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Sample records for reveals widespread occurrence

  1. Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases.

    PubMed

    Ellis, Mark J; Grossmann, J Günter; Eady, Robert R; Hasnain, S Samar

    2007-11-01

    Recently, the structure of a Cu-containing nitrite reductase (NiR) from Hyphomicrobium denitrificans (HdNiR) has been reported, establishing the existence of a new family of Cu-NiR where an additional type 1 Cu (T1Cu) containing cupredoxin domain is located at the N-terminus (Nojiri et al. in Proc. Natl. Acad. Sci. USA 104:4315-4320, 2007). HdNiR retains the well-characterised coupled T1Cu-type 2 Cu (T2Cu) core, where the T2Cu catalytic site is also built utilising ligands from neighbouring monomers. We have undertaken a genome analysis and found the wide occurrence of these NiRs, with members clustering in two groups, one showing an amino acid sequence similarity of around 80% with HdNiR, and a second group, including the NiR from the extremophile Acidothermus cellulolyticus, clustering around 50% similarity to HdNiR. This is reminiscent of the difference observed between the blue (Alcaligenes xylosoxidans) and green (Achromobacter cycloclastes and Alcaligenes faecalis) NiRs which have been extensively studied and may indicate that these also form two distinct subclasses of the new family. Genome analysis also showed the presence of Cu-NiRs with a C-terminal extension of 160-190 residues containing a class I cytochrome c domain with a characteristic beta-sheet extension. Currently no structural information exists for any member of this family. Genome analysis suggests the widespread occurrence of these novel NiRs with representatives in the alpha, beta and gamma subclasses of the Proteobacteria and in two species of the fungus Aspergillus. We selected the enzyme from Ralstonia pickettii for comparative modelling and produced a plausible structure highlighting an electron transfer mode in which the cytochrome c haem at the C-terminus can come within 16-A reach of the T1Cu centre of the T1Cu-T2Cu core. PMID:17712582

  2. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells.

    PubMed

    Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas; Lyon, David; Mullari, Meeli; Madsen, Maria V; Daniel, Jeremy A; Jensen, Lars J; Nielsen, Michael L

    2016-01-01

    The posttranslational modification of proteins by arginine methylation is functionally important, yet the breadth of this modification is not well characterized. Using high-resolution mass spectrometry, we identified 8030 arginine methylation sites within 3300 human proteins in human embryonic kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified by methylation. Through quantitative proteomics and RNA interference to examine arginine methylation stoichiometry, we unexpectedly found that the protein arginine methyltransferase (PRMT) family of arginine methyltransferases catalyzed methylation independently of arginine sequence context. In contrast to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially regulated the functions of the pre-mRNA splicing factor SRSF2 (serine/arginine-rich splicing factor 2) and the RNA transport ribonucleoprotein HNRNPUL1 (heterogeneous nuclear ribonucleoprotein U-like 1). Knocking down PRMT5 impaired the RNA binding function of SRSF2, whereas knocking down PRMT4 [also known as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human arginine methylome provides a missing piece in the global and integrative view of cellular physiology and protein regulation. PMID:27577262

  3. Widespread Natural Occurrence of Hydroxyurea in Animals.

    PubMed

    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.

  4. 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

  5. Widespread Natural Occurrence of Hydroxyurea in Animals.

    PubMed

    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

  6. Tetrahymanol: Its widespread occurrence and geochemical significance

    NASA Astrophysics Data System (ADS)

    Venkatesan, M. I.

    1989-11-01

    The occurrence of tetrahymanol (gammaceran-3β-ol) in sediments from various marine depositional environments such as the Santa Monica Basin and Palos Verdes shelf (southern California Bight), the Santa Barbara Basin (off the northern California Borderland), the Atlantic shelf, slope, and rise, and the Antarctic region, as well as in bacterial/algal mats from the Santa Barbara Basin and Baja California, together with its detection in sediments from the Peru upwelling region (ODP Leg 112) and Baffin Bay (ODP Leg 105) suggests that tetrahymanol occurs ubiquitously in marine samples. Tetrahymanol is the only known likely biological precursor of gammacerane, which is found in many petroleums and shales. The common occurrence of tetrahymanol in marine environments implies that primitive organisms similar to Tetrahymena, or organisms other than Tetrahymena (other protozoa, bacteria?), are also likely to contain this compound. Its isomer, diplopterol, has also been detected in several sediment sections.

  7. Widespread occurrence of ranavirus in pond-breeding amphibian populations.

    PubMed

    Hoverman, Jason T; Gray, Matthew J; Miller, Debra L; Haislip, Nathan A

    2012-03-01

    Ranaviruses are an emerging threat for many amphibian populations, yet their distribution in amphibian communities and the association of infection with possible stressors and species is not fully understood due to historically sparse surveillance. Agricultural practices that reduce the water quality of amphibian breeding habitats (e.g., cattle access to wetlands) and environmental stressors (e.g., lower temperatures) may contribute to ranavirus emergence. We tested larval amphibians for ranavirus infection across four seasons in farm ponds (n = 40) located in Tennessee, USA. Cattle at various densities were allowed access to half of the sampled ponds. Ranavirus infections were detected in nine species and in 33 of the sampled ponds (83%), illustrating widespread occurrence of the pathogen. Species within the family Ranidae were the most frequently infected. In 13 of the ponds containing infected individuals, prevalence exceeded 40% during at least one season. Infections were detected in multiple seasons in 20 of the sampled ponds containing infections, suggesting that ranaviruses are relatively persistent in these systems. Cattle had negative effects on water quality (turbidity and ammonia) and there was a positive association between cattle abundance and ranavirus prevalence in the summer. Counter to previous field studies in North America, we found a significant positive association between water temperature and ranavirus prevalence in the fall sampling events. Despite these findings, the influences of cattle and temperature on ranavirus prevalence were not consistent across seasons. As such, the mechanisms driving high ranavirus prevalence across the landscape and over time remain unclear. Given the widespread occurrence of ranaviruses in wild amphibians, we encourage the implementation of surveillance programs to help identify potential drivers of emergence. Sites with high ranavirus prevalence should be monitored annually for outbreaks, and the long

  8. 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.

  9. 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

  10. Widespread occurrence of bd in French Guiana, South America.

    PubMed

    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

  11. Widespread occurrence of bd in French Guiana, South America.

    PubMed

    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.

  12. 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.

  13. 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.

  14. Widespread Occurrence of Expressed Fungal Secretory Peroxidases in Forest Soils

    PubMed Central

    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. PMID:24763280

  15. 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

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

    PubMed Central

    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. PMID:26046534

  17. 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. PMID:26046534

  18. 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.

  19. Widespread occurrence of non-canonical transcription termination by human RNA polymerase III

    PubMed Central

    Orioli, Andrea; Pascali, Chiara; Quartararo, Jade; Diebel, Kevin W.; Praz, Viviane; Romascano, David; Percudani, Riccardo; van Dyk, Linda F.; Hernandez, Nouria; Teichmann, Martin; Dieci, Giorgio

    2011-01-01

    Human RNA polymerase (Pol) III-transcribed genes are thought to share a simple termination signal constituted by four or more consecutive thymidine residues in the coding DNA strand, just downstream of the RNA 3′-end sequence. We found that a large set of human tRNA genes (tDNAs) do not display any T≥4 stretch within 50 bp of 3′-flanking region. In vitro analysis of tDNAs with a distanced T≥4 revealed the existence of non-canonical terminators resembling degenerate T≥5 elements, which ensure significant termination but at the same time allow for the production of Pol III read-through pre-tRNAs with unusually long 3′ trailers. A panel of such non-canonical signals was found to direct transcription termination of unusual Pol III-synthesized viral pre-miRNA transcripts in gammaherpesvirus 68-infected cells. Genome-wide location analysis revealed that human Pol III tends to trespass into the 3′-flanking regions of tDNAs, as expected from extensive terminator read-through. The widespread occurrence of partial termination suggests that the Pol III primary transcriptome in mammals is unexpectedly enriched in 3′-trailer sequences with the potential to contribute novel functional ncRNAs. PMID:21421562

  20. Persistent and widespread occurrence of bioactive quinone pigments during post-Paleozoic crinoid diversification.

    PubMed

    Wolkenstein, Klaus

    2015-03-01

    Secondary metabolites often play an important role in the adaptation of organisms to their environment. However, little is known about the secondary metabolites of ancient organisms and their evolutionary history. Chemical analysis of exceptionally well-preserved colored fossil crinoids and modern crinoids from the deep sea suggests that bioactive polycyclic quinones related to hypericin were, and still are, globally widespread in post-Paleozoic crinoids. The discovery of hypericinoid pigments both in fossil and in present-day representatives of the order Isocrinida indicates that the pigments remained almost unchanged since the Mesozoic, also suggesting that the original color of hypericinoid-containing ancient crinoids may have been analogous to that of their modern relatives. The persistent and widespread occurrence, spatially as well as taxonomically, of hypericinoid pigments in various orders during the adaptive radiation of post-Paleozoic crinoids suggests a general functional importance of the pigments, contributing to the evolutionary success of the Crinoidea.

  1. Persistent and widespread occurrence of bioactive quinone pigments during post-Paleozoic crinoid diversification

    PubMed Central

    Wolkenstein, Klaus

    2015-01-01

    Secondary metabolites often play an important role in the adaptation of organisms to their environment. However, little is known about the secondary metabolites of ancient organisms and their evolutionary history. Chemical analysis of exceptionally well-preserved colored fossil crinoids and modern crinoids from the deep sea suggests that bioactive polycyclic quinones related to hypericin were, and still are, globally widespread in post-Paleozoic crinoids. The discovery of hypericinoid pigments both in fossil and in present-day representatives of the order Isocrinida indicates that the pigments remained almost unchanged since the Mesozoic, also suggesting that the original color of hypericinoid-containing ancient crinoids may have been analogous to that of their modern relatives. The persistent and widespread occurrence, spatially as well as taxonomically, of hypericinoid pigments in various orders during the adaptive radiation of post-Paleozoic crinoids suggests a general functional importance of the pigments, contributing to the evolutionary success of the Crinoidea. PMID:25730856

  2. Widespread occurrence of nitrate storage and denitrification among Foraminifera and Gromiida

    PubMed Central

    Piña-Ochoa, Elisa; Høgslund, Signe; Geslin, Emmanuelle; Cedhagen, Tomas; Revsbech, Niels Peter; Nielsen, Lars Peter; Schweizer, Magali; Jorissen, Frans; Rysgaard, Søren; Risgaard-Petersen, Nils

    2009-01-01

    Benthic foraminifers inhabit a wide range of aquatic environments including open marine, brackish, and freshwater environments. Here we show that several different and diverse foraminiferal groups (miliolids, rotaliids, textulariids) and Gromia, another taxon also belonging to Rhizaria, accumulate and respire nitrates through denitrification. The widespread occurrence among distantly related organisms suggests an ancient origin of the trait. The diverse metabolic capacity of these organisms, which enables them to respire with oxygen and nitrate and to sustain respiratory activity even when electron acceptors are absent from the environment, may be one of the reasons for their successful colonization of diverse marine sediment environments. The contribution of eukaryotes to the removal of fixed nitrogen by respiration may equal the importance of bacterial denitrification in ocean sediments. PMID:20080540

  3. 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. PMID:27087919

  4. 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

  5. Soils reveal widespread manganese enrichment from industrial inputs.

    PubMed

    Herndon, Elizabeth M; Jin, Lixin; Brantley, Susan L

    2011-01-01

    It is well-known that metals are emitted to the air by human activities and subsequently deposited to the land surface; however, we have not adequately evaluated the geographic extent and ecosystem impacts of industrial metal loading to soils. Here, we demonstrate that atmospheric inputs have widely contaminated soils with Mn in industrialized regions. Soils record elemental fluxes impacting the Earth's surface and can be analyzed to quantify inputs and outputs during pedogenesis. We use a mass balance model to interpret details of Mn enrichment by examining soil, bedrock, precipitation, and porefluid chemistry in a first-order watershed in central Pennsylvania, USA. This reveals that ∼ 53% of Mn in ridge soils can be attributed to atmospheric deposition from anthropogenic sources. An analysis of published data sets indicates that over half of the soils surveyed in Pennsylvania (70%), North America (60%), and Europe (51%) are similarly enriched in Mn. We conclude that soil Mn enrichment due to industrial inputs is extensive, yet patchy in distribution due to source location, heterogeneity of lithology, vegetation, and other attributes of the land surface. These results indicate that atmospheric transport must be considered a potentially critical component of the global Mn cycle during the Anthropocene.

  6. 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

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

    PubMed

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

    2013-09-01

    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 this is likely a global environmental issue

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

    PubMed

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

    2013-09-01

    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 this is likely a global environmental issue

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

    USGS Publications Warehouse

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

    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.

  10. Widespread occurrence of N6-methyladenosine in bacterial mRNA

    PubMed Central

    Deng, Xin; Chen, Kai; Luo, Guan-Zheng; Weng, Xiaocheng; Ji, Quanjiang; Zhou, Tianhong; He, Chuan

    2015-01-01

    N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent discoveries of demethylases and specific binding proteins of m6A as well as m6A methylomes obtained in mammals, yeast and plants have revealed regulatory functions of this RNA modification. Although m6A is present in the ribosomal RNA of bacteria, its occurrence in mRNA still remains elusive. Here, we have employed ultra-high pressure liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QQQ-MS/MS) to calculate the m6A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m6A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m6A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved m6A pattern that is distinct from those in eukaryotes. Most m6A peaks are located inside open reading frames and carry a unique consensus motif of GCCAU. Functional enrichment analysis of bacterial m6A peaks indicates that the majority of m6A-modified genes are associated with respiration, amino acids metabolism, stress response and small RNAs, suggesting potential functional roles of m6A in these pathways. PMID:26068471

  11. 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

  12. 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.

  13. 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

  14. 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. PMID:25850738

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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. PMID:19226299

  1. 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

  2. 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. PMID:21976755

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

    PubMed

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

    2014-12-16

    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.

  4. Widespread occurrence in frogs and toads of skin compounds interacting with the ouabain site of Na+, K+-ATPase.

    PubMed

    Flier, J; Edwards, M W; Daly, J W; Myers, C W

    1980-05-01

    Amphibians of the family Bufonidae contain high levels of skin compounds that both inhibit Na+- and K+-dependent adenosinetriphosphatase and antagonize the binding of ouabain to the enzyme. In species of Bufo and Atelopus, these compounds are relatively nonpolar bufodienolides, whereas Dendrophryniscus and Melanophryniscus contain more polar compounds of unknown structure. Skin extracts from 30 of 48 species of frogs representing an additional eight families contained relatively low levels of compounds that inhibit binding of ouabain to Na+,K+-adenosinetriphosphatase. The widespread occurrence of low levels of inhibitory compounds is consonant with the role for these compounds as physiological regulators of Na+,K+-adenosinetriphosphatase in amphibian skin; high levels in the Bufonidae probably also serve as a defense against some predators. PMID:6245447

  5. 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

  6. Genetic sequence data reveals widespread sharing of Leucocytozoon lineages in corvids.

    PubMed

    Freund, Dave; Wheeler, Sarah S; Townsend, Andrea K; Boyce, Walter M; Ernest, Holly B; Cicero, Carla; Sehgal, Ravinder N M

    2016-09-01

    Leucocytozoon, a widespread hemosporidian blood parasite that infects a broad group of avian families, has been studied in corvids (family: Corvidae) for over a century. Current taxonomic classification indicates that Leucocytozoon sakharoffi infects crows and related Corvus spp., while Leucocytozoon berestneffi infects magpies (Pica spp.) and blue jays (Cyanocitta sp.). This intrafamily host specificity was based on the experimental transmissibility of the parasites, as well as slight differences in their morphology and life cycle development. Genetic sequence data from Leucocytozoon spp. infecting corvids is scarce, and until the present study, sequence data has not been analyzed to confirm the current taxonomic distinctions. Here, we predict the phylogenetic relationships of Leucocytozoon cytochrome b lineages recovered from infected American Crows (Corvus brachyrhynchos), yellow-billed magpies (Pica nuttalli), and Steller's jays (Cyanocitta stelleri) to explore the host specificity pattern of L. sakharoffi and L. berestneffi. Phylogenetic reconstruction revealed a single large clade containing nearly every lineage recovered from the three host species, while showing no evidence of the expected distinction between L. sakharoffi and L. berestneffi. In addition, five of the detected lineages were recovered from both crows and magpies. This absence of the previously described host specificity in corvid Leucocytozoon spp. suggests that L. sakharoffi and L. berestneffi be reexamined from a taxonomic perspective.

  7. 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

  8. 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

  9. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes.

    PubMed

    Li, Bing; Yang, Ying; Ma, Liping; Ju, Feng; Guo, Feng; Tiedje, James M; Zhang, Tong

    2015-11-01

    A metagenomic approach and network analysis was used to investigate the wide-spectrum profiles of antibiotic resistance genes (ARGs) and their co-occurrence patterns in 50 samples from 10 typical environments. In total, 260 ARG subtypes belonging to 18 ARG types were detected with an abundance range of 5.4 × 10(-6)-2.2 × 10(-1) copy of ARG per copy of 16S-rRNA gene. The trend of the total ARG abundances in environments matched well with the levels of anthropogenic impacts on these environments. From the less impacted environments to the seriously impacted environments, the total ARG abundances increased up to three orders of magnitude, that is, from 3.2 × 10(-3) to 3.1 × 10(0) copy of ARG per copy of 16S-rRNA gene. The abundant ARGs were associated with aminoglycoside, bacitracin, β-lactam, chloramphenicol, macrolide-lincosamide-streptogramin, quinolone, sulphonamide and tetracycline, in agreement with the antibiotics extensively used in human medicine or veterinary medicine/promoters. The widespread occurrences and abundance variation trend of vancomycin resistance genes in different environments might imply the spread of vancomycin resistance genes because of the selective pressure resulting from vancomycin use. The simultaneous enrichment of 12 ARG types in adult chicken faeces suggests the coselection of multiple ARGs in this production system. Non-metric multidimensional scaling analysis revealed that samples belonging to the same environment generally possessed similar ARG compositions. Based on the co-occurrence pattern revealed by network analysis, tetM and aminoglycoside resistance protein, the hubs of the ARG network, are proposed to be indicators to quantitatively estimate the abundance of 23 other co-occurring ARG subtypes by power functions.

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

    PubMed

    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.

  11. Maize grain and soil surveys reveal suboptimal dietary selenium intake is widespread in Malawi

    PubMed Central

    Chilimba, Allan D. C.; Young, Scott D.; Black, Colin R.; Rogerson, Katie B.; Ander, E. Louise; Watts, Michael J.; Lammel, Joachim; Broadley, Martin R.

    2011-01-01

    Selenium is an essential element in human diets but the risk of suboptimal intake increases where food choices are narrow. Here we show that suboptimal dietary intake (i.e. 20–30 µg Se person−1 d−1) is widespread in Malawi, based on a spatial integration of Se concentrations of maize (Zea mays L.) grain and soil surveys for 88 field sites, representing 10 primary soil types and >75% of the national land area. The median maize grain Se concentration was 0.019 mg kg−1 (range 0.005–0.533), a mean intake of 6.7 µg Se person−1 d−1 from maize flour based on national consumption patterns. Maize grain Se concentration was up to 10-fold higher in crops grown on soils with naturally high pH (>6.5) (Eutric Vertisols). Under these less acidic conditions, Se becomes considerably more available to plants due to the greater solubility of Se(IV) species and oxidation to Se(VI). PMID:22355591

  12. 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

  13. Widespread Environmental Contamination with Mycobacterium tuberculosis Complex Revealed by a Molecular Detection Protocol

    PubMed Central

    Santos, Nuno; Santos, Catarina; Valente, Teresa; Gortázar, Christian; Almeida, Virgílio; Correia-Neves, Margarida

    2015-01-01

    Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70–0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area. PMID:26561038

  14. 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

  15. Widespread Environmental Contamination with Mycobacterium tuberculosis Complex Revealed by a Molecular Detection Protocol.

    PubMed

    Santos, Nuno; Santos, Catarina; Valente, Teresa; Gortázar, Christian; Almeida, Virgílio; Correia-Neves, Margarida

    2015-01-01

    Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70-0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area. PMID:26561038

  16. Widespread Environmental Contamination with Mycobacterium tuberculosis Complex Revealed by a Molecular Detection Protocol.

    PubMed

    Santos, Nuno; Santos, Catarina; Valente, Teresa; Gortázar, Christian; Almeida, Virgílio; Correia-Neves, Margarida

    2015-01-01

    Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70-0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area.

  17. 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

  18. 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. PMID:27267344

  19. 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.

  20. 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. PMID:25683740

  1. Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

    PubMed Central

    Salamov, Asaf; Zhang, Jiwei; Meng, Xiandong; Zhao, Zhiying; Kang, Dongwan; Underwood, Jason; Grigoriev, Igor V.; Figueroa, Melania; Schilling, Jonathan S.; Chen, Feng; Wang, Zhong

    2015-01-01

    Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly. PMID:26177194

  2. 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

  3. 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

  4. 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

  5. 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

  6. Widespread Occurrence of Diverse Human Pathogenic Types of the Fungus Fusarium Detected in Plumbing Drains ▿ †

    PubMed Central

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

    2011-01-01

    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. PMID:21976755

  7. 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

  8. A widespread low-latitude diurnal CO2 frost cycle on Mars revealed by Mars Climate Sounder observations

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Surface observations by the Mars Climate Sounder (MCS) onboard the Mars Reconnaissance Orbiter document the widespread occurrence of atmospherically-corrected ground temperatures consistent with the presence of extensive CO2 frost deposits at low latitudes at 3AM. While the detection of CO2 ice has previously been reported outside the polar regions, in discrete locations associated with very high elevation terrains (i.e. associated with Elysium, Olympus Mons and the Tharsis Montes), our observations provide the first observational evidence of a global-scale diurnal CO2 cycle involving the atmosphere and the surface. MCS surface temperatures consistent with the presence of ephemeral diurnal CO2 frost deposits are strongly correlated with geologic terrains characterized by high emissivity, high albedo, and low thermal inertia. All of these properties are conducive to low nighttime temperatures. Thermal modeling of these low inertia terrains (i.e. < 75 J m-2K-1s-1/2), which cover a large fraction of the Martian surface, confirms that the regolith frequently reaches CO2 frost point temperatures at all latitudes near 3AM, with seasonal variations noticed. In addition, models used in conjunction with MCS temperature retrievals also predict that right before sunrise, nearly all of the Martian dusty low thermal inertia units are frosted at some point during the Mars Year. Energy/mass balance modeling suggests deposits with depths of up to several hundreds of microns of CO2 (<<0.1% of the Martian atmosphere). This is not sufficient to generate a measurable diurnal pressure cycle. The discovery of this diurnal CO2 cycle may nonetheless represent an important step forward in our understanding of the way the Mars atmosphere interacts with the surface.

  9. Diversity and factors controlling widespread occurrence of syn-rift Ladinian microbialites in the western Tethys (Triassic Catalan Basin, NE Spain)

    NASA Astrophysics Data System (ADS)

    Mercedes-Martín, Ramon; Arenas, Concha; Salas, Ramon

    2014-11-01

    The fault-block carbonate ramps of the Ladinian (Middle Triassic) Catalan Basin hosted a wide variety of microbial deposits which formed during a syn-rift stage. Stratigraphical and sedimentological analyses of these microbialites allow us to reconstruct two depositional models for such microbial deposits. Moreover new insights into the interplay between the intrinsic and extrinsic factors that controlled the widespread development of these microbialites are provided. Stromatolites, ooidal-muddy microbial laminites and thrombolites were analyzed on the basis of their geometry, lamination and textural attributes. These microbialites are distributed over two Transgressive-Regressive sequences and coexisted during the Fassanian (Early Ladinian) regressive stage. Later, stromatolites and ooidal-muddy microbial laminites developed during the Longobardian (Late Ladinian) transgressive stage. Three types of lamina couplets reflect distinct accretion processes linked to water chemistry, sediment supply and hydrodynamic conditions. Thrombolite textures were produced by accretionary, binding and encrusting processes (microbially mediated) and pervasive cementation. The widespread occurrence of microbial deposits is explained as a consequence of a biogeochemical cascade of events (e.g., anoxic/dysoxic seawater conditions, volcanic activity, upwelling of alkaline waters, nutrient concentrations, and microbial blooms), which promoted favorable conditions for microbial growth in the Tethys during the Ladinian. Furthermore, in the Catalan Basin, syn-rift fault induced subsidence and local water energy gradients exerted an essential role in the distribution of the three types of microbialites through space and time. Thrombolites were prone to grow in the hanging wall block of a half-graben (subtidal conditions), whereas stromatolites and ooidal-muddy microbial laminites flourished preferably in a foot wall block setting (intertidal-shallow subtidal conditions). However, the fact

  10. Metabolomic analysis of bone morphogenetic protein receptor type 2 mutations in human pulmonary endothelium reveals widespread metabolic reprogramming.

    PubMed

    Fessel, Joshua P; Hamid, Rizwan; Wittmann, Bryan M; Robinson, Linda J; Blackwell, Tom; Tada, Yuji; Tanabe, Nobuhiro; Tatsumi, Koichiro; Hemnes, Anna R; West, James D

    2012-01-01

    Pulmonary arterial hypertension (PAH) is a progressive and fatal disease of the lung vasculature for which the molecular etiologies are unclear. Specific metabolic alterations have been identified in animal models and in PAH patients, though existing data focus mainly on abnormalities of glucose homeostasis. We hypothesized that analysis of the entire metabolome in PAH would reveal multiple other metabolic changes relevant to disease pathogenesis and possible treatment. Layered transcriptomic and metabolomic analyses of human pulmonary microvascular endothelial cells (hPMVEC) expressing two different disease-causing mutations in the bone morphogenetic protein receptor type 2 (BMPR2) confirmed previously described increases in aerobic glycolysis but also uncovered significant upregulation of the pentose phosphate pathway, increases in nucleotide salvage and polyamine biosynthesis pathways, decreases in carnitine and fatty acid oxidation pathways, and major impairment of the tricarboxylic acid (TCA) cycle and failure of anaplerosis. As a proof of principle, we focused on the TCA cycle, predicting that isocitrate dehydrogenase (IDH) activity would be altered in PAH, and then demonstrating increased IDH activity not only in cultured hPMVEC expressing mutant BMPR2 but also in the serum of PAH patients. These results suggest that widespread metabolic changes are an important part of PAH pathogenesis, and that simultaneous identification and targeting of the multiple involved pathways may be a more fruitful therapeutic approach than targeting of any one individual pathway.

  11. Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species

    PubMed Central

    Zhan, X; Dixon, A; Batbayar, N; Bragin, E; Ayas, Z; Deutschova, L; Chavko, J; Domashevsky, S; Dorosencu, A; Bagyura, J; Gombobaatar, S; Grlica, I D; Levin, A; Milobog, Y; Ming, M; Prommer, M; Purev-Ochir, G; Ragyov, D; Tsurkanu, V; Vetrov, V; Zubkov, N; Bruford, M W

    2015-01-01

    Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species. PMID:25074575

  12. Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species.

    PubMed

    Zhan, X; Dixon, A; Batbayar, N; Bragin, E; Ayas, Z; Deutschova, L; Chavko, J; Domashevsky, S; Dorosencu, A; Bagyura, J; Gombobaatar, S; Grlica, I D; Levin, A; Milobog, Y; Ming, M; Prommer, M; Purev-Ochir, G; Ragyov, D; Tsurkanu, V; Vetrov, V; Zubkov, N; Bruford, M W

    2015-01-01

    Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species. PMID:25074575

  13. Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

    PubMed Central

    2012-01-01

    Background Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. Results We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa). Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks. Conclusions Our study profiles an abundance of cis-NATs and nat-siRNAs in rice. These data are valuable for gaining insight into the complex function of the rice transcriptome. PMID:23259405

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

    PubMed

    Dubey, J P; Velmurugan, G V; Rajendran, 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

    2011-09-01

    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. PMID:21802422

  15. 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.

  16. 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.

