokarst development appears to be influenced by the interaction of tundra fire burn severity and near-surface, ground-ice content. Subsidence was greatest in severely burned, ice-rich upland terrain (yedoma), accounting for ~50% of the detected subsidence, despite representing only 30% of the fire disturbed study area. Microtopography increased by 340% in this terrain unit as a result of ice wedge degradation. Increases in the frequency, magnitude, and severity of tundra fires will contribute to future thermokarst development and associated landscape change in Arctic tundra regions.

  13. Recent Arctic tundra fire initiates widespread thermokarst development

    PubMed Central

    Jones, Benjamin M.; Grosse, Guido; Arp, Christopher D.; Miller, Eric; Liu, Lin; Hayes, Daniel J.; Larsen, Christopher F.

    2015-01-01

    Fire-induced permafrost degradation is well documented in boreal forests, but the role of fires in initiating thermokarst development in Arctic tundra is less well understood. Here we show that Arctic tundra fires may induce widespread thaw subsidence of permafrost terrain in the first seven years following the disturbance. Quantitative analysis of airborne LiDAR data acquired two and seven years post-fire, detected permafrost thaw subsidence across 34% of the burned tundra area studied, compared to less than 1% in similar undisturbed, ice-rich tundra terrain units. The variability in thermokarst development appears to be influenced by the interaction of tundra fire burn severity and near-surface, ground-ice content. Subsidence was greatest in severely burned, ice-rich upland terrain (yedoma), accounting for ~50% of the detected subsidence, despite representing only 30% of the fire disturbed study area. Microtopography increased by 340% in this terrain unit as a result of ice wedge degradation. Increases in the frequency, magnitude, and severity of tundra fires will contribute to future thermokarst development and associated landscape change in Arctic tundra regions. PMID:26511650

  14. Recent Arctic tundra fire initiates widespread thermokarst development

    USGS Publications Warehouse

    Jones, Benjamin M.; Grosse, Guido; Arp, Christopher D.; Miller, Eric K.; Liu, Lingli; Hayes, Daniel J.; Larsen, Christopher F.

    2015-01-01

    Fire-induced permafrost degradation is well documented in boreal forests, but the role of fires in initiating thermokarst development in Arctic tundra is less well understood. Here we show that Arctic tundra fires may induce widespread thaw subsidence of permafrost terrain in the first seven years following the disturbance. Quantitative analysis of airborne LiDAR data acquired two and seven years post-fire, detected permafrost thaw subsidence across 34% of the burned tundra area studied, compared to less than 1% in similar undisturbed, ice-rich tundra terrain units. The variability in thermokarst development appears to be influenced by the interaction of tundra fire burn severity and near-surface, ground-ice content. Subsidence was greatest in severely burned, ice-rich upland terrain (yedoma), accounting for ~50% of the detected subsidence, despite representing only 30% of the fire disturbed study area. Microtopography increased by 340% in this terrain unit as a result of ice wedge degradation. Increases in the frequency, magnitude, and severity of tundra fires will contribute to future thermokarst development and associated landscape change in Arctic tundra regions.

  15. Widespread transmission of independent cancer lineages within multiple bivalve species

    PubMed Central

    Metzger, Michael J.; Villalba, Antonio; Carballal, María J.; Iglesias, David; Sherry, James; Reinisch, Carol; Muttray, Annette F.; Baldwin, Susan A.; Goff, Stephen P.

    2016-01-01

    Most cancers arise from oncogenic changes in the genomes of somatic cells, and while the cells may migrate by metastasis, they remain within that single individual. Natural transmission of cancer cells from one individual to another has been observed in two distinctive cases in mammals (Tasmanian devils1 and dogs2,3), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria)4 suggested that this phenomenon might be more widespread. Here we analyzed disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and found that neoplasias in all three species are attributable to independent transmissible cancer lineages. In mussels and cockles, the cancer lineages are derived from their respective host species, but unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographic area. No cases of disseminated neoplasia have thus far been found in V. corrugata from the same region. These findings show that transmission of cancer cells in the marine environment is common in multiple species, that it has originated many times, and that while most transmissible cancers were found spreading within the species of origin, cross-species transmission of cancer cells can occur. PMID:27338791

  16. Widespread tau seeding activity at early Braak stages.

    PubMed

    Furman, Jennifer L; Vaquer-Alicea, Jaime; White, Charles L; Cairns, Nigel J; Nelson, Peter T; Diamond, Marc I

    2017-01-01

    Transcellular propagation of tau aggregates may underlie the progression of pathology in Alzheimer's disease (AD) and other tauopathies. Braak staging (B1, B2, B3) is based on phospho-tau accumulation within connected brain regions: entorhinal cortex (B1); hippocampus/limbic system (B2); and frontal and parietal lobes (B3). We previously developed a specific and sensitive assay that uses flow cytometry to quantify tissue seeding activity based on fluorescence resonance energy transfer (FRET) in cells that stably express tau reporter proteins. In a tauopathy mouse model, we have detected seeding activity far in advance of histopathological changes. It remains unknown whether individuals with AD also develop seeding activity prior to accumulation of phospho-tau. We measured tau seeding activity across four brain regions (hippocampus, frontal lobe, parietal lobe, and cerebellum) in 104 fresh-frozen human AD brain samples from all Braak stages. We observed widespread seeding activity, notably in regions predicted to be free of phospho-tau deposition, and in detergent-insoluble fractions that lacked tau detectable by ELISA. Seeding activity correlated positively with Braak stage and negatively with MMSE. Our results are consistent with early transcellular propagation of tau seeds that triggers subsequent development of neuropathology. The FRET-based seeding assay may also complement standard neuropathological classification of tauopathies.

  17. Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

    PubMed Central

    Sahni, Nidhi; Yi, Song; Taipale, Mikko; Fuxman Bass, Juan I.; Coulombe-Huntington, Jasmin; Yang, Fan; Peng, Jian; Weile, Jochen; Karras, Georgios I.; Wang, Yang; Kovács, István A.; Kamburov, Atanas; Krykbaeva, Irina; Lam, Mandy H.; Tucker, George; Khurana, Vikram; Sharma, Amitabh; Liu, Yang-Yu; Yachie, Nozomu; Zhong, Quan; Shen, Yun; Palagi, Alexandre; San-Miguel, Adriana; Fan, Changyu; Balcha, Dawit; Dricot, Amelie; Jordan, Daniel M.; Walsh, Jennifer M.; Shah, Akash A.; Yang, Xinping; Stoyanova, Ani; Leighton, Alex; Calderwood, Michael A.; Jacob, Yves; Cusick, Michael E.; Salehi-Ashtiani, Kourosh; Whitesell, Luke J.; Sunyaev, Shamil; Berger, Bonnie; Barabási, Albert-László; Charloteaux, Benoit; Hill, David E.; Hao, Tong; Roth, Frederick P.; Xia, Yu; Walhout, Albertha J.M.; Lindquist, Susan; Vidal, Marc

    2015-01-01

    SUMMARY How disease-associated mutations impair protein activities in the context of biological networks remains mostly undetermined. Although a few renowned alleles are well characterized, functional information is missing for over 100,000 disease-associated variants. Here we functionally profile several thousand missense mutations across a spectrum of Mendelian disorders using various interaction assays. The majority of disease-associated alleles exhibit wild-type chaperone binding profiles, suggesting they preserve protein folding or stability. While common variants from healthy individuals rarely affect interactions, two-thirds of disease-associated alleles perturb protein-protein interactions, with half corresponding to “edgetic” alleles affecting only a subset of interactions while leaving most other interactions unperturbed. With transcription factors, many alleles that leave protein-protein interactions intact affect DNA binding. Different mutations in the same gene leading to different interaction profiles often result in distinct disease phenotypes. Thus disease-associated alleles that perturb distinct protein activities rather than grossly affecting folding and stability are relatively widespread. PMID:25910212

  18. Occurrence of tar balls on the beaches of Fernando de Noronha Island, South Equatorial Atlantic.

    PubMed

    Baptista Neto, José Antônio; da Costa Campos, Thomas Ferreira; de Andrade, Carala Danielle Perreira; Sichel, Susanna Eleonora; da Fonseca, Estefan Monteiro; Motoki, Akihisa

    2014-12-01

    This work reports on the widespread occurrence of tar balls on a pebble beach of Sueste Bay on Fernando de Noronha Island, a Brazilian national marine park and a preserve in the South Equatorial Atlantic. Environmental regulations preclude regular visitors to the Sueste Bay beach, and the bay is a pristine area without any possible or potential sources of petroleum in the coastal zone. In this work, these tar balls were observed for the first time as they occurred as envelopes around beach pebbles. They are black in color, very hard, have a shell and coral fragment armor, and range in average size from 2 to 6 cm. The shape of the majority of the tar balls is spherical, but some can also be flattened ellipsoids. The polycyclic aromatic hydrocarbon analyses of the collected samples revealed the characteristics of a strongly weathered material, where only the most persistent compounds were detected: chrysene, benzo(b,k)fluoranthene, dibenzo(a,h)antracene and benzo(a)pyrene.

  19. Occurrence of regulated and emerging iodinated DBPs in the Shanghai drinking water.

    PubMed

    Wei, Xiao; Chen, Xin; Wang, Xia; Zheng, Weiwei; Zhang, Dong; Tian, Dajun; Jiang, Songhui; Ong, Choon Nam; He, Gengsheng; Qu, Weidong

    2013-01-01

    Drinking water chlorination plays a pivotal role in preventing pathogen contamination against water-borne disease. However, chemical disinfection leads to the formation of halogenated disinfection by products (DBPs). Many DBPs are highly toxic and are of health concern. In this study, we conducted a comprehensive measurements of DBPs, including iodoacetic acid (IAA), iodoform (IF), nine haloacetic acids and four trihalomethanes in drinking waters from 13 water plants in Shanghai, China. The results suggested that IAA and IF were found in all the water treatment plants, with maximum levels of 1.66 µg/L and 1.25 µg/L for IAA and IF, respectively. Owing to deterioration of water quality, the Huangpu River has higher IAA and IF than the Yangtze River. Our results also demonstrated that low pH, high natural organic matter, ammonia nitrogen, and iodide in source waters increased IAA and IF formation. Compared to chlorine, chloramines resulted in higher concentration of iodinated DBP, but reduced the levels of trihalomethanes. This is the first study to reveal the widespread occurrence of IAA and IF in drinking water in China. The data provide a better understanding on the formation of iodinated disinfection byproducts and the findings should be useful for treatment process improvement and disinfection byproducts controls.

  20. First natural occurrence of coesite

    USGS Publications Warehouse

    Chao, E.C.T.; Shoemaker, E.M.; Madsen, B.M.

    1960-01-01

    Coesite, the high-pressure polymorph of SiO2, hitherto known only as a synthetic compound, is identified as an abundant mineral in sheared Coconino sandstone at Meteor Crater, Arizona. This natural occurrence has important bearing on the recognition of meteorite impact craters in quartz-bearing geologic formations.

  1. Genomes of Abundant and Widespread Viruses from the Deep Ocean

    PubMed Central

    Mizuno, Carolina Megumi; Ghai, Rohit; Saghaï, Aurélien; López-García, Purificación

    2016-01-01

    ABSTRACT The deep sea is a massive, largely oligotrophic ecosystem, stretched over nearly 65% of the planet’s surface. Deep-sea planktonic communities are almost completely dependent upon organic carbon sinking from the productive surface, forming a vital component of global biogeochemical cycles. However, despite their importance, viruses from the deep ocean remain largely unknown. Here, we describe the first complete genomes of deep-sea viruses assembled from metagenomic fosmid libraries. “Candidatus Pelagibacter” (SAR11) phage HTVC010P and Puniceispirillum phage HMO-2011 are considered the most abundant cultured marine viruses known to date. Remarkably, some of the viruses described here recruited as many reads from deep waters as these viruses do in the photic zone, and, considering the gigantic scale of the bathypelagic habitat, these genomes provide information about what could be some of the most abundant viruses in the world at large. Their role in the viral shunt in the global ocean could be very significant. Despite the challenges encountered in inferring the identity of their hosts, we identified one virus predicted to infect members of the globally distributed SAR11 cluster. We also identified a number of putative proviruses from diverse taxa, including deltaproteobacteria, bacteroidetes, SAR11, and gammaproteobacteria. Moreover, our findings also indicate that lysogeny is the preferred mode of existence for deep-sea viruses inhabiting an energy-limited environment, in sharp contrast to the predominantly lytic lifestyle of their photic-zone counterparts. Some of the viruses show a widespread distribution, supporting the tenet “everything is everywhere” for the deep-ocean virome. PMID:27460793

  2. The Acraman impact and its widespread ejecta, South Australia

    NASA Technical Reports Server (NTRS)

    Gostin, V. A.; Keays, R. R.; Wallace, M. W.

    1992-01-01

    Discovery of a widespread horizon of shock-deformed volcaniclastic ejecta preserved in Late Proterozoic (approx. 600 Ma) shales in South Australia and its probable link to the Acraman impact structure in the Middle Proterozoic Gawler Range. Volcanics provide a rare opportunity to study the effects of a major terrestrial impact, including the sedimentology and distribution of an ejecta blanket and its precious-metal signature. The ejecta horizon occurs in the Bunyeroo Formation at many localities within the Adelaide Geosyncline, including the Wearing Hills, which are approx. 350 km northeast of the Acraman impact site. Following a search at the same stratigraphic level in other basins in South Australia, the ejecta has been located within the Lower Rodda beds of the Officer Basin, extending the limits of the ejecta to approx. 470 km northwest of the Acraman impact structure. The ejecta is therefore widely dispersed, and provides an important chronostratigraphic marker enabling precise correlation of Late Proterozoic sequences in southern Australia. In summary, the Bunyeroo ejecta is unique as the only known example of a widely dispersed, coarse-grained ejecta blanket that is, moreover, strongly linked to a known major impact structure. The marked Ir-PGE anomalies in the ejecta horizon provide support for the hypothesis that meteorite impact events can produce Ir anomalies interrestrial sediments. The findings also indicate that Ir can be mobilized and concentrated in sediments by low-temperature diagenetic processes. The identification of ejecta horizons in sedimentary rocks therefore should be based on the coincidence of shock-metamorphic features in the detritus and clear Ir anomalies.

  3. Widespread decline of Congo rainforest greenness in the past decade.

    PubMed

    Zhou, Liming; Tian, Yuhong; Myneni, Ranga B; Ciais, Philippe; Saatchi, Sassan; Liu, Yi Y; Piao, Shilong; Chen, Haishan; Vermote, Eric F; Song, Conghe; Hwang, Taehee

    2014-05-01

    Tropical forests are global epicentres of biodiversity and important modulators of climate change, and are mainly constrained by rainfall patterns. The severe short-term droughts that occurred recently in Amazonia have drawn attention to the vulnerability of tropical forests to climatic disturbances. The central African rainforests, the second-largest on Earth, have experienced a long-term drying trend whose impacts on vegetation dynamics remain mostly unknown because in situ observations are very limited. The Congolese forest, with its drier conditions and higher percentage of semi-evergreen trees, may be more tolerant to short-term rainfall reduction than are wetter tropical forests, but for a long-term drought there may be critical thresholds of water availability below which higher-biomass, closed-canopy forests transition to more open, lower-biomass forests. Here we present observational evidence for a widespread decline in forest greenness over the past decade based on analyses of satellite data (optical, thermal, microwave and gravity) from several independent sensors over the Congo basin. This decline in vegetation greenness, particularly in the northern Congolese forest, is generally consistent with decreases in rainfall, terrestrial water storage, water content in aboveground woody and leaf biomass, and the canopy backscatter anomaly caused by changes in structure and moisture in upper forest layers. It is also consistent with increases in photosynthetically active radiation and land surface temperature. These multiple lines of evidence indicate that this large-scale vegetation browning, or loss of photosynthetic capacity, may be partially attributable to the long-term drying trend. Our results suggest that a continued gradual decline of photosynthetic capacity and moisture content driven by the persistent drying trend could alter the composition and structure of the Congolese forest to favour the spread of drought-tolerant species.

  4. Widespread Chemical Detoxification of Alkaloid Venom by Formicine Ants.

    PubMed

    LeBrun, Edward G; Diebold, Peter J; Orr, Matthew R; Gilbert, Lawrence E

    2015-10-01

    The ability to detoxify defensive compounds of competitors provides key ecological advantages that can influence community-level processes. Although common in plants and bacteria, this type of detoxification interaction is extremely rare in animals. Here, using laboratory behavioral assays and analyses of videotaped interactions in South America, we report widespread venom detoxification among ants in the subfamily Formicinae. Across both data sets, nine formicine species, representing all major clades, used a stereotyped grooming behavior to self-apply formic acid (acidopore grooming) in response to fire ant (Solenopsis invicta and S. saevissima) venom exposure. In laboratory assays, this behavior increased the survivorship of species following exposure to S. invicta venom. Species expressed the behavior when exposed to additional alkaloid venoms, including both compositionally similar piperidine venom of an additional fire ant species and the pyrrolidine/pyrroline alkaloid venom of a Monomorium species. In addition, species expressed the behavior following exposure to the uncharacterized venom of a Crematogaster species. However, species did not express acidopore grooming when confronted with protein-based ant venoms or when exposed to monoterpenoid-based venom. This pattern, combined with the specific chemistry of the reaction of formic acid with venom alkaloids, indicates that alkaloid venoms are targets of detoxification grooming. Solenopsis thief ants, and Monomorium species stand out as brood-predators of formicine ants that produce piperidine, pyrrolidine, and pyrroline venom, providing an important ecological context for the use of detoxification behavior. Detoxification behavior also represents a mechanism that can influence the order of assemblage dominance hierarchies surrounding food competition. Thus, this behavior likely influences ant-assemblages through a variety of ecological pathways.

  5. Vertical transmission of fungal endophytes is widespread in forbs.

    PubMed

    Hodgson, Susan; de Cates, Catherine; Hodgson, Joshua; Morley, Neil J; Sutton, Brian C; Gange, Alan C

    2014-04-01

    To date, it has been thought that endophytic fungi in forbs infect the leaves of their hosts most commonly by air-borne spores (termed "horizontal transmission"). Here, we show that vertical transmission from mother plant to offspring, via seeds, occurs in six forb species (Centaurea cyanus, C. nigra,Papaver rhoeas,Plantago lanceolata,Rumex acetosa, and Senecio vulgaris), suggesting that this may be a widespread phenomenon. Mature seeds were collected from field-grown plants and endophytes isolated from these, and from subsequent cotyledons and true leaves of seedlings, grown in sterile conditions. Most seeds contain one species of fungus, although the identity of the endophyte differs between plant species. Strong evidence for vertical transmission was found for two endophyte species, Alternaria alternata and Cladosporium sphaerospermum. These fungi were recovered from within seeds, cotyledons, and true leaves, although the plant species they were associated with differed. Vertical transmission appears to be an imperfect process, and germination seems to present a bottleneck for fungal growth. We also found that A. alternata and C. sphaerospermum occur on, and within pollen grains, showing that endophyte transmission can be both within and between plant generations. Fungal growth with the pollen tube is likely to be the way in which endophytes enter the developing seed. The fact that true vertical transmission seems common suggests a more mutualistic association between these fungi and their hosts than has previously been thought, and possession of endophytes by seedling plants could have far-reaching ecological consequences. Seedlings may have different growth rates and be better protected against herbivores and pathogens, dependent on the fungi that were present in the mother plant. This would represent a novel case of trans-generational resistance in plants.

  6. Vertical transmission of fungal endophytes is widespread in forbs

    PubMed Central

    Hodgson, Susan; Cates, Catherine; Hodgson, Joshua; Morley, Neil J; Sutton, Brian C; Gange, Alan C

    2014-01-01

    To date, it has been thought that endophytic fungi in forbs infect the leaves of their hosts most commonly by air-borne spores (termed “horizontal transmission”). Here, we show that vertical transmission from mother plant to offspring, via seeds, occurs in six forb species (Centaurea cyanus, C. nigra,Papaver rhoeas,Plantago lanceolata,Rumex acetosa, and Senecio vulgaris), suggesting that this may be a widespread phenomenon. Mature seeds were collected from field-grown plants and endophytes isolated from these, and from subsequent cotyledons and true leaves of seedlings, grown in sterile conditions. Most seeds contain one species of fungus, although the identity of the endophyte differs between plant species. Strong evidence for vertical transmission was found for two endophyte species, Alternaria alternata and Cladosporium sphaerospermum. These fungi were recovered from within seeds, cotyledons, and true leaves, although the plant species they were associated with differed. Vertical transmission appears to be an imperfect process, and germination seems to present a bottleneck for fungal growth. We also found that A. alternata and C. sphaerospermum occur on, and within pollen grains, showing that endophyte transmission can be both within and between plant generations. Fungal growth with the pollen tube is likely to be the way in which endophytes enter the developing seed. The fact that true vertical transmission seems common suggests a more mutualistic association between these fungi and their hosts than has previously been thought, and possession of endophytes by seedling plants could have far-reaching ecological consequences. Seedlings may have different growth rates and be better protected against herbivores and pathogens, dependent on the fungi that were present in the mother plant. This would represent a novel case of trans-generational resistance in plants. PMID:24834319

  7. Chronic widespread pain in the spectrum of rheumatological diseases.

    PubMed

    Bliddal, Henning; Danneskiold-Samsøe, Bente

    2007-06-01

    Chronic pain is very common in all European countries, with musculoskeletal problems predominating. About 1% of the adult population develops a syndrome of chronic muscle pain, fibromyalgia (FMS), characterized by multiple tender points, back or neck pain, and a number of associated problems from other organs, including a high frequency of fatigue. Evidence points to central sensitization as an important neurophysiological aberration in the development of FMS. Importantly, these neurological changes may result from inadequately treated chronic focal pain problems such as osteoarthritis or myofascial pain. It is important for health professionals to be aware of this syndrome and to diagnose the patients to avoid a steady increase in diagnostic tests. On the other hand, patients with chronic widespread pain have an increased risk of developing malignancies, and new or changed symptoms should be diagnosed even in FMS. In rheumatology practice it is especially important to be aware of the existence of FMS in association with immune inflammatory diseases, most commonly lupus and rheumatoid arthritis. Differential diagnoses are other causes of chronic pain, e.g. thyroid disease. The costs of this syndrome are substantial due to loss of working capability and direct expenses of medication and health-system usage. Fibromyalgia patients need recognition of their pain syndrome if they are to comply with treatment. Lack of empathy and understanding by healthcare professionals often leads to patient frustration and inappropriate illness behavior, often associated with some exaggeration of symptoms in an effort to gain some legitimacy for their problem. FMS is multifaceted, and treatment consists of both medical interventions, with emphasis on agents acting on the central nervous system, and physical exercises.

  8. Widespread reductions in gray matter volume in depression☆

    PubMed Central

    Grieve, Stuart M.; Korgaonkar, Mayuresh S.; Koslow, Stephen H.; Gordon, Evian; Williams, Leanne M.

    2013-01-01

    Abnormalities in functional limbic–anterior cingulate–prefrontal circuits associated with emotional reactivity, evaluation and regulation have been implicated in the pathophysiology of major depressive disorder (MDD). However, existing knowledge about structural alterations in depression is equivocal and based on cohorts of limited sample size. This study used voxel-based morphometry (VBM) and surface-based cortical thickness to investigate the structure of these circuits in a large and well-characterized patient cohort with MDD. Non-geriatric MDD outpatients (n = 102) and age- and gender-matched healthy control participants (n = 34) provided T1-weighted magnetic resonance imaging data during their baseline visit as part of the International Study to Predict Optimized Treatment for Depression. Whole-brain VBM volumetric and surface-based cortical thickness assessments were performed voxel-wise and compared (at p < 0.05 corrected for multiple comparisons) between the MDD and control groups. MDD participants had reduced gray matter volume in the anterior cingulate cortex, regions of the prefrontal circuits, including dorsolateral and dorsomedial prefrontal cortices, and lateral and medial orbitofrontal cortices, but not in limbic regions. Additional reductions were observed cortically in the posterior temporal and parieto-occipital cortices and, subcortically in the basal ganglia and cerebellum. Focal cortical thinning in the medial orbitofrontal cortex was also observed for the MDD group. These alterations in volume and cortical thickness were not associated with severity of depressive symptoms. The findings demonstrate that widespread gray matter structural abnormalities are present in a well-powered study of patients with depression. The patterns of gray matter loss correspond to the same brain functional network regions that were previously established to be abnormal in MDD, which may support an underlying structural abnormality for these circuits. PMID

  9. Widespread decline of Congo rainforest greenness in the past decade

    NASA Astrophysics Data System (ADS)

    Zhou, Liming; Tian, Yuhong; Myneni, Ranga B.; Ciais, Philippe; Saatchi, Sassan; Liu, Yi Y.; Piao, Shilong; Chen, Haishan; Vermote, Eric F.; Song, Conghe; Hwang, Taehee

    2014-05-01

    Tropical forests are global epicentres of biodiversity and important modulators of climate change, and are mainly constrained by rainfall patterns. The severe short-term droughts that occurred recently in Amazonia have drawn attention to the vulnerability of tropical forests to climatic disturbances. The central African rainforests, the second-largest on Earth, have experienced a long-term drying trend whose impacts on vegetation dynamics remain mostly unknown because in situ observations are very limited. The Congolese forest, with its drier conditions and higher percentage of semi-evergreen trees, may be more tolerant to short-term rainfall reduction than are wetter tropical forests, but for a long-term drought there may be critical thresholds of water availability below which higher-biomass, closed-canopy forests transition to more open, lower-biomass forests. Here we present observational evidence for a widespread decline in forest greenness over the past decade based on analyses of satellite data (optical, thermal, microwave and gravity) from several independent sensors over the Congo basin. This decline in vegetation greenness, particularly in the northern Congolese forest, is generally consistent with decreases in rainfall, terrestrial water storage, water content in aboveground woody and leaf biomass, and the canopy backscatter anomaly caused by changes in structure and moisture in upper forest layers. It is also consistent with increases in photosynthetically active radiation and land surface temperature. These multiple lines of evidence indicate that this large-scale vegetation browning, or loss of photosynthetic capacity, may be partially attributable to the long-term drying trend. Our results suggest that a continued gradual decline of photosynthetic capacity and moisture content driven by the persistent drying trend could alter the composition and structure of the Congolese forest to favour the spread of drought-tolerant species.

  10. Widespread exploitation of the honeybee by early Neolithic farmers.

    PubMed

    Roffet-Salque, Mélanie; Regert, Martine; Evershed, Richard P; Outram, Alan K; Cramp, Lucy J E; Decavallas, Orestes; Dunne, Julie; Gerbault, Pascale; Mileto, Simona; Mirabaud, Sigrid; Pääkkönen, Mirva; Smyth, Jessica; Šoberl, Lucija; Whelton, Helen L; Alday-Ruiz, Alfonso; Asplund, Henrik; Bartkowiak, Marta; Bayer-Niemeier, Eva; Belhouchet, Lotfi; Bernardini, Federico; Budja, Mihael; Cooney, Gabriel; Cubas, Miriam; Danaher, Ed M; Diniz, Mariana; Domboróczki, László; Fabbri, Cristina; González-Urquijo, Jesus E; Guilaine, Jean; Hachi, Slimane; Hartwell, Barrie N; Hofmann, Daniela; Hohle, Isabel; Ibáñez, Juan J; Karul, Necmi; Kherbouche, Farid; Kiely, Jacinta; Kotsakis, Kostas; Lueth, Friedrich; Mallory, James P; Manen, Claire; Marciniak, Arkadiusz; Maurice-Chabard, Brigitte; Mc Gonigle, Martin A; Mulazzani, Simone; Özdoğan, Mehmet; Perić, Olga S; Perić, Slaviša R; Petrasch, Jörg; Pétrequin, Anne-Marie; Pétrequin, Pierre; Poensgen, Ulrike; Pollard, C Joshua; Poplin, François; Radi, Giovanna; Stadler, Peter; Stäuble, Harald; Tasić, Nenad; Urem-Kotsou, Dushka; Vuković, Jasna B; Walsh, Fintan; Whittle, Alasdair; Wolfram, Sabine; Zapata-Peña, Lydia; Zoughlami, Jamel

    2015-11-12

    The pressures on honeybee (Apis mellifera) populations, resulting from threats by modern pesticides, parasites, predators and diseases, have raised awareness of the economic importance and critical role this insect plays in agricultural societies across the globe. However, the association of humans with A. mellifera predates post-industrial-revolution agriculture, as evidenced by the widespread presence of ancient Egyptian bee iconography dating to the Old Kingdom (approximately 2400 BC). There are also indications of Stone Age people harvesting bee products; for example, honey hunting is interpreted from rock art in a prehistoric Holocene context and a beeswax find in a pre-agriculturalist site. However, when and where the regular association of A. mellifera with agriculturalists emerged is unknown. One of the major products of A. mellifera is beeswax, which is composed of a complex suite of lipids including n-alkanes, n-alkanoic acids and fatty acyl wax esters. The composition is highly constant as it is determined genetically through the insect's biochemistry. Thus, the chemical 'fingerprint' of beeswax provides a reliable basis for detecting this commodity in organic residues preserved at archaeological sites, which we now use to trace the exploitation by humans of A. mellifera temporally and spatially. Here we present secure identifications of beeswax in lipid residues preserved in pottery vessels of Neolithic Old World farmers. The geographical range of bee product exploitation is traced in Neolithic Europe, the Near East and North Africa, providing the palaeoecological range of honeybees during prehistory. Temporally, we demonstrate that bee products were exploited continuously, and probably extensively in some regions, at least from the seventh millennium cal BC, likely fulfilling a variety of technological and cultural functions. The close association of A. mellifera with Neolithic farming communities dates to the early onset of agriculture and may provide

  11. Widespread Refreezing of Both Surface and Basal Melt Water Beneath the Greenland Ice Sheet

    NASA Astrophysics Data System (ADS)

    Bell, R. E.; Tinto, K. J.; Das, I.; Wolovick, M.; Chu, W.; Creyts, T. T.; Frearson, N.

    2013-12-01

    Northeast Ice Stream. The contrasting rheology of glacial and interglacial ice may also enhance the deformation associated with freeze-on beneath large ice sheets. The occurrence of basal units both in the ice sheet interior and in the thermally very different ablation zone indicates refreezing is widespread and can occur in many environments beneath an ice sheet. This process appears to influence the morphology and behavior of the ice sheet from top to bottom.

  12. The Origin and Evolution of Parthenogenesis in Heteronotia Binoei (Gekkonidae): Evidence for Recent and Localized Origins of Widespread Clones

    PubMed Central

    Moritz, C.

    1991-01-01

    The parthenogenetic form of the gecko lizard species Heteronotia binoei has an unusually broad geographic range and high genetic diversity. Restriction enzyme analysis revealed two basic types of mitochondrial DNA (mtDNA) among the parthenogens. One type is restricted to western populations. The other type, analyzed in detail here, was widespread, being found in populations from central to western Australia. The diversity within this widespread type was low. The variation among parthenogens from central to western Australia was similar to that found within local populations of the sexual species that provided the mtDNA, and was an order of magnitude less than the differentiation shown between sexual populations across the same geographic distance. Phylogenetic analysis revealed that the widespread type of mtDNA in the parthenogens is most closely related to mtDNAs from western populations of the ``CA6'' sexual parent. These data suggest that these parthenogenetic clones arose recently within a small geographic area, most probably in Western Australia. The parthenogens must have spread rapidly to occupy much of the central and western Australian deserts. This rapid and extensive range expansion provides strong evidence that parthenogenesis can be a successful strategy for lizards in an environment with low and unpredictable rainfall. PMID:1682211

  13. Widespread purifying selection on RNA structure in mammals.

    PubMed

    Smith, Martin A; Gesell, Tanja; Stadler, Peter F; Mattick, John S

    2013-09-01

    Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5-22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1. This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.

  14. Widespread purifying selection on RNA structure in mammals

    PubMed Central

    Smith, Martin A.; Gesell, Tanja; Stadler, Peter F.; Mattick, John S.

    2013-01-01

    Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5–22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1. This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes. PMID:23847102

  15. Comparison of population genetic patterns in two widespread freshwater mussels with contrasting life histories in western North America.

    PubMed

    Mock, K E; Brim Box, J C; Chong, J P; Furnish, J; Howard, J K

    2013-12-01

    We investigate population genetic structuring in Margaritifera falcata, a freshwater mussel native to western North America, across the majority of its geographical range. We find shallow rangewide genetic structure, strong population-level structuring and very low population diversity in this species, using both mitochondrial sequence and nuclear microsatellite data. We contrast these patterns with previous findings in another freshwater mussel species group (Anodonta californiensis/A. nuttalliana) occupying the same continental region and many of the same watersheds. We conclude that differences are likely caused by contrasting life history attributes between genera, particularly host fish requirements and hermaphroditism. Further, we demonstrate the occurrence of a 'hotspot' for genetic diversity in both groups of mussels, occurring in the vicinity of the lower Columbia River drainage. We suggest that stream hierarchy may be responsible for this pattern and may produce similar patterns in other widespread freshwater species.

  16. Analysis of personnel error occurrence reports across Defense Program facilities

    SciTech Connect

    Stock, D.A.; Shurberg, D.A.; O`Brien, J.N.

    1994-05-01

    More than 2,000 reports from the Occurrence Reporting and Processing System (ORPS) database were examined in order to identify weaknesses in the implementation of the guidance for the Conduct of Operations (DOE Order 5480.19) at Defense Program (DP) facilities. The analysis revealed recurrent problems involving procedures, training of employees, the occurrence of accidents, planning and scheduling of daily operations, and communications. Changes to DOE 5480.19 and modifications of the Occurrence Reporting and Processing System are recommended to reduce the frequency of these problems. The primary tool used in this analysis was a coding scheme based on the guidelines in 5480.19, which was used to classify the textual content of occurrence reports. The occurrence reports selected for analysis came from across all DP facilities, and listed personnel error as a cause of the event. A number of additional reports, specifically from the Plutonium Processing and Handling Facility (TA55), and the Chemistry and Metallurgy Research Facility (CMR), at Los Alamos National Laboratory, were analyzed separately as a case study. In total, 2070 occurrence reports were examined for this analysis. A number of core issues were consistently found in all analyses conducted, and all subsets of data examined. When individual DP sites were analyzed, including some sites which have since been transferred, only minor variations were found in the importance of these core issues. The same issues also appeared in different time periods, in different types of reports, and at the two Los Alamos facilities selected for the case study.

  17. Rapid bottom melting widespread near Antarctic ice sheet grounding lines

    NASA Technical Reports Server (NTRS)

    Rignot, E.; Jacobs, S.

    2002-01-01

    As continental ice from Antartica reaches the grounding line and begins to float, its underside melts into the ocean. Results obtained with satellite radar interferometry reveal that bottom melt rates experienced by large outlet glaciers near their grounding lines are far higher than generally assumed.

  18. Clonal structure of the introduced freshwater snail Potamopyrgus antipodarum (Prosobranchia: Hydrobiidae), as revealed by DNA fingerprinting.

    PubMed

    Hauser, L; Carvalho, G R; Hughes, R N; Carter, R E

    1992-07-22

    Multi-locus DNA fingerprints were obtained from individuals of the hydrobiid snail, Potamopyrgus antipodarum (= P. jenkinsi), by using an RNA derivative (pSPT 18.15) of Jeffrey's 33.15 minisatellite core sequence. Whole-body homogenization of snails yielded 3.21 +/- 0.09 micrograms DNA per individual, producing complex profiles comprising 12-22 fragments within the 1.0-20.0 kilobase (kb) size range. Fingerprints from natural and experimental populations identified three distinct clonal genotypes corresponding to morphological strains A, B and C, with only rare mutational variants. Mother-offspring comparisons of genetic fingerprints revealed genetic stability during apomictic parthenogenesis. Data support the notion that British populations of P. antipodarum comprise three widespread obligate parthenogenetic clones resulting from a mid-19th Century introduction from Australasia. The present-day low levels of genotypic diversity are discussed in relation to the typical occurrence of P. antipodarum in man-made or immature habitats.

