WorldWideScience

Sample records for variation reveals relationships

  1. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)

    Genetic relationship among Musa genotypes revealed by microsatellite markers. NAP Abdullah, GB Saleh, ETS Putra, ZB Wahab. Abstract. A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect their genetic variation and to rule out duplicates among ...

  2. Genetic variation and geographical differentiation revealed using ...

    Indian Academy of Sciences (India)

    [Zhang L., Lu S., Sun D., and Peng J. 2015 Genetic variation and geographical differentiation revealed using ISSR markers in tung tree,. Vernicia fordii. J. Genet. 94, e5–e9. Online only: http://www.ias.ac.in/jgenet/OnlineResources/94/e5.pdf]. Introduction. Tung tree, Vernicia fordii is an oil-bearing woody plant species of ...

  3. Relationships between spatio-temporal environmental and genetic variation reveal an important influence of exogenous selection in a pupfish hybrid zone.

    Science.gov (United States)

    Carson, Evan W; Tobler, Michael; Minckley, W L; Ainsworth, Ryan J; Dowling, Thomas E

    2012-03-01

    The importance of exogenous selection in a natural hybrid zone between the pupfishes Cyprinodon atrorus and Cyprinodon bifasciatus was tested via spatio-temporal analyses of environmental and genetic change over winter, spring and summer for three consecutive years. A critical influence of exogenous selection on hybrid zone regulation was demonstrated by a significant relationship between environmental (salinity and temperature) and genetic (three diagnostic nuDNA loci) variation over space and time (seasons) in the Rio Churince system, Cuatro Ciénegas, Mexico. At sites environmentally more similar to parental habitats, the genetic composition of hybrids was stable and similar to the resident parental species, whereas complex admixtures of parental and hybrid genotypic classes characterized intermediate environments, as did the greatest change in allelic and genotypic frequencies across seasons. Within hybrids across the entire Rio Churince system, seasonal changes in allelic and genotypic frequencies were consistent with results from previous reciprocal transplant experiments, which showed C. bifasciatus to suffer high mortality (75%) when exposed to the habitat of C. atrorus in winter (extreme temperature lows and variability) and summer (abrupt salinity change and extreme temperature highs and variability). Although unconfirmed, the distributional limits of C. atrorus and C. atrorus-like hybrids appear to be governed by similar constraints (predation or competition). The argument favouring evolutionary significance of hybridization in animals is bolstered by the results of this study, which links the importance of exogenous selection in a contemporary hybrid zone between C. atrorus and C. bifasciatus to previous demonstration of the long-term evolutionary significance of environmental variation and introgression on the phenotypic diversification Cuatro Ciénegas Cyprinodon. © 2012 Blackwell Publishing Ltd.

  4. Long-term slip events in the Kanto district revealed from GNSS data during 1996—2011 and a relationship with variations in ocean bottom pressure

    Science.gov (United States)

    Tanaka, Y.; Yabe, S.; Ide, S.

    2016-12-01

    Recently, Mavrommatis et al. 2014 (MA2014 hereafter) reported that a long-term accelerative transient crustal deformation was occurring in eastern Japan before the 2011 M-9 earthquake. They revealed that the observed deformation could be explained by a fault slip on the plate boundary with depths of approximately 20—60 km where afterslip of the M-9 event was detected. Its characteristic time is at least 15 years, which is much longer than those of precursory deformations usually considered in numerical simulation and observation studies. The acceleration was more dominant below the Tohoku area, where the coseismic slip of the M-9 event was larger. In this study, GNSS data in the Kanto area were analyzed in detail and it was found that the acceleration was not necessarily uniform if seen at smaller spatial scales than in MA2014. The detrended GNSS data with co- and post-seismic deformations due to large earthquakes and published SSEs being removed showed i) a slower acceleration in north of Tokyo Bay during 1996—2000 (period A), ii) a deceleration over the same area during 2002—2006 (period B) and iii) a faster acceleration over northeast Kanto during 2007—2011 (period C). A result of slip inversion indicated that i) a fault slip on the plate boundary with the Philippine Sea Plate was more likely to cause the events during periods A and B because the observed displacement rate was parallel to the relative motion by the PHS to the continental plate. Similarly, a slip on the boundary with the Pacific Plate was more likely to generate the event during period C. If the slip during period A is ignored, our result is consistent with the result of MA2014 because amplitude and spatial scale of the slip during period C is larger. Temporal variations of these slips were well correlated with slip history predicted by a non-linear rock frictional law which considers combined effects of tides and non-tidal ocean bottom pressure (Tanaka et al. 2015). The same model can

  5. Phylogenomics reveals deep molluscan relationships.

    Science.gov (United States)

    Kocot, Kevin M; Cannon, Johanna T; Todt, Christiane; Citarella, Mathew R; Kohn, Andrea B; Meyer, Achim; Santos, Scott R; Schander, Christoffer; Moroz, Leonid L; Lieb, Bernhard; Halanych, Kenneth M

    2011-09-04

    Evolutionary relationships among the eight major lineages of Mollusca have remained unresolved despite their diversity and importance. Previous investigations of molluscan phylogeny, based primarily on nuclear ribosomal gene sequences or morphological data, have been unsuccessful at elucidating these relationships. Recently, phylogenomic studies using dozens to hundreds of genes have greatly improved our understanding of deep animal relationships. However, limited genomic resources spanning molluscan diversity has prevented use of a phylogenomic approach. Here we use transcriptome and genome data from all major lineages (except Monoplacophora) and recover a well-supported topology for Mollusca. Our results strongly support the Aculifera hypothesis placing Polyplacophora (chitons) in a clade with a monophyletic Aplacophora (worm-like molluscs). Additionally, within Conchifera, a sister-taxon relationship between Gastropoda and Bivalvia is supported. This grouping has received little consideration and contains most (>95%) molluscan species. Thus we propose the node-based name Pleistomollusca. In light of these results, we examined the evolution of morphological characters and found support for advanced cephalization and shells as possibly having multiple origins within Mollusca. © 2011 Macmillan Publishers Limited. All rights reserved

  6. Olivine-melt relationships and syneruptive redox variations in the 1959 eruption of K$\\bar{i}$lauea Volcano as revealed by XANES

    Energy Technology Data Exchange (ETDEWEB)

    Helz, R. T.; Cottrell, E.; Brounce, M. N.; Kelley, K. A.

    2017-03-01

    The 1959 summit eruption of K$\\bar{i}$lauea Volcano exhibited high lava fountains of gas-rich, primitive magma, containing olivine + chromian spinel in highly vesicular brown glass. Microprobe analysis of these samples shows that euhedral rims on olivine phenocrysts, in direct contact with glass, vary significantly in forsterite (Fo) content, at constant major-element melt composition, as do unzoned groundmass olivine crystals. Ferric/total iron (Fe+ 3/FeT)ratios for matrix and interstitial glasses, plus olivine-hosted glass inclusions in eight 1959 scoria samples have been determined by micro X-ray absorption near-edge structure spectroscopy (μ-XANES). These data show that much of the variation in Fo content reflects variation in oxidation state of iron in the melt, which varies with sulfur concentration in the glass and (locally) with proximity to scoria edges in contact with air. Data for 24 olivine-melt pairs in the better-equilibrated samples from later in the eruption show KD averaging 0.280 ± 0.03 for the exchange of Fe and Mg between olivine and melt, somewhat displaced from the value of 0.30 ± 0.03 given by Roeder and Emslie (1970). This may reflect the low SiO2 content of the 1959 magmas, which is lower than that in most K$\\bar{i}$lauea tholeiites. More broadly, we show the potential of μ-XANES and electron microprobe to revisit and refine the value of KD in natural systems.

  7. Olivine-melt relationships and syneruptive redox variations in the 1959 eruption of Kīlauea Volcano as revealed by XANES

    Science.gov (United States)

    Helz, Rosalind L.; Cottrell, Elizabeth; Brounce, Maryjo N.; Kelley, Katherine A.

    2017-01-01

    The 1959 summit eruption of Kīlauea Volcano exhibited high lava fountains of gas-rich, primitive magma, containing olivine + chromian spinel in highly vesicular brown glass. Microprobe analysis of these samples shows that euhedral rims on olivine phenocrysts, in direct contact with glass, vary significantly in forsterite (Fo) content, at constant major-element melt composition, as do unzoned groundmass olivine crystals. Ferric/total iron (Fe+ 3/FeT)ratios for matrix and interstitial glasses, plus olivine-hosted glass inclusions in eight 1959 scoria samples have been determined by micro X-ray absorption near-edge structure spectroscopy (μ-XANES). These data show that much of the variation in Fo content reflects variation in oxidation state of iron in the melt, which varies with sulfur concentration in the glass and (locally) with proximity to scoria edges in contact with air. Data for 24 olivine-melt pairs in the better-equilibrated samples from later in the eruption show KD averaging 0.280 ± 0.03 for the exchange of Fe and Mg between olivine and melt, somewhat displaced from the value of 0.30 ± 0.03 given by Roeder and Emslie (1970). This may reflect the low SiO2 content of the 1959 magmas, which is lower than that in most Kīlauea tholeiites. More broadly, we show the potential of μ-XANES and electron microprobe to revisit and refine the value of KD in natural systems.The observed variations of Fe+ 3/FeT ratios in the glasses reflect two distinct processes. The main process, sulfur degassing, produces steady decrease of the Fe+ 3/FeT ratio. Melt inclusions in olivine are high in sulfur (1060–1500 ppm S), with Fe+ 3/FeT = 0.160–0.175. Matrix glasses are degassed (mostly S < 200 ppm) with generally lower Fe+ 3/FeT(0.114–0.135). Interstitial glasses within clumps of olivine crystals locally show intermediate levels of sulfur and Fe+ 3/FeT ratio. The correlation suggests that (1) the 1959 magma was significantly reduced by sulfur

  8. Olivine-melt relationships and syneruptive redox variations in the 1959 eruption of Kīlauea Volcano as revealed by XANES

    Science.gov (United States)

    Helz, R. T.; Cottrell, E.; Brounce, M. N.; Kelley, K. A.

    2017-03-01

    The 1959 summit eruption of Kīlauea Volcano exhibited high lava fountains of gas-rich, primitive magma, containing olivine + chromian spinel in highly vesicular brown glass. Microprobe analysis of these samples shows that euhedral rims on olivine phenocrysts, in direct contact with glass, vary significantly in forsterite (Fo) content, at constant major-element melt composition, as do unzoned groundmass olivine crystals. Ferric/total iron (Fe+ 3/FeT)ratios for matrix and interstitial glasses, plus olivine-hosted glass inclusions in eight 1959 scoria samples have been determined by micro X-ray absorption near-edge structure spectroscopy (μ-XANES). These data show that much of the variation in Fo content reflects variation in oxidation state of iron in the melt, which varies with sulfur concentration in the glass and (locally) with proximity to scoria edges in contact with air. Data for 24 olivine-melt pairs in the better-equilibrated samples from later in the eruption show KD averaging 0.280 ± 0.03 for the exchange of Fe and Mg between olivine and melt, somewhat displaced from the value of 0.30 ± 0.03 given by Roeder and Emslie (1970). This may reflect the low SiO2 content of the 1959 magmas, which is lower than that in most Kīlauea tholeiites. More broadly, we show the potential of μ-XANES and electron microprobe to revisit and refine the value of KD in natural systems. The observed variations of Fe+ 3/FeT ratios in the glasses reflect two distinct processes. The main process, sulfur degassing, produces steady decrease of the Fe+ 3/FeT ratio. Melt inclusions in olivine are high in sulfur (1060-1500 ppm S), with Fe+ 3/FeT = 0.160-0.175. Matrix glasses are degassed (mostly S glasses within clumps of olivine crystals locally show intermediate levels of sulfur and Fe+ 3/FeT ratio. The correlation suggests that (1) the 1959 magma was significantly reduced by sulfur degassing during the eruption and (2) the melts originally had Fe+ 3/FeT ≥ 0.175, consistent with

  9. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum.

    Directory of Open Access Journals (Sweden)

    Xiuqing Zhang

    Full Text Available Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1-3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality

  10. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum

    Science.gov (United States)

    Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

    2017-01-01

    Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1–3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the

  11. Applications of Pharmacogenetics in Revealing Variations in ...

    African Journals Online (AJOL)

    acer

    In the past two decades many drugs were discovered through the developments taking place in molecular biology techniques. Drug action is now more defined. In addition to known pharmacogenetic variations on drug metabolism, variations in drug targets are also emerging. These targets include receptors, transporters,.

  12. Applications of Pharmacogenetics in Revealing Variations in ...

    African Journals Online (AJOL)

    This review article presents the latest findings of genetic variations in pharmacological targets related to disorders of major systems such as central nervous system, cardiovascular system, and the respiratory system especially in relation to asthma and the HLA antigen genotype in hypersensitivity reactions. East and Central ...

  13. Ruler arrays reveal haploid genomic structural variation.

    Directory of Open Access Journals (Sweden)

    P Alexander Rolfe

    Full Text Available Despite the known relevance of genomic structural variants to pathogen behavior, cancer, development, and evolution, certain repeat based structural variants may evade detection by existing high-throughput techniques. Here, we present ruler arrays, a technique to detect genomic structural variants including insertions and deletions (indels, duplications, and translocations. A ruler array exploits DNA polymerase's processivity to detect physical distances between defined genomic sequences regardless of the intervening sequence. The method combines a sample preparation protocol, tiling genomic microarrays, and a new computational analysis. The analysis of ruler array data from two genomic samples enables the identification of structural variation between the samples. In an empirical test between two closely related haploid strains of yeast ruler arrays detected 78% of the structural variants larger than 100 bp.

  14. Comparative RNA sequencing reveals substantial genetic variation in endangered primates

    Science.gov (United States)

    Perry, George H.; Melsted, Páll; Marioni, John C.; Wang, Ying; Bainer, Russell; Pickrell, Joseph K.; Michelini, Katelyn; Zehr, Sarah; Yoder, Anne D.; Stephens, Matthew; Pritchard, Jonathan K.; Gilad, Yoav

    2012-01-01

    Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of nonhuman primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerel's sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success. PMID:22207615

  15. Relationships among transforms, convolutions, and first variations

    Directory of Open Access Journals (Sweden)

    Jeong Gyoo Kim

    1999-01-01

    Full Text Available In this paper, we establish several interesting relationships involving the Fourier-Feynman transform, the convolution product, and the first variation for functionals F on Wiener space of the form F(x=f(〈α1,x〉,…,〈αn,x〉,                                                      (* where 〈αj,x〉 denotes the Paley-Wiener-Zygmund stochastic integral ∫0Tαj(tdx(t.

  16. Molecular variation in Cucumis melo as revealed by isoenzyme and ...

    African Journals Online (AJOL)

    Molecular variation in Cucumis melo as revealed by isoenzyme and RAPD markers. Tarek M Mohamed. Abstract. No Abstract. The Egyptian Journal of Biochemistry and Molecular Biology Vol. 23(2) 2005: 141-153. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT ...

  17. Revealing Relationships: First Graders Share Personal Literature

    Science.gov (United States)

    Weih, Timothy G.

    2014-01-01

    Literature holds the potential to significantly influence the lives of readers, but what is the nature of this influence for very young readers? This study investigated the question: What are the relationships between beginning readers and their personal literature? A first grade class of 18 students individually assembled a collection of personal…

  18. Cnidarian phylogenetic relationships as revealed by mitogenomics.

    Science.gov (United States)

    Kayal, Ehsan; Roure, Béatrice; Philippe, Hervé; Collins, Allen G; Lavrov, Dennis V

    2013-01-09

    Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in

  19. Cnidarian phylogenetic relationships as revealed by mitogenomics

    Science.gov (United States)

    2013-01-01

    Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that

  20. Transcriptomic variation in a coral reveals pathways of clonal organisation

    DEFF Research Database (Denmark)

    K Bay, Line; Nielsen, Henrik Bjørn; Jarmer, Hanne Østergaard

    2009-01-01

    A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base......) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5 x 10(-4)). These genes are associated with energy...... of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239 x 10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or levels...

  1. Genetic variations and evolutionary relationships among radishes ...

    African Journals Online (AJOL)

    To determine the genetic diversity and evolutionary relationships among red radishes, 37 accessions with different flesh colors were analyzed in terms of the red pigment content, karyotypes, and simple sequence repeat markers. Red pigment content of red radish was 3.4 to 28.8% with an average of 15.62%. The karyotype ...

  2. Variations in Wounding by Relationship Intimacy in Homicide Cases

    Science.gov (United States)

    Trojan, Carrie; Krull, Amy C.

    2012-01-01

    There are numerous examples in the homicide literature of a presumed connection between the victim-offender relationship and the manner, extent, and body location of wounds inflicted in homicides. The current study examined variations in wounding patterns according to the intimacy of the victim-offender relationship in a sample of urban homicides…

  3. Population genetic variation in sainfoin (Fabaceae) revealed by RAPD markers

    OpenAIRE

    Houshang NOSRATI; Mohammad Ali Hosseinpour FEIZI; Sona Seyed TARRAH; Ahmad Razban HAGHIGHI

    2012-01-01

    Studies on plants show that populations growing on the stressful environments indicate higher levels of genetic diversity, and that in outcrossing species majority of total genetic variation allocated to within population rather than between populations. We compared the level of genetic variation between populations growing in stressful and normal environments, and measured levels of within- and between population genetic variations in Onobrychis viciifolia L. (Sainfoin, Fabaceae) based on RA...

  4. Relationship between Indian and East Asian summer rainfall variations

    Science.gov (United States)

    Wu, Renguang

    2017-01-01

    The Indian and East Asian summer monsoons are two components of the whole Asian summer monsoon system. Previous studies have indicated in-phase and out-of-phase variations between Indian and East Asian summer rainfall. The present study reviews the current understanding of the connection between Indian and East Asian summer rainfall. The review covers the relationship of northern China, southern Japan, and South Korean summer rainfall with Indian summer rainfall; the atmospheric circulation anomalies connecting Indian and East Asian summer rainfall variations; the long-term change in the connection between Indian and northern China rainfall and the plausible reasons for the change; and the influence of ENSO on the relationship between Indian and East Asian summer rainfall and its change. While much progress has been made about the relationship between Indian and East Asian summer rainfall variations, there are several remaining issues that need investigation. These include the processes involved in the connection between Indian and East Asian summer rainfall, the non-stationarity of the connection and the plausible reasons, the influences of ENSO on the relationship, the performance of climate models in simulating the relationship between Indian and East Asian summer rainfall, and the relationship between Indian and East Asian rainfall intraseasonal fluctuations.

  5. Population genetic variation in sainfoin (Fabaceae revealed by RAPD markers

    Directory of Open Access Journals (Sweden)

    Houshang NOSRATI

    2012-05-01

    Full Text Available Studies on plants show that populations growing on the stressful environments indicate higher levels of genetic diversity, and that in outcrossing species majority of total genetic variation allocated to within population rather than between populations. We compared the level of genetic variation between populations growing in stressful and normal environments, and measured levels of within- and between population genetic variations in Onobrychis viciifolia L. (Sainfoin, Fabaceae based on RAPDs. Our results show that populations growing on he stressful environment i.e. saline soils indicated either the lowest 0.2466 or highest (0.3186 within-population genetic variation based on Nei’s diversity. That disagrees with Niche-Width Variation Theory, which expects highest genetic diversity within stressful populations. Partitioning the total genetic variation by analysis of molecular variance (AMOVA showed that 89.03% of total genetic diversity allocated to within populations while 10.97% of this variation dedicated to among populations, indicating predominantly outcrossing mode of pollination in sainfoin. The two population pairs growing under similar environmental stresses (cold climate and saline soil showed higher genetic similarity. This may suggest that RAPDs patterns reflex selection rather than random drift.

  6. Genetic relationships revealed by simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    Genetic relationships revealed by simple sequence repeat (SSR) markers among Ghanaian cassava cultivars released by different research groups. ... Genetic diversity was observed within populations (HS = 0.552) and, therefore, suggesting a low rate of inter-population gene flow among the individuals constituting the ...

  7. Identifying geographical variations in poverty-obesity relationships: empirical evidence from Taiwan

    Directory of Open Access Journals (Sweden)

    Tzai-Hung Wen

    2010-05-01

    Full Text Available There is an increasing interest in the relationship between area-based disadvantage and obesity but the extent to which the poverty-obesity relationship remains constant across geographical areas remains unclear. We examined geographical variations in the relationship between poverty and obesity in Taiwan using geographically weighted regression (GWR. A representative sample of 27,293 Taiwanese adults (21 to 64 years old from 262 townships was obtained from the 2001 Social Development Trend Survey on Health and Safety (SDSHS in Taiwan. GWR revealed that there were local variations in the poverty-obesity relationship and that poverty was only significantly associated with obesity in less-developed areas. Significant relationship between poverty and obesity was found only in less-developed areas, suggesting that the impact of poverty on obesity is area-specific.

  8. Variation and inter-relationship, between yield and, some agronomic ...

    African Journals Online (AJOL)

    Variation and inter-relationship, between yield and, some agronomic characters in induced rice ( Oryza sativa L.) mutants. ... Twenty three mutant lines in M5 and M6 generations plus two controls were sown in a randomised complete Block Design (RCBD) and replicated three times at the Sokoine University of Agriculture ...

  9. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

    Science.gov (United States)

    Ventura, Mario; Catacchio, Claudia R.; Alkan, Can; Marques-Bonet, Tomas; Sajjadian, Saba; Graves, Tina A.; Hormozdiari, Fereydoun; Navarro, Arcadi; Malig, Maika; Baker, Carl; Lee, Choli; Turner, Emily H.; Chen, Lin; Kidd, Jeffrey M.; Archidiacono, Nicoletta; Shendure, Jay; Wilson, Richard K.; Eichler, Evan E.

    2011-01-01

    Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes. PMID:21685127

  10. SSR markers reveal genetic variation between improved cassava ...

    African Journals Online (AJOL)

    Five SSR primers that have PIC values between 0.50 and 0.67 were selected and further assessed using simple arithmetic progression combination method. The results obtained revealed a combination of these 5 primers from SSR primers collection at IITA that could readily distinguish the 36 cassava genotypes at 0.93 ...

  11. Molar macrowear reveals Neanderthal eco-geographic dietary variation.

    Directory of Open Access Journals (Sweden)

    Luca Fiorenza

    Full Text Available Neanderthal diets are reported to be based mainly on the consumption of large and medium sized herbivores, while the exploitation of other food types including plants has also been demonstrated. Though some studies conclude that early Homo sapiens were active hunters, the analyses of faunal assemblages, stone tool technologies and stable isotopic studies indicate that they exploited broader dietary resources than Neanderthals. Whereas previous studies assume taxon-specific dietary specializations, we suggest here that the diet of both Neanderthals and early Homo sapiens is determined by ecological conditions. We analyzed molar wear patterns using occlusal fingerprint analysis derived from optical 3D topometry. Molar macrowear accumulates during the lifespan of an individual and thus reflects diet over long periods. Neanderthal and early Homo sapiens maxillary molar macrowear indicates strong eco-geographic dietary variation independent of taxonomic affinities. Based on comparisons with modern hunter-gatherer populations with known diets, Neanderthals as well as early Homo sapiens show high dietary variability in Mediterranean evergreen habitats but a more restricted diet in upper latitude steppe/coniferous forest environments, suggesting a significant consumption of high protein meat resources.

  12. Molar Macrowear Reveals Neanderthal Eco-Geographic Dietary Variation

    Science.gov (United States)

    Fiorenza, Luca; Benazzi, Stefano; Tausch, Jeremy; Kullmer, Ottmar; Bromage, Timothy G.; Schrenk, Friedemann

    2011-01-01

    Neanderthal diets are reported to be based mainly on the consumption of large and medium sized herbivores, while the exploitation of other food types including plants has also been demonstrated. Though some studies conclude that early Homo sapiens were active hunters, the analyses of faunal assemblages, stone tool technologies and stable isotopic studies indicate that they exploited broader dietary resources than Neanderthals. Whereas previous studies assume taxon-specific dietary specializations, we suggest here that the diet of both Neanderthals and early Homo sapiens is determined by ecological conditions. We analyzed molar wear patterns using occlusal fingerprint analysis derived from optical 3D topometry. Molar macrowear accumulates during the lifespan of an individual and thus reflects diet over long periods. Neanderthal and early Homo sapiens maxillary molar macrowear indicates strong eco-geographic dietary variation independent of taxonomic affinities. Based on comparisons with modern hunter-gatherer populations with known diets, Neanderthals as well as early Homo sapiens show high dietary variability in Mediterranean evergreen habitats but a more restricted diet in upper latitude steppe/coniferous forest environments, suggesting a significant consumption of high protein meat resources. PMID:21445243

  13. Doctor shopping reveals geographical variations in opioid abuse.

    Science.gov (United States)

    Nordmann, Sandra; Pradel, Vincent; Lapeyre-Mestre, Maryse; Frauger, Elisabeth; Pauly, Vanessa; Thirion, Xavier; Mallaret, Michel; Jouanjus, Emilie; Micallef, Joëlle

    2013-01-01

    results confirm important variations in the 3 French regions despite them being geographically close. Besides, they highlight different rates of opioid abuse between opioids for mild to moderate pain, opioids for moderately severe to severe pain, and opioid maintenance treatments, as well as differences within these groups.

  14. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

    OpenAIRE

    Wei Tong; Qiang He; Yong-Jin Park

    2017-01-01

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucle...

  15. The reciprocal relationship between competition and intraspecific trait variation

    DEFF Research Database (Denmark)

    A Bennett, Jonathan; Riibak, Kersti; Tamme, Riin

    2016-01-01

    tested how traits from different competitive environments influenced potential community assembly inferences. 3.The competitive environment had large effects on species’ traits, although many effects were species-specific. Differences among species in how competition affected trait expression was linked......1.Trait differences among plants are expected to influence the outcome of competition; competition should be strongest between similar species (or individuals) under limiting similarity, and between dissimilar species within competitive hierarchies. These hypotheses are often used to infer...... competitive dynamics from trait patterns within communities. However, plant traits are frequently plastic in response to competition. This variation is poorly accounted for in trait based studies of competition and community assembly. 2.To explore the relationship between trait responses and competitive...

  16. Nuclear microsatellite variation in Malagasy baobabs (Adansonia, Bombacoideae, Malvaceae) reveals past hybridization and introgression.

    Science.gov (United States)

    Leong Pock Tsy, Jean-Michel; Lumaret, Roselyne; Flaven-Noguier, Elodie; Sauve, Mathieu; Dubois, Marie-Pierre; Danthu, Pascal

    2013-12-01

    Adansonia comprises nine species, six of which are endemic to Madagascar. Genetic relationships between the Malagasy species remain unresolved due to conflicting results between nuclear and plastid DNA variation. Morphologically intermediate individuals between distinct species have been identified, indicative of interspecific hybridization. In this paper, microsatellite data are used to identify potential cases of hybridization and to provide insights into the evolutionary history of the genus on Madagascar. Eleven microsatellites amplified with new primers developed for Adansonia rubrostipa were used to analyse 672 individuals collected at 27 sites for the six Malagasy species and morphologically intermediate individuals. Rates of individual admixture were examined using three Bayesian clustering programs, STRUCTURE, BAPS and NewHybrids, with no a priori species assignment. Population differentiation was coherent, with recognized species boundaries. In the four Malagasy species of section Longitubae, 8·0, 9·0 and 9·5 % of individuals with mixed genotypes were identified by BAPS, NewHybrids and STRUCTURE, respectively. At sites with sympatric populations of A. rubrostipa and A. za, NewHybrids indicated these individuals to be F2 and, predominantly, backcrosses with both parental species. In northern Madagascar, two populations of trees combining A. za and A. perrieri morphology and microsatellite alleles were identified in the current absence of the parental species. The clear genetic differentiation observed between the six species may reflect their adaptation to different assortments of climate regimes and habitats during the colonization of the island. Microsatellite variation reveals that hybridization probably occurred in secondary contact between species of section Longitubae. This type of hybridization may also have been involved in the differentiation of a local new stabilized entity showing specific microsatellite alleles and morphological characters

  17. Genetic architecture of trout from Albania as revealed by mtDNA control region variation

    Science.gov (United States)

    2009-01-01

    To determine the genetic architecture of trout in Albania, 87 individuals were collected from 19 riverine and lacustrine sites in Albania, FYROM and Greece. All individuals were analyzed for sequence variation in the mtDNA control region. Among fourteen haplotypes detected, four previously unpublished haplotypes, bearing a close relationship to haplotypes of the Adriatic and marmoratus lineages of Salmo trutta, were revealed. Ten previously described haplotypes, characteristic of S. ohridanus, S. letnica and the Adriatic and Mediterranean lineages of S. trutta, were also detected. Haplotypes detected in this study were placed in a well supported branch of S. ohridanus, and a cluster of Mediterranean – Adriatic – marmoratus haplotypes, which were further delimited into three subdivisions of Mediterranean, marmoratus, and a previously non-described formation of four Adriatic haplotypes (Balkan cluster). Haplotypes of the Balkan cluster and the other Adriatic haplotypes, do not represent a contiguous haplotype lineage and appear not to be closely related, indicating independent arrivals into the Adriatic drainage and suggesting successive colonization events. Despite the presence of marmoratus haplotypes in Albania, no marbled phenotype was found, confirming previously reported findings that there is no association between this phenotype and marmoratus haplotypes. PMID:19284692

  18. Small-scale density variations in the lunar crust revealed by GRAIL

    Science.gov (United States)

    Jansen, J. C.; Andrews-Hanna, J. C.; Li, Y.; Lucey, P. G.; Taylor, G. J.; Goossens, S.; Lemoine, F. G.; Mazarico, E.; Head, J. W.; Milbury, C.; Kiefer, W. S.; Soderblom, J. M.; Zuber, M. T.

    2017-07-01

    Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that ∼98% of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2% of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10‧s of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by ± 10% over scales ranging from centimeters to 100‧s of kilometers.

  19. Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs

    NARCIS (Netherlands)

    Kappe, A.L.; van de Zande, L.; Vedder, E.J.; Bijlsma, R.; van Delden, Wilke

    Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands.

  20. Power graph compression reveals dominant relationships in genetic transcription networks.

    Science.gov (United States)

    Ahnert, Sebastian E

    2013-11-01

    We introduce a framework for the discovery of dominant relationship patterns in transcription networks, by compressing the network into a power graph with overlapping power nodes. Our application of this approach to the transcription networks of S. cerevisiae and E. coli, paired with GO term enrichment analysis, provides a highly informative overview of the most prominent relationships in the gene regulatory networks of these two organisms.

  1. Autosomal STR variations reveal genetic heterogeneity in the Mon-Khmer speaking group of Northern Thailand.

    Science.gov (United States)

    Kampuansai, Jatupol; Völgyi, Antónia; Kutanan, Wibhu; Kangwanpong, Daoroong; Pamjav, Horolma

    2017-03-01

    Since prehistoric times, Mon-Khmer speaking people have been recognized as indigenous ethnic groups living in northern Thailand. After the period of Tai colonization in the thirteenth century CE, the Mon-Khmer inhabitants were fragmented; some were expelled to rural areas while some were integrated into the mainstream of Tai society. Autosomal STR variations revealed that the present-day Mon-Khmer people could be genetically divided into two clusters. This finding appears to be consistent with the level of historical contact with the Tai majority ethnic groups. The cluster consisting of the Khamu, Lua, Paluang and Htin people, indicate that they have lived in remote areas and have had little historical contact with the Tai people. In this way, they appeared to have maintained aspects of their Mon-Khmer ancestral genetic bloodline but have genetically diverged from the Tai people. The cluster comprised of the Mon and Lawa people had an exclusively close relationship with the Tai people during the establishment of the prosperous Lan Na Kingdom. A fraction of the Tai genetic component investigated among the Mon people and some Lawa populations reflected the evidence of genetic admixture. However, some Lawa people, who have lived in the mountainous area of Mae Hong Son Province have exhibited a unique gene pool, which might have been shaped by the founder effect that occurred during their historical fragmentation. The rise of the genetic assimilation of the hill-tribe Karen people into the Mon-Khmer and the Tai gene pools indicated that different languages, cultures, and geographical distances have lost their power as barriers of inter-ethnic marriages in the present day. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. Phylogenetic Relationships in Actinidia as Revealed by RAPD Analysis

    Science.gov (United States)

    Hongwen Huang; Zuozhou Li; Jianqiang Li; Thomas L. Kubiisiak; Desmond R. Lavne

    2002-01-01

    Phylogenetic relationships within the Actinidia were investigated using randomly amplified polymorphic DNA (RAPD) markers. DNAs from 10 taxa, including31 species encompassing all four sections and four series of the traditional subdivisions within the genus, were amplified using 22 preselected 10-mer oligonucieotide primers. A total 204 DNA bands...

  3. Genetic relationship of a cucumber germplasm collection revealed ...

    Indian Academy of Sciences (India)

    c Indian Academy of Sciences. ONLINE RESOURCES. Genetic relationship of a ... cultivated vegetables, ranked fourth after tomato, onion and cabbage (Pitrat et al. 1999). It originates from India, and. China is .... Biosoft International, California, USA), primers were de- signed flanking the SSRs and allowed to generate PCR ...

  4. Genomic Mining Reveals Deep Evolutionary Relationships between Bornaviruses and Bats

    Directory of Open Access Journals (Sweden)

    Jie Cui

    2015-11-01

    Full Text Available Bats globally harbor viruses in order Mononegavirales, such as lyssaviruses and henipaviruses; however, little is known about their relationships with bornaviruses. Previous studies showed that viral fossils of bornaviral origin are embedded in the genomes of several mammalian species such as primates, indicative of an ancient origin of exogenous bornaviruses. In this study, we mined the available 10 bat genomes and recreated a clear evolutionary relationship of endogenous bornaviral elements and bats. Comparative genomics showed that endogenization of bornaviral elements frequently occurred in vesper bats, harboring EBLLs (endogenous bornavirus-like L elements in their genomes. Molecular dating uncovered a continuous bornavirus-bat interaction spanning 70 million years. We conclude that better understanding of modern exogenous bornaviral circulation in bat populations is warranted.

  5. Phylogenetic relationships within Aglaopheniidae (Cnidaria, Hydrozoa) reveal unexpected generic diversity

    OpenAIRE

    Postaire, Bautisse; Magalon, Hélène; Bourmaud, Chloé A.-F.,; Gravier-Bonnet, Nicole; Bruggemann, Henrich J.

    2015-01-01

    International audience; Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner-Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive struct...

  6. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

    Science.gov (United States)

    Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W.; Grubert, Fabian; Candille, Sophie I.; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L.; Tang, Hua; Ricci, Emiliano; Snyder, Michael P.

    2015-01-01

    Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy—many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. PMID:26297486

  7. Fronto-parietal network oscillations reveal relationship between working memory capacity and cognitive control

    NARCIS (Netherlands)

    Gulbinaite, R.; van Rijn, H.; Cohen, M.X.

    2014-01-01

    Executive-attention theory proposes a close relationship between working memory capacity (WMC) and cognitive control abilities. However, conflicting results are documented in the literature, with some studies reporting that individual variations in WMC predict differences in cognitive control and

  8. Variation in Carbohydrates between Cancer and Normal Cell Membranes Revealed by Super?Resolution Fluorescence Imaging

    OpenAIRE

    Chen, Junling; Liu, Tianzhou; Gao, Jing; Gao, Lan; Zhou, Lulu; Cai, Mingjun; Shi, Yan; Xiong, Wenyong; Jiang, Junguang; Tong, Ti; Wang, Hongda

    2016-01-01

    Carbohydrate alterations on cell membranes are associated with various cancer processes, including tumorigenesis, malignant transformation, and tumor dissemination. However, variations in the distributions of cancer?associated carbohydrates are unclear at the molecular level. Herein, direct stochastic optical reconstruction microscopy is used to reveal that seven major types of carbohydrates tended to form obvious clusters on cancer cell membranes compared with normal cell membranes (both cul...

  9. Identifying and explicating variation among friends with benefits relationships.

    Science.gov (United States)

    Mongeau, Paul A; Knight, Kendra; Williams, Jade; Eden, Jennifer; Shaw, Christina

    2013-01-01

    This two-study report identifies and validates a typology containing seven types of "friends with benefits relationships" (FWBRs). Study 1 asked heterosexual students to define the term FWBR and to describe their experience with the relationship type. Qualitative analysis of these data identified seven types of FWBRs (true friends, network opportunism, just sex, three types of transition in [successful, failed, and unintentional], and transition out). Study 2 quantitatively differentiates these relationship types in the amount of nonsexual interaction, strength of the friendship at the first sexual interaction, and history of romantic relationships with the FWBR partner (before the FWBR, after it, or both). Results from both studies clearly suggest that FWBRs represent a diverse set of relationship formulations where both the benefits (i.e., repeated sexual contact) and the friends (i.e., relationship between partners) vary widely. In many cases, FWBRs represent a desire for, or an attempt at, shifting the relationship from friends to a romantic partnership. Other implications are discussed, as are limitations and directions for future research. The diverse nature of FWBRs provides challenges for researchers that likely require multiple methods and theoretical frames.

  10. Stable isotopes reveal ecotypic variation of water uptake patterns in Aleppo pine

    Science.gov (United States)

    Ferrio, Juan Pedro; Lucabaugh, Devon; Chambel, Regina; Voltas, Jordi

    2014-05-01

    Aleppo pine (Pinus halepensis Mill.) has a large natural distribution range that encompasses a multitude of thermal and moisture conditions found in the Mediterranean basin. We hypothesized that due to the recurrent incidences of drought stress and high temperatures that occur at varying degrees along its distribution range, populations of Aleppo pine have undergone ecotypic differentiation in soil water uptake patterns. This study analyzed stable isotopic compositions (δ18O and δ2H) of xylem water to identify adaptive divergence associated to the pattern of soil water consumption by roots of Aleppo pine populations originating from the Mediterranean region. The results from this study show that genetic diversity in the extraction pattern of soil water can be found among populations and ecological regions of Aleppo pine under common garden conditions. However, the ability to detect such differences depended on the period of the year examined. In particular, data collection in full summer (end of July) proved to be the most adequate in revealing genetic divergence among populations, while end of spring and, to a lesser extent, end of summer, were less successful for this purpose. Both water uptake patterns (as estimated by δ18O and δ2H) and above-ground growth, exhibited significant relationships with both climatic and geographical variables. This suggests that the underlying variation among populations can be explained by certain characteristics at origin. In addition, we used a bayesian mixing model (SIAR package for R) that incorporated isotopic signatures from xylem and soil water in order to determine the predominant soil layer of water source consumption at the aforementioned periods of the growing season, where water availably ranged from lowest to highest. This allowed us to gain some understanding of Aleppo pines' differential reaction to drought, at the intraspecific level, across the fluctuating conditions of the growing season by comparing the

  11. Revealing Relationships among Relevant Climate Variables with Information Theory

    Science.gov (United States)

    Knuth, Kevin H.; Golera, Anthony; Curry, Charles T.; Huyser, Karen A.; Kevin R. Wheeler; Rossow, William B.

    2005-01-01

    The primary objective of the NASA Earth-Sun Exploration Technology Office is to understand the observed Earth climate variability, thus enabling the determination and prediction of the climate's response to both natural and human-induced forcing. We are currently developing a suite of computational tools that will allow researchers to calculate, from data, a variety of information-theoretic quantities such as mutual information, which can be used to identify relationships among climate variables, and transfer entropy, which indicates the possibility of causal interactions. Our tools estimate these quantities along with their associated error bars, the latter of which is critical for describing the degree of uncertainty in the estimates. This work is based upon optimal binning techniques that we have developed for piecewise-constant, histogram-style models of the underlying density functions. Two useful side benefits have already been discovered. The first allows a researcher to determine whether there exist sufficient data to estimate the underlying probability density. The second permits one to determine an acceptable degree of round-off when compressing data for efficient transfer and storage. We also demonstrate how mutual information and transfer entropy can be applied so as to allow researchers not only to identify relations among climate variables, but also to characterize and quantify their possible causal interactions.

  12. Variations in crowding, saccadic precision, and spatial localization reveal the shared topology of spatial vision.

    Science.gov (United States)

    Greenwood, John A; Szinte, Martin; Sayim, Bilge; Cavanagh, Patrick

    2017-04-25

    Visual sensitivity varies across the visual field in several characteristic ways. For example, sensitivity declines sharply in peripheral (vs. foveal) vision and is typically worse in the upper (vs. lower) visual field. These variations can affect processes ranging from acuity and crowding (the deleterious effect of clutter on object recognition) to the precision of saccadic eye movements. Here we examine whether these variations can be attributed to a common source within the visual system. We first compared the size of crowding zones with the precision of saccades using an oriented clock target and two adjacent flanker elements. We report that both saccade precision and crowded-target reports vary idiosyncratically across the visual field with a strong correlation across tasks for all participants. Nevertheless, both group-level and trial-by-trial analyses reveal dissociations that exclude a common representation for the two processes. We therefore compared crowding with two measures of spatial localization: Landolt-C gap resolution and three-dot bisection. Here we observe similar idiosyncratic variations with strong interparticipant correlations across tasks despite considerably finer precision. Hierarchical regression analyses further show that variations in spatial precision account for much of the variation in crowding, including the correlation between crowding and saccades. Altogether, we demonstrate that crowding, spatial localization, and saccadic precision show clear dissociations, indicative of independent spatial representations, whilst nonetheless sharing idiosyncratic variations in spatial topology. We propose that these topological idiosyncrasies are established early in the visual system and inherited throughout later stages to affect a range of higher-level representations.

  13. Interannual variations of total ozone and their relationship to variations of planetary wave activity

    Energy Technology Data Exchange (ETDEWEB)

    Fusco, A.C. (Univ. of Colorado, Boulder, CO (United States). Center for Atmospheric Theory and Analysis); Salby, M.L. (Bureau of Meteorology Research Centre, Melbourne, Victoria (Australia))

    1999-06-01

    Interannual variations of total ozone at midlatitudes of the Northern Hemisphere are shown to operate coherently wit h variations of upwelling planetary wave activity from the troposphere. Variations of upwelling wave activity, which modulate ozone transport and chemical production by the diabatic mean circulation of the stratosphere, account for much of the interannual variance of total ozone, including its systematic decline during the 1980s. Chemical depletion, enhanced by increasing halocarbon levels, accounts for the remainder of the midlatitude trend, consistent with values widely reported by chemical models that do not account for observed changes in upwelling planetary wave activity. Much of the chemical contribution comes from sharply enhanced depletion following the eruption of Mt. Pinatubo, during the final years of the satellite record. Incomplete representation of the 3--5-yr recovery toward normal aerosol and ozone after Pinatubo appears to distort the trend inferred from the overall satellite record to values that are unrepresentative of the rest of the record. The impact on ozone of interannual changes of upwelling planetary wave activity is evaluated in calculations with a three-dimensional model of stratospheric dynamics and photochemistry, which reproduce the magnitude and structure of observed interannual variations.

  14. The Relationship between MC1R Mutation and Plumage Color Variation in Pigeons

    Directory of Open Access Journals (Sweden)

    Jin-Shan Ran

    2016-01-01

    Full Text Available The polymorphisms of MC1R gene play a crucial role in coat color variation in mammals; however, the relationship is still unclear in pigeons. In this study, we sequenced 741 bp fragment of the MC1R for 39 individuals with five plumage color patterns (gray plumage, n=12; black plumage, n=9; white plumage, n=3; spotted plumage, n=12; red plumage, n=3. A total of three single nucleotide polymorphisms (SNPs were detected, including G199A, G225A, and A466G, which subsequently determined four haplotypes (H1–H4. Among them, H1 is the predominant haplotype. Association analysis revealed that H1 and H3 were significantly associated with the black plumage trait (P<0.05, while the H4 was significantly associated with gray plumage trait (P<0.05. Furthermore, only diplotype H1H1 was significantly associated with black and gray traits of pigeons. Collectively, our study suggested an association between genetic variation of MC1R and plumage color in pigeon.

  15. Variations in the origin of inferior phrenic arteries and their relationship to celiac axis variations on CT angiography

    Energy Technology Data Exchange (ETDEWEB)

    Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal [Dept. of Radiology, Tepecik Training and Research Hospital, Izmir (Turkmenistan); Toka, Onur [Dept. of Statistics, Hacettepe University, Ankara (Turkmenistan)

    2017-04-15

    Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18–94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation.

  16. Variations in the Origin of Inferior Phrenic Arteries and Their Relationship to Celiac Axis Variations on CT Angiography.

    Science.gov (United States)

    Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal; Toka, Onur

    2017-01-01

    Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18-94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation.

  17. Spatial and temporal variation of total electron content as revealed by principal component analysis

    Science.gov (United States)

    Talaat, Elsayed R.; Zhu, Xun

    2016-11-01

    Eleven years of global total electron content (TEC) data derived from the assimilated thermosphere-ionosphere electrodynamics general circulation model are analyzed using empirical orthogonal function (EOF) decomposition and the corresponding principal component analysis (PCA) technique. For the daily averaged TEC field, the first EOF explains more than 89 % and the first four EOFs explain more than 98 % of the total variance of the TEC field, indicating an effective data compression and clear separation of different physical processes. The effectiveness of the PCA technique for TEC is nearly insensitive to the horizontal resolution and the length of the data records. When the PCA is applied to global TEC including local-time variations, the rich spatial and temporal variations of field can be represented by the first three EOFs that explain 88 % of the total variance. The spectral analysis of the time series of the EOF coefficients reveals how different mechanisms such as solar flux variation, change in the orbital declination, nonlinear mode coupling and geomagnetic activity are separated and expressed in different EOFs. This work demonstrates the usefulness of using the PCA technique to assimilate and monitor the global TEC field.

  18. Intraspecific genetic variation in Paramecium revealed by mitochondrial cytochrome C oxidase I sequences.

    Science.gov (United States)

    Barth, Dana; Krenek, Sascha; Fokin, Sergei I; Berendonk, Thomas U

    2006-01-01

    Studies of intraspecific genetic diversity of ciliates, such as population genetics and biogeography, are particularly hampered by the lack of suitable DNA markers. For example, sequences of the non-coding ribosomal internal transcribed spacer (ITS) regions are often too conserved for intraspecific analyses. We have therefore identified primers for the mitochondrial cytochrome c oxidase I (COI) gene and applied them for intraspecific investigations in Paramecium caudatum and Paramecium multimicronucleatum. Furthermore, we obtained sequences of the ITS regions from the same strains and carried out comparative sequence analyses of both data sets. The mitochondrial sequences revealed substantially higher variation in both Paramecium species, with intraspecific divergences up to 7% in P. caudatum and 9.5% in P. multimicronucleatum. Moreover, an initial survey of the population structure discovered different mitochondrial haplotypes of P. caudatum in one pond, thereby demonstrating the potential of this genetic marker for population genetic analyses. Our primers successfully amplified the COI gene of other Paramecium. This is the first report of intraspecific variation in free-living protozoans based on mitochondrial sequence data. Our results show that the high variation in mitochondrial DNA makes it a suitable marker for intraspecific and population genetic studies.

  19. Metabolomics reveals variation and correlation among different tissues of olive (Olea europaea L.).

    Science.gov (United States)

    Guodong, Rao; Xiaoxia, Liu; Weiwei, Zha; Wenjun, Wu; Jianguo, Zhang

    2017-09-15

    Metabolites in olives are associated with nutritional value and physiological properties. However, comprehensive information regarding the olive metabolome is limited. In this study, we identified 226 metabolites from three different tissues of olive using a non-targeted metabolomic profiling approach, of which 76 named metabolites were confirmed. Further statistical analysis revealed that these 76 metabolites covered different types of primary metabolism and some of the secondary metabolism pathways. One-way analysis of variance (ANOVA) statistical assay was performed to calculate the variations within the detected metabolites, and levels of 65 metabolites were differentially expressed in different samples. Hierarchical cluster analysis (HCA) dendrograms showed variations among different tissues that were similar to the metabolite profiles observed in new leaves and fruit. Additionally, 5776 metabolite-metabolite correlations were detected by a Pearson correlation coefficient approach. Screening of the calculated correlations revealed 3136, 3025, and 5184 were determined to metabolites and had significant correlations in three different combinations, respectively. This work provides the first comprehensive metabolomic of olive, which will provide new insights into understanding the olive metabolism, and potentially help advance studies in olive metabolic engineering. © 2017. Published by The Company of Biologists Ltd.

  20. Metabolomics reveals variation and correlation among different tissues of olive (Olea europaea L.

    Directory of Open Access Journals (Sweden)

    Rao Guodong

    2017-09-01

    Full Text Available Metabolites in olives are associated with nutritional value and physiological properties. However, comprehensive information regarding the olive metabolome is limited. In this study, we identified 226 metabolites from three different tissues of olive using a non-targeted metabolomic profiling approach, of which 76 named metabolites were confirmed. Further statistical analysis revealed that these 76 metabolites covered different types of primary metabolism and some of the secondary metabolism pathways. One-way analysis of variance (ANOVA statistical assay was performed to calculate the variations within the detected metabolites, and levels of 65 metabolites were differentially expressed in different samples. Hierarchical cluster analysis (HCA dendrograms showed variations among different tissues that were similar to the metabolite profiles observed in new leaves and fruit. Additionally, 5776 metabolite-metabolite correlations were detected by a Pearson correlation coefficient approach. Screening of the calculated correlations revealed 3136, 3025, and 5184 were determined to metabolites and had significant correlations in three different combinations, respectively. This work provides the first comprehensive metabolomic of olive, which will provide new insights into understanding the olive metabolism, and potentially help advance studies in olive metabolic engineering.

  1. Structural variations in prefrontal cortex mediate the relationship between early childhood stress and spatial working memory

    National Research Council Canada - National Science Library

    Hanson, Jamie L; Chung, Moo K; Avants, Brian B; Rudolph, Karen D; Shirtcliff, Elizabeth A; Gee, James C; Davidson, Richard J; Pollak, Seth D

    2012-01-01

    .... Analysis of variations in brain structure revealed that cumulative life stress and spatial working memory were related to smaller volumes in the PFC, specifically prefrontal gray and white matter...

  2. Peritonsillar abscess: epidemiology and relationship with climate variations.

    Science.gov (United States)

    Freire, G S M; Dos Santos, J H Z; Rolón, P A; Pinheiro, G B; Sampaio, A L L

    2017-07-01

    Peritonsillar abscess is the most common deep infection of the head and neck in young adults. It is considered a purulent complication of acute tonsillitis, but other mechanisms have been proposed. There is no consensus as to whether seasonality affects peritonsillar abscess incidence. This observational, descriptive, retrospective study explored the epidemiology of peritonsillar abscess and its relationship with seasonality. The cases were selected from the emergency otolaryngology service of a tertiary hospital. The sample comprised 528 patients (42.61 per cent males, mean age = 26.63 years). A moderate positive correlation was found between peritonsillar abscess incidence and monthly average temperature. No associations were found with insolation, precipitation or humidity. In this sample, peritonsillar abscess was more likely to occur in warmer months. The findings corroborate the theory that peritonsillar abscess is not a direct complication of acute tonsillitis and may improve understanding of peritonsillar abscess aetiology.

  3. Latitudinal and seasonal variations of lower atmospheric inertial gravity wave energy revealed by US radiosonde data

    Directory of Open Access Journals (Sweden)

    S. D. Zhang

    2010-05-01

    Full Text Available The latitudinal and seasonal variations of gravity wave (GW potential energy density (EP, kinetic energy density (EK, and total energy density (ET, i.e, the sum of potential and kinetic energy densities in the tropospheric (typically 2–10 km and lower stratospheric (typically 18–25 km segments have been derived from 10 years (1998–2007 of radiosonde observations over 92 United States stations in the Northern Hemisphere. The latitudinal variation of EP in the lower stratosphere is in good agreement with satellite observations. However, EK and ET in the lower stratosphere are different from satellite observations and the difference is believed to be linked with the latitudinal dependence of GW sources. Our analysis reveals that GW energy properties exhibit distinctive latitudinal and seasonal variations. The upward-propagating GW energy in the troposphere is larger than that in the lower stratosphere at low latitudes but the opposite holds true at high latitudes. The transition latitude, where the upward- propagating energies in the two altitude regions are the same, occurs at 35° N throughout the year. So striking differences between GW activity in the troposphere and lower stratosphere are not likely explained only by the background wind Doppler shifting due to strong tropospheric jets. Our analysis indicates that the region around tropopause, roughly from 10 km to 18 km, is an important source region, especially at latitudes below 35° N. Our studies strongly suggest that in order to fully understand the global GW activity in the lower atmosphere, the GW kinetic energy and its geographical and seasonal variations should be included, and more attention should be given to GWs in the troposphere and GW sources within the intermediate region, especially the upper troposphere.

  4. Taxonomic variation in size-density relationships challenges the notion of energy equivalence

    OpenAIRE

    Isaac, Nick J. B.; Storch, David; Carbone, Chris

    2011-01-01

    The relationship between body mass and abundance is a major focus for research in macroecology. The form of this relationship has been suggested to reflect the partitioning of energy among species. We revisit classical datasets to show that size–density relationships vary systematically among taxonomic groups, with most variation occurring at the order level. We use this knowledge to make a novel test of the ‘energy equivalence rule’, at the taxonomic scale appropriate for the data. We find n...

  5. Illumina based whole mitochondrial genome of Junonia iphita reveals minor intraspecific variation

    Directory of Open Access Journals (Sweden)

    Catherine Vanlalruati

    2015-12-01

    Full Text Available In the present study, the near complete mitochondrial genome (mitogenome of Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae was determined to be 14,892 bp. The gene order and orientation are identical to those in other butterfly species. The phylogenetic tree constructed from the whole mitogenomes using the 13 protein coding genes (PCGs defines the genetic relatedness of the two J. iphita species collected from two different regions. All the Junonia species clustered together, and were further subdivided into clade one consisting of J. almana and J. orithya and clade two comprising of the two J. iphita which were collected from Indo and Indochinese subregions separated by river barrier. Comparison between the two J. iphita sequences revealed minor variations and Single Nucleotide Polymorphisms were identified at 51 sites amounting to 0.4% of the entire mitochondrial genome.

  6. Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)

    Science.gov (United States)

    Oliver, Rebekah E.; Islamovic, Emir; Obert, Donald E.; Wise, Mitchell L.; Herrin, Lauri L.; Hang, An; Harrison, Stephen A.; Ibrahim, Amir; Marshall, Juliet M.; Miclaus, Kelci J.; Lazo, Gerard R.; Hu, Gongshe; Jackson, Eric W.

    2014-01-01

    Tocochromanols are recognized for nutritional content, plant stress response, and seed longevity. Here we present a systems biological approach to characterize and develop predictive assays for genes affecting tocochromanol variation in barley. Major QTL, detected in three regions of a SNP linkage map, affected multiple tocochromanol forms. Candidate genes were identified through barley/rice orthology and sequenced in genotypes with disparate tocochromanol profiles. Gene-specific markers, designed based on observed polymorphism, mapped to the originating QTL, increasing R2 values at the respective loci. Polymorphism within promoter regions corresponded to motifs known to influence gene expression. Quantitative PCR analysis revealed a trend of increased expression in tissues grown at cold temperatures. These results demonstrate utility of a novel method for rapid gene identification and characterization, and provide a resource for efficient development of barley lines with improved tocochromanol profiles. PMID:24820172

  7. A first glimpse of wild lupin karyotype variation as revealed by comparative cytogenetic mapping

    Directory of Open Access Journals (Sweden)

    Karolina Susek

    2016-07-01

    Full Text Available Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n=32-52, basic chromosome numbers (x=5-7, 9, 13 and in nuclear genome size (2C DNA=0.97-2.68 pg. Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution.In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all ‘single-locus’ in L. angustifolius, in the wild lupins these clones proved to be ‘single-locus’, ‘single-locus’ with additional signals, ‘repetitive’ or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g. L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the

  8. A First Glimpse of Wild Lupin Karyotype Variation As Revealed by Comparative Cytogenetic Mapping.

    Science.gov (United States)

    Susek, Karolina; Bielski, Wojciech K; Hasterok, Robert; Naganowska, Barbara; Wolko, Bogdan

    2016-01-01

    Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins (OWL) demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n = 32-52), basic chromosome numbers (x = 5-7, 9, 13) and in nuclear genome size (2C DNA = 0.97-2.68 pg). Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution. In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all "single-locus" in L. angustifolius, in the wild lupins these clones proved to be "single-locus," "single-locus" with additional signals, "repetitive" or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g., L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the relationships between the

  9. Genome-size Variation in Switchgrass (Panicum virgatum: Flow Cytometry and Cytology Reveal Rampant Aneuploidy

    Directory of Open Access Journals (Sweden)

    Denise E. Costich

    2010-11-01

    Full Text Available Switchgrass ( L., a native perennial dominant of the prairies of North America, has been targeted as a model herbaceous species for biofeedstock development. A flow-cytometric survey of a core set of 11 primarily upland polyploid switchgrass accessions indicated that there was considerable variation in genome size within each accession, particularly at the octoploid (2 = 8 = 72 chromosome ploidy level. Highly variable chromosome counts in mitotic cell preparations indicated that aneuploidy was more common in octoploids (86.3% than tetraploids (23.2%. Furthermore, the incidence of hyper- versus hypoaneuploidy is equivalent in tetraploids. This is clearly not the case in octoploids, where close to 90% of the aneuploid counts are lower than the euploid number. Cytogenetic investigation using fluorescent in situ hybridization (FISH revealed an unexpected degree of variation in chromosome structure underlying the apparent genomic instability of this species. These results indicate that rapid advances in the breeding of polyploid biofuel feedstocks, based on the molecular-genetic dissection of biomass characteristics and yield, will be predicated on the continual improvement of our understanding of the cytogenetics of these species.

  10. Genome sequencing of Chlamydia trachomatis serovars E and F reveals substantial genetic variation.

    Science.gov (United States)

    Eder, Thomas; Kobus, Stefanie; Stallmann, Sonja; Stepanow, Stefanie; Köhrer, Karl; Hegemann, Johannes H; Rattei, Thomas

    2017-12-29

    Chlamydia trachomatis (Ctr) is a bacterial pathogen that causes ocular, urogenital and lymph system infections in humans. It is highly abundant and among its serovars, E, F and D are most prevalent in sexually transmitted disease. However, the number of publicly available genome sequences of the serovars E and F, and thereby our knowledge about the molecular architecture of these serovars, is low. Here we sequenced the genomes of six E and F clinical isolates and one E lab strain, in order to study the genetic variance in these serovars. As observed before, the genomic variation inside the Ctr genomes is very low and the phylogenetic placement in comparison to publicly available genomes is as expected by ompA gene serotyping. However, we observed a large InDel carrying four to five open reading frames in one clinical E sample and in the E lab strain. We have also observed substantial variation on nucleotide and amino acid levels, especially in membrane proteins and secreted proteins. Furthermore, these two groups of proteins are also target for recombination events. One clinical F isolate was genetically heterogeneous and revealed the highest differences on nucleotide level in the pmpE gene. © FEMS 2017.

  11. Deficiencies in jasmonate-mediated plant defense reveal quantitative variation in Botrytis cinerea pathogenesis.

    Directory of Open Access Journals (Sweden)

    Heather C Rowe

    2010-04-01

    Full Text Available Despite the described central role of jasmonate signaling in plant defense against necrotrophic pathogens, the existence of intraspecific variation in pathogen capacity to activate or evade plant jasmonate-mediated defenses is rarely considered. Experimental infection of jasmonate-deficient and jasmonate-insensitive Arabidopsis thaliana with diverse isolates of the necrotrophic fungal pathogen Botrytis cinerea revealed pathogen variation for virulence inhibition by jasmonate-mediated plant defenses and induction of plant defense metabolites. Comparison of the transcriptional effects of infection by two distinct B. cinerea isolates showed only minor differences in transcriptional responses of wild-type plants, but notable isolate-specific transcript differences in jasmonate-insensitive plants. These transcriptional differences suggest B. cinerea activation of plant defenses that require plant jasmonate signaling for activity in response to only one of the two B. cinerea isolates tested. Thus, similar infection phenotypes observed in wild-type plants result from different signaling interactions with the plant that are likely integrated by jasmonate signaling.

  12. Bioinformatic analysis of the neprilysin (M13 family of peptidases reveals complex evolutionary and functional relationships

    Directory of Open Access Journals (Sweden)

    Pinney John W

    2008-01-01

    Full Text Available Abstract Background The neprilysin (M13 family of endopeptidases are zinc-metalloenzymes, the majority of which are type II integral membrane proteins. The best characterised of this family is neprilysin, which has important roles in inactivating signalling peptides involved in modulating neuronal activity, blood pressure and the immune system. Other family members include the endothelin converting enzymes (ECE-1 and ECE-2, which are responsible for the final step in the synthesis of potent vasoconstrictor endothelins. The ECEs, as well as neprilysin, are considered valuable therapeutic targets for treating cardiovascular disease. Other members of the M13 family have not been functionally characterised, but are also likely to have biological roles regulating peptide signalling. The recent sequencing of animal genomes has greatly increased the number of M13 family members in protein databases, information which can be used to reveal evolutionary relationships and to gain insight into conserved biological roles. Results The phylogenetic analysis successfully resolved vertebrate M13 peptidases into seven classes, one of which appears to be specific to mammals, and insect genes into five functional classes and a series of expansions, which may include inactive peptidases. Nematode genes primarily resolved into groups containing no other taxa, bar the two nematode genes associated with Drosophila DmeNEP1 and DmeNEP4. This analysis reconstructed only one relationship between chordate and invertebrate clusters, that of the ECE sub-group and the DmeNEP3 related genes. Analysis of amino acid utilisation in the active site of M13 peptidases reveals a basis for their biochemical properties. A relatively invariant S1' subsite gives the majority of M13 peptidases their strong preference for hydrophobic residues in P1' position. The greater variation in the S2' subsite may be instrumental in determining the specificity of M13 peptidases for their substrates

  13. Intimate relationship status variations in violence against women: urban, suburban, and rural differences.

    Science.gov (United States)

    Rennison, Callie Marie; DeKeseredy, Walter S; Dragiewicz, Molly

    2013-11-01

    Woman abuse varies across intimate relationship categories (e.g., marriage, divorce, separation). However, it is unclear whether relationship status variations in violence against women differ across urban, suburban, and rural areas. We test the hypothesis that rural females, regardless of their intimate partner relationship status, are at higher risk of intimate violence than their urban and suburban counterparts. Results indicate that marital status is an important aspect of the relationship between intimate victimization and geographic area and that rural divorced and separated females are victimized at rates exceeding their urban counterparts.

  14. The relationship between diurnal variations in intraocular pressure measurements and central corneal thickness and corneal hysteresis.