  17. 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

  18. 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. PMID:24497033

  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. Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum

    PubMed Central

    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

    2014-01-01

    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. PMID:24497033

  2. An Extensive Field Survey Combined with a Phylogenetic Analysis Reveals Rapid and Widespread Invasion of Two Alien Whiteflies in China

    PubMed Central

    Hu, Jian; De Barro, Paul; Zhao, Hua; Wang, Jia; Nardi, Francesco; Liu, Shu-Sheng

    2011-01-01

    Background To understand the processes of invasions by alien insects is a pre-requisite for improving management. The whitefly Bemisia tabaci is a cryptic species complex that contains some of the most invasive pests worldwide. However, extensive field data to show the geographic distribution of the members of this species complex as well as the invasion by some of its members are scarce. Methodology/Principal Findings We used field surveys and published data to assess the current diversity and distribution of B. tabaci cryptic species in China and relate the indigenous members to other Asian and Australian members of the complex. The survey covered the 16 provinces where indigenous B. tabaci occur and extends this with published data for the whole of China. We used molecular markers to identify cryptic species. The evolutionary relationships between the different Asian B. tabaci were reconstructed using Bayesian methods. We show that whereas in the past the exotic invader Middle East-Asia Minor 1 was predominant across China, another newer invader Mediterranean is now the dominant species in the Yangtze River Valley and eastern coastal areas, and Middle East-Asia Minor 1 is now predominant only in the south and south eastern coastal areas. Based on mtCO1 we identified four new cryptic species, and in total we have recorded 13 indigenous and two invasive species from China. Diversity was highest in the southern and southeastern provinces and declined to north and west. Only the two invasive species were found in the northern part of the country where they occur primarily in protected cropping. By 2009, indigenous species were mainly found in remote mountainous areas and were mostly absent from extensive agricultural areas. Conclusions/Significance Invasions by some members of the whitefly B. tabaci species complex can be rapid and widespread, and indigenous species closely related to the invaders are replaced. PMID:21283707

  3. 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

  4. Comparative genomic de-convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionation.

    PubMed

    Wang, Xiyin; Guo, Hui; Wang, Jinpeng; Lei, Tianyu; Liu, Tao; Wang, Zhenyi; Li, Yuxian; Lee, Tae-Ho; Li, Jingping; Tang, Haibao; Jin, Dianchuan; Paterson, Andrew H

    2016-02-01

    The 'apparently' simple genomes of many angiosperms mask complex evolutionary histories. The reference genome sequence for cotton (Gossypium spp.) revealed a ploidy change of a complexity unprecedented to date, indeed that could not be distinguished as to its exact dosage. Herein, by developing several comparative, computational and statistical approaches, we revealed a 5× multiplication in the cotton lineage of an ancestral genome common to cotton and cacao, and proposed evolutionary models to show how such a decaploid ancestor formed. The c. 70% gene loss necessary to bring the ancestral decaploid to its current gene count appears to fit an approximate geometrical model; that is, although many genes may be lost by single-gene deletion events, some may be lost in groups of consecutive genes. Gene loss following cotton decaploidy has largely just reduced gene copy numbers of some homologous groups. We designed a novel approach to deconvolute layers of chromosome homology, providing definitive information on gene orthology and paralogy across broad evolutionary distances, both of fundamental value and serving as an important platform to support further studies in and beyond cotton and genomics communities. PMID:26756535

  5. 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

  6. Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization.

    PubMed

    Rodríguez-Molina, Juan B; Tseng, Sandra C; Simonett, Shane P; Taunton, Jack; Ansari, Aseem Z

    2016-08-01

    During transcription initiation, the TFIIH-kinase Kin28/Cdk7 marks RNA polymerase II (Pol II) by phosphorylating the C-terminal domain (CTD) of its largest subunit. Here we describe a structure-guided chemical approach to covalently and specifically inactivate Kin28 kinase activity in vivo. This method of irreversible inactivation recapitulates both the lethal phenotype and the key molecular signatures that result from genetically disrupting Kin28 function in vivo. Inactivating Kin28 impacts promoter release to differing degrees and reveals a "checkpoint" during the transition to productive elongation. While promoter-proximal pausing is not observed in budding yeast, inhibition of Kin28 attenuates elongation-licensing signals, resulting in Pol II accumulation at the +2 nucleosome and reduced transition to productive elongation. Furthermore, upon inhibition, global stabilization of mRNA masks different degrees of reduction in nascent transcription. This study resolves long-standing controversies on the role of Kin28 in transcription and provides a rational approach to irreversibly inhibit other kinases in vivo. PMID:27477907

  7. Population Polymorphism of Nuclear Mitochondrial DNA Insertions Reveals Widespread Diploidy Associated with Loss of Heterozygosity in Debaryomyces hansenii ▿ †

    PubMed Central

    Jacques, Noémie; Sacerdot, Christine; Derkaoui, Meriem; Dujon, Bernard; Ozier-Kalogeropoulos, Odile; Casaregola, Serge

    2010-01-01

    Debaryomyces hansenii, a yeast that participates in the elaboration of foodstuff, displays important genetic diversity. Our recent phylogenetic classification of this species led to the subdivision of the species into three distinct clades. D. hansenii harbors the highest number of nuclear mitochondrial DNA (NUMT) insertions known so far for hemiascomycetous yeasts. Here we assessed the intraspecific variability of the NUMTs in this species by testing their presence/absence first in 28 strains, with 21 loci previously detected in the completely sequenced strain CBS 767T, and second in a larger panel of 77 strains, with 8 most informative loci. We were able for the first time to structure populations in D. hansenii, although we observed little NUMT insertion variability within the clades. We determined the chronology of the NUMT insertions, which turned out to correlate with the previously defined taxonomy and provided additional evidence that colonization of nuclear genomes by mitochondrial DNA is a dynamic process in yeast. In combination with flow cytometry experiments, the NUMT analysis revealed the existence of both haploid and diploid strains, the latter being heterozygous and resulting from at least four crosses among strains from the various clades. As in the diploid pathogen Candida albicans, to which D. hansenii is phylogenetically related, we observed a differential loss of heterozygosity in the diploid strains, which can explain some of the large genetic diversity found in D. hansenii over the years. PMID:20048048

  8. 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. PMID:26096550

  9. Emotions in motion: dynamic compared to static facial expressions of disgust and happiness reveal more widespread emotion-specific activations.

    PubMed

    Trautmann, Sina Alexa; Fehr, Thorsten; Herrmann, Manfred

    2009-08-11

    In social contexts, facial expressions are dynamic in nature and vary rapidly in relation to situational requirements. However, there are very few fMRI studies using dynamic emotional stimuli. The aim of this study was (1) to introduce and evaluate a new stimulus database of static and dynamic emotional facial expressions according to arousal and recognizability investigated by a rating by both participants of the present fMRI study and by an external sample of 30 healthy women, (2) to examine the neural networks involved in emotion perception of static and dynamic facial stimuli separately, and (3) to examine the impact of motion on the emotional processing of dynamic compared to static face stimuli. A total of 16 females participated in the present fMRI study performing a passive emotion perception task including static and dynamic faces of neutral, happy and disgusted expressions. Comparing dynamic stimuli to static faces indicated enhanced emotion-specific brain activation patterns in the parahippocampal gyrus (PHG) including the amygdala (AMG), fusiform gyrus (FG), superior temporal gyrus (STG), inferior frontal gyrus (IFG), and occipital and orbitofrontal cortex (OFC). These regions have been discussed to be associated with emotional memory encoding, the perception of threat, facial identity, biological motion, the mirror neuron system, an increase of emotional arousal, and reward processing, respectively. Post hoc ratings of the dynamic stimuli revealed a better recognizability in comparison to the static stimuli. In conclusion, dynamic facial expressions might provide a more appropriate approach to examine the processing of emotional face perception than static stimuli. PMID:19501062

  10. Occurrence of poly(alpha2,8-deaminoneuraminic acid) in mammalian tissues: widespread and developmentally regulated but highly selective expression on glycoproteins.

    PubMed Central

    Ziak, M; Qu, B; Zuo, X; Zuber, C; Kanamori, A; Kitajima, K; Inoue, S; Inoue, Y; Roth, J

    1996-01-01

    In tissues of higher organisms homopolymers of alpha2,8-linked N-acetylneuraminic acid can be found as a posttranslational modification on selected proteins. We report here the discovery of homopolymers of alpha2,8-linked deaminoneuraminic acid [poly(alpha2,8-KDN)] in various tissues derived from all three germ layers in vertebrates including mammals. The monoclonal antibody kdn8kdn in conjunction with a bacterial KDNase permitted the detection of poly(alpha2,8-KDN) by immunohistochemistry and immunoblotting. Further evidence for the existence of poly(alpha2,8-KDN) was obtained by gas/liquid chromatography. The poly(alpha2,8-KDN) glycan was detectable in all tissues studied with the exception of mucus-producing cells present in various organs, the extracellular matrix, and basement membranes. However, in certain organs such as muscle, kidney, lung, and brain its expression was developmentally regulated. Despite its widespread tissue distribution, the poly(alpha2,8-KDN) glycan was detected on a single 150-kDa glycoprotein except for a single >350-kDa glycoprotein in kidney, which makes it most distinctive among polysialic acids. The ubiquitous yet selective expression may be indicative of a general function of the poly(alpha2,8-KDN)-bearing glycoproteins. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 Fig. 6 PMID:8610115

  11. Widespread occurrence and accumulation of bisphenol A diglycidyl ether (BADGE), bisphenol F diglycidyl ether (BFDGE) and their derivatives in human blood and adipose fat.

    PubMed

    Wang, Lei; Xue, Jingchuan; Kannan, Kurunthachalam

    2015-03-01

    Despite the widespread use of bisphenol A diglycidyl ether (BADGE) and bisphenol F diglycidyl ether (BFDGE) in various consumer products, studies on human exposure to these compounds are scarce. In this study, BADGE, BFDGE, and seven of their derivatives were determined in human adipose fat and blood plasma samples collected from New York City, NY. Bisphenol A bis (2,3-dihydroxypropyl) ether [BADGE·2H2O] was the major BADGE derivative found in 60% of the adipose samples and 70% of the plasma samples analyzed. High concentrations and detection frequencies of BFDGE were found in both adipose and plasma samples. BFDGE concentrations in adipose fat ranged from 19.1 to 4500 ng/g wet weight. A significant correlation between BADGE or BFDGE and their derivatives in adipose and plasma samples suggested hydration of these reactive compounds in humans. A significant positive correlation existed between BADGEs (i.e., the sum of BADGE and its five derivatives) and BFDGEs in adipose samples, which suggested similar exposure sources and pathways for these compounds in humans. Bisphenol A (BPA) also was analyzed in adipose fat and plasma, and its concentrations were positively correlated with those of BADGEs, which confirmed coexposure of BADGEs and BPA in humans.

  12. Analysis of Asn-linked glycans from vegetable foodstuffs: widespread occurrence of Lewis a, core alpha1,3-linked fucose and xylose substitutions.

    PubMed

    Wilson, I B; Zeleny, R; Kolarich, D; Staudacher, E; Stroop, C J; Kamerling, J P; Altmann, F

    2001-04-01

    The N-glycans from 27 "plant" foodstuffs, including one from a gymnospermic plant and one from a fungus, were prepared by a new procedure and examined by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). For several samples, glycan structures were additionally investigated by size-fractionation and reverse-phase high-performance liquid chromatography in conjunction with exoglycosidase digests and finally also (1)H-nuclear magnetic resonance spectroscopy. The glycans found ranged from the typical vacuolar "horseradish peroxidase" type and oligomannose to complex Le(a)-carrying structures. Though the common mushroom exclusively contained N-glycans of the oligomannosidic type, all plant foods contained mixtures of the above-mentioned types. Apple, asparagus, avocado, banana, carrot, celery, hazelnut, kiwi, onion, orange, pear, pignoli, strawberry, and walnut were particularly rich in Le(a)-carrying N-glycans. Although traces of Le(a)-containing structures were also present in almond, pistachio, potato, and tomato, no such glycans could be found in cauliflower. Coconut exhibited almost exclusively N-glycans containing only xylose but no fucose. Oligomannosidic N-glycans dominated in buckwheat and especially in the legume seeds mung bean, pea, peanut, and soybean. Papaya presented a unique set of hybrid type structures partially containing the Le(a) determinant. These results are not only compatible with the hypothesis that the carbohydrate structures are another potential source of immunological cross-reaction between different plant allergens, but they also demonstrate that the Le(a)-type structure is very widespread among plants. PMID:11358875

  13. Analysis of Asn-linked glycans from vegetable foodstuffs: widespread occurrence of Lewis a, core alpha1,3-linked fucose and xylose substitutions.

    PubMed

    Wilson, I B; Zeleny, R; Kolarich, D; Staudacher, E; Stroop, C J; Kamerling, J P; Altmann, F

    2001-04-01

    The N-glycans from 27 "plant" foodstuffs, including one from a gymnospermic plant and one from a fungus, were prepared by a new procedure and examined by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). For several samples, glycan structures were additionally investigated by size-fractionation and reverse-phase high-performance liquid chromatography in conjunction with exoglycosidase digests and finally also (1)H-nuclear magnetic resonance spectroscopy. The glycans found ranged from the typical vacuolar "horseradish peroxidase" type and oligomannose to complex Le(a)-carrying structures. Though the common mushroom exclusively contained N-glycans of the oligomannosidic type, all plant foods contained mixtures of the above-mentioned types. Apple, asparagus, avocado, banana, carrot, celery, hazelnut, kiwi, onion, orange, pear, pignoli, strawberry, and walnut were particularly rich in Le(a)-carrying N-glycans. Although traces of Le(a)-containing structures were also present in almond, pistachio, potato, and tomato, no such glycans could be found in cauliflower. Coconut exhibited almost exclusively N-glycans containing only xylose but no fucose. Oligomannosidic N-glycans dominated in buckwheat and especially in the legume seeds mung bean, pea, peanut, and soybean. Papaya presented a unique set of hybrid type structures partially containing the Le(a) determinant. These results are not only compatible with the hypothesis that the carbohydrate structures are another potential source of immunological cross-reaction between different plant allergens, but they also demonstrate that the Le(a)-type structure is very widespread among plants.

  14. Novel Finding of Widespread Occurrence and Accumulation of Bisphenol A Diglycidyl Ethers (BADGEs) and Novolac Glycidyl Ethers (NOGEs) in Marine Mammals from the United States Coastal Waters.

    PubMed

    Xue, Jingchuan; Kannan, Kurunthachalam

    2016-02-16

    Bisphenol A diglycidyl ether (BADGE)- and bisphenol F diglycidyl ether (BFDGE)-based epoxy resins have a broad range of applications, including serving as inner coatings of food and beverage cans and as protective coatings in marine construction. Prior to this study, no studies had examined the occurrence and bioaccumulation of BADGEs or BFDGEs in aquatic organisms. In this study, BADGE, BFDGE, and nine of their derivatives were determined in 121 tissue (liver, kidney, blubber, and brain) samples from eight species of marine mammals collected from the U.S. coastal waters of Florida, California, Washington, and Alaska. BADGE·2HCl was the predominant compound found in the majority (78.5%) of the marine mammal tissues analyzed, at concentrations of up to 2950 ng/g (wet weight (wt)) found in the liver of a sea otter from Kachemak Bay, Alaska. The measured concentrations of BADGE·2HCl in marine mammals were on the order of hundreds of nanograms per gram tissue, which are some of the highest concentrations ever reported for this compound in biota. Males contained greater concentrations of BADGE·2HCl than did females. BADGE·2HCl also was found in the brain tissues of sea otters. Trace levels of BADGE·2HCl were found in the livers of polar bears from Alaska, which suggested that BADGEs are widely distributed in the oceanic environment. PMID:26800265

  15. Novel Finding of Widespread Occurrence and Accumulation of Bisphenol A Diglycidyl Ethers (BADGEs) and Novolac Glycidyl Ethers (NOGEs) in Marine Mammals from the United States Coastal Waters.

    PubMed

    Xue, Jingchuan; Kannan, Kurunthachalam

    2016-02-16

    Bisphenol A diglycidyl ether (BADGE)- and bisphenol F diglycidyl ether (BFDGE)-based epoxy resins have a broad range of applications, including serving as inner coatings of food and beverage cans and as protective coatings in marine construction. Prior to this study, no studies had examined the occurrence and bioaccumulation of BADGEs or BFDGEs in aquatic organisms. In this study, BADGE, BFDGE, and nine of their derivatives were determined in 121 tissue (liver, kidney, blubber, and brain) samples from eight species of marine mammals collected from the U.S. coastal waters of Florida, California, Washington, and Alaska. BADGE·2HCl was the predominant compound found in the majority (78.5%) of the marine mammal tissues analyzed, at concentrations of up to 2950 ng/g (wet weight (wt)) found in the liver of a sea otter from Kachemak Bay, Alaska. The measured concentrations of BADGE·2HCl in marine mammals were on the order of hundreds of nanograms per gram tissue, which are some of the highest concentrations ever reported for this compound in biota. Males contained greater concentrations of BADGE·2HCl than did females. BADGE·2HCl also was found in the brain tissues of sea otters. Trace levels of BADGE·2HCl were found in the livers of polar bears from Alaska, which suggested that BADGEs are widely distributed in the oceanic environment.

  16. Evidence for the Widespread Occurrence of Massive Ground Ice in the Northern Plains of Mars: A Potential Relic of a Former Ocean?

    NASA Astrophysics Data System (ADS)

    Clifford, Stephen; Costard, Francois; PetitJean, Mouna; Mouginit, Jeremie; Parker, Tim

    2013-04-01

    The possibility that a large ocean once occupied the northern plains of Mars has been proposed based on the interpretive identification of various landforms, including sedimentary deposits, outwash plains and shorelines - the latter based largely on the work of Parker et al., who identified evidence of a series of nested levels, which they interpreted as shorelines, located along the highland/lowland boundary. The combination of high-resolution orbiter images with MOLA gridded topography has enabled the compilation of regional and global maps of the proposed shorelines. The highest and oldest of these was called the 'Arabian Level' and is believed to date back to the Late Noachian. In high-resolution MOC, HiRISE and HRSC images, the Arabian Level exhibits evidence of terracing (potentially indicative of wave-cut erosion); however, the topographically lower, younger 'shorelines' do not. The interior plains encompassed by these lower levels include vast expanses of cold-climate landforms, such as polygonal ground and scalloped depressions, a relationship that is consistent with either an initially warm, but progressively cooling, aqueous environment - or initial conditions that were cold from the outset. In either case, the flow-front-like morphologies associated with the lower levels may have resulted from ice-shoving due to short-lived transgressive events caused by later episodes of outflow channel activity around the northern plains. Persuasive new support for the ocean hypothesis comes from surface permittivities derived from the global observations of the MARSIS orbital radar sounding investigation on Mars Express. These permittivities, which are a measure of how strongly a radar pulse is reflected from the Martian surface, are unexpectedly low throughout the northern plains, consistent with the occurrence of thick deposits (at least ~60-80 m) of either highly-porous or ice-rich sediment. Further insight into the origin of these low permittivities is provided

  17. High resolution integrative analysis reveals widespread genetic and epigenetic changes after chronic in-vitro acid and bile exposure in Barrett's epithelium cells.

    PubMed

    Bajpai, Manisha; Kessel, Rachel; Bhagat, Tushar; Nischal, Sangeeta; Yu, Yiting; Verma, Amit; Das, Kiron M

    2013-12-01

    Barrett's epithelium (BE) is a premalignant condition resulting from chronic gastroesophageal reflux that may progress to esophageal adenocarcinoma (EAC). Early intervention holds promise in preventing BE progression. However, identification of high-risk BE patients remains challenging due to inadequate biomarkers for early diagnosis. We investigated the effect of prolonged chronic acid and bile exposure on transcriptome, methylome, and mutatome of cells in an in-vitro BE carcinogenesis (BEC) model. Twenty weeks acid and bile exposed cells from the BEC model (BEC20w) were compared with their naïve predecessors HiSeq Illumina based RNA sequencing was performed on RNA from both the cells for gene expression and mutational analysis. HELP Tagging Assay was performed for DNA methylation analysis. Ingenuity pathway, Gene Ontology, and KEGG PATHWAY analyses were then performed on datasets. Widespread aberrant genetic and epigenetic changes were observed in the BEC20w cells. Combinatorial analyses revealed 433 from a total of 863 downregulated genes had accompanying hypermethylation of promoters. Simultaneously, 690 genes from a total of 1,492 were upregulated with accompanying promoter hypomethylation. In addition, 763 mutations were identified on 637 genes. Ingenuity pathway analysis, Gene Ontology, and KEGG PATHWAY analyses associated the genetic and epigenetic changes in BEC20w cells with cellular and biological functions. Integration of high resolution comparative analyses of naïve BAR-T and BEC20w cells revealed striking genetic and epigenetic changes induced by chronic acid and bile exposure that may disrupt normal cellular functions and promote carcinogenesis. This novel study reveals several potential targets for future biomarkers and therapeutic development.

  18. 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.

  19. 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. PMID:26340076

  20. Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography.

    PubMed

    Latch, Emily K; Reding, Dawn M; Heffelfinger, James R; Alcalá-Galván, Carlos H; Rhodes, Olin E

    2014-07-01

    Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analysed 10 microsatellite loci from over 1900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses, we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles, and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation and management.

  1. 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

  2. reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells.

    PubMed

    Kinkley, Sarah; Helmuth, Johannes; Polansky, Julia K; Dunkel, Ilona; Gasparoni, Gilles; Fröhler, Sebastian; Chen, Wei; Walter, Jörn; Hamann, Alf; Chung, Ho-Ryun

    2016-01-01

    The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4(+) memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP-seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action. PMID:27530917

  3. 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

  4. 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. PMID:25821451

  5. 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 PAGESBeta

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

    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

  6. 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

  7. 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 Central

    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. PMID:25821451

  8. Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways.

    PubMed

    Smirnova, Julia B; Selley, Julian N; Sanchez-Cabo, Fatima; Carroll, Kathleen; Eddy, A Alan; McCarthy, John E G; Hubbard, Simon J; Pavitt, Graham D; Grant, Chris M; Ashe, Mark P

    2005-11-01

    Global inhibition of protein synthesis is a hallmark of many cellular stress conditions. Even though specific mRNAs defy this (e.g., yeast GCN4 and mammalian ATF4), the extent and variation of such resistance remain uncertain. In this study, we have identified yeast mRNAs that are translationally maintained following either amino acid depletion or fusel alcohol addition. Both stresses inhibit eukaryotic translation initiation factor 2B, but via different mechanisms. Using microarray analysis of polysome and monosome mRNA pools, we demonstrate that these stress conditions elicit widespread yet distinct translational reprogramming, identifying a fundamental role for translational control in the adaptation to environmental stress. These studies also highlight the complex interplay that exists between different stages in the gene expression pathway to allow specific preordained programs of proteome remodeling. For example, many ribosome biogenesis genes are coregulated at the transcriptional and translational levels following amino acid starvation. The transcriptional regulation of these genes has recently been connected to the regulation of cellular proliferation, and on the basis of our results, the translational control of these mRNAs should be factored into this equation.

  9. reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells

    PubMed Central

    Kinkley, Sarah; Helmuth, Johannes; Polansky, Julia K.; Dunkel, Ilona; Gasparoni, Gilles; Fröhler, Sebastian; Chen, Wei; Walter, Jörn; Hamann, Alf; Chung, Ho-Ryun

    2016-01-01

    The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4+ memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP-seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action. PMID:27530917

  10. 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.

  11. Isolation and characterization of a bacteriocin (Butyrivibriocin AR10) from the ruminal anaerobe Butyrivibrio fibrisolvens AR10: evidence in support of the widespread occurrence of bacteriocin-like activity among ruminal isolates of B. fibrisolvens.

    PubMed Central

    Kalmokoff, M L; Teather, R M

    1997-01-01

    Forty-nine isolates of Butyrivibrio fibrisolvens and a single isolate of Butyrivibrio crossotus were screened for the production of inhibitors by a deferred plating procedure. Twenty-five isolates produced factors which, to various degrees, inhibited the growth of the other Butyrivibrio isolates. None of the inhibitory activity was due to bacteriophages. The inhibitory products from 18 of the producing strains were sensitive to protease digestion. Differences in the ranges of activity among the Butyrivibrio isolates and protease sensitivity profiles suggest that a number of different inhibitory compounds are produced. These findings suggest that the production of bacteriocin-like inhibitors may be a widespread characteristic throughout the genus Butyrivibrio. The bacteriocin-like activity from one isolate, B. fibrisolvens AR10, was purified and confirmed to reside in a single peptide. Crude bacteriocin extracts were prepared by ammonium sulfate and methanol precipitation of spent culture supernatants, followed by dialysis and high-speed centrifugation. The active component was isolated from the semicrude extract by reverse-phase chromatography. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis confirmed that the peptide was purified to homogeneity, having an estimated molecular mass of approximately 4,000 Da. The N terminus of the peptide was blocked. A cyanogen bromide cleavage fragment of the native peptide yielded a sequence of 20 amino acids [(M)GIQLAPAXYQDIVNXVAAG]. No homology with previously reported bacteriocins was found. Butyrivibriocin AR10 represents the first bacteriocin isolated from a ruminal anaerobe. PMID:9023920

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. Structural and Functional Studies of gpX of Escherichia coli Phage P2 Reveal a Widespread Role for LysM Domains in the Baseplates of Contractile-Tailed Phages

    PubMed Central

    Fatehi Hassanabad, Mostafa; Chang, Tom; Pirani, Nawaz; Bona, Diane; Edwards, Aled M.

    2013-01-01

    A variety of bacterial pathogenicity determinants, including the type VI secretion system and the virulence cassettes from Photorhabdus and Serratia, share an evolutionary origin with contractile-tailed myophages. The well-characterized Escherichia coli phage P2 provides an excellent system for studies related to these systems, as its protein composition appears to represent the “minimal” myophage tail. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of gpX, a 68-residue tail baseplate protein. Although the sequence and structure of gpX are similar to those of LysM domains, which are a large family associated with peptidoglycan binding, we did not detect a peptidoglycan-binding activity for gpX. However, bioinformatic analysis revealed that half of all myophages, including all that possess phage T4-like baseplates, encode a tail protein with a LysM-like domain, emphasizing a widespread role for this domain in baseplate function. While phage P2 gpX comprises only a single LysM domain, many myophages display LysM domain fusions with other tail proteins, such as the DNA circulation protein found in Mu-like phages and gp53 of T4-like phages. Electron microscopy of P2 phage particles with an incorporated gpX-maltose binding protein fusion revealed that gpX is located at the top of the baseplate, near the junction of the baseplate and tail tube. gpW, the orthologue of phage T4 gp25, was also found to localize to this region. A general colocalization of LysM-like domains and gpW homologues in diverse phages is supported by our bioinformatic analysis. PMID:24097944

  17. Fluorescence spectroscopy reveals accompanying occurrence of ammonium with fulvic acid-like organic matter in a fluvio-lacustrine aquifer of Jianhan Plain.

    PubMed

    Huang, Shuangbing; Wang, Yanxin; Ma, Teng; Wang, Yanyan; Zhao, Long

    2016-05-01

    This study is the first to investigate the simultaneous presence of NH4 (+) and fluorescent organic matter components (FOCs) from a fluvio-lacustrine aquifer in Central Jianghan Plain. Sediment, groundwater, and surface water samples were collected for the sediment organic matter extraction, 3D fluorescence spectroscopy characterization, and/or hydrochemical analysis. NH4 (+) and dissolved organic carbon was ubiquitous in the groundwater. The fluorescence spectroscopy revealed good relationships between NH4 (+) and fulvic acid-like components (FALCs) in the groundwater and sediment-extracted organic matter (SEOM) solutions. NH4 (+) also exhibited significant positive correlation with protein-like component (PLC) (p < 0.001), with the stronger in the SEOM solutions than that in groundwater. Comparisons of spectroscopic indices [e.g., humification index (HIX), biological index (BIX), spectra slope (S275-295), and specific UV absorbance (SUVA254)] between the groundwater and SEOM solutions revealed more labile properties of SEOM. This result indicates that the decreasing NH4 (+)-FOCs correlations of groundwater relative to sediments may be attributed to microbial degradation. Factor analysis identifies important factors that cause NH4 (+) occurrence in the groundwater. The accompanying increase of FALC (C1) and NH4-N with the mole concentration of the normalized HCO3 (-)/(Ca(2+)+Mg(2+)) and [H(+)] suggests that couple effects of various biodegradations simultaneously occur in the aquifer, promoting the occurrence of NH4-DOMs.

  18. 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. PMID:23877177

  19. Widespread occurrence of norspermidine and norspermine in eukaryotic algae.

    PubMed

    Hamana, K; Matsuzaki, S

    1982-04-01

    Seven phyla of eukaryotic algae were analyzed to determine their contents of diamines and polyamines. The algae examined included Rhodophyta, Pyrrophyta, Chrysophyta, Phaeophyta, Euglenophyta, Chlorophyta, and Charophyta. Both putrescine and spermidine were detected in all the algae studied, while appreciable amounts of spermine were detected only in a few species of algae. 1,3-Diaminopropane, norspermidine, and norspermine, which are chemical analogs of putrescine, spermidine, and spermine, respectively, were widely distributed in various species of algae. There was no parallelism between the distribution patterns of putrescine derivatives and those of 1,3-diaminopropane derivatives. Cadaverine and agmatine were detected in multicellular marine algae. Homospermidine was detected sporadically in some algae. The biological and phylogenetical significance of polyamines in these lower eukaryotes is discussed.