  19. DNA phosphorothioation is widespread and quantized in bacterial genomes

    PubMed Central

    Wang, Lianrong; Chen, Shi; Vergin, Kevin L.; Giovannoni, Stephen J.; Chan, Simon W.; DeMott, Michael S.; Taghizadeh, Koli; Cordero, Otto X.; Cutler, Michael; Timberlake, Sonia; Alm, Eric J.; Polz, Martin F.; Pinhassi, Jarone; Deng, Zixin; Dedon, Peter C.

    2011-01-01

    Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes. PMID:21285367

  20. Chronic widespread pain is associated with worsening frailty in European men

    PubMed Central

    Wade, Katie Fredrika; Lee, David M.; McBeth, John; Ravindrarajah, Rathi; Gielen, Evelien; Pye, Stephen R.; Vanderschueren, Dirk; Pendleton, Neil; Finn, Joseph D.; Bartfai, György; Casanueva, Felipe F.; Forti, Gianni; Giwercman, Aleksander; Huhtaniemi, Ilpo T.; Kula, Krzysztof; Punab, Margus; Wu, Frederick C. W.; O'Neill, Terence W.

    2016-01-01

    Background: we hypothesised that chronic widespread pain (CWP), by acting as a potential stressor, may predispose to the development of, or worsening, frailty. Setting: longitudinal analysis within the European Male Ageing Study (EMAS). Participants: a total of 2,736 community-dwelling men aged 40–79. Methods: subjects completed a pain questionnaire and shaded a manikin, with the presence of CWP defined using the American College of Rheumatology criteria. Physical activity, smoking, alcohol consumption and depression were measured. Repeat assessments took place a median of 4.3 years later. A frailty index (FI) was used, with frail defined as an FI >0.35. The association between CWP at baseline and the new occurrence of frailty was examined using logistic regression; the association between CWP at baseline and change in FI was examined using negative binomial regression. Results: at baseline, 218 (8.3%) men reported CWP. Of the 2,631 men who were defined as non-frail at baseline, 112 (4.3%) were frail at follow-up; their mean FI was 0.12 (SD 0.1) at baseline and 0.15 (SD 0.1) at follow-up, with a mean change of 0.03 (SD 0.08) P ≤ 0.001. Among men who were non-frail at baseline, those with CWP were significantly more likely to develop frailty. After adjustment for age and centre, compared with those with no pain, those with CWP at baseline had a 70% higher FI at follow-up; these associations remained significant after further adjustment for smoking, body mass index, depression, physical activity and FI at baseline. Conclusion: the presence of CWP is associated with an increased risk of frailty in older European men. PMID:26679698

  1. Widespread effects of middle Mississippian deformation in the Great Basin of western North America

    USGS Publications Warehouse

    Trexler, J.H.; Cashman, P.H.; Cole, J.C.; Snyder, W.S.; Tosdal, R.M.; Davydov, V.I.

    2003-01-01

    Stratigraphic analyses in central and eastern Nevada reveal the importance of a deformation event in middle Mississippian time that caused widespread deformation, uplift, and erosion. It occurred between middle Osagean and late Meramecian time and resulted in deposition of both synorogenic and postorogenic sediments. The deformation resulted in east-west shortening, expressed as east-vergent folding and east-directed thrusting; it involved sedimentary rocks of the Antler foredeep as well as strata associated with the Roberts Mountains allochthon. A latest Meramecian to early Chesterian unconformity, with correlative conformable lithofacies changes, postdates this deformation and occurs throughout Nevada. A tectonic highland-created in the middle Mississippian and lasting into the Pennsylvanian and centered in the area west and southwest of Carlin, Nevada- shed sediments eastward across the Antler foreland, burying the unconformity. Postorogenic strata are late Meramecian to early Chesterian at the base and are widespread throughout the Great Basin. The tectonism therefore occurred 20 to 30 m.y. after inception of the Late Devonian Antler orogeny, significantly extending the time span of this orogeny or representing a generally unrecognized orogenic event in the Paleozoic evolution of western North America. We propose a revised stratigraphic nomenclature for Mississippian strata in Nevada, based on detailed age control and the recognition of unconformities. This approach resolves the ambiguity of some stratigraphic names and emphasizes genetic relationships within the upper Paleozoic section. We take advantage of better stratigraphic understanding to propose two new stratigraphic units for southern and eastern Nevada: the middle Mississippian Gap Wash and Late Mississippian Captain Jack Formations.

  2. Linking global climate and temperature variability to widespread amphibian declines putatively caused by disease

    PubMed Central

    Rohr, Jason R.; Raffel, Thomas R.

    2010-01-01

    The role of global climate change in the decline of biodiversity and the emergence of infectious diseases remains controversial, and the effect of climatic variability, in particular, has largely been ignored. For instance, it was recently revealed that the proposed link between climate change and widespread amphibian declines, putatively caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), was tenuous because it was based on a temporally confounded correlation. Here we provide temporally unconfounded evidence that global El Niño climatic events drive widespread amphibian losses in genus Atelopus via increased regional temperature variability, which can reduce amphibian defenses against pathogens. Of 26 climate variables tested, only factors associated with temperature variability could account for the spatiotemporal patterns of declines thought to be associated with Bd. Climatic predictors of declines became significant only after controlling for a pattern consistent with epidemic spread (by temporally detrending the data). This presumed spread accounted for 59% of the temporal variation in amphibian losses, whereas El Niño accounted for 59% of the remaining variation. Hence, we could account for 83% of the variation in declines with these two variables alone. Given that global climate change seems to increase temperature variability, extreme climatic events, and the strength of Central Pacific El Niño episodes, climate change might exacerbate worldwide enigmatic declines of amphibians, presumably by increasing susceptibility to disease. These results suggest that changes to temperature variability associated with climate change might be as significant to biodiversity losses and disease emergence as changes to mean temperature. PMID:20404180

  3. Genetic Markers of Widespread Extensively Drug-Resistant Pseudomonas aeruginosa High-Risk Clones

    PubMed Central

    Cabot, Gabriel; Ocampo-Sosa, Alain A.; Domínguez, M. Angeles; Gago, Juan F.; Juan, Carlos; Tubau, Fe; Rodríguez, Cristina; Moyà, Bartolomé; Peña, Carmen; Martínez-Martínez, Luis

    2012-01-01

    Recent reports have revealed the existence of widespread extensively drug-resistant (XDR) P. aeruginosa high-risk clones in health care settings, but there is still scarce information on their specific chromosomal (mutational) and acquired resistance mechanisms. Up to 20 (10.5%) of 190 bloodstream isolates collected from 10 Spanish hospitals met the XDR criteria. A representative number (15 per group) of isolates classified as multidrug-resistant (MDR) (22.6%), resistant to 1 to 2 classes (moderately resistant [modR]) (23.7%), or susceptible to all antibiotics (multiS) (43.2%) were investigated in parallel. Multilocus sequence typing (MLST) analysis revealed that all XDR isolates belonged to sequence type 175 (ST175) (n = 19) or ST111 (n = 1), both recognized as international high-risk clones. Clonal diversity was higher among the 15 MDR isolates (4 ST175, 2 ST111, and 8 additional STs) and especially high among the 15 modR (13 different STs) and multiS (14 STs) isolates. The XDR/MDR pattern in ST111 isolates correlated with the production of VIM-2, but none of the ST175 isolates produced acquired β-lactamases. In contrast, the analysis of resistance markers in 12 representative isolates (from 7 hospitals) of ST175 revealed that the XDR pattern was driven by the combination of AmpC hyperproduction, OprD inactivation (Q142X), 3 mutations conferring high-level fluoroquinolone resistance (GyrA T83I and D87N and ParC S87W), a G195E mutation in MexZ (involved in MexXY-OprM overexpression), and the production of a class 1 integron harboring the aadB gene (gentamicin and tobramycin resistance). Of particular interest, in nearly all the ST175 isolates, AmpC hyperproduction was driven by a novel AmpR-activating mutation (G154R), as demonstrated by complementation studies using an ampR mutant of PAO1. This work is the first to describe the specific resistance markers of widespread P. aeruginosa XDR high-risk clones producing invasive infections. PMID:23045355

  4. Evidence for Widespread Gene Control Function by the ydaO Riboswitch Candidate▿ †

    PubMed Central

    Block, Kirsten F.; Hammond, Ming C.; Breaker, Ronald R.

    2010-01-01

    Nearly all representatives of experimentally validated riboswitch classes in bacteria control the expression of genes for the transport or synthesis of key metabolic compounds. Recent findings have revealed that some riboswitches also regulate genes involved in physiological changes, virulence, and stress responses. Many novel RNA motifs are being identified by using bioinformatics algorithms that search for conserved sequence and structural features located in intergenic regions. Some of these RNAs are likely to function as riboswitches for metabolites or signaling compounds, and confirmation of this function would reveal the basis of the genetic control of new regulons. Herein we describe the analysis of the ydaO riboswitch candidate, which represents one of the most widespread candidates remaining to be validated. These RNAs are common in Gram-positive bacteria, and their genomic associations with diverse genes suggest that they sense a compound that signals broader physiological changes. We determined that the ydaO motif exhibits sequence- and structure-dependent gene control, and reporter assays indicate that its natural ligand is present even when cells are grown in defined media. A transposon-mediated knockout screen resulted in mutants with a dysregulated expression of genes controlled by the RNA motif. The mutations disrupt genes that drastically modulate energy-generating pathways, suggesting that the intracellular concentration of the ligand sensed by the ydaO motif is altered under these stress conditions. PMID:20511502

  5. Shortened cortical silent period in adductor spasmodic dysphonia: evidence for widespread cortical excitability.

    PubMed

    Samargia, Sharyl; Schmidt, Rebekah; Kimberley, Teresa Jacobson

    2014-02-07

    The purpose of this study was to compare cortical inhibition in the hand region of the primary motor cortex between subjects with focal hand dystonia (FHD), adductor spasmodic dysphonia (AdSD), and healthy controls. Data from 28 subjects were analyzed (FHD n=11, 53.25 ± 8.74 y; AdSD: n=8, 56.38 ± 7.5 y; and healthy controls: n=941.67 ± 10.85 y). All subjects received single pulse TMS to the left motor cortex to measure cortical silent period (CSP) in the right first dorsal interosseus (FDI) muscle. Duration of the CSP was measured and compared across groups. A one-way ANCOVA with age as a covariate revealed a significant group effect (p<0.001). Post hoc analysis revealed significantly longer CSP duration in the healthy group vs. AdSD group (p<0.001) and FHD group (p<0.001). These results suggest impaired intracortical inhibition is a neurophysiologic characteristic of FHD and AdSD. In addition, the shortened CSP in AdSD provides evidence to support a widespread decrease in cortical inhibition in areas of the motor cortex that represent an asymptomatic region of the body. These findings may inform future investigations of differential diagnosis as well as alternative treatments for focal dystonias.

  6. Assessing the impact of climate-change scenarios on landslide occurrence in Umbria Region, Italy

    NASA Astrophysics Data System (ADS)

    Ciabatta, L.; Camici, S.; Brocca, L.; Ponziani, F.; Stelluti, M.; Berni, N.; Moramarco, T.

    2016-10-01

    Landslides are frequent and widespread geomorphological phenomena causing loss of human life and damage to property. The main tool for assessing landslide risk relies on rainfall thresholds and thus, many countries established early warning systems aimed to landslide hazard assessment. The Umbria Region Civil Protection Centre developed an operational early warning system for landslide risk assessment, named PRESSCA, based on the soil saturation conditions to identify rainfall thresholds. These thresholds, currently used by the Civil Protection operators for the day-by-day landslide hazard assessment, provided satisfactory results with more than 86% of the landslides events correctly identified during the period 1990-2013. In this study, the PRESSCA system was employed for the assessment of climate change impact on landslide hazard in Central Italy. The outputs of five different Global Circulation Models (GCMs) were downscaled and weather generators were used for obtaining hourly rainfall and temperature time series from daily GCMs projection. Then, PRESSCA system was employed to estimate the number of landslide occurrence per year. By comparing results obtained for three different periods (1990-2013 (baseline), 2040-2069 and 2070-2099), for the Umbria territory a general increase in events occurrence was expected (up to more than 40%) in the future period, mainly during the winter season. The results also revealed that the effect of climate change on landslides was not straightforward to identify and the close interaction between rainfall magnitude/intensity, temperature and soil moisture should be analysed in depth. Overall, soil moisture was projected to decrease throughout the year but during the wet season the variations with respect to the present period were very small. Specifically, it was found that during the warm-dry season, due to the strong decrease of soil moisture, even for a sensible increase in rainfall intensity, the landslide occurrence was

  7. Widespread refertilization of cratonic and circum-cratonic lithospheric mantle

    NASA Astrophysics Data System (ADS)

    Tang, Yan-Jie; Zhang, Hong-Fu; Ying, Ji-Feng; Su, Ben-Xun

    2013-03-01

    Studies of mantle xenoliths have confirmed that Archean subcontinental lithospheric mantle (SCLM) is highly depleted in basaltic components (such as Al, Ca and Na) due to high-degree extraction of mafic and ultramafic melts and thus is refractory and buoyant, which made it chronically stable as tectonically independent units. However, increasing studies show that ancient SCLM can be refertilized by episodic rejuvenation events like infiltration of upwelling fertile material. The North China Craton is one of the most typical cases for relatively complete destruction of its Archean keel since the eruption of Paleozoic kimberlites, as is evidenced by a dramatic change in the compositions of mantle xenoliths sampled by Paleozoic to Cenozoic magmas, reflecting significant lithospheric thinning and the change in the character of the SCLM. The compositional change has been interpreted as the result of refertilization of Archean SCLM via multiple-stage peridotite-melt reactions, suggested by linear correlations between MgO and indices of fertility, covariations of Al2O3 with CaO, La/Yb, 87Sr/86Sr, 143Nd/144Nd, 187Os/188Os and Re-depletion ages (TRD), high Re abundances, scatter in Re-Os isotopic plot, variable in situ TRD ages of sulfides, and correlation between TRD ages and olivine Fo of peridotite xenoliths in Paleozoic kimberlites and Cenozoic basalts on the craton. By integrating major and trace element, Sr, Nd and Os isotopic compositions of peridotite xenoliths and orogenic massif peridotites from the continents of Europe, Asia, America, Africa and Australia, together with previous studies of petrology and geochemistry of global peridotites, we suggest that (1) refertilization of cratonic and circum-cratonic lithospheric mantle is widespread; (2) Archean SCLM worldwide has experienced a multi-stage history of melt depletion and refertilization since segregation from the convecting mantle; (3) cratonic SCLM may be more susceptible to compositional change caused by

  8. Rapid bottom melting widespread near Antarctic Ice Sheet grounding lines.

    PubMed

    Rignot, Eric; Jacobs, Stanley S

    2002-06-14

    As continental ice from Antarctica reaches the grounding line and begins to float, its underside melts into the ocean. Results obtained with satellite radar interferometry reveal that bottom melt rates experienced by large outlet glaciers near their grounding lines are far higher than generally assumed. The melting rate is positively correlated with thermal forcing, increasing by 1 meter per year for each 0.1 degrees C rise in ocean temperature. Where deep water has direct access to grounding lines, glaciers and ice shelves are vulnerable to ongoing increases in ocean temperature.

  9. Distribution and occurrence of arsenic in two typical Chinese coals

    SciTech Connect

    Mi, J.; Ren, J.; Zhang, H.J.; Bao, W.R.; Xie, K.C.

    2008-07-01

    Two complementary methods, float-sink experience and sequential chemical leaching were used to probe into the occurrence of arsenic in two Chinese coals: Yima (YM) and Datong (DT). Flow injection-hydride generation atomic fluorescence spectrometry was employed to measure the arsenic content in parent coals as well as the size and density-fraction samples. Float-sink experiment indicated that the heavy density fractions were enriched mineral containing arsenic in two bituminous coals studied, as confirmed by the sequential chemical leaching method. Sequential chemical leaching revealed that sulfide arsenic was the primary mode of occurrence (>50%) stable from also abounded in coal with content between 30 and 40%, and a small amount of arsenic took the occurrence of arganic form.

  10. Occurrence reporting and processing of operations information

    SciTech Connect

    1997-07-21

    DOE O 232.1A, Occurrence Reporting and Processing of Operations Information, and 10 CFR 830.350, Occurrence Reporting and Processing of Operations Information (when it becomes effective), along with this manual, set forth occurrence reporting requirements for Department of Energy (DOE) Departmental Elements and contractors responsible for the management and operation of DOE-owned and -leased facilities. These requirements include categorization of occurrences related to safety, security, environment, health, or operations (``Reportable Occurrences``); DOE notification of these occurrences; and the development and submission of documented follow-up reports. This Manual provides detailed information for categorizing and reporting occurrences at DOE facilities. Information gathered by the Occurrence Reporting and processing System is used for analysis of the Department`s performance in environmental protection, safeguards and security, and safety and health of its workers and the public. This information is also used to develop lessons learned and document events that significantly impact DOE operations.

  11. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations

    PubMed Central

    Southwell, Colin; Emmerson, Louise; McKinlay, John; Newbery, Kym; Takahashi, Akinori; Kato, Akiko; Barbraud, Christophe; DeLord, Karine; Weimerskirch, Henri

    2015-01-01

    Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980’s and have been increasing since the earliest counts in the 1960’s. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations. PMID:26488299

  12. Metabolic profiling reveals that PNPLA3 induces widespread effects on metabolism beyond triacylglycerol remodeling in Huh-7 hepatoma cells

    PubMed Central

    Min, Hae-Ki; Sookoian, Silvia; Pirola, Carlos J.; Cheng, Jianfeng; Mirshahi, Faridoddin

    2014-01-01

    PNPLA3 was recently associated with the susceptibility to nonalcoholic fatty liver disease, a common cause of chronic liver disease characterized by abnormal triglyceride accumulation. Although it is established that PNPLA3 has both triacylglycerol lipase and acylglycerol O-acyltransferase activities, is still unknown whether the gene has any additional role in the modulation of the human liver metabolome. To uncover the functional role of PNPLA3 on liver metabolism, we performed high-throughput metabolic profiling of PNPLA3 siRNA-silencing and overexpression of wild-type and mutant Ile148Met variants (isoleucine/methionine substitution at codon 148) in Huh-7 cells. Metabolomic analysis was performed by using GC/MS and LC/MS platforms. Silencing of PNPLA3 was associated with a global perturbation of Huh-7 hepatoma cells that resembled a catabolic response associated with protein breakdown. A significant decrease in amino- and γ-glutamyl-amino acids and dipeptides and a significant increase in cysteine sulfinic acid, myo-inositol, lysolipids, sphingolipids, and polyunsaturated fatty acids were observed. Overexpression of the PNPLA3 Met148 variant mirrored many of the metabolic changes observed during gene silencing, but in the opposite direction. These findings were replicated by the exploration of canonical pathways associated with PNPLA3 silencing and Met148 overexpression. Overexpression of the PNPLA3 Met148 variant was associated with a 1.75-fold increase in lactic acid, suggesting a shift to anaerobic metabolism and mitochondrial dysfunction. Together, these results suggest a critical role of PNPLA3 in the modulation of liver metabolism beyond its classical participation in triacylglycerol remodeling. PMID:24763554

  13. Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

    PubMed Central

    Papadopulos, Alexander S. T.; Kaye, Maria; Devaux, Céline; Hipperson, Helen; Lighten, Jackie; Dunning, Luke T.; Hutton, Ian; Baker, William J.; Butlin, Roger K.; Savolainen, Vincent

    2014-01-01

    It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry. PMID:24958917

  14. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

    PubMed

    Southwell, Colin; Emmerson, Louise; McKinlay, John; Newbery, Kym; Takahashi, Akinori; Kato, Akiko; Barbraud, Christophe; DeLord, Karine; Weimerskirch, Henri

    2015-01-01

    Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

  15. Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression at the human fetal–maternal interface

    PubMed Central

    Buckberry, Sam; Bianco-Miotto, Tina; Bent, Stephen J.; Dekker, Gustaaf A.; Roberts, Claire T.

    2014-01-01

    As males and females share highly similar genomes, the regulation of many sexually dimorphic traits is constrained to occur through sex-biased gene regulation. There is strong evidence that human males and females differ in terms of growth and development in utero and that these divergent growth strategies appear to place males at increased risk when in sub-optimal conditions. Since the placenta is the interface of maternal–fetal exchange throughout pregnancy, these developmental differences are most likely orchestrated by differential placental function. To date, progress in this field has been hampered by a lack of genome-wide information on sex differences in placental gene expression. Therefore, our motivation in this study was to characterize sex-biased gene expression in the human placenta. We obtained gene expression data for >300 non-pathological placenta samples from 11 microarray datasets and applied mapping-based array probe re-annotation and inverse-variance meta-analysis methods which showed that >140 genes (false discovery rate (FDR) <0.05) are differentially expressed between male and female placentae. A majority of these genes (>60%) are autosomal, many of which are involved in high-level regulatory processes such as gene transcription, cell growth and proliferation and hormonal function. Of particular interest, we detected higher female expression from all seven genes in the LHB-CGB cluster, which includes genes involved in placental development, the maintenance of pregnancy and maternal immune tolerance of the conceptus. These results demonstrate that sex-biased gene expression in the normal human placenta occurs across the genome and includes genes that are central to growth, development and the maintenance of pregnancy. PMID:24867328

  16. Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish.

    PubMed

    Martin, A P; Bermingham, E

    2000-06-07

    The lower Central American landscape was fully emergent approximately three million years ago, an event which marked the beginning of the Great American biotic interchange. Freshwater fishes participated in the biotic interchange. Because primary freshwater fishes are restricted to freshwater, they provide an excellent system for investigating the interplay of historical and recent processes on the assembly, structure and diversity of the regions' aquatic ecosystems. We focused on examining the history of diversification for a species of catfish (Pimelodella chagresi) whose distribution spans multiple, isolated drainage basins across the Isthmian landscape and into north-western South America. Analysis of mitochondrial DNA haplotypes and morphological traits indicated that P. chagresi, as currently recognized, comprises a species complex. In addition, along the Pacific slope of Panama, repeated dispersion, diversification, extinction and possibly hybridization are thought to underlie a complex distribution of haplotypes. Overall, the results underscore the tremendous importance of historical processes on regional biodiversity.

  17. Genetic characterization of Toxoplasma gondii in wildlife from North America revealed widespread and high prevalence of the fourth clonal type

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Little is known of the genetic diversity of Toxoplasma gondii circulating in wildlife. In the present study, wild animals, including dolphins from the USA were examined for T. gondii infection. Tissues of naturally exposed animals were bioassayed in mice for isolation of viable parasites. Viable T. ...

  18. New evidence for widespread mass transport on the Northeast Newfoundland Shelf revealed by Olex single-beam echo sounding

    NASA Astrophysics Data System (ADS)

    Shaw, John; Piper, David J. W.; Skulski, Thomas; Lamplugh, Michael J.; Craft, Andrew; Roy, André

    2012-02-01

    Based on Olex single-beam sounder data, multibeam sonar surveys, and sparse seismic reflection profiles, we recognize a large area of anomalous bathymetry on the Northeast Newfoundland Shelf as having formed as a result of mass-transport processes. Transported masses include (1) an arcuate ridge of deformed material with an area of 430 km2, which has moved distances of ~20 km; (2) a 70-km2 mass of deformed material displaced 50 km along a nearly horizontal track flanked by 90-m-high berms. The movement of these and other sediment bodies has created a 150-m-high headwall escarpment extending 110 km along the north flank of the Notre Dame glacial trough. In addition, a 35-km2 block of undeformed material has moved 5 km to the southeast, away from the headwall, creating a gap of the same dimensions, while a smaller block of material originating in this vicinity has been displaced 24 km in the opposite direction, creating a 20-m-deep groove on the seafloor. There is evidence for mass transport and headwall formation elsewhere on the Northeast Newfoundland Shelf. Analysis of seismic reflection data indicates that the transported material most likely consists of stacked Quaternary till sheets that overlie Cenozoic, Mesozoic and older sedimentary rocks. Given the very low gradients involved, glaciotectonism is the most likely process to account for transport and deformation of the large sediment masses. However, some mass transport may have resulted from submarine sliding away from the headwalls that were created by the glacial transport.

  19. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background Maize exhibits a wealth of epigenetic phenomena, from transposon silencing, cycling and presetting, to gene imprinting and paramutation. Furthermore, despite the complexity and sophistication of maize breeding, there is a large degree of “hidden” variation for many traits that is difficul...

  20. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

    PubMed

    Batut, Philippe; Dobin, Alexander; Plessy, Charles; Carninci, Piero; Gingeras, Thomas R

    2013-01-01

    Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5'-complete cDNA sequencing with an integrated data analysis workflow, to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive data set that represents the first available developmental time-course of promoter usage. We found that >40% of developmentally expressed genes have at least two promoters and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes.

  1. Colorado quartz: occurrence and discovery

    USGS Publications Warehouse

    Kile, D.E.; Modreski, P.J.; Kile, D.L.

    1991-01-01

    The many varieties and associations of quartz found throughout the state rank it as one of the premier worldwide localities for that species. This paper briefly outlines the historical importance of the mineral, the mining history and the geological setting before discussing the varieties of quartz present, its crystallography and the geological enviroments in which it is found. The latter include volcanic rocks and near surface igneous rocks; pegmatites; metamorphic and plutonic rocks; hydrothermal veins; skarns and sedimentary deposits. Details of the localities and mode of occurrence of smoky quartz, amethyst, milky quartz, rock crystal, rose quartz, citrine, agate and jasper are then given. -S.J.Stone

  2. Protein Delivery of an Artificial Transcription Factor Restores Widespread Ube3a Expression in an Angelman Syndrome Mouse Brain.

    PubMed

    Bailus, Barbara J; Pyles, Benjamin; McAlister, Michelle M; O'Geen, Henriette; Lockwood, Sarah H; Adams, Alexa N; Nguyen, Jennifer Trang T; Yu, Abigail; Berman, Robert F; Segal, David J

    2016-03-01

    Angelman syndrome (AS) is a neurological genetic disorder caused by loss of expression of the maternal copy of UBE3A in the brain. Due to brain-specific genetic imprinting at this locus, the paternal UBE3A is silenced by a long antisense transcript. Inhibition of the antisense transcript could lead to unsilencing of paternal UBE3A, thus providing a therapeutic approach for AS. However, widespread delivery of gene regulators to the brain remains challenging. Here, we report an engineered zinc finger-based artificial transcription factor (ATF) that, when injected i.p. or s.c., crossed the blood-brain barrier and increased Ube3a expression in the brain of an adult mouse model of AS. The factor displayed widespread distribution throughout the brain. Immunohistochemistry of both the hippocampus and cerebellum revealed an increase in Ube3a upon treatment. An ATF containing an alternative DNA-binding domain did not activate Ube3a. We believe this to be the first report of an injectable engineered zinc finger protein that can cause widespread activation of an endogenous gene in the brain. These observations have important implications for the study and treatment of AS and other neurological disorders.

  3. Sporothrix globosa, a pathogenic fungus with widespread geographical distribution.

    PubMed

    Madrid, Hugo; Cano, Josep; Gené, Josepa; Bonifaz, Alexandro; Toriello, Conchita; Guarro, Josep

    2009-09-30

    Sporothrix globosa, reported from the USA, Europe, and Asia, is a recently described pathogenic species morphologically similar to Sporothrix schenckii. In this study, the phylogenetic affinities of 32 clinical and environmental isolates morphologically identified as S. schenckii, from Mexico, Guatemala, and Colombia, were assessed by cladistic analysis of partial sequences of the calmodulin gene using the maximum parsimony and neighbor-joining methods. The study revealed that one out of 25 isolates from Mexico (4%), one out of three isolates from Guatemala (33.3%), and two out of four isolates from Colombia (50%) belonged to S. globosa, while the other isolates belonged to S. schenckii sensu stricto. This is the first record of S. globosa from Mexico, and Central and South America.

  4. Widespread endometriosis mimicking ovarian malignancy: a case report.

    PubMed

    Akinola, R A; Akinola, O I; Alakija, A; Wright, K O

    2012-03-01

    A 26 year old Nigerian nulliparous woman who presented in the medical emergency unit of a teaching hospital was referred after two weeks of management to the gynecology casualty with a diagnosis of malignant left ovarian cyst, because of the ascites, massive haemorrhagic pleural effusion, a left ovarian mass and an elevated C-125 marker. However, exploratory laparotomy, cytologic and histological examination of the pleural fluid and biopsied specimens revealed endometriosis. We present a case of intra and extra-pelvic endometriosis which simulated a malignant ovarian lesion and was histologically confirmed by cytology of the haemorrhagic pleural effusion and biopsy of the ovarian mass and peritoneal deposits obtained at laparotomy. This is to draw the attention of clinicians to endometriosis as a cause of pleural effusion, ascites and groin swelling which can simulate ovarian cancer.

  5. Widespread spin polarization effects in photoemission from topological insulators

    SciTech Connect

    Jozwiak, C.; Chen, Y. L.; Fedorov, A. V.; Analytis, J. G.; Rotundu, C. R.; Schmid, A. K.; Denlinger, J. D.; Chuang, Y.-D.; Lee, D.-H.; Fisher, I. R.; Birgeneau, R. J.; Shen, Z.-X.; Hussain, Z.; Lanzara, A.

    2011-06-22

    High-resolution spin- and angle-resolved photoemission spectroscopy (spin-ARPES) was performed on the three-dimensional topological insulator Bi{sub 2}Se{sub 3} using a recently developed high-efficiency spectrometer. The topological surface state's helical spin structure is observed, in agreement with theoretical prediction. Spin textures of both chiralities, at energies above and below the Dirac point, are observed, and the spin structure is found to persist at room temperature. The measurements reveal additional unexpected spin polarization effects, which also originate from the spin-orbit interaction, but are well differentiated from topological physics by contrasting momentum and photon energy and polarization dependencies. These observations demonstrate significant deviations of photoelectron and quasiparticle spin polarizations. Our findings illustrate the inherent complexity of spin-resolved ARPES and demonstrate key considerations for interpreting experimental results.

  6. Biochemistry and Occurrence of O-Demethylation in Plant Metabolism

    PubMed Central

    Hagel, Jillian M.; Facchini, Peter J.

    2010-01-01

    Demethylases play a pivitol role in numerous biological processes from covalent histone modification and DNA repair to specialized metabolism in plants and microorganisms. Enzymes that catalyze O- and N-demethylation include 2-oxoglutarate (2OG)/Fe(II)-dependent dioxygenases, cytochromes P450, Rieske-domain proteins and flavin adenine dinucleotide (FAD)-dependent oxidases. Proposed mechanisms for demethylation by 2OG/Fe(II)-dependent enzymes involve hydroxylation at the O- or N-linked methyl group followed by formaldehyde elimination. Members of this enzyme family catalyze a wide variety of reactions in diverse plant metabolic pathways. Recently, we showed that 2OG/Fe(II)-dependent dioxygenases catalyze the unique O-demethylation steps of morphine biosynthesis in opium poppy, which provides a rational basis for the widespread occurrence of demethylases in benzylisoquinoline alkaloid metabolism. PMID:21423357

  7. Cerulean Warbler occurrence and habitat use of Oklahoma

    USGS Publications Warehouse

    Leslie,, David M.; O'Connell, Timothy J.; Cavalieri, Vincent S.

    2011-01-01

    Dendroica cerulea (Cerulean Warbler) is a migrant songbird that has declined rangewide in recent decades. We surveyed 150 sites in 2006–2007 to determine if this species still occupied its former breeding range in Oklahoma. We located Cerulean Warblers at 5 sites and confirmed breeding on north slopes of two heavily forested ridges in the Ouachita Mountains. We did not encounter Cerulean Warblers in any bottomland hardwoods, despite the former widespread distribution and abundance of the species in such habitats. While habitat loss and degradation may limit occurrence of Cerulean Warbler in some areas, the pattern of decline for this species at the edge of its range in Oklahoma is also consistent with abandonment of peripheral range as the range-wide population declines.

  8. Ulnar neuropathy caused by a widespread synovial cyst of the elbow joint in a patient with rheumatoid arthritis.

    PubMed

    Scholz, Christoph; Gierthmuehlen, Mortimer; Egger, Karl; Hauschild, Oliver; van Velthoven-Wurster, V

    2014-11-01

    A 53-year-old man with rheumatoid arthritis presented with radiating pain, numbness, and diminished motor strength in the right hand according to the ulnar nerve functions. Magnetic resonance imaging and peripheral nerve ultrasound revealed a widespread cystic lesion descending from the elbow joint along the ulnar nerve over a length of 8 cm. After relapse under a therapeutic attempt with antirheumatic drugs, neurosurgical exploration was done using peripheral nerve ultrasound. A synovial cyst of the elbow was extirpated as a whole with subsequent anterior synovectomy. The postoperative course was uneventful with gradual recovery of function.

  9. Widespread flat warts associated with human papillomavirus type 5: a cutaneous manifestation of human immunodeficiency virus infection.

    PubMed

    Prose, N S; von Knebel-Doeberitz, C; Miller, S; Milburn, P B; Heilman, E

    1990-11-01

    Numerous flat and tinea versicolor-like warts developed on the face, trunk, and upper extremities of a 10-year-old boy with human immunodeficiency virus infection. Nucleic acid analysis of involved skin revealed human papillomavirus type 5, which has sometimes been associated with epidermodysplasia verruciformis. This human papillomavirus type has also been described in patients with common variable immunodeficiency and dyskeratosis congenita and in renal allograft recipients. Human immunodeficiency virus infection should be added to the list of immune-related disorders that predispose to widespread flat warts.

  10. Widespread Nanoparticle-Assay Interference: Implications for Nanotoxicity Testing

    PubMed Central

    Ong, Kimberly J.; MacCormack, Tyson J.; Clark, Rhett J.; Ede, James D.; Ortega, Van A.; Felix, Lindsey C.; Dang, Michael K. M.; Ma, Guibin; Fenniri, Hicham; Veinot, Jonathan G. C.; Goss, Greg G.

