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Sample records for reveals widespread occurrence

  1. Widespread Natural Occurrence of Hydroxyurea in Animals

    PubMed Central

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

    2015-01-01

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

  2. 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.

  3. 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.

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

    USGS Publications Warehouse

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

    2015-01-01

    Perchlorate (ClO− 4 ) and chlorate (ClO− 3 ) are ubiquitous on Earth and ClO− 4 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 ClO− 4 and ClO− 3 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 ClO− 4 and ClO− 3 within some of the samples, and their relative abundance with respect to other soluble species (e.g., NO− 3 ) 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 ClO− 4 and ClO− 3 could be present throughout the Solar System.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. Anaerobic Oxalate Degradation: Widespread Natural Occurrence in Aquatic Sediments

    PubMed Central

    Smith, Richard L.; Oremland, Ronald S.

    1983-01-01

    Significant concentrations of oxalate (dissolved plus particulate) were present in sediments taken from a diversity of aquatic environments, ranging from 0.1 to 0.7 mmol/liter of sediment. These included pelagic and littoral sediments from two freshwater lakes (Searsville Lake, Calif., and Lake Tahoe, Calif.), a hypersaline, meromictic, alkaline lake (Big Soda Lake, Nev.), and a South San Francisco Bay mud flat and salt marsh. The oxalate concentration of several plant species which are potential detrital inputs to these aquatic sediments ranged from 0.1 to 5.0% (wt/wt). In experiments with litter bags, the oxalate content of Myriophyllum sp. samples buried in freshwater littoral sediments decreased to 7% of the original value in 175 days. This suggests that plant detritus is a potential source of the oxalate within these sediments. [14C]oxalic acid was anaerobically degraded to 14CO2 in all sediment types tested, with higher rates evident in littoral sediments than in the pelagic sediments of the lakes studied. The turnover time of the added [14C]oxalate was less than 1 day in Searsville Lake littoral sediments. The total sediment oxalate concentration did not vary significantly between littoral and pelagic sediments and therefore did not appear to be controlling the rate of oxalate degradation. However, depth profiles of [14C]oxalate mineralization and dissolved oxalate concentration were closely correlated in freshwater littoral sediments; both were greatest in the surface sediments (0 to 5 cm) and decreased with depth. The dissolved oxalate concentration (9.1 μmol/liter of sediment) was only 3% of the total extractable oxalate (277 μmol/liter of sediment) at the sediment surface. These results suggest that anaerobic oxalate degradation is a widespread phenomenon in aquatic sediments and may be limited by the dissolved oxalate concentration within these sediments. PMID:16346332

  10. 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

  11. Thinking critically about the occurrence of widespread participation in poor nursing care.

    PubMed

    Roberts, Marc; Ion, Robin

    2015-04-01

    A discussion of how Arendt's work can be productively re-contextualized to provide a critical analysis of the occurrence of widespread participation in poor nursing care and what the implications of this are for the providers of nursing education. While the recent participation of nurses in healthcare failings, such as that detailed in the Francis report, has been universally condemned, there has been an absence of critical analyses in the literature that attempt to understand the occurrence of such widespread participation in poor nursing care. This is a significant omission in so far as such analyses will form an integral part of the strategy to limit the occurrence of such widespread participation of nurses in future healthcare failings. Discussion paper. Arendt's 'Eichmann in Jerusalem: A Report on the Banality of Evil' and 'Thinking and Moral Considerations: A Lecture'. In addition, a literature search was conducted and articles published in English relating to the terms care, compassion, ethics, judgement and thinking between 2004-2014 were included. It is anticipated that this discussion will stimulate further critical debate about the role of Arendt's work for an understanding of the occurrence of poor nursing care, and encouraging additional detailed analyses of the widespread participation of nurses in healthcare failings more generally. This article provides a challenging analysis of the widespread participation of nurses in poor care and discusses the opportunities confronting the providers of nursing education in limiting future healthcare failings. © 2014 John Wiley & Sons Ltd.

  12. 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.

  13. 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

  14. Widespread Occurrence of Pneumocystis carinii in Commercial Rat Colonies Detected Using Targeted PCR and Oral Swabs

    PubMed Central

    Icenhour, Crystal R.; Rebholz, Sandra L.; Collins, Margaret S.; Cushion, Melanie T.

    2001-01-01

    The genus Pneumocystis contains a family of fungal organisms that infect a wide variety of mammalian species. Although it is a cause of pneumonia in immunocompromised hosts, recent evidence suggests that these organisms colonize nonimmunosuppressed hosts. Detection of cryptic colonization with Pneumocystis becomes important in animal studies when infection-free animals are necessary. Provocation by chronic immunosuppression, histology, and serology has been widely used to detect the presence of Pneumocystis in rat colonies, requiring lengthy time periods and/or postmortem tissue. We conducted a study to evaluate the use of PCR amplification of oral swabs for the antemortem detection of Pneumocystis in 12 rat groups from three commercial vendors. Sera were collected upon arrival, and the oral cavity was swabbed for PCR analysis. Ten of these groups of rats were then housed in pairs under barrier and immunosuppressed to provoke Pneumocystis growth. Once moribund, the rats were sacrificed, and the lungs were collected to evaluate the presence of Pneumocystis by PCR and microscopic enumeration. DNA was extracted from oral swabs and lung homogenates, and PCR was performed using primers targeting a region within the mitochondrial large-subunit rRNA of Pneumocystis carinii f. sp. carinii. Upon receipt, 64% of rats were positive for P. carinii f. sp. carinii-specific antibodies, while P. carinii f. sp. carinii DNA was amplified from 98% of oral swabs. Postmortem PCR analysis of individual lungs revealed P. carinii f. sp. carinii DNA in all rat lungs, illustrating widespread occurrence of Pneumocystis in commercial rat colonies. Thus, oral swab/PCR is a rapid, nonlethal, and sensitive method for the assessment of Pneumocystis exposure. PMID:11574552

  15. 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

  16. A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria.

    PubMed

    Raymann, Kasie; Bobay, Louis-Marie; Doak, Thomas G; Lynch, Michael; Gribaldo, Simonetta

    2013-03-01

    Bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. However, the diversity, occurrence, and mechanisms of these interactions often are not fully known. The obligate bacterial endosymbionts of Paramecium provide their hosts with the ability to kill sensitive Paramecium strains through the production of R-bodies, highly insoluble coiled protein ribbons. R-bodies have been observed in a number of free-living bacteria, where their function is unknown. We have performed an exhaustive survey of genes coding for homologs of Reb proteins (R-body components) in complete bacterial genomes. We found that reb genes are much more widespread than previously thought, being present in representatives of major Proteobacterial subdivisions, including many free-living taxa, as well as taxa known to be involved in various kinds of interactions with eukaryotes, from mutualistic associations to pathogenicity. Reb proteins display very good conservation at the sequence level, suggesting that they may produce functional R-bodies. Phylogenomic analysis indicates that reb genes underwent a complex evolutionary history and allowed the identification of candidates potentially involved in R-body assembly, functioning, regulation, or toxicity. Our results strongly suggest that the ability to produce R-bodies is likely widespread in Proteobacteria. The potential involvement of R-bodies in as yet unexplored interactions with eukaryotes and the consequent ecological implications are discussed.

  17. A Genomic Survey of Reb Homologs Suggests Widespread Occurrence of R-Bodies in Proteobacteria

    PubMed Central

    Raymann, Kasie; Bobay, Louis-Marie; Doak, Thomas G.; Lynch, Michael; Gribaldo, Simonetta

    2013-01-01

    Bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. However, the diversity, occurrence, and mechanisms of these interactions often are not fully known. The obligate bacterial endosymbionts of Paramecium provide their hosts with the ability to kill sensitive Paramecium strains through the production of R-bodies, highly insoluble coiled protein ribbons. R-bodies have been observed in a number of free-living bacteria, where their function is unknown. We have performed an exhaustive survey of genes coding for homologs of Reb proteins (R-body components) in complete bacterial genomes. We found that reb genes are much more widespread than previously thought, being present in representatives of major Proteobacterial subdivisions, including many free-living taxa, as well as taxa known to be involved in various kinds of interactions with eukaryotes, from mutualistic associations to pathogenicity. Reb proteins display very good conservation at the sequence level, suggesting that they may produce functional R-bodies. Phylogenomic analysis indicates that reb genes underwent a complex evolutionary history and allowed the identification of candidates potentially involved in R-body assembly, functioning, regulation, or toxicity. Our results strongly suggest that the ability to produce R-bodies is likely widespread in Proteobacteria. The potential involvement of R-bodies in as yet unexplored interactions with eukaryotes and the consequent ecological implications are discussed. PMID:23450193

  18. 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.

  19. 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

  20. Widespread distribution of encapsulin nanocompartments reveals functional diversity.

    PubMed

    Giessen, Tobias W; Silver, Pamela A

    2017-03-06

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

  1. Widespread alternative and aberrant splicing revealed by lariat sequencing

    PubMed Central

    Stepankiw, Nicholas; Raghavan, Madhura; Fogarty, Elizabeth A.; Grimson, Andrew; Pleiss, Jeffrey A.

    2015-01-01

    Alternative splicing is an important and ancient feature of eukaryotic gene structure, the existence of which has likely facilitated eukaryotic proteome expansions. Here, we have used intron lariat sequencing to generate a comprehensive profile of splicing events in Schizosaccharomyces pombe, amongst the simplest organisms that possess mammalian-like splice site degeneracy. We reveal an unprecedented level of alternative splicing, including alternative splice site selection for over half of all annotated introns, hundreds of novel exon-skipping events, and thousands of novel introns. Moreover, the frequency of these events is far higher than previous estimates, with alternative splice sites on average activated at ∼3% the rate of canonical sites. Although a subset of alternative sites are conserved in related species, implying functional potential, the majority are not detectably conserved. Interestingly, the rate of aberrant splicing is inversely related to expression level, with lowly expressed genes more prone to erroneous splicing. Although we validate many events with RNAseq, the proportion of alternative splicing discovered with lariat sequencing is far greater, a difference we attribute to preferential decay of aberrantly spliced transcripts. Together, these data suggest the spliceosome possesses far lower fidelity than previously appreciated, highlighting the potential contributions of alternative splicing in generating novel gene structures. PMID:26261211

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

    PubMed

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

    2011-01-01

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

  3. 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

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

    PubMed

    Kim, Ki-Joong; Lee, Hae-Lim

    2005-02-28

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

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

    USGS Publications Warehouse

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

    2014-01-01

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

  6. 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

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

    PubMed

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

    2003-02-01

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

  8. Widespread occurrence of both metabolic and target-site herbicide resistance mechanisms in Lolium rigidum populations.

    PubMed

    Han, Heping; Yu, Qin; Owen, Mechelle J; Cawthray, Gregory R; Powles, Stephen B

    2016-02-01

    Lolium rigidum populations in Australia and globally have demonstrated rapid and widespread evolution of resistance to acetyl coenzyme A carboxylase (ACCase)-inhibiting and acetolactate synthase (ALS)-inhibiting herbicides. Thirty-three resistant L. rigidum populations, randomly collected from crop fields in a most recent resistance survey, were analysed for non-target-site diclofop metabolism and all known target-site ACCase gene resistance-endowing mutations. The HPLC profile of [(14) C]-diclofop-methyl in vivo metabolism revealed that 79% of these resistant L. rigidum populations showed enhanced capacity for diclofop acid metabolism (metabolic resistance). ACCase gene sequencing identified that 91% of the populations contain plants with ACCase resistance mutation(s). Importantly, 70% of the populations exhibit both non-target-site metabolic resistance and target-site ACCase mutations. This work demonstrates that metabolic herbicide resistance is commonly occurring in L. rigidum, and coevolution of both metabolic resistance and target-site resistance is an evolutionary reality. Metabolic herbicide resistance can potentially endow resistance to many herbicides and poses a threat to herbicide sustainability and thus crop production, calling for major research and management efforts. © 2015 Society of Chemical Industry.

  9. 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

  10. 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.

  11. Widespread rocky reef occurrence in the central English Channel and the implications for predictive habitat mapping

    NASA Astrophysics Data System (ADS)

    Diesing, Markus; Coggan, Roger; Vanstaen, Koen

    2009-08-01

    Reefs are one of the marine habitats listed in Annex I of the European Union's Habitats Directive, which aims to establish a coherent European ecological network of Special Areas of Conservation. EU Member States are required to prepare and propose a national list of sites for evaluation under the scheme, but currently the occurrence of reefs in the United Kingdom's nearshore and offshore areas is not well documented. Here we report on our search for rocky reefs in the central English Channel, which unexpectedly revealed an extensive reef system covering an area of 1100 km 2. Prior to our work, it was generally perceived that the seabed in this area comprised mostly gravel, with a few isolated rock outcrops. Our approach to determining the location, extent and character of these reefs incorporated broad, medium and fine-scale analyses over a 3200 km 2 area of seabed, using single- and multi-beam acoustic data, ground-truthed by underwater video and stills imagery. A benthic terrain model was developed in ArcGIS to map topographic features at the broad and medium scales. Biotope assignments were made at the fine scale through detailed analysis of video footage obtained from 30 sampling stations. The study area has a complex geological history and lies at the centre of a major bedload-parting zone. Together, these strongly influence the seabed character and the distribution of biotopes. An integrated assessment of the physical and biological features was used to map the study area to level 4 of the EUNIS habitat classification system. Similar physical conditions exist in other areas of the UK continental shelf, raising the prospect of predicting where other rocky reef systems might occur. In the absence of a co-ordinated national seabed survey programme, such predictions, coupled with interpretation of existing single-beam bathymetry data, can help prioritise areas where limited survey resources could be most effectively deployed.

  12. 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

  13. Widespread occurrence of chemical residues in beehive matrices from apiaries located in different landscapes of Western France.

    PubMed

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

    2013-01-01

    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. 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. 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 alone or in combination on honey bee health.

  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.

  15. 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

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

    SciTech Connect

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

    1987-07-01

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

  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 power-law distributions in inter-repeat distances shaped by genome dynamics.

    PubMed

    Klimopoulos, Alexandros; Sellis, Diamantis; Almirantis, Yannis

    2012-05-10

    Repetitive DNA sequences derived from transposable elements (TE) are distributed in a non-random way, co-clustering with other classes of repeat elements, genes and other genomic components. In a previous work we reported power-law-like size distributions (linearity in log-log scale) in the spatial arrangement of Alu and LINE1 elements in the human genome. Here we investigate the large-scale features of the spatial arrangement of all principal classes of TEs in 14 genomes from phylogenetically distant organisms by studying the size distribution of inter-repeat distances. Power-law-like size distributions are found to be widespread, extending up to several orders of magnitude. In order to understand the emergence of this distributional pattern, we introduce an evolutionary scenario, which includes (i) Insertions of DNA segments (e.g., more recent repeats) into the considered sequence and (ii) Eliminations of members of the studied TE family. In the proposed model we also incorporate the potential for transposition events (characteristic of the DNA transposons' life-cycle) and segmental duplications. Simulations reproduce the main features of the observed size distributions. Furthermore, we investigate the effects of various genomic features on the presence and extent of power-law size distributions including TE class and age, mode of parental TE transmission, GC content, deletion and recombination rates in the studied genomic region, etc. Our observations corroborate the hypothesis that insertions of genomic material and eliminations of repeats are at the basis of power-laws in inter-repeat distances. The existence of these power-laws could facilitate the formation of the recently proposed "fractal globule" for the confined chromatin organization. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    Yamazaki, T.; Roberts, A. P.

    2013-12-01

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

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

    PubMed

    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

    2008-10-16

    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.

  1. 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.

  2. 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.

  3. 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.

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

    PubMed

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

    2017-01-01

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

  5. THE WIDE-SPREAD DISTRIBUTION OF DIPHTHEROIDS AND THEIR OCCURRENCE IN VARIOUS LESIONS OF HUMAN TISSUES.

    PubMed

    Harris, W H; Wade, H W

    1915-05-01

    It is evident from this work and from the work of others that organisms having diphtheroidal morphology are wide-spread in their distribution in the human body. They are readily isolated from miscellaneous skin lesions, probably thriving better in pathological soils as saprophytes than in normal skin, although they can be obtained quite easily from the latter. Various strains can also be cultivated from the air, at least in this environment. Aside from the air and superficial parts of the human body, diphtheroids have frequently been isolated from the deeper regions. Hoag, working on general paresis and certain conditions of the lung, cultivated 199 diphtheroids, the majority of which were from the lungs and respiratory tract, also in some instances from the liver and spleen. He considered 146 of these isolations to be identical and classified them as organism x. Robertson, McRae, and Jeffry likewise in cases of dementia paralytica isolated what they considered an identical strain which was closely related to the Klebs-Loeffler bacillus, from the inflamed ileum, stomach, tonsils or pharynx, bronchi, lung, and brain. They differentiated their organism from Bacillus hoffmanni and Bacillus xerosis. The fact that these organisms have a somewhat unusual morphology, resembling as they do an organism of known pathogenicity, namely. Bacillus diphtherioe, should form no basis for assuming that they, too, are apt to possess these qualities. When we consider the number of simple bacillary contaminators analogous to such organisms as Bacillus anthracis, Bacillus typhosus, etc., we can readily see how frequently this occurs. The majority of the diphtheroids isolated by us stai??? by Gram's method; nearly all fail to resist the standard acid-fast methods, although use of the very low strengths of mineral acids allows the fixed stain to remain in whole or in part. There is consequently nothing unique in their tinctorial properties. These bacillary strains differ considerably in

  6. 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

  7. 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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    PubMed

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

    2011-12-01

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

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

    PubMed

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

    2016-01-01

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

  10. 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

  11. Widespread occurrence of Batrachochytrium dendrobatidis in contemporary and historical samples of the endangered Bombina pachypus along the Italian peninsula.

    PubMed

    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.

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

    PubMed Central

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

    2008-01-01

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

  13. Antigen retrieval reveals widespread basolateral expression of syntaxin 3 in renal epithelia.

    PubMed

    Breton, Sylvie; Inoue, Takeaki; Knepper, Mark A; Brown, Dennis

    2002-03-01

    Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins play a key role in docking and fusion of intracellular transport vesicles and may regulate apical and basolateral membrane protein delivery in epithelial cells. In a previous study, syntaxin 3 (a target SNARE) protein was detectable in the kidney only in intercalated cells. We now report a more widespread distribution of syntaxin 3 in a variety of renal epithelial cells after antigen retrieval. Sections of rat kidney were treated with SDS and incubated with antisyntaxin 3 antibodies. Strong basolateral membrane staining was seen in descending and ascending thin limbs of Henle, thick ascending limbs of Henle, the macula densa, distal and connecting tubules, and all cells of the collecting duct including A- and B-intercalated cells. The papillary surface epithelium and the transitional epithelium of the ureter were also stained, but proximal tubules were negative. Western blotting revealed a strong signal at 37 kDa in all regions, and the antigen was restricted to membrane fractions. SDS treatment was not necessary to reveal syntaxin 3 in intercalated cells. These data show that syntaxin 3 might be involved in basolateral trafficking pathways in most renal epithelial cell types. The exclusive basolateral location of syntaxin 3 in situ, however, contrasts with the apical location of this SNARE protein in some kidney epithelial cells in culture.

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

    PubMed Central

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

    2016-01-01

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

  15. 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.

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

    PubMed

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

    2013-02-01

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

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

    PubMed

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

    2017-01-01

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

  18. 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

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

    PubMed

    Ghobrial, Lora; Lankester, Felix; Kiyang, John A; Akih, Akih E; de Vries, Simone; Fotso, Roger; Gadsby, Elizabeth L; Jenkins, Peter D; Gonder, Mary K

    2010-01-22

    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. 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. 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 samples may reveal 'hotspots

  20. Widespread occurrence of magnetic nanoparticle inclusions in marine sediments and their importance in paleomagnetism and environmental magnetism

    NASA Astrophysics Data System (ADS)

    Chang, Liao; Roberts, Andrew; Heslop, David; Hayashida, Akira; Li, Jinhua; Zhao, Xiang; Huang, Qinghua

    2017-04-01

    Magnetic mineral inclusions occur commonly within other larger mineral phases in igneous rocks and have been demonstrated to preserve important paleomagnetic signals. While the usefulness of magnetic inclusions in igneous rocks have been explored extensively, their presence in sediments has only been speculated upon. The contribution of magnetic inclusions to the magnetization of sediments, therefore, has been elusive. In this study, we use transmission electron microscope (TEM) and magnetic methods to demonstrate the widespread preservation of silicate-hosted magnetic inclusions in marine sedimentary settings. TEM analysis reveals detailed information about the microstructure, chemical composition, grain size, and spatial arrangement of nanoscale magnetic mineral inclusions within larger silicate particles. Our results confirm the expectation that silicate minerals can protect magnetic mineral inclusions from sulfate-reducing diagenesis, and increase significantly the preservation potential of iron oxides in inclusions. Magnetic inclusions should, therefore, be considered as a potentially important source of fine-grained magnetic mineral assemblages, and represent a missing link in a wide range of sedimentary paleomagnetic and environmental magnetic studies. In addition, we present depositional remanent magnetization (DRM) modeling results to assess the paleomagnetic recording capability of magnetic inclusions. Our simulation demonstrates that deposition of larger silicate particles with magnetic inclusions will be controlled by gravitational and hydrodynamic forces rather than by geomagnetic torques. Thus, even though these large silicates may contain ideal single domain particles, they can not contribute meaningfully to paleomagnetic recording. However, smaller silicate grains (e.g., silt- and clay-sized) silicates with unidirectionally magnetized magnetic inclusions can potentially record a reliable DRM.