  20. 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.

  1. 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.

  2. 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. PMID:20413241

  3. 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. PMID:27209415

  4. Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes.

    PubMed

    Chen, Jing; Zhou, Zhi-Chao; Gu, Ji-Dong

    2014-06-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) process is unique in linking the microbial carbon and nitrogen cycles, but the presence of n-damo bacteria in marine ecosystem and the associated environmental factors are still poorly understood. In the present study, detection of n-damo bacteria using 16S rRNA and pmoA gene-based PCR primers was successfully employed to reveal their diversity and distribution in the surface and subsurface sediments of the South China Sea (SCS). The widespread occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity has been confirmed in this study. The pmoA gene-amplified sequences clustered within three newly erected subclusters, namely SCS-1, SCS-2, and SCS-3, suggesting the unique niche specificity of n-damo bacteria in the marine ecosystem. Results indicated the presence of n-damo bacteria in the west Pacific Ocean with a wide distribution from the continental shelf (E201S) to the deep abyss (E407S and E407B). Community structures of n-damo bacteria in SCS are clearly different from those of nonmarine ones known. It is also found that NO x (-) and NH4 (+) affected the community structures and distribution of n-damo bacteria in the SCS sediments differently. Salinity is another important factor identified, shaping the n-damo communities in marine environments. The community based on pmoA gene-amplified sequences, and community richness and diversity based on 16S rRNA gene-amplified sequences correlated with temperature. PMID:24769903

  5. Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes.

    PubMed

    Chen, Jing; Zhou, Zhi-Chao; Gu, Ji-Dong

    2014-06-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) process is unique in linking the microbial carbon and nitrogen cycles, but the presence of n-damo bacteria in marine ecosystem and the associated environmental factors are still poorly understood. In the present study, detection of n-damo bacteria using 16S rRNA and pmoA gene-based PCR primers was successfully employed to reveal their diversity and distribution in the surface and subsurface sediments of the South China Sea (SCS). The widespread occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity has been confirmed in this study. The pmoA gene-amplified sequences clustered within three newly erected subclusters, namely SCS-1, SCS-2, and SCS-3, suggesting the unique niche specificity of n-damo bacteria in the marine ecosystem. Results indicated the presence of n-damo bacteria in the west Pacific Ocean with a wide distribution from the continental shelf (E201S) to the deep abyss (E407S and E407B). Community structures of n-damo bacteria in SCS are clearly different from those of nonmarine ones known. It is also found that NO x (-) and NH4 (+) affected the community structures and distribution of n-damo bacteria in the SCS sediments differently. Salinity is another important factor identified, shaping the n-damo communities in marine environments. The community based on pmoA gene-amplified sequences, and community richness and diversity based on 16S rRNA gene-amplified sequences correlated with temperature.

  6. 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.

  7. 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

  8. Widespread pain in chronic epicondylitis.

    PubMed

    Pienimäki, Tuomo; Siira, Pertti; Vanharanta, Heikki

    2011-10-01

    We studied the associations of widespread pain with other pain and functional measures among patients with chronic epicondylitis. A total of 190 patients (66% females) participated in the study; with a mean age 43.7, mean duration of symptoms 48weeks, chronic lateral (n=160) and medial (n=30) epicondylitis. We analysed clinical status, grip strength and cubital pain thresholds and interviewed pain and disability, leisure time physical activity, strenuous hobby activities for arms, duration of symptoms, other systemic and upper extremity disorders, arm operations, and work ability. The location of pain was analysed using a whole-body pain drawing, categorized into three groups; the highest of which was classified as widespread pain. A total of 85 patients (45%) reported widespread pain. It was highly associated with female gender, high pain scores, decreased grip strength and pain thresholds (p<0.001 for all), with increased number of positive manual tests, low level of hobby strain for arms and physical activity, long duration of symptoms, and sick leave (p for all <0.05). It was also related to upper extremity disorders and arm surgery, but not with operated epicondylitis, other systemic diseases, workload or work ability. In addition, 39% of patients without other disease reported widespread pain. Widespread pain is common in chronic epicondylitis with and without other diseases, and is related to high pain scores, decreased function of the arm, long duration of symptoms, sick leave, and with a low level of physical activity.

  9. Widespread bullous fixed drug eruption

    PubMed Central

    Patell, Rushad D; Dosi, Rupal V; Shah, Purav C; Joshi, Harshal S

    2014-01-01

    A 53-year-old man developed a widespread erythematous eruption which rapidly evolved into fluid-filled bulla mostly involving the distal areas of all four limbs and erosions on the oral as well as anogenital mucosa. Based on clinical presentation, chronology of drug exposure, past events and histopathology as diagnosis of widespread bullous fixed drug eruption was made over Steven Johnson-toxic epidermal necrolysis syndrome. Steroids were deferred and the lesions healed with minimal pigmentation within a week. Differentiating between the two entities has been historically difficult, and yet can have significant therapeutic and prognostic implications. PMID:24510691

  10. Widespread bullous fixed drug eruption.

    PubMed

    Patell, Rushad D; Dosi, Rupal V; Shah, Purav C; Joshi, Harshal S

    2014-02-07

    A 53-year-old man developed a widespread erythematous eruption which rapidly evolved into fluid-filled bulla mostly involving the distal areas of all four limbs and erosions on the oral as well as anogenital mucosa. Based on clinical presentation, chronology of drug exposure, past events and histopathology as diagnosis of widespread bullous fixed drug eruption was made over Steven Johnson-toxic epidermal necrolysis syndrome. Steroids were deferred and the lesions healed with minimal pigmentation within a week. Differentiating between the two entities has been historically difficult, and yet can have significant therapeutic and prognostic implications.

  11. 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.

  12. 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.

  13. A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease

    PubMed Central

    2013-01-01

    Background Sequencing of the genome of Propionibacterium acnes produced a catalogue of genes many of which enable this organism to colonise skin and survive exposure to the elements. Despite this platform, there was little understanding of the gene regulation that gives rise to an organism that has a major impact on human health and wellbeing and causes infections beyond the skin. To address this situation, we have undertaken a genome–wide study of gene regulation using a combination of improved differential and global RNA-sequencing and an analytical approach that takes into account the inherent noise within the data. Results We have produced nucleotide-resolution transcriptome maps that identify and differentiate sites of transcription initiation from sites of stable RNA processing and mRNA cleavage. Moreover, analysis of these maps provides strong evidence for ‘pervasive’ transcription and shows that contrary to initial indications it is not biased towards the production of antisense RNAs. In addition, the maps reveal an extensive array of riboswitches, leaderless mRNAs and small non-protein-coding RNAs alongside vegetative promoters and post-transcriptional events, which includes unusual tRNA processing. The identification of such features will inform models of complex gene regulation, as illustrated here for ribonucleotide reductases and a potential quorum-sensing, two-component system. Conclusions The approach described here, which is transferable to any bacterial species, has produced a step increase in whole-cell knowledge of gene regulation in P. acnes. Continued expansion of our maps to include transcription associated with different growth conditions and genetic backgrounds will provide a new platform from which to computationally model the gene expression that determines the physiology of P. acnes and its role in human disease. PMID:24034785

  14. 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.

  15. Hearing Loss Widespread, 'Progressive' in Older Americans

    MedlinePlus

    ... page: https://medlineplus.gov/news/fullstory_160985.html Hearing Loss Widespread, 'Progressive' in Older Americans Rates accelerate especially ... 2016 (HealthDay News) -- A new study finds widespread hearing loss among elderly Americans, with an especially high rate ...

  16. 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

  17. Widespread horizontal transfer of retrotransposons.

    PubMed

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

    2013-01-15

    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

  18. Widespread horizontal transfer of retrotransposons.

    PubMed

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

    2013-01-15

    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.

  19. 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

  20. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment.

    PubMed Central

    Liesack, W; Stackebrandt, E

    1992-01-01

    A molecular ecological study was performed on an Australian soil sample to unravel a substantial portion of the bacterial diversity. A large fragment of the 16S rRNA gene was amplified, using DNA isolated by lysing the microorganisms directly within the soil matrix, and a clone library was generated. Comparative sequence analysis of 30 clones and dot blot hybridization of 83 additional clones with defined oligonucleotide probes revealed the presence of three major groups of prokaryotes of the domain Bacteria. The first one comprises 57 clones that indicate relatives of nitrogen-fixing bacteria of the alpha-2 subclass of the class Proteobacteria; the second group of 7 clones originates from members of the order Planctomycetales that, however, reveal no close relationship to any of the described Planctomycetales species; 22 clones of the third group are indicative of members of a novel main line of descent, sharing a common ancestry with members of planctomycetes and chlamydiae. Images PMID:1629164

  1. 16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization

    PubMed Central

    Ragon, Marie; Benzerara, Karim; Moreira, David; Tavera, Rosaluz; López-García, Purificación

    2014-01-01

    Cyanobacteria are mainly thought to induce carbonate precipitation extracellularly via their photosynthetic activity combined with the nucleation potential of exopolymeric substances. The discovery in microbialites of the alkaline lake Alchichica (Mexico) of Candidatus Gloeomargarita lithophora, a cyanobacterium forming large amounts of intracellular Mg-Ca-Sr-Ba carbonate spherules, showed that intracellular biomineralization in cyanobacteria is also possible. A second cyanobacterium isolated from the same environment, Candidatus Synechococcus calcipolaris G9, has been recently shown to also form intracellular calcium carbonates at the cell poles, a capability shared by all cultured species of the Thermosynechococcus clade, to which it belongs. To explore the diversity of these two distant cyanobacterial lineages representing two different patterns of intracellular calcification, we designed specific primers against their 16S rRNA genes and looked for their occurrence in a wide variety of samples. We identified the presence of members of the Gloeomargarita and Thermosynechococcus/S. calcipolaris lineages in microbialites collected from Lake Alchichica and three other neighboring Mexican lakes. The two clades also occurred in karstic areas and in some thermophilic or hypersaline microbial mats collected in South America and/or Southern Europe. Surprisingly, the within-group diversity in the two clades was low, especially within the S. calcipolaris clade, with all 16S rRNA gene sequences retrieved sharing more than 97% identity. This suggests that these clades are composed of a limited number of operational taxonomic units (OTUs) with cosmopolitan distribution. Moreover, scanning electron microscopy coupled with energy dispersive x-ray spectrometry showed the presence of intracellularly calcifying Gloeomargarita-like cyanobacteria in fresh samples where this clade was relatively abundant, suggesting that these cyanobacteria do precipitate carbonates intracellularly

  2. 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. PMID:26147218

  3. 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.

  4. 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

  5. Widespread morning drizzle on Titan.

    PubMed

    Adámkovics, Máté; Wong, Michael H; Laver, Conor; de Pater, Imke

    2007-11-01

    Precipitation is expected in Titan's atmosphere, yet it has not been directly observed, and the geographical regions where rain occurs are unknown. Here we present near-infrared spectra from the Very Large Telescope and W. M. Keck Observatories that reveal an enhancement of opacity in Titan's troposphere on the morning side of the leading hemisphere. Retrieved extinction profiles are consistent with condensed methane in clouds at an altitude near 30 kilometers and concomitant methane drizzle below. The moisture encompasses the equatorial region over Titan's brightest continent, Xanadu. Diurnal temperature gradients that cause variations in methane relative humidity, winds, and topography may each be a contributing factor to the condensation mechanism. The clouds and precipitation are optically thin at 2.0 micrometers, and models of "subvisible" clouds suggest that the droplets are 0.1 millimeter or larger.

  6. Occurrence of potentially pathogenic arcobacters in shellfish.

    PubMed

    Mottola, Anna; Bonerba, Elisabetta; Figueras, Maria José; Pérez-Cataluña, Alba; Marchetti, Patrizia; Serraino, Andrea; Bozzo, Giancarlo; Terio, Valentina; Tantillo, Giuseppina; Di Pinto, Angela

    2016-08-01

    Considering that several recent cases of human gastroenteritis have been associated with species from the Arcobacter genus, and that few data are currently available about the occurrence of this genus in Italian shellfish, the aim of the present study was to evaluate the occurrence of Arcobacter spp. and the presence of virulence-associated genes. The approach consisted of cultural and biomolecular (multiplex-PCR and 16S-RFLP) methods identifying isolates, followed by PCR assays aimed at the cadF, ciaB, cjl349, irgA, hecA putative virulence genes. Arcobacter spp. was detected in 16/70 (22.8%) shellfish samples. Specifically, Arcobacter spp. was highlighted in 10/42 (23.8%) mussel and in 6/28 (21.4%) clam samples. Subsequently, biomolecular assays revealed Arcobacter butzleri in 12/16 (75%) and Arcobacter cryaerophilus 1B in 4/16 (25%) isolates. PCRs aimed at the five putative virulence genes demonstrated widespread distribution of these genes among Arcobacter isolates and some differences from the results published by other authors. Our research provides more information regarding the health risks associated with the consumption of raw bivalve molluscs and underlines the need to implement an adequate control plan by performing intensive and continuous monitoring in order to guarantee human health. PMID:27052698

  7. 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.

  8. 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

  9. Widespread noncoding circular RNAs in plants.

    PubMed

    Ye, Chu-Yu; Chen, Li; Liu, Chen; Zhu, Qian-Hao; Fan, Longjiang

    2015-10-01

    A large number of noncoding circular RNAs (circRNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circRNAs. We performed genome-wide identification of circRNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circRNAs. circRNAs (12037 and 6012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56% (10/18) of the sampled rice exonic circRNAs validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNAs in plants. The introns flanking plant circRNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circRNAs. Plant circRNAs showed diverse expression patterns, and 27 rice exonic circRNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circRNAs and their parent genes. Our results demonstrated that circRNAs are widespread in plants, revealed the common and distinct features of circRNAs between plants and animals, and suggested that circRNAs could be a critical class of noncoding regulators in plants.

  10. 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

  11. Widespread formation of cherts during the early Eocene climate optimum

    NASA Astrophysics Data System (ADS)

    Muttoni, G.; Kent, D. V.

    2007-12-01

    Radiolarian cherts in the Tethyan realm of Jurassic age were recently interpreted as resulting from high biosiliceous productivity along upwelling zones in subequatorial paleolatitudes the locations of which were confirmed by revised paleomagnetic estimates. However, the widespread occurrence of cherts in the Eocene suggests that cherts may not always be reliable proxies of latitude and upwelling zones. In a new survey of the global spatiotemporal distribution of Cenozoic cherts in Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP) sediment cores, we found that cherts occur most frequently in the Paleocene and early Eocene, with a peak in occurrences at ~50 Ma that is coincident with the time of highest bottom water temperatures of the early Eocene climatic optimum (EECO) when the global ocean was presumably characterized by reduced upwelling efficiency and biosiliceous productivity. Cherts occur less commonly during the subsequent Eocene global cooling trend. Primary paleoclimatic factors rather than secondary diagenetic processes seem therefore to control chert formation. This timing of peak Eocene chert occurrence, which is supported by detailed stratigraphic correlations, contradicts currently accepted models that involve an initial loading of large amounts of dissolved silica from enhanced weathering and/or volcanism in a supposedly sluggish ocean of the EECO, followed during the subsequent middle Eocene global cooling by more vigorous oceanic circulation and consequent upwelling that made this silica reservoir available for enhanced biosilicification, with the formation of chert as a result of biosilica transformation during diagenesis. Instead, we suggest that basin-basin fractionation by deep-sea circulation could have raised the concentration of EECO dissolved silica especially in the North Atlantic, where an alternative mode of silica burial involving widespread direct precipitation and/or absorption of silica by clay minerals could have

  12. Widespread use of neuraminidase inhibitors in Japan.

    PubMed

    Sugaya, Norio

    2011-10-01

    Almost all patients with an influenza-like illness in Japan are now tested with rapid diagnostic tests, and when positive, they are treated with a neuraminidase inhibitor (NAI). Japan may have had the lowest case fatality rate for symptomatic illness (<0.001%, 198/20.7 million) in the H1N1/09 pandemic because of the universal implementation of early treatment with NAI. A study of 1,000 children hospitalized because of a H1N1/09 infection revealed that NAIs, primarily oseltamivir, had been used to treat 984 (98.4%) of the 1,000 patients. In 88.9% of the patients, treatment with NAIs was initiated within 48 h after the onset of illness. In addition to oseltamivir and zanamivir, the newly approved inhalant drug, laninamivir, and the newly approved intravenous drug, peramivir, were used in Japan during the 2010-2011 season. Neuropsychiatric disorders that were suspected of being adverse reactions to oseltamivir became a cause of concern in 2007. The Health, Labour and Welfare Ministry issued an emergency instruction to suspend the use of oseltamivir to treat patients between the ages of 10 and 19 years. However, according to the Vital Statistics data, the widespread use of oseltamivir has not caused an increase in deaths as a result of accidental falls or intentional jumps from buildings. Although oseltamivir is widely used in Japan, no outbreaks have been caused by oseltamivir-resistant viruses, and no serious illness caused by oseltamivir-resistant viruses has ever been reported.

  13. Widespread Wolbachia infection in terrestrial isopods and other crustaceans.

    PubMed

    Cordaux, Richard; Pichon, Samuel; Hatira, Houda Ben Afia; Doublet, Vincent; Grève, Pierre; Marcadé, Isabelle; Braquart-Varnier, Christine; Souty-Grosset, Catherine; Charfi-Cheikhrouha, Faouzia; Bouchon, Didier

    2012-01-01

    Wolbachia bacteria are obligate intracellular alpha-Proteobacteria of arthropods and nematodes. Although widespread among isopod crustaceans, they have seldom been found in non-isopod crustacean species. Here, we report Wolbachia infection in fourteen new crustacean species. Our results extend the range of Wolbachia infections in terrestrial isopods and amphipods (class Malacostraca). We report the occurrence of two different Wolbachia strains in two host species (a terrestrial isopod and an amphipod). Moreover, the discovery of Wolbachia in the goose barnacle Lepas anatifera (subclass Thecostraca) establishes Wolbachia infection in class Maxillopoda. The new bacterial strains are closely related to B-supergroup Wolbachia strains previously reported from crustacean hosts. Our results suggest that Wolbachia infection may be much more widespread in crustaceans than previously thought. The presence of related Wolbachia strains in highly divergent crustacean hosts suggests that Wolbachia endosymbionts can naturally adapt to a wide range of crustacean hosts. Given the ability of isopod Wolbachia strains to induce feminization of genetic males or cytoplasmic incompatibility, we speculate that manipulation of crustacean-borne Wolbachia bacteria might represent potential tools for controlling crustacean species of commercial interest and crustacean or insect disease vectors.

  14. Widespread Wolbachia infection in terrestrial isopods and other crustaceans

    PubMed Central

    Cordaux, Richard; Pichon, Samuel; Hatira, Houda Ben Afia; Doublet, Vincent; Grève, Pierre; Marcadé, Isabelle; Braquart-Varnier, Christine; Souty-Grosset, Catherine; Charfi-Cheikhrouha, Faouzia; Bouchon, Didier

    2012-01-01

    Abstract Wolbachia bacteria are obligate intracellular alpha-Proteobacteria of arthropods and nematodes. Although widespread among isopod crustaceans, they have seldom been found in non-isopod crustacean species. Here, we report Wolbachia infection in fourteen new crustacean species. Our results extend the range of Wolbachia infections in terrestrial isopods and amphipods (class Malacostraca). We report the occurrence of two different Wolbachia strains in two host species (a terrestrial isopod and an amphipod). Moreover, the discovery of Wolbachia in the goose barnacle Lepas anatifera (subclass Thecostraca) establishes Wolbachia infection in class Maxillopoda. The new bacterial strains are closely related to B-supergroup Wolbachia strains previously reported from crustacean hosts. Our results suggest that Wolbachia infection may be much more widespread in crustaceans than previously thought. The presence of related Wolbachia strains in highly divergent crustacean hosts suggests that Wolbachia endosymbionts can naturally adapt to a wide range of crustacean hosts. Given the ability of isopod Wolbachia strains to induce feminization of genetic males or cytoplasmic incompatibility, we speculate that manipulation of crustacean-borne Wolbachia bacteria might represent potential tools for controlling crustacean species of commercial interest and crustacean or insect disease vectors. PMID:22536103

  15. Widespread co-occurrence of virulent pathogens within California amphibian communities.

    PubMed

    Hoverman, Jason T; Mihaljevic, Joseph R; Richgels, Katherine L D; Kerby, Jacob L; Johnson, Pieter T J

    2012-09-01

    The chytrid fungus Batrachochytrium dendrobatidis, ranaviruses, and trematodes (Ribeiroia ondatrae and echinostomes) are highly virulent pathogens known to infect amphibians, yet the extent to which they co-occur within amphibian communities remains poorly understood. Using field surveillance of 85 wetlands in the East Bay region of California, USA, we found that 68% of wetlands had ≥2 pathogens and 36% had ≥3 pathogens. Wetlands with high pathogen species richness also tended to cluster spatially. Our results underscore the need for greater integration of multiple pathogens and their interactions into amphibian disease research and conservation efforts.

  16. Widespread occurrence and diversity of Cassava brown streak virus (Potyviridae: Ipomovirus) in Tanzania.

    PubMed

    Rwegasira, G M; Momanyi, G; Rey, M E C; Kahwa, G; Legg, J P

    2011-10-01

    Cassava brown streak disease (CBSD) has been a problem in Tanzania since 1936. Existing literature indicated limited distribution of the disease to low altitudes, usually <100 m above sea level, but the current geographical distribution of the disease was not known. Whether a single or many strains for the virus exist in Tanzania had not been reported to date. In this study, CBSD was recorded from sea level to ≈1,800 m above sea level. In total, 2,730 cassava plants were assessed for CBSD leaf symptoms in 91 fields and root symptoms were assessed at 81 sites. A sample was taken from each site for laboratory screening for Cassava brown streak virus (CBSV). CBSD mean foliar and root incidences were 38 and 36%, respectively. Reverse-transcription polymerase chain reaction of a partial 3'-terminal coat protein (CP) region of CBSV indicated the presence of CBSV in 67 of the 91 (73%) samples. Forty-three amplicons were sequenced, and phylogenetic comparisons with nucleotide sequences from GenBank (National Center for Biotechnology Information database) suggested that one major clade of CBSV primarily exists in Tanzania. However, there was nucleotide sequence divergence of up to 19% among the 42 isolates. In all, 42 of the 43 sequences had 80 to 100% nucleotide identity with 6 previously reported CP-CBSV sequences (from Mozambique and Tanzania). In total, 13 of 42 isolates had <80% nucleotide identities with three previously reported Ugandan CBSV sequences. One isolate, FJ687177, shared <78% sequence identity with the other Tanzanian sequences but was closely related (93%) to Ugandan isolates. It is likely that isolate FJ687177 may belong to a less widely distributed recently described species (clade 2) of CBSV, named Ugandan cassava brown streak virus (UCBSV).

  17. 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. PMID:21939283

  18. 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.

  19. 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.

  20. 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 ...

  1. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata).

    PubMed

    Guillou, L; Viprey, M; Chambouvet, A; Welsh, R M; Kirkham, A R; Massana, R; Scanlan, D J; Worden, A Z

    2008-12-01

    Syndiniales are a parasitic order within the eukaryotic lineage Dinophyceae (Alveolata). Here, we analysed the taxonomy of this group using 43655 18S rRNA gene sequences obtained either from environmental data sets or cultures, including 6874 environmental sequences from this study derived from Atlantic and Mediterranean waters. A total of 5571 out of the 43655 sequences analysed fell within the Dinophyceae. Both bayesian and maximum likelihood phylogenies placed Syndiniales in five main groups (I-V), as a monophyletic lineage at the base of 'core' dinoflagellates (all Dinophyceae except Syndiniales), although the latter placement was not bootstrap supported. Thus, the two uncultured novel marine alveolate groups I and II, which have been highlighted previously, are confirmed to belong to the Syndiniales. These groups were the most diverse and highly represented in environmental studies. Within each, 8 and 44 clades were identified respectively. Co-evolutionary trends between parasitic Syndiniales and their putative hosts were not clear, suggesting they may be relatively 'general' parasitoids. Based on the overall distribution patterns of the Syndiniales-affiliated sequences, we propose that Syndiniales are exclusively marine. Interestingly, sequences belonging to groups II, III and V were largely retrieved from the photic zone, while Group I dominated samples from anoxic and suboxic ecosystems. Nevertheless, both groups I and II contained specific clades preferentially, or exclusively, retrieved from these latter ecosystems. Given the broad distribution of Syndiniales, our work indicates that parasitism may be a major force in ocean food webs, a force that is neglected in current conceptualizations of the marine carbon cycle.

  2. Widespread occurrence of non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase among gram-positive bacteria.

    PubMed

    Iddar, Abdelghani; Valverde, Federico; Assobhei, Omar; Serrano, Aurelio; Soukri, Abdelaziz

    2005-12-01

    The non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase (GAPDHN, NADP+-specific, EC 1.2.1.9) is present in green eukaryotes and some Streptococcus strains. The present report describes the results of activity and immunoblot analyses, which were used to generate the first survey of bacterial GAPDHN distribution in a number of Bacillus, Streptococcus and Clostridium strains. Putative gapN genes were identified after PCR amplification of partial 700-bp sequences using degenerate primers constructed from highly conserved protein regions. Alignment of the amino acid sequences of these fragments with those of known sequences from other eukaryotic and prokaryotic GAPDHNs, demonstrated the presence of conserved residues involved in catalytic activity that are not conserved in aldehyde dehydrogenases, a protein family closely linked to GAPDHNs. The results confirm that the basic structural features of the members of the GAPDHN family have been conserved throughout evolution and that no identity exists with phosphorylating GAPDHs. Furthermore, phylogenetic trees generated from multiple sequence alignments suggested a close relationship between plant and bacterial GAPDHN families.

  3. 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. PMID:26498102

  4. 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.

  5. 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.

  6. Widespread cytoskeletal pathology characterizes corticobasal degeneration.

    PubMed Central

    Feany, M. B.; Dickson, D. W.

    1995-01-01

    Corticobasal degeneration (CBD) is a rare, progressive neurological disorder characterized by widespread neuronal and glial pathology. Using immunohistochemistry and laser confocal microscopy, we demonstrate that the nonamyloid cortical plaques of CBD are actually collections of abnormal tau in the distal processes of astrocytes. These glial cells express both vimentin and CD44, markers of astrocyte activation. Glial pathology also includes tau-positive cytoplasmic inclusions, here localized to Leu 7-expressing oligodendrocytes. In addition, a wide array of neuronal pathology is defined with tau-positive inclusions in multiple domains of a variety of cortical neurons. CBD thus exhibits widespread glial and neuronal cytoskeletal pathology, including a novel structure, the astrocytic plaque. CBD is a disease of generalized cytoskeletal disruption affecting several cell types and multiple domains of these cells. The further definition of CBD pathology refines the diagnosis and pathophysiological understanding of this unique disease and has important implications for other neurodegenerative diseases, like Alzheimer's disease, characterized by abnormal tau deposition. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:7778678

  7. 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

  8. Genealogy and Demographic History of a Widespread Amphibian throughout Indochina.

    PubMed

    Blair, Christopher; Davy, Christina M; Ngo, Andre; Orlov, Nikolai L; Shi, Hai-tao; Lu, Shun-qing; Gao, Lan; Rao, Ding-qi; Murphy, Robert W

    2013-01-01

    Relatively little is known about spatial patterns of cryptic diversity in tropical species and the processes that generate them. Few studies examine the geographic distribution of genetic lineages in Southeast Asia, an area hypothesized to harbor substantial cryptic diversity. We investigated the evolutionary history of Asian tree frogs of the Polypedates leucomystax complex (n = 172) based on 1800 bp of the mtDNA genes ND1 and cytochrome b and tested hypotheses pertaining to climate, geology, and dispersal patterns. Analyses revealed substantial genetic diversity and lineage divergence throughout the region with evidence for widespread sympatric lineages and a general north versus south clustering. Relaxed molecular clock analysis and tests for demographic expansion identified an initial cladogenesis during the Miocene with subsequent Plio-Pleistocene diversification, with the former corresponding to periods of increased aridity and the onset of monsoonal weather systems. Rates of diversification were relatively constant until the Early Pleistocene when rates increased exponentially. We found equivocal evidence for isolation-by-distance and a potential role of some landscape features as partial barriers to dispersal. Finally, our analyses showed that divergence between insular and mainland populations occurred before Homo sapiens colonized Southeast Asia, suggesting that historical human-mediated dispersal did not drive insular diversification. Our results suggested that demographic expansion in the Late Pleistocene resulted in widespread sympatric lineages in the P. leucomystax complex throughout southern China and Indochina and further clarified the evolutionary history of lineages within P. leucomystax.