    2014-01-01

    The evaluation of engineered nanomaterial safety has been hindered by conflicting reports demonstrating differential degrees of toxicity with the same nanoparticles. The unique properties of these materials increase the likelihood that they will interfere with analytical techniques, which may contribute to this phenomenon. We tested the potential for: 1) nanoparticle intrinsic fluorescence/absorbance, 2) interactions between nanoparticles and assay components, and 3) the effects of adding both nanoparticles and analytes to an assay, to interfere with the accurate assessment of toxicity. Silicon, cadmium selenide, titanium dioxide, and helical rosette nanotubes each affected at least one of the six assays tested, resulting in either substantial over- or under-estimations of toxicity. Simulation of realistic assay conditions revealed that interference could not be predicted solely by interactions between nanoparticles and assay components. Moreover, the nature and degree of interference cannot be predicted solely based on our current understanding of nanomaterial behaviour. A literature survey indicated that ca. 95% of papers from 2010 using biochemical techniques to assess nanotoxicity did not account for potential interference of nanoparticles, and this number had not substantially improved in 2012. We provide guidance on avoiding and/or controlling for such interference to improve the accuracy of nanotoxicity assessments. PMID:24618833

  11. Widespread DNA hypomethylation and differential gene expression in Turner syndrome

    PubMed Central

    Trolle, Christian; Nielsen, Morten Muhlig; Skakkebæk, Anne; Lamy, Philippe; Vang, Søren; Hedegaard, Jakob; Nordentoft, Iver; Ørntoft, Torben Falck; Pedersen, Jakob Skou; Gravholt, Claus Højbjerg

    2016-01-01

    Adults with 45,X monosomy (Turner syndrome) reflect a surviving minority since more than 99% of fetuses with 45,X monosomy die in utero. In adulthood 45,X monosomy is associated with increased morbidity and mortality, although strikingly heterogeneous with some individuals left untouched while others suffer from cardiovascular disease, autoimmune disease and infertility. The present study investigates the leukocyte DNAmethylation profile by using the 450K-Illumina Infinium assay and the leukocyte RNA-expression profile in 45,X monosomy compared with karyotypically normal female and male controls. We present results illustrating that genome wide X-chromosome RNA-expression profile, autosomal DNA-methylation profile, and the X-chromosome methylation profile clearly distinguish Turner syndrome from controls. Our results reveal genome wide hypomethylation with most differentially methylated positions showing a medium level of methylation. Contrary to previous studies, applying a single loci specific analysis at well-defined DNA loci, our results indicate that the hypomethylation extend to repetitive elements. We describe novel candidate genes that could be involved in comorbidity in TS and explain congenital urinary malformations (PRKX), premature ovarian failure (KDM6A), and aortic aneurysm formation (ZFYVE9 and TIMP1). PMID:27687697

  12. Islands of Complex DNA Are Widespread in Drosophila Centric Heterochromatin

    PubMed Central

    Le, M. H.; Duricka, D.; Karpen, G. H.

    1995-01-01

    Heterochromatin is a ubiquitous yet poorly understood component of multicellular eukaryotic genomes. Major gaps exist in our knowledge of the nature and overall organization of DNA sequences present in heterochromatin. We have investigated the molecular structure of the 1 Mb of centric heterochromatin in the Drosophila minichromosome Dp1187. A genetic screen of irradiated minichromosomes yielded rearranged derivatives of Dp1187 whose structures were determined by pulsed-field Southern analysis and PCR. Three Dp1187 deletion derivatives and an inversion had one breakpoint in the euchromatin and one in the heterochromatin, providing direct molecular access to previously inaccessible parts of the heterochromatin. End-probed pulsed-field restriction mapping revealed the presence of at least three ``islands'' of complex DNA, Tahiti, Moorea, and Bora Bora, constituting approximately one half of the Dp1187 heterochromatin. Pulsed-field Southern analysis demonstrated that Drosophila heterochromatin in general is composed of alternating blocks of complex DNA and simple satellite DNA. Cloning and sequencing of a small part of one island, Tahiti, demonstrated the presence of a retroposon. The implications of these findings to heterochromatin structure and function are discussed. PMID:8536977

  13. Recent and widespread rapid morphological change in rodents.

    PubMed

    Pergams, Oliver R W; Lawler, Joshua J

    2009-07-31

    In general, rapid morphological change in mammals has been infrequently documented. Examples that do exist are almost exclusively of rodents on islands. Such changes are usually attributed to selective release or founder events related to restricted gene flow in island settings. Here we document rapid morphological changes in rodents in 20 of 28 museum series collected on four continents, including 15 of 23 mainland sites. Approximately 17,000 measurements were taken of 1302 rodents. Trends included both increases and decreases in the 15 morphological traits measured, but slightly more trends were towards larger size. Generalized linear models indicated that changes in several of the individual morphological traits were associated with changes in human population density, current temperature gradients, and/or trends in temperature and precipitation. When we restricted these analyses to samples taken in the US (where data on human population trends were presumed to be more accurate), we found changes in two additional traits to be positively correlated with changes in human population density. Principle component analysis revealed general trends in cranial and external size, but these general trends were uncorrelated with climate or human population density. Our results indicate that over the last 100+ years, rapid morphological change in rodents has occurred quite frequently, and that these changes have taken place on the mainland as well as on islands. Our results also suggest that these changes may be driven, at least in part, by human population growth and climate change.

  14. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis

    SciTech Connect

    Ansong, Charles; Ortega, Corrie; Payne, Samuel H.; Haft, Daniel H.; Chauvigne-Hines, Lacie M.; Lewis, Michael P.; Ollodart, Anja R.; Purvine, Samuel O.; Shukla, Anil K.; Fortuin, Suereta; Smith, Richard D.; Adkins, Joshua N.; Grundner, Christoph; Wright, Aaron T.

    2013-01-24

    The annotation of protein function is almost completely performed by in silico approaches. However, computational prediction of protein function is frequently incomplete and error prone. In Mycobacterium tuberculosis (Mtb), ~25% of all genes have no predicted function and are annotated as hypothetical proteins. This lack of functional information severely limits our understanding of Mtb pathogenicity. Current tools for experimental functional annotation are limited and often do not scale to entire protein families. Here, we report a generally applicable chemical biology platform to functionally annotate bacterial proteins by combining activity-based protein profiling (ABPP) and quantitative LC-MS-based proteomics. As an example of this approach for high-throughput protein functional validation and discovery, we experimentally annotate the families of ATP-binding proteins in Mtb. Our data experimentally validate prior in silico predictions of >250 ATPases and adenosine nucleotide-binding proteins, and reveal 73 hypothetical proteins as novel ATP-binding proteins. We identify adenosine cofactor interactions with many hypothetical proteins containing a diversity of unrelated sequences, providing a new and expanded view of adenosine nucleotide binding in Mtb. Furthermore, many of these hypothetical proteins are both unique to Mycobacteria and essential for infection, suggesting specialized functions in mycobacterial physiology and pathogenicity. Thus, we provide a generally applicable approach for high throughput protein function discovery and validation, and highlight several ways in which application of activity-based proteomics data can improve the quality of functional annotations to facilitate novel biological insights.

  15. Widespread genomic signatures of natural selection in hominid evolution.

    PubMed

    McVicker, Graham; Gordon, David; Davis, Colleen; Green, Phil

    2009-05-01

    Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19-26% on the autosomes and 12-40% on the X chromosome. The overall trends are broadly consistent with "background selection" or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events.

  16. Lineaments and Mineral Occurrences in Pennsylvania

    NASA Technical Reports Server (NTRS)

    Mcmurtry, G. J.; Petersen, G. W. (Principal Investigator); Kowalik, W. S.; Gold, D. P.

    1975-01-01

    The author has identified the following significant results. A conservative lineament map of Pennsylvania interpreted from ERTS-1 channel 7 (infrared) imagery and Skylab photography was compared with the distribution of known metallic mines and mineral occurrences. Of 383 known mineral occurrences, 116 show a geographical association to 1 km wide lineaments, another 24 lie at the intersection of two lineaments, and one lies at the intersection of three lineaments. The Perkiomen Creek lineament in the Triassic Basin is associated with 9 Cu-Fe occurrences. Six Pb-Zn occurrences are associated with the Tyrone-Mount Union lineament. Thirteen other lineaments are associated with 3, 4, or 5 mineral occurrences each.

  17. Evidence for widespread endemism among Antarctic micro-organisms

    NASA Astrophysics Data System (ADS)

    Vyverman, Wim; Verleyen, Elie; Wilmotte, Annick; Hodgson, Dominic A.; Willems, Anne; Peeters, Karolien; Van de Vijver, Bart; De Wever, Aaike; Leliaert, Frederik; Sabbe, Koen

    2010-08-01

    Understanding the enormous diversity of microbes, their multiple roles in the functioning of ecosystems, and their response to large-scale environmental and climatic changes, are at the forefront of the international research agenda. In Antarctica, where terrestrial and lacustrine environments are predominantly microbial realms, an active and growing community of microbial ecologists is probing this diversity and its role in ecosystem processes. In a broader context, this work has the potential to make a significant contribution to the long-standing debate as to whether microbes are fundamentally different from macroorganisms in their biogeography. According to the ubiquity hypothesis, microbial community composition is not constrained by dispersal limitation and is solely the result of species sorting along environmental gradients. However, recent work on several groups of microalgae is challenging this view. Global analyses using morphology-based diatom inventories have demonstrated that, in addition to environmental harshness, geographical isolation underlies the strong latitudinal gradients in local and regional diversity in the Southern hemisphere. Increasing evidence points to a strong regionalization of diatom floras in the Antarctic and sub-Antarctic regions, mirroring the biogeographical regions that have been recognized for macroorganisms. Likewise, the application of molecular-phylogenetic techniques to cultured and uncultured diversity revealed a high number of Antarctic endemics among cyanobacteria and green algae. Calibration of these phylogenies suggests that several clades have an ancient evolutionary history within the Antarctic continent, possibly dating back to 330 Ma. These findings are in line with the current view on the origin of Antarctic terrestrial metazoa, including springtails, chironomids and mites, with most evidence suggesting a long history of geographic isolation on a multi-million year, even pre-Gondwana break-up timescale.

  18. Human and biophysical influences on fire occurrence in the United States.

    PubMed

    Hawbaker, Todd J; Radeloff, Volker C; Stewart, Susan I; Hammer, Roger B; Keuler, Nicholas S; Clayton, Murray K

    2013-04-01

    National-scale analyses of fire occurrence are needed to prioritize fire policy and management activities across the United States. However, the drivers of national-scale patterns of fire occurrence are not well understood, and how the relative importance of human or biophysical factors varies across the country is unclear. Our research goal was to model the drivers of fire occurrence within ecoregions across the conterminous United States. We used generalized linear models to compare the relative influence of human, vegetation, climate, and topographic variables on fire occurrence in the United States, as measured by MODIS active fire detections collected between 2000 and 2006. We constructed models for all fires and for large fires only and generated predictive maps to quantify fire occurrence probabilities. Areas with high fire occurrence probabilities were widespread in the Southeast, and localized in the Mountain West, particularly in southern California, Arizona, and New Mexico. Probabilities for large-fire occurrence were generally lower, but hot spots existed in the western and south-central United States The probability of fire occurrence is a critical component of fire risk assessments, in addition to vegetation type, fire behavior, and the values at risk. Many of the hot spots we identified have extensive development in the wildland--urban interface and are near large metropolitan areas. Our results demonstrated that human variables were important predictors of both all fires and large fires and frequently exhibited nonlinear relationships. However, vegetation, climate, and topography were also significant variables in most ecoregions. If recent housing growth trends and fire occurrence patterns continue, these areas will continue to challenge policies and management efforts seeking to balance the risks generated by wildfires with the ecological benefits of fire.

  19. Human and biophysical influences on fire occurrence in the United States

    USGS Publications Warehouse

    Hawbaker, Todd J.; Radeloff, Volker C.; Stewart, Susan I.; Hammer, Roger B.; Keuler, Nicholas S.; Clayton, Murray K.

    2013-01-01

    National-scale analyses of fire occurrence are needed to prioritize fire policy and management activities across the United States. However, the drivers of national-scale patterns of fire occurrence are not well understood, and how the relative importance of human or biophysical factors varies across the country is unclear. Our research goal was to model the drivers of fire occurrence within ecoregions across the conterminous United States. We used generalized linear models to compare the relative influence of human, vegetation, climate, and topographic variables on fire occurrence in the United States, as measured by MODIS active fire detections collected between 2000 and 2006. We constructed models for all fires and for large fires only and generated predictive maps to quantify fire occurrence probabilities. Areas with high fire occurrence probabilities were widespread in the Southeast, and localized in the Mountain West, particularly in southern California, Arizona, and New Mexico. Probabilities for large-fire occurrence were generally lower, but hot spots existed in the western and south-central United States The probability of fire occurrence is a critical component of fire risk assessments, in addition to vegetation type, fire behavior, and the values at risk. Many of the hot spots we identified have extensive development in the wildland–urban interface and are near large metropolitan areas. Our results demonstrated that human variables were important predictors of both all fires and large fires and frequently exhibited nonlinear relationships. However, vegetation, climate, and topography were also significant variables in most ecoregions. If recent housing growth trends and fire occurrence patterns continue, these areas will continue to challenge policies and management efforts seeking to balance the risks generated by wildfires with the ecological benefits of fire.

  20. Global occurrences of gas hydrate

    USGS Publications Warehouse

    Kvenvolden, K.A.; Lorenson, T.D.

    2001-01-01

    Natural gas hydrate is found worldwide in sediments of outer continental margins of all oceans and in polar areas with continuous permafrost. There are currently 77 localities identified globally where geophysical, geochemical and/or geological evidence indicates the presence of gas hydrate. Details concerning individual gas-hydrate occurrences are compiled at a new world-wide-web (www) site (http://walrus.wr.usgs.gov/globalhydrate). This site has been created to facilitate global gas-hydrate research by providing information on each of the localities where there is evidence for gas hydrate. Also considered are the implications of gas hydrate as a potential (1) energy resource, (2) factor in global climate change, and (3) geohazard.

  1. Intelligence in childhood and chronic widespread pain in middle age: the National Child Development Survey.

    PubMed

    Gale, Catharine R; Deary, Ian J; Cooper, Cyrus; Batty, G David

    2012-12-01

    Psychological factors are thought to play a part in the aetiology of chronic widespread pain. We investigated the relationship between intelligence in childhood and risk of chronic widespread pain in adulthood in 6902 men and women from the National Child Development Survey (1958 British Birth Cohort). Participants took a test of general cognitive ability at age 11 years; and chronic widespread pain, defined according to the American College of Rheumatology criteria, was assessed at age 45 years. Risk ratios (RRs) and 95% confidence intervals (CIs) were estimated using log-binomial regression, adjusting for sex and potential confounding or mediating factors. Risk of chronic widespread pain, defined according to the American College of Rheumatology criteria, rose in a stepwise fashion as intelligence fell (P for linear trend <0.0001). In sex-adjusted analyses, for an SD lower intelligence quotient, the RR of chronic widespread pain was 1.26 (95% CI 1.17-1.35). In multivariate backwards stepwise regression, lower childhood intelligence remained as an independent predictor of chronic widespread pain (RR 1.10; 95% CI 1.01-1.19), along with social class, educational attainment, body mass index, smoking status, and psychological distress. Part of the effect of lower childhood intelligence on risk of chronic widespread pain in midlife was significantly mediated through greater body mass index and more disadvantaged socioeconomic position. Men and women with higher intelligence in childhood are less likely as adults to report chronic widespread pain.

  2. Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803

    PubMed Central

    Liberton, Michelle; Chrisler, William B.; Nicora, Carrie D.; Moore, Ronald J.; Smith, Richard D.; Koppenaal, David W.; Pakrasi, Himadri B.; Jacobs, Jon M.

    2017-01-01

    In cyanobacteria such as Synechocystis sp. PCC 6803, large antenna complexes called phycobilisomes (PBS) harvest light and transfer the energy to the photosynthetic reaction centers. Modification of the light harvesting machinery in cyanobacteria has widespread consequences, causing changes in cell morphology and physiology. In the current study, we investigated the effects of PBS truncation on the proteomes of three Synechocystis 6803 PBS antenna mutants. These range from the progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of PBS in the PAL mutant. Comparative quantitative protein results revealed surprising changes in protein abundances in the mutant strains. Our results showed that PBS truncation in Synechocystis 6803 broadly impacted core cellular mechanisms beyond light harvesting and photosynthesis. Specifically, we observed dramatic alterations in membrane transport mechanisms, where the most severe PBS truncation in the PAL strain appeared to suppress the cellular utilization and regulation of bicarbonate and iron. These changes point to the role of PBS as a component critical to cell function, and demonstrate the continuing need to assess systems-wide protein based abundances to understand potential indirect phenotypic effects. PMID:28253354

  3. Seismic evidence for widespread western-US deep-crustal deformation caused by extension

    USGS Publications Warehouse

    Moschetti, M.P.; Ritzwoller, M.H.; Lin, F.; Yang, Y.

    2010-01-01

    Laboratory experiments have established that many of the materials comprising the Earth are strongly anisotropic in terms of seismic-wave speeds. Observations of azimuthal and radial anisotropy in the upper mantle are attributed to the lattice-preferred orientation of olivine caused by the shear strains associated with deformation, and provide some of the most direct evidence for deformation and flow within the Earths interior. Although observations of crustal radial anisotropy would improve our understanding of crustal deformation and flow patterns resulting from tectonic processes, large-scale observations have been limited to regions of particularly thick crust. Here we show that observations from ambient noise tomography in the western United States reveal strong deep (middle to lower)-crustal radial anisotropy that is confined mainly to the geological provinces that have undergone significant extension during the Cenozoic Era (since 65 Myr ago). The coincidence of crustal radial anisotropy with the extensional provinces of the western United States suggests that the radial anisotropy results from the lattice-preferred orientation of anisotropic crustal minerals caused by extensional deformation. These observations also provide support for the hypothesis that the deep crust within these regions has undergone widespread and relatively uniform strain in response to crustal thinning and extension. ?? 2010 Macmillan Publishers Limited. All rights reserved.

  4. Seismic evidence for widespread western-US deep-crustal deformation caused by extension.

    PubMed

    Moschetti, M P; Ritzwoller, M H; Lin, F; Yang, Y

    2010-04-08

    Laboratory experiments have established that many of the materials comprising the Earth are strongly anisotropic in terms of seismic-wave speeds. Observations of azimuthal and radial anisotropy in the upper mantle are attributed to the lattice-preferred orientation of olivine caused by the shear strains associated with deformation, and provide some of the most direct evidence for deformation and flow within the Earth's interior. Although observations of crustal radial anisotropy would improve our understanding of crustal deformation and flow patterns resulting from tectonic processes, large-scale observations have been limited to regions of particularly thick crust. Here we show that observations from ambient noise tomography in the western United States reveal strong deep (middle to lower)-crustal radial anisotropy that is confined mainly to the geological provinces that have undergone significant extension during the Cenozoic Era (since approximately 65 Myr ago). The coincidence of crustal radial anisotropy with the extensional provinces of the western United States suggests that the radial anisotropy results from the lattice-preferred orientation of anisotropic crustal minerals caused by extensional deformation. These observations also provide support for the hypothesis that the deep crust within these regions has undergone widespread and relatively uniform strain in response to crustal thinning and extension.

  5. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

    PubMed Central

    Smith, Christopher D.; Zimin, Aleksey; Holt, Carson; Abouheif, Ehab; Benton, Richard; Cash, Elizabeth; Croset, Vincent; Currie, Cameron R.; Elhaik, Eran; Elsik, Christine G.; Fave, Marie-Julie; Fernandes, Vilaiwan; Gadau, Jürgen; Gibson, Joshua D.; Graur, Dan; Grubbs, Kirk J.; Hagen, Darren E.; Helmkampf, Martin; Holley, Jo-Anne; Hu, Hao; Viniegra, Ana Sofia Ibarraran; Johnson, Brian R.; Johnson, Reed M.; Khila, Abderrahman; Kim, Jay W.; Laird, Joseph; Mathis, Kaitlyn A.; Moeller, Joseph A.; Muñoz-Torres, Monica C.; Murphy, Marguerite C.; Nakamura, Rin; Nigam, Surabhi; Overson, Rick P.; Placek, Jennifer E.; Rajakumar, Rajendhran; Reese, Justin T.; Robertson, Hugh M.; Suarez, Andrew V.; Suen, Garret; Suhr, Elissa L.; Tao, Shu; Torres, Candice W.; van Wilgenburg, Ellen; Viljakainen, Lumi; Walden, Kimberly K. O.; Wild, Alexander L.; Yandell, Mark; Yorke, James A.; Tsutsui, Neil D.

    2011-01-01

    Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism. PMID:21282631

  6. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile).

    PubMed

    Smith, Christopher D; Zimin, Aleksey; Holt, Carson; Abouheif, Ehab; Benton, Richard; Cash, Elizabeth; Croset, Vincent; Currie, Cameron R; Elhaik, Eran; Elsik, Christine G; Fave, Marie-Julie; Fernandes, Vilaiwan; Gadau, Jürgen; Gibson, Joshua D; Graur, Dan; Grubbs, Kirk J; Hagen, Darren E; Helmkampf, Martin; Holley, Jo-Anne; Hu, Hao; Viniegra, Ana Sofia Ibarraran; Johnson, Brian R; Johnson, Reed M; Khila, Abderrahman; Kim, Jay W; Laird, Joseph; Mathis, Kaitlyn A; Moeller, Joseph A; Muñoz-Torres, Monica C; Murphy, Marguerite C; Nakamura, Rin; Nigam, Surabhi; Overson, Rick P; Placek, Jennifer E; Rajakumar, Rajendhran; Reese, Justin T; Robertson, Hugh M; Smith, Chris R; Suarez, Andrew V; Suen, Garret; Suhr, Elissa L; Tao, Shu; Torres, Candice W; van Wilgenburg, Ellen; Viljakainen, Lumi; Walden, Kimberly K O; Wild, Alexander L; Yandell, Mark; Yorke, James A; Tsutsui, Neil D

    2011-04-05

    Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.

  7. Widespread of H5N1 infections in apparently healthy backyard poultry.

    PubMed

    Abozaid, Khaled G A; Aly, Mona M; Abdel-Moneim, Ahmed S; El-Kady, Magdy F

    2016-08-01

    Highly pathogenic avian influenza subtype H5N1 represents a threat to the poultry industry and human health worldwide. Inapparently infected birds are suspected to play an essential role in the spread of avian influenza virus. In the current study, a total of 25,646 samples (16,185 chicken, 4696 ducks, 1633 geese and 3132 turkeys) from apparently healthy birds were screened for the presence of positive samples for H5N1 during 2009-2014. The samples were examined by reverse transcriptase real-time polymerase chain reaction (rRT-PCR) for M, H5 and N1 genes of avian influenza viruses. The results revealed that the HPAI H5N1 existed in an inapparent manner in ducks (4.68 %), geese (4.10 %), chickens (2.48 %) and turkeys (2.29 %). The current finding highlights the serious impact of such type on birds in the epidemiology of H5N1 in birds, animals and humans. It also highlights the existence of another reason other than vaccination that contributes to the widespread of inapparent infection of H5N1 in Egypt.

  8. Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome

    PubMed Central

    Beilharz, Traude H.; Preiss, Thomas

    2007-01-01

    Control of poly(A) tail length can affect translation and stability of eukaryotic mRNAs. Although well established for individual cases, it was not known to what extent this type of adjustable gene control is used to shape expression of eukaryotic transcriptomes. Here we report on microarray-based measurements of mRNA poly(A) tail lengths and association with the poly(A)-binding protein Pab1 in S. cerevisiae, revealing extensive correlation between tail length and other physical and functional mRNA characteristics. Gene ontology analyses and further directed experiments indicate coregulation of tail length on functionally and cytotopically related mRNAs to coordinate cell-cycle progression, ribosome biogenesis, and retrotransposon expression. We show that the 3′-untranslated region drives transcript-specific adenylation control and translational efficiency of multiple mRNAs. Our findings suggest a wide-spread interdependence between 3′-untranslated region-mediated poly(A) tail length control, Pab1 binding, and mRNA translation in budding yeast. They further provide a molecular explanation for deadenylase function in the cell cycle and suggest additional cellular processes that depend on control of mRNA polyadenylation. PMID:17586758

  9. Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex.

    PubMed

    Papakostas, Spiros; Michaloudi, Evangelia; Proios, Konstantinos; Brehm, Michaela; Verhage, Laurens; Rota, Jadranka; Peña, Carlos; Stamou, Georgia; Pritchard, Victoria L; Fontaneto, Diego; Declerck, Steven A J

    2016-05-01

    Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and 4 nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.

  10. Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803.

    PubMed

    Liberton, Michelle; Chrisler, William B; Nicora, Carrie D; Moore, Ronald J; Smith, Richard D; Koppenaal, David W; Pakrasi, Himadri B; Jacobs, Jon M

    2017-01-01

    In cyanobacteria such as Synechocystis sp. PCC 6803, large antenna complexes called phycobilisomes (PBS) harvest light and transfer the energy to the photosynthetic reaction centers. Modification of the light harvesting machinery in cyanobacteria has widespread consequences, causing changes in cell morphology and physiology. In the current study, we investigated the effects of PBS truncation on the proteomes of three Synechocystis 6803 PBS antenna mutants. These range from the progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of PBS in the PAL mutant. Comparative quantitative protein results revealed surprising changes in protein abundances in the mutant strains. Our results showed that PBS truncation in Synechocystis 6803 broadly impacted core cellular mechanisms beyond light harvesting and photosynthesis. Specifically, we observed dramatic alterations in membrane transport mechanisms, where the most severe PBS truncation in the PAL strain appeared to suppress the cellular utilization and regulation of bicarbonate and iron. These changes point to the role of PBS as a component critical to cell function, and demonstrate the continuing need to assess systems-wide protein based abundances to understand potential indirect phenotypic effects.

  11. Climate controls the distribution of a widespread invasive species: Implications for future range expansion

    USGS Publications Warehouse

    McDowell, W.G.; Benson, A.J.; Byers, J.E.

    2014-01-01

    1. Two dominant drivers of species distributions are climate and habitat, both of which are changing rapidly. Understanding the relative importance of variables that can control distributions is critical, especially for invasive species that may spread rapidly and have strong effects on ecosystems. 2. Here, we examine the relative importance of climate and habitat variables in controlling the distribution of the widespread invasive freshwater clam Corbicula fluminea, and we model its future distribution under a suite of climate scenarios using logistic regression and maximum entropy modelling (MaxEnt). 3. Logistic regression identified climate variables as more important than habitat variables in controlling Corbicula distribution. MaxEnt modelling predicted Corbicula's range expansion westward and northward to occupy half of the contiguous United States. By 2080, Corbicula's potential range will expand 25–32%, with more than half of the continental United States being climatically suitable. 4. Our combination of multiple approaches has revealed the importance of climate over habitat in controlling Corbicula's distribution and validates the climate-only MaxEnt model, which can readily examine the consequences of future climate projections. 5. Given the strong influence of climate variables on Corbicula's distribution, as well as Corbicula's ability to disperse quickly and over long distances, Corbicula is poised to expand into New England and the northern Midwest of the United States. Thus, the direct effects of climate change will probably be compounded by the addition of Corbicula and its own influences on ecosystem function.

  12. Widespread Volumetric Brain Changes following Tooth Loss in Female Mice

    PubMed Central

    Avivi-Arber, Limor; Seltzer, Ze'ev; Friedel, Miriam; Lerch, Jason P.; Moayedi, Massieh; Davis, Karen D.; Sessle, Barry J.

    2017-01-01

    and 21 BXA24 mice revealed significant volumetric differences between the two strains in several brain regions. These findings highlight the utility of high-resolution sMRI for studying tooth loss-induced structural brain plasticity in mice, and provide a foundation for further phenotyping structural brain changes following tooth loss in the full AXB-BXA panel to facilitate mapping genes that control brain plasticity following orofacial injury. PMID:28119577

  13. Widespread grey matter pathology dominates the longitudinal cerebral MRI and clinical landscape of amyotrophic lateral sclerosis.

    PubMed

    Menke, Ricarda A L; Körner, Sonja; Filippini, Nicola; Douaud, Gwenaëlle; Knight, Steven; Talbot, Kevin; Turner, Martin R

    2014-09-01

    Diagnosis, stratification and monitoring of disease progression in amyotrophic lateral sclerosis currently rely on clinical history and examination. The phenotypic heterogeneity of amyotrophic lateral sclerosis, including extramotor cognitive impairments is now well recognized. Candidate biomarkers have shown variable sensitivity and specificity, and studies have been mainly undertaken only cross-sectionally. Sixty patients with sporadic amyotrophic lateral sclerosis (without a family history of amyotrophic lateral sclerosis or dementia) underwent baseline multimodal magnetic resonance imaging at 3 T. Grey matter pathology was identified through analysis of T1-weighted images using voxel-based morphometry. White matter pathology was assessed using tract-based spatial statistics analysis of indices derived from diffusion tensor imaging. Cross-sectional analyses included group comparison with a group of healthy controls (n = 36) and correlations with clinical features, including regional disability, clinical upper motor neuron signs and cognitive impairment. Patients were offered 6-monthly follow-up MRI, and the last available scan was used for a separate longitudinal analysis (n = 27). In cross-sectional study, the core signature of white matter pathology was confirmed within the corticospinal tract and callosal body, and linked strongly to clinical upper motor neuron burden, but also to limb disability subscore and progression rate. Localized grey matter abnormalities were detected in a topographically appropriate region of the left motor cortex in relation to bulbar disability, and in Broca's area and its homologue in relation to verbal fluency. Longitudinal analysis revealed progressive and widespread changes in the grey matter, notably including the basal ganglia. In contrast there was limited white matter pathology progression, in keeping with a previously unrecognized limited change in individual clinical upper motor neuron scores, despite advancing disability

  14. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  15. Antepartum Mastitis: A Rare Occurrence.

    PubMed

    Malik, Sushma; Patil, Varsha Anant; Korday, Charusheela Sujit; Shah, Dipti Parag

    2015-08-01

    Puerperal or lactational mastitis is an inflammatory condition of the breast that is commonly encountered in breastfeeding mothers. It occurs most commonly in the postpartum period, generally in the first 6 weeks of breastfeeding. In contrast, antepartum mastitis is an uncommon condition, and if not treated adequately, it may be complicated by the formation of a breast abscess. The authors present a case of a 24-year-old, second gravida mother who developed unilateral antepartum mastitis with abscess formation at 34 weeks of gestation, which was initially treated with antibiotics and surgical drainage. However, her symptoms persisted over the next 2 weeks, and she was referred to the authors' institution, where she was managed with antibiotics and surgical drainage after delivering a healthy near-term infant. The abscesses healed completely 2 months later, with sequelae of residual scarring and a nonprotractile nipple. The authors wish to emphasize that health care providers should be aware of the occurrence of mastitis in the antepartum period. Early recognition with adequate treatment of mastitis is the key to avoiding complications, and this will prevent lactation issues and also reduce morbidity in the mother and neonate.

  16. Unequal Contribution of Widespread and Narrow-Ranged Species to Botanical Diversity Patterns

    PubMed Central

    Raes, Niels; Wieringa, Jan J.; Sosef, Marc S. M.

    2016-01-01

    In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are overrepresented in species-rich areas. Based on distribution models of Gabonese plant species, we defined sequential subsets from narrow-ranged-to-widespread, widespread-to-narrow-ranged, and 100 randomly arranged species sequences using the range sizes of species in tropical Africa and within Gabon. Along these sequences, correlations between subsets and the total species richness and total weighted endemism patterns were computed. Random species subsets best represent the total species richness pattern, whereas subsets of narrow-ranged species best represent the total weighted endemism pattern. For species ordered according to their range sizes in tropical Africa, subsets of narrow-ranged species represented the total species richness pattern better than widespread species subsets did. However, the opposite was true when range sizes were truncated by the Gabonese national country borders. Correcting for the information content of the subset results in a skew of the sequential correlations, its direction depending on the range-size frequency distribution. Finally, we find a strong, positive, non-linear relation between weighted endemism and total species richness. Observed differences in the contribution of narrow-ranged, widespread and randomly selected species to species richness and weighted endemism patterns can be explained by the range-size frequency distribution and the use of different definitions of widespread or narrow-ranged. We

  17. Occurrence of oral deformities in larval anurans

    USGS Publications Warehouse

    Drake, D.L.; Altig, R.; Grace, J.B.; Walls, S.C.

    2007-01-01

    We quantified deformities in the marginal papillae, tooth rows, and jaw sheaths of tadpoles from 13 population samples representing three families and 11 sites in the southeastern United States. Oral deformities were observed in all samples and in 13.5-98% of the specimens per sample. Batrachochytrium dendrobatidis (chytrid) infections were detected in three samples. There was high variability among samples in the pattern and number of discovered deformities. Pairwise associations between oral structures containing deformities were nonrandom for several populations, especially those with B. dendrobatidis infections or high total numbers of deformities. Comparisons of deformities among samples using multivariate analyses revealed that tadpole samples grouped together by family. Analyses of ordination indicated that three variables, the number of deformities, the number of significant associations among deformity types within populations, and whether populations were infected with B. dendrobatidis, were significantly correlated with the pattern of deformities. Our data indicate that the incidence of oral deformities can be high in natural populations and that phylogeny and B. dendrobatidis infection exert a strong influence on the occurrence and type of oral deformities in tadpoles. ?? by the American Society of Ichthyologists and Herperologists.

  18. Aichi Virus 1: Environmental Occurrence and Behavior

    PubMed Central

    Kitajima, Masaaki; Gerba, Charles P.

    2015-01-01

    Aichi virus 1 (AiV-1), belonging to the genus Kobuvirus in the family Picornaviridae, has been proposed as a causative agent of human gastroenteritis potentially transmitted by fecal-oral routes through contaminated food or water. AiV-1 is globally distributed and has been detected in various types of environmental samples, such as sewage, river water, groundwater, and shellfish. Recent environmental studies revealed that this virus could be detected in higher frequency and greater abundance than other human enteric viruses. These findings suggest that AiV-1 could potentially be an appropriate indicator of viral contamination in the environment because of its high prevalence in water environments as well as structural and genetic similarity with some of the other important enteric viruses. Further studies on the occurrence and fate of AiV-1 in environments, even in combination with clinical studies of many regions, are needed for a better understanding of their epidemiology, temporal and geographical distribution, environmental stability, and potential health risks to humans. PMID:25996404

  19. Foreshock occurrence rates before large earthquakes worldwide

    USGS Publications Warehouse

    Reasenberg, P.A.

    1999-01-01

    Global rates of foreshock occurrence involving shallow M ??? 6 and M ??? 7 mainshocks and M ??? 5 foreshocks were measured, using earthquakes listed in the Harvard CMT catalog for the period 1978-1996. These rates are similar to rates ones measured in previous worldwide and regional studies when they are normalized for the ranges of magnitude difference they each span. The observed worldwide rates were compared to a generic model of earthquake clustering, which is based on patterns of small and moderate aftershocks in California, and were found to exceed the California model by a factor of approximately 2. Significant differences in foreshock rate were found among subsets of earthquakes defined by their focal mechanism and tectonic region, with the rate before thrust events higher and the rate before strike-slip events lower than the worldwide average. Among the thrust events a large majority, composed of events located in shallow subduction zones, registered a high foreshock rate, while a minority, located in continental thrust belts, measured a low rate. These differences may explain why previous surveys have revealed low foreshock rates among thrust events in California (especially southern California), while the worldwide observations suggest the opposite: California, lacking an active subduction zone in most of its territory, and including a region of mountain-building thrusts in the south, reflects the low rate apparently typical for continental thrusts, while the worldwide observations, dominated by shallow subduction zone events, are foreshock-rich.

  20. Widespread occurrence and low genetic diversity of Colombian datura virus in Brugmansia suggest an anthropogenic role in virus selection and spread.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Colombian datura virus was identified in Brugmansia and Datura metel plants from multiple regions of the U.S. using serological and molecular tests including ELISA and PCR. The low genetic diversity of CDV detected suggests that worldwide diversity of the virus has developed in a relatively short p...

  1. Widespread occurrence of N-terminal acylation in animal globins and possible origin of respiratory globins from a membrane-bound ancestor.