    Science.gov (United States)

    Kotecha, Aachal; Crabb, David P; Spratt, Alexander; Garway-Heath, David F

    2009-09-01

    To examine the relationship between office-hour changes in IOP, measured with the Goldmann applanation tonometer (GAT) and dynamic contour tonometer (DCT), and the corneal characteristics central corneal thickness (CCT) and corneal hysteresis (CH). Sixty-two eyes of 62 untreated normal subjects and patients with untreated glaucoma had IOP measurements performed with the GAT (mm Hg) and DCT (mm Hg) over an 8-hour period at 2-hour intervals beginning at 9 AM. CCT (micrometers) was measured using a noncontact optical low-coherence reflectometry (OLCR) pachymeter, and CH (mm Hg) was measured with an ocular response analyzer (ORA). The associations between IOP measurements and corneal characteristics for each patient over the measurement period were assessed by using multilevel modeling. GAT and DCT IOP and CCT changed significantly during office hours (ANOVA; GAT: F = 19.9, P IOP measurements revealed that both CCT and CH changes were significantly associated with GAT IOP changes (GAT IOP/CCT slope, 0.04 mm Hg/microm; 95% confidence intervals [CIs], 0.02-0.06; GAT IOP/CH slope, 0.20 mm Hg/mm Hg; 95% CI, 0.01-0.39). CCT, but not CH, changes were significantly associated with DCT IOP changes (DCT IOP/CCT slope, 0.03 mm Hg/microm; 95% CI, 0.00-0.05). However, although the association between CCT and GAT IOP was relatively uniform between subjects, association between CCT and DCT IOP showed greater intersubject variability. Age had no effect on the diurnal variation of IOP measured with either device. Measured IOP and corneal characteristics covary during office hours. Changes in CCT and CH are associated with changes in GAT IOP and, less consistently, with DCT IOP. The data suggest that variations in corneal characteristics explain a small proportion of the change in IOP measurements made with the GAT during office hours.

  15. Genetic variation and phylogenetic relationships in oil palm (Elaeis guineensis Jacq. based on RAPD analysis

    Directory of Open Access Journals (Sweden)

    Nualsri, C.

    2005-05-01

    Full Text Available The genetic variability and phylogenetic relationships in oil palm (Elaeis guineensis Jacq. were studied using RAPD (Random Amplified Polymorphic DNA. Leaf samples of 151 plants were collected from different areas in southern Thailand. DNA from the leaf samples was isolated using CTAB buffer and screened by decamer oligonucleotide primers. Among the total of 160 primers screened, 7 primers (OPB-08, OPR-11, OPT-06, OPT-19, OPAB-01, OPAB-09 and OPAB-14 were chosen to analyse for genetic variation in 151 individuals representing 52 dura, 60 tenera and 39 pisifera. Two hundred and nine amplified fragments were obtained from 7 primers with an average of 29.85 RAPD markers per primer. A dendrogram showing genetic similarities among oil palm was constructed based on polymorphic bands using UPGMA (Unweighted Pair-Group Method Using Arithmetic Average. Cluster analysis was performed using the SPSS program, which revealed four major clusters: 1 dura, tenera and pisifera from Paorong Oil Palm Company, Oil Palm Research Center, dura and tenera from private plantation in Krabi, and dura from Thepa Research Station;2 dura and tenera from Thai Boonthong Company, pisifera and tenera from Thepa Research Station, dura, tenera and pisifera from Klong Hoi Khong Research Station; 3 and 4 dura and tenera from Univanit Company, respectively. In general, a similarity index showed relatively high levels of 0.6 or greater.

  16. Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau.

    Science.gov (United States)

    Xing, Rui; Gao, Qing-Bo; Zhang, Fa-Qi; Fu, Peng-Cheng; Wang, Jiu-Li; Yan, Hui-Ying; Chen, Shi-Long

    2017-08-01

    Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.

  17. Functional Coding Variation in Recombinant Inbred Mouse Lines Reveals Novel Serotonin Transporter-Associated Phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Carneiro, Ana [Vanderbilt University; Airey, David [University of Tennessee Health Science Center, Memphis; Thompson, Brent [Vanderbilt University; Zhu, C [Vanderbilt University; Rinchik, Eugene M [ORNL; Lu, Lu [University of Tennessee Health Science Center, Memphis; Chesler, Elissa J [ORNL; Erikson, Keith [University of North Carolina; Blakely, Randy [Vanderbilt University

    2009-01-01

    The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT, SLC6A4) figures prominently in the etiology or treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism and obsessive-compulsive disorder (OCD). Here we utilize naturally occurring polymorphisms in recombinant inbred (RI) lines to identify novel phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by two nonsynonymous coding variants (Gly39 and Lys152 (GK)). At these positions, many other mouse lines, including DBA/2J, encode Glu39 and Arg152 (ER haplotype), assignments found also in hSERT. Synaptosomal 5-HT transport studies revealed reduced uptake associated with the GK variant. Heterologous expression studies confirmed a reduced SERT turnover rate for the GK variant. Experimental and in silico approaches using RI lines (C57Bl/6J X DBA/2J=BXD) identifies multiple anatomical, biochemical and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are multiple traits associated with anxiety and alcohol consumption, as well as of the control of dopamine (DA) signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates ironregulated DA phenotypes. Our studies provide a novel example of the power of coordinated in vitro, in vivo and in silico approaches using murine RI lines to elucidate and quantify the system-level impact of gene variation.

  18. Vp-Vs relationship and amplitude variation with offset modelling of glauconitic greensand

    DEFF Research Database (Denmark)

    Hossain, Zakir; Mukerji, Tapan; Fabricius, Ida Lykke

    2012-01-01

    The relationship between Vp and Vs may be used to predict Vs where only Vp is known. Vp/Vs is also used to identify pore fluids from seismic data and amplitude variation with offset analysis. Theoretical, physical, as well as statistical empirical Vp-Vs relationships have been proposed...... for reservoir characterization when shearwave data are not available. In published work, the focus is primarily on the Vp-Vs relationship of quartzitic sandstone. In order to broaden the picture we present Vp-Vs relationships of greensand composed of quartz and glauconite by using data from the Paleocene...... greensand Nini oil field in the North Sea. A Vp-Vs relationship derived from modelling is compared with empirical Vp-Vs regressions from laboratory data as well as from log data. The accuracy of Vs prediction is quantified in terms of rootmean- square error. We find that the Vp-Vs relationship derived from...

  19. Natural variation in petal color in Lycoris longituba revealed by anthocyanin components.

    Directory of Open Access Journals (Sweden)

    Qiuling He

    Full Text Available Lycoris longituba is one of the species belonging to the Amaryllidaceae family. Despite its limited distribution, endemic to central eastern China, this species displays an exceptionally wide diversity of flower colors from purple, red, orange, to yellow, in nature. We study the natural variation of floral color in L. longituba by testing the components of water-soluble vacuolar pigments--anthocyanins--in its petals using high-performance liquid chromatography coupled with photodiode array detection and electrospray ionization mass spectrometry. Four anthocyanins were identified, cyanidin-3-sophoroside (Cy3So, cyanidin-3-xylosylglucoside (Cy3XyGlc, cyanidin-3-sambubioside (Cy3Sa, and pelargonidin-3-xylosylglucoside (Pg3XyGlc, which occur at various amounts in L. longituba petals of different colors. A multivariate analysis was used to explore the relationship between pigments and flower color. Anthocyanins have been thought to play a major role in acting as a UV screen that protects the plant's DNA from sunlight damage and attracting insects for the purpose of pollination. Thus, knowledge about the content and type of anthocyanins determining the petal coloration of Lycoris longituba will help to study the adaptive evolution of flowers and provide useful information for the ornamental breeding of this species.

  20. Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma.

    Science.gov (United States)

    Cheng, Caixia; Zhou, Yong; Li, Hongyi; Xiong, Teng; Li, Shuaicheng; Bi, Yanghui; Kong, Pengzhou; Wang, Fang; Cui, Heyang; Li, Yaoping; Fang, Xiaodong; Yan, Ting; Li, Yike; Wang, Juan; Yang, Bin; Zhang, Ling; Jia, Zhiwu; Song, Bin; Hu, Xiaoling; Yang, Jie; Qiu, Haile; Zhang, Gehong; Liu, Jing; Xu, Enwei; Shi, Ruyi; Zhang, Yanyan; Liu, Haiyan; He, Chanting; Zhao, Zhenxiang; Qian, Yu; Rong, Ruizhou; Han, Zhiwei; Zhang, Yanlin; Luo, Wen; Wang, Jiaqian; Peng, Shaoliang; Yang, Xukui; Li, Xiangchun; Li, Lin; Fang, Hu; Liu, Xingmin; Ma, Li; Chen, Yunqing; Guo, Shiping; Chen, Xing; Xi, Yanfeng; Li, Guodong; Liang, Jianfang; Yang, Xiaofeng; Guo, Jiansheng; Jia, JunMei; Li, Qingshan; Cheng, Xiaolong; Zhan, Qimin; Cui, Yongping

    2016-02-04

    Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  1. Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat.

    Science.gov (United States)

    Teng, Huajing; Zhang, Yaohua; Shi, Chengmin; Mao, Fengbiao; Hou, Lingling; Guo, Hongling; Sun, Zhongsheng; Zhang, Jianxu

    2016-07-07

    Whole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches. Copyright © 2016 Teng et al.

  2. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves.

    Science.gov (United States)

    Schweizer, Rena M; Robinson, Jacqueline; Harrigan, Ryan; Silva, Pedro; Galverni, Marco; Musiani, Marco; Green, Richard E; Novembre, John; Wayne, Robert K

    2016-01-01

    In an era of ever-increasing amounts of whole-genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct grey wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1-kb nongenic neutral regions, and resequenced these regions in 107 wolves. Selection tests revealed striking patterns of variation within candidate genes relative to noncandidate regions and identified potentially functional variants related to local adaptation. We found 27% and 47% of candidate genes from the previous SNP array study had functional changes that were outliers in sweed and bayenv analyses, respectively. This result verifies the use of genomewide SNP surveys to tag genes that contain functional variants between populations. We highlight nonsynonymous variants in APOB, LIPG and USH2A that occur in functional domains of these proteins, and that demonstrate high correlation with precipitation seasonality and vegetation. We find Arctic and High Arctic wolf ecotypes have higher numbers of genes under selection, which highlight their conservation value and heightened threat due to climate change. This study demonstrates that combining genomewide genotyping arrays with large-scale resequencing and environmental data provides a powerful approach to discern candidate functional variants in natural populations. © 2015 John Wiley & Sons Ltd.

  3. Genetic variation in the popular lab worm Lumbriculus variegatus (Annelida: Clitellata: Lumbriculidae) reveals cryptic speciation.

    Science.gov (United States)

    Gustafsson, Daniel R; Price, David A; Erséus, Christer

    2009-05-01

    Genetic variation in the freshwater oligochaete Lumbriculus variegatus from Europe, North America and Japan was studied by sequencing and analysing the mitochondrial 16S and COI genes, and the nuclear ITS region. What hitherto has been regarded as L. variegatus was found to consist of at least two distinct clades (I and II), both of which occur in Europe as well as North America (clade I also in Japan). Specimens from a single locality in Sierra Nevada, California, also morphologically identified as L. variegatus, represent a third clade, which appears to be more closely related to clade II than to clade I, based on 16S data only. Average COI genetic distances were 17.7% between clades I and II, 0.6% within clade I, and 1.3% within clade II. Further, for these two clades, the mitochondrial (16S and COI) gene trees, which consider only the maternal lineages, are congruent with the ITS gene tree, which is the result of recombinations of paternal as well as maternal genomes. Finally, chromosome counts revealed clade I specimens to be highly polyploid, and clade II specimens to be diploid. We therefore conclude that clades I-II are separately evolving lineages, and that they should be regarded as separate species. This will have to be taken into account in the continued use of L. variegatus as a model organism in biological sciences.

  4. Fronto-parietal network oscillations reveal relationship between working memory capacity and cognitive control

    OpenAIRE

    Rasa eGulbinaite; Hedderik evan Rijn; Cohen, Michael X

    2014-01-01

    Executive-attention theory proposes a close relationship between working memory capacity (WMC) and cognitive control abilities. However, conflicting results are documented in the literature, with some studies reporting that individual variations in WMC predict differences in cognitive control and trial-to-trial control adjustments (operationalized as the size of the congruency effect and congruency sequence effects, respectively), while others report no WMC-related differences. We hypothesize...

  5. Spatial variation in the ecological relationships among the components of Beijing's carbon metabolic system.

    Science.gov (United States)

    Xia, Linlin; Fath, Brian D; Scharler, Ursula M; Zhang, Yan

    2016-02-15

    In this paper, we construct a spatially explicit model of carbon metabolism for the flows of carbon among the components of an urban area. We used the model to identify spatial heterogeneity in the ecological relationships within a carbon metabolic network. We combined land-use and cover type maps for Beijing from 1990 to 2010 with empirical coefficients and socioeconomic data to quantify the flows. We used utility analysis to determine the ecological relationships between the components of the system and analyzed their changes during urban development. We used ArcGIS to analyze their spatial variation. We found that the positive utilities in Beijing decreased over time and that negative relationships mostly outweighed positive relationships after 2000. The main ecological relationships were distributed throughout the entire urban area before 2000; subsequently, exploitation, control, and mutualism relationships became concentrated in the southeast, leaving competition relationships to dominate the northwest. Mutualism relationships were most common for natural components, but were not stable because they were easily disturbed by urban expansion. Transportation and industrial land and urban land were the most important contributors to exploitation and control relationships and may be important indicators of spatial adjustment. Increasing competition relationships unbalanced the carbon metabolism, and limitations on the area of land available for development and on the water resources led to increasingly serious competition. The results provide an objective basis for planning adjustments to Beijing's land-use patterns to improve its carbon metabolism and reduce carbon emission. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil

    Science.gov (United States)

    Luo, Jinming; Bai, Yaohui; Liang, Jinsong; Qu, Jiuhui

    2014-01-01

    Microbes have great potential for arsenic (As) and antimony (Sb) bioremediation in heavily contaminated soil because they have the ability to biotransform As and Sb to species that have less toxicity or are more easily removed. In this study, we integrated a metagenomic method with physicochemical characterization to elucidate the composition of microbial community and functional genes (related to As and Sb) in a high As (range from 34.11 to 821.23 mg kg−1) and Sb (range from 226.67 to 3923.07 mg kg−1) contaminated mine field. Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb. Moreover, redundancy analysis (RDA) of the relationship between the 18 phyla and the concentration of As and Sb demonstrated that 5 phyla of microbes, i.e. Actinobacteria, Firmicutes, Nitrospirae, Tenericutes and Gemmatimonadetes were positively correlated with As and Sb concentration. The distribution, diversity and abundance of functional genes (including arsC, arrA, aioA, arsB and ACR3) were much higher for the samples containing higher As and Sb concentrations. Based on correlation analysis, the results showed a positive relationship between arsC-like (R2 = 0.871) and aioA-like (R2 = 0.675) gene abundance and As concentration, and indicated that intracellular As(V) reduction and As(III) oxidation could be the dominant As detoxification mechanism enabling the microbes to survive in the environment. This study provides a direct and reliable reference on the diversity of microbial community and functional genes in an extremely high concentration As- and Sb-contaminated environment. PMID:25299175

  7. Relationship between winter AO/NAO and temperature in China: intraseasonal and interdecadal variations

    Science.gov (United States)

    Ren, Hong-Li; Zuo, Jinqing; Li, Weijing

    2017-04-01

    In this study, we focus on the intraseasonal and interdecadal variations in the relationship between winter AO/NAO (Arctic Oscillation / North Atlantic Oscillation) and surface air temperature (SAT) in China. On one hand, our results show that there is an intraseasonal contrast in impacts of AO/NAO on SAT in the central-southern China between early and mid-late winter. The linkage between AO and central-southern China SAT strongly depends on the AO-associated changes in Middle-East Jet Stream (MEJS) and the AO-MEJS relationship is significantly different between early and mid-late winter. On the other hand, our results also clearly show that inter-decadal changes have occurred in the relationship between the winter NAO and southern China surface air temperature anomalies in the past decades. A weak in-phase relationship occurred before the early 1970s, but a significant out-of-phase relationship dominated during 1979-1998, though it has been clearly weaker from the late 1990s onwards. Observational evidence shows that such interdecadal variations are mainly related to variations in the spatial pattern and amplitude of the NAO. The eastward shift and amplitude intensification of the NAO favored a north-south Asian dipole structure of circulation anomalies, which tended to produce cold SAT anomalies in central-southern China in the positive NAO phase and warm in the negative NAO phase.

  8. Trends in genome dynamics among major orders of insects revealed through variations in protein families.

    Science.gov (United States)

    Rappoport, Nadav; Linial, Michal

    2015-08-07

    Insects belong to a class that accounts for the majority of animals on earth. With over one million identified species, insects display a huge diversity and occupy extreme environments. At present, there are dozens of fully sequenced insect genomes that cover a range of habitats, social behavior and morphologies. In view of such diverse collection of genomes, revealing evolutionary trends and charting functional relationships of proteins remain challenging. We analyzed the relatedness of 17 complete proteomes representative of proteomes from insects including louse, bee, beetle, ants, flies and mosquitoes, as well as an out-group from the crustaceans. The analyzed proteomes mostly represented the orders of Hymenoptera and Diptera. The 287,405 protein sequences from the 18 proteomes were automatically clustered into 20,933 families, including 799 singletons. A comprehensive analysis based on statistical considerations identified the families that were significantly expanded or reduced in any of the studied organisms. Among all the tested species, ants are characterized by an exceptionally high rate of family gain and loss. By assigning annotations to hundreds of species-specific families, the functional diversity among species and between the major clades (Diptera and Hymenoptera) is revealed. We found that many species-specific families are associated with receptor signaling, stress-related functions and proteases. The highest variability among insects associates with the function of transposition and nucleic acids processes (collectively coined TNAP). Specifically, the wasp and ants have an order of magnitude more TNAP families and proteins relative to species that belong to Diptera (mosquitoes and flies). An unsupervised clustering methodology combined with a comparative functional analysis unveiled proteomic signatures in the major clades of winged insects. We propose that the expansion of TNAP families in Hymenoptera potentially contributes to the accelerated

  9. Revisiting the returns-volume relationship: Time variation, alternative measures and the financial crisis

    Science.gov (United States)

    Cook, Steve; Watson, Duncan

    2017-03-01

    Following its introduction in the seminal study of Osborne (1959), a voluminous literature has emerged examining the returns-volume relationship for financial assets. The present paper revisits this relationship in an examination of the FTSE100 which extends the existing literature in two ways. First, alternative daily measures of the FTSE100 index are used to create differing returns and absolute returns series to employ in an examination of returns-volume causality. Second, rolling regression analysis is utilised to explore potential time variation in the returns-volume relationship. The findings obtained depict a hitherto unconsidered complexity in this relationship with the type of returns series considered and financial crisis found to be significant underlying factors. The implications of the newly derived results for both the understanding of the nature of the returns-volume relationship and the development of theories in connection to it are discussed.

  10. Stable H and O isotope variations reveal sources of recharge in Dhofar, Sultanate of Oman.

    Science.gov (United States)

    Strauch, Gerhard; Al-Mashaikhi, Khalid S; Bawain, Abdullah; Knöller, Kay; Friesen, Jan; Müller, Thomas

    2014-01-01

    Due to the ability of stable water isotopes to characterize the origin of water and connected processes of groundwater recharge, we used the isotope variations of hydrogen and oxygen in different water sources for assessing the recharge process in the Dhofar region. δ(18)O and δ(2)H of precipitation, spring water, and groundwater cover a range from -10 to +2 and from -70 to +7 ‰ (vs Vienna Standard Mean Ocean Water), respectively, and correlate in a linear relationship close to the Global Meteoric Water Line. No obvious evaporation processes are detected. A clear signal of the recent precipitation is given by the annual monsoon. The monsoon signal is confirmed by several springs existing in the south at the foot of the Dhofar mountains and sources at Gogub above 450 m and Tawi Atir at 650 m above sea level. They occur here first in the form of water intercepted by trees as stemflow and throughflow. The isotope signature of groundwater in the Dhofar mountains reflects the climatic conditions at the time of recharge and the lithological features of the limestone matrix. To the north, the isotope patterns of the groundwater are continuously depleted from the monsoon signal along the outcropping aquifer D (Lower Umm Er Radhuma). Here, a more negative signature towards the wells in the Najd desert region was observed. Cyclone water that flooded wadis in the Dhofar region occasionally, as observed in November 2011, falls isotopically into the same range as we observed in the fossil groundwater. Taking into account the different sources of precipitation and groundwater and thus a clear distinction of the isotopic composition of the water sources, we conclude a recharge process divided into a southward and a northward component in the Dhofar region.

  11. Genetic basis of hidden phenotypic variation revealed by increased translational readthrough in yeast.

    Directory of Open Access Journals (Sweden)

    Noorossadat Torabi

    Full Text Available Eukaryotic release factors 1 and 3, encoded by SUP45 and SUP35, respectively, in Saccharomyces cerevisiae, are required for translation termination. Recent studies have shown that, besides these two key factors, several genetic and epigenetic mechanisms modulate the efficiency of translation termination. These mechanisms, through modifying translation termination fidelity, were shown to affect various cellular processes, such as mRNA degradation, and in some cases could confer a beneficial phenotype to the cell. The most studied example of such a mechanism is [PSI+], the prion conformation of Sup35p, which can have pleiotropic effects on growth that vary among different yeast strains. However, genetic loci underlying such readthrough-dependent, background-specific phenotypes have yet to be identified. Here, we used sup35(C653R, a partial loss-of-function allele of the SUP35 previously shown to increase readthrough of stop codons and recapitulate some [PSI+]-dependent phenotypes, to study the genetic basis of phenotypes revealed by increased translational readthrough in two divergent yeast strains: BY4724 (a laboratory strain and RM11_1a (a wine strain. We first identified growth conditions in which increased readthrough of stop codons by sup35(C653R resulted in different growth responses between these two strains. We then used a recently developed linkage mapping technique, extreme QTL mapping (X-QTL, to identify readthrough-dependent loci for the observed growth differences. We further showed that variation in SKY1, an SR protein kinase, underlies a readthrough-dependent locus observed for growth on diamide and hydrogen peroxide. We found that the allelic state of SKY1 interacts with readthrough level and the genetic background to determine growth rate in these two conditions.

  12. Meteorological variation in daily travel behaviour: evidence from revealed preference data from the Netherlands

    Science.gov (United States)

    Creemers, Lieve; Wets, Geert; Cools, Mario

    2015-04-01

    This study investigates the meteorological variation in revealed preference travel data. The main objective of this study is to investigate the impact of weather conditions on daily activity participation (trip motives) and daily modal choices in the Netherlands. To this end, data from the Dutch National Travel Household Survey of 2008 were matched to hourly weather data provided by the Royal Dutch Meteorological Institute and were complemented with thermal indices to indicate the level of thermal comfort and additional variables to indicate the seasonality of the weather conditions. Two multinomial logit-generalised estimation equations (MNL-GEE) models were constructed, one to assess the impact of weather conditions on trip motives and one to assess the effect of weather conditions on modal choice. The modelling results indicate that, depending on the travel attribute of concern, other factors might play a role. Nonetheless, the thermal component, as well as the aesthetical component and the physical component of weather play a significant role. Moreover, the parameter estimates indicate significant differences in the impact of weather conditions when different time scales are considered (e.g. daily versus hourly based). The fact that snow does not play any role at all was unexpected. This finding can be explained by the relatively low occurrence of this weather type in the study area. It is important to consider the effects of weather in travel demand modelling frameworks because this will help to achieve higher accuracy and more realistic traffic forecasts. These will in turn allow policy makers to make better long-term and short-term decisions to achieve various political goals, such as progress towards a sustainable transportation system. Further research in this respect should emphasise the role of weather conditions and activity-scheduling attributes.

  13. Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

    National Research Council Canada - National Science Library

    Hines, Heather M; Papa, Riccardo; Ruiz, Mayte; Papanicolaou, Alexie; Wang, Charles; Nijhout, H Frederik; McMillan, W Owen; Reed, Robert D

    2012-01-01

    .... Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater...

  14. Understanding Students' Transition to High School: Demographic Variation and the Role of Supportive Relationships.

    Science.gov (United States)

    Benner, Aprile D; Boyle, Alaina E; Bakhtiari, Farin

    2017-10-01

    The transition to high school is disruptive for many adolescents, yet little is known about the supportive relational processes that might attenuate the challenges students face as they move from middle to high school, particularly for students from more diverse backgrounds. Identifying potential buffers that protect youth across this critical educational transition is important for informing more effective support services for youth. In this study, we investigated how personal characteristics (gender, nativity, parent education level) and changes in support from family, friends, and school influenced changes in socioemotional adjustment and academic outcomes across the transition from middle to high school. The data were drawn from 252 students (50% females, 85% Latina/o). The results revealed declines in students' grades and increases in depressive symptoms and feelings of loneliness across the high school transition, with key variation by student nativity and gender. Additionally, stable/increasing friend support and school belonging were both linked to less socioemotional disruptions as students moved from middle to high school. Increasing/stable school belonging was also linked to increases in school engagement across the high school transition. These findings suggest that when high school transitions disrupt supportive relationships with important others in adolescents' lives, adolescents' socioemotional well-being and, to a lesser extent, their academic engagement are also compromised. Thus, in designing transition support activities, particularly for schools serving more low-income and race/ethnic minority youth, such efforts should strive to acclimate new high school students by providing inclusive, caring environments and positive connections with educators and peers.

  15. Genetic variation and relationships of seven sturgeon species and ten interspecific hybrids.

    Science.gov (United States)

    Zhang, Xiaomin; Wu, Wenhua; Li, Linmiao; Ma, Xufa; Chen, Jinping

    2013-06-28

    Sturgeon cultivation is important for both industry and aquaculture in China. To date, more than 17 species or strains have been farmed for fillets and caviar production. Crossbreeding among different sturgeon species is frequent and the F2 hybrids are fertile. However, large-scale farming can have negative impacts on wild populations i.e. escape of exotic sturgeons and must be taken into consideration. Escape of exotic sturgeons can cause severe ecological problems, including threatening native sturgeon species once the exotic varieties become established or hybridize with native individuals. However, little is known about their genetic resources and variation. Genetic diversity and introgression of seven sturgeon species were analyzed using mitochondrial DNA cytochrome oxidase subunit I (COI) and nine microsatellite markers. This study included 189 individuals from seven sturgeon species and 277 individuals from ten lineages of F2 hybrid strains. MtDNA COI sequences (632 bp long) were generated from 91 individuals across the 17 sturgeon strains and produced 23 different haplotypes. Haplotype diversity was high (h = 0.915 ± 0.015) and nucleotide diversity was low (π = 0.03680 ± 0.00153) in the seven sturgeon species and ten interspecific hybrids. Phylogenetic analyses resulted in almost identical tree topologies, and different haplotype structures were mainly related with sturgeons of different female parents. Analysis of molecular variance revealed that 81.73% of the genetic variance was due to matrilineal differences, while 9.40% resulted from strain variation. Pairwise Fst values obtained with POLYSAT software, were high among strains and ranged from 0.031 to 0.164. Admixture analysis assigned seven distinct groups and ten genotypes of admixed clusters composed of hybrid strains using STRUCTURE when assuming K = 7. The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions. These relationships were also supported by the results from

  16. In vivo quantification reveals extensive natural variation in mitochondrial form and function in Caenorhabditis briggsae.

    Directory of Open Access Journals (Sweden)

    Kiley A Hicks

    Full Text Available We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.

  17. Relationship between the variations of hydrogen in HCNG fuel and the oxygen in exhausted gas

    OpenAIRE

    Preecha Yaom; Sarawoot Watechagit

    2015-01-01

    The variation of the mixing ratio between hydrogen and compressed natural gas (CNG) in hydrogen enriched compressed natural gas fuel (HCNG) gives different results in terms of engine performances, fuel consumption, and emission characteristics. Therefore, the engine performance using HCNG as fuel can be optimized if the mixing ratio between the two fuels in HCNG can be adjusted in real time while the engine is being operated. In this research, the relationship between the amount of oxygen in ...

  18. Long-Term Measurements of Human Inflammatory Cytokines Reveal Complex Baseline Variations between Individuals.

    Science.gov (United States)

    Wu, Danlu; Dinh, Trinh L; Bausk, Bruce P; Walt, David R

    2017-12-01

    Comprehensive characterization of the healthy human proteome baseline is essential for personalized medicine. Baseline data are necessary to understand the variation between individuals, as well as longitudinal variation within individuals. Many important protein biomarkers, such as cytokines, exist at extremely low or undetectable levels in the healthy state. This paper describes results from a 14-week study of healthy human subjects using ultrasensitive single-molecule array (Simoa) assays to measure both intra and intersubject variation of 15 cytokines. The results show a wide variation in the ranges of some cytokines between individuals and demonstrate that individual baseline values will be essential for predicting disease presence and progression. Although all of the studied cytokines demonstrated high temporal stability (or low intrasubject variation) over the entire study period, there were two distinct groups of cytokines that demonstrated either high (IL-8, IFN-γ, IL-2, IL-6, and IL-1β) or low (IL-15, TNF-α, IL-12 p70, IL-17A, GM-CSF, IL-12 p40, IL-10, IL-7, IL-1α, and IL-5) subject-to-subject variation. This work demonstrates that ultrasensitive assays are essential for characterizing human cytokines in healthy subjects. The results show that some cytokines vary by more than two orders of magnitude between individuals, making it an imperative to obtain individual baseline measurements if they are to play a role in health and disease diagnosis. Copyright © 2017 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  19. Spatial and species variations in bacterial communities associated with corals from the Red Sea as revealed by pyrosequencing.

    Science.gov (United States)

    Lee, On On; Yang, Jiangke; Bougouffa, Salim; Wang, Yong; Batang, Zenon; Tian, Renmao; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

    2012-10-01

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  20. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  1. Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences.

    Science.gov (United States)

    Guo, Guo-Ye; Chen, Fang; Shi, Xiao-Dong; Tian, Yin-Shuai; Yu, Mao-Qun; Han, Xue-Qin; Yuan, Li-Chun; Zhang, Ying

    2016-01-01

    Genetic variation and phylogenetic relationships among 102 Jatropha curcas accessions from Asia, Africa, and the Americas were assessed using the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS). The average G+C content (65.04%) was considerably higher than the A+T (34.96%) content. The estimated genetic diversity revealed moderate genetic variation. The pairwise genetic divergences (GD) between haplotypes were evaluated and ranged from 0.000 to 0.017, suggesting a higher level of genetic differentiation in Mexican accessions than those of other regions. Phylogenetic relationships and intraspecific divergence were inferred by Bayesian inference (BI), maximum parsimony (MP), and median joining (MJ) network analysis and were generally resolved. The J. curcas accessions were consistently divided into three lineages, groups A, B, and C, which demonstrated distant geographical isolation and genetic divergence between American accessions and those from other regions. The MJ network analysis confirmed that Central America was the possible center of origin. The putative migration route suggested that J. curcas was distributed from Mexico or Brazil, via Cape Verde and then split into two routes. One route was dispersed to Spain, then migrated to China, eventually spreading to southeastern Asia, while the other route was dispersed to Africa, via Madagascar and migrated to China, later spreading to southeastern Asia. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  2. Taxonomic variation in size-density relationships challenges the notion of energy equivalence.

    Science.gov (United States)

    Isaac, Nick J B; Storch, David; Carbone, Chris

    2011-08-23

    The relationship between body mass and abundance is a major focus for research in macroecology. The form of this relationship has been suggested to reflect the partitioning of energy among species. We revisit classical datasets to show that size-density relationships vary systematically among taxonomic groups, with most variation occurring at the order level. We use this knowledge to make a novel test of the 'energy equivalence rule', at the taxonomic scale appropriate for the data. We find no obvious relationship between order-specific exponents for abundance and metabolic rate, although most orders show substantially shallower (less negative) scaling than predicted by energy equivalence. This finding implies greater energy flux among larger-bodied animals, with the largest species using two orders of magnitude more energy than the smallest. Our results reject the traditional interpretation of energy equivalence as a predictive rule. However, some variation in size-density exponents is consistent with a model of geometric constraints on foraging. This journal is © 2011 The Royal Society

  3. Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection.

    Science.gov (United States)

    Huang, Huateng; Rabosky, Daniel L

    2015-09-16

    Sexual dichromatism is the tendency for sexes to differ in color pattern and represents a striking form of within-species morphological variation. Conspicuous intersexual differences in avian plumage are generally thought to result from Darwinian sexual selection, to the extent that dichromatism is often treated as a surrogate for the intensity of sexual selection in phylogenetic comparative studies. Intense sexual selection is predicted to leave a footprint on genetic evolution by reducing the relative genetic diversity on sex chromosome to that on the autosomes. In this study, we test the association between plumage dichromatism and sex-linked genetic diversity using eight species pairs with contrasting levels of dichromatism. We estimated Z-linked and autosomal genetic diversity for these non-model avian species using restriction-site associated (RAD) loci that covered ~3 % of the genome. We find that monochromatic birds consistently have reduced sex-linked genomic variation relative to phylogenetically-paired dichromatic species and this pattern is robust to mutational biases. Our results are consistent with several interpretations. If present-day sexual selection is stronger in dichromatic birds, our results suggest that its impact on sex-linked genomic variation is offset by other processes that lead to proportionately lower Z-linked variation in monochromatic species. We discuss possible factors that may contribute to this discrepancy between phenotypes and genomic variation. Conversely, it is possible that present-day sexual selection -- as measured by the variance in male reproductive success -- is stronger in the set of monochromatic taxa we have examined, potentially reflecting the importance of song, behavior and other non-plumage associated traits as targets of sexual selection. This counterintuitive finding suggests that the relationship between genomic variation and sexual selection is complex and highlights the need for a more comprehensive survey

  4. Cross-cultural variations in big five relationships with religiosity: a sociocultural motives perspective.

    Science.gov (United States)

    Gebauer, Jochen E; Bleidorn, Wiebke; Gosling, Samuel D; Rentfrow, Peter J; Lamb, Michael E; Potter, Jeff

    2014-12-01

    A sociocultural motives perspective (SMP) on Big Five relationships is introduced. According to the SMP, Agreeableness and Conscientiousness elicit assimilation to sociocultural norms, Openness elicits contrast from these norms, and Extraversion and Neuroticism are independent of sociocultural assimilation and contrast. Due to sociocultural assimilation, then, relationships of Agreeableness and Conscientiousness with an outcome wax (become more positive or less negative) with that outcome's increasing sociocultural normativeness. Due to sociocultural contrast, relationships of Openness with an outcome wane (become less positive or more negative) with that outcome's increasing sociocultural normativeness. We tested the SMP using religiosity as our outcome. Study 1 included 4 cross-sectional self-report data sets across 66 countries (N = 1,129,334), 50 U.S. states (N = 1,057,342), 15 German federal states (N = 20,885), and 121 British urban areas (N = 386,315). Study 2 utilized informant-report data across 37 countries (N = 544,512). Study 3 used longitudinal data across 15 German federal states (N = 14,858). Results consistently supported the SMP. Relationships of Agreeableness and Conscientiousness with religiosity were more positive in religious sociocultural contexts than in secular contexts. Relationships of Openness with religiosity were more negative in religious sociocultural contexts than in secular contexts. At a more general level, the SMP offers theory-driven explanations for cross-cultural variations in Big Five relationships with their outcomes.

  5. Genetic variation in structure-function relationships for the inbred mouse lumbar vertebral body.

    Science.gov (United States)

    Tommasini, Steven M; Morgan, Timothy G; van der Meulen, Marjolein Ch; Jepsen, Karl J

    2005-05-01

    Structure-function relationships were determined for L(5) vertebral bodies from three inbred mouse strains. Genetic variability in whole bone mechanical properties could be explained by a combination of the traits specifying the amount, distribution, and quality of the cortical and trabecular bone tissue. Although phenotypically correlated with fracture, BMD may be disadvantageous to use in genetic and biomechanical analyses because BMD does not distinguish the contributions of the underlying morphological and compositional bone traits. Developing functional relationships between the underlying bone traits and whole bone mechanical properties should further our understanding of the genetics of bone fragility. Microarchitecture and composition of L(5) vertebral bodies (n = 10/strain) from A/J, C57BL/6J, and C3H/HeJ inbred mouse strains were determined using muCT with an isotropic voxel size of 16 mum(3). Failure load, stiffness, and total deformation as a measure of ductility were measured in compression using a noncontact strain extensometer imaging system. A correlation analysis related morphological and compositional bone traits to whole bone mechanical properties. A multivariate analysis identified structure-function relationships for each genotype. No single bone trait accurately explained the genetic variation in mechanical properties. However, a combination of traits describing the amount, distribution, and quality of cortical and trabecular bone tissue explained >70% of the variation in vertebral mechanical properties. Importantly, structure-function relationships were unique among genotypes. Different genetic backgrounds use different combinations of underlying bone traits to create mechanically functional structures. Using a single complex trait such as BMD or BV/TV as the sole phenotypic marker in genetic analyses may prove to be disadvantageous because of the complex relationship between mechanical properties and the underlying bone traits. Therefore

  6. Network modeling reveals prevalent negative regulatory relationships between signaling sectors in Arabidopsis immune signaling.

    Directory of Open Access Journals (Sweden)

    Masanao Sato

    Full Text Available Biological signaling processes may be mediated by complex networks in which network components and network sectors interact with each other in complex ways. Studies of complex networks benefit from approaches in which the roles of individual components are considered in the context of the network. The plant immune signaling network, which controls inducible responses to pathogen attack, is such a complex network. We studied the Arabidopsis immune signaling network upon challenge with a strain of the bacterial pathogen Pseudomonas syringae expressing the effector protein AvrRpt2 (Pto DC3000 AvrRpt2. This bacterial strain feeds multiple inputs into the signaling network, allowing many parts of the network to be activated at once. mRNA profiles for 571 immune response genes of 22 Arabidopsis immunity mutants and wild type were collected 6 hours after inoculation with Pto DC3000 AvrRpt2. The mRNA profiles were analyzed as detailed descriptions of changes in the network state resulting from the genetic perturbations. Regulatory relationships among the genes corresponding to the mutations were inferred by recursively applying a non-linear dimensionality reduction procedure to the mRNA profile data. The resulting static network model accurately predicted 23 of 25 regulatory relationships reported in the literature, suggesting that predictions of novel regulatory relationships are also accurate. The network model revealed two striking features: (i the components of the network are highly interconnected; and (ii negative regulatory relationships are common between signaling sectors. Complex regulatory relationships, including a novel negative regulatory relationship between the early microbe-associated molecular pattern-triggered signaling sectors and the salicylic acid sector, were further validated. We propose that prevalent negative regulatory relationships among the signaling sectors make the plant immune signaling network a "sector

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

    Directory of Open Access Journals (Sweden)

    Aurélien Chateigner

    2015-07-01

    Full Text Available 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.

  8. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.

    Directory of Open Access Journals (Sweden)

    James B Pease

    2016-02-01

    Full Text Available Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon, we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

  9. Molecular variation of Trypanosoma brucei subspecies as revealed by AFLP fingerprinting

    NARCIS (Netherlands)

    Agbo, E.E.C.; Majiwa, P.A.O.; Claassen, H.J.H.M.; Pas, te M.F.W.

    2002-01-01

    Genetic analysis of Trypanosoma spp. depends on the detection of variation between strains. We have used the amplified fragment length polymorphism (AFLP) technique to develop a convenient and reliable method for genetic characterization of Trypanosome (sub)species. AFLP accesses multiple

  10. Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

    Directory of Open Access Journals (Sweden)

    Hines Heather M

    2012-06-01

    Full Text Available Abstract Background Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato. Results We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern “switch gene” optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns. Conclusions This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.

  11. Variations in the labyrinthine segment of facial nerve canal revealed by high-resolution computed tomography.

    Science.gov (United States)

    Jin, Aiyan; Xu, Peng; Qu, Fengqin

    2017-08-09

    To study variations in the labyrinthine segment of fallopian canal and the associated middle and inner ear malformations. The high-resolution computed tomography (HRCT) images of the temporal bone in 24 patients with congenital variations in the labyrinthine segment of fallopian canal were analyzed retrospectively. The length of labyrinthine segment of the facial nerve and angle of the first genu of 10 normal subjects were also measured. Based on the original axial images, multi-planar reformation (MPR) and curved-planar reformation (CPR) images of bilateral ossicular chains, inner ear structure and fallopian canal were reconstructed. HRCT features of congenital variations in the labyrinthine segment of the facial nerve were analyzed, including its beginning site, dehiscence, length, angle of the first genu and the associated middle and inner ear malformations. Among the normal subjects, the length of labyrinthine segment of the facial nerve was 3.56±0.41mm, and angle of the first genu was 71.87±8.09°. Five types of variations in the labyrinthine segment of the facial nerve were found in 45 ears of 24 cases, including dehiscence in geniculate fossa in 25 ears, anteromedial displacement at the beginning site in 27 ears (widening of Bill's bar in 7 cases), enlargement of the angle of the first genu in 30 ears with an average value of 107.2° (96.0-126.0°), increase of length in 30 ears with an average length of 6.8mm (5.2-8.3mm) and bifurcation in one ear. Associated middle ear malformation in 6 ears and inner ear malformation in 36 ears were also found. A variety of congenital variations may occur in the labyrinthine segment of the facial nerve and they are often associated with middle or inner ear malformations, which can be clearly displayed by HRCT with MPR or CPR images. Copyright © 2017. Published by Elsevier B.V.

  12. Spatial variation in the relationship between performance and metabolic rate in wild juvenile Atlantic salmon.

    Science.gov (United States)

    Robertsen, Grethe; Armstrong, John D; Nislow, Keith H; Herfindal, Ivar; McKelvey, Simon; Einum, Sigurd

    2014-07-01

    Maintenance of metabolic rate (MR, the energy cost of self-maintenance) is linked to behavioural traits and fitness and varies substantially within populations. Despite having received much attention, the causes and consequences of this variation remain obscure. Theoretically, such within-population variation in fitness-related traits can be maintained by environmental heterogeneity in selection patterns, but for MR, this has rarely been tested in nature. Here, we experimentally test whether the relationship between MR and performance can vary spatially by assessing survival, growth rate and movement of Atlantic salmon (Salmo salar L.) juveniles from 10 family groups differing in MR (measured as egg metabolism) that were stocked in parallel across 10 tributaries of a single watershed. The relationship between MR and relative survival and growth rate varied significantly among tributaries. Specifically, the effect of MR ranged from negative to positive for relative survival, whereas it was negative for growth rate. The association between MR and movement was positive and did not vary significantly among tributaries. These results are consistent with a fitness cost of traits associated with behavioural dominance that varies across relatively small spatial scales (within a single watershed). More generally, our results support the hypothesis that spatial heterogeneity in environmental conditions contributes to maintain within-population variation in fitness-related traits, such as MR. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

  13. Geographic variation in the relationship between body mass index and the built environment.

    Science.gov (United States)

    Adachi-Mejia, Anna M; Lee, Chanam; Lee, Chunkuen; Carlos, Heather A; Saelens, Brian E; Berke, Ethan M; Doescher, Mark P

    2017-07-01

    Studies examining associations between weight status and neighborhood built environment (BE) have shown inconsistent results and have generally focused on urban settings. However, many Americans do not live in metropolitan areas and BE impacts may be different outside of metropolitan areas. We sought to examine whether the relationship between body mass index (BMI) and neighborhood BE exists and varies by geographic region across small towns in the United States. We conducted telephone surveys with 2156 adults and geographic information systems data in nine towns located within three geographic regions (Northeast, Texas, Washington) in 2011 and 2012. Multiple regression models examined the relationship between individual BMI and BE measures. Most physical activity variables were significantly associated with lower BMI in all geographic regions. We saw variation across geographic region in the relationship between characteristics of the BE variables and BMI. Some perceived and objectively-measured characteristics of the BE were significantly associated with adult BMI, but significant relationships varied by geographic region. For example, in the Northeast, perceived attractiveness of the neighborhood as a reason for why they chose to live there was associated with lower BMI; in Texas, the perceived presence of a fast food restaurant was negatively associated with BMI; in Washington, perceived presence of trees along the streets was associated with lower BMI. Our findings suggest that regional variation plays a role in the relationship between adult BMI and BE characteristics in small towns. Regardless of geographic location, interventions should encourage utilitarian walking and other forms of physical activity. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Temporal variation of Black Carbon concentration using Aethalometer observations and its relationships with meteorological variables in Karachi, Pakistan

    Science.gov (United States)

    Bibi, Samina; Alam, Khan; Chishtie, Farrukh; Bibi, Humera; Rahman, Said

    2017-05-01

    Black Carbon (BC) mass concentration was measured continuously for every five-minute interval with ground-based Aethalometer at an urban site in Karachi for the period from 2006 to 2008. In this study, the temporal (diurnal, monthly and seasonal) variations of BC and its relationship with meteorological variables were analyzed. Monthly averaged concentrations of BC ranged from 2.2 to 12.5 μg/m3, with maximum in the month of January 2007 and minimum in the month of June 2006. BC showed higher concentrations during the months of January, February and November while lower during the months of May, June, July and August throughout the years. It also displayed comparatively high concentrations during winter and postmonsoon, while moderate during premonsoon and low during summer. Diurnal analysis of BC concentration showed sharp peaks between 07:00 and 09:00 LST and again around 22:00 during all the months. Moreover, the relationship between BC concentration and meteorological variables such as Temperature (Temp), Relative Humidity (RH), Wind Speed (WS), Visibility (VIS) and RainFall (RF) was found and it was observed that BC concentration showed an inverse relationship with all these meteorological variables. Finally, the analysis of the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) cluster trajectories revealed that almost all the clusters were originating from southwest of the study site.

  15. Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae).

    Science.gov (United States)

    Hamon, Perla; Duroy, Pierre-Olivier; Dubreuil-Tranchant, Christine; Mafra D'Almeida Costa, Paulo; Duret, Caroline; Razafinarivo, Norosoa J; Couturon, Emmanuel; Hamon, Serge; de Kochko, Alexandre; Poncet, Valérie; Guyot, Romain

    2011-06-01

    In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution.

  16. {sup 1}H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    Energy Technology Data Exchange (ETDEWEB)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D., E-mail: bernard.lemire@ualberta.ca [University of Alberta, Department of Biochemistry, School of Molecular and Systems Medicine (Canada)

    2011-04-15

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in {sup 1}H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

  17. Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola.

    Science.gov (United States)

    Raman, H; Raman, R; Coombes, N; Song, J; Prangnell, R; Bandaranayake, C; Tahira, R; Sundaramoorthi, V; Killian, A; Meng, J; Dennis, E S; Balasubramanian, S

    2016-06-01

    Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes. ©2015 The Authors. Plant, Cell & Environment published by JohnWiley & Sons Ltd.

  18. Analysis of natural variation in bermudagrass (Cynodon dactylon) reveals physiological responses underlying drought tolerance.

    Science.gov (United States)

    Shi, Haitao; Wang, Yanping; Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

    2012-01-01

    Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H₂O₂ content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system.

  19. Analysis of natural variation in bermudagrass (Cynodon dactylon reveals physiological responses underlying drought tolerance.

    Directory of Open Access Journals (Sweden)

    Haitao Shi

    Full Text Available Bermudagrass (Cynodon dactylon is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon showed relative higher water loss, more severe cell membrane damage (EL, and more accumulation of hydrogen peroxide (H₂O₂ and malondialdehyde (MDA, while drought tolerant variety (Tifgreen exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen exhibited liner correlation with leaf water content (LWC, H₂O₂ content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system.

  20. Spatiotemporal variation in avian migration phenology: citizen science reveals effects of climate change.

    Directory of Open Access Journals (Sweden)

    Allen H Hurlbert

    Full Text Available A growing number of studies have documented shifts in avian migratory phenology in response to climate change, and yet there is a large amount of unexplained variation in the magnitude of those responses across species and geographic regions. We use a database of citizen science bird observations to explore spatiotemporal variation in mean arrival dates across an unprecedented geographic extent for 18 common species in North America over the past decade, relating arrival dates to mean minimum spring temperature. Across all species and geographic locations, species shifted arrival dates 0.8 days earlier for every °C of warming of spring temperature, but it was common for some species in some locations to shift as much as 3-6 days earlier per °C. Species that advanced arrival dates the earliest in response to warming were those that migrate more slowly, short distance migrants, and species with broader climatic niches. These three variables explained 63% of the interspecific variation in phenological response. We also identify a latitudinal gradient in the average strength of phenological response, with species shifting arrival earlier at southern latitudes than northern latitudes for the same degree of warming. This observation is consistent with the idea that species must be more phenologically sensitive in less seasonal environments to maintain the same degree of precision in phenological timing.

  1. Analysis of Natural Variation in Bermudagrass (Cynodon dactylon) Reveals Physiological Responses Underlying Drought Tolerance

    Science.gov (United States)

    Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

    2012-01-01

    Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H2O2) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H2O2 content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system. PMID:23285294

  2. Independent variations of plant and soil mixtures reveal soil feedback effects on plant community overyielding

    NARCIS (Netherlands)

    Hendriks, M.; Mommer, L.; Caluwe, de H.; Smit-Tiekstra, A.E.; Putten, van der W.H.; Kroon, de H.

    2013-01-01

    1. Recent studies have shown that the positive relationship between plant diversity and plant biomass ('overyielding') can be explained by soil pathogens depressing productivity more in low than in high diverse plant communities. However, tests of such soil effects in field studies were constrained

  3. Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand.

    Directory of Open Access Journals (Sweden)

    Thanwa Wongsuk

    Full Text Available The Scedosporium apiospermum species complex is an emerging filamentous fungi that has been isolated from environment. It can cause a wide range of infections in both immunocompetent and immunocompromised individuals. We aimed to study the genetic variation and relationships between 48 strains of S. apiospermum sensu stricto isolated from soil in Bangkok, Thailand. For PCR, sequencing and phylogenetic analysis, we used the following genes: actin; calmodulin exons 3 and 4; the second largest subunit of the RNA polymerase II; ß-tubulin exon 2-4; manganese superoxide dismutase; internal transcribed spacer; transcription elongation factor 1α; and beta-tubulin exons 5 and 6. The present study is the first phylogenetic analysis of relationships among S. apiospermum sensu stricto in Thailand and South-east Asia. This result provides useful information for future epidemiological study and may be correlated to clinical manifestation.

  4. Localising loci underlying complex trait variation using Regional Genomic Relationship Mapping.

    Directory of Open Access Journals (Sweden)

    Yoshitaka Nagamine

    Full Text Available The limited proportion of complex trait variance identified in genome-wide association studies may reflect the limited power of single SNP analyses to detect either rare causative alleles or those of small effect. Motivated by studies that demonstrate that loci contributing to trait variation may contain a number of different alleles, we have developed an analytical approach termed Regional Genomic Relationship Mapping that, like linkage-based family methods, integrates variance contributed by founder gametes within a pedigree. This approach takes advantage of very distant (and unrecorded relationships, and this greatly increases the power of the method, compared with traditional pedigree-based linkage analyses. By integrating variance contributed by founder gametes in the population, our approach provides an estimate of the Regional Heritability attributable to a small genomic region (e.g. 100 SNP window covering ca. 1 Mb of DNA in a 300000 SNP GWAS and has the power to detect regions containing multiple alleles that individually contribute too little variance to be detectable by GWAS as well as regions with single common GWAS-detectable SNPs. We use genome-wide SNP array data to obtain both a genome-wide relationship matrix and regional relationship ("identity by state" or IBS matrices for sequential regions across the genome. We then estimate a heritability for each region sequentially in our genome-wide scan. We demonstrate by simulation and with real data that, when compared to traditional ("individual SNP" GWAS, our method uncovers new loci that explain additional trait variation. We analysed data from three Southern European populations and from Orkney for exemplar traits - serum uric acid concentration and height. We show that regional heritability estimates are correlated with results from genome-wide association analysis but can capture more of the genetic variance segregating in the population and identify additional trait loci.

  5. Spatiotemporal variations of Venus middle atmosphere revealed by Subaru/COMICS

    Science.gov (United States)

    Sato, T. M.; Sagawa, H.; Kouyama, T.; Imamura, T.; Satoh, T.

    2013-09-01

    We report the spatiotemporal variations of brightness temperatures of Venus at cloud top altitudes (~70 km) obtained by the Cooled Mid-Infrared Camera and Spectrometer (COMICS), mounted on the 8.2-m Subaru Telescope. The two important findings are (1) the brightness temperatures at north polar regions were synchronized with those at south polar regions at least in the three observation nights and (2) there were some streaky patterns as were seen in UV and these patterns varied from day to day.

  6. Experimental reintroduction reveals novel life-history variation in Laysan Ducks (Anas laysanensis)

    Science.gov (United States)

    Walters, Jeffrey R.; Reynolds, Michelle H.

    2013-01-01

    Subfossil remains indicate that the Laysan Duck (Anas laysanensis) formerly occurred throughout the Hawaiian archipelago, but for more than 150 years it has been confined to a single, small atoll in the northwestern chain, Laysan Island. In 2004–2005, 42 ducks were reintroduced from Laysan to Midway Atoll, where they exhibited variation in life history never observed on Laysan. On Laysan, females have never been observed to breed successfully at age 1 year and few attempt it, whereas on Midway, females routinely raised young at reintroductions of this species may provide opportunities to test hypotheses about mechanisms underlying phenotypic plasticity.

  7. Phylogenetic variation of Aggregatibacter actinomycetemcomitans serotype e reveals an aberrant distinct evolutionary stable lineage

    NARCIS (Netherlands)

    van der Reijden, Wil A.; Brunner, Jorg; Bosch-Tijhof, Carolien J.; van Trappen, Stefanie; Rijnsburger, Martine C.; de Graaff, Marcel P. W.; van Winkelhoff, Arie J.; Cleenwerck, Ilse; de Vos, Paul

    2010-01-01

    The periodontal pathogen Aggregatibacter actinomycetemcomitans that comprises six serotypes (a-f), is often identified by PCR-based techniques targeting the 16S rRNA gene. In this study, 16S rRNA gene sequence analysis revealed an aberrant cluster of 19 strains within serotype e, denoted as serotype

  8. Comparative transcriptomics reveal host-specific nucleotide variation in entomophthoralean fungi

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Jensen, Annette Bruun; Eilenberg, Jørgen

    2017-01-01

    of toxins that interfere with the host immune response. Phylogenetic comparison with the nonobligate generalist insect-pathogenic fungus Conidiobolus coronatus revealed a gene-family expansion of trehalase enzymes in E. muscae. The main sugar in insect haemolymph is trehalose, and efficient sugar...

  9. Fathers' Participation in Parenting and Maternal Parenting Stress: Variation by Relationship Status.

    Science.gov (United States)

    Nomaguchi, Kei; Brown, Susan L; Leyman, Tanya M

    2017-06-01

    The growing diversity in mother-father relationship status has led to a debate over the role of fathers in parenting. Little is known, however, about how fathers' participation in parenting is linked to maternal well-being across different mother-father relationship statuses. Using data from the Fragile Families and Child Wellbeing Study (N = 2,062), fixed-effects as well as random-effects regression models show that overall fathers' engagement with children and sharing in child-related chores are negatively related to maternal parenting stress. Fathers' cooperative coparenting is negatively related to maternal parenting stress only in the random-effects model, suggesting that the association is driven by selection factors. There is little variation in these associations by mother-father relationship status, once selection factors are controlled for. These findings extend support for the current cultural emphasis on benefits of fathers' active participation in parenting for mothers and children even after the mother-father relationship dissolved.

  10. Multi-tissue analyses reveal limited inter-annual and seasonal variation in mercury exposure in an Antarctic penguin community.

    Science.gov (United States)

    Brasso, Rebecka L; Polito, Michael J; Emslie, Steven D

    2014-10-01

    Inter-annual variation in tissue mercury concentrations in birds can result from annual changes in the bioavailability of mercury or shifts in dietary composition and/or trophic level. We investigated potential annual variability in mercury dynamics in the Antarctic marine food web using Pygoscelis penguins as biomonitors. Eggshell membrane, chick down, and adult feathers were collected from three species of sympatrically breeding Pygoscelis penguins during the austral summers of 2006/2007-2010/2011. To evaluate the hypothesis that mercury concentrations in penguins exhibit significant inter-annual variation and to determine the potential source of such variation (dietary or environmental), we compared tissue mercury concentrations with trophic levels as indicated by δ(15)N values from all species and tissues. Overall, no inter-annual variation in mercury was observed in adult feathers suggesting that mercury exposure, on an annual scale, was consistent for Pygoscelis penguins. However, when examining tissues that reflected more discrete time periods (chick down and eggshell membrane) relative to adult feathers, we found some evidence of inter-annual variation in mercury exposure during penguins' pre-breeding and chick rearing periods. Evidence of inter-annual variation in penguin trophic level was also limited suggesting that foraging ecology and environmental factors related to the bioavailability of mercury may provide more explanatory power for mercury exposure compared to trophic level alone. Even so, the variable strength of relationships observed between trophic level and tissue mercury concentrations across and within Pygoscelis penguin species suggest that caution is required when selecting appropriate species and tissue combinations for environmental biomonitoring studies in Antarctica.

  11. Single-subject analysis reveals variation in knee mechanics during step landing.

    Science.gov (United States)

    Scholes, Corey J; McDonald, Michael D; Parker, Anthony W

    2012-08-09

    Evidence concerning the alteration of knee function during landing suffers from a lack of consensus. This uncertainty can be attributed to methodological flaws, particularly in relation to the statistical analysis of variable human movement data. The aim of this study was to compare single-subject and group analyses in detecting changes in knee stiffness and coordination during step landing that occur independent of an experimental intervention. A group of healthy men (N=12) stepped-down from a knee-high platform for 60 consecutive trials, each trial separated by a 1-minute rest. The magnitude and within-participant variability of sagittal stiffness and coordination of the landing knee were evaluated with both group and single-subject analyses. The group analysis detected significant changes in knee coordination. However, the single-subject analyses detected changes in all dependent variables, which included increases in variability with task repetition. Between-individual variation was also present in the timing, size and direction of alterations. The results have important implications for the interpretation of existing information regarding the adaptation of knee mechanics to interventions such as fatigue, footwear or landing height. It is proposed that a participant's natural variation in knee mechanics should be analysed prior to an intervention in future experiments. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Inner disc rearrangement revealed by dramatic brightness variations in the young star PV Cep

    Science.gov (United States)

    Kun, M.; Szegedi-Elek, E.; Moór, A.; Kóspál, Á.; Ábrahám, P.; Apai, D.; Kiss, Z. T.; Klagyivik, P.; Magakian, T. Yu.; Mező, Gy.; Movsessian, T. A.; Pál, A.; Rácz, M.; Rogers, J.

    2011-06-01

    Young Sun-like stars at the beginning of the pre-main-sequence (PMS) evolution are surrounded by accretion discs and remnant protostellar envelopes. Photometric and spectroscopic variations of these stars are driven by interactions of the star with the disc. Time-scales and wavelength dependence of the variability carry information on the physical mechanisms behind these interactions. We conducted multi-epoch, multiwavelength study of PV Cep, a strongly variable, accreting PMS star. By combining our own observations from 2004 to 2010 with archival and literature data, we show that PV Cep started a spectacular fading in 2005, reaching an IC-band amplitude of 4 mag. Analysis of variation of the optical and infrared fluxes, colour indices and emission line fluxes suggests that the photometric decline in 2005-2009 resulted from an interplay between variable accretion and circumstellar extinction: since the central luminosity of the system is dominated by accretion, a modest drop in the accretion rate could induce the drastic restructuring of the inner disc. Dust condensation in the inner disc region might have resulted in the enhancement of the circumstellar extinction.

  13. Interannual variation of the Indonesian throughflow in the Timor Passage as revealed in SODA: 1958 - 2008

    Science.gov (United States)

    Iskandar, I.; Mardiansyah, W.; Setiabudidaya, D.; Poerwono, P.; Syamsuddin, F.

    2015-09-01

    Temporal variability of the Indonesian Throughflow (ITF) in the Timor Passage was evaluated with special focus on its interannual variation. The ITF transport was estimated as a latitudinal averaged of an along strait currents in the Timor Passage based on the output of Simple Ocean Data Assimilation (SODA) experiment from 1958 - 2008. A Complex Empirical Orthogonal Function (CEOF), then, was applied to the interannual estimated ITF transport to extract the dominant mode of variability. The result has shown that the leading CEOF mode was explaining 67.2% of the total interannual variation. The reconstructed first CEOF time series shows strong positive anomalies (towards the Pacific Ocean) during 1962 - 1969, 1972 - 1978, 1997 - 1999, 2002 - 2005 and 2007. The transport was reversed (towards the Indian Ocean) during other periods. The upper layer transport above ˜200m depth is significantly correlated with the zonal wind stress in the western equatorial Pacific Ocean, with the transport lagging the winds by about 10 months. The middle layer transport between about 200 - 600m depth is significantly influenced by the zonal wind from the eastern equatorial Indian Ocean in which the zonal winds lag the ITF by about 5 months. In addition, the deeper layer transport below about 600m depth shows significant zero lag correlation with the zonal wind stress in the western equatorial Pacific Ocean, though the impact of the equatorial Indian Ocean zonal wind stress is not negligible.

  14. Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum.

    Directory of Open Access Journals (Sweden)

    Peter A Bron

    Full Text Available Lactic acid bacteria (LAB are utilized widely for the fermentation of foods. In the current post-genomic era, tools have been developed that explore genetic diversity among LAB strains aiming to link these variations to differential phenotypes observed in the strains investigated. However, these genotype-phenotype matching approaches fail to assess the role of conserved genes in the determination of physiological characteristics of cultures by environmental conditions. This manuscript describes a complementary approach in which Lactobacillus plantarum WCFS1 was fermented under a variety of conditions that differ in temperature, pH, as well as NaCl, amino acid, and O(2 levels. Samples derived from these fermentations were analyzed by full-genome transcriptomics, paralleled by the assessment of physiological characteristics, e.g., maximum growth rate, yield, and organic acid profiles. A data-storage and -mining suite designated FermDB was constructed and exploited to identify correlations between fermentation conditions and industrially relevant physiological characteristics of L. plantarum, as well as the associated transcriptome signatures. Finally, integration of the specific fermentation variables with the transcriptomes enabled the reconstruction of the gene-regulatory networks involved. The fermentation-genomics platform presented here is a valuable complementary approach to earlier described genotype-phenotype matching strategies which allows the identification of transcriptome signatures underlying physiological variations imposed by different fermentation conditions.