  9. 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.

  10. 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

  11. 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

  12. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

    PubMed

    Yang, Xinping; Coulombe-Huntington, Jasmin; Kang, Shuli; Sheynkman, Gloria M; Hao, Tong; Richardson, Aaron; Sun, Song; Yang, Fan; Shen, Yun A; Murray, Ryan R; Spirohn, Kerstin; Begg, Bridget E; Duran-Frigola, Miquel; MacWilliams, Andrew; Pevzner, Samuel J; Zhong, Quan; Trigg, Shelly A; Tam, Stanley; Ghamsari, Lila; Sahni, Nidhi; Yi, Song; Rodriguez, Maria D; Balcha, Dawit; Tan, Guihong; Costanzo, Michael; Andrews, Brenda; Boone, Charles; Zhou, Xianghong J; Salehi-Ashtiani, Kourosh; Charloteaux, Benoit; Chen, Alyce A; Calderwood, Michael A; Aloy, Patrick; Roth, Frederick P; Hill, David E; Iakoucheva, Lilia M; Xia, Yu; Vidal, Marc

    2016-02-11

    While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms" are functionally divergent (i.e., "functional alloforms"). PMID:26871637

  13. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

    PubMed

    Yang, Xinping; Coulombe-Huntington, Jasmin; Kang, Shuli; Sheynkman, Gloria M; Hao, Tong; Richardson, Aaron; Sun, Song; Yang, Fan; Shen, Yun A; Murray, Ryan R; Spirohn, Kerstin; Begg, Bridget E; Duran-Frigola, Miquel; MacWilliams, Andrew; Pevzner, Samuel J; Zhong, Quan; Trigg, Shelly A; Tam, Stanley; Ghamsari, Lila; Sahni, Nidhi; Yi, Song; Rodriguez, Maria D; Balcha, Dawit; Tan, Guihong; Costanzo, Michael; Andrews, Brenda; Boone, Charles; Zhou, Xianghong J; Salehi-Ashtiani, Kourosh; Charloteaux, Benoit; Chen, Alyce A; Calderwood, Michael A; Aloy, Patrick; Roth, Frederick P; Hill, David E; Iakoucheva, Lilia M; Xia, Yu; Vidal, Marc

    2016-02-11

    While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms" are functionally divergent (i.e., "functional alloforms").

  14. 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. PMID:21396373

  15. Widespread Gene Conversion in Centromere Cores

    PubMed Central

    Shi, Jinghua; Wolf, Sarah E.; Burke, John M.; Presting, Gernot G.; Ross-Ibarra, Jeffrey; Dawe, R. Kelly

    2010-01-01

    Centromeres are the most dynamic regions of the genome, yet they are typified by little or no crossing over, making it difficult to explain the origin of this diversity. To address this question, we developed a novel CENH3 ChIP display method that maps kinetochore footprints over transposon-rich areas of centromere cores. A high level of polymorphism made it possible to map a total of 238 within-centromere markers using maize recombinant inbred lines. Over half of the markers were shown to interact directly with kinetochores (CENH3) by chromatin immunoprecipitation. Although classical crossing over is fully suppressed across CENH3 domains, two gene conversion events (i.e., non-crossover marker exchanges) were identified in a mapping population. A population genetic analysis of 53 diverse inbreds suggests that historical gene conversion is widespread in maize centromeres, occurring at a rate >1×10−5/marker/generation. We conclude that gene conversion accelerates centromere evolution by facilitating sequence exchange among chromosomes. PMID:20231874

  16. Widespread vestibular activation of the rodent cortex.

    PubMed

    Rancz, Ede A; Moya, Javier; Drawitsch, Florian; Brichta, Alan M; Canals, Santiago; Margrie, Troy W

    2015-04-15

    Much of our understanding of the neuronal mechanisms of spatial navigation is derived from chronic recordings in rodents in which head-direction, place, and grid cells have all been described. However, despite the proposed importance of self-reference information to these internal representations of space, their congruence with vestibular signaling remains unclear. Here we have undertaken brain-wide functional mapping using both fMRI and electrophysiological methods to directly determine the spatial extent, strength, and time course of vestibular signaling across the rat forebrain. We find distributed activity throughout thalamic, limbic, and particularly primary sensory cortical areas in addition to known head-direction pathways. We also observe activation of frontal regions, including infralimbic and cingulate cortices, indicating integration of vestibular information throughout functionally diverse cortical regions. These whole-brain activity maps therefore suggest a widespread contribution of vestibular signaling to a self-centered framework for multimodal sensorimotor integration in support of movement planning, execution, spatial navigation, and autonomic responses to gravito-inertial changes. PMID:25878265

  17. Thermal acclimation in widespread heterotrophic soil microbes.

    PubMed

    Crowther, Thomas W; Bradford, Mark A

    2013-04-01

    Respiration by plants and microorganisms is primarily responsible for mediating carbon exchanges between the biosphere and atmosphere. Climate warming has the potential to influence the activity of these organisms, regulating exchanges between carbon pools. Physiological 'down-regulation' of warm-adapted species (acclimation) could ameliorate the predicted respiratory losses of soil carbon under climate change scenarios, but unlike plants and symbiotic microbes, the existence of this phenomenon in heterotrophic soil microbes remains controversial. Previous studies using complex soil microbial communities are unable to distinguish physiological acclimation from other community-scale adjustments. We explored the temperature-sensitivity of individual saprotrophic basidiomycete fungi growing in agar, showing definitively that these widespread heterotrophic fungi can acclimate to temperature. In almost all cases, the warm-acclimated individuals had lower growth and respiration rates at intermediate temperatures than cold-acclimated isolates. Inclusion of such microbial physiological responses to warming is essential to enhance the robustness of global climate-ecosystem carbon models. PMID:23331708

  18. 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

  19. 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

  20. 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. PMID:26044348

  1. Transglutaminases: Widespread Cross-linking Enzymes in Plants

    PubMed Central

    Serafini-Fracassini, Donatella; Del Duca, Stefano

    2008-01-01

    Background Transglutaminases have been studied in plants since 1987 in investigations aimed at interpreting some of the molecular mechanisms by which polyamines affect growth and differentiation. Transglutaminases are a widely distributed enzyme family catalysing a myriad of biological reactions in animals. In plants, the post-translational modification of proteins by polyamines forming inter- or intra-molecular cross-links has been the main transglutaminase reaction studied. Characteristics of Plant Transglutaminases The few plant transglutaminases sequenced so far have little sequence homology with the best-known animal enzymes, except for the catalytic triad; however, they share a possible structural homology. Proofs of their catalytic activity are: (a) their ability to produce glutamyl-polyamine derivatives; (b) their recognition by animal transglutaminase antibodies; and (c) biochemical features such as calcium-dependency, etc. However, many of their fundamental biochemical and physiological properties still remain elusive. Transglutaminase Activity is Ubiquitous It has been detected in algae and in angiosperms in different organs and sub-cellular compartments, chloroplasts being the best-studied organelles. Possible Roles Possible roles concern the structural modification of specific protein substrates. In chloroplasts, transglutaminases appear to stabilize the photosynthetic complexes and Rubisco, being regulated by light and other factors, and possibly exerting a positive effect on photosynthesis and photo-protection. In the cytosol, they modify cytoskeletal proteins. Preliminary reports suggest an involvement in the cell wall construction/organization. Other roles appear to be related to fertilization, abiotic and biotic stresses, senescence and programmed cell death, including the hypersensitive reaction. Conclusions The widespread occurrence of transglutaminases activity in all organs and cell compartments studied suggests a relevance for their still

  2. 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.

  3. 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.

  4. Developmental dyslexia and widespread activation across the cerebellar hemispheres.

    PubMed

    Baillieux, Hanne; Vandervliet, Everhard J M; Manto, Mario; Parizel, Paul M; De Deyn, Peter P; Mariën, Peter

    2009-02-01

    Developmental dyslexia is the most common learning disability in school-aged children with an estimated incidence of five to ten percent. The cause and pathophysiological substrate of this developmental disorder is unclear. Recently, a possible involvement of the cerebellum in the pathogenesis of dyslexia has been postulated. In this study, 15 dyslexic children and 7 age-matched control subjects were investigated by means of functional neuroimaging (fMRI) using a noun-verb association paradigm. Comparison of activation patterns between dyslexic and control subjects revealed distinct and significant differences in cerebral and cerebellar activation. Control subjects showed bilaterally well-defined and focal activation patterns in the frontal and parietal lobes and the posterior regions of the cerebellar hemispheres. The dyslexic children, however, presented widespread and diffuse activations on the cerebral and cerebellar level. Cerebral activations were found in frontal, parietal, temporal and occipital regions. Activations in the cerebellum were found predominantly in the cerebellar cortex, including Crus I, Crus II, hemispheric lobule VI, VII and vermal lobules I, II, III, IV and VII. This preliminary study is the first to reveal a significant difference in cerebellar functioning between dyslexic children and controls during a semantic association task. As a result, we propose a new hypothesis regarding the pathophysiological mechanisms of developmental dyslexia. Given the sites of activation in the cerebellum in the dyslexic group, a defect of the intra-cerebellar distribution of activity is suspected, suggesting a disorder of the processing or transfer of information within the cerebellar cortex. PMID:18986695

  5. Chronic widespread pain: clinical comorbidities and psychological correlates.

    PubMed

    Burri, Andrea; Ogata, Soshiro; Vehof, Jelle; Williams, Frances

    2015-08-01

    Recent studies have provided consistent evidence for a genetic influence on chronic widespread pain (CWP). The aim of this study was to investigate (1) the etiological structure underlying CWP by examining the covariation between CWP and psychological comorbidities and psychoaffective correlates and (2) the decomposition of the covariation into genetic and environmental components. A total of 3266 female twins (mean age 56.6 years) were subject to multivariate analyses. Using validated questionnaires to classify twins as having CWP, the prevalence of CWP was 20.8%. In the multivariate analysis, the most suitable model was the common pathway model. This model revealed 2 underlying latent variables, one common to anxiety, emotional intelligence, and emotional instability (f1) and the other common to depression and CWP (f2), the latter being highly heritable (86%). Both latent variables (f1 and f2) shared an additive genetic and a nonshared environmental factor. In addition, a second additive genetic factor loading only on f2 was found. This study reveals the structure of genetic and environmental influences of CWP and its psychoaffective correlates. The results show that the clustering of CWP and depression is due to a common, highly heritable, underlying latent trait. In addition, we found evidence that CWP, anxiety, emotional instability, and emotional intelligence are influenced by different underlying latent traits sharing the same genetic and nonshared environmental factors. This is the first study to reveal the structure and relative importance of genetic and environmental influences on complex etiological mechanisms of CWP and its correlates. PMID:25851458

  6. 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.

  7. No current evidence for widespread dosage compensation in S. cerevisiae

    PubMed Central

    Torres, Eduardo M; Springer, Michael; Amon, Angelika

    2016-01-01

    Previous studies of laboratory strains of budding yeast had shown that when gene copy number is altered experimentally, RNA levels generally scale accordingly. This is true when the copy number of individual genes or entire chromosomes is altered. In a recent study, Hose et al. (2015) reported that this tight correlation between gene copy number and RNA levels is not observed in recently isolated wild Saccharomyces cerevisiae variants. To understand the origins of this proposed difference in gene expression regulation between natural variants and laboratory strains of S. cerevisiae, we evaluated the karyotype and gene expression studies performed by Hose et al. on wild S. cerevisiae strains. In contrast to the results of Hose et al., our reexamination of their data revealed a tight correlation between gene copy number and gene expression. We conclude that widespread dosage compensation occurs neither in laboratory strains nor in natural variants of S. cerevisiae. DOI: http://dx.doi.org/10.7554/eLife.10996.001 PMID:26949255

  8. 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.

  9. 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

  10. Common occurrence of antibacterial agents in human intestinal microbiota.

    PubMed

    Drissi, Fatima; Buffet, Sylvain; Raoult, Didier; Merhej, Vicky

    2015-01-01

    Laboratory experiments have revealed many active mechanisms by which bacteria can inhibit the growth of other organisms. Bacteriocins are a diverse group of natural ribosomally synthesized antimicrobial peptides produced by a wide range of bacteria and which seem to play an important role in mediating competition within bacterial communities. In this study, we have identified and established the structural classification of putative bacteriocins encoded by 317 microbial genomes in the human intestine. On the basis of homologies to available bacteriocin sequences, mainly from lactic acid bacteria, we report the widespread occurrence of bacteriocins across the gut microbiota: 175 bacteriocins were found to be encoded in Firmicutes, 79 in Proteobacteria, 34 in Bacteroidetes, and 25 in Actinobacteria. Bacteriocins from gut bacteria displayed wide differences among phyla with regard to class distribution, net positive charge, hydrophobicity and secondary structure, but the α-helix was the most abundant structure. The peptide structures and physiochemical properties of bacteriocins produced by the most abundant bacteria in the gut, the Firmicutes and the Bacteroidetes, seem to ensure low antibiotic activity and participate in permanent intestinal host defense against the proliferation of harmful bacteria. Meanwhile, the potentially harmful bacteria, including the Proteobacteria, displayed highly effective bacteriocins, probably supporting the virulent character of diseases. These findings highlight the eventual role played by bacteriocins in gut microbial competition and their potential place in antibiotic therapy.

  11. 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.

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

    PubMed

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

    2014-03-01

    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.

  13. Worldwide occurrence of integrative conjugative element encoding multidrug resistance determinants in epidemic Vibrio cholerae O1.

    PubMed

    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.

  14. 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

  15. Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite

    PubMed Central

    Cobbold, Simon A.; Santos, Joana M.; Ochoa, Alejandro; Perlman, David H.; Llinás, Manuel

    2016-01-01

    Lysine acetylation is a ubiquitous post-translational modification in many organisms including the malaria parasite Plasmodium falciparum, yet the full extent of acetylation across the parasite proteome remains unresolved. Moreover, the functional significance of acetylation or how specific acetyl-lysine sites are regulated is largely unknown. Here we report a seven-fold expansion of the known parasite ‘acetylome’, characterizing 2,876 acetylation sites on 1,146 proteins. We observe that lysine acetylation targets a diverse range of protein complexes and is particularly enriched within the Apicomplexan AP2 (ApiAP2) DNA-binding protein family. Using quantitative proteomics we determined that artificial perturbation of the acetate/acetyl-CoA balance alters the acetyl-lysine occupancy of several ApiAP2 DNA-binding proteins and related transcriptional proteins. This metabolic signaling could mediate significant downstream transcriptional responses, as we show that acetylation of an ApiAP2 DNA-binding domain ablates its DNA-binding propensity. Lastly, we investigated the acetyl-lysine targets of each class of lysine deacetylase in order to begin to explore how each class of enzyme contributes to regulating the P. falciparum acetylome. PMID:26813983

  16. 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.

  17. Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation.

    PubMed

    Chatterjee, Aniruddha; Stockwell, Peter A; Rodger, Euan J; Duncan, Elizabeth J; Parry, Matthew F; Weeks, Robert J; Morison, Ian M

    2015-11-27

    The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript.

  18. 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

  19. HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses.

    PubMed

    Contreras-Galindo, Rafael; Kaplan, Mark H; He, Shirley; Contreras-Galindo, Angie C; Gonzalez-Hernandez, Marta J; Kappes, Ferdinand; Dube, Derek; Chan, Susana M; Robinson, Dan; Meng, Fan; Dai, Manhong; Gitlin, Scott D; Chinnaiyan, Arul M; Omenn, Gilbert S; Markovitz, David M

    2013-09-01

    Human endogenous retroviruses (HERVs) make up 8% of the human genome. The HERV-K (HML-2) family is the most recent group of these viruses to have inserted into the genome, and we have detected the activation of HERV-K (HML-2) proviruses in the blood of patients with HIV-1 infection. We report that HIV-1 infection activates expression of a novel HERV-K (HML-2) provirus, termed K111, present in multiple copies in the centromeres of chromosomes throughout the human genome yet not annotated in the most recent human genome assembly. Infection with HIV-1 or stimulation with the HIV-1 Tat protein leads to the activation of K111 proviruses. K111 is present as a single copy in the genome of the chimpanzee, yet K111 is not found in the genomes of other primates. Remarkably, K111 proviruses appear in the genomes of the extinct Neanderthal and Denisovan, while modern humans have at least 100 K111 proviruses spread across the centromeres of 15 chromosomes. Our studies suggest that the progenitor K111 integrated before the Homo-Pan divergence and expanded in copy number during the evolution of hominins, perhaps by recombination. The expansion of K111 provides sequence evidence suggesting that recombination between the centromeres of various chromosomes took place during the evolution of humans. K111 proviruses show significant sequence variations in each individual centromere, which may serve as markers in future efforts to annotate human centromere sequences. Further, this work is an example of the potential to discover previously unknown genomic sequences through the analysis of nucleic acids found in the blood of patients.

  20. A genome-wide panel of congenic mice reveals widespread epistasis of behavior quantitative trait loci.

    PubMed

    Gale, G D; Yazdi, R D; Khan, A H; Lusis, A J; Davis, R C; Smith, D J

    2009-06-01

    Understanding the genetics of behavioral variation remains a fascinating but difficult problem with considerable theoretical and practical implications. We used the genome-tagged mice (GTM) and an extensive test battery of well-validated behavioral assays to scan the genome for behavioral quantitative trait loci (QTLs). The GTM are a panel of 'speed congenic' mice consisting of over 60 strains spanning the entire autosomal genome. Each strain harbors a small (approximately 23 cM) DBA/2J donor segment on a uniform C57BL/6J background. The panel allows for mapping to regions as small as 5 cM and provides a powerful new tool for increasing mapping power and replicability in the analysis of QTLs. A total of 97 loci were mapped for a variety of complex behavioral traits including hyperactivity, anxiety, prepulse inhibition, avoidance and conditional fear. A larger number of loci were recovered than generally attained from standard mapping crosses. In addition, a surprisingly high proportion of loci, 63%, showed phenotypes unlike either of the parental strains. These data suggest that epistasis decreases sensitivity of locus detection in traditional crosses and demonstrate the utility of the GTM for mapping complex behavioral traits with high sensitivity and precision.

  1. Retrospective survey of museum specimens reveals historically widespread presence of Batrachochytrium dendrobatidis in China.

    PubMed

    Zhu, Wei; Bai, Changming; Wang, Supen; Soto-Azat, Claudio; Li, Xianping; Liu, Xuan; Li, Yiming

    2014-06-01

    Chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has been implicated in amphibian population declines worldwide. However, no amphibian declines or extinctions associated with Bd have been reported in Asia. To investigate the history of this pathogen in China, we examined 1,007 museum-preserved amphibian specimens of 80 species collected between 1933 and 2009. Bd was detected in 60 individuals (6.0%), with the earliest case of Bd infection occurring in one specimen of Bufo gargarizans and two Fejervarya limnocharis, all collected in 1933 from Chongqing, southwest China. Although mainly detected in non-threatened native amphibians, Bd was also found in four endangered species. We report the first evidence of Bd for Taiwan and the first detection of Bd in the critically endangered Chinese giant salamander (Andrias davidianus). Bd appears to have been present at a low rate of infection since at least the 1930s in China, and no significant differences in prevalence were detected between decades or provinces, suggesting that a historical steady endemic relationship between Bd and Chinese amphibians has occurred. Our results add new insights on the global emergence of Bd and suggest that this pathogen has been more widely distributed in the last century than previously believed.

  2. 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

  3. Widespread seasonal gene expression reveals annual differences in human immunity and physiology

    PubMed Central

    Dopico, Xaquin Castro; Evangelou, Marina; Ferreira, Ricardo C.; Guo, Hui; Pekalski, Marcin L.; Smyth, Deborah J.; Cooper, Nicholas; Burren, Oliver S.; Fulford, Anthony J.; Hennig, Branwen J.; Prentice, Andrew M.; Ziegler, Anette-G.; Bonifacio, Ezio; Wallace, Chris; Todd, John A.

    2015-01-01

    Seasonal variations are rarely considered a contributing component to human tissue function or health, although many diseases and physiological process display annual periodicities. Here we find more than 4,000 protein-coding mRNAs in white blood cells and adipose tissue to have seasonal expression profiles, with inverted patterns observed between Europe and Oceania. We also find the cellular composition of blood to vary by season, and these changes, which differ between the United Kingdom and The Gambia, could explain the gene expression periodicity. With regards to tissue function, the immune system has a profound pro-inflammatory transcriptomic profile during European winter, with increased levels of soluble IL-6 receptor and C-reactive protein, risk biomarkers for cardiovascular, psychiatric and autoimmune diseases that have peak incidences in winter. Circannual rhythms thus require further exploration as contributors to various aspects of human physiology and disease. PMID:25965853

  4. 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.

  5. Revealing Mercury

    NASA Astrophysics Data System (ADS)

    Prockter, L. M.; Solomon, S. C.; Head, J. W.; Watters, T. R.; Murchie, S. L.; Robinson, M. S.; Chapman, C. R.; McNutt, R. L.

    2009-04-01

    The MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft, developed under NASA's Discovery Program, launched in August 2004. En route to insertion into orbit about Mercury in 2011, MESSENGER flies by Mercury three times. The first and second of these encounters were accomplished in January and October of 2008. These flybys viewed portions of Mercury's surface that were not observed by Mariner 10 during its reconnaissance of somewhat less than half of the planet in 1974-1975. All MESSENGER instruments operated during each flyby and returned a wealth of new data. Many of the new observations were focused on the planet's geology, including monochrome imaging at resolutions as high as 100 m/pixel, multispectral imaging in 11 filters at resolutions as high as 500 m/pixel, laser altimetry tracks extending over several thousands of kilometers, and high-resolution spectral measurements of several types of terrain. Here we present an overview of the first inferences on the global geology of Mercury from the MESSENGER observations. Whereas evidence for volcanism was equivocal from Mariner 10 data, the new MESSENGER images and altimetry provide compelling evidence that volcanism was widespread and protracted on Mercury. Color imaging reveals three common spectral units on the surface: a higher-reflectance, relatively red material occurring as a distinct class of smooth plains, typically with distinct embayment relationships interpreted to indicate volcanic emplacement; a lower-reflectance, relatively blue material typically excavated by impact craters and therefore inferred to be more common at depth; and a spectrally intermediate terrain that constitutes much of the uppermost crust. Three more minor spectral units are also seen: fresh crater ejecta, reddish material associated with rimless depressions interpreted to be volcanic centers, and high-reflectance deposits seen in some crater floors. Preliminary measurements of crater size

  6. 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.

  7. 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). PMID:27248576

  8. Widespread occurrence of phthalic acid esters in raw oilseeds in China used for edible vegetable oil production.

    PubMed

    Hu, Ai-Peng; Liu, Yu-Lan; Shi, Long-Kai

    2016-09-01

    Seven different phthalic acid esters (PAEs) were quantified in 124 samples of 16 types of oilseeds from China using a simplified GC-MS method. Di-2-ethylhexyl phthalate and di-n-butyl phthalate were found in all tested oilseed samples. Each made a high contribution to the summed total PAEs. Total PAE concentrations in 124 oilseeds ranged from 0.14 to 3.05 mg kg(-1), and the mean was 0.99 mg kg(-1). Mandulapalka (Cyperus esculentus) samples were the most severely contaminated among all the tested specimens; maize germ samples were least contaminated. Di-n-octyl phthalate and butylbenzyl phthalate were not detected in 12 and five types of oilseeds, respectively. Only eight samples contained all seven analytes. No difference was observed between woody oil-bearing plant and herbaceous oil-bearing plant in terms of PAEs content.

  9. 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. PMID:27289504

  10. Intersex in the clam Scrobicularia plana (Da Costa): Widespread occurrence in English Channel estuaries and surrounding areas.

    PubMed

    Pope, N D; Childs, K; Dang, C; Davey, M S; O'Hara, S C M; Langston, K; Minier, C; Pascoe, P L; Shortridge, E; Langston, W J

    2015-06-30

    Estuarine clams Scrobicularia plana were sampled from 108 intertidal locations around the English Channel and adjacent areas. Although S. plana is believed to be a strict gonochorist, 58% of the populations sampled included intersexed individuals (described as male clams exhibiting ovotestis). Over the entire region, on average, 8.6% of male clams exhibited intersex, although proportions of affected males ranged from 0% to 53% depending on location. The severity of intersex was assessed using a simple classification scale, with the majority of individuals showing low levels of impact. Sex ratios were significantly skewed at some sites. There were no significant relationships between incidence or severity of intersex; or with size or parasitism of individual clams. Intersex in S. plana is a useful tool to assess endocrine disruptive effects in estuaries, although mechanisms of impact and causative agents remain uncertain.

  11. 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).

  12. 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.

  13. Widespread occurrence of phthalic acid esters in raw oilseeds in China used for edible vegetable oil production.

    PubMed

    Hu, Ai-Peng; Liu, Yu-Lan; Shi, Long-Kai

    2016-09-01

    Seven different phthalic acid esters (PAEs) were quantified in 124 samples of 16 types of oilseeds from China using a simplified GC-MS method. Di-2-ethylhexyl phthalate and di-n-butyl phthalate were found in all tested oilseed samples. Each made a high contribution to the summed total PAEs. Total PAE concentrations in 124 oilseeds ranged from 0.14 to 3.05 mg kg(-1), and the mean was 0.99 mg kg(-1). Mandulapalka (Cyperus esculentus) samples were the most severely contaminated among all the tested specimens; maize germ samples were least contaminated. Di-n-octyl phthalate and butylbenzyl phthalate were not detected in 12 and five types of oilseeds, respectively. Only eight samples contained all seven analytes. No difference was observed between woody oil-bearing plant and herbaceous oil-bearing plant in terms of PAEs content. PMID:27603777

  14. 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. PMID:23603470

  15. Distribution of sulfated glycosaminoglycans in the animal kingdom: widespread occurrence of heparin-like compounds in invertebrates.

    PubMed

    Medeiros, G F; Mendes, A; Castro, R A; Baú, E C; Nader, H B; Dietrich, C P

    2000-07-26

    Sulfated glycosaminoglycans were isolated from 23 species of 13 phyla of invertebrates and characterized by their electrophoretic migration in three different buffer systems coupled with enzymatic degradation using bacterial heparinase, heparitinases and chondroitinase AC. Heparan sulfate is a ubiquitous compound present in all species analyzed whereas chondroitin sulfate was present in 20 species and heparin-like compounds in 12 species of the invertebrates. The heparin-like compounds were purified from the echinoderm Mellita quinquisperforata (sand dollar) and the crustacean Ucides cordatus (crab) with anticoagulant activities of 60 and 52 IU/mg, respectively. Degradation of these heparins with heparinase produced significant amounts of the trisulfated disaccharide typical of mammalian heparins. This was confirmed by 13C-NMR spectroscopy of the crab heparin. An updated phylogenetic tree of the distribution of sulfated glycosaminoglycans in the animal kingdom is also presented. PMID:10913828

  16. 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.

  17. Marine ciliates as a widespread source of tetrahymanol and hopan-3. beta. -ol in sediments

    SciTech Connect

    Harvey, H.R.; McManus, G.B. )

    1991-11-01

    The authors observed tetrahymanol (gammaceran-3{beta}-ol) as a principal neutral lipid in eight marine ciliate species, most of which were scuticociliates, a group of ciliates that feeds mainly on bacteria. Tetrahymanol abundance in pure cultures and field samples (sediment traps, water column particulates, and enrichments from coastal and estuarine environments) shows good agreement with ciliate biovolume (R{sup 2} = 0.89), suggesting that tetrahymanol is a specific marker for marine ciliates that feed on bacteria. Hopan-3{beta}-ol was also positively identified in several ciliates, but did not occur in all species examined. Because of their widespread distribution in modern marine systems, these organisms provide a likely source for the common appearance of tetrahymanol in many marine sediments. By analogy, the presumed presence of ciliates in ancient seas may explain the occurrence of its diagenetic product, gammacerane, in more mature sediments and crude oils.

  18. Widespread, prolonged late Middle to Late Ordovician upwelling in North America: A proxy record of glaciation?

    NASA Astrophysics Data System (ADS)

    Pope, Michael C.; Steffen, Jessica B.

    2003-01-01

    Late Middle to Late Ordovician subtidal ramp carbonates of New Mexico, Texas, and Oklahoma contain abundant spiculitic chert (to 70% chert by volume) and phosphate (1 5 wt%), indicating that these rocks formed in an extensive upwelling zone. Upwelling began in the late Middle Ordovician (ca. 454 Ma) and persisted until the end of the Ordovician. Late Ordovician cherty carbonates also occur along the U.S. Cordilleran margin, in board of organic-rich graptolitic shale and chert. The widespread occurrence of Late Ordovician cherty and phosphatic carbonates on southern and western Laurentia, in addition to phosphate-rich, cool-water carbonates over much of the North American Midcontinent, suggests vigorous thermohaline circulation related to prolonged (10 14 Ma) Gondwana glaciation.