    PubMed

    Blank, Miriam; Burmester, Thorsten

    2012-11-01

    Proteins of the (hemo-)globin superfamily have been identified in many different animals but also occur in plants, fungi, and bacteria. Globins are renowned for their ability to store and to transport oxygen, but additional globin functions such as sensing, signaling, and detoxification have been proposed. Recently, we found that the zebrafish globin X protein is myristoylated and palmitoylated at its N-terminus. The addition of fatty acids results in an association with the cellular membranes, suggesting a previously unrecognized globin function. In this study, we show that N-terminal acylation likely occurs in globin proteins from a broad range of phyla. An N-terminal myristoylation site was identified in 90 nonredundant globins from Chlorophyta, Heterokontophyta, Cnidaria, Mollusca, Arthropoda, Nematoda, Echinodermata, Hemichordata, and Chordata (including Cephalochordata), of which 66 proteins carry an additional palmitoylation site. Bayesian phylogenetic analyses identified five major globin families, which may mirror the ancient globin diversity of the Metazoa. Globin X-like proteins form two related clades, which diverged before the radiation of the Eumetazoa. Vertebrate hemoglobin (Hb), myoglobin, cytoglobin, globin E, and globin Y form a strongly supported common clade, which is the sister group of a clade consisting of invertebrate Hbs and relatives. The N-terminally acylated globins do not form a single monophyletic group but are distributed to four distinct clades. This pattern may be either explained by multiple introduction of an N-terminal acylation site into distinct globin lineages or by the origin of animal respiratory globins from a membrane-bound ancestor. Similarly, respiratory globins were not monophyletic. This suggests that respiratory globins might have emerged independently several times and that the early metazoan globins might have been associated with a membrane and carried out a function that was related to lipid protection or signaling.

  2. THE WIDESPREAD OCCURRENCE OF WATER VAPOR IN THE CIRCUMSTELLAR ENVELOPES OF CARBON-RICH ASYMPTOTIC GIANT BRANCH STARS: FIRST RESULTS FROM A SURVEY WITH HERSCHEL /HIFI

    SciTech Connect

    Neufeld, D. A.; Gonzalez-Alfonso, E.; Melnick, G.; Szczerba, R.; Schmidt, M.; Decin, L.; Alcolea, J.; De Koter, A.; Dominik, C.; Waters, L. B. F. M.; Schoeier, F. L.; Justtanont, K.; Olofsson, H.; Bujarrabal, V.; Planesas, P.; Cernicharo, J.; Teyssier, D.; Marston, A. P.; Menten, K.

    2011-02-01

    We report the preliminary results of a survey for water vapor in a sample of eight C stars with large mid-IR continuum fluxes: V384 Per, CIT 6, V Hya, Y CVn, IRAS 15194-5115, V Cyg, S Cep, and IRC+40540. This survey, performed using the HIFI instrument on board the Herschel Space Observatory, entailed observations of the lowest transitions of both ortho- and para-water: the 556.936 GHz 1{sub 10}-1{sub 01} and 1113.343 GHz 1{sub 11}-0{sub 00} transitions, respectively. Water vapor was unequivocally detected in all eight of the target stars. Prior to this survey, IRC+10216 was the only carbon-rich asymptotic giant branch (AGB) star from which thermal water emissions had been discovered, in that case with the use of the Submillimeter Wave Astronomy Satellite (SWAS). Our results indicate that IRC+10216 is not unusual, except insofar as its proximity to Earth leads to a large line flux that was detectable with SWAS. The water spectral line widths are typically similar to those of CO rotational lines, arguing against the vaporization of a Kuiper Belt analog being the general explanation for water vapor in carbon-rich AGB stars. There is no apparent correlation between the ratio of the integrated water line fluxes to the 6.3 {mu}m continuum flux-a ratio which measures the water outflow rate-and the total mass-loss rate for the stars in our sample.

  3. Specificity of interaction between carcinogenic polynuclear aromatic hydrocarbons and nuclear proteins: widespread occurrence of a restricted pattern of histone-binding in intact cells

    SciTech Connect

    MacLeod, M.C.; Pelling, J.C.; Slaga, T.J.; Nikbakht-Noghrei, P.A.; Mansfield, B.K.; Selkirk, J.K.

    1982-01-01

    Metabolic activation of benzo(a)pyrene (B(a)P) produces a number of potentially reactive metabolites. The endproducts of one metabolic pathway, 7,8-dihydroxy-9,10-oxy-7,8,9,10-tetrahydro-B(a)P (BPDE) are responsible for essentially all DNA adduct formation in animal cells treated with B(a)P, and a particular stereoisomer, designated (+)-anti-BPDE is thought to be the ultimate carcinogenic derivative of B(a)P. In hamster embryo cell nuclei treated with (+)-anti-BPDE, two of the histones of the nucleosomal core, H3 and H2A, are covalently modified, while the remaining core histones, H4 and H2B, are essentially unmodified. All four purified core histones, however, serve as targets. 7,12-dimethylbenz(a)anthracene and 3-methylcholanthrene show the same pattern of histone binding in hamster embryo cells. Treatment of mouse embryo cells with (/sup 3/H)-BPDE results in covalent binding of the hydrocarbon to histones H3 and H2A among the many cellular targets, while histones H2B and H4 are not bound. Similar binding patterns are seen in mouse embryo cells, a permanent murine, fibroblastic cell line, and a human mammary epithelial cell line, T47D, treated with (/sup 3/H)B(a)P. Again, the histones are unevenly labeled, displaying the H3 and H2A pattern. Histone-binding in the human cells may also be mediated by BPDE. Similar BPDE binding patterns were observed in other murine and human cell lines and in primary cultures of murine epidermal epithelial cells. The restriction of histone H2B and H4 binding appears to be general when intact cultured cells are studied. This specificity was not observed in a mixed reconstituted system in which rat liver microsomes were used to activate B(a)P. This finding reinforces reservations concerning the use of microsomal systems to probe the interactions of carcinogens with macromolecules and the relationships of adduct formation with the processes of carcinogenesis. (ERB)

  4. Widespread occurrence of bisphenol A diglycidyl ethers, p-hydroxybenzoic acid esters (parabens), benzophenone type-UV filters, triclosan, and triclocarban in human urine from Athens, Greece.

    PubMed

    Asimakopoulos, Alexandros G; Thomaidis, Nikolaos S; Kannan, Kurunthachalam

    2014-02-01

    Biomonitoring of human exposure to bisphenol A diglycidyl ethers (BADGEs; resin coating for food cans), p-hydroxybenzoic acid esters (parabens; preservatives), benzophenone-type UV filters (BP-UV filters; sunscreen agents), triclosan (TCS; antimicrobials), and triclocarban (TCC; antimicrobials) has been investigated in western European countries and North America. Nevertheless, little is known about the exposure of Greek populations to these environmental chemicals. In this study, 100 urine samples collected from Athens, Greece, were analyzed by liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) for the determination of total concentrations of five derivatives of BADGEs, six parabens and their metabolite (ethyl-protocatechuate), five derivatives of BP-UV filters, TCS, and TCC. Urinary concentrations of BADGEs, parabens, ethyl-protocatechuate, BP-UV filters, TCS and TCC (on a volume basis) ranged 0.3-20.9 (geometric mean: 0.9), 1.6-1010 (24.2), <2-71.0 (2.1), 0.5-1120 (4.4), <0.5-2580 (8.0) and <0.5-1.9 (0.6) ng/mL, respectively. All 19 target chemicals were found in urine, and the highest detection rates were observed for methyl paraben (100%), bisphenol A bis (2,3-dihydroxypropyl) ether (90%), ethyl paraben (87%), 2,4-dihydroxybenzophenone (78%), propyl paraben (72%), and TCS (71%). Estimated daily intakes (EDIurine), calculated on the basis of the measured urinary concentrations, ranged from 0.023 μg/kg bw/day for Σ5BADGEs to 31.4 μg/kg bw/day for Σ6Parabens.

  5. Evidence for the role of an invasive weed in widespread occurrence of phytoplasmal diseases in diverse vegetable crops: implications from lineage-specific molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the period from 2011 to 2013, several plant diseases repeatedly occurred in vegetable crops grown in Yuanmou County, Yunnan Province, China. Affected plants included cowpea, sword bean, string bean, tomato, lettuce, and water spinach. The diseased plants exhibited symptoms of witches’-broom...

  6. Corrigendum to "Widespread occurrence of (per)chlorate in the Solar System" [Earth Planet. Sci. Lett. 430 (2015) 470-476

    NASA Astrophysics Data System (ADS)

    Jackson, W. Andrew; Davila, Alfonso F.; Sears, Derek; Coates, John D.; McKay, Christopher P.; Brundrett, Maeghan; Estrada, Nubia; Böhlke, J. K.

    2016-02-01

    The authors regret that two sets of data (Atacama (Rao et al., 2010) and Mars Meteorite Range (Kounaves et al., 2014)) in Fig. 2 of our article were plotted in the wrong units. The correction does not change the relationship between ClO3- and ClO4- ; it only shifts the magnitude of the concentrations. The conclusions of the article are not affected. The corrected Fig. 2 appears below.

  7. Widespread occurrence and phylogenetic placement of a soil clone group adds a prominant new branch to the fungal tree of life

    SciTech Connect

    Porter, Terri M.; Schadt, Christopher Warren; Rizvi, L; Martin, Andrew P.; Schmidt, Steven K.; Scott-Denton, Laura; Vilgalys, Rytas; Moncalvo, Jean-Marc

    2008-01-01

    Fungi are one of the most diverse groups of Eukarya and play essential roles in terrestrial ecosystems as decomposers, pathogens and mutualists. This study unifies disparate reports of unclassified fungal sequences from soils of diverse origins and anchors many of them in a well-supported clade of the Ascomycota equivalent to a subphylum. We refer to this clade as Soil Clone Group I (SCGI). We expand the breadth of environments surveyed and develop a taxon-specific primer to amplify 2.4 kbp rDNA fragments directly from soil. Our results also expand the known range of this group from North America to Europe and Australia. The ancient origin of SCGI implies that it may represent an important transitional form among the basal Ascomycota groups. SCGI is unusual because it currently represents the only major fungal lineage known only from sequence data. This is an important contribution towards building a more complete fungal phylogeny and highlights the need for further work to determine the function and biology of SCGI taxa.

  8. Widespread Occurrence of Glyphosate and its Degradation Product (AMPA) in U.S. Soils, Surface Water, Groundwater, and Precipitation, 2001-2009

    NASA Astrophysics Data System (ADS)

    Brauman, K. A.; Flörke, M.; Mueller, N. D.; Foley, J. A.

    2011-12-01

    Water is integral to agricultural production, and agriculture is by far the largest human use of water, so food security and water sustainability are inexorably linked. When water goes to food production, however, the benefits and costs are not uniformly distributed across the globe. We quantify the magnitude and global range of the multidimensional tradeoffs among food production, water consumption, and water quality impairment. To evaluate the productivity of water consumption in agriculture, we quantified the magnitude and global range of crop water productivity, the amount of food produced per unit of water consumed, for 16 major food crops (Brauman et al., 2013). We now expand on this, contextualizing the impact of high or low water productivity with information about water availability. Using outputs from the WaterGAP3 model (Flörke et al., 2013, Verzano et al. 2012), we map the burden of agricultural water consumption on total water availability. To incorporate impacts of agriculture on water quality, we include areas of excess nutrient application (Mueller et al., 2012). The integrated information about yield, water consumption, water availability, and nutrient application shows that benefits and impacts to water quantity and quality are not evenly distributed. Analogous to previous investigations of 'yield gaps,' which identified areas where biophysical conditions are sufficient for achieving yields higher than those that are attained (Licker et al., 2010), we show that in many places, for the given impacts to water, food production could be increased.

  9. Radiation-Induced Defects in Kaolinite as Tracers of Past Occurrence of Radionuclides in a Natural Analogue of High Level Nuclear Waste Repository

    NASA Astrophysics Data System (ADS)

    Allard, T.; Fourdrin, C.; Calas, G.

    2007-05-01

    Understanding the processes controlling migrations of radioelements at the Earth's surface is an important issue for the long-term safety assessment of high level nuclear waste repositories (HLNWR). Evidence of past occurrence and transfer of radionuclides can be found using radiation-induced defects in minerals. Clay minerals are particularly relevant because of their widespread occurrence at the Earth's surface and their finely divided nature which provides high contact area with radioactive fluids. Owing to its sensitivity to radiations, kaolinite can be used as natural, in situ dosimeter. Kaolinite is known to contain radiation-induced defects which are detected by Electron Paramagnetic Resonance. They are differentiated by their nature, their production kinetics and their thermal stability. One of these defects is stable at the scale of geological periods and provides a record of past radionuclide occurrence. Based on artificial irradiations, a methodology has been subsequently proposed to determine paleodose cumulated by kaolinite since its formation. The paleodose can be used to derive equivalent radioelement concentrations, provided that the age of kaolinite formation can be constrained. This allows quantitative reconstruction of past transfers of radioelements in natural systems. An example is given for the Nopal I U-deposit (Chihuahua, Mexico), hosted in hydrothermally altered volcanic tufs and considered as analogue of the Yucca Mountain site. The paleodoses experienced by kaolinites were determined from the concentration of defects and dosimetry parameters of experimental irradiations. Using few geochemical assumption, a equivalent U-content responsible for defects in kaolinite was calculated from the paleodose, a dose rate balance and model ages of kaolinites constrained by tectonic phases. In a former study, the ages were assumptions derived from regional tectonic events. In thepresent study, ages of mineralization events are measured from U

  10. Foreshock occurrence before large earthquakes

    USGS Publications Warehouse

    Reasenberg, P.A.

    1999-01-01

    Rates of foreshock occurrence involving shallow M ??? 6 and M ??? 7 mainshocks and M ??? 5 foreshocks were measured in two worldwide catalogs over ???20-year intervals. The overall rates observed are similar to ones measured in previous worldwide and regional studies when they are normalized for the ranges of magnitude difference they each span. The observed worldwide rates were compared to a generic model of earthquake clustering based on patterns of small and moderate aftershocks in California. The aftershock model was extended to the case of moderate foreshocks preceding large mainshocks. Overall, the observed worldwide foreshock rates exceed the extended California generic model by a factor of ???2. Significant differences in foreshock rate were found among subsets of earthquakes defined by their focal mechanism and tectonic region, with the rate before thrust events higher and the rate before strike-slip events lower than the worldwide average. Among the thrust events, a large majority, composed of events located in shallow subduction zones, had a high foreshock rate, while a minority, located in continental thrust belts, had a low rate. These differences may explain why previous surveys have found low foreshock rates among thrust events in California (especially southern California), while the worldwide observations suggests the opposite: California, lacking an active subduction zone in most of its territory, and including a region of mountain-building thrusts in the south, reflects the low rate apparently typical for continental thrusts, while the worldwide observations, dominated by shallow subduction zone events, are foreshock-rich. If this is so, then the California generic model may significantly underestimate the conditional probability for a very large (M ??? 8) earthquake following a potential (M ??? 7) foreshock in Cascadia. The magnitude differences among the identified foreshock-mainshock pairs in the Harvard catalog are consistent with a uniform

  11. Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity

    PubMed Central

    Delrieu-Trottin, Erwan; Maynard, Jeffrey; Planes, Serge

    2014-01-01

    Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability. PMID:25355471

  12. Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity.

    PubMed

    Delrieu-Trottin, Erwan; Maynard, Jeffrey; Planes, Serge

    2014-12-22

    Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability.

  13. WIDESPREAD AND HIDDEN ACTIVE GALACTIC NUCLEI IN STAR-FORMING GALAXIES AT REDSHIFT >0.3

    SciTech Connect

    Juneau, Stephanie; Bournaud, Frederic; Daddi, Emanuele; Elbaz, David; Alexander, David M.; Mullaney, James R.; Magnelli, Benjamin; Hwang, Ho Seong; Willner, S. P.; Coil, Alison L.; Rosario, David J.; Trump, Jonathan R.; Faber, S. M.; Kocevski, Dale D.; Cooper, Michael C.; Frayer, David T.; and others

    2013-02-20

    We characterize the incidence of active galactic nuclei (AGNs) in 0.3 < z < 1 star-forming galaxies by applying multi-wavelength AGN diagnostics (X-ray, optical, mid-infrared, radio) to a sample of galaxies selected at 70 {mu}m from the Far-Infrared Deep Extragalactic Legacy survey (FIDEL). Given the depth of FIDEL, we detect 'normal' galaxies on the specific star formation rate (sSFR) sequence as well as starbursting systems with elevated sSFR. We find an overall high occurrence of AGN of 37% {+-} 3%, more than twice as high as in previous studies of galaxies with comparable infrared luminosities and redshifts but in good agreement with the AGN fraction of nearby (0.05 < z < 0.1) galaxies of similar infrared luminosities. The more complete census of AGNs comes from using the recently developed Mass-Excitation (MEx) diagnostic diagram. This optical diagnostic is also sensitive to X-ray weak AGNs and X-ray absorbed AGNs, and reveals that absorbed active nuclei reside almost exclusively in infrared-luminous hosts. The fraction of galaxies hosting an AGN appears to be independent of sSFR and remains elevated both on the sSFR sequence and above. In contrast, the fraction of AGNs that are X-ray absorbed increases substantially with increasing sSFR, possibly due to an increased gas fraction and/or gas density in the host galaxies.

  14. Drought's legacy: multiyear hydraulic deterioration underlies widespread aspen forest die-off and portends increased future risk.

    PubMed

    Anderegg, William R L; Plavcová, Lenka; Anderegg, Leander D L; Hacke, Uwe G; Berry, Joseph A; Field, Christopher B

    2013-04-01

    Forest mortality constitutes a major uncertainty in projections of climate impacts on terrestrial ecosystems and carbon-cycle feedbacks. Recent drought-induced, widespread forest die-offs highlight that climate change could accelerate forest mortality with its diverse and potentially severe consequences for the global carbon cycle, ecosystem services, and biodiversity. How trees die during drought over multiple years remains largely unknown and precludes mechanistic modeling and prediction of forest die-off with climate change. Here, we examine the physiological basis of a recent multiyear widespread die-off of trembling aspen (Populus tremuloides) across much of western North America. Using observations from both native trees while they are dying and a rainfall exclusion experiment on mature trees, we measure hydraulic performance over multiple seasons and years and assess pathways of accumulated hydraulic damage. We test whether accumulated hydraulic damage can predict the probability of tree survival over 2 years. We find that hydraulic damage persisted and increased in dying trees over multiple years and exhibited few signs of repair. This accumulated hydraulic deterioration is largely mediated by increased vulnerability to cavitation, a process known as cavitation fatigue. Furthermore, this hydraulic damage predicts the probability of interyear stem mortality. Contrary to the expectation that surviving trees have weathered severe drought, the hydraulic deterioration demonstrated here reveals that surviving regions of these forests are actually more vulnerable to future droughts due to accumulated xylem damage. As the most widespread tree species in North America, increasing vulnerability to drought in these forests has important ramifications for ecosystem stability, biodiversity, and ecosystem carbon balance. Our results provide a foundation for incorporating accumulated drought impacts into climate-vegetation models. Finally, our findings highlight the

  15. Common and unique associated factors for medically unexplained chronic widespread pain and chronic fatigue☆

    PubMed Central

    McBeth, J.; Tomenson, B.; Chew-Graham, C.A.; Macfarlane, G.J.; Jackson, J.; Littlewood, A.; Creed, F.H.

    2015-01-01

    Objective Chronic widespread pain and chronic fatigue share common associated factors but these associations may be explained by the presence of concurrent depression and anxiety. Methods We mailed questionnaires to a randomly selected sample of people in the UK to identify participants with chronic widespread pain (ACR 1990 definition) and those with chronic fatigue. The questionnaire assessed sociodemographic factors, health status, healthcare use, childhood factors, adult attachment, and psychological stress including anxiety and depression. To identify persons with unexplained chronic widespread pain or unexplained chronic fatigue; we examined participant's medical records to exclude medical illness that might cause these symptoms. Results Of 1443 participants (58.0% response rate) medical records of 990 were examined. 9.4% (N = 93) had unexplained chronic widespread pain and 12.6% (N = 125) had unexplained chronic fatigue. Marital status, childhood psychological abuse, recent threatening experiences and other somatic symptoms were commonly associated with both widespread pain and fatigue. No common effect was found for few years of education and current medical illnesses (more strongly associated with chronic widespread pain) or recent illness in a close relative, neuroticism, depression and anxiety scores (more strongly associated with chronic fatigue). Putative associated factors with a common effect were associated with unexplained chronic widespread pain or unexplained chronic fatigue only when there was concurrent anxiety and/or depression. Discussion This study suggests that the associated factors for chronic widespread pain and chronic fatigue need to be studied in conjunction with concurrent depression/anxiety. Clinicians should be aware of the importance of concurrent anxiety or depression. PMID:26652592

  16. Shaping of the Southern Adriatic Continental Margin Through Widespread Mass Wasting and Bottom Currents

    NASA Astrophysics Data System (ADS)

    Trincardi, F.; Cattaneo, A.; Correggiari, A.; Verdicchio, G.; Tobi, T.

    2003-12-01

    New TOBI seafloor images and VHR Chirp sonar profiles reveal widespread collapsing of the South Adriatic continental slope including: multiple overlapping slide scars affecting more than 100 km of Pleistocene regressive shelf-margin deposits below the shelf edge, extensive blocky slides on the lower slope (block sizes up to 200 x 500 m), and a basin wide acoustically-transparent deposit up to 40 m thick, buried under a late-Pleistocene-Holocene mud section, in water depths greater than 1000 m. Lateral variations in internal geometry and seafloor morphology likely reflects along margin differences in sediment composition and thickness of the mass-transport deposits and variable run outs (up to 40 km). Preliminary correlation to published cores in the area indicates that the main mass transport deposit reached the basin floor during the Last Glacial Maximum, but younger failures of smaller size may have affected the slope in more recent times. The new data show that the entire slope area is swept by bottom currents generating furrowed areas up to several tens of km2 in extent, moats on the downdrift side of seafloor irregularities (slide blocks) and preferential sediment deposition on the inferred updrift side, and growth of upslope-migrating sediment waves. In particular, two fields of sediment waves can be mapped in water depths of 400-600 and 1000 m. The former may reflect the activity of the Levantine Intermediate Waters, while the latter may be linked to the downslope flow of the Northern Adriatic Dense Waters. Future work will focus on the definition of intervals of growth vs quiescence of the sediment waves, their possible relation to paleoceanographic reconfigurations, and their interplay with seafloor irregularities dictated by slope instability. A smaller-scale possibly comparable interaction of seafloor morphology generated by sediment deformation and differential deposition of muddy deposits on the shelf emphasizes the importance of bottom

  17. Neuropathic pain as part of chronic widespread pain: environmental and genetic influences.

    PubMed

    Momi, Sukhleen K; Fabiane, Stella Maris; Lachance, Genevieve; Livshits, Gregory; Williams, Frances M K

    2015-10-01

    Chronic widespread pain (CWP) has complex aetiology and forms part of the fibromyalgia syndrome. Recent evidence suggests a higher frequency of neuropathic pain features in those with CWP than previously thought. The aim of this study was to determine the prevalence of neuropathic pain features in individuals with CWP and to estimate the influence of genetic and environmental factors on neuropathic pain in CWP. Validated questionnaires (the London Fibromyalgia Screening Study questionnaire and PainDETECT questionnaire) were used to classify twins as having CWP and neuropathic pain, respectively. The prevalence of CWP was 14.7% (n = 4324), and of the 1357 twins invited to complete neuropathic pain screening, 15.9% of those having CWP demonstrated features of neuropathic pain. Neuropathic pain was found to be heritable (A = 37%; 95% confidence interval [CI]: 23%-50%) with unique environmental factors accounting for 63% (95% CI: 49%-79%) of the variance. Heritability of neuropathic pain and CWP were found to be correlated, 0.54 (95% CI: 0.42-0.65). Increasing age, raised body mass index, female gender, and smoking were all risk factors for neuropathic pain (P < 0.05), and CWP (P < 0.05). High socioeconomic status showed negative correlation with neuropathic pain (P = 0.003) and CWP (P = 0.001). Bivariate analysis of the 2 pain traits revealed that genetic predisposition to neuropathic pain is shared with that for CWP. This is the first study to provide formal heritability estimates for neuropathic pain in CWP. The findings suggest that at least some of the genetic factors underlying the development of neuropathic pain and CWP are the same.

  18. Widespread use and frequent detection of neonicotinoid insecticides in wetlands of Canada's Prairie Pothole Region.

    PubMed

    Main, Anson R; Headley, John V; Peru, Kerry M; Michel, Nicole L; Cessna, Allan J; Morrissey, Christy A

    2014-01-01

    Neonicotinoids currently dominate the insecticide market as seed treatments on Canada's major Prairie crops (e.g., canola). The potential impact to ecologically significant wetlands in this dominantly agro-environment has largely been overlooked while the distribution of use, incidence and level of contamination remains unreported. We modelled the spatial distribution of neonicotinoid use across the three Prairie Provinces in combination with temporal assessments of water and sediment concentrations in wetlands to measure four active ingredients (clothianidin, thiamethoxam, imidacloprid and acetamiprid). From 2009 to 2012, neonicotinoid use was increasing; by 2012, applications covered an estimated ∼11 million hectares (44% of Prairie cropland) with >216,000 kg of active ingredients. Thiamethoxam, followed by clothianidin, were the dominant seed treatments by mass and area. Areas of high neonicotinoid use were identified as high density canola or soybean production. Water sampled four times from 136 wetlands (spring, summer, fall 2012 and spring 2013) across four rural municipalities in Saskatchewan similarly revealed clothianidin and thiamethoxam in the majority of samples. In spring 2012 prior to seeding, 36% of wetlands contained at least one neonicotinoid. Detections increased to 62% in summer 2012, declined to 16% in fall, and increased to 91% the following spring 2013 after ice-off. Peak concentrations were recorded during summer 2012 for both thiamethoxam (range:

  19. Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function

    PubMed Central

    Naeem, Villian; Chen, Yanmei; Lee, Terrance; Angeloni, Nicholas; Wang, Yin; Xu, Eugene Yujun

    2010-01-01

    Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. Examination of Boule evolution within insect and mammalian lineages revealed little evidence for accelerated evolution, unlike most reproductive genes. Instead, purifying selection was the major force behind Boule evolution. Furthermore, loss of function of mammalian Boule resulted in male-specific infertility and a global arrest of sperm development remarkably similar to the phenotype in an insect boule mutation. This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis. PMID:20657660

  20. Widespread distribution and unexpected variation among science faculty with education specialties (SFES) across the United States.

    PubMed

    Bush, Seth D; Pelaez, Nancy J; Rudd, James A; Stevens, Michael T; Tanner, Kimberly D; Williams, Kathy S

    2013-04-30

    College and university science departments are increasingly taking an active role in improving science education. Perhaps as a result, a new type of specialized science faculty position within science departments is emerging--referred to here as science faculty with education specialties (SFES)--where individual scientists focus their professional efforts on strengthening undergraduate science education, improving kindergarten-through-12th grade science education, and conducting discipline-based education research. Numerous assertions, assumptions, and questions about SFES exist, yet no national studies have been published. Here, we present findings from a large-scale study of US SFES, who are widespread and increasing in numbers. Contrary to many assumptions, SFES were indeed found across the nation, across science disciplines, and, most notably, across primarily undergraduate, master of science-granting, and PhD-granting institutions. Data also reveal unexpected variations among SFES by institution type. Among respondents, SFES at master of science-granting institutions were almost twice as likely to have formal training in science education compared with other SFES. In addition, SFES at PhD-granting institutions were much more likely to have obtained science education funding. Surprisingly, formal training in science education provided no advantage in obtaining science education funding. Our findings show that the SFES phenomenon is likely more complex and diverse than anticipated, with differences being more evident across institution types than across science disciplines. These findings raise questions about the origins of differences among SFES and are useful to science departments interested in hiring SFES, scientific trainees preparing for SFES careers, and agencies awarding science education funding.

  1. Cytotype differences modulate eco-geographical differentiation in the widespread plant Centaurea stoebe.

    PubMed

    Hahn, Min A; Müller-Schärer, Heinz

    2013-05-01

    The evolution of optimal life history strategies is central for the fitness of organisms in a given environment. Besides divergent selection, other factors may determine regional patterns of differentiation and contribute to life history evolution. In a common-garden environment over three years, we examined life history differentiation across different eco-geographical regions and effects of a specialist root-insect herbivore in the widespread European plant Centaurea stoebe, spotted knapweed. This plant occurs as two cytotypes with contrasting life cycles: monocarpic diploids and polycarpic tetraploids. In addition, the tetraploid cytotype has more recently become invasive in North America. We found significant regional differentiation in traits related to the timing of reproduction and reproductive allocation, but contrasting patterns in diploids and tetraploids. In diploids the degree of regional differentiation was higher compared to native tetraploids, and in the latter compared to invasive tetraploids. Furthermore, a pronounced shift in environmental conditions between the native and introduced range could have contributed to the differentiation between native and invasive tetraploids. The study also revealed the potential of the root-mining insect herbivore Agapeta zoegana, used as a biological control organism, to increase plant performance (presumably through overcompensatory growth), especially in the polycarpic tetraploids, and more so in the introduced populations. These findings suggest that patterns of regional differentiation in C. stoebe may be partly determined by divergent selection, but also strongly modulated by life cycle differences among geo-cytotypes. Furthermore, our study highlights the importance in applying a comprehensive and long-term approach when studying regional differentiation in plants.

  2. The Psychoactive Designer Drug and Bath Salt Constituent MDPV Causes Widespread Disruption of Brain Functional Connectivity.

    PubMed

    Colon-Perez, Luis M; Tran, Kelvin; Thompson, Khalil; Pace, Michael C; Blum, Kenneth; Goldberger, Bruce A; Gold, Mark S; Bruijnzeel, Adriaan W; Setlow, Barry; Febo, Marcelo

    2016-08-01

    The abuse of 'bath salts' has raised concerns because of their adverse effects, which include delirium, violent behavior, and suicide ideation in severe cases. The bath salt constituent 3,4-methylenedioxypyrovalerone (MDPV) has been closely linked to these and other adverse effects. The abnormal behavioral pattern produced by acute high-dose MDPV intake suggests possible disruptions of neural communication between brain regions. Therefore, we determined if MDPV exerts disruptive effects on brain functional connectivity, particularly in areas of the prefrontal cortex. Male rats were imaged following administration of a single dose of MDPV (0.3, 1.0, or 3.0 mg/kg) or saline. Resting state brain blood oxygenation level-dependent (BOLD) images were acquired at 4.7 T. To determine the role of dopamine transmission in MDPV-induced changes in functional connectivity, a group of rats received the dopamine D1/D2 receptor antagonist cis-flupenthixol (0.5 mg/kg) 30 min before MDPV. MDPV dose-dependently reduced functional connectivity. Detailed analysis of its effects revealed that connectivity between frontal cortical and striatal areas was reduced. This included connectivity between the prelimbic prefrontal cortex and other areas of the frontal cortex and the insular cortex with hypothalamic, ventral, and dorsal striatal areas. Although the reduced connectivity appeared widespread, connectivity between these regions and somatosensory cortex was not as severely affected. Dopamine receptor blockade did not prevent the MDPV-induced decrease in functional connectivity. The results provide a novel signature of MDPV's in vivo mechanism of action. Reduced brain functional connectivity has been reported in patients suffering from psychosis and has been linked to cognitive dysfunction, audiovisual hallucinations, and negative affective states akin to those reported for MDPV-induced intoxication. The present results suggest that disruption of functional connectivity networks

  3. Serological, Molecular and Entomological Surveillance Demonstrates Widespread Circulation of West Nile Virus in Turkey

    PubMed Central

    Ergunay, Koray; Gunay, Filiz; Erisoz Kasap, Ozge; Oter, Kerem; Gargari, Sepandar; Karaoglu, Taner; Tezcan, Seda; Cabalar, Mehmet; Yildirim, Yakup; Emekdas, Gürol; Alten, Bulent; Ozkul, Aykut

    2014-01-01

    West Nile virus (WNV), a mosquito-borne flavivirus with significant impact on human and animal health, has recently demonstrated an expanded zone of activity globally. The aim of this study is to investigate the frequency and distribution of WNV infections in potential vectors and several mammal and avian species in Turkey, where previous data indicate viral circulation. The study was conducted in 15 provinces across Turkey during 2011–2013. In addition, the entomological study was extended to 4 districts of the Turkish Republic of Northern Cyprus. WNV exposure was determined in humans, horses, sheep and ducks from Mersin, Sanliurfa, Van and Kars provinces of Turkey, via the detection of neutralizing antibodies. WNV RNA was sought in human and equine samples from Mersin, Adana and Mugla provinces. Field-collected mosquitoes from 92 sites at 46 locations were characterized morphologically and evaluated for viral RNA. Neutralizing antibodies were identified in 10.5% of the 1180 samples studied and detected in all species evaluated. Viral nucleic acids were observed in 5.9% of 522 samples but only in horses. A total of 2642 mosquito specimens belonging to 15 species were captured, where Ochlerotatus caspius (52.4%), Culex pipiens sensu lato (24.2%) comprise the most frequent species. WNV RNA was detected in 4 mosquito pools (1.9%), that comprise Oc. caspius Cx. pipiens s.l. and DNA barcoding revealed the presence of Cx. quinquefasciatus and Cx. perexiguus mosquitoes in infected Culex pools. All WNV partial sequences were characterized as lineage 1 clade 1a. These findings indicate a widespread WNV activity in Turkey, in Eastern Thrace and Mediterranean-Aegean regions as well as Southeastern and Northeastern Anatolia. PMID:25058465

  4. Widespread differences in cortex DNA methylation of the "language gene" CNTNAP2 between humans and chimpanzees.

    PubMed

    Schneider, Eberhard; El Hajj, Nady; Richter, Steven; Roche-Santiago, Justin; Nanda, Indrajit; Schempp, Werner; Riederer, Peter; Navarro, Bianca; Bontrop, Ronald E; Kondova, Ivanela; Scholz, Claus Jürgen; Haaf, Thomas

    2014-04-01

    CNTNAP2, one of the largest genes in the human genome, has been linked to human-specific language abilities and neurodevelopmental disorders. Our hypothesis is that epigenetic rather than genetic changes have accelerated the evolution of the human brain. To compare the cortex DNA methylation patterns of human and chimpanzee CNTNAP2 at ultra-high resolution, we combined methylated DNA immunoprecipitation (MeDIP) with NimbleGen tiling arrays for the orthologous gene and flanking sequences. Approximately 1.59 Mb of the 2.51 Mb target region could be aligned and analyzed with a customized algorithm in both species. More than one fifth (0.34 Mb) of the analyzed sequence throughout the entire gene displayed significant methylation differences between six human and five chimpanzee cortices. One of the most striking interspecies differences with 28% methylation in human and 59% in chimpanzee cortex (by bisulfite pyrosequencing) lies in a region 300 bp upstream of human SNP rs7794745 which has been associated with autism and parent-of-origin effects. Quantitative real-time RT PCR revealed that the protein-coding splice variant CNTNAP2-201 is 1.6-fold upregulated in human cortex, compared with the chimpanzee. Transcripts CNTNAP2-001, -002, and -003 did not show skewed allelic expression, which argues against CNTNAP2 imprinting, at least in adult human brain. Collectively, our results suggest widespread cortex DNA methylation changes in CNTNAP2 since the human-chimpanzee split, supporting a role for CNTNAP2 fine-regulation in human-specific language and communication traits.