  1. 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

  2. Widespread Brain Areas Engaged during a Classical Auditory Streaming Task Revealed by Intracranial EEG

    PubMed Central

    Dykstra, Andrew R.; Halgren, Eric; Thesen, Thomas; Carlson, Chad E.; Doyle, Werner; Madsen, Joseph R.; Eskandar, Emad N.; Cash, Sydney S.

    2011-01-01

    The auditory system must constantly decompose the complex mixture of sound arriving at the ear into perceptually independent streams constituting accurate representations of individual sources in the acoustic environment. How the brain accomplishes this task is not well understood. The present study combined a classic behavioral paradigm with direct cortical recordings from neurosurgical patients with epilepsy in order to further describe the neural correlates of auditory streaming. Participants listened to sequences of pure tones alternating in frequency and indicated whether they heard one or two “streams.” The intracranial EEG was simultaneously recorded from sub-dural electrodes placed over temporal, frontal, and parietal cortex. Like healthy subjects, patients heard one stream when the frequency separation between tones was small and two when it was large. Robust evoked-potential correlates of frequency separation were observed over widespread brain areas. Waveform morphology was highly variable across individual electrode sites both within and across gross brain regions. Surprisingly, few evoked-potential correlates of perceptual organization were observed after controlling for physical stimulus differences. The results indicate that the cortical areas engaged during the streaming task are more complex and widespread than has been demonstrated by previous work, and that, by-and-large, correlates of bistability during streaming are probably located on a spatial scale not assessed – or in a brain area not examined – by the present study. PMID:21886615

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

    PubMed Central

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

    2014-01-01

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

  4. [Granulomatous hepatitis revealing a Mycobacterium bovis widespread infection following intravesical BCG therapy].

    PubMed

    Raffray, L; Rivière, P; Bonnet, H; Duffau, P; Longy-Boursier, M

    2015-09-01

    Intravesical therapy with bacillus Calmette-Guérin (BCG) has proved to be effective in the treatment of superficial bladder tumors. Side-effects include local infections and rarely disseminated BCG infection with multiple end organ complications such as granulomatous hepatitis, pneumonitis, aortitis and bone marrow involvement. We report an 83-year-old man who presented with chronic granulomatous hepatitis. This was related to intravesical BCG therapy received two years earlier for superficial bladder cancer. Aortitis, splenic infarction and hematopoietic involvement were also diagnosed. Outcome was favorable following adapted antibiotic course. This case report highlights the possibility of widespread BCG infection following intravesical treatment, and the need for vigilance in patients with a history of such a therapy even several years later. Copyright © 2014 Société nationale française de médecine interne (SNFMI). Published by Elsevier SAS. All rights reserved.

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

    PubMed

    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)).

  6. 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

  7. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity

    PubMed Central

    Chang, Matthew T.; Asthana, Saurabh; Gao, Sizhi Paul; Lee, Byron H.; Chapman, Jocelyn S.; Kandoth, Cyriac; Gao, JianJiong; Socci, Nicholas D.; Solit, David B.; Olshen, Adam B.; Schultz, Nikolaus; Taylor, Barry S.

    2015-01-01

    Mutational hotspots indicate selective pressure across a population of tumor samples, but their prevalence within and across cancer types is incompletely characterized. An approach to detect significantly mutated residues, rather than methods that identify recurrently mutated genes, may uncover new biologically and therapeutically relevant driver mutations. Here we developed a statistical algorithm to identify recurrently mutated residues in tumour samples. We applied the algorithm to 11,119 human tumors, spanning 41 cancer types, and identified 470 hotspot somatic substitutions in 275 genes. We find that half of all human tumors possess one or more mutational hotspots with widespread lineage-, position-, and mutant allele-specific differences, many of which are likely functional. In total, 243 hotspots were novel and appeared to affect a broad spectrum of molecular function, including hotspots at paralogous residues of Ras-related small GTPases RAC1 and RRAS2. Redefining hotspots at mutant amino acid resolution will help elucidate the allele-specific differences in their function and could have important therapeutic implications. PMID:26619011

  8. 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

  9. 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

  10. 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

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

    PubMed

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

    2006-07-01

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

  12. New GEOPHYSICAL MAPPING of the CHUKCHI MARGIN reveals widespread GLACIAL EROSION

    NASA Astrophysics Data System (ADS)

    Dove, D.; Polyak, L. V.; Coakley, B.

    2012-12-01

    Multibeam bathymetry, multi-channel, and chirp seismic data were acquired in a broad grid from R/V Marcus G. Langseth in September, 2011 over the outer Chukchi shelf, Chukchi Rise, Northwind Basin, and Northwind Ridge at water depths between 40 to 4,000 m. In the bathymetric data, iceberg scouring is dominant at depths less than 350 m, and multiple glacigenic bedforms are observed on the top and slopes (350-900 m) of Chukchi Rise and Borderland. The distribution mega-scale glacial lineations and ice-marginal moraines reveal a complex erosional history. The glacial lineations record two patterns of erosion which are likely formed by local and Laurentide sourced ice streams, recurrent over several glacial episodes. In the areas affected by glacial erosion, the chirp sub-bottom data reveal multiple sedimentary units including: well stratified post and inter-glacial deposits, transparent units interpreted as deformable tills, lenticular and fan shaped units interpreted as ice-marginal features and re-deposited sediments, and pre-glacial strata. A broadly observed buried erosional surface(s) exhibits high-frequency scouring and broad channelling also reveals multiple episodes of glacial erosion. A deeper erosional channel observed in the multi-channel seismic data is tunnel-valley like in form, and may be genetically linked to the large, buried erosional/drainage channels recently observed in the Bering Sea. The data obtained suggest that a Pleistocene ice sheet(s) existed on the northern Chukchi Shelf, and supports earlier conclusions of multiple erosions of the Borderland by SE-NW trending ice flows. The data greatly expand our knowledge on the Quaternary history of the Chukchi-Beringian region, and raise further questions about: the interaction of ice masses from the Laurentide, and potentially Chukchi and East-Siberian Shelf ice sheets, the glacio-isostatic history in the Bering region, and the implications for oceanic and atmospheric circulation, especially the

  13. Widespread occurrence of a covalent linkage between xyloglucan and acidic polysaccharides in suspension-cultured angiosperm cells.

    PubMed

    Popper, Zoë A; Fry, Stephen C

    2005-07-01

    Covalent linkages between xyloglucan and rhamnogalacturonan-I (RG-I) have been reported in the primary cell walls of cultured Rosa cells and may contribute to wall architecture. This study investigated whether this chemical feature is general to angiosperms or whether Rosa is unusual. * Xyloglucan was alkali-extracted from the walls of l-[1-3H]arabinose-fed suspension-cultured cells of Arabidopsis, sycamore, rose, tomato, spinach, maize and barley. The polysaccharide was precipitated with 50 % ethanol and subjected to anion-exchange chromatography in 8 m urea. Eluted fractions were Driselase-digested, yielding [3H]isoprimeverose (diagnostic of [3H]xyloglucan). The Arabidopsis cells were also fed [6-14C]glucuronic acid, and radiolabelled pectins were extracted with ammonium oxalate. * [3H]Xyloglucan was detected in acidic (galacturonate-containing) as well as non-anionic polysaccharide fractions. The proportion of the [3H]isoprimeverose units that were in anionic fractions was: Arabidopsis, 45 %; sycamore, 60 %; rose, 44 %; tomato, 75 %; spinach, 70 %; maize, 50 %; barley, 70 %. In Arabidopsis cultures fed d-[6-(14)C]glucuronate, 20 % of the (galacturonate-14C)-labelled pectins were found to hydrogen-bond to cellulose, a characteristic normally restricted to hemicelluloses such as xyloglucan. * Alkali-stable, anionic complexes of xyloglucan (reported in the case of Rosa to be xyloglucan-RG-I covalent complexes) are widespread in the cell walls of angiosperms, including gramineous monocots.

  14. Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

    PubMed

    Hurley, Jennifer M; Dasgupta, Arko; Emerson, Jillian M; Zhou, Xiaoying; Ringelberg, Carol S; Knabe, Nicole; Lipzen, Anna M; Lindquist, Erika A; Daum, Christopher G; Barry, Kerrie W; Grigoriev, Igor V; Smith, Kristina M; Galagan, James E; Bell-Pedersen, Deborah; Freitag, Michael; Cheng, Chao; Loros, Jennifer J; Dunlap, Jay C

    2014-12-02

    Neurospora crassa has been for decades a principal model for filamentous fungal genetics and physiology as well as for understanding the mechanism of circadian clocks. Eukaryotic fungal and animal clocks comprise transcription-translation-based feedback loops that control rhythmic transcription of a substantial fraction of these transcriptomes, yielding the changes in protein abundance that mediate circadian regulation of physiology and metabolism: Understanding circadian control of gene expression is key to understanding eukaryotic, including fungal, physiology. Indeed, the isolation of clock-controlled genes (ccgs) was pioneered in Neurospora where circadian output begins with binding of the core circadian transcription factor WCC to a subset of ccg promoters, including those of many transcription factors. High temporal resolution (2-h) sampling over 48 h using RNA sequencing (RNA-Seq) identified circadianly expressed genes in Neurospora, revealing that from ∼10% to as much 40% of the transcriptome can be expressed under circadian control. Functional classifications of these genes revealed strong enrichment in pathways involving metabolism, protein synthesis, and stress responses; in broad terms, daytime metabolic potential favors catabolism, energy production, and precursor assembly, whereas night activities favor biosynthesis of cellular components and growth. Discriminative regular expression motif elicitation (DREME) identified key promoter motifs highly correlated with the temporal regulation of ccgs. Correlations between ccg abundance from RNA-Seq, the degree of ccg-promoter activation as reported by ccg-promoter-luciferase fusions, and binding of WCC as measured by ChIP-Seq, are not strong. Therefore, although circadian activation is critical to ccg rhythmicity, posttranscriptional regulation plays a major role in determining rhythmicity at the mRNA level.

  15. 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.

  16. Widespread Occurrence of a Covalent Linkage Between Xyloglucan and Acidic Polysaccharides in Suspension-cultured Angiosperm Cells

    PubMed Central

    POPPER, ZOË A.; FRY, STEPHEN C.

    2005-01-01

    • Background and Aims Covalent linkages between xyloglucan and rhamnogalacturonan-I (RG-I) have been reported in the primary cell walls of cultured Rosa cells and may contribute to wall architecture. This study investigated whether this chemical feature is general to angiosperms or whether Rosa is unusual. • Methods Xyloglucan was alkali-extracted from the walls of l-[1-3H]arabinose-fed suspension-cultured cells of Arabidopsis, sycamore, rose, tomato, spinach, maize and barley. The polysaccharide was precipitated with 50 % ethanol and subjected to anion-exchange chromatography in 8 m urea. Eluted fractions were Driselase-digested, yielding [3H]isoprimeverose (diagnostic of [3H]xyloglucan). The Arabidopsis cells were also fed [6-14C]glucuronic acid, and radiolabelled pectins were extracted with ammonium oxalate. • Key Results [3H]Xyloglucan was detected in acidic (galacturonate-containing) as well as non-anionic polysaccharide fractions. The proportion of the [3H]isoprimeverose units that were in anionic fractions was: Arabidopsis, 45 %; sycamore, 60 %; rose, 44 %; tomato, 75 %; spinach, 70 %; maize, 50 %; barley, 70 %. In Arabidopsis cultures fed d-[6-14C]glucuronate, 20 % of the (galacturonate-14C)-labelled pectins were found to hydrogen-bond to cellulose, a characteristic normally restricted to hemicelluloses such as xyloglucan. • Conclusions Alkali-stable, anionic complexes of xyloglucan (reported in the case of Rosa to be xyloglucan–RG-I covalent complexes) are widespread in the cell walls of angiosperms, including gramineous monocots. PMID:15837720

  17. Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds

    PubMed Central

    Jiang, Yu; Shi, Tao; Cai, Hanfang; Lan, Xianyong; Zhao, Xin; Plath, Martin; Chen, Hong

    2017-01-01

    Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97.86% and 98.98% coverage of genomes, respectively. Comparison with the Bos_taurus_UMD_3.1 reference assembly yielded 9,010,096 SNPs for Nanyang, and 6,965,062 for Qinchuan cattle, 51% and 29% of which were novel SNPs, respectively. A total of 154,934 and 115,032 small indels (1 to 3 bp) were found in the Nanyang and Qinchuan genomes, respectively. The SNP and indel distribution revealed that Nanyang showed a genetically high diversity as compared to Qinchuan cattle. Furthermore, a total of 2,907 putative cases of copy number variation (CNV) were identified by aligning Nanyang to Qinchuan genome, 783 of which (27%) encompassed the coding regions of 495 functional genes. The gene ontology (GO) analysis revealed that many CNV genes were enriched in the immune system and environment adaptability. Among several CNV genes related to lipid transport and fat metabolism, Lepin receptor gene (LEPR) overlapping with CNV_1815 showed remarkably higher copy number in Qinchuan than Nanyang (log2 (ratio) = -2.34988; P value = 1.53E-102). Further qPCR and association analysis investigated that the copy number of the LEPR gene presented positive correlations with transcriptional expression and phenotypic traits, suggesting the LEPR CNV may contribute to the higher fat deposition in muscles of Qinchuan cattle. Our findings provide evidence that the distinct phenotypes of Nanyang and Qinchuan breeds may be due to the different genetic variations including SNPs, indels

  18. 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

  19. 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

  20. 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

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

    PubMed

    Cai, Haiyuan

    2012-01-01

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

  2. 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

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

    PubMed

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

    2014-04-01

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

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

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

  6. Widespread Occurrence of Plant Perchlorate

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  7. 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

  8. Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network.

    PubMed

    Richard, Arianne C; Peters, James E; Lee, James C; Vahedi, Golnaz; Schäffer, Alejandro A; Siegel, Richard M; Lyons, Paul A; Smith, Kenneth G C

    2016-07-19

    hits. This systematic analysis of the influence of regulatory genetic variants in the TNF superfamily network reveals widespread and diverse roles for these cytokines in susceptibility to a number of immune-mediated diseases.

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

    PubMed Central

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

    2015-01-01

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

  10. High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination.

    PubMed

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

    2015-05-13

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

  11. 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.

  12. SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy.

    PubMed

    Didion, John P; Buus, Ryan J; Naghashfar, Zohreh; Threadgill, David W; Morse, Herbert C; de Villena, Fernando Pardo-Manuel

    2014-10-03

    The crisis of Misidentified and contaminated cell lines have plagued the biological research community for decades. Some repositories and journals have heeded calls for mandatory authentication of human cell lines, yet misidentification of mouse cell lines has received little publicity despite their importance in sponsored research. Short tandem repeat (STR) profiling is the standard authentication method, but it may fail to distinguish cell lines derived from the same inbred strain of mice. Additionally, STR profiling does not reveal karyotypic changes that occur in some high-passage lines and may have functional consequences. Single nucleotide polymorphism (SNP) profiling has been suggested as a more accurate and versatile alternative to STR profiling; however, a high-throughput method for SNP-based authentication of mouse cell lines has not been described. We have developed computational methods (Cell Line Authentication by SNP Profiling, CLASP) for cell line authentication and copy number analysis based on a cost-efficient SNP array, and we provide a reference database of commonly used mouse strains and cell lines. We show that CLASP readily discriminates among cell lines of diverse taxonomic origins, including multiple cell lines derived from a single inbred strain, intercross or wild caught mouse. CLASP is also capable of detecting contaminants present at concentrations as low as 5%. Of the 99 cell lines we tested, 15 exhibited substantial divergence from the reported genetic background. In all cases, we were able to distinguish whether the authentication failure was due to misidentification (one cell line, Ba/F3), the presence of multiple strain backgrounds (five cell lines), contamination by other cells and/or the presence of aneuploid chromosomes (nine cell lines). Misidentification and contamination of mouse cell lines is potentially as widespread as it is in human cell culture. This may have substantial implications for studies that are dependent on the

  13. Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata, Asteraceae)

    Treesearch

    Bryce A. Richardson; Justin T. Page; Prabin Bajgain; Stewart C. Sanderson; Joshua A. Udall

    2012-01-01

    Premise of the study: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid...

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

    PubMed

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

    2017-03-01

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

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

    PubMed

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

    2014-06-24

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

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

    PubMed

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

    2015-01-01

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

  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 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

  19. 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

  20. 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.

  1. Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting

    PubMed Central

    Loeb, Gabriel B.; Khan, Aly A.; Canner, David; Hiatt, Joseph B.; Shendure, Jay; Darnell, Robert B.; Leslie, Christina S.; Rudensky, Alexander Y.

    2012-01-01

    microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3′ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. We found that approximately forty percent of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these non-canonical sites feature extensive complementarity to the miRNA seed with one mismatch. These non-canonical sites confer regulation of gene expression albeit less potently than canonical sites. Thus, non-canonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation. PMID:23142080

  2. Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae).

    PubMed

    Richardson, Bryce A; Page, Justin T; Bajgain, Prabin; Sanderson, Stewart C; Udall, Joshua A

    2012-12-01

    Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. • We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana, and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high-read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor-net network analyses. • Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis, are polyphyletic occurring within and between diploid subspecies groups. • Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.

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

    PubMed

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

    2014-09-01

    To examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia. Neotropics. 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. 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. 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 particular the presence of genetically uniform

  4. 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

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

    PubMed Central

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

    2016-01-01

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

  7. Population polymorphism of nuclear mitochondrial DNA insertions reveals widespread diploidy associated with loss of heterozygosity in Debaryomyces hansenii.

    PubMed

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

    2010-03-01

    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 767(T), 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.

  8. 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

  9. 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. © 2015 John Wiley & Sons Ltd.

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

    PubMed

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

    2017-03-01

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

  11. Comparative Genomics of the Mating-Type Loci of the Mushroom Flammulina velutipes Reveals Widespread Synteny and Recent Inversions

    PubMed Central

    van Peer, Arend F.; Park, Soon-Young; Shin, Pyung-Gyun; Jang, Kab-Yeul; Yoo, Young-Bok; Park, Young-Jin; Lee, Byoung-Moo; Sung, Gi-Ho; James, Timothy Y.; Kong, Won-Sik

    2011-01-01

    Background Mating-type loci of mushroom fungi contain master regulatory genes that control recognition between compatible nuclei, maintenance of compatible nuclei as heterokaryons, and fruiting body development. Regions near mating-type loci in fungi often show adapted recombination, facilitating the generation of novel mating types and reducing the production of self-compatible mating types. Compared to other fungi, mushroom fungi have complex mating-type systems, showing both loci with redundant function (subloci) and subloci with many alleles. The genomic organization of mating-type loci has been solved in very few mushroom species, which complicates proper interpretation of mating-type evolution and use of those genes in breeding programs. Methodology/Principal Findings We report a complete genetic structure of the mating-type loci from the tetrapolar, edible mushroom Flammulina velutipes mating type A3B3. Two matB3 subloci, matB3a that contains a unique pheromone and matB3b, were mapped 177 Kb apart on scaffold 1. The matA locus of F. velutipes contains three homeodomain genes distributed over 73 Kb distant matA3a and matA3b subloci. The conserved matA region in Agaricales approaches 350 Kb and contains conserved recombination hotspots showing major rearrangements in F. velutipes and Schizophyllum commune. Important evolutionary differences were indicated; separation of the matA subloci in F. velutipes was diverged from the Coprinopsis cinerea arrangement via two large inversions whereas separation in S. commune emerged through transposition of gene clusters. Conclusions/Significance In our study we determined that the Agaricales have very large scale synteny at matA (∼350 Kb) and that this synteny is maintained even when parts of this region are separated through chromosomal rearrangements. Four conserved recombination hotspots allow reshuffling of large fragments of this region. Next to this, it was revealed that large distance subloci can exist in matB as

  12. 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. © 2015 John Wiley & Sons Ltd.

  13. Genetic alterations in mesiodens as revealed by targeted next-generation sequencing and gene co-occurrence network analysis.