  15. Transcriptomes Reveal Genetic Signatures Underlying Physiological Variations Imposed by Different Fermentation Conditions in Lactobacillus plantarum

    Science.gov (United States)

    Bongers, Roger S.; van Bokhorst-van de Veen, Hermien; Wiersma, Anne; Overmars, Lex; Marco, Maria L.; Kleerebezem, Michiel

    2012-01-01

    Lactic acid bacteria (LAB) are utilized widely for the fermentation of foods. In the current post-genomic era, tools have been developed that explore genetic diversity among LAB strains aiming to link these variations to differential phenotypes observed in the strains investigated. However, these genotype-phenotype matching approaches fail to assess the role of conserved genes in the determination of physiological characteristics of cultures by environmental conditions. This manuscript describes a complementary approach in which Lactobacillus plantarum WCFS1 was fermented under a variety of conditions that differ in temperature, pH, as well as NaCl, amino acid, and O2 levels. Samples derived from these fermentations were analyzed by full-genome transcriptomics, paralleled by the assessment of physiological characteristics, e.g., maximum growth rate, yield, and organic acid profiles. A data-storage and -mining suite designated FermDB was constructed and exploited to identify correlations between fermentation conditions and industrially relevant physiological characteristics of L. plantarum, as well as the associated transcriptome signatures. Finally, integration of the specific fermentation variables with the transcriptomes enabled the reconstruction of the gene-regulatory networks involved. The fermentation-genomics platform presented here is a valuable complementary approach to earlier described genotype-phenotype matching strategies which allows the identification of transcriptome signatures underlying physiological variations imposed by different fermentation conditions. PMID:22802930

  16. Fronto-parietal network oscillations reveal relationship between working memory capacity and cognitive control

    Directory of Open Access Journals (Sweden)

    Rasa eGulbinaite

    2014-09-01

    Full Text Available Executive-attention theory proposes a close relationship between working memory capacity (WMC and cognitive control abilities. However, conflicting results are documented in the literature, with some studies reporting that individual variations in WMC predict differences in cognitive control and trial-to-trial control adjustments (operationalized as the size of the congruency effect and congruency sequence effects, respectively, while others report no WMC-related differences. We hypothesized that brain network dynamics might be a more sensitive measure of WMC-related differences in cognitive control abilities. Thus, in the present study, we measured human EEG during the Simon task to characterize WMC-related differences in the neural dynamics of conflict processing and adaptation to conflict. Although high- and low-WMC individuals did not differ behaviorally, there were substantial WMC-related differences in theta (4-8 Hz and delta (1-3 Hz connectivity in fronto-parietal networks. Group differences in local theta and delta power were relatively less pronounced. These results suggest that the relationship between WMC and cognitive control abilities is more strongly reflected in large-scale oscillatory network dynamics than in spatially localized activity or in behavioral task performance.

  17. Fronto-parietal network oscillations reveal relationship between working memory capacity and cognitive control.

    Science.gov (United States)

    Gulbinaite, Rasa; van Rijn, Hedderik; Cohen, Michael X

    2014-01-01

    Executive-attention theory proposes a close relationship between working memory capacity (WMC) and cognitive control abilities. However, conflicting results are documented in the literature, with some studies reporting that individual variations in WMC predict differences in cognitive control and trial-to-trial control adjustments (operationalized as the size of the congruency effect and congruency sequence effects, respectively), while others report no WMC-related differences. We hypothesized that brain network dynamics might be a more sensitive measure of WMC-related differences in cognitive control abilities. Thus, in the present study, we measured human EEG during the Simon task to characterize WMC-related differences in the neural dynamics of conflict processing and adaptation to conflict. Although high- and low-WMC individuals did not differ behaviorally, there were substantial WMC-related differences in theta (4-8 Hz) and delta (1-3 Hz) connectivity in fronto-parietal networks. Group differences in local theta and delta power were relatively less pronounced. These results suggest that the relationship between WMC and cognitive control abilities is more strongly reflected in large-scale oscillatory network dynamics than in spatially localized activity or in behavioral task performance.

  18. Multilocus nuclear sequences reveal intra- and interspecific relationships among chromosomally polymorphic species of cactophilic Drosophila.

    Science.gov (United States)

    Machado, Carlos A; Matzkin, Luciano M; Reed, Laura K; Markow, Therese A

    2007-07-01

    Drosophila mojavensis and Drosophila arizonae, a pair of sibling species endemic to North America, constitute an important model system to study ecological genetics and the evolution of reproductive isolation. This species pair can produce fertile hybrids in some crosses and are sympatric in a large part of their ranges. Despite the potential for hybridization in nature, however, evidence of introgression has not been rigorously sought. Further, the evolutionary relationships within and among the geographically distant populations of the two species have not been characterized in detail using high-resolution molecular studies. Both species have six chromosomes: five large acrocentrics and one 'dot' chromosome. Fixed inversion differences between the species exist in three chromosomes (X, 2 and 3) while three are colinear (4, 5 and 6), suggesting that were introgression to occur, it would be most likely in the colinear chromosomes. We utilized nucleotide sequence variation at multiple loci on five chromosomes to test for evidence of introgression, and to test various scenarios for the evolutionary relationships of these two species and their populations. While we do not find evidence of recent introgression, loci in the colinear chromosomes appear to have participated in exchange in the past. We also found considerable population structure within both species. The level of differentiation discovered among D. arizonae populations was unexpectedly high and suggests that its populations, as well as those of D. mojavensis, may be themselves undergoing incipient speciation and merit further attention.

  19. The Genetic Relationship between Leishmania aethiopica and Leishmania tropica Revealed by Comparing Microsatellite Profiles.

    Science.gov (United States)

    Krayter, Lena; Schnur, Lionel F; Schönian, Gabriele

    2015-01-01

    Leishmania (Leishmania) aethiopica and L. (L.) tropica cause cutaneous leishmaniases and appear to be related. L. aethiopica is geographically restricted to Ethiopia and Kenya; L. tropica is widely dispersed from the Eastern Mediterranean, through the Middle East into eastern India and in north, east and south Africa. Their phylogenetic inter-relationship is only partially revealed. Some studies indicate a close relationship. Here, eight strains of L. aethiopica were characterized genetically and compared with 156 strains of L. tropica from most of the latter species' geographical range to discern the closeness. Twelve unlinked microsatellite markers previously used to genotype strains of L. tropica were successfully applied to the eight strains of L. aethiopica and their microsatellite profiles were compared to those of 156 strains of L. tropica from various geographical locations that were isolated from human cases of cutaneous and visceral leishmaniasis, hyraxes and sand fly vectors. All the microsatellite profiles were subjected to various analytical algorithms: Bayesian statistics, distance-based and factorial correspondence analysis, revealing: (i) the species L. aethiopica, though geographically restricted, is genetically very heterogeneous; (ii) the strains of L. aethiopica formed a distinct genetic cluster; and (iii) strains of L. aethiopica are closely related to strains of L. tropica and more so to the African ones, although, by factorial correspondence analysis, clearly separate from them. The successful application of the 12 microsatellite markers, originally considered species-specific for the species L. tropica, to strains of L. aethiopica confirmed the close relationship between these two species. The Bayesian and distance-based methods clustered the strains of L. aethiopica among African strains of L. tropica, while the factorial correspondence analysis indicated a clear separation between the two species. There was no correlation between

  20. Structural variations in prefrontal cortex mediate the relationship between early childhood stress and spatial working memory.

    Science.gov (United States)

    Hanson, Jamie L; Chung, Moo K; Avants, Brian B; Rudolph, Karen D; Shirtcliff, Elizabeth A; Gee, James C; Davidson, Richard J; Pollak, Seth D

    2012-06-06

    A large corpus of research indicates that exposure to stress impairs cognitive abilities, specifically executive functioning dependent on the prefrontal cortex (PFC). We collected structural MRI scans (n = 61), well-validated assessments of executive functioning, and detailed interviews assessing stress exposure in humans to examine whether cumulative life stress affected brain morphometry and one type of executive functioning, spatial working memory, during adolescence-a critical time of brain development and reorganization. Analysis of variations in brain structure revealed that cumulative life stress and spatial working memory were related to smaller volumes in the PFC, specifically prefrontal gray and white matter between the anterior cingulate and the frontal poles. Mediation analyses revealed that individual differences in prefrontal volumes accounted for the association between cumulative life stress and spatial working memory. These results suggest that structural changes in the PFC may serve as a mediating mechanism through which greater cumulative life stress engenders decrements in cognitive functioning.

  1. Metabolomics reveals significant variations in metabolites and correlations regarding the maturation of walnuts (Juglans regia L.

    Directory of Open Access Journals (Sweden)

    Guodong Rao

    2016-06-01

    Full Text Available The content of walnut metabolites is related to its nutritive value and physiological characteristics, however, comprehensive information concerning the metabolome of walnut kernels is limited. In this study we analyzed the metabolites of walnut kernels at five developmental stages from filling to ripening using GC-MS-based untargeted metabolomics; of a total 252 peaks identified, 85 metabolites were positively identified. Further statistical analysis revealed that these 85 metabolites covered different types of metabolism pathways. PCA scores revealed that the metabolic compositions of the embryo are different at each stage, while the metabolic composition of the endotesta could not be significantly separated into distinct groups. Additionally, 7225 metabolite-metabolite correlations were detected in walnut kernel by a Pearson correlation coefficient approach; during screening of the calculated correlations, 463 and 1047 were determined to be significant with r2≥0.49 and had a false discovery rate (FDR ≤0.05 in endotesta and embryo, respectively. This work provides the first comprehensive metabolomic study of walnut kernels and reveals that most of the carbohydrate and protein-derived carbon was transferred into other compounds, such as fatty acids, during the maturation of walnuts, which may potentially provide the basis for further studies on walnut kernel metabolism.

  2. PHYLOGENETIC ANALYSIS REVEALS GENETIC VARIATIONS OF DENSOVIRUS ISOLATED FROM FIELD MOSQUITOES IN BANGKOK AND SURROUNDING REGIONS.

    Science.gov (United States)

    Boonnak, Kobporn; Suttitheptumrong, Aroonroong; Jotekratok, Ubonwan; Pattanakitsakul, Sa-Nga

    2015-03-01

    Screening for densoviruses (DNVs) from Aedes, Culex and Toxorhynchites mosquitoes collected in Bangkok and surrounding regions identified two clades of Aedes DNV; Ae. aegypti DNV (AaeDNV) and Ae. albopictus DNV (AalDNV) by PCR-restriction fragment length polymorphism (PCR-RFLP). From nucleotide sequencing and phylogenetic analysis of PCR amplicons of a fragment of DNV capsid gene, these DNVs were shown to be new DNV genetic variations similar to AaeDNV. Isolation and identification of densoviruses from indigenous field mosquitoes reside in natural habitat should be helpful in monitoring the distribution of DNVs in important mosquitoes, especially Ae. aegypti and Ae. albopictus, vector for dengue and yellow fever viruses.

  3. Natural Genetic Variation for Growth and Development Revealed by High-Throughput Phenotyping in Arabidopsis thaliana.

    Science.gov (United States)

    Zhang, Xu; Hause, Ronald J; Borevitz, Justin O

    2012-01-01

    Leaf growth and development determines a plant's capacity for photosynthesis and carbon fixation. These morphological traits are the integration of genetic and environmental factors through time. Yet fine dissection of the developmental genetic basis of leaf expansion throughout a growing season is difficult, due to the complexity of the trait and the need for real time measurement. In this study, we developed a time-lapse image analysis approach, which traces leaf expansion under seasonal light variation. Three growth traits, rosette leaf area, circular area, and their ratio as compactness, were measured and normalized on a linear timescale to control for developmental heterogeneity. We found high heritability for all growth traits that changed over time. Our study highlights a cost-effective, high-throughput phenotyping approach that facilitates the dissection of genetic basis of plant shoot growth and development under dynamic environmental conditions.

  4. Temporal genetic variation as revealed by a microsatellite analysis of European sardine ( Sardina pilchardus) archived samples

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara

    2012-01-01

    ) that explain the genetic diversity variation, while the same parameters turned out to be more stable in the southern samples. In addition, we detected the presence of a genetic bottleneck and low effective population size ( Ne) values in several northern samples. Even if the northern and southern Adriatic...... of otoliths and scales from sampling locations of northern (Chioggia) and southern (Vieste) Adriatic Sea, with the aim to investigate the genetic effects of these stock biomass fluctuations. The northern samples showed significant reduction in observed heterozygosity ( HO) and mean number of alleles ( Na...... sardine samples belong to the same genetic stock, the more pronounced decrease in genetic variability recorded in the northern sample led us to speculate that a more intensive fishing pressure and a more pronounced oceanographic isolation of this area could have accentuated the effects of the genetic...

  5. Diurnal microstructural variations in healthy adult brain revealed by diffusion tensor imaging.

    Directory of Open Access Journals (Sweden)

    Chunxiang Jiang

    Full Text Available Biorhythm is a fundamental property of human physiology. Changes in the extracellular space induced by cell swelling in response to the neural activity enable the in vivo characterization of cerebral microstructure by measuring the water diffusivity using diffusion tensor imaging (DTI. To study the diurnal microstructural alterations of human brain, fifteen right-handed healthy adult subjects were recruited for DTI studies in two repeated sessions (8∶30 AM and 8∶30 PM within a 24-hour interval. Fractional anisotropy (FA, apparent diffusion coefficient (ADC, axial (λ// and radial diffusivity (λ⊥ were compared pixel by pixel between the sessions for each subject. Significant increased morning measurements in FA, ADC, λ// and λ⊥ were seen in a wide range of brain areas involving frontal, parietal, temporal and occipital lobes. Prominent evening dominant λ⊥ (18.58% was detected in the right inferior temporal and ventral fusiform gyri. AM-PM variation of λ⊥ was substantially left side hemisphere dominant (p<0.05, while no hemispheric preference was observed for the same analysis for ADC (p = 0.77, λ// (p = 0.08 or FA (p = 0.25. The percentage change of ADC, λ//, λ⊥, and FA were 1.59%, 2.15%, 1.20% and 2.84%, respectively, for brain areas without diurnal diffusivity contrast. Microstructural variations may function as the substrates of the phasic neural activities in correspondence to the environment adaptation in a light-dark cycle. This research provided a baseline for researches in neuroscience, sleep medicine, psychological and psychiatric disorders, and necessitates that diurnal effect should be taken into account in following up studies using diffusion tensor quantities.

  6. Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns.

    Science.gov (United States)

    Grusz, Amanda L; Rothfels, Carl J; Schuettpelz, Eric

    2016-08-30

    Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns-an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection. We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution. Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.

  7. Indifference to dissonance in native Amazonians reveals cultural variation in music perception.

    Science.gov (United States)

    McDermott, Josh H; Schultz, Alan F; Undurraga, Eduardo A; Godoy, Ricardo A

    2016-07-28

    by biology remains debated. One widely discussed phenomenon is that some combinations of notes are perceived by Westerners as pleasant, or consonant, whereas others are perceived as unpleasant,or dissonant. The contrast between consonance and dissonance is central to Western music and its origins have fascinated scholars since the ancient Greeks. Aesthetic responses to consonance are commonly assumed by scientists to have biological roots, and thus to be universally present in humans. Ethnomusicologists and composers, in contrast, have argued that consonance is a creation of Western musical culture. The issue has remained unresolved, partly because little is known about the extent of cross-cultural variation in consonance preferences. Here we report experiments with the Tsimane'--a native Amazonian society with minimal exposure to Western culture--and comparison populations in Bolivia and the United States that varied in exposure to Western music. Participants rated the pleasantness of sounds. Despite exhibiting Western-like discrimination abilities and Western-like aesthetic responses to familiar sounds and acoustic roughness, the Tsimane' rated consonant and dissonant chords and vocal harmonies as equally pleasant. By contrast, Bolivian city- and town-dwellers exhibited significant preferences for consonance,albeit to a lesser degree than US residents. The results indicate that consonance preferences can be absent in cultures sufficiently isolated from Western music, and are thus unlikely to reflect innate biases or exposure to harmonic natural sounds. The observed variation in preferences is presumably determined by exposure to musical harmony, suggesting that culture has a dominant role in shaping aesthetic responses to music.

  8. Longitudinal imaging of Caenorhabditis elegans in a microfabricated device reveals variation in behavioral decline during aging

    OpenAIRE

    Churgin, Matthew A.; Jung, Sang-Kyu; Yu, Chih-Chieh; Chen, Xiangmei; Raizen, David M.; Fang-Yen, Christopher

    2017-01-01

    eLife digest Aging affects almost all living things, yet little is known about the biological changes that occur as we get older. Scientists often study aging in the microscopic roundworm Caenorhabditis elegans because it reproduces quickly and its lifespan is short (about 2?3 weeks on average). To date, investigations have helped to reveal genes that affect overall lifespan. However, it is not known how much these genes also affect the animal?s healthy lifespan or ?healthspan?, that is to sa...

  9. RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat

    Directory of Open Access Journals (Sweden)

    Shenghui Zhou

    2017-09-01

    Full Text Available Agropyron cristatum, which is a wild grass of the tribe Triticeae, grows widely in harsh environments and provides many desirable genetic resources for wheat improvement. However, unclear interspecific phylogeny and genome-wide variation has limited the utilization of A. cristatum in the production of superior wheat varieties. In this study, by sequencing the transcriptome of the representative tetraploid A. cristatum Z559 and the common wheat variety Fukuhokomugi (Fukuho, which are often used as parents in a wide cross, their phylogenetic relationship and interspecific variation were dissected. First, 214,854 transcript sequences were assembled, and 3,457 orthologous genes related to traits of interest were identified in A. cristatum. Second, a total of 72 putative orthologous gene clusters were used to construct phylogenetic relationships among A. cristatum, Triticeae and other genomes. A clear division between A. cristatum and the other Triticeae species was revealed. Third, the sequence similarity of most genes related to traits of interest is greater than 95% between A. cristatum and wheat. Therefore, using the 5% mismatch parameter for A. cristatum, we mapped the transcriptome sequencing data to wheat reference sequences to discover the variations between A. cristatum and wheat and 862,340 high-quality variants were identified. Additionally, compared with the wheat A and B genomes, the P and D genomes displayed an obviously larger variant density and a longer evolutionary distance, suggesting that A. cristatum is more distantly related to the wheat D genome. Finally, by using Kompetitive Allele Specific PCR array (KASPar technology, 37 of 53 (69.8% SNPs were shown to be genuine in Z559, Fukuho, and additional lines with seven different P chromosomes, and function of the genes in which these SNPs are located were also determined. This study provides not only the first insights into the phylogenetic relationships between the P genome and

  10. RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat.

    Science.gov (United States)

    Zhou, Shenghui; Yan, Baiqiang; Li, Fei; Zhang, Jinpeng; Zhang, Jing; Ma, Huihui; Liu, Weihua; Lu, Yuqing; Yang, Xinming; Li, Xiuquan; Liu, Xu; Li, Lihui

    2017-01-01

    Agropyron cristatum, which is a wild grass of the tribe Triticeae, grows widely in harsh environments and provides many desirable genetic resources for wheat improvement. However, unclear interspecific phylogeny and genome-wide variation has limited the utilization of A. cristatum in the production of superior wheat varieties. In this study, by sequencing the transcriptome of the representative tetraploid A. cristatum Z559 and the common wheat variety Fukuhokomugi (Fukuho), which are often used as parents in a wide cross, their phylogenetic relationship and interspecific variation were dissected. First, 214,854 transcript sequences were assembled, and 3,457 orthologous genes related to traits of interest were identified in A. cristatum. Second, a total of 72 putative orthologous gene clusters were used to construct phylogenetic relationships among A. cristatum, Triticeae and other genomes. A clear division between A. cristatum and the other Triticeae species was revealed. Third, the sequence similarity of most genes related to traits of interest is greater than 95% between A. cristatum and wheat. Therefore, using the 5% mismatch parameter for A. cristatum, we mapped the transcriptome sequencing data to wheat reference sequences to discover the variations between A. cristatum and wheat and 862,340 high-quality variants were identified. Additionally, compared with the wheat A and B genomes, the P and D genomes displayed an obviously larger variant density and a longer evolutionary distance, suggesting that A. cristatum is more distantly related to the wheat D genome. Finally, by using Kompetitive Allele Specific PCR array (KASPar) technology, 37 of 53 (69.8%) SNPs were shown to be genuine in Z559, Fukuho, and additional lines with seven different P chromosomes, and function of the genes in which these SNPs are located were also determined. This study provides not only the first insights into the phylogenetic relationships between the P genome and Triticeae but also

  11. Variation in facial masculinity and symmetry preferences across the menstrual cycle is moderated by relationship context.

    Science.gov (United States)

    Little, Anthony C; Jones, Benedict C

    2012-07-01

    In women, changes in preference during the menstrual cycle have been documented for attractiveness judgements of odour and various physical and behavioural male traits. Although many studies have demonstrated greater attraction to masculine traits, such as male faces, bodies, and voices, at high fertility, several recent studies present null results for these shifts in preferences. Moreover, evidence for stronger attraction to symmetric faces at high fertility is equivocal. Here we examined variation in preferences across the cycle for both facial masculinity and symmetry according to relationship context. Using both within-subject (Study 1) and between-subject (Study2) designs, we show that women prefer masculinity and symmetry in male faces at times when their fertility is likely to be highest (during the follicular phase of their cycle) when judging the faces for short-term relationship attractiveness. No effect of cycle was seen for long-term judgements. These results indicate that cyclic shifts in women are most apparent when judging for short-term relationships, which may explain the null results in studies where only general attractiveness was assessed. Cyclical preferences could influence women to select a partner who possesses traits that may enhance her offspring's quality at times when conception is most likely and/or serve to improve partner investment when investment is important. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Spatial Variation of the Relationship between PM2.5 Concentrations and Meteorological Parameters in China

    Directory of Open Access Journals (Sweden)

    Gang Lin

    2015-01-01

    Full Text Available Epidemiological studies around the world have reported that fine particulate matter (PM2.5 is closely associated with human health. The distribution of PM2.5 concentrations is influenced by multiple geographic and socioeconomic factors. Using a remote-sensing-derived PM2.5 dataset, this paper explores the relationship between PM2.5 concentrations and meteorological parameters and their spatial variance in China for the period 2001–2010. The spatial variations of the relationships between the annual average PM2.5, the annual average precipitation (AAP, and the annual average temperature (AAT were evaluated using the Geographically Weighted Regression (GWR model. The results indicated that PM2.5 had a strong and stable correlation with meteorological parameters. In particular, PM2.5 had a negative correlation with precipitation and a positive correlation with temperature. In addition, the relationship between the variables changed over space, and the strong negative correlation between PM2.5 and the AAP mainly appeared in the warm temperate semihumid region and northern subtropical humid region in 2001 and 2010, with some localized differences. The strong positive correlation between the PM2.5 and the AAT mainly occurred in the mid-temperate semiarid region, the humid, semihumid, and semiarid warm temperate regions, and the northern subtropical humid region in 2001 and 2010.

  13. Satellite measurements reveal strong anisotropy in spatial coherence of climate variations over the Tibet Plateau.

    Science.gov (United States)

    Chen, Deliang; Tian, Yudong; Yao, Tandong; Ou, Tinghai

    2016-08-24

    This study uses high-resolution, long-term satellite observations to evaluate the spatial scales of the climate variations across the Tibet Plateau (TP). Both land surface temperature and precipitation observations of more than 10 years were analysed with a special attention to eight existing ice-core sites in the TP. The temporal correlation for the monthly or annual anomalies between any two points decreases exponentially with their spatial distance, and we used the e-folding decay constant to quantify the spatial scales. We found that the spatial scales are strongly direction-dependent, with distinctive patterns in the west-east and south-north orientations, for example. Meanwhile, in the same directions the scales are largely symmetric backward and forward. Focusing on the west-east and south-north directions, we found the spatial coherence in the first is generally stronger than in the second. The annual surface temperature had typical spatial scales of 302-480 km, while the annual precipitation showed smaller scales of 111-182 km. The majority of the eight ice-core sites exhibit scales much smaller than the typical scales over the TP as a whole. These results provide important observational basis for the selection of appropriate downscaling strategies, deployment of climate-data collection networks, and interpreting paleoclimate reconstructions.

  14. Variation in canopy duration in the perennial biofuel crop Miscanthus reveals complex associations with yield

    Science.gov (United States)

    Robson, Paul R.H.; Farrar, Kerrie; Gay, Alan P.; Jensen, Elaine F.; Clifton-Brown, John C.; Donnison, Iain S.

    2013-01-01

    Energy crops can provide a sustainable source of power and fuels, and mitigate the negative effects of CO2 emissions associated with fossil fuel use. Miscanthus is a perennial C4 energy crop capable of producing large biomass yields whilst requiring low levels of input. Miscanthus is largely unimproved and therefore there could be significant opportunities to increase yield. Further increases in yield will improve the economics, energy balance, and carbon mitigation of the crop, as well as reducing land-take. One strategy to increase yield in Miscanthus is to maximize the light captured through an extension of canopy duration. In this study, canopy duration was compared among a diverse collection of 244 Miscanthus genotypes. Canopy duration was determined by calculating the number of days between canopy establishment and senescence. Yield was positively correlated with canopy duration. Earlier establishment and later senescence were also both separately correlated with higher yield. However, although genotypes with short canopy durations were low yielding, not all genotypes with long canopy durations were high yielding. Differences of yield between genotypes with long canopy durations were associated with variation in stem and leaf traits. Different methodologies to assess canopy duration traits were investigated, including visual assessment, image analysis, light interception, and different trait thresholds. The highest correlation coefficients were associated with later assessments of traits and the use of quantum sensors for canopy establishment. A model for trait optimization to enable yield improvement in Miscanthus and other bioenergy crops is discussed. PMID:23599277

  15. Diversity and Variation of Bacterial Community Revealed by MiSeq Sequencing in Chinese Dark Teas.

    Directory of Open Access Journals (Sweden)

    Jianyu Fu

    Full Text Available Chinese dark teas (CDTs are now among the popular tea beverages worldwide due to their unique health benefits. Because the production of CDTs involves fermentation that is characterized by the effect of microbes, microorganisms are believed to play critical roles in the determination of the chemical characteristics of CDTs. Some dominant fungi have been identified from CDTs. In contrast, little, if anything, is known about the composition of bacterial community in CDTs. This study was set to investigate the diversity and variation of bacterial community in four major types of CDTs from China. First, the composition of the bacterial community of CDTs was determined using MiSeq sequencing. From the four typical CDTs, a total of 238 genera that belong to 128 families of bacteria were detected, including most of the families of beneficial bacteria known to be associated with fermented food. While different types of CDTs had generally distinct bacterial structures, the two types of brick teas produced from adjacent regions displayed strong similarity in bacterial composition, suggesting that the producing environment and processing condition perhaps together influence bacterial succession in CDTs. The global characterization of bacterial communities in CDTs is an essential first step for us to understand their function in fermentation and their potential impact on human health. Such knowledge will be important guidance for improving the production of CDTs with higher quality and elevated health benefits.

  16. Molecular variation of Trypanosoma brucei subspecies as revealed by AFLP fingerprinting.

    Science.gov (United States)

    Agbo, E E C; Majiwa, P A O; Claassen, H J H M; te Pas, M F W

    2002-04-01

    Genetic analysis of Trypanosoma spp. depends on the detection of variation between strains. We have used the amplified fragment length polymorphism (AFLP) technique to develop a convenient and reliable method for genetic characterization of Trypanosome (sub)species. AFLP accesses multiple independent sites within the genome and would allow a better definition of the relatedness of different Trypanosome (sub)species. Nine isolates (3 from each T. brucei subspecies) were tested with 40 AFLP primer combinations to identify the most appropriate pairs of restriction endonucleases and selective primers. Primers based on the recognition sequences of EcoRI and BglII were chosen and used to analyse 31 T. brucei isolates. Similarity levels calculated with the Pearson correlation coefficient ranged from 15 to 98%, and clusters were determined using the unweighted pair-group method using arithmetic averages (UPGMA). At the intraspecific level, AFLP fingerprints were grouped by numerical analysis in 2 main clusters, allowing a clear separation of T. b. gambiense (cluster I) from T. b. brucei and T. b. rhodesiense isolates (cluster II). Interspecies evaluation of this customized approach produced heterogeneous AFLP patterns, with unique genetic markers, except for T. evansi and T. equiperdum, which showed identical patterns and clustered together.

  17. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

    Directory of Open Access Journals (Sweden)

    James W Kijas

    Full Text Available The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

  18. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

    Science.gov (United States)

    Kijas, James W; Townley, David; Dalrymple, Brian P; Heaton, Michael P; Maddox, Jillian F; McGrath, Annette; Wilson, Peter; Ingersoll, Roxann G; McCulloch, Russell; McWilliam, Sean; Tang, Dave; McEwan, John; Cockett, Noelle; Oddy, V Hutton; Nicholas, Frank W; Raadsma, Herman

    2009-01-01

    The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

  19. Diel Variation in Flower Scent Reveals Poor Consistency of Diurnal and Nocturnal Pollination Syndromes in Sileneae.

    Science.gov (United States)

    Prieto-Benítez, Samuel; Dötterl, Stefan; Giménez-Benavides, Luis

    2015-12-01

    The composition of flower scent and the timing of emission are crucial for chemical communication between plants and their pollinators; hence, they are key traits for the characterization of pollination syndromes. In many plants, however, plants are assigned to a syndrome based on inexpensive to measure flower traits, such as color, time of flower opening, and shape. We compared day and night scents from 31 Sileneae species and tested for quantitative and semi-quantitative differences in scent among species classified a priori as diurnal or nocturnal. As most Sileneae species are not only visited by either diurnal or nocturnal animals as predicted by their syndrome, we hypothesized that, even if flower scent were preferentially emitted during the day or at night, most species also would emit some scents during the opposing periods of the day. This phenomenon would contribute to the generalized assemblage of flower visitors usually observed in Sileneae species. We found that diel variations of scent often were not congruent with the syndrome definition, but could partially be explained by taxonomy and sampling times. Most species emitted compounds with attractive potential to insects during both the night and day. Our results highlight the current opinion that syndromes are not watertight compartments evolved to exclude some flower visitors. Thus, important information may be lost when scents are collected either during day- or night-time, depending on the a priori classification of the species as diurnal or nocturnal.

  20. Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy

    DEFF Research Database (Denmark)

    Kaas, Christian Schrøder; Kristensen, Claus; Betenbaugh, Michael J.

    2015-01-01

    depths of 0x, 16x, 33x and 49x coverage corresponding to a copy number in the genome of 0, 1, 2 and 3 copies. This indicate that 17% of the genes are haploid revealing a large number of genes which can be knocked out with relative ease. This tendency of haploidy was furthermore shown to be present...... in eight additional analyzed CHO genomes (15-20% haploidy) but not in the genome of the Chinese hamster. The dhfr gene is confirmed to be haploid in CHO DXB11; transcriptionally active and the remaining allele contains a G410C point mutation causing a Thr137Arg missense mutation. We find similar to 2...

  1. Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence.

    Science.gov (United States)

    Setoh, Yin Xiang; Amarilla, Alberto A; Peng, Nias Y; Slonchak, Andrii; Periasamy, Parthiban; Figueiredo, Luiz T M; Aquino, Victor H; Khromykh, Alexander A

    2017-09-22

    Rocio virus (ROCV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae. We present an updated sequence of ROCV strain SPH 34675 (GenBank: AY632542.4), the only available full genome sequence prior to this study. Using next-generation sequencing of the entire genome, we reveal substantial sequence variation from the prototype sequence, with 30 nucleotide differences amounting to 14 amino acid changes, as well as significant changes to predicted 3'UTR RNA structures. Our results present an updated and corrected sequence of a potential emerging human-virulent flavivirus uniquely indigenous to Brazil (GenBank: MF461639).

  2. Revealing textural variations at the groundwater-surface water interface using induced polarisation techniques

    Science.gov (United States)

    McLachlan, P.; Binley, A. M.; Chambers, J. E.

    2016-12-01

    The groundwater-surface water (GW-SW) interface actively governs the transfer of water, nutrients and contaminants between groundwater systems and surface water environments. It is capable of mitigating environmental pollution by attenuating and transforming contaminants transported by groundwater discharging to the surface or by surface water recharging to the subsurface. The ability of the GW-SW interface to mitigate pollution is linked to its hydrological and physiochemical properties, the presence of grain surfaces, and its consequent ability to host diverse microbial populations. Despite its importance, characterising the GW-SW interface remains a challenge as traditional methods are often intrusive, environmentally damaging or labour intensive and so they often provide spatially sparse, or spatially restricted, information. There is therefore a requirement for methods which can provide information about the GW-SW interface at high spatial resolution and over large areas. In recent years there has been increased interest in using induced polarisation in field based exploration to characterise grain surface properties of unconsolidated geological materials. Induced polarisation may offer the potential to interrogate textural properties of the GW-SW interface, such as cation exchange and grain surface area which are important for determining the biogeochemical properties of the subsurface. Here we demonstrate the ability of induced polarisation measurements to reveal contrasts in the textural properties of two sites on a 200 m river meander (River Leith, Cumbria, UK). Previous work has revealed that both sites are distinctive in terms of their hydrology, fluvial deposits and biogeochemistry. We present in-stream induced polarisation measurements in addition to lab based measurements of induced polarisation, cation exchange capacity, grain size distribution and surface area on samples obtained from drilling.

  3. In situ cardiac perfusion reveals interspecific variation of intraventricular flow separation in reptiles.

    Science.gov (United States)

    Joyce, William; Axelsson, Michael; Altimiras, Jordi; Wang, Tobias

    2016-07-15

    The ventricles of non-crocodilian reptiles are incompletely divided and provide an opportunity for mixing of oxygen-poor blood and oxygen-rich blood (intracardiac shunting). However, both cardiac morphology and in vivo shunting patterns exhibit considerable interspecific variation within reptiles. In the present study, we develop an in situ double-perfused heart approach to characterise the propensity and capacity for shunting in five reptile species: the turtle Trachemys scripta, the rock python Python sebae, the yellow anaconda Eunectes notaeus, the varanid lizard Varanus exanthematicus and the bearded dragon Pogona vitticeps To simulate changes in vascular bed resistance, pulmonary and systemic afterloads were independently manipulated and changes in blood flow distribution amongst the central outflow tracts were monitored. As previously demonstrated in Burmese pythons, rock pythons and varanid lizards exhibited pronounced intraventricular flow separation. As pulmonary or systemic afterload was raised, flow in the respective circulation decreased. However, flow in the other circulation, where afterload was constant, remained stable. This correlates with the convergent evolution of intraventricular pressure separation and the large intraventricular muscular ridge, which compartmentalises the ventricle, in these species. Conversely, in the three other species, the pulmonary and systemic flows were strongly mutually dependent, such that the decrease in pulmonary flow in response to elevated pulmonary afterload resulted in redistribution of perfusate to the systemic circuit (and vice versa). Thus, in these species, the muscular ridge appeared labile and blood could readily transverse the intraventricular cava. We conclude that relatively minor structural differences between non-crocodilian reptiles result in the fundamental changes in cardiac function. Further, our study emphasises that functionally similar intracardiac flow separation evolved independently in

  4. Fish habitat selection in a large hydropeaking river: Strong individual and temporal variations revealed by telemetry.

    Science.gov (United States)

    Capra, Hervé; Plichard, Laura; Bergé, Julien; Pella, Hervé; Ovidio, Michaël; McNeil, Eric; Lamouroux, Nicolas

    2017-02-01

    Modeling individual fish habitat selection in highly variable environments such as hydropeaking rivers is required for guiding efficient management decisions. We analyzed fish microhabitat selection in the heterogeneous hydraulic and thermal conditions (modeled in two-dimensions) of a reach of the large hydropeaking Rhône River locally warmed by the cooling system of a nuclear power plant. We used modern fixed acoustic telemetry techniques to survey 18 fish individuals (five barbels, six catfishes, seven chubs) signaling their position every 3s over a three-month period. Fish habitat selection depended on combinations of current microhabitat hydraulics (e.g. velocity, depth), past microhabitat hydraulics (e.g. dewatering risk or maximum velocities during the past 15days) and to a lesser extent substrate and temperature. Mixed-effects habitat selection models indicated that individual effects were often stronger than specific effects. In the Rhône, fish individuals appear to memorize spatial and temporal environmental changes and to adopt a "least constraining" habitat selection. Avoiding fast-flowing midstream habitats, fish generally live along the banks in areas where the dewatering risk is high. When discharge decreases, however, they select higher velocities but avoid both dewatering areas and very fast-flowing midstream habitats. Although consistent with the available knowledge on static fish habitat selection, our quantitative results demonstrate temporal variations in habitat selection, depending on individual behavior and environmental history. Their generality could be further tested using comparative experiments in different environmental configurations. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Pauses in Striatal Cholinergic Interneurons: What is Revealed by Their Common Themes and Variations?

    Directory of Open Access Journals (Sweden)

    Yan-Feng Zhang

    2017-10-01

    Full Text Available Striatal cholinergic interneurons, the so-called tonically active neurons (TANs, pause their firing in response to sensory cues and rewards during classical conditioning and instrumental tasks. The respective pause responses observed can demonstrate many commonalities, such as constant latency and duration, synchronous occurrence in a population of cells, and coincidence with phasic activities of midbrain dopamine neurons (DANs that signal reward predictions and errors. Pauses can however also show divergent properties. Pause latencies and durations can differ in a given TAN between appetitive vs. aversive outcomes in classical conditioning, initial excitation can be present or absent, and a second pause can variably follow a rebound. Despite more than 20 years of study, the functions of these pause responses are still elusive. Our understanding of pause function is hindered by an incomplete understanding of how pauses are generated. In this mini-review article, we compare pause types, as well as current key hypotheses for inputs underlying pauses that include dopamine-induced inhibition through D2-receptors, a GABA input from ventral tegmental area, and a prolonged afterhyperpolarization induced by excitatory input from the cortex or from the thalamus. We review how each of these mechanisms alone explains some but not all aspects of pause responses. These mechanisms might need to operate in specific but variable sets of sequences to generate a full range of pause responses. Alternatively, these mechanisms might operate in conjunction with an underlying control mechanism within cholinergic interneurons which could potentially provide a framework to generate the common themes and variations seen amongst pause responses.

  6. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes.

    Science.gov (United States)

    Glessner, Joseph T; Wang, Kai; Cai, Guiqing; Korvatska, Olena; Kim, Cecilia E; Wood, Shawn; Zhang, Haitao; Estes, Annette; Brune, Camille W; Bradfield, Jonathan P; Imielinski, Marcin; Frackelton, Edward C; Reichert, Jennifer; Crawford, Emily L; Munson, Jeffrey; Sleiman, Patrick M A; Chiavacci, Rosetta; Annaiah, Kiran; Thomas, Kelly; Hou, Cuiping; Glaberson, Wendy; Flory, James; Otieno, Frederick; Garris, Maria; Soorya, Latha; Klei, Lambertus; Piven, Joseph; Meyer, Kacie J; Anagnostou, Evdokia; Sakurai, Takeshi; Game, Rachel M; Rudd, Danielle S; Zurawiecki, Danielle; McDougle, Christopher J; Davis, Lea K; Miller, Judith; Posey, David J; Michaels, Shana; Kolevzon, Alexander; Silverman, Jeremy M; Bernier, Raphael; Levy, Susan E; Schultz, Robert T; Dawson, Geraldine; Owley, Thomas; McMahon, William M; Wassink, Thomas H; Sweeney, John A; Nurnberger, John I; Coon, Hilary; Sutcliffe, James S; Minshew, Nancy J; Grant, Struan F A; Bucan, Maja; Cook, Edwin H; Buxbaum, Joseph D; Devlin, Bernie; Schellenberg, Gerard D; Hakonarson, Hakon

    2009-05-28

    Autism spectrum disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies focusing on candidate genes or genomic regions have identified several copy number variations (CNVs) that are associated with an increased risk of ASDs. Here we present the results from a whole-genome CNV study on a cohort of 859 ASD cases and 1,409 healthy children of European ancestry who were genotyped with approximately 550,000 single nucleotide polymorphism markers, in an attempt to comprehensively identify CNVs conferring susceptibility to ASDs. Positive findings were evaluated in an independent cohort of 1,336 ASD cases and 1,110 controls of European ancestry. Besides previously reported ASD candidate genes, such as NRXN1 (ref. 10) and CNTN4 (refs 11, 12), several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls (P = 9.5 x 10(-3)). Furthermore, CNVs within or surrounding genes involved in the ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40, were affected by CNVs not observed in controls (P = 3.3 x 10(-3)). We also identified duplications 55 kilobases upstream of complementary DNA AK123120 (P = 3.6 x 10(-6)). Although these variants may be individually rare, they target genes involved in neuronal cell-adhesion or ubiquitin degradation, indicating that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.

  7. Massive stars reveal variations of the stellar initial mass function in the Milky Way stellar clusters

    Science.gov (United States)

    Dib, Sami; Schmeja, Stefan; Hony, Sacha

    2017-01-01

    We investigate whether the stellar initial mass function (IMF) is universal, or whether it varies significantly among young stellar clusters in the Milky Way. We propose a method to uncover the range of variation of the parameters that describe the shape of the IMF for the population of young Galactic clusters.These parameters are the slopes in the low and high stellar mass regimes, γ and Γ, respectively, and the characteristic mass, Mch. The method relies exclusively on the high-mass content of the clusters, but is able to yield information on the distributions of parameters that describe the IMF over the entire stellar mass range. This is achieved by comparing the fractions of single and lonely massive O stars in a recent catalogue of the Milky Way clusters with a library of simulated clusters built with various distribution functions of the IMF parameters. The synthetic clusters are corrected for the effects of the binary population, stellar evolution, sample incompleteness, and ejected O stars. Our findings indicate that broad distributions of the IMF parameters are required in order to reproduce the fractions of single and lonely O stars in Galactic clusters. They also do not lend support to the existence of a cluster mass-maximum stellar mass relation. We propose a probabilistic formulation of the IMF whereby the parameters of the IMF are described by Gaussian distribution functions centred around γ = 0.91, Γ = 1.37, and Mch = 0.41 M⊙, and with dispersions of σγ = 0.25, σΓ = 0.60, and σ _{M_{ch}}=0.27 M⊙ around these values.

  8. Metabolomics reveals amino acids contribute to variation in response to simvastatin treatment.

    Directory of Open Access Journals (Sweden)

    Miles Trupp

    Full Text Available Statins are widely prescribed for reducing LDL-cholesterol (C and risk for cardiovascular disease (CVD, but there is considerable variation in therapeutic response. We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism. Analyses were conducted in 148 participants in the Cholesterol and Pharmacogenetics study who were profiled pre and six weeks post treatment with 40 mg/day simvastatin: 100 randomly selected from the full range of the LDL-C response distribution and 24 each from the top and bottom 10% of this distribution ("good" and "poor" responders, respectively. The metabolic signature of drug exposure in the full range of responders included essential amino acids, lauric acid (p<0.0055, q<0.055, and alpha-tocopherol (p<0.0003, q<0.017. Using the HumanCyc database and pathway enrichment analysis, we observed that the metabolites of drug exposure were enriched for the pathway class amino acid degradation (p<0.0032. Metabolites whose change correlated with LDL-C lowering response to simvastatin in the full range responders included cystine, urea cycle intermediates, and the dibasic amino acids ornithine, citrulline and lysine. These dibasic amino acids share plasma membrane transporters with arginine, the rate-limiting substrate for nitric oxide synthase (NOS, a critical mediator of cardiovascular health. Baseline metabolic profiles of the good and poor responders were analyzed by orthogonal partial least square discriminant analysis so as to determine the metabolites that best separated the two response groups and could be predictive of LDL-C response. Among these were xanthine, 2-hydroxyvaleric acid, succinic acid, stearic acid, and fructose. Together, the findings from this study indicate that clusters of metabolites involved in multiple pathways not directly connected with cholesterol metabolism may play a role in modulating the response

  9. SPATIAL VARIATIONS OF PAH PROPERTIES IN M17SW REVEALED BY SPITZER /IRS SPECTRAL MAPPING

    Energy Technology Data Exchange (ETDEWEB)

    Yamagishi, M. [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Chuo-ku, Sagamihara 252-5210 (Japan); Kaneda, H.; Ishihara, D.; Oyabu, S.; Suzuki, T.; Nishimura, A.; Kohno, M. [Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Onaka, T.; Ohashi, S. [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Nagayama, T.; Matsuo, M. [Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065 (Japan); Umemoto, T.; Minamidani, T.; Fujita, S. [Nobeyama Radio Observatory, National Astronomical Observatory of Japan (NAOJ), National Institutes of Natural Sciences (NINS), 462-2, Nobeyama, Minamimaki, Minamisaku, Nagano 384-1305 (Japan); Tsuda, Y., E-mail: yamagish@ir.isas.jaxa.jp [Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-0042 (Japan)

    2016-12-20

    We present Spitzer /IRS mid-infrared spectral maps of the Galactic star-forming region M17 as well as IRSF/SIRIUS Br γ and Nobeyama 45 m/FOREST {sup 13}CO ( J = 1–0) maps. The spectra show prominent features due to polycyclic aromatic hydrocarbons (PAHs) at wavelengths of 6.2, 7.7, 8.6, 11.3, 12.0, 12.7, 13.5, and 14.2  μ m. We find that the PAH emission features are bright in the region between the H ii region traced by Br γ and the molecular cloud traced by {sup 13}CO, supporting that the PAH emission originates mostly from photo-dissociation regions. Based on the spatially resolved Spitzer /IRS maps, we examine spatial variations of the PAH properties in detail. As a result, we find that the interband ratio of PAH 7.7  μ m/PAH 11.3  μ m varies locally near M17SW, but rather independently of the distance from the OB stars in M17, suggesting that the degree of PAH ionization is mainly controlled by local conditions rather than the global UV environments determined by the OB stars in M17. We also find that the interband ratios of the PAH 12.0  μ m, 12.7  μ m, 13.5  μ m, and 14.2  μ m features to the PAH 11.3  μ m feature are high near the M17 center, which suggests structural changes of PAHs through processing due to intense UV radiation, producing abundant edgy irregular PAHs near the M17 center.

  10. Nuclear receptor engineering based on novel structure activity relationships revealed by farnesyl pyrophosphate.

    Science.gov (United States)

    Goyanka, Ritu; Das, Sharmistha; Samuels, Herbert H; Cardozo, Timothy

    2010-11-01

    Nuclear receptors (NRs) comprise the second largest protein family targeted by currently available drugs, acting via specific ligand interactions within the ligand binding domain (LBD). Recently, farnesyl pyrophosphate (FPP) was shown to be a unique promiscuous NR ligand, activating a subset of NR family members and inhibiting wound healing in skin. The current study aimed at visualizing the unique basis of FPP interaction with multiple receptors in order to identify general structure-activity relationships that operate across the NR family. Docking of FPP to the 3D structures of the LBDs of a diverse set of NRs consistently revealed an electrostatic FPP pyrophosphate contact with an NR arginine conserved in the NR family, a hydrophobic farnesyl contact with NR helix-12 and a ligand binding pocket volume between 300 and 430 Å(3) as the minimal requirements for FPP activation of any NR. Lack of any of these structural features appears to render a given NR resistant to FPP activation. We used these structure-activity relationships to rationally design and successfully engineer several mutant human estrogen receptors that retain responsiveness to estradiol but no longer respond to FPP.

  11. Genepool Variation in Genus Glycine Subgenus Soja Revealed by Polymorphic Nuclear and Chloroplast Microsatellites

    Science.gov (United States)

    Powell, W.; Morgante, M.; Doyle, J. J.; McNicol, J. W.; Tingey, S. V.; Rafalski, A. J.

    1996-01-01

    A combination of nuclear and chloroplast simple sequence repeats (SSRs) have been used to investigate the levels and pattern of variability detected in Glycine max and G. soja genotypes. Based on the analysis of 700 soybean genotypes with 115 restriction fragment length polymorphism (RFLP) probes, 12 accessions were identified that represent 92% of the allelic variability detected in this genepool. These 12 core genotypes together with a sample of G. max and G. soja accessions were evaluated with 11 nuclear SSRs that detected 129 alleles. Compared with the other G. max and G. soja genotypes sampled, the core genotypes represent 40% of the allelic variability detected with SSRs. Despite the multi-allelic nature of soybean SSRs, dendrograms representing phenetic relationships between accessions clustered according to their subspecies origin. In addition to biparentally inherited nuclear SSRs, two uniparentally (maternally) transmitted chloroplast SSRs were also studied. A total of seven haplotypes were identified, and diversity indices of 0.405 +/- 0.088 and 0.159 +/- 0.071 were obtained for the two chloroplast SSRs. The availability of polymorphic SSR loci in the chloroplast genome provides new opportunities to investigate cytonuclear interactions in plants. PMID:8889540

  12. Revealing Spatial Variation and Correlation of Urban Travels from Big Trajectory Data

    Science.gov (United States)

    Li, X.; Tu, W.; Shen, S.; Yue, Y.; Luo, N.; Li, Q.

    2017-09-01

    With the development of information and communication technology, spatial-temporal data that contain rich human mobility information are growing rapidly. However, the consistency of multi-mode human travel behind multi-source spatial-temporal data is not clear. To this aim, we utilized a week of taxies' and buses' GPS trajectory data and smart card data in Shenzhen, China to extract city-wide travel information of taxi, bus and metro and tested the correlation of multi-mode travel characteristics. Both the global correlation and local correlation of typical travel indicator were examined. The results show that: (1) Significant differences exist in of urban multi-mode travels. The correlation between bus travels and taxi travels, metro travel and taxi travels are globally low but locally high. (2) There are spatial differences of the correlation relationship between bus, metro and taxi travel. These findings help us understanding urban travels deeply therefore facilitate both the transport policy making and human-space interaction research.

  13. Adolescent overweight, social relationships and the transition to first sex: gender and racial variations.

    Science.gov (United States)

    Cheng, Yen-hsin Alice; Landale, Nancy S

    2011-03-01

    Being overweight influences adolescents' relationships by increasing their likelihood of experiencing social alienation and discrimination. Its role in sexual development is relatively understudied, as are potential mechanisms through which weight may influence early sexual activity. Data from the National Longitudinal Study of Adolescent Health were used in discrete-time event history analyses investigating the association between body weight, social relationships and timing of sexual debut among 8,197 respondents who were in grades 7-12 in 1994-1995 (Wave 1) and were young adults in 2001-2002 (Wave 3). Subgroup analyses explored gender and racial and ethnic variations in the association. Overweight adolescents were less likely than their normal-weight peers to report first intercourse between Waves 1 and 3 (odds ratio, 0.9). Characteristics reflecting social alienation, including having relatively few close friends and no experience with romantic relationships, were negatively associated with first intercourse among overweight youths. Results differed by gender and race and ethnicity. Overweight females had a lower likelihood than normal-weight females of experiencing first intercourse (0.8), but no such association was evident among males. Similarly, overweight white youths--but not those from other racial and ethnic groups--had reduced odds of sexual debut (0.7). Future studies should seek to understand the broader implications of adolescent weight status for social relationships and subsequent development, and practitioners should apply this knowledge to prevention programs. Postponement of sexual activity may benefit youths, but potential benefits and risks may depend upon the social processes involved. Copyright © 2010 by the Guttmacher Institute.

  14. Striking variations in consultation rates with general practice reveal family influence

    Directory of Open Access Journals (Sweden)

    Spreeuwenberg Peter

    2007-01-01

    Full Text Available Abstract Background The reasons why patients decide to consult a general practitioner vary enormously. While there may be individual reasons for this variation, the family context has a significant and unique influence upon the frequency of individuals' visits. The objective of this study was to explore which family factors can explain the differences between strikingly high, and correspondingly low, family consultation rates in families with children aged up to 21. Methods Data were used from the second Dutch national survey of general practice. This survey extracted from the medical records of 96 practices in the Netherlands, information on all consultations with patients during 2001. We defined, through multilevel analysis, two groups of families. These had respectively, predominantly high, and low, contact frequencies due to a significant family influence upon the frequency of the individual's first contacts. Binomial logistic regression analyses were used to analyse which of the family factors, related to shared circumstances and socialisation conditions, can explain the differences in consultation rates between the two groups of families. Results In almost 3% of all families, individual consultation rates decrease significantly due to family influence. In 11% of the families, individual consultation rates significantly increase due to family influence. While taking into account the health status of family members, family factors can explain family consultation rates. These factors include circumstances such as their economic status and number of children, as well as socialisation conditions such as specific health knowledge and family beliefs. The chance of significant low frequencies of contact due to family influences increases significantly with factors such as, paid employment of parents in the health care sector, low expectations of general practitioners' care for minor ailments and a western cultural background. Conclusion Family

  15. Robust hierarchical state-space models reveal diel variation in travel rates of migrating leatherback turtles.

    Science.gov (United States)

    Jonsen, Ian D; Myers, Ransom A; James, Michael C

    2006-09-01

    1. Biological and statistical complexity are features common to most ecological data that hinder our ability to extract meaningful patterns using conventional tools. Recent work on implementing modern statistical methods for analysis of such ecological data has focused primarily on population dynamics but other types of data, such as animal movement pathways obtained from satellite telemetry, can also benefit from the application of modern statistical tools. 2. We develop a robust hierarchical state-space approach for analysis of multiple satellite telemetry pathways obtained via the Argos system. State-space models are time-series methods that allow unobserved states and biological parameters to be estimated from data observed with error. We show that the approach can reveal important patterns in complex, noisy data where conventional methods cannot. 3. Using the largest Atlantic satellite telemetry data set for critically endangered leatherback turtles, we show that the diel pattern in travel rates of these turtles changes over different phases of their migratory cycle. While foraging in northern waters the turtles show similar travel rates during day and night, but on their southward migration to tropical waters travel rates are markedly faster during the day. These patterns are generally consistent with diving data, and may be related to changes in foraging behaviour. Interestingly, individuals that migrate southward to breed generally show higher daytime travel rates than individuals that migrate southward in a non-breeding year. 4. Our approach is extremely flexible and can be applied to many ecological analyses that use complex, sequential data.

  16. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes.

    Science.gov (United States)

    Starkenburg, Shawn R; Kwon, Kyungyoon J; Jha, Ramesh K; McKay, Cedar; Jacobs, Michael; Chertkov, Olga; Twary, Scott; Rocap, Gabrielle; Cattolico, Rose Ann

    2014-03-19

    Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776. The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome). Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.

  17. Nuclear DNA Content Variation and Species Relationships in the Genus Lupinus (Fabaceae)

    Science.gov (United States)

    NAGANOWSKA, BARBARA; WOLKO, BOGDAN; ŚLIWIŃSKA, ELWIRA; KACZMAREK, ZYGMUNT

    2003-01-01

    The 2C nuclear DNA content has been estimated by flow cytometry in 18 species and botanical forms of the genus Lupinus (family Fabaceae), using propidium iodide as a fluorescent dye. They represented distinct infrageneric taxonomic groups and differed in somatic chromosome numbers. Estimated 2C DNA values ranged from 0·97 pg in L. princei to 2·44 pg in L. luteus, which gives a more than 2·5-fold variation. Statistical analysis of the data obtained resulted in a grouping that supports the generally accepted taxonomic classification of the Old World lupins. The rough-seeded L. princei turned out to be an interesting exception, getting closer to smooth-seeded species. Results of DNA content analyses are discussed with regards to the phylogenetic relationships among the Old World lupins and some aspects of the evolution of the genus. PMID:12853281

  18. Lithologic variation within bright material on Vesta revealed by linear spectral unmixing

    Science.gov (United States)

    Zambon, F.; Tosi, F.; Carli, C.; De Sanctis, M. C.; Blewett, D. T.; Palomba, E.; Longobardo, A.; Frigeri, A.; Ammannito, E.; Russell, C. T.; Raymond, C. A.

    2016-07-01

    Vesta's surface is mostly composed of pyroxene-rich lithologies compatible with howardite, eucrite and diogenite (HED) meteorites (e.g., McCord et al. [1970] Science, 168, 1445-1447; Feierberg & Drake [1980] Science, 209, 805-807). Data provided by the Visible and Infrared (VIR) spectrometer, onboard the NASA Dawn spacecraft, revealed that all Vesta reflectance spectra show absorption bands at ∼0.9 and ∼1.9 μm, which are typical of iron-bearing pyroxenes (De Sanctis et al. [2012] Science, 336, 697-700). Other minerals may be present in spectrally significant concentrations; these include olivine and opaque phases like those found in carbonaceous chondrites. These additional components modify the dominant pyroxene absorptions. We apply linear spectral unmixing on bright material (BM) units of Vesta to identify HEDs and non-HED phases. We explore the limits of applicability of linear spectral unmixing, testing it on laboratory mixtures. We find that the linear method is applicable at the VIR pixel resolution and it is useful when the surface is composed of pyroxene-rich lithologies containing moderate quantities of carbonaceous chondrite, olivine, and plagioclase. We found three main groups of BM units: eucrite-rich, diogenite-rich, and olivine-rich. For the non-HED spectral endmember, we choose either olivine or a featureless component. Our work confirms that Vesta's surface contains a high content of pyroxenes mixed with a lower concentration of other phases. In many cases, the non-HED endmember that gives the best fit is the featureless phase, which causes a reduction in the strength of both bands. The anticorrelation between albedo and featureless endmember indicates that this phase is associated with low-albedo, CC-like opaque material. Large amounts of olivine have been detected in Bellicia, Arruntia and BU14 BM units. Other sites present low olivine content (<30%) mostly with a high concentration of diogenite.

  19. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

    Directory of Open Access Journals (Sweden)

    Yanliang Jiang

    Full Text Available The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

  20. Fecal genotyping and contaminant analyses reveal variation in individual river otter exposure to localized persistent contaminants.

    Science.gov (United States)

    Guertin, Daniel A; Harestad, Alton S; Ben-David, Merav; Drouillard, Ken G; Elliott, John E

    2010-02-01

    The present study investigated polyhalogenated aromatic hydrocarbon (PHAH) concentrations in feces of known river otters (Lontra canadensis) along the coast of southern Vancouver Island, British Columbia, Canada. Specifically, we combined microsatellite genotyping of DNA from feces for individual identification with fecal contaminant analyses to evaluate exposure of 23 wild otters to organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and polybrominated diphenylethers (PBDEs). Overall, feces collected from otters in urban/industrial Victoria Harbor had the greatest concentrations of nearly all compounds assessed. Fecal concentrations of OCPs and PBDEs were generally low throughout the region, whereas PCBs dominated in all locations. Re-sampling of known otters over space and time revealed that PCB exposure varied with movement and landscape use. Otters with the highest fecal PCB concentrations were those inhabiting the inner reaches of Victoria Harbor and adjacent Esquimalt Harbor, and those venturing into the harbor systems. Over 50% of samples collected from eight known otters in Victoria Harbor had total-PCB concentrations above the maximum allowable concentration as established for Eurasian otter (Lutra lutra) feces, with a geometric mean value (10.6 mg/kg lipid wt) that exceeded the reproductive toxicity threshold (9 mg/kg lipid wt). Those results are consistent with our findings from 1998 and 2004, and indicate that the harbors of southern Vancouver Island, particularly Victoria Harbor, are a chronic source of PCB exposure for otters. The present study further demonstrates the suitability of using otter feces as a noninvasive/destructive biomonitoring tool in contaminant studies, particularly when sampling of the same individuals at the local population-level is desired. Copyright 2009 SETAC.

  1. Relationship of Mycotoxins Accumulation and Bioactive Components Variation in Ginger after Fungal Inoculation

    Directory of Open Access Journals (Sweden)

    Zhixin Yang

    2017-06-01

    Full Text Available Ginger has got increasing worldwide interests due to its extensive biological activities, along with high medical and edible values. But fungal contamination and mycotoxin residues have brought challenges to its quality and safety. In the present study, the relationship of content of mycotoxins accumulation and bioactive components variation in ginger after infection by toxigenic fungi were investigated for the first time to elucidate the influence of fungal contamination on the inherent quality of ginger. After being infected by Aspergillus flavus and Aspergillus carbonarius for different periods, the produced mycotoxins was determined by an immunoaffinity column clean-up based ultra-fast liquid chromatography coupled with tandem mass spectrometry, and the main bioactive components in ginger were analyzed by ultra performance liquid chromatography-photodiode array detection. The results showed that consecutive incubation of ginger with A. flavus and A. carbonarius within 20 days resulted in the production and accumulation of aflatoxins (especially AFB1 and ochratoxin A, as well as the constant content reduction of four bioactive components, which were confirmed through the scanning electron microscope images. Significantly negative correlation was expressed between the mycotoxins accumulation and bioactive components variation in ginger, which might influence the quality and safety of it. Furthermore, a new compound was detected after inoculation for 6 days, which was found in our study for the first time.

  2. A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape.

    Science.gov (United States)

    Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; Del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

    2017-01-04

    We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.

  3. A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape

    Science.gov (United States)

    Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

    2017-01-01

    We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk. PMID:28051113

  4. Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

    Science.gov (United States)

    Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth

    2011-01-01

    Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements. PMID:21765983

  5. Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains

    Science.gov (United States)

    Davidson, Rebecca M.; Hasan, Nabeeh A.; de Moura, Vinicius Calado Nogueira; Duarte, Rafael Silva; Jackson, Mary; Strong, Michael

    2013-01-01

    Rapidly growing, non-tuberculous mycobacteria (NTM) in the Mycobacterium abscessus (MAB) species are emerging pathogens that cause various diseases including skin and respiratory infections. The species has undergone recent taxonomic nomenclature refinement, and is currently recognized as two subspecies, M. abscessus subsp. abscessus (MAB-A) and M. abscessus subsp. bolletii (MAB-B). The recently reported outbreaks of MAB-B in surgical patients in Brazil from 2004 to 2009 and in cystic fibrosis patients in the United Kingdom (UK) in 2006 to 2012 underscore the need to investigate the genetic diversity of clinical MAB strains. To this end, we sequenced the genomes of two Brazilian MAB-B epidemic isolates (CRM-0019 and CRM-0020) derived from an outbreak of skin infections in Rio de Janeiro, two unrelated MAB strains from patients with pulmonary infections in the United States (US) (NJH8 and NJH11) and one type MAB-B strain (CCUG 48898) and compared them to 25 publically available genomes of globally diverse MAB strains. Genome-wide analyses of 27,598 core genome single nucleotide polymorphisms (SNPs) revealed that the two Brazilian derived CRM strains are nearly indistinguishable from one another and are more closely related to UK outbreak isolates infecting CF patients than to strains from the US, Malaysia or France. Comparative genomic analyses of six closely related outbreak strains revealed geographic-specific large-scale insertion/deletion variation that corresponds to bacteriophage insertions and recombination hotspots. Our study integrates new genome sequence data with existing genomic information to explore the global diversity of infectious M. abscessus isolates and to compare clinically relevant outbreak strains from different continents. PMID:24055961

  6. Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

    Science.gov (United States)

    Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama-Jr, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

    2017-04-21

    Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA2s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA2s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not efficiently

  7. Seasonal variation of the Beaufort shelfbreak jet and its relationship to Arctic cetacean occurrence

    Science.gov (United States)

    Lin, Peigen; Pickart, Robert S.; Stafford, Kathleen M.; Moore, G. W. K.; Torres, Daniel J.; Bahr, Frank; Hu, Jianyu

    2016-12-01

    Using mooring time series from September 2008 to August 2012, together with ancillary atmospheric and satellite data sets, we quantify the seasonal variations of the shelfbreak jet in the Alaskan Beaufort Sea and explore connections to the occurrences of bowhead and beluga whales. Wind patterns during the 4 year study period are different from the long-term climatological conditions that the springtime peak in easterly winds shifted from May to June and the autumn peak was limited to October instead of extending farther into the fall. These changes were primarily due to the behavior of the two regional atmospheric centers of action, the Aleutian Low and Beaufort High. The volume transport of the shelfbreak jet, which peaks in the summer, was decomposed into a background (weak wind) component and a wind-driven component. The wind-driven component is correlated to the Pt. Barrow, AK alongcoast wind speed record although a more accurate prediction is obtained when considering the ice thickness at the mooring site. An upwelling index reveals that wind-driven upwelling is enhanced in June and October when storms are stronger and longer-lasting. The seasonal variation of Arctic cetacean occurrence is dominated by the eastward migration in spring, dictated by pack-ice patterns, and westward migration in fall, coincident with the autumn peak in shelfbreak upwelling intensity.