  5. Out of Africa: Phylogeny and biogeography of the widespread genus Acanthodactylus (Reptilia: Lacertidae).

    PubMed

    Tamar, Karin; Carranza, Salvador; Sindaco, Roberto; Moravec, Jiří; Trape, Jean-François; Meiri, Shai

    2016-10-01

    Acanthodactylus lizards are among the most diverse and widespread diurnal reptiles in the arid regions spanning from North Africa across to western India. Acanthodactylus constitutes the most species-rich genus in the family Lacertidae, with over 40 recognized species inhabiting a wide variety of dry habitats. The genus has seldom undergone taxonomic revisions, and although there are a number of described species and species-groups, their boundaries, as well as their interspecific relationships, remain largely unresolved. We constructed a multilocus phylogeny, combining data from two mitochondrial (12S, cytb) and three nuclear (MC1R, ACM4, c-mos) markers for 302 individuals belonging to 36 known species, providing the first large-scale time-calibrated molecular phylogeny of the genus. We evaluated phylogenetic relationships between and within species-groups, and assessed Acanthodactylus biogeography across its known range. Acanthodactylus cladogenesis is estimated to have originated in Africa due to vicariance and dispersal events from the Oligocene onwards. Radiation started with the separation into three clades: the Western and scutellatus clades largely distributed in North Africa, and the Eastern clade occurring mostly in south-west Asia. Most Acanthodactylus species diverged during the Miocene, possibly as a result of regional geological instability and climatic changes. We support most of the current taxonomic classifications and phylogenetic relationships, and provide genetic validity for most species. We reveal a new distinct blanfordii species-group, suggest new phylogenetic positions (A. hardyi, A. masirae), and synonymize several species and subspecies (A. lineomaculatus, A. boskianus khattensis and A. b. nigeriensis) with their phylogenetically closely-related species. We recommend a thorough systematic revision of taxa, such as A. guineensis, A. grandis, A. dumerilii, A. senegalensis and the pardalis and erythrurus species-groups, which exhibit high

  6. Widespread Use and Frequent Detection of Neonicotinoid Insecticides in Wetlands of Canada's Prairie Pothole Region

    PubMed Central

    Main, Anson R.; Headley, John V.; Peru, Kerry M.; Michel, Nicole L.; Cessna, Allan J.; Morrissey, Christy A.

    2014-01-01

    Neonicotinoids currently dominate the insecticide market as seed treatments on Canada's major Prairie crops (e.g., canola). The potential impact to ecologically significant wetlands in this dominantly agro-environment has largely been overlooked while the distribution of use, incidence and level of contamination remains unreported. We modelled the spatial distribution of neonicotinoid use across the three Prairie Provinces in combination with temporal assessments of water and sediment concentrations in wetlands to measure four active ingredients (clothianidin, thiamethoxam, imidacloprid and acetamiprid). From 2009 to 2012, neonicotinoid use was increasing; by 2012, applications covered an estimated ∼11 million hectares (44% of Prairie cropland) with >216,000 kg of active ingredients. Thiamethoxam, followed by clothianidin, were the dominant seed treatments by mass and area. Areas of high neonicotinoid use were identified as high density canola or soybean production. Water sampled four times from 136 wetlands (spring, summer, fall 2012 and spring 2013) across four rural municipalities in Saskatchewan similarly revealed clothianidin and thiamethoxam in the majority of samples. In spring 2012 prior to seeding, 36% of wetlands contained at least one neonicotinoid. Detections increased to 62% in summer 2012, declined to 16% in fall, and increased to 91% the following spring 2013 after ice-off. Peak concentrations were recorded during summer 2012 for both thiamethoxam (range:

  7. Neuropathic pain as part of chronic widespread pain: environmental and genetic influences

    PubMed Central

    Momi, Sukhleen K.; Fabiane, Stella Maris; Lachance, Genevieve; Livshits, Gregory; Williams, Frances M. K.

    2015-01-01

    Abstract Chronic widespread pain (CWP) has complex aetiology and forms part of the fibromyalgia syndrome. Recent evidence suggests a higher frequency of neuropathic pain features in those with CWP than previously thought. The aim of this study was to determine the prevalence of neuropathic pain features in individuals with CWP and to estimate the influence of genetic and environmental factors on neuropathic pain in CWP. Validated questionnaires (the London Fibromyalgia Screening Study questionnaire and PainDETECT questionnaire) were used to classify twins as having CWP and neuropathic pain, respectively. The prevalence of CWP was 14.7% (n = 4324), and of the 1357 twins invited to complete neuropathic pain screening, 15.9% of those having CWP demonstrated features of neuropathic pain. Neuropathic pain was found to be heritable (A = 37%; 95% confidence interval [CI]: 23%-50%) with unique environmental factors accounting for 63% (95% CI: 49%-79%) of the variance. Heritability of neuropathic pain and CWP were found to be correlated, 0.54 (95% CI: 0.42-0.65). Increasing age, raised body mass index, female gender, and smoking were all risk factors for neuropathic pain (P < 0.05), and CWP (P < 0.05). High socioeconomic status showed negative correlation with neuropathic pain (P = 0.003) and CWP (P = 0.001). Bivariate analysis of the 2 pain traits revealed that genetic predisposition to neuropathic pain is shared with that for CWP. This is the first study to provide formal heritability estimates for neuropathic pain in CWP. The findings suggest that at least some of the genetic factors underlying the development of neuropathic pain and CWP are the same. PMID:26121255

  8. Widespread alterations in the synaptic proteome of the adolescent cerebral cortex following prenatal immune activation in rats.

    PubMed

    Györffy, Balázs A; Gulyássy, Péter; Gellén, Barbara; Völgyi, Katalin; Madarasi, Dóra; Kis, Viktor; Ozohanics, Olivér; Papp, Ildikó; Kovács, Péter; Lubec, Gert; Dobolyi, Árpád; Kardos, József; Drahos, László; Juhász, Gábor; Kékesi, Katalin A

    2016-08-01

    An increasing number of studies have revealed associations between pre- and perinatal immune activation and the development of schizophrenia and autism spectrum disorders (ASDs). Accordingly, neuroimmune crosstalk has a considerably large impact on brain development during early ontogenesis. While a plethora of heterogeneous abnormalities have already been described in established maternal immune activation (MIA) rodent and primate animal models, which highly correlate to those found in human diseases, the underlying molecular background remains obscure. In the current study, we describe the long-term effects of MIA on the neocortical pre- and postsynaptic proteome of adolescent rat offspring in detail. Molecular differences were revealed in sub-synaptic fractions, which were first thoroughly characterized using independent methods. The widespread proteomic examination of cortical samples from offspring exposed to maternal lipopolysaccharide administration at embryonic day 13.5 was conducted via combinations of different gel-based proteomic techniques and tandem mass spectrometry. Our experimentally validated proteomic data revealed more pre- than postsynaptic protein level changes in the offspring. The results propose the relevance of altered synaptic vesicle recycling, cytoskeletal structure and energy metabolism in the presynaptic region in addition to alterations in vesicle trafficking, the cytoskeleton and signal transduction in the postsynaptic compartment in MIA offspring. Differing levels of the prominent signaling regulator molecule calcium/calmodulin-dependent protein kinase II in the postsynapse was validated and identified specifically in the prefrontal cortex. Finally, several potential common molecular regulators of these altered proteins, which are already known to be implicated in schizophrenia and ASD, were identified and assessed. In summary, unexpectedly widespread changes in the synaptic molecular machinery in MIA rats were demonstrated which

  9. Occurrence and amount of microplastic ingested by fishes in watersheds of the Gulf of Mexico.

    PubMed

    Phillips, Melissa B; Bonner, Timothy H

    2015-11-15

    Ingestion of microplastics by fishes could be an emerging environmental crisis because of the proliferation of plastic pollution in aquatic environments. Microplastics in marine ecosystems are well documented, however only one study has reported percent occurrence of microplastics in freshwater fishes. The purpose of this study was to quantify the occurrences and types of microplastics ingested by fishes within several freshwater drainages of the Gulf of Mexico and an estuary of the Gulf of Mexico. Among 535 fishes examined in this study, 8% of the freshwater fishes and 10% of the marine fishes had microplastics in their gut tract. Percentage occurrence of microplastics ingested by fishes in non-urbanized streams (5%) was less than that of one of the urbanized streams (Neches River; 29%). Percent occurrence of microplastics by habitat (i.e., benthic, pelagic) and trophic guilds (herbivore/omnivore, invertivore, carnivore) were similar. Low but widespread occurrences among drainages, habitat guilds, and trophic guilds indicate proliferation of plastic pollution within watersheds of the Gulf of Mexico, but consequences to fish health are unknown at this time.

  10. UMTRA project list of reportable occurrences

    SciTech Connect

    Not Available

    1994-04-01

    This UMTRA Project List of Reportable occurrences is provided to facilitate efficient categorization of reportable occurrences. These guidelines have been established in compliance with DOE minimum reporting requirements under DOE Order 5000.3B. Occurrences are arranged into nine groups relating to US Department of Energy (DOE) Uranium Mill Tailings Remedial Action (UMTRA) Project operations for active sites. These nine groupings are provided for reference to determined whether an occurrence meets reporting requirement criteria in accordance with the minimum reporting requirements. Event groups and significance categories that cannot or will not occur, and that do not apply to UMTRA Project operations, are omitted. Occurrence categorization shall be as follows: Group 1. Facility Condition; Group 2. Environmental; Group 3. Personnel Safety; Group 4. Personnel Radiation Protection; Group 5. Safeguards and Security; Group 6. Transportation; Group 7. Value Basis Reporting; Group 8. Facility Status; and Group 9. Cross-Category Items.

  11. DETECTION OF WIDESPREAD HYDRATED MATERIALS ON VESTA BY THE VIR IMAGING SPECTROMETER ON BOARD THE DAWN MISSION

    SciTech Connect

    De Sanctis, M. C.; Ammannito, E.; Palomba, E.; Longobardo, A.; Capaccioni, F.; Capria, M. T.; Tosi, F.; Zambon, F.; Carraro, F.; Fonte, S.; Frigeri, A.; Magni, G.; Combe, J.-Ph.; McCord, T. B.; Marchi, S.; Mittlefehldt, D. W.; Pieters, C. M.; Sunshine, J.; Raymond, C. A.; Russell, C. T.; and others

    2012-10-20

    Water plays a key role in the evolution of terrestrial planets, and notably in the occurrence of Earth's oceans. However, the mechanism by which water has been incorporated into these bodies-including Earth-is still extensively debated. Here we report the detection of widespread 2.8 {mu}m OH absorption bands on the surface of the asteroid Vesta by the VIR imaging spectrometer on board Dawn. These observations are surprising as Vesta is fully differentiated with a basaltic surface. The 2.8 {mu}m OH absorption is distributed across Vesta's surface and shows areas enriched and depleted in hydrated materials. The uneven distribution of hydrated mineral phases is unexpected and indicates ancient processes that differ from those believed to be responsible for OH on other airless bodies, like the Moon. The origin of Vestan OH provides new insight into the delivery of hydrous materials in the main belt and may offer new scenarios on the delivery of hydrous minerals in the inner solar system, suggesting processes that may have played a role in the formation of terrestrial planets.

  12. Hassallidins, antifungal glycolipopeptides, are widespread among cyanobacteria and are the end-product of a nonribosomal pathway.

    PubMed

    Vestola, Johanna; Shishido, Tania K; Jokela, Jouni; Fewer, David P; Aitio, Olli; Permi, Perttu; Wahlsten, Matti; Wang, Hao; Rouhiainen, Leo; Sivonen, Kaarina

    2014-05-06

    Cyanobacteria produce a wide variety of cyclic peptides, including the widespread hepatotoxins microcystins and nodularins. Another class of peptides, cyclic glycosylated lipopeptides called hassallidins, show antifungal activity. Previously, two hassallidins (A and B) were reported from an epilithic cyanobacterium Hassallia sp. and found to be active against opportunistic human pathogenic fungi. Bioinformatic analysis of the Anabaena sp. 90 genome identified a 59-kb cryptic inactive nonribosomal peptide synthetase gene cluster proposed to be responsible for hassallidin biosynthesis. Here we describe the hassallidin biosynthetic pathway from Anabaena sp. SYKE748A, as well as the large chemical variation and common occurrence of hassallidins in filamentous cyanobacteria. Analysis demonstrated that 20 strains of the genus Anabaena carry hassallidin synthetase genes and produce a multitude of hassallidin variants that exhibit activity against Candida albicans. The compounds discovered here were distinct from previously reported hassallidins A and B. The IC50 of hassallidin D was 0.29-1.0 µM against Candida strains. A large variation in amino acids, sugars, their degree of acetylation, and fatty acid side chain length was detected. In addition, hassallidins were detected in other cyanobacteria including Aphanizomenon, Cylindrospermopsis raciborskii, Nostoc, and Tolypothrix. These compounds may protect some of the most important bloom-forming and globally distributed cyanobacteria against attacks by parasitic fungi.

  13. A specialist’s audit of aggregated occurrence records

    PubMed Central

    Mesibov, Robert

    2013-01-01

    Abstract Occurrence records for named, native Australian millipedes from the Global Biodiversity Information Facility (GBIF) and the Atlas of Living Australia (ALA) were compared with the same records from the Millipedes of Australia (MoA) website, compiled independently by the author. The comparison revealed some previously unnoticed errors in MoA, and a much larger number of errors and other problems in the aggregated datasets. Errors have been corrected in MoA and in some data providers’ databases, but will remain in GBIF and ALA until data providers have supplied updates to these aggregators. An audit by a specialist volunteer, as reported here, is not a common occurrence. It is suggested that aggregators should do more, or more effective, data checking and should query data providers when possible errors are detected, rather than simply disclaim responsibility for aggregated content. PMID:23794864

  14. Modeling fire occurrence as a function of landscape

    NASA Astrophysics Data System (ADS)

    Loboda, T. V.; Carroll, M.; DiMiceli, C.

    2011-12-01

    area impacted by fire from the total available area within a given value of the Fire Occurrence Index (FOI) increased from 9.e-06 at FOI < 3 to 28.e-06 at 25 < FOI <= 28. Additionally, the model has revealed a new important relationship between fire occurrence, anthropogenic activity, and fire weather. Data analysis has demonstrated that human activity can alter the expected weather/fire occurrence relationships and result in considerable modifications of fire regimes contrary to the assumed ecological parameters. Specifically, between 2001 and 2009 over 50% of total fire impacted area burned during the low fire danger conditions (Canadian Fire Weather Index < 5). These findings and the FOM capabilities offer a new theoretical construct and an advanced tool for assessing the potential impacts of climate changes on fire regimes, particularly within landscapes which are impacted strongly by human activities. Future development of the FOM will focus on ingesting and internal downscaling of climate variables produced by General or Regional Circulation Models to develop scenarios of potential future change in fire occurrence under the influence of projected climate change at the appropriate regional or landscape scales.

  15. A simple physical model for deep moonquake occurrence times

    USGS Publications Warehouse

    Weber, R.C.; Bills, B.G.; Johnson, C.L.

    2010-01-01

    The physical process that results in moonquakes is not yet fully understood. The periodic occurrence times of events from individual clusters are clearly related to tidal stress, but also exhibit departures from the temporal regularity this relationship would seem to imply. Even simplified models that capture some of the relevant physics require a large number of variables. However, a single, easily accessible variable - the time interval I(n) between events - can be used to reveal behavior not readily observed using typical periodicity analyses (e.g., Fourier analyses). The delay-coordinate (DC) map, a particularly revealing way to display data from a time series, is a map of successive intervals: I(n+. 1) plotted vs. I(n). We use a DC approach to characterize the dynamics of moonquake occurrence. Moonquake-like DC maps can be reproduced by combining sequences of synthetic events that occur with variable probability at tidal periods. Though this model gives a good description of what happens, it has little physical content, thus providing only little insight into why moonquakes occur. We investigate a more mechanistic model. In this study, we present a series of simple models of deep moonquake occurrence, with consideration of both tidal stress and stress drop during events. We first examine the behavior of inter-event times in a delay-coordinate context, and then examine the output, in that context, of a sequence of simple models of tidal forcing and stress relief. We find, as might be expected, that the stress relieved by moonquakes influences their occurrence times. Our models may also provide an explanation for the opposite-polarity events observed at some clusters. ?? 2010.

  16. Long-term changes to the frequency of occurrence of British moths are consistent with opposing and synergistic effects of climate and land-use changes

    PubMed Central

    Fox, Richard; Oliver, Tom H; Harrower, Colin; Parsons, Mark S; Thomas, Chris D; Roy, David B

    2014-01-01

    Species’ distributions are likely to be affected by a combination of environmental drivers. We used a data set of 11 million species occurrence records over the period 1970–2010 to assess changes in the frequency of occurrence of 673 macro-moth species in Great Britain. Groups of species with different predicted sensitivities showed divergent trends, which we interpret in the context of land-use and climatic changes. A diversity of responses was revealed: 260 moth species declined significantly, whereas 160 increased significantly. Overall, frequencies of occurrence declined, mirroring trends in less species-rich, yet more intensively studied taxa. Geographically widespread species, which were predicted to be more sensitive to land use than to climate change, declined significantly in southern Britain, where the cover of urban and arable land has increased. Moths associated with low nitrogen and open environments (based on their larval host plant characteristics) declined most strongly, which is also consistent with a land-use change explanation. Some moths that reach their northern (leading edge) range limit in southern Britain increased, whereas species restricted to northern Britain (trailing edge) declined significantly, consistent with a climate change explanation. Not all species of a given type behaved similarly, suggesting that complex interactions between species’ attributes and different combinations of environmental drivers determine frequency of occurrence changes. Synthesis and applications. Our findings are consistent with large-scale responses to climatic and land-use changes, with some species increasing and others decreasing. We suggest that land-use change (e.g. habitat loss, nitrogen deposition) and climate change are both major drivers of moth biodiversity change, acting independently and in combination. Importantly, the diverse responses revealed in this species-rich taxon show that multifaceted conservation strategies are needed to

  17. A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae)

    PubMed Central

    2011-01-01

    Background Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. Results Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. Conclusions The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological

  18. The Effects of Daily Co-Occurrence of Affect on Older Adults’ Reactivity to Health Stressors

    PubMed Central

    Ramsey, Jennifer L.; Neupert, Shevaun D.; Mroczek, Daniel K.; Spiro, Avron

    2015-01-01

    Objectives The present study examined age differences among older adults in the daily co-occurrence of affect and its potential role in buffering the negative effects of health stressors. Design Participants were from the Veterans Affairs Normative Aging Study (NAS) and included 249 young-old adults (age = 60–79 years, M=71.6) and 64 old-old adults (age = 80–89, M = 82.9) who completed questionnaires assessing stressors, physical health symptoms, and positive and negative affect on eight consecutive days. Results An independent samples t-test showed young-old and old-old adults did not significantly differ in their mean levels of daily co-occurrence of affect. The between-person relationships among stressors, health, and daily co-occurrence of affect revealed that neither stressors nor health were significantly related to daily co-occurrence of affect. However, results from a multilevel model revealed a three-way cross-level interaction (Health Stressor X Age Group X Co-Occurrence of Affect) where old-old adults with higher levels of co-occurrence of affect were less emotionally reactive to health stressors than young-old adults. Conclusion These findings provide support for the assertion that co-occurrence of affect functions in an adaptive capacity and highlight the importance of examining domain specific stressors. PMID:26518259

  19. Occurrence of acid precipitation on the West Coast of the United States

    SciTech Connect

    Powers, C.F.; Rambo, D.L.

    1981-01-01

    Compilation of published and unpublished data shows acid precipitation to be more widespread in the Pacific coastal states than is generally recognized. Although information is scattered and discontinuous, precipitation is definitely acidic in the Los Angeles Basin and north-central California and in the Puget Sound region in Washington. Acid-rain occurrences were observed in western and eastern Oregon, but data are inadequate for regional generalization. New stations currently being established in Washington and Oregon, largely in response to the recently renewed activity of Mount St. Helens, will greatly facilitate assessment of precipitation acidity in the Northwest.

  20. Report to Congress on abnormal occurrences

    SciTech Connect

    Not Available

    1991-03-01

    Section 208 of the Energy Reorganization Act of 1974 identified an abnormal occurrence as an unscheduled incident or event that the Nuclear Regulatory Commission determines to be significant from the standpoint of public health or safety and requires a quarterly report of such events to be made to Congress. This report covers the period from October 1 through December 31, 1990. The report discusses five abnormal occurrences, none of which involved a nuclear power plant. Two involved significant overexposures to the hands of two radiographers, two involved medical therapy misadministrations, and one involved a medical diagnostic misadministration. No abnormal occurrences were reported by the Agreement States. The report also contains information that updates a previously reported abnormal occurrence. 8 refs.

  1. Managing occurrence branching in qualitative simulation

    SciTech Connect

    Tokuda, L.

    1996-12-31

    Qualitative simulators can produce common sense abstractions of complex behaviors given only partial knowledge about a system. One of the problems which limits the applicability of qualitative simulators is the intractable branching of successor states encountered with model of even modest size. Some branches may be unavoidable due to the complex nature of a system. Other branches may be accidental results of the model chosen. A common source of intractability is occurrence branching. Occurrence branching occurs when the state transitions of two variables are unordered with respect to each other. This paper extends the QSIM model to distinguish between interesting occurrence branching and uninteresting occurrence branching. A representation, algorithm, and simulator for efficiently handling uninteresting branching is presented.

  2. Occurrence of pneumomediastinum due to dental procedures.

    PubMed

    Aslaner, Mehmet Ali; Kasap, Gül Nihal; Demir, Cihat; Akkaş, Meltem; Aksu, Nalan M

    2015-01-01

    The occurrence of pneumomediastinum and massive subcutaneous emphysema due to dental procedures is quite rare. We present a case of pneumomediastinum and massive subcutaneous emphysema that occurred during third molar tooth extraction with air-turbine handpiece.

  3. Occurrence and distribution of Indian primates

    USGS Publications Warehouse

    Karanth, K.K.; Nichols, J.D.; Hines, J.E.

    2010-01-01

    Global and regional species conservation efforts are hindered by poor distribution data and range maps. Many Indian primates face extinction, but assessments of population status are hindered by lack of reliable distribution data. We estimated the current occurrence and distribution of 15 Indian primates by applying occupancy models to field data from a country-wide survey of local experts. We modeled species occurrence in relation to ecological and social covariates (protected areas, landscape characteristics, and human influences), which we believe are critical to determining species occurrence in India. We found evidence that protected areas positively influence occurrence of seven species and for some species are their only refuge. We found evergreen forests to be more critical for some primates along with temperate and deciduous forests. Elevation negatively influenced occurrence of three species. Lower human population density was positively associated with occurrence of five species, and higher cultural tolerance was positively associated with occurrence of three species. We find that 11 primates occupy less than 15% of the total land area of India. Vulnerable primates with restricted ranges are Golden langur, Arunachal macaque, Pig-tailed macaque, stump-tailed macaque, Phayre's leaf monkey, Nilgiri langur and Lion-tailed macaque. Only Hanuman langur and rhesus macaque are widely distributed. We find occupancy modeling to be useful in determining species ranges, and in agreement with current species ranking and IUCN status. In landscapes where monitoring efforts require optimizing cost, effort and time, we used ecological and social covariates to reliably estimate species occurrence and focus species conservation efforts. ?? Elsevier Ltd.

  4. The occurrence of gonadal dysgenesis in association with monozygotic twinning.

    PubMed Central

    Karp, L; Bryant, J I; Tagatz, G; Giblett, E; Fialkow, P J

    1975-01-01

    A case is presented of a monozygotic twin pair, discordant for phenotypic sex, in which the female member showed gonadal dysgenesis and chromosomal mosaicism. Review of the pertinent literature reveals that in monozygotic twin pairs, phenotypic and karyotypic concordance is the usual occurrence for Down's and Klinefelter's syndromes, whereas discordance often accompanies gonadal dysgenesis. Mosaicism is a frequent concomitant of gonadal dysgenesis in monozygotic twins. Our case strengthens the probability of a real association between mosaicism and monozygotic twinning in gonadal dysgenesis. Images PMID:1121022

  5. [Metabolic correction of structural changes in adrenal glands during experimental widespread purulent peritonitis].

    PubMed

    Kosinets, V A; Fedotov, D N

    2012-01-01

    Experiments on 55 male chinchilla rabbits with model widespread purulent peritonitis have been performed for determinig structural changes in adrenal glands with the aid of optical microscopy. The introduction of aerobic-anaerobic culture of E. Coli and B. Fragilis into the abdominal cavity causes expressed structural changes in parenchyma of adrenal glands within 6 hours. It is established for the first time that the administration of metabolic drugs citoflavin (containing succinic acid) and neoton (containing creatine phosphate) prevents the development of pathological structural changes in adrenal glands under conditions of experimental widespread purulent peritonitis.

  6. Molecular characterization of a naturally occurring intraspecific recombinant begomovirus with close relatives widespread in southern Arabia

    PubMed Central

    2014-01-01

    Background Tomato leaf curl Sudan virus (ToLCSDV) is a single-stranded DNA begomovirus of tomato that causes downward leaf curl, yellowing, and stunting. Leaf curl disease results in significant yield reduction in tomato crops in the Nile Basin. ToLCSDV symptoms resemble those caused by Tomato yellow leaf curl virus, a distinct and widespread begomovirus originating in the Middle East. In this study, tomato samples exhibiting leaf curl symptoms were collected from Gezira, Sudan. The associated viral genome was molecularly characterized, analyzed phylogenetically, and an infectious clone for one isolate was constructed. Findings The complete genomes for five newly discovered variants of ToLCSDV, ranging in size from 2765 to 2767-bp, were cloned and sequenced, and subjected to pairwise and phylogenetic analyses. Pairwise analysis indicated that the five Gezira isolates shared 97-100% nucleotide identity with each other. Further, these variants of ToLCSDV shared their highest nucleotide identity at 96-98%, 91-95%, 91-92%, and 91-92% with the Shambat, Gezira, Oman and Yemen strains of ToLCSDV, respectively. Based on the high maximum nucleotide identities shared between these ToLCSDV variants from Gezira and other previously recognized members of this taxonomic group, they are considered isolates of the Shambat strain of ToLCSDV. Analysis of the complete genome sequence for these new variants revealed that they were naturally occurring recombinants between two previously reported strains of ToLCSDV. Finally, a dimeric clone constructed from one representative ToLCSV genome from Gezira was shown to be infectious following inoculation to tomato and N. benthamiana plants. Conclusion Five new, naturally occurring recombinant begomovirus variants (>96% shared nt identity) were identified in tomato plants from Gezira in Sudan, and shown to be isolates of the Shambat strain of ToLCSDV. The cloned viral genome was infectious in N. benthamiana and tomato plants, and symptoms in

  7. The widespread ~10ka Saksunarvatn tephra is not a product single eruption

    NASA Astrophysics Data System (ADS)

    Thordarson, T.

    2014-12-01

    Since its identification as a 45 cm-thick basaltic ash horizon in a sediment core from Lake Saksunarvatn on Streymoy in the Faeroe archipelago the ~10 ka Saksunarvatn ash has been taken to represent one discrete stratigraphic marker horizon in early Holocene sedimentary sequences across the North Atlantic; from Greenland to Western Europe, carrying the inference that it was produced by one continuous eruption. If taken at face value, the volume of this basaltic tephra would be >450 km3, which not only makes it - by far - the largest tephra fall deposit produced by an explosive eruption at an Icelandic volcano but also puts it in the category of 'super-eruptions'. It also implies that the inferred 'Saksunarvatn eruption' would have been about 40 times bigger than the ~3 ka H3 and ~4.2 ka H4 events, two of largest post-glacial silicic explosive eruptions in Iceland. Also, the largest known post-glacial basaltic explosive eruption in Iceland produced tephra volumes of 5-8 km3, or factor of 60 smaller than the anticipated 'Saksunarvatn' event. Although the geological record in Iceland contains ample examples of volcanic events with magnitudes in the range of VEI5-7, it does not reveal evidence of events on the super-eruption scale. These question the validity of the inference that the tephra referred to as the Saksunarvatn ash is a product of a single eruption. New studies on lake sediment cores and soil profiles in Iceland have identified several tephra layers in the time interval 10.4 - 9.9 ka that exhibit major element composition identical to that of the Saksunarvatn ash. Thus, over a period of ~500-years the Grímsvötn volcano produced a series of events erupting tephra of composition identical to that of the Saksunarvatn ash and we will present stratigraphic and geochemical evidence to demonstrate that the 10.4 - 9.9 ka interval of the early Holocene sediment archives contains at least six widespread tephra layers of Saksunarvatn composition and that an early

  8. Occurrence and Biodegradation of Nonylphenol in the Environment

    PubMed Central

    Mao, Zhen; Zheng, Xiao-Fei; Zhang, Yan-Qiu; Tao, Xiu-Xiang; Li, Yan; Wang, Wei

    2012-01-01

    Nonylphenol (NP) is an ultimate degradation product of nonylphenol polyethoxylates (NPE) that is primarily used in cleaning and industrial processes. Its widespread use has led to the wide existence of NP in various environmental matrices, such as water, sediment, air and soil. NP can be decreased by biodegradation through the action of microorganisms under aerobic or anaerobic conditions. Half-lives of biodegradation ranged from a few days to almost one hundred days. The degradation rate for NP was influenced by temperature, pH and additions of yeast extracts, surfactants, aluminum sulfate, acetate, pyruvate, lactate, manganese dioxide, ferric chloride, sodium chloride, hydrogen peroxide, heavy metals, and phthalic acid esters. Although NP is present at low concentrations in the environment, as an endocrine disruptor the risks of long-term exposure to low concentrations remain largely unknown. This paper reviews the occurrence of NP in the environment and its aerobic and anaerobic biodegradation in natural environments and sewage treatment plants, which is essential for assessing the potential risk associated with low level exposure to NP and other endocrine disruptors. PMID:22312266

  9. [Relationships between summer drought and strong typhoon events and pine wilt disease occurrence in East Asia].

    PubMed

    Wang, Fei

    2012-06-01

    The occurrence and prevalence of pine wilt disease cause huge losses to Japan, China, and South Korea in East Asia, and have received concerns from many countries. By the methods of field observation and meteorological data analysis, this paper studied the characteristics of the occurrence and prevalence of pine wilt disease and their relations to the meteorological disaster events. In Japan, China and South Korea, the meteorological extreme events of persistent summer drought and strong typhoon could trigger the occurrence of pine wilt. In extremely dry and hot environment, pine trees often appeared energy metabolism imbalance and entire tree wilt. However, in the years with lower temperature and more rainfall, less or nearly no pine wilt event occurred. It was suggested that before the attack by pine wood nematode and its vectors, the vigor of the pines had already declined, and thus, pine wilt disease could be confined in the areas often hit by summer drought and strong typhoon events. In the areas with suitable natural environment characterized by less summer drought and strong typhoon events and no improperly enlarged pine planting, there would be little possibility of widespread occurrence of pine wilt disease.

  10. Widespread subcutaneous emphysema and barotrauma resulting from high pressure gas injection.

    PubMed

    Smith, Barnaby; Brown, Troy

    2012-09-21

    Widespread subcutaneous emphysema is an unusual emergency presentation. We present a case of accidental high pressure insufflation, the pathophysiology and subsequent medical management in the acute setting. Such presentations are rare but dramatic and can have important life-threatening consequences that require immediate treatment.

  11. Landscape heterogeneity predicts gene flow in a widespread polymorphic bumble bee, Bombus bifarius (Hymentoptera: Apidae).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bombus bifarius is a widespread bumble bee that occurs in montane regions of western North America. This species has several major color polymorphisms, and shows evidence of genetic structuring among regional populations. We test whether this structure is evidence for discrete gene flow barriers tha...

  12. 77 FR 30877 - Aging Airplane Program: Widespread Fatigue Damage; Technical Amendment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-24

    ..., 121, and 129 [Docket No. FAA-2006-24281; Amendment Nos. 26-6, 121-360, 129-51] RIN 2120-AI05 Aging... On November 15, 2010, the FAA published a final rule entitled, ``Aging Airplane Program: Widespread... Airbus to comply with Sec. 26.21. As stated in the preamble of the rule entitled, ``Aging...

  13. Climate change and forest fires synergistically drive widespread melt events of the Greenland Ice Sheet.

    PubMed

    Keegan, Kaitlin M; Albert, Mary R; McConnell, Joseph R; Baker, Ian

    2014-06-03

    In July 2012, over 97% of the Greenland Ice Sheet experienced surface melt, the first widespread melt during the era of satellite remote sensing. Analysis of six Greenland shallow firn cores from the dry snow region confirms that the most recent prior widespread melt occurred in 1889. A firn core from the center of the ice sheet demonstrated that exceptionally warm temperatures combined with black carbon sediments from Northern Hemisphere forest fires reduced albedo below a critical threshold in the dry snow region, and caused the melting events in both 1889 and 2012. We use these data to project the frequency of widespread melt into the year 2100. Since Arctic temperatures and the frequency of forest fires are both expected to rise with climate change, our results suggest that widespread melt events on the Greenland Ice Sheet may begin to occur almost annually by the end of century. These events are likely to alter the surface mass balance of the ice sheet, leaving the surface susceptible to further melting.

  14. Federal policies to promote the widespread utilization of photovoltaic systems. Supplement: Review and critique

    NASA Technical Reports Server (NTRS)

    Smith, J. L.

    1980-01-01

    Review comments of the Congressional report entitled 'Federal Policies to Promote the Widespread Utilization of Photovoltaic Systems' are presented. Responses to the review comments by the Jet Propulsion Laboratory, preparer of the Congressional report, are also presented. The Congressional report discussed various issues related to promoting the deployment of photovoltaic systems through the Federal Photovoltaic Program. Various program strategies and funding levels were examined.

  15. 77 FR 28772 - Air Quality: Widespread Use for Onboard Refueling Vapor Recovery and Stage II Waiver

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-16

    ... determined that onboard refueling vapor recovery (ORVR) technology is in widespread use throughout the motor vehicle fleet for purposes of controlling motor vehicle refueling emissions, and, therefore, by this... West Building, located at 1301 Constitution Ave. NW., Washington, DC. The Public Reading Room is...

  16. Preoperative widespread pain sensitization and chronic pain after hip and knee replacement: a cohort analysis

    PubMed Central

    Wylde, Vikki; Sayers, Adrian; Lenguerrand, Erik; Gooberman-Hill, Rachael; Pyke, Mark; Beswick, Andrew D.; Dieppe, Paul; Blom, Ashley W.

    2015-01-01

    Abstract Chronic pain after joint replacement is common, affecting approximately 10% of patients after total hip replacement (THR) and 20% of patients after total knee replacement (TKR). Heightened generalized sensitivity to nociceptive input could be a risk factor for the development of this pain. The primary aim of this study was to investigate whether preoperative widespread pain sensitivity was associated with chronic pain after joint replacement. Data were analyzed from 254 patients receiving THR and 239 patients receiving TKR. Pain was assessed preoperatively and at 12 months after surgery using the Western Ontario and McMaster Universities Osteoarthritis Pain Scale. Preoperative widespread pain sensitivity was assessed through measurement of pressure pain thresholds (PPTs) at the forearm using an algometer. Statistical analysis was conducted using linear regression and linear mixed models, and adjustments were made for confounding variables. In both the THR and TKR cohort, lower PPTs (heightened widespread pain sensitivity) were significantly associated with higher preoperative pain severity. Lower PPTs were also significantly associated with higher pain severity at 12 months after surgery in the THR cohort. However, PPTs were not associated with the change in pain severity from preoperative to 12 months postoperative in either the TKR or THR cohort. These findings suggest that although preoperative widespread pressure pain sensitivity is associated with pain severity before and after joint replacement, it is not a predictor of the amount of pain relief that patients gain from joint replacement surgery, independent of preoperative pain severity. PMID:25599300

  17. The origin of widespread species in a poor dispersing lineage (diving beetle genus Deronectes)

    PubMed Central

    García-Vázquez, David

    2016-01-01

    In most lineages, most species have restricted geographic ranges, with only few reaching widespread distributions. How these widespread species reached their current ranges is an intriguing biogeographic and evolutionary question, especially in groups known to be poor dispersers. We reconstructed the biogeographic and temporal origin of the widespread species in a lineage with particularly poor dispersal capabilities, the diving beetle genus Deronectes (Dytiscidae). Most of the ca. 60 described species of Deronectes have narrow ranges in the Mediterranean area, with only four species with widespread European distributions. We sequenced four mitochondrial and two nuclear genes of 297 specimens of 109 different populations covering the entire distribution of the four lineages of Deronectes, including widespread species. Using Bayesian probabilities with an a priori evolutionary rate, we performed (1) a global phylogeny/phylogeography to estimate the relationships of the main lineages within each group and root them, and (2) demographic analyses of the best population coalescent model for each species group, including a reconstruction of the geographical history estimated from the distribution of the sampled localities. We also selected 56 specimens to test for the presence of Wolbachia, a maternally transmitted parasite that can alter the patterns of mtDNA variability. All species of the four studied groups originated in the southern Mediterranean peninsulas and were estimated to be of Pleistocene origin. In three of the four widespread species, the central and northern European populations were nested within those in the northern areas of the Anatolian, Balkan and Iberian peninsulas respectively, suggesting a range expansion at the edge of the southern refugia. In the Mediterranean peninsulas the widespread European species were replaced by vicariant taxa of recent origin. The fourth species (D. moestus) was proven to be a composite of unrecognised lineages with

  18. The Occurrence Rate of Hot Jupiters

    NASA Astrophysics Data System (ADS)

    Rampalli, Rayna; Catanzarite, Joseph; Batalha, Natalie M.