    PubMed

    Kim, Y Y; Hwang, J; Kim, H-S; Kwon, H J; Kim, S; Lee, J H; Lee, J H

    2017-04-17

    Mesiodens is the most common type of supernumerary tooth which includes a population prevalence of 0.15%-1.9%. Alongside evidence that the condition is heritable, mutations in single genes have been reported in few human supernumerary tooth cases. Gene sequencing methods in tradition way are time-consuming and labor-intensive, whereas next-generation sequencing and bioinformatics are cost-effective for large samples and target sizes. We describe the application of a targeted next-generation sequencing (NGS) and bioinformatics approach to samples from 17 mesiodens patients. Subjects were diagnosed on the basis of panoramic radiograph. A total of 101 candidate genes which were captured custom genes were sequenced on the Illumina HiSeq 2500. Multistep bioinformatics processing was performed including variant identification, base calling, and in silico analysis of putative disease-causing variants. Targeted capture identified 88 non-synonymous, rare, exonic variants involving 42 of the 101 candidate genes. Moreover, we investigated gene co-occurrence relationships between the genomic alterations and identified 88 significant relationships among 18 most recurrent driver alterations. Our search for co-occurring genetic alterations revealed that such alterations interact cooperatively to drive mesiodens. We discovered a gene co-occurrence network in mesiodens patients with functionally enriched gene groups in the sonic hedgehog (SHH), bone morphogenetic proteins (BMP), and wingless integrated (WNT) signaling pathways. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. All rights reserved.

  14. 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

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

    PubMed

    Petrovan, Silviu O; Schmidt, Benedikt R

    2016-01-01

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

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

    SciTech Connect

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

    2016-05-19

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

  17. 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

  18. 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.

  19. 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

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

    DOE PAGES

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

    2016-05-19

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

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

    PubMed

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

    2008-04-24

    The neuropeptide PDF is released by sixteen clock neurons in Drosophila and helps maintain circadian activity rhythms by coordinating a network of approximately 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, DH31, stimulates large cAMP increases in all PDF-expressing clock neurons. Thus, the network of approximately 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 subcellular resolution. Specifically, it experimentally confirms the longstanding hypothesis that PDF is a direct modulator of most neurons in the Drosophila clock network.

  2. 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

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

    SciTech Connect

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

    2016-05-19

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

  4. Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis.

    PubMed

    Csoka, Antonei B; English, Sangeeta B; Simkevich, Carl P; Ginzinger, David G; Butte, Atul J; Schatten, Gerald P; Rothman, Frank G; Sedivy, John M

    2004-08-01

    Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease with widespread phenotypic features resembling premature aging. HGPS was recently shown to be caused by dominant mutations in the LMNA gene, resulting in the in-frame deletion of 50 amino acids near the carboxyl terminus of the encoded lamin A protein. Children with this disease typically succumb to myocardial infarction or stroke caused by severe atherosclerosis at an average age of 13 years. To elucidate further the molecular pathogenesis of this disease, we compared the gene expression patterns of three HGPS fibroblast cell strains heterozygous for the LMNA mutation with three normal, age-matched cell strains. We defined a set of 361 genes (1.1% of the approximately 33,000 genes analysed) that showed at least a 2-fold, statistically significant change. The most prominent categories encode transcription factors and extracellular matrix proteins, many of which are known to function in the tissues severely affected in HGPS. The most affected gene, MEOX2/GAX, is a homeobox transcription factor implicated as a negative regulator of mesodermal tissue proliferation. Thus, at the gene expression level, HGPS shows the hallmarks of a developmental disorder affecting mesodermal and mesenchymal cell lineages. The identification of a large number of genes implicated in atherosclerosis is especially valuable, because it provides clues to pathological processes that can now be investigated in HGPS patients or animal models.

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

    PubMed

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

    2017-02-03

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

  6. Characterization of Enteroviruses from Non-Human Primates in Cameroon Revealed Virus Types Widespread in Humans along with Candidate New Types and Species

    PubMed Central

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

    2014-01-01

    Enteroviruses (EVs) infecting African Non-Human Primates (NHP) are still poorly documented. This study was designed to characterize the genetic diversity of EVs among captive and wild NHP in Cameroon and to compare this diversity with that found in humans. Stool specimens were collected in April 2008 in NHP housed in sanctuaries in Yaounde and neighborhoods. Moreover, stool specimens collected from wild NHP from June 2006 to October 2008 in the southern rain forest of Cameroon were considered. RNAs purified directly from stool samples were screened for EVs using a sensitive RT-nested PCR targeting the VP1 capsid coding gene whose nucleotide sequence was used for molecular typing. Captive chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla) were primarily infected by EV types already reported in humans in Cameroon and elsewhere: Coxsackievirus A13 and A24, Echovirus 15 and 29, and EV-B82. Moreover EV-A119, a novel virus type recently described in humans in central and west Africa, was also found in a captive Chimpanzee. EV-A76, which is a widespread virus in humans, was identified in wild chimpanzees, thus suggesting its adaptation and parallel circulation in human and NHP populations in Cameroon. Interestingly, some EVs harbored by wild NHP were genetically distinct from all existing types and were thus assigned as new types. One chimpanzee-derived virus was tentatively assigned as EV-J121 in the EV-J species. In addition, two EVs from wild monkeys provisionally registered as EV-122 and EV-123 were found to belong to a candidate new species. Overall, this study indicates that the genetic diversity of EVs among NHP is more important than previously known and could be the source of future new emerging human viral diseases. PMID:25079078

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

    PubMed

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

    2014-01-01

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

  8. 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.

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

    PubMed Central

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

    2015-01-01

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

  10. Extended-spectrum beta-lactamase-producing Escherichia coli in turkey meat production farms in the Czech Republic: national survey reveals widespread isolates with bla(SHV-12) genes on IncFII plasmids.

    PubMed

    Dolejska, M; Matulova, M; Kohoutova, L; Literak, I; Bardon, J; Cizek, A

    2011-09-01

    The occurrence and epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in the environment of turkey farms in the Czech Republic were studied. Extended-spectrum beta-lactamase-producing E. coli isolates were found on 8 (20%) of 40 turkey farms surveyed. A total of 200 environmental smears were examined, and a total of 25 ESBL-producing E. coli were isolated. These isolates were analysed using XbaI pulsed-field gel electrophoresis and divided into nine pulsotypes. Most of the isolates harboured the gene bla(SHV-12) on a 40-kb plasmid of the IncFII group with an identical EcoRV restriction profile. Indistinguishable or clonally related SHV-12-producing isolates belonging to the same pulsotypes were found at some unrelated farms. Widespread occurrence of ESBL-producing E. coli isolates with bla(SHV-12) carried on IncFII plasmids in meat production flocks in the Czech Republic was demonstrated. Results indicate vertical transmission of ESBL-producing E. coli within the turkey production pyramid. The study shows the risk of multiresistant ESBL-producing bacteria and antibiotic-resistance genes being transmitted to humans via the food chain. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

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

    PubMed

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

    2017-02-01

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

  12. A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques.

    PubMed

    Lei, Haiyan; Fukushige, Tetsunari; Niu, Wei; Sarov, Mihail; Reinke, Valerie; Krause, Michael

    2010-12-29

    Identifying transcription factor binding sites genome-wide using chromatin immunoprecipitation (ChIP)-based technology is becoming an increasingly important tool in addressing developmental questions. However, technical problems associated with factor abundance and suitable ChIP reagents are common obstacles to these studies in many biological systems. We have used two completely different, widely applicable methods to determine by ChIP the genome-wide binding sites of the master myogenic regulatory transcription factor HLH-1 (CeMyoD) in C. elegans embryos. The two approaches, ChIP-seq and ChIP-chip, yield strongly overlapping results revealing that HLH-1 preferentially binds to promoter regions of genes enriched for E-box sequences (CANNTG), known binding sites for this well-studied class of transcription factors. HLH-1 binding sites were enriched upstream of genes known to be expressed in muscle, consistent with its role as a direct transcriptional regulator. HLH-1 binding was also detected at numerous sites unassociated with muscle gene expression, as has been previously described for its mouse homolog MyoD. These binding sites may reflect several additional functions for HLH-1, including its interactions with one or more co-factors to activate (or repress) gene expression or a role in chromatin organization distinct from direct transcriptional regulation of target genes. Our results also provide a comparison of ChIP methodologies that can overcome limitations commonly encountered in these types of studies while highlighting the complications of assigning in vivo functions to identified target sites.

  13. A Widespread Distribution of Genomic CeMyoD Binding Sites Revealed and Cross Validated by ChIP-Chip and ChIP-Seq Techniques

    PubMed Central

    Lei, Haiyan; Fukushige, Tetsunari; Niu, Wei; Sarov, Mihail; Reinke, Valerie; Krause, Michael

    2010-01-01

    Identifying transcription factor binding sites genome-wide using chromatin immunoprecipitation (ChIP)-based technology is becoming an increasingly important tool in addressing developmental questions. However, technical problems associated with factor abundance and suitable ChIP reagents are common obstacles to these studies in many biological systems. We have used two completely different, widely applicable methods to determine by ChIP the genome-wide binding sites of the master myogenic regulatory transcription factor HLH-1 (CeMyoD) in C. elegans embryos. The two approaches, ChIP-seq and ChIP-chip, yield strongly overlapping results revealing that HLH-1 preferentially binds to promoter regions of genes enriched for E-box sequences (CANNTG), known binding sites for this well-studied class of transcription factors. HLH-1 binding sites were enriched upstream of genes known to be expressed in muscle, consistent with its role as a direct transcriptional regulator. HLH-1 binding was also detected at numerous sites unassociated with muscle gene expression, as has been previously described for its mouse homolog MyoD. These binding sites may reflect several additional functions for HLH-1, including its interactions with one or more co-factors to activate (or repress) gene expression or a role in chromatin organization distinct from direct transcriptional regulation of target genes. Our results also provide a comparison of ChIP methodologies that can overcome limitations commonly encountered in these types of studies while highlighting the complications of assigning in vivo functions to identified target sites. PMID:21209968

  14. Computer assisted analysis of MR-mammography reveals association between contrast enhancement and occurrence of distant metastasis.

    PubMed

    Baltzer, Pascal A T; Zoubi, Ramy; Burmeister, Hartmut P; Gajda, Mieczyslaw; Camara, Oumar; Kaiser, Werner A; Dietzel, Matthias

    2012-12-01

    Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is able to detect breast cancer with high sensitivity. Furthermore, this method provides functional information on tissue composition and vascularization. This study aims to identify the potential of DCE-MRI to predict distant metastasis in breast cancer patients using computer assisted interpretation of dynamic enhancement data. For this purpose, 59 consecutive patients with newly diagnosed invasive breast cancer received pretherapeutic DCE-MRI at 1.5 Tesla according to international recommendations. In all patients, follow up interval and occurrence of distant metastasis was documented. For DCE-MRI analysis dedicated software was used (Brevis, Siemens Healthcare, Erlangen, Germany). It allows semiautomatic identification of the most suspect curve in a lesion analyzed. Enhancement parameters assessed were "Initial Enhancement", "Washout", "Peak-Enhancement", and "Time to Peak Enhancement". Cox proportional hazards regression (CPHR) was used to analyze the effect of these parameters on the probability of metachronous distant metastasis. Median follow up period was 52.0 months. 6 patients developed distant metastases between 11 and 35 months after breast cancer diagnosis. In CPHR, Washout could be identified as significant and independent predictor for occurrence of distant metastasis (P = 0.0134). Our initial data demonstrate an association between computer measured enhancement parameters in DCE-MRI and occurrence of distant metastasis by quantification of Washout.

  15. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential.

    PubMed

    Pal, Chandan; Bengtsson-Palme, Johan; Kristiansson, Erik; Larsson, D G Joakim

    2015-11-17

    Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems. Co-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE∆1 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (<0.7 %) but more common on those of human and domestic animal origin (5 % and 7 %, respectively). Finally, plasmids with both BMRGs and ARGs were more likely to be conjugative (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes. This is the first large-scale identification of

  16. Good pitch memory is widespread.

    PubMed

    Schellenberg, E Glenn; Trehub, Sandra E

    2003-05-01

    Here we show that good pitch memory is widespread among adults with no musical training. We tested unselected college students on their memory for the pitch level of instrumental soundtracks from familiar television programs. Participants heard 5-s excerpts either at the original pitch level or shifted upward or downward by 1 or 2 semitones. They successfully identified the original pitch levels. Other participants who heard comparable excerpts from unfamiliar recordings could not do so. These findings reveal that ordinary listeners retain fine-grained information about pitch level over extended periods. Adults' reportedly poor memory for pitch is likely to be a by-product of their inability to name isolated pitches.

  17. 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

  18. 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.

  19. K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores.

    PubMed

    Emerson, Arnold I; Andrews, Simeon; Ahmed, Ikhlak; Azis, Thasni Ka; Malek, Joel A

    2015-01-01

    Network biology currently focuses primarily on metabolic pathways, gene regulatory, and protein-protein interaction networks. While these approaches have yielded critical information, alternative methods to network analysis will offer new perspectives on biological information. A little explored area is the interactions between domains that can be captured using domain co-occurrence networks (DCN). A DCN can be used to study the function and interaction of proteins by representing protein domains and their co-existence in genes and by mapping cancer mutations to the individual protein domains to identify signals. The domain co-occurrence network was constructed for the human proteome based on PFAM domains in proteins. Highly connected domains in the central cores were identified using the k-core decomposition technique. Here we show that these domains were found to be more evolutionarily conserved than the peripheral domains. The somatic mutations for ovarian, breast and prostate cancer diseases were obtained from the TCGA database. We mapped the somatic mutations to the individual protein domains and the local false discovery rate was used to identify significantly mutated domains in each cancer type. Significantly mutated domains were found to be enriched in cancer disease pathways. However, we found that the inner cores of the DCN did not contain any of the significantly mutated domains. We observed that the inner core protein domains are highly conserved and these domains co-exist in large numbers with other protein domains. Mutations and domain co-occurrence networks provide a framework for understanding hierarchal designs in protein function from a network perspective. This study provides evidence that a majority of protein domains in the inner core of the DCN have a lower mutation frequency and that protein domains present in the peripheral regions of the k-core contribute more heavily to the disease. These findings may contribute further to drug development.

  20. 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.

  1. 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

  2. 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

  3. 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

    Maxwell, Karen L; Fatehi Hassanabad, Mostafa; Chang, Tom; Paul, Vivek D; Pirani, Nawaz; Bona, Diane; Edwards, Aled M; Davidson, Alan R

    2013-12-01

    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.

  4. Latent Class Analysis Reveals Distinct Subgroups of Patients Based on Symptom Occurrence and Demographic and Clinical Characteristics.

    PubMed

    Miaskowski, Christine; Dunn, Laura; Ritchie, Christine; Paul, Steven M; Cooper, Bruce; Aouizerat, Bradley E; Alexander, Kimberly; Skerman, Helen; Yates, Patsy

    2015-07-01

    Cancer patients experience a broad range of physical and psychological symptoms as a result of their disease and its treatment. On average, these patients report 10 unrelieved and co-occurring symptoms. The aims were to determine if subgroups of oncology outpatients receiving active treatment (n = 582) could be identified based on their distinct experience with 13 commonly occurring symptoms; to determine whether these subgroups differed on select demographic and clinical characteristics; and to determine if these subgroups differed on quality of life (QOL) outcomes. Demographic, clinical, and symptom data from one Australian and two U.S. studies were combined. Latent class analysis was used to identify patient subgroups with distinct symptom experiences based on self-report data on symptom occurrence using the Memorial Symptom Assessment Scale. Four distinct latent classes were identified (i.e., all low [28.0%], moderate physical and lower psych [26.3%], moderate physical and higher psych [25.4%], and all high [20.3%]). Age, gender, education, cancer diagnosis, and presence of metastatic disease differentiated among the latent classes. Patients in the all high class had the worst QOL scores. Findings from this study confirm the large amount of interindividual variability in the symptom experience of oncology patients. The identification of demographic and clinical characteristics that place patients at risk for a higher symptom burden can be used to guide more aggressive and individualized symptom management interventions. Copyright © 2015 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

  5. 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.

  6. 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.

  7. Widespread occurrence of the mycotoxin fumonisin b(2) in wine.

    PubMed

    Mogensen, Jesper Mølgaard; Larsen, Thomas Ostenfeld; Nielsen, Kristian Fog

    2010-04-28

    Fumonisins are important mycotoxins because they are suspected to cause human and animal toxicoses by the consumption of contaminated corn-based food and feeds. However, with the discovery of fumonisin production in grapes by Aspergillus niger , wine may also be a fumonisin-containing commodity. In the present study, we have developed a simple and quantitative cation-exchange-based purification method for the subsequent isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) determination of fumonisins in wine. A comparative study of seven different solid-phase extraction (SPE) columns showed that polymeric mixed-mode reversed-phase (RP) cation-exchange columns were superior to classic silica-based cation and mixed-mode cation-exchange columns. A total of 77 wine samples from 13 countries were subsequently tested, and surprisingly, 18 (23%) were found to contain fumonisin B(2) in the range of 1-25 microg/L. These findings were further confirmed by immunoaffinity purification and re-analysis of the positive cation-exchanged extracts.

  8. 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.

  9. 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.

  10. 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.

  11. Trypanosoma cruzi reservoir—triatomine vector co-occurrence networks reveal meta-community effects by synanthropic mammals on geographic dispersal

    PubMed Central

    Valiente-Banuet, Leopoldo; Sánchez-Cordero, Víctor; Stephens, Christopher R.

    2017-01-01

    Contemporary patterns of land use and global climate change are modifying regional pools of parasite host species. The impact of host community changes on human disease risk, however, is difficult to assess due to a lack of information about zoonotic parasite host assemblages. We have used a recently developed method to infer parasite-host interactions for Chagas Disease (CD) from vector-host co-occurrence networks. Vector-host networks were constructed to analyze topological characteristics of the network and ecological traits of species’ nodes, which could provide information regarding parasite regional dispersal in Mexico. Twenty-eight triatomine species (vectors) and 396 mammal species (potential hosts) were included using a data-mining approach to develop models to infer most-likely interactions. The final network contained 1,576 links which were analyzed to calculate centrality, connectivity, and modularity. The model predicted links of independently registered Trypanosoma cruzi hosts, which correlated with the degree of parasite-vector co-occurrence. Wiring patterns differed according to node location, while edge density was greater in Neotropical as compared to Nearctic regions. Vectors with greatest public health importance (i.e., Triatoma dimidiata, T. barberi, T. pallidipennis, T. longipennis, etc), did not have stronger links with particular host species, although they had a greater frequency of significant links. In contrast, hosts classified as important based on network properties were synanthropic mammals. The latter were the most common parasite hosts and are likely bridge species between these communities, thereby integrating meta-community scenarios beneficial for long-range parasite dispersal. This was particularly true for rodents, >50% of species are synanthropic and more than 20% have been identified as T. cruzi hosts. In addition to predicting potential host species using the co-occurrence networks, they reveal regions with greater

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  13. 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

  14. 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.

  15. 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.

  16. Integrative Conjugative Elements Are Widespread in Field Isolates of Mycoplasma Species Pathogenic for Ruminants

    PubMed Central

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

    2014-01-01

    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. PMID:25527550

  17. 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.

  18. Autocorrelation analysis reveals widespread spatial biases in microarray experiments

    PubMed Central

    Koren, Amnon; Tirosh, Itay; Barkai, Naama

    2007-01-01

    Background DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes. Results In order to assess the prevalence of this effect and better understand its origins, we applied an autocorrelation analysis of the relationship between chromosomal position and expression level to a database of over 2000 individual yeast microarray experiments. We show that at least 60% of these experiments exhibit spurious chromosomal position-dependent gene correlations, which nonetheless appear in a stochastic manner within each experimental dataset. Using computer simulations, we show that large spatial biases caused in the microarray hybridization step and independently of printing procedures can exclusively account for the observed spurious correlations, in contrast to previous suggestions. Our data suggest that such biases may generate more than 15% false data per experiment. Importantly, spatial biases are expected to occur regardless of microarray design and over a wide range of microarray platforms, organisms and experimental procedures. Conclusions Spatial biases comprise a major source of noise in microarray studies; revision of routine experimental practices and normalizations to account for these biases may significantly and comprehensively improve the quality of new as well as existing DNA microarray data. PMID:17565680

  19. Autocorrelation analysis reveals widespread spatial biases in microarray experiments.

    PubMed

    Koren, Amnon; Tirosh, Itay; Barkai, Naama

    2007-06-12

    DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes. In order to assess the prevalence of this effect and better understand its origins, we applied an autocorrelation analysis of the relationship between chromosomal position and expression level to a database of over 2000 individual yeast microarray experiments. We show that at least 60% of these experiments exhibit spurious chromosomal position-dependent gene correlations, which nonetheless appear in a stochastic manner within each experimental dataset. Using computer simulations, we show that large spatial biases caused in the microarray hybridization step and independently of printing procedures can exclusively account for the observed spurious correlations, in contrast to previous suggestions. Our data suggest that such biases may generate more than 15% false data per experiment. Importantly, spatial biases are expected to occur regardless of microarray design and over a wide range of microarray platforms, organisms and experimental procedures. Spatial biases comprise a major source of noise in microarray studies; revision of routine experimental practices and normalizations to account for these biases may significantly and comprehensively improve the quality of new as well as existing DNA microarray data.