  8. ¹³C MRS reveals a small diurnal variation in the glycogen content of human thigh muscle.

    Science.gov (United States)

    Takahashi, Hideyuki; Kamei, Akiko; Osawa, Takuya; Kawahara, Takashi; Takizawa, Osamu; Maruyama, Katsuya

    2015-06-01

    There is marked diurnal variation in the glycogen content of skeletal muscles of animals, but few studies have addressed such variations in human muscles. (13)C MRS can be used to noninvasively measure the glycogen content of human skeletal muscle, but no study has explored the diurnal variations in this parameter. This study aimed to investigate whether a diurnal variation in glycogen content occurs in human muscles and, if so, to what extent it can be identified using (13)C MRS. Six male volunteers were instructed to maintain their normal diet and not to perform strenuous exercise for at least 3 days before and during the experiment. Muscle glycogen and blood glucose concentrations were measured six times in 24 h under normal conditions in these subjects. The glycogen content in the thigh muscle was determined noninvasively by natural abundance (13)C MRS using a clinical MR system at 3 T. Nutritional analysis revealed that the subjects' mean carbohydrate intake was 463 ± 137 g, being approximately 6.8 ± 2.4 g/kg body weight. The average sleeping time was 5.9 ± 1.0 h. The glycogen content in the thigh muscle at the starting point was 64.8 ± 20.6 mM. Although absolute and relative individual variations in muscle glycogen content were 7.0 ± 2.1 mM and 11.3 ± 4.6%, respectively, no significant difference in glycogen content was observed among the different time points. This study demonstrates that normal food intake (not fat and/or carbohydrate rich), sleep and other daily activities have a negligible influence on thigh muscle glycogen content, and that the diurnal variation of the glycogen content in human muscles is markedly smaller than that in animal muscles. Moreover, the present results also support the reproducibility and availability of (13)C MRS for the evaluation of the glycogen content in human muscles. Copyright © 2015 John Wiley & Sons, Ltd.

  9. Variations on a theme: sources of heterogeneity in the form of the interspecific relationship between abundance and distribution.

    Science.gov (United States)

    Blackburn, Tim M; Cassey, Phillip; Gaston, Kevin J

    2006-11-01

    1. A positive interspecific relationship between abundance and distribution is widely considered to be one of the most general patterns in ecology. However, the relationship appears to vary considerably across assemblages, from significant positive to significant negative correlations and all shades in between. 2. This variation has led to the suggestion that the abundance-distribution relationship has multiple forms, with the corollary that different patterns may inform about, or have different, causes. However, this variation has never been formally quantified, nor has it been determined whether the observed variation is indicative of sampling error in estimating a single effect or of real heterogeneity in such relationships. Here, we use the meta-analytical approach to assess variation in abundance-distribution relationships, and to test different hypotheses for it. 3. Analysis of 279 relationships found a mean effect size of 0.655, which was both highly significantly different from zero and indicative of a strong positive association between abundance and distribution. However, effect sizes were highly heterogeneous, supporting the contention that this relationship does indeed have multiple forms. 4. Most notably, relationships vary significantly in strength across realms, with the strongest in the marine and intertidal, intermediate relationships for terrestrial and parasitic assemblages, and the weakest relationships in freshwater systems. Effect sizes in all of the aquatic realms are homogeneous, suggesting that realm is an important source of the heterogeneity observed across all studies. We posit that this may be because the different spatial structure of the environment in each realm affects the opportunity for the dispersal of individuals between sites. 5. Some of the remaining heterogeneity in effect sizes for terrestrial assemblages could be explained by partitioning assemblages by habitat, scale, biogeographical region and taxon, but considerable

  10. Variation in the diversity-productivity relationship in young forests of the eastern United States.

    Directory of Open Access Journals (Sweden)

    Santosh Ojha

    Full Text Available The diversity-productivity relationship has not been studied as extensively in forests as in other ecosystems. We address this gap in our knowledge by examining the relationship of productivity (primarily the periodic annual increment in aboveground biomass, but also the mean annual increment with five species diversity indices, stand, and environmental factors. We used 967 naturally regenerated Forest Inventory and Analysis plots with stand age ≤30 years, located in the conterminous thirty-one eastern states, and satisfying strict selection requirements. Generally, mixed-species (heterospecific stands were as productive as or even somewhat more productive than pure (monospecific stands. The periodic and mean annual increments were both positively correlated with species richness (R2 = 0.04 and 0.20, p<0.001. Similarly, the zero-order and partial correlations with productivity were positive for four of the diversity indices (species richness, functional diversity, phylogenetic diversity, and phylogenetic species richness and not significant for the fifth (functional dispersion. Greater diversity was more important on low-productivity sites and in stands with low stocking. As forests generally get more diverse and productive away from the poles, we tested if the nature of the productivity-diversity relationship changed latitudinally. Productivity was weakly positively correlated with four of the diversity indices north of 40° latitude, but weakly negatively with three of the indices to the south. Our examination of the productivity-diversity relationship in stands containing either of the two most dominant species, quaking aspen or loblolly pine, revealed that pure loblolly pine stands were somewhat more productive than only three of the eight mixtures with loblolly in the composition, while pure aspen stands were no more productive than any of the aspen mixtures. Overall, monospecific stands did not seem to have a clear productivity advantage

  11. Variation in the diversity-productivity relationship in young forests of the eastern United States.

    Science.gov (United States)

    Ojha, Santosh; Dimov, Luben

    2017-01-01

    The diversity-productivity relationship has not been studied as extensively in forests as in other ecosystems. We address this gap in our knowledge by examining the relationship of productivity (primarily the periodic annual increment in aboveground biomass, but also the mean annual increment) with five species diversity indices, stand, and environmental factors. We used 967 naturally regenerated Forest Inventory and Analysis plots with stand age ≤30 years, located in the conterminous thirty-one eastern states, and satisfying strict selection requirements. Generally, mixed-species (heterospecific) stands were as productive as or even somewhat more productive than pure (monospecific) stands. The periodic and mean annual increments were both positively correlated with species richness (R2 = 0.04 and 0.20, pcorrelations with productivity were positive for four of the diversity indices (species richness, functional diversity, phylogenetic diversity, and phylogenetic species richness) and not significant for the fifth (functional dispersion). Greater diversity was more important on low-productivity sites and in stands with low stocking. As forests generally get more diverse and productive away from the poles, we tested if the nature of the productivity-diversity relationship changed latitudinally. Productivity was weakly positively correlated with four of the diversity indices north of 40° latitude, but weakly negatively with three of the indices to the south. Our examination of the productivity-diversity relationship in stands containing either of the two most dominant species, quaking aspen or loblolly pine, revealed that pure loblolly pine stands were somewhat more productive than only three of the eight mixtures with loblolly in the composition, while pure aspen stands were no more productive than any of the aspen mixtures. Overall, monospecific stands did not seem to have a clear productivity advantage over mixtures. The findings of this study have implications

  12. Histone-DNA contacts in structure/function relationships of nucleosomes as revealed by crosslinking

    Energy Technology Data Exchange (ETDEWEB)

    Usachenko, S.I. [Univ. of California, Davis, CA (United States); Bradbury, E.M. [Los Alamos National Lab., NM (United States). Life Science Div.]|[Univ. of California, Davis, CA (United States)

    1998-12-31

    The magnitude of the problem of understanding the structure/function relationships of eukaryotic chromosomes can be appreciated from the fact that the human diploid genome contains more than 2 meters of DNA packaged into 46 chromosomes, each at metaphase being several microns in length. Each chromatid of a chromosome contains a single DNA molecule several centimeters in length. In addition to the DNA, chromosomes contain an equal weight of histones and an equal weight of non-histone chromosomal proteins. These histones are the major chromosomal structural proteins. The non-histone chromosomal proteins are involved in the DNA processes of transcription and replication, in chromosome organization and in nuclear architecture. Polytene chromosomes with their bands and interbands and puffs of active genetic loci provide visual evidence for long range order as do the bands and interbands of mammalian metaphase chromosomes. The gentle removal of histones and all but the most tightly bound 2--3% of non-histone proteins from metaphase chromosomes revealed by electron microscopy a residual protein scaffold constraining a halo of DNA loops extending out from the scaffold.

  13. Metagenomic analysis reveals symbiotic relationship among bacteria in Microcystis-dominated community

    Directory of Open Access Journals (Sweden)

    Meili eXie

    2016-02-01

    Full Text Available Microcystis bloom, a cyanobacterial mass occurrence often found in eutrophicated water bodies, is one of the most serious threats to freshwater ecosystems worldwide. In nature, Microcystis forms aggregates or colonies that contain heterotrophic bacteria. The Microcystis-bacteria colonies were persistent even when they were maintained in lab culture for a long period. The relationship between Microcystis and the associated bacteria was investigated by a metagenomic approach in this study. We developed a visualization-guided method of binning for genome assembly after total colony DNA sequencing. We found that the method was effective in grouping sequences and it did not require reference genome sequence. Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures. Analysis of metabolic pathways based on these genomes revealed that while all heterotrophic bacteria were dependent upon Microcystis for carbon and energy, Vitamin B12 biosynthesis, which is required for growth by Microcystis, was accomplished in a cooperative fashion among the bacteria. Our analysis also suggests that individual bacteria in the colony community contributed a complete pathway for degradation of benzoate, which is inhibitory to the cyanobacterial growth, and its ecological implication for Microcystis bloom is discussed.

  14. Widespread, focal copy number variations (CNV and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Flibotte Stephane

    2011-03-01

    Full Text Available Abstract Background Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America. T. cruzi is diploid, almost exclusively asexual, and displays an extraordinarily diverse population structure both genetically and phenotypically. Yet, to date the genotypic diversity of T. cruzi and its relationship, if any, to biological diversity have not been studied at the whole genome level. Results In this study, we used whole genome oligonucleotide tiling arrays to compare gene content in biologically disparate T. cruzi strains by comparative genomic hybridization (CGH. We observed that T. cruzi strains display widespread and focal copy number variations (CNV and a substantially greater level of diversity than can be adequately defined by the current genetic typing methods. As expected, CNV were particularly frequent in gene family-rich regions containing mucins and trans-sialidases but were also evident in core genes. Gene groups that showed little variation in copy numbers among the strains tested included those encoding protein kinases and ribosomal proteins, suggesting these loci were less permissive to CNV. Moreover, frequent variation in chromosome copy numbers were observed, and chromosome-specific CNV signatures were shared by genetically divergent T. cruzi strains. Conclusions The large number of CNV, over 4,000, reported here uphold at a whole genome level the long held paradigm of extraordinary genome plasticity among T. cruzi strains. Moreover, the fact that these heritable markers do not parse T. cruzi strains along the same lines as traditional typing methods is strongly suggestive of genetic exchange playing a major role in T. cruzi population structure and biology.

  15. Genetic variation and relationships of old maize genotypes (Zea mays l. detected using SDS-page

    Directory of Open Access Journals (Sweden)

    Martin Vivodík

    2016-11-01

    Full Text Available The assessment of genetic diversity among the members of a species is of vital importance for successful breeding and adaptability. In the present study 40 old genotypes of maize from Hungary, Union of Soviet Socialist Republics, Poland, Czechoslovakia, Yugoslavia and Slovak Republic  were evaluated for the total seed storage proteins using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE through vertical slab unit. The number of total scorable protein bands was twentythree as a result of SDS-PAGE technique but those that were not cosistent in reproducibility and showed occasional variation in sharpness and density were not considered. Out of twentythree polypeptide bands, 6 (31% were commonly present in all accessions and considered as monomorphic, while 17 (65% showed variations and considered as polymorphic. On the basis of banding profiles of proteins of different kDa, gel was divided into zones A, B and C. The major protein bands were lied in zones A and B, while minor bands were present in zones C. In zone A out of 10 protein bands, 1 were monomorphic and 9 were polymorphic. In zone B out of 8 protein bands, 3 was monomorphic and 5 was polymorphic and in zone C out of 5 protein bands, 2 were monomorphic whereas 3 polymorphic. The dendrogram tree demonstrated the relationship among the forty registered old maize genotypes according to the similarity index, using UPGMA cluster analysis. The dendrogram was divided into two main clusters. The first one contained eleven genotypes from maize, while the second cluster contained the twentynine genotypes of maize. Similarly the present study of genetic variability in the seed storage polypeptide determined by SDS-PAGE technique proved that it is fruitful to identify genetic diversity among accessions of maize. 

  16. Strong lateral variation of ground temperature revealed by a large network of boreholes in the Slave Geological Province of Canada

    Science.gov (United States)

    Gruber, Stephan; Riddick, Julia; Brown, Nick; Karunaratne, Kumari; Kokelj, Steve V.

    2017-04-01

    The Slave Geological Province is a key region in the Canadian North. Its tundra areas form a large and resource-rich landscape in which comparably few systematic permafrost observations exist. Because the region contains layers of ice-rich till, the ground is susceptible to subsidence during thaw. Consequently, possible impacts of permafrost thawing on infrastructure and the natural environment motivate baseline investigations and simulation studies. In this context, the spatial variation of ground temperatures is relevant: How well can we extrapolate from one or few locations of observation? How well can we describe permafrost characteristics with coarse-grid (e.g., 50 km) models assuming relatively homogenous conditions? In July 2015, an observation network of more than 40 plots was installed to monitor ground thermal regime and to detect surface subsidence. Plots are within few tens of meters to few tens of kilometers from each other and were chosen to represent a distinct combination of surficial geology, vegetation, drainage conditions, and snow accumulation. In each plot (15 m x 15 m), temperatures are recorded in a borehole as well as about 10 cm deep at four locations. Data on surface and subsurface properties has been recorded as well. In September 2016, data was downloaded from the loggers and the conditions of the instruments were described. This contribution presents the first year of temperature data. In the annual averages, it reveals more than 7°C lateral variation between plots as well as within-plot variations of more than 2.5°C. This underscores the need for carefully designing measurement campaigns and methods when aiming to test coarse-scale permafrost simulations, even in gentle topography. The data resulting from this observational network will be made available publicly in the near future.

  17. Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species

    Science.gov (United States)

    Hoedjes, K M; Smid, H M; Vet, L E M; Werren, J H

    2014-01-01

    Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the parasitic wasp genus Nasonia. After a single olfactory conditioning trial, N. vitripennis consolidates long-term memory that lasts at least 6 days. Memory of the closely related species N. giraulti is present at 24 h but is lost within 2 days after a single trial. The genetic basis of this interspecific difference in memory retention was studied in a backcrossing experiment in which the phenotype of N. giraulti was selected for in the background of N. vitripennis for up to five generations. A genotyping microarray revealed five regions that were retained in wasps with decreased memory retention. Independent introgressions of individual candidate regions were created using linked molecular markers and tested for memory retention. One region on chromosome 1 (spanning ∼5.8 cM) and another on chromosome 5 (spanning ∼25.6 cM) resulted in decreased memory after 72 h, without affecting 24-h-memory retention. This phenotype was observed in both heterozygous and homozygous individuals. Transcription factor CCAAT/enhancer-binding protein and a dopamine receptor, both with a known function in memory formation, are within these genomic regions and are candidates for the regulation of memory retention. Concluding, this study demonstrates a powerful approach to study variation in memory retention and provides a basis for future research on its genetic basis. PMID:25052416

  18. Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study

    Directory of Open Access Journals (Sweden)

    Quanxiu Wang

    2017-10-01

    Full Text Available The photoprotective processes conferred by nonphotochemical quenching (NPQ serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa, and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified. To check the validity of the GWAS signals, three F2 mapping populations with parents selected from the association panel were constructed and assayed. All QTLs detected in mapping populations could correspond to at least one GWAS signal, indicating the GWAS results were quite reliable. OsPsbS1 was repeatedly detected and explained more than 40% of the variation in the whole association population in two years, and demonstrated to be a common major QTL in all three mapping populations derived from inter-group crosses. We revealed 43 single nucleotide polymorphisms (SNPs and 7 insertions and deletions (InDels within a 6,997-bp DNA fragment of OsPsbS1, but found no non-synonymous SNPs or InDels in the coding region, indicating the PsbS1 protein sequence is highly conserved. Haplotypes with the 2,674-bp insertion in the promoter region exhibited significantly higher NPQ values and higher expression levels of OsPsbS1. The OsPsbS1 RNAi plants and CRISPR/Cas9 mutants exhibited drastically decreased NPQ values. OsPsbS1 had specific and high-level expression in green tissues of rice. However, we didn't find significant function for OsPsbS2, the other rice PsbS homologue. Manipulation of the significant loci or candidate genes identified may enhance photoprotection and improve photosynthesis and yield in rice.

  19. High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.

    Science.gov (United States)

    Sim, Sung-Chur; Van Deynze, Allen; Stoffel, Kevin; Douches, David S; Zarka, Daniel; Ganal, Martin W; Chetelat, Roger T; Hutton, Samuel F; Scott, John W; Gardner, Randolph G; Panthee, Dilip R; Mutschler, Martha; Myers, James R; Francis, David M

    2012-01-01

    The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F(st) supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st) outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.

  20. Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species.

    Science.gov (United States)

    Hoedjes, K M; Smid, H M; Vet, L E M; Werren, J H

    2014-12-01

    Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the parasitic wasp genus Nasonia. After a single olfactory conditioning trial, N. vitripennis consolidates long-term memory that lasts at least 6 days. Memory of the closely related species N. giraulti is present at 24 h but is lost within 2 days after a single trial. The genetic basis of this interspecific difference in memory retention was studied in a backcrossing experiment in which the phenotype of N. giraulti was selected for in the background of N. vitripennis for up to five generations. A genotyping microarray revealed five regions that were retained in wasps with decreased memory retention. Independent introgressions of individual candidate regions were created using linked molecular markers and tested for memory retention. One region on chromosome 1 (spanning ∼5.8 cM) and another on chromosome 5 (spanning ∼25.6 cM) resulted in decreased memory after 72 h, without affecting 24-h-memory retention. This phenotype was observed in both heterozygous and homozygous individuals. Transcription factor CCAAT/enhancer-binding protein and a dopamine receptor, both with a known function in memory formation, are within these genomic regions and are candidates for the regulation of memory retention. Concluding, this study demonstrates a powerful approach to study variation in memory retention and provides a basis for future research on its genetic basis.

  1. [Relationships between coefficient of variation of diameter and height and competition index of main coniferous trees in Changbai Mountains].

    Science.gov (United States)

    Zhao, Jun-Hui; Kang, Xin-Gang; Zhang, Hui-Dong; Liu, Yan

    2009-08-01

    A total of 1139 trees from 8 clear-cut stands dominated by fir, spruce, and pine in the Changbai Mountains were selected to study the relationships between the coefficient of variation of diameter and height and the competition index of the three main coniferous tree species in the Mountains. For the test tree species, the variation of height vs. diameter class was relatively small, while the variations of diameter and height vs. age class were larger, with the largest coefficient of variation of diameter vs. age class. The traditional height-diameter models could better reflect the real growth of trees, whereas the diameter-age or height-age models were not good enough. Competition was the main factor inducing the variations of tree diameter and height, suggesting that incorporating the competition index to the traditional models of tree growth and height could improve the model accuracy significantly.

  2. Regional Variation in Neonatal Intensive Care Admissions and the Relationship to Bed Supply.

    Science.gov (United States)

    Harrison, Wade N; Wasserman, Jared R; Goodman, David C

    2018-01-01

    To characterize geographic variation in neonatal intensive care unit (NICU) admission rates across the entire birth cohort and evaluate the relationship between regional bed supply and NICU admission rates. This was a population-based, cross-sectional study. 2013 US birth certificate and 2012 American Hospital Association data were used to assign newborns and NICU beds to neonatal intensive care regions. Descriptive statistics of admission rates were calculated across neonatal intensive care regions. Multilevel logistic regression was used to examine the relationship between bed supply and individual odds of admission, with adjustment for maternal and newborn characteristics. Among 3 304 364 study newborns, the NICU admission rate was 7.2 per 100 births and varied across regions for all birth weight categories. IQRs in admission rates were 84.5-93.2 per 100 births for 500-1499 g, 35.3-46.1 for 1500-2499 g, and 3.5-5.5 for ≥2500 g. Adjusted odds of admission for newborns of very low birth weight were unrelated to regional bed supply; however, newborns ≥2500 g in regions with the highest NICU bed supply were significantly more likely to be admitted to a NICU than those in regions with the lowest (aOR 1.20 [1.03-1.40]). There is persistent underuse of NICU care for newborns of very low birth weight that is not associated with regional bed supply. Among larger newborns, we find evidence of supply-sensitive care, raising concerns about the potential overuse of expensive and unnecessary care. Rather than improving access to needed care, NICU expansion may instead further deregionalize neonatal care, exacerbating underuse. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Relationships of bovine ephemeral fever epizootics to population immunity and virus variation.

    Science.gov (United States)

    Ting, Lu-Jen; Lee, Ming-Shiuh; Lee, Shu-Hwae; Tsai, Hsiang-Jung; Lee, Fan

    2014-10-10

    Bovine ephemeral fever is an arthropod-borne bovine viral disease caused by infection with bovine ephemeral fever virus which belongs to genus Ephemerovirus within the family Rhabdoviridae. In this study, serological data and virological information about the disease and the virus, spanning from 2001 to 2013, were employed to analyze the relationships of bovine ephemeral fever epizootics to population immunity and virus variation. National and regional surveillance data indicated that 2 of the 3 major epizootics and 87% regional outbreaks were associated with lower neutralizing antibody titers and immunity coverage, reflecting the importance of population immunity for the control of bovine ephemeral fever. Phylogenetic analysis and sequence comparison demonstrated that Taiwanese bovine ephemeral fever viruses were >96.0% and >97.6% similar to the East Asian isolates in nucleotide and amino acid sequences, respectively. These analyses supported that the Taiwanese viruses shared the same gene pool with the strains of the other East Asian countries, mainly Japan. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Relationship between acromial morphological variation and subacromial impingement: A three-dimensional analysis.

    Science.gov (United States)

    Li, Xinyu; Xu, Wei; Hu, Ning; Liang, Xi; Huang, Wei; Jiang, Dianming; Chen, Hong

    2017-01-01

    To evaluate the association of acromial morphology and subacromial impingement. Bilateral shoulder computed tomography was performed in 138 patients who received shoulder arthroscopy. Measured parameters included: acromial tilt (AT), modified acromial tilt (mAT), acromial slope (AS), acromiohumeral interval (AHI), lateral acromial angle (LAA), acromial index (AI), critical shoulder angle (CSA), acromial anterior protrusion (AAP), and acromial inferior protrusion (AIP). Acromial morphological characteristics were compared between groups. Side-to-side differences were assessed between affected and non-affected shoulders. Intra- and inter-observer agreements for each parameter were calculated. AT (25.90 vs. 29.41°), mAT (18.88 vs. 22.64°), and AHI (5.46 vs. 6.47 mm) were significantly smaller in impinged patients. The impingement group demonstrated significantly larger AI (63.50 vs. 59.84%), CSA (31.78 vs. 28.74°), AAP (7.13 vs. 5.32 mm), and AIP (5.51 vs. 4.04 mm). Regarding side-to-side comparison, the acromial morphology was significantly different between the affected and non-affected shoulders in impinged patients, while the difference was slight and insignificant in control patients. All, except AS and LAA, measured parameters demonstrated good intra- and inter-observer agreements. Three-dimensional reconstructed CT scan is a reliable method to measure shoulder morphology. The acromial morphological variation is related with sub acromial impingement, however, the causal relationship of them should be further explored.

  5. Relationship between the variations of hydrogen in HCNG fuel and the oxygen in exhausted gas

    Directory of Open Access Journals (Sweden)

    Preecha Yaom

    2015-09-01

    Full Text Available The variation of the mixing ratio between hydrogen and compressed natural gas (CNG in hydrogen enriched compressed natural gas fuel (HCNG gives different results in terms of engine performances, fuel consumption, and emission characteristics. Therefore, the engine performance using HCNG as fuel can be optimized if the mixing ratio between the two fuels in HCNG can be adjusted in real time while the engine is being operated. In this research, the relationship between the amount of oxygen in the exhausted gas and the mixing composition between the hydrogen and CNG in HCNG is investigated based on the equilibrium equation of combustion. It is found that the main factors affecting the amount of oxygen in exhausted gas when using HCNG as fuel include the error from the air-fuel-ratio (AFR control, the error from the HCNG composition control, and the intended change of the HCNG composition. Theoretically, the amount of the oxygen in the exhaust should increase by 0.78% for every 5% addition of H2 at stoichiometric condition. This value can be higher or lower for lean and rich engine operation, respectively. The experimental results found that at the equivalent ratio around 0.8 the amount of O2 in the exhaust gas increases about 1.23% for every 5% H2 addition, which inclines with the proposed calculations.

  6. Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships.

    Science.gov (United States)

    Koton, Yael; Gordon, Michal; Chalifa-Caspi, Vered; Bisharat, Naiel

    2014-01-01

    In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59 and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C) and environmental (E), all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins) were present in all human pathogenic strains (both biotype 3 and non-biotype 3) and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS) proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and formed a genetically

  7. Comparative Genomic Analysis of Clinical and Environmental Vibrio Vulnificus Isolates Revealed Biotype 3 Evolutionary Relationships

    Directory of Open Access Journals (Sweden)

    Yael eKotton

    2015-01-01

    Full Text Available In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59% and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 kbp to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C and environmental (E, all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins were present in all human pathogenic strains (both biotype 3 and non-biotype 3 and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and

  8. Structure-Dynamics Relationships in Bursting Neuronal Networks Revealed Using a Prediction Framework

    Science.gov (United States)

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Ruohonen, Keijo; Linne, Marja-Leena

    2013-01-01

    The question of how the structure of a neuronal network affects its functionality has gained a lot of attention in neuroscience. However, the vast majority of the studies on structure-dynamics relationships consider few types of network structures and assess limited numbers of structural measures. In this in silico study, we employ a wide diversity of network topologies and search among many possibilities the aspects of structure that have the greatest effect on the network excitability. The network activity is simulated using two point-neuron models, where the neurons are activated by noisy fluctuation of the membrane potential and their connections are described by chemical synapse models, and statistics on the number and quality of the emergent network bursts are collected for each network type. We apply a prediction framework to the obtained data in order to find out the most relevant aspects of network structure. In this framework, predictors that use different sets of graph-theoretic measures are trained to estimate the activity properties, such as burst count or burst length, of the networks. The performances of these predictors are compared with each other. We show that the best performance in prediction of activity properties for networks with sharp in-degree distribution is obtained when the prediction is based on clustering coefficient. By contrast, for networks with broad in-degree distribution, the maximum eigenvalue of the connectivity graph gives the most accurate prediction. The results shown for small () networks hold with few exceptions when different neuron models, different choices of neuron population and different average degrees are applied. We confirm our conclusions using larger () networks as well. Our findings reveal the relevance of different aspects of network structure from the viewpoint of network excitability, and our integrative method could serve as a general framework for structure-dynamics studies in biosciences. PMID:23935998

  9. Variation of partial transferrin sequences and phylogenetic relationships among hares (Lepus capensis, Lagomorpha) from Tunisia.

    Science.gov (United States)

    Awadi, Asma; Suchentrunk, Franz; Makni, Mohamed; Ben Slimen, Hichem

    2016-10-01

    North African hares are currently included in cape hares, Lepus capensis sensu lato, a taxon that may be considered a superspecies or a complex of closely related species. The existing molecular data, however, are not unequivocal, with mtDNA control region sequences suggesting a separate species status and nuclear loci (allozymes, microsatellites) revealing conspecificity of L. capensis and L. europaeus. Here, we study sequence variation in the intron 6 (468 bp) of the transferrin nuclear gene, of 105 hares with different coat colour from different regions in Tunisia with respect to genetic diversity and differentiation, as well as their phylogenetic status. Forty-six haplotypes (alleles) were revealed and compared phylogenetically to all available TF haplotypes of various Lepus species retrieved from GenBank. Maximum Likelihood, neighbor joining and median joining network analyses concordantly grouped all currently obtained haplotypes together with haplotypes belonging to six different Chinese hare species and the African scrub hare L. saxatilis. Moreover, two Tunisian haploypes were shared with L. capensis, L timidus, L. sinensis, L. yarkandensis, and L. hainanus from China. These results indicated the evolutionary complexity of the genus Lepus with the mixing of nuclear gene haplotypes resulting from introgressive hybridization or/and shared ancestral polymorphism. We report the presence of shared ancestral polymorphism between North African and Chinese hares. This has not been detected earlier in the mtDNA sequences of the same individuals. Genetic diversity of the TF sequences from the Tunisian populations was relatively high compared to other hare populations. However, genetic differentiation and gene flow analyses (AMOVA, FST, Nm) indicated little divergence with the absence of geographically meaningful phylogroups and lack of clustering with coat colour types. These results confirm the presence of a single hare species in Tunisia, but a sound inference on

  10. Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition.

    Science.gov (United States)

    Diboun, Ilhame; Mathew, Sweety; Al-Rayyashi, Maryam; Elrayess, Mohamed; Torres, Maria; Halama, Anna; Méret, Michaël; Mohney, Robert P; Karoly, Edward D; Malek, Joel; Suhre, Karsten

    2015-12-16

    Dates are tropical fruits with appreciable nutritional value. Previous attempts at global metabolic characterization of the date metabolome were constrained by small sample size and limited geographical sampling. In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabolome. Multivariate analysis revealed a first principal component (PC1) significantly associated with the dates' countries of production. The availability of a smaller dataset featuring immature dates from different development stages served to build a model of the ripening process in dates, which helped reveal a strong ripening signature in PC1. Analysis revealed enrichment in the dry type of dates amongst fruits with early ripening profiles at one end of PC1 as oppose to an overrepresentation of the soft type of dates with late ripening profiles at the other end of PC1. Dry dates are typical to the North African region whilst soft dates are more popular in the Gulf region, which partly explains the observed association between PC1 and geography. Analysis of the loading values, expressing metabolite correlation levels with PC1, revealed enrichment patterns of a comprehensive range of metabolite classes along PC1. Three distinct metabolic phases corresponding to known stages of date ripening were observed: An early phase enriched in regulatory hormones, amines and polyamines, energy production, tannins, sucrose and anti-oxidant activity, a second phase with on-going phenylpropanoid secondary metabolism, gene expression and phospholipid metabolism and a late phase with marked sugar dehydration activity and degradation reactions leading to increased volatile synthesis. These data indicate the importance of date ripening as a main driver of variation in the date metabolome responsible for their diverse nutritional and

  11. MDA and GSH-Px activity in transition dairy cows under seasonal variations and their relationship with reproductive performance

    Directory of Open Access Journals (Sweden)

    Colakoglu Hatice Esra

    2017-12-01

    Full Text Available Introduction: The purpose of the current study was to evaluate the blood glutathione peroxidase (GSH-Px and malondialdehyde (MDA levels under seasonal variations in dairy cows during transition period, and to assess the relationship between chosen reproductive parameters, GSH-Px, and MDA.

  12. Integrative Variation Analysis Reveals that a Complex Genotype May Specify Phenotype in Siblings with Syndromic Autism Spectrum Disorder.

    Directory of Open Access Journals (Sweden)

    Viviane Neri de Souza Reis

    Full Text Available It has been proposed that copy number variations (CNVs are associated with increased risk of autism spectrum disorder (ASD and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations-single nucleotide variants (SNVs or small insertions and deletions (indels-with probable functional impacts. With aCGH, we identified, in both siblings, a duplication in the 4p16.3 region and a deletion at 8p23.3, inherited by a paternal balanced translocation, t(4, 8 (p16; p23. Exome variant analysis found a total of 316 variants, of which 102 were shared by both siblings, 128 were in the male sibling exome data, and 86 were in the female exome data. Our integrative network analysis showed that the siblings' shared translocation could explain their similar syndromic phenotype, including overgrowth, macrocephaly, and intellectual disability. However, exome data aggregate genes to those already connected from their translocation, which are important to the robustness of the network and contribute to the understanding of the broader spectrum of psychiatric symptoms. This study shows the importance of using an integrative approach to explore genotype-phenotype variability.

  13. Variability of tropical cyclone rapid intensification in the North Atlantic and its relationship with climate variations

    Science.gov (United States)

    Wang, Chunzai; Wang, Xidong; Weisberg, Robert H.; Black, Michael L.

    2017-02-01

    The paper uses observational data from 1950 to 2014 to investigate rapid intensification (RI) variability of tropical cyclones (TCs) in the North Atlantic and its relationships with large-scale climate variations. RI is defined as a TC intensity increase of at least 15.4 m/s (30 knots) in 24 h. The seasonal RI distribution follows the seasonal TC distribution, with the highest number in September. Although an RI event can occur anywhere over the tropical North Atlantic (TNA), there are three regions of maximum RI occurrence: (1) the western TNA of 12°N-18°N and 60°W-45°W, (2) the Gulf of Mexico and the western Caribbean Sea, and (3) the open ocean southeast and east of Florida. RI events also show a minimum value in the eastern Caribbean Sea north of South America—a place called a hurricane graveyard due to atmospheric divergence and subsidence. On longer time scales, RI displays both interannual and multidecadal variability, but RI does not show a long-term trend due to global warming. The top three climate indices showing high correlations with RI are the June-November ENSO and Atlantic warm pool indices, and the January-March North Atlantic oscillation index. It is found that variabilities of vertical wind shear and TC heat potential are important for TC RI in the hurricane main development region, whereas relative humidity at 500 hPa is the main factor responsible for TC RI in the eastern TNA. However, the large-scale oceanic and atmospheric variables analyzed in this study do not show an important role in TC RI in the Gulf of Mexico and the open ocean southeast and east of Florida. This suggests that other factors such as small-scale changes of oceanic and atmospheric variables or TC internal processes may be responsible for TC RI in these two regions. Additionally, the analyses indicate that large-scale atmospheric and oceanic variables are not critical to TC genesis and formation; however, once a tropical depression forms, large-scale climate

  14. Variability of tropical cyclone rapid intensification in the North Atlantic and its relationship with climate variations

    Science.gov (United States)

    Wang, Chunzai; Wang, Xidong; Weisberg, Robert H.; Black, Michael L.

    2017-12-01

    The paper uses observational data from 1950 to 2014 to investigate rapid intensification (RI) variability of tropical cyclones (TCs) in the North Atlantic and its relationships with large-scale climate variations. RI is defined as a TC intensity increase of at least 15.4 m/s (30 knots) in 24 h. The seasonal RI distribution follows the seasonal TC distribution, with the highest number in September. Although an RI event can occur anywhere over the tropical North Atlantic (TNA), there are three regions of maximum RI occurrence: (1) the western TNA of 12°N-18°N and 60°W-45°W, (2) the Gulf of Mexico and the western Caribbean Sea, and (3) the open ocean southeast and east of Florida. RI events also show a minimum value in the eastern Caribbean Sea north of South America—a place called a hurricane graveyard due to atmospheric divergence and subsidence. On longer time scales, RI displays both interannual and multidecadal variability, but RI does not show a long-term trend due to global warming. The top three climate indices showing high correlations with RI are the June-November ENSO and Atlantic warm pool indices, and the January-March North Atlantic oscillation index. It is found that variabilities of vertical wind shear and TC heat potential are important for TC RI in the hurricane main development region, whereas relative humidity at 500 hPa is the main factor responsible for TC RI in the eastern TNA. However, the large-scale oceanic and atmospheric variables analyzed in this study do not show an important role in TC RI in the Gulf of Mexico and the open ocean southeast and east of Florida. This suggests that other factors such as small-scale changes of oceanic and atmospheric variables or TC internal processes may be responsible for TC RI in these two regions. Additionally, the analyses indicate that large-scale atmospheric and oceanic variables are not critical to TC genesis and formation; however, once a tropical depression forms, large-scale climate

  15. Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

    Science.gov (United States)

    Li, Dezhu; Sun, Yongzhen; Niu, Yunyun; Chen, Zhiduan; Luo, Hongmei; Pang, Xiaohui; Sun, Zhiying; Liu, Chang; Lv, Aiping; Deng, Youping; Larson-Rabin, Zachary; Wilkinson, Mike; Chen, Shilin

    2012-01-01

    Background Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. Methodology/Principal Findings In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. Conclusions Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification. PMID:22952830

  16. Seasonal variations of phytoplankton dynamics in Nunatsiavut fjords (Labrador, Canada) and their relationships with environmental conditions

    Science.gov (United States)

    Simo-Matchim, Armelle-Galine; Gosselin, Michel; Blais, Marjolaine; Gratton, Yves; Tremblay, Jean-Éric

    2016-04-01

    We assessed phytoplankton dynamics and its environmental control in four Labrador fjords (Nachvak, Saglek, Okak, and Anaktalak) during summer, early fall and late fall. Primary production and chlorophyll a (chl a) biomass were measured at seven optical depths, including the depth of subsurface chl a maximum (SCM). Phytoplankton abundance, size structure and taxonomy were determined at the SCM. Principal component analysis and non-metric multidimensional scaling were used to analyze relationships between production, biomass and community composition in relation to environmental variables. We observed a marked seasonal variability, with significant differences in phytoplankton structure and function between summer and fall. Surprisingly, primary production and chl a biomass were not significantly different from one fjord to another. The highest values of primary production (1730 mg C m- 2 day- 1) and chl a biomass (96 mg chl a m- 2) were measured during the summer bloom, and those high values indicate that Labrador fjords are highly productive ecosystems. The summer community showed relatively high abundance of nanophytoplankton (2-20 μm) while the fall community was characterized by low primary production and chl a biomass as well as relatively high abundance of picophytoplankton (diatoms and flagellates in summer, whereas the fall community was largely dominated by flagellates. Seasonal variations in phytoplankton dynamics were mainly controlled by the strength of the vertical stratification and by the large differences in day length due to the northerly location of Labrador fjords. This study documents for the very first time phytoplankton structure and function in Labrador fjords, and provides an essential foundation for further research and for monitoring environmental changes in arctic and subarctic coastal areas.

  17. Exploring the relationship between malaria, rainfall intermittency, and spatial variation in rainfall seasonality

    Science.gov (United States)

    Merkord, C. L.; Wimberly, M. C.; Henebry, G. M.; Senay, G. B.

    2014-12-01

    Malaria is a major public health problem throughout tropical regions of the world. Successful prevention and treatment of malaria requires an understanding of the environmental factors that affect the life cycle of both the malaria pathogens, protozoan parasites, and its vectors, anopheline mosquitos. Because the egg, larval, and pupal stages of mosquito development occur in aquatic habitats, information about the spatial and temporal distribution of rainfall is critical for modeling malaria risk. Potential sources of hydrological data include satellite-derived rainfall estimates (TRMM and GPM), evapotranspiration derived from a simplified surface energy balance, and estimates of soil moisture and fractional water cover from passive microwave imagery. Previous studies have found links between malaria cases and total monthly or weekly rainfall in areas where both are highly seasonal. However it is far from clear that monthly or weekly summaries are the best metrics to use to explain malaria outbreaks. It is possible that particular temporal or spatial patterns of rainfall result in better mosquito habitat and thus higher malaria risk. We used malaria case data from the Amhara region of Ethiopia and satellite-derived rainfall estimates to explore the relationship between malaria outbreaks and rainfall with the goal of identifying the most useful rainfall metrics for modeling malaria occurrence. First, we explored spatial variation in the seasonal patterns of both rainfall and malaria cases in Amhara. Second, we assessed the relative importance of different metrics of rainfall intermittency, including alternation of wet and dry spells, the strength of intensity fluctuations, and spatial variability in these measures, in determining the length and severity of malaria outbreaks. We also explored the sensitivity of our results to the choice of method for describing rainfall intermittency and the spatial and temporal scale at which metrics were calculated. Results

  18. Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations.

    Science.gov (United States)

    Ma, Zhihong; Yang, Xuefen; Bercsenyi, Miklos; Wu, Junjie; Yu, Yongyao; Wei, Kaijian; Fan, Qixue; Yang, Ruibin

    2015-10-20

    To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.

  19. Distinct intraspecific variations of garlic (Allium sativum L.) revealed by the exon-intron sequences of the alliinase gene.

    Science.gov (United States)

    Endo, Aki; Imai, Yukiko; Nakamura, Mizuho; Yanagisawa, Eri; Taguchi, Takaaki; Torii, Kosuke; Okumura, Hidenobu; Ichinose, Koji

    2014-04-01

    Garlic (Allium sativum L.) has been used worldwide as a food and for medicinal purposes since early times. Garlic cultivars exhibit considerable morphological diversity despite the fact that they are mostly sterile and are grown only by vegetative propagation of cloves. Considerable recombination occurs in garlic genomes, including the genes involved in secondary metabolites. We examined the genomic DNAs (gDNAs) from garlic, encoding alliinase, a key enzyme involved in organosulfur metabolism in Allium plants. The 1.7-kb gDNA fragments, covering three exons (2, 3, and 4) and all four introns, were amplified from total DNAs prepared from garlic samples produced in Asia and Europe, leading to 73 sequences in total: Japan (JPN), China (CHN), India (IND), Spain (ESP), and France (FRA). The exon sequences were highly conserved among all the sequences, probably reflecting the fully functional alliinase associated with the flavor quality. Distinct intraspecific variations were detected for all four intron sequences, leading to the haplotype classifications. A close relationship between JPN and CHN was observed for all four introns, whereas IND showed a more divergent distribution. ESP and FRA afforded clearly different variants compared with those from Asian sequences. The present study provides information that could be useful in the development of an additional molecular marker for garlic authentication and quality control.

  20. Accounting for stimulus-specific variation in precision reveals a discrete capacity limit in visual working memory.

    Science.gov (United States)

    Pratte, Michael S; Park, Young Eun; Rademaker, Rosanne L; Tong, Frank

    2017-01-01

    If we view a visual scene that contains many objects, then momentarily close our eyes, some details persist while others seem to fade. Discrete models of visual working memory (VWM) assume that only a few items can be actively maintained in memory, beyond which pure guessing will emerge. Alternatively, continuous resource models assume that all items in a visual scene can be stored with some precision. Distinguishing between these competing models is challenging, however, as resource models that allow for stochastically variable precision (across items and trials) can produce error distributions that resemble random guessing behavior. Here, we evaluated the hypothesis that a major source of variability in VWM performance arises from systematic variation in precision across the stimuli themselves; such stimulus-specific variability can be incorporated into both discrete-capacity and variable-precision resource models. Participants viewed multiple oriented gratings, and then reported the orientation of a cued grating from memory. When modeling the overall distribution of VWM errors, we found that the variable-precision resource model outperformed the discrete model. However, VWM errors revealed a pronounced "oblique effect," with larger errors for oblique than cardinal orientations. After this source of variability was incorporated into both models, we found that the discrete model provided a better account of VWM errors. Our results demonstrate that variable precision across the stimulus space can lead to an unwarranted advantage for resource models that assume stochastically variable precision. When these deterministic sources are adequately modeled, human working memory performance reveals evidence of a discrete capacity limit. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  1. Fluctuating monsoonal precipitation as revealed by foraminiferal variations in a core from shelf regime off Karwar (India)

    Digital Repository Service at National Institute of Oceanography (India)

    Nigam, R.

    Variations in the percentage frequency of the foraminifera Cavarotalia annectens in the sediments collected by box core in the shelf region of Karwar, infront of the mouth of the Kalinadi river, India were used to map paleomonsoonal variations...

  2. Spatio-Temporal Variation in Length-Weight Relationships and Condition of the Ribbonfish Trichiurus lepturus (Linnaeus, 1758): Implications for Fisheries Management.

    Science.gov (United States)

    Al Nahdi, Abdullah; Garcia de Leaniz, Carlos; King, Andrew J

    2016-01-01

    Knowledge of length-weight relationships for commercially exploited fish is an important tool for assessing and managing of fish stocks. However, analyses of length-weight relationship fisheries data typically do not consider the inherent differences in length-weight relationships for fish caught from different habitats, seasons, or years, and this can affect the utility of these data for developing condition indices or calculating fisheries biomass. Here, we investigated length-weight relationships for ribbonfish Trichiurus lepturus in the waters of the Arabian Sea off Oman collected during three periods (2001-02, 2007-08, and 2014-15) and showed that a multivariate modelling approach that considers the areas and seasons in which ribbonfish were caught improved estimation of length-weight relationships. We used the outputs of these models to explore spatio-temporal variations in condition indices and relative weights among ribbonfish, revealing fish of 85-125 cm were in the best overall condition. We also found that condition differed according to where and when fish were caught, with condition lowest during spring and pre-south-west monsoon periods and highest during and after the south-west monsoons. We interpret these differences to be a consequence of variability in temperature and food availability. Based on our findings, we suggest fishing during seasons that have the lowest impact on fish condition and which are commercially most viable; such fishery management would enhance fisheries conservation and economic revenue in the region.

  3. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution.

    Science.gov (United States)

    Razumova, Olga V; Alexandrov, Oleg S; Divashuk, Mikhail G; Sukhorada, Tatiana I; Karlov, Gennady I

    2016-05-01

    Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants.

  4. Deciding to Reveal Sexual Information and Sexuality Education in Mother-Daughter Relationships

    Science.gov (United States)

    Coffelt, Tina A.

    2017-01-01

    Communication privacy management theory informed this study of nine mothers and their 18- or 19-year-old daughters who were interviewed to understand privacy rule foundations that influence their decisions to reveal or conceal sexual information. Findings reveal the salience of motivation and the risk-benefit ratio when making decisions about…

  5. Spatial variation in the relationship between performance and metabolic rate in wild juvenile Atlantic salmon

    Science.gov (United States)

    Grethe Robertsen; John D. Armstrong; Keith H. Nislow; Ivar Herfindal; Simon McKelvey; Sigurd Einum; Martin. Genner

    2014-01-01

    Maintenance of metabolic rate (MR, the energy cost of self-maintenance) is linked to behavioural traits and fitness and varies substantially within populations. Despite having received much attention, the causes and consequences of this variation remain obscure. Theoretically, such within-population variation in fitness-related traits can be maintained by environmental...

  6. Relationship between the composition of flavonoids and flower colors variation in tropical water lily (Nymphaea cultivars.

    Directory of Open Access Journals (Sweden)

    Manlan Zhu

    Full Text Available Water lily, the member of the Nymphaeaceae family, is the symbol of Buddhism and Brahmanism in India. Despite its limited researches on flower color variations and formation mechanism, water lily has background of blue flowers and displays an exceptionally wide diversity of flower colors from purple, red, blue to yellow, in nature. In this study, 34 flavonoids were identified among 35 tropical cultivars by high-performance liquid chromatography (HPLC with photodiode array detection (DAD and electrospray ionization mass spectrometry (ESI-MS. Among them, four anthocyanins: delphinidin 3-O-rhamnosyl-5-O-galactoside (Dp3Rh5Ga, delphinidin 3-O-(2"-O-galloyl-6"-O-oxalyl-rhamnoside (Dp3galloyl-oxalylRh, delphinidin 3-O-(6"-O-acetyl-β-glucopyranoside (Dp3acetylG and cyanidin 3- O-(2"-O-galloyl-galactopyranoside-5-O-rhamnoside (Cy3galloylGa5Rh, one chalcone: chalcononaringenin 2'-O-galactoside (Chal2'Ga and twelve flavonols: myricetin 7-O-rhamnosyl-(1 → 2-rhamnoside (My7RhRh, quercetin 7-O-galactosyl-(1 → 2-rhamnoside (Qu7GaRh, quercetin 7-O-galactoside (Qu7Ga, kaempferol 7-O-galactosyl-(1 → 2-rhamnoside (Km7GaRh, myricetin 3-O-galactoside (My3Ga, kaempferol 7-O-galloylgalactosyl-(1 → 2-rhamnoside (Km7galloylGaRh, myricetin 3-O-galloylrhamnoside (My3galloylRh, kaempferol 3-O-galactoside (Km3Ga, isorhamnetin 7-O-galactoside (Is7Ga, isorhamnetin 7-O-xyloside (Is7Xy, kaempferol 3-O-(3"-acetylrhamnoside (Km3-3"acetylRh and quercetin 3-O-acetylgalactoside (Qu3acetylGa were identified in the petals of tropic water lily for the first time. Meanwhile a multivariate analysis was used to explore the relationship between pigments and flower color. By comparing, the cultivars which were detected delphinidin 3-galactoside (Dp3Ga presented amaranth, and detected delphinidin 3'-galactoside (Dp3'Ga presented blue. However, the derivatives of delphinidin and cyanidin were more complicated in red group. No anthocyanins were detected within white and yellow group

  7. Relationship between the composition of flavonoids and flower colors variation in tropical water lily (Nymphaea) cultivars.

    Science.gov (United States)

    Zhu, Manlan; Zheng, Xuchen; Shu, Qingyan; Li, Hui; Zhong, Peixing; Zhang, Huijin; Xu, Yanjun; Wang, Lijin; Wang, Liangsheng

    2012-01-01

    Water lily, the member of the Nymphaeaceae family, is the symbol of Buddhism and Brahmanism in India. Despite its limited researches on flower color variations and formation mechanism, water lily has background of blue flowers and displays an exceptionally wide diversity of flower colors from purple, red, blue to yellow, in nature. In this study, 34 flavonoids were identified among 35 tropical cultivars by high-performance liquid chromatography (HPLC) with photodiode array detection (DAD) and electrospray ionization mass spectrometry (ESI-MS). Among them, four anthocyanins: delphinidin 3-O-rhamnosyl-5-O-galactoside (Dp3Rh5Ga), delphinidin 3-O-(2"-O-galloyl-6"-O-oxalyl-rhamnoside) (Dp3galloyl-oxalylRh), delphinidin 3-O-(6"-O-acetyl-β-glucopyranoside) (Dp3acetylG) and cyanidin 3- O-(2"-O-galloyl-galactopyranoside)-5-O-rhamnoside (Cy3galloylGa5Rh), one chalcone: chalcononaringenin 2'-O-galactoside (Chal2'Ga) and twelve flavonols: myricetin 7-O-rhamnosyl-(1 → 2)-rhamnoside (My7RhRh), quercetin 7-O-galactosyl-(1 → 2)-rhamnoside (Qu7GaRh), quercetin 7-O-galactoside (Qu7Ga), kaempferol 7-O-galactosyl-(1 → 2)-rhamnoside (Km7GaRh), myricetin 3-O-galactoside (My3Ga), kaempferol 7-O-galloylgalactosyl-(1 → 2)-rhamnoside (Km7galloylGaRh), myricetin 3-O-galloylrhamnoside (My3galloylRh), kaempferol 3-O-galactoside (Km3Ga), isorhamnetin 7-O-galactoside (Is7Ga), isorhamnetin 7-O-xyloside (Is7Xy), kaempferol 3-O-(3"-acetylrhamnoside) (Km3-3"acetylRh) and quercetin 3-O-acetylgalactoside (Qu3acetylGa) were identified in the petals of tropic water lily for the first time. Meanwhile a multivariate analysis was used to explore the relationship between pigments and flower color. By comparing, the cultivars which were detected delphinidin 3-galactoside (Dp3Ga) presented amaranth, and detected delphinidin 3'-galactoside (Dp3'Ga) presented blue. However, the derivatives of delphinidin and cyanidin were more complicated in red group. No anthocyanins were detected within white and

  8. Examining genotypic variation in autism spectrum disorder and its relationship to parental age and phenotype

    Directory of Open Access Journals (Sweden)

    Geier DA

    2016-07-01

    Full Text Available David A Geier,1,2 Janet K Kern,1,3 Lisa K Sykes,2 Mark R Geier1,2 1Research Department, The Institute of Chronic Illnesses, Inc, 2Research Department, CoMeD, Inc, Silver Spring, MD, 3Research Department, CONEM US Autism Research Group, Allen, TX, USA Background: Previous studies on genetic testing of chromosomal abnormalities in individuals diagnosed with autism spectrum disorder (ASD found that ~80% have negative genetic test results (NGTRs and ~20% have positive genetic test results (PGTRs, of which ~7% were probable de novo mutations (PDNMs. Research suggests that parental age is a risk factor for an ASD diagnosis. This study examined genotypic variation in ASD and its relationship to parental age and phenotype.Methods: Phenotype was derived from detailed clinical information, and genotype was derived from high-resolution blood chromosome and blood whole-genome copy number variant genetic testing on a consecutive cohort (born: 1983–2009 of subjects diagnosed with ASD (N=218.Results: Among the subjects examined, 80.3% had NGTRs and 19.7% had PGTRs, of which 6.9% had PDNMs. NGTR subjects were born more recently (the risk of PDNMs decreasing by 12% per more recent birth year and tended to have an increased male–female ratio compared to PDNM subjects. PDNM subjects had significantly increased mean parental age and paternal age at subject’s birth (the risk of a PDNM increasing by 7%–8% per year of parental or paternal age compared to NGTR subjects. PGTR and NGTR subjects showed significant improvements in speech/language/communication with increasing age. PGTR subjects showed significant improvements in sociability, a core feature of an ASD diagnosis, with increasing age, whereas NGTR subjects showed significant worsening in sociability with increasing age.Conclusion: This study helps to elucidate different phenotypic ASD subtypes and may even indicate the need for differential diagnostic classifications. Keywords: genotype, phenotype

  9. Why You Go Reveals Who You Know: Disclosing Social Relationship by Cooccurrence

    Directory of Open Access Journals (Sweden)

    Feng Yi

    2017-01-01

    Full Text Available The popularity of location-based services (LBS and the ubiquity of sensor device have resulted in rich spatiotemporal data. A large number of human behaviors had been recorded including cooccurrence which refers to the phenomenon that two people have been to the same places at the same time. These data enable attackers to infer people’s social relationship based on their cooccurrences and many attack models were proposed. However, current attack models still cannot effectively address the following two challenges: How to distinguish cooccurrences between acquaintances and strangers? What kind of cooccurrence contributes to strong social strength? In this paper, we present a novel social relationship attack model—the Mobility Intention-based Relationship Inference (MIRI model—which can solve the above two issues. Firstly, we extract mobility intentions and adopt them to characterize cooccurrences. A classification model is trained for attacking social relationship. The experimental results on two real-world datasets demonstrate that the proposed MIRI model can properly differentiate cooccurrences by simultaneously considering spatial and temporal features. The comparison results also indicate that MIRI model significantly outperforms state-of-the-art social relationship attack models.

  10. Generalised power graph compression reveals dominant relationship patterns in complex networks

    Science.gov (United States)

    Ahnert, Sebastian E.

    2014-03-01

    We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified.

  11. Allozymic Variation and Relationships within Viola sect. Viola (Violaceae in Iran

    Directory of Open Access Journals (Sweden)

    Mehrvarz Shahryar Saeidi

    2016-12-01

    Full Text Available Genetic variation and differentiation in taxa of the genus Viola L. sect. Viola, subsections Viola and Rostratae (Kupffer W. Becker, were studied from natural populations occurring in Iran. Two isoenzyme systems, Phosphoglucoisomerase (PGI and Aconitase (ACO, encoding four putative loci, were employed to detect interspecific and intraspecific genetic variation. Considering the patterns of isoenzyme variation in the studied taxa, it is evident that V. caspia (Rupr. Freyn subsp. caspia and V. capia subsp. sylvestroides Marcussen are closely related. The species V. alba Bess. subsp. alba and V. sintenisii W. Becker are isoenzymatically well characterized as distinct genetic entities.

  12. Relationship between the composition of flavonoids and flower colors variation in tropical water lily (Nymphaea) cultivars

    National Research Council Canada - National Science Library

    Zhu, Manlan; Zheng, Xuchen; Shu, Qingyan; Li, Hui; Zhong, Peixing; Zhang, Huijin; Xu, Yanjun; Wang, Lijin; Wang, Liangsheng

    2012-01-01

    .... Despite its limited researches on flower color variations and formation mechanism, water lily has background of blue flowers and displays an exceptionally wide diversity of flower colors from purple...

  13. Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species

    NARCIS (Netherlands)

    Hoedjes, K.M.; Smid, H.M.; Vet, L.E.M.; Werren, J.H.

    2014-01-01

    Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the

  14. Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

    Directory of Open Access Journals (Sweden)

    Marco Scortichini

    2010-11-01

    Full Text Available Forty-five Xanthomonas arboricola pv. juglandis (Xaj strains originating from Juglans regia cultivation in different countries were molecularly typed by means of MultiLocus Sequence Typing (MLST, using acnB, gapA, gyrB and rpoD gene fragments. A total of 2.5 kilobases was used to infer the phylogenetic relationship among the strains and possible recombination events. Haplotype diversity, linkage disequilibrium analysis, selection tests, gene flow estimates and codon adaptation index were also assessed. The dendrograms built by maximum likelihood with concatenated nucleotide and amino acid sequences revealed two major and two minor phylotypes. The same haplotype was found in strains originating from different continents, and different haplotypes were found in strains isolated in the same year from the same location. A recombination breakpoint was detected within the rpoD gene fragment. At the pathovar level, the Xaj populations studied here are clonal and under neutral selection. However, four Xaj strains isolated from walnut fruits with apical necrosis are under diversifying selection, suggesting a possible new adaptation. Gene flow estimates do not support the hypothesis of geographic isolation of the strains, even though the genetic diversity between the strains increases as the geographic distance between them increases. A triplet deletion, causing the absence of valine, was found in the rpoD fragment of all 45 Xaj strains when compared with X. axonopodis pv. citri strain 306. The codon adaptation index was high in all four genes studied, indicating a relevant metabolic activity.

  15. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas L Turner

    2011-03-01

    Full Text Available Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size.

  16. Cross-cultural variations in Big Five relationships with religiosity : A sociocultural motives perspective

    NARCIS (Netherlands)

    Gebauer, Jochen E.; Bleidorn, Wiebke; Gosling, Samuel D.; Rentfrow, Peter J.; Lamb, Michael E.; Potter, Jeff

    2014-01-01

    A sociocultural motives perspective (SMP) on Big Five relationships is introduced. According to the SMP, Agreeableness and Conscientiousness elicit assimilation to sociocultural norms, Openness elicits contrast from these norms, and Extraversion and Neuroticism are independent of sociocultural

  17. Utility of canine microsatellites in revealing the relationships of pure bred dogs.

    Science.gov (United States)

    Zajc, I; Sampson, J

    1999-01-01

    The variability of 19 canine microsatellite loci was examined within and between three pure breeds of dog. Their phylogenetic relationships were estimated by microsatellite and conventional genetic distances which indicated that greyhounds and German shepherds had longer diverse evolutionary histories, whereas Labrador retrievers were established much later. Our three breeds differ mainly in the relative frequencies of alleles at a locus and in distribution of alleles across loci. As a consequence of sampling strategy, greyhounds express significantly lower polymorphism than the other two breeds. However, some highly polymorphic microsatellite loci were common to all three breeds. High exclusion power of such loci made them valuable for parentage testing. Although the exclusion probability at a single locus is relatively low, it increases by every added microsatellite. The six most polymorphic ones sufficed to reach the exclusion probability of 99% in all three breeds tested here. As the majority of pedigree dogs have similar population structures, the data presented can be used to estimate the probability of biological paternity for any dog breed, despite the absence of appropriate population data. Polymorphic canine microsatellites proved to be valuable descriptors of population structure, and evolutionary and filial relationships.

  18. Muscle contraction phenotypic analysis enabled by optogenetics reveals functional relationships of sarcomere components in Caenorhabditis elegans

    Science.gov (United States)

    Hwang, Hyundoo; Barnes, Dawn E.; Matsunaga, Yohei; Benian, Guy M.; Ono, Shoichiro; Lu, Hang

    2016-01-01

    The sarcomere, the fundamental unit of muscle contraction, is a highly-ordered complex of hundreds of proteins. Despite decades of genetics work, the functional relationships and the roles of those sarcomeric proteins in animal behaviors remain unclear. In this paper, we demonstrate that optogenetic activation of the motor neurons that induce muscle contraction can facilitate quantitative studies of muscle kinetics in C. elegans. To increase the throughput of the study, we trapped multiple worms in parallel in a microfluidic device and illuminated for photoactivation of channelrhodopsin-2 to induce contractions in body wall muscles. Using image processing, the change in body size was quantified over time. A total of five parameters including rate constants for contraction and relaxation were extracted from the optogenetic assay as descriptors of sarcomere functions. To potentially relate the genes encoding the sarcomeric proteins functionally, a hierarchical clustering analysis was conducted on the basis of those parameters. Because it assesses physiological output different from conventional assays, this method provides a complement to the phenotypic analysis of C. elegans muscle mutants currently performed in many labs; the clusters may provide new insights and drive new hypotheses for functional relationships among the many sarcomere components.

  19. Genetic relationships among Enterococcus faecalis isolates from different sources as revealed by multilocus sequence typing.