  19. Occurrence of ultrasonic cavitation in sewage sludge

    NASA Astrophysics Data System (ADS)

    Zielewicz-Madej, E.; Sorys, P.

    2006-11-01

    The study revealed considerable differences in the susceptibility of the sludge to preliminary treatment by two kind of mixing and expressed as changes in the initial properties of the sludge and thus conditions for the occurrence of ultrasonic disintegration in particular sludge from wastewater treatment plants G, K andZ. The susceptibility of sludge to ultrasounds which depends on the sludge properties was explained by the higher COD of dissolved matter after ultrasonic disintegration of sludge.

  20. 77 FR 55105 - Aging Airplane Program: Widespread Fatigue Damage; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-07

    ... establish a limit of validity of the engineering data that supports the structural maintenance program... tables. This document corrects the errors in those tables. DATES: This corrective action becomes... entitled ``Aging Airplane Program: Widespread Fatigue Damage'' (77 FR 30877), which corrected a final...

  1. Assessment of the feasibility of the widespread photovoltaic retrofits

    NASA Astrophysics Data System (ADS)

    Jackson, J. L.

    Some of the economic implications of retrofits and retrofit designs which might be employed are considered. Residential and commercial retrofits may represent a significant national market for photovoltaic (PV) systems. Techniques for estimating the photovoltaic retrofits market and present preliminary conclusions about physical market size are discussed. Possible institutional barriers to widespread retrofits are reviewed.

  2. 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

  3. A monomorphic halotype of chromosome Ia is associated with widespread success in clonal and nonclonal populations of Toxoplasma gondii

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Toxoplasma gondii is a widespread parasite of animals that causes zoonotic infection in humans. Previous studies have revealed a strongly clonal population structure in North America and Europe, while strains from South American are genetically divergent and show greater evidence of recombination. ...

  4. Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap)

    PubMed Central

    Vetriani, Costantino; Voordeckers, James W; Crespo-Medina, Melitza; O'Brien, Charles E; Giovannelli, Donato; Lutz, Richard A

    2014-01-01

    Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body. PMID:24430487

  5. Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap).

    PubMed

    Vetriani, Costantino; Voordeckers, James W; Crespo-Medina, Melitza; O'Brien, Charles E; Giovannelli, Donato; Lutz, Richard A

    2014-07-01

    Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

    2011-01-01

    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. PMID:21209662

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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. PMID:19345016

  18. 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

  19. 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.

  20. The tad locus: postcards from the widespread colonization island.

    PubMed

    Tomich, Mladen; Planet, Paul J; Figurski, David H

    2007-05-01

    The Tad (tight adherence) macromolecular transport system, which is present in many bacterial and archaeal species, represents an ancient and major new subtype of type II secretion. The tad genes are present on a genomic island named the widespread colonization island (WCI), and encode the machinery that is required for the assembly of adhesive Flp (fimbrial low-molecular-weight protein) pili. The tad genes are essential for biofilm formation, colonization and pathogenesis in the genera Aggregatibacter (Actinobacillus), Haemophilus, Pasteurella, Pseudomonas, Yersinia, Caulobacter and perhaps others. Here we review the structure, function and evolution of the Tad secretion system.

  1. Pharmacogenetics in Psychiatry: Are We Ready for Widespread Clinical Use?

    PubMed Central

    Arranz, Maria J.; Kapur, Shitij

    2008-01-01

    There are high expectations about the capabilities of pharmacogenetics to tailor psychotropic treatment and “personalize” treatment. While a large number of associations, with generally small effect size, have been discovered, a “test” with widespread use and adoption is still missing. A more realistic picture, recognizing the important contribution of clinical and environmental factors toward overall clinical outcome has emerged. In this emerging view, genetic findings, if considered individually, may have limited clinical applications. Thus, in recent years, combinations of information in several genes have been used for the selection of appropriate therapeutic doses and for the prediction of agranulocytosis, hyperlipidemia, and response to antipsychotic and antidepressant medications. While these tests based on multiple genes show greater predictive ability than individual allele tests, their net impact on clinical consequence and costs is limited, thus leading to limited penetration into widespread clinical use. As one looks at other branches of medicine, there are successful examples of pharmacogenetic tests guiding treatment, and thus, it is reasonable to hope that with the incorporation of clinical and environmental information and the identification of new genes drawn from genome-wide analysis, will improve the predictive utility of these tests leading to their increased use by clinicians. PMID:18753306

  2. Geographically contrasting biodiversity reductions in a widespread New Zealand seabird.

    PubMed

    Rawlence, Nicolas J; Kennedy, Martyn; Anderson, Christian N K; Prost, Stefan; Till, Charlotte E; Smith, Ian W G; Scofield, R Paul; Tennyson, Alan J D; Hamel, Jill; Lalas, Chris; Matisoo-Smith, Elizabeth A; Waters, Jonathan M

    2015-09-01

    Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines.

  3. Geographically contrasting biodiversity reductions in a widespread New Zealand seabird.

    PubMed

    Rawlence, Nicolas J; Kennedy, Martyn; Anderson, Christian N K; Prost, Stefan; Till, Charlotte E; Smith, Ian W G; Scofield, R Paul; Tennyson, Alan J D; Hamel, Jill; Lalas, Chris; Matisoo-Smith, Elizabeth A; Waters, Jonathan M

    2015-09-01

    Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines. PMID:26227633

  4. Widespread methanotrophic primary production in lowland chalk rivers

    PubMed Central

    Shelley, Felicity; Grey, Jonathan; Trimmer, Mark

    2014-01-01

    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. PMID:24695425

  5. 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.

  6. Human DNA methylomes at base resolution show widespread epigenomic differences

    PubMed Central

    Lister, Ryan; Pelizzola, Mattia; Dowen, Robert H.; Hawkins, R. David; Hon, Gary; Tonti-Filippini, Julian; Nery, Joseph R.; Lee, Leonard; Ye, Zhen; Ngo, Que-Minh; Edsall, Lee; Antosiewicz-Bourget, Jessica; Stewart, Ron; Ruotti, Victor; Millar, A. Harvey; Thomson, James A.; Ren, Bing; Ecker, Joseph R.

    2010-01-01

    Summary DNA cytosine methylation is a central epigenetic modification that plays essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of mRNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors. Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes. Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that they may utilize different methylation mechanisms to affect gene regulation. Methylation in non-CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers. Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity. These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development. PMID:19829295

  7. 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

  8. 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.

  9. Widespread distribution of extensive chromosomal fragmentation in ciliates.

    PubMed

    Riley, J L; Katz, L A

    2001-07-01

    Ciliates are a diverse group of eukaryotes characterized by their division of nuclear function into a "germ line" micronucleus and a "somatic" macronucleus. After conjugation, chromosomes in the transcriptionally active macronucleus develop by fragmentation, elimination, and amplification of germ line chromosomes. Extensive chromosomal processing that generates a macronucleus with gene-sized fragments has thus far been well documented in members of only one class of ciliates, the Spirotrichea. Here we establish the broad distribution of extensive fragmentation among members of the class Phyllopharyngea and the genera Metopus (order Armophorida) and Nyctotherus (order Clevelandellida). Moreover, analyses of small-subunit rDNA genealogies indicate that gene-sized chromosomes occur in members of the three separate clades: (1) the class Spirotrichea, (2) the class Phyllopharyngea, and (3) the two orders Clevelandellida and Armophorida. Together, these data indicate that the generation of gene-sized chromosomes is widespread and demonstrate multiple origins of extensive fragmentation within ciliates.

  10. 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

  11. 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.

  12. 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.

  13. 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. PMID:19039134

  14. 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. PMID:27276229

  15. Hypoxia in paradise: widespread hypoxia tolerance in coral reef fishes.

    PubMed Central

    Nilsson, Göran E; Ostlund-Nilsson, Sara

    2004-01-01

    Using respirometry, we examined the hypoxia tolerance of 31 teleost fish species (seven families) inhabiting coral reefs at a 2-5 m depth in the lagoon at Lizard Island (Great Barrier Reef, Australia). All fishes studied maintained their rate of oxygen consumption down to relatively severe hypoxia (20-30% air saturation). Indeed, most fishes appeared unaffected by hypoxia until the oxygen level fell below 10% of air saturation. This, hitherto unrecognized, hypoxia tolerance among coral reef fishes could reflect adaptations to nocturnal hypoxia in tide pools. It may also be needed to enable fishes to reside deep within branching coral at night to avoid predation. Widespread hypoxia tolerance in a habitat with such an extreme biodiversity as coral reefs indicate that there is a wealth of hypoxia related adaptations to be discovered in reef fishes. PMID:15101411

  16. 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.

  17. Occurrence of emerging food-borne pathogenic Arcobacter spp. isolated from pre-cut (ready-to-eat) vegetables.

    PubMed

    Mottola, Anna; Bonerba, Elisabetta; Bozzo, Giancarlo; Marchetti, Patrizia; Celano, Gaetano Vitale; Colao, Valeriana; Terio, Valentina; Tantillo, Giuseppina; Figueras, Maria José; Di Pinto, Angela

    2016-11-01

    Given that changes in consumer food behaviours have led to an increase in the demand for pre-cut ready-to-eat (RTE) vegetables, and that few data are currently available on the occurrence of Arcobacter spp. in such foods, the aim of the present study was to assess the occurrence of Arcobacter spp. that carry virulence-associated genes on pre-cut RTE vegetables, using cultural and molecular methods. Arcobacter was detected using biomolecular identification methods in 44/160 (27.5%) of the samples, of which 40/44 (90.9%) isolates corresponded to A. butzleri and 4/44 (9.1%) to A. cryaerophilus. Studying the incidence of 9 virulence-associated genes revealed the widespread distribution of these genes among the Arcobacter isolates tested. The results obtained in our research provided plenty of information on the health risks associated with the direct consumption of raw vegetables, and highlight the need to implement further studies at each level of the production chain, in order to obtain further information to help protect human health. PMID:27442848

  18. Occurrence of emerging food-borne pathogenic Arcobacter spp. isolated from pre-cut (ready-to-eat) vegetables.

    PubMed

    Mottola, Anna; Bonerba, Elisabetta; Bozzo, Giancarlo; Marchetti, Patrizia; Celano, Gaetano Vitale; Colao, Valeriana; Terio, Valentina; Tantillo, Giuseppina; Figueras, Maria José; Di Pinto, Angela

    2016-11-01

    Given that changes in consumer food behaviours have led to an increase in the demand for pre-cut ready-to-eat (RTE) vegetables, and that few data are currently available on the occurrence of Arcobacter spp. in such foods, the aim of the present study was to assess the occurrence of Arcobacter spp. that carry virulence-associated genes on pre-cut RTE vegetables, using cultural and molecular methods. Arcobacter was detected using biomolecular identification methods in 44/160 (27.5%) of the samples, of which 40/44 (90.9%) isolates corresponded to A. butzleri and 4/44 (9.1%) to A. cryaerophilus. Studying the incidence of 9 virulence-associated genes revealed the widespread distribution of these genes among the Arcobacter isolates tested. The results obtained in our research provided plenty of information on the health risks associated with the direct consumption of raw vegetables, and highlight the need to implement further studies at each level of the production chain, in order to obtain further information to help protect human health.

  19. Widespread osteoblastic metastases and marked elevation of CA19-9 as a presentation of signet ring cell gastric carcinoma

    PubMed Central

    Romano, Asaf; Bejar, Jacob; Schiff, Elad; Dotan, Yaniv

    2016-01-01

    Widespread osteoblastic metastases, as well as marked elevations of CA19-9 and carcino-embryonic antigen (CEA), are the initial manifestations of gastric signet ring cell carcinoma. CT Imaging revealed diffuse sclerotic metastases in the axial skeleton. It was only following gastric biopsy that the primary site of metastatic bone tumor was identified. Recent studies suggest that early diagnosis of cancer origin, including tumor molecular profiling, may dictate specific therapy, improve prognosis and increase patient survival rates. PMID:27034800

  20. Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water.

    PubMed

    Narciso-da-Rocha, Carlos; Manaia, Célia M

    2016-09-01

    The environment is the original and most ancient source of the antibiotic resistance determinants that threat the human health nowadays. In the environment, water is a privileged habitat and mode of dissemination of bacteria of different origins. Freshwater bodies that cross urban areas are supposed to hold a complex mixture of both human/animal origin and strictly environmental bacteria. In this study, we were interested in unveiling the bacterial diversity in urban river transects and, simultaneously, investigate the occurrence of antibiotic resistant bacteria, in particular the multidrug resistant (MDR). With this aim, water and sediments of two rivers were sampled from an urban transect and the bacterial diversity was assessed based on 16S rRNA gene-based community analysis and, simultaneously, total heterotrophic bacteria were isolated in the presence and in the absence of antibiotics. The three predominant phyla were Proteobacteria, Bacteroidetes and Actinobacteria, in water, or Acidobacteria, in sediments. MDR bacteria were observed to belong to the predominant phyla observed in water, mostly of the classes Gamma- and Betaproteobacteria (Proteobacteria) and Sphingobacteriia and Flavobacteriia (Bacteroidetes) and belonged to genera of ubiquitous (Pseudomonas, Acinetobacter, Stenotrophomonas) or mainly environmental (Chitinophaga, Chryseobacterium) bacteria. The observation that MDR bacteria are widespread in the environment and over distinct phylogenetic lineages has two relevant implications: i) the potential of environmental bacteria as source or facilitators for antibiotic resistance acquisition; ii) the need to complement culture-independent methods with culture-based approaches in order to identify major sources of MDR profiles.

  1. 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.

  2. 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. PMID:27358768

  3. 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

  4. 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.

  5. 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

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

    PubMed

    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

  7. 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.

  8. 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. PMID:25644484

  9. 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

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

    PubMed

    van der Heijden, Marcel G A; de Bruin, Susanne; Luckerhoff, Ludo; van Logtestijn, Richard S P; Schlaeppi, Klaus

    2016-02-01

    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.

  11. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface.

    PubMed

    Probst, Alexander J; Weinmaier, Thomas; Raymann, Kasie; Perras, Alexandra; Emerson, Joanne B; Rattei, Thomas; Wanner, Gerhard; Klingl, Andreas; Berg, Ivan A; Yoshinaga, Marcos; Viehweger, Bernhard; Hinrichs, Kai-Uwe; Thomas, Brian C; Meck, Sandra; Auerbach, Anna K; Heise, Matthias; Schintlmeister, Arno; Schmid, Markus; Wagner, Michael; Gribaldo, Simonetta; Banfield, Jillian F; Moissl-Eichinger, Christine

    2014-11-26

    Subsurface microbial life contributes significantly to biogeochemical cycling, yet it remains largely uncharacterized, especially its archaeal members. This 'microbial dark matter' has been explored by recent studies that were, however, mostly based on DNA sequence information only. Here, we use diverse techniques including ultrastuctural analyses to link genomics to biology for the SM1 Euryarchaeon lineage, an uncultivated group of subsurface archaea. Phylogenomic analyses reveal this lineage to belong to a widespread group of archaea that we propose to classify as a new euryarchaeal order ('Candidatus Altiarchaeales'). The representative, double-membraned species 'Candidatus Altiarchaeum hamiconexum' has an autotrophic metabolism that uses a not-yet-reported Factor420-free reductive acetyl-CoA pathway, confirmed by stable carbon isotopic measurements of archaeal lipids. Our results indicate that this lineage has evolved specific metabolic and structural features like nano-grappling hooks empowering this widely distributed archaeon to predominate anaerobic groundwater, where it may represent an important carbon dioxide sink.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23628889

  13. 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.

  14. 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.

  15. Occurrence of Regulated and Emerging Iodinated DBPs in the Shanghai Drinking Water

    PubMed Central

    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. PMID:23555742

  16. 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.

  17. 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. PMID:23247041

  18. 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.

  19. 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

  20. 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

  1. 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.

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

    PubMed

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

    2016-06-30

    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 distinct cases in mammals (Tasmanian devils and dogs), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria) suggested that this phenomenon might be more widespread. Here we analyse disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and find 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; however, unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographical 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 are found spreading within the species of origin, cross-species transmission of cancer cells can occur. PMID:27338791

  3. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria.

    PubMed

    Reisch, Chris R; Stoudemayer, Melissa J; Varaljay, Vanessa A; Amster, I Jonathan; Moran, Mary Ann; Whitman, William B

    2011-05-12

    Dimethylsulphoniopropionate (DMSP) accounts for up to 10% of carbon fixed by marine phytoplankton in ocean surface waters, producing an estimated 11.7-103 Tmol S per year, most of which is processed by marine bacteria through the demethylation/demethiolation pathway. This pathway releases methanethiol (MeSH) instead of the climatically active gas dimethylsulphide (DMS) and enables marine microorganisms to assimilate the reduced sulphur. Despite recognition of this critical microbial transformation for over two decades, the biochemical pathway and enzymes responsible have remained unidentified. Here we show that three new enzymes related to fatty acid β-oxidation constitute the pathway that assimilates methylmercaptopropionate (MMPA), the first product of DMSP demethylation/demethiolation, and that two previously unknown coenzyme A (CoA) derivatives, 3-methylmercaptopropionyl-CoA (MMPA-CoA) and methylthioacryloyl-CoA (MTA-CoA), are formed as novel intermediates. A member of the marine roseobacters, Ruegeria pomeroyi DSS-3, requires the MMPA-CoA pathway for MMPA assimilation and MeSH production. This pathway and the ability to produce MeSH from MMPA are present in diverse bacteria, and the ubiquitous SAR11 clade bacterium Pelagibacter ubique possesses enzymes for at least the first two steps. Analysis of marine metagenomic data indicates that the pathway is widespread among bacterioplankton in the ocean surface waters, making it one of the most important known routes for acquisition of reduced carbon and sulphur by surface ocean heterotrophs.

  4. 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.

  5. Widespread use of real-time PCR for rickettsial diagnosis.

    PubMed

    Renvoisé, Aurélie; Rolain, Jean-Marc; Socolovschi, Cristina; Raoult, Didier

    2012-02-01

    We report 2 years of experience with rickettsial molecular diagnosis using real-time PCR at the French National Reference Center. All Rickettsia genomes available were compared to discover specific sequences to design new sets of primers and probes. The specificity was verified in silico and against a panel of 30 rickettsial species. Sensitivity was determined using 10-fold serial dilutions. Finally, primers and probes that were both specific and sensitive were routinely used for the diagnosis of rickettsial infections from clinical specimens. We retained sets of primers and probes to detect spotted fever group Rickettsia, typhus group Rickettsia,Rickettsia conorii,Rickettsia slovaca,Rickettsia africae and Rickettsia australis; 643 clinical samples were screened for the presence of Rickettsia DNA. Overall, 45 positive samples were detected, including 15 Rickettsia africae, nine R. conorii, five Rickettsia sibirica mongolitimonae, four R. slovaca, two R. australis, four Rickettsia massiliae, one Rickettsia honei, one Rickettsia typhi and eight Rickettsia sp. Positive samples were detected mainly from cutaneous biopsies and swabs (31/45). Widespread use of real-time PCR is inexpensive and reduces delay in the diagnosis of rickettsial infections. These real-time PCR assays could be implemented easily in laboratories that have molecular facilities and may be added to existing molecular tools as a point-of-care strategy.

  6. Hydrothermal Occurrences in Gusev Crater

    NASA Astrophysics Data System (ADS)

    Ruff, S. W.; Farmer, J. D.; Milliken, R.; Mills, V. W.; Shock, E.

    2011-12-01

    Exploration of the Gusev crater landing site by the Spirit rover has revealed for the first time, in situ evidence of hydrothermal activity on Mars. Most compelling are eroded outcrops of opaline silica found adjacent to "Home Plate" [1], an eroded stack of volcaniclastic deposits stratigraphically overlain by a vesicular basalt unit [2]. Recent work [3] demonstrates that the silica outcrops occur in a stratiform unit that possibly surrounds Home Plate. The outcrops are dominated by opal-A with no evidence for diagenesis to other silica phases. No other hydrous or alteration phases have been identified within the outcrops; most notable is a lack of sulfur phases. The outcrops have porous and in some cases, brecciated microtextures. Taken together, these observations support the interpretation that the opaline silica outcrops were produced in a hot spring or perhaps geyser environment. In this context, they are silica sinter deposits precipitated from silica-rich hydrothermal fluids, possibly related to the volcanism that produced the Home Plate volcanic rocks. On Earth, debris aprons in which sinter is brecciated, reworked, and cemented, are common features of hot springs and geysers and are good analogs for the Martian deposits. An alternative hypothesis is that the silica resulted from acid-sulfate leaching of precursor rocks by fumarolic steam condensates. But stratigraphic, textural, and chemical observations tend to diminish this possibility [3]. We are conducting extensive laboratory and field investigations of silica from both hot spring/geyser and fumarole environments to understand the full range of mineralogical, chemical, textural, and morphological variations that accompany its production, in order to shed more light on the Home Plate occurrence. The recent discovery of abundant Mg-Fe carbonate (16-34 wt%) in outcrops named Comanche provides possible evidence for additional hydrothermal activity in Gusev [4]. However, the carbonate is hosted by olivine

  7. Statistics of ionospheric scintillation occurrence over European high latitudes

    NASA Astrophysics Data System (ADS)

    Sreeja, V.; Aquino, M.

    2014-12-01

    Rapid fluctuation in the amplitude and phase of transionospheric radio signals caused by small scale ionospheric plasma density irregularities is known as scintillation. Over the high latitudes, irregularities causing scintillation are associated with large scale plasma structures and scintillation occurrence is mainly enhanced during geomagnetic storms. This paper presents a statistical analysis of scintillation occurrence on GPS L1C/A signal at a high latitude station located in Bronnoysund (geographic latitude 65.5°N, geographic longitude 12.2°E; corrected geomagnetic (CGM) latitude 62.77°N), Norway, during the periods around the peaks of solar cycles 23 (2002-2003) and 24 (2011-2013). The analysis revealed that the scintillation occurrence at Bronnoysund during both the solar maximum periods maximises close to the midnight magnetic local time (MLT) sector. A higher occurrence of scintillation is observed on geomagnetically active days during both the solar maximum periods. The seasonal pattern of scintillation occurrence indicated peaks during the summer and equinoctial months. A comparison with the interplanetary magnetic field (IMF) components By and Bz showed an association of scintillation occurrence with the southward IMF Bz conditions.

  8. Yeast biogeography and the effects of species recognition approaches: the case study of widespread basidiomycetous species from birch forests in Russia.

    PubMed

    Yurkov, Andrey; Inácio, João; Chernov, Ivan Yu; Fonseca, Álvaro

    2015-04-01

    Understanding diversity and distribution patterns of fungi, including yeasts, ultimately depends on accuracy of species recognition. However, different approaches to yeast species recognition often result in different entities or operational taxonomic units. We studied the effects of using different yeast species recognition approaches, namely morphological species recognition (MSR) and phylogenetic species recognition (PSR), on the distribution patterns of widespread basidiomycetous yeasts. Hence, we have revised a collection of yeast fungi isolated from spatially remote birch forests in the Moscow Region and Western Siberia with molecular typing and identification tools. PCR fingerprinting and rDNA sequencing analyses of strains of nine species previously identified on the basis of morphological and physiological tests (MSR) yielded 21 phylogenetic species (PSR), including three currently undescribed taxa. The number of distinct phylogenetic species comprised within a single morphospecies ranged from one to seven. A total of ten species were found in both regions, whereas the distribution of 11 yeasts was restricted to a single region only. Both geographical region and type of substrate (plant or soil) influence yeast distribution. Cryptococcus wieringae, C. victoriae, C. magnus, and Leucosporidium scottii were frequently found on plant substrates, whereas C. terricola and C. podzolicus were associated to soil substrates. Occurrence of C. magnus, C. albidus and Sporobolomyces roseus was found to depend on the geographical region. Microsatellite-PCR fingerprinting, MSP-PCR, applied to studying yeast intraspecific variability revealed three different types of distribution: (a) variability that depends on geographical factors (Curvibasidium cygneicollum, C. podzolicus, C. victoriae), (b) genetic identity irrespectively of the region of isolation (Rhodotorula pinicola, C. terricola), and (c) high degree of genetic variability that did not correlate with region of

  9. 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

  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 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. PMID:24759324

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Gene name errors are widespread in the scientific literature.

    PubMed

    Ziemann, Mark; Eren, Yotam; El-Osta, Assam

    2016-01-01

    The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.

  4. Gene name errors are widespread in the scientific literature.

    PubMed

    Ziemann, Mark; Eren, Yotam; El-Osta, Assam

    2016-01-01

    The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions. PMID:27552985

  5. Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate.

    PubMed

    Kelly, David W; MacIsaac, Hugh J; Heath, Daniel D

    2006-02-01

    Vicariance and dispersal can strongly influence population genetic structure and allopatric speciation, but their importance in the origin of marine biodiversity is unresolved. In transitional estuarine environments, habitat discreteness and dispersal barriers could enhance divergence and provide insight to evolutionary mechanisms underlying marine and freshwater biodiversity. We examined this by assessing phylogeographic structure in the widespread amphipod Gammarus tigrinus across 13 estuaries spanning its northwest Atlantic range from Quebec to Florida. Mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 1 phylogenies supported deep genetic structure consistent with Pliocene separation and cryptic northern and southern species. This break occurred across the Virginian-Carolinian coastal biogeographic zone, where an oceanographic discontinuity may restrict gene flow. Ten estuarine populations of the northern species occurred in four distinct clades, supportive of Pleistocene separation. Glaciation effects on genetic structure of estuarine populations are largely unknown, but analysis of molecular variance (AMOVA) supported a phylogeographic break among clades in formerly glaciated versus nonglaciated areas across Cape Cod, Massachusetts. This finding was concordant with patterns in other coastal species, though there was no significant relationship between latitude and genetic diversity. This supports Pleistocene vicariance events and divergence of clades in different northern glacial refugia. AMOVA results and private haplotypes in most populations support an allopatric distribution across estuaries. Clade mixture zones are consistent with historical colonization and human-mediated transfer. An isolation-by-distance model of divergence was detected after we excluded a suspected invasive haplotype in the St. Lawrence estuary. The occurrence of cryptic species and divergent population structure support limited dispersal, dispersed habitat

  6. First survey for the amphibian chytrid fungus Batrachochytrium dendrobatidis in Connecticut (USA) finds widespread prevalence.

    PubMed

    Richards-Hrdlicka, Kathryn L; Richardson, Jonathan L; Mohabir, Leon

    2013-02-28

    The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is an emerging infectious fungal pathogen of amphibians and is linked to global population declines. Until now, there has only been 1 survey for the fungus in the northeastern USA, which focused primarily on northern New England. We tested for Bd in a large number of samples (916 individuals from 116 sites) collected throughout the state of Connecticut, representing 18 native amphibian species. In addition, 239 preserved wood frog Lithobates sylvaticus tadpoles from throughout the state were screened for the fungus. Bd presence was assessed in both the fresh field swabs and the preserved samples using a sensitive quantitative PCR assay. Our contemporary survey found widespread Bd prevalence throughout Connecticut, occurring in 14 species and in 28% of all sampled animals. No preserved L. sylvaticus specimens tested positive for the fungus. Two common species, bullfrogs R. catesbeiana and green frogs R. clamitans had particularly high infection rates (0.21-0.39 and 0.33-0.42, respectively), and given their wide distribution throughout the state, we suggest they may serve as sentinels for Bd occurrence in this region. Further analyses found that several other factors increase the likelihood of infection, including life stage, host sex, and host family. Within sites, ponds with ranids, especially green frogs, increased the likelihood of Bd prevalence. By studying Bd in populations not facing mass declines, the results from this study are an important contribution to our understanding of how some amphibian species and populations remain infected yet exhibit no signs of chytridiomycosis even when Bd is widely distributed.

  7. Optimal full matching for survival outcomes: a method that merits more widespread use.

    PubMed

    Austin, Peter C; Stuart, Elizabeth A

    2015-12-30

    Matching on the propensity score is a commonly used analytic method for estimating the effects of treatments on outcomes. Commonly used propensity score matching methods include nearest neighbor matching and nearest neighbor caliper matching. Rosenbaum (1991) proposed an optimal full matching approach, in which matched strata are formed consisting of either one treated subject and at least one control subject or one control subject and at least one treated subject. Full matching has been used rarely in the applied literature. Furthermore, its performance for use with survival outcomes has not been rigorously evaluated. We propose a method to use full matching to estimate the effect of treatment on the hazard of the occurrence of the outcome. An extensive set of Monte Carlo simulations were conducted to examine the performance of optimal full matching with survival analysis. Its performance was compared with that of nearest neighbor matching, nearest neighbor caliper matching, and inverse probability of treatment weighting using the propensity score. Full matching has superior performance compared with that of the two other matching algorithms and had comparable performance with that of inverse probability of treatment weighting using the propensity score. We illustrate the application of full matching with survival outcomes to estimate the effect of statin prescribing at hospital discharge on the hazard of post-discharge mortality in a large cohort of patients who were discharged from hospital with a diagnosis of acute myocardial infarction. Optimal full matching merits more widespread adoption in medical and epidemiological research. © 2015 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

  8. First survey for the amphibian chytrid fungus Batrachochytrium dendrobatidis in Connecticut (USA) finds widespread prevalence.