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

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

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

  1. 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.

  2. 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

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

    PubMed

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

    2008-01-01

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

  4. 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

  5. 16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization.

    PubMed

    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

  6. Organohalogens in nature: More widespread than previously assumed

    SciTech Connect

    Asplund, G.; Grimvall, A. )

    1991-08-01

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

  7. 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.

  8. 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

  9. 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

  10. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    PubMed

    Asada, Tetsuhiro

    2013-06-01

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

  12. Genetic differentiation in the soil-feeding termite Cubitermes sp. affinis subarquatus: occurrence of cryptic species revealed by nuclear and mitochondrial markers

    PubMed Central

    Roy, Virginie; Demanche, Christine; Livet, Alexandre; Harry, Myriam

    2006-01-01

    Background Soil-feeding termites are particularly interesting models for studying the effects of fragmentation, a natural or anthropic phenomenon described as promoting genetic differentiation. However, studying the link between fragmentation and genetics requires a method for identifying species unambiguously, especially when morphological diagnostic characters are lacking. In humivorous termites, which contribute to the fertility of tropical soils, molecular taxonomy and phylogenetic relationships are rarely studied, though mitochondrial and nuclear molecular markers are widely used in studies of pest termites. Here, we attempt to clarify the taxonomy of soil-feeding colonies collected throughout the naturally fragmented Lopé Reserve area (Gabon) and morphologically affiliated to Cubitermes sp. affinis subarquatus. The mitochondrial gene of cytochrome oxidase II (COII), the second nuclear rDNA internal transcribed spacer (ITS2) and five microsatellites were analyzed in 19 colonies. Results Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenetic analyses, which were applied to the COII and ITS2 sequences, and Neighbor-Joining reconstructions, applied to the microsatellite data, reveal four major lineages in the Cubitermes sp. affinis subarquatus colonies. The concordant genealogical pattern of these unlinked markers strongly supports the existence of four cryptic species. Three are sympatric in the Reserve and are probably able to disperse within a mosaic of forests of variable ages and savannahs. One is limited to a very restricted gallery forest patch located in the North, outside the Reserve. Conclusion Our survey highlights the value of combined mitochondrial and nuclear markers for exploring unknown groups such as soil-feeding termites, and their relevance for resolving the taxonomy of organisms with ambiguous morphological diagnostic characters. PMID:17123444

  13. 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. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  14. 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

  15. Type 2 Diabetes Widespread in Adults

    MedlinePlus

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

  16. Widespread surface meltwater drainage in Antarctica

    NASA Astrophysics Data System (ADS)

    Kingslake, J.; Ely, J.; Das, I.; Bell, R. E.

    2016-12-01

    Surface meltwater is thought to cause ice-shelf disintegration, which accelerates the contribution of ice sheets to sea-level rise. Antarctic surface melting is predicted to increase and trigger further ice-shelf disintegration during this century. These climate-change impacts could be modulated by an active hydrological network analogous to the one in operation in Greenland. Despite some observations of Antarctic surface and sub-surface hydrological systems, large-scale active surface drainage in Antarctica has rarely been studied. We use satellite imagery and aerial photography to reveal widespread active hydrology on the surface of the Antarctic Ice Sheet as far south as 85o and as high as 1800 m a.s.l., often near mountain peaks that protrude through the ice (nunataks) and relatively low-albedo `blue-ice areas'. Despite predominantly sub-zero regional air temperatures, as simulated by a regional climate model, Antarctic active drainage has persisted for decades, transporting water through surface streams and feeding vast melt ponds up to 80 km long. Drainage networks (the largest are over 100 km in length) form on flat ice shelves, steep outlet glaciers and ice-sheet flanks across the West and East Antarctica Ice Sheets. Motivated by the proximity of many drainage systems to low-albedo rock and blue-ice areas, we hypothesize a positive feedback between exposed-rock extent, BIA formation, melting and ice-sheet thinning. This feedback relies on drainage moving water long distances from areas near exposed rock, across the grounding line onto and across ice shelves - a process we observe, but had previously thought to be unlikely in Antarctica. This work highlights previously-overlooked processes, not captured by current regional-scale models, which may accelerate the retreat of the Antarctic Ice Sheet.

  17. Remote detection of widespread indigenous water in lunar pyroclastic deposits

    NASA Astrophysics Data System (ADS)

    Milliken, Ralph E.; Li, Shuai

    2017-08-01

    Laboratory analyses of lunar samples provide a direct means to identify indigenous volatiles and have been used to argue for the presence of Earth-like water content in the lunar interior. Some volatile elements, however, have been interpreted as evidence for a bulk lunar mantle that is dry. Here we demonstrate that, for a number of lunar pyroclastic deposits, near-infrared reflectance spectra acquired by the Moon Mineralogy Mapper instrument onboard the Chandrayaan-1 orbiter exhibit absorptions consistent with enhanced OH- and/or H2O-bearing materials. These enhancements suggest a widespread occurrence of water in pyroclastic materials sourced from the deep lunar interior, and thus an indigenous origin. Water abundances of up to 150 ppm are estimated for large pyroclastic deposits, with localized values of about 300 to 400 ppm at potential vent areas. Enhanced water content associated with lunar pyroclastic deposits and the large areal extent, widespread distribution and variable chemistry of these deposits on the lunar surface are consistent with significant water in the bulk lunar mantle. We therefore suggest that water-bearing volcanic glasses from Apollo landing sites are not anomalous, and volatile loss during pyroclastic eruptions may represent a significant pathway for the transport of water to the lunar surface.

  18. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. 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 ...

  20. High diverstiy and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales

    Treesearch

    R.A. Healy; M.E. Smith; G.M. Bonito; D.H. Pfister; Z.-W. Ge; G.G. Guevara; G. Williams; K. Stafford; L. Kumar; T. Lee; C. Hobart; J. Trappe; R. Vilgalys; D.J. McLaughlin

    2013-01-01

    Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both...

  1. Widespread occurrence and potential for biodegradation of bioactive contaminants in Congaree National Park, USA

    USGS Publications Warehouse

    Bradley, Paul M.; Battaglin, William A.; Clark, Jimmy M.; Henning, Frank; Hladik, Michelle; Iwanowicz, Luke; Journey, Celeste; Riley, Jeffrey W.; Romanok, Kristin

    2017-01-01

    Organic contaminants with designed molecular bioactivity, such as pesticides and pharmaceuticals, originate from human and agricultural sources, occur frequently in surface waters, and threaten the structure and function of aquatic and terrestrial ecosystems. Congaree National Park in South Carolina (USA) is a vulnerable park unit due to its location downstream of multiple urban and agricultural contaminant sources and its hydrologic setting, being composed almost entirely of floodplain and aquatic environments. Seventy-two water and sediment samples were collected from 16 sites in Congaree National Park during 2013 to 2015, and analyzed for 199 and 81 targeted organic contaminants, respectively. More than half of these water and sediment analytes were not detected or potentially had natural sources. Pharmaceutical contaminants were detected (49 total) frequently in water throughout Congaree National Park, with higher detection frequencies and concentrations at Congaree and Wateree River sites, downstream from major urban areas. Forty-seven organic wastewater indicator chemicals were detected in water, and 36 were detected in sediment, of which approximately half are distinctly anthropogenic. Endogenous sterols and hormones, which may originate from humans or wildlife, were detected in water and sediment samples throughout Congaree National Park, but synthetic hormones were detected only once, suggesting a comparatively low risk of adverse impacts. Assessment of the biodegradation potentials of 8 14C-radiolabeled model contaminants indicated poor potentials for some contaminants, particularly under anaerobic sediments conditions.

  2. 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 ...

  3. Widespread occurrence and potential for biodegradation of bioactive contaminants in Congaree National Park, USA.

    PubMed

    Bradley, Paul M; Battaglin, William A; Clark, Jimmy M; Henning, Frank P; Hladik, Michelle L; Iwanowicz, Luke R; Journey, Celeste A; Riley, Jeffrey W; Romanok, Kristin M

    2017-06-21

    Organic contaminants with designed molecular bioactivity, such as pesticides and pharmaceuticals, originate from human and agricultural sources, occur frequently in surface waters, and threaten the structure and function of aquatic and terrestrial ecosystems. Congaree National Park in South Carolina (USA) is a vulnerable park unit due to its location downstream of multiple urban and agricultural contaminant sources and its hydrologic setting, being composed almost entirely of floodplain and aquatic environments. Seventy-two water and sediment samples were collected from 16 sites in Congaree National Park during 2013 to 2015, and analyzed for 199 and 81 targeted organic contaminants, respectively. More than half of these water and sediment analytes were not detected or potentially had natural sources. Pharmaceutical contaminants were detected (49 total) frequently in water throughout Congaree National Park, with higher detection frequencies and concentrations at Congaree and Wateree River sites, downstream from major urban areas. Forty-seven organic wastewater indicator chemicals were detected in water, and 36 were detected in sediment, of which approximately half are distinctly anthropogenic. Endogenous sterols and hormones, which may originate from humans or wildlife, were detected in water and sediment samples throughout Congaree National Park, but synthetic hormones were detected only once, suggesting a comparatively low risk of adverse impacts. Assessment of the biodegradation potentials of 8 (14) C-radiolabeled model contaminants indicated poor potentials for some contaminants, particularly under anaerobic sediments conditions. Environ Toxicol Chem 2017;9999:1-12. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America. Published 2017 Wiley Periodicals Inc., on behalf of SETAC.

  4. 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.

  5. Microwave Photonics: current challenges towards widespread application.

    PubMed

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

    2013-09-23

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

  6. Laser light scattering in diagnostics of widespread diseases

    NASA Astrophysics Data System (ADS)

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

    2002-08-01

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

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

    PubMed

    McBride, Mark J; Zhu, Yongtao

    2013-01-01

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

  8. Pain and the brain: chronic widespread pain.

    PubMed

    Arnold, Lesley M

    2009-04-01

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

  9. Widespread Antarctic glaciation during the Late Eocene

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  10. 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.

  11. Weird Weather: Large Abrupt Widespread Climate Changes

    SciTech Connect

    Alley, Richard B.

    2001-01-24

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

  12. International arrivals: widespread bioinvasions in European Seas.

    PubMed

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

    2014-04-01

    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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. The characterization of widespread fatigue damage in fuselage structure

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  18. The characterization of widespread fatigue damage in fuselage structure

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  19. Widespread RNA 3′-end oligouridylation in mammals

    PubMed Central

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

    2012-01-01

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

  20. Radiation therapy for widespread actinic keratoses.

    PubMed

    Dinehart, Scott M; Graham, Matt; Maners, Ann

    2011-07-01

    To profile 16 patients with widespread and resistant actinic keratoses (AKs) treated with radiation therapy. Chart review and phone interviews of 16 patients who were treated with radiation therapy between 2003 and 2010. A specialized dermatological practice primarily treating patients with skin cancer. The study population at the time of treatment was aged 70 to 87 with a mean age of 79.6 years and included 14 men and two women. Patients were followed at two weeks and six months after treatment to assess clinical outcome. All adverse effects were recorded. Patients were contacted for phone interview to assess patient satisfaction after treatment. Patients all had significant reduction of AKs in the radiation field with a majority (90%) reporting they were "very satisfied" with their treatment outcome. Of 16 patients at two weeks post-treatment, 13 had complete clinical resolution of their AK after radiation therapy. Three of 16 patients had significant reduction (50-99%) in AK in the treatment field. Patients reported improved quality of life, a reduced need for frequent clinic visits, and long-term remission from the development of new AKs within the treatment field. Patients meeting suggested specific criteria developed by the authors may be treated successfully with radiation therapy with good outcomes at six-month follow up and high levels of patient satisfaction.

  1. Neurobiology of fibromyalgia and chronic widespread pain.

    PubMed

    Sluka, Kathleen A; Clauw, Daniel J

    2016-12-03

    Fibromyalgia is the current term for chronic widespread musculoskeletal pain for which no alternative cause can be identified. The underlying mechanisms, in both human and animal studies, for the continued pain in individuals with fibromyalgia will be explored in this review. There is a substantial amount of support for alterations of central nervous system nociceptive processing in people with fibromyalgia, and that psychological factors such as stress can enhance the pain experience. Emerging evidence has begun exploring other potential mechanisms including a peripheral nervous system component to the generation of pain and the role of systemic inflammation. We will explore the data and neurobiology related to the role of the CNS in nociceptive processing, followed by a short review of studies examining potential peripheral nervous system changes and cytokine involvement. We will not only explore the data from human subjects with fibromyalgia but will relate this to findings from animal models of fibromyalgia. We conclude that fibromyalgia and related disorders are heterogenous conditions with a complicated pathobiology with patients falling along a continuum with one end a purely peripherally driven painful condition and the other end of the continuum is when pain is purely centrally driven. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  2. Widespread Vestibular Activation of the Rodent Cortex

    PubMed Central

    Moya, Javier; Drawitsch, Florian; Brichta, Alan M.

    2015-01-01

    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

  3. 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.

  4. Widespread ectopic expression of olfactory receptor genes

    PubMed Central

    Feldmesser, Ester; Olender, Tsviya; Khen, Miriam; Yanai, Itai; Ophir, Ron; Lancet, Doron

    2006-01-01

    Background Olfactory receptors (ORs) are the largest gene family in the human genome. Although they are expected to be expressed specifically in olfactory tissues, some ectopic expression has been reported, with special emphasis on sperm and testis. The present study systematically explores the expression patterns of OR genes in a large number of tissues and assesses the potential functional implication of such ectopic expression. Results We analyzed the expression of hundreds of human and mouse OR transcripts, via EST and microarray data, in several dozens of human and mouse tissues. Different tissues had specific, relatively small OR gene subsets which had particularly high expression levels. In testis, average expression was not particularly high, and very few highly expressed genes were found, none corresponding to ORs previously implicated in sperm chemotaxis. Higher expression levels were more common for genes with a non-OR genomic neighbor. Importantly, no correlation in expression levels was detected for human-mouse orthologous pairs. Also, no significant difference in expression levels was seen between intact and pseudogenized ORs, except for the pseudogenes of subfamily 7E which has undergone a human-specific expansion. Conclusion The OR superfamily as a whole, show widespread, locus-dependent and heterogeneous expression, in agreement with a neutral or near neutral evolutionary model for transcription control. These results cannot reject the possibility that small OR subsets might play functional roles in different tissues, however considerable care should be exerted when offering a functional interpretation for ectopic OR expression based only on transcription information. PMID:16716209

  5. Control of the geomorphology and gas hydrate extent on widespread gas emissions offshore Romania (Black Sea)

    NASA Astrophysics Data System (ADS)

    Riboulot, V.; Cattaneo, A.; Sultan, N.; Ker, S.; Scalabrin, C.; Gaillot, A.; Jouet, G.; Marsset, B.; Thomas, Y.; Ballas, G.; Marsset, T.; Garziglia, S.; Ruffine, L.; Boulart, C.

    2016-12-01

    The Romanian sector of the Black Sea deserves attention because the Danube deep-sea fan is one of the largest sediment depositional systems worldwide and is considered the world's most isolated sea, the largest anoxic water body on the planet and a unique energy-rich sea. Due to the high sediment accumulation rate, presence of organic matter and anoxic conditions, the Black sea sediment offshore the Danube delta is rich in gas and thus show BSR. The cartography of the BSR over the last 20 years, exhibits its widespread occurrence, indicative of extensive development of hydrate accumulations and a huge gas hydrate potential. By combining old and new datasets acquired in 2015 during the GHASS expedition, we performed a geomorphological analysis of the continental slope north-east of the Danube canyon that reveals the presence of several landslides inside and outside several canyons incising the seafloor. It is a complex study area presenting sedimentary processes such as seafloor erosion and instability, mass wasting, formation of gas hydrates, fluid migration, gas escape, where the imprint of geomorphology seems to dictate the location where gas seep occurs. . Some 1409 gas seeps within the water column acoustic records are observed between 200 m and 800 m water depth. No gas flares were detected in deeper areas where gas hydrates are stable. Overall, 93% of the all gas seeps observed are above geomorphological structures. 78% are right above escarpment induced by sedimentary destabilizations inside or outside canyons. The results suggest a geomorphological control of degassing at the seafloor and gas seeps are thus constrained by the gas hydrates stability zone. The stability of the gas hydrates is dependent on the salinity gradient through the sedimentary column and thus on the Black Sea recent geological history. The extent and the dynamics of gas hydrates have a probable impact on the sedimentary destabilization observed at the seafloor.

  6. 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

  7. 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

  8. Spatial and temporal variability in fire occurrence within the Las Bayas Forestry Reserve, Durango, Mexico

    Treesearch

    S. A. Drury; T. T. Veblen

    2008-01-01

    Patterns of fire occurrence within the Las Bayas Forestry Reserve, Mexico are analyzed in relation to variability in climate, topography, and human land-use. Significantly more fires with shorter fire return intervals occurred from 1900 to 1950 than from 1950 to 2001. However, the frequency of widespread fire years (25% filter) was unchanged over time, as widespread...

  9. 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.

  10. Transglutaminases: widespread cross-linking enzymes in plants.

    PubMed

    Serafini-Fracassini, Donatella; Del Duca, Stefano

    2008-08-01

    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. 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. It has been detected in algae and in angiosperms in different organs and sub-cellular compartments, chloroplasts being the best-studied organelles. 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. The widespread occurrence of transglutaminases activity in all organs and cell compartments studied suggests a relevance for their still incompletely defined physiological roles. At present, it is not possible to classify this enzyme family in plants owing to

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Shen, Bin; Li, Yixiao

    2014-12-01

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

  13. 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.

  14. Viewing a forelimb induces widespread cortical activations.

    PubMed

    Raos, Vassilis; Kilintari, Marina; Savaki, Helen E

    2014-04-01

    cortical network is recruited even by mere observation of an arm executing goalless movements, which partially overlaps with the cortical network supporting the execution and observation of goal-directed forelimb actions. Interestingly, this overlap concerns mainly lower order sensory-motor rather than higher order association prefrontal and parietal cortices. Our results demonstrate that in order to reveal the net effects specifically induced by observation of a purposeful reaching-to-grasp action, the use of an appropriate control taking into account the effects of viewing the object to be grasped, the reaching arm and the static hand is crucial. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  16. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife

    PubMed Central

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

    2016-01-01

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

  17. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  18. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife.

    PubMed

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

    2016-12-13

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

  19. Widespread episodic thiamine deficiency in Northern Hemisphere wildlife

    USGS Publications Warehouse

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

    2016-01-01

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

  20. Widespread plasticity in CTCF occupancy linked to DNA methylation.

    PubMed

    Wang, Hao; Maurano, Matthew T; Qu, Hongzhu; Varley, Katherine E; Gertz, Jason; Pauli, Florencia; Lee, Kristen; Canfield, Theresa; Weaver, Molly; Sandstrom, Richard; Thurman, Robert E; Kaul, Rajinder; Myers, Richard M; Stamatoyannopoulos, John A

    2012-09-01

    CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor.

  1. Widespread plasticity in CTCF occupancy linked to DNA methylation

    PubMed Central

    Wang, Hao; Maurano, Matthew T.; Qu, Hongzhu; Varley, Katherine E.; Gertz, Jason; Pauli, Florencia; Lee, Kristen; Canfield, Theresa; Weaver, Molly; Sandstrom, Richard; Thurman, Robert E.; Kaul, Rajinder; Myers, Richard M.; Stamatoyannopoulos, John A.

    2012-01-01

    CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor. PMID:22955980

  2. 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

  3. 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

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

    PubMed Central

    2014-01-01

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

  5. 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.

  6. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Concise Review: Cell Therapies: The Route to Widespread Adoption

    PubMed Central

    Foley, Lucy

    2012-01-01

    We identify three dimensions with which to classify heuristically the routes to widespread adoption of cellular therapies. The first dimension is based on the relative involvement of clinicians and companies in a particular cellular therapy. The second dimension is based on cell type and consequent scale of manufacture. The third dimension classifies the therapeutic intervention as a procedure or product and has perhaps received less attention. We suggest that for those cellular therapies that require therapeutic procedures, close collaboration between companies and clinicians will reduce the time to widespread adoption. For selected cellular therapies we make predictions of the likely time to widespread adoption. PMID:23197823

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

    PubMed Central

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

    2014-01-01

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

  9. The Logic of Occurrence

    DTIC Science & Technology

    1986-12-01

    determining the consequences of assumptions about the behavior of a system . If the space of behaviors is represented by an envisionment , many such...consequences can be represented by pruning states from the envisionment . This paper provides a formal logic of occurrence which justifies the...algorithms involved and provides a language for relating specific histories to envisionments . The concepts and axioms are general enough to be applicable to

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

    PubMed Central

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

    2014-01-01

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

  11. Microbial survey of ready-to-eat salad ingredients sold at retail reveals the occurrence and the persistence of Listeria monocytogenes Sequence Types 2 and 87 in pre-packed smoked salmon.