    Science.gov (United States)

    Chen, X; Song, Y Q; Xu, H Y; Menghe, B L G; Zhang, H P; Sun, Z H

    2015-08-01

    Enterococcus faecalis is part of the natural gut flora of humans and other mammals; some isolates are also used in food production. So, it is important to evaluate the genetic diversity and phylogenetic relationships among E. faecalis isolates from different sources. Multilocus sequence typing protocol was used to compare 39 E. faecalis isolates from Chinese traditional food products (including dairy products, acidic gruel) and 4 published E. faecalis isolates from other sources including human-derived isolates employing 5 housekeeping genes (groEL, clpX, recA, rpoB, and pepC). A total of 23 unique sequence types were identified, which were grouped into 5 clonal complexes and 10 singletons. The value of standardized index of association of the alleles (IA(S)=0.1465) and network structure indicated a high frequency of intraspecies recombination across these isolates. Enterococcus faecalis lineages also exhibited clearly source-clustered distributions. The isolates from dairy source were clustered together. However, the relationship between isolates from acidic gruel and one isolate from a human source was close. The MLST scheme presented in this study provides a sharable and continuously growing sequence database enabling global comparison of strains from different sources, and will further advance our understanding of the microbial ecology of this important species. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  20. Relationship between Genetic Variation at PPP1R3B and Liver Glycogen and Triglyceride Levels

    DEFF Research Database (Denmark)

    Stender, Stefan; Smagris, Eriks; Lauridsen, Bo K

    2018-01-01

    Genetic variation at rs4240624 on chromosome 8 is associated with an attenuated signal on hepatic computerized tomography (CT), which has been attributed to changes in hepatic fat. The closest coding gene to rs4240624, PPP1R3B, encodes a protein that promotes hepatic glycogen synthesis. Here we...

  1. Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species

    OpenAIRE

    Hoedjes, K.M.; Smid, H.M.; Vet, L.E.M.; Werren, J. H.

    2014-01-01

    Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the parasitic wasp genus Nasonia. After a single olfactory conditioning trial, N. vitripennis consolidates long-term memory that lasts at least 6 days. Memory of the closely related species N. giraulti is...

  2. An investigation into the relationship between thickness variations and manufacturing techniques of mouthguards.

    Science.gov (United States)

    Farrington, Timothy; Coward, Trevor; Onambele-Pearson, Gladys; Taylor, Rebecca L; Earl, Philip; Winwood, Keith

    2016-02-01

    The aim of this study was to measure the finished thickness of a single identical 4-mm EVA mouthguard model from a large fabricated sample group and to evaluate the degree of material thinning and variations during the fabrication process. Twenty boxes were distributed to dental technician participants, each containing five duplicated dental models (n = 100), alongside 5 × 4 mm mouthguard blanks and a questionnaire. The mouthguards were measured using electronic callipers (resolution: ±0.01 mm) at three specific points. The five thickest and thinnest mouthguards were examined using a CT scanner to describe the surface typography unique to each mouthguard, highlighting dimensional thinning patterns during the fabrication process. Of the three measurement points, the anterior sulcus point of the mouthguard showed a significant degree of variation (up to 34% coefficient of variation), in finished mouthguard thickness between individuals. The mean thickness of the mouthguards in the anterior region was 1.62 ± 0.38 mm with a range of 0.77-2.80 mm. This variation was also evident in the occlusion and posterior lingual regions but to a lesser extent (up to 12.2% and 9.8% variations, respectively). This study highlights variability in the finished thickness of the mouthguards especially in the anterior sulcus region measurement point, both within and between individuals. At the anterior region measurement point of the mouthguard, the mean thickness was 1.62 mm, equating to an overall material thinning of 59.5% when using a single 4-mm EVA blank. This degree of thinning is comparative to previous single operator research studies. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Spatio-temporal variation in vegetation biomass and its relationships with climate factors in the Xilingol grasslands, Northern China.

    Directory of Open Access Journals (Sweden)

    Tian Gao

    Full Text Available Knowledge about grassland biomass and its dynamics is critical for studying regional carbon cycles and for the sustainable use of grassland resources. In this study, we investigated the spatio-temporal variation of biomass in the Xilingol grasslands of northern China. Field-based biomass samples and MODIS time series data sets were used to establish two empirical models based on the relationship of the normalized difference vegetation index (NDVI with above-ground biomass (AGB as well as that of AGB with below-ground biomass (BGB. We further explored the climatic controls of these variations. Our results showed that the biomass averaged 99.01 Tg (1 Tg=10(12 g over a total area of 19.6 × 10(4 km(2 and fluctuated with no significant trend from 2001 to 2012. The mean biomass density was 505.4 g/m(2, with 62.6 g/m(2 in AGB and 442.8 g/m(2 in BGB, which generally decreased from northeast to southwest and exhibited a large spatial heterogeneity. The year-to-year AGB pattern was generally consistent with the inter-annual variation in the growing season precipitation (GSP, showing a robust positive correlation (R(2=0.82, P<0.001, but an opposite coupled pattern was observed with the growing season temperature (GST (R(2=0.61, P=0.003. Climatic factors also affected the spatial distribution of AGB, which increased progressively with the GSP gradient (R(2=0.76, P<0.0001 but decreased with an increasing GST (R(2=0.70, P<0.0001. An improved moisture index that combined the effects of GST and GSP explained more variation in AGB than did precipitation alone (R(2=0.81, P<0.0001. The relationship between AGB and GSP could be fit by a power function. This increasing slope of the GSP-AGB relationships along the GSP gradient may be partly explained by the GST-GSP spatial pattern in Xilingol. Our findings suggest that the relationships between climatic factors and AGB may be scale-dependent and that multi-scale studies and sufficient long-term field data are needed

  4. Antigenic relationships within the genus Salmonella as revealed by anti-Salmonella enteritidis monoclonal antibodies.

    Science.gov (United States)

    Malik, M; Butchaiah, G; Bansal, M P; Siddiqui, M Z; Bakshi, C S; Singh, R K

    2002-04-01

    A panel of 38 monoclonal antibodies (MAbs) that react with outer membrane proteins (OMPs) of Salmonella enteritidis was produced. On the basis of their binding pattern in ELISA, the MAbs were divided into three groups. The first group, consisting of 15 MAbs, was found to be Salmonella-specific as they did not cross-react with Escherichia coli or Pasteurella multocida. The second group of 15 MAbs cross-reacted with E. coli but not with P. multocida, reflecting the closer antigenic relationship of E. coli with Salmonella. The third group of 8 MAbs cross-reacted with both E. coli and P. multocida, indicating that the antigenic determinants identified by these MAbs are conserved in all the three genera. The antigenic relationship of the Salmonella serovars (S. enteritidis, S. gallinarum, S. typhimurium, S. dublin, S. agona, S. indiana and S. choleraesuis) was studied using OMPs prepared from them and the anti-S. enteritidis MAbs. Three MAbs appeared to be specific for S. enteritidis as they did not cross-react with any of the other Salmonella serovars. Twelve of the 38 MAbs cross-reacted with all the serovars tested. Six of these were specific to the Salmonella genus as they did not cross-react with any of the other Gram-negative bacteria tested. The reactivity pattern of the other MAbs indicated that S. gallinarum was antigenically close to S. enteritidis, followed in order by S. dublin, S. agona, S. typhimurium and S. indiana, whereas S. choleraesuis seemed to be antigenically quite distant from S. enteritidis.

  5. The relationship between sign production and sign comprehension: What handedness reveals.

    Science.gov (United States)

    Watkins, Freya; Thompson, Robin L

    2017-07-01

    Unlike the phonological loop in spoken language monitoring, sign language users' own production provides mostly proprioceptive feedback and only minimal visual feedback. Here we investigate whether sign production influences sign comprehension by exploiting hand dominance in a picture-sign matching task performed by left-handed signers and right-handed signers. Should all signers perform better to right-handed input, this would suggest that a frequency effect in sign perception drives comprehension. However, if signers perform better to congruent-handed input, this would implicate the production system's role in comprehension. We found evidence for both hypotheses, with variation dependent on sign type. All signers performed faster to right-handers for phonologically simple, one-handed signs. However, left-handed signers preferred congruent-handed input for phonologically complex, two-handed asymmetrical signs. These results are in line with a weak version of the motor theory of speech perception, where the motor system is only engaged when comprehending complex input. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  6. Size at the onset of maturity (SOM) revealed in length-weight relationships of brackish amphipods and isopods: An information theory approach

    Science.gov (United States)

    Longo, Emanuela; Mancinelli, Giorgio

    2014-01-01

    In amphipods and other small-sized crustaceans, allometric relationships are conventionally analysed by fitting the standard model Y = a·Xb (X and Y are, e.g., body length and weight, respectively) whose scaling exponent b is assumed to be constant. However, breakpoints in allometric relationships have long been documented in large-sized crustaceans, ultimately determined by ontogenetic, abrupt variations in the value of b. Here, the existence of breakpoints in length-weight relationships was investigated in four amphipod (i.e., Gammarus aequicauda, Gammarus insensibilis, Microdeutopus gryllotalpa, and Dexamine spinosa) and three isopod species (i.e., Lekanesphaera hookeri, Sphaeroma serratum, and Cymodoce truncata) from three Mediterranean lagoons. The power of two candidate linear models fitted to log10-transformed data - a simple model assuming a constant exponent b and a segmented model assuming b to vary after a breakpoint - was compared using a parsimonious selection strategy based on the Akaike information criterion. The segmented model with a breakpoint provided the most accurate fitting of length-weight data in the majority of the species analysed; non-conclusive results were obtained only for D. spinosa and C. truncata, of which a limited number of specimens was examined. Model parameters were consistent for amphipod and isopod species collected across the three different habitats; the generality of the results was further supported by a literature search confirming that the identified breakpoints corresponded with ontogenetic discontinuities related with sexual maturation in all the species investigated. In this study, segmented regression models were revealed to provide a statistically accurate and biologically meaningful description of length-weight relationships of common amphipod and isopod species. The methodological limitations of the approach are considered, while the practical implications for secondary production estimates are discussed.

  7. Seasonal Variation in the NDVI–Species Richness Relationship in a Prairie Grassland Experiment (Cedar Creek

    Directory of Open Access Journals (Sweden)

    Ran Wang

    2016-02-01

    Full Text Available Species richness generally promotes ecosystem productivity, although the shape of the relationship varies and remains the subject of debate. One reason for this uncertainty lies in the multitude of methodological approaches to sampling biodiversity and productivity, some of which can be subjective. Remote sensing offers new, objective ways of assessing productivity and biodiversity. In this study, we tested the species richness–productivity relationship using a common remote sensing index, the Normalized Difference Vegetation Index (NDVI, as a measure of productivity in experimental prairie grassland plots (Cedar Creek. Our study spanned a growing season (May to October, 2014 to evaluate dynamic changes in the NDVI–species richness relationship through time and in relation to environmental variables and phenology. We show that NDVI, which is strongly associated with vegetation percent cover and biomass, is related to biodiversity for this prairie site, but it is also strongly influenced by other factors, including canopy growth stage, short-term water stress and shifting flowering patterns. Remarkably, the NDVI-biodiversity correlation peaked at mid-season, a period of warm, dry conditions and anthesis, when NDVI reached a local minimum. These findings confirm a positive, but dynamic, productivity–diversity relationship and highlight the benefit of optical remote sensing as an objective and non-invasive tool for assessing diversity–productivity relationships.

  8. Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases

    Energy Technology Data Exchange (ETDEWEB)

    P Lombardi; H Angell; D Whittington; E Flynn; K Rajashankar; D Christianson

    2011-12-31

    Polyamines are a ubiquitous class of polycationic small molecules that can influence gene expression by binding to nucleic acids. Reversible polyamine acetylation regulates nucleic acid binding and is required for normal cell cycle progression and proliferation. Here, we report the structures of Mycoplana ramosa acetylpolyamine amidohydrolase (APAH) complexed with a transition state analogue and a hydroxamate inhibitor and an inactive mutant complexed with two acetylpolyamine substrates. The structure of APAH is the first of a histone deacetylase-like oligomer and reveals that an 18-residue insert in the L2 loop promotes dimerization and the formation of an 18 {angstrom} long 'L'-shaped active site tunnel at the dimer interface, accessible only to narrow and flexible substrates. The importance of dimerization for polyamine deacetylase function leads to the suggestion that a comparable dimeric or double-domain histone deacetylase could catalyze polyamine deacetylation reactions in eukaryotes.

  9. 13C-detection in RNA bases: revealing structure-chemical shift relationships.

    Science.gov (United States)

    Farès, Christophe; Amata, Irene; Carlomagno, Teresa

    2007-12-26

    The chemical shifts of the unprotonated carbons in the proton-deficient nucleobases of RNA are rarely reported, despite the valuable information that they contain about base-pairing and base-stacking. We have developed 13C-detected 2D-experiments to identify the unprotonated 13C in the RNA bases and have assigned all the base nuclei of uniformly 13C,15N-labeled HIV-2 TAR-RNA. The 13C chemical shift distributions revealed perturbations correlated with the base-pairing and base-stacking properties of all four base-types. From this work, we conclude that the information contained in the chemical shift perturbations within the base rings can provide valuable restraint information for solving RNA structures, especially in conformational averaged regions, where NOE-based information is not available.

  10. Past and Present-day Ice Mass Variation on Svalbard Revealed by Superconducting Gravimeter, GPS and VLBI Measurements

    Science.gov (United States)

    Kierulf, H. P.; Omang, O.

    2012-12-01

    The measured uplift in Ny-Alesund has varied with geodetic technique, analyzed strategy, and the time period used. This has caused problems for both reference frame issues as well as the geophysical interpretations of the results. In Arctic areas deglaciation after the last glacial maximum, Holocene ice mass variation, and present day ice melt contribute to the land uplift. In addition, tectonic contributions cannot be excluded. We use both geometric and gravity data from the observatory in Ny-Alesund as well as in-situ mass balance measurements of local glaciers to separate the different processes contributing to the land uplift in Ny-Alesund and Svalbard. Measurements from the geodetic observatory in Ny-Alesund indicate land uplift much larger than expected from traditional models of glacial isostatic adjustment. In addition, the land uplift shows large variations from year to year. A combination of the measured variations in the land uplift along with local ice mass variations give a good constraint on the land uplift caused by the present day ice melt. However, we are still not able to explain all the measured uplift. The changes in measured gravity are consistent with the geometric measurements but also much larger than expected from the glacial isostatic adjustment and the present day ice melt. The ratio of unexplained gravity change and unexplained geometric uplift indicate a viscoelastic process. The unexplained uplift is most likely caused by late Holocene ice mass variations.

  11. An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci

    Science.gov (United States)

    Li, Baohua; Zhang, Yuanyuan; Mohammadi, Seyed Abolghasem; Huai, Dongxin; Zhou, Yongming; Kliebenstein, Daniel J.

    2016-07-01

    Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.

  12. Climate variations in greenhouse cultivated with gerbera and relationship with external conditions

    OpenAIRE

    Andrade Júnior,Aderson S. de; Damasceno,Lisânea M. O.; Dias,Nildo da S.; Gheyi,Hans R.; Guiselini,Cristiane

    2011-01-01

    Black meshes used in greenhouses provide shade to plants, affecting photosynthesis and presenting certain properties that change the microclimatic conditions in these environments. The objective of this study was to evaluate the variation in climate elements in greenhouse cultivated with gerbera (Gerbera jamesonii, Vr. Rambo) in relation to external conditions and the reference evapotranspiration (ETo) at Teresina, State of Piauí, Brazil. The measurements were obtained from July to October 20...

  13. Relationships Among Ecologically Important Dimensions of Plant Trait Variation in Seven Neotropical Forests

    Science.gov (United States)

    Wright, Ian J.; Ackerly, David D.; Bongers, Frans; Harms, Kyle E.; Ibarra-Manriquez, Guillermo; Martinez-Ramos, Miguel; Mazer, Susan J.; Muller-Landau, Helene C.; Paz, Horacio; Pitman, Nigel C. A.; Poorter, Lourens; Silman, Miles R.; Vriesendorp, Corine F.; Webb, Cam O.; Westoby, Mark; Wright, S. Joseph

    2007-01-01

    Background and Aims When ecologically important plant traits are correlated they may be said to constitute an ecological ‘strategy’ dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait combinations are favoured over others and into the implications of trait differences among species. Here we investigated relationships among several traits, and thus the strategy dimensions they represented, across 2134 woody species from seven Neotropical forests. Methods Six traits were studied: specific leaf area (SLA), the average size of leaves, seed and fruit, typical maximum plant height, and wood density (WD). Trait relationships were quantified across species at each individual forest as well as across the dataset as a whole. ‘Phylogenetic’ analyses were used to test for correlations among evolutionary trait-divergences and to ascertain whether interspecific relationships were biased by strong taxonomic patterning in the traits. Key Results The interspecific and phylogenetic analyses yielded congruent results. Seed and fruit size were expected, and confirmed, to be tightly related. As expected, plant height was correlated with each of seed and fruit size, albeit weakly. Weak support was found for an expected positive relationship between leaf and fruit size. The prediction that SLA and WD would be negatively correlated was not supported. Otherwise the traits were predicted to be largely unrelated, being representatives of putatively independent strategy dimensions. This was indeed the case, although WD was consistently, negatively related to leaf size. Conclusions The dimensions represented by SLA, seed/fruit size and leaf size were essentially independent and thus conveyed largely independent information about plant strategies. To a lesser extent the same was true for plant height and WD. Our tentative explanation for negative WD–leaf size relationships, now also known from other

  14. [Relationship between genetic variation of furin gene and hypercholesterolemia and hyper-low-density lipoprotein cholesterolemia in Kazakh general population].

    Science.gov (United States)

    Wang, Hong-mei; Li, Nan-fang; Hong, Jing; Luo, Wen-li; Yan, Zhi-tao; Wang, Xin-ling; Zhu, Yi; Shen, Yan

    2014-04-01

    To investigate the relationship between the genetic variation of Furin gene and the hypercholesterolemia and hyper-low-density lipoprotein cholesterolemia in Kazakh general population. Based on a cross-sectional epidemiological study in a Kazakh general population, a case-control study including 878 subjects was conducted. All the sequence variant-located promoters and exon regions of Furin gene were identified by the direct sequencing of PCR products in 48 randomly selected hypercholesterolemic individuals (24 males and 24 females). After having genotyped the representative polymorphisms in 878 subjects by TaqMan PCR, we investigated the relationship between genetic variation of Furin and hypercholesterolemia/hyper-low-density lipoprotein cholesterolemia in these subjects. Twelve genetic variations in Furin gene were identified by sequencing 48 hypercholesterolemic individuals and 4 common single nucleotide polymorphisms (rs6226, rs6227, rs2071410, and rs4932178)were selected as the representatives for genotyping in these subjects. The rs6226, rs6227, rs2071410, and rs4932178 polymorphisms were successfully genotyped. The distribution of the genotypes, alleles, and haplotypes of rs6226, rs6227, rs2071410, and rs4932178 polymorphisms did not differ significantly between the hypercholesterolemia group and the control groups or between the hyper-low-density lipoprotein cholesterolemia group and the control groups (all P>0.05). The cholesterol and low-density lipoprotein cholesterol levels did not differ significantly among individuals with different genotypes (all P>0.05). The genetic variation of Furin may not be associated with hypercholesterolemia or hyper-low-density lipoprotein cholesterolemia in Kazakh general population.

  15. Genetic diversity and relationships in mulberry (genus Morus as revealed by RAPD and ISSR marker assays

    Directory of Open Access Journals (Sweden)

    Thangavelu K

    2004-01-01

    Full Text Available Abstract Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species. Results RAPD analysis using 19 random primers generated 128 discrete markers ranging from 500–3000 bp in size. One-hundred-nineteen of these were polymorphic (92%, with an average of 6.26 markers per primer. Among these were a few putative species-specific amplification products which could be useful for germplasm classification and introgression studies. The ISSR analysis employed six anchored primers, 4 of which generated 93 polymorphic markers with an average of 23.25 markers per primer. Cluster analysis of RAPD and ISSR data using the WINBOOT package to calculate the Dice coefficient resulted into two clusters, one comprising polyploid wild species and the other with domesticated (mostly diploid species. Conclusion These results suggest that RAPD and ISSR markers are useful for mulberry genetic diversity analysis and germplasm characterization, and that putative species-specific markers may be obtained which can be converted to SCARs after further studies.

  16. Relationship between thunderstorm electrification and storm kinetics revealed by phased array weather radar

    Science.gov (United States)

    Yoshida, S.; Adachi, T.; Kusunoki, K.; Hayashi, S.; Wu, T.; Ushio, T.; Yoshikawa, E.

    2017-04-01

    We examine 3-D lightning location data and radar data obtained through multiple radar observation stations, including two X-band phased array weather radars (PAWRs), in order to understand the relationship between thunderstorm electrification and storm kinetics. In an investigated convective cell, both intracloud (IC) and cloud-to-ground (CG) flash rates drastically change within 25 min. First, the IC flash rate shows a steep increase with a peak at 10 min-1, and then, the CG flash rate peaks 7 min afterward. During the increase phase of the IC flash rate, the radar observation indicates that the echo top height and updraft echo volume in the upper level increase. The upper positive charge regions removed by IC flashes are located in or near the updraft region at high altitudes. On the contrary, the IC flash rate decreases when the updraft at high altitudes weakens. The IC flash rate is well correlated with a proxy for updraft volume in 1 min interval comparison. These results indicate that the IC flash rate has a strong connection with updraft at high altitudes. The CG flash rate peaks when precipitation particles, probably involving graupel, from high altitudes arrive at approximately the -10°C isotherm level. We speculate that graupel from high altitudes might contribute to the initiations of CG flashes. We show an abrupt ascent of the upper positive charge region involved in IC flashes. PAWR observation results indicate that the updraft might have contributed to the ascent of the upper positive lightning charge region.

  17. Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes.

    Directory of Open Access Journals (Sweden)

    Kean Chong Lim

    Full Text Available Elucidating the phylogenetic relationships of the current but problematic Dasyatidae (Order Myliobatiformes was the first priority of the current study. Here, we studied three molecular gene markers of 43 species (COI gene, 33 species (ND2 gene and 34 species (RAG1 gene of stingrays to draft out the phylogenetic tree of the order. Nine character states were identified and used to confirm the molecularly constructed phylogenetic trees. Eight or more clades (at different hierarchical level were identified for COI, ND2 and RAG1 genes in the Myliobatiformes including four clades containing members of the present Dasyatidae, thus rendering the latter non-monophyletic. The uncorrected p-distance between these four 'Dasytidae' clades when compared to the distance between formally known families confirmed that these four clades should be elevated to four separate families. We suggest a revision of the present classification, retaining the Dasyatidae (Dasyatis and Taeniurops species but adding three new families namely, Neotrygonidae (Neotrygon and Taeniura species, Himanturidae (Himantura species and Pastinachidae (Pastinachus species. Our result indicated the need to further review the classification of Dasyatis microps. By resolving the non-monophyletic problem, the suite of nine character states enables the natural classification of the Myliobatiformes into at least thirteen families based on morphology.

  18. Relationship between blood oxygenation and lactate in human skeletal muscle revealed by near-infrared spectroscopy

    Science.gov (United States)

    Xu, Guodong; Luo, Qingming; Ge, Xinfa; Gong, Hui; Zeng, Shaoqun

    2002-04-01

    Near-infrared spectroscopy (NIRS) is a focus of attention in the research field of biomedical photonics. The concentration of HbO2 in human skeletal muscle has been measured noninvasive NIRS using a portable tissue oximeter continuously when the subjects did incremental exercises on a power bicycle. Blood lactate is one of traditional physical research subjects which is applied most widely. We study blood volume in the tissue of sportsmen when they are subjected by the incremental physical load, simultaneously detecting some parameters such as the heart rate, maximal oxygen absorption and the concentration of blood lactate. As the intensity of exercises was heightened, the concentration of blood lactate and blood volume in tissue increased, while the concentration of HbO2 decreased. Thus the rudimental characteristics of energy consumption and supply during hypoxia and aerobic exercises are investigated. By discovering the relationship between blood lactate in human skeletal muscle and blood oxygenation, a novel approach for measuring blood lactate noninvasively and assessing the sports ability could be provided. Furthermore, it is possible to assess the fatigue state with tissue oximeter to monitor the human sports intensity noninvasively and dynamically.

  19. Polygenic risk score and heritability estimates reveals a genetic relationship between ASD and OCD.

    Science.gov (United States)

    Guo, W; Samuels, J F; Wang, Y; Cao, H; Ritter, M; Nestadt, P S; Krasnow, J; Greenberg, B D; Fyer, A J; McCracken, J T; Geller, D A; Murphy, D L; Knowles, J A; Grados, M A; Riddle, M A; Rasmussen, S A; McLaughlin, N C; Nurmi, E L; Askland, K D; Cullen, B A; Piacentini, J; Pauls, D L; Bienvenu, O J; Stewart, S E; Goes, F S; Maher, B; Pulver, A E; Valle, D; Mattheisen, M; Qian, J; Nestadt, G; Shugart, Y Y

    2017-07-01

    Obsessive-compulsive disorder (OCD) and Autism spectrum disorder (ASD) are both highly heritable neurodevelopmental disorders that conceivably share genetic risk factors. However, the underlying genetic determinants remain largely unknown. In this work, the authors describe a combined genome-wide association study (GWAS) of ASD and OCD. The OCD dataset includes 2998 individuals in nuclear families. The ASD dataset includes 6898 individuals in case-parents trios. GWAS summary statistics were examined for potential enrichment of functional variants associated with gene expression levels in brain regions. The top ranked SNP is rs4785741 (chromosome 16) with P value=6.9×10-7 in our re-analysis. Polygenic risk score analyses were conducted to investigate the genetic relationship within and across the two disorders. These analyses identified a significant polygenic component of ASD, predicting 0.11% of the phenotypic variance in an independent OCD data set. In addition, we examined the genomic architecture of ASD and OCD by estimating heritability on different chromosomes and different allele frequencies, analyzing genome-wide common variant data by using the Genome-wide Complex Trait Analysis (GCTA) program. The estimated global heritability of OCD is 0.427 (se=0.093) and 0.174 (se=0.053) for ASD in these imputed data. Published by Elsevier B.V.

  20. Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae.

    Science.gov (United States)

    Zhang, W Q; Zhang, M H

    2013-09-03

    Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.

  1. A metabonomic study of transgenic maize (Zea mays) seeds revealed variations in osmolytes and branched amino acids.

    Science.gov (United States)

    Manetti, Cesare; Bianchetti, Cristiano; Casciani, Lorena; Castro, Cecilia; Di Cocco, Maria Enrica; Miccheli, Alfredo; Motto, Mario; Conti, Filippo

    2006-01-01

    The aim of the research was to investigate metabolic variations associated with genetic modifications in the grains of Zea mays using metabonomic techniques. With this in mind, the non-targeted characteristic of the technique is useful to identify metabolites peculiar to the genetic modification and initially undefined. The results obtained showed that the genetic modification, introducing Cry1Ab gene expression, induces metabolic variations involving the primary nitrogen pathway. Concerning the methodological aspects, the experimental protocol used has been applied in this field for the first time. It consists of a combination of partial least square-discriminant analysis and principal component analysis. The most important metabolites for discrimination were selected and the metabolic correlations linking them are identified. Principal component analysis on selected signals confirms metabolic variations, highlighting important details about the changes induced on the metabolic network by the presence of a Bt transgene in the maize genome.

  2. Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks.

    Science.gov (United States)

    Brion, Christian; Ambroset, Chloé; Sanchez, Isabelle; Legras, Jean-Luc; Blondin, Bruno

    2013-10-04

    Variation of gene expression can lead to phenotypic variation and have therefore been assumed to contribute the diversity of wine yeast (Saccharomyces cerevisiae) properties. However, the molecular bases of this variation of gene expression are unknown. We addressed these questions by carrying out an integrated genetical-genomic study in fermentation conditions. We report here quantitative trait loci (QTL) mapping based on expression profiling in a segregating population generated by a cross between a derivative of the popular wine strain EC1118 and the laboratory strain S288c. Most of the fermentation traits studied appeared to be under multi-allelic control. We mapped five phenotypic QTLs and 1465 expression QTLs. Several expression QTLs overlapped in hotspots. Among the linkages unraveled here, several were associated with metabolic processes essential for wine fermentation such as glucose sensing or nitrogen and vitamin metabolism. Variations affecting the regulation of drug detoxification and export (TPO1, PDR12 or QDR2) were linked to variation in four genes encoding transcription factors (PDR8, WAR1, YRR1 and HAP1). We demonstrated that the allelic variation of WAR1 and TPO1 affected sorbic and octanoic acid resistance, respectively. Moreover, analysis of the transcription factors phylogeny suggests they evolved with a specific adaptation of the strains to wine fermentation conditions. Unexpectedly, we found that the variation of fermentation rates was associated with a partial disomy of chromosome 16. This disomy resulted from the well known 8-16 translocation. This large data set made it possible to decipher the effects of genetic variation on gene expression during fermentation and certain wine fermentation properties. Our findings shed a new light on the adaptation mechanisms required by yeast to cope with the multiple stresses generated by wine fermentation. In this context, the detoxification and export systems appear to be of particular importance

  3. The relationship between DTCA, drug requests, and prescriptions: Uncovering variation in specialty and space

    NARCIS (Netherlands)

    S. Stremersch (Stefan); V. Schwartz-Landsman (Vardit); S. Venkataraman (Sriram)

    2013-01-01

    textabstractPatients increasingly request their physicians to prescribe specific brands of pharmaceutical drugs. A popular belief is that requests are triggered by direct-to-consumer advertising (DTCA). We examine the relationship between DTCA, patient requests, and prescriptions for statins. We

  4. Relationships among ecologically important dimensions of plant trait variation in seven neotropical forests

    NARCIS (Netherlands)

    Wright, I.J.; Ackerly, D.D.; Bongers, F.J.J.M.; Harms, K.E.; Ibarra-Manriquez, G.; Martinez-Ramos, M.; Mazer, S.J.; Muller-Landau, H.C.; Paz, H.; Pitman, N.C.A.; Poorter, L.; Silman, M.R.; Vriesendorp, C.F.; Webb, C.O.; Westoby, M.; Wright, S.J.

    2007-01-01

    Background and Aims When ecologically important plant traits are correlated they may be said to constitute an ecological 'strategy' dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait combinations are favoured over

  5. Coparenting Relationships after Divorce: Variations by Type of Marital Violence and Fathers' Role Differentiation

    Science.gov (United States)

    Hardesty, Jennifer L.; Khaw, Lyndal; Chung, Grace H.; Martin, Jennifer M.

    2008-01-01

    Using grounded theory methods, we examined coparenting relationships for 25 divorced mothers who experienced violence during their marriages. How well former husbands were able to differentiate, or keep separate, their parental and spousal roles emerged as central to coparenting dynamics and was partly related to type of marital violence. Linking…

  6. 45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus.

    Science.gov (United States)

    Rodrigues, Joana; Viegas, Wanda; Silva, Manuela

    2017-01-01

    The genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity-A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5' external transcribed spacer (5'-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5'-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5'-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5'-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5'-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.

  7. Karyotype relationships among selected deer species and cattle revealed by bovine FISH probes.

    Directory of Open Access Journals (Sweden)

    Jan Frohlich

    Full Text Available The Cervidae family comprises more than fifty species divided into three subfamilies: Capreolinae, Cervinae and Hydropotinae. A characteristic attribute for the species included in this family is the great karyotype diversity, with the chromosomal numbers ranging from 2n = 6 observed in female Muntiacus muntjak vaginalis to 2n = 70 found in Mazama gouazoubira as a result of numerous Robertsonian and tandem fusions. This work reports chromosomal homologies between cattle (Bos taurus, 2n = 60 and nine cervid species using a combination of whole chromosome and region-specific paints and BAC clones derived from cattle. We show that despite the great diversity of karyotypes in the studied species, the number of conserved chromosomal segments detected by 29 cattle whole chromosome painting probes was 35 for all Cervidae samples. The detailed analysis of the X chromosomes revealed two different morphological types within Cervidae. The first one, present in the Capreolinae is a sub/metacentric X with the structure more similar to the bovine X. The second type found in Cervini and Muntiacini is an acrocentric X which shows rearrangements in the proximal part that have not yet been identified within Ruminantia. Moreover, we characterised four repetitive sequences organized in heterochromatic blocks on sex chromosomes of the reindeer (Rangifer tarandus. We show that these repeats gave no hybridization signals to the chromosomes of the closely related moose (Alces alces and are therefore specific to the reindeer.

  8. Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine

    Science.gov (United States)

    Hong, Xutao; Chen, Jing; Liu, Lin; Wu, Huan; Tan, Haiqin; Xie, Guangfa; Xu, Qian; Zou, Huijun; Yu, Wenjing; Wang, Lan; Qin, Nan

    2016-01-01

    Chinese Rice Wine (CRW) is a common alcoholic beverage in China. To investigate the influence of microbial composition on the quality of CRW, high throughput sequencing was performed for 110 wine samples on bacterial 16S rRNA gene and fungal Internal Transcribed Spacer II (ITS2). Bioinformatic analyses demonstrated that the quality of yeast starter and final wine correlated with microbial taxonomic composition, which was exemplified by our finding that wine spoilage resulted from a high proportion of genus Lactobacillus. Subsequently, based on Lactobacillus abundance of an early stage, a model was constructed to predict final wine quality. In addition, three batches of 20 representative wine samples selected from a pool of 110 samples were further analyzed in metagenomics. The results revealed that wine spoilage was due to rapid growth of Lactobacillus brevis at the early stage of fermentation. Gene functional analysis indicated the importance of some pathways such as synthesis of biotin, malolactic fermentation and production of short-chain fatty acid. These results led to a conclusion that metabolisms of microbes influence the wine quality. Thus, nurturing of beneficial microbes and inhibition of undesired ones are both important for the mechanized brewery. PMID:27241862

  9. Puffins reveal contrasting relationships between forage fish and ocean climate in the North Pacific

    Science.gov (United States)

    Sydeman, William J.; Piatt, John F.; Thompson, Sarah Ann; Garcia-Reyes, Marisol; Hatch, Scott A.; Arimitsu, Mayumi; Slater, Leslie; Williams, Jeffrey C.; Rojek, Nora A.; Zador, Stephani G.; Renner, Heather M.

    2017-01-01

    Long-term studies of predator food habits (i.e., ‘predator-based sampling’) are useful for identifying patterns of spatial and temporal variability of forage nekton in marine ecosystems. We investigated temporal changes in forage fish availability and relationships to ocean climate by analyzing diet composition of three puffin species (horned puffin Fratercula corniculata, tufted puffin Fratercula cirrhata, and rhinoceros auklet Cerorhinca monocerata) from five sites in the North Pacific from 1978–2012. Dominant forage species included squids and hexagrammids in the western Aleutians, gadids and Pacific sand lance (Ammodytes personatus) in the eastern Aleutians and western Gulf of Alaska (GoA), and sand lance and capelin (Mallotus villosus) in the northern and eastern GoA. Interannual fluctuations in forage availability dominated variability in the western Aleutians, whereas lower-frequency shifts in forage fish availability dominated elsewhere. We produced regional multivariate indicators of sand lance, capelin, and age-0 gadid availability by combining data across species and sites using Principal Component Analysis, and related these indices to environmental factors including sea level pressure (SPL), winds, and sea surface temperature (SST). There was coherence in the availability of sand lance and capelin across the study area. Sand lance availability increased linearly with environmental conditions leading to warmer ocean temperatures, whereas capelin availability increased in a non-linear manner when environmental changes led to lower ocean temperatures. Long-term studies of puffin diet composition appear to be a promising tool for understanding the availability of these difficult-to-survey forage nekton in remote regions of the North Pacific.

  10. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences.

    Science.gov (United States)

    Regier, Jerome C; Shultz, Jeffrey W; Zwick, Andreas; Hussey, April; Ball, Bernard; Wetzer, Regina; Martin, Joel W; Cunningham, Clifford W

    2010-02-25

    The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.

  11. A Qualitative Study Revealing the Relationship Between Cultural Indicators and Attitudes Toward the Ads

    Directory of Open Access Journals (Sweden)

    Emine Sahin

    2014-12-01

    Full Text Available The companies, in International markets, are required to examine the attitudes and the behaviours to recognize the consumer to be able to make their products preferable under constantly growing competitive conditions. Therefore, it is of great importance to know cultural values of the customers in the country's where global brands compete and to shape ads which is one of the marketing communication tools in this direction. In this respect, knowing the cultural similarities or differences of the countries where the ads are used (such as that country's religion, language, norms and cultural values gains importance. The consumer attitudes towards the ads change in accordance with their cultural similarities or dissimilarities and this attitude change determines the tendency of shopping. According to Geert Hofstede, social anthropologist who analyzes the cultural levels and the relationships among them the basic elements of the culture consists of symbols, heroes, rituals and values underlying them. Thorough symbols, a number of cultural values are conveyed to ads. The problem of this study which was carried out in order to determine attitude change towards the ads including cultural differences is “Is there a difference in the attitudes towards the ads including different cultural symbols? How it is distributed according to gender differences?" In this study, a qualitative research method was applied and interviewed with 20 test subject. 20 students studying in one of the universities in Turkey were selected with formal sampling, they were asked questions, and it was tried to determine the difference between the ad of Doğuş Çay-a tea brand which uses the symbols and local accent of Black sea region in Turkey in its ads- and the ad of Lipton which is an international British tea brand. At the end of the study, it was found out that sample’s the attitude was positive towards ad of Doğuş Çay, not Lipton.

  12. Second-harmonic generation reveals a relationship between metastatic potential and collagen fiber structure

    Science.gov (United States)

    Burke, Kathleen A.; Dawes, Ryan P.; Cheema, Mehar K.; Perry, Seth; Brown, Edward

    2014-02-01

    Second Harmonic Generation (SHG) of collagen signals allows for the analysis of collagen structural changes throughout metastatic progression. The directionality of coherent SHG signals, measured through the ratio of the forward-propagating to backward propagating signal (F/B ratio), is affected by fibril diameter, spacing, and order versus disorder of fibril packing within a fiber. As tumors interact with their microenvironment and metastasize, it causes changes in these parameters, and concurrent changes in the F/B ratio. Specifically, the F/B ratio of breast tumors that are highly metastatic to the lymph nodes is significantly higher than those in tumors with restricted lymph node involvement. We utilized in vitro analysis of tumor cell motility through collagen gels of different microstructures, and hence different F/B ratios, to explore the relationship between collagen microstructures and metastatic capabilities of the tumor. By manipulating environmental factors of fibrillogenesis and biochemical factors of fiber composition we created methods of varying the average F/B ratio of the gel, with significant changes in fiber structure occurring as a result of alterations in incubation temperature and increasing type III collagen presence. A migration assay was performed using simultaneous SHG and fluorescent imaging to measure average penetration depth of human tumor cells into the gels of significantly different F/B ratios, with preliminary data demonstrating that cells penetrate deeper into gels of higher F/B ratio caused by lower type III collagen concentration. Determining the role of collagen structure in tumor cell motility will aid in the future prediction metastatic capabilities of a primary tumor.

  13. 45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

    Science.gov (United States)

    Rodrigues, Joana; Viegas, Wanda

    2017-01-01

    The genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity–A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5’ external transcribed spacer (5’-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5’-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5’-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5’-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5’-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways. PMID:28448637

  14. An integrative genetic study of rice metabolism, growth and stochastic variation reveals potential C/N partitioning loci

    DEFF Research Database (Denmark)

    Li, Baohua; Zhang, Yuanyuan; Mohammadi, Seyed Abolghasem

    2016-01-01

    on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we...

  15. Low temporal variation in the intact polar lipid composition of North Sea coastal marine water reveals limited chemotaxonomic value

    NARCIS (Netherlands)

    Brandsma, J.; Hopmans, E.C.; Philippart, C.J.M.; Veldhuis, M.J.W.; Schouten, S.; Sinninghe Damsté, J.S.S.

    2012-01-01

    Temporal variations in the abundance and composition of intact polar lipids (IPLs) in North Sea coastal marine water were assessed over a one-year seasonal cycle, and compared with environmental parameters and the microbial community composition. Sulfoquinovosyldiacylglycerol (SQDG) was the most

  16. Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma.

    Directory of Open Access Journals (Sweden)

    Stine H Kresse

    Full Text Available BACKGROUND: Osteosarcomas are the most common non-haematological primary malignant tumours of bone, and all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. PRINCIPAL FINDINGS: The cell lines showed complex patterns of DNA copy number changes, where genomic copy number gains were significantly associated with gene-rich regions and losses with gene-poor regions. By integrating the datasets, 350 genes were identified as having two types of aberrations (gain/over-expression, hypo-methylation/over-expression, loss/under-expression or hyper-methylation/under-expression using a recurrence threshold of 6/19 (>30% cell lines. The genes showed in general alterations in either DNA copy number or DNA methylation, both within individual samples and across the sample panel. These 350 genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. The aberrations of three selected genes, CXCL5, DLX5 and RUNX2, were validated in five cell lines and five tumour samples using PCR techniques. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2'-deoxycytidine treatment for four genes tested; AKAP12, CXCL5, EFEMP1 and IL11RA. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for detrimental genes. CONCLUSIONS: Integrative analysis of genome-wide genetic and epigenetic alterations identified dependencies and relationships between

  17. Revealing genetic relationships between compounds affecting boar taint and reproduction in pigs.

    Science.gov (United States)

    Grindflek, E; Meuwissen, T H E; Aasmundstad, T; Hamland, H; Hansen, M H S; Nome, T; Kent, M; Torjesen, P; Lien, S

    2011-03-01

    Boar taint is characterized by an unpleasant taste or odor in intact male pigs and is primarily attributed to increased concentrations of androstenone and skatole and to a lesser extent by increased indole. The boar taint compounds skatole and indole are produced by gut bacteria, metabolized in the liver, and stored in the fat tissue. Androstenone, on the other hand, is synthesized in the testis along with testosterone and estrogens, which are known to be important factors affecting fertility. The main goal of this study was to investigate the relationship between genetic factors involved in the primary boar taint compounds in an attempt to discover ways to reduce boar taint without decreasing fertility-related compounds. Heritabilities and genetic correlations between traits were estimated for compounds related to boar taint (androstenone, skatole, indole) and reproduction (testosterone, 17β-estradiol, and estrone sulfate). Heritabilities in the range of 0.47 to 0.67 were detected for androstenone concentrations in both fat and plasma, whereas those for skatole and indole were slightly less (0.27 to 0.41). The genetic correlations between androstenone in plasma and fat were extremely high (0.91 to 0.98) in Duroc and Landrace. In addition, genetic correlations between androstenone (both plasma and fat) and the other sex steroids (estrone sulfate, 17β-estradiol, and testosterone) were very high, in the range of 0.80 to 0.95. Furthermore, a genome-wide association study (GWA) and a combined linkage disequilibrium and linkage analysis (LDLA) were conducted on 1,533 purebred Landrace and 1,027 purebred Duroc to find genome regions involved in genetic control of the boar taint compounds androstenone, skatole, and indole, and sex hormones related to fertility traits. Up to 3,297 informative SNP markers were included for both breeds, including SNP from several boar taint candidate genes. From the GWA study, we found that altogether 27 regions were significant at a

  18. [The relationship between the variation rate of MODIS land surface temperature and AMSR-E soil moisture and its application to downscaling].

    Science.gov (United States)

    Wang, An-Qi; Xie, Chao; Shi, Jian-Cheng; Gong, Hui-Li

    2013-03-01

    Using AMSR-E soil moisture, MODIS land surface temperature (Ts) and vegetation index product, the authors discuss the relationship between the variation rate of land surface temperature and surface soil moisture. Selecting the plains region of central United States as the study area, the authors propose the distribution triangle of the variation rate of land surface temperature and soil moisture. In the present paper, temperature variation and vegetation index (TVVI), a new index containing the information of temperature variation and vegetation, is introduced. The authors prove that TVVI and soil moisture show a steady relationship of exponential function; and build a quantitative model of soil moisture(SM) and instantaneous surface temperature variation (VTs). The authors later achieve downscaling of AMSR-E soil moisture data, through the above stated functional relationships and high-resolution MODIS data. Comparison with measured data on ground surface indicates that this method of downscaling is of high precision

  19. Past and Present-day Ice Mass Variation on Svalbard Revealed by Superconducting Gravimeter and GPS Measurements

    Science.gov (United States)

    Omang, O. D.; Kierulf, H. P.

    2012-12-01

    In Arctic areas deglaciation after the last glacial maximum, holocene ice-mass variation as well as present day ice melt, contribute to the land uplift. We use both geometric (GPS) and gravity (Superconducting Gravimeter) data from the observatory in Ny-Ålesund, Svalbard, as well as in-situ mass balance measurements of the local glaciers, to separate the different processes contributing to the land uplift in Ny-Ålesund and Svalbard. Geometric measurements from Ny-Ålesund indicate a land uplift much larger than expected from traditional models of glacial isostatic adjustment (GIA). In addition the land uplift shows large year-to-year variations. A combination of the measured variations in the land uplift with local ice-mass variations give us a good constraint on the land uplift caused by the present day ice melt. However, we are still not able to explain all of the measured uplift. We compare 10 years of Superconducting Gravimeter measurements with geometric data and find that they are consistent. We also find, as with the geometric data, that the measured gravity change is much larger than expected from glacial isostatic adjustment and present day ice melt. The ratio between unexplained gravity change and unexplained geometric uplift indicates a viscoelastic process. Most likely is the unexplained uplift caused by late holocene ice-mass variations. Daily SG measurements (in red) overlaid by 4 harmonic constituents and piecewise trends (in black), piecewise trends only (in green) and AG measurements with 1 σ uncertainties (in blue). Daily GPS measurements (in red) overlaid by 4 harmonic constituents and piecewise trends (in black) and piecewise trends only (in green).

  20. Relationship Between Imposex and Morphological Variation of the Shell in Nucella lapillus (Gastropoda: Thaididae)

    Science.gov (United States)

    Son, M. H.; Hughes, R. N.

    2000-05-01

    The relationship between imposex and shell morphology of the common dogwhelk, Nucella lapillus, was examined in populations from North Wales. Degree of imposex, morphometry of the shell, habitat-exposure to wave action and substratum type were subjected to multivariate statistical analyses. Shell size increased significantly with increasing degree of imposex. This trend possibly is caused by a diversion of energy allocation from reproduction to shell growth when reproductive effort is blocked or disturbed by imposex.

  1. Seasonal variation of Legionella in Taiwan's reservoir and its relationships with environmental factors.

    Science.gov (United States)

    Kao, Po-Min; Hsu, Bing-Mu; Chang, Tien-Yu; Hsu, Tsui-Kang; Tzeng, Kai-Jiun; Huang, Yu-Li

    2015-04-01

    In this study, the presence of Legionella in major water reservoirs of Taiwan was examined with respect to seasonal variation, geographical variation, and water quality parameters using TaqMan real-time qPCR. Water samples were collected quarterly at 19 reservoirs in Taiwan between November 2012 and August 2013. The detection rate for Legionella was 35.5% (27/76), and Legionella was detected in all seasons. The Legionella concentration was relatively high in spring and summer, reaching 3.86 × 10(8) and 7.35 × 10(8) cells/L, respectively. By sampling the area, Legionella was detected at a higher proportion in reservoirs in the northern and southern areas, and the difference was consistent in all seasons. Significant association was found between detection of Legionella and various water quality parameters, including conductivity, chlorophyll a, and dissolved oxygen (Mann-Whitney U test, P Legionella detection with pH (P = 0.030, R = -0.497) and dissolved oxygen (P = 0.007, R = -0.596) in fall and positive correlation with Carlson's trophic state index (P = 0.049, R = 0.457) in spring. The identified species included Legionella pneumophila and Legionella drancourtii. The detection of Legionella in reservoirs was indicative of a potential public health risk and should be further evaluated.

  2. Joint cross-correlation analysis reveals complex, time-dependent functional relationship between cortical neurons and arm electromyograms

    Science.gov (United States)

    Zhuang, Katie Z.; Lebedev, Mikhail A.

    2014-01-01

    Correlation between cortical activity and electromyographic (EMG) activity of limb muscles has long been a subject of neurophysiological studies, especially in terms of corticospinal connectivity. Interest in this issue has recently increased due to the development of brain-machine interfaces with output signals that mimic muscle force. For this study, three monkeys were implanted with multielectrode arrays in multiple cortical areas. One monkey performed self-timed touch pad presses, whereas the other two executed arm reaching movements. We analyzed the dynamic relationship between cortical neuronal activity and arm EMGs using a joint cross-correlation (JCC) analysis that evaluated trial-by-trial correlation as a function of time intervals within a trial. JCCs revealed transient correlations between the EMGs of multiple muscles and neural activity in motor, premotor and somatosensory cortical areas. Matching results were obtained using spike-triggered averages corrected by subtracting trial-shuffled data. Compared with spike-triggered averages, JCCs more readily revealed dynamic changes in cortico-EMG correlations. JCCs showed that correlation peaks often sharpened around movement times and broadened during delay intervals. Furthermore, JCC patterns were directionally selective for the arm-reaching task. We propose that such highly dynamic, task-dependent and distributed relationships between cortical activity and EMGs should be taken into consideration for future brain-machine interfaces that generate EMG-like signals. PMID:25210153

  3. Morphology and temporal variation of the polar oval of Venus revealed by VMC/Venus express visible and UV images

    Science.gov (United States)

    Muto, Keishiro; Imamura, Takeshi

    2017-10-01

    The morphology of the dark polar oval seen at the Venus cloud top in visible and ultraviolet wavelengths has been unclear because the portion of the oval on the nightside is invisible. We analyzed in detail the variability of the whole shape of the oval by connecting VMC/Venus Express visible images taken on different days after shifting the images in zonal direction based on the estimated zonal advection speed. The shape of the oval was found to be changing over time between elongated shape and near-circular shape. The dominant period of this variation changes with time in the range of 200-350 Earth days, and does not seem to coincide with the orbital period, the rotation period, and the length of the day. This suggests that the variation of the oval shape is driven by some internal nonlinear process. The mechanism of oval formation is discussed.

  4. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

    Science.gov (United States)

    Daniel L. Lindner; Mark T. Banik

    2011-01-01

    Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus...

  5. Variation in testosterone and corticosterone in amphibians and reptiles: relationships with latitude, elevation, and breeding season length.

    Science.gov (United States)

    Eikenaar, Cas; Husak, Jerry; Escallón, Camilo; Moore, Ignacio T

    2012-11-01

    Latitudinal variation in life-history traits has been the focus of numerous investigations, but underlying hormonal mechanisms have received much less attention. Steroid hormones play a central role in vertebrate reproduction and may be associated with life-history trade-offs. Consequently, circulating concentrations of these hormones vary tremendously across vertebrates, yet interspecific geographic variation in male hormone concentrations has been studied in detail only in birds. We here report on such variation in amphibians and reptiles, confirming patterns observed in birds. Using phylogenetic comparative analyses, we found that in amphibians, but not in reptiles, testosterone and baseline corticosterone were positively related to latitude. Baseline corticosterone was negatively related to elevation in amphibians but not in reptiles. For both groups, testosterone concentrations were negatively related to breeding-season length. In addition, testosterone concentrations were positively correlated with baseline corticosterone in both groups. Our findings may best be explained by the hypothesis that shorter breeding seasons increase male-male competition, which may favor increased testosterone concentrations that modulate secondary sexual traits. Elevated energetic demands resulting from greater reproductive intensity may require higher baseline corticosterone. Thus, the positive relationship between testosterone and corticosterone in both groups suggests an energetic demand for testosterone-regulated behavior that is met with increased baseline glucocorticoid concentrations.

  6. Seasonal blood pressure variation and its relationship to environmental temperature in healthy elderly Japanese studied by home measurements.

    Science.gov (United States)

    Kimura, Toshiaki; Senda, Shoichi; Masugata, Hisashi; Yamagami, Ayumu; Okuyama, Hiroyuki; Kohno, Takeaki; Hirao, Tomohiro; Fukunaga, Megumu; Okada, Hiroki; Goda, Fuminori

    2010-01-01

    The purpose of the present study was to examine seasonal blood pressure variation and its relationship to environmental temperature in healthy elderly Japanese, as studied by home measurements. Fifteen healthy elderly Japanese (79.3 +/- 5.9 yrs) measured their blood pressure at home each morning for more than 25 times per month for 3 years. Monthly mean outdoor temperatures were obtained from the Takamatsu meteorological Observatory. The highest levels of systolic and diastolic blood pressure measured at home were observed in February (129 +/- 14 and 81 +/- 13 mmHg). The lowest levels of systolic and diastolic blood pressure measured at home were observed in August (117 +/- 11 and 73 +/- 10 mmHg). Likewise, the lowest and highest means of outdoor temperature were observed in February (5.0 degrees C) and August (29.2 degrees C), respectively. Hence, both systolic and diastolic blood pressure demonstrated a close inverse correlation with the means of outdoor temperature (r = -0.973, p blood pressure (SBP) and 0.29 mmHg in diastolic blood pressure (DBP). Seasonal variations in home blood pressure and outdoor temperature showed complete correspondence in healthy elderly Japanese, with the blood pressures being inversely related to the ambient temperature. These seasonal home blood pressure variations should be kept in mind when controlling blood pressure in elderly patients.

  7. Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats.

    Directory of Open Access Journals (Sweden)

    Manisha Brahmachary

    2014-06-01

    Full Text Available Tandem repeats are common in eukaryotic genomes, but due to difficulties in assaying them remain poorly studied. Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. We observed extreme variability in copy number of tandemly repeated genes, with many loci showing 5-10 fold variation in copy number among humans. Many of these loci show hallmarks of genome assembly errors, and the true copy number of many large tandem repeats is significantly under-represented even in the high quality 'finished' human reference assembly. Importantly, we demonstrate that most large tandem repeat variations are not tagged by nearby SNPs, and are therefore essentially invisible to SNP-based GWAS approaches. Using association analysis we identify many cis correlations of large tandem repeat variants with nearby gene expression and DNA methylation levels, indicating that variations of tandem repeat length are associated with functional effects on the local genomic environment. This includes an example where expansion of a macrosatellite repeat is associated with increased DNA methylation and suppression of nearby gene expression, suggesting a mechanism termed "repeat induced gene silencing", which has previously been observed only in transgenic organisms. We also observed multiple signatures consistent with altered selective pressures at tandemly repeated loci, suggesting important biological functions. Our studies show that tandemly repeated loci represent a highly variable fraction of the genome that have been systematically ignored by most previous studies, copy number variation of which can exert functionally significant effects. We suggest that future studies of tandem repeat loci will lead to many novel insights into their

  8. Digital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats

    Science.gov (United States)

    Quilez, Javier; Hasson, Dan; Borel, Christelle; Warburton, Peter; Sharp, Andrew J.

    2014-01-01

    Tandem repeats are common in eukaryotic genomes, but due to difficulties in assaying them remain poorly studied. Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. We observed extreme variability in copy number of tandemly repeated genes, with many loci showing 5–10 fold variation in copy number among humans. Many of these loci show hallmarks of genome assembly errors, and the true copy number of many large tandem repeats is significantly under-represented even in the high quality ‘finished’ human reference assembly. Importantly, we demonstrate that most large tandem repeat variations are not tagged by nearby SNPs, and are therefore essentially invisible to SNP-based GWAS approaches. Using association analysis we identify many cis correlations of large tandem repeat variants with nearby gene expression and DNA methylation levels, indicating that variations of tandem repeat length are associated with functional effects on the local genomic environment. This includes an example where expansion of a macrosatellite repeat is associated with increased DNA methylation and suppression of nearby gene expression, suggesting a mechanism termed “repeat induced gene silencing”, which has previously been observed only in transgenic organisms. We also observed multiple signatures consistent with altered selective pressures at tandemly repeated loci, suggesting important biological functions. Our studies show that tandemly repeated loci represent a highly variable fraction of the genome that have been systematically ignored by most previous studies, copy number variation of which can exert functionally significant effects. We suggest that future studies of tandem repeat loci will lead to many novel insights into their role in

  9. Spatio-temporal genetic variation in populations of wild emmer wheat, Triticum turgidum ssp. dicoccoides, as revealed by AFLP analysis.

    Science.gov (United States)

    Ozbek, O; Millet, E; Anikster, Y; Arslan, O; Feldman, M

    2007-06-01

    Genetic structure of natural populations of wild crop relatives has been the subject of many studies. Yet, most of them focused on the assessment of spatial genetic diversity, while information on long-term variation, affected by yearly changes, has been considered only in few cases. The present study aimed therefore, to estimate the spatio-temporal genetic variation in populations of wild emmer wheat, the progenitor of domesticated wheat, and to assess the contribution of spatial versus temporal factors to the maintenance of genetic variation in a population. Single spikes were collected in the years 1988 and 2002 from plants that grew in the same sampling points, from six different habitats in the Ammiad conservation site, Eastern Galilee, Israel. Seeds were planted in a nursery and DNA was extracted from each plant and analyzed by the AFLP method. Fourteen primer combinations yielded 1,545 bands of which 50.0 and 48.8% were polymorphic in the years 1988 and 2002, respectively. Genetic diversity was much larger within populations than between populations and the temporal genetic diversity was considerably smaller than the spatial one. Nevertheless, population genetic structure may vary to some degree in different years, mainly due to fluctuations in population size because of yearly rainfall variations. This may lead to predominance of different genotypes in different years. Clustering the plants by their genetic distances grouped them according to their habitats, indicating the existence of genotype-environment affinities. The significance of the results in relation to factors affecting the maintenance of polymorphism in natural populations is discussed.

  10. Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes.

    Science.gov (United States)

    O'Neal, Wanda K; Gallins, Paul; Pace, Rhonda G; Dang, Hong; Wolf, Whitney E; Jones, Lisa C; Guo, XueLiang; Zhou, Yi-Hui; Madar, Vered; Huang, Jinyan; Liang, Liming; Moffatt, Miriam F; Cutting, Garry R; Drumm, Mitchell L; Rommens, Johanna M; Strug, Lisa J; Sun, Wei; Stonebraker, Jaclyn R; Wright, Fred A; Knowles, Michael R

    2015-02-05

    Variation in cystic fibrosis (CF) phenotypes, including lung disease severity, age of onset of persistent Pseudomonas aeruginosa (P. aeruginosa) lung infection, and presence of meconium ileus (MI), has been partially explained by genome-wide association studies (GWASs). It is not expected that GWASs alone are sufficiently powered to uncover all heritable traits associated with CF phenotypic diversity. Therefore, we utilized gene expression association from lymphoblastoid cells lines from 754 p.Phe508del CF-affected homozygous individuals to identify genes and pathways. LPAR6, a G protein coupled receptor, associated with lung disease severity (false discovery rate q value = 0.0006). Additional pathway analyses, utilizing a stringent permutation-based approach, identified unique signals for all three phenotypes. Pathways associated with lung disease severity were annotated in three broad categories: (1) endomembrane function, containing p.Phe508del processing genes, providing evidence of the importance of p.Phe508del processing to explain lung phenotype variation; (2) HLA class I genes, extending previous GWAS findings in the HLA region; and (3) endoplasmic reticulum stress response genes. Expression pathways associated with lung disease were concordant for some endosome and HLA pathways, with pathways identified using GWAS associations from 1,978 CF-affected individuals. Pathways associated with age of onset of persistent P. aeruginosa infection were enriched for HLA class II genes, and those associated with MI were related to oxidative phosphorylation. Formal testing demonstrated that genes showing differential expression associated with lung disease severity were enriched for heritable genetic variation and expression quantitative traits. Gene expression provided a powerful tool to identify unrecognized heritable variation, complementing ongoing GWASs in this rare disease. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All

  11. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding.

    Science.gov (United States)

    Sim, Sung-Chur; Robbins, Matthew D; Chilcott, Charles; Zhu, Tong; Francis, David M

    2009-10-09

    Cultivated tomato (Solanum lycopersicum L.) has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP) discovery as a high-throughput approach for marker development in cultivated tomato. Three varieties, FL7600 (fresh-market), OH9242 (processing), and PI114490 (cherry) were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (alpha) used to define the confidence interval (CI), and ranged from 76% for polymorphisms identified at alpha or= 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of theta (Fst) suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace), and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka) to synonymous substitutions (Ks) for 20 loci with multiple SNPs (>or= 4 per locus). Six of 20 loci showed ratios of Ka/Ks >or= 0.9. Array-based SFP discovery was an efficient method to identify a large number of molecular markers for genetics and breeding in elite tomato germplasm. Patterns of sequence variation across five major tomato groups provided insight into to the effect of human selection on genetic variation.

  12. Genetic variation and relationships among Ulex (Fabaceae) species in southern Spain and northern Morocco assessed by chloroplast microsatellite (cpSSR) markers.

    Science.gov (United States)

    Cubas, Paloma; Pardo, Cristina; Tahiri, Hikmat

    2005-12-01

    Genetic variation in 27 populations of Ulex species from southern Spain and northern Morocco (Betic-Rif arc) was assessed using 11 chloroplast microsatellite (cpSSR) markers, which revealed 47 different haplotypes. These nonrecombinant, haploid markers allow measurement of genetic variation in closely related species of Ulex where molecular phylogenetic analyses have not provided a clear view of interspecific relationships. Discriminant analysis indicates that the haplotypes are useful to differentiate among species, and analysis of molecular variance (AMOVA) shows high levels of differentiation among populations. The minimum spanning tree (MST), that represents the connections between the haplotypes, suggests that the eastern Rifean U. africanus haplotypes are more genetically related than those from southern Spain. The latter may have lost genetic diversity while colonizing new habitats, eventually differentiating into U. baeticus and U. scaber. Hybridization between these populations, followed by polyploidization, may have originated the tetraploids (U. congestus and U. borgiae) that colonized new habitats associated with acidic rocks. Separate groupings of U. scaber populations may indicate multiple origins from different stocks. Diversification in this group of Ulex species could be related to the opening of the Alboran Sea by Middle Miocene, when the populations from Morocco and Spain became isolated from each other.

  13. Temporal and spatial variations in the relationship between urbanization and water quality.

    Science.gov (United States)

    Ren, Lijun; Cui, Erqian; Sun, Haoyu

    2014-12-01

    With the development of economy, most of Chinese cities are at the stage of rapid urbanization in recent years, which has caused many environmental problems, especially the serious deterioration of water quality. Therefore, the research of the relationship between urbanization and water quality has important theoretical and practical significance, and it is also the main restriction factor in the urbanization advancement. In this work, we investigated the impact of urbanization on the water quality of the nearby river. We established a comprehensive environmental assessment framework by combining urbanization and water quality, and one model was designed to examine the impact of urbanization on the water quality in Jinan from 2001 to 2010 with factor component analysis. The assessment of urbanization level was accomplished using a comprehensive index system, which was based on four aspects: demographic urbanization, economic urbanization, land urbanization, and social urbanization. In addition, synthetic pollution index method was utilized to assess the water pollution of Xiaoqing River in the study area. Through the analysis of regression curves, we conclude that (1) when the urbanization level is below 25 %, the relationship is low and irregular; (2) if the urbanization level varies between 25 and 40 %, there will be an irreversible degradation of stream water quality; (3) there is a positive correlation between urbanization and pollution levels of urban river after the adjustment period; and (4) land and demographic aspects have the highest independent contribution. This study is a useful reference for policymakers in terms of economic and environmental management.