    2017-01-01

    As the first kind of exoplanet to be discovered, hot Jupiters have always been objects of interest. Despite being prevalent in radial velocity and ground-based surveys, they were found to be much rarer based on Kepler observations. These data show a pile-up at radii of 9-22 Rearth and orbital periods of 1-10 days. Computing accurate occurrence rates can lend insight into planet-formation and migration-theories. To get a more accurate look, the idea of reliability was introduced. Each hot Jupiter candidate was assigned a reliability based on its location in the galactic plane and likelihood of being a false positive. Numbers were updated if ground-based follow-up indicated a candidate was indeed a false positive. These reliabilities were introduced into an occurrence rate calculation and yielded about a 12% decrease in occurrence rate for each period bin examined and a 25% decrease across all the bins. To get a better idea of the cause behind the pileup, occurrence rates based on parent stellar metallicity were calculated. As expected from previous work, higher metallicity stars yield higher occurrence rates. Future work includes examining period distributions in both the high metallicity and low metallicity sample for a better understanding and confirmation of the pile-up effect.

  19. Widespread structural brain involvement in ALS is not limited to the C9orf72 repeat expansion

    PubMed Central

    Westeneng, Henk-Jan; Walhout, Renée; Straathof, Milou; Schmidt, Ruben; Hendrikse, Jeroen; Veldink, Jan H; van den Heuvel, Martijn P; van den Berg, Leonard H

    2016-01-01

    Background In patients with a C9orf72 repeat expansion (C9+), a neuroimaging phenotype with widespread structural cerebral changes has been found. We aimed to investigate the specificity of this neuroimaging phenotype in patients with amyotrophic lateral sclerosis (ALS). Methods 156 C9− and 14 C9+ patients with ALS underwent high-resolution T1-weighted MRI; a subset (n=126) underwent diffusion-weighted imaging. Cortical thickness, subcortical volumes and white matter integrity were compared between C9+ and C9− patients. Using elastic net logistic regression, a model defining the neuroimaging phenotype of C9+ was determined and applied to C9− patients with ALS. Results C9+ patients showed cortical thinning outside the precentral gyrus, extending to the bilateral pars opercularis, fusiform, lingual, isthmus-cingulate and superior parietal cortex, and smaller volumes of the right hippocampus and bilateral thalamus, and reduced white matter integrity of the inferior and superior longitudinal fasciculus compared with C9− patients (p<0.05). Among 128 C9− patients, we detected a subgroup of 27 (21%) with a neuroimaging phenotype congruent to C9+ patients, while 101 (79%) C9− patients showed cortical thinning restricted to the primary motor cortex. C9− patients with a ‘C9+’ neuroimaging phenotype had lower performance on the frontal assessment battery, compared with other C9− patients with ALS (p=0.004). Conclusions This study shows that widespread structural brain involvement is not limited to C9+ patients, but also presents in a subgroup of C9− patients with ALS and relates to cognitive deficits. Our neuroimaging findings reveal an intermediate phenotype that may provide insight into the complex relationship between genetic factors and clinical characteristics. PMID:27756805

  20. Evidence for widespread effusive volcanism near the Noachian-Hesperian transition in circum-Hellas cratered uplands of Mars

    NASA Astrophysics Data System (ADS)

    Fergason, R. L.; Rogers, D.

    2011-12-01

    that these represent low-viscosity flood lavas that buried their vents, similar to lunar mare. The morphologic similarities between the various occurrences of this unit suggest that they were likely emplaced nearly contemporaneously, which would imply relatively widespread magmatism that post-dates the formation of the primary crust. There is morphologic evidence for enhanced fluvial activity during this time period [Irwin et al., 2005, JGR-Planets]; significant volcanism near this time period (such as that described here) may have provided the climatic conditions needed to enable intense fluvial activity. The distinct compositional difference between these volcanic materials and the olivine-poor materials they overlie raises the question of whether the older crust-forming materials were 1) relatively deficient in olivine at the time of crystallization, or 2) compositionally similar to the younger materials, but altered to remove olivine. Based on observations of crater ejecta that impact into the older materials, we present evidence suggesting that the older materials were indeed less mafic than the younger volcanic units, but also that they have experienced some surficial alteration.

  1. Paleomagnetic and paleoenvironmental implications of magnetofossil occurrences in late Miocene marine sediments from the Guadalquivir Basin, SW Spain

    PubMed Central

    Larrasoaña, Juan C.; Liu, Qingsong; Hu, Pengxiang; Roberts, Andrew P.; Mata, Pilar; Civis, Jorge; Sierro, Francisco J.; Pérez-Asensio, José N.

    2014-01-01

    Although recent studies have revealed more widespread occurrences of magnetofossils in pre-Quaternary sediments than have been previously reported, their significance for paleomagnetic and paleoenvironmental studies is not fully understood. We present a paleo- and rock-magnetic study of late Miocene marine sediments recovered from the Guadalquivir Basin (SW Spain). Well-defined paleomagnetic directions provide a robust magnetostratigraphic chronology for the two studied sediment cores. Rock magnetic results indicate the dominance of intact magnetosome chains throughout the studied sediments. These results provide a link between the highest-quality paleomagnetic directions and higher magnetofossil abundances. We interpret that bacterial magnetite formed in the surface sediment mixed layer and that these magnetic particles gave rise to a paleomagnetic signal in the same way as detrital grains. They, therefore, carry a magnetization that is essentially identical to a post-depositional remanent magnetization, which we term a bio-depositional remanent magnetization. Some studied polarity reversals record paleomagnetic directions with an apparent 60–70 kyr recording delay. Magnetofossils in these cases are interpreted to carry a biogeochemical remanent magnetization that is locked in at greater depth in the sediment column. A sharp decrease in magnetofossil abundance toward the middle of the studied boreholes coincides broadly with a major rise in sediment accumulation rates near the onset of the Messinian salinity crisis (MSC), an event caused by interruption of the connection between the Mediterranean Sea and the Atlantic Ocean. This correlation appears to have resulted from dilution of magnetofossils by enhanced terrigenous inputs that were driven, in turn, by sedimentary changes triggered in the basin at the onset of the MSC. Our results highlight the importance of magnetofossils as carriers of high-quality paleomagnetic and paleoenvironmental signals even in

  2. Occurrence of Coxiella burnetii and Chlamydiales species in abortions of domestic ruminants and in wild ruminants in Hungary, Central Europe.

    PubMed

    Kreizinger, Zsuzsa; Szeredi, Levente; Bacsadi, Árpád; Nemes, Csaba; Sugár, László; Varga, Tamás; Sulyok, Kinga M; Szigeti, Alexandra; Ács, Kornél; Tóbiás, Enikő; Borel, Nicole; Gyuranecz, Miklós

    2015-03-01

    Coxiella burnetii and certain members of the Chlamydiales order are zoonotic, intracellular, Gram-negative bacteria, with abortigenic potential in ruminants. These pathogens have a broad host range and worldwide geographical distribution. The current study aimed to reveal the importance of C. burnetii and Chlamydiales spp. in abortions in domestic ruminants and their occurrence in wild ruminants with real-time polymerase chain reaction (qPCR) assays, histology, and immunohistochemical staining (IHC). From the 111 abortion cases of domestic ruminants examined, C. burnetii was detected in 33 placenta samples (cattle, n = 22; sheep, n = 10; goat, n = 1), and members of the Chlamydiales order were detected in 32 placenta samples (cattle, n = 14; sheep, n = 16; goat, n = 2) using qPCR. Coinfection with both C. burnetii and Chlamydiales spp. were identified in 12 cases (cattle, n = 3; sheep, n = 8; goat, n = 1) out of the qPCR-positive samples. The presence of the relevant antigen was confirmed by IHC in 20 cases (C. burnetii, n = 2, in sheep; Chlamydiaceae, n = 17, in sheep [n = 15] and goat [n = 2]; and both pathogens in 1 sheep). Coxiella burnetii was identified in 2.2% (2/91) of the wild ruminants, but the samples were negative by IHC. Uncultured Chlamydiales spp. were detected in 4.4% (4/91) of the placenta samples by qPCR. In conclusion, Q fever is widespread among domestic ruminants in Hungary, and, in several cases, C. burnetii was implicated as the primary cause of abortions. Waddlia chondrophila, Parachlamydia spp., and uncultured Chlamydiales spp. were present only sporadically in samples from cattle and wild ruminants.

  3. Occurrence of emerging contaminants, priority substances (2008/105/CE) and heavy metals in treated wastewater and groundwater at Depurbaix facility (Barcelona, Spain).

    PubMed

    Teijon, Gloria; Candela, Lucila; Tamoh, Karim; Molina-Díaz, Antonio; Fernández-Alba, A R

    2010-08-01

    The presence of 170 pharmaceuticals, personal care products, priority substances according to the 2008/105EU Directive and four metals (Cd, Ni, Hg, Pb) have been investigated at the Llobregat delta, south of Barcelona (Spain). In the area, reclaimed water is destined to satisfy environmental uses, irrigation and the construction of a hydraulic barrier against seawater intrusion in the deep aquifer of the delta. A monitoring survey was undertaken of water samples from a tertiary wastewater treatment plant (Depurbaix), treated waste water with an additional treatment of ultrafiltration, reverse osmosis, and UV disinfection (WWATP, for the hydraulic barrier injection). Groundwater samples from the aquifer receiving recharge were also investigated. The pharmaceutical group of substances was detected in sampled waters at concentrations rarely exceeding a few microg/L, among the compounds Caffeine, Nicotine and Galaxolide (musk fragrance) were found to be present in more than 60% of the samples. Diuron was the only priority substance detected. The four metals were always present in a variable concentration. After the WWATP treatment the majority of analytes are removed from tertiary treated wastewater or their concentration is reduced below 0.1 microg/L. Monitoring revealed a widespread occurrence of analysed compounds in groundwater. Among them Codeine (analgesic), Ibuprofen (anti-inflammatory), Iopamidol, Iopromide (contrast agent) and Paraxanthine (metabolite of caffeine) have only been detected in groundwater, and are not present in water currently being injected in the deep aquifer.

  4. A Sweet Tasting Demonstration of Random Occurrences.

    ERIC Educational Resources Information Center

    Christopher, Andrew N.; Marek, Pam

    2002-01-01

    Discusses a game in which students must guess the flavor of LifeSaver candy without the aid of sight and smell. Explains that this demonstration assists students to understand the phenomenon of random occurrences. Describes how the presentation is conducted as well as the outcomes of the demonstration. (CMK)

  5. Occurrence of Crohn's disease with Parkinson's disease.

    PubMed

    Fujioka, Shinsuke; Curry, Sadie E; Kennelly, Kathleen D; Tacik, Pawel; Heckman, Michael G; Tsuboi, Yoshio; Strongosky, Audrey J; van Gerpen, Jay A; Uitti, Ryan J; Ross, Owen A; Ikezu, Tsuneya; Wszolek, Zbigniew K

    2017-02-10

    We retrospectively investigated the co-occurrence of Crohn's disease in a cohort of 876 patients with Parkinson's disease, based on the observation that LRRK2 is a shared genetic risk factor. We identified 2 patients with Crohn's disease; this number was consistent with the number of cases expected in the general population.

  6. Tectonic implications of Archean anorthosite occurrences

    NASA Technical Reports Server (NTRS)

    Phinney, W. C.; Morrison, D. A.; Maczuga, D. E.

    1988-01-01

    The occurrences of megacrystic anorthosite and basalt in a variety of geologic settings were reviewed and it was found that these rock types occur in a variety of tectonic settings. Anorthosites and megacrystic basalts are petrogenetically related and are found in oceanic volcanic crust, cratons, and shelf environments. Although megacrystic basalts are most common in Archean terranes, similar occurrences are observed in rocks of early Proterozoic age, and even in young terranes such as the Galapagos hotspot. Based on inferences from experimental petrology, all of the occurrences are apparently associated with similar parental melts that are relatively Fe-rich tholeiites. The megacrystic rocks exhibit a two- (or more)-stage development of plagioclase, with the megacrysts having relatively uniform composition produced under nearly isothermal and isochemical conditions over substantial periods of time. The anorthosites appear to have intruded various crustal levels from very deep to very shallow. The petrogenetic indicators, however, suggest that conditions of formation of the Precambrian examples were different from Phanerozoic occurrences.

  7. OCCURRENCE OF GERMANIUM AND ARSENIC IN METEORITES.

    PubMed

    Papish, J; Hanford, Z M

    1930-03-07

    1. Spectroscopic evidence has been obtained of the occurrence of germanium in certain siderites, siderolites and aerolites. 2. Judging from the number and intensity of spectral lines the germanium in these meteorites is present in traces. 3. Germanium has been extracted from Toluca and Welland siderites. 4. Arsenic has been extracted from Toluca and Welland siderites.

  8. Occurrence of Biotypes in Radopholus citrophilus.

    PubMed

    Kaplan, D T; O'Bannon, J H

    1985-04-01

    Two morphologically and karyotypically identical populations of the citrus burrowing nematode, Radopholus citrophilus, differed in their ability to damage and reproduce in roots of citrus rootstocks previously identified as either resistant or tolerant. These populations are considered to be biotypes, and their occurrence may explain the appearance of spreading decline symptoms in plantings of rootstocks previously considered resistant.

  9. Species occurrence data for the nation

    USGS Publications Warehouse

    ,

    2015-09-28

    BISON's size is unprecedented, including records for most living species found in the U.S. and encompassing the efforts of more than a million professional and citizen scientists. And the vast majority of BISON's species occurrence records are specific locations, not just county or state records.

  10. Technique for Evaluating Multiple Probability Occurrences /TEMPO/

    NASA Technical Reports Server (NTRS)

    Mezzacappa, M. A.

    1970-01-01

    Technique is described for adjustment of engineering response information by broadening the application of statistical subjective stimuli theory. The study is specifically concerned with a mathematical evaluation of the expected probability of relative occurrence which can be identified by comparison rating techniques.

  11. Thermoregulatory behavior is widespread in the embryos of reptiles and birds.

    PubMed

    Li, Teng; Zhao, Bo; Zhou, Yong-Kang; Hu, Rui; Du, Wei-Guo

    2014-03-01

    Recent studies have demonstrated that thermoregulatory behavior occurs not only in posthatching turtles but also in turtles prior to hatching. Does thermoregulatory behavior also occur in the embryos of other reptile and bird species? Our experiments show that such behavior is widespread but not universal in reptile and bird embryos. We recorded repositioning within the egg, in response to thermal gradients, in the embryos of three species of snakes (Xenochrophis piscator, Elaphe bimaculata, and Zaocys dhumnades), two turtles (Chelydra serpentina and Ocadia sinensis), one crocodile (Alligator sinensis), and four birds (Coturnix coturnix, Gallus gallus domesticus, Columba livia domestica, and Anas platyrhynchos domestica). However, we detected no significant thermoregulation by the embryos of two lizard species (Takydromus septentrionalis and Phrynocephalus frontalis). Overall, embryonic thermoregulatory behavior is widespread in reptile as well as bird species but may be unimportant in the small eggs laid by most lizards.

  12. Calvarial malignant melanotic neuroectodermal tumour of infancy presenting with widespread intracranial metastasis.

    PubMed

    Furtado, Sunil V; Ghosal, Nandita; Hegde, Alangar S

    2012-09-01

    The piamater, branchial arch derivatives and melanocytes, derivatives of the neural crest, are associated with rare, sporadic, non-inherited embryonic neuroectodermal dysplasia. We report a case of a 13 year-old girl with a malignant melanotic neuroectodermal tumour of infancy, an uncommon malignant extra-axial pigmented tumour with an aggressive clinical course. The clinical presentation, radiology, surgical management, adjuvant therapy are discussed along with a brief review of literature. The patient had widespread intracranial metastasis at presentation and rapidly deteriorated while on adjuvant therapy. A hyperdense extra-axial tumour on plain computed tomogram in a child could suggest a melanotic neuroectodermal tumour. Its malignant variant is associated with a poor prognosis when associated with widespread intracranial metastasis.

  13. Chronic partial denervation is more widespread than is suspected clinically in paralytic poliomyelitis. Electrophysiological study.

    PubMed

    Cruz Martínez, A; Pérez Conde, M C; Ferrer, M T

    1983-01-01

    Clinical evaluation, quantitative analysis of the EMG, and motor unit fiber density were carried out on 34 selected patients that suffered paralytic poliomyelitis. 50% of the subjects developed a late and slowly progressive weakness. Automatic analysis of the electromyogram showed a great increase in mean amplitude in weak muscles but also in hypertrophic ones, and in other muscles that had normal strength. Increase in mean amplitude and in motor unit fiber density was greater in the weaker muscles. The increased amplitude ad motor unit fiber density found in clinically unaffected muscles confirms that neurogenic atrophy is more widespread than is suspected clinically. Thus, the late deterioration of function developed in some of the patients always takes place in muscles which are previously damaged and partially depleted in motor units. Widespread neurogenic involvement of the muscles can play an important role in the late deterioration of these patients.

  14. Democratizing an electroluminescence imaging apparatus and analytics project for widespread data acquisition in photovoltaic materials

    NASA Astrophysics Data System (ADS)

    Fada, Justin S.; Wheeler, Nicholas R.; Zabiyaka, Davis; Goel, Nikhil; Peshek, Timothy J.; French, Roger H.

    2016-08-01

    We present a description of an electroluminescence (EL) apparatus, easily sourced from commercially available components, with a quantitative image processing platform that demonstrates feasibility for the widespread utility of EL imaging as a characterization tool. We validated our system using a Gage R&R analysis to find a variance contribution by the measurement system of 80.56%, which is typically unacceptable, but through quantitative image processing and development of correction factors a variance contribution by the measurement system of 2.41% was obtained. We further validated the system by quantifying the signal-to-noise ratio (SNR) and found values consistent with other systems published in the literature, at SNR values of 10-100, albeit at exposure times of greater than 1 s compared to 10 ms for other systems. This SNR value range is acceptable for image feature recognition, providing the opportunity for widespread data acquisition and large scale data analytics of photovoltaics.

  15. Democratizing an electroluminescence imaging apparatus and analytics project for widespread data acquisition in photovoltaic materials.

    PubMed

    Fada, Justin S; Wheeler, Nicholas R; Zabiyaka, Davis; Goel, Nikhil; Peshek, Timothy J; French, Roger H

    2016-08-01

    We present a description of an electroluminescence (EL) apparatus, easily sourced from commercially available components, with a quantitative image processing platform that demonstrates feasibility for the widespread utility of EL imaging as a characterization tool. We validated our system using a Gage R&R analysis to find a variance contribution by the measurement system of 80.56%, which is typically unacceptable, but through quantitative image processing and development of correction factors a variance contribution by the measurement system of 2.41% was obtained. We further validated the system by quantifying the signal-to-noise ratio (SNR) and found values consistent with other systems published in the literature, at SNR values of 10-100, albeit at exposure times of greater than 1 s compared to 10 ms for other systems. This SNR value range is acceptable for image feature recognition, providing the opportunity for widespread data acquisition and large scale data analytics of photovoltaics.

  16. Puzzles in modern biology. I. Male sterility, failure reveals design.

    PubMed

    Frank, Steven A

    2016-01-01

    Many human males produce dysfunctional sperm. Various plants frequently abort pollen. Hybrid matings often produce sterile males. Widespread male sterility is puzzling. Natural selection prunes reproductive failure. Puzzling failure implies something that we do not understand about how organisms are designed. Solving the puzzle reveals the hidden processes of design.

  17. Puzzles in modern biology. I. Male sterility, failure reveals design

    PubMed Central

    Frank, Steven A.

    2016-01-01

    Many human males produce dysfunctional sperm. Various plants frequently abort pollen. Hybrid matings often produce sterile males. Widespread male sterility is puzzling. Natural selection prunes reproductive failure. Puzzling failure implies something that we do not understand about how organisms are designed. Solving the puzzle reveals the hidden processes of design. PMID:28004842

  18. Widespread erosive tinea corporis by Arthroderma benhamiae in a renal transplant recipient: case report.

    PubMed

    Budihardja, Debby; Freund, Viviane; Mayser, Peter

    2010-11-01

    Superficial fungal infections are expected to be more prevalent in renal transplant recipients because of graft-preserving immunosuppressive therapy. Here we report the case of a 45-year-old patient with widespread erosive tinea corporis transmitted by domestic animals. Sequencing of the internal transcribed spacer region identified Arthroderma benhamiae (teleomorph of Trichophyton mentagrophytes) in the patient, her husband and her domestic animals. A combination therapy with systemic terbinafine hydrochloride and topically applied ciclopiroxolamine was successful.

  19. THE WIDESPREAD OF Fe(III)-REDUCING BACTERIA IN NATURAL ECOSYSTEMS OF ECUADOR.

    PubMed

    Tashyrev, O B; Govorukha, V M

    2015-01-01

    The widespread of Fe(III)-reducing microorganisms in natural ecosystems of Ecuador of La Favorita, Tungurahua volcano and Papallacta areas was experimentally proved. High efficiency of microbial precipitation of soluble iron compounds was also demonstrated. Obtained results indicate the potential ability of Fe(III)-reducing microorganisms to influence the formation of carbon and iron vector fluxes in ecosystems, as well as development of effective biotechnologies of water purification from iron compounds.

  20. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes

    PubMed Central

    Delrieu-Trottin, Erwan; Mona, Stefano; Maynard, Jeffrey; Neglia, Valentina; Veuille, Michel; Planes, Serge

    2017-01-01

    Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism. PMID:28091580

  1. A comparison of inbreeding depression in tropical and widespread Drosophila species.

    PubMed

    Bechsgaard, Jesper S; Hoffmann, Ary A; Sgró, Carla; Loeschcke, Volker; Bilde, Trine; Kristensen, Torsten N

    2013-01-01

    The evolutionary history of widespread and specialized species is likely to cause a different genetic architecture of key ecological traits in the two species groups. This may affect how these two groups respond to inbreeding. Here we investigate inbreeding effects in traits related to performance in 5 widespread and 5 tropical restricted species of Drosophila with the aim of testing whether the two species groups suffered differently from inbreeding depression. The traits investigated were egg-to-adult viability, developmental time and resistance to heat, cold and desiccation. Our results showed that levels of inbreeding depression were species and trait specific and did not differ between the species groups for stress resistance traits. However, for the life history traits developmental time and egg-to adult viability, more inbreeding depression was observed in the tropical species. The results reported suggest that for life history traits tropical species of Drosophila will suffer more from inbreeding depression than widespread species in case of increases in the rate of inbreeding e.g. due to declines in population sizes.

  2. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes.

    PubMed

    Delrieu-Trottin, Erwan; Mona, Stefano; Maynard, Jeffrey; Neglia, Valentina; Veuille, Michel; Planes, Serge

    2017-01-16

    Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.

  3. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes

    NASA Astrophysics Data System (ADS)

    Delrieu-Trottin, Erwan; Mona, Stefano; Maynard, Jeffrey; Neglia, Valentina; Veuille, Michel; Planes, Serge

    2017-01-01

    Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.

  4. Visualizing the Structure of Medical Informatics Using Term Co-Occurrence Analysis: II. INSPEC Perspective.

    ERIC Educational Resources Information Center

    Morris, Theodore

    2001-01-01

    Term co-occurrence analysis of INSPEC classification codes and thesaurus terms used to index Medical Informatics literature reveals an information science and technology perspective on the field, to accompany the biomedical perspective previously reported. This study continues the search for a better understanding of the structure of Medical…

  5. Deep divergence and structure in the Tropical Oceanic Pacific: a multilocus phylogeography of a widespread gekkonid lizard (Squamata: Gekkonidae: Gehyra oceanica)

    USGS Publications Warehouse

    Tonione, Maria A.; Fisher, Robert N.; Zhu, Catherine; Moritz, Craig

    2016-01-01

    Aim The islands of the Tropical Oceanic Pacific (TOP) host both local radiations and widespread, colonizing species. The few phylogeographical analyses of widespread species often point to recent human-aided expansions through the Pacific, suggesting that the communities are recently assembled. Here we apply multilocus data to infer biogeographical history of the gekkonid lizard, Gehyra oceanica, which is widespread, but for which prior analyses suggested a pre-human history and in situ diversification. Location Tropical Oceanic Pacific. Methods We generated a data set including mtDNA and diagnostic SNPs for 173 individuals of G. oceanica spanning Micronesia, Melanesia, and Polynesia. For a subset of these individuals, we also sequenced nuclear loci. From these data, we performed maximum likelihood and Bayesian inference to reveal major clades. We also performed Bayesian clustering analyses and coalescence–based species delimitation tests to infer the number of species in this area. Results We found evidence for six independent evolutionary lineages (candidate species) within G. oceanica that diverged between the Pliocene and the early Pleistocene, with high diversity through northern Melanesia, and pairing of northern Melanesian endemic taxa with widespread lineages across Micronesia and Polynesia. Main conclusions The islands of northern Melanesia not only have unrecognized diversity, but also were the source of independent expansions of lineages through the more remote northern and eastern Pacific. These results highlight the very different evolutionary histories of island faunas on remote archipelagos versus those across Melanesia and point to the need for more intensive studies of fauna within Melanesia if we are to understand the evolution of diversity across the tropical Pacific.

  6. Sinkhole occurrence in consequence of heavy rainstorms

    NASA Astrophysics Data System (ADS)

    Parise, Mario; Pisano, Luca; Vennari, Carmela

    2016-04-01

    Sinkholes, the most typical geological hazard in karst, are widespread in Apulia (south-eastern Italy), due to the presence in about the whole region of soluble rocks. Sinkholes can cause damage to private property and civil infrastructures such as buildings and roads. Detailed mapping of sinkholes is critical in understanding the hydrological processes, beside being extremely useful to mitigate the related geological risk. Sinkholes typically function as a major connection between the water flowing at the surface and the groundwaters, by collecting rainfall and rapidly draining it within the bedrock. In Apulia, the main risk to the humans is generally linked to anthropogenic sinkholes, with the possibility of collapses related to man-made caves (quarries, mines, civil settlements, etc.; see Parise, 2012, 2015a). Natural sinkholes are less frequent, or appears at least to be less reported, since they generally occur in rural areas, and often are rapidly canceled by landowners. During the first week of September 2014, the Gargano Promontory (northern Apulia) was affected by an intense storm, characterized by rainfall cumulates well above the seasonal mean values. The total amount of measured rainfall for the whole event (covering the period from September 1, to September 6, 2014) reached a peak of over 500 mm (Martinotti et al., 2015). As a response to the storm, and due to peculiarity of the Gargano karst setting, several geo-hazards (different types of slope failures, floods and sinkholes) were recorded over an area of 2300 km2. As regards sinkholes, during the September 2014 storm, at least a dozen of phenomena, mostly of small size, were documented. These are prevailingly concentrated in two areas in the surroundings of the towns of San Marco in Lamis and Monte Sant'Angelo. In particular, at San Marco in Lamis, four sinkholes (the deepest about 6 m-deep and 5 m-wide, showing at the bottom the upper portion of the epikarst, with pinnacles of limestone rocks

  7. Reanalyzing Head et al. (2015): investigating the robustness of widespread p-hacking

    PubMed Central

    2017-01-01

    Head et al. (2015) provided a large collection of p-values that, from their perspective, indicates widespread statistical significance seeking (i.e., p-hacking). This paper inspects this result for robustness. Theoretically, the p-value distribution should be a smooth, decreasing function, but the distribution of reported p-values shows systematically more reported p-values for .01, .02, .03, .04, and .05 than p-values reported to three decimal places, due to apparent tendencies to round p-values to two decimal places. Head et al. (2015) correctly argue that an aggregate p-value distribution could show a bump below .05 when left-skew p-hacking occurs frequently. Moreover, the elimination of p = .045 and p = .05, as done in the original paper, is debatable. Given that eliminating p = .045 is a result of the need for symmetric bins and systematically more p-values are reported to two decimal places than to three decimal places, I did not exclude p = .045 and p = .05. I conducted Fisher’s method .04 < p < .05 and reanalyzed the data by adjusting the bin selection to .03875 < p ≤ .04 versus .04875 < p ≤ .05. Results of the reanalysis indicate that no evidence for left-skew p-hacking remains when we look at the entire range between .04 < p < .05 or when we inspect the second-decimal. Taking into account reporting tendencies when selecting the bins to compare is especially important because this dataset does not allow for the recalculation of the p-values. Moreover, inspecting the bins that include two-decimal reported p-values potentially increases sensitivity if strategic rounding down of p-values as a form of p-hacking is widespread. Given the far-reaching implications of supposed widespread p-hacking throughout the sciences Head et al. (2015), it is important that these findings are robust to data analysis choices if the conclusion is to be considered unequivocal. Although no evidence of widespread left-skew p-hacking is found in this

  8. Reanalyzing Head et al. (2015): investigating the robustness of widespread p-hacking.

    PubMed

    Hartgerink, Chris H J

    2017-01-01

    Head et al. (2015) provided a large collection of p-values that, from their perspective, indicates widespread statistical significance seeking (i.e., p-hacking). This paper inspects this result for robustness. Theoretically, the p-value distribution should be a smooth, decreasing function, but the distribution of reported p-values shows systematically more reported p-values for .01, .02, .03, .04, and .05 than p-values reported to three decimal places, due to apparent tendencies to round p-values to two decimal places. Head et al. (2015) correctly argue that an aggregate p-value distribution could show a bump below .05 when left-skew p-hacking occurs frequently. Moreover, the elimination of p = .045 and p = .05, as done in the original paper, is debatable. Given that eliminating p = .045 is a result of the need for symmetric bins and systematically more p-values are reported to two decimal places than to three decimal places, I did not exclude p = .045 and p = .05. I conducted Fisher's method .04 < p < .05 and reanalyzed the data by adjusting the bin selection to .03875 < p ≤ .04 versus .04875 < p ≤ .05. Results of the reanalysis indicate that no evidence for left-skew p-hacking remains when we look at the entire range between .04 < p < .05 or when we inspect the second-decimal. Taking into account reporting tendencies when selecting the bins to compare is especially important because this dataset does not allow for the recalculation of the p-values. Moreover, inspecting the bins that include two-decimal reported p-values potentially increases sensitivity if strategic rounding down of p-values as a form of p-hacking is widespread. Given the far-reaching implications of supposed widespread p-hacking throughout the sciences Head et al. (2015), it is important that these findings are robust to data analysis choices if the conclusion is to be considered unequivocal. Although no evidence of widespread left-skew p-hacking is found in this

  9. A population-based study of the associations of stroke occurrence with weather parameters in Siberia, Russia (1982-92).

    PubMed

    Feigin, V L; Nikitin, Y P; Bots, M L; Vinogradova, T E; Grobbee, D E

    2000-03-01

    Previous studies have established a seasonal variation in stroke occurrence, but none have assessed the influence of inclement weather conditions on stroke incidence in a general population of Russia. We performed a stroke population-based study in the Oktiabrsky District of Novosibirsk, Siberia, Russia. Included in the analysis were 1929 patients with their first occurrence of ischemic stroke (IS), 215 patients with their first occurrence of intracerebral hemorrhage (ICH) and 64 patients with their first occurrence of subarachnoid hemorrhage (SAH): all patients were aged between 25 and 74 years. The cumulative daily occurrence of total strokes and stroke subtypes was evaluated in relation to aggregated daily mean values of ambient temperature, relative humidity and air pressure by means of Poisson regression analysis to estimate the rate ratio (RR) with corresponding confidence interval (CI) and to identify the weather parameters of most importance. In a multivariate analysis, with adjustment for the effects of season, solar and geomagnetic activity, and age of the patients, low ambient temperature (RR 1.32; 95% CI 1.05-1.66) and mean value of air pressure (RR 0.986; 95% CI 0.972-0.999) were important predictors of IS occurrence, while mild ambient temperature (RR 1.52; 95% CI 1. 04-2.22) was an important predictor of ICH occurrence. No relationship between SAH occurrence and any one of the weather parameters studied was revealed. There was no interaction between any meteorological variables that was statistically significant. Inclement weather conditions are associated with the occurrence of IS and ICH in Siberia, Russia. Among the meteorological parameters studied, low ambient temperature and mean air pressure are the most important predictors of IS occurrence, whereas the occurrence of ICH is associated with mild ambient temperature. There is no association between any one of the weather parameters studied and the occurrence of SAH.

  10. Predicting occurrence of juvenile shark habitat to improve conservation planning.

    PubMed

    Oh, Beverly Z L; Sequeira, Ana M M; Meekan, Mark G; Ruppert, Jonathan L W; Meeuwig, Jessica J

    2016-11-30

    Fishing and habitat degradation have increased the extinction risk of sharks, and conservation strategies recognize that survival of juveniles is critical for the effective management of shark populations. Despite the rapid expansion of marine protected areas (MPAs) globally, the paucity of shark-monitoring data on large scales (100s-1000s km) means that the effectiveness of MPAs in halting shark declines remains unclear. Using data collected by baited remote underwater video systems (BRUVS) in northwestern Australia, we developed generalized linear models to elucidate the ecological drivers of habitat suitability for juvenile sharks. We assessed occurrence patterns at the order and species levels. We included all juvenile sharks sampled and the 3 most abundant species sampled separately (grey reef [Carcharhinus amblyrhynchos], sandbar [Carcharhinus plumbeus], and whitetip reef sharks [Triaenodon obesus]). We predicted the occurrence of juvenile sharks across 490,515 km(2) of coastal waters and quantified the representation of highly suitable habitats within MPAs. Our species-level models had higher accuracy (ĸ ≥ 0.69) and deviance explained (≥48%) than our order-level model (ĸ = 0.36 and deviance explained of 10%). Maps of predicted occurrence revealed different species-specific patterns of highly suitable habitat. These differences likely reflect different physiological or resource requirements between individual species and validate concerns over the utility of conservation targets based on aggregate species groups as opposed to a species-focused approach. Highly suitable habitats were poorly represented in MPAs with the most restrictions on extractive activities. This spatial mismatch possibly indicates a lack of explicit conservation targets and information on species distribution during the planning process. Non-extractive BRUVS provided a useful platform for building the suitability models across large scales to assist conservation planning across

  11. A mu-delta opioid receptor brain atlas reveals neuronal co-occurrence in subcortical networks.

    PubMed

    Erbs, Eric; Faget, Lauren; Scherrer, Gregory; Matifas, Audrey; Filliol, Dominique; Vonesch, Jean-Luc; Koch, Marc; Kessler, Pascal; Hentsch, Didier; Birling, Marie-Christine; Koutsourakis, Manoussos; Vasseur, Laurent; Veinante, Pierre; Kieffer, Brigitte L; Massotte, Dominique

    2015-03-01

    Opioid receptors are G protein-coupled receptors (GPCRs) that modulate brain function at all levels of neural integration, including autonomic, sensory, emotional and cognitive processing. Mu (MOR) and delta (DOR) opioid receptors functionally interact in vivo, but whether interactions occur at circuitry, cellular or molecular levels remains unsolved. To challenge the hypothesis of MOR/DOR heteromerization in the brain, we generated redMOR/greenDOR double knock-in mice and report dual receptor mapping throughout the nervous system. Data are organized as an interactive database offering an opioid receptor atlas with concomitant MOR/DOR visualization at subcellular resolution, accessible online. We also provide co-immunoprecipitation-based evidence for receptor heteromerization in these mice. In the forebrain, MOR and DOR are mainly detected in separate neurons, suggesting system-level interactions in high-order processing. In contrast, neuronal co-localization is detected in subcortical networks essential for survival involved in eating and sexual behaviors or perception and response to aversive stimuli. In addition, potential MOR/DOR intracellular interactions within the nociceptive pathway offer novel therapeutic perspectives.