    PubMed

    Chau, Man Ling; Aung, Kyaw Thu; Hapuarachchi, Hapuarachchige Chanditha; Lee, Pei Sze Valarie; Lim, Pei Ying; Kang, Joanne Su Lin; Ng, Youming; Yap, Hooi Ming; Yuk, Hyun-Gyun; Gutiérrez, Ramona Alikiiteaga; Ng, Lee Ching

    2017-02-28

    As the preparation of salads involves extensive handling and the use of uncooked ingredients, they are particularly vulnerable to microbial contamination. This study aimed to determine the microbial safety and quality of pre-packed salads and salad bar ingredients sold in Singapore, so as to identify public health risks that could arise from consuming salads and to determine areas for improvement in the management of food safety. The most frequently encountered organism in pre-packed salad samples was B. cereus, particularly in pasta salads (33.3%, 10/30). The most commonly detected organism in salad bar ingredients was L. monocytogenes, in particular seafood ingredients (44.1%, 15/34), largely due to contaminated smoked salmon. Further investigation showed that 21.6% (37/171) of the pre-packed smoked salmon sold in supermarkets contained L. monocytogenes. Significantly higher prevalence of L. monocytogenes and higher Standard Plate Count were detected in smoked salmon at salad bars compared to pre-packed smoked salmon in supermarkets, which suggested multiplication of the organism as the products move down the supply chain. Further molecular analysis revealed that L. monocytogenes Sequence Type (ST) 2 and ST87 were present in a particular brand of pre-packed salmon products over a 4-year period, implying a potential persistent contamination problem at the manufacturing level. Our findings highlighted a need to improve manufacturing and retail hygiene processes as well as to educate vulnerable populations to avoid consuming food prone to L. monocytogenes contamination.

  12. EPA is proposing a program under which certain widespread ...

    EPA Pesticide Factsheets

    EPA is proposing a program under which certain widespread post-user items that are hazardous wastes would be collected under greatly streamlined requirements, to facilitate separation of these materials from the municipal waste stream.

  13. Widespread West Nile virus activity, eastern United States, 2000.

    PubMed

    Marfin, A A; Petersen, L R; Eidson, M; Miller, J; Hadler, J; Farello, C; Werner, B; Campbell, G L; Layton, M; Smith, P; Bresnitz, E; Cartter, M; Scaletta, J; Obiri, G; Bunning, M; Craven, R C; Roehrig, J T; Julian, K G; Hinten, S R; Gubler, D J

    2001-01-01

    In 1999, the U.S. West Nile (WN) virus epidemic was preceded by widespread reports of avian deaths. In 2000, ArboNET, a cooperative WN virus surveillance system, was implemented to monitor the sentinel epizootic that precedes human infection. This report summarizes 2000 surveillance data, documents widespread virus activity in 2000, and demonstrates the utility of monitoring virus activity in animals to identify human risk for infection.

  14. Direct chemical evidence for widespread dairying in prehistoric Britain

    PubMed Central

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

    2003-01-01

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

  15. Widespread HCO Emission in the Nuclear Starburst of M82

    NASA Astrophysics Data System (ADS)

    García-Burillo, S.; Martín-Pintado, J.; Fuente, A.; Usero, A.; Neri, R.

    2002-08-01

    We present a high-resolution (~5") image of the nucleus of M82 showing the presence of widespread emission of the formyl radical (HCO). The HCO map, the first obtained in an external galaxy, reveals the existence of a structured disk of ~650 pc full diameter. The HCO distribution in the plane mimics the ring morphology displayed by other molecular/ionized gas tracers in M82. More precisely, rings traced by HCO, CO, and H II regions are nested, with the HCO ring lying in the outer edge of the molecular torus. Observations of HCO in Galactic clouds indicate that the abundance of HCO is strongly enhanced in the interfaces between the ionized and molecular gas. The surprisingly high overall abundance of HCO measured in M82 [X(HCO)~4×10-10] indicates that its nuclear disk can be viewed as a giant photon-dominated region (PDR) of ~650 pc size. The existence of various nested gas rings, with the highest HCO abundance occurring at the outer ring [X(HCO)~0.8×10-9], suggests that PDR chemistry is propagating in the disk. We discuss the inferred large abundances of HCO in M82 in the context of a starburst evolutionary scenario, picturing the M82 nucleus as an evolved starburst. Based on observations carried out with the Institut de Radioastronomie Millimétrique (IRAM) Plateau de Bure Interferometer. IRAM is supported by the Institut National des Sciences de l'Univers/Centre National de la Recherche Scientifique (France), the Max-Planck-Gesellschaft (Germany), and the Instituto Geográfico Nacional (Spain).

  16. 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

  17. Occurrence of polycadinene in fossil and recent resins

    NASA Astrophysics Data System (ADS)

    Van Aarssen, B. G. K.; de Leeuw, J. W.; Collinson, M.; Boon, J. J.; Goth, K.

    1994-01-01

    Dammars produced by Dipterocarpaceae growing in Southeast Asia are partly composed of a macromolecule with a polycadinene structure. This polymer is the precursor of many specific compounds encountered in crude oils and sediment extracts from South Asia. Until recently there was no evidence for a more widespread geographical occurrence of this resinous polymer. Using different pyrolysis methods it is shown that the polymers present in a resinite from Utah, USA, and in resins contained in resin canals of Eocene fossil fruits from Germany and England are also polycadinenes. The fossil fruits were undoubtedly produced by ancient representatives of mastixioid Cornaceae, a group of plants which was widespread in the Tertiary of Europe and North America and which is not related to Dipterocarpaceae. These findings extend the known occurrence and origin of the sesquiterpenoid type resin polymer. It is to be expected that catagenetic products of these resin polymers should be present in oils, coals, and sediment extracts from areas outside Southeast Asia.

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

    USGS Publications Warehouse

    Barron, J.A.; Keller, G.

    1982-01-01

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

  19. 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.

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

    PubMed

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

    2012-09-01

    We conducted a pilot survey of genetic variation of A. cantonensis using small subunit (SSU) ribosomal (r) RNA and mitochondrial cytochrome c oxidase subunit I (coxI) gene sequences. Two distinct SSU genotypes (G1 and G2) were identified among 17 individual A. cantonensis worms from 17 different geographical localities in Japan, Mainland China, Taiwan, and Thailand. The partial coxI sequences were determined for 83 worms from 18 different geographical localities from Japan, Mainland China, Taiwan, and Thailand. Phylogenetic analysis showed eight distinct coxI haplotypes (ac1 to ac8). In 16 out of 18 localities, only a single coxI haplotype was found. However, in two localities, two coxI haplotypes coexisted. The common haplotypes found were: haplotype ac1 (Tokyo, Chiba, Kanagawa, Amamioshima Island, and Taichung), haplotype ac2 (Ishikawa, Shenzhen, and Lianjiang), haplotype ac5 (the Okinawa and the Ogasawara Islands), and haplotype ac7 (Miyagi, Aichi, and Kanagawa). Each of these regions is separated from the others by high mountain ranges or oceans. In addition, the lower genetic variation and particular geographical distribution of A. cantonensis in each location could indicate a founder effect, which may have resulted from multiple independent origins, and suggests that haplotypes migrated from endemic areas via human-related transportation. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26612583

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

    PubMed Central

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

    2016-01-01

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

  3. 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

  4. 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

  5. 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

  6. Perceptions of health risks of cigarette smoking: A new measure reveals widespread misunderstanding

    PubMed Central

    Krosnick, Jon A.; Malhotra, Neil; Bruera, Eduardo F.; Chang, LinChiat; Pasek, Josh; Thomas, Randall K.

    2017-01-01

    Most Americans recognize that smoking causes serious diseases, yet many Americans continue to smoke. One possible explanation for this paradox is that perhaps Americans do not accurately perceive the extent to which smoking increases the probability of adverse health outcomes. This paper examines the accuracy of Americans’ perceptions of the absolute risk, attributable risk, and relative risk of lung cancer, and assesses which of these beliefs drive Americans’ smoking behavior. Using data from three national surveys, statistical analyses were performed by comparing means, medians, and distributions, and by employing Generalized Additive Models. Perceptions of relative risk were associated as expected with smoking onset and smoking cessation, whereas perceptions of absolute risk and attributable risk were not. Additionally, the relation of relative risk with smoking status was stronger among people who held their risk perceptions with more certainty. Most current smokers, former smokers, and never-smokers considerably underestimated the relative risk of smoking. If, as this paper suggests, people naturally think about the health consequences of smoking in terms of relative risk, smoking rates might be reduced if public understanding of the relative risks of smoking were more accurate and people held those beliefs with more confidence. PMID:28806420

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

    PubMed

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

    2008-12-19

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

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

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2011-10-01

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

  11. 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.

  12. Widespread low rates of Antarctic glacial isostatic adjustment revealed by GPS observations

    NASA Astrophysics Data System (ADS)

    Thomas, Ian D.; King, Matt A.; Bentley, Michael J.; Whitehouse, Pippa L.; Penna, Nigel T.; Williams, Simon D. P.; Riva, Riccardo E. M.; Lavallee, David A.; Clarke, Peter J.; King, Edward C.; Hindmarsh, Richard C. A.; Koivula, Hannu

    2011-11-01

    Bedrock uplift in Antarctica is dominated by a combination of glacial isostatic adjustment (GIA) and elastic response to contemporary mass change. Here, we present spatially extensive GPS observations of Antarctic bedrock uplift, using 52% more stations than previous studies, giving enhanced coverage, and with improved precision. We observe rapid elastic uplift in the northern Antarctic Peninsula. After considering elastic rebound, the GPS data suggests that modeled or empirical GIA uplift signals are often over-estimated, particularly the magnitudes of the signal maxima. Our observation that GIA uplift is misrepresented by modeling (weighted root-mean-squares of observation-model differences: 4.9-5.0 mm/yr) suggests that, apart from a few regions where large ice mass loss is occurring, the spatial pattern of secular ice mass change derived from Gravity Recovery and Climate Experiment (GRACE) data and GIA models may be unreliable, and that several recent secular Antarctic ice mass loss estimates are systematically biased, mainly too high.

  13. Perceptions of health risks of cigarette smoking: A new measure reveals widespread misunderstanding.

    PubMed

    Krosnick, Jon A; Malhotra, Neil; Mo, Cecilia Hyunjung; Bruera, Eduardo F; Chang, LinChiat; Pasek, Josh; Thomas, Randall K

    2017-01-01

    Most Americans recognize that smoking causes serious diseases, yet many Americans continue to smoke. One possible explanation for this paradox is that perhaps Americans do not accurately perceive the extent to which smoking increases the probability of adverse health outcomes. This paper examines the accuracy of Americans' perceptions of the absolute risk, attributable risk, and relative risk of lung cancer, and assesses which of these beliefs drive Americans' smoking behavior. Using data from three national surveys, statistical analyses were performed by comparing means, medians, and distributions, and by employing Generalized Additive Models. Perceptions of relative risk were associated as expected with smoking onset and smoking cessation, whereas perceptions of absolute risk and attributable risk were not. Additionally, the relation of relative risk with smoking status was stronger among people who held their risk perceptions with more certainty. Most current smokers, former smokers, and never-smokers considerably underestimated the relative risk of smoking. If, as this paper suggests, people naturally think about the health consequences of smoking in terms of relative risk, smoking rates might be reduced if public understanding of the relative risks of smoking were more accurate and people held those beliefs with more confidence.

  14. Single cell transcriptome analysis of muscle satellite cells reveals widespread transcriptional heterogeneity.

    PubMed

    Cho, Dong Seong; Doles, Jason D

    2017-09-08

    Tissue specific stem cells are indispensable contributors to adult tissue maintenance, repair, and regeneration. In skeletal muscle, satellite cells (SCs) are the resident muscle stem cell population and are required to maintain skeletal muscle homeostasis throughout life. Increasing evidence suggests that SCs are a heterogeneous cell population with substantial biochemical and functional diversity. A major limitation in the field is an incomplete understanding of the nature and extent of this cellular heterogeneity. Single cell analyses are well suited to addressing this issue, especially when coupled to unbiased profiling paradigms such as high throughout RNA sequencing. We performed single cell RNA sequencing (scRNA-seq) on freshly isolated muscle satellite cells and found a surprising degree of heterogeneity at multiple levels, from muscle-specific transcripts to the broader SC transcriptome. We leveraged several comparative bioinformatics techniques and found that individual SCs enrich for unique transcript clusters. We propose that these gene expression "fingerprints" may contribute to observed functional SC diversity. Overall, these studies underscore the importance of several established SC signaling pathways/processes on a single cell level, implicate novel regulators of SC heterogeneity, and lay the groundwork for further investigation into SC heterogeneity in health and disease. Copyright © 2017. Published by Elsevier B.V.

  15. 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

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

    PubMed

    Cheng, Kun; Rong, Xiaoying; Huang, Ying

    2016-09-01

    Homologous recombination is increasingly being recognized as a driving force in microbial evolution. However, recombination in streptomycetes, a rich source of diverse secondary metabolites, particularly among different species, remains minimally investigated. In this study, the largest sample of Streptomyces species to date, consisting of 142 type strains spanning the genus, with available sequences of 16S rRNA, atpD, gyrB, recA, rpoB and trpB genes, were collected and subjected to a comprehensive population genetic analysis to generate an overall estimate of the level of Streptomyces interspecies genetic exchange and its effect on the evolution of this genus. The results indicate frequent homologous recombination among Streptomyces species, which occurred three times more frequently and was nearly 14 times more important than point mutation in nucleotide sequence divergence (ρ/θw=3.10, r/m=13.74). As a result, a facilitating effect on the evolutionary process and confusion in phylogenetic relationships were observed, as well as a number of specific transfer events of the six gene fragments. A resultant phylogenetic network depicted extensive horizontal genetic exchange which decays clonality in streptomycetes. Moreover, seven evolutionary lineage groups were identified in the present sample in the Structure analysis, generally consistent with morphological and physiological data, and the contribution of recombination was detected to be varied among them. Our analyses demonstrated a reticulate evolution within Streptomyces due to the high level of interspecies gene exchange, which greatly challenges the traditional tree-shaped phylogeny in this genus and may advance our evolutionary understanding of a genuine Streptomyces species. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    PubMed

    Larson, Courtney L; Reed, Sarah E; Merenlender, Adina M; Crooks, Kevin R

    2016-01-01

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

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

    PubMed

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

    2015-02-01

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

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

    PubMed

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

    2012-06-01

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

  20. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade.

    PubMed

    de Boer, Hugo J; Ghorbani, Abdolbaset; Manzanilla, Vincent; Raclariu, Ancuta-Cristina; Kreziou, Anna; Ounjai, Sarawut; Osathanunkul, Maslin; Gravendeel, Barbara

    2017-09-27

    In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient Cyamopsis tetraganoloba (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids. © 2017 The Author(s).

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

    PubMed Central

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

    2010-01-01

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

  2. 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.

  3. Global relationship of fire occurrence and fire intensity: A test of intermediate fire occurrence-intensity hypothesis

    NASA Astrophysics Data System (ADS)

    Luo, Ruisen; Hui, Dafeng; Miao, Ning; Liang, Chuan; Wells, Nicholas

    2017-05-01

    Fire plays a significant role in global atmosphere and biosphere carbon and nutrient cycles. Globally, there are substantially different distributions and impacts between fire occurrence and fire intensity. It is prominent to have a thorough investigation of global relationship between fire occurrence and fire intensity for future fire prediction and management. In this study, we proposed an intermediate fire occurrence-intensity (IFOI) hypothesis for the global relationship between fire occurrence and fire intensity, suggesting that fire occurrence changes with fire intensity following a humped relationship. We examined this hypothesis via satellite data from January 2001 to December 2013 at a global scale, and in small and large fire intensity zones, respectively. Furthermore, the fire occurrence and fire intensity relationship was developed among different vegetation types to reveal the changes of parameters and strengths. Finally, the environmental factors (including climatic, hydraulic, biological, and anthropogenic variables) underpinning the fire occurrence and intensity pattern were evaluated for the underlying mechanisms. The results supported our IFOI hypothesis and demonstrated that the humped relationship is driven by different causes among vegetation types. Fire occurrence increases with fire intensity in small fire intensity zones due to alleviation of the factors limiting both fire occurrence and intensity. Beyond a certain fire intensity threshold, fire occurrence is constrained, probably due to the limitation of available fuels. The information generated in this study could be helpful for understanding global variation of fire occurrence and fire intensity due to fire-vegetation-climate-human interactions and facilitating future fire management.

  4. 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).

  5. 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.

  6. 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.

  7. 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.

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

    DTIC Science & Technology

    2010-08-01

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

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

    PubMed

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

    2016-04-01

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

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

    PubMed

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

    2015-11-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Brewer, John

    1994-09-01

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

  13. Women with Chronic and Episodic Migraine Exhibit Similar Widespread Pressure Pain Sensitivity.

    PubMed

    Palacios-Ceña, María; Lima Florencio, Lidiane; Natália Ferracini, Gabriela; Barón, Johanna; Guerrero, Ángel L; Ordás-Bandera, Carlos; Arendt-Nielsen, Lars; Fernández-de-Las-Peñas, César

    2016-11-01

    To investigate widespread pressure hyperalgesia in the trigemino-cervical and extra-trigeminal (distant pain-free) regions in women with episodic and chronic migraine. Fifty-one women with episodic migraine, 52 women with chronic migraine, and 52 healthy women without headache history were recruited. Pressure pain thresholds (PPT) were bilaterally assessed over the trigeminal area (i.e., temporalis muscle), cervical area (i.e., C5/C6 zygapophyseal joint), and two extra-trigeminal areas (i.e., second metacarpal, tibialis anterior muscle) in a blinded design. Clinical features of migraine and anxiety/depression (Hospital Anxiety and Depression Scale, HADS) were also assessed. The multivariate analysis of covariance (ANCOVA) revealed that PPTs were significantly decreased bilaterally over trigeminal and extra-trigeminal points in migraine patients compared to healthy women (all sites, P < 0.001). No differences between episodic and chronic migraine were observed (all, P > 0.919). The presence of neck pain (all, P > 0.282), anxiety (P > 0.425) or depression (all, P > 0.316) did not influence the results. The intensity of migraine pain was negatively associated with widespread pressure pain sensitivity: The greater the intensity of migraine attacks, the lower the widespread PPT levels, i.e., the greater the widespread sensitization. This study found similar widespread pressure hypersensitivity in women with episodic or chronic migraine suggesting that central manifestations are involved both in episodic and chronic migraine. © 2016 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    NASA Astrophysics Data System (ADS)

    Harvey, H. Rodger; Mcmanus, George B.

    1991-11-01

    We observed tetrahymanol (gammaceran-3β-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 ( R2 = 0.89), suggesting that tetrahymanol is a specific marker for marine ciliates that feed on bacteria. Hopan-3β-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.

  15. 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.

  16. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

    SciTech Connect

    Lobanov, Alexei V.; Heaphy, Stephen M.; Turanov, Anton A.; Gerashchenko, Maxim V.; Pucciarelli, Sandra; Devaraj, Raghul R.; Xie, Fang; Petyuk, Vladislav A.; Smith, Richard D.; Klobutcher, Lawrence A.; Atkins, John F.; Miceli, Cristina; Hatfield, Dolph L.; Baranov, Pavel V.; Gladyshev, Vadim N.

    2016-11-21

    The ribosome can change its reading frame during translation in a process known as programmed ribosomal frameshifting. These rare events are supported by complex mRNA signals. However, we found that the ciliates Euplotes crassus and Euplotes focardii exhibit widespread frameshifting at stop codons. 47 different codons preceding stop signals resulted in either +1 or +2 frameshifts, and +1 frameshifting at AAA was the most frequent. The frameshifts showed unusual plasticity and rapid evolution, and had little influence on translation rates. The proximity of a stop codon to the 3' mRNA end, rather than its occurrence or sequence context, appeared to designate termination. Thus, a ‘stop codon’ is not a sufficient signal for translation termination, and the default function of stop codons in Euplotes is frameshifting, whereas termination is specific to certain mRNA positions and probably requires additional factors.