  14. Theoretical and empirical evidence for the relationship between stem diameter variations and the water status of mature temperate trees

    Science.gov (United States)

    Dietrich, Lars; Zweifel, Roman; Kahmen, Ansgar

    2017-04-01

    Assessing a trees' water status is essential to evaluate its water status during drought. In particular for mature trees it is extremely difficult to monitor the water status throughout the growing season because of the difficulty of canopy access. Daily variations of stem diameter (SDV) are discussed to provide a powerful alternative in measuring a trees' water status. SDV have been shown to incorporate both radial growth and the diurnal shrinkage and swelling of bark tissue, which is caused by daytime transpiration and nighttime refilling, respectively. During dry periods, bark tissue that is depleted in water cannot entirely refill at night resulting in a progressive overall shrinkage of the tree's stem diameter often called tree water deficit (TWD). Comprehensive comparisons of SDV-based values for TWD and reliable values of stem water potential are yet missing for mature trees. As such, TWD has not yet been fully established as a simple and continuous proxy for a trees' water status. Using a canopy crane situated in Northern Switzerland, we calculated TWD based on SDV for six Central European forest tree species during one moist (2014) and one exceptionally dry (2015) growing season and compared these values to the trees' branch water potential. We found a tight relationship between branch water potential and TWD in all six species. We further employed four different mathematical approaches to calculate TWD and tested what approach yielded the best relationship with water potential. Most approaches resulted in significant relationships (p logistic functions. We propose that, based on such a function, TWD can be employed to estimate stem water potential of trees for an entire growing season. We conclude from our data that TWD is tightly correlated to the stem water potential of mature tree species and can, thus, be used to describe continuous seasonal variations in a tree's water status. Because of its relatively easy application and deployment, there is high

  15. An Examination of the Relationship between Visual Fatigue Symptoms with Flicker Value Variations in Video Display Terminal Users

    Directory of Open Access Journals (Sweden)

    Ehsanollah Habibi

    2015-01-01

    Full Text Available In most sensitive occupations such as nuclear, military and chemical industries closed circuit systems and visual display terminals (VDTs are used to carefully control and assess sensitive processes. Visual fatigue is one of the factors decreasing accuracy and concentration in operators causing faulty perception. This study aimed to find out a relationship between visual fatigue symptoms (VFS of Flicker value variations in video display terminal (VDT operators. This cross-sectional study, conducted in 2011, aimed to examine visual fatigue and determine the relationship between its symptoms and visual flicker value changes in 248 operators of VDTs in several occupations. The materials used in this study were a visual fatigue questionnaire of VDTs and a VFM-90.1 device. Visual fatigue was measured in two stages (prior to beginning to work and 60 min later. The data were analyzed by SPSS11.5, using descriptive statistics, paired t-test, simple and multiple linear regressions, correlation and recognition coefficients. Then regression equations of changes in flicker value depending on the changes in the main domains and the changes in final score before the questionnaire were obtained. Paired t-test indicated significant differences in the mean score of visual fatigue symptoms and the mean score of flicker value between the two stages, respectively (P ≤ 0.001. Simple and multiple regressions of flicker value variations, for the last visual fatigue changes in questionnaire score and the four main domains of the questionnaire were obtained R2 = 0.851 and R2 = 0.853, respectively. Correlation coefficient in the above tests indicated reverse and significant relationships among flicker value changes with changes in questionnaire score and visual fatigue symptoms. Diagnosing the first symptoms of visual fatigue could be an appropriate warning for VDTs operators in sensitive occupations to react suitably, in behavior and management, to control or treat

  16. Relationships between morphology, diet and spatial distribution: testing the effects of intra and interspecific morphological variations on the patterns of resource use in two Neotropical Cichlids

    Directory of Open Access Journals (Sweden)

    Ana Lúcia A. Sampaio

    Full Text Available Considering th e morphology, diet and spatial distribution of Satanoperca pappaterraand Crenicichla britskii (Perciformes: Cichlidae in the Upper Paraná River floodplain (Brazil, the following questions were investigated: (1 Could the body shape predict the use of trophic resources and habitat by C. britskiiand S. pappaterra? (2 Could the relationship between morphology and use of trophic resources and habitat be also extended to the intraspecific scale? (3 What are the most important morphological traits used to predict the variation on diet and habitat occupation within and between species? We hypothesized that intra and interspecific differences in morphological patterns imply in different forms of resource exploitation and that the ecomorphological analysis enables the identification of trophic and spatial niche segregation. Fish samplings were performed in different types of habitats (rivers, secondary channels, connected and disconnected lagoons in the Upper Paraná River floodplain. Analyses of the stomach content was conducted to characterize the feeding patterns and twenty-two ecomorphological indices were calculated from linear morphological measurements and areas. A principal component analysis (PCA run with these indices evidenced the formation of two significant axes, revealing in the axis 1 an ecomorphological ordination according to the type of habitat, regardless the species. The individuals of both species exploiting lotic habitats tended to have morphological traits that enable rapid progressive and retrograde movements, braking and continuous swimming, whereas individuals found in lentic and semi-lotic habitats presented morphology adapted to a greater maneuverability and stabilization in deflections. On the other hand the axis 2 evidenced a segregation related to the feeding ecology, between S. pappaterra and C. britskii. The relationship between morphology and use of spatial and feeding resource was corroborated by the

  17. Spatial variations of bacterial community and its relationship with water chemistry in Sanya Bay, South China Sea as determined by DGGE fingerprinting and multivariate analysis.

    Science.gov (United States)

    Ling, Juan; Zhang, Yan-Ying; Dong, Jun-De; Wang, You-Shao; Feng, Jing-Bing; Zhou, Wei-Hua

    2015-10-01

    Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted

  18. Metabolomics Reveals Relationship between Plasma Inositols and Birth Weight: Possible Markers for Fetal Programming of Type 2 Diabetes

    Directory of Open Access Journals (Sweden)

    Pia Marlene Nissen

    2011-01-01

    Full Text Available Epidemiological studies in man and with experimental animal models have shown that intrauterine growth restriction (IUGR resulting in low birth weight is associated with higher risk of programming welfare diseases in later life. In the pig, severe IUGR occurs naturally and contribute substantially to a large intralitter variation in birth weight and may therefore be a good model for man. In the present paper the natural form of IUGR in pigs was studied close to term by nuclear magnetic resonance (NMR-based metabolomics. The NMR-based investigations revealed different metabolic profiles of plasma samples from low-birth weight (LW and high-birth weight (HW piglets, respectively, and differences were assigned to levels of glucose and myo-inositol. Further studies by GC-MS revealed that LW piglets had a significant higher concentration of myoinositol and D-chiro-inositol in plasma compared to larger littermates. Myo-inositol and D-chiro-inositol have been coupled with glucose intolerance and insulin resistance in adults, and the present paper therefore suggests that IUGR is related to impaired glucose metabolism during fetal development, which may cause type 2 diabetes in adulthood.

  19. Metabolomics reveals relationship between plasma inositols and birth weight: possible markers for fetal programming of type 2 diabetes.

    Science.gov (United States)

    Nissen, Pia Marlene; Nebel, Caroline; Oksbjerg, Niels; Bertram, Hanne Christine

    2011-01-01

    Epidemiological studies in man and with experimental animal models have shown that intrauterine growth restriction (IUGR) resulting in low birth weight is associated with higher risk of programming welfare diseases in later life. In the pig, severe IUGR occurs naturally and contribute substantially to a large intralitter variation in birth weight and may therefore be a good model for man. In the present paper the natural form of IUGR in pigs was studied close to term by nuclear magnetic resonance (NMR-)based metabolomics. The NMR-based investigations revealed different metabolic profiles of plasma samples from low-birth weight (LW) and high-birth weight (HW) piglets, respectively, and differences were assigned to levels of glucose and myo-inositol. Further studies by GC-MS revealed that LW piglets had a significant higher concentration of myoinositol and D-chiro-inositol in plasma compared to larger littermates. Myo-inositol and D-chiro-inositol have been coupled with glucose intolerance and insulin resistance in adults, and the present paper therefore suggests that IUGR is related to impaired glucose metabolism during fetal development, which may cause type 2 diabetes in adulthood.

  20. When confidence comes and goes: How variation in self-efficacy moderates stressor-strain relationships.

    Science.gov (United States)

    Peng, Ann C; Schaubroeck, John M; Xie, Jia Lin

    2015-07-01

    Inconsistent published findings regarding a proposed buffering role of self-efficacy in stress coping led us to develop a model in which within-person variability in self-efficacy over time affects how individuals' mean levels of self-efficacy moderate the relationship between demands and psychological symptoms. Results from two independent samples (manufacturing workers and college students) supported the hypothesized interaction between demands, self-efficacy mean level, and self-efficacy variability. Demands were more positively associated with psychological strain among those with high and stable self-efficacy than those with high and variable self-efficacy. We discuss the implications of intrapersonal variability in self-efficacy for research on stress coping. (c) 2015 APA, all rights reserved).

  1. Variations on a classical theme: On the formal relationship between magnitudes per square arcsecond and luminance

    Directory of Open Access Journals (Sweden)

    Salvador Bará

    2017-12-01

    Full Text Available The formal link between magnitudes per square arcsecond and luminance is discussed in this paper. Directly related to the human visual system, luminance is defined in terms of the spectral radiance of the source, weighted by the CIE V(l luminous efficiency function, and scaled by the 683 lm/W luminous efficacy constant. In consequence, any exact and spectrum-independent relationship between luminance and magnitudes per square arcsecond requires that the last ones be measured precisely in the CIE V(l band. The luminance value corresponding to mVC=0 (zero-point of the CIE V(l magnitude scale depends on the reference source chosen for the definition of the magnitude system. Using absolute AB magnitudes, the zero point luminance of the CIE V(l photometric band is 10.96 x 104 cd·m-2.

  2. Explaining cross-national variation in the relationship between priority congruence and satisfaction with democracy

    DEFF Research Database (Denmark)

    Reher, Stefanie

    2015-01-01

    countries and older democracies. The hypotheses are empirically tested in a multilevel regression framework, where voter survey data from the 2009 European Election Study is linked with candidate survey data. The results indicate that citizens are indeed more satisfied with democracy if elites share......Previous research has shown that citizens tend to be more satisfied with the functioning of democracy when their ideological positions are more proximate to representatives’.This article argues that congruence in policy priorities between citizens and political elites should have a similar effect......: citizens whose concerns are shared by elites should perceive them to be more attentive and responsive to public concerns and societal needs. Yet, the relationship might vary with differences in expectations towards democracy and representation. Specifically, it should be stronger in more democratic...

  3. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L. reveals patterns of SNP variation associated with breeding

    Directory of Open Access Journals (Sweden)

    Zhu Tong

    2009-10-01

    Full Text Available Abstract Background Cultivated tomato (Solanum lycopersicum L. has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP discovery as a high-throughput approach for marker development in cultivated tomato. Results Three varieties, FL7600 (fresh-market, OH9242 (processing, and PI114490 (cherry were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (α used to define the confidence interval (CI, and ranged from 76% for polymorphisms identified at α ≤ 10-6 to 60% for those identified at α ≤ 10-2. Validation percentage reached a plateau between α ≤ 10-4 and α ≤ 10-7, but failure to identify known SFPs (Type II error increased dramatically at α ≤ 10-6. Trough sequence validation, we identified 279 SNPs and 27 InDels in 111 loci. Sixty loci contained ≥ 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of θ (Fst suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace, and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka to synonymous substitutions (Ks for 20 loci with multiple SNPs (≥ 4 per

  4. Individual variation in sow aggressive behavior and its relationship with sow welfare.

    Science.gov (United States)

    Verdon, M; Morrison, R S; Rice, M; Hemsworth, P H

    2016-03-01

    This study examined the relationships between individual sow aggressive behavior and sow welfare, based on aggression, skin injuries, and stress, in a total of 275 pregnant domestic sows. Over 4 time replicates, sows were randomly mixed into groups of 10 (floor space of 1.8 m/sow) within 7 d of insemination in both their first and second gestations (200 sows per gestation with 126 sows observed in both gestations). Measurements were taken on aggression (both delivered and received) at feeding, skin injuries, and plasma cortisol concentrations at d 2, 9, and 51 after mixing. Live weight gain, nonreproductive removals, litter size (born alive, total born, and stillborn piglets), and farrowing rate were also recorded. In both the first and the second gestations, sows were classified at d 2 after mixing as "submissive" (delivered little or no aggression at feeding relative to aggression received), "subdominant" (received more aggression at feeding than delivered), and "dominant" (delivered more aggression at feeding than received). In both gestations, sows classified as dominant at d 2 subsequently delivered more (gestation 1, gained the most weight (gestation 1, cortisol concentrations at d 2 of gestation 2, but there were no differences between classifications at d 9 and 51 in either gestation (gestation 1, > 0.05; gestation 2, = 0.02). There were no significant relationships between aggression classification and reproduction and nonreproductive removals ( > 0.05). In conclusion, sows classified as dominant at feeding at d 2 subsequently received less aggression at feeding, sustained fewer skin injuries, and had higher live weight gain. Submissive and subdominant sows in groups are likely to benefit from the provision of increased resources such as space and access to feed.

  5. Implications of Variation in the Relationships between Beneficiary Characteristics and Medicare Advantage CAHPS Measures.

    Science.gov (United States)

    Hatfield, Laura A; Zaslavsky, Alan M

    2017-08-01

    To study how differences in quality score adjustments across Medicare Advantage contracts change comparisons for individuals and contracts. Responses to the Medicare Advantage implementation of the Consumer Assessments of Healthcare Providers and Systems (CAHPS) survey from 2010 to 2014. We fit national-and state-level hierarchical models to predict CAHPS scores for individuals and contracts, adjusted for self-reported education, general health, and mental health. We allow the effects of these variables on quality measures to vary across contracts with a hierarchical model. We perform secondary data analysis. For average consumers, standard adjustment is sufficient to represent variation in contract quality standardized to a common population. For people with characteristics far from average, personalized reporting using their characteristics and contract-specific coefficients can substantially change the expected quality measures across contracts. This effect is stronger when comparing among contracts within a state than across all contracts. Customized reporting may help consumers select the best Medicare Advantage plan, but policies should protect against unintended consequences. © Health Research and Educational Trust.

  6. Relationship between Stroke Volume Variation and Blood Transfusion during Liver Transplantation.

    Science.gov (United States)

    Choi, Jae Moon; Lee, Yoon Kyung; Yoo, Hwanhee; Lee, Sukyung; Kim, Hee Yeong; Kim, Young-Kug

    2016-01-01

    Intraoperative blood transfusion increases the risk for perioperative mortality and morbidity in liver transplant recipients. A high stroke volume variation (SVV) method has been proposed to reduce blood loss during living donor hepatectomy. Herein, we investigated whether maintaining high SVV could reduce the need for blood transfusion and also evaluated the effect of the high SVV method on postoperative outcomes in liver transplant recipients. We retrospectively analyzed 332 patients who underwent liver transplantation, divided into control (maintaining blood transfusion requirement and hemodynamic parameters, including SVV, as well as postoperative outcomes, such as incidences of acute kidney injury, durations of postoperative intensive care unit and hospital stay, and rates of 1-year mortality. Mean SVV values were 7.0% ± 1.3% in the control group (n = 288) and 11.2% ± 1.8% in the high SVV group (n = 44). The median numbers of transfused packed red blood cells and fresh frozen plasmas in the high SVV group were significantly lower than those in control group (0 vs. 2 units, P = 0.003; and 0 vs. 3 units, P = 0.033, respectively). No significant between-group differences were observed for postoperative outcomes. Maintaining high SVV can reduce the blood transfusion requirement during liver transplantation without worsening postoperative outcomes. These findings provide insights into improving perioperative management in liver transplant recipients.

  7. Caribbean-wide, long-term study of seagrass beds reveals local variations, shifts in community structure and occasional collapse.

    Directory of Open Access Journals (Sweden)

    Brigitta I van Tussenbroek

    Full Text Available The CARICOMP monitoring network gathered standardized data from 52 seagrass sampling stations at 22 sites (mostly Thalassia testudinum-dominated beds in reef systems across the Wider Caribbean twice a year over the period 1993 to 2007 (and in some cases up to 2012. Wide variations in community total biomass (285 to >2000 g dry m(-2 and annual foliar productivity of the dominant seagrass T. testudinum (2000 g dry m(-2 were found among sites. Solar-cycle related intra-annual variations in T. testudinum leaf productivity were detected at latitudes > 16°N. Hurricanes had little to no long-term effects on these well-developed seagrass communities, except for 1 station, where the vegetation was lost by burial below ∼1 m sand. At two sites (5 stations, the seagrass beds collapsed due to excessive grazing by turtles or sea-urchins (the latter in combination with human impact and storms. The low-cost methods of this regional-scale monitoring program were sufficient to detect long-term shifts in the communities, and fifteen (43% out of 35 long-term monitoring stations (at 17 sites showed trends in seagrass communities consistent with expected changes under environmental deterioration.

  8. Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation.

    Science.gov (United States)

    Shimada, Makoto K; Panchapakesan, Karuna; Tishkoff, Sarah A; Nato, Alejandro Q; Hey, Jody

    2007-03-01

    The population genetic history of a 10.1-kbp noncoding region of the human X chromosome was studied using the males of the HGDP-CEPH Human Genome Diversity Panel (672 individuals from 52 populations). The geographic distribution of patterns of variation was roughly consistent with previous studies, with the major exception that 1 highly divergent haplotype (haplotype X, hX) was observed at low frequency in widely scattered non-African populations and not at all observed in sub-Saharan African populations. Microsatellite (short tandem repeat) variation within the sequenced region was low among copies of hX, even though the estimated time of ancestry of hX and other sequences was 1.44 Myr. The estimated age of the common ancestor of all hX copies was 5,230 years (95% consistency index: 2,000-75,480 years). To further address the presence of hX in Africa, additional samples from Chad and Tanzania were screened. Five additional copies of hX were observed, consistent with a history in which hX was present in Africa prior to the migration of modern humans out of Africa and with eastern Africa being the source of non-African modern human populations. Taken together, these features of hX-that it is much older than other haplotypes and uncommon and patchily distributed throughout Africa, Europe, and Asia-present a cautionary tale for interpretations of human history.

  9. Five willow varieties cultivated across diverse field environments reveal stem density variation associated with high tension wood abundance

    Directory of Open Access Journals (Sweden)

    Nicolas eBerthod

    2015-10-01

    Full Text Available Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice (SRC willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec to determine their bioenergy potential in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood, suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50 % of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry

  10. Five willow varieties cultivated across diverse field environments reveal stem density variation associated with high tension wood abundance.

    Science.gov (United States)

    Berthod, Nicolas; Brereton, Nicholas J B; Pitre, Frédéric E; Labrecque, Michel

    2015-01-01

    Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood), suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50% of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry.

  11. Genome-Wide Detection of SNP and SV Variations to Reveal Early Ripening-Related Genes in Grape.

    Directory of Open Access Journals (Sweden)

    Yanshuai Xu

    Full Text Available Early ripening in grape (Vitis vinifera L. is a crucial agronomic trait. The fruits of the grape line 'Summer Black' (SBBM, which contains a bud mutation, can be harvested approximately one week earlier than the 'Summer Black' (SBCcontrol. To investigate the molecular mechanism of the bud mutation related to early ripening, we detected genome-wide genetic variations based on re-sequencing. In total, 3,692,777 single nucleotide polymorphisms (SNPs and 81,223 structure variations (SVs in the SBC genome and 3,823,464 SNPs and 85,801 SVs in the SBBM genome were detected compared with the reference grape sequence. Of these, 635 SBC-specific genes and 665 SBBM-specific genes were screened. Ripening and colour-associated unigenes with non-synonymous mutations (NS, SVs or frame-shift mutations (F were analysed. The results showed that 90 unigenes in SBC, 76 unigenes in SBBM and 13 genes that mapped to large fragment indels were filtered. The expression patterns of eight genes were confirmed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR.The re-sequencing data showed that 635 SBC-specific genes and 665 SBBM-specific genes associated with early ripening were screened. Among these, NCED6 expression appears to be related to NCED1 and is involved in ABA biosynthesis in grape, which might play a role in the onset of anthocyanin accumulation. The SEP and ERF genes probably play roles in ethylene response.

  12. Isotopic niche variation from the Holocene to today reveals minimal partitioning and individualistic dynamics among four sympatric desert mice.

    Science.gov (United States)

    Terry, Rebecca C

    2018-01-01

    Species interact with each other and their environment over a range of temporal scales, yet our understanding of resource partitioning and the mechanisms of species coexistence is largely restricted to modern time-scales of years to decades. Furthermore, the relative magnitudes of inter- vs. intraspecific variation in resource use are rarely considered, despite the potential for the latter to influence a species' ability to cope with changing environmental conditions. Modern desert rodent communities are thought to be strongly structured by competitive interactions, with niche partitioning of food resources hypothesized to explain the coexistence of multiple sympatric granivores. Yet the stability of niche dynamics over extended temporal scales within desert rodent communities is unknown. I examined the isotopic niche dynamics of four common sympatric desert mice (three granivores: Chaetodipus formosus, Perognathus longimembris and Reithrodontomys megalotis, and one omnivore: Peromyscus maniculatus) in the Smoke Creek Desert of northwestern Nevada using 13 C and 15 N isotopes obtained from "Modern" (2008-2013 CE), "Historical" (1989-2005 CE) and Holocene fossil specimens spanning the last c. 7,500 years. I found significant variation in niche position, niche breadth and interspecific niche overlap of these species through time. The niche breadth dynamics of the cricetids (P. maniculatus and R. megalotis) were positively correlated with one another, while the niche breadth dynamics of the heteromyid C. formosus were negatively correlated with those of all other species. Body size, dietary functional group, palaeoenvironmental trends and time-averaging provided little explanatory power. Importantly, Modern and Historical patterns of resource use and partitioning differed from Holocene baselines in terms of decreased niche overlap and in the absolute and relative position of each species' niche in at least one isotopic axis. These observations suggest that each

  13. Revealing important nocturnal and day-to-day variations in fire smoke emissions through a multiplatform inversion

    Energy Technology Data Exchange (ETDEWEB)

    Saide, Pablo E.; Peterson, David A.; de Silva, Arlindo; Anderson, Bruce; Ziemba, Luke D.; Diskin, Glenn; Sachse, Glen; Hair, Jonathan; Butler, Carolyn; Fenn, Marta; Jimenez, Jose L.; Campuzano-Jost, Pedro; Perring, Anne E.; Schwarz, Joshua P.; Markovic, Milos Z.; Russell, Phil; Redemann, Jens; Shinozuka, Yohei; Streets, David G.; Yan, Fang; Dibb, Jack; Yokelson, Robert; Toon, O. Brian; Hyer, Edward; Carmichael, Gregory R.

    2015-05-16

    We couple airborne, ground-based, and satellite observations; conduct regional simulations; and develop and apply an inversion technique to constrain hourly smoke emissions from the Rim Fire, the third largest observed in California, USA. Emissions constrained with multiplatform data show notable nocturnal enhancements (sometimes over a factor of 20), correlate better with daily burned area data, and are a factor of 2–4 higher than a priori estimates, highlighting the need for improved characterization of diurnal profiles and day-to-day variability when modeling extreme fires. Constraining only with satellite data results in smaller enhancements mainly due to missing retrievals near the emissions source, suggesting that top-down emission estimates for these events could be underestimated and a multiplatform approach is required to resolve them. Predictions driven by emissions constrained with multiplatform data present significant variations in downwind air quality and in aerosol feedback on meteorology, emphasizing the need for improved emissions estimates during exceptional events.

  14. Spatial and temporal variations in nitrogen export from a New Zealand pastoral catchment revealed by stream water nitrate isotopic composition

    Science.gov (United States)

    Wells, Naomi S.; Baisden, W. Troy; Horton, Travis; Clough, Tim J.

    2016-04-01

    Viable indicators of nitrogen (N) attenuation at the catchment scale are needed in order to sustainably manage global agricultural intensification. We hypothesized that the dominance of a single land use (pasture production) and strong ground-to-surface water connectivity would combine to create a system in which surface water nitrate isotopes (δ15N and δ18O of NO3-) could be used to monitor variations in catchment-scale attenuation. Nitrate isotopes were measured monthly over a 2 year period in four reaches along a spring-fed, gaining stream (mean NO3-N of 6 mg L-1) in Canterbury, New Zealand. The stream water NO3- pool indicated that the highest degree of denitrification occurred in the shallow upper reaches. Moving downstream through increasingly sandy soils, the isotopic signature of denitrification became progressively weaker. The lowest reaches fell into the expected range for NO3- produced from the nitrification of pasture N sources (urine and fertilizers), implying that the attenuation capacity of the groundwater and riparian systems was lower than the rate of N inputs. After excluding months affected by effluent spills or extreme weather (n = 4), variations in the degree of denitrification over stream distance were combined with the measured NO3- discharge to estimate N attenuation over time in the subcatchment. Attenuation was highly responsive to rainfall: 93% of calculated attenuation (20 kg NO3-N ha-1 yr-1) occurred within 48 h of rainfall. These findings demonstrate the potential for detailed NO3- stable isotope data to provide integrative measures of catchment NO3- loss pathways.

  15. Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity.

    Directory of Open Access Journals (Sweden)

    Rhys A Farrer

    Full Text Available Pathogenic fungi constitute a growing threat to both plant and animal species on a global scale. Despite a clonal mode of reproduction dominating the population genetic structure of many fungi, putatively asexual species are known to adapt rapidly when confronted by efforts to control their growth and transmission. However, the mechanisms by which adaptive diversity is generated across a clonal background are often poorly understood. We sequenced a global panel of the emergent amphibian pathogen, Batrachochytrium dendrobatidis (Bd, to high depth and characterized rapidly changing features of its genome that we believe hold the key to the worldwide success of this organism. Our analyses show three processes that contribute to the generation of de novo diversity. Firstly, we show that the majority of wild isolates manifest chromosomal copy number variation that changes over short timescales. Secondly, we show that cryptic recombination occurs within all lineages of Bd, leading to large regions of the genome being in linkage equilibrium, and is preferentially associated with classes of genes of known importance for virulence in other pathosystems. Finally, we show that these classes of genes are under directional selection, and that this has predominantly targeted the Global Panzootic Lineage (BdGPL. Our analyses show that Bd manifests an unusually dynamic genome that may have been shaped by its association with the amphibian host. The rates of variation that we document likely explain the high levels of phenotypic variability that have been reported for Bd, and suggests that the dynamic genome of this pathogen has contributed to its success across multiple biomes and host-species.

  16. NMR spectroscopy reveals unexpected structural variation at the protein-protein interface in MHC class I molecules

    Energy Technology Data Exchange (ETDEWEB)

    Beerbaum, Monika; Ballaschk, Martin; Erdmann, Natalja [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany); Schnick, Christina [Freie Universitaet Berlin, Institut fuer Immungenetik, Charite-Universitaetsmedizin Berlin (Germany); Diehl, Anne [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany); Uchanska-Ziegler, Barbara; Ziegler, Andreas [Freie Universitaet Berlin, Institut fuer Immungenetik, Charite-Universitaetsmedizin Berlin (Germany); Schmieder, Peter, E-mail: schmieder@fmp-berlin.de [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany)

    2013-10-15

    {beta}{sub 2}-Microglobulin ({beta}{sub 2}m) is a small, monomorphic protein non-covalently bound to the heavy chain (HC) in polymorphic major histocompatibility complex (MHC) class I molecules. Given the high evolutionary conservation of structural features of {beta}{sub 2}m in various MHC molecules as shown by X-ray crystallography, {beta}{sub 2}m is often considered as a mere scaffolding protein. Using nuclear magnetic resonance (NMR) spectroscopy, we investigate here whether {beta}{sub 2}m residues at the interface to the HC exhibit changes depending on HC polymorphisms and the peptides bound to the complex in solution. First we show that human {beta}{sub 2}m can effectively be produced in deuterated form using high-cell-density-fermentation and we employ the NMR resonance assignments obtained for triple-labeled {beta}{sub 2}m bound to the HLA-B*27:09 HC to examine the {beta}{sub 2}m-HC interface. We then proceed to compare the resonances of {beta}{sub 2}m in two minimally distinct subtypes, HLA-B*27:09 and HLA-B*27:05, that are differentially associated with the spondyloarthropathy Ankylosing Spondylitis. Each of these subtypes is complexed with four distinct peptides for which structural information is already available. We find that only the resonances at the {beta}{sub 2}m-HC interface show a variation of their chemical shifts between the different complexes. This indicates the existence of an unexpected plasticity that enables {beta}{sub 2}m to accommodate changes that depend on HC polymorphism as well as on the bound peptide through subtle structural variations of the protein-protein interface.

  17. Genotype variation and genetic relationship among Escherichia coli from nursery pigs located in different pens in the same farm

    DEFF Research Database (Denmark)

    Herrero-Fresno, Ana; Ahmed, Shahana; Hansen, Monica Hegstad

    2017-01-01

    evaluated the genotype variation of E. coli isolated from swine fecal samples at the single pig and pen level, as well as between pens using repetitive extragenic palindromic (REP) PCR fingerprinting and pulsed field gel electrophoresis (PFGE). The genetic diversity of strains collected from media......BACKGROUND: So far, little is known about the genetic diversity and relatedness among Escherichia coli (E. coli) populations in the gut of swine. Information on this is required to improve modeling studies on antimicrobial resistance aiming to fight its occurrence and development. This work...... supplemented with ampicillin or tetracycline was also investigated. Besides, the genetic relationship of strains within each pen, between pens, as well as among strains within each group isolated from media with or without antibiotic, was assessed. RESULTS: REP-PCR patterns (N = 75) were generated for all...

  18. Investigation of the Relationship Between Ionospheric TEC Anomaly Variations and Fault Types Before the Earthquakes

    Science.gov (United States)

    Ulukavak, M.; Yalçınkaya, M.

    2017-11-01

    Earthquakes are natural phenomena that shake the earth and cause many damage. Since the time of arrival of the earthquakes cannot be determined directly, some signs before the earthquake should be examined and interpreted by examining the environmental changes. One of the methods used for this is monitoring the ionospheric total electron content (TEC) changes in total electron content unit (TECU). GPS satellites have begun to be used as a means of monitoring ionospheric TEC anomalies before earthquakes since they began to be used as sensors around the world. In this study, three fault type (normal, thrust and strike-slip faulting) of 28 earthquakes with a magnitude greater than 7 (Mw) and the percentage changes of TEC anomalies before the earthquakes were investigated. The ionospheric TEC anomalies before the earthquake were calculated according to the 15-day running median statistical analysis method. Different solar and geomagnetic indices have been investigated to determine the active space weather conditions and quiet days before and after the earthquake. The TEC anomalies were determined during the quiet days before the earthquake by comparing the ionospheric anomalies that occurred before the earthquake after the determination of quiet days with the indices of the space weather conditions. The results show that there is a relationship between fault type and the earthquake precursor percentage changes and were determined as 47.6 % TECU for regions where normal faulting, 50.4 % TECU for regions where thrust faulting, and 44.2 % TECU for regions where strike-slip faulting occurred, respectively.

  19. Tri-Variate Relationships among Vegetation, Soil, and Topography along Gradients of Fluvial Biogeomorphic Succession.

    Directory of Open Access Journals (Sweden)

    Daehyun Kim

    Full Text Available This research investigated how the strength of vegetation-soil-topography couplings varied along a gradient of biogeomorphic succession in two distinct fluvial systems: a forested river floodplain and a coastal salt marsh creek. The strength of couplings was quantified as tri-variance, which was calculated by correlating three singular axes, one each extracted using three-block partial least squares from vegetation, soil, and topography data blocks. Within each system, tri-variance was examined at low-, mid-, and high-elevation sites, which represented early-, intermediate-, and late-successional phases, respectively, and corresponded to differences in ongoing disturbance frequency and intensity. Both systems exhibited clearly increasing tri-variance from the early- to late-successional stages. The lowest-lying sites underwent frequent and intense hydrogeomorphic forcings that dynamically reworked soil substrates, restructured surface landforms, and controlled the colonization of plant species. Such conditions led vegetation, soil, and topography to show discrete, stochastic, and individualistic behaviors over space and time, resulting in a loose coupling among the three ecosystem components. In the highest-elevation sites, in contrast, disturbances that might disrupt the existing biotic-abiotic relationships were less common. Hence, ecological succession, soil-forming processes, and landform evolution occurred in tight conjunction with one another over a prolonged period, thereby strengthening couplings among them; namely, the three behaved in unity over space and time. We propose that the recurrence interval of physical disturbance is important to-and potentially serves as an indicator of-the intensity and mechanisms of vegetation-soil-topography feedbacks in fluvial biogeomorphic systems.

  20. Diversity of 16S-23S rDNA internal transcribed spacer (ITS reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors.

    Directory of Open Access Journals (Sweden)

    Andrew P Liguori

    Full Text Available Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.

  1. Phenotypic Variation Is Almost Entirely Independent of the Host-Pathogen Relationship in Clinical Isolates of S. aureus.

    Directory of Open Access Journals (Sweden)

    Adrian D Land

    Full Text Available A key feature of Staphylococcus aureus biology is its ability to switch from an apparently benign colonizer of ~30% of the population to a cutaneous pathogen, to a deadly invasive pathogen. Little is known about the mechanisms driving this transition or the propensity of different S. aureus strains to engender different types of host-pathogen interactions. At the same time, significant weight has been given to the role of specific in vitro phenotypes in S. aureus virulence. Biofilm formation, hemolysis and pigment formation have all been associated with virulence in mice.To determine if there is a correlation between in vitro phenotype and the three types of host-pathogen relationships commonly exhibited by S. aureus in the context of its natural human host, we assayed 300 clinical isolates for phenotypes implicated in virulence including hemolysis, sensitivity to autolysis, and biofilm formation. For comparative purposes, we also assayed phenotype in 9 domesticated S. aureus strains routinely used for analysis of virulence determinants in laboratory settings.Strikingly, the clinical strains exhibited significant phenotypic uniformity in each of the assays evaluated in this study. One exception was a small, but significant, correlation between an increased propensity for biofilm formation and isolation from skin and soft tissue infections (SSTIs. In contrast, we observed a high degree of phenotypic variation between common laboratory strains that exhibit virulence in mouse models. These data suggest the existence of significant evolutionary pressure on the S. aureus genome and highlight a role for host factors as a strong determinant of the host-pathogen relationship. In addition, the high degree of variation between laboratory strains emphasizes the need for caution when applying data obtained in one lab strain to the analysis of another.

  2. Genetic diversity and relationship in American and African oil palm as revealed by RFLP and AFLP molecular markers

    Directory of Open Access Journals (Sweden)

    Barcelos Edson

    2002-01-01

    Full Text Available The objective of this work was to evaluate the genetic diversity, its organization and the genetic relationships within oil palm (Elaeis oleifera (Kunth Cortés, from America, and E. guineensis (Jacq., from Africa germplasm using Restriction Fragment Length Polymorphism (RFLP and Amplified Fragment Length Polymorphism (AFLP. In complement to a previous RFLP study on 241 E. oleifera accessions, 38 E. guineensis accessions were analyzed using the same 37 cDNA probes. These accessions covered a large part of the geographical distribution areas of these species in America and Africa. In addition, AFLP analysis was performed on a sub-set of 40 accessions of E. oleifera and 22 of E. guineensis using three pairs of enzyme/primer combinations. Data were subjected to Factorial Analysis of Correspondence (FAC and cluster analysis, with parameters of genetic diversity being also studied. Results appeared congruent between RFLP and AFLP. In the E. oleifera, AFLP confirmed the strong structure of genetic diversity revealed by RFLP, according to geographical origin of the studied material, with the identification of the same four distinct genetic groups: Brazil, French Guyana/Surinam, Peru, north of Colombia/Central America. Both markers revealed that genetic divergence between the two species is of the same magnitude as that among provenances of E. oleifera. This finding is in discrepancy with the supposed early tertiary separation of the two species.

  3. Genetic relationships among ten endod types as revealed by a combination of morphological, RAPD and AFLP markers.

    Science.gov (United States)

    Semagn, Kassa

    2002-01-01

    The genetic relationships among ten types of endod (Phytolacca dodecandra) cultivated by the Institute of Pathobiology of the Addis Ababa University to combat the disease bilharzia in Ethiopia were studied using morphology and molecular markers. A total of 18 morphological characters, 194 amplified fragment length polymorphism (AFLP) and 42 random amplified polymorphic DNA (RAPD) markers were used to determine genetic proximity between types. Genetic distance and cluster analysis of the AFLP data revealed the lack of genetic difference between E47 and E48 but relatively wider genetic difference among the other endod types. Cluster and principal component analyses performed on the AFLP and RAPD markers demonstrated the presence of distinct separation of E56 but not that of E44 from the others. The AFLP and RAPD data, thcrefore, did not support the hypothesis that the superiority of E44 in agronomic traits and molluscicidal potency is linked to its distinct genetic difference from the other endod types. Matrices correspondence tests demonstrated the presence of greater correspondence between AFLP and RAPD data (r = 0.842) but not between the morphology and that of AFLP and RAPD. This indicates the correspondence more between the two DNA markers systems than either of them with morphological traits. The cophenetic correlation coefficients also revealed poor fit for morphology (r = 0.716), good fit for RAPD (r = 0.872) and very good fit for AFLP (r = 0.975), reflecting the hyper-variability and higher resolving power of AFLP.

  4. Relationship between human physiological parameters and geomagnetic variations of solar origin

    Science.gov (United States)

    Dimitrova, S.

    Results presented concern influence of increased geomagnetic activity on some human physiological parameters. The blood pressure and heart rate of 86 volunteers were measured on working days in autumn 2001 (01/10 09/11) and in spring 2002 (08/04 28/05). These periods were chosen because of maximal expected geomagnetic activity. Altogether 2799 recordings were obtained and analysed. Questionnaire information about subjective psycho-physiological complaints was also gathered. MANOVA was employed to check the significance of the influence of three factors on the physiological parameters under consideration. The factors were the following: (1) planetary geomagnetic activity level estimated by Ap-index and divided into five levels; (2) gender males and females; (3) blood pressure degree persons in the group examined were divided into hypotensive, normotensive and hypertensive. Post hoc analysis was performed to elicit the significance of differences in the factors’ levels. The average arterial blood pressure of the group was found to increase significantly with the increase of geomagnetic activity level. The average increment of systolic and diastolic blood pressure of the group examined reached 9%. This effect was present irrespectively of gender. Results obtained suppose that hypertensive persons have the highest sensitivity and the hypotensive persons have the lowest sensitivity of the arterial blood pressure to increase of geomagnetic activity. The results did not show significant changes in the heart rate. The percentage of the persons who reported subjective psycho-physiological complaints was also found to increase significantly with the geomagnetic activity increase and the highest sensitivity was revealed for the hypertensive females.

  5. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia

    Science.gov (United States)

    2014-01-01

    Background Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. Results We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. Conclusion The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15

  6. Sediment budget variation at watershed scale due to anthropogenic pressures, and its relationship to coastal erosion

    Science.gov (United States)

    Aiello, Antonello; Adamo, Maria; Canora, Filomena

    2014-05-01

    forecast coastline fluctuations caused by such anthropogenic interventions. These are valuable information for both the management of and development of future plans for coastal environments and for reducing exposure risk to coastal erosion. The purpose of this study was to compare and to evaluate the suitability of the RUSLE (Revised Universal Soil Loss Equation), RUSLE 3D and USPED (Unit Stream Power-based Erosion Deposition) models in assessing the sediment budget variation at watershed scale. In order to assess the rate of net soil erosion, the three models were applied to the Bradano river basin and to the sub-basin subtended by the San Giuliano Dam. To this end, digital terrain model, products derived from satellite remote sensing (multi-temporal Landsat imagery), soil texture maps and ancillary data were integrated and processed in a GIS. To test the models, the computed soil erosion rates were integrated over the San Giuliano sub-basin surface, and compared with the dam silting value provided by an interregional authority responsible for its management. The three models have proven to be effective in quantifying the soil erosion at watershed scale.

  7. Trophic calculations reveal the mechanism of population-level variation in mercury concentrations between marine ecosystems: case studies of two polar seabirds.

    Science.gov (United States)

    Brasso, Rebecka L; Polito, Michael J

    2013-10-15

    The incorporation of quantitative trophic level analysis in ecotoxicological studies provides explanatory power to identify the factors, trophic or environmental, driving population-level variation in mercury exposure at large geographic scales. In the Antarctic marine ecosystem, mercury concentrations and stable isotope values in Adélie penguins (Pygoscelis adeliae) were compared between the Antarctic Peninsula and the Ross Sea. Correcting tissue δ(15)N values for baseline δ(15)N values revealed population-level differences in trophic position which contributes to differences in mercury. Data from Thick-billed murres (Uria lomvia) were synthesized from published values from Baffin Bay and Svalbard to demonstrate the utility of baseline δ(15)N values in identifying differences in environmental mercury exposure independent of diet. Here, we demonstrate the importance of calculating population-specific trophic level data to uncover the source of variation in mercury concentrations between geographically distinct populations of marine predators. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Genetic diversity and phylogenetic relationships of seven Amorphophallus species in southwestern China revealed by chloroplast DNA sequences.

    Science.gov (United States)

    Gao, Yong; Yin, Si; Yang, Huixiao; Wu, Lifang; Yan, Yuehui

    2017-07-15

    Plants species in the genus Amorphophallus are of great economic importance, as they are the only plants known to produce glucomannan. Although southwestern China has been recognized as one of the origin centres of Amorphophallus, only a few studies assessing its genetic diversity have been reported. To aid in the utilization and conservation of Amorphophallus species, we evaluated the genetic diversity and phylogenetic relationships among seven edible Amorphophallus species using three chloroplast DNA regions (rbcL, trnL and trnK-matK). The results showed that the genetic diversity at the population level was relatively low, with over half of the populations harbouring only one haplotype. The widely scattered species, A. konjac, had the largest genetic diversity, while the narrow endemic species, A. yuloensis, possessed only one haplotype. Phylogeny analysis identified three well-supported major lineages. Our study suggested that habitat fragmentation might be a driver of the genetic variation patterns within and between populations of Amorphophallus. A conservation strategy consisting of in situ conservation and germplasm collection is recommended.

  9. Vulnerability of Agriculture to Climate Change as Revealed by Relationships between Simulated Crop Yield and Climate Change Indices

    Science.gov (United States)

    King, A. W.; Absar, S. M.; Nair, S.; Preston, B. L.

    2012-12-01

    The vulnerability of agriculture is among the leading concerns surrounding climate change. Agricultural production is influenced by drought and other extremes in weather and climate. In regions of subsistence farming, worst case reductions in yield lead to malnutrition and famine. Reduced surplus contributes to poverty in agrarian economies. In more economically diverse and industrialized regions, variations in agricultural yield can influence the regional economy through market mechanisms. The latter grows in importance as agriculture increasingly services the energy market in addition to markets for food and fiber. Agriculture is historically a highly adaptive enterprise and will respond to future changes in climate with a variety of adaptive mechanisms. Nonetheless, the risk, if not expectation, of increases in climate extremes and hazards exceeding historical experience motivates scientifically based anticipatory assessment of the vulnerability of agriculture to climate change. We investigate the sensitivity component of that vulnerability using EPIC, a well established field-scale model of cropping systems that includes the simulation of economic yield. The core of our analysis is the relationship between simulated yield and various indices of climate change, including the CCI/CLIVAR/JCOM ETCCDI indices, calculated from weather inputs to the model. We complement this core with analysis using the DSSAT cropping system model and exploration of relationships between historical yield statistics and climate indices calculated from weather records. Our analyses are for sites in the Southeast/Gulf Coast region of the United States. We do find "tight" monotonic relationships between annual yield and climate for some indices, especially those associated with available water. More commonly, however, we find an increase in the variability of yield as the index value becomes more extreme. Our findings contribute to understanding the sensitivity of crop yield as part of

  10. RNA sequencing analysis reveals transcriptomic variations in tobacco (Nicotiana tabacum) leaves affected by climate, soil, and tillage factors.

    Science.gov (United States)

    Lei, Bo; Lu, Kun; Ding, Fuzhang; Zhang, Kai; Chen, Yi; Zhao, Huina; Zhang, Lin; Ren, Zhu; Qu, Cunmin; Guo, Wenjing; Wang, Jing; Pan, Wenjie

    2014-04-11

    The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq) analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs), soil factors (SFs), and tillage factors (TFs). We detected 4980, 2916, and 1605 differentially expressed genes (DEGs) that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs), respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.

  11. Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.

    Science.gov (United States)

    Zhuang, Jiali; Weng, Zhiping

    2015-09-30

    Genomic structural variations (SVs) are pervasive in many types of cancers. Characterizing their underlying mechanisms and potential molecular consequences is crucial for understanding the basic biology of tumorigenesis. Here, we engineered a local assembly-based algorithm (laSV) that detects SVs with high accuracy from paired-end high-throughput genomic sequencing data and pinpoints their breakpoints at single base-pair resolution. By applying laSV to 97 tumor-normal paired genomic sequencing datasets across six cancer types produced by The Cancer Genome Atlas Research Network, we discovered that non-allelic homologous recombination is the primary mechanism for generating somatic SVs in acute myeloid leukemia. This finding contrasts with results for the other five types of solid tumors, in which non-homologous end joining and microhomology end joining are the predominant mechanisms. We also found that the genes recursively mutated by single nucleotide alterations differed from the genes recursively mutated by SVs, suggesting that these two types of genetic alterations play different roles during cancer progression. We further characterized how the gene structures of the oncogene JAK1 and the tumor suppressors KDM6A and RB1 are affected by somatic SVs and discussed the potential functional implications of intergenic SVs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Region-specific variation in the properties of skeletal adipocytes reveals regulated and constitutive marrow adipose tissues.

    Science.gov (United States)

    Scheller, Erica L; Doucette, Casey R; Learman, Brian S; Cawthorn, William P; Khandaker, Shaima; Schell, Benjamin; Wu, Brent; Ding, Shi-Ying; Bredella, Miriam A; Fazeli, Pouneh K; Khoury, Basma; Jepsen, Karl J; Pilch, Paul F; Klibanski, Anne; Rosen, Clifford J; MacDougald, Ormond A

    2015-08-06

    Marrow adipose tissue (MAT) accumulates in diverse clinical conditions but remains poorly understood. Here we show region-specific variation in MAT adipocyte development, regulation, size, lipid composition, gene expression and genetic determinants. Early MAT formation in mice is conserved, whereas later development is strain dependent. Proximal, but not distal tibial, MAT is lost with 21-day cold exposure. Rat MAT adipocytes from distal sites have an increased proportion of monounsaturated fatty acids and expression of Scd1/Scd2, Cebpa and Cebpb. Humans also have increased distal marrow fat unsaturation. We define proximal 'regulated' MAT (rMAT) as single adipocytes interspersed with active haematopoiesis, whereas distal 'constitutive' MAT (cMAT) has low haematopoiesis, contains larger adipocytes, develops earlier and remains preserved upon systemic challenges. Loss of rMAT occurs in mice with congenital generalized lipodystrophy type 4, whereas both rMAT and cMAT are preserved in mice with congenital generalized lipodystrophy type 3. Consideration of these MAT subpopulations may be important for future studies linking MAT to bone biology, haematopoiesis and whole-body metabolism.

  13. Genetic Variation in Quercus acutissima Carruth., in Traditional Japanese Rural Forests and Agricultural Landscapes, Revealed by Chloroplast Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Yoko Saito

    2017-11-01

    Full Text Available Quercus acutissima Carruth. is an economically important species that has long been cultivated in Japan, so is a valuable subject for investigating the impact of human activities on genetic variation in trees. In total, 2152 samples from 18 naturally regenerated populations and 28 planted populations in Japan and 13 populations from the northeastern part of Eurasia, near Japan, were analyzed using six maternally inherited chloroplast (cpDNA simple sequence repeat (SSR markers. Although 23 haplotypes were detected in total, both the Japanese natural and artificial populations exhibited much lower genetic diversity than the continental populations. The level of genetic differentiation among natural populations in Japan was also much lower (G’ST = 0.261 than that on the continent (G’ST = 0.856. These results suggest that human activities, such as historical seed transfer, have reduced genetic diversity within and among populations and resulted in a homogeneous genetic structure in Japan. The genetic characteristics of natural and artificial populations of Quercus acutissima in Japan are almost the same and it is likely that most of the natural populations are thought to have originated from individuals that escaped from plantations.

  14. RNA Sequencing Analysis Reveals Transcriptomic Variations in Tobacco (Nicotiana tabacum Leaves Affected by Climate, Soil, and Tillage Factors

    Directory of Open Access Journals (Sweden)

    Bo Lei

    2014-04-01

    Full Text Available The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs, soil factors (SFs, and tillage factors (TFs. We detected 4980, 2916, and 1605 differentially expressed genes (DEGs that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs, respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.

  15. Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes.

    Science.gov (United States)

    Kushwaha, Basdeo; Kumar, Ravindra; Agarwal, Suyash; Pandey, Manmohan; Nagpure, N S; Singh, Mahender; Srivastava, Shreya; Joshi, C G; Das, P; Sahoo, L; Jayasankar, P; Meher, P K; Shah, T M; Patel, A B; Patel, Namrata; Koringa, P; Das, Sofia Priyadarsani; Patnaik, Siddhi; Bit, Amrita; Sarika; Iquebal, M A; Kumar, Dinesh; Jena, J K

    2015-09-01

    Whole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequence the mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data of Clarias batrachus, generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome using both de novo and reference based approaches. Both the methods yielded almost similar results and the best assembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotation resulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order was found to be identical with other catfishes. Variation analyses between assembled and the reference (GenBank Acc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequences and tRNA supports the monophyly of catfishes. Two SSRs were identified in C. batrachus mitogenome, out of which one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrial genes were found to evolve at a much faster pace than the d-loop, which in turn are followed by the rRNAs; the tRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among the coding genes, ND2 evolves most rapidly. The variations present in the coding regions of the mitogenome and their comparative analyses with other catfish species may be useful in species conservation and management programs.

  16. Spatial Variation of Regional Sustainable Development and its Relationship to the Allocation of Science and Technology Resources

    Directory of Open Access Journals (Sweden)

    Jian Wu

    2014-09-01

    Full Text Available With the increasing of labor salaries, the RMB exchange rate, resource product prices and requirements of environmental protection, inexpensive labor and land are no longer the decisive factor of regional competitiveness. From this perspective, China needs to shift from the extensive development mode to the sustainable development mode. Science and technology resources rational allocation is one of the key issues in sustainable development. Based on the counties (districts data of Zhejiang Province in China, this paper portrays the spatial variation of regional sustainable development level of this area. This paper finds that counties tend to cluster in groups with the same sustainable development level, and this agglomeration trend has been enforced during the past several years. It then testifies to the relationship between the allocation of science and technology resources and local sustainable development, identifies science and technology human resources, financial resources and environmental resource are positively related to local sustainable development, except government financial support. The economic level has a negative relationship with regional sustainable development. This is because the development of the Zhejiang economy grown at the expense of the environment and ecosystem. Some advice is given according to the empirical analysis result.

  17. [RAPD analysis of the intraspecific and interspecific variation and phylogenetic relationships of Aegilops L. species with the U genome].

    Science.gov (United States)

    Goriunova, S V; Chikida, N N; Kochieva, E Z

    2010-07-01

    RAPD analysis was used to study the genetic variation and phylogenetic relationships of polyploid Aegilops species with the U genome. In total, 115 DNA samples of eight polyploid species containing the U genome and the diploid species Ae. umbellulata (U) were examined. Substantial interspecific polymorphism was observed for the majority of the polyploid species with the U genome (interspecific differences, 0.01-0,2; proportion of polymorphic loci, 56.6-88.2%). Aegilops triuncialis was identified as the only alloploid species with low interspecific polymorphism (interspecific differences, 0-0.01, P = 50%) in the U-genome group. The U-genome Aegilops species proved to be separated from other species of the genus. The phylogenetic relationships were established for the U-genome species. The greatest separation within the U-genome group was observed for the US-genome species Ae. kotschyi and Ae. variabilis. The tetraploid species Ae. triaristata and Ae. columnaris, which had the UX genome, and the hexaploid species Ae. recta (UXN) were found to be related to each other and separate from the UM-genome species. A similarity was observed between the U M-genome species Ae. ovata and Ae. biuncialis, which had the UM genome, and the ancestral diploid U-genome species Ae. umbellulata. The UC-genome species Ae. triuncialis was rather separate and slightly similar to the UX-genome species.

  18. Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep.

    Science.gov (United States)

    Harbison, Susan T; Serrano Negron, Yazmin L; Hansen, Nancy F; Lobell, Amanda S

    2017-12-01

    Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown. We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations. At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper. Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways-EGFR, Wnt, Hippo, and MAPK. The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive.

  19. Single Cell Quantification of Reporter Gene Expression in Live Adult Caenorhabditis elegans Reveals Reproducible Cell-Specific Expression Patterns and Underlying Biological Variation.

    Directory of Open Access Journals (Sweden)

    Alexander R Mendenhall

    Full Text Available In multicellular organisms such as Caenorhabditis elegans, differences in complex phenotypes such as lifespan correlate with the level of expression of particular engineered reporter genes. In single celled organisms, quantitative understanding of responses to extracellular signals and of cell-to-cell variation in responses has depended on precise measurement of reporter gene expression. Here, we developed microscope-based methods to quantify reporter gene expression in cells of Caenorhabditis elegans with low measurement error. We then quantified expression in strains that carried different configurations of Phsp-16.2-fluorescent-protein reporters, in whole animals, and in all 20 cells of the intestine tissue, which is responsible for most of the fluorescent signal. Some animals bore more recently developed single copy Phsp-16.2 reporters integrated at defined chromosomal sites, others, "classical" multicopy reporter gene arrays integrated at random sites. At the level of whole animals, variation in gene expression was similar: strains with single copy reporters showed the same amount of animal-to-animal variation as strains with multicopy reporters. At the level of cells, in animals with single copy reporters, the pattern of expression in cells within the tissue was highly stereotyped. In animals with multicopy reporters, the cell-specific expression pattern was also stereotyped, but distinct, and somewhat more variable. Our methods are rapid and gentle enough to allow quantification of expression in the same cells of an animal at different times during adult life. They should allow investigators to use changes in reporter expression in single cells in tissues as quantitative phenotypes, and link those to molecular differences. Moreover, by diminishing measurement error, they should make possible dissection of the causes of the remaining, real, variation in expression. Understanding such variation should help reveal its contribution to

  20. Relationship between geographical origin, seed size and genetic diversity in faba bean (Vicia faba L.) as revealed by SSR markers.

    Science.gov (United States)

    Göl, Şurhan; Doğanlar, Sami; Frary, Anne

    2017-05-11

    Faba bean (Vicia faba L.) is an important legume species because of its high protein and starch content. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the nitrogen fixing bacteria in its roots. In this work, 255 faba bean germplasm accessions were characterized using 32 SSR primers which yielded 302 polymorphic fragments. According to the results, faba bean individuals were divided into two main groups based on the neighbor-joining algorithm (r = 0.91) with some clustering based on geographical origin as well as seed size. Population structure was also determined and agreed with the dendrogram analysis in splitting the accessions into two subpopulations. Analysis of molecular variance (AMOVA) revealed high levels of within population genetic variation. Genetic similarity and geographical proximity were related with separation of European accessions from African and Asian ones. Interestingly, there was no significant difference between landrace (38%) and cultivar (40%) diversity indicating that genetic variability has not yet been lost due to breeding. A total of 44 genetically well-characterized faba bean individuals were selected for a core collection to be further examined for yield and nutritional traits.

  1. Remote acoustic monitoring of North Atlantic right whales (Eubalaena glacialis) reveals seasonal and diel variations in acoustic behavior.

    Science.gov (United States)

    Matthews, Leanna P; McCordic, Jessica A; Parks, Susan E

    2014-01-01

    Remote acoustic monitoring is a non-invasive tool that can be used to study the distribution, behavior, and habitat use of sound-producing species. The North Atlantic right whale (Eubalaena glacialis) is an endangered baleen whale species that produces a variety of stereotyped acoustic signals. One of these signals, the "gunshot" sound, has only been recorded from adult male North Atlantic right whales and is thought to function for reproduction, either as reproductive advertisement for females or as an agonistic signal toward other males. This study uses remote acoustic monitoring to analyze the presence of gunshots over a two-year period at two sites on the Scotian Shelf to determine if there is evidence that North Atlantic right whales may use these locations for breeding activities. Seasonal analyses at both locations indicate that gunshot sound production is highly seasonal, with an increase in the autumn. One site, Roseway West, had significantly more gunshot sounds overall and exhibited a clear diel trend in production of these signals at night. The other site, Emerald South, also showed a seasonal increase in gunshot production during the autumn, but did not show any significant diel trend. This difference in gunshot signal production at the two sites indicates variation either in the number or the behavior of whales at each location. The timing of the observed seasonal increase in gunshot sound production is consistent with the current understanding of the right whale breeding season, and our results demonstrate that detection of gunshots with remote acoustic monitoring can be a reliable way to track shifts in distribution and changes in acoustic behavior including possible mating activities.

  2. Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.

    Science.gov (United States)

    Gerstner, Jason R; Koberstein, John N; Watson, Adam J; Zapero, Nikolai; Risso, Davide; Speed, Terence P; Frank, Marcos G; Peixoto, Lucia

    2016-10-25

    Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep). In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV). RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1-3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h) do so on average with a time constant that is similar to the time constant for the discharge of sleep need. We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally distinct classes of genes.

  3. Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in ploidy and nutrient utilisation potential amongst wine isolates.

    Science.gov (United States)

    Borneman, Anthony R; Zeppel, Ryan; Chambers, Paul J; Curtin, Chris D

    2014-02-01

    The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations, such as those used for the production of biofuel and wine, where it outlasts and, under some conditions, outcompetes the major industrial yeast Saccharomyces cerevisiae. In order to investigate the level of inter-strain variation that is present within this economically important species, the genomes of four diverse D. bruxellensis isolates were compared. While each of the four strains was shown to contain a core diploid genome, which is clearly sufficient for survival, two of the four isolates have a third haploid complement of chromosomes. The sequences of these additional haploid genomes were both highly divergent from those comprising the diploid core and divergent between the two triploid strains. Similar to examples in the Saccharomyces spp. clade, where some allotriploids have arisen on the basis of enhanced ability to survive a range of environmental conditions, it is likely these strains are products of two independent hybridisation events that may have involved multiple species or distinct sub-species of Dekkera. Interestingly these triploid strains represent the vast majority (92%) of isolates from across the Australian wine industry, suggesting that the additional set of chromosomes may confer a selective advantage in winery environments that has resulted in these hybrid strains all-but replacing their diploid counterparts in Australian winery settings. In addition to the apparent inter-specific hybridisation events, chromosomal aberrations such as strain-specific insertions and deletions and loss-of-heterozygosity by gene conversion were also commonplace. While these events are likely to have affected many phenotypes across these strains, we have been able to link a specific deletion to the inability to utilise nitrate by some strains of D. bruxellensis, a phenotype that may have direct impacts in the ability for these strains to compete with S. cerevisiae.

  4. Remote Acoustic Monitoring of North Atlantic Right Whales (Eubalaena glacialis) Reveals Seasonal and Diel Variations in Acoustic Behavior

    Science.gov (United States)

    Matthews, Leanna P.; McCordic, Jessica A.; Parks, Susan E.

    2014-01-01

    Remote acoustic monitoring is a non-invasive tool that can be used to study the distribution, behavior, and habitat use of sound-producing species. The North Atlantic right whale (Eubalaena glacialis) is an endangered baleen whale species that produces a variety of stereotyped acoustic signals. One of these signals, the “gunshot” sound, has only been recorded from adult male North Atlantic right whales and is thought to function for reproduction, either as reproductive advertisement for females or as an agonistic signal toward other males. This study uses remote acoustic monitoring to analyze the presence of gunshots over a two-year period at two sites on the Scotian Shelf to determine if there is evidence that North Atlantic right whales may use these locations for breeding activities. Seasonal analyses at both locations indicate that gunshot sound production is highly seasonal, with an increase in the autumn. One site, Roseway West, had significantly more gunshot sounds overall and exhibited a clear diel trend in production of these signals at night. The other site, Emerald South, also showed a seasonal increase in gunshot production during the autumn, but did not show any significant diel trend. This difference in gunshot signal production at the two sites indicates variation either in the number or the behavior of whales at each location. The timing of the observed seasonal increase in gunshot sound production is consistent with the current understanding of the right whale breeding season, and our results demonstrate that detection of gunshots with remote acoustic monitoring can be a reliable way to track shifts in distribution and changes in acoustic behavior including possible mating activities. PMID:24646524

  5. Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in ploidy and nutrient utilisation potential amongst wine isolates.

    Directory of Open Access Journals (Sweden)

    Anthony R Borneman

    2014-02-01

    Full Text Available The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations, such as those used for the production of biofuel and wine, where it outlasts and, under some conditions, outcompetes the major industrial yeast Saccharomyces cerevisiae. In order to investigate the level of inter-strain variation that is present within this economically important species, the genomes of four diverse D. bruxellensis isolates were compared. While each of the four strains was shown to contain a core diploid genome, which is clearly sufficient for survival, two of the four isolates have a third haploid complement of chromosomes. The sequences of these additional haploid genomes were both highly divergent from those comprising the diploid core and divergent between the two triploid strains. Similar to examples in the Saccharomyces spp. clade, where some allotriploids have arisen on the basis of enhanced ability to survive a range of environmental conditions, it is likely these strains are products of two independent hybridisation events that may have involved multiple species or distinct sub-species of Dekkera. Interestingly these triploid strains represent the vast majority (92% of isolates from across the Australian wine industry, suggesting that the additional set of chromosomes may confer a selective advantage in winery environments that has resulted in these hybrid strains all-but replacing their diploid counterparts in Australian winery settings. In addition to the apparent inter-specific hybridisation events, chromosomal aberrations such as strain-specific insertions and deletions and loss-of-heterozygosity by gene conversion were also commonplace. While these events are likely to have affected many phenotypes across these strains, we have been able to link a specific deletion to the inability to utilise nitrate by some strains of D. bruxellensis, a phenotype that may have direct impacts in the ability for these strains to compete with S

  6. Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex

    Directory of Open Access Journals (Sweden)

    Jason R. Gerstner

    2016-10-01

    Full Text Available Abstract Background Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep. Results In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV. RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1–3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h do so on average with a time constant that is similar to the time constant for the discharge of sleep need. Conclusions We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally

  7. Natural Genetic Variation of Xanthomonas campestris pv. campestris Pathogenicity on Arabidopsis Revealed by Association and Reverse Genetics

    Science.gov (United States)

    Guy, Endrick; Genissel, Anne; Hajri, Ahmed; Chabannes, Matthieu; David, Perrine; Carrere, Sébastien; Lautier, Martine; Roux, Brice; Boureau, Tristan; Arlat, Matthieu; Poussier, Stéphane; Noël, Laurent D.