    PubMed

    Richards-Hrdlicka, Kathryn L; Richardson, Jonathan L; Mohabir, Leon

    2013-02-28

    The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is an emerging infectious fungal pathogen of amphibians and is linked to global population declines. Until now, there has only been 1 survey for the fungus in the northeastern USA, which focused primarily on northern New England. We tested for Bd in a large number of samples (916 individuals from 116 sites) collected throughout the state of Connecticut, representing 18 native amphibian species. In addition, 239 preserved wood frog Lithobates sylvaticus tadpoles from throughout the state were screened for the fungus. Bd presence was assessed in both the fresh field swabs and the preserved samples using a sensitive quantitative PCR assay. Our contemporary survey found widespread Bd prevalence throughout Connecticut, occurring in 14 species and in 28% of all sampled animals. No preserved L. sylvaticus specimens tested positive for the fungus. Two common species, bullfrogs R. catesbeiana and green frogs R. clamitans had particularly high infection rates (0.21-0.39 and 0.33-0.42, respectively), and given their wide distribution throughout the state, we suggest they may serve as sentinels for Bd occurrence in this region. Further analyses found that several other factors increase the likelihood of infection, including life stage, host sex, and host family. Within sites, ponds with ranids, especially green frogs, increased the likelihood of Bd prevalence. By studying Bd in populations not facing mass declines, the results from this study are an important contribution to our understanding of how some amphibian species and populations remain infected yet exhibit no signs of chytridiomycosis even when Bd is widely distributed. PMID:23446966

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

    PubMed

    Rohr, Jason R; Raffel, Thomas R

    2010-05-01

    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.

  10. Widespread Distribution of Disinfectant Resistance Genes among Staphylococci of Bovine and Caprine Origin in Norway

    PubMed Central

    Bjorland, Jostein; Steinum, Terje; Kvitle, Bjørg; Waage, Steinar; Sunde, Marianne; Heir, Even

    2005-01-01

    We demonstrate here a widespread distribution of genes mediating efflux-based resistance to quaternary ammonium compounds (QACs) in staphylococci from unpasteurized milk from 127 dairy cattle herds and 70 dairy goat herds. QAC resistance genes were identified in 21% of the cattle herds (qacA/B, smr, qacG, and qacJ) and in 10% of the goat herds (qacA/B and smr). Further examination of 42 QAC-resistant bovine and caprine isolates revealed the following genes: qacA/B (12 isolates) was present in four different species of coagulase-negative staphylococci (CoNS), smr (27 isolates) was detected in eight different CoNS species and in Staphylococcus aureus on a previously reported plasmid (pNVH99), qacG (two isolates) was detected on two plasmids (pST94-like) in Staphylococcus cohnii and Staphylococcus warneri, and qacJ (two isolates) was found in Staphylococcus hominis and Staphylococcus delphini on a plasmid (pNVH01) previously found in equine staphylococci. Isolation of indistinguishable pulsed-field gel electrophoresis (PFGE) CoNS types from tank milk and mammary quarter milk samples in a dairy cattle herd suggested that these QAC-resistant staphylococci were of intramammary origin. Indistinguishable or closely related PFGE types of bovine QAC-resistant CoNS were observed in different herds. One particular bovine S. warneri PFGE type was isolated repeatedly from samples collected during a 30-month period in a herd, showing long-term persistence. In conclusion, it seems that the widespread distribution of staphylococci carrying QAC resistance genes in Norwegian dairy cattle and goat herds is the result of both the intra- and interspecies spread of QAC resistance plasmids and the clonal spread of QAC-resistant strains. PMID:16145078

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

    PubMed

    Rohr, Jason R; Raffel, Thomas R

    2010-05-01

    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

  12. Tracheal Perforation and Widespread Subcutaneous Emphysema in a Horse

    PubMed Central

    Caron, J. P.; Townsend, H. G. G.

    1984-01-01

    A twelve year old Quarterhorse mare exhibited subcutaneous emphysema of the head, neck, upper forelimbs and thorax, and walked with a stiff gait, characterized by decreased flexion of the forelimbs. Endoscopy of the trachea revealed a small tracheal wound ninety centimeters from the external nares. The location of the lesion corresponded with a seroma present at the base of the neck. The subcutaneous emphysema and the seroma resolved without specific therapy. Blunt trauma was suggested as the cause of the tracheal lesion and subsequent subcutaneous emphysema. ImagesFigure 1. PMID:17422449

  13. 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.

  14. 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

  15. 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

  16. Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis

    PubMed Central

    Liu, Ming-Jung; Wu, Szu-Hsien; Chen, Ho-Ming; Wu, Shu-Hsing

    2012-01-01

    Environmental ‘light' has a vital role in regulating plant growth and development. Transcriptomic profiling has been widely used to examine how light regulates mRNA levels on a genome-wide scale, but the global role of translational regulation in the response to light is unknown. Through a transcriptomic comparison of steady-state and polysome-bound mRNAs, we reveal a clear impact of translational control on thousands of genes, in addition to transcriptomic changes, during photomorphogenesis. Genes encoding ribosomal protein are preferentially regulated at the translational level, which possibly contributes to the enhanced translation efficiency. We also reveal that mRNAs regulated at the translational level share characteristics of longer half-lives and shorter cDNA length, and that transcripts with a cis-element, TAGGGTTT, in their 5′ untranslated region have higher translatability. We report a previously neglected aspect of gene expression regulation during Arabidopsis photomorphogenesis. The identities and molecular signatures associated with mRNAs regulated at the translational level also offer new directions for mechanistic studies of light-triggered translational enhancement in Arabidopsis. PMID:22252389

  17. Epizootic hemorrhagic disease: analysis of tissues by amplification and in situ hybridization reveals widespread orbivirus infection at low copy numbers.

    PubMed

    Brodie, S J; Bardsley, K D; Diem, K; Mecham, J O; Norelius, S E; Wilson, W C

    1998-05-01

    A recent outbreak of hemorrhagic fever in wild ruminants in the northwest United States was characterized by rapid onset of fever, followed shortly thereafter by hemorrhage and death. As a result, a confirmed 1,000 white-tailed deer and pronghorn antelope died over the course of 3 months. Lesions were multisystemic and included severe edema, congestion, acute vascular necrosis, and hemorrhage. Animals that died with clinical signs and/or lesions consistent with hemorrhagic fever had antibody to epizootic hemorrhagic disease virus serotype 2 (EHDV-2) by radioimmune precipitation but the antibody was limited exclusively to class immunoglobulin M. These findings, indicative of acute infection, were corroborated by the observation that numerous deer were found dead; however, clinically affected deer were rarely seen during the outbreak. Furthermore, only in animals with hemorrhagic lesions was EHDV-2 isolated and/or erythrocyte-associated EHDV-2 RNA detected by serotype-specific reverse transcription (RT)-PCR. By using a novel RT in situ PCR assay, viral nucleic acid was localized to the cytoplasm of large numbers of tissue leukocytes and vascular endothelium in tissues with hemorrhage and to vessels, demonstrating acute intimal and medial necrosis. Because PCR amplification prior to in situ hybridization was essential for detecting EHDV, the virus copy number within individual cells was low, <20 virus copies. These findings suggest that massive covert infection characterized by rapid dissemination of virus facilitates the severe and lethal nature of this disease. PMID:9557671

  18. 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

  19. Multiplex real-time PCR monitoring of intestinal helminths in humans reveals widespread polyparasitism in Northern Samar, the Philippines.

    PubMed

    Gordon, Catherine A; McManus, Donald P; Acosta, Luz P; Olveda, Remigio M; Williams, Gail M; Ross, Allen G; Gray, Darren J; Gobert, Geoffrey N

    2015-06-01

    The global socioeconomic importance of helminth parasitic disease is underpinned by the considerable clinical impact on millions of people. While helminth polyparasitism is considered common in the Philippines, little has been done to survey its extent in endemic communities. High morphological similarity of eggs between related species complicates conventional microscopic diagnostic methods which are known to lack sensitivity, particularly in low intensity infections. Multiplex quantitative PCR diagnostic methods can provide rapid, simultaneous identification of multiple helminth species from a single stool sample. We describe a multiplex assay for the differentiation of Ascaris lumbricoides, Necator americanus, Ancylostoma, Taenia saginata and Taenia solium, building on our previously published findings for Schistosoma japonicum. Of 545 human faecal samples examined, 46.6% were positive for at least three different parasite species. High prevalences of S. japonicum (90.64%), A. lumbricoides (58.17%), T. saginata (42.57%) and A. duodenale (48.07%) were recorded. Neither T. solium nor N. americanus were found to be present. The utility of molecular diagnostic methods for monitoring helminth parasite prevalence provides new information on the extent of polyparasitism in the Philippines municipality of Palapag. These methods and findings have potential global implications for the monitoring of neglected tropical diseases and control measures.

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

    PubMed

    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

    2014-08-01

    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.

  1. 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

  2. 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

  3. 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.

  4. 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...

  5. 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

  6. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

    PubMed

    Schwartz, Schraga; Bernstein, Douglas A; Mumbach, Maxwell R; Jovanovic, Marko; Herbst, Rebecca H; León-Ricardo, Brian X; Engreitz, Jesse M; Guttman, Mitchell; Satija, Rahul; Lander, Eric S; Fink, Gerald; Regev, Aviv

    2014-09-25

    Pseudouridine is the most abundant RNA modification, yet except for a few well-studied cases, little is known about the modified positions and their function(s). Here, we develop Ψ-seq for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with spike-ins and de novo identification of previously reported positions and discover hundreds of unique sites in human and yeast mRNAs and snoRNAs. Perturbing pseudouridine synthases (PUS) uncovers which pseudouridine synthase modifies each site and their target sequence features. mRNA pseudouridinylation depends on both site-specific and snoRNA-guided pseudouridine synthases. Upon heat shock in yeast, Pus7p-mediated pseudouridylation is induced at >200 sites, and PUS7 deletion decreases the levels of otherwise pseudouridylated mRNA, suggesting a role in enhancing transcript stability. rRNA pseudouridine stoichiometries are conserved but reduced in cells from dyskeratosis congenita patients, where the PUS DKC1 is mutated. Our work identifies an enhanced, transcriptome-wide scope for pseudouridine and methods to dissect its underlying mechanisms and function.

  7. Transcriptome-wide mapping reveals widespread dynamic regulated pseudouridylation of ncRNA and mRNA

    PubMed Central

    Schwartz, Schraga; Bernstein, Douglas A.; Mumbach, Maxwell R.; Jovanovic, Marko; Herbst, Rebecca H.; León-Ricardo, Brian X.; Engreitz, Jesse M.; Guttman, Mitchell; Satija, Rahul; Lander, Eric S.; Fink, Gerald; Regev, Aviv

    2014-01-01

    SUMMARY Pseudouridine is the most abundant RNA modification, yet except for a few well-studied cases, little is known about the modified positions and their function(s). Here, we develop Ψ-seq for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with spike-ins and de novo identification of previously reported positions and discover hundreds of novel sites in human and yeast mRNAs and snoRNAs. Perturbing pseudouridine synthases (PUSs) uncovers which PUSs modify each site and their target sequence features. mRNA pseudouridinylation depends on both site-specific and snoRNA-guided PUSs. Upon heat shock in yeast, Pus7-mediated pseudouridylation is induced at >200 sites and Pus7 deletion decreases the levels of otherwise pseudouridylated mRNA, suggesting a role in enhancing transcript stability. rRNA pseudouridine stoichiometries are conserved, but reduced in cells from dyskeratosis congenita patients, where the PUS DKC1 is mutated. Our work identifies an enhanced, transcritome-wide scope for pseudouridine, and methods to dissect its underlying mechanisms and function. PMID:25219674

  8. Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species

    PubMed Central

    Eshoo, Mark W.; Carolan, Heather E.; Massire, Christian; Chou, Danny M.; Crowder, Chris D.; Rounds, Megan A.; Phillipson, Curtis A.; Schutzer, Steven E.; Ecker, David J.

    2015-01-01

    Ixodes pacificus ticks can harbor a wide range of human and animal pathogens. To survey the prevalence of tick-borne known and putative pathogens, we tested 982 individual adult and nymphal I. pacificus ticks collected throughout California between 2007 and 2009 using a broad-range PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to detect a wide range of tick-borne microorganisms. Overall, 1.4% of the ticks were found to be infected with Borrelia burgdorferi, 2.0% were infected with Borrelia miyamotoi and 0.3% were infected with Anaplasma phagocytophilum. In addition, 3.0% were infected with Babesia odocoilei. About 1.2% of the ticks were co-infected with more than one pathogen or putative pathogen. In addition, we identified a novel Anaplasmataceae species that we characterized by sequencing of its 16S rRNA, groEL, gltA, and rpoB genes. Sequence analysis indicated that this organism is phylogenetically distinct from known Anaplasma species with its closest genetic near neighbors coming from Asia. The prevalence of this novel Anaplasmataceae species was as high as 21% at one site, and it was detected in 4.9% of ticks tested statewide. Based upon this genetic characterization we propose that this organism be called ‘Candidatus Cryptoplasma californiense’. Knowledge of this novel microbe will provide awareness for the community about the breadth of the I. pacificus microbiome, the concept that this bacterium could be more widely spread; and an opportunity to explore whether this bacterium also contributes to human or animal disease burden. PMID:26375033

  9. 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. PMID:26488299

  10. 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. ...

  11. Multiplex real-time PCR monitoring of intestinal helminths in humans reveals widespread polyparasitism in Northern Samar, the Philippines.

    PubMed

    Gordon, Catherine A; McManus, Donald P; Acosta, Luz P; Olveda, Remigio M; Williams, Gail M; Ross, Allen G; Gray, Darren J; Gobert, Geoffrey N

    2015-06-01

    The global socioeconomic importance of helminth parasitic disease is underpinned by the considerable clinical impact on millions of people. While helminth polyparasitism is considered common in the Philippines, little has been done to survey its extent in endemic communities. High morphological similarity of eggs between related species complicates conventional microscopic diagnostic methods which are known to lack sensitivity, particularly in low intensity infections. Multiplex quantitative PCR diagnostic methods can provide rapid, simultaneous identification of multiple helminth species from a single stool sample. We describe a multiplex assay for the differentiation of Ascaris lumbricoides, Necator americanus, Ancylostoma, Taenia saginata and Taenia solium, building on our previously published findings for Schistosoma japonicum. Of 545 human faecal samples examined, 46.6% were positive for at least three different parasite species. High prevalences of S. japonicum (90.64%), A. lumbricoides (58.17%), T. saginata (42.57%) and A. duodenale (48.07%) were recorded. Neither T. solium nor N. americanus were found to be present. The utility of molecular diagnostic methods for monitoring helminth parasite prevalence provides new information on the extent of polyparasitism in the Philippines municipality of Palapag. These methods and findings have potential global implications for the monitoring of neglected tropical diseases and control measures. PMID:25858090

  12. 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

  13. 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.

  14. 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. PMID:26727042

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Widespread Layers in Arabia Terra: Implications for Martian Geologic History

    NASA Technical Reports Server (NTRS)

    Venechuk, Elizabeth M.; Oehler, D. Z.

    2006-01-01

    Layered rocks in Arabia Terra have been the focus of several recent papers. Studies have focused on the layers found in crater basins located in the southwest portion of the region. However, Mars Orbiter Camera (MOC) images have identified layered deposits across the region. Terrestrial layered rocks are usually sedimentary, and often deposited in water. Thus extensive layered sequences in Arabia Terra may indicate locations of past, major depositional basins on Mars. Other mechanisms can also create layered rocks, or the appearance of layered rocks, including volcanism (both lava flows and ash falls), wind-blown deposits, and wave-cut terraces at shorelines. By identifying where in the region layers occur, and classifying the layers according to morphology and albedo, past depositional environments may be identified. Arabia Terra is characterized by heavily cratered Noachian plains, as well as a rise from -4000 m in the northwest to 4000 m in the southeast (Mars Orbital Laser Altimeter [MOLA] datum). This slope may have provided a constraint on sediment deposition and thus layer formation. While most of the region is Noachian in age, a significant percentage of the area is identified as Hesperian. Although the history of the Arabia Terra initially seems to be straightforward cratered plains with several younger units atop them analysis of high-resolution imagery may reveal a more complex history.

  2. 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

  3. Recent and Widespread Rapid Morphological Change in Rodents

    PubMed Central

    Pergams, Oliver R. W.; Lawler, Joshua J.

    2009-01-01

    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. PMID:19649284

  4. 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.

  5. Natural occurrence of Fusarium and subsequent fumonisin contamination in preharvest and stored maize in Benin, West Africa.

    PubMed

    Fandohan, P; Gnonlonfin, B; Hell, K; Marasas, W F O; Wingfield, M J

    2005-03-15

    The natural occurrence of Fusarium and fumonisin contamination was evaluated from 1999 to 2003 in both preharvest and stored maize produced by small-scale farmers in four agroecological zones of Benin. Mycological analyses revealed a predominance of both Fusarium and Aspergillus in maize samples compared to other genera. The two Fusarium species most commonly isolated from maize were Fusarium verticillioides (68%) and Fusarium proliferatum (31%). Atypical isolates of F. verticillioides with some characteristics of Fusarium andiyazi but apparently closer to F. verticillioides, because the isolates were all high fumonisin producers, were also found only on preharvest maize. Study of F. verticillioides strains showed the presence of extremely high fumonisin producers in Benin with total fumonisin levels ranging from 8240 to 16,690 mg/kg. Apart from 2002-2003, Fusarium occurrence was not significantly different from one zone to another, although a slight decrease was observed from south, humid, to north, drier. Fusarium occurrence varied somewhat from one season to another. It significantly decreased over the 6 months of storage. Widespread fumonisin occurrence in maize was observed. Most of the maize samples collected were found positive for fumonisin with levels ranging from not detected to 12 mg/kg in 1999-2000, 6.7 mg/kg in 2000-2001 and 6.1 mg/kg in 2002-2003. Fumonisin levels in maize were found to be significantly higher in the two southern zones during all the surveys. The highest mean total fumonisin level was detected in 1999-2000 in maize samples from the southern Guinea Savannah (SGS) (12 mg/kg), whereas in both 2000-2001 and 2002-2003, it was in samples from the forest mosaic savannah (FMS) (6.7 and 6.1 mg/kg, respectively). Fumonisin levels varied from one season to another and, throughout the storage time, showing a decreasing trend in each zone. However, this decrease was not significant every season. An increasing trend was observed during some seasons

  6. 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.

  7. Widespread expression of conserved small RNAs in small symbiont genomes

    PubMed Central

    Hansen, Allison K; Degnan, Patrick H

    2014-01-01

    Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for ∼65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution. PMID:25012903

  8. Widespread establishment and regulatory impact of Alu exons in human genes.

    PubMed

    Shen, Shihao; Lin, Lan; Cai, James J; Jiang, Peng; Kenkel, Elizabeth J; Stroik, Mallory R; Sato, Seiko; Davidson, Beverly L; Xing, Yi

    2011-02-15

    The Alu element has been a major source of new exons during primate evolution. Thousands of human genes contain spliced exons derived from Alu elements. However, identifying Alu exons that have acquired genuine biological functions remains a major challenge. We investigated the creation and establishment of Alu exons in human genes, using transcriptome profiles of human tissues generated by high-throughput RNA sequencing (RNA-Seq) combined with extensive RT-PCR analysis. More than 25% of Alu exons analyzed by RNA-Seq have estimated transcript inclusion levels of at least 50% in the human cerebellum, indicating widespread establishment of Alu exons in human genes. Genes encoding zinc finger transcription factors have significantly higher levels of Alu exonization. Importantly, Alu exons with high splicing activities are strongly enriched in the 5'-UTR, and two-thirds (10/15) of 5'-UTR Alu exons tested by luciferase reporter assays significantly alter mRNA translational efficiency. Mutational analysis reveals the specific molecular mechanisms by which newly created 5'-UTR Alu exons modulate translational efficiency, such as the creation or elongation of upstream ORFs that repress the translation of the primary ORFs. This study presents genomic evidence that a major functional consequence of Alu exonization is the lineage-specific evolution of translational regulation. Moreover, the preferential creation and establishment of Alu exons in zinc finger genes suggest that Alu exonization may have globally affected the evolution of primate and human transcriptomes by regulating the protein production of master transcriptional regulators in specific lineages.

  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. Widespread ability of fungi to drive quinone redox cycling for biodegradation.

    PubMed

    Krueger, Martin C; Bergmann, Michael; Schlosser, Dietmar

    2016-06-01

    Wood-rotting fungi possess remarkably diverse extracellular oxidation mechanisms, including enzymes, such as laccase and peroxidases, and Fenton chemistry. The ability to biologically drive Fenton chemistry by the redox cycling of quinones has previously been reported to be present in both ecologically diverging main groups of wood-rotting basidiomycetes. Therefore, we investigated whether it is even more widespread among fungal organisms. Screening of a diverse selection of a total of 18 ascomycetes and basidiomycetes for reduction of the model compound 2,6-dimethoxy benzoquinone revealed that all investigated strains were capable of reducing it to its corresponding hydroquinone. In a second step, depolymerization of the synthetic polymer polystyrene sulfonate was used as a proxy for quinone-dependent Fenton-based biodegradation capabilities. A diverse subset of the strains, including environmentally ubiquitous molds, white-rot fungi, as well as peatland and aquatic isolates, caused substantial depolymerization indicative for the effective employment of quinone redox cycling as biodegradation tool. Our results may also open up new paths to utilize diverse fungi for the bioremediation of recalcitrant organic pollutants. PMID:27190290

  11. Human vision fails to distinguish widespread sexual dichromatism among sexually "monochromatic" birds.

    PubMed

    Eaton, Muir D

    2005-08-01

    Historical scenarios of evolution of avian plumage coloration have been called into question with the discoveries that most birds can see UV light (which normal humans cannot), and that UV-reflecting plumages are widespread in birds. Several examples of sexual dichromatism not detectable with human visual capabilities suggest that our categorizations of plumages as sexually mono- or dichromatic might often be incorrect. Nonetheless, given the limited taxonomic scope of those examples, the vast majority of sexually monochromatic birds are still treated as such without question in avian research. Herein, I show that >90% of 139 species, in a broad sampling of presumed sexually monochromatic passerine birds, were actually sexually dichromatic from an avian visual perspective, based on comparisons of plumage reflectance data using a visual model of color discrimination thresholds. The taxonomic ubiquity of this result suggests that many existing interpretations of evolutionary patterns of sexual dichromatism in birds are erroneous. The visual model used herein provides a method for quantifying sexual dichromatism, revealing that most (58.7%) feather patches sampled lie along a continuum of dichromatism between avian and human discriminatory abilities and could represent unrecognized sexually selected signals. Sexual dichromatism in this study rarely resulted from intersexual differences in UV coloration alone, emphasizing the need for analysis of bird coloration in relation to the full extent of avian visual discriminatory abilities, including, but not limited to, UV-visual capabilities.

  12. 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. PMID:27170296

  13. 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.

  14. Widespread ability of fungi to drive quinone redox cycling for biodegradation.

    PubMed

    Krueger, Martin C; Bergmann, Michael; Schlosser, Dietmar

    2016-06-01

    Wood-rotting fungi possess remarkably diverse extracellular oxidation mechanisms, including enzymes, such as laccase and peroxidases, and Fenton chemistry. The ability to biologically drive Fenton chemistry by the redox cycling of quinones has previously been reported to be present in both ecologically diverging main groups of wood-rotting basidiomycetes. Therefore, we investigated whether it is even more widespread among fungal organisms. Screening of a diverse selection of a total of 18 ascomycetes and basidiomycetes for reduction of the model compound 2,6-dimethoxy benzoquinone revealed that all investigated strains were capable of reducing it to its corresponding hydroquinone. In a second step, depolymerization of the synthetic polymer polystyrene sulfonate was used as a proxy for quinone-dependent Fenton-based biodegradation capabilities. A diverse subset of the strains, including environmentally ubiquitous molds, white-rot fungi, as well as peatland and aquatic isolates, caused substantial depolymerization indicative for the effective employment of quinone redox cycling as biodegradation tool. Our results may also open up new paths to utilize diverse fungi for the bioremediation of recalcitrant organic pollutants.

  15. 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.

  16. Widespread Iron Oxidizing Bacterial Communities in a late Paleoproterozoic Marine Environment

    NASA Astrophysics Data System (ADS)

    Planavsky, N.; Rouxel, O.; Bekker, A.

    2007-12-01

    Discovery of exceptionally well-preserved microfossils in the Gunflint Iron Formation provided the first evidence for diverse and abundant life in the Precambrian oceans. However, whether the Gunflint microbial communities were dominated by cyanobacteria or represent an archaic, lithotrophic ecosystem is a matter of longstanding debate. Here, we present Fe isotope and rare earth element (REE) data for microfossiliferous stromatolites that are consistent with the Gunflint biota being an iron-oxidizing bacterial community. The lack of or positive Ce anomalies in REE data indicate that the benthic community grew below a redoxcline and positive iron isotope compositions reveal that the microbial community only oxidized a fraction of the dissolved iron load. This depositional setting and Fe isotope evidence for incomplete iron oxidation are inconsistent with a cyanobacterial interpretation and provide strong support that the Gunflint biota was indeed a microaerophilic lithotrophic microbial ecosystem. An apparently restricted temporal distribution of the Gunflint biota coupled with a widespread spatial distribution signals a significant ecosystem evolutionary event in the late Paleoproterozoic when the ocean was redox-stratified and Fe-rich anoxic waters impinged onto the shallow shelf.

  17. Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes

    PubMed Central

    Andreeva, Alexandra V; Kutuzov, Mikhail A

    2004-01-01

    Background In eukaryotes, PPP (protein phosphatase P) family is one of the two known protein phosphatase families specific for Ser and Thr. The role of PPP phosphatases in multiple signaling pathways in eukaryotic cell has been extensively studied. Unlike eukaryotic PPP phosphatases, bacterial members of the family have broad substrate specificity or may even be Tyr-specific. Moreover, one group of bacterial PPPs are diadenosine tetraphosphatases, indicating that bacterial PPP phosphatases may not necessarily function as protein phosphatases. Results We describe the presence in eukaryotes of three groups of expressed genes encoding "non-conventional" phosphatases of the PPP family. These enzymes are more closely related to bacterial PPP phosphatases than to the known eukaryotic members of the family. One group, found exclusively in land plants, is most closely related to PPP phosphatases from some α-Proteobacteria, including Rhizobiales, Rhodobacterales and Rhodospirillaceae. This group is therefore termed Rhizobiales / Rhodobacterales / Rhodospirillaceae-like phosphatases, or Rhilphs. Phosphatases of the other group are found in Viridiplantae, Rhodophyta, Trypanosomatidae, Plasmodium and some fungi. They are structurally related to phosphatases from psychrophilic bacteria Shewanella and Colwellia, and are termed Shewanella-like phosphatases, or Shelphs. Phosphatases of the third group are distantly related to ApaH, bacterial diadenosine tetraphosphatases, and are termed ApaH-like phosphatases, or Alphs. Patchy distribution of Alphs in animals, plants, fungi, diatoms and kinetoplasts suggests that these phosphatases were present in the common ancestor of eukaryotes but were independently lost in many lineages. Rhilphs, Shelphs and Alphs form PPP clades, as divergent from "conventional" eukaryotic PPP phosphatases as they are from each other and from major bacterial clades. In addition, comparison of primary structures revealed a previously unrecognised (I

  18. 77 FR 30877 - Aging Airplane Program: Widespread Fatigue Damage; Technical Amendment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-24

    ... Airplane Program: Widespread Fatigue Damage,'' (75 FR 69746). In that final rule the FAA revised the... actions (see Damage Tolerance Data for Repairs and Alterations, 72 FR 70486). Change to Table 1 of Sec... Administration 14 CFR Parts 26, 121, and 129 RIN 2120-AI05 Aging Airplane Program: Widespread Fatigue...

  19. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria

    PubMed Central

    Anantharaman, Karthik; Breier, John A.; Sheik, Cody S.; Dick, Gregory J.