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

    PubMed

    Witting, N; Duno, M; Vissing, J

    2013-01-01

    Becker muscular dystrophy features progressive proximal weakness, wasting and often focal hypertrophy. We present a patient with pain and cramps from adolescence. Widespread muscle hypertrophy, preserved muscle strength and a 10-20-fold raised CPK were noted. Muscle biopsy was dystrophic, and Western blot showed a 95% reduction of dystrophin levels. Genetic analyses revealed a non-sense mutation in exon 2 of the dystrophin gene. This mutation is predicted to result in a Duchenne phenotype, but resulted in a mild Becker muscular dystrophy with widespread muscle hypertrophy. We suggest that this unusual phenotype is caused by translation re-initiation downstream from the mutation site. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    PubMed Central

    Kristan, William B.

    2014-01-01

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

  19. 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

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

    PubMed

    Ahmad, Jowairiyya; Tagoe, Clement E

    2014-07-01

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

  1. Are neonicotinoid insecticides driving declines of widespread butterflies?

    PubMed

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

    2015-01-01

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

  2. DCAA Audits: Widespread Problems with Audit Quality Require Significant Reform

    DTIC Science & Technology

    2009-09-01

    GAO United States Government Accountability Office Report to the Committee on Homeland Security and Governmental Affairs...U.S. Senate DCAA AUDITS Widespread Problems with Audit Quality Require Significant Reform September 2009 GAO-09-468 Report ...Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to average 1 hour per response

  3. Keystone Targets for Change: Planning for Widespread Positive Consequences.

    ERIC Educational Resources Information Center

    Barnett, David W.; And Others

    1996-01-01

    Elaborates the concept of "keystone target variable selection" for school psychological practice. "Keystone variables" refers to relatively narrow targets for change having the most widespread benefits to clients. The hypothesized benefits of selecting keystone targets for change include more effective and efficient interventions. (KW)

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

    PubMed Central

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

    2014-01-01

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

  5. 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

  6. Active Longitude and Coronal Mass Ejection Occurrences

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  7. Familial occurrence of dystocia.

    PubMed

    Berg-Lekås, M L; Högberg, U; Winkvist, A

    1998-07-01

    A cohort study was conducted to determine the risk of dystocia for women whose mothers, sisters, or twin sisters had dystocia during childbirth. A linked database was constructed between 2 separate Swedish birth registries. Obstetric data on mothers giving birth to daughters during the period 1955 to 1972 were studied. Among these daughters, sister-couples and twins were identified. The daughters subsequently became mothers during 1973 and 1990 and obstetric data on the first deliveries were also studied. If a mother had dystocia when delivering her eldest daughter, this daughter had an increased risk of dystocia during her own first childbirth (odds ratio 1.7, 95% confidence interval 1.2 to 2.4). If the mother had an assisted instrumental delivery (vacuum extraction, forceps, or cesarean section) because of dystocia, there was a higher risk for her daughter to have an instrumental delivery because of dystocia (odds ratio 1.8, 95% confidence interval 1.0 to 3.1). Among primiparous sisters the risk of an instrumental delivery because of dystocia in a younger sister was more than tripled (odds ratio 3.5, 95% confidence interval 2.1 to 5.8) if her elder sister had a dystocic labor requiring instrumental intervention. The risk among twins increased more than 20-fold (odds ratio 24.0, 95% confidence interval 1.5 to 794.5) if 1 twin sister had dystocia during her first childbirth. Dystocia has a familial occurrence, suggesting a possible genetic factor explaining inefficient uterine action.

  8. 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

  9. 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

  10. Evidence of widespread axonal pathology in Wolfram syndrome.

    PubMed

    Shannon, P; Becker, L; Deck, J

    1999-09-01

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

  11. 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.

  12. 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.

  13. Bilateral widespread mechanical pain hypersensitivity as sign of central sensitization in patients with cluster headache.

    PubMed

    Fernández-de-Las-Peñas, César; Ortega-Santiago, Ricardo; Cuadrado, María L; López-de-Silanes, Carlos; Pareja, Juan A

    2011-03-01

    To investigate bilateral widespread pressure pain hyperalgesia in deep tissues over symptomatic (trigemino-cervical) and nonsymptomatic (distant pain-free) regions in patients with cluster headache (CH). Central sensitization is claimed to play a relevant role in CH. No study has previously searched for widespread pressure hyperalgesia in deep tissues over both symptomatic (trigemino-cervical) and nonsymptomatic (distant pain-free) regions in patients with CH. Sixteen men (mean age: 43 ± 11 years) with CH in a remission phase and 16 matched controls were recruited. Pressure pain thresholds (PPTs) were bilaterally measured over the supra-orbital (V1), infra-orbital (V2), mental (V3), median (C5), radial (C6), and ulnar (C7) nerves, C5-C6 zygapophyseal joint, mastoid process, and tibialis anterior muscle by an assessor blinded to the subjects' condition. The results showed that PPT levels were significantly decreased bilaterally in patients with CH as compared with healthy controls (all sites, P < .001). A greater degree of sensitization over the mastoid process (P < .001) and a lower degree of sensitization over the tibialis anterior muscle (P < .01) was found. Our findings revealed bilateral widespread pressure pain hypersensitivity in patients with CH confirming the presence of central sensitization mechanisms in this headache condition. © 2010 American Headache Society.

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

    PubMed

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

    2009-06-01

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

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

    PubMed Central

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

    2016-01-01

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

  16. Widespread pressure pain hypersensitivity in elderly subjects with unilateral thumb carpometacarpal osteoarthritis.

    PubMed

    Chiarotto, Alessandro; Fernandez-de-Las-Peñas, Cesar; Castaldo, Matteo; Negrini, Stefano; Villafañe, Jorge Hugo

    2013-12-01

    Widespread pressure hypersensitivity is one of the signs that characterize central pain sensitization in subjects with knee and hip osteoarthritis (OA). The purpose of this study was to evaluate whether widespread pressure pain hyperalgesia is a feature of individuals with unilateral symptomatic thumb carpometacarpal (CMC) OA. A total of 16 patients with unilateral symptomatic thumb CMC OA and 16 healthy sex- and age-matched controls were recruited. Pressure pain thresholds (PPTs) were assessed bilaterally over the first CMC joint; the C5-C6 zygapophyseal joint; the median, ulnar, and radial nerves; and tibialis anterior muscle. Grip and key strength, intensity of pain, and function QuickDASH were also measured. The analyses showed that patients with thumb CMC OA present bilaterally decreased PPTs over the first CMC joint, the C5-C6 zygapophyseal joint, and the tibialis anterior, median, ulnar and radial nerve as compared to controls (all, P < 0.01). Patients with thumb CMC OA also exhibited a bilateral reduction in pinch and grip strength than controls (P < 0.05). A significant correlation was found between PPT over the radial nerve and QuickDASH (r = 0.546, P = 0.029). This study revealed bilateral widespread pressure pain hypersensitivity in individuals with unilateral symptomatic thumb CMC OA, suggesting that central pain processing mechanisms might be a feature of this pain population. These results should be taken into consideration when addressing future treatment approaches.

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

    PubMed

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

    2016-11-10

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

  18. Unemployment and widespread influenza in America, 1999–2010

    PubMed Central

    Cornwell, Benjamin

    2011-01-01

    Please cite this paper as: Cornwell B. (2012) Unemployment and widespread influenza in America, 1999–2010. Influenza and Other Respiratory Viruses 6(1), 63–70. Background  Research shows that unemployment reduces access to health care and vaccines and increases financial difficulty, family conflict, and other sources of stress that are known to suppress immune function. In addition, seasonal unemployment rates parallel seasonal influenza activity. Following a theory that argues that macroeconomic conditions affect population health, this paper examines whether there is an association between monthly unemployment rates and influenza activity. Methods  Data from influenza activity surveillance reports from the Centers for Disease Control and Prevention are combined with information from the Bureau of Labor Statistics on state‐level unemployment rates in the U.S. for the flu seasons between 1999 and 2010. Pooled time‐series cross‐section logistic regression analyses are conducted to examine the effect of the unemployment rate on the likelihood of widespread and/or regional influenza activity in the 48 contiguous states throughout this period. A total of 3712 state‐month observations are examined. Results  Net of other factors included in the multivariate regression analysis, a one‐percentage‐point increment in the unemployment rate is associated with between a 7·1% and 37·0% increment in the odds of widespread influenza (Odds ratio = 1·21). Likewise, a one‐percentage‐point increment in the unemployment rate is associated with between a 17·1% and 44·7% increment in the odds of at least regional influenza (Odds ratio = 1·30). Results hold regardless of whether time‐varying state‐level characteristics are included. Conclusions  Higher state‐level unemployment increases the likelihood of regional and widespread influenza activity. PMID:21718460

  19. Identifying patients with chronic widespread pain in primary care

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2011-01-06

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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Weather, Chinook, and stroke occurrence.

    PubMed

    Field, Thalia S; Hill, Michael D

    2002-07-01

    Changes in weather and season have been linked to stroke occurrence. However, the association has been inconsistent across stroke types. Calgary is a city in the Chinook belt and is subject to high variability in weather conditions. We obtained hourly weather data over a 5-year period from 1996 to 2000; Chinook events were identified according to the accepted definition. We reviewed administrative data to determine stroke occurrence and defined stroke types to maximize specificity of diagnosis. To examine the hypothesis that weather affected the number of strokes occurring in a given day, we compared average daily stroke occurrence on Chinook days and non-Chinook days; we compared mean daily temperature, relative humidity, barometric pressure, and wind speed by the number of strokes occurring on any given day. Annual variation in stroke frequency was observed. No seasonal, monthly, or weekly variation in overall stroke occurrence or occurrence by type was evident. No relationship with changes in weather parameters was observed. We found no association between weather changes and stroke occurrence. A cause-and-effect relationship between weather and stroke occurrence is dubious because of a lack of consistency across studies.

  7. 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.

  8. Insecure attachment style is associated with chronic widespread pain

    PubMed Central

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

    2009-01-01

    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

  9. 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.

  10. 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.

  11. 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.

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

    PubMed Central

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

    2016-01-01

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

  13. A WIDESPREAD B CHROMOSOME POLYMORPHISM MAINTAINED WITHOUT APPARENT DRIVE.

    PubMed

    Lopez-Leon, M D; Cabrero, J; Camacho, J P M; Cano, M I; Santos, J L

    1992-04-01

    The transmission rates of the three main types of B chromosome present in the grasshopper Eyprepocnemis plorans were studied by two different methods: (i) cytological observation of their meiotic behavior in males and females and (ii) karyological analysis of the embryo offspring obtained either from gravid females collected in the field or from controlled crosses. We conclude that Bs are inherited in a random manner with no tendency toward accumulation or loss from either sex. The possible factors that might be responsible for the maintenance of this widespread polymorphism are discussed. © 1992 The Society for the Study of Evolution.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

    Martin, Michael D.

    2016-01-01

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

  16. 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.

  17. 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

  18. Widespread methanotrophic primary production in lowland chalk rivers.

    PubMed

    Shelley, Felicity; Grey, Jonathan; Trimmer, Mark

    2014-05-22

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

  19. Widespread effects of alcohol on white matter microstructure

    PubMed Central

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

    2014-01-01

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

  20. Tobacco Smoking Produces Widespread Dominant Brain Wave Alpha Frequency Increases

    PubMed Central

    Domino, Edward F.; Ni, Lisong; Thompson, Michael; Zhang, Huilea; Shikata, Hiroki; Fukai, Hiromi; Sakaki, Takeshi; Ohya, Ippei

    2009-01-01

    The major pharmacological ingredient in tobacco smoke is nicotine, a mild stimulant known to alter brain electrical activity. The object of this study was to determine if tobacco smoking in humans produces localized or widespread neocortical dominant alpha electroencephalographic (EEG) frequency increases consistent with nicotine stimulation of the brainstem activating system in animals. Twenty-two male volunteer non-deprived tobacco smokers were studied. They were asked not to smoke for at least 1 hr before the experiment in mid-morning as part of their usual smoking schedule. In the laboratory, they sham smoked and then smoked their favorite tobacco cigarette. Two experimental sessions (#1 and #2) were conducted, separated by a one to two month interval. In both sessions, there were minor statistically significant increases in the dominant alpha frequencies after sham smoking. In both sessions, after the subjects smoked a favorite tobacco cigarette there was a significant generalized increase in dominant alpha EEG frequencies in most scalp recording sites. This study demonstrates that tobacco smoking produces widespread bilateral neocortical increases in dominant alpha EEG frequencies consistent with the stimulant effects of nicotine on the brainstem reticular activating system. PMID:19765621

  1. 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.

  2. Occurrence of hemocyanin in ostracod crustaceans.

    PubMed

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

    2014-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed Central

    1987-01-01

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

  5. 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.

  6. Widespread Losses of Vomeronasal Signal Transduction in Bats

    PubMed Central

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

    2011-01-01

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

  7. Serologic Evidence of Widespread Everglades Virus Activity in Dogs, Florida

    PubMed Central

    Coffey, Lark L.; Crawford, Cynda; Dee, James; Miller, Ryan; Freier, Jerome

    2006-01-01

    Everglades virus (EVEV), an alphavirus in the Venezuelan equine encephalitis complex, circulates among rodents and vector mosquitoes in Florida and occasionally infects humans. It causes febrile disease, sometimes accompanied by neurologic manifestations. Although previous surveys showed high seroprevalence in humans, EVEV infections may be underdiagnosed because the disease is not severe enough to warrant a clinic visit or the undifferentiated presentations complicate diagnosis. Documented EVEV activity, as recent as 1993, was limited to south Florida. Using dogs as sentinels, a serosurvey was conducted to evaluate whether EVEV circulated recently in Florida and whether EVEV's spatial distribution parallels that of the mosquito vector, Culex cedecei. Four percent of dog sera contained neutralizing EVEV antibodies, and many seropositive animals lived farther north than both recorded EVEV activity and the principal vector. These results indicate that EVEV is widespread in Florida and may be an important, unrecognized cause of human illness. PMID:17326938

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

    USGS Publications Warehouse

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

    2011-01-01

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

  9. NASCENT-SEQ INDICATES WIDESPREAD COTRANSCRIPTIONAL RNA EDITING IN DROSOPHILA

    PubMed Central

    Rodriguez, Joseph; Menet, Jerome S.; Rosbash, Michael

    2012-01-01

    SUMMARY The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila, by isolating nascent RNA from adult fly heads and subjecting samples to high throughput sequencing. There are a large number of edited sites within nascent exons. Nascent RNA from an ADAR null mutant strain was also sequenced, indicating that almost all A-to-I events require ADAR. Moreover, mRNA editing levels correlate with editing levels within the cognate nascent RNA sequence, indicating that the extent of editing is set cotranscriptionally. Surprisingly, the nascent data also identify an excess of intronic over exonic editing sites. These intronic sites occur preferentially within introns that are poorly spliced cotranscriptionally, suggesting a link between editing and splicing. We conclude that ADAR-mediated editing is more widespread than previously indicated and largely occurs cotranscriptionally. PMID:22658416

  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. 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.

  12. Widespread Decrease of Nicotinic Acetylcholine Receptors in Parkinson's Disease

    PubMed Central

    Ichise, Masanori; Zoghbi, Sami S; Liow, Jeih-San; Ghose, Subroto; Vines, Douglass C; Sangare, Janet; Lu, Jian-Qiang; Cropley, Vanessa L; Iida, Hidehiro; Kim, Kyeong Min; Cohen, Robert M; Bara-Jimenez, William; Ravina, Bernard; Innis, Robert B

    2005-01-01

    Nicotinic acetylcholine receptors (nAChRs) have close interactions with the dopaminergic system and play critical roles in cognitive function. nAChRs were imaged in 10 non-demented Parkinson's disease (PD) patients and 15 age-matched healthy subjects using a single photon emission computed tomography ligand [123I]5-iodo-3-[2(S)-2-azetidinylmethoxy]pyridine. Using an arterial input function, we measured the total distribution volume (V; specific plus non-displaceable) as well as the delivery (K1). PD showed a widespread significant decrease (∼10%) of V in both cortical and subcortical regions without a significant change in K1. These results indicate the importance of extending the study to demented patients. PMID:16374823

  13. 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.

  14. Neurodegenerative diseases and widespread aggregation are associated with supersaturated proteins

    PubMed Central

    Ciryam, Prajwal; Tartaglia, Gian Gaetano; Morimoto, Richard I.; Dobson, Christopher M.; Vendruscolo, Michele

    2013-01-01

    Summary The maintenance of protein solubility is a fundamental aspect of protein homeostasis, as aggregation is associated with cytotoxicity and a variety of human diseases. Numerous proteins unrelated in sequence and structure, however, can misfold and aggregate, and widespread aggregation can occur in living systems under stress or ageing. A crucial question in this context is why only certain proteins aggregate in vivo while others do not. We identify here the proteins most vulnerable to aggregation as those whose cellular concentrations are high relative to their solubilities. These supersaturated proteins represent a metastable sub-proteome involved in pathological aggregation during stress and ageing, and are overrepresented in biochemical processes associated with neurodegenerative disorders. Consequently, such cellular processes become dysfunctional when the ability to keep intrinsically supersaturated proteins soluble is compromised. Thus, the simultaneous analysis of abundance and solubility can rationalize the diverse cellular pathologies linked to neurodegenerative diseases and aging. PMID:24183671

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

    PubMed Central

    de Freitas, Camila Fernanda Novak Pinheiro; 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. PMID:24068140

  16. 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

  17. Widespread and Indiscriminate Nanosilver Use: Genuine Potential for Microbial Resistance.

    PubMed

    Gunawan, Cindy; Marquis, Christopher P; Amal, Rose; Sotiriou, Georgios A; Rice, Scott A; Harry, Elizabeth J

    2017-04-25

    In this era of increasing antibiotic resistance, the use of alternative antimicrobials such as silver has become more widespread. Superior antimicrobial activity has been provided through fabrication of silver nanoparticles or nanosilver (NAg), which imparts cytotoxic actions distinct from those of bulk silver. In the wake of the recent discoveries of bacterial resistance to NAg and its rising incorporation in medical and consumer goods such as wound dressings and dietary supplements, we argue that there is an urgent need to monitor the prevalence and spread of NAg microbial resistance. In this Perspective, we describe how the use of NAg in commercially available products facilitates prolonged microorganism exposure to bioavailable silver, which underpins the development of resistance. Furthermore, we advocate for a judicial approach toward NAg use in order to preserve its efficacy and to avoid environmental disruption.

  18. Widespread movement of meltwater onto and across Antarctic ice shelves

    NASA Astrophysics Data System (ADS)

    Kingslake, Jonathan; Ely, Jeremy C.; Das, Indrani; Bell, Robin E.

    2017-04-01

    Surface meltwater drains across ice sheets, forming melt ponds that can trigger ice-shelf collapse, acceleration of grounded ice flow and increased sea-level rise. Numerical models of the Antarctic Ice Sheet that incorporate meltwater’s impact on ice shelves, but ignore the movement of water across the ice surface, predict a metre of global sea-level rise this century in response to atmospheric warming. To understand the impact of water moving across the ice surface a broad quantification of surface meltwater and its drainage is needed. Yet, despite extensive research in Greenland and observations of individual drainage systems in Antarctica, we have little understanding of Antarctic-wide surface hydrology or how it will evolve. Here we show widespread drainage of meltwater across the surface of the ice sheet through surface streams and ponds (hereafter ‘surface drainage’) as far south as 85° S and as high as 1,300 metres above sea level. Our findings are based on satellite imagery from 1973 onwards and aerial photography from 1947 onwards. Surface drainage has persisted for decades, transporting water up to 120 kilometres from grounded ice onto and across ice shelves, feeding vast melt ponds up to 80 kilometres long. Large-scale surface drainage could deliver water to areas of ice shelves vulnerable to collapse, as melt rates increase this century. While Antarctic surface melt ponds are relatively well documented on some ice shelves, we have discovered that ponds often form part of widespread, large-scale surface drainage systems. In a warming climate, enhanced surface drainage could accelerate future ice-mass loss from Antarctic, potentially via positive feedbacks between the extent of exposed rock, melting and thinning of the ice sheet.

  19. Widespread movement of meltwater onto and across Antarctic ice shelves.

    PubMed

    Kingslake, Jonathan; Ely, Jeremy C; Das, Indrani; Bell, Robin E

    2017-04-19

    Surface meltwater drains across ice sheets, forming melt ponds that can trigger ice-shelf collapse, acceleration of grounded ice flow and increased sea-level rise. Numerical models of the Antarctic Ice Sheet that incorporate meltwater's impact on ice shelves, but ignore the movement of water across the ice surface, predict a metre of global sea-level rise this century in response to atmospheric warming. To understand the impact of water moving across the ice surface a broad quantification of surface meltwater and its drainage is needed. Yet, despite extensive research in Greenland and observations of individual drainage systems in Antarctica, we have little understanding of Antarctic-wide surface hydrology or how it will evolve. Here we show widespread drainage of meltwater across the surface of the ice sheet through surface streams and ponds (hereafter 'surface drainage') as far south as 85° S and as high as 1,300 metres above sea level. Our findings are based on satellite imagery from 1973 onwards and aerial photography from 1947 onwards. Surface drainage has persisted for decades, transporting water up to 120 kilometres from grounded ice onto and across ice shelves, feeding vast melt ponds up to 80 kilometres long. Large-scale surface drainage could deliver water to areas of ice shelves vulnerable to collapse, as melt rates increase this century. While Antarctic surface melt ponds are relatively well documented on some ice shelves, we have discovered that ponds often form part of widespread, large-scale surface drainage systems. In a warming climate, enhanced surface drainage could accelerate future ice-mass loss from Antarctic, potentially via positive feedbacks between the extent of exposed rock, melting and thinning of the ice sheet.