    2013-01-01

    ABSTRACT The pathogenic bacterium Xanthomonas campestris pv. campestris, the causal agent of black rot of Brassicaceae, manipulates the physiology and the innate immunity of its hosts. Association genetic and reverse-genetic analyses of a world panel of 45 X. campestris pv. campestris strains were used to gain understanding of the genetic basis of the bacterium’s pathogenicity to Arabidopsis thaliana. We found that the compositions of the minimal predicted type III secretome varied extensively, with 18 to 28 proteins per strain. There were clear differences in aggressiveness of those X. campestris pv. campestris strains on two Arabidopsis natural accessions. We identified 3 effector genes (xopAC, xopJ5, and xopAL2) and 67 amplified fragment length polymorphism (AFLP) markers that were associated with variations in disease symptoms. The nature and distribution of the AFLP markers remain to be determined, but we observed a low linkage disequilibrium level between predicted effectors and other significant markers, suggesting that additional genetic factors make a meaningful contribution to pathogenicity. Mutagenesis of type III effectors in X. campestris pv. campestris confirmed that xopAC functions as both a virulence and an avirulence gene in Arabidopsis and that xopAM functions as a second avirulence gene on plants of the Col-0 ecotype. However, we did not detect the effect of any other effector in the X. campestris pv. campestris 8004 strain, likely due to other genetic background effects. These results highlight the complex genetic basis of pathogenicity at the pathovar level and encourage us to challenge the agronomical relevance of some virulence determinants identified solely in model strains. PMID:23736288

  8. Gene copy number variations in adaptive evolution: The genomic distribution of gene copy number variations revealed by genetic mapping and their adaptive role in an undomesticated species, white spruce (Picea glauca).

    Science.gov (United States)

    Prunier, Julien; Caron, Sébastien; Lamothe, Manuel; Blais, Sylvie; Bousquet, Jean; Isabel, Nathalie; MacKay, John

    2017-11-01

    Gene copy number variation (CNV) has been associated with phenotypic variability in animals and plants, but a genomewide understanding of their impacts on phenotypes is largely restricted to human and agricultural systems. As such, CNVs have rarely been considered in investigations of the genomic architecture of adaptation in wild species. Here, we report on the genetic mapping of gene CNVs in white spruce, which lacks a contiguous assembly of its large genome (~20 Gb), and their relationships with adaptive phenotypic variation. We detected 3,911 gene CNVs including de novo structural variations using comparative genome hybridization on arrays (aCGH) in a large progeny set. We inferred the heterozygosity at CNV loci within parents by comparing haploid and diploid tissues and genetically mapped 82 gene CNVs. Our analysis showed that CNVs were distributed over 10 linkage groups and identified four CNV hotspots that we predict to occur in other species of the Pinaceae. Significant relationships were found between 29 of the gene CNVs and adaptive traits based on regression analyses with timings of bud set and bud flush, and height growth, suggesting a role for CNVs in climate adaptation. The importance of CNVs in adaptive evolution of white spruce was also indicated by functional gene annotations and the clustering of 31% of the mapped adaptive gene CNVs in CNV hotspots. Taken together, these results illustrate the feasibility of studying CNVs in undomesticated species and represent a major step towards a better understanding of the roles of CNVs in adaptive evolution. © 2017 John Wiley & Sons Ltd.

  9. Spatial variations in fluvial incision across the eastern margin of Tibet reveal locus of deformation in the deep crust

    Science.gov (United States)

    Kirby, Eric

    2017-04-01

    The manifestation of coupling among climate, erosion and tectonics along steep topographic margins of orogenic plateaus is strongly dependent on the processes driving crustal thickening. Along the eastern margin of the Tibetan Plateau, a long-standing and vigorous debate persists over whether mountain building occurred largely along upper-crustal faults or was the consequence of distributed thickening in the lower crust. Here I revisit this debate and show how surface deformation recorded by geomorphology over millennial timescales (10^4-105 yr) can yield insight into the role the deep crust along plateau margins. In contrast to the intensively studied Longmen Shan, the topographic margin of the Tibetan Plateau north of the Sichuan Basin follows the north-south Min Shan and cuts orthogonally across the structural grain of the Mesozoic West Qinling orogen. The lack of a direct association of topography with upper crustal faults affords an opportunity to evaluate the patterns of differential rock uplift from geomorphology. First, I employ an empirical calibration of river profile steepness (channel gradient normalized for drainage basin area) and erosion rate from cosmogenic 10Be concentrations in modern sediment. Application to the channels draining the plateau margin reveals a locus of high (300-500 m/Myr) erosion rate coincident with the Min Shan. Second, I present new results of surveying and dating of fluvial terraces developed along the Bailong Jiang, one of the major rivers draining across the plateau margin. A preliminary chronology of terrace formation and abandonment based on radiocarbon and OSL dating of fluvial deposits reveals systematic spatial gradients in fluvial incision, with highest incision rates (1000-2000 m/Myr) localized along the axis of the Min Shan and decreasing toward both the foreland and the plateau. This locus of incision has apparently been sustained through multiple generations of terrace formation and abandonment since at least 80 ka

  10. Morphological and biochemical analyses of original and regenerated lizard tails reveal variation in protein and lipid composition.

    Science.gov (United States)

    Boozalis, Ted S; LaSalle, Landon T; Davis, Jon R

    2012-01-01

    Caudal autotomy, or voluntary self-amputation of the tail, is a common and effective predator evasion mechanism used by most lizard species. The tail contributes to a multitude of biological functions such as locomotion, energetics, and social interactions, and thus there are often costs associated with autotomy. Notably, relatively little is known regarding bioenergetic costs of caudal autotomy in lizards, though key morphological differences exist between the original and regenerated tail that could alter the biochemistry and energetics. Therefore, we investigated lizard caudal biochemical content before and after regeneration in three gecko and one skink species. Specifically, we integrated biochemical and morphological analyses to quantify protein and lipid content in original and regenerated tails. All lizards lost significant body mass, mostly protein, due to autotomy and biochemical results indicated that original tails of all species contained a greater proportion of protein than lipid. Morphological analyses of two gecko species revealed interspecific differences in protein and lipid content of regenerated lizard tails. Results of this study contribute to our understanding of the biochemical consequences of a widespread predator evasion mechanism. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification.

    Science.gov (United States)

    Siler, Cameron D; Diesmos, Arvin C; Alcala, Angel C; Brown, Rafe M

    2011-04-01

    The spectacular, virtually endemic radiation of Philippine semi-fossorial skinks of the genus Brachymeles represent one of the few radiations of scincid lizards to possess both fully limbed and limbless species. And yet, nothing is known of the phylogenetic relationships of this exceptional group. Morphologically similar body plans have made it difficult to assess species-level diversity, and the genus has long been recognized as one of the more modest radiations of southeast Asian lizards. However, recent large-scale survey efforts have resulted in the discovery of numerous new species, and taxonomic studies indicate that the diversity within the genus Brachymeles is grossly underestimated. In this study we provide the first robust estimate of phylogenetic relationships within the genus Brachymeles using a multi-locus dataset and nearly complete taxonomic sampling. We provide statistical tests of monophyly for all polytypic species and two widespread limb-reduced species and our results indicate wholesale deviations from past summaries and taxonomic evaluations of the genus. With few exceptions, we are able to reject the monophyly of all polytypic and widespread species, thereby validating the need for large-scale taxonomic revisions. Our results reveal that the limbless, monotypic, genus Davewakeum is nested within Brachymeles. Mapping of body form on our preferred phylogenetic tree suggests that limb-reduction and digit loss has occurred on multiple occasions in the history of the genus. A Bayesian reconstruction of ancestral areas indicates strong statistical support for a minimum of five major dispersal events that have given rise to a major component of the observed species diversity on separate Pleistocene aggregate island platforms of the archipelago. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Dynamics of Dual Infection with Campylobacter jejuni Strains in Chickens Reveals Distinct Strain-to-Strain Variation in Infection Ecology

    Science.gov (United States)

    Wigley, Paul; Humphrey, Suzanne; Kemmett, Kirsty; Lacharme-Lora, Lizeth; Humphrey, Tom; Williams, Nicola

    2014-01-01

    Although multiple genotypes of Campylobacter jejuni may be isolated from the same commercial broiler flock, little is known about the infection dynamics of different genotypes within individuals or their colonization sites within the gut. Single experimental infections with C. jejuni M1 (sequence type 137, clonal complex 45) and C. jejuni 13126 (sequence type 21, clonal complex 21) revealed that 13126 colonized the ceca at significantly higher levels. The dissemination and colonization sites of the two C. jejuni strains then were examined in an experimental broiler flock. Two 33-day-old broiler chickens were infected with M1 and two with 13126, and 15 birds were left unchallenged. Cloacal swabs were taken postinfection to determine the colonization and shedding of each strain. By 2 days postinfection (dpi), 8/19 birds were shedding M1 whereas none were shedding 13126. At 8 dpi, all birds were shedding both strains. At 18 dpi, liver and cecal levels of each isolate were quantified, while in 10 birds they also were quantified at nine sites throughout the gastrointestinal (GI) tract. 13126 was found throughout the GI tract, while M1 was largely restricted to the ceca and colon. The livers of 7/19 birds were culture positive for 13126 only. These data show that 13126 has a distinctly different infection biology than strain M1. It showed slower colonization of the lower GI tract but was more invasive and able to colonize at a high level throughout the GI tract. The finding that C. jejuni strains have markedly different infection ecologies within the chicken has implications for control in the poultry industry and suggests that the contamination risk of edible tissues is dependent on the isolate involved. PMID:25107966

  13. [Spatial variation of soil moisture/salinity and the relationship with vegetation under natural conditions in Yancheng coastal wetland].

    Science.gov (United States)

    Zhang, Hua-Bing; Liu, Hong-Yu; Li, Yu-Feng; An, Jing; Xue, Xing-Yu; Hou, Ming-Hang

    2013-02-01

    Taking the core part of Yancheng national nature reserve as the study area, according to soil sampling analysis of coastal wetlands in April and May 2011 land the 2011 ETM + remote sensing image, the spatial difference characteristic of coastal wetlands soil moisture and salinity, and the relationship with vegetation under natural conditions, were investigated with the model of correspondence analysis (CCA), linear regression simulation and geo-statistical method. The results showed: Firstly, the average level of the soil moisture was fluctuating between 36.820% and 46.333% , and the soil salinity was between 0.347% and 1.328% , in a more detailed sense, the Spartina swamp was the highest, followed by the mudflats swamp, the Suaeda salsa swamp, and the Reed marsh. Secondly, the spatial variation of soil moisture was consistent with that of the salinity, and the degree of variation in the east-west direction was greater than that in the north-south. The maximum soil moisture and salinity were found in the southwest Spartina swamp. The minimum was in the Reed swamp. The soil moisture and salinity were divided into 5 levels, from I to V. Level IV occupied the highest proportion, which were 36.156% and 28.531% , respectively. Finally, different landscape types with the combination of soil moisture and salinity showed a common feature that the moisture and salinity were from both high to low. The soil moisture value of Reed marshes was lower than 40.116% and the salinity value was lower than 0. 676% . The soil moisture value of Suaeda salsa marshes was between 38. 162% and 46. 403% and the salinity value was between 0.417% and 1.295%. The soil moisture value of Spartina swamp was higher than 43.214% and the salinity was higher than 1.090%. The soil moisture value of beach was higher than 43.214% and the salinity was higher than 0.677%.

  14. Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements

    Science.gov (United States)

    Grundberg, Elin; Meduri, Eshwar; Sandling, Johanna K.; Hedman, Åsa K.; Keildson, Sarah; Buil, Alfonso; Busche, Stephan; Yuan, Wei; Nisbet, James; Sekowska, Magdalena; Wilk, Alicja; Barrett, Amy; Small, Kerrin S.; Ge, Bing; Caron, Maxime; Shin, So-Youn; Ahmadi, Kourosh R.; Ainali, Chrysanthi; Barrett, Amy; Bataille, Veronique; Bell, Jordana T.; Buil, Alfonso; Deloukas, Panos; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Durbin, Richard; Glass, Daniel; Grundberg, Elin; Hassanali, Neelam; Hedman, Åsa K.; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lindgren, Cecilia M.; Lowe, Christopher E.; McCarthy, Mark I.; Meduri, Eshwar; di Meglio, Paola; Min, Josine L.; Montgomery, Stephen B.; Nestle, Frank O.; Nica, Alexandra C.; Nisbet, James; O’Rahilly, Stephen; Parts, Leopold; Potter, Simon; Sandling, Johanna; Sekowska, Magdalena; Shin, So-Youn; Small, Kerrin S.; Soranzo, Nicole; Spector, Tim D.; Surdulescu, Gabriela; Travers, Mary E.; Tsaprouni, Loukia; Tsoka, Sophia; Wilk, Alicja; Yang, Tsun-Po; Zondervan, Krina T.; Lathrop, Mark; Dermitzakis, Emmanouil T.; McCarthy, Mark I.; Spector, Timothy D.; Bell, Jordana T.; Deloukas, Panos

    2013-01-01

    Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, and function of methylation variation and how it is regulated by genetic and environmental factors. We utilized the Multiple Tissue Human Expression Resource (MuTHER) and generated Illumina 450K adipose methylome data from 648 twins. We found that individual CpGs had low variance and that variability was suppressed in promoters. We noted that DNA methylation variation was highly heritable (h2median = 0.34) and that shared environmental effects correlated with metabolic phenotype-associated CpGs. Analysis of methylation quantitative-trait loci (metQTL) revealed that 28% of CpGs were associated with nearby SNPs, and when overlapping them with adipose expression quantitative-trait loci (eQTL) from the same individuals, we found that 6% of the loci played a role in regulating both gene expression and DNA methylation. These associations were bidirectional, but there were pronounced negative associations for promoter CpGs. Integration of metQTL with adipose reference epigenomes and disease associations revealed significant enrichment of metQTL overlapping metabolic-trait or disease loci in enhancers (the strongest effects were for high-density lipoprotein cholesterol and body mass index [BMI]). We followed up with the BMI SNP rs713586, a cg01884057 metQTL that overlaps an enhancer upstream of ADCY3, and used bisulphite sequencing to refine this region. Our results showed widespread population invariability yet sequence dependence on adipose DNA methylation but that incorporating maps of regulatory elements aid in linking CpG variation to gene regulation and disease risk in a tissue-dependent manner. PMID:24183450

  15. High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate.

    Directory of Open Access Journals (Sweden)

    Roberto Bobadilla Landey

    Full Text Available Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant. Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee

  16. Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

    Science.gov (United States)

    Homburger, Julian R.; Green, Eric M.; Caleshu, Colleen; Sunitha, Margaret S.; Taylor, Rebecca E.; Ruppel, Kathleen M.; Metpally, Raghu Prasad Rao; Colan, Steven D.; Michels, Michelle; Day, Sharlene M.; Olivotto, Iacopo; Bustamante, Carlos D.; Dewey, Frederick E.; Ho, Carolyn Y.; Spudich, James A.; Ashley, Euan A.

    2016-01-01

    Myosin motors are the fundamental force-generating elements of muscle contraction. Variation in the human β-cardiac myosin heavy chain gene (MYH7) can lead to hypertrophic cardiomyopathy (HCM), a heritable disease characterized by cardiac hypertrophy, heart failure, and sudden cardiac death. How specific myosin variants alter motor function or clinical expression of disease remains incompletely understood. Here, we combine structural models of myosin from multiple stages of its chemomechanical cycle, exome sequencing data from two population cohorts of 60,706 and 42,930 individuals, and genetic and phenotypic data from 2,913 patients with HCM to identify regions of disease enrichment within β-cardiac myosin. We first developed computational models of the human β-cardiac myosin protein before and after the myosin power stroke. Then, using a spatial scan statistic modified to analyze genetic variation in protein 3D space, we found significant enrichment of disease-associated variants in the converter, a kinetic domain that transduces force from the catalytic domain to the lever arm to accomplish the power stroke. Focusing our analysis on surface-exposed residues, we identified a larger region significantly enriched for disease-associated variants that contains both the converter domain and residues on a single flat surface on the myosin head described as the myosin mesa. Notably, patients with HCM with variants in the enriched regions have earlier disease onset than patients who have HCM with variants elsewhere. Our study provides a model for integrating protein structure, large-scale genetic sequencing, and detailed phenotypic data to reveal insight into time-shifted protein structures and genetic disease. PMID:27247418

  17. Geographic variation and genetic relationships in populations of the Androniscus dentiger complex from Central Italy (Isopoda, Oniscidea, Trichoniscidae

    Directory of Open Access Journals (Sweden)

    Gabriele Gentile

    1997-01-01

    Full Text Available Androniscus dentiger is a terrestrial isopod distributed from Great Britain to North Africa, inhabiting humid edafic environments, superficial underground compartments and both natural and artificial caves. In this study allozyme data have been used to investigate the geographic variation and the genetic relationships of several populations of A. dentiger from Central Italy, using as outgroups populations from four congeneric species, A. calcivagus, A. cfr. subterraneus, A. spelaeorum, and A. degener. Multivariate analysis of A. dentiger allele frequencies indicates the existence of a group of populations (group A distributed in a wide geographic area which are genetically slightly differentiated, and several populations (arbitrarily defined as group B which show differentiation levels comparable to those observed between the morphologically well differentiated species. The low valley of the river Tiber seems to act as an effective geographic barrier between the populations from group A and the remaining ones. The genetic divergence between populations within the group A seems to have a recent origin. This is suggested by the low genetic distances and heterozygosity values within the group A, and by the very low number of private alleles occurring in this group. The high degree of intraspecific and interspecific genetic differentiation is not consistent with the levels of morphological differentiation traditionally used to distinguish different species within this genus. On the whole, these data suggest that A. dentiger might be considered as a complex of cryptic/sibling species.

  18. Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

    Science.gov (United States)

    Cui, Henglin; Yang, Kun; Pagaling, Eulyn

    2013-01-01

    Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand. PMID:23563940

  19. Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.

    Directory of Open Access Journals (Sweden)

    Minjun Yang

    Full Text Available Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC. Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.

  20. Modeling genetic and non-genetic variation of feed efficiency and its partial relationships between component traits as a function of management and environmental factors

    Science.gov (United States)

    Feed efficiency (FE), characterized as the ability to convert feed nutrients into saleable milk or meat directly affects the profitability of dairy production, is of increasing economic importance in the dairy industry. We conjecture that FE is a complex trait whose variation and relationships or pa...

  1. Modeling genetic and nongenetic variation of feed efficiency and its partial relationships between component traits as a function of management and environmental factors

    NARCIS (Netherlands)

    Lu, Y.; Vandehaar, M.J.; Spurlock, D.M.; Weigel, K.A.; Armentano, L.E.; Staples, C.R.; Connor, E.E.; Wang, Z.; Coffey, M.; Veerkamp, R.F.; Haas, de Y.; Tempelman, R.J.

    2017-01-01

    Feed efficiency (FE), characterized as the fraction of feed nutrients converted into salable milk or meat, is of increasing economic importance in the dairy industry. We conjecture that FE is a complex trait whose variation and relationships or partial efficiencies (PE) involving the conversion of

  2. Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations.

    Science.gov (United States)

    Zhou, Yang; Utsunomiya, Yuri T; Xu, Lingyang; Hay, El Hamidi Abdel; Bickhart, Derek M; Sonstegard, Tad S; Van Tassell, Curtis P; Garcia, Jose Fernando; Liu, George E

    2016-07-06

    We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.

  3. Cobra venom proteome and glycome determined from individual snakes of Naja atra reveal medically important dynamic range and systematic geographic variation.

    Science.gov (United States)

    Huang, Hsuan-Wei; Liu, Bing-Sin; Chien, Kun-Yi; Chiang, Liao-Chun; Huang, Sheng-Yu; Sung, Wang-Chou; Wu, Wen-Guey

    2015-10-14

    Recent progress in snake venomics has shed much light on the intra-species variation among the toxins from different geographical regions and has provided important information for better snakebite management. Most previous reports on snake venomics were based on venoms pooled from different snakes. In this study, we present the proteomic and glycomic profiles of venoms from individual Naja atra snakes. The results reveal wide dynamic range of three-finger toxins. Systematic classification based on cardiotoxin (CTX-) profiles of A2/A4 and A6, respectively, allowed the identification of two putative subspecies of Taiwan cobra from the eastern and western regions. We also identified four major N-glycan moieties on cobra snake venom metalloproteinase on the bi-antennary glycan core. ELISA showed that these glycoproteins (cobra venom toxins such as small molecular weight CTXs (~60%). By removing these high-molecular weight glycoproteins from the immunogen, we demonstrated better protection than that achieved with conventional crude venom immunization in mice challenged by crude venom. We conclude that both intra-species and inter-individual variations of proteomic and glycomic profiles of snake venomics should be considered to provide better antivenomic approach for snakebite management. Based on the proteomic and glycomic profiles of venoms obtained from individual snakes, we demonstrated a surprisingly wide dynamic range and geographical variation of three-finger toxins in cobra venomics. This provides a reasonable explanation for the variable neutralization effects of antivenom treatment on victims suffering from cobra snakebite and suggests a simple and economic method to produce potent antivenom with better efficacy. Since two major venomic profiles with distinct dynamic ranges were observed for Taiwan cobra venoms isolated from the eastern and western regions, the current venomic profile should be used as a quality control for future production of antivenom in

  4. Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions.

    Directory of Open Access Journals (Sweden)

    Matthew C Dulik

    Full Text Available Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*. In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13(th century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.

  5. Strong genetic structure revealed by multilocus patterns of variation in Giardia duodenalis isolates of patients from Galicia (NW-Iberian Peninsula).

    Science.gov (United States)

    Gabín-García, Luis B; Bartolomé, Carolina; Abal-Fabeiro, José L; Méndez, Santiago; Llovo, José; Maside, Xulio

    2017-03-01

    We report a survey of genetic variation at three coding loci in Giardia duodenalis of assemblages A and B obtained from stool samples of patients from Santiago de Compostela (Galicia, NW-Iberian Peninsula). The mean pooled synonymous diversity for assemblage A was nearly five times lower than for assemblage B (0.77%±0.30% and 4.14%±1.65%, respectively). Synonymous variation in both assemblages was in mutation-drift equilibrium and an excess of low-frequency nonsynonymous variants suggested the action of purifying selection at the three loci. Differences between isolates contributed to 40% and 60% of total genetic variance in assemblages A and B, respectively, which revealed a significant genetic structure. These results, together with the lack of evidence for recombination, support that (i) Giardia assemblages A and B are in demographic equilibrium and behave as two genetically isolated populations, (ii) infections are initiated by a reduced number of individuals, which may be genetically diverse and even belong to different assemblages, and (iii) parasites reproduce clonally within the host. However, the observation of invariant loci in some isolates means that mechanisms for the homogenization of the genetic content of the two diploid nuclei in each individual must exist. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Of mice and the 'Age of Discovery': the complex history of colonization of the Azorean archipelago by the house mouse (Mus musculus) as revealed by mitochondrial DNA variation.

    Science.gov (United States)

    Gabriel, S I; Mathias, M L; Searle, J B

    2015-01-01

    Humans have introduced many species onto remote oceanic islands. The house mouse (Mus musculus) is a human commensal and has consequently been transported to oceanic islands around the globe as an accidental stowaway. The history of these introductions can tell us not only about the mice themselves but also about the people that transported them. Following a phylogeographic approach, we used mitochondrial D-loop sequence variation (within an 849- to 864-bp fragment) to study house mouse colonization of the Azores. A total of 239 sequences were obtained from all nine islands, and interpretation was helped by previously published Iberian sequences and 66 newly generated Spanish sequences. A Bayesian analysis revealed presence in the Azores of most of the D-loop clades previously described in the domesticus subspecies of the house mouse, suggesting a complex colonization history of the archipelago as a whole from multiple geographical origins, but much less heterogeneity (often single colonization?) within islands. The expected historical link with mainland Portugal was reflected in the pattern of D-loop variation of some of the islands but not all. A more unexpected association with a distant North European source area was also detected in three islands, possibly reflecting human contact with the Azores prior to the 15th century discovery by Portuguese mariners. Widening the scope to colonization of the Macaronesian islands as a whole, human linkages between the Azores, Madeira, the Canaries, Portugal and Spain were revealed through the sharing of mouse sequences between these areas. From these and other data, we suggest mouse studies may help resolve historical uncertainties relating to the 'Age of Discovery'. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  7. Molecular phylogenetic relationships among four species of the mangrove tree genus Bruguiera (Rhizophoraceae, as revealed by chromosome and RAPD markers

    Directory of Open Access Journals (Sweden)

    Pragnya Sahoo

    2007-06-01

    Full Text Available Analysis of karyotype, nuclear DNA content and RAPD markers were performed in four species of Bruguiera (Rhizophoraceae of Bhitarkanika mangrove forests, Orissa, India. Detailed karyotype analysis revealing 2n=34 in B. cylindrica and 2n=36 in B. gymnorrhiza was reported for the first time and 2n=34 in B. parviflora and B. sexangula was confirmed. On the basis of the common types of chromosomes present among Bruguiera, two distinct groups were found; one consists of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula. The symmetrical karyotype with same chromosome types grouped B. cylindrica and B. parviflora together and presence of Type E chromosomes placed B. gymnorrhiza and B. sexangula in a separate group, suggesting their closer affinity in their respective group. Analysis of chromosome length, volume, INV and 4C DNA content confirmed this division. Nuclear DNA content was two-fold higher (~17.0 pg in the second group than in the first (~8.0 pg. The amplification products generated through RAPD revealed 1-9 amplicons with size variations from 600 bp to 2 500 bp with 49.31% genetic similarity between B. gymnorrhiza and B. sexangula and 47.10% in between B. cylindrica and B. parviflora. The high copy number marker band (~ 1 100 bp yielded in OPN-15 primer in B. parviflora the characteristic DNA marker, which was cloned and used as probes for assessment of genetic diversity, and demonstrated its close genetic affinity to B. cylindrica. B. gymnorrhiza and B. sexangula also produced similar marker bands of ~600 bp and ~2 200 bp in the same primer. All of the cytological, 4C DNA content and RAPD data confirmed the existence of two taxonomically distinct groups of Bruguiera: one consisting of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula as placed earlier (1862 in the tribe Rhizophoreae by Bentham and Hooker, on the basis of the flowering habits of Bruguiera. Genetically, the B

  8. Composition, peat-forming vegetation and kerogen paraffinicity of Cenozoic coals: Relationship to variations in the petroleum generation potential (Hydrogen Index)

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, H.I.; Lindstroem, S.; Nytoft, H.P.; Rosenberg, P. [Geological Survey of Denmark and Greenland (GEUS), Oester Voldgade 10, DK-1350 Copenhagen (Denmark)

    2009-04-01

    Coals with similar thermal maturity and from the same deposit normally show a considerable range in petroleum generation potential as measured by the Hydrogen Index (HI). This variation may partly be related to variations in plant input to the precursor mires and organic matter preservation. It is widely accepted that some Cenozoic coals and coaly sediments have the potential to generate oil, which is related to the coal's paraffinicity. Coal paraffinicity is not readily reflected in the bulk HI. In this paper, the relationships between measured HI and coal composition, coal kerogen paraffinicity and floral input have been investigated in detail for three sets of coals from Colombia/Venezuela, Indonesia, and Vietnam. The samples in each coal set are largely of iso-rank. The petroleum generation potential was determined by Rock-Eval pyrolysis. Reflected light microscopy was used to analyse the organic matter (maceral) composition and the thermal maturity was determined by vitrinite reflectance (VR) measurements. The botanical affinity of pollen and spores was analysed by palynology. Coal kerogen paraffinicity was determined by ruthenium tetroxide-catalysed oxidation (RTCO) followed by chain length analysis and quantification (mg/g TOC) of the liberated aliphatic chains. The coals are dominated by huminite, in particular detrohuminite. Only the Vietnamese coals are rich in microscopically visible liptinite. The pollen and spores suggest that the coals were derived principally from complex angiosperm mire vegetations, with subordinate proportions of ferns that generally grew in a subtropical to tropical climate. Measured HI values vary considerably, but for the majority of the coals the values lie between approximately 200 mg HC/g TOC and 300 mg HC/g TOC. Aliphatics yielding monocarboxylic acids dominate in the coal kerogen, whereas aliphatics yielding dicarboxylic acids are secondary. However, the dicarboxylic acids show that cross-linking long-chain aliphatics

  9. Variations of GHGs from the lower-troposphere to the UT/LS revealed by two Japanese regular aircraft observation programs

    Science.gov (United States)

    Niwa, Yosuke; Machida, Toshinobu; Sawa, Yousuke; Tsuboi, Kazuhiro; Matsueda, Hidekazu; Imasu, Ryoichi

    2014-05-01

    A Japan-centered observation network consisting of two regular aircraft programs have revealed the greenhouse gases variations from the lower-troposphere to the upper-troposphere/lower-stratosphere (UT/LS) regions. In the Comprehensive Observation Network for Trace gases by Airliner (CONTRAIL) project, in-situ continuous measurement equipment (CME) onboard commercial passenger aircraft world-widely observes CO2 profiles in vertical over tens of airports and in horizontal in the UT/LS regions. The CONTRAIL-CME has revealed three-dimensional structure of the global CO2 distribution and has exposed significant inter-hemispheric transport of CO2 through the upper-troposphere. In inverse modeling, the CME data have provided strong constraints on CO2 flux estimation especially for the Asian tropics. Automatic flask air sampling equipment (ASE) is also onboard the CONTRAIL aircraft and has been observing CO2 mixing ratios as well as those of methane, carbon monoxide, nitrous oxide and other trace species in the upper-troposphere between Japan and Australia. The observation period of the ASE has reached 20 years. In recent years, the ASE program has extended to the northern subarctic UT/LS region and has given an insight of transport mechanisms in the UT/LS by observing seasonal GHGs variations. In the other aircraft observation program by Japan Meteorological Agency, variations of GHGs have been observed by flask-sampling onboard a C-130H aircraft horizontally in the mid-troposphere over the western North Pacific as well as vertically over Minamitorishima-Island. The C-130H aircraft has persistently observed high mixing ratios of CH4 in the mid-troposphere, which seems to be originated from fossil fuel combustion throughout the year as well as from biogenic sources during summer in the Asian regions. Those above aircraft observation programs have a significant role for constraining GHGs flux estimates by filling the data gap of the existing surface measurement network

  10. Variation of gas exchange within native plant species of Switzerland and relationships with ozone injury: an open-top experiment.

    Science.gov (United States)

    Zhang, J; Ferdinand, J A; Vanderheyden, D J; Skelly, J M; Innes, J L

    2001-01-01

    Gas exchange and ozone-induced foliar injury were intensively measured during a 6-day period in mid-August 1998 on leaves of Acer pseudoplatanus, Betula pendula, Corylus avellana, Fagus sylvatica, Fraxinus excelsior, Morus nigra, Prunus avium, Prunus serotina, Rhamnus cathartica, and Viburnum lantana at a forest nursery site in Canton Ticino, Switzerland. Plants were grown in four open plots (AA), four open-top chambers receiving carbon-filtered (CF) air, and four receiving non-filtered (NF) air. Significant variation in gas exchange (F > 12.7, P photosynthesis and average stomatal conductance differing by a factor of two. Species also varied significantly in foliar injury for those leaves for which we measured gas exchange (F = 39.6, P Plants grown in CF chambers had significantly higher net photosynthesis (A) and stomatal conductance to water vapor (gwv), and lower foliar injury than plants grown in NF chambers and AA plots; interactions between species and ozone treatments were significant for all variables (F > or = 2.2, P 0.1). Although A and gwv decreased and foliar injury increased with leaf age, the magnitude of these changes was lower for plants grown in CF chambers than for plants grown in NF chambers and AA plots. Neither ozone uptake threshold (r = 0.26, P > 0.20) nor whole-plant injury (r = -0.15, P > 0.41) was significantly correlated with stomatal conductance across these species. It appears that the relationships between stomatal conductance and foliar injury are species-specific and interactions between physiology and environments and leaf biochemical processes must be considered in determining species sensitivity to ambient ozone exposures.

  11. Genotype variation and genetic relationship among Escherichia coli from nursery pigs located in different pens in the same farm.

    Science.gov (United States)

    Herrero-Fresno, Ana; Ahmed, Shahana; Hansen, Monica Hegstad; Denwood, Matthew; Zachariasen, Camilla; Olsen, John Elmerdahl

    2017-01-05

    So far, little is known about the genetic diversity and relatedness among Escherichia coli (E. coli) populations in the gut of swine. Information on this is required to improve modeling studies on antimicrobial resistance aiming to fight its occurrence and development. This work evaluated the genotype variation of E. coli isolated from swine fecal samples at the single pig and pen level, as well as between pens using repetitive extragenic palindromic (REP) PCR fingerprinting and pulsed field gel electrophoresis (PFGE). The genetic diversity of strains collected from media supplemented with ampicillin or tetracycline was also investigated. Besides, the genetic relationship of strains within each pen, between pens, as well as among strains within each group isolated from media with or without antibiotic, was assessed. REP-PCR patterns (N = 75) were generated for all the isolates (N = 720). Two profiles (REP_2 and REP_5) dominated, accounting for 23.7 and 23.3% of all isolates, respectively. At the pig and at the pen level, the number of different strains ranged from two to eight, and from 27 to 31, respectively, and multiple isolates from a single pen were found to be identical; however, in some of the pens, additional strains occurred at a lower frequency. E. coli isolates yielding different REP profiles were subjected to PFGE and led to 41 different genotypes which were also compared. Despite the presence of dominant strains, our results suggest a high genetic diversity of E. coli strains exist at the pen level and between pens. Selection with antibiotic seems to not affect the genetic diversity. The dominant REP profiles were the same found in a previous study in Denmark, which highlights that the same predominant strains are circulating in pigs of this country and might represent the archetypal E.coli commensal in pigs.

  12. Phylogeography of Yersinia ruckeri reveals effects of past evolutionary events on the current strain distribution and explains variations in the global transmission of Enteric Redmouth (ERM disease.

    Directory of Open Access Journals (Sweden)

    Asmine eBastardo

    2015-10-01

    Full Text Available Phylogeographic patterns and population genetic structure of Yersinia ruckeri, the pathological agent of enteric redmouth disease (ERM in salmonids, were investigated on the basis of concatenated multiloci sequences from isolates of different phenotypes obtained between 1965-2009 from diverse areas and hosts. Sequence analyses revealed genetic differentiation among subpopulations with the largest genetic distance occurring between subpopulations of Europe and Canada and/or South America. Bayesian analysis indicated the presence of three ancestral population clusters. Mismatch distribution displayed signatures characteristic of changes in size due to demographic and spatial expansions in the overall Y. ruckeri population, and also in the geographically separate subpopulations. Furthermore, a weak signal of isolation by distance was determined. A significant positive correlation between genetic and geographical distances was observed. These results revealed that the population of Y. ruckeri has undergone both ancient and recent population changes that were probably induced by biogeography forces in the past and, much more recently, by adaptive processes forced by aquaculture expansion. These findings have important implications for future studies on Y. ruckeri population dynamics, on the potential role of genetic structure to explain variations in ERM transmission, and on the effect of past evolutionary events on current estimations of gene flow.

  13. Comparative Proteomic and Physiological Analysis Reveals the Variation Mechanisms of Leaf Coloration and Carbon Fixation in a Xantha Mutant of Ginkgo biloba L.

    Science.gov (United States)

    Liu, Xinliang; Yu, Wanwen; Wang, Guibin; Cao, Fuliang; Cai, Jinfeng; Wang, Huanli

    2016-10-27

    Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. The chlorophyll content of YL was remarkably lower than that in GL. The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL. Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching. To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS. In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes. Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves. The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL. These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants.

  14. Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling.

    Directory of Open Access Journals (Sweden)

    Srikanth Ryali

    2016-12-01

    Full Text Available Little is currently known about dynamic brain networks involved in high-level cognition and their ontological basis. Here we develop a novel Variational Bayesian Hidden Markov Model (VB-HMM to investigate dynamic temporal properties of interactions between salience (SN, default mode (DMN, and central executive (CEN networks-three brain systems that play a critical role in human cognition. In contrast to conventional models, VB-HMM revealed multiple short-lived states characterized by rapid switching and transient connectivity between SN, CEN, and DMN. Furthermore, the three "static" networks occurred in a segregated state only intermittently. Findings were replicated in two adult cohorts from the Human Connectome Project. VB-HMM further revealed immature dynamic interactions between SN, CEN, and DMN in children, characterized by higher mean lifetimes in individual states, reduced switching probability between states and less differentiated connectivity across states. Our computational techniques provide new insights into human brain network dynamics and its maturation with development.

  15. Low level of genetic variation within Melica transsilvanica populations from the Kraków-Częstochowa Upland and the Pieniny Mts revealed by AFLPs analysis

    Directory of Open Access Journals (Sweden)

    Magdalena Szczepaniak

    2011-01-01

    Full Text Available Fragmented distribution, the breeding system and effects of genetic drift in small-size populations occurring at edge of the species range play an important role in shaping genetic diversity of such a species. Melica transsilvanica is a plant rare in the flora of Poland, where it reaches the northern limit of its continuous range. Amplified Fragment Length Polymorphism (AFLP DNA profiling method was applied to measure genetic diversity among and within populations of M. transsilvanica. Additionally, genetic relationships between M. transsilvanica and Melica ciliata, two closely related species, were explored. A total of 68 plants from 7 populations of M. transsilvanica and 24 plants from 2 populations of M. ciliata, collected in Poland and outside it, were analyzed. Using 294 AFLP fragments from 3 primer combinations, accessions were grouped into two major clusters associating with M. ciliata and M. transsilvanica, respectively. Further, two subclusters, corresponding to the samples collected from the Pieniny Mts and from the Kraków - Częstochowa Upland were clearly distinguished within the M. transsilvanica group. The hierarchical AMOVA exhibited significant genetic distinction between these geographic regions (60.89%, p < 0.001. The obtained results showed that the most genetic diversity resided between the populations of M. transsilvanica (86.03% while considerably lower genetic variation was found within the populations (13.97%, which is consistent with the results reported for self-plants. The low level of AFLP genetic variation of M. transsilvanica can be caused by the geographic isolation of populations, which preserves the dominant self-mating breeding system of the species. Individual populations of M. transsilvanica are characterized by isolated gene pools differing by a small number of loci.

  16. Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation

    DEFF Research Database (Denmark)

    Yusim, K.; Kesmir, Can; Gaschen, B.

    2002-01-01

    The human cytotoxic T-lymphocyte (CTL) response to human immunodeficiency virus type 1 (HIV-1) has been intensely studied, and hundreds of CTL epitopes have been experimentally defined, published, and compiled in the HIV Molecular Immunology Database. Maps of CTL epitopes on HIV-1 protein sequences...... reveal that defined epitopes tend to cluster. Here we integrate the global sequence and immunology databases to systematically explore the relationship between HIV-1 amino acid sequences and CTL epitope distributions. CTL responses to five HIV-1 proteins, Gag p17, Gag p24, reverse transcriptase (RT), Env......, and Nef, have been particularly well characterized in the literature to date. Through comparing CTL epitope distributions in these five proteins to global protein sequence alignments, we identified distinct characteristics of HIV amino acid sequences that correlate with CTL epitope localization. First...

  17. Spatial patterns of neutral and functional genetic variations reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies.

    Science.gov (United States)

    Kyle, Christopher J; Rico, Yessica; Castillo, Sarrah; Srithayakumar, Vythegi; Cullingham, Catherine I; White, Bradley N; Pond, Bruce A

    2014-05-01

    Local adaptation is necessary for population survival and depends on the interplay between responses to selective forces and demographic processes that introduce or retain adaptive and maladaptive attributes. Host-parasite systems are dynamic, varying in space and time, where both host and parasites must adapt to their ever-changing environment in order to survive. We investigated patterns of local adaptation in raccoon populations with varying temporal exposure to the raccoon rabies virus (RRV). RRV infects approximately 85% of the population when epizootic and has been presumed to be completely lethal once contracted; however, disease challenge experiments and varying spatial patterns of RRV spread suggest some level of immunity may exist. We first assessed patterns of local adaptation in raccoon populations along the eastern seaboard of North America by contrasting spatial patterns of neutral (microsatellite loci) and functional, major histocompatibility complex (MHC) genetic diversity and structure. We explored variation of MHC allele frequencies in the light of temporal population exposure to RRV (0-60 years) and specific RRV strains in infected raccoons. Our results revealed high levels of MHC variation (66 DRB exon 2 alleles) and pronounced genetic structure relative to neutral microsatellite loci, indicative of local adaptation. We found a positive association linking MHC genetic diversity and temporal RRV exposure, but no association with susceptibility and resistance to RRV strains. These results have implications for landscape epidemiology studies seeking to predict the spread of RRV and present an example of how population demographics influence the degree to which populations adapt to local selective pressures. © 2014 John Wiley & Sons Ltd.

  18. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

    Directory of Open Access Journals (Sweden)

    Rajani Rai

    2015-11-01

    Full Text Available Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR and Classification and Regression Tree Analysis (CRT to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634; FAS (rs2234767; FASL (rs763110; DCC (rs2229080, rs4078288, rs7504990, rs714; PSCA (rs2294008, rs2978974; ADRA2A (rs1801253; ADRB1 (rs1800544; ADRB3 (rs4994; CYP17 (rs2486758 involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634, DCC (rs714, rs2229080, rs4078288 and ADRB3 (rs4994 polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994 to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10 or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10. Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

  19. High sensitivity detection of Plasmodium species reveals positive correlations between infections of different species, shifts in age distribution and reduced local variation in Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Smith Thomas A

    2009-03-01

    Full Text Available Abstract Background When diagnosed by standard light microscopy (LM, malaria prevalence can vary significantly between sites, even at local scale, and mixed species infections are consistently less common than expect in areas co-endemic for Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae. The development of a high-throughput molecular species diagnostic assay now enables routine PCR-based surveillance of malaria infections in large field and intervention studies, and improves resolution of species distribution within and between communities. Methods This study reports differences in the prevalence of infections with all four human malarial species and of mixed infections as diagnosed by LM and post-PCR ligase detection reaction – fluorescent microsphere (LDR-FMA assay in 15 villages in the central Sepik area of Papua New Guinea. Results Significantly higher rates of infection by P. falciparum, P. vivax, P. malariae and Plasmodium ovale were observed in LDR-FMA compared to LM diagnosis (p P. malariae (3.9% vs 13.4% and P. ovale (0.0% vs 4.8%. In contrast to LM diagnosis, which suggested a significant deficit of mixed species infections, a significant excess of mixed infections over expectation was detected by LDR-FMA (p P. falciparum (LM: 7–9 yrs 47.5%, LDR-FMA: 10–19 yrs 74.2% and P. vivax (LM: 4–6 yrs 24.2%, LDR-FMA: 7–9 yrs 50.9% but not P. malariae infections (10–19 yrs, LM: 7.7% LDR-FMA: 21.6%. Significant geographical variation in prevalence was found for all species (except for LM-diagnosed P. falciparum, with the extent of this variation greater in LDR-FMA than LM diagnosed infections (overall, 84.4% vs. 37.6%. Insecticide-treated bednet (ITN coverage was also the dominant factor linked to geographical differences in Plasmodium species infection prevalence explaining between 60.6% – 74.5% of this variation for LDR-FMA and 81.8% – 90.0% for LM (except P. falciparum, respectively. Conclusion The present study

  20. Social Network Analysis: Applied Tool to Enhance Effective Collaboration between Child Protection Organisations by Revealing and Strengthening Work Relationships

    National Research Council Canada - National Science Library

    Beáta Dávid

    2013-01-01

    .... The qualitative approach was complemented by social network analysis. Revealing the mechanism based on the actors' perception on how the child protection network operates, we identifi ed and named the strengths and weaknesses of its structure...

  1. Using Negative Emotions to Trace the Experience of Borderline Personality Pathology: Interconnected Relationships Revealed in an Experience Sampling Study.

    Science.gov (United States)

    Law, Mary Kate; Fleeson, William; Arnold, Elizabeth Mayfield; Furr, R Michael

    2016-02-01

    While emotional difficulties are highly implicated in borderline personality disorder (BPD), the dynamic relationships between emotions and BPD symptoms that occur in everyday life are unknown. The current paper examined the function of negative emotions as they relate to BPD symptoms in real time. Experience sampling methodology with 281 participants measured negative emotions and borderline symptoms, expressed as a spectrum of experiences, five times daily for two weeks. Overall, having a BDP diagnosis was associated with experiencing more negative emotions. Multilevel modeling supported positive concurrent relationships between negative emotions and BPD symptoms. Lagged models showed that even after 3 hours negative emotions and several symptoms continued to influence each other. Therefore, results indicated that negative emotions and BPD symptoms are intricately related; some evidenced long-lasting relationships. This research supports emotion-symptom contingencies within BPD and provides insight regarding the reactivity and functionality of negative emotions in borderline pathology.

  2. Using negative emotions to trace the experience of borderline personality pathology: Interconnected relationships revealed in an experience sampling study

    Science.gov (United States)

    Law, Mary Kate; Fleeson, William; Arnold, Elizabeth Mayfield; Furr, R. Michael

    2015-01-01

    While emotional difficulties are highly implicated in borderline personality disorder (BPD), the dynamic relationships between emotions and BPD symptoms that occur in everyday life are unknown. The current paper examined the function of negative emotions as they relate to BPD symptoms in real time. Experience sampling methodology with 281 participants measured negative emotions and borderline symptoms, expressed as a spectrum of experiences, five times daily for two weeks. Overall, having a BDP diagnosis was associated with experiencing more negative emotions. Multilevel modeling supported positive concurrent relationships between negative emotions and BPD symptoms. Lagged models showed that even after three hours negative emotions and several symptoms continued to influence each other. Therefore, results indicated that negative emotions and BPD symptoms are intricately related; some evidenced long-lasting relationships. This research supports emotion-symptom contingencies within BPD and provides insight regarding the reactivity and functionality of negative emotions in borderline pathology. PMID:25710731

  3. Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.

    Science.gov (United States)

    Cesnik, Anthony J; Shortreed, Michael R; Sheynkman, Gloria M; Frey, Brian L; Smith, Lloyd M

    2016-03-04

    Mass-spectrometry-based proteomic analysis underestimates proteomic variation due to the absence of variant peptides and posttranslational modifications (PTMs) from standard protein databases. Each individual carries thousands of missense mutations that lead to single amino acid variants, but these are missed because they are absent from generic proteomic search databases. Myriad types of protein PTMs play essential roles in biological processes but remain undetected because of increased false discovery rates in variable modification searches. We address these two fundamental shortcomings of bottom-up proteomics with two recently developed software tools. The first consists of workflows in Galaxy that mine RNA sequencing data to generate sample-specific databases containing variant peptides and products of alternative splicing events. The second tool applies a new strategy that alters the variable modification approach to consider only curated PTMs at specific positions, thereby avoiding the combinatorial explosion that traditionally leads to high false discovery rates. Using RNA-sequencing-derived databases with this Global Post-Translational Modification (G-PTM) search strategy revealed hundreds of single amino acid variant peptides, tens of novel splice junction peptides, and several hundred posttranslationally modified peptides in each of ten human cell lines.

  4. De novo genetic variation revealed in somatic sectors of single Arabidopsis plants [v1; ref status: indexed, http://f1000r.es/kw

    Directory of Open Access Journals (Sweden)

    Marianne T Hopkins

    2013-01-01

    Full Text Available Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives. Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.

  5. De novo genetic variation revealed in somatic sectors of single Arabidopsis plants [v2; ref status: indexed, http://f1000r.es/1ii

    Directory of Open Access Journals (Sweden)

    Marianne T Hopkins

    2013-07-01

    Full Text Available Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives. Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.

  6. High-resolution arrays reveal burden of copy number variations on Parkinson disease genes associated with increased disease risk in random cohorts.

    Science.gov (United States)

    Murthy, Megha N; Veerappa, Avinash M; Seshachalam, Keshava B; Ramachandra, Nallur B

    2016-09-01

    Parkinson disease (PD) is a neurological disease responsible for a considerable rate of mortality and morbidity in the society. Since the symptoms of the disease appear much later than the actual onset of neuron degeneration, a majority of cases remain undiagnosed until the manifestation of the symptoms. In order to investigate the existence of such susceptibility in the population, we analyzed Copy Number Variation (CNV) influences on PD genes in 1715 individuals from 12 different populations. Overall, 16 CNV-PD genes, 3 known to be causal and 13 associated, were found to be significantly enriched. PARK2, was under heavy burden with ~1% of the population containing CNV in the exonic region. The impact of these genes on the genome and disease pathway was analyzed using several genome analysis tools. Protein interaction network of CNV-PD genes revealed a complex interaction of molecules forming a major hub by the α-Synuclein, whose direct interactors, LRRK2, PARK2 and ATP13A2 are under CNV influence. We hypothesize that CNVs may not be the initiating event in the pathogenesis of PD and remain latent until additional secondary hits are acquired and also propose novel genes that may fall under the PD pathway which contribute in pathogenesis.

  7. Variations in brachial plexus and the relationship of median nerve with the axillary artery: a case report

    Directory of Open Access Journals (Sweden)

    Rao Vani

    2007-10-01

    Full Text Available Abstract Background Brachial Plexus innervates the upper limb. As it is the point of formation of many nerves, variations are common. Knowledge of these is important to anatomists, radiologists, anesthesiologists and surgeons. The presence of anatomical variations of the peripheral nervous system is often used to explain unexpected clinical signs and symptoms. Case Presentation On routine dissection of an embalmed 57 year old male cadaver, variations were found in the formation of divisions and cords of the Brachial Plexus of the right side. Some previously unreported findings observed were; direct branches to the muscles Pectoralis Minor and Latissimus dorsi from C6, innervation of deltoid by C6 and C7 roots and the origin of lateral pectoral nerve from the posterior division of upper trunk. The median nerve was present lateral to axillary artery. The left side brachial plexus was also inspected and found to have normal anatomy. Conclusion The probable cause for such variations and their embryological basis is discussed in the paper. It is also concluded that although these variations may not have affected the functioning of upper limb in this individual, knowledge of such variations is essential in evaluation of unexplained sensory and motor loss after trauma and surgical interventions to the upper limb.

  8. A little similarity goes a long way: the effects of peripheral but self-revealing similarities on improving and sustaining interracial relationships.

    Science.gov (United States)

    West, Tessa V; Magee, Joe C; Gordon, Sarah H; Gullett, Lindy

    2014-07-01

    Integrating theory on close relationships and intergroup relations, we construct a manipulation of similarity that we demonstrate can improve interracial interactions across different settings. We find that manipulating perceptions of similarity on self-revealing attributes that are peripheral to the interaction improves interactions in cross-race dyads and racially diverse task groups. In a getting-acquainted context, we demonstrate that the belief that one's different-race partner is similar to oneself on self-revealing, peripheral attributes leads to less anticipatory anxiety than the belief that one's partner is similar on peripheral, nonself-revealing attributes. In another dyadic context, we explore the range of benefits that perceptions of peripheral, self-revealing similarity can bring to different-race interaction partners and find (a) less anxiety during interaction, (b) greater interest in sustained contact with one's partner, and (c) stronger accuracy in perceptions of one's partners' relationship intentions. By contrast, participants in same-race interactions were largely unaffected by these manipulations of perceived similarity. Our final experiment shows that among small task groups composed of racially diverse individuals, those whose members perceive peripheral, self-revealing similarity perform superior to those who perceive dissimilarity. Implications for using this approach to improve interracial interactions across different goal-driven contexts are discussed.

  9. Spatial variations in the relationships between land use and water quality across an urbanization gradient in the watersheds of Northern Georgia, USA.

    Science.gov (United States)

    Tu, Jun

    2013-01-01

    A spatial statistical technique, Geographically Weighted Regression (GWR) is applied to study the spatial variations in the relationships between four land use indicators, including percentages of urban land, forest, agricultural land, and wetland, and eight water quality indicators including specific conductance (SC), dissolved oxygen, dissolved nutrients, and dissolved organic carbon, in the watersheds of northern Georgia, USA. The results show that GWR has better model performance than ordinary least squares regression (OLS) to analyze the relationships between land use and water quality. There are great spatial variations in the relationships affected by the urbanization level of watersheds. The relationships between urban land and SC are stronger in less-urbanized watersheds, while those between urban land and dissolved nutrients are stronger in highly-urbanized watersheds. Percentage of forest is an indicator of good water quality. Agricultural land is usually associated with good water quality in highly-urbanized watersheds, but might be related to water pollution in less-urbanized watersheds. This study confirms the results obtained from a similar study in eastern Massachusetts, and so suggest that GWR technique is a very useful tool in water environmental research and also has the potential to be applied to other fields of environmental studies and management in other regions.

  10. The relationship between female brooding and male nestling provisioning: does climate underlie geographic variation in sex roles?

    Science.gov (United States)

    Yoon, Jongmin; Sofaer, Helen R.; Sillett, T. Scott; Morrison, Scott A.; Ghalambor, Cameron K.

    2017-01-01

    Comparative studies of populations occupying different environments can provide insights into the ecological conditions affecting differences in parental strategies, including the relative contributions of males and females. Male and female parental strategies reflect the interplay between ecological conditions, the contributions of the social mate, and the needs of offspring. Climate is expected to underlie geographic variation in incubation and brooding behavior, and can thereby affect both the absolute and relative contributions of each sex to other aspects of parental care such as offspring provisioning. However, geographic variation in brooding behavior has received much less attention than variation in incubation attentiveness or provisioning rates. We compared parental behavior during the nestling period in populations of orange-crowned warblers Oreothlypis celata near the northern (64°N) and southern (33°N) boundaries of the breeding range. In Alaska, we found that males were responsible for the majority of food delivery whereas the sexes contributed equally to provisioning in California. Higher male provisioning in Alaska appeared to facilitate a higher proportion of time females spent brooding the nestlings. Surprisingly, differences in brooding between populations could not be explained by variation in ambient temperature, which was similar between populations during the nestling period. While these results represent a single population contrast, they suggest additional hypotheses for the ecological correlates and evolutionary drivers of geographic variation in brooding behavior, and the factors that shape the contributions of each sex.

  11. Introgression evidence and phylogenetic relationships among three (ParaMisgurnus species as revealed by mitochondrial and nuclear DNA markers

    Directory of Open Access Journals (Sweden)

    Jakovlić I.

    2013-01-01

    Full Text Available The taxonomy of (ParaMisgurnus genera is still debated. We therefore used mitochondrial and nuclear DNA markers to analyze the phylogenetic relationships among Misgurnus anguillicaudatus, Paramisgurnus dabryanus and Misgurnus fossilis. Differing phylogenetic signals from mitochondrial and nuclear marker data suggest an introgression event in the history of M. anguillicaudatus and M. mohoity. No substantial genetic evidence was found that Paramisgurnus dabryanus should be classified as a separate genus.

  12. Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes.

    Directory of Open Access Journals (Sweden)

    David J Allen

    Full Text Available BACKGROUND: Human noroviruses are a highly diverse group of viruses classified into three of the five currently recognised Norovirus genogroups, and contain numerous genotypes or genetic clusters. Noroviruses are the major aetiological agent of endemic gastroenteritis in all age groups, as well as the cause of periodic epidemic gastroenteritis. The noroviruses most commonly associated with outbreaks of gastroenteritis are genogroup II genotype 4 (GII-4 strains. The relationship between genotypes of noroviruses with their phenotypes and antigenic profile remains poorly understood through an inability to culture these viruses and the lack of a suitable animal model. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe a study of the diversity of amino acid sequences of the highly variable P2 region in the major capsid protein, VP1, of the GII-4 human noroviruses strains using sequence analysis and homology modelling techniques. CONCLUSIONS/SIGNIFICANCE: Our data identifies two sites in this region, which show significant amino acid substitutions associated with the appearance of variant strains responsible for epidemics with major public health impact. Homology modelling studies revealed the exposed nature of these sites on the capsid surface, providing supportive structural data that these two sites are likely to be associated with putative variant-specific epitopes. Furthermore, the patterns in the evolution of these viruses at these sites suggests that noroviruses follow a neutral network pattern of evolution.

  13. Variation of Binge Eating One Year after Roux-en-Y Gastric Bypass and Its Relationship with Excess Weight Loss.

    Science.gov (United States)

    Luiz, Luciano Billodre; Brito, César Luis de Souza; Debon, Letícia Manoel; Brandalise, Lívia Nora; Azevedo, Juliana Tainski de; Monbach, Karin Daniele; Heberle, Luísa Schmidt; Mottin, Cláudio Corá

    2016-01-01

    Bariatric surgery is the most effective treatment for obesity classes II and III. However, some patients do not get the desired results or initially lose and then regain the lost weight. Identifying these individuals early on and treating them adequately remains a challenge. As binge eating directly affects food intake, the study of this symptom and its relation to bariatric surgery and its results is increasing, because it appears to have an influence on the results of surgery. This study aimed to see how binge eating changes, measured with the Binge Eating Scale, interferes in the % excess weight loss one year after Roux-en-Y gastric bypass. We conducted a cross-sectional study with 149 patients older than 18 years who were evaluated one year after undergoing Roux-en-Y gastric bypass. The variation in the intensity of binge eating was measured with the pre- and postoperative Binge Eating Scale scores. The variation of one unit in the Binge Eating Scale implied an inverse variation of 0.41% of % excess weight loss (p<0.05). The correlation coefficient between the variation of binge eating and the % excess weight loss was -0.186 (p = 0.033). The correlation coefficient between the binge eating symptoms one year after surgery and the % excess weight loss was -0.353 (p<0.001). There was a correlation between the variation of binge eating one year after gastric bypass and the % excess weight loss. The correlation between binge eating and the % excess weight loss was greater after the surgery than it was at the preoperative stage. This study provides new, valuable information on the intensity and variation of binge eating symptoms one year after gastric bypass, which, to the best of our knowledge, have not been studied in depth earlier.

  14. Variation of Binge Eating One Year after Roux-en-Y Gastric Bypass and Its Relationship with Excess Weight Loss.

    Directory of Open Access Journals (Sweden)

    Luciano Billodre Luiz

    Full Text Available Bariatric surgery is the most effective treatment for obesity classes II and III. However, some patients do not get the desired results or initially lose and then regain the lost weight. Identifying these individuals early on and treating them adequately remains a challenge. As binge eating directly affects food intake, the study of this symptom and its relation to bariatric surgery and its results is increasing, because it appears to have an influence on the results of surgery.This study aimed to see how binge eating changes, measured with the Binge Eating Scale, interferes in the % excess weight loss one year after Roux-en-Y gastric bypass.We conducted a cross-sectional study with 149 patients older than 18 years who were evaluated one year after undergoing Roux-en-Y gastric bypass. The variation in the intensity of binge eating was measured with the pre- and postoperative Binge Eating Scale scores.The variation of one unit in the Binge Eating Scale implied an inverse variation of 0.41% of % excess weight loss (p<0.05. The correlation coefficient between the variation of binge eating and the % excess weight loss was -0.186 (p = 0.033. The correlation coefficient between the binge eating symptoms one year after surgery and the % excess weight loss was -0.353 (p<0.001.There was a correlation between the variation of binge eating one year after gastric bypass and the % excess weight loss. The correlation between binge eating and the % excess weight loss was greater after the surgery than it was at the preoperative stage. This study provides new, valuable information on the intensity and variation of binge eating symptoms one year after gastric bypass, which, to the best of our knowledge, have not been studied in depth earlier.

  15. Quantitative Detection and Genotyping of Helicobacter pylori from Stool using Droplet Digital PCR Reveals Variation in Bacterial Loads that Correlates with cagA Virulence Gene Carriage.

    Science.gov (United States)

    Talarico, Sarah; Safaeian, Mahboobeh; Gonzalez, Paula; Hildesheim, Allan; Herrero, Rolando; Porras, Carolina; Cortes, Bernal; Larson, Ann; Fang, Ferric C; Salama, Nina R

    2016-08-01

    Epidemiologic studies of the carcinogenic stomach bacterium Helicobacter pylori have been limited by the lack of noninvasive detection and genotyping methods. We developed a new stool-based method for detection, quantification, and partial genotyping of H. pylori using droplet digital PCR (ddPCR), which allows for increased sensitivity and absolute quantification by PCR partitioning. Stool-based ddPCR assays for H. pylori 16S gene detection and cagA virulence gene typing were tested using a collection of 50 matched stool and serum samples from Costa Rican volunteers and 29 H. pylori stool antigen-tested stool samples collected at a US hospital. The stool-based H. pylori 16S ddPCR assay had a sensitivity of 84% and 100% and a specificity of 100% and 71% compared to serology and stool antigen tests, respectively. The stool-based cagA genotyping assay detected cagA in 22 (88%) of 25 stools from CagA antibody-positive individuals and four (16%) of 25 stools from CagA antibody-negative individuals from Costa Rica. All 26 of these samples had a Western-type cagA allele. Presence of serum CagA antibodies was correlated with a significantly higher load of H. pylori in the stool. The stool-based ddPCR assays are a sensitive, noninvasive method for detection, quantification, and partial genotyping of H. pylori. The quantitative nature of ddPCR-based H. pylori detection revealed significant variation in bacterial load among individuals that correlates with presence of the cagA virulence gene. These stool-based ddPCR assays will facilitate future population-based epidemiologic studies of this important human pathogen. © 2015 John Wiley & Sons Ltd.

  16. How Do People Become W.E.I.R.D.? Migration Reveals the Cultural Transmission Mechanisms Underlying Variation in Psychological Processes.

    Science.gov (United States)

    Mesoudi, Alex; Magid, Kesson; Hussain, Delwar

    2016-01-01

    Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD) countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal 'natural experiment' for uncovering such mechanisms. We used a battery of psychological measures previously shown to vary cross-culturally to compare the social orientation and cognitive style of 286 residents of East London from three cultural backgrounds: (i) 1st-generation British Bangladeshi immigrants; (ii) 2nd-generation British Bangladeshis raised in the UK to Bangladeshi-raised parents; and (iii) non-migrants whose parents were born and raised in the UK. Model comparison revealed that individualism and dispositional attribution, typical of Western societies, are driven primarily by horizontal cultural transmission (e.g. via mass media), with parents and other family members having little or no effect, while collectivism, social closeness and situational attribution were driven by a mix of vertical/oblique cultural transmission (e.g. via family contact) and horizontal cultural transmission. These individual-level transmission dynamics can explain hitherto puzzling population-level phenomena, such as the partial acculturation of 2nd-generation immigrants on measures such as collectivism (due to the mix of vertical and horizontal cultural transmission), or the observation in several countries of increasing individualism (which is transmitted horizontally and therefore rapidly) despite little corresponding change in collectivism (which is transmitted partly vertically and therefore more slowly). Further consideration of cultural transmission mechanisms, in conjunction with the study of migrant

  17. Large-scale analysis of variation in the insulin-like growth factor family in humans reveals rare disease links and common polymorphisms.