  12. The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton.

    PubMed

    Lefèvre, Emilie; Roussel, Balbine; Amblard, Christian; Sime-Ngando, Télesphore

    2008-06-11

    Eukaryotic microorganisms have been undersampled in biodiversity studies in freshwater environments. We present an original 18S rDNA survey of freshwater picoeukaryotes sampled during spring/summer 2005, complementing an earlier study conducted in autumn 2004 in Lake Pavin (France). These studies were designed to detect the small unidentified heterotrophic flagellates (HF, 0.6-5 microm) which are considered the main bacterivores in aquatic systems. Alveolates, Fungi and Stramenopiles represented 65% of the total diversity and differed from the dominant groups known from microscopic studies. Fungi and Telonemia taxa were restricted to the oxic zone which displayed two fold more operational taxonomic units (OTUs) than the oxycline. Temporal forcing also appeared as a driving force in the diversification within targeted organisms. Several sequences were not similar to those in databases and were considered as new or unsampled taxa, some of which may be typical of freshwater environments. Two taxa known from marine systems, the genera Telonema and Amoebophrya, were retrieved for the first time in our freshwater study. The analysis of potential trophic strategies displayed among the targeted HF highlighted the dominance of parasites and saprotrophs, and provided indications that these organisms have probably been wrongfully regarded as bacterivores in previous studies. A theoretical exercise based on a new 'parasite/saprotroph-dominated HF hypothesis' demonstrates that the inclusion of parasites and saprotrophs may increase the functional role of the microbial loop as a link for carbon flows in pelagic ecosystems. New interesting perspectives in aquatic microbial ecology are thus opened.

  13. Geological features of the northeastern Canadian Arctic margin revealed from analysis of potential field data

    NASA Astrophysics Data System (ADS)

    Anudu, Goodluck K.; Stephenson, Randell A.; Macdonald, David I. M.; Oakey, Gordon N.

    2016-11-01

    The northeastern Canadian Arctic margin is bordered to the north by Alpha Ridge, a dominantly magmatic complex within the Amerasia Basin of the Arctic Ocean, which forms part of the High Arctic Large Igneous Province (HALIP). The characteristics of the gravity and magnetic anomaly fields change notably along the Arctic margin, with two main segments recognised. Aeromagnetic and gravity data in the transition zone between these contrasting domains of the Canadian Arctic margin are analysed here in detail. Results obtained using a variety of edge enhancement (derivative) methods highlight several magnetic domains and a major offshore sedimentary basin as well as some known and a number of previously unknown tectonic and magmatic elements. A magmatic intrusion distribution map derived from the edge enhanced magnetic anomaly maps reveals that magmatic rocks are much more widespread in the relatively shallow subsurface than implied by surface geological mapping. Magmatic intrusions (mainly dykes) and other geological structures have NW-SE, NE-SW and N-S major trends. Broad gravity and pseudogravity lows across most of the Sverdrup Basin region are due to thick, less dense sedimentary succession and low magnetised crust. Magnetic and pseudogravity highs observed over Alpha Ridge indicate high crustal magnetisation associated with the occurrence of extensive and voluminous crustal magmatic bodies. Absence of these volcanic and intrusive rocks in the imaged sedimentary basin beneath the northeast Canadian Arctic margin region suggests that the basin probably formed after the cessation of HALIP magmatism.

  14. Gain and Loss of Phototrophic Genes Revealed by Comparison of Two Citromicrobium Bacterial Genomes

    PubMed Central

    Zheng, Qiang; Zhang, Rui; Fogg, Paul C. M.; Beatty, J. Thomas; Wang, Yu; Jiao, Nianzhi

    2012-01-01

    Proteobacteria are thought to have diverged from a phototrophic ancestor, according to the scattered distribution of phototrophy throughout the proteobacterial clade, and so the occurrence of numerous closely related phototrophic and chemotrophic microorganisms may be the result of the loss of genes for phototrophy. A widespread form of bacterial phototrophy is based on the photochemical reaction center, encoded by puf and puh operons that typically are in a ‘photosynthesis gene cluster’ (abbreviated as the PGC) with pigment biosynthesis genes. Comparison of two closely related Citromicrobial genomes (98.1% sequence identity of complete 16S rRNA genes), Citromicrobium sp. JL354, which contains two copies of reaction center genes, and Citromicrobium strain JLT1363, which is chemotrophic, revealed evidence for the loss of phototrophic genes. However, evidence of horizontal gene transfer was found in these two bacterial genomes. An incomplete PGC (pufLMC-puhCBA) in strain JL354 was located within an integrating conjugative element, which indicates a potential mechanism for the horizontal transfer of genes for phototrophy. PMID:22558224

  15. Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates.

    PubMed Central

    Anderson, A J; Dawes, E A

    1990-01-01

    Polyhydroxyalkanoates (PHAs), of which polyhydroxybutyrate (PHB) is the most abundant, are bacterial carbon and energy reserve materials of widespread occurrence. They are composed of 3-hydroxyacid monomer units and exist as a small number of cytoplasmic granules per cell. The properties of the C4 homopolymer PHB as a biodegradable thermoplastic first attracted industrial attention more than 20 years ago. Copolymers of C4 (3-hydroxybutyrate [3HB]) and C5 (3-hydroxyvalerate [3HV]) monomer units have modified physical properties; e.g., the plastic is less brittle than PHB, whereas PHAs containing C8 to C12 monomers behave as elastomers. This family of materials is the centre of considerable commercial interest, and 3HB-co-3HV copolymers have been marketed by ICI plc as Biopol. The known polymers exist as 2(1) helices with the fiber repeat decreasing from 0.596 nm for PHB to about 0.45 nm for C8 to C10 polymers. Novel copolymers with a backbone of 3HB and 4HB have been obtained. The native granules contain noncrystalline polymer, and water may possibly act as a plasticizer. Although the biosynthesis and regulation of PHB are generally well understood, the corresponding information for the synthesis of long-side-chain PHAs from alkanes, alcohols, and organic acids is still incomplete. The precise mechanisms of action of the polymerizing and depolymerizing enzymes also remain to be established. The structural genes for the three key enzymes of PHB synthesis from acetyl coenzyme A in Alcaligenes eutrophus have been cloned, sequenced, and expressed in Escherichia coli. Polymer molecular weights appear to be species specific. The factors influencing the commercial choice of organism, substrate, and isolation process are discussed. The physiological functions of PHB as a reserve material and in symbiotic nitrogen fixation and its presence in bacterial plasma membranes and putative role in transformability and calcium signaling are also considered. PMID:2087222

  16. Occurrence, activity and contribution of anammox in some freshwater extreme environments.

    PubMed

    Zhu, Guibing; Xia, Chao; Shanyun, Wang; Zhou, Leiliu; Liu, Lu; Zhao, Siyan

    2015-12-01

    Anaerobic ammonium oxidation (anammox) widely occurs in marine ecosystems, and it plays an important role in the global nitrogen cycle. But in freshwater ecosystems its occurrence, distribution and contribution, especially in extreme environments, are still not well known. In this study, anammox process was investigated in some extreme environments of freshwater ecosystems, such as those with high (above 75°C) and low (below -35°C) temperature, high (pH > 8) and low (pH < 4) pH and eutrophy (the concentration of NH4 (+) -N > 300 mg kg(-1) ). The polymerase chain reaction (PCR) screening results showed that anammox bacteria were widespread in the examined sediments from freshwater extreme environments. Quantitative PCR showed that the abundance of anammox bacteria ranged from 6.94 × 10(4) to 8.05 × 10(6) hydrazine synthase (hzsB) gene copies g(-1) dry soil. (15) N-labelled incubation experiments indicated the occurrence of anammox in all examined sediments and the potential anammox rates ranged from 0.02 to 6.24 nmol N g(-1)  h(-1) , with a contribution of 3.45-58.74% of the total N2 production. In summary, these results demonstrate the occurrence of anammox in these extreme environments, inferring that anammox may harbour a wide ecological niche in the freshwater ecosystems.

  17. Human error and time of occurrence in hazardous material events in mining and manufacturing.

    PubMed

    Ruckart, Perri Zeitz; Burgess, Paula A

    2007-04-11

    Human error has played a role in several large-scale hazardous materials events. To assess how human error and time of occurrence may have contributed to acute chemical releases, data from the Hazardous Substances Emergency Events Surveillance (HSEES) system for 1996-2003 were analyzed. Analyses were restricted to events in mining or manufacturing where human error was a contributing factor. The temporal distribution of releases was also evaluated to determine if the night shift impacted releases due to human error. Human error-related events in mining and manufacturing resulted in almost four times as many events with victims and almost three times as many events with evacuations compared with events in these industries where human error was not a contributing factor (10.3% versus 2.7% and 11.8% versus 4.5%, respectively). Time of occurrence of events attributable to human error in mining and manufacturing showed a widespread distribution for number of events, events with victims and evacuations, and hospitalizations and deaths, without apparent increased occurrence during the night shift. Utilizing human factor engineering in both front-end ergonomic design and retrospective incident investigation provides one potential systematic approach that may help minimize human error in workplace-related acute chemical releases and their resulting injuries.

  18. Analysis of climatic and environmental variables associated with the occurrence of West Nile virus in Morocco.

    PubMed

    Calistri, Paolo; Ippoliti, Carla; Candeloro, Luca; Benjelloun, Abdennasser; El Harrak, Mehdi; Bouchra, Belkadi; Danzetta, Maria Luisa; Di Sabatino, Daria; Conte, Annamaria

    2013-07-01

    West Nile disease (WND) is one of the most widespread mosquito-borne infectious diseases in the World. In Morocco the first WND cases were reported in equines in 1996. After an apparent epidemiological silence, WND re-occurred in 2003 and in 2010, when the disease was reported in equines living in the central and north-western part of the country. Eco-climatic variables are known to influence the mosquito presence and abundance and, therefore, the probability of occurrence of mosquito-borne infections. The remote sensed values of Land Surface Temperature (LST), Normalised Difference Vegetation Index (NDVI) and rainfall registered from 2001 to 2010 were evaluated for a possible association with the occurrence of WND cases in 2003 and in 2010. In the zones where WND cases occurred, NDVI values recorded in 2003 and 2010, from June to November, were significantly higher than those registered during the same months in the rest of the decade. Rainfall data showed higher peaks in 2003 and 2010, when the number of days with extreme rainfall was significantly higher during 1-2 months before the occurrence of WND cases. Temperature does not seem to play an important role in Moroccan epidemiological conditions.

  19. Modified Fusarium mycotoxins unmasked: From occurrence in cereals to animal and human excretion.

    PubMed

    Broekaert, Nathan; Devreese, Mathias; De Baere, Siegrid; De Backer, Patrick; Croubels, Siska

    2015-06-01

    Modified mycotoxins formed by plants, fungi and during some food processing steps may remain undetected by analytical methods, potentially causing underestimation of mycotoxin exposure and risk. Furthermore, due to altered physico-chemical characteristics of modified mycotoxins, these compounds might have different gastro-intestinal absorption compared to the unmodified forms, leading to altered modified mycotoxin plasma concentrations. Additionally, modified mycotoxins can be converted back into their corresponding unmodified forms by in vivo hydrolysis upon oral ingestion. This review aims to describe the current knowledge on the production, occurrence, toxicity and toxicokinetic properties of the modified Fusarium mycotoxins. The need for more occurrence data to correctly assess the risks associated with these modified mycotoxins is clearly indicated, including differences between commodities as well as geographical and climatological influences. Research on toxicity of these modified forms demonstrates the possibility of significant decreases as well as increases in the toxic effects of these compounds compared with those of the unmodified forms. Their toxicokinetics demonstrates that a decreased (increased) polarity of modified mycotoxins might cause enhanced (decreased) oral absorption. The possibility of in vivo hydrolysis, altered toxicity and their wide-spread occurrence makes modified mycotoxins a complex threat for which a risk assessment will require prospective multi-disciplinary efforts.

  20. Factors influencing the occurrence and distribution of neonicotinoid insecticides in surface waters of southern Ontario, Canada.

    PubMed

    Struger, John; Grabuski, Josey; Cagampan, Steve; Sverko, Ed; McGoldrick, Daryl; Marvin, Christopher H

    2017-02-01

    The widespread use of neonicotinoid insecticides and recent increased regulatory scrutiny requires the generation of monitoring data with sufficient scope and resolution to provide decision makers with a better understanding of occurrence and distribution in the environment. This study presents a wide-scale investigation of neonicotinoid insecticides used across the range of agricultural activities from fifteen surface water sites in southern Ontario. Using statistical analysis, the correlation of individual compounds with land use was investigated, and the relationship between neonicotinoid occurrence and hydrologic parameters in calibrated water courses was also assessed. Of the five neonicotinoids studied, imidacloprid, clothianidin and thiamethoxam exhibited detection rates above 90% at over half the sites sampled over a three year period (2012-2014). At two sites in southwestern Ontario, the Canadian Federal freshwater guideline value for imidacloprid (230 ng/L) was exceeded in roughly 75% of the samples collected. For some watersheds, there were correlations between the occurrence of neonicotinoids and precipitation and/or stream discharge. Some watersheds exhibited seasonal maxima in concentrations of neonicotinoids in spring and fall, particularly for those areas where row crop agriculture is predominant; these seasonal patterns were absent in some areas characterized by a broad range of agricultural activities.

  1. Male vulnerability explains the occurrence of sexual cannibalism in a moderately sexually dimorphic wolf spider.

    PubMed

    Fernández-Montraveta, Carmen; González, José Miguel; Cuadrado, Mariano

    2014-06-01

    Sexual cannibalism is a widespread phenomenon among a few animal taxa. Its occurrence is interpreted as female and/or male optimal reproductive decisions or as a non-adaptive side effect of selection for efficiently foraging females. In spite of the amount of research addressed at understanding its evolutionary origins, we lack accurate information about the proximate causes of sexual cannibalism. In a moderately sexually dimorphic wolf spider (Hogna radiata, Araneae, Lycosidae) we assessed the factors mediating the occurrence of sexual cannibalism and its fitness benefits to females. Sexual cannibalism was a rather common outcome of laboratory mating interactions, occurring in more than a quarter percent of courtship interactions involving virgin females. Sexual cannibalism mostly followed mating. Occurrence of sexual cannibalism depended on male vulnerability to female attacks: relatively smaller males were at higher risk of being attacked and older males were less likely to avoid female attacks. Sexual cannibalism had direct and positive effects on female fitness, as sexually cannibalistic females exhibited increased fecundity irrespective of their size, condition and foraging rate. Male consumption was almost complete and represented a relevant food intake to females. We interpret sexual cannibalism as a strategic foraging decision for H. radiata females that adjust their aggressive behaviour towards males so as to limit its potential costs.

  2. Environmental occurrence of arsenic in Colombia: a review.

    PubMed

    Alonso, David L; Latorre, Sergio; Castillo, Elianna; Brandão, Pedro F B

    2014-03-01

    The international literature on the presence of arsenic (As) in Latin America does not disclose the true magnitude of the presence of As in Colombia. In this paper, we summarize the literature on As occurrence in Colombia. The data reveal that As is present in matrices such as soil, sediments and water and in the food chain. Some of the As concentrations exceed the limits specified by national and international regulations. Arsenic higher concentrations are associated with mining regions (e.g., soils, up to 148 mg/kg; sediments, up to 1400 mg/kg) and agricultural areas (e.g., vegetables, up to 5.40 mg/kg; irrigation water, up to 255 μg/L), and underscore the potential human and environmental risks associated with the presence of As in the country. This review highlights the importance of focusing research on understanding the occurrence, origin and distribution of As in Colombia to better understand its environmental and public health impact.

  3. Occurrence of phosphatidyl-D-serine in the rat cerebrum.

    PubMed

    Omori, Taketo; Mihara, Hisaaki; Kurihara, Tatsuo; Esaki, Nobuyoshi

    2009-05-01

    Phosphatidylserine (PS), a relatively abundant component of mammalian cell membranes, plays important roles in biological processes including apoptosis and cell signaling. It is believed that phosphatidyl-L-serine is the only naturally occurring PS. Here, we describe for the first time the occurrence of phosphatidyl-D-serine (D-PS) in rat cerebrum. Quantitative HPLC analysis of the derivatives of serine liberated from PS by hydrolysis revealed that the amount of D-PS was approximately 1% of the total PS in the cerebrum. Enzymatic cleavage of cerebrum PS with phospholipase D and phospholipase C resulted in the release of both isomers of serine and phosphoserine, respectively, providing additional evidence for the existence of D-PS. Free D-serine was incorporated into PS in an in vitro system using a cerebrum extract, and this activity was inhibited by EDTA, suggesting the occurrence of a divalent cation-dependent enzyme that synthesizes D-PS by a base-exchange reaction.

  4. Idaho National Laboratory Quarterly Occurrence Analysis

    SciTech Connect

    Mitchell, Lisbeth Ann

    2015-11-01

    This report is published quarterly by the Idaho National Laboratory (INL) Quality and Performance Management Organization. The Department of Energy (DOE) Occurrence Reporting and Processing System (ORPS), as prescribed in DOE Order 232.2, “Occurrence Reporting and Processing of Operations Information,” requires a quarterly analysis of events, both reportable and not reportable, for the previous 12 months. This report is the analysis of 85 reportable events (18 from the 4th Qtr FY-15 and 67 from the prior three reporting quarters), as well as 25 other issue reports (including events found to be not reportable and Significant Category A and B conditions) identified at INL during the past 12 months (8 from this quarter and 17 from the prior three quarters).

  5. Tidal triggering effect on earthquakes occurrence

    NASA Astrophysics Data System (ADS)

    Contadakis, M. E.; Arabelos, D.; Spatalas, S. D.

    2016-01-01

    In this review we present the investigation for the tidal triggering evidence on the earthquakes at various seismic areas of Greece. The result of our analysis using the HiCum method, indicate that the monthly variation of the frequencies of earthquake occurrence is in accordance with the period of the tidal lunar monthly (Mm) variations. The same happens with the corresponding diurnal and semi-diurnal variations of the frequencies of earthquake occurrence with the diurnal (K1), (O1) and semi-diurnal solar (S2) and semidiurnal lunar (M2) tidal variations. The confidence level of the Tidal-Earthquake frequency period compliance is very sensitive to the seismicity of the area and we call it Tidal - Earthquake frequency compliance parameter. We suggest that this parameter may be used in earthquake risk evaluation.

  6. Genetic differentiation associated with host plants and geography among six widespread species of South American Blepharoneura fruit flies (Tephritidae).

    PubMed

    Ottens, K; Winkler, I S; Lewis, M L; Scheffer, S J; Gomes-Costa, G A; Condon, M A; Forbes, A A

    2017-04-01

    Tropical herbivorous insects are astonishingly diverse, and many are highly host-specific. Much evidence suggests that herbivorous insect diversity is a function of host plant diversity; yet, the diversity of some lineages exceeds the diversity of plants. Although most species of herbivorous fruit flies in the Neotropical genus Blepharoneura are strongly host-specific (they deposit their eggs in a single host plant species and flower sex), some species are collected from multiple hosts or flowers and these may represent examples of lineages that are diversifying via changes in host use. Here, we investigate patterns of diversification within six geographically widespread Blepharoneura species that have been collected and reared from at least two host plant species or host plant parts. We use microsatellites to (1) test for evidence of local genetic differentiation associated with different sympatric hosts (different plant species or flower sexes) and (2) examine geographic patterns of genetic differentiation across multiple South American collection sites. In four of the six fly species, we find evidence of local genetic differences between flies collected from different hosts. All six species show evidence of geographic structure, with consistent differences between flies collected in the Guiana Shield and flies collected in Amazonia. Continent-wide analyses reveal - in all but one instance - that genetically differentiated flies collected in sympatry from different host species or different sex flowers are not one another's closest relatives, indicating that genetic differences often arise in allopatry before, or at least coincident with, the evolution of novel host use.

  7. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

    PubMed

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H; Hugenholtz, Philip

    2016-04-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0-1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms.

  8. Local changes in rates of group A Streptococcus disease and antibiotic resistance are associated with geographically widespread strain turnover events.

    PubMed

    Metzgar, David; McDonough, Erin A; Hansen, Christian J; Blaesing, Carl R; Baynes, Darcie; Hawksworth, Anthony W; Blair, Patrick J; Faix, Dennis J; Russell, Kevin L

    2010-01-01

    This study addresses the effects of dynamic strain turnover and antibiotic prophylaxis on rates of group A Streptococcus (GAS) antibiotic resistance and disease. The authors analyzed the strain distributions, disease rates, and patterns of antibiotic resistance of 802 GAS isolates collected from 2002 through 2007. These samples were collected from patients with GAS infection symptoms at 10 military facilities. Macrolide resistance peaked at 25% during 2004, due to the geographically widespread dominance of a single resistant strain (M75). The resistant strain was not retained regardless of local patterns of macrolide use, and resistance rates decreased upon replacement of M75 with macrolide-susceptible strains. Disease rates were similarly correlated with dominance of specific M types. Statistical analysis revealed temporal correlations between strain distributions at multiple locations. Only the most common strains yielded enough data at multiple sites for statistically significant comparison of temporal fluctuations in dominance, but these (including M44, M3, M18, M118, and M6) all yielded highly significant temporal correlations of 90% or greater on yearly scales. As expected given the complexity and variability of strain distributions on shorter time scales, analysis on a monthly scale yielded lower degrees of positive correlation (31-62%), but in this case all significant correlations were still positive. Shifts in antibiotic resistance profiles and disease rates at specific sites appear to be associated with strain replacements happening on larger scales, independent of antibiotic use at individual sites.

  9. Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype

    PubMed Central

    Langlois, Rebecca; Großkopf, Tobias; Mills, Matthew; Takeda, Shigenobu; LaRoche, Julie

    2015-01-01

    Marine dinitrogen (N2) fixation studies have focused nearly exclusively on cyanobacterial diazotrophs; however γ-proteobacteria are an abundant component of the marine community and have been largely overlooked until recently. Here we present a phylogenetic analysis of all nifH γ-proteobacterial sequences available in public databases and qPCR data of a γ-proteobacterial phylotype, Gamma A (UMB), obtained during several research cruises. Our analysis revealed a complex diversity of diazotrophic γ-proteobacteria. One phylotype in particular, Gamma A, was described in several traditional and quantitative PCR studies. Though several γ-proteobacterial nifH sequences have been described as laboratory contaminants, Gamma A is part of a large cluster of sequences isolated from marine environments and distantly related to the clade of contaminants. Using a TaqMan probe and primer set, Gamma A nifH DNA abundance and expression were analyzed in nearly 1000 samples collected during 15 cruises to the Atlantic and Pacific Oceans. The data showed that Gamma A is an active, cosmopolitan diazotroph found throughout oxygenated, oligotrophic waters reaching maximum abundances of 8 x 104 nifH DNA copies l-1 and 5 x 105 nifH transcript copies l-1. Gamma A nifH transcript abundances were on average 3 fold higher than nifH DNA abundances. The widespread distribution and activity of Gamma A indicate that it has potential to be a globally important N2 fixing organism. PMID:26103055

  10. Keratin subsets in spindle cell sarcomas. Keratins are widespread but synovial sarcoma contains a distinctive keratin polypeptide pattern and desmoplakins.

    PubMed Central

    Miettinen, M.

    1991-01-01

    The presence of individual keratin polypeptides and desmoplakins was immunohistochemically studied in 25 spindle cell sarcomas of different types using acetone-fixed frozen sections. Results revealed that keratins 8 and 18 were present in a high number of tumors: 9 of 9 synovial sarcomas, 5 of 7 leiomyosarcomas, 5 of 5 malignant schwannomas, and 1 of 4 undifferentiated spindle cell sarcomas. In addition to keratins 8 and 18, the glandular component of synovial sarcoma showed prominent reactivity with antibodies to keratins 7 and 19. Also the glandular epithelial cells in synovial sarcoma showed desmoplakin immunoreactivity preferentially in a luminal distribution, but desmoplakin was absent in other spindle cell sarcomas. Furthermore keratin 13 was seen focally in 4 of 9 synovial sarcomas. In contrast, keratins 7, 13, and 19 were practically absent in leiomyosarcomas, malignant schwannomas, and undifferentiated spindle cell sarcomas. The widespread presence of keratins 8 and 18 in various spindle cell sarcomas may reflect aberrant keratin expression in mesenchymal cells, previously described in cultured transformed fibroblasts. The presence of keratins 7 and 19 and desmoplakin is highly associated with morphologically observable epithelial differentiation restricted to synovial sarcoma among spindle cell sarcomas. Images Figure 1 Figure 2 Figure 3 PMID:1704194

  11. Evolution on the move: specialization on widespread resources associated with rapid range expansion in response to climate change.

    PubMed

    Bridle, Jon R; Buckley, James; Bodsworth, Edward J; Thomas, Chris D

    2014-02-07

    Generalist species and phenotypes are expected to perform best under rapid environmental change. In contrast to this view that generalists will inherit the Earth, we find that increased use of a single host plant is associated with the recent climate-driven range expansion of the UK brown argus butterfly. Field assays of female host plant preference across the UK reveal a diversity of adaptations to host plants in long-established parts of the range, whereas butterflies in recently colonized areas are more specialized, consistently preferring to lay eggs on one host plant species that is geographically widespread throughout the region of expansion, despite being locally rare. By common-garden rearing of females' offspring, we also show an increase in dispersal propensity associated with the colonization of new sites. Range expansion is therefore associated with an increase in the spatial scale of adaptation as dispersive specialists selectively spread into new regions. Major restructuring of patterns of local adaptation is likely to occur across many taxa with climate change, as lineages suited to regional colonization rather than local success emerge and expand.

  12. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage

    PubMed Central

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H.; Hugenholtz, Philip

    2016-01-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0–1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms. PMID:26615204

  13. Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments.

    PubMed

    He, Y; Li, M; Perumal, V; Feng, X; Fang, J; Xie, J; Sievert, S M; Wang, F

    2016-04-04

    Members of the archaeal phylum Bathyarchaeota are widespread and abundant in the energy-deficient marine subsurface sediments. However, their life strategies have remained largely elusive. Here, we provide genetic evidence that some lineages of Bathyarchaeota are acetogens, being capable of homoacetogenesis, a metabolism so far restricted to the domain Bacteria. Metabolic reconstruction based on genomic bins assembled from the metagenome of deep-sea subsurface sediments shows that the metabolism of some lineages of Bathyarchaeota is similar to that of bona fide bacterial homoacetogens, by having pathways for acetogenesis and for the fermentative utilization of a variety of organic substrates. Heterologous expression and activity assay of the acetate kinase gene ack from Bathyarchaeota, demonstrate further the capability of these Bathyarchaeota to grow as acetogens. The presence and expression of bathyarchaeotal genes indicative of active acetogenesis was also confirmed in Peru Margin subsurface sediments where Bathyarchaeota are abundant. The analyses reveal that this ubiquitous and abundant subsurface archaeal group has adopted a versatile life strategy to make a living under energy-limiting conditions. These findings further expand the metabolic potential of Archaea and argue for a revision of the role of Archaea in the carbon cycle of marine sediments.

  14. Is It Easy to Be Urban? Convergent Success in Urban Habitats among Lineages of a Widespread Native Ant

    PubMed Central

    Menke, Sean B.; Booth, Warren; Dunn, Robert R.; Schal, Coby; Vargo, Edward L.; Silverman, Jules

    2010-01-01

    The most rapidly expanding habitat globally is the urban habitat, yet the origin and life histories of the populations of native species that inhabit this habitat remain poorly understood. We use DNA barcoding of the COI gene in the widespread native pest ant Tapinoma sessile to test two hypotheses regarding the origin of urban populations and traits associated with their success. First, we determine if urban samples of T. sessile have a single origin from natural populations by looking at patterns of haplotype clustering from across their range. Second, we examine whether polygynous colony structure – a trait associated with invasion success – is correlated with urban environments, by studying the lineage dependence of colony structure. Our phylogenetic analysis of 49 samples identified four well supported geographic clades. Within clades, Kimura-2 parameter pairwise genetic distances revealed <2.3% variation; however, between clade genetic distances were 7.5–10.0%, suggesting the possibility of the presence of cryptic species. Our results indicate that T. sessile has successfully colonized urban environments multiple times. Additionally, polygynous colony structure is a highly plastic trait across habitat, clade, and haplotype. In short, T. sessile has colonized urban habitats repeatedly and appears to do so using life history strategies already present in more natural populations. Whether similar results hold for other species found in urban habitats has scarcely begun to be considered. PMID:20169204

  15. A mid-Permian chert event: widespread deposition of biogenic siliceous sediments in coastal, island arc and oceanic basins

    USGS Publications Warehouse

    Murchey, B.L.; Jones, D.L.

    1992-01-01

    Radiolarian and conodont of Permian siliceous rocks from twenty-three areas in teh the circum-Pacific and Mediterranean regions reveal a widespread Permian Chert Event during the middle Leonardian to Wordian. Radiolarian- and (or) sponge spicule-rich siliceous sediments accumulated beneath high productivity zones in coastal, island arc and oceanic basins. Most of these deposits now crop out in fault-bounded accreted terranes. Biogenic siliceous sediments did not accumulate in terranes lying beneath infertile waters including the marine sequences in terranes of northern and central Alaska. The Permian Chert Event is coeval with major phosphorite deposition along the western margin of Pangea (Phosphoria Formation and related deposits). A well-known analogue for this event is middle Miocene deposition of biogenic siliceous sediments beneath high productivity zones in many parts of the Pacific and concurrent deposition of phosphatic as well as siliceous sediments in basins along the coast of California. Interrelated factors associated with both the Miocene and Permian depositional events include plate reorientations, small sea-level rises and cool polar waters. ?? 1992.

  16. Mine and mineral occurrences of Afghanistan

    USGS Publications Warehouse

    Orris, G.J.; Bliss, J.D.

    2002-01-01

    This inventory of more than 1000 mines and mineral occurrences in Afghanistan was compiled from published literature and the files of project members of the National Industrial Minerals project of the U.S. Geological Survey. The compiled data have been edited for consistency and most duplicates have been deleted. The data cover metals, industrial minerals, coal, and peat. Listings in the table represent several levels of information, including mines, mineral showings, deposits, and pegmatite fields.

  17. Mycotoxins: occurrence, toxicology, and exposure assessment.

    PubMed

    Marin, S; Ramos, A J; Cano-Sancho, G; Sanchis, V

    2013-10-01

    Mycotoxins are abiotic hazards produced by certain fungi that can grow on a variety of crops. Consequently, their prevalence in plant raw materials may be relatively high. The concentration of mycotoxins in finished products is usually lower than in raw materials. In this review, occurrence and toxicology of the main mycotoxins are summarised. Furthermore, methodological approaches for exposure assessment are described. Existing exposure assessments, both through contamination and consumption data and biomarkers of exposure, for the main mycotoxins are also discussed.

  18. Meteotsunami occurrence frequency along the Mediterranean coasts

    NASA Astrophysics Data System (ADS)

    Masina, Marinella; Archetti, Renata; Lamberti, Alberto

    2016-04-01

    A number of research studies describe exceptional destructive meteotsunami events since long time whereas no systematic database is available of moderate events because sea level data were recorded with insufficient resolution. Sea level measurements recently collected with high sampling rate, one per minute or less, by tide gauges positioned along the Mediterranean coasts are examined, aiming to analyze the occurrence of oscillation events in the tsunami frequency range. Sea level data from operating tide stations inside the Mediterranean basin are made publicly available through the Intergovernmental Oceanographic Commission Sea Level Monitoring Facility web site (http://www.ioc-sealevelmonitoring.org/). After the implementation of a rigorous quality check procedure to the raw water level time series, Hilbert transform is applied to two hour high-pass filtered observations to identify tsunami-like oscillation events. Events of seismic origin are identified by consistency between earthquake occurrence and tsunami wave travel time from the earthquake epicenter to the specific tide gauge. Similar analyses are performed to exclude sea waves induced harbor seiches events. A list of probable meteotsunami episodes occurred in the Mediterranean region is so compiled and their occurrence frequency and intensity statistics are evaluated at the different tide gauge sites over the time period of high frequency water level data availability ranging from five to seven years. The effects of atmospheric conditions and seabed topography are discussed. Detection and characterization of meteotsunamis, both of exceptional character and of weak intensity, represent an essential step toward improved assessments of coastal flooding risk along the Mediterranean coasts.

  19. Hierarchical models of animal abundance and occurrence

    USGS Publications Warehouse

    Royle, J. Andrew; Dorazio, R.M.

    2006-01-01

    Much of animal ecology is devoted to studies of abundance and occurrence of species, based on surveys of spatially referenced sample units. These surveys frequently yield sparse counts that are contaminated by imperfect detection, making direct inference about abundance or occurrence based on observational data infeasible. This article describes a flexible hierarchical modeling framework for estimation and inference about animal abundance and occurrence from survey data that are subject to imperfect detection. Within this framework, we specify models of abundance and detectability of animals at the level of the local populations defined by the sample units. Information at the level of the local population is aggregated by specifying models that describe variation in abundance and detection among sites. We describe likelihood-based and Bayesian methods for estimation and inference under the resulting hierarchical model. We provide two examples of the application of hierarchical models to animal survey data, the first based on removal counts of stream fish and the second based on avian quadrat counts. For both examples, we provide a Bayesian analysis of the models using the software WinBUGS.

  20. Occurrence, Distribution and Frequency of Riparian Fire in California

    NASA Astrophysics Data System (ADS)

    Bendix, J.; Commons, M. G.