  20. Widespread homologous recombination within and between Streptomyces species.

    PubMed

    Doroghazi, James R; Buckley, Daniel H

    2010-09-01

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

  1. Are Epigenetic Factors Implicated in Chronic Widespread Pain?

    PubMed Central

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

    2016-01-01

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

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Asakereh, Hossein; Shadman, Hassan

    2016-12-01

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

  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 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

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

    PubMed

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

    2017-04-15

    Our aim was to quantify microplastic ingestion by fish assemblages in two tropical Brazilian estuaries and to evaluate whether biological and ecological factors influence the ingestion of microplastics by fish species. Of 2233 fish from both estuaries (from 69 species) examined in this study, 9% of the individuals (24 species) had microplastics in their gut contents. Microplastic ingestion occurred irrespective of fish size and functional group. The diet of fish species was analyzed based on prey items identified in the fish's full stomach contents and five feeding guilds were defined. Microplastics were common throughout all feeding guilds. Low (average ingestion values 1.06±0.30 items/total fish) but widespread occurrence among estuaries also indicates proliferation of microplastic pollution. Our findings highlight the need to focus on assemblage level studies to understand the real magnitude of the problem and emphasize the urgency of mitigation measures directed at microplastic pollution in estuarine ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Glycolipids: Occurrence, Significance, and Properties

    NASA Astrophysics Data System (ADS)

    Holst, Otto

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

  9. 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.

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

    SciTech Connect

    Frostenson, C.K.

    1995-07-01

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

  11. 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

  12. Transient widespread cortical and splenial lesions in acute encephalitis/encephalopathy associated with primary Epstein-Barr virus infection.

    PubMed

    Zhang, Shuo; Feng, Juan; Shi, Yifang

    2016-01-01

    Infection with Epstein-Barr virus (EBV) is very common and usually occurs in childhood or early adulthood. Encephalitis/encephalopathy is an uncommon but serious neurological complication of EBV. A case of EBV-associated encephalitis/encephalopathy with involvement of reversible widespread cortical and splenial lesions is presented herein. An 8-year-old Chinese girl who presented with fever and headache, followed by seizures and drowsiness, was admitted to the hospital. Magnetic resonance imaging revealed high signal intensities on diffusion-weighted imaging in widespread cortical and splenial lesions. The clinical and laboratory examination results together with the unusual radiology findings suggested acute encephalitis/encephalopathy due to primary EBV infection. After methylprednisolone pulse therapy together with ganciclovir, the patient made a full recovery without any brain lesions. The hallmark clinical-radiological features of this patient included severe encephalitis/encephalopathy at onset, the prompt and complete recovery, and rapidly reversible widespread involvement of the cortex and splenium. Patients with EBV encephalitis/encephalopathy who have multiple lesions, even with the widespread involvement of cortex and splenium of the corpus callosum, may have a favorable outcome with complete disappearance of all brain lesions. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  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. First Natural Occurrence of Coesite.

    PubMed

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

    1960-07-22

    Coesite, the high-pressure polymorph of SiO(2), 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.

  15. 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; Technical Amendment AGENCY: Federal Aviation Administration... Fatigue Damage,'' (75 FR 69746). In that final rule the FAA revised the regulations pertaining to certification and operation of transport category airplanes to prevent widespread fatigue damage in...

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

    PubMed Central

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

    2013-01-01

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2013-01-01

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

  2. 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.

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

    PubMed

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

    2013-05-01

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

  4. Widespread tau seeding activity at early Braak stages.

    PubMed

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

    2017-01-01

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

  5. Recent Arctic tundra fire initiates widespread thermokarst development

    DOE PAGES

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

    2015-10-29

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

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

    PubMed

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

    2013-03-01

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

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

    PubMed Central

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

    2016-01-01

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

  8. Recent Arctic tundra fire initiates widespread thermokarst development

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  9. Widespread intron retention in mammals functionally tunes transcriptomes

    PubMed Central

    Pan, Qun; Nachman, Emil N.; Alipanahi, Babak; Gonatopoulos-Pournatzis, Thomas; Frey, Brendan

    2014-01-01

    Alternative splicing (AS) of precursor RNAs is responsible for greatly expanding the regulatory and functional capacity of eukaryotic genomes. Of the different classes of AS, intron retention (IR) is the least well understood. In plants and unicellular eukaryotes, IR is the most common form of AS, whereas in animals, it is thought to represent the least prevalent form. Using high-coverage poly(A)+ RNA-seq data, we observe that IR is surprisingly frequent in mammals, affecting transcripts from as many as three-quarters of multiexonic genes. A highly correlated set of cis features comprising an “IR code” reliably discriminates retained from constitutively spliced introns. We show that IR acts widely to reduce the levels of transcripts that are less or not required for the physiology of the cell or tissue type in which they are detected. This “transcriptome tuning” function of IR acts through both nonsense-mediated mRNA decay and nuclear sequestration and turnover of IR transcripts. We further show that IR is linked to a cross-talk mechanism involving localized stalling of RNA polymerase II (Pol II) and reduced availability of spliceosomal components. Collectively, the results implicate a global checkpoint-type mechanism whereby reduced recruitment of splicing components coupled to Pol II pausing underlies widespread IR-mediated suppression of inappropriately expressed transcripts. PMID:25258385

  10. 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

  11. 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.

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

    PubMed

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

    1993-02-01

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

  13. Widespread Distribution of Reticulon-3 in Various Neurodegenerative Diseases

    PubMed Central

    Heath, Jonathon E.; Siedlak, Sandra L.; Zhu, Xiongwei; Lee, Hyoung-gon; Thakur, Akanksha; Yan, Riqiang; Perry, George; Smith, Mark A.; Castellani, Rudy J.

    2010-01-01

    Reticulons are a group of membrane-bound proteins involved in diverse cellular functions, and are suggested to act as inhibitors of β-secretase enzyme 1 (BACE1) activity that cleaves amyloid precursor protein. Reticulons are known to accumulate in the dystrophic neurites of Alzheimer disease, and studies have suggested that alterations in reticulons, such as increased aggregation, impair BACE1 binding, increasing amyloid-β production, and facilitating reticulon deposition in dystrophic neurites. To further characterize the cellular distribution of reticulon, we examined reticulon-3 expression in cases of Alzheimer disease, Parkinson disease, and diffuse Lewy body disease. A more widespread cellular distribution of reticulon-3 was noted than in previous reports, including deposits in dystrophic neurites, neuropil threads, granulovacuolar degeneration, glial cells, morphologically normal neurons in both hippocampal pyramidal cell layer and cerebral neocortex, and specifically neurofibrillary tangles and Lewy bodies. These results are compatible with reticulon alterations as nonspecific downstream stress responses, consistent with its expression during periods of endoplasmic reticulum stress. This emphasizes the increasing recognition that much of the AD pathological spectrum represents a response to the disease rather than cause, and emphasizes the importance of examining upstream processes, such as oxidative stress, that have functional effects prior to the onset of structural alterations. PMID:20374499

  14. 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.

  15. Recent Arctic tundra fire initiates widespread thermokarst development

    SciTech Connect

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

    2015-10-29

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

  16. 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

  17. 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.

  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. Non-pharmacological treatment of chronic widespread musculoskeletal pain.

    PubMed

    Mannerkorpi, Kaisa; Henriksson, Chris

    2007-06-01

    Non-pharmacological treatment for patients with chronic widespread pain (CWP) and fibromyalgia (FM) aims to enhance overall health. This chapter reviews studies of exercise, education, movement therapies and sensory stimulation. Based on a systematic review of randomized controlled trials (RCTs), we suggest that aerobic exercise of low to moderate intensity, such as walking and pool exercise, can improve symptoms and distress in patients with CWP and FM, and it may improve physical capacity in sedentary patients. Aerobic exercise of moderate to high intensity has been shown to improve aerobic capacity and tender-point status. Educational programmes have been shown to enhance self-efficacy and health perception. There is no conclusive evidence about the type of educational programme that works best, but a small-group format and interactive discussions appear to be important components. Exercise combined with education appears to produce synergies. Studies of movement therapies (such as qigong) and sensory treatments (such as acupuncture and massage) are few in number. There is today no conclusive evidence about the effects of these treatments in CWP, although positive effects have been reported in a few studies.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

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

    PubMed

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

    2014-04-01

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

  6. Vertical transmission of fungal endophytes is widespread in forbs

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Bliddal, Henning; Danneskiold-Samsøe, Bente

    2007-06-01

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

  8. Widespread reductions in gray matter volume in depression☆

    PubMed Central

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

    2013-01-01

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

  9. Widespread 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.

  10. 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.

  11. The prevalence of widespread central hypersensitivity in chronic pain patients.

    PubMed

    Schliessbach, J; Siegenthaler, A; Streitberger, K; Eichenberger, U; Nüesch, E; Jüni, P; Arendt-Nielsen, L; Curatolo, M

    2013-11-01

    Chronic pain is associated with generalized hypersensitivity and impaired endogenous pain modulation (conditioned pain modulation; CPM). Despite extensive research, their prevalence in chronic pain patients is unknown. This study investigated the prevalence and potential determinants of widespread central hypersensitivity and described the distribution of CPM in chronic pain patients. We examined 464 consecutive chronic pain patients for generalized hypersensitivity and CPM using pressure algometry at the second toe and cold pressor test. Potential determinants of generalized central hypersensitivity were studied using uni- and multivariate regression analyses. Prevalence of generalized central hypersensitivity was calculated for the 5th, 10th and 25th percentile of normative values for pressure algometry obtained by a previous large study on healthy volunteers. CPM was addressed on a descriptive basis, since normative values are not available. Depending on the percentile of normative values considered, generalized central hypersensitivity affected 17.5-35.3% of patients. 23.7% of patients showed no increase in pressure pain threshold after cold pressor test. Generalized central hypersensitivity was more frequent and CPM less effective in women than in men. Unclearly classifiable pain syndromes showed higher frequencies of generalized central hypersensitivity than other pain syndromes. Although prevalent in chronic pain, generalized central hypersensitivity is not present in every patient. An individual assessment is therefore required in order to detect altered pain processing. The broad basic knowledge about central hypersensitivity now needs to be translated into concrete clinical consequences, so that patients can be offered an individually tailored mechanism-based treatment. © 2013 European Federation of International Association for the Study of Pain Chapters.

  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. Widespread production of nonmicrobial greenhouse gases in soils.

    PubMed

    Wang, Bin; Lerdau, Manuel; He, Yongli

    2017-06-06

    Carbon dioxide (CO2 ), methane (CH4 ), and nitrous oxide (N2 O) are the three most important greenhouse gases (GHGs), and all show large uncertainties in their atmospheric budgets. Soils of natural and managed ecosystems play an extremely important role in modulating their atmospheric abundance. Mechanisms underlying the exchange of these GHGs at the soil-atmosphere interface are often assumed to be exclusively microbe-mediated (M-GHGs). We argue that it is a widespread phenomenon for soil systems to produce GHGs through nonmicrobial pathways (NM-GHGs) based on a review of the available evidence accumulated over the past half century. We find that five categories of mechanistic process, including photodegradation, thermal degradation, reactive oxidative species (ROS) oxidation, extracellular oxidative metabolism (EXOMET), and inorganic chemical reactions, can be identified as accounting for their production. These pathways are intricately coupled among themselves and with M-GHGs production and are subject to strong influences from regional and global change agents including, among others, climate warming, solar radiation, and alterations of atmospheric components. Preliminary estimates have suggested that NM-GHGs could play key roles in contributing to budgets of GHGs in the arid regions, whereas their global importance would be enhanced with accelerated global environmental changes. Therefore, more research should be undertaken, with a differentiation between NM-GHGs and M-GHGs, to further elucidate the underlying mechanisms, to investigate the impacts of various global change agents, and to quantify their contributions to regional and global GHGs budgets. These efforts will contribute to a more complete understanding of global carbon and nitrogen cycling and a reduction in the uncertainty of carbon-climate feedbacks in the Earth system. © 2017 John Wiley & Sons Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  15. Recent Widespread Tree Growth Decline Despite Increasing Atmospheric CO2

    PubMed Central

    Silva, Lucas C. R.; Anand, Madhur; Leithead, Mark D.

    2010-01-01

    Background The synergetic effects of recent rising atmospheric CO2 and temperature are expected to favor tree growth in boreal and temperate forests. However, recent dendrochronological studies have shown site-specific unprecedented growth enhancements or declines. The question of whether either of these trends is caused by changes in the atmosphere remains unanswered because dendrochronology alone has not been able to clarify the physiological basis of such trends. Methodology/Principal Findings Here we combined standard dendrochronological methods with carbon isotopic analysis to investigate whether atmospheric changes enhanced water use efficiency (WUE) and growth of two deciduous and two coniferous tree species along a 9° latitudinal gradient across temperate and boreal forests in Ontario, Canada. Our results show that although trees have had around 53% increases in WUE over the past century, growth decline (measured as a decrease in basal area increment – BAI) has been the prevalent response in recent decades irrespective of species identity and latitude. Since the 1950s, tree BAI was predominantly negatively correlated with warmer climates and/or positively correlated with precipitation, suggesting warming induced water stress. However, where growth declines were not explained by climate, WUE and BAI were linearly and positively correlated, showing that declines are not always attributable to warming induced stress and additional stressors may exist. Conclusions Our results show an unexpected widespread tree growth decline in temperate and boreal forests due to warming induced stress but are also suggestive of additional stressors. Rising atmospheric CO2 levels during the past century resulted in consistent increases in water use efficiency, but this did not prevent growth decline. These findings challenge current predictions of increasing terrestrial carbon stocks under climate change scenarios. PMID:20657763

  16. Recent widespread tree growth decline despite increasing atmospheric CO2.

    PubMed

    Silva, Lucas C R; Anand, Madhur; Leithead, Mark D

    2010-07-21

    The synergetic effects of recent rising atmospheric CO(2) and temperature are expected to favor tree growth in boreal and temperate forests. However, recent dendrochronological studies have shown site-specific unprecedented growth enhancements or declines. The question of whether either of these trends is caused by changes in the atmosphere remains unanswered because dendrochronology alone has not been able to clarify the physiological basis of such trends. Here we combined standard dendrochronological methods with carbon isotopic analysis to investigate whether atmospheric changes enhanced water use efficiency (WUE) and growth of two deciduous and two coniferous tree species along a 9 degrees latitudinal gradient across temperate and boreal forests in Ontario, Canada. Our results show that although trees have had around 53% increases in WUE over the past century, growth decline (measured as a decrease in basal area increment--BAI) has been the prevalent response in recent decades irrespective of species identity and latitude. Since the 1950s, tree BAI was predominantly negatively correlated with warmer climates and/or positively correlated with precipitation, suggesting warming induced water stress. However, where growth declines were not explained by climate, WUE and BAI were linearly and positively correlated, showing that declines are not always attributable to warming induced stress and additional stressors may exist. Our results show an unexpected widespread tree growth decline in temperate and boreal forests due to warming induced stress but are also suggestive of additional stressors. Rising atmospheric CO2 levels during the past century resulted in consistent increases in water use efficiency, but this did not prevent growth decline. These findings challenge current predictions of increasing terrestrial carbon stocks under climate change scenarios.

  17. 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

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

    SciTech Connect

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

    1994-05-01

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

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  1. Bioprospecting: evolutionary implications from a post-olmec pharmacopoeia and the relevance of widespread taxa.

    PubMed

    Leonti, Marco; Cabras, Stefano; Castellanos, Maria Eugenia; Challenger, Antony; Gertsch, Jürg; Casu, Laura

    2013-05-02

    "Nothing in biology makes sense except in the light of evolution" The historical legacy and relevance of ethnopharmacology in drug discovery is undisputed. Here we connect the parameters influencing the selection of plant derived medicines by human culture with the concept of evolution. In the present contribution we compare global data with local data and try to answer the questions, to what extent are the taxonomic clades included in indigenous pharmacopoeias associated with certain ailment groups, and to what extent can ecology and phylogeny, which we consider a proxy for chemical relatedness and convergence, account for the observed bias? We use an approximated chi-square test (χ(2)) to check for associations between 12 ethnomedical use-categories and 15 taxonomical clades. With cluster analyses we test for correlations between phylogeny and use-categories. We compare the 67 drug-productive families identified by Zhu et al. with the medicinal flora of the Popoluca and the APG database and compare our results with the phylogenetic target classes evidenced by Zhu et al. Furthermore, we compare the medicinal flora of the Popoluca with the world's weeds (cf. Holm et al.) and discuss our results in relation to anthropological rationales for plant selection. The null-hypothesis "species from the 15 taxonomic clades are selected proportionally to their share in the treatment of the twelve organ- and symptom-defined use-categories" is rejected. The cluster dendrogram for the clades shows that the use patterns are to a certain extent associated with Angiosperm phylogeny. With the occurrence of 53 families the 67 drug-productive families are overrepresented in the regional flora of the Popoluca. The importance of these families in terms of their share is even more pronounced with the medicinal flora holding around 70% of all individual Popoluca informant responses. The overall phylogenetic use pattern is influenced by both the inherent pharmacological properties, which

  2. 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

  3. 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

  4. 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.

  5. 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. © 2013 John Wiley & Sons Ltd.

  6. 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.

  7. 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.

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

    PubMed

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

    1992-07-22

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

  9. Climate-driven diversification in two widespread Galerida larks

    PubMed Central

    2008-01-01

    Background The major impact of Plio-Pleistocene climatic oscillations on the current genetic structure of many species is widely recognised but their importance in driving speciation remains a matter of controversies. In addition, since most studies focused on Europe and North America, the influence of many other biogeographic barriers such as the Sahara remains poorly understood. In this paper, climate-driven diversification was investigated by using a comparative phylogeographic approach in combination with phenotypic data in two avian species groups distributed on both sides of the deserts belt of Africa and Asia. In particular, we tested whether: 1) vicariance diversification events are concomitant with past climatic events; and 2) current ecological factors (using climate and competition as proxies) contribute to phenotypic divergence between allopatric populations. Results Mitochondrial and nuclear sequence data indicated that the crested and Thekla lark species groups diverged in the early Pliocene and that subsequent speciation events were congruent with major late Pliocene and Pleistocene climatic events. In particular, steep increase in aridity in Africa near 2.8 and 1.7 million years ago were coincident with two north-south vicariance speciation events mediated by the Sahara. Subsequent glacial cycles of the last million years seem to have shaped patterns of genetic variation within the two widespread species (G. cristata and G. theklae). The Sahara appears to have allowed dispersal from the tropical areas during climatic optima but to have isolated populations north and south of it during more arid phases. Phenotypic variation did not correlate with the history of populations, but was strongly influenced by current ecological conditions. In particular, our results suggested that (i) desert-adapted plumage evolved at least three times and (ii) variation in body size was mainly driven by interspecific competition, but the response to competition was

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

    PubMed

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

    2016-07-26

    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. The deep sea is among the largest known habitats and a critical cog in biogeochemical cycling but remains underexplored in its microbiology. Even more than is the case for its prokaryotic community, our knowledge of its viral component has remained limited by the paucity of information

  11. Sanukitoids Record the Onset of Widespread Neoarchean Supracrustal Recycling

    NASA Astrophysics Data System (ADS)

    Bjorkman, K. E.; Kemp, A. I.; Lu, Y. J.; McCuaig, T. C.; Hollings, P. N.