    Science.gov (United States)

    Rotwein, Peter

    2017-06-02

    The insulin-like growth factors IGF1 and IGF2 are closely related proteins that are essential for normal growth and development in humans and other species and play critical roles in many physiological and pathophysiological processes. IGF actions are mediated by transmembrane receptors and modulated by IGF-binding proteins. The importance of IGF actions in human physiology is strengthened by the rarity of inactivating mutations in their genes and by the devastating impact caused by such mutations on normal development and somatic growth. Large-scale genome sequencing has the potential to provide new insights into human variation and disease susceptibility. Toward this end, the availability of DNA sequence data from 60,706 people through the Exome Aggregation Consortium has prompted the analyses presented here. Results reveal a broad range of potential missense and other alterations in the coding regions of every IGF family gene, but the vast majority of predicted changes were uncommon. The total number of different alleles detected per gene in the population varied over an ∼15-fold range, from 57 for IGF1 to 872 for IGF2R, although when corrected for protein length the rate ranged from 0.22 to 0.59 changes/codon among the 11 genes evaluated. Previously characterized disease-causing mutations in IGF2, IGF1R, IGF2R, or IGFALS all were found in the general population but with allele frequencies of <1:30,000. A few new highly prevalent amino acid polymorphisms were also identified. Collectively, these data provide a wealth of opportunities to understand the intricacies of IGF signaling and action in both physiological and pathological contexts. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs.

    Science.gov (United States)

    Karali, Marianthi; Persico, Maria; Mutarelli, Margherita; Carissimo, Annamaria; Pizzo, Mariateresa; Singh Marwah, Veer; Ambrosio, Concetta; Pinelli, Michele; Carrella, Diego; Ferrari, Stefano; Ponzin, Diego; Nigro, Vincenzo; di Bernardo, Diego; Banfi, Sandro

    2016-02-29

    MicroRNAs play a fundamental role in retinal development and function. To characterise the miRNome of the human retina, we carried out deep sequencing analysis on sixteen individuals. We established the catalogue of retina-expressed miRNAs, determined their relative abundance and found that a small number of miRNAs accounts for almost 90% of the retina miRNome. We discovered more than 3000 miRNA variants (isomiRs), encompassing a wide range of sequence variations, which include seed modifications that are predicted to have an impact on miRNA action. We demonstrated that a seed-modifying isomiR of the retina-enriched miR-124-3p was endowed with different targeting properties with respect to the corresponding canonical form. Moreover, we identified 51 putative novel, retina-specific miRNAs and experimentally validated the expression for nine of them. Finally, a parallel analysis of the human Retinal Pigment Epithelium (RPE)/choroid, two tissues that are known to be crucial for retina homeostasis, yielded notably distinct miRNA enrichment patterns compared to the retina. The generated data are accessible through an ad hoc database. This study is the first to reveal the complexity of the human retina miRNome at nucleotide resolution and constitutes a unique resource to assess the contribution of miRNAs to the pathophysiology of the human retina. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. How Do People Become W.E.I.R.D.? Migration Reveals the Cultural Transmission Mechanisms Underlying Variation in Psychological Processes.

    Directory of Open Access Journals (Sweden)

    Alex Mesoudi

    Full Text Available Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal 'natural experiment' for uncovering such mechanisms. We used a battery of psychological measures previously shown to vary cross-culturally to compare the social orientation and cognitive style of 286 residents of East London from three cultural backgrounds: (i 1st-generation British Bangladeshi immigrants; (ii 2nd-generation British Bangladeshis raised in the UK to Bangladeshi-raised parents; and (iii non-migrants whose parents were born and raised in the UK. Model comparison revealed that individualism and dispositional attribution, typical of Western societies, are driven primarily by horizontal cultural transmission (e.g. via mass media, with parents and other family members having little or no effect, while collectivism, social closeness and situational attribution were driven by a mix of vertical/oblique cultural transmission (e.g. via family contact and horizontal cultural transmission. These individual-level transmission dynamics can explain hitherto puzzling population-level phenomena, such as the partial acculturation of 2nd-generation immigrants on measures such as collectivism (due to the mix of vertical and horizontal cultural transmission, or the observation in several countries of increasing individualism (which is transmitted horizontally and therefore rapidly despite little corresponding change in collectivism (which is transmitted partly vertically and therefore more slowly. Further consideration of cultural transmission mechanisms, in conjunction with the study of

  20. How Do People Become W.E.I.R.D.? Migration Reveals the Cultural Transmission Mechanisms Underlying Variation in Psychological Processes

    Science.gov (United States)

    Mesoudi, Alex; Magid, Kesson; Hussain, Delwar

    2016-01-01

    Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD) countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal ‘natural experiment’ for uncovering such mechanisms. We used a battery of psychological measures previously shown to vary cross-culturally to compare the social orientation and cognitive style of 286 residents of East London from three cultural backgrounds: (i) 1st-generation British Bangladeshi immigrants; (ii) 2nd-generation British Bangladeshis raised in the UK to Bangladeshi-raised parents; and (iii) non-migrants whose parents were born and raised in the UK. Model comparison revealed that individualism and dispositional attribution, typical of Western societies, are driven primarily by horizontal cultural transmission (e.g. via mass media), with parents and other family members having little or no effect, while collectivism, social closeness and situational attribution were driven by a mix of vertical/oblique cultural transmission (e.g. via family contact) and horizontal cultural transmission. These individual-level transmission dynamics can explain hitherto puzzling population-level phenomena, such as the partial acculturation of 2nd-generation immigrants on measures such as collectivism (due to the mix of vertical and horizontal cultural transmission), or the observation in several countries of increasing individualism (which is transmitted horizontally and therefore rapidly) despite little corresponding change in collectivism (which is transmitted partly vertically and therefore more slowly). Further consideration of cultural transmission mechanisms, in conjunction with the study of migrant

  1. Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

    NARCIS (Netherlands)

    Homburger, J.R. (Julian R.); Green, E.M. (Eric M.); Caleshu, C. (Colleen); Sunitha, M.S. (Margaret S.); Taylor, R.E. (Rebecca E.); Ruppel, K.M. (Kathleen M.); Metpally, R.P.R. (Raghu Prasad Rao); S.D. Colan (Steven); M. Michels (Michelle); Day, S.M. (Sharlene M.); I. Olivotto (Iacopo); Bustamante, C.D. (Carlos D.); Dewey, F.E. (Frederick E.); Ho, C.Y. (Carolyn Y.); Spudich, J.A. (James A.); Ashley, E.A. (Euan A.)

    2016-01-01

    textabstractMyosin motors are the fundamental force-generating elements of muscle contraction. Variation in the human β-cardiac myosin heavy chain gene (MYH7) can lead to hypertrophic cardiomyopathy (HCM), a heritable disease characterized by cardiac hypertrophy, heart failure, and sudden cardiac

  2. Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.

    Science.gov (United States)

    Ohtana, Yuki; Abdullah, Azian Azamimi; Altaf-Ul-Amin, Md; Huang, Ming; Ono, Naoaki; Sato, Tetsuo; Sugiura, Tadao; Horai, Hisayuki; Nakamura, Yukiko; Morita Hirai, Aki; Lange, Klaus W; Kibinge, Nelson K; Katsuragi, Tetsuo; Shirai, Tsuyoshi; Kanaya, Shigehiko

    2014-12-01

    Developing database systems connecting diverse species based on omics is the most important theme in big data biology. To attain this purpose, we have developed KNApSAcK Family Databases, which are utilized in a number of researches in metabolomics. In the present study, we have developed a network-based approach to analyze relationships between 3D structure and biological activity of metabolites consisting of four steps as follows: construction of a network of metabolites based on structural similarity (Step 1), classification of metabolites into structure groups (Step 2), assessment of statistically significant relations between structure groups and biological activities (Step 3), and 2-dimensional clustering of the constructed data matrix based on statistically significant relations between structure groups and biological activities (Step 4). Applying this method to a data set consisting of 2072 secondary metabolites and 140 biological activities reported in KNApSAcK Metabolite Activity DB, we obtained 983 statistically significant structure group-biological activity pairs. As a whole, we systematically analyzed the relationship between 3D-chemical structures of metabolites and biological activities. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. The relationship between county variation in macro contextual factors and the performance of public health practice in regional public health systems in Nebraska.

    Science.gov (United States)

    Chen, Li-Wu; Xu, Liyan; Yu, Fang; Jacobson, Janelle; Roberts, Sara; Palm, David

    2012-01-01

    This study examined the relationship between county variation in macro contextual variables and the performance of public health practice in regional local health departments (LHDs) in Nebraska. DESIGN AND MAIN OUTCOMES MEASURES: County-level data from the US Census Bureau, the Nebraska Department of Health and Human Services, and the University of Nebraska Medical Center's Health Professions Tracking Services were used to create macro context variables (eg, demographic, geographic, social, economic, population health status). The public health performance data were collected through a mail survey of the directors of regional LHDs in Nebraska in 2008. Public health performance measures were created to indicate LHD's general performance as well as core function specific performance (ie, assessment, assurance, policy development). The coefficients of variation were estimated and used to categorize each regional LHD into either a larger county variation group or a smaller county variation group for each domain of macro context variables. Statistical comparisons of public health performance measures were then made between these 2 groups for each domain. The results suggest that the county variation in macro contextual variables within a regional public health district, in general, is negatively associated with the performance of public health practice in regional LHDs. The regional LHD's performance in specific public health core function (eg, assurance) is negatively associated with the county variation in specific types of macro context factors (eg, geographic factors such as land size and population density). Regional LHDs may design and implement their public health programs on the basis of the type and degree of heterogeneity among the member counties within their jurisdiction. The formation of regional LHDs, if possible, should follow geographic boundaries that minimize the heterogeneity of county composition in terms of macro contextual factors.

  4. Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment

    KAUST Repository

    Rapakoulia, Trisevgeni

    2017-08-09

    Motivation: Drug combination therapy for treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect, while reducing the likelihood of drug resistance. In order to reduce time and cost spent in comprehensive screens, methods are needed which can model additive effects of possible drug combinations. Results: We here show that the transcriptional response to combinatorial drug treatment at promoters, as measured by single molecule CAGE technology, is accurately described by a linear combination of the responses of the individual drugs at a genome wide scale. We also find that the same linear relationship holds for transcription at enhancer elements. We conclude that the described approach is promising for eliciting the transcriptional response to multidrug treatment at promoters and enhancers in an unbiased genome wide way, which may minimize the need for exhaustive combinatorial screens.

  5. Relationship between Late Pleistocene sea-level variations, carbonate platform morphology and aragonite production (Maldives, Indian Ocean)

    DEFF Research Database (Denmark)

    Paul, A.; Reijmer, J.J.G.; Fürstenau, J.

    2012-01-01

    A piston core from the Maldives carbonate platform was investigated for carbonate mineralogy, grain-size distributions, calcium carbonate content and organic carbon. The sedimentary record was linked to Late Pleistocene sea-level variations, using an age model based on oxygen isotopes obtained from...... of the atolls of the Maldives carbonate platform. Platform flooding events were characterized by strongly increased deposition of aragonite and mud within the Inner Sea of the Maldives. Exposure events, in contrast, can be recognized by rapid decreases in the values of both proxy records. The results show...... that sediments on the Maldives carbonate platform contain a continuous record of Pleistocene sea-level variations. These sediments may, therefore, contribute to a better understanding of regional and even global sea-level changes, and yield new insights into the interplay between ocean currents and carbonate...

  6. What I experienced yesterday is who I am today: relationship of work motivations and behaviors to within-individual variation in the five-factor model of personality.

    Science.gov (United States)

    Judge, Timothy A; Simon, Lauren S; Hurst, Charlice; Kelley, Ken

    2014-03-01

    Historically, organizational and personality psychologists have ignored within-individual variation in personality across situations or have treated it as measurement error. However, we conducted a 10-day experience sampling study consistent with whole trait theory (Fleeson, 2012), which conceptualizes personality as a system of stable tendencies and patterns of intraindividual variation along the dimensions of the Big Five personality traits (Costa & McCrae, 1992). The study examined whether (a) internal events (i.e., motivation), performance episodes, and interpersonal experiences at work predict deviations from central tendencies in trait-relevant behavior, affect, and cognition (i.e., state personality), and (b) there are individual differences in responsiveness to work experiences. Results revealed that personality at work exhibited both stability and variation within individuals. Trait measures predicted average levels of trait manifestation in daily behavior at work, whereas daily work experiences (i.e., organizational citizenship, interpersonal conflict, and motivation) predicted deviations from baseline tendencies. Additionally, correlations of neuroticism with standard deviations in the daily personality variables suggest that, although work experiences influence state personality, people higher in neuroticism exhibit higher levels of intraindividual variation in personality than do those who are more emotionally stable.

  7. FTIR-ATR-based prediction and modelling of lignin and energy contents reveals independent intra-specific variation of these traits in bioenergy poplars

    Directory of Open Access Journals (Sweden)

    Taylor Gail

    2011-04-01

    estimations in large data sets. Our study revealed that the intra-specific variations in lignin and energy contents were unrelated to each other and that the lignin content, therefore, was no predictor of the energy content. Employing principle component analyses we showed that factor loadings for the energy content were mainly associated with carbohydrate ring vibrations, whereas those for lignin were mainly related to aromatic compounds. Therefore, our analysis suggests that it may be possible to optimize the energy content of trees without concomitant increase in lignin.

  8. Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.

    Science.gov (United States)

    Rapakoulia, Trisevgeni; Gao, Xin; Huang, Yi; de Hoon, Michiel; Okada-Hatakeyama, Mariko; Suzuki, Harukazu; Arner, Erik

    2017-12-01

    Drug combination therapy for treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect, while reducing the likelihood of drug resistance. In order to reduce time and cost spent in comprehensive screens, methods are needed which can model additive effects of possible drug combinations. We here show that the transcriptional response to combinatorial drug treatment at promoters, as measured by single molecule CAGE technology, is accurately described by a linear combination of the responses of the individual drugs at a genome wide scale. We also find that the same linear relationship holds for transcription at enhancer elements. We conclude that the described approach is promising for eliciting the transcriptional response to multidrug treatment at promoters and enhancers in an unbiased genome wide way, which may minimize the need for exhaustive combinatorial screens. The CAGE sequence data used in this study is available in the DDBJ Sequence Read Archive (http://trace.ddbj.nig.ac.jp/index_e.html), accession number DRP001113. xin.gao@kaust.edu.sa or erik.arner@riken.jp. Supplementary data are available at Bioinformatics online.

  9. Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms.

    Science.gov (United States)

    Gong, Li; Paris, Harry S; Nee, Michael H; Stift, Gertraud; Pachner, Martin; Vollmann, Johann; Lelley, Tamas

    2012-03-01

    Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo probably driven by a common desire to consume the young fruits. Among the accessions tested, there was no evidence for crossing between subspecies after domestication.

  10. ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity.

    Science.gov (United States)

    Reddy, Ch Surendhar; Babu, A Prasad; Swamy, B P Mallikarjuna; Kaladhar, K; Sarla, N

    2009-02-01

    Drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to drought, flood, or salinity using inter-simple sequence repeat (ISSR) markers. Based on all markers, the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties. The salt-tolerant varieties were closest to two flood-tolerant varieties, and together they were distinct from the drought-tolerant varieties. (GA)(8)YG was the most informative primer, showing the highest polymorphic information content (PIC) and resolving power (Rp). The drought-, flood-, and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties, when (GA)(8)YG was used. Sabita was the only exception. The two aus varieties, Nagina22 and FR13A, were separated and grouped with the drought- and flood-tolerant varieties, respectively, but they were together in dendrograms based on other primers. The results show that ISSR markers associated with (GA)(8)YG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.

  11. Connectivity profiles reveal the relationship between brain areas for social cognition in human and monkey temporoparietal cortex.

    Science.gov (United States)

    Mars, Rogier B; Sallet, Jérôme; Neubert, Franz-Xaver; Rushworth, Matthew F S

    2013-06-25

    The human ability to infer the thoughts and beliefs of others, often referred to as "theory of mind," as well as the predisposition to even consider others, are associated with activity in the temporoparietal junction (TPJ) area. Unlike the case of most human brain areas, we have little sense of whether or how TPJ is related to brain areas in other nonhuman primates. It is not possible to address this question by looking for similar task-related activations in nonhuman primates because there is no evidence that nonhuman primates engage in theory-of-mind tasks in the same manner as humans. Here, instead, we explore the relationship by searching for areas in the macaque brain that interact with other macaque brain regions in the same manner as human TPJ interacts with other human brain regions. In other words, we look for brain regions with similar positions within a distributed neural circuit in the two species. We exploited the fact that human TPJ has a unique functional connectivity profile with cortical areas with known homologs in the macaque. For each voxel in the macaque temporal and parietal cortex we evaluated the similarity of its functional connectivity profile to that of human TPJ. We found that areas in the middle part of the superior temporal cortex, often associated with the processing of faces and other social stimuli, have the most similar connectivity profile. These results suggest that macaque face processing areas and human mentalizing areas might have a similar precursor.

  12. Comparative Mitochondrial Genome Analysis of Eligma narcissus and other Lepidopteran Insects Reveals Conserved Mitochondrial Genome Organization and Phylogenetic Relationships.

    Science.gov (United States)

    Dai, Li-Shang; Zhu, Bao-Jian; Zhao, Yue; Zhang, Cong-Fen; Liu, Chao-Liang

    2016-05-25

    In this study, we sequenced the complete mitochondrial genome of Eligma narcissus and compared it with 18 other lepidopteran species. The mitochondrial genome (mitogenome) was a circular molecule of 15,376 bp containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an adenine (A) + thymine (T) - rich region. The positive AT skew (0.007) indicated the occurrence of more As than Ts. The arrangement of 13 PCGs was similar to that of other sequenced lepidopterans. All PCGs were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which was initiated by the CGA sequence, as observed in other lepidopterans. The results of the codon usage analysis indicated that Asn, Ile, Leu, Tyr and Phe were the five most frequent amino acids. All tRNA genes were shown to be folded into the expected typical cloverleaf structure observed for mitochondrial tRNA genes. Phylogenetic relationships were analyzed based on the nucleotide sequences of 13 PCGs from other insect mitogenomes, which confirmed that E. narcissus is a member of the Noctuidae superfamily.

  13. Group structure predicts variation in proximity relationships between male-female and male-infant pairs of mountain gorillas (Gorilla beringei beringei).

    Science.gov (United States)

    Rosenbaum, S; Maldonado-Chaparro, A A; Stoinski, T S

    2016-01-01

    Relationships between conspecifics are influenced by both ecological factors and the social organization they live in. Systematic variation of both--consistent with predictions derived from socioecology models--is well documented, but there is considerable variation within species and populations that is poorly understood. The mountain gorilla (Gorilla beringei) is unusual because, despite possessing morphology associated with male contest competition (e.g., extreme sexual dimorphism), they are regularly observed in both single-male and multimale groups. Both male-female and male-infant bonds are strong because males provide protection against infanticide and/or predation. Risk of these threats varies with social structure, which may influence the strength of social relationships among group members (including females and offspring, if females with lower infant mortality risk are less protective of infants). Here, we investigate the relationship between group structure and the strength of proximity relationships between males and females, males and infants, and females and offspring. Data come from 10 social groups containing 1-7 adult males, monitored by the Dian Fossey Gorilla Fund's Karisoke Research Center in Volcanoes National Park, Rwanda. After controlling for group size and infant age, association strength was similar for male-female pairs across group types with both dominant and nondominant males, but male-infant relationships were strongest in single-male groups where paternity certainty was high and animals had fewer social partners to choose from. The male:female and male:infant ratios better predicted both male-female and male-infant associations than the absolute number of males, females, or infants did. The fewer the number of males per female or infant, the more both pair types associated. Dominant males in groups containing fewer males had higher eigenvector centrality (a measure of importance in a social network) than dominant males in groups

  14. Relationship of serum interleukin-10 and its genetic variations with ischemic stroke in a Chinese general population.

    Directory of Open Access Journals (Sweden)

    Gaoqiang Xie

    Full Text Available BACKGROUND AND PURPOSE: Anti-inflammatory cytokine and its genetic variations may play an important role in the process of atherosclerosis. We assessed whether serum interleukin-10 (IL-10 and its genetic variations are associated with ischemic stroke in a Chinese general population. METHODS: An epidemiological survey on cardiovascular diseases and their risk factors was carried in a general population in Beijing in 2005. Serum IL-10, IL-6, p-selectin, soluble intercellular adhesion molecule-1 and C-reactive protein were analyzed using ELISA kits, while three IL-10 Single Nucleotide Polymorphisms (SNP (rs1800872, rs1554286 and rs3021094 were genotyped in 1475 participants. RESULTS: A high serum IL-10 (top tertile was significantly associated with ischemic stroke (multivariable adjusted odds ratio (OR =0.50; 95%CI 0.31-0.81. Rs1800872 (AA vs. AC+CC genotype, OR=1.60; 1.06-2.39, rs1554286(TT vs. CT+CC genotype, OR=1.59; 1.06-2.39, and rs3021094 (CC/CA vs. AA genotype, OR=1.64; 1.04-2.60 were all significantly associated with ischemic stroke even after controlling for age, sex, smoking, systolic blood pressure, total cholesterol, glucose, body mass index and serum IL-10. The SNP score (a summary index of these SNPs and IL-10 (top tertile together significantly improved the discriminative power in predicting ischemic stroke by 3.3% (95%CI: 0.2-6.4, p=0.0398 compared to predictions based on conventional risk factors alone. CONCLUSIONS: The lower serum IL-10 concentration and its selected genetic variations were significantly associated with an increased likelihood of ischemic stroke in this cross-sectional study. Our results suggest that more prospective studies should be conducted to provide stronger evidence justifying the use of IL-10 and its SNPs as new biomarkers to identify a predisposition towards ischemic stroke.

  15. Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions.

    Science.gov (United States)

    Porth, Ilga; Klápště, Jaroslav; Skyba, Oleksandr; Friedmann, Michael C; Hannemann, Jan; Ehlting, Juergen; El-Kassaby, Yousry A; Mansfield, Shawn D; Douglas, Carl J

    2013-11-01

    High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Wood traits are polygenic in nature, but gene hierarchies can be assessed to identify the most important gene variants controlling specific traits within complex networks defining the overall wood phenotype. We tested a large set of genetic, genomic, and phenotypic information in an integrative approach to predict wood properties in Populus trichocarpa. Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49k Nimblegen (Roche NimbleGen Inc., Madison, WI, USA) array elements and for 28,831 polymorphic single nucleotide polymorphisms (SNPs). Pre-selected transcripts and SNPs with high statistical dependence on phenotypic traits were used in Bayesian network learning procedures with a stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at a much lower logarithm of Bayes factor (logBF) threshold than SNPs and were not accommodated in the networks. Using persistent variables, we constructed cross-validated networks for variability in wood attributes, which contained four to six variables with 94-100% predictive accuracy. Accommodated gene variants revealed the hierarchy in the genetic architecture that underpins substantial phenotypic variability, and represent new tools to support the maximization of response to selection. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  16. Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

    Directory of Open Access Journals (Sweden)

    Maggie CY Lau

    2014-10-01

    Full Text Available Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1 screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S and N; (2 to characterize the biodiversity represented by the common functional genes; (3 to investigate the subsurface biogeography as revealed by this subset of genes; and (4 to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAP reductase, NifH, NifD, NifK, NifE and NifN genes. Although these 8 common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with either geographical, environmental or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.

  17. Relationship between antigenicity and pathogenicity for Burkholderia pseudomallei and Burkholderia mallei revealed by a large panel of mouse MAbs.

    Science.gov (United States)

    Zou, Nianxiang; Tsai, Shien; Feng, Shaw-Huey; Newsome, Tamara; Kim, Hyung-Yong; Li, Bingjie; Zhang, Shimin; Lo, Shyh-Ching

    2008-08-01

    Burkholderia pseudomallei and Burkholderia mallei are two closely related gram-negative bacterial species classified by the CDC as category B biowarfare agents. To develop monoclonal antibodies (MAbs) that can recognize as many different strains and/or clinical isolates of these two pathogens as possible, we immunized mice with heat-killed bacterial whole cells and membrane preparations from multiple strains and/or clinical isolates of B. pseudomallei and B. mallei. More than 100 different hybridoma clones that produced MAbs strongly reacting to B. pseudomallei and/or B. mallei have been developed. These MAbs were categorized into eight different groups according to their reaction specificity against different species of Burkholderia bacteria as well as the different nature of target antigens (LPS, capsule polysaccharides, proteins, and glycoproteins) on the bacteria they recognized. Characterization of this large panel of MAbs has demonstrated an interesting pattern of various antigenic epitopes shared by the different species of Burkholderia bacteria. More importantly, this study has revealed a pathogenicity-linked antigen epitope(s) on capsule-like polysaccharides found only in the pathogenic species of Burkholderia bacteria and a Burkholderia-specific antigen epitope(s) that did not exist in other gram-negative bacterial species. Our MAbs should prove to be highly valuable in the development of detection, diagnosis, and therapeutic applications against B. mallei and B. pseudomallei infections.

  18. Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Xie, Fang-Fei; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Hong; Wu, Jian; Guo, Yu-Fan; Zeng, Ke-Qin; Wang, Ming-Jun; Zhu, Xiao-Wei; Xia, Wei; Wang, Lan; He, Pei; Bing, Peng-Fei; Lu, Xin; Zhang, Yong-Hong; Lei, Shu-Feng

    2017-07-22

    DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P correlation (R T4 > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

  19. Revealing natural relationships among arbuscular mycorrhizal fungi: culture line BEG47 represents Diversispora epigaea, not Glomus versiforme.

    Science.gov (United States)

    Schüssler, Arthur; Krüger, Manuela; Walker, Christopher

    2011-01-01

    Understanding the mechanisms underlying biological phenomena, such as evolutionarily conservative trait inheritance, is predicated on knowledge of the natural relationships among organisms. However, despite their enormous ecological significance, many of the ubiquitous soil inhabiting and plant symbiotic arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are incorrectly classified. Here, we focused on a frequently used model AMF registered as culture BEG47. This fungus is a descendent of the ex-type culture-lineage of Glomus epigaeum, which in 1983 was synonymised with Glomus versiforme. It has since then been used as 'G. versiforme BEG47'. We show by morphological comparisons, based on type material, collected 1860-61, of G. versiforme and on type material and living ex-type cultures of G. epigaeum, that these two AMF species cannot be conspecific, and by molecular phylogenetics that BEG47 is a member of the genus Diversispora. This study highlights that experimental works published during the last >25 years on an AMF named 'G. versiforme' or 'BEG47' refer to D. epigaea, a species that is actually evolutionarily separated by hundreds of millions of years from all members of the genera in the Glomerales and thus from most other commonly used AMF 'laboratory strains'. Detailed redescriptions substantiate the renaming of G. epigaeum (BEG47) as D. epigaea, positioning it systematically in the order Diversisporales, thus enabling an evolutionary understanding of genetical, physiological, and ecological traits, relative to those of other AMF. Diversispora epigaea is widely cultured as a laboratory strain of AMF, whereas G. versiforme appears not to have been cultured nor found in the field since its original description.

  20. Family relationship of female breeders reduce the systematic inter-individual variation in the gut microbiota of inbred laboratory mice

    DEFF Research Database (Denmark)

    Hufeldt, Majbritt Ravn; Nielsen, Dennis Sandris; Vogensen, Finn Kvist

    2010-01-01

    The gut microbiota (GM) may influence disease expression in several animal models for inflammatory diseases. It may therefore seem reasonable to pursue reduction in the number of animals used for individual studies by reducing the variation in the GM. Previous studies have shown that the composit......The gut microbiota (GM) may influence disease expression in several animal models for inflammatory diseases. It may therefore seem reasonable to pursue reduction in the number of animals used for individual studies by reducing the variation in the GM. Previous studies have shown...... that the composition of the GM is related to genetics to a certain extent. We hypothesized that the GM similarity in a group of mice born by mothers not being sisters would be lower than that in a group born by mothers being sisters. The lower similarity could lead to clustering of the GM of mice born by non......-sisters according to their mothers, while such clustering would not be visible if the mothers were sisters. We used 16S rRNA gene (V3 region) polymerase chain reaction-derived amplicon profiling by denaturing gradient gel electrophoresis (DGGE) to study the GM composition in caecum samples of 33 eight-week-old C57...

  1. Dorsal Scapular Artery Variations and Relationship to the Brachial Plexus, and a Related Thoracic Outlet Syndrome Case.

    Science.gov (United States)

    Verenna, Anne-Marie A; Alexandru, Daniela; Karimi, Afshin; Brown, Justin M; Bove, Geoffrey M; Daly, Frank J; Pastore, Anthony M; Pearson, Helen E; Barbe, Mary F

    2016-01-01

    Rationale Knowledge of the relationship of the dorsal scapular artery (DSA) with the brachial plexus is limited. Objective We report a case of a variant DSA path, and revisit DSA origins and under-investigated relationship with the plexus in cadavers. Methods The DSA was examined in a male patient and 106 cadavers. Results In the case, we observed an unusual DSA compressing the lower plexus trunk, that resulted in intermittent radiating pain and paresthesia. In the cadavers, the DSA originated most commonly from the subclavian artery (71%), with 35% from the thyrocervical trunk. Nine sides of eight cadavers (seven females) had two DSA branches per side, with one branch from each origin. The most typical DSA path was a subclavian artery origin before passing between upper and middle brachial plexus trunks (40% of DSAs), versus between middle and lower trunks (23%), or inferior (4%) or superior to the plexus (1%). Following a thyrocervical trunk origin, the DSA passed most frequently superior to the plexus (23%), versus between middle and lower trunks (6%) or upper and middle trunks (4%). Bilateral symmetry in origin and path through the brachial plexus was observed in 13 of 35 females (37%) and 6 of 17 males (35%), with the most common bilateral finding of a subclavian artery origin and a path between upper and middle trunks (17%). Conclusion Variability in the relationship between DSA and trunks of the brachial plexus has surgical and clinical implications, such as diagnosis of thoracic outlet syndrome.

  2. Transcriptional profiling reveals developmental relationship and distinct biological functions of CD16+ and CD16- monocyte subsets

    Directory of Open Access Journals (Sweden)

    Zhou Xiaobo

    2009-08-01

    Full Text Available Abstract Background Human peripheral blood monocytes (Mo consist of subsets distinguished by expression of CD16 (FCγRIII and chemokine receptors. Classical CD16- Mo express CCR2 and migrate in response to CCL2, while a minor CD16+ Mo subset expresses CD16 and CX3CR1 and migrates into tissues expressing CX3CL1. CD16+ Mo produce pro-inflammatory cytokines and are expanded in certain inflammatory conditions including sepsis and HIV infection. Results To gain insight into the developmental relationship and functions of CD16+ and CD16- Mo, we examined transcriptional profiles of these Mo subsets in peripheral blood from healthy individuals. Of 16,328 expressed genes, 2,759 genes were differentially expressed and 228 and 250 were >2-fold upregulated and downregulated, respectively, in CD16+ compared to CD16- Mo. CD16+ Mo were distinguished by upregulation of transcripts for dendritic cell (DC (SIGLEC10, CD43, RARA and macrophage (MΦ (CSF1R/CD115, MafB, CD97, C3aR markers together with transcripts relevant for DC-T cell interaction (CXCL16, ICAM-2, LFA-1, cell activation (LTB, TNFRSF8, LST1, IFITM1-3, HMOX1, SOD-1, WARS, MGLL, and negative regulation of the cell cycle (CDKN1C, MTSS1, whereas CD16- Mo were distinguished by upregulation of transcripts for myeloid (CD14, MNDA, TREM1, CD1d, C1qR/CD93 and granulocyte markers (FPR1, GCSFR/CD114, S100A8-9/12. Differential expression of CSF1R, CSF3R, C1QR1, C3AR1, CD1d, CD43, CXCL16, and CX3CR1 was confirmed by flow cytometry. Furthermore, increased expression of RARA and KLF2 transcripts in CD16+ Mo coincided with absence of cell surface cutaneous lymphocyte associated antigen (CLA expression, indicating potential imprinting for non-skin homing. Conclusion These results suggest that CD16+ and CD16- Mo originate from a common myeloid precursor, with CD16+ Mo having a more MΦ – and DC-like transcription program suggesting a more advanced stage of differentiation. Distinct transcriptional programs, together

  3. Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a very-low-carbohydrate low-fat ketogenic diet

    Science.gov (United States)

    2010-01-01

    Background The prevalence of type 2 diabetes is increasing worldwide, accounting for 85-95% of all diagnosed cases of diabetes. Clinical trials provide evidence of benefits of low-carbohydrate ketogenic diets in terms of clinical outcomes on type 2 diabetes patients. However, the molecular events responsible for these improvements still remain unclear in spite of the high amount of knowledge on the primary mechanisms of both the diabetes and the metabolic state of ketosis. Molecular network analysis of conditions, diseases and treatments might provide new insights and help build a better understanding of clinical, metabolic and molecular relationships among physiological conditions. Accordingly, our aim is to reveal such a relationship between a ketogenic diet and type 2 diabetes through systems biology approaches. Methods Our systemic approach is based on the creation and analyses of the cell networks representing the metabolic state in a very-low-carbohydrate low-fat ketogenic diet. This global view might help identify unnoticed relationships often overlooked in molecule or process-centered studies. Results A strong relationship between the insulin resistance pathway and the ketosis main pathway was identified, providing a possible explanation for the improvement observed in clinical trials. Moreover, the map analyses permit the formulation of some hypothesis on functional relationships between the molecules involved in type 2 diabetes and induced ketosis, suggesting, for instance, a direct implication of glucose transporters or inflammatory processes. The molecular network analysis performed in the ketogenic-diet map, from the diabetes perspective, has provided insights on the potential mechanism of action, but also has opened new possibilities to study the applications of the ketogenic diet in other situations such as CNS or other metabolic dysfunctions. PMID:21143928

  4. Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a very-low-carbohydrate low-fat ketogenic diet

    Directory of Open Access Journals (Sweden)

    Naval Jordi

    2010-12-01

    Full Text Available Abstract Background The prevalence of type 2 diabetes is increasing worldwide, accounting for 85-95% of all diagnosed cases of diabetes. Clinical trials provide evidence of benefits of low-carbohydrate ketogenic diets in terms of clinical outcomes on type 2 diabetes patients. However, the molecular events responsible for these improvements still remain unclear in spite of the high amount of knowledge on the primary mechanisms of both the diabetes and the metabolic state of ketosis. Molecular network analysis of conditions, diseases and treatments might provide new insights and help build a better understanding of clinical, metabolic and molecular relationships among physiological conditions. Accordingly, our aim is to reveal such a relationship between a ketogenic diet and type 2 diabetes through systems biology approaches. Methods Our systemic approach is based on the creation and analyses of the cell networks representing the metabolic state in a very-low-carbohydrate low-fat ketogenic diet. This global view might help identify unnoticed relationships often overlooked in molecule or process-centered studies. Results A strong relationship between the insulin resistance pathway and the ketosis main pathway was identified, providing a possible explanation for the improvement observed in clinical trials. Moreover, the map analyses permit the formulation of some hypothesis on functional relationships between the molecules involved in type 2 diabetes and induced ketosis, suggesting, for instance, a direct implication of glucose transporters or inflammatory processes. The molecular network analysis performed in the ketogenic-diet map, from the diabetes perspective, has provided insights on the potential mechanism of action, but also has opened new possibilities to study the applications of the ketogenic diet in other situations such as CNS or other metabolic dysfunctions.

  5. Analysis of the Relationship between Changes in Meteorological Conditions and the Variation in Summer Ozone Levels over the Central Kanto Area

    Directory of Open Access Journals (Sweden)

    Mai Khiem

    2010-01-01

    Full Text Available An increasing trend in ground-level ozone (O3 concentrations has recently been recognized in Japan, although concentrations of ozone precursors, nitrogen oxides (NOx, volatile organic compounds (VOCs and nonmethane hydrocarbons (NMHCs have decreased. In this paper, the relationship between meteorological factors (temperature and wind speed and ground-level ozone concentrations in the summer over the central Kanto area of Japan was examined using both statistical analyses and numerical models. The Fifth-Generation NCAR/Penn State Mesoscale Model (MM5 and the Community Multiscale Air Quality (CMAQ model were employed in this study. It was found that there is a close relationship between meteorological conditions and ground-level ozone concentrations over the central Kanto area. In summer, up to 84% of the long-term variation in peak ozone concentrations may be accounted for by changes in the seasonally averaged daily maximum temperature and seasonally averaged wind speed, while about 70% of the recent short-term variation in peak ozone depends on the daily maximum temperature and the daily averaged wind speed. The results of numerical simulations also indicate that urban heat island (UHI phenomena can play an important role in the formation of high ozone concentrations in this area.

  6. Ground-level ozone in urban Beijing over a 1-year period: Temporal variations and relationship to atmospheric oxidation

    Science.gov (United States)

    Wang, Zhanshan; Li, Yunting; Chen, Tian; Zhang, Dawei; Sun, Feng; Wei, Qiang; Dong, Xin; Sun, Ruiwen; Huan, Ning; Pan, Libo

    2015-10-01

    Regional ozone pollution has become a major environmental concern in China, especially in densely populated and economically vibrant regions such as North China, including Beijing. To address this issue, surface ozone and its precursors (CO, NO, and NO2) from December 2012 to November 2013 at 12 sites in urban Beijing and 2 sites in suburban Beijing were analyzed. The annual average concentrations of O3, CO, NO, and NO2 in urban Beijing were 45.5 ± 50.2 μg m- 3, 1.5 ± 1.3 mg m- 3, 27.3 ± 42.7 μg m- 3, and 58.3 + 32.0 μg m- 3, respectively. The concentration of ozone was highest during summer, whereas concentrations of its precursors were highest during winter. Diurnal variations in ozone presented as a single-peak curve, with the peak appearing at about 15:00-16:00. Diurnal variations in most ozone precursors showed bimodal curves; the first peak appeared at about 08:00-09:00, and the second peak appeared at night. Hourly concentrations of ozone on the weekend were higher than those on weekdays between 11:00 and 24:00 in urban Beijing, which was suggestive of a significant weekend effect. This may be because NO inhibition on the weekend is weaker than that on weekdays during the ozone formation phase. Diurnal variations in OX (NO2 + O3) showed a single peak, which appeared at 15:00 or 16:00. The results of correlation analysis among OX, O3, and NO2 suggested that OX was mainly controlled by O3 during the day and by NO2 during the night throughout the year. OX was controlled by NO2 during both the day and night during winter due to the low concentration of O3. The regional transport of ozone along the upwind direction was found in a typical ozone pollution event in summer in Beijing.

  7. Genetic variation of wild and hatchery populations of the catla Indian major carp (Catla catla Hamilton 1822: Cypriniformes, Cyprinidae revealed by RAPD markers

    Directory of Open Access Journals (Sweden)

    S.M. Zakiur Rahman

    2009-01-01

    Full Text Available Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822 in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001 departure from homogeneity and the F ST values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.

  8. Potential relationship between phenotypic and molecular characteristics in revealing livestock-associated Staphylococcus aureus in Chinese humans without occupational livestock contact

    Directory of Open Access Journals (Sweden)

    Yanping Fan

    2016-09-01

    Full Text Available While some studies have defined Staphylococcus aureus based on its clonal complex and resistance pattern, few have explored the relations between the genetic lineages and antibiotic resistance patterns and immune evasion cluster (IEC genes. Our aim was to investigate the potential relationship between phenotypic and molecular characteristics so as to reveal livestock-associated S. aureus in humans. The study participants were interviewed, and they provided two nasal swabs for S. aureus analysis. All S. aureus and methicillin-resistant S. aureus (MRSA were tested for antibiotic susceptibility, multilocus sequence type and IEC genes. Of the 1162 participants, 9.3% carried S. aureus, including MRSA (1.4% and multidrug-resistant S. aureus (MDRSA, 2.8%. The predominant multidrug-resistant pattern among MDRSA isolates was nonsusceptibility to erythromycin, clindamycin and tetracycline. The most common S. aureus genotypes were ST7, ST6, ST188 and ST59, and the predominant MRSA genotype was ST7. Notably, the livestock-associated S. aureus isolates (IEC-negative CC9, IEC-negative tetracycline-resistant CC398, and IEC-negative tetracycline-resistant CC5 were found in people with no occupational livestock contact. These findings reveal a potential relationship between S. aureus CCs and IEC genes and antibiotic resistance patterns in defining livestock-associated S. aureus in humans and support growing concern about the potential livestock-to-human transmission of livestock-associated S. aureus by non-occupational livestock contact.

  9. RFLP Marker Variation of Cytocrome b Gene and Genetic Relationship among Batur, Merino and Local Sheep Breeds

    Directory of Open Access Journals (Sweden)

    Prayitno Prayitno

    2011-09-01

    Full Text Available RFLP analysis of mitochondrial DNA cytochrome b gene was conducted to determine the diversity, status and close genetic relationships in a population of Batur sheep with the Merino and local sheep breeds (Garut, Thin Tail and Fat Tail. The research used genomic DNA of 27 samples of Batur, 15 Merino, 17 Garut, 15 Thin Tails and 15 Fat Tails sheep. The PCR process used two types of 25 nucleotides primers. The PCR products were checked by using 2% agarose gel electrophoresis. The PCR DNA fragment was digested by using Hae III at 37 oC and incubated for 10 hours. Similarities and differences of cytochrome b gene RFLP bands between individual samples of one and across populations, genetic distance, and close genetic relationship, were identified. The PCR process of the cytochrome b gene metochondrial DNA of the 45 samples of sheep yielded 359 bp band types. The digestion (cutting of the PCR products of mitochondrial DNA cytochrome b gene by using Hae III resulted in RFLP band profiles of 128 up to 231 bp polymorphisms of cytochrome b gene. Although the Hae III restriction enzyme recognized only one restriction site, however, between samples of Batur, Merino, Garut, Thin Tail, and Fat Tails, there were monomorphism and polymorphism Hae III loci. Key Words:  RFLP, cytochrome b gene, genetic markers, genetic similarity, Batur shee Animal Production 13(3:156-165 (2011

  10. Spatial-Temporal Variations of Water Quality and Its Relationship to Land Use and Land Cover in Beijing, China.

    Science.gov (United States)

    Chen, Xiang; Zhou, Weiqi; Pickett, Steward T A; Li, Weifeng; Han, Lijian

    2016-04-27

    Rapid urbanization with intense land use and land cover (LULC) change and explosive population growth has a great impact on water quality. The relationship between LULC characteristics and water quality provides important information for non-point sources (NPS) pollution management. In this study, we first quantified the spatial-temporal patterns of five water quality variables in four watersheds with different levels of urbanization in Beijing, China. We then examined the effects of LULC on water quality across different scales, using Pearson correlation analysis, redundancy analysis, and multiple regressions. The results showed that water quality was improved over the sampled years but with no significant difference (p > 0.05). However, water quality was significantly different among nonurban and both exurban and urban sites (p < 0.05). Forest land was positively correlated with water quality and affected water quality significantly (p < 0.05) within a 200 m buffer zone. Impervious surfaces, water, and crop land were negatively correlated with water quality. Crop land and impervious surfaces, however, affected water quality significantly (p < 0.05) for buffer sizes greater than 800 m. Grass land had different effects on water quality with the scales. The results provide important insights into the relationship between LULC and water quality, and thus for controlling NPS pollution in urban areas.

  11. Relationships between morphology, diet and spatial distribution: testing the effects of intra and interspecific morphological variations on the patterns of resource use in two Neotropical Cichlids

    Directory of Open Access Journals (Sweden)

    Ana Lúcia A. Sampaio

    Full Text Available Considering th e morphology, diet and spatial distribution of Satanoperca pappaterra and Crenicichla britskii (Perciformes: Cichlidae in the Upper Paraná River floodplain (Brazil, the following questions were investigated: (1 Could the body shape predict the use of trophic resources and habitat by C. britskii and S. pappaterra? (2 Could the relationship between morphology and use of trophic resources and habitat be also extended to the intraspecific scale? (3 What are the most important morphological traits used to predict the variation on diet and habitat occupation within and between species? We hypothesized that intra and interspecific differences in morphological patterns imply in different forms of resource exploitation and that the ecomorphological analysis enables the identification of trophic and spatial niche segregation. Fish samplings were performed in different types of habitats (rivers, secondary channels, connected and disconnected lagoons in the Upper Paraná River floodplain. Analyses of the stomach content was conducted to characterize the feeding patterns and twenty-two ecomorphological indices were calculated from linear morphological measurements and areas. A principal component analysis (PCA run with these indices evidenced the formation of two significant axes, revealing in the axis 1 an ecomorphological ordination according to the type of habitat, regardless the species. The individuals of both species exploiting lotic habitats tended to have morphological traits that enable rapid progressive and retrograde movements, braking and continuous swimming, whereas individuals found in lentic and semi-lotic habitats presented morphology adapted to a greater maneuverability and stabilization in deflections. On the other hand the axis 2 evidenced a segregation related to the feeding ecology, between S. pappaterra and C. britskii. The relationship between morphology and use of spatial and feeding resource was corroborated by the

  12. Detailed analysis of variation at and around mitochondrial position 16189 in a large Finnish cohort reveals no significant associations with early growth or metabolic phenotypes at age 31 years.

    Science.gov (United States)

    Das, Sreena; Bennett, Amanda J; Sovio, Ulla; Ruokonen, Aimo; Martikainen, Hannu; Pouta, Anneli; Hartikainen, Anna-Liisa; Franks, Stephen; Elliott, Paul; Poulton, Joanna; Järvelin, Marjo-Riitta; McCarthy, Mark I

    2007-08-01

    Mitochondrial dysfunction is increasingly implicated in pathogenesis of adult metabolic disease. Rare mitochondrial (mt) DNA mutations impair glucose homeostasis, but the contribution of common variants is unclear. In small studies, variation within the OriB origin of replication (at mt16189 in particular) has been associated with both early growth and adult metabolic phenotypes and may contribute to life-course relationships between the two. The aim was to study a large well-characterized cohort to determine whether previously reported small-scale associations between OriB sequence variation and early growth and adult metabolic phenotypes are robust. This was a genetic association study of 5470 individuals from the population-based Northern Finland Birth Cohort of 1966, followed prospectively from pregnancy to age 31 yr. We measured indices of early growth (including birth weight, placental weight, and ponderal index) and adult metabolic homeostasis (including body mass index, fasting glucose and insulin, indices of insulin action and secretion) and their relationship to variation in the OriB region. Previously reported associations could not be confirmed. There were no significant (P < 0.01, uncorrected) associations between OriB sequence variation and measures of early growth including birth weight (P = 0.52, comparing individuals with mt16189T to those with a homopolymeric C-tract) and placental weight (P = 0.49). There were no significant associations with adult metabolic phenotypes including fasting glucose (P = 0.07), fasting insulin (P = 0.42), and homeostatic model assessment-derived measures of insulin sensitivity or secretion (P = 0.45 and P = 0.56, respectively). Despite substantial power to detect previously reported effects, mtDNA variations around OriB are not major contributors to variation in early growth and metabolic phenotypes during early adulthood.

  13. Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation.

    Science.gov (United States)

    Pereira, Tiago José; Baldwin, James Gordon

    2016-05-01

    Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Interdecadal variation of tropical cyclone genesis and its relationship to the convective activities over the central Pacific

    Science.gov (United States)

    Huangfu, Jingliang; Huang, Ronghui; Chen, Wen

    2017-04-01

    Using the outgoing longwave radiation (OLR) data from the National Oceanic and Atmospheric Administration archives, this paper analyzes the interdecadal variation of convective activities over the central Pacific (CP) from July to October of 1979-2013 and its impact on tropical cyclone (TC) genesis in the western North Pacific (WNP). Concurrent with the interdecadal decrease of TC genesis, the tropical convection underwent a significant interdecadal change in the late 1990s. Overall, the first leading empirical orthogonal function mode of the tropical OLR during July-October turned from a zonal dipole pattern during 1979-1997 to a tripole pattern during 1998-2013. Concomitant to this change, the boreal part of the Walker circulation shrank westward, with its downdraft branch located over the CP. The downward motion anomalies over the CP increased after the late 1990s, as did the trade easterlies. Consistent with the CP convective activity anomalies, the negative low-level relative vorticity anomalies and upper-level divergence anomalies, positive vertical wind shear anomalies and anomalous abundant water vapor can be observed over the southeastern part of the WNP. Additionally, the tropical depression (TD)-type waves associated with the CP convective activities are significantly different before and after the late 1990s. Before the late 1990s, the off-equatorial TD-type waves could be distinctly observed, with clear transitions located along the WNP monsoon trough. However, these transitions were vague after the late 1990s. Therefore, the convective activities over the CP may have played an important role in affecting the interdecadal change of TC genesis by affecting the genesis of TD-type waves.

  15. Heterogeneity in genetic and nongenetic variation and energy sink relationships for residual feed intake across research stations and countries.

    Science.gov (United States)

    Tempelman, R J; Spurlock, D M; Coffey, M; Veerkamp, R F; Armentano, L E; Weigel, K A; de Haas, Y; Staples, C R; Connor, E E; Lu, Y; VandeHaar, M J

    2015-03-01

    Our long-term objective is to develop breeding strategies for improving feed efficiency in dairy cattle. In this study, phenotypic data were pooled across multiple research stations to facilitate investigation of the genetic and nongenetic components of feed efficiency in Holstein cattle. Specifically, the heritability of residual feed intake (RFI) was estimated and heterogeneous relationships between RFI and traits relating to energy utilization were characterized across research stations. Milk, fat, protein, and lactose production converted to megacalories (milk energy; MilkE), dry matter intakes (DMI), and body weights (BW) were collected on 6,824 lactations from 4,893 Holstein cows from research stations in Scotland, the Netherlands, and the United States. Weekly DMI, recorded between 50 to 200 d in milk, was fitted as a linear function of MilkE, BW0.75, and change in BW (ΔBW), along with parity, a fifth-order polynomial on days in milk (DIM), and the interaction between this polynomial and parity in a first-stage model. The residuals from this analysis were considered to be a phenotypic measure of RFI. Estimated partial regression coefficients of DMI on MilkE and on BW0.75 ranged from 0.29 to 0.47 kg/Mcal for MilkE across research stations, whereas estimated partial regression coefficients on BW0.75 ranged from 0.06 to 0.16 kg/kg0.75. Estimated partial regression coefficients on ΔBW ranged from 0.06 to 0.39 across stations. Heritabilities for country-specific RFI were based on fitting second-stage random regression models and ranged from 0.06 to 0.24 depending on DIM. The overall heritability estimate across all research stations and all DIM was 0.15±0.02, whereas an alternative analysis based on combining the first- and second-stage model as 1 model led to an overall heritability estimate of 0.18±0.02. Hence future genomic selection programs on feed efficiency appear to be promising; nevertheless, care should be taken to allow for potentially

  16. Variation in functional connectivity along anterior-to-posterior intraparietal sulcus, and relationship with age across late childhood and adolescence

    Directory of Open Access Journals (Sweden)

    Sarah A. Vinette

    2015-06-01

    Full Text Available The intraparietal sulcus (IPS, a region in the dorsal attention network (DAN, has been implicated in multi-sensory attention and working memory. Working memory and attention develop across childhood; changes in functional connectivity within the DAN may relate to this maturation. Previous findings regarding fronto-parietal intrinsic functional connectivity age-effects were mixed. Our study aimed to circumvent limitations of previous work using a large cross-sectional sample, 183 typically developing participants 6.5–20 years, from the Autism Brain Imaging Data Exchange, and seed regions along the anterior-to-posterior axis of the IPS. These seeds, IPS0-4, were entered into functional connectivity models. Group-level models investigated differential connectivity along the IPS and relationships with age. Anterior IPS3/4 exhibited greater connectivity with sensorimotor/pre-motor regions. Posterior IPS0/1 demonstrated greater connectivity with dorsal and ventral visual regions. Positive age-effects were found between IPS3-4 and visual regions. Negative age-effects were found between IPS and superior parietal and medial orbitofrontal cortices. Follow-up region of interest analyses were used to estimate age-effects for DAN and anticorrelated default mode network regions. Results suggest age-effects on IPS functional connectivity are relatively modest, and may differ pre- and across-adolescence. Studying typical age-related connectivity variability within this network may help to understand neurodevelopmental disorders marked by impaired attention.

  17. How Do People Become W.E.I.R.D.? Migration Reveals the Cultural Transmission Mechanisms Underlying Variation in Psychological Processes

    OpenAIRE

    Mesoudi, Alex; Magid, Kesson; Hussain, Delwar

    2016-01-01

    Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD) countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal ‘natural experiment’ for uncov...

  18. How do people become W.E.I.R.D.? Migration reveals the cultural transmission mechanisms underlying variation in psychological processes.

    OpenAIRE

    Alex Mesoudi; Kesson Magid; Delwar Hussain

    2016-01-01

    Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD) countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal 'natural experiment' for uncov...

  19. Theoretical model explaining the relationship between the molecular mass and the activation energy of the enzyme revealed by a large-scale analysis of bioinformatics data.

    Science.gov (United States)

    Pawlowski, Piotr H; Zielenkiewicz, Piotr

    2013-01-01

    A general dependence of the enzyme catalytic rate on its mass was revealed when a statistical analysis of 17065 records from the EMP database was performed. The estimated activation energy of the catalytic process decreases asymptotically with the enzyme molecular mass increase. The proposed theoretical model postulates the existence of an intermediate complex of the enzyme and the departing product. It allows for the explanation of the discovered mass-energy relationship, as an effect of the global enzyme-product interactions during complex dissociation. Fitted parameters of the model seem to be in agreement with those widely accepted for the van der Waals energy of molecular interactions. Their values also agree with the picture of the hydrogen bonding in the catalytic process and suggest that surface walk can be the favorable way of the product departure.

  20. Personal exposure to PM2.5, black smoke and NO2 in Copenhagen: relationship to bedroom and outdoor concentrations covering seasonal variation

    DEFF Research Database (Denmark)

    Sørensen, Mette; Loft, Steffen; Andersen, Helle Vibeke

    2005-01-01

    concentrations of PM(2.5), black smoke (BS), and nitrogen dioxide (NO(2)) were measured during 2-day periods in 30 subjects (20-33 years old) living and studying in central parts of Copenhagen. The measurements were repeated in the four seasons. Information on indoor exposure sources such as environmental...... factor. Seasons were defined as a dichotomised grouping of outdoor temperature (above and below 8 degrees C). For NO(2) there was a significant association between personal exposure and both the bedroom, the front door and the background concentrations, whereas for PM(2.5) and BS only the bedroom...... three measurements, and the association between the front door and the background concentrations was significant for PM(2.5) and NO(2), but not for BS, indicating greater spatial variation for BS than for PM(2.5) and NO(2). For NO(2), the relationship between the personal exposure and the front door...

  1. Standardized deceased donor kidney donation rates in the UK reveal marked regional variation and highlight the potential for increasing kidney donation: a prospective cohort study†

    Science.gov (United States)

    Summers, D. M.; Johnson, R. J.; Hudson, A. J.; Collett, D.; Murphy, P.; Watson, C. J. E.; Neuberger, J. M.; Bradley, J. A.

    2014-01-01

    Background The UK has implemented a national strategy for organ donation that includes a centrally coordinated network of specialist nurses in organ donation embedded in all intensive care units and a national organ retrieval service for deceased organ donors. We aimed to determine whether despite the national approach to donation there is significant regional variation in deceased donor kidney donation rates. Methods The UK prospective audit of deaths in critical care was analysed for a cohort of patients who died in critical care between April 2010 and December 2011. Multivariate logistic regression was used to identify the factors associated with kidney donation. The logistic regression model was then used to produce risk-adjusted funnel plots describing the regional variation in donation rates. Results Of the 27 482 patients who died in a critical care setting, 1528 (5.5%) became kidney donors. Factors found to influence donation rates significantly were: type of critical care [e.g. neurointensive vs general intensive care: OR 1.53, 95% confidence interval (CI) 1.34–1.75, P69 vs age 18–39 yr: OR 0.2, 0.15–0.25, Pdeath [e.g. ‘other’ (excluding ‘stroke’ and ‘trauma’) vs ‘trauma’: OR 0.04, 95% CI 0.03–0.05, Pdonation rates for the 20 UK kidney donor regions showed marked variation. The overall standardized donation rate ranged from 3.2 to 7.5%. Four regions had donation rates of >2 standard deviations (sd) from the mean (two below and two above). Regional variation was most marked for donation after circulatory death (DCD) kidney donors with 9 of the 20 regions demonstrating donation rates of >2 sd from the mean (5 below and 4 above). Conclusions The marked regional variation in kidney donation rates observed in this cohort after adjustment for factors strongly associated with donation rates suggests that there is considerable scope for further increasing kidney donation rates in the UK, particularly DCD. PMID:24335581

  2. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

    Directory of Open Access Journals (Sweden)

    Vining Kelly J

    2012-01-01

    Full Text Available Abstract Background DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem in the reference tree species black cottonwood (Populus trichocarpa. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq, we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation" had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. Conclusions We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

  3. Mapping the Relationship of Inter-Village Variation in Agroforestry Tree Survival with Social and Ecological Characteristics: The Case of the Vi Agroforestry Project, Mara Region, Tanzania

    Directory of Open Access Journals (Sweden)

    Karl-Erik Johansson

    2013-12-01

    Full Text Available Agroforestry practices can improve the adaptive capacity and resilience of local farming and subsistence systems while providing livelihood benefits to households. However, scaling up of agroforestry technology has often proved difficult. Many studies have been carried out to explain the lack of tangible impact, based mainly on formal household/farm surveys comparing characteristics of non-adopters with that of adopters. In this study, we mapped the relationship between agroforestry tree survival in villages that were a part of the Vi Agroforestry project in the Mara region, Tanzania with key social-ecological variables. A random sample of 21 households from each of 89 investigated project villages was used. The proportion of households with surviving agroforestry trees, varied from 10%–90% among villages. Social and ecological differences between villages were important explanations to this variation. Variables related to the project and its operations explained most of the inter-village variation in households with few surviving trees. To encourage the majority of village households to practice agroforestry their perceptions of tree ownership and the benefit of agroforestry were additional key factors to the project showing the importance of socio-cultural issues to the households’ decisions to continue beyond the initial tree planting and testing phase.

  4. The relationship of glutathione-S-transferases copy number variation and indoor air pollution to symptoms and markers of respiratory disease

    DEFF Research Database (Denmark)

    Hersoug, Lars-Georg; Brasch-Andersen, Charlotte; Husemoen, Lise Lotte Nystrup

    2012-01-01

    Introduction: Exposure to particulate matter (PM) may induce inflammation and oxidative stress in the airways. Carriers of null polymorphisms of glutathione S-transferases (GSTs), which detoxify reactive oxygen species, may be particularly susceptible to the effects of PM. Objectives: To investig....... The relationship of glutathione-S-transferases copy number variation and indoor air pollution to symptoms and markers of respiratory disease. Clin Respir J 2011; DOI:10.1111/j.1752-699X.2011.00258.x.......: To investigate whether deletions of GSTM1 and GSTT1 modify the potential effects of exposure to indoor sources of PM on symptoms and objective markers of respiratory disease. Methods: We conducted a population-based, cross-sectional study of 3471 persons aged 18-69 years. Information about exposure to indoor...... volume in 1 s (FEV(1) ), but these trends were not statistically significant. Furthermore, we did not observe any statistically significant interactions between GST copy number variation and exposure to indoor sources of PM in relation to respiratory symptoms and markers. Conclusions: In this adult...

  5. Variation of summer phytoplankton community composition and its relationship to nitrate and regenerated nitrogen assimilation across the North Atlantic Ocean

    Science.gov (United States)

    Van Oostende, N.; Fawcett, S. E.; Marconi, D.; Lueders-Dumont, J.; Sabadel, A. J. M.; Woodward, E. M. S.; Jönsson, B. F.; Sigman, D. M.; Ward, B. B.

    2017-03-01

    The North Atlantic Ocean is considered a nitrogen (N) limited system once vernal stabilisation of the water column alleviates light limitation and allows phytoplankton growth to deplete surface nutrients to virtually undetectable levels. Ammonium and other regenerated N forms are then the main surface N source for phytoplankton production. The effort to determine which phytoplankton groups contribute to long-term biological export production would be greatly aided by information on which phytoplankton groups are responsible for the assimilation of nitrate, as opposed to those assimilating predominantly regenerated N. In this study, we used the natural abundance N isotopes to examine basin-scale patterns of nitrate and regenerated N assimilation and evaluated the relationships between these trends and phytoplankton community composition. Samples were collected during a summertime cruise transect (August-September 2013) from the subtropical (36°N 73°W) to the subarctic (54°N 20°W) North Atlantic and analysed for the N isotopic composition (δ15N vs. N2 in air) of particulate nitrogen (PN) and nitrate, size-fractionated chlorophyll a, and phytoplankton group biomass using flow cytometry. The depth of the 300 nmol l-1 nitrate isopleth shoaled from the subtropics (79 m), where phytoplankton stripped surface waters of nitrate, to the subarctic, where it intersected with the surface and the upward nutrient supply drove a summer phytoplankton bloom. The δ15N of PN above the nitracline increased from the subtropics (-0.3‰) to the subarctic (4.2‰), reflecting both a change in the δ15N of the subsurface nitrate source (from 2.4‰ to 5.1‰) and increased reliance by phytoplankton on nitrate relative to regenerated N. Throughout the transect, the phytoplankton community was mainly composed of pico- and nano-sized cells (>88% of chlorophyll a in the pico- and nanophytoplankton biomass. Pico- and nanoeukaryotes showed the opposite pattern, becoming more important

  6. The variation of dust content with intrinsic galaxy properties: revealing strong dust biases in many commonly-used galaxy property measurements

    Science.gov (United States)

    Devour, Brian; Bell, Eric F.

    2018-01-01

    Dust strongly affects many observations of galaxy properties, and quantifying galaxy dust content and correcting for its effects is a delicate and often uncertain task. In particular, both the impact of dust on commonly-used metrics of galaxy structure and the variation of dust content with intrinsic galaxy properties are poorly quantified. The inclination dependence of dust attenuation is a powerful tool to quantify dust amounts and the effects of dust on galaxy property measurements; this requires the construction of dust and inclination-independent selection techniques to isolate samples of intrinsically similar galaxies for study. To this end we construct dust and inclination-independent measurements of galaxy mass and star formation rate using dust-penetrated infrared datasets, and we develop novel dust and inclination-independent galaxy ‘linear’ size and concentration measur