    2013-01-01

    Hydrothermal vents are a well-known source of energy that powers chemosynthesis in the deep sea. Recent work suggests that microbial chemosynthesis is also surprisingly pervasive throughout the dark oceans, serving as a significant CO2 sink even at sites far removed from vents. Ammonia and sulfur have been identified as potential electron donors for this chemosynthesis, but they do not fully account for measured rates of dark primary production in the pelagic water column. Here we use metagenomic and metatranscriptomic analyses to show that deep-sea populations of the SUP05 group of uncultured sulfur-oxidizing Gammaproteobacteria, which are abundant in widespread and diverse marine environments, contain and highly express genes encoding group 1 Ni, Fe hydrogenase enzymes for H2 oxidation. Reconstruction of near-complete genomes of two cooccurring SUP05 populations in hydrothermal plumes and deep waters of the Gulf of California enabled detailed population-specific metatranscriptomic analyses, revealing dynamic patterns of gene content and transcript abundance. SUP05 transcripts for genes involved in H2 and sulfur oxidation are most abundant in hydrothermal plumes where these electron donors are enriched. In contrast, a second hydrogenase has more abundant transcripts in background deep-sea samples. Coupled with results from a bioenergetic model that suggest that H2 oxidation can contribute significantly to the SUP05 energy budget, these findings reveal the potential importance of H2 as a key energy source in the deep ocean. This study also highlights the genomic plasticity of SUP05, which enables this widely distributed group to optimize its energy metabolism (electron donor and acceptor) to local geochemical conditions. PMID:23263870

  20. Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river.

    PubMed

    Rodriguez-Mozaz, Sara; Chamorro, Sara; Marti, Elisabet; Huerta, Belinda; Gros, Meritxell; Sànchez-Melsió, Alexandre; Borrego, Carles M; Barceló, Damià; Balcázar, Jose Luis

    2015-02-01

    Antibiotic resistance has become a major health concern; thus, there is a growing interest in exploring the occurrence of antibiotic resistance genes (ARGs) in the environment as well as the factors that contribute to their emergence. Aquatic ecosystems provide an ideal setting for the acquisition and spread of ARGs due to the continuous pollution by antimicrobial compounds derived from anthropogenic activities. We investigated, therefore, the pollution level of a broad range of antibiotics and ARGs released from hospital and urban wastewaters, their removal through a wastewater treatment plant (WWTP) and their presence in the receiving river. Several antimicrobial compounds were detected in all water samples collected. Among antibiotic families, fluoroquinolones were detected at the highest concentration, especially in hospital effluent samples. Although good removal efficiency by treatment processes was observed for several antimicrobial compounds, most antibiotics were still present in WWTP effluents. The results also revealed that copy numbers of ARGs, such as blaTEM (resistance to β-lactams), qnrS (reduced susceptibility to fluoroquinolones), ermB (resistance to macrolides), sulI (resistance to sulfonamides) and tetW (resistance to tetracyclines), were detected at the highest concentrations in hospital effluent and WWTP influent samples. Although there was a significant reduction in copy numbers of these ARGs in WWTP effluent samples, this reduction was not uniform across analyzed ARGs. Relative concentration of ermB and tetW genes decreased as a result of wastewater treatment, whereas increased in the case of blaTEM, sulI and qnrS genes. The incomplete removal of antibiotics and ARGs in WWTP severely affected the receiving river, where both types of emerging pollutants were found at higher concentration in downstream waters than in samples collected upstream from the discharge point. Taken together, our findings demonstrate a widespread occurrence of

  1. Galactoxylomannan-mediated immunological paralysis results from specific B cell depletion in the context of widespread immune system damage

    PubMed Central

    De Jesus, Magdia; Nicola, André Moraes; Frases, Susana; Lee, Ian R.; Mieses, Steven; Casadevall, Arturo

    2009-01-01

    The mechanisms responsible for polysaccharide-induced immunological paralysis have remained unexplained almost a century after this phenomenon was first described. Cryptococcus neoformans capsular polysaccharides glucuronoxylomannan (GXM) and galactoxylomannan (GalXM) elicit little or no antibody responses. This study investigates the immunological and biological effects of GalXM in mice. GalXM immunization elicits a state of immunological paralysis in mice characterized by the disappearance of antibody-producing cells in the spleen. Immunological paralysis and lack of immunogenicity could not be overcome by immunization with GalXM conjugated to a protein carrier, Bacillus anthracis protective antigen. Additionally, immunization with GalXM in either complete or incomplete Freund's adjuvant was associated with spleen enlargement in Balb/c mice. Terminal deoxynucleotidyl Transferase Biotin-dUTP Nick End Labeling (TUNEL) and flow cytometry revealed widespread apoptosis in the spleen after GalXM administration. Administration of a cocktail of Caspase-3 Inhibitor Z-DEVD-FMK and General Caspase Inhibitor Z-VAD-FMK or Fas-deficient mice abrogated the complete disappearance of antibody producing cells. Analysis of spleen cytokine expression in response to GalXM systemic injection revealed that GalXM down-regulated the production of inflammatory cytokines. Hence, we conclude that GalXM-induced immune paralysis is a result of specific B-cell depletion mediated by its pro-apoptotic properties in the context of widespread dysregulation of immune function. PMID:19684080

  2. Galactoxylomannan-mediated immunological paralysis results from specific B cell depletion in the context of widespread immune system damage.

    PubMed

    De Jesus, Magdia; Nicola, André Moraes; Frases, Susana; Lee, Ian R; Mieses, Steven; Casadevall, Arturo

    2009-09-15

    The mechanisms responsible for polysaccharide-induced immunological paralysis have remained unexplained almost a century after this phenomenon was first described. Cryptococcus neoformans capsular polysaccharides glucuronoxylomannan and galactoxylomannan (GalXM) elicit little or no Ab responses. This study investigates the immunological and biological effects of GalXM in mice. GalXM immunization elicits a state of immunological paralysis in mice characterized by the disappearance of Ab-producing cells in the spleen. Immunological paralysis and lack of immunogenicity could not be overcome by immunization with GalXM conjugated to a protein carrier, Bacillus anthracis protective Ag. Additionally, immunization with GalXM in either complete or IFA was associated with spleen enlargement in BALB/c mice. TUNEL and flow cytometry revealed widespread apoptosis in the spleen after GalXM administration. Administration of a cocktail of caspase-3 inhibitor Z-DEVD-FMK and general caspase inhibitor Z-VAD-FMK or Fas-deficient mice abrogated the complete disappearance of Ab-producing cells. Analysis of spleen cytokine expression in response to GalXM systemic injection revealed that GalXM down-regulated the production of inflammatory cytokines. Hence, we conclude that GalXM-induced immune paralysis is a result of specific B cell depletion mediated by its proapoptotic properties in the context of widespread dysregulation of immune function.

  3. High latitudes and high genetic diversity: phylogeography of a widespread boreal bird, the gray jay (Perisoreus canadensis).

    PubMed

    van Els, Paul; Cicero, Carla; Klicka, John

    2012-05-01

    We describe range-wide phylogeographic variation in gray jays (Perisoreus canadensis), a boreal Nearctic corvid that occurs today primarily in recently glaciated regions. Phylogenetic analysis of mitochondrial DNA (1041 base pairs ND2 gene; N=205, 50 localities) revealed four reciprocally monophyletic groups. One widespread clade occurs across the North American boreal zone, from Newfoundland to Alaska and southwest into Utah. Three other clades occur at lower latitudes in the montane West in Colorado, the northern Rocky Mountains, and the Pacific Northwest respectively. The geographic distribution of clades in gray jays corresponds with a general pattern that is emerging for boreal taxa, having one widespread northern clade and one or more geographically restricted southwestern clades. Population genetic analyses indicate that the larger boreal clade is genetically structured and harbors significantly more genetic diversity than those clades occurring at lower latitudes. Species distribution modeling (SDM) revealed multiple putative Pleistocene refugia including several occurring at higher latitudes. We suggest that multiple post-glacial colonization routes, some of which originate from these northern refugia, are responsible for the relatively high genetic diversity at high latitudes. Conversely, lower latitude clades show little variation, probably as a result of historical restriction to smaller geographical areas with smaller long-term population sizes. This 'upside-down' pattern of genetic diversity contrasts with the conventional view that populations of north-temperate species occupying previously glaciated habitats should possess lower levels of diversity than their southern counterparts. PMID:22321688

  4. 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

  5. On-off intermittency in earthquake occurrence

    SciTech Connect

    Bottiglieri, M.; Godano, C.

    2007-02-15

    The clustered occurrence of earthquakes is viewed as an intermittent phenomenon, interpreting the clusters of events as chaotic bursts combined to the Poissonian occurrence of background seismicity. In particular, we suggest that it can be interpreted as an example of on-off intermittency. This kind of intermittency is parameter driven and exhibits certain universal statistical properties. The study of a Californian catalogue allows to interpret earthquake occurrence as an on-off intermittent phenomenon. Our results suggest the existence of a branching mechanism in earthquake occurrence well explained by epidemic type models.

  6. 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

  7. 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.

  8. Aichi virus 1: environmental occurrence and behavior.

    PubMed

    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.

  9. 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.

  10. 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

  11. 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

  12. 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. PMID:22718912

  13. 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.

  14. 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.

  15. Widespread occurrence of benzophenone-type UV light filters in personal care products from China and the United States: an assessment of human exposure.

    PubMed

    Liao, Chunyang; Kannan, Kurunthachalam

    2014-04-01

    Benzophenone-3 (BP-3) is a sunscreen agent used in a variety of personal care products (PCPs) for the protection of human skin and hair from damage by ultraviolet (UV) radiation. Concerns have been raised over exposure of humans to BP-3, owing to the estrogenic potential of this compound. Nevertheless, the levels and profiles of BP-3 in PCPs and sources of exposure of humans to this estrogenic compound are not well-known. In this study, concentrations of BP-3 were determined in seven categories of 231 PCPs collected from several cities in China (n = 117) and the United States (U.S.) (n = 114), using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). BP-3 was found in the majority (81%) of the samples analyzed, at concentrations as high as 0.148%. The highest BP-3 concentrations (geometric mean [GM]: 548; median: 530 ng/g) were found in skin lotions (including sunscreen lotions), followed by makeup products (284; 221 ng/g). PCPs collected from the U.S. contained higher concentrations of BP-3 than those collected from China. On the basis of the concentrations measured and daily usage rates of PCPs, we estimated the daily intake of BP-3 through dermal absorption from the use of PCPs. The GM and 95th percentile exposure doses to BP-3 were 0.978 and 25.5 μg/day, respectively, for adult women in China, which were 2 orders of magnitude lower than those found for adult women in the U.S. (24.4 and 5160 μg/day). Skin lotions and face creams contributed to the preponderance of daily BP-3 exposures (>80%). PMID:24588714

  16. 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)

  17. 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

    NASA Astrophysics Data System (ADS)

    Neufeld, D. A.; González-Alfonso, E.; Melnick, G.; Szczerba, R.; Schmidt, M.; Decin, L.; Alcolea, J.; de Koter, A.; Schöier, F. L.; Bujarrabal, V.; Cernicharo, J.; Dominik, C.; Justtanont, K.; Marston, A. P.; Menten, K.; Olofsson, H.; Planesas, P.; Teyssier, D.; Waters, L. B. F. M.

    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 110-101 and 1113.343 GHz 111-000 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 μm continuum flux—a ratio which measures the water outflow rate—and the total mass-loss rate for the stars in our sample. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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. PMID:26388444

  5. 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.

  6. Widespread drought episodes in the western Great Lakes region during the past 2000 years: Geographic extent and potential mechanisms

    NASA Astrophysics Data System (ADS)

    Booth, Robert K.; Notaro, Michael; Jackson, Stephen T.; Kutzbach, John E.

    2006-02-01

    We compared high-resolution reconstructions of peatland water-table depth at two raised bogs in the western Great Lakes region separated by ˜1000 km. The sites included Minden Bog in southeastern Michigan and Hole-in-the-Bog in north-central Minnesota. Our objectives were to 1) determine whether large, decadal to multidecadal droughts of the past 2000 yrs were spatially and temporally coherent across the region, and 2) assess the underlying mechanisms of widespread droughts in the region. We found a strong correlation between bog-inferred records of moisture variability in the two regions ( r = 0.53). Between 2100 and 600 BP, extreme drought events centered on 1850, 1800, 1650, 1000, 800, and 700 BP are recorded in both regions. Many of these drought events were contemporaneous with large droughts already documented at sites far to the west in the Great Plains and Rocky Mountains. To identify potential modern climate analogues, we used empirical orthogonal function (EOF) analysis to reveal spatial modes of variability in drought and precipitation records of North America for the past century. The first EOFs of annual precipitation and Palmer Drought Severity Index (PDSI) were similar to each other, and consistent with a pattern of widespread continental drought. Correlations between these EOFs and annual sea surface temperatures (SSTs) indicate strong relationships to SSTs in both the Atlantic and Pacific basins. We hypothesize that widespread droughts between 1000 and 700 BP were related to amplification of a spatial mode of moisture variability associated with an anomalously warm North Atlantic, a warm mid-latitude North Pacific, and an anomalously cold Tropical Pacific. A more extensive network of hydroclimate records, developed using a consistent set of methods and proxies, could be used in conjunction with high-resolution records of past SSTs to test this hypothesis.

  7. 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

  8. 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

  9. Formation and occurrence of dopamine-derived betacyanins.

    PubMed

    Kobayashi, N; Schmidt, J; Wray, V; Schliemann, W

    2001-03-01

    In light of the fact that the main betaxanthin (miraxanthin V) and the major betacyanin (2-descarboxy-betanidin) in hairy root cultures of yellow beet (Beta vulgaris L.) are both dopamine-derived, the occurrence of similar structures for the minor betacyanins was also suggested. By HPLC comparison with the betacyanins obtained by dopamine administration to beet seedlings, enzymatic hydrolysis, LCMS and 1H NMR analyses, the minor betacyanins from hairy roots were identified as 2-descarboxy-betanin and its 6'-O-malonyl derivative. A short-term dopamine administration experiment with fodder beet seedlings revealed that the condensation step between 2-descarboxy-cyclo-Dopa and betalamic acid is the decisive reaction, followed by glucosylation and acylation. From these data a pathway for the biosynthesis of dopamine-derived betalains is proposed. Furthermore, the occurrence of these compounds in various cell and hairy root cultures as well as beet plants (Fodder and Garden Beet Group) is shown.

  10. Landscape characteristics influence morphological and genetic differentiation in a widespread raptor (Buteo jamaicensis).

    PubMed

    Hull, Joshua M; Hull, Angus C; Sacks, Benjamin N; Smith, Jeff P; Ernest, Holly B

    2008-02-01

    Landscape-scale population genetic structure in vagile vertebrates was commonly considered to be a contradiction in terms whereas recent studies have demonstrated behaviour and habitat associated structure in several such species. We investigate whether landscape features influence morphological and genetic differentiation in a widespread, mobile raptor. To accurately describe genetic differentiation associated with regional landscape factors, we first investigated subspecies relationships at a continental scale. We used 17 microsatellite loci and five morphological measurements to investigate differentiation between eastern and western subspecies of red-tailed hawks (Buteo jamaicensis) and to identify patterns between differentiation and habitat within western North America. Bayesian and frequency-based analyses of microsatellite data revealed clear distinctions between B. j. borealis (eastern) and B. j. calurus (western) samples. Furthermore, hawks sampled in Texas were stouter than those collected from the Rocky Mountains and farther west. Among western samples, birds from the Great Basin, Rocky Mountains, and Washington were significantly different in morphology than those from Oregon and California. We identified a pattern of isolation by distance among western breeding sites around the Sierra Nevada. Given the long-range dispersal capabilities of raptors, this pattern suggests that population-specific habitat preferences, corresponding with habitat breaks between eastern and western slopes of the Sierra Nevada, and/or regionally variable population densities limit migration between the Mediterranean habitat of central California and the xeric habitats of southern California and interior west. We suggest habitat preferences and regionally disparate population densities may play a role in shaping genetic structure in vagile avian taxa.

  11. 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.

  12. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses.

    PubMed

    Pritham, Ellen J; Putliwala, Tasneem; Feschotte, Cédric

    2007-04-01

    We previously identified a group of atypical mobile elements designated Mavericks from the nematodes Caenorhabditis elegans and C. briggsae and the zebrafish Danio rerio. Here we present the results of comprehensive database searches of the genome sequences available, which reveal that Mavericks are widespread in invertebrates and non-mammalian vertebrates but show a patchy distribution in non-animal species, being present in the fungi Glomus intraradices and Phakopsora pachyrhizi and in several single-celled eukaryotes such as the ciliate Tetrahymena thermophila, the stramenopile Phytophthora infestans and the trichomonad Trichomonas vaginalis, but not detectable in plants. This distribution, together with comparative and phylogenetic analyses of Maverick-encoded proteins, is suggestive of an ancient origin of these elements in eukaryotes followed by lineage-specific losses and/or recurrent episodes of horizontal transmission. In addition, we report that Maverick elements have amplified recently to high copy numbers in T. vaginalis where they now occupy as much as 30% of the genome. Sequence analysis confirms that most Mavericks encode a retroviral-like integrase, but lack other open reading frames typically found in retroelements. Nevertheless, the length and conservation of the target site duplication created upon Maverick insertion (5- or 6-bp) is consistent with a role of the integrase-like protein in the integration of a double-stranded DNA transposition intermediate. Mavericks also display long terminal-inverted repeats but do not contain ORFs similar to proteins encoded by DNA transposons. Instead, Mavericks encode a conserved set of 5 to 9 genes (in addition to the integrase) that are predicted to encode proteins with homology to replication and packaging proteins of some bacteriophages and diverse eukaryotic double-stranded DNA viruses, including a DNA polymerase B homolog and putative capsid proteins. Based on these and other structural similarities, we

  13. 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:

  14. The Association between Chronic Widespread Musculoskeletal Pain, Depression and Fatigue Is Genetically Mediated

    PubMed Central

    Burri, Andrea; Ogata, Soshiro; Livshits, Gregory; Williams, Frances

    2015-01-01

    Background Chronic widespread muscoloskeletal pain (CWP) is prevalent in the general population and associated with high health care costs, so understanding the risk factors for chronic pain is important for both those affected and for society. In the present study we investigated the underlying etiological structure of CWP to understand better the association between the major clinical features of fatigue, depression and dihydroepiandrosterone sulphate (DHEAS) using a multivariate twin design. Methodology/Principle Findings Data were available in 463 UK female twin pairs including CWP status and information on depression, chronic fatigue and serum DHEAS levels. High to moderate heritabilities for all phenotypes were obtained (42.58% to 74.24%). The highest phenotypic correlation was observed between fatigue and CWP (r = 0.45), and the highest genetic correlation between CWP and fatigue (rg = 0.78). Structural equation modeling revealed the AE Cholesky model to provide the best model of the observed data. In this model, two additive genetic factors could be detected loading heavily on CWP—A2 explaining 40% of the variance and A3 20%. The factor loading heaviest on DHEAS showed only a small loading on the other phenotypes and none on fatigue at all. Furthermore, one distinct non-shared environmental factor loading specifically on CWP—but not on any of the other phenotypes—could be detected suggesting that the association between CWP and the other phenotypes is due only to genetic factors. Conclusions/Significance Our results suggest that CWP and its associated features share a genetic predisposition but that they are relatively distinct in their environmental determinants. PMID:26599910

  15. 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:

  16. Niphargus–Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania

    PubMed Central

    Flot, Jean-François; Bauermeister, Jan; Brad, Traian; Hillebrand-Voiculescu, Alexandra; Sarbu, Serban M; Dattagupta, Sharmishtha

    2014-01-01

    Niphargus is a speciose amphipod genus found in groundwater habitats across Europe. Three Niphargus species living in the sulphidic Frasassi caves in Italy harbour sulphur-oxidizing Thiothrix bacterial ectosymbionts. These three species are distantly related, implying that the ability to form ectosymbioses with Thiothrix may be common among Niphargus. Therefore, Niphargus–Thiothrix associations may also be found in sulphidic aquifers other than Frasassi. In this study, we examined this possibility by analysing niphargids of the genera Niphargus and Pontoniphargus collected from the partly sulphidic aquifers of the Southern Dobrogea region of Romania, which are accessible through springs, wells and Movile Cave. Molecular and morphological analyses revealed seven niphargid species in this region. Five of these species occurred occasionally or exclusively in sulphidic locations, whereas the remaining two were restricted to nonsulphidic areas. Thiothrix were detected by PCR on all seven Dobrogean niphargid species and observed using microscopy to be predominantly attached to their hosts' appendages. 16S rRNA gene sequences of the Thiothrix epibionts fell into two main clades, one of which (herein named T4) occurred solely on niphargids collected in sulphidic locations. The other Thiothrix clade was present on niphargids from both sulphidic and nonsulphidic areas and indistinguishable from the T3 ectosymbiont clade previously identified on Frasassi-dwelling Niphargus. Although niphargids from Frasassi and Southern Dobrogea are not closely related, the patterns of their association with Thiothrix are remarkably alike. The finding of similar Niphargus–Thiothrix associations in aquifers located 1200 km apart suggests that they may be widespread in European groundwater ecosystems. PMID:24044653

  17. 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:

  18. 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

  19. 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

  20. Landscape characteristics influence morphological and genetic differentiation in a widespread raptor (Buteo jamaicensis).

    PubMed

    Hull, Joshua M; Hull, Angus C; Sacks, Benjamin N; Smith, Jeff P; Ernest, Holly B

    2008-02-01

    Landscape-scale population genetic structure in vagile vertebrates was commonly considered to be a contradiction in terms whereas recent studies have demonstrated behaviour and habitat associated structure in several such species. We investigate whether landscape features influence morphological and genetic differentiation in a widespread, mobile raptor. To accurately describe genetic differentiation associated with regional landscape factors, we first investigated subspecies relationships at a continental scale. We used 17 microsatellite loci and five morphological measurements to investigate differentiation between eastern and western subspecies of red-tailed hawks (Buteo jamaicensis) and to identify patterns between differentiation and habitat within western North America. Bayesian and frequency-based analyses of microsatellite data revealed clear distinctions between B. j. borealis (eastern) and B. j. calurus (western) samples. Furthermore, hawks sampled in Texas were stouter than those collected from the Rocky Mountains and farther west. Among western samples, birds from the Great Basin, Rocky Mountains, and Washington were significantly different in morphology than those from Oregon and California. We identified a pattern of isolation by distance among western breeding sites around the Sierra Nevada. Given the long-range dispersal capabilities of raptors, this pattern suggests that population-specific habitat preferences, corresponding with habitat breaks between eastern and western slopes of the Sierra Nevada, and/or regionally variable population densities limit migration between the Mediterranean habitat of central California and the xeric habitats of southern California and interior west. We suggest habitat preferences and regionally disparate population densities may play a role in shaping genetic structure in vagile avian taxa. PMID:18208488

  1. Widespread deuteration across the IRDC G035.39-00.33

    NASA Astrophysics Data System (ADS)

    Barnes, A. T.; Kong, S.; Tan, J. C.; Henshaw, J. D.; Caselli, P.; Jiménez-Serra, I.; Fontani, F.

    2016-05-01

    Infrared Dark Clouds (IRDCs) are cold, dense regions that are usually found within Giant Molecular Clouds. Ongoing star formation within IRDCs is typically still deeply embedded within the surrounding molecular gas. Characterizing the properties of relatively quiescent IRDCs may therefore help us to understand the earliest phases of the star formation process. Studies of local molecular clouds have revealed that deuterated species are enhanced in the earliest phases of star formation. In this paper, we test this towards IRDC G035.39-00.33. We present an 80 arcsec by 140 arcsec map of the J = 2 → 1 transition of N2D+, obtained with the Institut de Radioastronomie Millimétrique 30 m telescope telescope. We find that N2D+ is widespread throughout G035.39-00.33. Complementary observations of N2H+ (1 - 0) are used to estimate the deuterium fraction, D_frac^N_2H^+ ≡ N(N2D+)/N(N2H+). We report a mean D_frac^N_2H^+ = 0.04 ± 0.01, with a maximum of D_frac^N_2H^+ = 0.09 ± 0.02. The mean deuterium fraction is ˜3 orders of magnitude greater than the interstellar [D]/[H] ratio. High angular resolution observations are required to exclude beam dilution effects of compact deuterated cores. Using chemical modelling, we find that the average observed values of D_frac^N_2H^+are in agreement with an equilibrium deuterium fraction, given the general properties of the cloud. This implies that the IRDC is at least ˜3 Myr old, which is ˜8 times longer than the mean free-fall time of the observed deuterated region.

  2. 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

  3. "Nested" cryptic diversity in a widespread marine ecosystem engineer: a challenge for detecting biological invasions

    PubMed Central

    2011-01-01

    Background Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit. Results Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within Pyura stolonifera in the different coastal communities they dominate. Conclusions This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the

  4. Widespread presence of human BOULE homologs among animals and conservation of their ancient reproductive function.

    PubMed

    Shah, Chirag; Vangompel, Michael J W; Naeem, Villian; Chen, Yanmei; Lee, Terrance; Angeloni, Nicholas; Wang, Yin; Xu, Eugene Yujun

    2010-07-15

    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.

  5. Serological, molecular and entomological surveillance demonstrates widespread circulation of West Nile virus in Turkey.

    PubMed

    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

    2014-07-01

    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.

  6. 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

  7. 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.

  8. Hassallidins, antifungal glycolipopeptides, are widespread among cyanobacteria and are the end-product of a nonribosomal pathway

    PubMed Central

    Vestola, Johanna; Shishido, Tania K.; Jokela, Jouni; Fewer, David P.; Aitio, Olli; Permi, Perttu; Wahlsten, Matti; Wang, Hao; Rouhiainen, Leo; Sivonen, Kaarina

    2014-01-01

    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. PMID:24742428

  9. Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes[W

    PubMed Central

    Wenke, Torsten; Döbel, Thomas; Sörensen, Thomas Rosleff; Junghans, Holger; Weisshaar, Bernd; Schmidt, Thomas

    2011-01-01

    Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5′ truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3′ end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families. PMID:21908723

  10. 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.

  11. 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

  12. Arsenic occurrence in Brazil and human exposure.

    PubMed

    de Figueiredo, Bernardino Ribeiro; Borba, Ricardo Perobelli; Angélica, Rômulo Simões

    2007-04-01

    Environmental exposure to arsenic (As) in terms of public health is receiving increasing attention worldwide following cases of mass contamination in different parts of the world. However, there is a scarcity of data available on As geochemistry in Brazilian territory, despite the known occurrence of As in some of the more severely polluted areas of Brazil. The purpose of this paper is to discuss existing data on As distribution in Brazil based on recent investigations in three contaminated areas as well as results from the literature. To date, integrated studies on environmental and anthropogenic sources of As contamination have been carried out only in three areas in Brazil: (1) the Southeastern region, known as the Iron Quadrangle, where As was released into the drainage systems, soils and atmosphere as a result of gold mining; (2) the Ribeira Valley, where As occurs in Pb-Zn mine wastes and naturally in As-rich rocks and soils; (3) the Amazon region, including the Santana area, where As is associated with manganese ores mined over the last 50 years. Toxicological studies revealed that the populations were not exposed to elevated levels of As, with the As concentrations in surface water in these areas rarely exceeding 10 microg/L. Deep weathering of bedrocks along with formation of Fe/Al-enriched soils and sediments function as a chemical barrier that prevents the release of As into the water. In addition, the tropical climate results in high rates of precipitation in the northern and southeastern regions and, hence, the As contents of drinking water is diluted. Severe cases of human As exposure related to non-point pollution sources have not been reported in Brazil. However, increasing awareness of the adverse health effects of As will eventually lead to a more complete picture of the distribution of As in Brazil. PMID:17351814

  13. Arsenic occurrence in Brazil and human exposure.

    PubMed

    de Figueiredo, Bernardino Ribeiro; Borba, Ricardo Perobelli; Angélica, Rômulo Simões

    2007-04-01

    Environmental exposure to arsenic (As) in terms of public health is receiving increasing attention worldwide following cases of mass contamination in different parts of the world. However, there is a scarcity of data available on As geochemistry in Brazilian territory, despite the known occurrence of As in some of the more severely polluted areas of Brazil. The purpose of this paper is to discuss existing data on As distribution in Brazil based on recent investigations in three contaminated areas as well as results from the literature. To date, integrated studies on environmental and anthropogenic sources of As contamination have been carried out only in three areas in Brazil: (1) the Southeastern region, known as the Iron Quadrangle, where As was released into the drainage systems, soils and atmosphere as a result of gold mining; (2) the Ribeira Valley, where As occurs in Pb-Zn mine wastes and naturally in As-rich rocks and soils; (3) the Amazon region, including the Santana area, where As is associated with manganese ores mined over the last 50 years. Toxicological studies revealed that the populations were not exposed to elevated levels of As, with the As concentrations in surface water in these areas rarely exceeding 10 microg/L. Deep weathering of bedrocks along with formation of Fe/Al-enriched soils and sediments function as a chemical barrier that prevents the release of As into the water. In addition, the tropical climate results in high rates of precipitation in the northern and southeastern regions and, hence, the As contents of drinking water is diluted. Severe cases of human As exposure related to non-point pollution sources have not been reported in Brazil. However, increasing awareness of the adverse health effects of As will eventually lead to a more complete picture of the distribution of As in Brazil.

  14. 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.

  15. The occurrence of acid precipitation on the west coast of the United States.

    PubMed

    Powers, C F; Rambo, D L

    1981-06-01

    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 have been observed in western and eastern Oregon, but data are inadequate for regional generalization. New stations currently being established in Washington and Oregon, largely in resposnse to the recently renewed activity of Mount St. Helens, will greatly facilitate assessment of precipitation acidity in the Northwest.

  16. 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.

  17. Brief Communication: Freaque wave occurrences in 2013

    NASA Astrophysics Data System (ADS)

    Liu, P. C.

    2014-11-01

    Documenting freaque waves when they occured around the globe in 2013 is based here on news reports on the internet. It was found that there were a total 22 cases of freaque waves in 2013, based on those reported in clearly-defined physically specific environments. There were three cases in the deep ocean, six in nearshore areas, seven on sandy beaches, and seven on rocky shore areas. Note that most of the academic research has been on freaque waves in the deep ocean, which accounts for 13% of all occurrences. The majority of reported occurrences, 87%, are in the nearshore areas or along the beach area. Geographically, these cases are also fairly evenly spread around the globe. As of now, there is no general knowledge regarding the frequency of occurrence of these freaque waves, so that one may assume that 2013 was a customary year for freaque wave occurrences.

  18. 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

  19. 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.

  20. Nonspecific Adherence by Actinobacillus actinomycetemcomitans Requires Genes Widespread in Bacteria and Archaea

    PubMed Central

    Kachlany, Scott C.; Planet, Paul J.; Bhattacharjee, Mrinal K.; Kollia, Evyenia; DeSalle, Rob; Fine, Daniel H.; Figurski, David H.

    2000-01-01

    The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is the putative agent for localized juvenile periodontitis, a particularly destructive form of periodontal disease in adolescents. This bacterium has also been isolated from a variety of other infections, notably endocarditis. Fresh clinical isolates of A. actinomycetemcomitans form tenacious biofilms, a property likely to be critical for colonization of teeth and other surfaces. Here we report the identification of a locus of seven genes required for nonspecific adherence of A. actinomycetemcomitans to surfaces. The recently developed transposon IS903φkan was used to isolate mutants of the rough clinical isolate CU1000 that are defective in tight adherence to surfaces (Tad−). Unlike wild-type cells, Tad− mutant cells adhere poorly to surfaces, fail to form large autoaggregates, and lack long, bundled fibrils. Nucleotide sequencing and genetic complementation analysis revealed a 6.7-kb region of the genome with seven adjacent genes (tadABCDEFG) required for tight adherence. The predicted TadA polypeptide is similar to VirB11, an ATPase involved in macromolecular transport. The predicted amino acid sequences of the other Tad polypeptides indicate membrane localization but no obvious functions. We suggest that the tad genes are involved in secretion of factors required for tight adherence of A. actinomycetemcomitans. Remarkably, complete and highly conserved tad gene clusters are present in the genomes of the bubonic plague bacillus Yersinia pestis and the human and animal pathogen Pasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteria and Archaea. Our results show that the tad genes are required for tight adherence of A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a wide array of microorganisms indicates that they have important functions. We propose that tad

  1. Recognition of the Script in Serbian Documents Using Frequency Occurrence and Co-Occurrence Analysis

    PubMed Central

    Brodić, Darko; Milivojević, Zoran N.; Maluckov, Čedomir A.

    2013-01-01

    Any document in Serbian language can be written in two different scripts: Latin or Cyrillic. Although characteristics of these scripts are similar, some of their statistical measures are quite different. The paper proposed a method for the extraction of certain script from document according to the occurrence and co-occurrence of the script types. First, each letter is modeled with the certain script type according to characteristics concerning its position in baseline area. Then, the frequency analysis of the script types occurrence is performed. Due to diversity of Latin and Cyrillic script, the occurrence of modeled letters shows substantial statistics dissimilarity. Furthermore, the co-occurrence matrix is computed. The analysis of the co-occurrence matrix draws a strong margin as a criteria to distinguish and recognize the certain script. The proposed method is analyzed on the case of a database which includes different types of printed and web documents. The experiments gave encouraging results. PMID:24385887

  2. Occurrence of Six Honeybee Viruses in Diseased Austrian Apiaries

    PubMed Central

    Berényi, Olga; Bakonyi, Tamás; Derakhshifar, Irmgard; Köglberger, Hemma; Nowotny, Norbert

    2006-01-01

    The occurrence, prevalence, and distribution patterns of acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Kashmir bee virus (KBV), and sacbrood virus (SBV) were investigated in 90 Austrian honeybee colonies suffering from symptoms of depopulation, sudden collapse, paralysis, or dark coloring by employing reverse transcription-PCR. Infestation with parasites was also recorded. The samples originated from all parts of Austria. The most prevalent virus was DWV, present in 91% of samples, followed by ABPV, SBV, and BQCV (68%, 49%, and 30%, respectively). CBPV was detected in 10% of colonies, while KBV was not present in any sample. In most samples, more than one virus was identified. The distribution pattern of ABPV, BQCV, CBPV, and SBV varied considerably in the different geographic regions investigated, while DWV was widespread in all Austrian federal states. In bees that showed dark coloring and disorientation, CBPV was always detected. Simultaneous infections of DWV and ABPV were most frequently observed in colonies suffering from weakness, depopulation, and sudden collapse. Bees obtained from apparently healthy colonies within the same apiaries showed a similar distribution pattern of viruses; however, the relative virus load was 10 to 126 times lower than in bees from diseased colonies. A limited number of bee samples from surrounding central European countries (Germany, Poland, Hungary, and Slovenia) were also tested for the presence of the above viruses. Variances were found in the distribution of BQCV and SBV. PMID:16597939

  3. 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

  4. [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.

  5. 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

  6. Barriers and opportunities to the widespread adoption of telemedicine: a bi-country evaluation.

    PubMed

    Vimarlund, Vivian; Le Rouge, Cynthia

    2013-01-01

    Recognizing that current practices for healthcare delivery are no longer sustainable, OECD governments are focusing more and more on how to leverage ICT to facilitate superior healthcare delivery. One such possibility is the use of Telemedicine. A major goal of telemedicine today is to develop next-generation telemedicine tools and technologies. However, key "classic" barriers continue to challenge widespread telemedicine adoption by health care organizations. These barriers include technology, financial, legal/standards, business strategy, and human resources issues. This comparative study explores the current status of barriers and opportunities to the widespread adoption of telemedicine in two different countries: Sweden, and USA. PMID:23920707

  7. Barriers and opportunities to the widespread adoption of telemedicine: a bi-country evaluation.

    PubMed

    Vimarlund, Vivian; Le Rouge, Cynthia

    2013-01-01

    Recognizing that current practices for healthcare delivery are no longer sustainable, OECD governments are focusing more and more on how to leverage ICT to facilitate superior healthcare delivery. One such possibility is the use of Telemedicine. A major goal of telemedicine today is to develop next-generation telemedicine tools and technologies. However, key "classic" barriers continue to challenge widespread telemedicine adoption by health care organizations. These barriers include technology, financial, legal/standards, business strategy, and human resources issues. This comparative study explores the current status of barriers and opportunities to the widespread adoption of telemedicine in two different countries: Sweden, and USA.

  8. [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.

  9. Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families

    PubMed Central

    Quistgaard, Esben M; Thirup, Søren S

    2009-01-01

    Background The Asp-box is a short sequence and structure motif that folds as a well-defined β-hairpin. It is present in different folds, but occurs most prominently as repeats in β-propellers. Asp-box β-propellers are known to be characteristically irregular and to occur in many medically important proteins, most of which are glycosidase enzymes, but they are otherwise not well characterized and are only rarely treated as a distinct β-propeller family. We have analyzed the sequence, structure, function and occurrence of the Asp-box and s-Asp-box -a related shorter variant, and provide a comprehensive classification and computational analysis of the Asp-box β-propeller family. Results We find that all conserved residues of the Asp-box support its structure, whereas the residues in variable positions are generally used for other purposes. The Asp-box clearly has a structural role in β-propellers and is highly unlikely to be involved in ligand binding. Sequence analysis of the Asp-box β-propeller family reveals it to be very widespread especially in bacteria and suggests a wide functional range. Disregarding the Asp-boxes, sequence conservation of the propeller blades is very low, but a distinct pattern of residues with specific properties have been identified. Interestingly, Asp-boxes are occasionally found very close to other propeller-associated repeats in extensive mixed-motif stretches, which strongly suggests the existence of a novel class of hybrid β-propellers. Structural analysis reveals that the top and bottom faces of Asp-box β-propellers have striking and consistently different loop properties; the bottom is structurally conserved whereas the top shows great structural variation. Interestingly, only the top face is used for functional purposes in known structures. A structural analysis of the 10-bladed β-propeller fold, which has so far only been observed in the Asp-box family, reveals that the inner strands of the blades are unusually far apart

  10. 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

    2014-06-01

    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. PMID:24843158

  11. Achieving Widespread, Democratic Education in the United States Today: Dewey's Ideas Reconsidered

    ERIC Educational Resources Information Center

    Meadows, Elizabeth; Blatchford, Katherine

    2009-01-01

    Excellent, democratic education that furthers each person's potential, success and happiness for her own and others' well-being is not yet widespread in the U.S. today. Dewey's The Public and Its Problems has much to say about the possibilities and challenges of achieving this goal. This paper examines Dewey's ideas about how a public for…

  12. 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

    2014-06-01

    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.

  13. Climate change and forest fires synergistically drive widespread melt events of the Greenland Ice Sheet

    PubMed Central

    Keegan, Kaitlin M.; Albert, Mary R.; McConnell, Joseph R.; Baker, Ian

    2014-01-01

    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. PMID:24843158

  14. 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

  15. 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.

  16. 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...

  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. Forest Pest Occurrence Predictionca-Markov Model

    NASA Astrophysics Data System (ADS)

    Xie, Fangyi; Zhang, Xiaoli; Chen, Xiaoyan

    Since the spatial pattern of forest pest occurrence is determined by biological characteristics and habitat conditions, this paper introduced construction of a cellular automaton model combined with Markov model to predicate the forest pest occurrence. Rules of the model includes the cell states rules, neighborhood rules and transition rules which are defined according to the factors from stand conditions, stand structures, climate and the influence of the factors on the state conversion. Coding for the model is also part of the implementations of the model. The participants were designed including attributes and operations of participants expressed with a UML diagram. Finally, the scale issues on forest pest occurrence prediction, of which the core are the prediction of element size and time interval, are partly discussed in this paper.

  19. Fresh Shallow Valleys in Northern Arabia Terra: Evidence for a Late, Widespread Period of Aqueous Activity on Mars

    NASA Astrophysics Data System (ADS)

    Wilson, S. A.; Howard, A. D.; Moore, J. M.; Grant, J. A., III

    2015-12-01

    Concentrations of fresh shallow valleys (FSVs) on Mars occur between ~30-45° in both hemispheres as well as near the equator (e.g., Gale crater and vicinity). FSVs in the northern hemisphere occur along the dichotomy boundary, with the highest concentration in northern Arabia Terra from 35-40°N between 0-20ºE. In this region, FSVs developed both on and away from ejecta of relatively fresh craters, making the direct association between impact processes and formation less likely. Crater statistics and cross-cutting relationships indicate the formation of FSVs terminated prior to about 1.4 Ga, suggesting they may be contemporaneous with alluvial fan and delta formation in the equatorial and mid-latitudes. Many FSV systems are 150+ km long, and in several cases appear to cross depressions that were likely filled with ice or water during FSV formation. Most FSV systems could have formed from a single episode of erosion but incision of the main channel in some locations may imply episodic formation. One long valley system in N. Arabia Terra with an incised channel (100 m wide, up to 10 m deep) yields formative discharges in the range of 100-200 m3/s assuming sand sized particles and a flow depth of 0.25 m, consistent with formation via snowmelt. The grain size is unknown, therefore discharges could range from 10s m3/s for active transport of fine sand to 1000 m3/s for gravel sized grains. Approximately 25 small craters (diameters ranging from ~2-10 km) have single channels extending outward from their rim, implying overflow of the crater and the possible presence of a deep lake. Widespread occurrence of FSVs, their similar morphology, and modest state of degradation is consistent with most forming during one or more global intervals of favorable climate, likely through snowmelt from surface or sub-ice flows during the Hesperian.

  20. The occurrence of multidrug-resistant Pseudomonas aeruginosa on hydrocarbon-contaminated sites.

    PubMed

    Kaszab, Edit; Kriszt, Balázs; Atzél, Béla; Szabó, Gabriella; Szabó, István; Harkai, Péter; Szoboszlay, Sándor

    2010-01-01

    The main aim of this paper was the comprehensive estimation of the occurrence rate and the antibiotic-resistance conditions of opportunistic pathogen Pseudomonas aeruginosa in hydrocarbon-contaminated environments. From 2002 to 2007, 26 hydrocarbon-contaminated sites of Hungary were screened for the detection of environmental isolates. Altogether, 156 samples were collected and examined for the determination of appearance, representative cell counts, and antibiotic-resistance features of P. aeruginosa. The detected levels of minimal inhibitory concentrations of ten different drugs against 36 environmental strains were compared to the results of a widely used reference strain ATCC 27853 and four other clinical isolates of P. aeruginosa. Based on our long-term experiment, it can be established that species P. aeruginosa was detectable in case of 61.5% of the investigated hydrocarbon-contaminated sites and 35.2% of the examined samples that shows its widespread occurrence in polluted soil-groundwater systems. In the course of the antibiotic-resistance assay, our results determined that 11 of the examined 36 environmental strains had multiple drug-resistance against several clinically effective antimicrobial classes: cephalosporins, wide spectrum penicillins, carbapenems, fluoroquinolones, and aminoglycosides. The fact that these multiresistant strains were isolated from 8 different hydrocarbon-contaminated sites, mainly from outskirts, confirms that multiple drug-resistance of P. aeruginosa is widespread not only in clinical, but also in natural surroundings as well. PMID:19597862

  1. 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.

  2. 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.

  3. 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.

  4. [T-2 toxin: occurrence and detection].

    PubMed

    Dohnal, V; Jezková, A; Kuca, K; Jun, D

    2007-07-01

    The paper is focused on the occurrence and methods for the detection of T-2 toxin, one of the most toxic trichothecene Fusarium mycotoxin. Due to its physical-chemical properties and high toxicity, T-2 toxin is classified as a potential biological warfare agent. PMID:17969315

  5. 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)

  6. 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.

  7. 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

  8. 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.

  9. Alleviating Search Uncertainty through Concept Associations: Automatic Indexing, Co-Occurrence Analysis, and Parallel Computing.

    ERIC Educational Resources Information Center

    Chen, Hsinchun; Martinez, Joanne; Kirchhoff, Amy; Ng, Tobun D.; Schatz, Bruce R.

    1998-01-01

    Grounded on object filtering, automatic indexing, and co-occurrence analysis, an experiment was performed using a parallel supercomputer to analyze over 400,000 abstracts in an INSPEC computer engineering collection. A user evaluation revealed that system-generated thesauri were better than the human-generated INSPEC subject thesaurus in concept…

  10. 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…

  11. 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.

  12. 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. PMID:27587162

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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. PMID:26422925

  19. OCCURRENCE OF Blastocystis spp. IN UBERABA, MINAS GERAIS, BRAZIL.

    PubMed

    Cabrine-Santos, Marlene; Cintra, Eduardo do Nascimento; do Carmo, Rafaela Andrade; Nascentes, Gabriel Antônio Nogueira; Pedrosa, André Luiz; Correia, Dalmo; Oliveira-Silva, Márcia Benedita de

    2015-01-01

    Intestinal parasites are a problem for public health all over the world. The infection with Blastocystis, a protozoan of controversial pathogenicity, is one of the most common among them all. In this study, the occurrence of intestinal parasites, with emphasis on Blastocystis, in patients at the Universidade Federal do Triângulo Mineiro was investigated in Uberaba (MG) through microscopy of direct smears and fecal concentrates using Ritchie's method. Feces of 1,323 patients were examined from April 2011 to May 2012. In 28.7% of them at least one intestinal parasite was identified, and the most frequent organisms were Blastocystis spp. (17.8%) and Giardia intestinalis (7.4%). The occurrence of parasitism was higher in children aged 6 -10 years old, and the infection with Blastocystis spp. was higher above the age of six (p < 0.001). The exclusive presence of G. intestinalis and of Blastocystis spp. was observed in 5.4% and 12.2% of the patients, respectively. Regarding patients with diarrheic feces, 8% revealed unique parasitism of Blastocystis spp. Other intestinal parasites observed in children were Ascaris lumbricoides (0.3%) and Entamoeba histolytica/dispar/moshkovskii (1.4%). The Ritchie's method was more sensitive (92.8%) when compared to direct microscopy (89.8%), with high agreement between them (97.7%, kappa = 0.92). In conclusion, the occurrence of Blastocystis spp. in Uberaba is high and the presence of diarrheic feces with exclusive presence of the parasite of Blastocystis spp. was observed. PMID:26200960

  20. OCCURRENCE OF Blastocystis spp. IN UBERABA, MINAS GERAIS, BRAZIL

    PubMed Central

    CABRINE-SANTOS, Marlene; CINTRA, Eduardo do Nascimento; do CARMO, Rafaela Andrade; NASCENTES, Gabriel Antônio Nogueira; PEDROSA, André Luiz; CORREIA, Dalmo; de OLIVEIRA-SILVA, Márcia Benedita

    2015-01-01

    Intestinal parasites are a problem for public health all over the world. The infection with Blastocystis, a protozoan of controversial pathogenicity, is one of the most common among them all. In this study, the occurrence of intestinal parasites, with emphasis on Blastocystis, in patients at the Universidade Federal do Triângulo Mineiro was investigated in Uberaba (MG) through microscopy of direct smears and fecal concentrates using Ritchie’s method. Feces of 1,323 patients were examined from April 2011 to May 2012. In 28.7% of them at least one intestinal parasite was identified, and the most frequent organisms were Blastocystis spp. (17.8%) and Giardia intestinalis (7.4%). The occurrence of parasitism was higher in children aged 6 -10 years old, and the infection with Blastocystis spp. was higher above the age of six (p < 0.001). The exclusive presence of G. intestinalis and of Blastocystis spp. was observed in 5.4% and 12.2% of the patients, respectively. Regarding patients with diarrheic feces, 8% revealed unique parasitism of Blastocystis spp. Other intestinal parasites observed in children were Ascaris lumbricoides(0.3%) and Entamoeba histolytica/dispar/moshkovskii (1.4%). The Ritchie’s method was more sensitive (92.8%) when compared to direct microscopy (89.8%), with high agreement between them (97.7%, kappa = 0.92). In conclusion, the occurrence of Blastocystis spp. in Uberaba is high and the presence of diarrheic feces with exclusive presence of the parasite of Blastocystis spp. was observed. PMID:26200960

  1. Chronic widespread musculoskeletal pain - a comparison of those who meet criteria for fibromyalgia and those who do not.

    PubMed

    Cöster, Lars; Kendall, Sally; Gerdle, Björn; Henriksson, Chris; Henriksson, Karl G; Bengtsson, Ann

    2008-07-01

    Fibromyalgia is currently classified as chronic widespread pain with widespread allodynia to pressure pain. There are few data describing pain characteristics, quality of life, consequences for daily living, and psychosocial status in patients who meet the classification criteria for fibromyalgia proposed by the American College of Rheumatology compared with patients with chronic widespread pain but not widespread allodynia. This study used a randomly selected sample from the general population. A postal questionnaire and a pain mannequin were sent to 9952 people. The response rate was 76.7%. The pain drawings showed that 345 people had widespread pain; that is, they noted pain in all four extremities and axially. Clinical examination, which included a manual tender point examination, was performed in 125 subjects. These people answered commonly used questionnaires on pain, quality of life, coping strategies, depression, and anxiety. Compared with chronic widespread pain without widespread allodynia, fibromyalgia was associated with more severe symptoms/consequences for daily life and higher pain severity. Similar coping strategies were found. Chronic widespread pain without widespread allodynia to pressure pain was found in 4.5% in the population and fibromyalgia in 2.5%.

  2. 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.

  3. Evidence of widespread selection on standing variation in Europe at height-associated SNPs.

    PubMed

    Turchin, Michael C; Chiang, Charleston W K; Palmer, Cameron D; Sankararaman, Sriram; Reich, David; Hirschhorn, Joel N

    2012-09-01

    Strong signatures of positive selection at newly arising genetic variants are well documented in humans(1-8), but this form of selection may not be widespread in recent human evolution(9). Because many human traits are highly polygenic and partly determined by common, ancient genetic variation, an alternative model for rapid genetic adaptation has been proposed: weak selection acting on many pre-existing (standing) genetic variants, or polygenic adaptation(10-12). By studying height, a classic polygenic trait, we demonstrate the first human signature of widespread selection on standing variation. We show that frequencies of alleles associated with increased height, both at known loci and genome wide, are systematically elevated in Northern Europeans compared with Southern Europeans (P < 4.3 × 10(-4)). This pattern mirrors intra-European height differences and is not confounded by ancestry or other ascertainment biases. The systematic frequency differences are consistent with the presence of widespread weak selection (selection coefficients ∼10(-3)-10(-5) per allele) rather than genetic drift alone (P < 10(-15)). PMID:22902787

  4. Subjects with Knee Osteoarthritis Exhibit Widespread Hyperalgesia to Pressure and Cold.

    PubMed

    Moss, Penny; Knight, Emma; Wright, Anthony

    2016-01-01

    Hyperalgesia to mechanical and thermal stimuli are characteristics of a range of disorders such as tennis elbow, whiplash and fibromyalgia. This study evaluated the presence of local and widespread mechanical and thermal hyperalgesia in individuals with knee osteoarthritis, compared to healthy control subjects. Twenty-three subjects with knee osteoarthritis and 23 healthy controls, matched for age, gender and body mass index, were recruited for the study. Volunteers with any additional chronic pain conditions were excluded. Pain thresholds to pressure, cold and heat were tested at the knee, ipsilateral heel and ipsilateral elbow, in randomized order, using standardised methodology. Significant between-groups differences for pressure pain and cold pain thresholds were found with osteoarthritic subjects demonstrating significantly increased sensitivity to both pressure (p = .018) and cold (p = .003) stimuli, compared with controls. A similar pattern of results extended to the pain-free ipsilateral ankle and elbow indicating widespread pressure and cold hyperalgesia. No significant differences were found between groups for heat pain threshold, although correlations showed that subjects with greater sensitivity to pressure pain were also likely to be more sensitive to both cold pain and heat pain. This study found widespread elevated pain thresholds in subjects with painful knee osteoarthritis, suggesting that altered nociceptive system processing may play a role in ongoing arthritic pain for some patients. PMID:26809009

  5. Subjects with Knee Osteoarthritis Exhibit Widespread Hyperalgesia to Pressure and Cold

    PubMed Central

    Moss, Penny; Knight, Emma; Wright, Anthony

    2016-01-01

    Hyperalgesia to mechanical and thermal stimuli are characteristics of a range of disorders such as tennis elbow, whiplash and fibromyalgia. This study evaluated the presence of local and widespread mechanical and thermal hyperalgesia in individuals with knee osteoarthritis, compared to healthy control subjects. Twenty-three subjects with knee osteoarthritis and 23 healthy controls, matched for age, gender and body mass index, were recruited for the study. Volunteers with any additional chronic pain conditions were excluded. Pain thresholds to pressure, cold and heat were tested at the knee, ipsilateral heel and ipsilateral elbow, in randomized order, using standardised methodology. Significant between-groups differences for pressure pain and cold pain thresholds were found with osteoarthritic subjects demonstrating significantly increased sensitivity to both pressure (p = .018) and cold (p = .003) stimuli, compared with controls. A similar pattern of results extended to the pain-free ipsilateral ankle and elbow indicating widespread pressure and cold hyperalgesia. No significant differences were found between groups for heat pain threshold, although correlations showed that subjects with greater sensitivity to pressure pain were also likely to be more sensitive to both cold pain and heat pain. This study found widespread elevated pain thresholds in subjects with painful knee osteoarthritis, suggesting that altered nociceptive system processing may play a role in ongoing arthritic pain for some patients. PMID:26809009

  6. Deciphering microbial interactions and detecting keystone species with co-occurrence networks.

    PubMed

    Berry, David; Widder, Stefanie

    2014-01-01

    Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.

  7. Deciphering microbial interactions and detecting keystone species with co-occurrence networks.

    PubMed

    Berry, David; Widder, Stefanie

    2014-01-01

    Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets. PMID:24904535

  8. 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.

  9. 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

    2008-01-01

    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. PMID:18545660

  10. Syndrome disintegration: Exome sequencing reveals that Fitzsimmons syndrome is a co-occurrence of multiple events.

    PubMed

    Armour, Christine M; Smith, Amanda; Hartley, Taila; Chardon, Jodi Warman; Sawyer, Sarah; Schwartzentruber, Jeremy; Hennekam, Raoul; Majewski, Jacek; Bulman, Dennis E; Suri, Mohnish; Boycott, Kym M

    2016-07-01

    In 1987 Fitzsimmons and Guilbert described identical male twins with progressive spastic paraplegia, brachydactyly with cone shaped epiphyses, short stature, dysarthria, and "low-normal" intelligence. In subsequent years, four other patients, including one set of female identical twins, a single female child, and a single male individual were described with the same features, and the eponym Fitzsimmons syndrome was adopted (OMIM #270710). We performed exome analysis of the patient described in 2009, and one of the original twins from 1987, the only patients available from the literature. No single genetic etiology exists that explains Fitzsimmons syndrome; however, multiple different genetic causes were identified. Specifically, the twins described by Fitzsimmons had heterozygous mutations in the SACS gene, the gene responsible for autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS), as well as a heterozygous mutation in the TRPS1, the gene responsible in Trichorhinophalangeal syndrome type 1 (TRPS1 type 1) which includes brachydactyly as a feature. A TBL1XR1 mutation was identified in the patient described in 2009 as contributing to his cognitive impairment and autistic features with no genetic cause identified for his spasticity or brachydactyly. The findings show that these individuals have multiple different etiologies giving rise to a similar phenotype, and that "Fitzsimmons syndrome" is in fact not one single syndrome. Over time, we anticipate that continued careful phenotyping with concomitant genome-wide analysis will continue to identify the causes of many rare syndromes, but it will also highlight that previously delineated clinical entities are, in fact, not syndromes at all. © 2016 Wiley Periodicals, Inc. PMID:27133561

  11. The Molecular Diversity of Freshwater Picoeukaryotes Reveals High Occurrence of Putative Parasitoids in the Plankton

    PubMed Central

    Lefèvre, Emilie; Roussel, Balbine; Amblard, Christian; Sime-Ngando, Télesphore

    2008-01-01

    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 µm) 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. PMID:18545660

  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. Multi-mycotoxin screening reveals separate occurrence of aflatoxins and ochratoxin a in Asian rice.

    PubMed

    Lim, Chee Wei; Yoshinari, Tomoya; Layne, Jeff; Chan, Sheot Harn

    2015-04-01

    The determination of important regulated mycotoxins in rice has been reported previously but not in the individual matrix of white, brown, red, and basmati rice with respect to the matrix effect, recovery, and stability. A total of 190 Asian rices were examined for regulated mycotoxin contamination by the LC-ESI-MS/MS method. Significant variation (p < 0.05) in the matrix effect was observed for fumonisins. Methanol improved the limits of detection (LOD) for HT-2 from 50 μg/kg to 2.3 μg/kg by promoting ionization efficiency of the ammonium-adduct. LOD and limits of quantitation ranged from 0.1 to 18 μg/kg and 0.2-31 μg/kg, respectively. All analytes degraded by more than 50% on storage, except fumonisins. Acetic acid (1%) provided significant improvement (p < 0.05) in recovery for all analytes in selected white rice from Thailand and China. Mean recovery ranged from 70 to 120%. RSD values were lower than 15% for all analytes. Five AFB1 and single OTA positive samples were detected. No correlation between mycotoxin contamination and rice species (r = 0) exists.

  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. Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames

    PubMed Central

    Janich, Peggy; Arpat, Alaaddin Bulak; Castelo-Szekely, Violeta; Lopes, Maykel; Gatfield, David

    2015-01-01

    Mammalian gene expr