    2013-12-01

    In recent years, there has been increasing attention to the role of fire as a disturbance agent in riparian ecosystems. That role seems to be quite variable, as fire has been shown to profoundly affect some riparian plant communities and their hydrogeomorphic settings, while in other instances its impact has been described as negligible. Our knowledge thus far is based on scattered field studies in a variety of locations; a systematic evaluation of the actual extent and frequency of riparian fire is lacking. In this paper, we use data from the Monitoring Trends in Burn Severity (MTBS), LANDFIRE and Fire and Resource Assessment Program (FRAP) databases to characterize the occurrence of riparian fire in California. We used the MTBS and LANDFIRE data to identify fires that had burned at varying levels of severity in areas classified as having riparian vegetation, and matched those fires with the FRAP data to obtain additional information regarding each fire (such as date of occurrence). We analyzed 21 years of data (1990-2010). During this period, an average of 1197 ha of riparian vegetation burned per year, approximately 0.12% of the total area mapped as riparian vegetation in the state. This compares to 125750 ha/year of upland vegetation, thus riparian fire accounts for 0.94% of the area burned annually in California. Statewide, the extrapolated return interval for riparian fire is 843 years, compared to 318 years for upland fire. The statewide totals are misleading, however, because there is substantial geographic variance in the occurrence of riparian (as well as upland) fire. Analysis of fire in different ecoregions of the state reveals how dramatic that variance is. In southern California ecoregions, between .82% and 1.35% of the riparian vegetation burns each year, contrasting with the Cascades and Basin and Range ecoregions, where < .05% of the riparian zone burns annually. There is also considerable regional variation in the season of burning. Overall, the

  1. Occurrence of Trichinella spp. in wild animals in northwestern Libya.

    PubMed

    Hosni, M M; Maghrbi, A A El; Ganghish, K S

    2013-01-01

    The present study determined the occurrence of Trichinella spp. in captured and some perished wildlife animals which included 70 hedgehogs, 19 red foxes, 13 common jackals and 8 crested porcupines in northwestern Libya. Muscle samples of these animals were examined by trichinoscopy. Trichinella larvae were detected only in 4 (5.7%) of the hedgehogs (Erinaceus algirus) and 2 (10.5%) of the red foxes (Vulpes vulpes). Larvae were found in the muscles of the diaphragm, abdomen, tongue, forelimb, hindlimb and intercostal muscles. Examination of tissue sections revealed the presence of numerous cysts within the muscle fibers containing one or more coiled or elongated larvae. Inflammatory cell infiltration was observed around the cysts especially at their poles. Results indicated the importance of wild animals as reservoirs of Trichinella larvae and their role in the transmission of the disease to other wild and domestic animals as well as humans.

  2. Citrobocter kasori spinal epidural abscess: a rare occurrence.

    PubMed

    Kumar, Ashok; Jain, Pramod; Singh, Pritish; Divthane, Rupam; Badole, C M

    2013-01-01

    Pyogenic spinal epidural abscess Is an uncommon Infectious occurrence. Clinical prospects of pyogenic spinal epidural abscess are graver if not promptly diagnosed and treated appropriately. A case of spinal epidural abscess has been presented with sinus tract formation at L4-L5 level, of pyogenic aetiology that progressed to paraplegia over the course of the disease. MRI pointed towards an epidural abscess extending from T12 vertebral level to S1 vertebral level. Surgical decompression in the form of laminectomy and evacuation of pus was done and antibiotics were given according to culture and sensitivity. Histopathological analysis revealed the acute suppurative nature of the abscess. Citrobacter kasori was isolated on pus culture. Pyogenic epidural abscess with causative organism being Citrobacter kasori has least been documented.

  3. A new occurrence of telluride minerals in South Carolina.

    USGS Publications Warehouse

    Bell, H.; Larson, R.R.

    1984-01-01

    A study of drill cores from the Haile gold mine, Lancaster County, South Carolina, has revealed grains containing large amounts of Te with various combinations of Pb, Ag and Au in pyrite. These telluride minerals have so far not been identified. The nearby Brewer mine, on the basis of chemical evidence, also contains tellurides. The probable telluride localities in South Carolina are now expanded to three, significantly increasing the few reports of Te minerals from the Au deposits of the southeastern Piedmont, many of which are now considered to be volcanogenic. The occurrence of telluride minerals in gold ore from the Haile-Brewer area may help to explain the divergence in Au/Ag ratios reported in chemical analyses of drill core, ore samples and production records. Te, in addition, may be useful in geochemical exploration programmes in the SE Piedmont, including programmes using heavy mineral concentrates derived from stream alluvium. -R.S.M.

  4. White Matter Disruptions in Schizophrenia Are Spatially Widespread and Topologically Converge on Brain Network Hubs.

    PubMed

    Klauser, Paul; Baker, Simon T; Cropley, Vanessa L; Bousman, Chad; Fornito, Alex; Cocchi, Luca; Fullerton, Janice M; Rasser, Paul; Schall, Ulrich; Henskens, Frans; Michie, Patricia T; Loughland, Carmel; Catts, Stanley V; Mowry, Bryan; Weickert, Thomas W; Shannon Weickert, Cynthia; Carr, Vaughan; Lenroot, Rhoshel; Pantelis, Christos; Zalesky, Andrew

    2016-08-17

    White matter abnormalities associated with schizophrenia have been widely reported, although the consistency of findings across studies is moderate. In this study, neuroimaging was used to investigate white matter pathology and its impact on whole-brain white matter connectivity in one of the largest samples of patients with schizophrenia. Fractional anisotropy (FA) and mean diffusivity (MD) were compared between patients with schizophrenia or schizoaffective disorder (n = 326) and age-matched healthy controls (n = 197). Between-group differences in FA and MD were assessed using voxel-based analysis and permutation testing. Automated whole-brain white matter fiber tracking and the network-based statistic were used to characterize the impact of white matter pathology on the connectome and its rich club. Significant reductions in FA associated with schizophrenia were widespread, encompassing more than 40% (234ml) of cerebral white matter by volume and involving all cerebral lobes. Significant increases in MD were also widespread and distributed similarly. The corpus callosum, cingulum, and thalamic radiations exhibited the most extensive pathology according to effect size. More than 50% of cortico-cortical and cortico-subcortical white matter fiber bundles comprising the connectome were disrupted in schizophrenia. Connections between hub regions comprising the rich club were disproportionately affected. Pathology did not differ between patients with schizophrenia and schizoaffective disorder and was not mediated by medication. In conclusion, although connectivity between cerebral hubs is most extensively disturbed in schizophrenia, white matter pathology is widespread, affecting all cerebral lobes and the cerebellum, leading to disruptions in the majority of the brain's fiber bundles.

  5. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines.

    PubMed

    Whittall, J B; Syring, J; Parks, M; Buenrostro, J; Dick, C; Liston, A; Cronn, R

    2010-03-01

    Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world's rarest pines - Torrey pine (Pinus torreyana) - due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% ( approximately 105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/ approximately 21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants.

  6. Widespread Changes in White Matter Microstructure after a Day of Waking and Sleep Deprivation

    PubMed Central

    Elvsåshagen, Torbjørn; Norbom, Linn B.; Pedersen, Per Ø.; Quraishi, Sophia H.; Bjørnerud, Atle; Malt, Ulrik F.; Groote, Inge R.; Westlye, Lars T.

    2015-01-01

    Background Elucidating the neurobiological effects of sleep and waking remains an important goal of the neurosciences. Recently, animal studies indicated that sleep is important for cell membrane and myelin maintenance in the brain and that these structures are particularly susceptible to insufficient sleep. Here, we tested the hypothesis that a day of waking and sleep deprivation would be associated with changes in diffusion tensor imaging (DTI) indices of white matter microstructure sensitive to axonal membrane and myelin alterations. Methods Twenty-one healthy adult males underwent DTI in the morning [7:30AM; time point (TP)1], after 14 hours of waking (TP2), and then after another 9 hours of waking (TP3). Whole brain voxel-wise analysis was performed with tract based spatial statistics. Results A day of waking was associated with widespread increases in white matter fractional anisotropy, which were mainly driven by radial diffusivity reductions, and sleep deprivation was associated with widespread fractional anisotropy decreases, which were mainly explained by reductions in axial diffusivity. In addition, larger decreases in axial diffusivity after sleep deprivation were associated with greater sleepiness. All DTI changes remained significant after adjusting for hydration measures. Conclusions This is the first DTI study of sleep deprivation in humans. Although previous studies have observed localized changes in DTI indices of cerebral microstructure over the course of a few hours, further studies are needed to confirm widespread DTI changes within hours of waking and to clarify whether such changes in white matter microstructure serve as neurobiological substrates of sleepiness. PMID:26020651

  7. Species limits and phylogeography of Newportia (Scolopendromorpha) and implications for widespread morphospecies

    PubMed Central

    Edgecombe, Gregory D.; Vahtera, Varpu; Giribet, Gonzalo; Kaunisto, Pipsa

    2015-01-01

    Abstract The genus Newportia Gervais, 1847, includes some 60 nominal species distributed in the Caribbean islands and from Mexico to central South America. Modern keys to species and subspecies are available, greatly facilitating identification, but some species are based on few specimens and have incomplete documentation of taxonomically-informative characters. In order to explore genetic variability and evolutionary relationships within geographically-widespread morphospecies, specimens of Newportia (Newportia) stolli (Pocock, 1896) and Newportia (Newportia) divergens Chamberlin, 1922, two nominal species distinguished principally by differences in suture patterns on T1, were sequenced for mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI) genes from populations in southern Mexico, Guatemala, Honduras and Brazil. Newportia (Newportia) stolli is paraphyletic with respect to Newportia (Newportia) divergens within a clade from Guatemala, Honduras, and Chiapas (Mexico), most trees being consistent with a single loss of a connection between the anterior transverse suture on T1, whereas specimens of “Newportia (Newportia) stolli” from Brazil are not closely allied to those from the Mesomerican type area. The widespread morphospecies Newportia (Newportia) monticola Pocock, 1890, was sequenced for the same loci from populations in Costa Rica, Colombia and Brazil, finding that specimens from these areas do not unite as a monophyletic group. Samples of Newportia (Newportia) oreina Chamberlin, 1915, from different regions of Mexico form geographic clusters that resolve as each other’s closest relatives. These results suggest that some widespread species of Newportia may be taxa of convenience more so than natural groupings. In several cases geographic proximity fits the phylogeny better than taxonomy, suggesting that non-monophyletic species do not result from use of inappropriate molecular markers. Molecular identification is possible for specimens

  8. Species limits and phylogeography of Newportia (Scolopendromorpha) and implications for widespread morphospecies.

    PubMed

    Edgecombe, Gregory D; Vahtera, Varpu; Giribet, Gonzalo; Kaunisto, Pipsa

    2015-01-01

    The genus Newportia Gervais, 1847, includes some 60 nominal species distributed in the Caribbean islands and from Mexico to central South America. Modern keys to species and subspecies are available, greatly facilitating identification, but some species are based on few specimens and have incomplete documentation of taxonomically-informative characters. In order to explore genetic variability and evolutionary relationships within geographically-widespread morphospecies, specimens of Newportia (Newportia) stolli (Pocock, 1896) and Newportia (Newportia) divergens Chamberlin, 1922, two nominal species distinguished principally by differences in suture patterns on T1, were sequenced for mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI) genes from populations in southern Mexico, Guatemala, Honduras and Brazil. Newportia (Newportia) stolli is paraphyletic with respect to Newportia (Newportia) divergens within a clade from Guatemala, Honduras, and Chiapas (Mexico), most trees being consistent with a single loss of a connection between the anterior transverse suture on T1, whereas specimens of "Newportia (Newportia) stolli" from Brazil are not closely allied to those from the Mesomerican type area. The widespread morphospecies Newportia (Newportia) monticola Pocock, 1890, was sequenced for the same loci from populations in Costa Rica, Colombia and Brazil, finding that specimens from these areas do not unite as a monophyletic group. Samples of Newportia (Newportia) oreina Chamberlin, 1915, from different regions of Mexico form geographic clusters that resolve as each other's closest relatives. These results suggest that some widespread species of Newportia may be taxa of convenience more so than natural groupings. In several cases geographic proximity fits the phylogeny better than taxonomy, suggesting that non-monophyletic species do not result from use of inappropriate molecular markers. Molecular identification is possible for specimens missing

  9. Evidence of Small-Fiber Polyneuropathy in Unexplained, Juvenile-Onset, Widespread Pain Syndromes

    PubMed Central

    Klein, Max M.

    2013-01-01

    OBJECTIVE: We tested the hypothesis that acquired small-fiber polyneuropathy (SFPN), previously uncharacterized in children, contributes to unexplained pediatric widespread pain syndromes. METHODS: Forty-one consecutive patients evaluated for unexplained widespread pain beginning before age 21 had medical records comprehensively analyzed regarding objective diagnostic testing for SFPN (neurodiagnostic skin biopsy, nerve biopsy, and autonomic function testing), plus histories, symptoms, signs, other tests, and treatments. Healthy, demographically matched volunteers provided normal controls for SFPN tests. RESULTS: Age at illness onset averaged 12.3 ± 5.7 years; 73% among this poly-ethnic sample were female (P = .001). Sixty-eight percent were chronically disabled, and 68% had hospitalizations. Objective testing diagnosed definite SFPN in 59%, probable SFPN in 17%, and possible SFPN in 22%. Only 1 of 41 had entirely normal SFPN test results. Ninety-eight percent of patients had other somatic complaints consistent with SFPN dysautonomia (90% cardiovascular, 82% gastrointestinal, and 34% urologic), 83% reported chronic fatigue, and 63% had chronic headache. Neurologic examinations identified reduced sensation in 68% and vasomotor abnormalities in 55%, including 23% with erythromelalgia. Exhaustive investigations for SFPN causality identified only history of autoimmune illnesses in 33% and serologic markers of disordered immunity in 89%. Treatment with corticosteroids and/or intravenous immune globulin objectively and subjectively benefited 80% of patients (12/15). CONCLUSIONS: More than half among a large series of patients with childhood-onset, unexplained chronic widespread pain met rigorous, multitest, diagnostic criteria for SFPN, which extends the age range of acquired SFPN into early childhood. Some cases appeared immune-mediated and improved with immunomodulatory therapies. PMID:23478869

  10. Drought characteristics drive patterns in widespread aspen forest mortality across the western United States

    NASA Astrophysics Data System (ADS)

    Anderegg, W.; Anderegg, L.; Abatzoglou, J. T.; Berry, J. A.

    2011-12-01

    Widespread drought-induced forest mortality has been documented across the globe in the last few decades and influences land-atmosphere interactions, biodiversity, carbon sequestration, and biophysical and biogeochemical feedbacks to climate change. These rapid mortality events are currently not well-captured in current vegetation models, limiting the ability to predict them. While many studies have focused on the plant physiological mechanisms that mediate vegetation mortality, the characteristics of drought seasonality, sequence, severity and duration that drive mortality events have received much less attention. These characteristics are particularly relevant in light of changing precipitation regimes, changes to snowpack and snowmelt, and increasing temperature stress associated with climate change. We examine the characteristics of drought associated with the recent widespread mortality of trembling aspen (Populus tremuloides) across much of the western United States. We combine a regional model of watershed-level aspen mortality with in situ tissue isotopic analysis of water source to analyze the roles of drought seasonality, severity, and duration in this mortality event, including raw climate variables, derived drought indices, and variables generated by a climate envelope approach. We found that variables pertaining to spring temperatures and spring-summer water deficit, especially during the peak severity of drought, best capture regional mortality patterns, though multi-year drought variables did improve the model. Field water isotopic analysis of aspen water source over a growing season and during moderate seasonal water stress corroborate the regional model by indicating that aspen clones generally utilize surface water with little plasticity during drought stress. These results suggest that drought characteristics can play an important role in mediating widespread forest mortality and have implications for the future vulnerability of trembling aspen

  11. Widespread Use of TATA Elements in the Core Promoters for RNA Polymerases III, II, and I in Fission Yeast

    PubMed Central

    Hamada, Mitsuhiro; Huang, Ying; Lowe, Todd M.; Maraia, Richard J.

    2001-01-01

    In addition to directing transcription initiation, core promoters integrate input from distal regulatory elements. Except for rare exceptions, it has been generally found that eukaryotic tRNA and rRNA genes do not contain TATA promoter elements and instead use protein-protein interactions to bring the TATA-binding protein (TBP), to the core promoter. Genomewide analysis revealed TATA elements in the core promoters of tRNA and 5S rRNA (Pol III), U1 to U5 snRNA (Pol II), and 37S rRNA (Pol I) genes in Schizosaccharomyces pombe. Using tRNA-dependent suppression and other in vivo assays, as well as in vitro transcription, we demonstrated an obligatory requirement for upstream TATA elements for tRNA and 5S rRNA expression in S. pombe. The Pol III initiation factor Brf is found in complexes with TFIIIC and Pol III in S. pombe, while TBP is not, consistent with independent recruitment of TBP by TATA. Template commitment assays are consistent with this and confirm that the mechanisms of transcription complex assembly and initiation by Pol III in S. pombe differ substantially from those in other model organisms. The results were extended to large-rRNA synthesis, as mutation of the TATA element in the Pol I promoter also abolishes rRNA expression in fission yeast. A survey of other organisms' genomes reveals that a substantial number of eukaryotes may use widespread TATAs for transcription. These results indicate the presence of TATA-unified transcription systems in contemporary eukaryotes and provide insight into the residual need for TBP by all three Pols in other eukaryotes despite a lack of TATA elements in their promoters. PMID:11564871

  12. Periodic and aperiodic traveling pulses in population dynamics: An example from the occurrence of epidemic infections

    NASA Astrophysics Data System (ADS)

    Vecchio, A.; Primavera, L.; Carbone, V.

    2006-03-01

    The dynamics of the occurrence of the dengue hemorrhagic fever in the 72 provinces of Thailand is investigated by performing a proper orthogonal decomposition (POD) on spatiotemporal data. Using this technique, we are able to identify and select the contribution of different modes, selected according to the energy content, to the evolution of the epidemic during 14 years. We found that the phenomenon is characterized by periodic cycles of yearly occurrence characterized by spatial scales of about 420 km. Superimposed on this basic mode, POD analysis is able to reveal the presence of high-energetic aperiodic traveling pulses of the epidemic, which extend spatially for about 510 km from Bangkok.

  13. Occurrence of diopside and Cr-Zr-armalcolite on the moon.

    NASA Technical Reports Server (NTRS)

    Steele, I. M.; Smith, J. V.

    1972-01-01

    Petrographic and electron-microprobe examination of the sample of 1 to 2 mm fines, Apollo 14166,6, has revealed a fragment with the unique lunar mineralogy of plagioclase, olivine, diopside, a Ti-Fe-Zr phase, and a trace of ilminite. The second occurrence of diopside is reported together with the third occurrence of a recently identified Ti-Fe-Zr phase. Microprobe analyses of the principal phases of the fragment studied are presented in a table. The relatively pure diopside analyses reported represent the most Mg-rich calcic pyroxene found in lunar material.

  14. Satellite-based multi-spectral detection of the Widespread and Persistent Winter Fog over the Indo-Gangetic Plains

    NASA Astrophysics Data System (ADS)

    Gautam, R.; Rizvi, S.

    2015-12-01

    The Indo-Gangetic Plains (IGP), in the northern parts of south Asia, are subjected to dense haze/fog during winter months, on an annual basis. The thick fog prevalent during December/January months is both persistent and widespread in nature, often covering the entire IGP which stretches over 1500km in length. This study used multi-spectral imagery from MODIS data, to develop algorithms for daytime as well as nighttime detection of fog during winter 2000 to 2014 over the IGP. Specifically, our nighttime detection algorithm employs a bispectral thresholding technique, involving brightness temperature difference (BTD) between two spectral channels- 3.9 and 11.02μm. The theoretical basis for the detection using the 3.9 μm and 11.02 μm channels rely on the particular emissive properties of the two channels for fog droplets (Bendix and Bachmann, 1991). The small droplets found in fog are less emissive at 3.9 μm than at 11.02 μm. Brightness temperatures computed from corresponding radiance data (MODIS Level-1B) of band 22 (3.9 μm) and band 31 (11.02 μm), in conjunction with theoretical calculations from a radiative transfer (RT) model, were utilized to evaluate threshold value of BTD. Using theoretical RT calculations and automated analysis of hundreds of moderately high resolution satellite imagery (pixel resolution of 1km), our threshold cutoff for foggy pixels results in BTD value of 4 (deg) K. Additionally, to minimize contamination, we apply a spatial variability filter to discriminate the uniform texture of fog from other low-level clouds. A similar methodology based on BTD is also tested for daytime fog detection and separation from other cloud types. Furthermore, on the basis of operational multispectral retrievals of cloud properties (cloud effective radius, cloud top pressure, and cloud fraction) from MODIS, we have also processed spatial occurrences of fog climatology from 2000 to 2014. To validate our satellite retrieval algorithm of fog detection from

  15. Testing Chemical Safety: What Is Needed to Ensure the Widespread Application of Non-animal Approaches?

    PubMed

    Burden, Natalie; Sewell, Fiona; Chapman, Kathryn

    2015-05-01

    Scientists face growing pressure to move away from using traditional animal toxicity tests to determine whether manufactured chemicals are safe. Numerous ethical, scientific, business, and legislative incentives will help to drive this shift. However, a number of hurdles must be overcome in the coming years before non-animal methods are adopted into widespread practice, particularly from regulatory, scientific, and global perspectives. Several initiatives are nevertheless underway that promise to increase the confidence in newer alternative methods, which will support the move towards a future in which less data from animal tests is required in the assessment of chemical safety.

  16. City of Camden, New Jersey Program offering widespread energy recovery (power): Final report

    SciTech Connect

    Witkowski, Stanley

    2013-12-31

    The Camden Residential POWER Program, Program Offering Widespread Energy Recovery, is a program designed to benefit Camden homeowners, stabilize neighborhoods and put local contractors to work. Camden POWER granted up to $18,600 to fund energy efficient home improvements and necessary life/safety rehabilitation repairs. The program was designed as a self-sustaining, neighborhood approach to bringing long-term energy and financial savings to the community. Valuable home upgrades were completed, including high-efficiency furnaces, hot water heaters, insulation, insulated roofs and blower door guided air-sealing. The goal of all improvements were to reduce energy consumption, lower utility bills, improve property values and promote neighborhood stabilization.

  17. Testing Chemical Safety: What Is Needed to Ensure the Widespread Application of Non-animal Approaches?

    PubMed Central

    Burden, Natalie; Sewell, Fiona; Chapman, Kathryn

    2015-01-01

    Scientists face growing pressure to move away from using traditional animal toxicity tests to determine whether manufactured chemicals are safe. Numerous ethical, scientific, business, and legislative incentives will help to drive this shift. However, a number of hurdles must be overcome in the coming years before non-animal methods are adopted into widespread practice, particularly from regulatory, scientific, and global perspectives. Several initiatives are nevertheless underway that promise to increase the confidence in newer alternative methods, which will support the move towards a future in which less data from animal tests is required in the assessment of chemical safety. PMID:26018957

  18. Widespread Rift Valley Fever Emergence in Senegal in 2013–2014

    PubMed Central

    Sow, Abdourahmane; Faye, Ousmane; Ba, Yamar; Diallo, Diawo; Fall, Gamou; Faye, Oumar; Bob, Ndeye Sakha; Loucoubar, Cheikh; Richard, Vincent; Dia, Anta Tal; Diallo, Mawlouth; Malvy, Denis; Sall, Amadou Alpha

    2016-01-01

    Rift Valley fever (RVF), which caused epizootics and epidemics among human and livestock populations, occurred in Senegal in 2013–2014. A multidisciplinary field investigation was carried out in 3 regions of Senegal. We found 11 confirmed human cases of Rift Valley fever, including severe cases with encephalitis and retinitis, 1 pool of mosquito (Aedes ochraceus), and 52 animals tested positive for the disease. Symptoms such as encephalitis and macular retinitis were the most severe cases reported so far in Senegal. The outbreak was widespread due to animals' movements, leading to the largest RVF outbreak in Senegal in terms of geographic spreading and reaching areas that never reported RVF activity previously. PMID:27704007

  19. 1918 pandemic influenza virus and Streptococcus pneumoniae co-infection results in activation of coagulation and widespread pulmonary thrombosis in mice and humans.

    PubMed

    Walters, Kathie-Anne; D'Agnillo, Felice; Sheng, Zong-Mei; Kindrachuk, Jason; Schwartzman, Louis M; Kuestner, Rolf E; Chertow, Daniel S; Golding, Basil T; Taubenberger, Jeffery K; Kash, John C

    2016-01-01

    To study bacterial co-infection following 1918 H1N1 influenza virus infection, mice were inoculated with the 1918 influenza virus, followed by Streptococcus pneumoniae (SP) 72 h later. Co-infected mice exhibited markedly more severe disease, shortened survival time and more severe lung pathology, including widespread thrombi. Transcriptional profiling revealed activation of coagulation only in co-infected mice, consistent with the extensive thrombogenesis observed. Immunohistochemistry showed extensive expression of tissue factor (F3) and prominent deposition of neutrophil elastase on endothelial and epithelial cells in co-infected mice. Lung sections of SP-positive 1918 autopsy cases showed extensive thrombi and prominent staining for F3 in alveolar macrophages, monocytes, neutrophils, endothelial and epithelial cells, in contrast to co-infection-positive 2009 pandemic H1N1 autopsy cases. This study reveals that a distinctive feature of 1918 influenza virus and SP co-infection in mice and humans is extensive expression of tissue factor and activation of the extrinsic coagulation pathway leading to widespread pulmonary thrombosis.

  20. The widespread role of non-enzymatic reactions in cellular metabolism

    PubMed Central

    Keller, Markus A; Piedrafita, Gabriel; Ralser, Markus

    2015-01-01

    Enzymes shape cellular metabolism, are regulated, fast, and for most cases specific. Enzymes do not however prevent the parallel occurrence of non-enzymatic reactions. Non-enzymatic reactions were important for the evolution of metabolic pathways, but are retained as part of the modern metabolic network. They divide into unspecific chemical reactivity and specific reactions that occur either exclusively non-enzymatically as part of the metabolic network, or in parallel to existing enzyme functions. Non-enzymatic reactions resemble catalytic mechanisms as found in all major enzyme classes and occur spontaneously, small molecule (e.g. metal-) catalyzed or light-induced. The frequent occurrence of non-enzymatic reactions impacts on stability and metabolic network structure, and has thus to be considered in the context of metabolic disease, network modeling, biotechnology and drug design. PMID:25617827

  1. The widespread role of non-enzymatic reactions in cellular metabolism.

    PubMed

    Keller, Markus A; Piedrafita, Gabriel; Ralser, Markus

    2015-08-01

    Enzymes shape cellular metabolism, are regulated, fast, and for most cases specific. Enzymes do not however prevent the parallel occurrence of non-enzymatic reactions. Non-enzymatic reactions were important for the evolution of metabolic pathways, but are retained as part of the modern metabolic network. They divide into unspecific chemical reactivity and specific reactions that occur either exclusively non-enzymatically as part of the metabolic network, or in parallel to existing enzyme functions. Non-enzymatic reactions resemble catalytic mechanisms as found in all major enzyme classes and occur spontaneously, small molecule (e.g. metal-) catalyzed or light-induced. The frequent occurrence of non-enzymatic reactions impacts on stability and metabolic network structure, and has thus to be considered in the context of metabolic disease, network modeling, biotechnology and drug design.

  2. Genetically depauperate but widespread: the case of an emblematic Mediterranean pine.

    PubMed

    Vendramin, Giovanni G; Fady, Bruno; González-Martínez, Santiago C; Hu, Feng Sheng; Scotti, Ivan; Sebastiani, Federico; Soto, Alvaro; Petit, Rémy J

    2008-03-01

    Genetic variation is generally considered a prerequisite for adaptation to new environmental conditions. Thus the discovery of genetically depauperate but geographically widespread species is unexpected. We used 12 paternally inherited chloroplast microsatellites to estimate population genetic variation across the full range of an emblematic circum-Mediterranean conifer, stone pine (Pinus pinea L.). The same chloroplast DNA haplotype is fixed in nearly all of the 34 investigated populations. Such a low level of variation is consistent with a previous report of very low levels of diversity at nuclear loci in this species. Stone pine appears to have passed through a severe and prolonged demographic bottleneck, followed by subsequent natural- and human-mediated dispersal across the Mediterranean Basin. No other abundant and widespread plant species has as little genetic diversity as P. pinea at both chloroplast and nuclear markers. However, the species harbors a nonnegligible amount of variation at adaptive traits. Thus a causal relationship between genetic diversity, as measured by marker loci, and the evolutionary precariousness of a species, cannot be taken for granted.

  3. Natural variation of fecundity components in a widespread plant with dimorphic seeds

    NASA Astrophysics Data System (ADS)

    Braza, Rita; Arroyo, J.; García, M. B.

    2010-09-01

    The number and size of seeds are the basis of the quantity and quality components of female reproductive fitness in plants, playing a central role in the evolutionary ecology of life history diversification. In this study we show and analyze the natural variability of several fecundity variables (fruit set, seed production per fruit, seed size, total seed production per plant, and proportion of small seeds) in Plantago coronopus, a widespread, short-lived herb with dimorphic seeds. The structure of such variability was examined at the individual, population (eight locations with different environments within the same region), and life history levels (annual vs perennial), and correlated to soil fertility. There was no divergence associated to the life history for any of the variables studied. Total seed production (the quantity component of female fitness) was correlated with maternal resources, while the size of the large mucilaginous, basal seeds, and the proportion of the small apical seeds (quality component) were more associated to environmental resources. Thus, internal and external resources shape different fitness components, maximizing seed production, and fitting the size and proportion of different kind of seeds to local conditions irrespective of life history. P. coronopus illustrates the versatility of short-lived widespread plants to combine fecundity traits in a flexible manner, in order to increase fitness at each of the many possible habitats they occupy over heterogeneous environments.

  4. Widespread white matter and conduction defects in PSEN1-related spastic paraparesis.

    PubMed

    Soosman, Steffan K; Joseph-Mathurin, Nelly; Braskie, Meredith N; Bordelon, Yvette M; Wharton, David; Casado, Maria; Coppola, Giovanni; McCallum, Holly; Nuwer, Marc; Coutin-Churchman, Pedro; Apostolova, Liana G; Benzinger, Tammie; Ringman, John M

    2016-11-01

    The mechanisms underlying presenilin 1 (PSEN1) mutation-associated spastic paraparesis (SP) are not clear. We compared diffusion and volumetric magnetic resonance measures between 3 persons with SP associated with the A431E mutation and 7 symptomatic persons with PSEN1 mutations without SP matched for symptom duration. We performed amyloid imaging and central motor and somatosensory conduction studies in 1 subject with SP. We found decreases in fractional anisotropy and increases in mean diffusivity in widespread white-matter areas including the corpus callosum, occipital, parietal, and frontal lobes in PSEN1 mutation carriers with SP. Volumetric measures were not different, and amyloid imaging showed low signal in sensorimotor cortex and other areas in a single subject with SP. Electrophysiological studies demonstrated both slowed motor and sensory conduction in the lower extremities in this same subject. Our results suggest that SP in carriers of the A431E PSEN1 mutation is a manifestation of widespread white-matter abnormalities not confined to the corticospinal tract that is at most indirectly related to the mutation's effect on amyloid precursor protein processing and amyloid deposition.

  5. Sex in troubled waters: Widespread agricultural contaminant disrupts reproductive behaviour in fish.

    PubMed

    Bertram, Michael G; Saaristo, Minna; Baumgartner, John B; Johnstone, Christopher P; Allinson, Mayumi; Allinson, Graeme; Wong, Bob B M

    2015-04-01

    Chemical pollution is a pervasive and insidious agent of environmental change. One class of chemical pollutant threatening ecosystems globally is the endocrine disrupting chemicals (EDCs). The capacity of EDCs to disrupt development and reproduction is well established, but their effects on behaviour have received far less attention. Here, we investigate the impact of a widespread androgenic EDC on reproductive behaviour in the guppy, Poecilia reticulata. We found that short-term exposure of male guppies to an environmentally relevant concentration of 17β-trenbolone-a common environmental pollutant associated with livestock production-influenced the amount of male courtship and forced copulatory behaviour (sneaking) performed toward females, as well as the receptivity of females toward exposed males. Exposure to 17β-trenbolone was also associated with greater male mass. However, no effect of female exposure to 17β-trenbolone was detected on female reproductive behaviour, indicating sex-specific vulnerability at this dosage. Our study is the first to show altered male reproductive behaviour following exposure to an environmentally realistic concentration of 17β-trenbolone, demonstrating the possibility of widespread disruption of mating systems of aquatic organisms by common agricultural contaminants.

  6. Diversification and phylogeographic structure in widespread Azteca plant-ants from the northern Neotropics.

    PubMed

    Pringle, Elizabeth G; Ramírez, Santiago R; Bonebrake, Timothy C; Gordon, Deborah M; Dirzo, Rodolfo

    2012-07-01

    The Neotropical myrmecophytic tree Cordia alliodora hosts symbiotic Azteca ants in most of its widespread range. The taxonomy of the genus Azteca is notoriously difficult, which has frequently obscured species identity in ecological studies. We used sequence data from one mitochondrial and four nuclear loci to infer phylogenetic relationships, patterns of geographic distribution, and timing of diversification for 182 colonies of five C. alliodora-dwelling Azteca species from Mexico to Colombia. All morphological species were recovered as monophyletic, but we identified at least five distinct genetic lineages within the most abundant and specialized species, Azteca pittieri. Mitochondrial and nuclear data were concordant at the species level, but not within species. Divergence time analyses estimated that C. alliodora-dwelling Azteca shared a common ancestor approximately 10-22million years ago, prior to the proposed arrival of the host tree in Middle America. Diversification in A. pittieri occurred in the Pleistocene and was not correlated with geographic distance, which suggests limited historical gene flow among geographically restricted populations. This contrasts with the previously reported lack of phylogeographic structure at this spatial scale in the host tree. Climatic niches, and particularly precipitation-related variables, did not overlap between the sites occupied by northern and southern lineages of A. pittieri. Together, these results suggest that restricted gene flow among ant populations may facilitate local adaptation to environmental heterogeneity. Differences in population structure between the ants and their host trees may profoundly affect the evolutionary dynamics of this widespread ant-plant mutualism.

  7. Widespread ground motion distribution caused by rupture directivity during the 2015 Gorkha, Nepal earthquake

    NASA Astrophysics Data System (ADS)

    Koketsu, Kazuki; Miyake, Hiroe; Guo, Yujia; Kobayashi, Hiroaki; Masuda, Tetsu; Davuluri, Srinagesh; Bhattarai, Mukunda; Adhikari, Lok Bijaya; Sapkota, Soma Nath

    2016-06-01

    The ground motion and damage caused by the 2015 Gorkha, Nepal earthquake can be characterized by their widespread distributions to the east. Evidence from strong ground motions, regional acceleration duration, and teleseismic waveforms indicate that rupture directivity contributed significantly to these distributions. This phenomenon has been thought to occur only if a strike-slip or dip-slip rupture propagates to a site in the along-strike or updip direction, respectively. However, even though the earthquake was a dip-slip faulting event and its source fault strike was nearly eastward, evidence for rupture directivity is found in the eastward direction. Here, we explore the reasons for this apparent inconsistency by performing a joint source inversion of seismic and geodetic datasets, and conducting ground motion simulations. The results indicate that the earthquake occurred on the underthrusting Indian lithosphere, with a low dip angle, and that the fault rupture propagated in the along-strike direction at a velocity just slightly below the S-wave velocity. This low dip angle and fast rupture velocity produced rupture directivity in the along-strike direction, which caused widespread ground motion distribution and significant damage extending far eastwards, from central Nepal to Mount Everest.

  8. Widespread ground motion distribution caused by rupture directivity during the 2015 Gorkha, Nepal earthquake

    PubMed Central

    Koketsu, Kazuki; Miyake, Hiroe; Guo, Yujia; Kobayashi, Hiroaki; Masuda, Tetsu; Davuluri, Srinagesh; Bhattarai, Mukunda; Adhikari, Lok Bijaya; Sapkota, Soma Nath

    2016-0