    2016-12-01

    The sudden appearance of sanukitoid magmatism marks a chemical and isotopic turning point in the late Archean. Petrogenetic models call for mixing between primitive and evolved sources to account for their enrichment in both compatible and incompatible elements. TTG melts and the mantle wedge are the most commonly cited end members, but previous study of oxygen isotopes hinted at a supracrustal contribution. Clarifying the nature of endmembers may illuminate the significance of this shift for crustal growth and geodynamics. Heavy oxygen isotope signatures in zircons from 15 sanukitoid intrusions across 4 terranes in the southwestern Superior Craton of Canada (average δ18Ozrc=6.6‰, extending to 7.4‰) unequivocally fingerprint a supracrustal contribution to the host magmas. This contrasts with the mantle-like oxygen of pre-collisional TTG magmatism. Hafnium isotopes measured in the same zircon domains are less radiogenic than the estimated Superior mantle at 2.7 Ga, with ɛHf ranging from +1.5 to +4.1. Hf-O isotope mixing models require <50% local Archean sediment (δ18OWR=10.6‰, ɛHf 1.5±1) addition to mantle peridotite. Within-sample isotope homogeneity indicates a well-mixed magma during zircon crystallisation. A correlation in ɛHf to local crust implies local sediment input or additional contamination by crustal assimilation. As the terranes are roughly parallel to the Kenoran Orogeny, the local Hf signature is unlikely to be derived from subducted sediments. Rather these data permit (i) extensive mixing of sediment melts with the mantle wedge followed by crustal assimilation, registering the onset of widespread erosion and subduction of sediments, or (ii) assimilation of local supracrustal rocks at depth, and by implication, late crustal overturn. These results are incongruent with the current paradigm for late Archaean magmatism, which links sanukitoid generation to extensive TTG metasomatism of the mantle. Sanukitoid emplacement thus records a

  12. Effects of urbanization on the occurrence of Batrachochytrium dendrobatidis: do urban environments provide refuge from the amphibian chytrid fungus?

    Treesearch

    Daniel Saenz; Taylor L. Hall; Matthew A. Kwiatkowski

    2015-01-01

    Batrachochytrium dendrobatidis (Bd) is a widespread pathogenic fungus that is known to cause the disease, chytridiomycosis, which can be lethal to many amphibians. We compared occurrence rates on spring peepers (Pseudacris crucifer) in urban and forested breeding sites in eastern Texas, USA. All study sites were at...

  13. Patch size but not short-term isolation influences occurrence of westslope cutthroat trout above human-made barriers

    Treesearch

    Douglas P. Peterson; Bruce E. Rieman; Dona L. Horan; Michael K. Young

    2014-01-01

    Habitat fragmentation in aquatic systems has led to widespread isolation of stream fishes. Metapopulation theory predicts that persistence is directly related to local patch size and its characteristics, but because these relationships tend to be taxon-specific, empirical data are important. We assembled 246 observations of occurrence of westslope cutthroat trout (WCT...

  14. Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages

    PubMed Central

    2013-01-01

    Background Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimicrobial susceptibility of isolates from a UK-wide survey of Campylobacter in retail poultry in 2001 and 2004–5 was investigated. The occurrence of phenotypes resistant to tetracycline, quinolones (ciprofloxacin and naladixic acid), erythromycin, chloramphenicol and aminoglycosides was quantified. This was compared with a phylogeny for these isolates based upon Multi Locus Sequence Typing (MLST) to investigate the pattern of antimicrobial resistance acquisition. Results Antimicrobial resistance was present in all lineage clusters, but statistical testing showed a non-random distribution. Erythromycin resistance was associated with Campylobacter coli. For all antimicrobials tested, resistant isolates were distributed among relatively distant lineages indicative of widespread acquisition. There was also evidence of clustering of resistance phenotypes within lineages; indicative of local expansion of resistant strains. Conclusions These results are consistent with the widespread acquisition of antimicrobial resistance among chicken associated Campylobacter isolates, either through mutation or horizontal gene transfer, and the expansion of these lineages as a proportion of the population. As Campylobacter are not known to multiply outside of the host and long-term carriage in humans is extremely infrequent in industrialized countries, the most likely location for the proliferation of resistant lineages is in farmed chickens. PMID:23855904

  15. DNA phosphorothioation is widespread and quantized in bacterial genomes

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  18. Identification of subgroups of patients with tension type headache with higher widespread pressure pain hyperalgesia.

    PubMed

    Fernández-de-Las-Peñas, César; Benito-González, Elena; Palacios-Ceña, María; Wang, Kelun; Castaldo, Matteo; Arendt-Nielsen, Lars

    2017-12-01

    Identification of subgroups of patients with different levels of sensitization and clinical features can help to identify groups at risk and the development of better therapeutic strategies. The aim of this study was to identify subgroups of patients with tension type headache (TTH) with different levels of sensitization, clinical pain features, and psychological outcomes. A total of 197 individuals with TTH participated. Headache intensity, frequency, and duration and medication intake were collected with a 4-weeks diary. Pressure pain thresholds were assessed bilaterally over the temporalis muscle, C5-C6 joint, second metacarpal and tibialis anterior muscle to determine widespread pressure pain hyperalgesia. The Hospital Anxiety and Depression Scale assessed anxiety and depression. The State-Trait Anxiety Inventory evaluated the state and trait levels of anxiety. The Headache Disability Inventory evaluated the burden of headache. Health-related quality of life was determined with the SF-36 questionnaire. Groups were considered as positive (three or more criteria) or negative (less than three criteria) on a clinical prediction rule: headache duration <8.5 h/day; headache frequency <5.5 days/week; bodily pain <47 and vitality <47.5. The ANCOVA revealed that subjects in group 1 (positive rule, n = 89) exhibited longer headache history, shorter headache duration, lower headache frequency, higher widespread pressure hyperalgesia, higher anxiety trait levels, and lower quality of life (all, P < 0.01) than those subjects within group 2 (negative rule, n = 108). Differences were similar between men and women. This study identified a subgroup of patients with TTH with higher sensitization, higher chronicity of headaches and worse quality of life but lower frequency and duration of headache episodes. This subgroup of individuals with TTH may need particular attention and specific therapeutic programs for avoiding potential chronification.

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

    PubMed

    Rohr, Jason R; Raffel, Thomas R

    2010-05-04

    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.

  20. Widespread pressure pain hypersensitivity and ultrasound imaging evaluation of abdominal area after colon cancer treatment.

    PubMed

    Sánchez-Jiménez, Antonio; Cantarero-Villanueva, Irene; Molina-Barea, Rocio; Fernández-Lao, Carolina; Galiano-Castillo, Noelia; Arroyo-Morales, Manuel

    2014-02-01

    To investigate the presence of widespread pressure pain sensitivity in cancer patients following partial colorectal resection in the abdominal and lower back area and to describe the presence of abnormalities in abdominal and lower back muscle morphology. Twenty colon cancer survivors (eight females, mean age 56.60 ± 7.76 years) and 20 matched healthy controls (10 females, mean age 54.22 ± 8.12 years) participated. Abdominal and lower back pain was assessed after undergoing surgery using a Visual Analogue Scale (VAS) and Brief Pain Inventory (BPI). Pressure pain thresholds (PPTs) were bilaterally assessed over the supraumbilical, infraumbilical, and lower back areas and the second metacarpal. Ultrasound imaging was used to measure the depth of the abdominal muscles, the width of the midline abdominal fascia and the width of the lumbar multifidus. Ten months after finishing oncological treatments, patients who underwent partial colorectal resection reported significantly higher pain levels in the low-back area (P = 0.003) but not in the abdominal area (P = 0.426) compared with the matched controls. After surgery, the colon patients reported significantly higher BPI-intensity (P < 0.001) and BPI-interference scores (P = 0.009) compared with the matched controls. An analysis of variance (ANOVA) revealed significant between-groups difference in dominant-side lumbar, supraumbilical and infraumbilical (P ≥ 0.01), and second-metacarpal (P < 0.05) PPT levels. A significant between-groups difference was found by the ANOVA in ultrasound imaging of the depth of the internal oblique muscle (F = 4.887, P = 0.035) but not in the other ultrasound imaging measurements. Ten months after oncology treatment, colon cancer survivors show widespread pressure pain muscle hyperalgesia and reduced depths of dominant-side internal oblique muscles compared with matched controls. Wiley Periodicals, Inc.

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

    USGS Publications Warehouse

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

    2003-01-01

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

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

    PubMed Central

    Rohr, Jason R.; Raffel, Thomas R.

    2010-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2014-02-07

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

  5. Widespread abundance of functional bacterial amyloid in mycolata and other gram-positive bacteria.

    PubMed

    Jordal, Peter Bruun; Dueholm, Morten Simonsen; Larsen, Poul; Petersen, Steen Vang; Enghild, Jan Johannes; Christiansen, Gunna; Højrup, Peter; Nielsen, Per Halkjaer; Otzen, Daniel Erik

    2009-06-01

    Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella, and the gram-positive organism Streptomyces coelicolor. Here we probed gram-positive bacteria with conformationally specific antibodies and revealed the existence of FuBA in 12 of 14 examined mycolata species, as well as six other distantly related species examined belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbriae, sometimes copious amounts of them, and in two cases large extracellular fibrils were also produced. In three cases, FuBA was revealed only after extensive removal of extracellular material by saponification, indicating that there is integrated attachment within the cellular envelope. Spores of species in the genera Streptomyces, Bacillus, and Nocardia were all coated with amyloids. FuBA was purified from Gordonia amarae (from the cell envelope) and Geodermatophilus obscurus, and they had the morphology, tinctorial properties, and beta-rich structure typical of amyloid. The presence of approximately 9-nm-wide amyloids in the cell envelope of G. amarae was visualized by transmission electron microscopy analysis. We conclude that amyloid is widespread among gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spore and the cellular envelope.

  6. Widespread Abundance of Functional Bacterial Amyloid in Mycolata and Other Gram-Positive Bacteria▿

    PubMed Central

    Jordal, Peter Bruun; Dueholm, Morten Simonsen; Larsen, Poul; Petersen, Steen Vang; Enghild, Jan Johannes; Christiansen, Gunna; Højrup, Peter; Nielsen, Per Halkjær; Otzen, Daniel Erik

    2009-01-01

    Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella, and the gram-positive organism Streptomyces coelicolor. Here we probed gram-positive bacteria with conformationally specific antibodies and revealed the existence of FuBA in 12 of 14 examined mycolata species, as well as six other distantly related species examined belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbriae, sometimes copious amounts of them, and in two cases large extracellular fibrils were also produced. In three cases, FuBA was revealed only after extensive removal of extracellular material by saponification, indicating that there is integrated attachment within the cellular envelope. Spores of species in the genera Streptomyces, Bacillus, and Nocardia were all coated with amyloids. FuBA was purified from Gordonia amarae (from the cell envelope) and Geodermatophilus obscurus, and they had the morphology, tinctorial properties, and β-rich structure typical of amyloid. The presence of approximately 9-nm-wide amyloids in the cell envelope of G. amarae was visualized by transmission electron microscopy analysis. We conclude that amyloid is widespread among gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spore and the cellular envelope. PMID:19395568

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

    PubMed Central

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

    2010-01-01

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

  8. 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

  9. 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

  10. Occurrence reporting and processing of operations information

    SciTech Connect

    1997-07-21

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

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

    PubMed

    Rignot, Eric; Jacobs, Stanley S

    2002-06-14

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

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

    SciTech Connect

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

    2008-07-01

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

  13. 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

  14. Substorm statistics: Occurrences and amplitudes

    SciTech Connect

    Borovsky, J.E.; Nemzek, R.J.

    1994-05-01

    The occurrences and amplitudes of substorms are statistically investigated with the use of three data sets: the AL index, the Los Alamos 3-satellite geosynchronous energetic-electron measurements, and the GOES-5 and -6 geosynchronous magnetic-field measurements. The investigation utilizes {approximately} 13,800 substorms in AL, {approximately} 1400 substorms in the energetic-electron flux, and {approximately} 100 substorms in the magnetic field. The rate of occurrence of substorms is determined as a function of the time of day, the time of year, the amount of magnetotail bending, the orientation of the geomagnetic dipole, the toward/away configuration of the IMF, and the parameters of the solar wind. The relative roles of dayside reconnection and viscous coupling in the production of substorms are assessed. Three amplitudes are defined for a substorms: the jump in the AL index, the peak of the >30-keV integral electron flux at geosynchronous orbit near midnight, and the angle of rotation of the geosynchronous magnetic field near midnight. The substorm amplitudes are statistically analyzed, the amplitude measurements are cross correlated with each other, and the substorm amplitudes are determined as functions of the solar-wind parameters. Periodically occurring and randomly occurring substorms are analyzed separately. The energetic-particle-flux amplitudes are consistent with unloading and the AL amplitudes are consistent with direct driving plus unloading.

  15. Ictal kissing: occurrence and etiology.

    PubMed

    Asadi-Pooya, Ali A; Fletman, Elizabeth W

    2017-02-01

    Ictal kissing is a rare semiological manifestation in patients with epilepsy. We tried to estimate its occurrence and characterize the underlying etiology. We retrospectively reviewed all video-EEG reports from Jefferson Comprehensive Epilepsy Center over a 12-year period (2004-2015) for the occurrence of the term "kiss". We then searched the electronic database PubMed on September 21, 2016 using the following search terms in the English language: "ictal" OR "seizure" OR "epilepsy" AND "kiss" OR "kissing". Relevant original studies were included. During the study period, 5133 patients were investigated in our epilepsy monitoring unit. One patient (0.02%) had one episode of documented ictal kissing. He had drug-resistant right mesial temporal lobe epilepsy. In total, five studies met the criteria for inclusion in the review. These studies described nine patients with drug-resistant focal epilepsy and ictal kissing behavior. Six out of ten patients with ictal kissing had hippocampal sclerosis. We add to the literature on ictal kissing by providing additional information on its frequency and etiology. The most common underlying etiology for ictal kissing is hippocampal sclerosis. However, this semiological ictal phenomenon is not pathognomonic for any etiology or localization.

  16. 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

  17. 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.

  18. A 3-year survey of Italian honey bee-collected pollen reveals widespread contamination by agricultural pesticides.

    PubMed

    Tosi, Simone; Costa, Cecilia; Vesco, Umberto; Quaglia, Giancarlo; Guido, Giovanni

    2017-09-29

    Honey bee (Apis mellifera L.) health is compromised by complex interactions between multiple stressors, among which pesticides play a major role. To better understand the extent of honey bee colonies' exposure to pesticides in time and space, we conducted a survey by collecting corbicular pollen from returning honey bee foragers in 53 Italian apiaries during the active beekeeping season of 3 subsequent years (2012-2014). Of 554 pollen samples analysed for pesticide residues, 62% contained at least one pesticide. The overall rate of multiresidual samples (38%) was higher than the rate of single pesticide samples (24%), reaching a maximum of 7 pesticides per sample (1%). Over 3years, 18 different pesticides were detected (10 fungicides and 8 insecticides) out of 66 analysed. Pesticide concentrations reached the level of concern for bee health (Hazard Quotient (HQ) higher than 1000) at least once in 13% of the apiaries and exceeded the thresholds of safety for human dietary intake (Acute Reference Dose (ARfD), the Acceptable Daily Intake (ADI), and the Maximum Residue Limit (MRL)) in 39% of the analysis. The pesticide which was most frequently detected was the insecticide chlorpyrifos (30% of the samples overall, exceeding ARfD, ADI, or MRL in 99% of the positive ones), followed by the fungicides mandipropamid (19%), metalaxyl (16%), spiroxamine (15%), and the neonicotinoid insecticide imidacloprid (12%). Imidacloprid had also the highest HQ level (5054, with 12% of its positive samples with HQ higher than 1000). This 3year survey provides further insights on the contamination caused by agricultural pesticide use on honey bee colonies. Bee-collected pollen is shown to be a valuable tool for environmental monitoring, and for the detection of illegal uses of pesticides. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  1. 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. Copyright © 2015 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  2. 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

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

    USDA-ARS?s Scientific Manuscript database

    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. ...

  4. 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

  5. Magnetic resonance microscopy and immunohistochemistry of the CNS of the mutant SOD murine model of ALS reveals widespread neural deficits.

    PubMed

    Petrik, M S; Wilson, J M B; Grant, S C; Blackband, S J; Tabata, R C; Shan, X; Krieger, C; Shaw, C A

    2007-01-01

    Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that primarily affects motor neurons and descending motor tracts of the CNS. We have evaluated the CNS of a murine model of familial ALS based on the over-expression of mutant human superoxide dismutase (mSOD; G93A) using magnetic resonance microscopy (MRM) and immunohistochemistry (IHC). Three-dimensional volumetric analysis was performed from 3D T2*-weighted images acquired at 17.6 T at isotropic resolutions of 40 mum. Compared to controls, mSOD mice had significant reductions in the volumes of total brain, substantia nigra, striatum, hippocampus, and internal capsule, with decreased cortical thickness in primary motor and somatosensory cortices. In the spinal cord, mSOD mice had significantly decreased volume of both the total grey and white matter; in the latter case, the volume change was confined to the dorsal white matter. Increased apoptosis, GFAP positive astrocytes, and/or activated microglia were observed in all those CNS regions that showed volume loss except for the hippocampus. The MRM findings in mSOD over-expressing mice are similar to data previously obtained from a model of ALS-parkinsonism dementia complex (ALS-PDC), in which neural damage occurred following a diet of washed cycad flour containing various neurotoxins. The primary difference between the two models involves a significantly greater decrease in spinal cord white matter volume in mSOD mice, perhaps reflecting variations in degeneration of the descending motor tracts. The extent to which several CNS structures are impacted in both murine models of ALS argues for a reevaluation of the nature of the pathogenesis of ALS since CNS structures involved in Parkinson's and Alzheimer's diseases appear to be affected as well.

  6. 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

  7. 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

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

    PubMed Central

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

    2013-01-01

    Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5′-complete cDNA sequencing with an integrated data analysis workflow, to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive data set that represents the first available developmental time-course of promoter usage. We found that >40% of developmentally expressed genes have at least two promoters and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes. PMID:22936248

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

    PubMed

    Martin, A P; Bermingham, E

    2000-06-07

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

  10. 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

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

    PubMed

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

    2013-01-01

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

  12. Veronica officinalis Product Authentication Using DNA Metabarcoding and HPLC-MS Reveals Widespread Adulteration with Veronica chamaedrys

    PubMed Central

    Raclariu, Ancuta C.; Mocan, Andrei; Popa, Madalina O.; Vlase, Laurian; Ichim, Mihael C.; Crisan, Gianina; Brysting, Anne K.; de Boer, Hugo

    2017-01-01

    Studying herbal products derived from local and traditional knowledge and their value chains is one of the main challenges in ethnopharmacology. The majority of these products have a long history of use, but non-harmonized trade and differences in regulatory policies between countries impact their value chains and lead to concerns over product efficacy, safety and quality. Veronica officinalis L. (common speedwell), a member of Plantaginaceae family, has a long history of use in European traditional medicine, mainly in central eastern Europe and the Balkans. However, no specified control tests are available either to establish the quality of derived herbal products or for the discrimination of its most common substitute, V. chamaedrys L. (germander speedwell). In this study, we use DNA metabarcoding and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS) to authenticate sixteen V. officinalis herbal products and compare the potential of the two approaches to detect substitution, adulteration and the use of unreported constituents. HPLC-MS showed high resolution in detecting phytochemical target compounds, but did not enable detection of specific plant species in the products. DNA metabarcoding detected V. officinalis in only 15% of the products, whereas it detected V. chamaedrys in 62% of the products. The results confirm that DNA metabarcoding can be used to test for the presence of Veronica species, and detect substitution and/or admixture of other Veronica species, as well as simultaneously detect all other species present. Our results confirm that none of the herbal products contained exactly the species listed on the label, and all included substitutes, contaminants or fillers. This study highlights the need for authentication of raw herbals along the value chain of these products. An integrative methodology can assess both the quality of herbal products in terms of target compound concentrations and species composition, as well as admixture and substitution with other chemical compounds and plants. PMID:28674497

  13. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.

    PubMed

    Byrne, Ashley; Beaudin, Anna E; Olsen, Hugh E; Jain, Miten; Cole, Charles; Palmer, Theron; DuBois, Rebecca M; Forsberg, E Camilla; Akeson, Mark; Vollmers, Christopher

    2017-07-19

    Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification. After benchmarking our approach, we analyse individual murine B1a cells using a custom multiplexing strategy. We identify thousands of unannotated transcription start and end sites, as well as hundreds of alternative splicing events in these B1a cells. We also identify hundreds of genes expressed across B1a cells that display multiple complex isoforms, including several B cell-specific surface receptors. Our results show that we can identify and quantify complex isoforms at the single cell level.

  14. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

    PubMed Central

    Byrne, Ashley; Beaudin, Anna E.; Olsen, Hugh E.; Jain, Miten; Cole, Charles; Palmer, Theron; DuBois, Rebecca M.; Forsberg, E. Camilla; Akeson, Mark; Vollmers, Christopher

    2017-01-01

    Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification. After benchmarking our approach, we analyse individual murine B1a cells using a custom multiplexing strategy. We identify thousands of unannotated transcription start and end sites, as well as hundreds of alternative splicing events in these B1a cells. We also identify hundreds of genes expressed across B1a cells that display multiple complex isoforms, including several B cell-specific surface receptors. Our results show that we can identify and quantify complex isoforms at the single cell level. PMID:28722025

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

    USDA-ARS?s Scientific Manuscript database

    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...

  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. Widespread endometriosis mimicking ovarian malignancy: a case report.

    PubMed

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

    2012-03-01

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

  18. 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.

  19. 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.

  20. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

    DOE PAGES

    Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar; ...

    2016-11-16

    Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded