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Sample records for variation reveals relationships

  1. Intra- and interspecific trait variations reveal functional relationships between specific leaf area and soil niche within a subtropical forest.

    Science.gov (United States)

    He, Dong; Chen, Yongfa; Zhao, Kangning; Cornelissen, J H C; Chu, Chengjin

    2018-02-03

    How functional traits vary with environmental conditions is of fundamental importance in trait-based community ecology. However, how intraspecific variability in functional traits is connected to species distribution is not well understood. This study investigated inter- and intraspecific variation of a key functional trait, i.e. specific leaf area (leaf area per unit dry mass; SLA), in relation to soil factors and tested if trait variation is more closely associated with specific environmental regimes for low-variability species than for high-variability species. In a subtropical evergreen forest plot (50 ha, southern China), 106 700 leaves from 5335 individuals of 207 woody species were intensively collected, with 30 individuals sampled for most species to ensure a sufficient sample size representative of intraspecific variability. Soil conditions for each plant were estimated by kriging from more than 1700 observational soil locations across the plot. Intra- and interspecific variation in SLA were separately related to environmental factors. Based on the species-specific variation of SLA, species were categorized into three groups: low-, intermediate- and high-intraspecific variability. Intraspecific habitat ranges and the strength of SLA-habitat relationships were compared among these three groups. Interspecific variation in SLA overrides the intraspecific variation (77 % vs. 8 %). Total soil nitrogen (TN, positively) and total organic carbon (TOC, negatively) are the most important explanatory factors for SLA variation at both intra- and interspecific levels. SLA, both within and between species, decreases with decreasing soil nitrogen availability. As predicted, species with low intraspecific variability in SLA have narrower habitat ranges with respect to soil TOC and TN and show a stronger SLA-habitat association than high-variability species. For woody plants low SLA is a phenotypic and probably adaptive response to nitrogen stress, which drives the

  2. 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.

  3. 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 eruption and (2) the melts originally had Fe+ 3/FeT ≥ 0.175, consistent with oxygen fugacity (fO2) at least 0.4 log units above the fayalite-magnetite-quartz (FMQ) buffer at 1 atm and magmatic temperature of 1200 °C.The second process is interaction between the

  4. 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

  5. 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

  6. Applications of Pharmacogenetics in Revealing Variations in ...

    African Journals Online (AJOL)

    acer

    taking place in molecular biology techniques. Drug action is now more ... the latest findings of genetic variations in pharmacological targets related to disorders of major .... Similarly, Gly 9 allele. (Ser9Gly) of the dopamine D3 receptor gene.

  7. 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 ...

  8. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species.

    Science.gov (United States)

    Chang, Chia-Hao; Li, Fan; Shao, Kwang-Tsao; Lin, Yeong-Shin; Morosawa, Takahiro; Kim, Sungmin; Koo, Hyeyoung; Kim, Won; Lee, Jae-Seong; He, Shunping; Smith, Carl; Reichard, Martin; Miya, Masaki; Sado, Tetsuya; Uehara, Kazuhiko; Lavoué, Sébastien; Chen, Wei-Jen; Mayden, Richard L

    2014-12-01

    Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Genetic variation in pea (Pisum sativum L.) demonstrates the importance of root but not shoot C/N ratios in the control of plant morphology and reveals a unique relationship between shoot length and nodulation intensity.

    Science.gov (United States)

    Ludidi, Ndiko N; Pellny, Till K; Kiddle, Guy; Dutilleul, Christelle; Groten, Karin; VAN Heerden, Philippus D R; Dutt, Som; Powers, Stephen J; Römer, Peter; Foyer, Christine H

    2007-10-01

    Nodule numbers are regulated through systemic auto-regulatory signals produced by shoots and roots. The relative effects of shoot and root genotype on nodule numbers together with relationships to organ biomass, carbon (C) and nitrogen (N) status, and related parameters were measured in pea (Pisum sativum) exploiting natural genetic variation in maturity and apparent nodulation intensity. Reciprocal grafting experiments between the early (Athos), intermediate (Phönix) and late (S00182) maturity phenotypes were performed and Pearson's correlation coefficients for the parameters were calculated. No significant correlations were found between shoot C/N ratios and plant morphology parameters, but the root C/N ratio showed a strong correlation with root fresh and dry weights as well as with shoot fresh weight with less significant interactions with leaf number. Hence, the root C/N ratio rather than shoot C/N had a predominant influence on plant morphology when pea plants are grown under conditions of symbiotic nitrogen supply. The only phenotypic characteristic that showed a statistically significant correlation with nodulation intensity was shoot length, which accounted for 68.5% of the variation. A strong linear relationship was demonstrated between shoot length and nodule numbers. Hence, pea nodule numbers are controlled by factors related to shoot extension, but not by shoot or root biomass accumulation, total C or total N. The relationship between shoot length and nodule numbers persisted under field conditions. These results suggest that stem height could be used as a breeding marker for the selection of pea cultivars with high nodule numbers and high seed N contents.

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

    African Journals Online (AJOL)

    enoh

    2012-03-29

    Mar 29, 2012 ... 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 cultivar, microsatellite markers were used in their analysis. The microsatellite profiles of 44 Musa genotypes of various origins.

  11. 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…

  12. 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...

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

    African Journals Online (AJOL)

    vera 1

    To determine the genetic diversity and evolutionary relationships among red radishes, 37 accessions ... determined that plant height, fresh leaf weight, and root ... Flower-shaped. Red .... according to Levan's karyotype classification standards.

  14. 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 ...

  15. 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…

  16. The Relationship of Gender and Academic Performance to Motivation: Within-Ethnic-Group Variations.

    Science.gov (United States)

    Rouse, Kimberly A. Gordon; Austin, James T.

    2002-01-01

    Three studies examined within-ethnic-group variations in the relationship of grade point average and gender to motivation among African American, Hispanic American, and Euro-American students. Survey data revealed patterns of significant within-ethnic-group differences that varied across ethnic groups. In general, males demonstrated more…

  17. Variation and Inter-relationship ,Between Yield aJld,SQQl

    African Journals Online (AJOL)

    Variation and Inter-relationship ,Between Yield aJld,SQQl~ ",,,',, ... Analysis of variance revealed sigiiificaiit'differences, among the-teSted. • .:' '. J ~ I .... Successful use of. muta~ "number of panicles,~r~~ metre,', 100Q,grain ... ponents and to assess genetic x ,environment inter- , individual traits, estimates of error phenotYpic,.

  18. In vitro adaptation of Plasmodium falciparum reveal variations in cultivability

    OpenAIRE

    White, John; Mascarenhas, Anjali; Pereira, Ligia; Dash, Rashmi; Walke, Jayashri T.; Gawas, Pooja; Sharma, Ambika; Manoharan, Suresh Kumar; Guler, Jennifer L.; Maki, Jennifer N.; Kumar, Ashwani; Mahanta, Jagadish; Valecha, Neena; Dubhashi, Nagesh; Vaz, Marina

    2016-01-01

    Background Culture-adapted Plasmodium falciparum parasites can offer deeper understanding of geographic variations in drug resistance, pathogenesis and immune evasion. To help ground population-based calculations and inferences from culture-adapted parasites, the complete range of parasites from a study area must be well represented in any collection. To this end, standardized adaptation methods and determinants of successful in vitro adaption were sought. Methods Venous blood was collected f...

  19. The reciprocal relationship between competition and intraspecific trait variation

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... with larger leaves and lower specific leaf area than their neighbours. Switching to more stress tolerant strategies by increasing root diameter and leaf tissue density also reduced competition. However, dissimilarity in root tissue density also minimized competition, consistent with limiting similarity...... suggest that considering the effect of competition on trait expression is critical to understanding the relationship between traits and community assembly....

  20. In vitro adaptation of Plasmodium falciparum reveal variations in cultivability.

    Science.gov (United States)

    White, John; Mascarenhas, Anjali; Pereira, Ligia; Dash, Rashmi; Walke, Jayashri T; Gawas, Pooja; Sharma, Ambika; Manoharan, Suresh Kumar; Guler, Jennifer L; Maki, Jennifer N; Kumar, Ashwani; Mahanta, Jagadish; Valecha, Neena; Dubhashi, Nagesh; Vaz, Marina; Gomes, Edwin; Chery, Laura; Rathod, Pradipsinh K

    2016-01-22

    Culture-adapted Plasmodium falciparum parasites can offer deeper understanding of geographic variations in drug resistance, pathogenesis and immune evasion. To help ground population-based calculations and inferences from culture-adapted parasites, the complete range of parasites from a study area must be well represented in any collection. To this end, standardized adaptation methods and determinants of successful in vitro adaption were sought. Venous blood was collected from 33 P. falciparum-infected individuals at Goa Medical College and Hospital (Bambolim, Goa, India). Culture variables such as whole blood versus washed blood, heat-inactivated plasma versus Albumax, and different starting haematocrit levels were tested on fresh blood samples from patients. In vitro adaptation was considered successful when two four-fold or greater increases in parasitaemia were observed within, at most, 33 days of attempted culture. Subsequently, parasites from the same patients, which were originally cryopreserved following blood draw, were retested for adaptability for 45 days using identical host red blood cells (RBCs) and culture media. At a new endemic area research site, ~65% of tested patient samples, with varied patient history and clinical presentation, were successfully culture-adapted immediately after blood collection. Cultures set up at 1% haematocrit and 0.5% Albumax adapted most rapidly, but no single test condition was uniformly fatal to culture adaptation. Success was not limited by low patient parasitaemia nor by patient age. Some parasites emerged even after significant delays in sample processing and even after initiation of treatment with anti-malarials. When 'day 0' cryopreserved samples were retested in parallel many months later using identical host RBCs and media, speed to adaptation appeared to be an intrinsic property of the parasites collected from individual patients. Culture adaptation of P. falciparum in a field setting is formally shown to be

  1. 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.

  2. Speed, speed variation and crash relationships for urban arterials.

    Science.gov (United States)

    Wang, Xuesong; Zhou, Qingya; Quddus, Mohammed; Fan, Tianxiang; Fang, Shou'en

    2018-04-01

    Speed and speed variation are closely associated with traffic safety. There is, however, a dearth of research on this subject for the case of urban arterials in general, and in the context of developing nations. In downtown Shanghai, the traffic conditions in each direction are very different by time of day, and speed characteristics during peak hours are also greatly different from those during off-peak hours. Considering that traffic demand changes with time and in different directions, arterials in this study were divided into one-way segments by the direction of flow, and time of day was differentiated and controlled for. In terms of data collection, traditional fixed-based methods have been widely used in previous studies, but they fail to capture the spatio-temporal distributions of speed along a road. A new approach is introduced to estimate speed variation by integrating spatio-temporal speed fluctuation of a single vehicle with speed differences between vehicles using taxi-based high frequency GPS data. With this approach, this paper aims to comprehensively establish a relationship between mean speed, speed variation and traffic crashes for the purpose of formulating effective speed management measures, specifically using an urban dataset. From a total of 234 one-way road segments from eight arterials in Shanghai, mean speed, speed variation, geometric design features, traffic volume, and crash data were collected. Because the safety effects of mean speed and speed variation may vary at different segment lengths, arterials with similar signal spacing density were grouped together. To account for potential correlations among these segments, a hierarchical Poisson log-normal model with random effects was developed. Results show that a 1% increase in mean speed on urban arterials was associated with a 0.7% increase in total crashes, and larger speed variation was also associated with increased crash frequency. Copyright © 2018 Elsevier Ltd. All rights

  3. 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...... modelling works well for greensand shear-wave velocity prediction. We model the seismic response of glauconitic greensand by using laboratory data from the Nini field. Our studies here reveal that brine-saturated glauconitic greensand can have a similar seismic response to that from oil-saturated quartzitic...

  4. 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...

  5. Relationships among and variation within rare breeds of swine.

    Science.gov (United States)

    Roberts, K S; Lamberson, W R

    2015-08-01

    Extinction of rare breeds of livestock threatens to reduce the total genetic variation available for selection in the face of the changing environment and new diseases. Swine breeds facing extinction typically share characteristics such as small size, slow growth rate, and high fat percentage, which limit them from contributing to commercial production. Compounding the risk of loss of variation is the lack of pedigree information for many rare breeds due to inadequate herd books, which increases the chance that producers are breeding closely related individuals. By making genetic data available, producers can make more educated breeding decisions to preserve genetic diversity in future generations, and conservation organizations can prioritize investments in breed preservation. The objective of this study was to characterize genetic variation within and among breeds of swine and prioritize heritage breeds for preservation. Genotypes from the Illumina PorcineSNP60 BeadChip (GeneSeek, Lincoln, NE) were obtained for Guinea, Ossabaw Island, Red Wattle, American Saddleback, Mulefoot, British Saddleback, Duroc, Landrace, Large White, Pietrain, and Tamworth pigs. A whole-genome analysis toolset was used to construct a genomic relationship matrix and to calculate inbreeding coefficients for the animals within each breed. Relatedness and average inbreeding coefficient differed among breeds, and pigs from rare breeds were generally more closely related and more inbred ( Guinea pigs. Tamworth, Duroc, and Mulefoot tended to not cluster with the other 7 breeds.

  6. 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.

  7. 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., III; Milbury, C.; hide

    2017-01-01

    Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that approximately 98 percent of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2 percent 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 plus or minus 10 percent over scales ranging from centimeters to 100’s of kilometers.

  8. Mitochondrial DNA variation and genetic relationships of Populus species.

    Science.gov (United States)

    Barrett, J W; Rajora, O P; Yeh, F C; Dancik, B P; Strobeck, C

    1993-02-01

    We examined variation in and around the region coding for the cytochrome c oxidase I (coxI) and ATPase 6 (atp6) genes in the mitochondrial genomes of four Populus species (P. nigra, P. deltoides, P. maximowiczii, and P. tremuloides) and the natural hybrid P. x canadensis (P. deltoides x P. nigra). Total cellular DNAs of these poplars were digested with 16 restriction endonucleases and probed with maize mtDNA-specific probes (CoxI and Atp6). The only variant observed for Atp6 was interspecific, with P. maximowiczii separated from the other species as revealed by EcoRI digestions. No intraspecific mtDNA variation was observed among individuals of P. nigra, P. maximowiczii, P. x canadensis, or P. tremuloides for the CoxI probe. However, two varieties of P. deltoides were distinct because of a single site change in the KpnI digestions, demonstrating that P. deltoides var. deltoides (eastern cottonwood) and var. occidentalis (plains cottonwood) have distinct mitochondrial genomes in the region of the coxI gene. Populus x canadensis shared the same restriction fragment patterns as its suspected maternal parent P. deltoides. Nucleotide substitutions per base in and around the coxI and atp6 genes among the Populus species and the hybrid ranged from 0.0017 to 0.0077. The interspecific estimates of nucleotide substitution per base suggested that P. tremuloides was furthest removed from P. deltoides and P. x canadensis and least diverged from P. nigra. Populus maximowiczii was placed between these two clusters.

  9. 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.

  10. Socializing by Gaming : Revealing Social Relationships in Multiplayer Online Games

    NARCIS (Netherlands)

    Jia, L.; Shen, S.; van de Bovenkamp, R.; Iosup, A.; Kuipers, F.A.; Epema, D.H.J.

    2015-01-01

    Multiplayer Online Games (MOGs) like Defense of the Ancients and StarCraft II have attracted hundreds of millions of users who communicate, interact, and socialize with each other through gaming. In MOGs, rich social relationships emerge and can be used to improve gaming services such as match

  11. Phylogenetic relationships among anuran trypanosomes as revealed by riboprinting.

    Science.gov (United States)

    Clark, C G; Martin, D S; Diamond, L S

    1995-01-01

    Twenty trypanosome isolates from Anura (frogs and toads) assigned to several species were characterized by riboprinting-restriction enzyme digestion of polymerase chain reaction amplified small subunit ribosomal RNA genes. Restriction site polymorphisms allowed distinction of all the recognized species and no intraspecific variation in riboprint patterns was detected. Phylogenetic reconstruction using parsimony and distance estimates based on restriction fragment comigration showed Trypanosoma chattoni to be only distantly related to the other species, while T. ranarum and T. fallisi appear to be sister taxa despite showing non-overlapping host specificities.

  12. Genetic relationships among Orobanche species as revealed by RAPD analysis.

    Science.gov (United States)

    Román, B; Alfaro, C; Torres, A M; Moreno, M T; Satovic, Z; Pujadas, A; Rubiales, D

    2003-05-01

    RAPD markers were used to study variation among 20 taxa in the genus OROBANCHE: O. alba, O. amethystea, O. arenaria, O. ballotae, O. cernua, O. clausonis, O. cumana, O. crenata, O. densiflora, O. foetida, O. foetida var. broteri, O. gracilis, O. haenseleri, O. hederae, O. latisquama, O. mutelii, O. nana, O. ramosa, O. rapum-genistae and O. santolinae. A total of 202 amplification products generated with five arbitrary RAPD primers was obtained and species-specific markers were identified. The estimated Jaccard's differences between the species varied between 0 and 0.864. The pattern of interspecific variation obtained is in general agreement with previous taxonomic studies based on morphology, and the partition into two different sections (Trionychon and Orobanche) is generally clear. However, the position in the dendrogram of O. clausonis did not fit this classification since it clustered with members of section TRIONYCHON: Within this section, O. arenaria was relatively isolated from the other members of the section: O. mutelii, O. nana and O. ramosa. Within section Orobanche, all O. ramosa populations showed a similar amplification pattern, whereas differences among O. crenata populations growing on different hosts were found. Orobanche foetida and O. densiflora clustered together, supporting the morphological and cytological similarities and the host preferences of these species.

  13. 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

    2015-11-01

    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. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

  14. Peak flow variation in childhood asthma : Relationship to symptoms, atopy, airways obstruction and hyperresponsiveness

    NARCIS (Netherlands)

    Brand, PLP; Duiverman, EJ; Postma, DS; Waalkens, HJ; Kerrebijn, KF; vanEssenZandvliet, EEM; Quanjer, PH; Sluiter, HJ; Pouw, EM; Schoonbrood, DFME; Roos, CM; Jansen, HM; DeGooijer, A; Kerstjens, HAM; vanderMark, TW; Koeter, GH; deJong, PM; Sterk, PJ; Weaver, AMJ; Dijkman, JH; Dekhuijzen, PNR; Folgering, HTM; vanHerwaarden, CLA; Overbeek, SE; Bogaard, JM; Hilvering, C; Gans, SJ; Mengelers, HJJ; vanderBruggenBogaarts, BAHA; Kreukniet, J; Kouwenberg, JM; Prinsen, JE; Gerritsen, J; Knol, K; deMonchy, JGR; Dekker, FW; Kaptein, AA; Merkus, PJFM; Pocock, SJ; Hughes, MD; Robinson, NJ; Bleecker, ER; Meyers, DA

    Although home recording of peak expiratory flow (PEF) is considered useful in managing asthma, little is known about the relationship of PEF variation to other indicators of disease activity, We examined the relationship of PEF variation, expressed in various ways, to symptoms, atopy, level of lung

  15. 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.

  16. Revisiting diversity: cultural variation reveals the constructed nature of emotion perception.

    Science.gov (United States)

    Gendron, Maria

    2017-10-01

    The extent of cultural variation in emotion perception has long been assumed to be bounded by underlying universality. A growing body of research reveals, however, that evidence of universality in emotion perception is method-bound. Without the assumption of underlying universality, new lines of inquiry become relevant. Accumulating evidence suggests that cultures vary in what cues are relevant to perceptions of emotion. Further, cultural groups vary in their spontaneous inferences; mental state inference does not appear to be the only, or even most routine, mode of perception across cultures. Finally, setting universality assumptions aside requires innovation in the theory and measurement of culture. Recent studies reveal the promise of refinements in psychological approaches to culture. Together, the available evidence is consistent with a view of emotion perceptions as actively constructed by perceivers to fit the social and physical constraints of their cultural worlds. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.

    Science.gov (United States)

    Simon, Lauriane; Rabanal, Fernando A; Dubos, Tristan; Oliver, Cecilia; Lauber, Damien; Poulet, Axel; Vogt, Alexander; Mandlbauer, Ariane; Le Goff, Samuel; Sommer, Andreas; Duborjal, Hervé; Tatout, Christophe; Probst, Aline V

    2018-04-06

    Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.

  18. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, S.D.; Yi, F. [Wuhan Univ., Hubei (China). School of Electronic Information; Ministry of Education, Wuhan, Hubei (China). Key Lab. of Geospace Environment and Geodesy; State Observatory for Atmospheric Remote Sensing, Wuhan (China); Huang, C.M. [Wuhan Univ., Hubei (China). School of Electronic Information; Ministry of Education, Wuhan, Hubei (China). Key Lab. of Geospace Environment and Geodesy; State Observatory for Atmospheric Remote Sensing, Wuhan (China); Miami Univ., Oxford, OH (United States). Electrical and Computer Engineering Dept.; Zhou, Q. [Miami Univ., Oxford, OH (United States). Electrical and Computer Engineering Dept.

    2010-07-01

    The latitudinal and seasonal variations of gravity wave (GW) potential energy density (E{sub P}), kinetic energy density (E{sub K}), and total energy density (E{sub T}), 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 E{sub P} in the lower stratosphere is in good agreement with satellite observations. However, E{sub K} and E{sub T} 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. (orig.)

  20. 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.

  1. 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.

  2. 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.

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

    International Nuclear Information System (INIS)

    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

  4. 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.

  5. Temporal and radial variation of the solar wind temperature-speed relationship

    Science.gov (United States)

    Elliott, H. A.; Henney, C. J.; McComas, D. J.; Smith, C. W.; Vasquez, B. J.

    2012-09-01

    The solar wind temperature (T) and speed (V) are generally well correlated at ˜1 AU, except in Interplanetary Coronal Mass Ejections where this correlation breaks down. We perform a comprehensive analysis of both the temporal and radial variation in the temperature-speed (T-V) relationship of the non-transient wind, and our analysis provides insight into both the causes of the T-V relationship and the sources of the temperature variability. Often at 1 AU the speed-temperature relationship is well represented by a single linear fit over a speed range spanning both the slow and fast wind. However, at times the fast wind from coronal holes can have a different T-V relationship than the slow wind. A good example of this was in 2003 when there was a very large and long-lived outward magnetic polarity coronal hole at low latitudes that emitted wind with speeds as fast as a polar coronal hole. The long-lived nature of the hole made it possible to clearly distinguish that some holes can have a different T-V relationship. In an earlier ACE study, we found that both the compressions and rarefactions T-V curves are linear, but the compression curve is shifted to higher temperatures. By separating compressions and rarefactions prior to determining the radial profiles of the solar wind parameters, the importance of dynamic interactions on the radial evolution of the solar wind parameters is revealed. Although the T-V relationship at 1 AU is often well described by a single linear curve, we find that the T-V relationship continually evolves with distance. Beyond ˜2.5 AU the differences between the compressions and rarefactions are quite significant and affect the shape of the overall T-V distribution to the point that a simple linear fit no longer describes the distribution well. Since additional heating of the ambient solar wind outside of interaction regions can be associated with Alfvénic fluctuations and the turbulent energy cascade, we also estimate the heating rate

  6. Genetic variability of environmental sensitivity revealed by phenotypic variation in body weight and (its correlations to physiological and behavioral traits.

    Directory of Open Access Journals (Sweden)

    Delphine Lallias

    Full Text Available Adaptive phenotypic plasticity is a key component of the ability of organisms to cope with changing environmental conditions. Fish have been shown to exhibit a substantial level of phenotypic plasticity in response to abiotic and biotic factors. In the present study, we investigate the link between environmental sensitivity assessed globally (revealed by phenotypic variation in body weight and more targeted physiological and behavioral indicators that are generally used to assess the sensitivity of a fish to environmental stressors. We took advantage of original biological material, the rainbow trout isogenic lines, which allowed the disentangling of the genetic and environmental parts of the phenotypic variance. Ten lines were characterized for the changes of body weight variability (weight measurements taken every month during 18 months, the plasma cortisol response to confinement stress (3 challenges and a set of selected behavioral indicators. This study unambiguously demonstrated the existence of genetic determinism of environmental sensitivity, with some lines being particularly sensitive to environmental fluctuations and others rather insensitive. Correlations between coefficient of variation (CV for body weight and behavioral and physiological traits were observed. This confirmed that CV for body weight could be used as an indicator of environmental sensitivity. As the relationship between indicators (CV weight, risk-taking, exploration and cortisol was shown to be likely depending on the nature and intensity of the stressor, the joint use of several indicators should help to investigate the biological complexity of environmental sensitivity.

  7. Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms

    Science.gov (United States)

    Young, Jodi N.; Heureux, Ana M.C.; Sharwood, Robert E.; Rickaby, Rosalind E.M.; Morel, François M.M.; Whitney, Spencer M.

    2016-01-01

    While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat c), oxygenation (k cat o), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23–68 µM), SC/O (57–116mol mol−1), and K O (413–2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat c for each diatom Rubisco showed less variation (2.1–3.7s−1), thus averting the canonical trade-off typically observed between K C and k cat c for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily. PMID:27129950

  8. 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.

  9. 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

  10. Study of morphological variation of northern Neotropical Ariidae reveals conservatism despite macrohabitat transitions.

    Science.gov (United States)

    Stange, Madlen; Aguirre-Fernández, Gabriel; Salzburger, Walter; Sánchez-Villagra, Marcelo R

    2018-03-27

    Morphological convergence triggered by trophic adaptations is a common pattern in adaptive radiations. The study of shape variation in an evolutionary context is usually restricted to well-studied fish models. We take advantage of the recently revised systematics of New World Ariidae and investigate skull shape evolution in six genera of northern Neotropical Ariidae. They constitute a lineage that diversified in the marine habitat but repeatedly adapted to freshwater habitats. 3D geometric morphometrics was applied for the first time in catfish skulls and phylogenetically informed statistical analyses were performed to test for the impact of habitat on skull diversification after habitat transition in this lineage. We found that skull shape is conserved throughout phylogeny. A morphospace analysis revealed that freshwater and marine species occupy extreme ends of the first principal component axis and that they exhibit similar Procrustes variances. Yet freshwater species occupy the smallest shape space compared to marine and brackish species (based on partial disparity), and marine and freshwater species have the largest Procrustes distance to each other. We observed a single case of shape convergence as derived from 'C-metrics', which cannot be explained by the occupation of the same habitat. Although Ariidae occupy such a broad spectrum of different habitats from sea to freshwater, the morphospace analysis and analyses of shape and co-variation with habitat in a phylogenetic context shows that conservatism dominates skull shape evolution among ariid genera.

  11. 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.

  12. Revealing metabolomic variations in Cortex Moutan from different root parts using HPLC-MS method.

    Science.gov (United States)

    Xiao, Chaoni; Wu, Man; Chen, Yongyong; Zhang, Yajun; Zhao, Xinfeng; Zheng, Xiaohui

    2015-01-01

    The distribution of metabolites in the different root parts of Cortex Moutan (the root bark of Paeonia suffruticosa Andrews) is not well understood, therefore, scientific evidence is not available for quality assessment of Cortex Moutan. To reveal metabolomic variations in Cortex Moutan in order to gain deeper insights to enable quality control. Metabolomic variations in the different root parts of Cortex Moutan were characterised using high-performance liquid chromatography combined with mass spectrometry (HPLC-MS) and multivariate data analysis. The discriminating metabolites in different root parts were evaluated by the one-way analysis of variance and a fold change parameter. The metabolite profiles of Cortex Moutan were largely dominated by five primary and 41 secondary metabolites . Higher levels of malic acid, gallic acid and mudanoside-B were mainly observed in the second lateral roots, whereas dihydroxyacetophenone, benzoyloxypaeoniflorin, suffruticoside-A, kaempferol dihexoside, mudanpioside E and mudanpioside J accumulated in the first lateral and axial roots. The highest contents of paeonol, galloyloxypaeoniflorin and procyanidin B were detected in the axial roots. Accordingly, metabolite compositions of Cortex Moutan were found to vary among different root parts. The axial roots have higher quality than the lateral roots in Cortex Moutan due to the accumulation of bioactive secondary metabolites associated with plant physiology. These findings provided important scientific evidence for grading Cortex Moutan on the general market. Copyright © 2014 John Wiley & Sons, Ltd.

  13. Within-Host Variations of Human Papillomavirus Reveal APOBEC-Signature Mutagenesis in the Viral Genome.

    Science.gov (United States)

    Hirose, Yusuke; Onuki, Mamiko; Tenjimbayashi, Yuri; Mori, Seiichiro; Ishii, Yoshiyuki; Takeuchi, Takamasa; Tasaka, Nobutaka; Satoh, Toyomi; Morisada, Tohru; Iwata, Takashi; Miyamoto, Shingo; Matsumoto, Koji; Sekizawa, Akihiko; Kukimoto, Iwao

    2018-03-28

    Persistent infection with oncogenic human papillomaviruses (HPVs) causes cervical cancer, accompanied with the accumulation of somatic mutations into the host genome. There are concomitant genetic changes in the HPV genome during viral infection; however, their relevance to cervical carcinogenesis is poorly understood. Here we explored within-host genetic diversity of HPV by performing deep sequencing analyses of viral whole-genome sequences in clinical specimens. The whole genomes of HPV types 16, 52 and 58 were amplified by type-specific PCR from total cellular DNA of cervical exfoliated cells collected from patients with cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC), and were deep-sequenced. After constructing a reference vial genome sequence for each specimen, nucleotide positions showing changes with > 0.5% frequencies compared to the reference sequence were determined for individual samples. In total, 1,052 positions of nucleotide variations were detected in HPV genomes from 151 samples (CIN1, n = 56; CIN2/3, n = 68; ICC, n = 27), with varying numbers per sample. Overall, C-to-T and C-to-A substitutions were the dominant changes observed across all histological grades. While C-to-T transitions were predominantly detected in CIN1, their prevalence was decreased in CIN2/3 and fell below that of C-to-A transversions in ICC. Analysis of the tri-nucleotides context encompassing substituted bases revealed that Tp C pN, a preferred target sequence for cellular APOBEC cytosine deaminases, was a primary site for C-to-T substitutions in the HPV genome. These results strongly imply that the APOBEC proteins are drivers of HPV genome mutation, particularly in CIN1 lesions. IMPORTANCE HPVs exhibit surprisingly high levels of genetic diversity, including a large repertoire of minor genomic variants in each viral genotype. Here, by conducting deep sequencing analyses, we show for the first time a comprehensive snapshot of the "within

  14. Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.

    Directory of Open Access Journals (Sweden)

    Kristoffer T Bæk

    Full Text Available Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8325 (NRS77/PS47 required correction of errors in the 8325 reference genome, and reassessment of variation previously attributed to chemical mutagenesis of the restriction-defective RN4220. Using an extensive strain pedigree analysis, we discovered that 8325-4 contains 16 single nucleotide polymorphisms (SNP arising prior to the construction of RN4220. We identified 5 indels in 8325-4 compared with 8325. Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly decrease (75% steady state sarS but not spa transcript levels in post-exponential phase. The sub-lineage 8325-4 was also found to harbor 4 additional SNPs. We also found large sequence variation between 8325, 8325-4 and RN4220 in a cluster of repetitive hypothetical proteins (SA0282 homologs near the Ess secretion cluster. The overall 8325-4 SNP set results in 17 alterations within coding sequences. Remarkably, we discovered that all tested strains of the 8325-4 lineage lack phenol soluble modulin α3 (PSMα3, a virulence determinant implicated in neutrophil chemotaxis, biofilm architecture and surface spreading. Collectively, our results clarify and define the 8325-4 pedigree and reveal clear evidence that mutations existing throughout all branches of this lineage, including the widely used RN6390 and SH1000 strains, could conceivably impact virulence regulation.

  15. 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.

  16. 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.

  17. Systematic Prioritization and Integrative Analysis of Copy Number Variations in Schizophrenia Reveal Key Schizophrenia Susceptibility Genes

    Science.gov (United States)

    Luo, Xiongjian; Huang, Liang; Han, Leng; Luo, Zhenwu; Hu, Fang; Tieu, Roger; Gan, Lin

    2014-01-01

    Schizophrenia is a common mental disorder with high heritability and strong genetic heterogeneity. Common disease-common variants hypothesis predicts that schizophrenia is attributable in part to common genetic variants. However, recent studies have clearly demonstrated that copy number variations (CNVs) also play pivotal roles in schizophrenia susceptibility and explain a proportion of missing heritability. Though numerous CNVs have been identified, many of the regions affected by CNVs show poor overlapping among different studies, and it is not known whether the genes disrupted by CNVs contribute to the risk of schizophrenia. By using cumulative scoring, we systematically prioritized the genes affected by CNVs in schizophrenia. We identified 8 top genes that are frequently disrupted by CNVs, including NRXN1, CHRNA7, BCL9, CYFIP1, GJA8, NDE1, SNAP29, and GJA5. Integration of genes affected by CNVs with known schizophrenia susceptibility genes (from previous genetic linkage and association studies) reveals that many genes disrupted by CNVs are also associated with schizophrenia. Further protein-protein interaction (PPI) analysis indicates that protein products of genes affected by CNVs frequently interact with known schizophrenia-associated proteins. Finally, systematic integration of CNVs prioritization data with genetic association and PPI data identifies key schizophrenia candidate genes. Our results provide a global overview of genes impacted by CNVs in schizophrenia and reveal a densely interconnected molecular network of de novo CNVs in schizophrenia. Though the prioritized top genes represent promising schizophrenia risk genes, further work with different prioritization methods and independent samples is needed to confirm these findings. Nevertheless, the identified key candidate genes may have important roles in the pathogenesis of schizophrenia, and further functional characterization of these genes may provide pivotal targets for future therapeutics and

  18. Variation in social relationships relates to song preferences and EGR1 expression in a female songbird.

    Science.gov (United States)

    Schubloom, Hannah E; Woolley, Sarah C

    2016-09-01

    Social experiences can profoundly shape social behavior and the underlying neural circuits. Across species, the formation of enduring social relationships is associated with both neural and behavioral changes. However, it remains unclear how longer-term relationships between individuals influence brain and behavior. Here, we investigated how variation in social relationships relates to variation in female preferences for and neural responses to song in a pair-bonding songbird. We assessed variation in the interactions between individuals in male-female zebra finch pairs and found that female preferences for their mate's song were correlated with the degree of affiliation and amount of socially modulated singing, but not with the frequency of aggressive interactions. Moreover, variation in measures of pair quality and preference correlated with variation in the song-induced expression of EGR1, an immediate early gene related to neural activity and plasticity, in brain regions important for auditory processing and social behavior. For example, females with weaker preferences for their mate's song had greater EGR1 expression in the nucleus Taeniae, the avian homologue of the mammalian medial amygdala, in response to playback of their mate's courtship song. Our data indicate that the quality of social interactions within pairs relates to variation in song preferences and neural responses to ethologically relevant stimuli and lend insight into neural circuits sensitive to social information. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 76: 1029-1040, 2016. © 2016 Wiley Periodicals, Inc.

  19. 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.

  20. Genetic variation and comparison of orchardgrass (Dactylis glomerata L.) cultivars and wild accessions as revealed by SSR markers.

    Science.gov (United States)

    Xie, W G; Lu, X F; Zhang, X Q; Huang, L K; Cheng, L

    2012-02-24

    Orchardgrass is a highly variable, perennial forage grass that is cultivated throughout temperate and subtropical regions of the world. Despite its economic importance, the genetic relationship and distance among and within cultivars are largely unknown but would be of great interest for breeding programs. We investigated the molecular variation and structure of cultivar populations, compared the level of genetic diversity among cultivars (Baoxing, Anba, Bote, and Kaimo), subspecies (Dactylis glomerata ssp Woronowii) and advanced breeding line (YA02-116) to determine whether there is still sufficient genetic diversity within presently used cultivars for future breeding progress in China. Twenty individuals were analyzed from each of six accessions using SSR markers; 114 easily scored bands were generated from 15 SSR primer pairs, with an average of 7.6 alleles per locus. The polymorphic rate was 100% among the 120 individuals, reflecting a high degree of genetic diversity. Among the six accessions, the highest genetic diversity was observed in Kaimo (H = 0.2518; I = 0.3916; P = 87.3%) and 02-116 had a lower level of genetic diversity (H = 0.1806; I = 0.2788; P = 58.73%) compared with other cultivars tested. An of molecular variance revealed a much larger genetic variation within accessions (65%) than between them (35%). This observation suggests that these cultivars have potential for providing rich genetic resource for further breeding program. Furthermore, the study also indicated that Chinese orchardgrass breeding has involved strong selection for adaptation to forage production, which may result in restricted genetic base of orchardgrass cultivar.

  1. Revealing the Relationship between Reading Interest and Critical Thinking Skills through Remap GI and Remap Jigsaw

    Science.gov (United States)

    Zubaidah, Siti; Corebima, Aloysius Duran; Mahanal, Susriyati; Mistianah

    2018-01-01

    The aim of this research was to reveal the relationship between student's reading interest and critical thinking skills through Reading Concept Map Group Investigation (Remap GI) and Reading Concept Map Jigsaw (Remap Jigsaw) learning models. To do so, two science classes from first grade of two Senior High Schools in Malang, Indonesia were…

  2. Intergroup Variation of Social Relationships in Wild Vervet Monkeys: A Dynamic Network Approach.

    Science.gov (United States)

    Borgeaud, Christèle; Sosa, Sebastian; Bshary, Redouan; Sueur, Cédric; van de Waal, Erica

    2016-01-01

    Social network analysis is a powerful tool that enables us to describe and quantify relationships between individuals. So far most of the studies rely on the analyses of various network snapshots, but do not capture changes over time. Here we use a stochastic actor-oriented model (SAOM) to test both the structure and the dynamics of relationships of three groups of wild vervet monkeys. We found that triadic closure (i.e., the friend of a friend is a friend) was significant in all three groups while degree popularity (i.e., the willingness to associate with individuals with high degree of connections) was significant in only two groups (AK, BD). The structure and dynamics of relationships according to the attributes of sex, matrilineand age differed significantly among groups. With respect to the structure, when analyzing the likelihood of bonds according to the different attributes, we found that individuals associate themselves preferably to individuals of the same sex only in two groups (AK, NH), while significant results for attachment to individuals of the same matriline were found also in two groups (BD, NH). With respect to the dynamics, i.e., how quickly relationships are modified, we found in two groups (AK, BD) that females' relationships were more prone to variation than males.' In the BD group, relationships within high-ranking matrilines were less stable than low-ranking ones while in the NH group, juveniles' relationships were also less stable than adults' ones. The intergroup variation indicates that establishing species-specific or even population specific characteristics of social networks for later between-species comparisons will be challenging. Although, such variation could also indicate some methodological issue, we are quite confident that data was collected similarly within the different groups. Our study therefore provides a potential new method to quantify social complexity according to natural demographic variation.

  3. Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops

    Directory of Open Access Journals (Sweden)

    Hongwei Wang

    2017-06-01

    Full Text Available Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges. However, identification of the key genetic components underlying the trait is critical and will serve as the foundation for future crop genetic improvement. Recently, genome-wide association studies have made significant contributions to facilitate the discovery of natural variation contributing to stress tolerance in crops. From these studies, the identified loci can serve as targets for genomic selection or editing to enable the molecular design of new cultivars. Here, we summarize research progress on this issue and focus on the genetic basis of drought tolerance as revealed by genome-wide association studies and quantitative trait loci mapping. Although many favorable loci have been identified, elucidation of their molecular mechanisms contributing to increased stress tolerance still remains a challenge. Thus, continuous efforts are still required to functionally dissect this complex trait through comprehensive approaches, such as system biological studies. It is expected that proper application of the acquired knowledge will enable the development of stress tolerant cultivars; allowing agricultural production to become more sustainable under dynamic environmental conditions.

  4. Influences of spatial and temporal variation on fish-habitat relationships defined by regression quantiles

    Science.gov (United States)

    Dunham, J.B.; Cade, B.S.; Terrell, J.W.

    2002-01-01

    We used regression quantiles to model potentially limiting relationships between the standing crop of cutthroat trout Oncorhynchus clarki and measures of stream channel morphology. Regression quantile models indicated that variation in fish density was inversely related to the width:depth ratio of streams but not to stream width or depth alone. The spatial and temporal stability of model predictions were examined across years and streams, respectively. Variation in fish density with width:depth ratio (10th-90th regression quantiles) modeled for streams sampled in 1993-1997 predicted the variation observed in 1998-1999, indicating similar habitat relationships across years. Both linear and nonlinear models described the limiting relationships well, the latter performing slightly better. Although estimated relationships were transferable in time, results were strongly dependent on the influence of spatial variation in fish density among streams. Density changes with width:depth ratio in a single stream were responsible for the significant (P 80th). This suggests that stream-scale factors other than width:depth ratio play a more direct role in determining population density. Much of the variation in densities of cutthroat trout among streams was attributed to the occurrence of nonnative brook trout Salvelinus fontinalis (a possible competitor) or connectivity to migratory habitats. Regression quantiles can be useful for estimating the effects of limiting factors when ecological responses are highly variable, but our results indicate that spatiotemporal variability in the data should be explicitly considered. In this study, data from individual streams and stream-specific characteristics (e.g., the occurrence of nonnative species and habitat connectivity) strongly affected our interpretation of the relationship between width:depth ratio and fish density.

  5. 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.

  6. 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.

  7. Black-White variations in the lagged reciprocal relationship between religiosity and perceived control.

    Science.gov (United States)

    Oates, Gary

    2013-06-01

    This national longitudinal data-based multi-population LISREL study, the most comprehensive assessment to date of racial variations in the (in)congruity between religiosity and perceived control, gauges variation among Black and White Americans in the lagged reciprocal relationship between religiosity dimensions and mastery. Racial variation in the reciprocal religiosity-perceived control relationship has hitherto gone un-addressed. Prior investigations have also typically utilised cross-sectional samples - often from regional or age-specific populations. The observed public religiosity-mastery relationship over time exhibits signs of mutual reinforcement among Blacks: public religiosity enhances Blacks' subsequent mastery, while prior mastery borderline-significantly enhances their public religiosity. The subjective religiosity-mastery relationship among Whites evinces a marginally countervailing pattern: Subjective religiosity diminishes Whites' mastery, while mastery borderline-significantly enhances their subjective religiosity. The inordinately positive public religiosity-effect on Blacks' mastery notably constitutes solid support for the " resource compensation " perspective on the impact of religiosity on mastery across dominant and subordinate groups.

  8. Genetic variation among isolates of Sarcocystis neurona, the agent of protozoal myeloencephalitis, as revealed by amplified fragment length polymorphism markers.

    Science.gov (United States)

    Elsheikha, H M; Schott, H C; Mansfield, L S

    2006-06-01

    Sarcocystis neurona causes serious neurological disease in horses and other vertebrates in the Americas. Based on epidemiological data, this parasite has recently emerged. Here, the genetic diversity of Sarcocystis neurona was evaluated using the amplified fragment length polymorphism (AFLP) method. Fifteen S. neurona taxa from different regions collected over the last 10 years were used; six isolates were from clinically diseased horses, eight isolates were from wild-caught opossums (Didelphis virginiana), and one isolate was from a cowbird (Molothrus ater). Additionally, four outgroup taxa were also fingerprinted. Nine primer pairs were used to generate AFLP patterns, with a total number of amplified fragments ranging from 30 to 60, depending on the isolate and primers tested. Based on the presence/absence of amplified AFLP fragments and pairwise similarity values, all the S. neurona isolates tested were clustered in one monophyletic group. No significant correlation could be found between genomic similarity and host origin of the S. neurona isolates. AFLP revealed significant intraspecific genetic variations, and S. neurona appeared as a highly variable species. Furthermore, linkage disequilibrium analysis suggested that S. neurona populations within Michigan have an intermediate type of population structure that includes characteristics of both clonal and panamictic population structures. AFLP is a reliable molecular technique that has provided one of the most informative approaches to ascertain phylogenetic relationships in S. neurona and its closest relatives, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis, which may be applicable to other related protozoal species.

  9. 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.

  10. Cross-site comparisons of concentration-discharge relationships reveal climate-driven chemostatic set points

    Science.gov (United States)

    Godsey, S.; Kirchner, J. W.

    2017-12-01

    Streamflow solute concentrations often vary predictably with flows, providing insight into processes controlling solute generation and export. Previous work by the authors showed that log-transformed concentration-discharge relationships of weathering-derived solutes in 59 headwater catchments had relatively low slopes, implying that these watersheds behaved almost like chemostats. That is, their rates of solute production and/or mobilization were nearly proportional to water fluxes, on both event and inter-annual time scales. Here we re-examine these findings using data from roughly 1000 catchments, ranging from ˜10 to >1,000,000 sq. km in drainage area, and spanning a wide range of lithologic and climatic settings.Concentration-discharge relationships among this much larger set of much larger catchments are broadly consistent with the chemostatic behavior described above. However, site-to-site variations in mean concentrations among these catchments are negatively correlated with long-term average precipitation and discharge, suggesting dilution of stream concentrations under long-term leaching of the critical zone. Thus, on event and inter-annual time scales, stream solute concentrations are chemostatically buffered by groundwater storage and fast chemical reactions (such as ion exchange), but on much longer time scales, the catchment's chemostatic "set point" is determined by climatically driven critical zone evolution. We present examples illustrating short-term and long-term controls on water quality consistent with variations in weather and climate, and discuss their implications.

  11. 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

  12. Possible relationship between the Earth's rotation variations and geomagnetic field reversals over the past 510 Myr

    OpenAIRE

    Pacca, Igor G.; Frigo, Everton; Hartmann, Gelvam A.

    2015-01-01

    The Earth's rotation can change as a result of several internal and external processes, each of which is at a different timescale. Here, we present some possible connections between the Earth's rotation variations and the geomagnetic reversal frequency rates over the past 120 Myr. In addition, we show the possible relationship between the geomagnetic field reversal frequency and the δ18O oscillations. Because the latter reflects the glacial and interglacial periods, we hypothesize that it can...

  13. Genetic variation in Aquaporin-4 moderates the relationship between sleep and brain Aβ-amyloid burden.

    Science.gov (United States)

    Rainey-Smith, Stephanie R; Mazzucchelli, Gavin N; Villemagne, Victor L; Brown, Belinda M; Porter, Tenielle; Weinborn, Michael; Bucks, Romola S; Milicic, Lidija; Sohrabi, Hamid R; Taddei, Kevin; Ames, David; Maruff, Paul; Masters, Colin L; Rowe, Christopher C; Salvado, Olivier; Martins, Ralph N; Laws, Simon M

    2018-02-26

    The glymphatic system is postulated to be a mechanism of brain Aβ-amyloid clearance and to be most effective during sleep. Ablation of the astrocytic end-feet expressed water-channel protein, Aquaporin-4, in mice, results in impairment of this clearance mechanism and increased brain Aβ-amyloid deposition, suggesting that Aquaporin-4 plays a pivotal role in glymphatic function. Currently there is a paucity of literature regarding the impact of AQP4 genetic variation on sleep, brain Aβ-amyloid burden and their relationship to each other in humans. To address this a cross-sectional observational study was undertaken in cognitively normal older adults from the Australian Imaging, Biomarkers and Lifestyle (AIBL) study. Genetic variants in AQP4 were investigated with respect to self-reported Pittsburgh Sleep Quality Index sleep parameters, positron emission tomography derived brain Aβ-amyloid burden and whether these genetic variants moderated the sleep-Aβ-amyloid burden relationship. One AQP4 variant, rs72878776, was associated with poorer overall sleep quality, while several SNPs moderated the effect of sleep latency (rs491148, rs9951307, rs7135406, rs3875089, rs151246) and duration (rs72878776, rs491148 and rs2339214) on brain Aβ-amyloid burden. This study suggests that AQP4 genetic variation moderates the relationship between sleep and brain Aβ-amyloid burden, which adds weight to the proposed glymphatic system being a potential Aβ-amyloid clearance mechanism and suggests that AQP4 genetic variation may impair this function. Further, AQP4 genetic variation should be considered when interpreting sleep-Aβ relationships.

  14. 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.

  15. 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.

  16. 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

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

    NARCIS (Netherlands)

    Cardol, M.; Dijk, L. van; Bosch, W.J.H.M. van den; Spreeuwenberg, P.; Bakker, D.H. de; Groenewegen, P.P.

    2007-01-01

    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

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

    NARCIS (Netherlands)

    Cardol, Mieke; Dijk, Liset van; Bosch, Wil J.H.M. van den; Spreeuwenberg, Peter; Bakker, Dinny H. de; Groenewegen, Peter P.

    2007-01-01

    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

  19. Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

    Science.gov (United States)

    Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

    2018-01-01

    Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships

  20. 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.

  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. How Facebook might reveal users' attitudes toward work and relationships with coworkers.

    Science.gov (United States)

    Chou, Hui-Tzu Grace; Hammond, Ron J; Johnson, Roberta

    2013-02-01

    With the spread of Facebook among people in many countries, some companies have started using applicants' Facebook profiles as a criterion of personnel selection, in an effort to identify good workers among job applicants. However, how using Facebook is connected to individuals' relationships with coworkers and work attitudes is unclear. The purpose of this study was to examine the relationship between using Facebook, relationships with coworkers, and some attitudes toward the current job. Undergraduate students at a state university in Utah were randomly chosen to participate in an online survey between April and May 2012. The results of a multivariate analysis, based on 516 currently employed respondents, revealed several findings. First, those more involved in using Facebook--often assumed as more people-oriented individuals--do not have better relationships with their coworkers than their counterparts. Second, those with more Facebook friends care less about their work performance than those with fewer Facebook friends. Third, those frequently update their Facebook profile like their current job less, and are more likely to think about changing their jobs, compared with those updating their Facebook profile less often. Although Facebook friendship usually begins with offline friendship, this research found that offline interaction with friends has a different impact on work attitudes than online interaction: Those spending more time with friends offline like their jobs more and are less likely to think about changing jobs. Implications are discussed.

  3. Anglo-Saxon animal husbandry techniques revealed though isotope and chemical variations in cattle teeth

    International Nuclear Information System (INIS)

    Evans, J.A.; Tatham, S.; Chenery, S.R.; Chenery, C.A.

    2007-01-01

    The Sr concentration and isotope composition of tooth enamel from domesticated animals from two neighbouring Anglo-Saxon settlements, at Empingham (6-7th century) and Ketton (10-12th century) in Rutland, central England, are compared both with each other, and with associated human populations. Data from the Empingham II site form discrete fields in Sr concentration and isotope composition space for cattle, pig and sheep with a partial overlap of the human and pig fields. By contrast there is significant overlap in all the animal and human data fields from the Ketton site. The differences in data distribution between the two sites are attributed to animal husbandry techniques, as the surface geology of the two areas is very similar, implying geological factors are an unlikely cause of the difference. It is suggested that the grazing and feeding patterns of animals at the Empingham II site were controlled and restricted, whereas at the Ketton site the animals grazed and foraged freely over a common area. Strontium isotope variation within cattle molars from the two settlements show marked differences that reflect the nature of their feeding and rearing. The enamel from a cattle molar from the Empingham II site has a well-defined, systematic variation of Sr isotope composition with Sr concentration, whereas no such patterns exist in a comparable cattle molar from Ketton. Chemical and O isotope variations in the cattle tooth from Empingham II show sympathetic variation of Sr and Ba concentrations with Sr isotope composition from cusp to cervix. The cusp has higher Sr and Ba concentrations log (Sr/Ca) ratio of -3.1 and 87 Sr/ 86 Sr ratio of 0.71151 where as the cervical region of the enamel has log (Sr/Ca) = -3.3 and 87 Sr/ 86 Sr = 0.71061

  4. Anglo-Saxon animal husbandry techniques revealed though isotope and chemical variations in cattle teeth

    Energy Technology Data Exchange (ETDEWEB)

    Evans, J.A. [NERC Isotope Geosciences Laboratory, BGS, Keyworth, Nottingham NG12 5GG (United Kingdom)], E-mail: je@nigl.nerc.ac.uk; Tatham, S. [School of Archaeology and Ancient History, University of Leicester, Leicester LE1 7RH (United Kingdom); Chenery, S.R. [British Geological Survey, Keyworth, Nottingham NG12 5GG (United Kingdom); Chenery, C.A. [NERC Isotope Geosciences Laboratory, BGS, Keyworth, Nottingham NG12 5GG (United Kingdom)

    2007-09-15

    The Sr concentration and isotope composition of tooth enamel from domesticated animals from two neighbouring Anglo-Saxon settlements, at Empingham (6-7th century) and Ketton (10-12th century) in Rutland, central England, are compared both with each other, and with associated human populations. Data from the Empingham II site form discrete fields in Sr concentration and isotope composition space for cattle, pig and sheep with a partial overlap of the human and pig fields. By contrast there is significant overlap in all the animal and human data fields from the Ketton site. The differences in data distribution between the two sites are attributed to animal husbandry techniques, as the surface geology of the two areas is very similar, implying geological factors are an unlikely cause of the difference. It is suggested that the grazing and feeding patterns of animals at the Empingham II site were controlled and restricted, whereas at the Ketton site the animals grazed and foraged freely over a common area. Strontium isotope variation within cattle molars from the two settlements show marked differences that reflect the nature of their feeding and rearing. The enamel from a cattle molar from the Empingham II site has a well-defined, systematic variation of Sr isotope composition with Sr concentration, whereas no such patterns exist in a comparable cattle molar from Ketton. Chemical and O isotope variations in the cattle tooth from Empingham II show sympathetic variation of Sr and Ba concentrations with Sr isotope composition from cusp to cervix. The cusp has higher Sr and Ba concentrations log (Sr/Ca) ratio of -3.1 and {sup 87}Sr/{sup 86}Sr ratio of 0.71151 where as the cervical region of the enamel has log (Sr/Ca) = -3.3 and {sup 87}Sr/{sup 86}Sr = 0.71061.

  5. Developmental constraints revealed by co-variation within and among molar rows in two murine rodents.

    Science.gov (United States)

    Renaud, Sabrina; Pantalacci, Sophie; Quéré, Jean-Pierre; Laudet, Vincent; Auffray, Jean-Christophe

    2009-01-01

    Morphological integration corresponds to interdependency between characters that can arise from several causes. Proximal causes of integration include that different phenotypic features may share common genetic sets and/or interact during their development. Ultimate causes may be the prolonged effect of selection favoring integration of functionally interacting characters, achieved by the molding of these proximal causes. Strong and direct interactions among successive teeth of a molar row are predicted by genetic and developmental evidences. Functional constraints related to occlusion, however, should have selected more strongly for a morphological integration of occluding teeth and a corresponding evolution of the underlying developmental and genetic pathways. To investigate how these predictions match the patterns of phenotypic integration, we studied the co-variation among the six molars of the murine molar row, focusing on two populations of house mice (Mus musculus domesticus) and wood mice (Apodemus sylvaticus). The size and shape of the three upper and lower molars were quantified and compared. Our results evidenced similar patterns in both species, size being more integrated than shape among all the teeth, and both size and shape co-varying strongly between adjacent teeth, but also between occluding teeth. Strong co-variation within each molar row is in agreement with developmental models showing a cascade influence of the first molar on the subsequent molars. In contrast, the strong co-variation between molars of the occluding tooth rows confirms that functional constraints molded patterns of integration and probably the underlying developmental pathways despite the low level of direct developmental interactions occurring among molar rows. These patterns of co-variation are furthermore conserved between the house mouse and the wood mouse that diverged >10 Ma, suggesting that they may constitute long-running constraints to the diversification of the murine

  6. 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

  7. 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.

  8. 1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    International Nuclear Information System (INIS)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D.

    2011-01-01

    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 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.

  9. {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.

  10. Arabian Sea GEOSECS stations revisited: Tracer-depth profiles reveal temporal variations?

    International Nuclear Information System (INIS)

    Mulsow, S.; Povinec, P.P.; Somayajulu, B.L.K.

    2002-01-01

    In March-April 1998, the Physical Research Laboratory and the Regional Research Laboratory (Ahmedabad, India) together with the IAEA Marine Environment Laboratory, Monaco, participated in the research mission to visit GEOSECS (Geochemical Ocean Sections Study) stations in the Arabian Sea. The main objective was to reoccupy these stations which were sampled in the early seventies to observe possible time variations in trace behaviour in this region. It is generally accepted that both natural (climate variations) and anthropogenic (greenhouse effect) changes can cause modifications of the oceanic characteristics and properties of deep waters on yearly and decadal scales. For long time-scales (100 to 1000 years) one needs to look at the sediments where these changes are subtly recorded. Tracers such as 14 C and 3 H (deep waters) and 228 Ra surface waters are useful markers of water circulation patterns and changes. Also man-made radiotracers such as 90 Sr, 137 Cs, 99 Tc, 238 Pu, 239 , 240 Pu and 241 Am, can give information on air-sea exchange as well as penetration (vertical change) rates in the open ocean [2]. We visited GEOSECS stations 415 to 419. In each station, CTD profiles, 3 H, 14 C, 90 Sr, 137 Cs, Pu and Am profiles, nutrients, Be, TOC and oxygen were determined from surface to bottom. Also uranium and trace elements were sampled in function of the oxygen minimum zone. In this paper we report the findings on the physical properties as well as the variations in water circulation patterns and also vertical exchange rates in the Arabian Sea. PSU profiles collected in this mission compared with those PSU profiles measured in 1974 (GEOSECS) showed marked differences in those stations located in the southeast part of the Arabian Sea. In contrast, those located more towards the north (415-416) showed little temporal variation. We think these changes may be real given that the PSU values at depth are comparable and reflect the presence of deep Antarctic bottom

  11. 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...

  12. Seismic tomography with P and S data reveals lateral variations in the rigidity of slabs

    NARCIS (Netherlands)

    Widiyantoro, S.; Kennett, B.L.N.; Hilst, R.D. van der

    1999-01-01

    Regional seismic tomography of the northwest Pacific island arcs using P- and S-wave arrival time data with similar path coverage reveals an oceanic lithospheric slab deflected in the mantle transition zone beneath the Izu Bonin region in good agreement with the results of earlier tomographic and

  13. 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

  14. 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.

  15. 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

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

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    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. Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers.

    Science.gov (United States)

    Wang, Hai-Fei; Zong, Xu-Xiao; Guan, Jian-Ping; Yang, Tao; Sun, Xue-Lian; Ma, Yu; Redden, Robert

    2012-03-01

    Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit.

  18. Environmental variation shifts the relationship between trees and scatterhoarders along the continuum from mutualism to antagonism.

    Science.gov (United States)

    Sawaya, Gina M; Goldberg, Adam S; Steele, Michael A; Dalgleish, Harmony J

    2018-05-01

    The conditional mutualism between scatterhoarders and trees varies on a continuum from mutualism to antagonism and can change across time and space, and among species. We examined 4 tree species (red oak [Quercus rubra], white oak [Quercus alba], American chestnut [Castanea dentata] and hybrid chestnut [C. dentata × Castanea mollissima) across 5 sites and 3 years to quantify the variability in this conditional mutualism. We used a published model to compare the rates of seed emergence with and without burial to the probability that seeds will be cached and left uneaten by scatterhoarders to quantify variation in the conditional mutualism that can be explained by environmental variation among sites, years, species, and seed provenance within species. All species tested had increased emergence when buried. However, comparing benefits of burial to the probability of caching by scatterhoarders indicated a mutualism in red oak, while white oak was nearly always antagonistic. Chestnut was variable around the boundary between mutualism and antagonism, indicating a high degree of context dependence in the relationship with scatterhoarders. We found that different seed provenances did not vary in their potential for mutualism. Temperature did not explain microsite differences in seed emergence in any of the species tested. In hybrid chestnut only, emergence on the surface declined with soil moisture in the fall. By quantifying the variation in the conditional mutualism that was not caused by changes in scatterhoarder behavior, we show that environmental conditions and seed traits are an important and underappreciated component of the variation in the relationship between trees and scatterhoarders. © 2018 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  19. 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.

  20. Complex pattern of variation in neurocranial ontogeny revealed by CT-scanning.

    Science.gov (United States)

    Anzelmo, Marisol; Ventrice, Fernando; Kelmansky, Diana; Sardi, Marina

    2018-05-01

    The neurocranium of hominid species has been largely studied with reference to the midsagittal plane, with variations being attributed to brain evolution. By contrast, there is limited information on variation in non-midsagittal regions, which are the points of insertion of muscles and bony structures related to mastication. This work aims to analyze ontogenetic changes and sexual dimorphism (SD) in midsagittal and non-midsagittal neurocranial structures from a contemporary human sample comprising 138 computed tomography (CT) cranial images of individuals ranging from infants to adults. Morphology of the vault and the base was assessed by registering landmarks and semilandmarks, which were analyzed by geometric morphometrics, and the endocranial volume (EV). The results of regressions and Kruskal-Wallis test indicate that the major size and shape changes in both midsagittal and non-midsagittal regions occur during infancy and juvenility; shape changes are also associated with an increase in EV. The size of the midsagittal vault, the shape of the non-midsagittal vault and the size of the base show an extension of ontogenetic trajectories. Sexes show similar changes in shape but different changes in size. We conclude that brain growth appears to be an important factor influencing the morphology of the neurocranium, at least during infancy and childhood. Subsequent changes may be attributed to osteogenic activity and the differential growth of the brain lobes. Masticatory-related bony structures and muscles may not be strong enough factors to induce independent modifications in non-midsagittal structures. The small influence of the cranial muscles would explain why the human neurocranium is a quite integrated structure.

  1. 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.

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

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    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.

  3. Long-term changes in abundances of Sonoran Desert lizards reveal complex responses to climatic variation.

    Science.gov (United States)

    Flesch, Aaron D; Rosen, Philip C; Holm, Peter

    2017-12-01

    Understanding how climatic variation affects animal populations and communities is essential for addressing threats posed by climate change, especially in systems where impacts are projected to be high. We evaluated abundance dynamics of five common species of diurnal lizards over 25 years in a Sonoran Desert transition zone where precipitation decreased and temperature increased across time, and assessed hypotheses for the influence of climatic flux on spatiotemporal variation in abundances. We repeatedly surveyed lizards in spring and summer of each year at up to 32 sites, and used hierarchical mixture models to estimate detection probabilities, abundances, and population growth rates. Among terrestrial species, abundances of a short-lived, winter-spring breeder increased markedly by an estimated 237%-285% across time, while two larger spring-summer breeders with higher thermal preferences declined by up to 64%. Abundances of two arboreal species that occupy shaded and thus sheltered microhabitats fluctuated but did not decline systematically. Abundances of all species increased with precipitation at short lag times (1-1.5 years) likely due to enhanced food availability, but often declined after periods of high precipitation at longer lag times (2-4 years) likely due to predation and other biotic pressures. Although rising maximum daily temperatures (T max ) are expected to drive global declines of lizards, associations with T max were variable and weak for most species. Instead, abundances of all species declined with rising daily minimum temperatures, suggesting degradation of cool refugia imposed widespread metabolic or other costs. Our results suggest climate warming and drying are having major impacts on lizard communities by driving declines in species with traits that augment exposure to abiotic extremes and by modifying species interactions. The complexity of patterns we report indicates that evaluating and responding to the influence of climate change

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

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    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.

  5. 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 study; n = 21 and 19, respectively) and triple brooding has never been observed. Other novel life history on Midway included early cessation of parental care to renest. Altered life history on Midway is likely related to better feeding conditions and low population density compared with Laysan. An especially intriguing possibility is that the phenotypic plasticity observed represents exposure of hidden reaction norms evolved when the species inhabited a range of environments, but several alternative explanations exist. Future reintroductions of this species may provide opportunities to test hypotheses about mechanisms underlying phenotypic plasticity.

  6. 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.

  7. Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci.

    Science.gov (United States)

    Korall, Petra; Pryer, Kathleen M; Metzgar, Jordan S; Schneider, Harald; Conant, David S

    2006-06-01

    Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed.

  8. Variations in the Phytophthora infestans Population in Nepal as Revealed by Nuclear and Mitochondrial DNA Polymorphisms.

    Science.gov (United States)

    Ghimire, S R; Hyde, K D; Hodgkiss, I J; Shaw, D S; Liew, E C Y

    2003-02-01

    ABSTRACT Phytophthora infestans isolates collected from potato and tomato crops from various parts of Nepal during the 1999 and 2000 crop seasons were characterized for nuclear and mitochondrial DNA polymorphisms using restriction fragment length polymorphism markers. The nuclear DNA probe RG57 detected 11 multilocus genotypes among 280 isolates. Three genotypes were detected 21 times or more, constituting 94% of the total population, whereas frequencies of other genotypes ranged from 0.004 to 0.014. The overall genotypic diversity as estimated by the Gleason index was 1.78. Most of the overall diversity was present at the highest level (i.e., interregional, 46%), indicating limited gene flow among regions. Cluster analysis of multilocus genotypes derived from RG57 and mating type data for Nepalese isolates and representative isolates worldwide showed Nepalese isolates grouping into four clusters. Characterization of 67 isolates for mitochondrial DNA polymorphisms revealed the presence of two mt-haplotypes, Ia and Ib with the proportions of 0.88 and 0.12, respectively. Polymorphisms in nuclear and mitochondrial DNA revealed a moderate level of diversity in this population. Genotype NP3 had an identical RG57 fingerprint to US1 and had mt-haplotype Ib, confirming the presence of an old population in Nepal. Most of the genotypes had a different RG57 fingerprint than that of US1 and mt-haplotype Ia, the common characteristics of new populations. The presence of a new population at high proportions in Nepal was consistent with the global trend of mt-haplotype distribution, and suggests the displacement of old populations. This study indicates at least three possible introductions of P. infestans to Nepal.

  9. Expression of cytokeratins in odontogenic jaw cysts: monoclonal antibodies reveal distinct variation between different cyst types.

    Science.gov (United States)

    Hormia, M; Ylipaavalniemi, P; Nagle, R B; Virtanen, I

    1987-08-01

    Immunostaining with monoclonal antibodies was used to study and compare the cytokeratin content of odontogenic cysts and normal gingival epithelium. Two monoclonal antibodies, PKK2 and KA1, stained the whole epithelium in all cyst samples. In gingiva, PKK2 gave a suprabasal staining and KA1 reacted with all epithelial cell layers. Antibodies PKK1, KM 4.62 and KS 8.12 gave a heterogeneous staining in follicular and radicular cysts. In keratocysts and in gingiva PKK1 and KM 4.62 reacted mainly with basal cells and KS 8.12 gave a suprabasal staining. Antibodies reacting with the simple epithelial cytokeratin polypeptide No. 18 (PKK3, KS 18.18) recognized in gingiva only solitary cells compatible with Merkel cells. In a case of follicular ameloblastoma a distinct staining of tumor epithelium was revealed with these antibodies. In 2 follicular cysts, but not in other cyst types, a layer of cytokeratin 18-positive cells was revealed. KA5 and KK 8.60 antibodies, reacting exclusively with keratinizing epithelia, including normal gingiva, gave no reaction in radicular cysts, keratocysts and ameloblastoma. Two of the follicular cysts, were negative for PKK3 and KS 18.18, but reacted strongly with KA5 and KK 8.60. The present results show that odontogenic jaw cysts have distinct differences in their cytokeratin content. With the exception of some follicular cysts, they lack signs of keratinizing epithelial differentiation. Only follicular cysts appear to share with some types of ameloblastoma the expression of cytokeratin polypeptide No. 18.

  10. Relationship of biomechanical factors to baseball pitching velocity: within pitcher variation.

    Science.gov (United States)

    Stodden, David F; Fleisig, Glenn S; McLean, Scott P; Andrews, James R

    2005-02-01

    To reach the level of elite, most baseball pitchers need to consistently produce high ball velocity but avoid high joint loads at the shoulder and elbow that may lead to injury. This study examined the relationship between fastball velocity and variations in throwing mechanics within 19 baseball pitchers who were analyzed via 3-D high-speed motion analysis. Inclusion in the study required each one to demonstrate a variation in velocity of at least 1.8 m/s (range 1.8-3.5 m/s) during 6 to 10 fastball pitch trials. Three mixed model analyses were performed to assess the independent effects of 7 kinetic, 11 temporal, and 12 kinematic parameters on pitched ball velocity. Results indicated that elbow flexion torque, shoulder proximal force, and elbow proximal force were the only three kinetic parameters significantly associated with increased ball velocity. Two temporal parameters (increased time to max shoulder horizontal adduction and decreased time to max shoulder internal rotation) and three kinematic parameters (decreased shoulder horizontal adduction at foot contact, decreased shoulder abduction during acceleration, and increased trunk tilt forward at release) were significantly related to increased ball velocity. These results point to variations in an individual's throwing mechanics that relate to pitched ball velocity, and also suggest that pitchers should focus on consistent mechanics to produce consistently high fastball velocities. In addition, pitchers should strengthen shoulder and elbow musculature that resist distraction as well as improve trunk strength and flexibility to maximize pitching velocity and help prevent injury.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. REVEALING SPATIAL VARIATION AND CORRELATION OF URBAN TRAVELS FROM BIG TRAJECTORY DATA

    Directory of Open Access Journals (Sweden)

    X. Li

    2017-09-01

    Full Text Available 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.

  18. Temporal variation of streamflow, sediment load and their relationship in the Yellow River basin, China.

    Directory of Open Access Journals (Sweden)

    Guangju Zhao

    Full Text Available Variation of streamflow and sediment load in the Yellow River basin has received considerable attention due to its drastic reduction during the past several decades. This paper presents a detailed investigation on the changes of streamflow and sediment load from 1952 to 2011 using monthly observations at four gauging stations along the Yellow River. The results show significant decreasing trends for both streamflow and sediment load at all four gauging stations over the past 60 years. The wavelet transform demonstrated discontinuous periodicities from 1969 to 1973 and after 1986 due to the construction of large reservoirs and implementation of numerous soil and water conservations practices. The sediment rating curves with the power-law function was applied to investigate the relationship between discharge and sediment load. The results indicate distinct variations of the relationship between streamflow and sediment and implied significant hydro-morphological changes within different periods. The reducing sediment supply from the source region and the increased erosive power of the river are detected at Lanzhou station, while the decrease of the transport capacity at Toudaoguai is caused by severe siltation. Significant changes in the relationship between streamflow and sediment load are found at Huayuankou and Gaocun stations, which are largely induced by evident sediment income and trapping effects of large reservoirs. It is estimated that numerous reservoirs have strongly altered the regime and magnitude of streamflow and trapped large amount of sediment, leading to severe siltation and evident reduction of their total volumes. A decrease in precipitation, incoming water from the upper reaches, soil and water conservation measures as well as water consumption contribute most to the significant reduction of streamflow. The decrease of sediment load mainly resulted from various soil and water conservation measures and trapping in reservoirs

  19. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars.

    Science.gov (United States)

    Lin, Hong; Rao, Jun; Shi, Jianxin; Hu, Chaoyang; Cheng, Fang; Wilson, Zoe A; Zhang, Dabing; Quan, Sheng

    2014-09-01

    Soybean [Glycine max (L.) Merr.] is one of the world's major crops, and soybean seeds are a rich and important resource for proteins and oils. While "omics" studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especially in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield. © 2014 Institute of Botany, Chinese Academy of Sciences.

  20. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars

    Institute of Scientific and Technical Information of China (English)

    Hong Lin; Jun Rao; Jianxin Shi; Chaoyang Hu; Fang Cheng; Zoe AWilson; Dabing Zhang; Sheng Quan

    2014-01-01

    Soybean [Glycine max (L.) Merr.] is one of the world’s major crops, and soybean seeds are a rich and important resource for proteins and oils. While “omics”studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especial y in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetical y related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

  1. Spatiotemporal mechanical variation reveals critical role for rho kinase during primitive streak morphogenesis.

    Science.gov (United States)

    Henkels, Julia; Oh, Jaeho; Xu, Wenwei; Owen, Drew; Sulchek, Todd; Zamir, Evan

    2013-02-01

    Large-scale morphogenetic movements during early embryo development are driven by complex changes in biochemical and biophysical factors. Current models for amniote primitive streak morphogenesis and gastrulation take into account numerous genetic pathways but largely ignore the role of mechanical forces. Here, we used atomic force microscopy (AFM) to obtain for the first time precise biomechanical properties of the early avian embryo. Our data reveal that the primitive streak is significantly stiffer than neighboring regions of the epiblast, and that it is stiffer than the pre-primitive streak epiblast. To test our hypothesis that these changes in mechanical properties are due to a localized increase of actomyosin contractility, we inhibited actomyosin contractility via the Rho kinase (ROCK) pathway using the small-molecule inhibitor Y-27632. Our results using several different assays show the following: (1) primitive streak formation was blocked; (2) the time-dependent increase in primitive streak stiffness was abolished; and (3) convergence of epiblast cells to the midline was inhibited. Taken together, our data suggest that actomyosin contractility is necessary for primitive streak morphogenesis, and specifically, ROCK plays a critical role. To better understand the underlying mechanisms of this fundamental process, future models should account for the findings presented in this study.

  2. 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

    Background: The DHFR negative CHO DXB11 cell line (also known as DUX-B11 and DUKX) was historically the first CHO cell line to be used for large scale production of heterologous proteins and is still used for production of a number of complex proteins.  Results: Here we present the genomic sequence...... of the CHO DXB11 genome sequenced to a depth of 33x. Overall a significant genomic drift was seen favoring GC -> AT point mutations in line with the chemical mutagenesis strategy used for generation of the cell line. The sequencing depth for each gene in the genome revealed distinct peaks at sequencing...... 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...

  3. 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

  4. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

    Directory of Open Access Journals (Sweden)

    McGuire Patrick E

    2010-12-01

    chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

  5. 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.

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

    Science.gov (United States)

    Jiang, Yanliang; Zhang, Songhao; Xu, Jian; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A; Sun, Xiaowen; Xu, Peng

    2014-01-01

    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.

  7. 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.

  8. 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

  9. Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study.

    Science.gov (United States)

    Wang, Quanxiu; Xie, Weibo; Xing, Hongkun; Yan, Ju; Meng, Xiangzhou; Li, Xinglei; Fu, Xiangkui; Xu, Jiuyue; Lian, Xingming; Yu, Sibin; Xing, Yongzhong; Wang, Gongwei

    2015-06-01

    Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

  10. 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.

  11. 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, 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 PLA 2 s 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 PLA 2 s. 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

  12. Biometrical studies upon hominoid teeth: the coefficient of variation, sexual dimorphism and questions of phylogenetic relationship.

    Science.gov (United States)

    Blumenberg, B

    1985-01-01

    Sexual dimorphism as a function of variation in hominoid tooth metrics has been investigated for four groups of taxa: Recent great apes (two subfamilies), Dryopiths (one subfamily), Ramapiths (one subfamily) and hominids (one family). Gorilla, and to a lesser extent Pan, appear characterized by very high levels of sexual dimorphism and meet several criteria for statistical outliers. Recent great apes are the only group exhibiting consistently high levels of sexual dimorphism. Ramapiths are the only group characterized by low levels of sexual dimorphism and their relative canine length is most similar to Dryopiths. Both Dryopiths and hominids contain taxa with low and intermediate levels of sexual dimorphism. The Gingerich and Shoeninger hypothesis relating coefficients of variation to occlusal complexity is supported. Non-parametric statistics suggest that homogeneity of coefficient of variation profiles over most of the tooth row is characteristic of only the Dryopiths and a composite data set composed of the Dryopith plus Ramapith tooth measurements. Oxnard's model for the multifactorial basis of multiple sexual dimorphisms is also supported. The Dryopith and hominid patterns of sexual dimorphism are similar, an observation that suggests phylogenetic relationship. At the taxonomic level of subfamily or family, sexual dimorphism is a character of cladistic usefulness and possible phylogenetic valence. Assuming that breeding system and sexual dimorphism are functional correlates as many workers suggest, then Ramapithecus sp. China, Sivapithecus indicus and possibly Australopithecus boisei are good candidates for having possessed monogamous breeding/social structures. All Dryopith taxa, S. sivalensis, Sivapithecus sp. China, A. afarensis, Homo habilis and H. erectus emerge as the best candidates for having possessed a polygynous breeding/social structure. No biometrical affinities of Ramapiths with hominids can be demonstrated and some phylogenetic relationship with

  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. Investigating output and energy variations and their relationship to delivery QA results using Statistical Process Control for helical tomotherapy.

    Science.gov (United States)

    Binny, Diana; Mezzenga, Emilio; Lancaster, Craig M; Trapp, Jamie V; Kairn, Tanya; Crowe, Scott B

    2017-06-01

    The aims of this study were to investigate machine beam parameters using the TomoTherapy quality assurance (TQA) tool, establish a correlation to patient delivery quality assurance results and to evaluate the relationship between energy variations detected using different TQA modules. TQA daily measurement results from two treatment machines for periods of up to 4years were acquired. Analyses of beam quality, helical and static output variations were made. Variations from planned dose were also analysed using Statistical Process Control (SPC) technique and their relationship to output trends were studied. Energy variations appeared to be one of the contributing factors to delivery output dose seen in the analysis. Ion chamber measurements were reliable indicators of energy and output variations and were linear with patient dose verifications. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  15. Metabolite Profiling of Peppers of Various Colors Reveals Relationships Between Tocopherol, Carotenoid, and Phytosterol Content.

    Science.gov (United States)

    Kim, Tae Jin; Choi, Jaehyuk; Kim, Kil Won; Ahn, Soon Kil; Ha, Sun-Hwa; Choi, Yongsoo; Park, Nam Il; Kim, Jae Kwang

    2017-12-01

    Peppers are widely consumed in Korea; the varietal development of peppers with increased content of beneficial plant metabolites is, therefore, of considerable interest. This requires a comprehensive understanding of the metabolic profile of pepper plants and the factors affecting this profile. To this end, we determined the content of various metabolites, such as hydrophilic and lipophilic compounds, phenolic acids, carotenoids, and capsaicinoids in peppers of various colors (green, red, pale green, and violet peppers) and in a high-pungency (green) pepper. We also performed principal component analysis (PCA), Pearson's correlation analysis, and hierarchical clustering analysis (HCA) to determine the relationships among these metabolites in peppers. PCA results indicated no significant variances among the 3 sample replicates. The HCA showed correlations between the metabolites resulting from common or closely linked biosynthesis pathways. Our results showed that carotenoids correlated positively with tocopherols and negatively with phytosterols; our findings also indicated a close relationship between the methylerythritol 4-phosphate and mevalonic acid biosynthesis pathways, providing evidence in favor of an earlier hypothesis regarding crosstalk across the chloroplast membrane. We, thus, demonstrate that metabolic profiling combined with multivariate analysis is a useful tool for analyzing metabolic networks. A total of 71 metabolites were measured in 5 peppers of different colors. The metabolic profiling with multivariate analysis revealed that tocopherol content had a positive correlation with the carotenoid content and a negative correlation with the phytosterol content. The results of this study may help in breeding programs to produce new germplasm with enhanced nutritional quality. © 2017 Institute of Food Technologists®.

  16. The Radial Variation of the Solar Wind Temperature-Speed Relationship

    Science.gov (United States)

    Elliott, H. A.; McComas, D. J.

    2010-12-01

    Generally, the solar wind temperature (T) and speed (V) are well correlated except in Interplanetary Coronal Mass Ejections where this correlation breaks down. We have shown that at 1 AU the speed-temperature relationship is often well represented by a linear fit for a speed range spanning both the slow and fast wind. By examining all of the ACE and OMNI measurements, we found that when coronal holes are large the fast wind can have a different T-V relationship than the slow wind. The best example of this was in 2003 when there was a very large and long-lived outward polarity coronal hole at low latitudes. The long-lived nature of the hole made it possible to clearly distinguish that large holes can have a different T-V relationship. We found it to be rare that holes are large enough and last long enough to have enough data points to clearly demonstrate this effect. In this study we compare the 2003 coronal hole observations from ACE with the Ulysses polar coronal hole measurements. In an even earlier ACE study we found that both the compressions and rarefactions curves are linear, but the compression curve is shifted to higher temperatures. In this presentation we use Helios, Ulysses, and ACE measurements to examine how the T-V relationship varies with distance. The dynamic evolution of the solar wind parameters is revealed when we first separate compressions and rarefactions and then determine the radial profiles of the solar wind parameters. We find that T-V relationship varies with distance and in particular beyond 3 AU the differences between the compressions and rarefactions are quite important and at such distances a simple linear fit does not represent the T-V distribution very well.

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

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    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.

  18. On the Relationship between Variational Level Set-Based and SOM-Based Active Contours

    Science.gov (United States)

    Abdelsamea, Mohammed M.; Gnecco, Giorgio; Gaber, Mohamed Medhat; Elyan, Eyad

    2015-01-01

    Most Active Contour Models (ACMs) deal with the image segmentation problem as a functional optimization problem, as they work on dividing an image into several regions by optimizing a suitable functional. Among ACMs, variational level set methods have been used to build an active contour with the aim of modeling arbitrarily complex shapes. Moreover, they can handle also topological changes of the contours. Self-Organizing Maps (SOMs) have attracted the attention of many computer vision scientists, particularly in modeling an active contour based on the idea of utilizing the prototypes (weights) of a SOM to control the evolution of the contour. SOM-based models have been proposed in general with the aim of exploiting the specific ability of SOMs to learn the edge-map information via their topology preservation property and overcoming some drawbacks of other ACMs, such as trapping into local minima of the image energy functional to be minimized in such models. In this survey, we illustrate the main concepts of variational level set-based ACMs, SOM-based ACMs, and their relationship and review in a comprehensive fashion the development of their state-of-the-art models from a machine learning perspective, with a focus on their strengths and weaknesses. PMID:25960736

  19. Form and function relationships revealed by long-term research in a semiarid mountain catchment

    Science.gov (United States)

    McNamara, J. P.; Benner, S. G.; Chandler, D. G.; Flores, A. N.; Marshall, H. P.; Seyfried, M. S.; Poulos, M. J.; Pierce, J. L.

    2017-12-01

    Fifteen years of cumulative research in the Dry Creek Experimental Watershed in southwest Idaho, USA has revealed relationships between catchment form and function and contributed to improved fundamental understanding of Critical Zone structure, function, and evolution that would not have been possible through independent short term projects alone. The impacts of aspect and elevation on incident energy and water, coupled with climate seasonality, has produced tightly connected landforms properties and hydrologic processes. North-facing hillslopes have steeper slopes, thicker soil mantles, and finer soil texture than their south-facing counterparts. Finer soils enable higher water holding capacities on north facing slopes, which when coupled with thicker soils produces higher soil water storage capacity. The storage of water first as snow, then as soil moisture determines how upland ecosystems survive the seasonal and persistent water stress that happens each year, and sustains streamflow throughout the year. The cumulative body of local knowledge has improved general understanding of catchment science, serves as a resource for developing, evaluating, and improving conceptual and numerical of process-based models, and for data-driven hydrologic education.

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

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    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.

  1. Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population.

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    Sofaer, Helen R; Sillett, T Scott; Langin, Kathryn M; Morrison, Scott A; Ghalambor, Cameron K

    2014-07-01

    Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong.

  2. Relationship between the morphological variation of sella turcica with age and gender: A digital radiographic study

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    Talkad Subbaiah Mahesh Kumar

    2017-01-01

    Full Text Available Introduction: Sella turcica is a saddle-shaped concavity located in the middle cranial fossa of the skull. The exact dimensions of sella turcica are an important consideration in the diagnosis, prognosis, and treatment of diseases related to the pituitary gland and brain. The sella turcica size and morphology is different from person to person. Thus, obtaining any data in this regard will be a great help in detecting abnormalities within this anatomic area. Aim: The objective of this study was to find out the correlation between the morphological variations of sella turcica with age and gender. Materials and Methods: Study sample consisted of 311 cephalograms of patients with age ranging 6–40 years. The contour of the sella turcica was traced and the linear measurements – length, depth, and diameter of sella turcica – were measured according to Silverman. Results: Morphology of sella turcica appeared to be normal shape in 27.3% of the study population followed by combination (26.7%, irregular (15.8%, pyramidal (10.6%, bridge (10%, oblique anterior wall (5.5%, and double contour (4.2%. Gender-wise comparison of the linear measurement was not statistically significant. Among the linear measurement, the parameter depth and diameter were statistically significant (P < 0.001 when correlated with age. On comparison of shape of sella turcica with linear measurements, the parameter length was statistically significant (P < 0.001. Conclusion: There is no significant relationship between the linear measurements and gender. There exists a significant relationship between the mean depth and mean diameter with age. That is, as age increases, the depth and diameter increase. There is a significant relationship between the length and the different shapes of sella turcica.

  3. Molecular modelling studies of kdr mutations in voltage gated sodium channel revealed significant conformational variations contributing to insecticide resistance.

    Science.gov (United States)

    Yellapu, Nanda Kumar; Gopal, Jeyakodi; Kasinathan, Gunasekaran; Purushothaman, Jambulingam

    2018-06-01

    Voltage gated sodium channels (VGSC) of mosquito vectors are the primary targets of dichlorodiphenyltrichloroethane (DDT) and other synthetic pyrethroids used in public health programmes. The knockdown resistant (kdr) mutations in VGSC are associated with the insecticide resistance especially in Anophelines. The present study is aimed to emphasize and demarcate the impact of three kdr-mutations such as L1014S, L1014F and L1014H on insecticide resistance. The membrane model of sodium transport domain of VGSC (STD-VGSC) was constructed using de novo approach based on domain and trans-membrane predictions. The comparative molecular modelling studies of wild type and mutant models of STD-VGSC revealed that L1014F mutant was observed to be near native to the wild type model in all the respects, but, L1014S and L1014H mutations showed drastic variations in the energy levels, root mean square fluctuations (RMSF) that resulted in conformational variations. The predicted binding sites also showed variable cavity volumes and RMSF in L1014S and L1014H mutants. Further, DDT also found be bound in near native manner to wild type in L1014F mutant and with variable orientation and affinities in L1014S and L1014H mutants. The variations and fluctuations observed in mutant structures explained that each mutation has its specific impact on the conformation of VGSC and its binding with DDT. The study provides new insights into the structure-function-correlations of mutant STD-VGSC structures and demonstrates the role and effects of kdr mutations on insecticide resistance in mosquito vectors.

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

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    Sung-Chur Sim

    Full Text Available 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.

  5. Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis.

    Science.gov (United States)

    Georgii, Elisabeth; Jin, Ming; Zhao, Jin; Kanawati, Basem; Schmitt-Kopplin, Philippe; Albert, Andreas; Winkler, J Barbro; Schäffner, Anton R

    2017-07-10

    Elevated temperature and reduced water availability are frequently linked abiotic stresses that may provoke distinct as well as interacting molecular responses. Based on non-targeted metabolomic and transcriptomic measurements from Arabidopsis rosettes, this study aims at a systematic elucidation of relevant components in different drought and heat scenarios as well as relationships between molecular players of stress response. In combined drought-heat stress, the majority of single stress responses are maintained. However, interaction effects between drought and heat can be discovered as well; these relate to protein folding, flavonoid biosynthesis and growth inhibition, which are enhanced, reduced or specifically induced in combined stress, respectively. Heat stress experiments with and without supplementation of air humidity for maintenance of vapor pressure deficit suggest that decreased relative air humidity due to elevated temperature is an important component of heat stress, specifically being responsible for hormone-related responses to water deprivation. Remarkably, this "dry air effect" is the primary trigger of the metabolomic response to heat. In contrast, the transcriptomic response has a substantial temperature component exceeding the dry air component and including up-regulation of many transcription factors and protein folding-related genes. Data level integration independent of prior knowledge on pathways and condition labels reveals shared drought and heat responses between transcriptome and metabolome, biomarker candidates and co-regulation between genes and metabolic compounds, suggesting novel players in abiotic stress response pathways. Drought and heat stress interact both at transcript and at metabolite response level. A comprehensive, non-targeted view of this interaction as well as non-interacting processes is important to be taken into account when improving tolerance to abiotic stresses in breeding programs. Transcriptome and metabolome

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

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    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

  7. Holocene hydrologic variation at Lake Titicaca, Bolivia/Peru, and its relationship to North Atlantic climate variation

    Science.gov (United States)

    Baker, P. A.; Fritz, S. C.; Garland, J.; Ekdahl, E.

    2005-10-01

    A growing number of sites in the Northern Hemisphere show centennial- to millennial-scale climate variation that has been correlated with change in solar variability or with change in North Atlantic circulation. However, it is unclear how (or whether) these oscillations in the climate system are manifest in the Southern Hemisphere because of a lack of sites with suitably high sampling resolution. In this paper, we reconstruct the lake-level history of Lake Titicaca, using the carbon isotopic content of sedimentary organic matter, to evaluate centennial- to millennial-scale precipitation variation and its phasing relative to sites in the Northern Hemisphere. The pattern and timing of lake-level change in Lake Titicaca is similar to the ice-rafted debris record of Holocene Bond events, demonstrating a possible coupling between precipitation variation on the Altiplano and North Atlantic sea-surface temperatures (SSTs). The cold periods of the Holocene Bond events correspond with periods of increased precipitation on the Altiplano. Holocene precipitation variability on the Altiplano is anti-phased with respect to precipitation in the Northern Hemisphere monsoon region. More generally, the tropical Andes underwent large changes in precipitation on centennial-to-millennial timescales during the Holocene.

  8. Giant ants and their shape: revealing relationships in the genus Titanomyrma with geometric morphometrics

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    Julian Katzke

    2018-01-01

    Full Text Available Shape is a natural phenomenon inherent to many different lifeforms. A modern technique to analyse shape is geometric morphometrics (GM, which offers a whole range of methods concerning the pure shape of an object. The results from these methods have provided new insights into biological problems and have become especially useful in the fields of entomology and palaeontology. Despite the conspicuous successes in other hymenopteran groups, GM analysis of wings and fossil wings of Formicidae has been neglected. Here we tested if landmarks defining the wing shape of fossil ants that belong to the genus Titanomyrma are reliable and if this technique is able to expose relationships among different groups of the largest Hymenoptera that ever lived. This study comprises 402 wings from 362 ants that were analysed and assigned with the GM methods linear discriminant function analysis, principal component analysis, canonical variate analysis, and regression. The giant ant genus Titanomyrma and the parataxon Formicium have different representatives that are all very similar but these modern methods were able to distinguish giant ant types even to the level of the sex. Thirty-five giant ant specimens from the Eckfeld Maar were significantly differentiable from a collection of Messel specimens that consisted of 187 Titanomyrma gigantea females and 42 T. gigantea males, and from 74 Titanomyrma simillima females and 21 T. simillima males. Out of the 324 Messel ants, 127 are newly assigned to a species and 223 giant ants are newly assigned to sex with GM analysis. All specimens from Messel fit to the two species. Moreover, shape affinities of these groups and the species Formicium brodiei, Formicium mirabile, and Formicium berryi, which are known only from wings, were investigated. T. gigantea stands out with a possible female relative in one of the Eckfeld specimens whereas the other groups show similar shape patterns that are possibly plesiomorphic. Formicidae

  9. Giant ants and their shape: revealing relationships in the genus Titanomyrma with geometric morphometrics.

    Science.gov (United States)

    Katzke, Julian; Barden, Phillip; Dehon, Manuel; Michez, Denis; Wappler, Torsten

    2018-01-01

    Shape is a natural phenomenon inherent to many different lifeforms. A modern technique to analyse shape is geometric morphometrics (GM), which offers a whole range of methods concerning the pure shape of an object. The results from these methods have provided new insights into biological problems and have become especially useful in the fields of entomology and palaeontology. Despite the conspicuous successes in other hymenopteran groups, GM analysis of wings and fossil wings of Formicidae has been neglected. Here we tested if landmarks defining the wing shape of fossil ants that belong to the genus Titanomyrma are reliable and if this technique is able to expose relationships among different groups of the largest Hymenoptera that ever lived. This study comprises 402 wings from 362 ants that were analysed and assigned with the GM methods linear discriminant function analysis, principal component analysis, canonical variate analysis, and regression. The giant ant genus Titanomyrma and the parataxon Formicium have different representatives that are all very similar but these modern methods were able to distinguish giant ant types even to the level of the sex. Thirty-five giant ant specimens from the Eckfeld Maar were significantly differentiable from a collection of Messel specimens that consisted of 187 Titanomyrma gigantea females and 42 T. gigantea males, and from 74 Titanomyrma simillima females and 21 T. simillima males. Out of the 324 Messel ants, 127 are newly assigned to a species and 223 giant ants are newly assigned to sex with GM analysis. All specimens from Messel fit to the two species. Moreover, shape affinities of these groups and the species Formicium brodiei , Formicium mirabile , and Formicium berryi , which are known only from wings, were investigated. T. gigantea stands out with a possible female relative in one of the Eckfeld specimens whereas the other groups show similar shape patterns that are possibly plesiomorphic. Formicidae are one of the

  10. Shifts in river-floodplain relationship reveal the impacts of river regulation: A case study of Dongting Lake in China

    Science.gov (United States)

    Lu, Cai; Jia, Yifei; Jing, Lei; Zeng, Qing; Lei, Jialin; Zhang, Shuanghu; Lei, Guangchun; Wen, Li

    2018-04-01

    Better understanding of the dynamics of hydrological connectivity between river and floodplain is essential for the ecological integrity of river systems. In this study, we proposed a regime-switch modelling (RSM) framework, which integrates change point analysis with dynamic linear regression, to detect and date change points in linear regression, and to quantify the relative importance of natural variations and anthropogenic disturbances. The approach was applied to the long-term hydrological time series to investigate the evolution of river-floodplain relation in Dongting Lake in the last five decades, during which the Yangtze River system experienced unprecedented anthropogenic manipulations. Our results suggested that 1) there were five distinct regimes during which the influence of inflows and local climate on lake water level changed significantly. The detected change points were well corresponding to the major events occurred upon the Yangtze; 2) although the importance of inflows from the Yangtze was greater than that of the tributaries flows over the five regimes, the relative contribution gradually decreased from regime 1 to regime 5. The weakening of hydrological forcing from the Yangtze was mainly attributed to the reduction in channel capacity resulting from sedimentation in the outfalls and water level dropping caused by river bed scour in the mainstream; 3) the effects of local climate was much smaller than these of inflows; and 4) since the operation of The Three Gorges Dam in 2006, the river-floodplain relationship entered a new equilibrium in that all investigated variables changed synchronously in terms of direction and magnitude. The results from this study reveal the mechanisms underlying the alternated inundation regime in Dongting Lake. The identified change points, some of which have not been previously reported, will allow a reappraisal of the current dam and reservoir operation strategies not only for flood/drought risk management but

  11. Relationships between Nutrient Heterogeneity, Root Growth, and Hormones: Evidence for Interspecific Variation.

    Science.gov (United States)

    Dong, Jia; Jones, Robert H; Mou, Pu

    2018-02-28

    (1) Background: Plant roots respond to nutrients through root architecture that is regulated by hormones. Strong inter-specific variation in root architecture has been well documented, but physiological mechanisms that may control the variation have not. (2) Methods: We examined correlations between root architecture and hormones to seek clues on mechanisms behind root foraging behavior. In the green house at Beijing Normal University, hydroponic culture experiments were used to examine the root responses of four species- Callistephus chinensis , Solidago canadensis , Ailanthus altissima , Oryza sativa- to two nitrogen types (NO₃ - or NH₄⁺), three nitrogen concentrations (low, medium, and high concentrations of 0.2, 1, and 18 mM, respectively) and two ways of nitrogen application (stable vs. variable). The plants were harvested after 36 days to measure root mass, 1st order root length, seminal root length for O. sativa , density of the 1st order laterals, seminal root number for O. sativa , the inter-node length of the 1st order laterals, and root hormone contents of indole-3-acetic acid, abscisic acid, and cytokinins (zeatin + zeatinriboside). (3) Results: Species differed significantly in their root architecture responses to nitrogen treatments. They also differed significantly in hormone responses to the nitrogen treatments. Additionally, the correlations between root architecture and hormone responses were quite variable across the species. Each hormone had highly species-specific relationships with root responses. (4) Conclusions: Our finding implies that a particular root foraging behavior is probably not controlled by the same biochemical pathway in all species.

  12. Relationships between Nutrient Heterogeneity, Root Growth, and Hormones: Evidence for Interspecific Variation

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    Jia Dong

    2018-02-01

    Full Text Available (1 Background: Plant roots respond to nutrients through root architecture that is regulated by hormones. Strong inter-specific variation in root architecture has been well documented, but physiological mechanisms that may control the variation have not. (2 Methods: We examined correlations between root architecture and hormones to seek clues on mechanisms behind root foraging behavior. In the green house at Beijing Normal University, hydroponic culture experiments were used to examine the root responses of four species—Callistephus chinensis, Solidago canadensis, Ailanthus altissima, Oryza sativa—to two nitrogen types (NO3− or NH4+, three nitrogen concentrations (low, medium, and high concentrations of 0.2, 1, and 18 mM, respectively and two ways of nitrogen application (stable vs. variable. The plants were harvested after 36 days to measure root mass, 1st order root length, seminal root length for O. sativa, density of the 1st order laterals, seminal root number for O. sativa, the inter-node length of the 1st order laterals, and root hormone contents of indole-3-acetic acid, abscisic acid, and cytokinins (zeatin + zeatinriboside. (3 Results: Species differed significantly in their root architecture responses to nitrogen treatments. They also differed significantly in hormone responses to the nitrogen treatments. Additionally, the correlations between root architecture and hormone responses were quite variable across the species. Each hormone had highly species-specific relationships with root responses. (4 Conclusions: Our finding implies that a particular root foraging behavior is probably not controlled by the same biochemical pathway in all species.

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

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    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. 

  14. 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

  15. 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.

  16. Observations of Co-variation in Cloud Properties and their Relationships with Atmospheric State

    Science.gov (United States)

    Sinclair, K.; van Diedenhoven, B.; Fridlind, A. M.; Arnold, T. G.; Yorks, J. E.; Heymsfield, G. M.; McFarquhar, G. M.; Um, J.

    2017-12-01

    Radiative properties of upper tropospheric ice clouds are generally not well represented in global and cloud models. Cloud top height, cloud thermodynamic phase, cloud optical thickness, cloud water path, particle size and ice crystal shape all serve as observational targets for models to constrain cloud properties. Trends or biases in these cloud properties could have profound effects on the climate since they affect cloud radiative properties. Better understanding of co-variation between these cloud properties and linkages with atmospheric state variables can lead to better representation of clouds in models by reducing biases in their micro- and macro-physical properties as well as their radiative properties. This will also enhance our general understanding of cloud processes. In this analysis we look at remote sensing, in situ and reanalysis data from the MODIS Airborne Simulator (MAS), Cloud Physics Lidar (CPL), Cloud Radar System (CRS), GEOS-5 reanalysis data and GOES imagery obtained during the Tropical Composition, Cloud and Climate Coupling (TC4) airborne campaign. The MAS, CPL and CRS were mounted on the ER-2 high-altitude aircraft during this campaign. In situ observations of ice size and shape were made aboard the DC8 and WB57 aircrafts. We explore how thermodynamic phase, ice effective radius, particle shape and radar reflectivity vary with altitude and also investigate how these observed cloud properties vary with cloud type, cloud top temperature, relative humidity and wind profiles. Observed systematic relationships are supported by physical interpretations of cloud processes and any unexpected differences are examined.

  17. Within crown variation in the relationship between foliage biomass and sapwood area in jack pine.

    Science.gov (United States)

    Schneider, Robert; Berninger, Frank; Ung, Chhun-Huor; Mäkelä, Annikki; Swift, D Edwin; Zhang, S Y

    2011-01-01

    The relationship between sapwood area and foliage biomass is the basis for a lot of research on eco-phyisology. In this paper, foliage biomass change between two consecutive whorls is studied, using different variations in the pipe model theory. Linear and non-linear mixed-effect models relating foliage differences to sapwood area increments were tested to take into account whorl location, with the best fit statistics supporting the non-linear formulation. The estimated value of the exponent is 0.5130, which is significantly different from 1, the expected value given by the pipe model theory. When applied to crown stem sapwood taper, the model indicates that foliage biomass distribution influences the foliage biomass to sapwood area at crown base ratio. This result is interpreted as being the consequence of differences in the turnover rates of sapwood and foliage. More importantly, the model explains previously reported trends in jack pine sapwood area at crown base to tree foliage biomass ratio.

  18. TREATMENT OF THE RELATIONSHIP BETWEEN VARIATION, CHANGE AND GRAMMAR IN TEXTBOOKS OF SECONDARY EDUCATION

    Directory of Open Access Journals (Sweden)

    Eliete Figueira BATISTA DA SILVEIRA

    2015-06-01

    Full Text Available The focus on variation and change is observed in sociolinguistic academic and scientific research and recommended in the guidelines of PCN. However, the negative valuation of the various standards and improper use of discoveries and linguistic terms are revealed in the textbooks examined. We treat this issue from a perspective of critical appreciation of the advances, inconsistencies and theoretical-descriptive deficiencies found in high school textbooks. We discuss the definition of the space of cultured norms and standard in the midst of a Brazilian reality of diverse discourses guided by various rules, and we have made explicit the contributions of sociolinguistic studies for teaching. Proved necessary to apply this knowledge to the development of teaching materials, regulated by an exploiter teaching of linguistic heterogeneity and deconstructing the discourse of monolithic and homogeneous language. The valuation of the various standards enable the citizen to the development of intellectual autonomy and critical by modifying the current reality of massive illiteracy. This will be possible with the dialogue between scientific knowledge and the authors/publishers of textbooks.

  19. Large regional-scale variation in C3/C4 distribution pattern of Inner Mongolia steppe is revealed by grazer wool carbon isotope composition

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    K. Auerswald

    2009-05-01

    Full Text Available This work explored the spatial variation of C3/C4 distribution in the Inner Mongolia, P. R. China, steppe by geostatistical analysis of carbon isotope data of vegetation and sheep wool. Standing community biomass (n=118 and sheep wool (n=146 were sampled in a ~0.2 Mio km2 area. Samples from ten consecutive years (1998–2007 were obtained. Community biomass samples represented the carbon isotopic composition of standing vegetation on about 1000 m2 ("community-scale", whereas the spatio-temporal scale of wool reflected the isotope composition of the entire area grazed by the herd during a 1-yr period (~5–10 km2, "farm-scale". Pair wise sampling of wool and vegetation revealed a 13C-enrichment of 2.7±0.7‰ (95% confidence interval in wool relative to vegetation, but this shift exhibited no apparent relationships with environmental parameters or stocking rate. The proportion of C4 plants in above-ground biomass (PC4, % was estimated with a two-member mixing model of 13C discrimination by C3 and C4 vegetation (13Δ3 and 13Δ4, respectively, in accounting for the effects of changing 13C in atmospheric CO2 on sample isotope composition, and of altitude and aridity on 13Δ3. PC4 averaged 19%, but the variation was enormous: full-scale (0% to 100% at community-scale, and 0% to 85% at farm-scale. The farm-scale variation of PC4 exhibited a clear regional pattern over a range of ~250 km. Importantly PC4 was significantly higher above the 22°C isotherm of the warmest month, which was obtained from annual high-resolution maps and averaged over the different sampling years. This is consistent with predictions from C3/C4 crossover temperature of quantum yield or light use efficiency in C3 and C4 plants. Still, temperature gradients accounted for only 10% of

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

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    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.

  1. RELATIONSHIP OF AIRWAY HYPERRESPONSIVENESS TO RESPIRATORY SYMPTOMS AND DIURNAL PEAK FLOW VARIATION IN PATIENTS WITH OBSTRUCTIVE LUNG-DISEASE

    NARCIS (Netherlands)

    BRAND, PLP; POSTMA, DS; KERSTJENS, HAM; KOETER, GH

    This study reports on the relationship of airway hyperresponsiveness (AH) with respiratory symptoms and diurnal peak flow expiratory (PEF) variation in 221 hyperresponsive patients with moderately severe airways obstruction. The disease was in a stable phase in all patients. Closely adhering to the

  2. Possible relationship between the Earth’s rotation variations and geomagnetic field reversals over the past 510 Myr

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    Igor Gil Pacca

    2015-04-01

    Full Text Available The Earth’s rotation can change as a result of several internal and external processes, each of which is at a different timescale. Here, we present some possible connections between the Earth’s rotation variations and the geomagnetic reversal frequency rates over the past 120 Myr. In addition, we show the possible relationship between the geomagnetic field reversal frequency and the δ18O oscillations. Because the latter reflects the glacial and interglacial periods, we hypothesize that it can be used as a possible indicator to explain the length of day (LOD variations and consequently the reversal field frequency over the past 510 Myr. Therefore, our analysis suggests that the relationships between the geomagnetic reversal frequency rates and the Earth’s rotation changes during the Phanerozoic. However, more reversal data are required for periods before the KRS to strengthen the perspective of using the geomagnetic reversal data as a marker for the LOD variations through geological times.

  3. 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

  4. 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.

  5. 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 (< 2 μm). The low value of carbon potentially exported out of the euphotic zone throughout the study (≤ 31% of total primary production) suggests that phytoplankton production was mainly grazed by microzooplankton rather than being exported to greater depths. We observed a mixed assemblage of 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

  6. 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.

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

    Science.gov (United States)

    Ahnert, Sebastian E

    2014-03-25

    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.

  8. Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness

    Science.gov (United States)

    Bauer, Christopher R; Li, Shuang; Siegal, Mark L

    2015-01-01

    The concept of robustness in biology has gained much attention recently, but a mechanistic understanding of how genetic networks regulate phenotypic variation has remained elusive. One approach to understand the genetic architecture of variability has been to analyze dispensable gene deletions in model organisms; however, the most important genes cannot be deleted. Here, we have utilized two systems in yeast whereby essential genes have been altered to reduce expression. Using high-throughput microscopy and image analysis, we have characterized a large number of morphological phenotypes, and their associated variation, for the majority of essential genes in yeast. Our results indicate that phenotypic robustness is more highly dependent upon the expression of essential genes than on the presence of dispensable genes. Morphological robustness appears to be a general property of a genotype that is closely related to pleiotropy. While the fitness profile across a range of expression levels is idiosyncratic to each gene, the global pattern indicates that there is a window in which phenotypic variation can be released before fitness effects are observable. PMID:25609648

  9. Relationship between the species-representative phenotype and intraspecific variation in Ranunculaceae floral organ and Asteraceae flower numbers.

    Science.gov (United States)

    Kitazawa, Miho S; Fujimoto, Koichi

    2016-04-01

    Phenotypic variation in floral morphologies contributes to speciation by testing various morphologies that might have higher adaptivity, leading eventually to phylogenetic diversity. Species diversity has been recognized, however, by modal morphologies where the variation is averaged out, so little is known about the relationship between the variation and the diversity. We analysed quantitatively the intraspecific variation of the organ numbers within flowers of Ranunculaceae, a family which branched near the monocot-eudicot separation, and the numbers of flowers within the capitula of Asteraceae, one of the most diverse families of eudicots. We used four elementary statistical quantities: mean, standard deviation (s.d.), degree of symmetry (skewness) and steepness (kurtosis). While these four quantities vary among populations, we found a common relationship between s.d. and the mean number of petals and sepals in Ranunculaceae and number of flowers per capitulum in Asteraceae. The s.d. is equal to the square root of the difference between the mean and specific number, showing robustness: for example, 3 in Ficaria sepals, 5 in Ranunculus petals and Anemone tepals, and 13 in Farfugium ray florets. This square-root relationship was not applicable to Eranthis petals which show little correlation between the s.d. and mean, and the stamens and carpels of Ranunculaceae whose s.d. is proportional to the mean. The specific values found in the square-root relationship provide a novel way to find the species-representative phenotype among varied morphologies. The representative phenotype is, in most cases, unique to the species or genus level, despite intraspecific differences of average phenotype among populations. The type of variation shown by the statistical quantities indicates not only the robustness of the morphologies but also how flowering plants changed during evolution among representative phenotypes that eventually led to phylogenetic diversification. © The

  10. 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...

  11. The relationship between temporal variation of hypoxia, polarographic measurements and predictions of tumour response to radiation

    Science.gov (United States)

    Toma-Dasu, Iuliana; Dasu, Alexandru; Karlsson, Mikael

    2004-10-01

    The polarographic oxygen sensor is one of the most used devices for in vivo measurements of oxygen and many other measurement techniques for measuring tumour hypoxia are correlated with electrode measurements. Little is known however about the relationship between electrode measurements and the real tissue oxygenation. This paper investigates the influence of the temporal change of the hypoxic pattern on the electrode measurements and the tumour response. Electrode measurements and tumour response were simulated using a computer program that allows both the calculation of the tissue oxygenation with respect to the two types of hypoxia that might arise in tumours and the virtual insertion of the electrode into the tissue. It was therefore possible to control the amount of each type of hypoxia in order to investigate their influence on the measurement results. Tissues with several vascular architectures ranging from well oxygenated to poorly oxygenated were taken into consideration as might be seen in practice. The influence of the electrode measurements on the treatment outcome was estimated by calculating the tumour control probability for the tumours characterized either by the real or by the measured tumour oxygenation. We have simulated electrode oxygen measurements in different types of tissues, covering a wide range of tumour oxygenations. The results of the simulations showed that the measured distribution depends on the details of the vascular network and not on the type of hypoxia. We have also simulated the effects of the temporal change of the acute hypoxic pattern due to the opening and the closure of different blood vessels during a full fractionated treatment. The results of this simulation suggested that the temporal variation of the hypoxic pattern does not lead to significantly different results for the electrode measurements or the predicted tumour control probabilities. In conclusion, it was found that the averaging effect of the electrode leads

  12. 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

  13. 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

  14. 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

  15. Linear and Non-Linear Dose-Response Functions Reveal a Hormetic Relationship Between Stress and Learning

    OpenAIRE

    Zoladz, Phillip R.; Diamond, David M.

    2008-01-01

    Over a century of behavioral research has shown that stress can enhance or impair learning and memory. In the present review, we have explored the complex effects of stress on cognition and propose that they are characterized by linear and non-linear dose-response functions, which together reveal a hormetic relationship between stress and learning. We suggest that stress initially enhances hippocampal function, resulting from amygdala-induced excitation of hippocampal synaptic plasticity, as ...

  16. Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers.

    Science.gov (United States)

    Korir, N K; Diao, W; Tao, R; Li, X; Kayesh, E; Li, A; Zhen, W; Wang, S

    2014-01-08

    The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

  17. 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

  18. 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.

  19. 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.

  20. Respiratory flow-sound relationship during both wakefulness and sleep and its variation in relation to sleep apnea.

    Science.gov (United States)

    Yadollahi, Azadeh; Montazeri, Aman; Azarbarzin, Ali; Moussavi, Zahra

    2013-03-01

    Tracheal respiratory sound analysis is a simple and non-invasive way to study the pathophysiology of the upper airway and has recently been used for acoustic estimation of respiratory flow and sleep apnea diagnosis. However in none of the previous studies was the respiratory flow-sound relationship studied in people with obstructive sleep apnea (OSA), nor during sleep. In this study, we recorded tracheal sound, respiratory flow, and head position from eight non-OSA and 10 OSA individuals during sleep and wakefulness. We compared the flow-sound relationship and variations in model parameters from wakefulness to sleep within and between the two groups. The results show that during both wakefulness and sleep, flow-sound relationship follows a power law but with different parameters. Furthermore, the variations in model parameters may be representative of the OSA pathology. The other objective of this study was to examine the accuracy of respiratory flow estimation algorithms during sleep: we investigated two approaches for calibrating the model parameters using the known data recorded during either wakefulness or sleep. The results show that the acoustical respiratory flow estimation parameters change from wakefulness to sleep. Therefore, if the model is calibrated using wakefulness data, although the estimated respiratory flow follows the relative variations of the real flow, the quantitative flow estimation error would be high during sleep. On the other hand, when the calibration parameters are extracted from tracheal sound and respiratory flow recordings during sleep, the respiratory flow estimation error is less than 10%.

  1. Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors.

    Directory of Open Access Journals (Sweden)

    Vítor Borges

    Full Text Available Research on the obligate intracellular bacterium Chlamydia trachomatis demands culture in cell-lines, but the adaptive process behind the in vivo to in vitro transition is not understood. We assessed the genomic and transcriptomic dynamics underlying C. trachomatis in vitro adaptation of strains representing the three disease groups (ocular, epithelial-genital and lymphogranuloma venereum propagated in epithelial cells over multiple passages. We found genetic features potentially underlying phase variation mechanisms mediating the regulation of a lipid A biosynthesis enzyme (CT533/LpxC, and the functionality of the cytotoxin (CT166 through an ON/OFF mechanism. We detected inactivating mutations in CT713/porB, a scenario suggesting metabolic adaptation to the available carbon source. CT135 was inactivated in a tropism-specific manner, with CT135-negative clones emerging for all epithelial-genital populations (but not for LGV and ocular populations and rapidly increasing in frequency (~23% mutants per 10 passages. RNA-sequencing analyses revealed that a deletion event involving CT135 impacted the expression of multiple virulence factors, namely effectors known to play a role in the C. trachomatis host-cell invasion or subversion (e.g., CT456/Tarp, CT694, CT875/TepP and CT868/ChlaDub1. This reflects a scenario of attenuation of C. trachomatis virulence in vitro, which may take place independently or in a cumulative fashion with the also observed down-regulation of plasmid-related virulence factors. This issue may be relevant on behalf of the recent advances in Chlamydia mutagenesis and transformation where culture propagation for selecting mutants/transformants is mandatory. Finally, there was an increase in the growth rate for all strains, reflecting gradual fitness enhancement over time. In general, these data shed light on the adaptive process underlying the C. trachomatis in vivo to in vitro transition, and indicates that it would be prudent to

  2. Lateral Variations of the Mantle Transition Zone Structure beneath the Southeastern Tibetan Plateau Revealed by P-wave Receiver Functions

    Science.gov (United States)

    Bai, Y.; Ai, Y.; Jiang, M.; He, Y.; Chen, Q.

    2017-12-01

    The deep structure of the southeastern Tibetan plateau is of great scientific importance to a better understanding of the India-Eurasia collision as well as the evolution of the magnificent Tibetan plateau. In this study, we collected 566 permanent and temporary seismic stations deployed in SE Tibet, with a total of 77853 high quality P-wave receiver functions been extracted by maximum entropy deconvolution method. On the basis of the Common Conversion Point (CCP) stacking technique, we mapped the topography of the 410km and 660km discontinuities (hereinafter called the `410' and the `660'), and further investigated the lateral variation of the mantle transition zone (MTZ) thickness beneath this region. The background velocity model deduced from H-κ stacking results and a previous body-wave tomographic research was applied for the correction of the crustal and upper mantle heterogeneities beneath SE Tibet for CCP stacking. Our results reveal two significantly thickened MTZ anomalies aligned nearly in the south-north direction. The magnitude of both anomalies are 30km above the global average of 250km. The southern anomaly located beneath the Dianzhong sub-block and the Indo-China block is characterized by a slightly deeper `410' and a greater-than-normal `660', while the northern anomaly beneath western Sichuan has an uplifted `410' and a depressed `660'. Combining with previous studies in the adjacent region, we suggest that slab break-off may occurred during the eastward subduction of the Burma plate, with the lower part of the cold slab penetrated into the MTZ and stagnated at the bottom of the `660' which may cause the southern anomaly in our receiver function images. The origin of the Tengchong volcano is probably connected to the upwelling of the asthenospheric material caused by the slab break-off or to the ascending of the hot and wet material triggered by the dehydration of stagnant slab in the MTZ. The anomaly in the north, on the other hand, might be

  3. Genetic variations and relationships of cultivated and weedy types of perilla species in Korea and Japan using multi DNA markers

    International Nuclear Information System (INIS)

    Sun, Y.; Zheng, S.; Lee, J.; Hong, S.

    2017-01-01

    The genus Perilla, known as an oil crop or a Chinese medicine, vegetable crop, is widely cultivated in East Asia. It occurs in two distinct varieties, var. frutescens and var. crispa, and their genetic relationship is still obscure. To understand the genetic diversity and relationships of the cultivated and weedy types of Perilla crops in Korea, Japan and China, we evaluated the genetic variation of 20 accessions by 3 rDNA markers. Among these three markers, the nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) region of Perilla crops showed less sequence variations than the 5S and 18S genes. There were abundant variable nucleotide sites appearing in the 5S and 18S genes. Especially in the 18S gene, the variable nucleotide sites showed specificity between some Perilla type and other varieties. JPN1 showed 6 special variable nucleotide sites differing from other varieties, resulting in the farthest phylogenetic relationship in the 18S tree. CHI15 shared 8 special variable sites, also showing far phylogenetic relationship with other varieties. According to the sequence analysis result, the cultivated types of Korean var. frutescens showed relatively more genetic diversity than those of Japanese var. frutescens, while Korean var. crispa showed lower genetic diversity than those of Japanese var. crispa. However, the intra- or inter-variety genetic distance did not have significant difference. This work provided more sequence resources of Perilla crops and evidences to evaluate the genetic variation and relationships. Our result would help molecular type identification, functional plant breeding and trait improvement of Perilla crops. (author)

  4. The Relationship of Temporal Variations in SMAP Vegetation Optical Depth to Plant Hydraulic Behavior

    Science.gov (United States)

    Konings, A. G.

    2016-12-01

    The soil emissions measured by L-band radiometers such as that on the NASA Soil Moisture Active/Passive mission are modulated by vegetation cover as quantified by the soil scattering albedo and the vegetation optical depth (VOD). The VOD is linearly proportional to the total vegetation water content, which is dependent on both the biomass and relative water content of the plant. Biomass is expected to vary more slowly than water content. Variations in vegetation water content are highly informative as they are directly indicative of the degree of hydraulic stress (or lack thereof) experienced by the plant. However, robust retrievals are needed in order for SMAP VOD observations to be useful. This is complicated by the fact that multiple unknowns (soil moisture, VOD, and albedo) need to be determined from two highly correlated polarizations. This presentation will discuss the application to SMAP of a recently developed timeseries algorithm for VOD and albedo retrieval - the Multi-Temporal Dual Channel Algorithm MTDCA, and its interpretation for plant hydraulic applications. The MT-DCA is based on the assumption that, for consecutive overpasses at a given time of day, VOD varies more slowly than soil moisture. A two-overpass moving average can then be used to determine variations in VOD that are less sensitive to high-frequency noise than classical dual-channel algorithms. Seasonal variations of SMAP VOD are presented and compared to expected patterns based on rainfall and radiation seasonality. Taking advantage of the large diurnal variation (relative to the seasonal variation) of canopy water potention, diurnal variations (between 6AM and 6PM observations) of SMAP VOD are then used to calculate global variations in ecosystem-scale isohydricity - the degree of stomatal closure and xylem conductivity loss in response to water stress. Lastly, the effect of satellite sensing frequency and overpass time on water content across canopies of different height will be

  5. 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.

  6. The multidecadal variations of the interannual relationship between the East Asian summer monsoon and ENSO in a coupled model

    Science.gov (United States)

    Liu, Bo; Huang, Gang; Hu, Kaiming; Wu, Renguang; Gong, Hainan; Wang, Pengfei; Zhao, Guijie

    2017-10-01

    This study investigates the multidecadal variations of the interannual relationship between the East Asian summer monsoon (EASM) and El Niño-Southern Oscillation (ENSO) in 1000-year simulation of a coupled climate model. The interannual relationship between ENSO and EASM has experienced pronounced changes throughout the 1000-year simulation. During the periods with significant ENSO-EASM relationship, the ENSO-related circulation anomalies show a Pacific-Japan (PJ)-like pattern with significant wave-activity flux propagating from the tropics to the north in lower troposphere and from the mid-latitudes to the south in upper troposphere. The resultant ENSO-related precipitation anomalies are more (less) than normal over the East Asia (western North Pacific) in the decaying summers of El Niño events. In contrast, the circulation and precipitation anomalies are weak over East Asia-western North Pacific during the periods with weak ENSO-EASM relationship. Based on the energy conversion analysis, the related anomalies achieve barotropic and baroclinic energy from the mean flow during the periods with strong ENSO-EASM relationship. On the contrary, during the low-correlation periods, the energy conversion is too weak to form the link between the tropics and mid-latitudes. The main reason for the multidecadal variations of ENSO-EASM relationship is the amplitude discrepancy of SST anomalies over the Indo-western Pacific Ocean which, in turn, leads to the intensity difference of the western North Pacific anomalous anticyclone (WPAC) and related climate anomalies.

  7. The complete mitochondrial genome of Sesarmops sinensis reveals gene rearrangements and phylogenetic relationships in Brachyura.

    Science.gov (United States)

    Tang, Bo-Ping; Xin, Zhao-Zhe; Liu, Yu; Zhang, Dai-Zhen; Wang, Zheng-Fei; Zhang, Hua-Bin; Chai, Xin-Yue; Zhou, Chun-Lin; Liu, Qiu-Ning

    2017-01-01

    Mitochondrial genome (mitogenome) is very important to understand molecular evolution and phylogenetics. Herein, in this study, the complete mitogenome of Sesarmops sinensis was reported. The mitogenome was 15,905 bp in size, and contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew and the GC skew are both negative in the mitogenomes of S. sinensis. The nucleotide composition of the S. sinensis mitogenome was also biased toward A + T nucleotides (75.7%). All tRNA genes displayed a typical mitochondrial tRNA cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. S. sinensis exhibits a novel rearrangement compared with the Pancrustacean ground pattern and other Brachyura species. Based on the 13 PCGs, the phylogenetic analysis showed that S. sinensis and Sesarma neglectum were clustered on one branch with high nodal support values, indicating that S. sinensis and S. neglectum have a sister group relationship. The group (S. sinensis + S. neglectum) was sister to (Parasesarmops tripectinis + Metopaulias depressus), suggesting that S. sinensis belongs to Grapsoidea, Sesarmidae. Phylogenetic trees based on amino acid sequences and nucleotide sequences of mitochondrial 13 PCGs using BI and ML respectively indicate that section Eubrachyura consists of four groups clearly. The resulting phylogeny supports the establishment of a separate subsection Potamoida. These four groups correspond to four subsections of Raninoida, Heterotremata, Potamoida, and Thoracotremata.

  8. 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.

  9. Phylogenetic relationships among East African haplochromine fish as revealed by short interspersed elements (SINEs).

    Science.gov (United States)

    Terai, Yohey; Takezaki, Naoko; Mayer, Werner E; Tichy, Herbert; Takahata, Naoyuki; Klein, Jan; Okada, Norihiro

    2004-01-01

    Genomic DNA libraries were prepared from two endemic species of Lake Victoria haplochromine (cichlid) fish and used to isolate and characterize a set of short interspersed elements (SINEs). The distribution and sequences of the SINEs were used to infer phylogenetic relationships among East African haplochromines. The SINE-based classification divides the fish into four groups, which, in order of their divergence from a stem lineage, are the endemic Lake Tanganyika flock (group 1); fish of the nonendemic, monotypic, widely distributed genus Astatoreochromis (group 2); the endemic Lake Malawi flock (group 3); and group 4, which contains fish from widely dispersed East African localities including Lakes Victoria, Edward, George, Albert, and Rukwa, as well as many rivers. The group 4 haplochromines are characterized by a subset of polymorphic SINEs, each of which is present in some individuals and absent in others of the same population at a given locality, the same morphologically defined species, and the same mtDNA-defined haplogroup. SINE-defined group 4 contains six of the seven previously described mtDNA haplogroups. One of the polymorphic SINEs appears to be fixed in the endemic Lake Victoria flock; four others display the presence-or-absence polymorphism within the species of this flock. These findings have implications for the origin of Lake Victoria cichlids and for their founding population sizes.

  10. Zebrafish syntenic relationship to human/mouse genomes revealed by radiation hybrid mapping

    International Nuclear Information System (INIS)

    Samonte, Irene E.

    2007-01-01

    Zebrafish (Danio rerio) is an excellent model system for vertebrate developmental analysis and a new model for human disorders. In this study, however, zebrafish was used to determine its syntenic relationship to human/mouse genomes using the zebrafish-hamster radiation hybrid panel. The focus was on genes residing on chromosomes 6 and 17 of human and mouse, respectively, and some other genes of either immunologic or evolutionary importance. Gene sequences of interest and zebrafish expressed sequence tags deposited in the GenBank were used in identifying zebrafish homologs. Polymerase chain reaction (PCR) amplification, cloning and subcloning, sequencing, and phylogenetic analysis were done to confirm the homology of the candidate genes in zebrafish. The promising markers were then tested in the 94 zebrafish-hamster radiation hybrid panel cell lines and submitted for logarithm of the odds (LOD) score analysis to position genes on the zebrafish map. A total of 19 loci were successfully mapped to zebrafish linkage groups 1, 14, 15, 19, and 20. Four of these loci were positioned in linkage group 20, whereas, 3 more loci were added in linkage group 19, thus increasing to 34 loci the number of human genes syntenic to the group. With the sequencing of the zebrafish genome, about 20 more MHC genes were reported linked on the same group. (Author)

  11. 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.

  12. 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.

  13. 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.

  14. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

    Science.gov (United States)

    Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B

    2015-11-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.

  15. Adolescents’ Gender Mistrust: Variations and Implications for the Quality of Romantic Relationships

    OpenAIRE

    Nomaguchi, Kei M.; Giordano, Peggy C.; Manning, Wendy D.; Longmore, Monica A.

    2011-01-01

    Recent research demonstrates that perceptions of gender mistrust are implicated in lower marriage rates among low-income populations. Yet few quantitative studies have examined the factors predicting gender mistrust during adolescence and whether it influences the quality of subsequent nonmarital romantic relationships. Analysis of three waves of data from the Toledo Adolescent Relationships Study (N = 1,106) indicates that in addition to neighborhood poverty rates, parents’ own gender mistru...

  16. Insights into intraspecific wood density variation and its relationship to growth, height and elevation in a treeline species.

    Science.gov (United States)

    Fajardo, A

    2018-05-01

    The wood economics spectrum provides a general framework for interspecific trait-trait coordination across wide environmental gradients. Whether global patterns are mirrored within species constitutes a poorly explored subject. In this study, I first determined whether wood density co-varies together with elevation, tree growth and height at the within-species level. Second, I determined the variation of wood density in different stem parts (trunk, branch and twigs). In situ trunk sapwood, trunk heartwood, branch and twig densities, in addition to stem growth rates and tree height were determined in adult trees of Nothofagus pumilio at four elevations in five locations spanning 18° of latitude. Mixed effects models were fitted to test relationships among variables. The variation in wood density reported in this study was narrow (ca. 0.4-0.6 g cm -3 ) relative to global density variation (ca. 0.3-1.0 g cm -3 ). There was no significant relationship between stem growth rates and wood density. Furthermore, the elevation gradient did not alter the wood density of any stem part. Trunk sapwood density was negatively related to tree height. Twig density was higher than branch and trunk densities. Trunk heartwood density was always significantly higher than sapwood density. Negative across-species trends found in the growth-wood density relationship may not emerge as the aggregate of parallel intraspecific patterns. Actually, trees with contrasting growth rates show similar wood density values. Tree height, which is tightly related to elevation, showed a negative relationship with sapwood density. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  17. 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

    2016-05-31

    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.

  18. Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera

    Science.gov (United States)

    Karpe, Snehal D.; Jain, Rikesh; Brockmann, Axel; Sowdhamini, Ramanathan

    2016-01-01

    Abstract We developed a computational pipeline for homology based identification of the complete repertoire of olfactory receptor (OR) genes in the Asian honey bee species, Apis florea. Apis florea is phylogenetically the most basal honey bee species and also the most distant sister species to the Western honey bee Apis mellifera, for which all OR genes had been identified before. Using our pipeline, we identified 180 OR genes in A. florea, which is very similar to the number of ORs identified in A. mellifera (177 ORs). Many characteristics of the ORs including gene structure, synteny of tandemly repeated ORs and basic phylogenetic clustering are highly conserved. The composite phylogenetic tree of A. florea and A. mellifera ORs could be divided into 21 clades which are in harmony with the existing Hymenopteran tree. However, we found a few nonorthologous OR relationships between both species as well as independent pseudogenization of ORs suggesting separate evolutionary changes. Particularly, a subgroup of the OR gene clade XI, which had been hypothesized to code cuticular hydrocarbon receptors showed a high number of species-specific ORs. RNAseq analysis detected a total number of 145 OR transcripts in male and 162 in female antennae. Most of the OR genes were highly expressed on the female antennae. However, we detected five distinct male-biased OR genes, out of which three genes (AfOr11, AfOr18, AfOr170P) were shown to be male-biased in A. mellifera, too, thus corroborating a behavioral function in sex-pheromone communication. PMID:27540087

  19. Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity.

    Science.gov (United States)

    Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

    2014-08-01

    To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to 'classical' hotspots based on species richness (SR) only. Global. SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global scale.

  20. 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.

  1. 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 L.; 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.

  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. Variation in the Asian monsoon intensity and dry-wet condition since the Little Ice Age in central China revealed by an aragonite stalagmite

    Science.gov (United States)

    Yin, J.-J.; Yuan, D.-X.; Li, H.-C.; Cheng, H.; Li, T.-Y.; Edwards, R. L.; Lin, Y.-S.; Qin, J.-M.; Tang, W.; Zhao, Z.-Y.; Mii, H.-S.

    2014-04-01

    Highlight: this paper focuses on the climate variability in central China since 1300 AD, involving: 1. A well-dated, 1.5 year resolution stalagmite δ18O record from Lianhua Cave, central China; 2. Links of the δ18O record with regional dry-wet condition, monsoon intensity, and temperature over eastern China; 3. Correlations among drought events in the Lianhua record, solar irradiation, and ENSO index. We present a highly precisely 230Th/U dated, 1.5 year resolution δ18O record of an aragonite stalagmite (LHD1) collected from Lianhua Cave in Wuling mountain area of central China. The comparison of the δ18O record with the local instrumental record and historical documents exhibits at least 15 drought events in the Wuling mountain and adjacent areas during the Little Ice Age, in which some of them were corresponding to megadrought events in the broad Asian monsoonal region of China. Thus, the stalagmite δ18O record reveals variations in the summer monsoon precipitation and dry-wet condition in Wuling mountain area. The eastern China temperature varied with the solar activity, showing higher temperature under stronger solar irradiation which produces stronger summer monsoon. During Maunder, Dalton and 1900 sunspot minima, more severe drought events occurred, indicating weakening of the summer monsoon when solar activity decreased on decadal time scales. On interannual time scale, dry conditions in the studying area were prevailing under El Niño condition, which is also supported by the spectrum analysis. Hence, our record illustrates the linkage of Asian summer monsoon precipitation to solar irradiation and ENSO: wetter condition under stronger summer monsoon during warm periods and vice versa; During cold periods, the Walker circulation will shift toward central Pacific under El Niño condition, resulting further weakening of Asian summer monsoon. However, the δ18O of LHD1 record is positively correlated with temperature after ~1940 AD which is opposite to the

  4. Seasonal and Daily Variations of Subsurface Velocity Revealed by the Air-gun Source in Binchuan, Yunnan, China

    Science.gov (United States)

    Luan, Y.; Yang, H.; Wang, B.

    2017-12-01

    We derive temporal variations of subsurface structure using a large-volume air-gun source excited in Binchuan, Yunnan, southwest China, the first transmitting seismic station that can generate high-quality repeating waveforms. The data were collected between January 2013 and December 2015 that were recorded by 40 stations within 150 km, including permanent and newly deployed air-gun array stations. Firstly, we conduct cluster analysis using the waveforms at the nearest station and find the clustering result is not only governed by the water level of the reservoir, but also has seasonal variations. Furthermore, we use the records of the nearest station to approximate the source time functions and then retrieve empirical Green's functions (EGF) by deconvolution. Then we obtain travel time difference by comparing the EGF. The travel time difference exhibits clear seasonal variation, and the pattern correlates the best with surface air temperature. The increasing temperature coincides with increasing delay time i.e. decreasing seismic velocity. We interpret the observed seasonal variation of subsurface velocity is partly caused by thermo-elastic strain. However, our calculated thermo-elastic strain is only half in amplitude of the observed strain, indicating other factors such as precipitation and ground water level may play a role in the subsurface changes. Moreover, we derive the daily variation of subsurface velocity in December 2015 when air-gun shots were made in every hour. The delay time clearly correlates with the barometric pressure change and the tidal strain. Here we demonstrate that both long-term (seasonal) and short-term (daily) structural variations can be derived using the newly constructed active source, which is a powerful tool to advance our understanding of rheological properties of the crust as well as well processes associated with earthquakes and other natural hazards.

  5. 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

  6. CpDNA haplotype variation reveals strong human influence on oak stands of the Veluwe forest in the Netherlands

    NARCIS (Netherlands)

    Buiteveld, J.; Koelewijn, H.P.

    2006-01-01

    We examined chloroplast DNA (cpDNA) variation in 78 oak stands of an important forest complex (the Veluwe) in The Netherlands. Based on historical maps and information oak stands were classified as planted or autochthonous. A genetic study by means of cpDNA haplotype characterisation was carried out

  7. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

    NARCIS (Netherlands)

    Zhang, Z.; Mao, L.; Chen, Junshi; Bu, F.; Li, G.; Sun, J.; Li, S.; Sun, H.; Jiao, C.; Blakely, R.; Pan, J.; Cai, R.; Luo, R.; Peer, Van de Y.; Jacobsen, E.; Fei, Z.; Huang, S.

    2015-01-01

    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep

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

    KAUST Repository

    Lee, O. O.; Yang, J.; Bougouffa, S.; Wang, Y.; Batang, Zenon B.; Tian, R.; Al-Suwailem, A.; Qian, P.-Y.

    2012-01-01

    -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

  9. 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

  10. Geographical variation in the age/length relationship in Baltic flounder ( Platichthys flesus )

    DEFF Research Database (Denmark)

    Drevs, T.; Kadakas, V; Lang, T.

    1999-01-01

    The age/length relationship in Baltic flounder (Platichthys flesus) was investigated by sex, based on otolith readings of 2925 individuals sampled from 11 stations along a transect from the Mecklenburg Eight to the Gulf of Finland in autumn 1994. A significant decrease in length at age was observ...

  11. 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

  12. Linear and non-linear dose-response functions reveal a hormetic relationship between stress and learning.

    Science.gov (United States)

    Zoladz, Phillip R; Diamond, David M

    2008-10-16

    Over a century of behavioral research has shown that stress can enhance or impair learning and memory. In the present review, we have explored the complex effects of stress on cognition and propose that they are characterized by linear and non-linear dose-response functions, which together reveal a hormetic relationship between stress and learning. We suggest that stress initially enhances hippocampal function, resulting from amygdala-induced excitation of hippocampal synaptic plasticity, as well as the excitatory effects of several neuromodulators, including corticosteroids, norepinephrine, corticotropin-releasing hormone, acetylcholine and dopamine. We propose that this rapid activation of the amygdala-hippocampus brain memory system results in a linear dose-response relation between emotional strength and memory formation. More prolonged stress, however, leads to an inhibition of hippocampal function, which can be attributed to compensatory cellular responses that protect hippocampal neurons from excitotoxicity. This inhibition of hippocampal functioning in response to prolonged stress is potentially relevant to the well-described curvilinear dose-response relationship between arousal and memory. Our emphasis on the temporal features of stress-brain interactions addresses how stress can activate, as well as impair, hippocampal functioning to produce a hormetic relationship between stress and learning.

  13. Trophic calculations reveal the mechanism of population-level variation in mercury concentrations between marine ecosystems: Case studies of two polar seabirds

    International Nuclear Information System (INIS)

    Brasso, Rebecka L.; Polito, Michael J.

    2013-01-01

    Highlights: • Ecosystem-specific baseline and consumer δ 15 N paired for population-specific trophic level. • Source of population-level variation in mercury exposure identified in two seabirds. • High mercury and trophic position suggests trophic driver of population-level variation. • Trophic similarities, differing mercury reveals geographic differences in bioavailability. -- Abstract: 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

  14. Relationship between climatic variables and the variation in bulk tank milk composition using canonical correlation analysis.

    Science.gov (United States)

    Stürmer, Morgana; Busanello, Marcos; Velho, João Pedro; Heck, Vanessa Isabel; Haygert-Velho, Ione Maria Pereira

    2018-06-04

    A number of studies have addressed the relations between climatic variables and milk composition, but these works used univariate statistical approaches. In our study, we used a multivariate approach (canonical correlation) to study the impact of climatic variables on milk composition, price, and monthly milk production at a dairy farm using bulk tank milk data. Data on milk composition, price, and monthly milk production were obtained from a dairy company that purchased the milk from the farm, while climatic variable data were obtained from the National Institute of Meteorology (INMET). The data are from January 2014 to December 2016. Univariate correlation analysis and canonical correlation analysis were performed. Few correlations between the climatic variables and milk composition were found using a univariate approach. However, using canonical correlation analysis, we found a strong and significant correlation (r c  = 0.95, p value = 0.0029). Lactose, ambient temperature measures (mean, minimum, and maximum), and temperature-humidity index (THI) were found to be the most important variables for the canonical correlation. Our study indicated that 10.2% of the variation in milk composition, pricing, and monthly milk production can be explained by climatic variables. Ambient temperature variables, together with THI, seem to have the most influence on variation in milk composition.

  15. 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.

  16. Additive genetic variation in the craniofacial skeleton of baboons (genus Papio) and its relationship to body and cranial size.

    Science.gov (United States)

    Joganic, Jessica L; Willmore, Katherine E; Richtsmeier, Joan T; Weiss, Kenneth M; Mahaney, Michael C; Rogers, Jeffrey; Cheverud, James M

    2018-02-01

    Determining the genetic architecture of quantitative traits and genetic correlations among them is important for understanding morphological evolution patterns. We address two questions regarding papionin evolution: (1) what effect do body and cranial size, age, and sex have on phenotypic (V P ) and additive genetic (V A ) variation in baboon crania, and (2) how might additive genetic correlations between craniofacial traits and body mass affect morphological evolution? We use a large captive pedigreed baboon sample to estimate quantitative genetic parameters for craniofacial dimensions (EIDs). Our models include nested combinations of the covariates listed above. We also simulate the correlated response of a given EID due to selection on body mass alone. Covariates account for 1.2-91% of craniofacial V P . EID V A decreases across models as more covariates are included. The median genetic correlation estimate between each EID and body mass is 0.33. Analysis of the multivariate response to selection reveals that observed patterns of craniofacial variation in extant baboons cannot be attributed solely to correlated response to selection on body mass, particularly in males. Because a relatively large proportion of EID V A is shared with body mass variation, different methods of correcting for allometry by statistically controlling for size can alter residual V P patterns. This may conflate direct selection effects on craniofacial variation with those resulting from a correlated response to body mass selection. This shared genetic variation may partially explain how selection for increased body mass in two different papionin lineages produced remarkably similar craniofacial phenotypes. © 2017 Wiley Periodicals, Inc.

  17. 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.

  18. Lateral Variations of Interplate Coupling along the Mexican Subduction Interface: Relationships with Long-Term Morphology and Fault Zone Mechanical Properties

    Science.gov (United States)

    Rousset, Baptiste; Lasserre, Cécile; Cubas, Nadaya; Graham, Shannon; Radiguet, Mathilde; DeMets, Charles; Socquet, Anne; Campillo, Michel; Kostoglodov, Vladimir; Cabral-Cano, Enrique; Cotte, Nathalie; Walpersdorf, Andrea

    2016-10-01

    Although patterns of interseismic strain accumulation above subduction zones are now routinely characterised using geodetic measurements, their physical origin, persistency through time, and relationships to seismic hazard and long-term deformation are still debated. Here, we use GPS and morphological observations from southern Mexico to explore potential mechanical links between variations in inter-SSE (in between slow slip events) coupling along the Mexico subduction zone and the long-term topography of the coastal regions from Guerrero to Oaxaca. Inter-SSE coupling solutions for two different geometries of the subduction interface are derived from an inversion of continuous GPS time series corrected from slow slip events. They reveal strong along-strike variations in the shallow coupling (i.e. at depths down to 25 km), with high-coupling zones (coupling >0.7) alternating with low-coupling zones (coupling 0.7) and transitions to uncoupled, steady slip at a relatively uniform ˜ 175-km inland from the trench. Along-strike variations in the coast-to-trench distances are strongly correlated with the GPS-derived forearc coupling variations. To explore a mechanical explanation for this correlation, we apply Coulomb wedge theory, constrained by local topographic, bathymetric, and subducting-slab slopes. Critical state areas, i.e. areas where the inner subduction wedge deforms, are spatially correlated with transitions at shallow depth between uncoupled and coupled areas of the subduction interface. Two end-member models are considered to explain the correlation between coast-to-trench distances and along-strike variations in the inter-SSE coupling. The first postulates that the inter-SSE elastic strain is partitioned between slip along the subduction interface and homogeneous plastic permanent deformation of the upper plate. In the second, permanent plastic deformation is postulated to depend on frictional transitions along the subduction plate interface. Based on the

  19. 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

  20. The relationship between growth of the aerial part and alkaloid content variation in cultivated Aconitum carmichaeli Debeaux.

    Science.gov (United States)

    Kawasaki, Ryoichi; Motoya, Wakako; Atsumi, Toshiyuki; Mouri, Chika; Kakiuchi, Nobuko; Mikage, Masayuki

    2011-01-01

    Processed root of aconite, Aconitum carmichaeli Debeaux--known as bushi in Japan--is indispensable for treating diseases among elderly persons in Japanese and Chinese traditional medicine. Its active component is bushi diester alkaloid (BDA), which consists of aconitine (ACO), mesaconitine (MES), hypaconitine (HYP), and jesaconitine (JES). Since an overdose of BDA results in severe side effects, the BDA content should be within safe limits. However, the BDA content of raw aconite root, even that produced by standard cultivation procedures, varies greatly. In this study, to clarify the cause of BDA variation, we examined the weight and BDA content of each part of cultivated A. carmichaeli: the aerial part, the mother tuberous root (MT), the daughter tuberous root (DT), and the rootlet (RL). We found the following positive relationships: between aerial part weight and DT weight, aerial part weight and BDA content in stem of apex, and BDA content in stem of apex and total BDA of DT attached to the plant. Furthermore, DT belonging to a higher weight group showed less BDA content variation. In addition, BDA of DT and those of MT and RL differ in both content and composition. In conclusion, it was suggested that the weight or the size of the aerial part was a good marker for monitoring BDA content and its variation in the tuberous root, and it was found to be desirable to prevent mixing MT and RL at harvest.

  1. 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.

  2. GPS-tracking and colony observations reveal variation in offshore habitat use and foraging ecology of breeding Sandwich Terns

    Science.gov (United States)

    Fijn, R. C.; de Jong, J.; Courtens, W.; Verstraete, H.; Stienen, E. W. M.; Poot, M. J. M.

    2017-09-01

    Breeding success of seabirds critically depends on their foraging success offshore. However, studies combining at-sea tracking and visual provisioning observations are scarce, especially for smaller species of seabirds. This study is the first in which breeding Sandwich Terns were tracked with GPS-loggers to collect detailed data on foraging habitat use in four breeding seasons. The maximum home range of individual Sandwich Terns comprised approximately 1900 km2 and the average foraging range was 27 km. Trip durations were on average 135 min with average trip lengths of 67 km. Actual foraging behaviour comprised 35% of the time budget of a foraging trip. Substantial year-to-year variation was found in habitat use and trip variables, yet with the exception of 2012, home range size remained similar between years. Food availability, chick age and environmental conditions are proposed as the main driving factors between inter- and intra-annual variations in trip variables. Our multi-method approach also provided geo-referenced information on prey presence and we conclude that future combining of colony observations and GPS-loggers deployments can potentially provide a near complete insight into the feeding ecology of breeding Sandwich Terns, including the behaviour of birds at sea.

  3. Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.

    Science.gov (United States)

    Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

    2014-03-01

    Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  4. 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

  5. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

    Science.gov (United States)

    Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J; Leitch, Ilia J

    2015-01-01

    The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

  6. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

    Directory of Open Access Journals (Sweden)

    Jiří Macas

    Full Text Available The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57% of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%. Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

  7. Mental and Active Preparation: Examining Variations in Women's Processes of Preparing to Leave Abusive Relationships.

    Science.gov (United States)

    Bermea, Autumn M; Khaw, Lyndal; Hardesty, Jennifer L; Rosenbloom, Lindsay; Salerno, Craig

    2017-02-01

    Although the process of leaving abusive relationships has received increased research attention, preparing to leave is still largely understudied. Despite an emphasis on safety planning, not all women take active steps to prepare, and the characteristics and experiences of those who do or do not actively prepare are unknown. We address this gap with a secondary data analysis of interviews with 25 abused mothers in the process of leaving. All women initially engaged in mental planning, where they had emotionally disconnected from their partners. Using constructivist grounded theory techniques, we identified two distinct groups: those whose mental planning led to active planning ( n = 11), and those who moved directly from mental planning to leaving ( n = 14) with little time or need to actively plan. The groups differed on several individual, relationship, and child factors, which may have impacted the ability or decisions to prepare. This study supports the feminist view that survivors are not helpless victims but active agents who strategize for safety. Those who engage solely in mental planning still prepare to leave, even if they do not engage in active planning. Practitioners should consider factors affecting preparations and acknowledge mental planning as a necessary effort in leaving.

  8. 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.

  9. Revealing the physical insight of a length-scale parameter in metamaterials by exploiting the variational formulation

    Science.gov (United States)

    Abali, B. Emek

    2018-04-01

    For micro-architectured materials with a substructure, called metamaterials, we can realize a direct numerical simulation in the microscale by using classical mechanics. This method is accurate, however, computationally costly. Instead, a solution of the same problem in the macroscale is possible by means of the generalized mechanics. In this case, no detailed modeling of the substructure is necessary; however, new parameters emerge. A physical interpretation of these metamaterial parameters is challenging leading to a lack of experimental strategies for their determination. In this work, we exploit the variational formulation based on action principles and obtain a direct relation between a parameter used in the kinetic energy and a metamaterial parameter in the case of a viscoelastic model.

  10. Genetic and biochemical analysis reveals linked QTLs determining natural variation for fruit post-harvest water loss in pepper (Capsicum).

    Science.gov (United States)

    Popovsky-Sarid, Sigal; Borovsky, Yelena; Faigenboim, Adi; Parsons, Eugene P; Lohrey, Gregory T; Alkalai-Tuvia, Sharon; Fallik, Elazar; Jenks, Matthew A; Paran, Ilan

    2017-02-01

    Molecular markers linked to QTLs controlling post-harvest fruit water loss in pepper may be utilized to accelerate breeding for improved shelf life and inhibit over-ripening before harvest. Bell pepper (Capsicum annuum L.) is an important vegetable crop world-wide. However, marketing is limited by the relatively short shelf life of the fruit due to water loss and decay that occur during prolonged storage. Towards breeding pepper with reduced fruit post-harvest water loss (PWL), we studied the genetic, physiological and biochemical basis for natural variation of PWL. We performed quantitative trait locus (QTL) mapping of fruit PWL in multiple generations of an interspecific cross of pepper, which resulted in the identification of two linked QTLs on chromosome 10 that control the trait. We further developed near-isogenic lines (NILs) for characterization of the QTL effects. Transcriptome analysis of the NILs allowed the identification of candidate genes associated with fruit PWL-associated traits such as cuticle biosynthesis, cell wall metabolism and fruit ripening. Significant differences in PWL between the NILs in the immature fruit stage, differentially expressed cuticle-associated genes and differences in the content of specific chemical constituents of the fruit cuticle, indicated a likely influence of cuticle composition on the trait. Reduced PWL in the NILs was associated with delayed over-ripening before harvest, low total soluble solids before storage, and reduced fruit softening after storage. Our study enabled a better understanding of the genetic and biological processes controlling natural variation in fruit PWL in pepper. Furthermore, the genetic materials and molecular markers developed in this study may be utilized to breed peppers with improved shelf life and inhibited over-ripening before harvest.

  11. Spatio-temporal dynamics of ocean conditions and forage taxa reveal regional structuring of seabird–prey relationships.

    Science.gov (United States)

    Santora, Jarrod A; Schroeder, Isaac D; Field, John C; Wells, Brian K; Sydeman, William J

    Studies of predator–prey demographic responses and the physical drivers of such relationships are rare, yet essential for predicting future changes in the structure and dynamics of marine ecosystems. Here, we hypothesize that predator–prey relationships vary spatially in association with underlying physical ocean conditions, leading to observable changes in demographic rates, such as reproduction. To test this hypothesis, we quantified spatio-temporal variability in hydrographic conditions, krill, and forage fish to model predator (seabird) demographic responses over 18 years (1990–2007). We used principal component analysis and spatial correlation maps to assess coherence among ocean conditions, krill, and forage fish, and generalized additive models to quantify interannual variability in seabird breeding success relative to prey abundance. The first principal component of four hydrographic measurements yielded an index that partitioned “warm/weak upwelling” and “cool/strong upwelling” years. Partitioning of krill and forage fish time series among shelf and oceanic regions yielded spatially explicit indicators of prey availability. Krill abundance within the oceanic region was remarkably consistent between years, whereas krill over the shelf showed marked interannual fluctuations in relation to ocean conditions. Anchovy abundance varied on the shelf, and was greater in years of strong stratification, weak upwelling and warmer temperatures. Spatio-temporal variability of juvenile forage fish co-varied strongly with each other and with krill, but was weakly correlated with hydrographic conditions. Demographic responses between seabirds and prey availability revealed spatially variable associations indicative of the dynamic nature of “predator–habitat” relationships. Quantification of spatially explicit demographic responses, and their variability through time, demonstrate the possibility of delineating specific critical areas where the

  12. 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.

  13. Aibika (Abelmoschus manihot L.): Genetic variation, morphology and relationships to micronutrient composition.

    Science.gov (United States)

    Rubiang-Yalambing, Lydia; Arcot, Jayashree; Greenfield, Heather; Holford, Paul

    2016-02-15

    Aibika (Abelmoschus manihot L.) is believed to be a good source of micronutrients. However, although many varieties of aibika are commonly consumed in Papua New Guinea, their micronutrient content is unknown. Therefore, the mineral (Ca, Fe, K, Mg, Mn, Na, Zn & Cu), folate composition and the genetic variation of 23 aibika accessions from the collection at the National Agricultural Research Institute were studied over a 3year period to provide data for nutritional studies and to inform breeding programs. The data showed that aibika is, potentially, a crop of high nutritional value with the potential to boost the micronutrient status of local PNG communities. However, there were substantial differences in the micronutrient concentrations of the accessions from year to year and accessions that had the highest concentration of a particular mineral in 1year did not have the high concentrations in other years. Clusters determined using unweighted pair group method with arithmetic mean analysis (UPGMA) of the micronutrient contents differed in each of the 3years. Genetic analysis made using random amplification of polymorphic DNA and directed amplification of mini satellite region DNA placed the accessions into five groups. There was no correlation between these groups and leaf morphology, nor were there correlations with the clusters determined from the UPGMA analyses. There appears to be considerable interaction between genotype and environmental factors determining micronutrient composition and environmental factors may play a greater role than genotype in influencing micronutrient composition. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. 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.

  15. 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

  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. Diversity of 16S-23S rDNA internal transcribed spacer (ITS reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors.

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    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.

  18. Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).

    Science.gov (United States)

    Hinsu, Ankit T; Parmar, Nidhi R; Nathani, Neelam M; Pandit, Ramesh J; Patel, Anand B; Patel, Amrutlal K; Joshi, Chaitanya G

    2017-04-01

    Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. 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

  20. Self esteem and self agency in first episode psychosis: Ethnic variation and relationship with clinical presentation.

    Science.gov (United States)

    Ciufolini, Simone; Morgan, Craig; Morgan, Kevin; Fearon, Paul; Boydell, Jane; Hutchinson, Gerard; Demjaha, Arsjme; Girardi, Paolo; Doody, Gill A; Jones, Peter B; Murray, Robin; Dazzan, Paola

    2015-06-30

    The impact of self esteem and Locus of Control (LoC) on clinical presentation across different ethnic groups of patients at their first psychotic episode (FEP) remains unknown. We explored these constructs in 257 FEP patients (Black n=95; White British n=119) and 341 controls (Black n=70; White British n=226), and examined their relationship with symptom dimensions and pathways to care. FEP patients presented lower self-esteem and a more external LoC than controls. Lower self esteem was associated with a specific symptoms profile (more manic and less negative symptoms), and with factors predictive of poorer outcome (longer duration of untreated psychosis (DUP) and compulsory mode of admission). A more external LoC was associated with more negative symptoms and an insidious onset. When we explored these constructs across different ethnic groups, we found that Black patients had significantly higher self esteem than White British. This was again associated with specific symptom profiles. While British patients with lower self esteem were more likely to report delusions, hallucinations and negative symptoms, Black patients with a lower self esteem showed less disorganization symptoms. These findings suggest that self esteem and LoC may represent one way in which social experiences and contexts differentially influence vulnerable individuals along the pathway to psychosis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  1. Nonlinear Variations of Net Primary Productivity and Its Relationship with Climate and Vegetation Phenology, China

    Directory of Open Access Journals (Sweden)

    Jian Yang

    2017-09-01

    Full Text Available Net primary productivity (NPP is an important component of the terrestrial carbon cycle. In this study, NPP was estimated based on two models and Moderate Resolution Imaging Spaectroradiometer (MODIS data. The spatiotemporal patterns of NPP and the correlations with climate factors and vegetation phenology were then analyzed. Our results showed that NPP derived from MODIS performed well in China. Spatially, NPP decreased from the southeast toward the northwest. Temporally, NPP showed a nonlinear increasing trend at a national scale, but the magnitude became slow after 2004. At a regional scale, NPP in Northern China and the Tibetan Plateau showed a nonlinear increasing trend, while the NPP decreased in most areas of Southern China. The decreases in NPP were more than offset by the increases. At the biome level, all vegetation types displayed an increasing trend, except for shrub and evergreen broad forests (EBF. Moreover, a turning point year occurred for all vegetation types, except for EBF. Generally, climatic factors and Length of Season were all positively correlated with the NPP, while the relationships were much more diverse at a regional level. The direct effect of solar radiation on the NPP was larger (0.31 than precipitation (0.25 and temperature (0.07. Our results indicated that China could mitigate climate warming at a regional and/or global scale to some extent during the time period of 2001–2014.

  2. 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.

  3. Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing.

    Science.gov (United States)

    Jo, Yeong Deuk; Choi, Yoomi; Kim, Dong-Hwan; Kim, Byung-Dong; Kang, Byoung-Cheorl

    2014-07-04

    Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Although large portion of sequence context was

  4. 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.

  5. Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep.

    Directory of Open Access Journals (Sweden)

    Susan T Harbison

    2017-12-01

    Full Text Available 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.

  6. Relationship Between Gender, Age, and Weight and the Serum Ionized Calcium Variations in Dog Periodontal Disease Evolution.

    Science.gov (United States)

    Carreira, L Miguel; Dias, Daniela; Azevedo, Pedro

    2015-06-01

    To analyze the relationships between gender, age, weight, and variations in the levels of serum ionized calcium ([iCa(2+)]) during periodontal disease (PD) evolution. In this study, dogs (n = 50) were divided into 5 groups according to the stage of PD: G0 (no PD), G1 (gingivitis), G2 (initial periodontitis), G3 (moderate periodontitis), and G4 (severe periodontitis). Statistically significant correlations were observed between age, [iCa(2+)] levels, and PD stage. Older dogs had lower [iCa(2+)] levels and more advanced PD stages (high positive correlation), and their body weight decreased as PD developed (negative correlation). Lower [iCa(2+)] values were associated with more severe PD. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Regional variation of white matter development in the cat brain revealed by ex vivo diffusion MR tractography.

    Science.gov (United States)

    Dai, Guangping; Das, Avilash; Hayashi, Emiko; Chen, Qin; Takahashi, Emi

    2016-11-01

    Three-dimensional reconstruction of developing fiber pathways is essential to assessing the developmental course of fiber pathways in the whole brain. We applied diffusion spectrum imaging (DSI) tractography to five juvenile ex vivo cat brains at postnatal day (P) 35, when the degree of myelination varies across brain regions. We quantified diffusion properties (fractional anisotropy [FA] and apparent diffusion coefficient [ADC]) and other measurements (number, volume, and voxel count) on reconstructed pathways for projection (cortico-spinal and thalamo-cortical), corpus callosal, limbic (cingulum and fornix), and association (cortico-cortical) pathways, and characterized regional differences in maturation patterns by assessing diffusion properties. FA values were significantly higher in cortico-cortical pathways within the right hemisphere compared to those within the left hemisphere, while the other measurements for the cortico-cortical pathways within the hemisphere did not show asymmetry. ADC values were not asymmetric in both types of pathways. Interestingly, tract count and volume were significantly larger in the left thalamo-cortical pathways compared to the right thalamo-cortical pathways. The bilateral thalamo-cortical pathways showed high FA values compared to the other fiber pathways. On the other hand, ADC values did not show any differences across pathways studied. These results demonstrate that DSI tractography successfully depicted regional variations of white matter tracts during development when myelination is incomplete. Low FA and high ADC values in the cingulum bundle suggest that the cingulum bundle is less mature than the others at this developmental stage. Copyright © 2016 ISDN. Published by Elsevier Ltd. All rights reserved.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Relationships between pigment composition variation and reflectance for plant species from a coastal savannah in California

    Science.gov (United States)

    Ustin, Susan L.; Sanderson, Eric W.; Grossman, Yaffa; Hart, Quinn J.

    1993-01-01

    Advances in imaging spectroscopy have indicated that remotely sensed reflectance measurements of the plant canopy may be used to identify and qualify some classes of canopy biochemicals; however, the manner in which differences in biochemical compositions translate into differences is not well understood. Most frequently, multiple linear regression routines have been used to correlate narrow band reflectance values with measured biochemical concentrations. Although some success has been achieved with such methods for given data sets, the bands selected by multiple regression are not consistent between data sets, nor is it always clear what physical or biological basis underlies the correlation. To examine the relationship between biochemical concentration and leaf reflectance signal we chose to focus on the visible spectrum where the primary biochemical absorbances are due to photosynthetic pigments. Pigments provide a range of absorbance features, occur over a range of concentrations in natural samples, and are ecophysiologically important. Concentrations of chlorophyll, for example, have been strongly correlated to foliar nitrogen levels within a species and to photosynthetic capacity across many species. In addition pigments effectively absorb most of the photosynthetically active radiation between 400-700 nm, a spectral region for which silicon detectors have good signal/noise characteristics. Our strategy has been to sample a variety of naturally occurring species to measure leaf reflectance and pigment compositions. We hope to extend our understanding of pigment reflectance effects to interpret small overlapping absorbances of other biochemicals in the infrared region. For this reason, selected samples were also tested to determine total nitrogen, crude protein, cellulose, and lignin levels. Leaf reflectance spectra measured with AVIRIS bandwidths and wavelengths were compared between species and within species and for differences between seasons, for changes

  14. Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing.

    Directory of Open Access Journals (Sweden)

    Zhen-Hui Wang

    Full Text Available BACKGROUND: Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs and 17,839 homozygous insertions/deletions (indels were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a

  15. PWR clad ballooning: The effect of circumferential clad temperature variations on the burst strain/burst temperature relationship

    International Nuclear Information System (INIS)

    Barlow, P.

    1983-01-01

    By experiment, it has been shown by other workers that there is a reduction in the creep ductility of Zircaloy 4 in the α+β phase transition region. Results from single rod burst tests also show a reduction in burst strain in the α+β phase region. In this report it is shown theoretically that for single rod burst tests in the presence of circumferential temperature gradients, the temperature dependence of the mean burst strain is not determined by temperature variations in creep ductility, but is governed by the temperature sensitivity of the creep strain rate, which is shown to be a maximum in the α+β phase transition region. To demonstrate this effect, the mean clad strain at burst was calculated for creep straining at different temperature levels in the α, α+β and β phase regions. Cross-pin temperature gradients were applied which produced strain variations around the clad which were greatest in the α+β phase region. The mean strain at burst was determined using a maximum local burst strain (i.e. a creep ductility) which is independent of temperature. By assuming cross-pin temperature gradients which are typical of those observed during burst tests, then the calculated mean burst strain/burst temperature relationship gave good agreement with experiment. The calculations also show that when circumferential temperature differences are present, the calculated mean strain at burst is not sensitive to variations in the magnitude of the assumed creep ductility. This reduces the importance of the assumed burst criterion in the calculations. Hence a temperature independent creep ductility (e.g. 100% local strain) is adequate as a burst criterion for calculations under PWR LOCA conditions. (author)

  16. Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

    Science.gov (United States)

    Jha, Aashish R; Miles, Cecelia M; Lippert, Nodia R; Brown, Christopher D; White, Kevin P; Kreitman, Martin

    2015-10-01

    Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Genetic characterisation of farmed rainbow trout in Norway: intra- and inter-strain variation reveals potential for identification of escapees

    Directory of Open Access Journals (Sweden)

    Glover Kevin A

    2008-12-01

    Full Text Available Abstract Background The rainbow trout (Oncorhynchus mykiss is one of the most important aquaculture species in the world, and Norway is one of the largest producers. The present study was initiated in response to a request from the Norwegian police authority to identify the farm of origin for 35 escaped rainbow trout captured in a fjord. Eleven samples, each consisting of approximately 47 fish, were collected from the three farms operating in the fjord where the escapees were captured. In order to gain a better general understanding of the genetic structure of rainbow trout strains used in Norwegian aquaculture, seven samples (47 fish per sample were collected from six farms located outside the region where the escapees were captured. All samples, including the escapees, were genotyped with 12 microsatellite loci. Results All samples displayed considerable genetic variability at all loci (mean number of alleles per locus per sample ranged from 5.4–8.6. Variable degrees of genetic differentiation were observed among the samples, with pair-wise FST values ranging from 0–0.127. Self-assignment tests conducted among the samples collected from farms outside the fjord where the escapees were observed gave an overall correct assignment of 82.5%, demonstrating potential for genetic identification of escapees. In the "real life" assignment of the 35 captured escapees, all were excluded from two of the samples included as controls in the analysis, and 26 were excluded from the third control sample. In contrast, only 1 of the escapees was excluded from the 11 pooled samples collected on the 3 farms operating in the fjord. Conclusion Considerable genetic variation exists within and among rainbow trout strains farmed in Norway. Together with modern statistical methods, this will provide commercial operators with a tool to monitor breeding and fish movements, and management authorities with the ability to identify the source of escapees. The data

  18. Genetic variation in Rhodomyrtus tomentosa (Kemunting) populations from Malaysia as revealed by inter-simple sequence repeat markers.

    Science.gov (United States)

    Hue, T S; Abdullah, T L; Abdullah, N A P; Sinniah, U R

    2015-12-14

    Kemunting (Rhodomyrtus tomentosa) from the Myrtaceae family, is native to Malaysia. It is widely used in traditional medicine to treat various illnesses and possesses significant antibacterial properties. In addition, it has great potential as ornamental in landscape design. Genetic variability studies are important for the rational management and conservation of genetic material. In the present study, inter-simple sequence repeat markers were used to assess the genetic diversity of 18 R. tomentosa populations collected from ten states of Peninsular Malaysia. The 11 primers selected generated 173 bands that ranged in size from 1.6 kb to 130 bp, which corresponded to an average of 15.73 bands per primer. Of these bands, 97.69% (169 in total) were polymorphic. High genetic diversity was documented at the species level (H(T) = 0.2705; I = 0.3973; PPB = 97.69%) but there was a low diversity at population level (H(S) = 0.0073; I = 0 .1085; PPB = 20.14%). The high level of genetic differentiation revealed by G(ST) (73%) and analysis of molecular variance (63%), together with the limited gene flow among population (N(m) = 0.1851), suggests that the populations examined are isolated. Results from an unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis clearly grouped the populations into two geographic groups. This clear grouping can also be demonstrated by the significant Mantel test (r = 0.581, P = 0.001). We recommend that all the R. tomentosa populations be preserved in conservation program.

  19. 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.

  20. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  1. Population variation in drought resistance and its relationship with adaptive and physiological seedling traits in Turkish red pine (Pinus brutia Ten.)

    OpenAIRE

    KANDEMİR, GAYE; ÖNDE, SERTAÇ; TEMEL, FATİH; KAYA, ZEKİ

    2017-01-01

    Variation in drought resistance and its relationship with adaptive and physiological traits in forest trees are important in choosing suitable seed sources for reforestation and afforestation programs. A common garden experiment using 240 half-sib families originating from coastal and inland populations of Turkish red pine (Pinus brutia) in Turkey was set up with three replicates. The aims were to determine variation of drought damage, height growth, and phenology among populations and to ...

  2. Racial and Ethnic Variation in the Relationship Between Student Loan Debt and the Transition to First Birth.

    Science.gov (United States)

    Min, Stella; Taylor, Miles G

    2018-02-01

    The present study employs discrete-time hazard regression models to investigate the relationship between student loan debt and the probability of transitioning to either marital or nonmarital first childbirth using the 1997 National Longitudinal Survey of Youth (NLSY97). Accounting for nonrandom selection into student loans using propensity scores, our study reveals that the effect of student loan debt on the transition to motherhood differs among white, black, and Hispanic women. Hispanic women holding student loans experience significant declines in the probability of transitioning to both marital and nonmarital motherhood, whereas black women with student loans are significantly more likely to transition to any first childbirth. Indebted white women experience only a decrease in the probability of a marital first birth. The results from this study suggest that student loans will likely play a key role in shaping future demographic patterns and behaviors.

  3. Variations in fuel characteristics of corn (Zea mays) stovers: General spatial patterns and relationships to soil properties

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Shaojun [Unit of Biomass Technology and Chemistry, Swedish University of Agricultural Sciences, SE-901 83 Umeaa (Sweden); College of Life Science, Beijing Normal University, Beijing (China); Zhang, Yufen [College of Life Science, Beijing Normal University, Beijing (China); Zhuo, Yue [Biomass Engineering Centre, China Agricultural University, Beijing (China); Lestander, Torbjoern; Geladi, Paul [Unit of Biomass Technology and Chemistry, Swedish University of Agricultural Sciences, SE-901 83 Umeaa (Sweden)

    2010-06-15

    The geographic variations in corn stover fuel and soil characteristics from 22 sites in the Kerchin region (43.8-45.0 N, 122.7-125.1 E), north-east China, were examined in both 2006 and 2007. The correlations between fuel characteristics and soil parameters were analysed using principal component analysis (PCA) and partial least squares regression (PLS). The main emphasis was on the feasibility of using corn stovers as feedstock in direct combustion for heat and power generation. The examined corn stovers from Kerchin generally have similar characteristics to energy grasses grown in Europe and may be used as biofuels. However, large variations, up to several orders of magnitude, in the fuel characteristics existed among the samples. With PCA, the studied soils showed a clear distinction between soluble and less soluble elements, with a trend for higher insoluble element (such as Si) concentrations in south-western soils and a higher pH in the more northern soils. The component for fuel characteristics showed a distinct trend with latitude that can be explained by the above-mentioned soil component pattern. PLS regression models suggested some important relationships that may be used to predict corn stover fuel characteristics using soil and environment properties; for example, latitude, soil pH and Si are the most important predictors for Ca content in corn stovers, but not for K that is best predicted by soil K. Although limited by numbers of samples and sites, this study indicated that this approach can be used to predict biofuel quality. (author)

  4. The variation in visibility and its relationship with surface wind speed in China from 1960 to 2009

    Science.gov (United States)

    Sun, Tianze; Che, Huizheng; Wu, Jian; Wang, Hong; Wang, Yaqiang; Zhang, Xiaoye

    2018-01-01

    This study used daily visibility and surface wind speed observational data over the 50-year period from 1960 to 2009, from 464 national meteorological stations in China, to examine the relationship between these two variables. Specifically, using the statistical methods of empirical orthogonal function (EOF) analysis and wavelet analysis, the data were processed into anomaly data to study their spatial and temporal distributions and the characteristics of each pattern's periodicity after EOF analysis of the whole country's visibility and surface wind speed. Correlation analysis and composite analysis were then used to elucidate the relationship between the two variables on different time scales. The results showed a gradual reduction in visibility nationally, with the nine-point moving mean implying decadal variability of the visibility with a downward trend. However, an irregular oscillation was found for the inter-annual variability of visibility. For the anomaly series of visibility during the 50-year period, a long-period oscillation of around 32 years was apparent. Up until the 1990s, there was an approximate 16-year medium-term oscillation period, whereas, after the 1990s, an approximate 8-year oscillation period was generated. In terms of high correlation between the two variables, for the decadal variability, the changes in visibility and surface wind speed at this time scale were almost in agreement. Meanwhile, with respect to the serious pollution in the Yangtze River Delta Economic Zone, the correlation between the two variables was reasonably high, suggesting that surface wind had a significant influence on the scattering of aerosol particles. However, in the Sichuan Basin, the correlation was relatively low, possibly on account of its landscape limiting the variation of wind speed.

  5. The relationship of age-adjusted Charlson comorbidity ındex and diurnal variation of blood pressure.

    Science.gov (United States)

    Kalaycı, Belma; Erten, Yunus Turgay; Akgün, Tunahan; Karabag, Turgut; Kokturk, Furuzan

    2018-03-05

    Charlson Comorbidity index (CCI) is a scoring system to predict prognosis and mortality. It exhibits better utility when combined with age, age-adjusted Charlson Comorbidity Index (ACCI). The aim of this study was to evaluate the relationship between ACCI and diurnal variation of blood pressure parameters in hypertensive patients and normotensive patients. We enrolled 236 patients. All patients underwent a 24-h ambulatory blood pressure monitoring (ABPM) for evaluation of dipper or non-dipper pattern. We searched the correlation between ACCI and dipper or non-dipper pattern and other ABPM parameters. To further investigate the role of these parameters in predicting survival, a multivariate analysis using the Cox proportional hazard model was performed. 167 patients were in the hypertensive group (87 patients in non-dipper status) and 69 patients were in the normotensive group (41 patients in non-dipper status) of all study patients. We found a significant difference and negative correlation between AACI and 24-h diastolic blood pressure (DBP), awake DBP, awake mean blood pressure (MBP) and 24-h MBP and awake systolic blood pressure(SBP). Night decrease ratio of blood pressure had also a negative correlation with ACCI (p = 0.003, r = -0.233). However, we found a relationship with non-dipper pattern and ACCI in the hypertensive patients (p = 0.050). In multivariate Cox analysis sleep MBP was found related to mortality like ACCI (p = 0.023, HR = 1.086, %95 CI 1.012-1.165) Conclusion: ACCI was statistically significantly higher in non-dipper hypertensive patients than dipper hypertensive patients while ACCI had a negative correlation with blood pressure. Sleep MBP may predict mortality.

  6. Family context, victimization, and child trauma symptoms: variations in safe, stable, and nurturing relationships during early and middle childhood.

    Science.gov (United States)

    Turner, Heather A; Finkelhor, David; Ormrod, Richard; Hamby, Sherry; Leeb, Rebecca T; Mercy, James A; Holt, Melissa

    2012-04-01

    Based on a nationally representative sample of 2,017 children age 2-9 years, this study examines variations in "safe, stable, and nurturing" relationships (SSNRs), including several forms of family perpetrated victimization, and documents associations between these factors and child trauma symptoms. Findings show that many children were exposed to multiple forms of victimization within the family (such as physical or sexual abuse, emotional maltreatment, child neglect, sibling victimization, and witnessing family violence), as evidenced by substantial intercorrelations among the different forms of victimization. Moreover, victimization exposure was significantly associated with several indices of parental dysfunction, family adversity, residential instability, and problematic parenting practices. Of all SSNR variables considered, emotional abuse and inconsistent or hostile parenting emerged as having the most powerful independent effects on child trauma symptoms. Also, findings supported a cumulative risk model, whereby trauma symptom levels increased with each additional SSNR risk factor to which children were exposed. Implications for research and practice are discussed. © 2012 American Orthopsychiatric Association.

  7. Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions.

    Science.gov (United States)

    Dulik, Matthew C; Osipova, Ludmila P; Schurr, Theodore G

    2011-03-11

    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.

  8. 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.

  9. Analyses of anatomical relationship between mandibular third molar roots and variations in lingual undercut of mandible using cone-beam computed tomography

    Directory of Open Access Journals (Sweden)

    Sertac Aktop

    2017-09-01

    Conclusion: The narrow angulation of the lingual balcony region and the relationship between roots and lingual soft tissues should be noted to avoid undesirable complication of displacement of a tooth or fragment into sublingual, submandibular, and pterygomandibular spaces. There was no relation in the floor of the mouth between the position of the impacted third molar roots and different lingual undercut angulation variations.

  10. Transcriptomic analysis of short-fruit 1 (sf1) reveals new insights into the variation of fruit-related traits in Cucumis sativus.

    Science.gov (United States)

    Wang, Lina; Cao, Chenxing; Zheng, Shuangshuang; Zhang, Haiyang; Liu, Panjing; Ge, Qian; Li, Jinrui; Ren, Zhonghai

    2017-06-07

    Fruit size is an important quality trait in different market classes of Cucumis sativus L., an economically important vegetable cultivated worldwide, but the genetic and molecular mechanisms that control fruit size are largely unknown. In this study, we isolated a natural cucumber mutant, short fruit 1 (sf1), caused by a single recessive Mendelian factor, from the North China-type inbred line CNS2. In addition to significantly decreased fruit length, other fruit-related phenotypic variations were also observed in sf1 compared to the wild-type (WT) phenotype, indicating that sf1 might have pleiotropic effects. Microscopic imaging showed that fruit cell size in sf1 was much larger than that in WT, suggesting that the short fruit phenotype in sf1 is caused by decreased cell number. Fine mapping revealed that sf1 was localized to a 174.3 kb region on chromosome 6. Similarly, SNP association analysis of bulked segregant RNA-Seq data showed increased SNP frequency in the same region of chromosome 6. In addition, transcriptomic analysis revealed that sf1 might control fruit length through the fine-tuning of cytokinin and auxin signalling, gibberellin biosynthesis and signal transduction in cucumber fruits. Overall, our results provide important information for further study of fruit length and other fruit-related features in cucumber.

  11. 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

  12. The Relationship Between Genetic Variations of the Cholesteryl Ester Transfer Protein Gene and Coronary Artery Disease in Turkish Subjects

    Science.gov (United States)

    Gundogdu, Fuat; Gurlertop, Yekta; Pirim, Ibrahim; Sevimli, Serdar; Dogan, Hasan; Arslan, Sakir; Aksoy, Hulya; Karakelloglu, Sule; Senocak, Huseyin

    2009-01-01

    Objective Although the relationship between cholesteryl ester transfer protein (CETP) and cholesterol metabolism has been characterized in recent years, the effect of CETP genetic variants associated with coronary artery disease (CAD) is still unclear. Therefore, we investigated the association between CETP gene polymorphism and levels of lipid in patients with CAD. Materials and Methods We conducted a case-control study that included 194 unrelated subjects who underwent coronary angiography for suspected ischemic heart disease. This group was divided into 96 patients with angiographically documented CAD and 98 subjects (individuals matched for age and gender) without angiographically documented CAD (CAD-free subjects), all of whom were studied to examine the genotypic distribution of the CETP gene polymorphism in CAD. Genotyping was performed via polymerase chain reaction. Results Of the 96 patients with CAD, 38 (40%) were B1B1, 42 (44%) B1B2 and 16 (16%) B2B2, compared with the control subjects, of which 35 (36%) were B1B1, 44 (45%) B1B2 and 19 (19%) B2B2. There were no significant differences between patients with CAD and control subjects in the distribution of the CETP gene polymorphism. Patients with the B1B1 genotype had lower high-density lipoprotein-cholesterol (HDL-C) and higher triglyceride (TG) levels than patients with the B2B2 genotype (p<0.05). In addition, among control subjects HDL-C levels were significantly higher in subjects with the B2B2 genotype than in subjects with the B1B1 genotype (p<0.01). Conclusion Our results suggest that genetic variations of the CTEP gene may be responsible for low HDL-C levels but may not be considered as a risk factor for CAD in the Turkish population. PMID:25610061

  13. 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.

  14. Variation in the biochemical response to l-thyroxine therapy and relationship with peripheral thyroid hormone conversion efficiency

    Science.gov (United States)

    Midgley, John E M; Larisch, Rolf; Dietrich, Johannes W; Hoermann, Rudolf

    2015-01-01

    Several influences modulate biochemical responses to a weight-adjusted levothyroxine (l-T4) replacement dose. We conducted a secondary analysis of the relationship of l-T4 dose to TSH and free T3 (FT3), using a prospective observational study examining the interacting equilibria between thyroid parameters. We studied 353 patients on steady-state l-T4 replacement for autoimmune thyroiditis or after surgery for malignant or benign thyroid disease. Peripheral deiodinase activity was calculated as a measure of T4–T3 conversion efficiency. In euthyroid subjects, the median l-T4 dose was 1.3 μg/kg per day (interquartile range (IQR) 0.94,1.60). The dose was independently associated with gender, age, aetiology and deiodinase activity (all P29 nmol/s revealed an increasing FT3–FT4 dissociation; the poorest converters showed the lowest FT3 levels in spite of the highest dose and circulating FT4 (P<0.001). An l-T4-related FT3–TSH disjoint was also apparent; some patients with fully suppressed TSH failed to raise FT3 above the median level. These findings imply that thyroid hormone conversion efficiency is an important modulator of the biochemical response to l-T4; FT3 measurement may be an additional treatment target; and l-T4 dose escalation may have limited success to raise FT3 appropriately in some cases. PMID:26335522

  15. Study on the relationship between the lake area variations of Qinghai-Tibetan Plateau and the corresponding climate change in their basins

    Science.gov (United States)

    Guozhuang, Shen; Jingjuan, Liao; Huadong, Guo; Yingkui, Li

    2014-03-01

    Qinghai-Tibetan Plateau is the largest lake area in China, with a total area of existing lakes of 36,900km2, accounting for 52% of the total lake area of China. Lakes on the Tibetan Plateau play critical roles in the water cycle and ecological and environment systems of the Plateau. The global trend of warming up is increasing obviously, which has led to major changes in the climate conditions in China, even in the world. Whereas, when they analyse the relationship they just use the weather station's recording data, without any spatial analysis of the climate data. Here, we will do some researches on the relationship between the 10 selected lakes' area variation and the corresponding climate change in their drainage basin and discuss how the lakes changes in recent 40 years using the climate data processed using the spatial kriging. Thus, the drainage area can be taken into account and a real relationship can be pointed out. In order to study the relationship, Landsat MSS data, Landsat TM, Landsat ETM images, the topographic map have been collected to extract the variation of lake area. The 131 weather stations climate data, including precipitation, temperature, sun shine duration, evaporation are chosen to study the relationship. After extraction of the area of the lakes, a multivariate statistical analysis method was used to test the relationship between the area of the lakes and the global climate change, including the change of the temperature, the precipitation, and other factors. The variation of lakes in Qinghai-Tibetan Plateau is related to the mean temperature, the precipitation and saturation vapour pressure. But the frozen soil may affect the lake area variation to some extent.

  16. Study on the relationship between the lake area variations of Qinghai-Tibetan Plateau and the corresponding climate change in their basins

    International Nuclear Information System (INIS)

    Guozhuang, Shen; Jingjuan, Liao; Huadong, Guo; Yingkui, Li

    2014-01-01

    Qinghai-Tibetan Plateau is the largest lake area in China, with a total area of existing lakes of 36,900km 2 , accounting for 52% of the total lake area of China. Lakes on the Tibetan Plateau play critical roles in the water cycle and ecological and environment systems of the Plateau. The global trend of warming up is increasing obviously, which has led to major changes in the climate conditions in China, even in the world. Whereas, when they analyse the relationship they just use the weather station's recording data, without any spatial analysis of the climate data. Here, we will do some researches on the relationship between the 10 selected lakes' area variation and the corresponding climate change in their drainage basin and discuss how the lakes changes in recent 40 years using the climate data processed using the spatial kriging. Thus, the drainage area can be taken into account and a real relationship can be pointed out. In order to study the relationship, Landsat MSS data, Landsat TM, Landsat ETM images, the topographic map have been collected to extract the variation of lake area. The 131 weather stations climate data, including precipitation, temperature, sun shine duration, evaporation are chosen to study the relationship. After extraction of the area of the lakes, a multivariate statistical analysis method was used to test the relationship between the area of the lakes and the global climate change, including the change of the temperature, the precipitation, and other factors. The variation of lakes in Qinghai-Tibetan Plateau is related to the mean temperature, the precipitation and saturation vapour pressure. But the frozen soil may affect the lake area variation to some extent

  17. Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae).

    Science.gov (United States)

    Moraes, Evandro M; Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Machado, Marlon C

    2012-09-01

    The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

  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. 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.

  1. Nonlinearity and thresholds in dose-response relationships for carcinogenicity due to sampling variation, logarithmic dose scaling, or small differences in individual susceptibility

    International Nuclear Information System (INIS)

    Lutz, W.K.; Gaylor, D.W.; Conolly, R.B.; Lutz, R.W.

    2005-01-01

    Nonlinear and threshold-like shapes of dose-response curves are often observed in tests for carcinogenicity. Here, we present three examples where an apparent threshold is spurious and can be misleading for low dose extrapolation and human cancer risk assessment. Case 1: For experiments that are not replicated, such as rodent bioassays for carcinogenicity, random variation can lead to misinterpretation of the result. This situation was simulated by 20 random binomial samplings of 50 animals per group, assuming a true linear dose response from 5% to 25% tumor incidence at arbitrary dose levels 0, 0.5, 1, 2, and 4. Linearity was suggested only by 8 of the 20 simulations. Four simulations did not reveal the carcinogenicity at all. Three exhibited thresholds, two showed a nonmonotonic behavior with a decrease at low dose, followed by a significant increase at high dose ('hormesis'). Case 2: Logarithmic representation of the dose axis transforms a straight line into a sublinear (up-bent) curve, which can be misinterpreted to indicate a threshold. This is most pronounced if the dose scale includes a wide low dose range. Linear regression of net tumor incidences and intersection with the dose axis results in an apparent threshold, even with an underlying true linear dose-incidence relationship. Case 3: Nonlinear shapes of dose-cancer incidence curves are rarely seen with epidemiological data in humans. The discrepancy to data in rodents may in part be explained by a wider span of individual susceptibilities for tumor induction in humans due to more diverse genetic background and modulation by co-carcinogenic lifestyle factors. Linear extrapolation of a human cancer risk could therefore be appropriate even if animal bioassays show nonlinearity

  2. Inter- and intra-specific cuticle variation between amphimictic and parthenogenetic species of root-knot nematode (Meloidogyne spp.) as revealed by a bacterial parasite (Pasteuria penetrans).

    Science.gov (United States)

    Davies, K G; Rowe, J A; Williamson, V M

    2008-06-01

    Specific host-parasite interactions exist between species and strains of plant parasitic root-knot nematodes and the Gram-positive bacterial hyperparasite Pasteuria penetrans. This bacterium produces endospores that adhere to the cuticle of migrating juveniles, germinate and colonise the developing female within roots. Endospore attachment of P. penetrans populations to second-stage juveniles of the root-knot nematode species Meloidogyne incognita and Meloidogyne hapla showed there were interactive differences between bacterial populations and nematode species. Infected females of M. incognita produced a few progeny which were used to establish two nematode lines from single infective juveniles encumbered with either three or 26 endospores. Single juvenile descent lines of each nematode species were produced to test whether cuticle variation was greater within M. hapla lines that reproduce by facultative meiotic parthenogenesis than within lines of M. incognita, which reproduces by obligate parthenogenesis. Assays revealed variability between broods of individual females derived from single second-stage juvenile descent lines of both M. incognita and M. hapla suggesting that progeny derived from a single individual can differ in spore adhesion in both sexual and asexual nematode species. These results suggest that special mechanisms that produced these functional differences in the cuticle surface may have evolved in both sexually and asexually reproducing nematodes as a strategy to circumvent infection by this specialised hyperparasite.

  3. 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.

  4. Modulation of the SSTA decadal variation on ENSO events and relationships of SSTA With LOD,SOI, etc

    Science.gov (United States)

    Liao, D. C.; Zhou, Y. H.; Liao, X. H.

    2007-01-01

    Interannual and decadal components of the length of day (LOD), Southern Oscillation Index (SOI) and Sea Surface Temperature anomaly (SSTA) in Nino regions are extracted by band-pass filtering, and used for research of the modulation of the SSTA on the ENSO events. Results show that besides the interannual components, the decadal components in SSTA have strong impacts on monitoring and representing of the ENSO events. When the ENSO events are strong, the modulation of the decadal components of the SSTA tends to prolong the life-time of the events and enlarge the extreme anomalies of the SST, while the ENSO events, which are so weak that they can not be detected by the interannual components of the SSTA, can also be detected with the help of the modulation of the SSTA decadal components. The study further draws attention to the relationships of the SSTA interannual and decadal components with those of LOD, SOI, both of the sea level pressure anomalies (SLPA) and the trade wind anomalies (TWA) in tropic Pacific, and also with those of the axial components of the atmospheric angular momentum (AAM) and oceanic angular momentum (OAM). Results of the squared coherence and coherent phases among them reveal close connections with the SSTA and almost all of the parameters mentioned above on the interannual time scales, while on the decadal time scale significant connections are among the SSTA and SOI, SLPA, TWA, ?3w and ?3w+v as well, and slight weaker connections between the SSTA and LOD, ?3pib and ?3bp

  5. Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing.

    Science.gov (United States)

    Khanshour, Anas M; Cothran, Ernest Gus

    2013-09-13

    Maternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East. The variability in the upstream region of the D-loop revealed additional differences among the haplotypes that had identical sequences in the hypervariable region 1 (HVR1). While the American-Arabians showed relatively low diversity, the Syrian population was the most variable and contained a very rare and old haplogroup. The Middle Eastern horses had major genetic contributions to the Western horses and there was no clear pattern of differentiation among all tested populations. Our results also showed that several individuals from different strains shared a single haplotype, and individuals from a single strain were represented in clearly separated haplogroups. The whole mtDNA D-loop sequence was more powerful for analysis of the maternal genetic diversity in the Arabian horses than using just the HVR1. Native populations from the Middle East, such as Syrians, could be suggested as a hot spot of genetic diversity and may help in understanding the evolution history of the Arabian horse breed. Most importantly, there was no evidence that the Arabian horse breed has clear subdivisions depending on the traditional maternal based strain classification system.

  6. 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.

  7. Variation in the Asian monsoon intensity and dry-wet conditions since the Little Ice Age in central China revealed by an aragonite stalagmite

    Science.gov (United States)

    Yin, J.-J.; Yuan, D.-X.; Li, H.-C.; Cheng, H.; Li, T.-Y.; Edwards, R. L.; Lin, Y.-S.; Qin, J.-M.; Tang, W.; Zhao, Z.-Y.; Mii, H.-S.

    2014-10-01

    This paper focuses on the climate variability in central China since AD 1300, involving: (1) a well-dated, 1.5-year resolution stalagmite δ18O record from Lianhua Cave, central China (2) links of the δ18O record with regional dry-wet conditions, monsoon intensity, and temperature over eastern China (3) correlations among drought events in the Lianhua record, solar irradiation, and ENSO (El Niño-Southern Oscillation) variation. We present a highly precise, 230Th / U-dated, 1.5-year resolution δ18O record of an aragonite stalagmite (LHD1) collected from Lianhua Cave in the Wuling Mountain area of central China. The comparison of the δ18O record with the local instrumental record and historical documents indicates that (1) the stalagmite δ18O record reveals variations in the summer monsoon intensity and dry-wet conditions in the Wuling Mountain area. (2) A stronger East Asian summer monsoon (EASM) enhances the tropical monsoon trough controlled by ITCZ (Intertropical Convergence Zone), which produces higher spring quarter rainfall and isotopically light monsoonal moisture in the central China. (3) The summer quarter/spring quarter rainfall ratio in central China can be a potential indicator of the EASM strength: a lower ratio corresponds to stronger EASM and higher spring rainfall. The ratio changed from 1 after 1950, reflecting that the summer quarter rainfall of the study area became dominant under stronger influence of the Northwestern Pacific High. Eastern China temperatures varied with the solar activity, showing higher temperatures under stronger solar irradiation, which produced stronger summer monsoons. During Maunder, Dalton and 1900 sunspot minima, more severe drought events occurred, indicating a weakening of the summer monsoon when solar activity decreased on decadal timescales. On an interannual timescale, dry conditions in the study area prevailed under El Niño conditions, which is also supported by the spectrum analysis. Hence, our record

  8. Karyotypic evolution and phylogenetic relationships in the order Chiroptera as revealed by G-banding comparison and chromosome painting.

    Science.gov (United States)

    Ao, Lei; Mao, Xiuguang; Nie, Wenhui; Gu, Xiaoming; Feng, Qing; Wang, Jinhuan; Su, Weiting; Wang, Yingxiang; Volleth, Marianne; Yang, Fengtang

    2007-01-01

    Bats are a unique but enigmatic group of mammals and have a world-wide distribution. The phylogenetic relationships of extant bats are far from being resolved. Here, we investigated the karyotypic relationships of representative species from four families of the order Chiroptera by comparative chromosome painting and banding. A complete set of painting probes derived from flow-sorted chromosomes of Myotis myotis (family Vespertilionidae) were hybridized onto metaphases of Cynopterus sphinx (2n = 34, family Pteropodidae), Rhinolophus sinicus (2n=36, family Rhinolophidae) and Aselliscus stoliczkanus (2n=30, family Hipposideridae) and delimited 27, 30 and 25 conserved chromosomal segments in the three genomes, respectively. The results substantiate that Robertsonian translocation is the main mode of chromosome evolution in the order Chiroptera, with extensive conservation of whole chromosomal arms. The use of M. myotis (2n=44) probes has enabled the integration of C. sphinx, R. sinicus and A. stoliczkanus chromosomes into the previously established comparative maps between human and Eonycteris spelaea (2n=36), Rhinolophus mehelyi (2n=58), Hipposideros larvatus (2n=32), and M. myotis. Our results provide the first cytogenetic signature rearrangement that supports the grouping of Pteropodidae and Rhinolophoidea in a common clade (i.e. Pteropodiformes or Yinpterochiroptera) and thus improve our understanding on the karyotypic relationships and genome phylogeny of these bat species.

  9. Variation in perceptions of physical dominance and trustworthiness predicts individual differences in the effect of relationship context on women's preferences for masculine pitch in men's voices.

    Science.gov (United States)

    Vukovic, Jovana; Jones, Benedict C; Feinberg, David R; Debruine, Lisa M; Smith, Finlay G; Welling, Lisa L M; Little, Anthony C

    2011-02-01

    Several studies have found that women tend to demonstrate stronger preferences for masculine men as short-term partners than as long-term partners, though there is considerable variation among women in the magnitude of this effect. One possible source of this variation is individual differences in the extent to which women perceive masculine men to possess antisocial traits that are less costly in short-term relationships than in long-term relationships. Consistent with this proposal, here we show that the extent to which women report stronger preferences for men with low (i.e., masculine) voice pitch as short-term partners than as long-term partners is associated with the extent to which they attribute physical dominance and low trustworthiness to these masculine voices. Thus, our findings suggest that variation in the extent to which women attribute negative personality characteristics to masculine men predicts individual differences in the magnitude of the effect of relationship context on women's masculinity preferences, highlighting the importance of perceived personality attributions for individual differences in women's judgments of men's vocal attractiveness and, potentially, their mate preferences. ©2010 The British Psychological Society.

  10. Mining routinely collected acute data to reveal non-linear relationships between nurse staffing levels and outcomes.

    Science.gov (United States)

    Leary, Alison; Cook, Rob; Jones, Sarahjane; Smith, Judith; Gough, Malcolm; Maxwell, Elaine; Punshon, Geoffrey; Radford, Mark

    2016-12-16

    Nursing is a safety critical activity but not easily quantified. This makes the building of predictive staffing models a challenge. The aim of this study was to determine if relationships between registered and non-registered nurse staffing levels and clinical outcomes could be discovered through the mining of routinely collected clinical data. The secondary aim was to examine the feasibility and develop the use of 'big data' techniques commonly used in industry for this area of healthcare and examine future uses. The data were obtained from 1 large acute National Health Service hospital trust in England. Routinely collected physiological, signs and symptom data from a clinical database were extracted, imported and mined alongside a bespoke staffing and outcomes database using Mathmatica V.10. The physiological data consisted of 120 million patient entries over 6 years, the bespoke database consisted of 9 years of daily data on staffing levels and safety factors such as falls. To discover patterns in these data or non-linear relationships that would contribute to modelling. To examine feasibility of this technique in this field. After mining, 40 correlations (pdata (such as the presence or absence of nausea) and staffing factors. Several inter-related factors demonstrated step changes where registered nurse availability appeared to relate to physiological parameters or outcomes such as falls and the management of symptoms. Data extraction proved challenging as some commercial databases were not built for extraction of the massive data sets they contain. The relationship between staffing and outcomes appears to exist. It appears to be non-linear but calculable and a data-driven model appears possible. These findings could be used to build an initial mathematical model for acute staffing which could be further tested. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  11. 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

  12. 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

  13. 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

  14. The potential of Tillandsia dune ecosystems for revealing past and present variations in advective fog along the coastal Atacama Desert, northern Chile

    Science.gov (United States)

    Latorre Hidalgo, C.; García, J. L.; Gonzalez, A. L.; Marquet, P. A.

    2015-12-01

    The coastal Atacama Desert is home to a complex geo-ecosystem supported by fog with multiple atmospheric and oceanic drivers. Fog collectors in place for the last 17 years reveal that monthly fog intensity and amount are significantly linked to the El Niño-Southern Oscillation (ENSO 1+2) with cold (warm) anomalies correlated to increased (decreased) fog (R2 = 0.41). Rainfall, however, can occur during extreme positive ENSO anomalies. Tillandsia landbeckii is an epiarenitic plant common to the coastal Atacama where fog is intercepted by the coastal escarpment between 950-1250 m.a.s.l. These plants possess multiple adaptations to survive exclusively on fog, including the construction of "dune" ecosystems known as "tillandsiales". Buried T. landbeckii layers in such dunes contain a record of past variations of fog over time (dunes can top 3 m in height) and alternating plant and sand layers are readily visible in dune stratigraphy. Stable N isotopes on modern plants and fog indicate that these plants reflect δ15N values of total N dissolved in fog. We measured δ15N values from buried T. landbeckii layers from five different tillandsiales found across c. 50 km the coastal escarpment. The isotope values in these buried plants indicate a prominent c. 8.0 ‰ shift towards more negative δ15N values on average over the last 3,200 years. Based on differences in δ15N between modern and more extensive "paleo" tillandsiales at one of our lowest elevation study sites, we interpret this shift as an increase in available moisture due to increased fog input during the late Holocene. Increased variability in ENSO as well as increased upwelling and southerly winds along the coastal Atacama would explain in part this increase. Clearly, the Atacama tillandsiales have considerable potential for monitoring past and present change of these large-scale ocean-atmosphere systems.

  15. Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma.

    Science.gov (United States)

    Wu, Ren-Chin; Chao, An-Shine; Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

    2017-07-18

    Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations.

  16. Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma

    Science.gov (United States)

    Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

    2017-01-01

    Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations. PMID:28533481

  17. Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Paraná river basins.

    Science.gov (United States)

    Claramunt, Santiago

    2014-09-01

    Relationships among genera in the tribe Synallaxini have proved difficult to resolve. In this study, I investigate relationships among Synallaxis, Certhiaxis and Schoeniophylax using DNA sequences from the mitochondrion and three nuclear regions. I implemented novel primers and protocols for amplifying and sequencing autosomal and sex-linked introns in Furnariidae that resolved basal relationships in the Synallaxini with strong support. Synallaxis propinqua is sister to Schoeniophylax phryganophilus, and together they form a clade with Certhiaxis. The results are robust to analytical approaches when all genomic regions are analyzed jointly (parsimony, maximum likelihood, and species-tree analysis) and the same basal relationships are recovered by most genomic regions when analyzed separately. A sister relationship between S. propinqua, an Amazonian river island specialist, and S. phryganophilus, from the Paraná River basin region, reveals a new biogeographic pattern shared by at least other four pairs of taxa with similar distributions and ecologies. Estimates of divergence times for these five pairs span from the late Miocene to the Pleistocene. Identification of the historical events that produced this pattern is difficult and further advances will require additional studies of the taxa involved and a better understanding of the recent environmental history of South America. A new classification is proposed for the Synallaxini, including the description of a new genus for S. propinqua. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. 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.

  19. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers

    DEFF Research Database (Denmark)

    Edwards, Arwyn; Mur, Luis A. J.; Girdwood, Susan E.

    2014-01-01

    Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction...... revealed Proteobacteria were particularly abundant, with Cyanobacteria likely acting as ecosystem engineers in both alpine and Arctic cryoconite communities. However, despite these generalities, significant differences in bacterial community structures, compositions and metabolomes are found between alpine...... fragment length polymorphism and Fourier transform infrared metabolite fingerprinting of cryoconite from glaciers in Austria, Greenland and Svalbard demonstrated cryoconite bacterial communities are closely correlated with cognate metabolite fingerprints. The influence of bacterial-associated fatty acids...

  20. 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.

  1. Anticipation of public speaking in virtual reality reveals a relationship between trait social anxiety and startle reactivity.

    Science.gov (United States)

    Cornwell, Brian R; Johnson, Linda; Berardi, Luciano; Grillon, Christian

    2006-04-01

    Startle reflex modification has become valuable to the study of fear and anxiety, but few studies have explored startle reactivity in socially threatening situations. Healthy participants ranging in trait social anxiety entered virtual reality (VR) that simulates standing center-stage in front of an audience to anticipate giving a speech and count backward. We measured startle and autonomic reactivity during anticipation of both tasks inside VR after a single baseline recording outside VR. Trait social anxiety, but not general trait anxiety, was positively correlated with startle before entering VR and most clearly during speech anticipation inside VR. Speech anticipation inside VR also elicited stronger physiologic responses relative to anticipation of counting. Under social-evaluative threat, startle reactivity showed robust relationships with fear of negative evaluation, a central aspect of social anxiety and clinical social phobia. Context-specific startle modification may be an endophenotype for subtypes of pathological anxiety.

  2. Comparative Proteomics Reveals Differences in Host-Pathogen Interaction between Infectious and Commensal Relationship with Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Juan J. Garrido

    2017-04-01

    Full Text Available Campylobacter jejuni is the leading food-borne poisoning in industrialized countries. While the bacteria causes disease in humans, it merely colonizes the gut in poultry or pigs, where seems to establish a commensal relationship. Until now, few studies have been conducted to elucidate the relationship between C. jejuni and its different hosts. In this work, a comparative proteomics approach was used to identify the underlying mechanisms involved in the divergent outcome following C. jejuni infection in human and porcine host. Human (INT-407 and porcine (IPEC-1 intestinal cell lines were infected by C. jejuni for 3 h (T3h and 24 h (T24h. C. jejuni infection prompted an intense inflammatory response at T3h in human intestinal cells, mainly characterized by expression of proteins involved in cell spreading, cell migration and promotion of reactive oxygen species (ROS. Proteomic analysis evidenced significantly regulated biofunctions in human cells related with engulfment and endocytosis, and supported by canonical pathways associated to infection such as caveolar- and clathrin-mediated endocytosis signaling. In porcine IPEC-1 cells, inflammatory response as well as signaling pathways that control cellular functions such as cell migration, endocytosis and cell cycle progression resulted downregulated. These differences in the host response to infection were supported by the different pattern of adhesion and invasion proteins expressed by C. jejuni in human and porcine cells. No marked differences in expression of virulence factors involved in adaptive response and iron acquisition functions were observed. Therefore, the results of this study suggest that both host and pathogen factors are responsible for commensal or infectious character of C. jejuni in different hosts.

  3. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar; Hasan, Zahra; Ali, Asho; McNerney, Ruth; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A.; Nair, Mridul; Clark, Taane G.; Zaver, Ambreen; Jafri, Sana; Hasan, Rumina

    2015-01-01

    Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  4. Assessing the relationship between the Driver Behavior Questionnaire and the Driver Skill Inventory: Revealing sub-groups of drivers

    DEFF Research Database (Denmark)

    Martinussen, Laila Marianne; Møller, Mette; Prato, Carlo Giacomo

    2014-01-01

    The Driver Behavior Questionnaire and the Driver Skill Inventory are two of the most frequently used measures of self-reported driving style and driving skill. The motivation behind the present study was to identify sub-groups of drivers that potentially act dangerously in traffic (as measured...... self-reported driving skills and whether the reported skill level was reflected in the reported aberrant driving behaviors. 3908 drivers aged 18–84 participated in the survey. K-means cluster analysis revealed four distinct sub-groups that differed in driving skills and frequency of aberrant driving...... by frequency of aberrant driving behaviors and level of driving skills), as well as to test whether the sub-groups differ in characteristics such as age, gender, annual mileage and accident involvement. Furthermore, the joint analysis of the two instruments was used to test drivers’ assessment of their own...

  5. 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 family relatedness of the breeding pairs....

  6. Geographic variation in body size and its relationship with environmental gradients in the Oriental Garden Lizard, Calotes versicolor.

    Science.gov (United States)

    Wei, Xiaomei; Yan, Linmiao; Zhao, Chengjian; Zhang, Yueyun; Xu, Yongli; Cai, Bo; Jiang, Ni; Huang, Yong

    2018-05-01

    Patterns of geographic variation in body size are predicted to evolve as adaptations to local environmental gradients. However, many of these clinal patterns in body size, such as Bergmann's rule, are controversial and require further investigation into ectotherms such as reptiles on a regional scale. To examine the environmental variables (temperature, precipitation, topography and primary productivity) that shaped patterns of geographic variation in body size in the reptile Calotes versicolor , we sampled 180 adult specimens (91 males and 89 females) at 40 locations across the species range in China. The MANOVA results suggest significant sexual size dimorphism in C. versicolor ( F 23,124  = 11.32, p  body size of C. versicolor differed for males and females, but mechanisms related to heat balance and water availability hypotheses were involved in both sexes. Temperature seasonality, precipitation of the driest month, precipitation seasonality, and precipitation of the driest quarter were the most important predictors of variation in body size in males, whereas mean precipitation of the warmest quarter, mean temperature of the wettest quarter, precipitation seasonality, and precipitation of the wettest month were most important for body size variation in females. The discrepancy between patterns of association between the sexes suggested that different selection pressures may be acting in males and females.

  7. 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

  8. Phylogenetic relationships among zooxanthellae (Symbiodinium) associated to excavating sponges (Cliona spp.) reveal an unexpected lineage in the Caribbean.

    Science.gov (United States)

    Granados, C; Camargo, C; Zea, S; Sánchez, J A

    2008-11-01

    Phylogenetic relationships of symbiotic dinoflagellate lineages, distributed in all tropical and subtropical seas, suggest strategies for long distance dispersal but at the same time strong host specialization. Zooxanthellae (Symbiodinium: Dinophyta), which are associated to diverse shallow-water cnidarians, also engage in symbioses with some sponge species of the genus Cliona. In the Caribbean, zooxanthellae-bearing Cliona has recently become abundant due to global warming, overfishing, and algae abundance. Using molecular techniques, the symbionts from five excavating species (Clionacaribbaea, C. tenuis, C. varians, C. aprica and C. laticavicola) from the southern and southwestern Caribbean were surveyed. Several DNA sequence regions were used in order to confirm zooxanthellae identity; 18S rDNA, domain V of chloroplast large subunit (cp23S), internal transcribed spacer 2 (ITS2), and ITS2 secondary structure. Sequence analyses corroborated the presence of three zooxanthellae clades: A, B, and G. Presence of clades A and B in common boring sponges of the Caribbean fit with the general pattern of the province. The discovery of clade G for the first time in any organism of the Atlantic Ocean leads us to consider this unusual finding as a phylogenetic relict through common ancestors of sponge clades or an invasion of the sponge from the Indo-Pacific.

  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. Revealing the relationships between chemistry, topology and stiffness of ultrastrong Co-based metallic glass thin films: A combinatorial approach

    International Nuclear Information System (INIS)

    Schnabel, Volker; Köhler, Mathias; Evertz, Simon; Gamcova, Jana; Bednarcik, Jozef; Music, Denis; Raabe, Dierk; Schneider, Jochen M.

    2016-01-01

    An efficient way to study the relationship between chemical composition and mechanical properties of thin films is to utilize the combinatorial approach, where spatially resolved mechanical property measurements are conducted along a concentration gradient. However, for thin film glasses many properties including the mechanical response are affected by chemical topology. Here a novel method is introduced which enables spatially resolved short range order analysis along concentration gradients of combinatorially synthesized metallic glass thin films. For this purpose a CoZrTaB metallic glass film of 3 μm thickness is deposited on a polyimide foil, which is investigated by high energy X-ray diffraction in transmission mode. Through the correlative chemistry-topology-stiffness investigation, we observe that an increase in metalloid concentration from 26.4 to 32.7 at% and the associated formation of localized (hybridized) metal – metalloid bonds induce a 10% increase in stiffness. Concomitantly, along the same composition gradient, a metalloid-concentration-induced increase in first order metal - metal bond distances of 1% is observed, which infers itinerant (metallic) bond weakening. Hence, the metalloid concentration induced increase in hybridized bonding dominates the corresponding weakening of metallic bonds.

  11. Structural organization of the genes for rat von Ebner's gland proteins 1 and 2 reveals their close relationship to lipocalins.

    Science.gov (United States)

    Kock, K; Ahlers, C; Schmale, H

    1994-05-01

    The rat von Ebner's gland protein 1 (VEGP 1) is a secretory protein, which is abundantly expressed in the small acinar von Ebner's salivary glands of the tongue. Based on the primary structure of this protein we have previously suggested that it is a member of the lipocalin superfamily of lipophilic-ligand carrier proteins. Although the physiological role of VEGP 1 is not clear, it might be involved in sensory or protective functions in the taste epithelium. Here, we report the purification of VEGP 1 and of a closely related secretory polypeptide, VEGP 2, the isolation of a cDNA clone encoding VEGP 2, and the isolation and structural characterization of the genes for both proteins. Protein purification by gel-filtration and anion-exchange chromatography using Mono Q revealed the presence of two different immunoreactive VEGP species. N-terminal sequence determination of peptide fragments isolated after protease Asp-N digestion allowed the identification of a new VEGP, named VEGP 2, in addition to the previously characterized VEGP 1. The complete VEGP 2 sequence was deduced from a cDNA clone isolated from a von Ebner's gland cDNA library. The VEGP 2 cDNA encodes a protein of 177 amino acids and is 94% identical to VEGP 1. DNA sequence analysis of the rat VEGP 1 and 2 genes isolated from rat genomic libraries revealed that both span about 4.5 kb and contain seven exons. The VEGP 1 and 2 genes are non-allelic distinct genes in the rat genome and probably arose by gene duplication. The high degree of nucleotide sequence identity in introns A-C (94-100%) points to a recent gene conversion event that included the 5' part of the genes. The genomic organization of the rat VEGP genes closely resembles that found in other lipocalins such as beta-lactoglobulin, mouse urinary proteins (MUPs) and prostaglandin D synthase, and therefore provides clear evidence that VEGPs belong to this superfamily of proteins.

  12. 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.

  13. 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

    2018-01-01

    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.

  14. The mean–variance relationship reveals two possible strategies for dynamic brain connectivity analysis in fMRI

    Science.gov (United States)

    Thompson, William H.; Fransson, Peter

    2015-01-01

    When studying brain connectivity using fMRI, signal intensity time-series are typically correlated with each other in time to compute estimates of the degree of interaction between different brain regions and/or networks. In the static connectivity case, the problem of defining which connections that should be considered significant in the analysis can be addressed in a rather straightforward manner by a statistical thresholding that is based on the magnitude of the correlation coefficients. More recently, interest has come to focus on the dynamical aspects of brain connectivity and the problem of deciding which brain connections that are to be considered relevant in the context of dynamical changes in connectivity provides further options. Since we, in the dynamical case, are interested in changes in connectivity over time, the variance of the correlation time-series becomes a relevant parameter. In this study, we discuss the relationship between the mean and variance of brain connectivity time-series and show that by studying the relation between them, two conceptually different strategies to analyze dynamic functional brain connectivity become available. Using resting-state fMRI data from a cohort of 46 subjects, we show that the mean of fMRI connectivity time-series scales negatively with its variance. This finding leads to the suggestion that magnitude- versus variance-based thresholding strategies will induce different results in studies of dynamic functional brain connectivity. Our assertion is exemplified by showing that the magnitude-based strategy is more sensitive to within-resting-state network (RSN) connectivity compared to between-RSN connectivity whereas the opposite holds true for a variance-based analysis strategy. The implications of our findings for dynamical functional brain connectivity studies are discussed. PMID:26236216

  15. The mean-variance relationship reveals two possible strategies for dynamic brain connectivity analysis in fMRI.

    Science.gov (United States)

    Thompson, William H; Fransson, Peter

    2015-01-01

    When studying brain connectivity using fMRI, signal intensity time-series are typically correlated with each other in time to compute estimates of the degree of interaction between different brain regions and/or networks. In the static connectivity case, the problem of defining which connections that should be considered significant in the analysis can be addressed in a rather straightforward manner by a statistical thresholding that is based on the magnitude of the correlation coefficients. More recently, interest has come to focus on the dynamical aspects of brain connectivity and the problem of deciding which brain connections that are to be considered relevant in the context of dynamical changes in connectivity provides further options. Since we, in the dynamical case, are interested in changes in connectivity over time, the variance of the correlation time-series becomes a relevant parameter. In this study, we discuss the relationship between the mean and variance of brain connectivity time-series and show that by studying the relation between them, two conceptually different strategies to analyze dynamic functional brain connectivity become available. Using resting-state fMRI data from a cohort of 46 subjects, we show that the mean of fMRI connectivity time-series scales negatively with its variance. This finding leads to the suggestion that magnitude- versus variance-based thresholding strategies will induce different results in studies of dynamic functional brain connectivity. Our assertion is exemplified by showing that the magnitude-based strategy is more sensitive to within-resting-state network (RSN) connectivity compared to between-RSN connectivity whereas the opposite holds true for a variance-based analysis strategy. The implications of our findings for dynamical functional brain connectivity studies are discussed.

  16. Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

    Science.gov (United States)

    Srinivasan, Sujatha; Hoffman, Noah G.; Morgan, Martin T.; Matsen, Frederick A.; Fiedler, Tina L.; Hall, Robert W.; Ross, Frederick J.; McCoy, Connor O.; Bumgarner, Roger; Marrazzo, Jeanne M.; Fredricks, David N.

    2012-01-01

    Background Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. Methodology/Principal Findings Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel’s criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. Conclusions/Significance The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in

  17. Natural variation at the FRD3 MATE transporter locus reveals cross-talk between Fe homeostasis and Zn tolerance in Arabidopsis thaliana

    OpenAIRE

    Pineau, Christophe; Loubet, Stéphanie; Lefoulon, Cécile; Chaliès, Claude; Fizames, Cécile; Lacombe, Benoît; Ferrand, Marina; Loudet, Olivier; Berthomieu, Pierre; Richard, Odile

    2012-01-01

    Author Summary Plants are adapted to soils in which the amounts of different nutrients vary widely, like Zn-deficient or Zn-contaminated soils. Exploring the molecular bases of plant adaptation to Zn-contaminated soils is important in determining strategies for phytoremediation. Here, we describe the mapping and characterization of a QTL for Zn tolerance in A. thaliana that underlies the natural variation of the root response to excess Zn. This physiological variation is controlled by differe...

  18. Seasonal variation of sperm quality and the relationship between spermatocrit and sperm concentration in yamú Brycon amazonicus

    DEFF Research Database (Denmark)

    Cruz-Casallas, Pablo E.; Medina-Robles, Víctor M.; Velasco-Santamaría, Yohana M.

    2007-01-01

    and sperm concentration were examined over two reproductive seasons. Activation time, spermatocrit, and sperm concentration were significantly higher in 2003 than in 2004. Spermatocrit and sperm concentration showed a significant positive relationship (r2=0.79). During the 2004 reproductive season......, a significant variation was observed for spermatocrit and sperm concentration between the initial period (February 15th to March 14th) and the middle and final periods (March 15th to April 14th and April 15th to May 14th, respectively). Neither the ion concentrations nor the glucose and cholesterol...... concentrations varied between any periods of the reproductive season. Osmolality and triglyceride concentrations showed significant variations between periods during the reproductive season....

  19. Self-Representations in Early Adolescence: Variations in Sibling Similarity by Sex Composition and Sibling Relationship Qualities

    Science.gov (United States)

    Gamble, Wendy C.; Card, Noel A.; Yu, Jeong Jin

    2010-01-01

    Self-representations play an important role in adolescent development. This study compared self-representations for siblings and explored whether sibling relationship characteristics are associated with similarities or differences in sibling self-concepts. We examined self-representations of 438 adolescent sibling dyads (M age younger sibling =…

  20. 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.

  1. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Thudi, Mahendar; Khan, Aamir W; Kumar, Vinay; Gaur, Pooran M; Katta, Krishnamohan; Garg, Vanika; Roorkiwal, Manish; Samineni, Srinivasan; Varshney, Rajeev K

    2016-01-27

    Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for

  2. 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.

  3. 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.

  4. Ethnic variations in the relationship between multiple stress domains and use of several types of tobacco/nicotine products among a diverse sample of adults

    Directory of Open Access Journals (Sweden)

    Christopher J. Rogers

    2018-06-01

    Full Text Available Introduction: Financial strain and discrimination are consistent predictors of negative health outcomes and maladaptive coping behaviors, including tobacco use. Although there is considerable information exploring stress and smoking, limited research has examined the relationship between patterns of stress domains and specific tobacco/nicotine product use. Even fewer studies have assessed ethnic variations in these relationships. Methods: This study investigated the relationship between discrimination and financial strain and current tobacco/nicotine product use and explored the ethnic variation in these relationships among diverse sample of US adults (N = 1068. Separate logistic regression models assessed associations between stress domains and tobacco/nicotine product use, adjusting for covariates (e.g., age, gender, race/ethnicity, and household income. Due to statistically significant differences, the final set of models was stratified by race/ethnicity. Results: Higher levels of discrimination were associated with higher odds of all three tobacco/nicotine product categories. Financial strain was positively associated with combustible tobacco and combined tobacco/nicotine product use. Financial strain was especially risky for Non-Hispanic Whites (AOR:1.191, 95%CI:1.083–1.309 and Blacks/African Americans (AOR:1.542, 95%CI:1.106–2.148, as compared to other groups, whereas discrimination was most detrimental for Asians/Pacific Islanders (AOR:3.827, 95%CI:1.832–7.997 and Hispanics/Latinas/Latinos (AOR:2.517, 95%CI:1.603–3.952. Conclusions: Findings suggest discrimination and financial stressors are risk factors for use of multiple tobacco/nicotine products, highlighting the importance of prevention research that accounts for these stressors. Because ethnic groups may respond differently to stress/strain, prevention research needs to identify cultural values, beliefs, and coping strategies that can buffer the negative consequences of

  5. Variation in the biochemical response to l-thyroxine therapy and relationship with peripheral thyroid hormone conversion efficiency

    OpenAIRE

    Midgley, John E M; Larisch, Rolf; Dietrich, Johannes W; Hoermann, Rudolf

    2015-01-01

    Several influences modulate biochemical responses to a weight-adjusted levothyroxine (l-T4) replacement dose. We conducted a secondary analysis of the relationship of l-T4 dose to TSH and free T3 (FT3), using a prospective observational study examining the interacting equilibria between thyroid parameters. We studied 353 patients on steady-state l-T4 replacement for autoimmune thyroiditis or after surgery for malignant or benign thyroid disease. Peripheral deiodinase activity was calculated a...

  6. Ecological variation in wealth-fertility relationships in Mongolia: the 'central theoretical problem of sociobiology' not a problem after all?

    Science.gov (United States)

    Alvergne, Alexandra; Lummaa, Virpi

    2014-12-07

    The negative wealth-fertility relationship brought about by market integration remains a puzzle to classic evolutionary models. Evolutionary ecologists have argued that this phenomenon results from both stronger trade-offs between reproductive and socioeconomic success in the highest social classes and the comparison of groups rather than individuals. Indeed, studies in contemporary low fertility settings have typically used aggregated samples that may mask positive wealth-fertility relationships. Furthermore, while much evidence attests to trade-offs between reproductive and socioeconomic success, few studies have explicitly tested the idea that such constraints are intensified by market integration. Using data from Mongolia, a post-socialist nation that underwent mass privatization, we examine wealth-fertility relationships over time and across a rural-urban gradient. Among post-reproductive women, reproductive fitness is the lowest in urban areas, but increases with wealth in all regions. After liberalization, a demographic-economic paradox emerges in urban areas: while educational attainment negatively impacts female fertility in all regions, education uniquely provides socioeconomic benefits in urban contexts. As market integration progresses, socio-economic returns to education increase and women who limit their reproduction to pursue education get wealthier. The results support the view that selection favoured mechanisms that respond to opportunities for status enhancement rather than fertility maximization. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  7. Study of living kidney donor-recipient relationships: variation with socioeconomic deprivation in the white population of England.

    Science.gov (United States)

    Bailey, Phillippa K; Tomson, Charles Rv; Ben-Shlomo, Yoav

    2013-01-01

    Socioeconomic deprivation is associated with higher renal replacement therapy acceptance rates in the UK but lower rates of living kidney transplantation. This study examines donor-recipient relationship patterns with socioeconomic deprivation in the white population of England. Demographic characteristics of all white live renal transplant donors and recipients between 2001 and 2010 in England were analyzed. Patterns of donor-recipient relationship were analyzed to see whether they differed according to an ecological measure of socioeconomic status (Index of Multiple Deprivation). Group comparisons were performed using chi-square tests and multivariable logistic regression. Sources of living kidney transplants differed with deprivation (p Recipients living in poorer areas were more likely to receive a kidney from a sibling, child, and "other relative" donor and less likely from spouses/partners. Logistic regression suggested differences seen with spouse/partner donations with deprivation were explained by differences in the age and gender of the recipients. The source of living kidneys differs by level of area deprivation. Given the disparity in rates of living kidney transplants between the most and least socioeconomically deprived, there is a need to understand the reasons behind these observed relationship differences, with the aim of increasing transplantation rates in the most deprived. © 2013 John Wiley & Sons A/S.

  8. Relationship and variation of qPCR and culturable enterococci estimates in ambient surface waters are predictable

    Science.gov (United States)

    Whitman, Richard L.; Ge, Zhongfu; Nevers, Meredith B.; Boehm, Alexandria B.; Chern, Eunice C.; Haugland, Richard A.; Lukasik, Ashley M.; Molina, Marirosa; Przybyla-Kelly, Kasia; Shively, Dawn A.; White, Emily M.; Zepp, Richard G.; Byappanahalli, Muruleedhara N.

    2010-01-01

    The quantitative polymerase chain reaction (qPCR) method provides rapid estimates of fecal indicator bacteria densities that have been indicated to be useful in the assessment of water quality. Primarily because this method provides faster results than standard culture-based methods, the U.S. Environmental Protection Agency is currently considering its use as a basis for revised ambient water quality criteria. In anticipation of this possibility, we sought to examine the relationship between qPCR-based and culture-based estimates of enterococci in surface waters. Using data from several research groups, we compared enterococci estimates by the two methods in water samples collected from 37 sites across the United States. A consistent linear pattern in the relationship between cell equivalents (CCE), based on the qPCR method, and colony-forming units (CFU), based on the traditional culturable method, was significant (P 10CFU > 2.0/100 mL) while uncertainty increases at lower CFU values. It was further noted that the relative error in replicated qPCR estimates was generally higher than that in replicated culture counts even at relatively high target levels, suggesting a greater need for replicated analyses in the qPCR method to reduce relative error. Further studies evaluating the relationship between culture and qPCR should take into account analytical uncertainty as well as potential differences in results of these methods that may arise from sample variability, different sources of pollution, and environmental factors.

  9. Hostile Attribution Bias Mediates the Relationship Between Structural Variations in the Left Middle Frontal Gyrus and Trait Angry Rumination

    Directory of Open Access Journals (Sweden)

    Yueyue Wang

    2018-04-01

    Full Text Available Angry rumination is a common mental phenomenon which may lead to negative social behaviors such as aggression. Although numerous neuroimaging studies have focused on brain area activation during angry rumination, to our knowledge no study has examined the neuroanatomical and cognitive mechanisms of this process. In this study, we conducted a voxel-based morphometry analysis, using a region of interest analysis to identify the structural and cognitive mechanisms underlying individual differences in trait angry rumination (as measured by the Angry Rumination Scale in a sample of 82 undergraduate students. We found that angry rumination was positively correlated with gray matter density in the left middle frontal gyrus (left-MFG, which is implicated in inhibition control, working memory, and emotional regulation. The mediation analysis further revealed that hostile attribution bias (as measured by the Social Information Processing–Attribution Bias Questionnaire acted as a cognitive mechanism underlying the positive association between the left-MFG gray matter density and trait angry rumination. These findings suggest that hostile attribution bias may contribute to trait angry rumination, while the left-MFG may play an important role in the development of hostile attribution bias and trait angry rumination. The study reveals the brain mechanisms of trait angry rumination and plays a role in revealing the cognitive mechanisms of the development of trait angry rumination.

  10. 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, 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

  11. Modelling lamb carcase pH and temperature decline parameters: relationship to shear force and abattoir variation.

    Science.gov (United States)

    Hopkins, David L; Holman, Benjamin W B; van de Ven, Remy J

    2015-02-01

    Carcase pH and temperature decline rates influence lamb tenderness; therefore pH decline parameters are beneficial when modelling tenderness. These include pH at temperature 18 °C (pH@Temp18), temperature when pH is 6 (Temp@pH6), and pH at 24 h post-mortem (pH24). This study aimed to establish a relationship between shear force (SF) as a proxy for tenderness and carcase pH decline parameters estimated using both linear and spline estimation models for the m. longissimus lumborum (LL). The study also compared abattoirs regarding their achievement of ideal pH decline, indicative of optimal tenderness. Based on SF measurements of LL and m. semimembranosus collected as part of the Information Nucleus slaughter programme (CRC for Sheep Industry Innovation) this study found significant relationships between tenderness and pH24LL, consistent across the meat cuts and ageing periods examined. Achievement of ideal pH decline was shown not to have significantly differed across abattoirs, although rates of pH decline varied significantly across years within abattoirs.

  12. 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

  13. Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut.

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    Vincent Raquin

    2017-12-01

    Full Text Available Dengue virus (DENV causes more human infections than any other mosquito-borne virus. The current lack of antiviral strategies has prompted genome-wide screens for host genes that are required for DENV infectivity. Earlier transcriptomic studies that identified DENV host factors in the primary vector Aedes aegypti used inbred laboratory colonies and/or pools of mosquitoes that erase individual variation. Here, we performed transcriptome sequencing on individual midguts in a field-derived Ae. aegypti population to identify new candidate host factors modulating DENV replication. We analyzed the transcriptomic data using an approach that accounts for individual co-variation between viral RNA load and gene expression. This approach generates a prediction about the agonist or antagonist effect of candidate genes on DENV replication based on the sign of the correlation between gene expression and viral RNA load. Using this method, we identified 39 candidate genes that went undetected by conventional pairwise comparison of gene expression levels between DENV-infected midguts and uninfected controls. Only four candidate genes were detected by both methods, emphasizing their complementarity. We demonstrated the value of our approach by functional validation of a candidate agonist gene encoding a sterol regulatory element-binding protein (SREBP, which was identified by correlation analysis but not by pairwise comparison. We confirmed that SREBP promotes DENV infection in the midgut by RNAi-mediated gene knockdown in vivo. We suggest that our approach for transcriptomic analysis can empower genome-wide screens for potential agonist or antagonist factors by leveraging inter-individual variation in gene expression. More generally, this method is applicable to a wide range of phenotypic traits displaying inter-individual variation.

  14. Relationships between abstract features and methodological quality explained variations of social media activity derived from systematic reviews about psoriasis interventions.

    Science.gov (United States)

    Ruano, J; Aguilar-Luque, M; Isla-Tejera, B; Alcalde-Mellado, P; Gay-Mimbrera, J; Hernandez-Romero, José Luis; Sanz-Cabanillas, J L; Maestre-López, B; González-Padilla, M; Carmona-Fernández, P J; Gómez-García, F; García-Nieto, A Vélez

    2018-05-24

    The aim of this study was to describe the relationship among abstract structure, readability, and completeness, and how these features may influence social media activity and bibliometric results, considering systematic reviews (SRs) about interventions in psoriasis classified by methodological quality. Systematic literature searches about psoriasis interventions were undertaken on relevant databases. For each review, methodological quality was evaluated using the Assessing the Methodological Quality of Systematic Reviews (AMSTAR) tool. Abstract extension, structure, readability, and quality and completeness of reporting were analyzed. Social media activity, which consider Twitter and Facebook mention counts, as well as Mendeley readers and Google scholar citations were obtained for each article. Analyses were conducted to describe any potential influence of abstract characteristics on review's social media diffusion. We classified 139 intervention SRs as displaying high/moderate/low methodological quality. We observed that abstract readability of SRs has been maintained high for last 20 years, although there are some differences based on their methodological quality. Free-format abstracts were most sensitive to the increase of text readability as compared with more structured abstracts (IMRAD or 8-headings), yielding opposite effects on their quality and completeness depending on the methodological quality: a worsening in low quality reviews and an improvement in those of high-quality. Both readability indices and PRISMA for Abstract total scores showed an inverse relationship with social media activity and bibliometric results in high methodological quality reviews but not in those of lower quality. Our results suggest that increasing abstract readability must be specially considered when writing free-format summaries of high-quality reviews, because this fact correlates with an improvement of their completeness and quality, and this may help to achieve broader

  15. The time series variations of tritium concentration in precipitation and its relationships to the rainfall-inducing air mass

    International Nuclear Information System (INIS)

    Shimada, Jun

    1978-01-01

    The author measured the tritium concentration in precipitation of Tokyo for every ten-day period from August 1972 to May 1974. Judging from the daily synoptic weather chart, the rainfall-inducing air masses in Japan were classified into five types; polar maritime air mass (Pm), polar continental air mass (Pc), tropical maritime air mass (Tm), tropical continental air mass (Tc), and equatorial maritime air mass (Em). And the precipitation for every ten-day period sampled for tritium measurement were classified into these five types. Based on this classification, it is confirmed that there exist clear difference in the tritium concentration between the rainfall from the continental air mass and ones from the maritime air mass. It is characteristic that the tritium concentration in rainfall induced by equatorial maritime air mass such as typhoon in summer and early fall season is very low whereas the tritium concentration in rainfall and snowfall induced directly by the polar continental air mass in late winter season is very high. The regional difference of the tritium concentration in intermonthly precipitation could considerably be explained by this synoptic meteological classification of rainfall-inducing air mass. In spite of these regional difference of tritium concentration in precipitation, use of the tritium concentration of Tokyo as a representative value of Japan may be allowed because of the similarities of the changing pattern and annual mean tritium concentration. The time series variations of tritium concentration in precipitation of Tokyo from August 1972 to December 1977, Tsukuba from December 1976 to April 1978, and Nagaoka from April 1977 to March 1978 are listed. (author)

  16. Genetic relationships between clinical and non-clinical strains of Yersinia enterocolitica biovar 1A as revealed by multilocus enzyme electrophoresis and multilocus restriction typing

    Directory of Open Access Journals (Sweden)

    Virdi Jugsharan S

    2010-05-01

    Full Text Available Abstract Background Genetic relationships among 81 strains of Y. enterocolitica biovar 1A isolated from clinical and non-clinical sources were discerned by multilocus enzyme electrophoresis (MLEE and multilocus restriction typing (MLRT using six loci each. Such studies may reveal associations between the genotypes of the strains and their sources of isolation. Results All loci were polymorphic and generated 62 electrophoretic types (ETs and 12 restriction types (RTs. The mean genetic diversity (H of the strains by MLEE and MLRT was 0.566 and 0.441 respectively. MLEE (DI = 0.98 was more discriminatory and clustered Y. enterocolitica biovar 1A strains into four groups, while MLRT (DI = 0.77 identified two distinct groups. BURST (Based Upon Related Sequence Types analysis of the MLRT data suggested aquatic serotype O:6,30-6,31 isolates to be the ancestral strains from which, clinical O:6,30-6,31 strains might have originated by host adaptation and genetic change. Conclusion MLEE revealed greater genetic diversity among strains of Y. enterocolitica biovar 1A and clustered strains in four groups, while MLRT grouped the strains into two groups. BURST analysis of MLRT data nevertheless provided newer insights into the probable evolution of clinical strains from aquatic strains.

  17. Genetic relationships among wild and cultivated accessions of curry leaf plant (Murraya koenigii (L.) Spreng.), as revealed by DNA fingerprinting methods.

    Science.gov (United States)

    Verma, Sushma; Rana, T S

    2013-02-01

    Murraya koenigii (L.) Spreng. (Rutaceae), is an aromatic plant and much valued for its flavor, nutritive and medicinal properties. In this study, three DNA fingerprinting methods viz., random amplification of polymorphic DNA (RAPD), directed amplification of minisatellite DNA (DAMD), and inter-simple sequence repeat (ISSR), were used to unravel the genetic variability and relationships across 92 wild and cultivated M. koenigii accessions. A total of 310, 102, and 184, DNA fragments were amplified using 20 RAPD, 5 DAMD, and 13 ISSR primers, revealing 95.80, 96.07, and 96.73% polymorphism, respectively, across all accessions. The average polymorphic information content value obtained with RAPD, DAMD, and ISSR markers was 0.244, 0.250, and 0.281, respectively. The UPGMA tree, based on Jaccard's similarity coefficient generated from the cumulative (RAPD, DAMD, and ISSR) band data showed two distinct clusters, clearly separating wild and cultivated accessions in the dendrogram. Percentage polymorphism, gene diversity (H), and Shannon information index (I) estimates were higher in cultivated accessions compared to wild accessions. The overall high level of polymorphism and varied range of genetic distances revealed a wide genetic base in M. koenigii accessions. The study suggests that RAPD, DAMD, and ISSR markers are highly useful to unravel the genetic variability in wild and cultivated accessions of M. koenigii.

  18. Characterizing the structure-function relationship reveals the mode of action of a novel antimicrobial peptide, P1, from jumper ant Myrmecia pilosula.

    Science.gov (United States)

    Tseng, Tien-Sheng; Tsai, Keng-Chang; Chen, Chinpan

    2017-06-01

    Microbial infections of antibiotic-resistant strains cause serious diseases and have a significant impact on public health worldwide, so novel antimicrobial drugs are urgently needed. Insect venoms, a rich source of bioactive components containing antimicrobial peptides (AMPs), are attractive candidates for new therapeutic agents against microbes. Recently, a novel peptide, P1, identified from the venom of the Australian jumper ant Myrmecia pilosula, showed potent antimicrobial activities against both Gram-negative and Gram-positive bacteria, but its structure-function relationship is unknown. Here, we used biochemical and biophysical techniques coupled with computational simulations to explore the mode of action of P1 interaction with dodecylphosphocholine (DPC) micelles as a model membrane system. Our circular dichroism (CD) and NMR studies revealed an amphipathic α-helical structure for P1 upon interaction with DPC micelles. A paramagnetic relaxation enhancement approach revealed that P1 orients its α-helix segment (F6-G14) into DPC micelles. In addition, the α-helix segment could be essential for membrane permeabilization and antimicrobial activity. Moreover, the arginine residues R8, R11, and R15 significantly contribute to helix formation and membrane-binding affinity. The lysine residue K19 of the C-terminus functionally guides P1 to interact with DPC micelles in the early interaction stage. Our study provides insights into the mode of action of P1, which is valuable in modifying and developing potent AMPs as antibiotic drugs.

  19. 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.

  20. Rumination mediates the relationship between structural variations in ventrolateral prefrontal cortex and sensitivity to negative life events.

    Science.gov (United States)

    Qiao, L; Wei, D T; Li, W F; Chen, Q L; Che, X W; Li, B B; Li, Y D; Qiu, J; Zhang, Q L; Liu, Y J

    2013-01-01

    Individuals have different levels of stress sensitivity. An individual's predisposition to experience negative life events (NLEs) may make him/her more vulnerable to a series of psychopathological and physical diseases. However, the neuroanatomical correlates of individual differences in sensitivity to NLEs remain unknown. In this study, voxel-based morphometry was used to identify the gray matter (GM) associations of individual differences in sensitivity to NLEs measured by adolescent self-rating life events checklist. Results showed that there was a positive association between individual NLEs sensitivity and regional GM volume (rGMV) in the ventrolateral prefrontal cortex (VLPFC). GM was mostly evident in the left frontal operculum and a small part of the left middle frontal gyrus. This region was thought to play an important role in introception. Importantly, our study revealed that rumination served as a mediator between the rGMV of the VLPFC and individual NLEs sensitivity. These findings suggest that people with greater VLPFC might be more inclined to ruminate and the ruminative response style might make them more sensitive to NLEs. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  1. The assessment of the relationship between variations in the apelin gene and coronary artery disease in Turkish population.

    Science.gov (United States)

    Pakizeh, Ebrahim; Çoşkunpınar, Ender; Oltulu, Yasemin Müşteri; Çakmak, Hüseyin Altuğ; İkitimur, Barış; Işık Sağlam, Zümrüt Mine; Karimova, Ayla; Vural, Vural Ali

    2015-09-01

    Apelin is a novel endogenous peptide with inotropic and vasodilatory properties and is the ligand for the angiotensin receptor-like 1 (APJ) receptor. The aim of the study was to investigate the association of 2 single-nucleotide polymorphisms (SNPs) in the apelin gene with susceptibility to coronary artery disease (CAD) in the Turkish population. The present observational case-control study consisted of 244 subjects (134 angiographically proven CAD patients and 110 healthy controls) aged 30-65 years. The association of 2 SNPs (rs3115758 and rs3115759) in the apelin gene and CAD risk was investigated. Real-time polymerase chain reaction (RT-PCR) was used to analyze the 2 SNPs in both the CAD and the healthy subjects. Allele and genotype frequencies between patients and control groups were compared using the Chi-square (χ2) test. The relationships of the 2 polymorphisms with the presence of CAD were determined with multiple binary logistic regression analysis after adjustment for CAD risk factors. TT and AA risk genotypes of the rs3115758 and rs3115759 variants in the apelin gene were found to be significantly related with the risk of CAD with the same power (OR: 6.36, 95% CI: 1.41-28.6) (p=0.007). After adjustments for traditional CAD risk factors, the homozygous TT genotype for rs3115758 and AA genotype for rs3115759 increased the CAD risk, both with an OR of 5.91. Genetic variants in the apelin gene are significantly associated with the risk of CAD in the Turkish population.

  2. Assessment of indoor radon, thoron concentrations, and their relationship with seasonal variation and geology of Udhampur district, Jammu & Kashmir, India.

    Science.gov (United States)

    Kumar, Ajay; Sharma, Sumit; Mehra, Rohit; Narang, Saurabh; Mishra, Rosaline

    2017-07-01

    Background The inhalation doses resulting from the exposure to radon, thoron, and their progeny are important quantities in estimating the radiation risk for epidemiological studies as the average global annual effective dose due to radon and its progeny is 1.3 mSv as compared to that of 2.4 mSv due to all other natural sources of ionizing radiation. Objectives The annual inhalation dose has been assessed with an aim of investigating the health risk to the inhabitants of the studied region. Methods Time integrated deposition based 222 Rn/ 220 Rn sensors have been used to measure concentrations in 146 dwellings of Udhampur district, Jammu and Kashmir. An active smart RnDuo monitor has also been used for comparison purposes. Results The range of indoor radon/thoron concentrations is found to vary from 11 to 58 Bqm -3 with an average value of 29 ± 9 Bqm -3 and from 25 to 185 Bqm -3 with an average value of 83 ± 32 Bqm -3 , respectively. About 10.7% dwellings have higher values than world average of 40 Bqm -3 prescribed by UNSCEAR. The relationship of indoor radon and thoron levels with different seasons, ventilation conditions, and different geological formations have been discussed. Conclusions The observed values of concentrations and average annual effective dose due to radon, thoron, and its progeny in the study area have been found to be below the recommended level of ICRP. The observed concentrations of 222 Rn and 220 Rn measured with active and passive techniques are found to be in good agreement.

  3. 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.

  4. DRD2 genotype-based variation of default mode network activity and of its relationship with striatal DAT binding.

    Science.gov (United States)

    Sambataro, Fabio; Fazio, Leonardo; Taurisano, Paolo; Gelao, Barbara; Porcelli, Annamaria; Mancini, Marina; Sinibaldi, Lorenzo; Ursini, Gianluca; Masellis, Rita; Caforio, Grazia; Di Giorgio, Annabella; Niccoli-Asabella, Artor; Popolizio, Teresa; Blasi, Giuseppe; Bertolino, Alessandro

    2013-01-01

    The default mode network (DMN) comprises a set of brain regions with "increased" activity during rest relative to cognitive processing. Activity in the DMN is associated with functional connections with the striatum and dopamine (DA) levels in this brain region. A functional single-nucleotide polymorphism within the dopamine D2 receptor gene (DRD2, rs1076560 G > T) shifts splicing of the 2 D2 isoforms, D2 short and D2 long, and has been associated with striatal DA signaling as well as with cognitive processing. However, the effects of this polymorphism on DMN have not been explored. The aim of this study was to evaluate the effects of rs1076560 on DMN and striatal connectivity and on their relationship with striatal DA signaling. Twenty-eight subjects genotyped for rs1076560 underwent functional magnetic resonance imaging during a working memory task and 123 55 I-Fluoropropyl-2-beta-carbomethoxy-3-beta(4-iodophenyl) nortropan Single Photon Emission Computed Tomography ([(123)I]-FP-CIT SPECT) imaging (a measure of dopamine transporter [DAT] binding). Spatial group-independent component (IC) analysis was used to identify DMN and striatal ICs. Within the anterior DMN IC, GG subjects had relatively greater connectivity in medial prefrontal cortex (MPFC), which was directly correlated with striatal DAT binding. Within the posterior DMN IC, GG subjects had reduced connectivity in posterior cingulate relative to T carriers. Additionally, rs1076560 genotype predicted connectivity differences within a striatal network, and these changes were correlated with connectivity in MPFC and posterior cingulate within the DMN. These results suggest that genetically determined D2 receptor signaling is associated with DMN connectivity and that these changes are correlated with striatal function and presynaptic DA signaling.

  5. Variation among sub-basins of the upper Nelson River in relationships between precipitation, runoff and the Pacific Decadal Oscillation

    International Nuclear Information System (INIS)

    McCullough, G.

    2008-01-01

    In this paper, I examine relationships between precipitation and river discharge in the Nelson River watershed and several global climate indices. Inter-decadal patterns in discharge and precipitation for several sub-basins closely tracked the Pacific Decadal Oscillation (PDO) through much of the 20th century. The PDO explained 53% of the variability in precipitation and 70% in discharge for the Red River (5-y averages) from 1915-1975. However, since 1975, both precipitation and discharge have increased relative to trend of the PDO. Winnipeg River discharge likewise increased relative to the PDO, but diverged earlier, beginning in 1965. The hydrograph of the Saskatchewan River followed the PDO only until mid-century, after which discharge declined relative to the PDO. The decline of discharge in the Saskatchewan River is not matched by consistent declines in precipitation, but may be partly due to consumptive use, mainly irrigation, and losses due to evaporation from large reservoirs created in the 1960s and 1970s. However, the increases in the Red and Winnipeg River are well-explained by increased spring and summer precipitation. For instance, precipitation was 20-30% higher in the decade 1996-2005 than in the previous decade. By examining historical data, we show the runoff coefficient to increase with increasing discharge, and that the proportional increase is greater in the Red than in the Winnipeg River basin. In the Red, the moderate difference in precipitation was amplified into a doubling of annual mean discharge. Comparing the same 2 periods, a smaller 10% increase in precipitation in the Winnipeg River basin explains a 27% increase in discharge. (author)

  6. Not everything is black and white: color and behavioral variation reveal a continuum between cryptic and aposematic strategies in a polymorphic poison frog.

    Science.gov (United States)

    Willink, Beatriz; Brenes-Mora, Esteban; Bolaños, Federico; Pröhl, Heike

    2013-10-01

    Aposematism and crypsis are often viewed as two extremes of a continuum of visual conspicuousness to predators. Theory predicts that behavioral and coloration conspicuousness should vary in tandem along the conspicuousness spectrum for antipredator strategies to be effective. Here we used visual modeling of contrast and behavioral observations to examine the conspicuousness of four populations of the granular poison frog, Oophaga granulifera, which exhibits almost continuous variation in dorsal color. The patterns of geographic variation in color, visual contrast, and behavior support a gradient of overall conspicuousness along the distribution of O. granulifera. Red and green populations, at the extremes of the color distribution, differ in all elements of color, contrast, and behavior, strongly reflecting aposematic and cryptic strategies. However, there is no smooth cline in any elements of behavior or coloration between the two extremes. Instead populations of intermediate colors attain intermediate conspicuousness by displaying different combinations of aposematic and cryptic traits. We argue that coloration divergence among populations may be linked to the evolution of a gradient of strategies to balance the costs of detection by predators and the benefits of learned aversion. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  7. Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L. as revealed by microsatellite DNA analysis

    Directory of Open Access Journals (Sweden)

    D. LOUKOVITIS

    2014-10-01

    Full Text Available Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.

  8. Temporal and spatial variations in sand and dust storm events in East Asia from 2007 to 2016: Relationships with surface conditions and climate change.

    Science.gov (United States)

    An, Linchang; Che, Huizheng; Xue, Min; Zhang, Tianhang; Wang, Hong; Wang, Yaqiang; Zhou, Chunhong; Zhao, Hujia; Gui, Ke; Zheng, Yu; Sun, Tianze; Liang, Yuanxin; Sun, Enwei; Zhang, Hengde; Zhang, Xiaoye

    2018-08-15

    We analyzed the frequency and intensity of sand and dust storms (SDSs) in East Asia from 2007 to 2016 using observational data from ground stations, numerical modeling, and vegetation indices obtained from both satellite and reanalysis data. The relationships of SDSs with surface conditions and the synoptic circulation pattern were also analyzed. The statistical analyses demonstrated that the number and intensity of SDS events recorded in spring during 2007 to 2016 showed a decreasing trend. The total number of spring SDSs decreased from at least ten events per year before 2011 to less than ten events per year after 2011. The overall average annual variation of the surface dust concentration in the main dust source regions decreased 33.24μg/m 3 (-1.75%) annually. The variation in the temperatures near and below the ground surface and the amount of precipitation and soil moisture all favored an improvement in vegetation coverage, which reduced the intensity and frequency of SDSs. The strong winds accompanying the influx of cold air from high latitudes showed a decreasing trend, leading to a decrease in the number of SDSs and playing a key role in the decadal decrease of SDSs. The decrease in the intensity of the polar vortex during study period was closely related to the decrease in the intensity and frequency of SDSs. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Novák, Petr; Pellicer, J.; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Vrbová, Iva; Doležel, Jaroslav; Kelly, L.J.; Leitch, I.J.

    2015-01-01

    Roč. 10, č. 11 (2015), e0143424 E-ISSN 1932-6203 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:60077344 ; RVO:61389030 Keywords : Generation sequencing reveals * transposable elements * satellite repeats * retrotransposons Subject RIV: EB - Genetics ; Molecular Biology; EB - Genetics ; Molecular Biology (UEB-Q) Impact factor: 3.057, year: 2015

  10. Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns.

    Science.gov (United States)

    De Laere, Bram; van Dam, Pieter-Jan; Whitington, Tom; Mayrhofer, Markus; Diaz, Emanuela Henao; Van den Eynden, Gert; Vandebroek, Jean; Del-Favero, Jurgen; Van Laere, Steven; Dirix, Luc; Grönberg, Henrik; Lindberg, Johan

    2017-08-01

    Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy. We performed profiling of circulating tumour DNA via low-pass whole-genome sequencing and targeted sequencing of the entire AR gene, including introns. Targeted RNA sequencing was performed on enriched circulating tumour cell fractions to assess the expression levels of seven AR splice variants (ARVs). Somatic AR variations, including copy-number alterations, structural variations, and point mutations, were combined with ARV expression patterns and correlated to clinicopathologic parameters. Collectively, any AR perturbation, including ARV, was detected in 25/30 patients. Surprisingly, intra-AR structural variation was present in 15/30 patients, of whom 14 expressed ARVs. The majority of ARV-positive patients expressed multiple ARVs, with AR-V3 the most abundantly expressed. The presence of any ARV was associated with progression-free survival after second-line endocrine treatment (hazard ratio 4.53, 95% confidence interval 1.424-14.41; p=0.0105). Six out of 17 poor responders were AR-V7-negative, but four carried other AR perturbations. Comprehensive AR profiling, which is feasible using liquid biopsies, is necessary to increase our understanding of the mechanisms underpinning resistance to endocrine treatment. Alterations in the androgen receptor are associated with endocrine treatment outcomes. This study demonstrates that it is possible to identify different types of alterations via simple blood draws. Follow-up studies are needed to determine the effect of

  11. Fourier transform infrared imaging microspectroscopy and tissue-level mechanical testing reveal intraspecies variation in mouse bone mineral and matrix composition.

    Science.gov (United States)

    Courtland, Hayden-William; Nasser, Philip; Goldstone, Andrew B; Spevak, Lyudmila; Boskey, Adele L; Jepsen, Karl J

    2008-11-01

    Fracture susceptibility is heritable and dependent upon bone morphology and quality. However, studies of bone quality are typically overshadowed by emphasis on bone geometry and bone mineral density. Given that differences in mineral and matrix composition exist in a variety of species, we hypothesized that genetic variation in bone quality and tissue-level mechanical properties would also exist within species. Sixteen-week-old female A/J, C57BL/6J (B6), and C3H/HeJ (C3H) inbred mouse femora were analyzed using Fourier transform infrared imaging and tissue-level mechanical testing for variation in mineral composition, mineral maturity, collagen cross-link ratio, and tissue-level mechanical properties. A/J femora had an increased mineral-to-matrix ratio compared to B6. The C3H mineral-to-matrix ratio was intermediate of A/J and B6. C3H femora had reduced acid phosphate and carbonate levels and an increased collagen cross-link ratio compared to A/J and B6. Modulus values paralleled mineral-to-matrix values, with A/J femora being the most stiff, B6 being the least stiff, and C3H having intermediate stiffness. In addition, work-to-failure varied among the strains, with the highly mineralized and brittle A/J femora performing the least amount of work-to-failure. Inbred mice are therefore able to differentially modulate the composition of their bone mineral and the maturity of their bone matrix in conjunction with tissue-level mechanical properties. These results suggest that specific combinations of bone quality and morphological traits are genetically regulated such that mechanically functional bones can be constructed in different ways.

  12. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-01-21

    Background Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multigene family. Although the function of PE_PGRS genes is unknown, it is hypothesized that the PE_PGRS genes may be associated with antigenic variability in MTB. Material and methods Whole genome sequencing analysis was performed on (n = 37) extensively drug-resistant (XDR) MTB strains from Pakistan, which included Lineage 1 (East African Indian, n = 2); Other lineage 1 (n = 3); Lineage 3 (Central Asian, n = 24); Other lineage 3 (n = 4); Lineage 4 (X3, n = 1) and T group (n = 3) MTB strains. Results There were 107 SNPs identified from the analysis of 42 PE_PGRS genes; of these, 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in PE_PGRS genes – 6, 9 and 10 – were common in all EAI, CAS, Other lineages (1 and 3), T1 and X3. Deletions (DELs) in PE_PGRS genes – 3 and 19 – were observed in 17 (80.9%) CAS1 and 6 (85.7%) in Other lineages (1 and 3) XDR MTB strains, while DELs in the PE_PGRS49 were observed in all CAS1, CAS, CAS2 and Other lineages (1 and 3) XDR MTB strains. All CAS, EAI and Other lineages (1 and 3) strains showed insertions (INS) in PE_PGRS6 gene, while INS in the PE_PGRS genes 19 and 33 were observed in 20 (95.2%) CAS1, all CAS, CAS2, EAI and Other lineages (1 and 3) XDR MTB strains. Conclusion Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  13. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-03-01

    Background: Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multi-gene family. Although the function of the members of the PE_PGRS multi-gene family is not yet known, it is hypothesized that the PE_PGRS genes may be associated with genetic variability. Material and methods: Whole genome sequencing analysis was performed on (n= 37) extensively drug resistant (XDR) MTB strains from Pakistan which included Central Asian (n= 23), East African Indian (n= 2), X3 (n= 1), T group (n= 3) and Orphan (n= 8) MTB strains. Results: By analyzing 42 PE_PGRS genes, 111 SNPs were identified, of which 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in the PE_PGRS genes were as follows: 6, 9, 10 and 55 present in each of the CAS, EAI, Orphan, T1 and X3 XDR MTB strains studied. Deletions in PE_PGRS genes: 19, 21 and 23 were observed in 7 (35.0%) CAS1 and 3 (37.5%) in Orphan XDR MTB strains, while deletions in the PE_PGRS genes: 49 and 50 were observed in 36 (95.0%) CAS1 and all CAS, CAS2 and Orphan XDR MTB strains. An insertion in PE_PGRS6 gene was observed in all CAS, EAI3 and Orphan, while insertions in the PE_PGRS genes 19 and 33 were observed in 19 (95%) CAS1 and all CAS, CAS2, EAI3 and Orphan XDR MTB strains. Conclusion: Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs, Insertions and Deletions in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  14. Morphological variation, phylogenetic relationships, and geographic distribution of the Baenidae (Testudines), based on new specimens from the Uinta Formation (Uinta Basin), Utah (USA)

    Science.gov (United States)

    Hutchison, J. Howard; Townsend, K. E. Beth; Adrian, Brent; Jager, Daniel

    2017-01-01

    We described newly discovered baenid specimens from the Uintan North American Land Mammal Age (NALMA), in the Uinta Formation, Uinta Basin, Utah. These specimens include a partial skull and several previously undescribed postcranial elements of Baena arenosa, and numerous well-preserved shells of B. arenosa and Chisternon undatum. Baenids from the Uintan NALMA (46.5–40 Ma) are critical in that they provide valuable insight into the morphology and evolution of the diverse and speciose baenid family near the end of its extensive radiation, just prior to the disappearance of this clade from the fossil record. These Uintan specimens greatly increase the known variation in these late-surviving taxa and indicate that several characters thought to define these species should be reassessed. The partial cranium of B. arenosa, including portions of the basicranium, neurocranium, face, and lower jaw, was recently recovered from Uinta B sediments. While its morphology is consistent with known specimens of B. arenosa, we observed several distinct differences: a crescent-shaped condylus occipitalis that is concave dorsally, tuberculum basioccipitale that flare out laterally, and a distinct frontal-nasal suture. The current sample of plastral and carapacial morphology considerably expands the documented variation in the hypodigms of B. arenosa and C. undatum. Novel shell characters observed include sigmoidal extragular-humeral sulci, and small, subtriangular gular scutes. Subadult specimens reveal ontogenetic processes in both taxa, and demonstrate that diagnostic morphological differences between them were present from an early developmental age. PMID:28686718

  15. Morphological variation, phylogenetic relationships, and geographic distribution of the Baenidae (Testudines, based on new specimens from the Uinta Formation (Uinta Basin, Utah (USA.

    Directory of Open Access Journals (Sweden)

    Heather F Smith

    Full Text Available We described newly discovered baenid specimens from the Uintan North American Land Mammal Age (NALMA, in the Uinta Formation, Uinta Basin, Utah. These specimens include a partial skull and several previously undescribed postcranial elements of Baena arenosa, and numerous well-preserved shells of B. arenosa and Chisternon undatum. Baenids from the Uintan NALMA (46.5-40 Ma are critical in that they provide valuable insight into the morphology and evolution of the diverse and speciose baenid family near the end of its extensive radiation, just prior to the disappearance of this clade from the fossil record. These Uintan specimens greatly increase the known variation in these late-surviving taxa and indicate that several characters thought to define these species should be reassessed. The partial cranium of B. arenosa, including portions of the basicranium, neurocranium, face, and lower jaw, was recently recovered from Uinta B sediments. While its morphology is consistent with known specimens of B. arenosa, we observed several distinct differences: a crescent-shaped condylus occipitalis that is concave dorsally, tuberculum basioccipitale that flare out laterally, and a distinct frontal-nasal suture. The current sample of plastral and carapacial morphology considerably expands the documented variation in the hypodigms of B. arenosa and C. undatum. Novel shell characters observed include sigmoidal extragular-humeral sulci, and small, subtriangular gular scutes. Subadult specimens reveal ontogenetic processes in both taxa, and demonstrate that diagnostic morphological differences between them were present from an early developmental age.

  16. Child abuse and the balance of power in parental relationships: an evolved domain-independent mental mechanism that accounts for behavioral variation.

    Science.gov (United States)

    Handwerker, W P

    2001-01-01

    Previous studies use zero-order analyses to show a link between child abuse and exposure to "stepfathers." These studies rest on a proposed evolved, domain-specific cognitive mechanism that induces adult males to abuse or kill offspring not their own and, so, contribute directly to reproductive success. However, child abuse may reflect an evolved neurological mechanism that creates behavioral plasticity and adaptability by assigning emotional weights (which in consciousness appear rationalized as costs and benefits) to choice alternatives in all behavioral domains. This mechanism should act as a selective mechanism to create enhanced ability to avoid predation (social exploitation) and to obtain access to resources, given the properties of specific ecosystems, and should control behavioral responses to variation in the balance of power in social relationships. Power equalities should elicit good treatment for both parties; power inequalities, by contrast, should elicit exploitative and coercive behavior on the part of those who hold the balance of power. This paper reports a test of both hypotheses simultaneously, controlling for a standard social science risk factor (growing up in poverty). Once we control for the balance of power in parental relationships, exposure to a stepfather and growing up in poverty show no effect on the intensity of child abuse. Powerful women negotiated affectionate behavior from their partners for both themselves and their children; powerless women's negotiations with partners usually left both themselves and their children open to violence.

  17. Investigating the relationship between costs and outcomes for English mental health providers: a bi-variate multi-level regression analysis.

    Science.gov (United States)

    Moran, Valerie; Jacobs, Rowena

    2018-06-01

    Provider payment systems for mental health care that incentivize cost control and quality improvement have been a policy focus in a number of countries. In England, a new prospective provider payment system is being introduced to mental health that should encourage providers to control costs and improve outcomes. The aim of this research is to investigate the relationship between costs and outcomes to ascertain whether there is a trade-off between controlling costs and improving outcomes. The main data source is the Mental Health Minimum Data Set (MHMDS) for the years 2011/12 and 2012/13. Costs are calculated using NHS reference cost data while outcomes are measured using the Health of the Nation Outcome Scales (HoNOS). We estimate a bivariate multi-level model with costs and outcomes simultaneously. We calculate the correlation and plot the pairwise relationship between residual costs and outcomes at the provider level. After controlling for a range of demographic, need, social, and treatment variables, residual variation in costs and outcomes remains at the provider level. The correlation between residual costs and outcomes is negative, but very small, suggesting that cost-containment efforts by providers should not undermine outcome-improving efforts under the new payment system.

  18. Variation of particulate organic carbon and its relationship with bio-optical properties during a phytoplankton bloom in the Pearl River estuary

    International Nuclear Information System (INIS)

    Wang Guifen; Zhou Wen; Cao Wenxi; Yin Jianping; Yang Yuezhong; Sun Zhaohua; Zhang Yuanzhi; Zhao Jun

    2011-01-01

    Highlights: → A study about relationship between POC and optical properties during a phytoplankton bloom. → Empirical algorithms for retrieving POC concentration from optical data were developed. → Phytoplankton carbon and it's ratio to Chl-a are estimated and discussed. → Demonstrates that marine optical buoy can be a new platform for monitoring biogeochemical cycle. - Abstract: In this study, variations in the particulate organic carbon (POC) were monitored during a phytoplankton bloom event, and the corresponding changes in bio-optical properties were tracked at one station (114.29 o E, 22.06 o N) located in the Pearl River estuary. A greater than 10-fold increase in POC (112.29-1173.36 mg m -3 ) was observed during the bloom, with the chlorophyll a concentration (Chl-a) varying from 0.984 to 25.941 mg m -3 . A power law function is used to describe the relationship between POC and Chl-a, and the POC:Chl-a ratio tends to change inversely with Chl-a. Phytoplankton carbon concentration is indirectly estimated using the conceptual model proposed by , and this carbon is found to contribute 47.21% (±10.65%) to total POC. The estimated carbon-to-chlorophyll ratio of phytoplankton in diatom-dominated waters is found to be comparable with results reported in the literature. Empirical algorithms for determining the concentrations of Chl-a and POC were developed based on the relationships of these variables with the blue-to-green reflectance ratio. With these bio-optical models, the levels of particulate organic carbon and Chl-a could be predicted from the radiometric data measured by a marine optical buoy, which showed much more detailed information about the variability in biogeochemical parameters during this bloom event.

  19. Mitochondrial DNA Variation Reveals a Sharp Genetic Break within the Distribution of the Blue Land Crab Cardisoma guanhumi in the Western Central Atlantic

    Directory of Open Access Journals (Sweden)

    Maria Rosimere Xavier Amaral

    2015-08-01

    Full Text Available The blue land crab Cardisoma guanhumi is widely distributed throughout tropical and subtropical estuarine regions in the Western Central Atlantic (WCA. Patterns of population genetic structure and historical demographics of the species were assessed by mtDNA control region sequence analysis to examine the connectivity among five populations (n = 97 within the region for future conservation strategies and decision-making of fishery management. A total of 234 polymorphic nucleotides were revealed within the sequence region, which have defined 93 distinct haplotypes. No dominant mtDNA haplotypes were found but instead a distribution of a few low-frequency recurrent haplotypes with a large number of singletons. A NJ-tree and a median-joining haplotype network revealed two distinct clusters, corresponding to individuals from estuaries located along the Caribbean Sea and Brazilian waters, respectively. AMOVA and FST statistics supported the hypothesis that two main geographic regions exists. Phylogeographical discontinuity was further demonstrated by the Bayesian assignment analysis and a significant pattern of isolation-by-distance. Additionally, tests of neutral evolution and analysis of mismatch distribution indicate a complex demographic history in the WCA, which corresponds to bottleneck and subsequent population growth. Overall, a sharp genetic break between Caribbean and Brazilian populations raised concerns over the conservation status of the blue land crab.

  20. Molecular identification of Anaplasma marginale in two autochthonous South American wild species revealed an identical new genotype and its phylogenetic relationship with those of bovines.

    Science.gov (United States)

    Guillemi, Eliana C; de la Fourniere, Sofía; Orozco, Marcela; Peña Martinez, Jorge; Correa, Elena; Fernandez, Javier; Lopez Arias, Ludmila; Paoletta, Martina; Corona, Belkis; Pinarello, Valérie; Wilkowsky, Silvina E; Farber, Marisa D

    2016-05-26

    Anaplasma marginale is a well-known cattle pathogen of tropical and subtropical world regions. Even though, this obligate intracellular bacterium has been reported in other host species different than bovine, it has never been documented in Myrmecophaga tridactyla (giant anteater) or Hippocamelus antisense (taruca), which are two native endangered species. Samples from two sick wild animals: a Myrmecophaga tridactyla (blood) and a Hippocamelus antisense (blood and serum) were studied for the presence of A. marginale DNA through msp5 gene fragment amplification. Further characterization was done through MSP1a tandem repeats analysis and MLST scheme and the genetic relationship among previously characterized A. marginale sequences were studied by applying, eBURST algorithm and AMOVA analysis. Anaplasma marginale DNA was identified in the Myrmecophaga tridactyla and Hippocamelus antisense samples. Through molecular markers, we identified an identical genotype in both animals that was not previously reported in bovine host. The analysis through eBURST and AMOVA revealed no differentiation between the taruca/anteater isolate and the bovine group. In the present publication we report the identification of A. marginale DNA in a novel ruminant (Hippocamelus antisense) and non-ruminant (Myrmecophaga tridactyla) host species. Genotyping analysis of isolates demonstrated the close relatedness of the new isolate with the circulation population of A. marginale in livestock. Further analysis is needed to understand whether these two hosts contribute to the anaplasmosis epidemiology.

  1. Synthesis and evaluation of 8,4'-dideshydroxy-leinamycin revealing new insights into the structure-activity relationship of the anticancer natural product leinamycin.

    Science.gov (United States)

    Liu, Tao; Ma, Ming; Ge, Hui-Ming; Yang, Chunying; Cleveland, John; Shen, Ben

    2015-11-01

    Leinamycin (LNM, 1) is a novel antitumor antibiotic produced by Streptomyces atroolivaceus S-140 and features an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. The 1,3-dioxo-1,2-dithiolane moiety of LNM is essential for its antitumor activity via an episulfonium ion-mediated DNA alkylation upon reductive activation in the presence of cellular thiols. We recently isolated leinamycin E1 (LNM E1, 2) from an engineered strain S. atroolivaceus SB3033, which lacks the 1,3-dioxo-1,2-dithiolane moiety. Here we report the chemical synthesis of 8,4'-dideshydroxy-LNM (5) from 2 and determination of the cytotoxicity of 5 against selected cancer cell lines in comparison with 1; 5 exhibits comparable activity as 1 with the EC50 values between 8.21 and 275 nM. This work reveals new insight into the structure-activity relationship of LNM and highlights the synergy between metabolic pathway engineering and medicinal chemistry for natural product drug discovery. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product.

    Science.gov (United States)

    Tran, Hai L; Lexa, Katrina W; Julien, Olivier; Young, Travis S; Walsh, Christopher T; Jacobson, Matthew P; Wells, James A

    2017-02-22

    Macrocycles are appealing drug candidates due to their high affinity, specificity, and favorable pharmacological properties. In this study, we explored the effects of chemical modifications to a natural product macrocycle upon its activity, 3D geometry, and conformational entropy. We chose thiocillin as a model system, a thiopeptide in the ribosomally encoded family of natural products that exhibits potent antimicrobial effects against Gram-positive bacteria. Since thiocillin is derived from a genetically encoded peptide scaffold, site-directed mutagenesis allows for rapid generation of analogues. To understand thiocillin's structure-activity relationship, we generated a site-saturation mutagenesis library covering each position along thiocillin's macrocyclic ring. We report the identification of eight unique compounds more potent than wild-type thiocillin, the best having an 8-fold improvement in potency. Computational modeling of thiocillin's macrocyclic structure revealed a striking requirement for a low-entropy macrocycle for activity. The populated ensembles of the active mutants showed a rigid structure with few adoptable conformations while inactive mutants showed a more flexible macrocycle which is unfavorable for binding. This finding highlights the importance of macrocyclization in combination with rigidifying post-translational modifications to achieve high-potency binding.

  3. Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India.

    Science.gov (United States)

    Imamura, Daisuke; Morita, Masatomo; Sekizuka, Tsuyoshi; Mizuno, Tamaki; Takemura, Taichiro; Yamashiro, Tetsu; Chowdhury, Goutam; Pazhani, Gururaja P; Mukhopadhyay, Asish K; Ramamurthy, Thandavarayan; Miyoshi, Shin-Ichi; Kuroda, Makoto; Shinoda, Sumio; Ohnishi, Makoto

    2017-02-01

    Cholera is an acute diarrheal disease and a major public health problem in many developing countries in Asia, Africa, and Latin America. Since the Bay of Bengal is considered the epicenter for the seventh cholera pandemic, it is important to understand the genetic dynamism of Vibrio cholerae from Kolkata, as a representative of the Bengal region. We analyzed whole genome sequence data of V. cholerae O1 isolated from cholera patients in Kolkata, India, from 2007 to 2014 and identified the heterogeneous genomic region in these strains. In addition, we carried out a phylogenetic analysis based on the whole genome single nucleotide polymorphisms to determine the genetic lineage of strains in Kolkata. This analysis revealed the heterogeneity of the Vibrio seventh pandemic island (VSP)-II in Kolkata strains. The ctxB genotype was also heterogeneous and was highly related to VSP-II types. In addition, phylogenetic analysis revealed the shifts in predominant strains in Kolkata. Two distinct lineages, 1 and 2, were found between 2007 and 2010. However, the proportion changed markedly in 2010 and lineage 2 strains were predominant thereafter. Lineage 2 can be divided into four sublineages, I, II, III and IV. The results of this study indicate that lineages 1 and 2-I were concurrently prevalent between 2007 and 2009, and lineage 2-III observed in 2010, followed by the predominance of lineage 2-IV in 2011 and continued until 2014. Our findings demonstrate that the epidemic of cholera in Kolkata was caused by several distinct strains that have been constantly changing within the genetic lineages of V. cholerae O1 in recent years.

  4. Genotypic variation in growth and physiological response to drought stress and re-watering reveals the critical role of recovery in drought adaptation in maize seedlings

    Directory of Open Access Journals (Sweden)

    Daoqian eChen

    2016-01-01

    Full Text Available Non-irrigated crops in temperate climates and irrigated crops in arid climates are subjected to continuous cycles of water stress and re-watering. Thus, fast and efficient recovery from water stress may be among the key determinants of plant drought adaptation. The present study was designed to comparatively analyze the roles of drought resistance and drought recovery in drought adaptation and to investigate the physiological basis of genotypic variation in drought adaptation in maize (Zea mays seedlings. As the seedlings behavior in growth associate with yield under drought, it could partly reflect the potential of drought adaptability. Growth and physiological responses to progressive drought stress and recovery were observed in seedlings of ten maize lines. The results showed that drought adaptability is closely related to drought recovery (r = 0.714**, but not to drought resistance (r = 0.332. Drought induced decreases in leaf water content, water potential, osmotic potential, gas exchange parameters, chlorophyll content, Fv/Fm and nitrogen content, and increased H2O2 accumulation and lipid peroxidation. After recovery, most of these physiological parameters rapidly returned to normal levels. The physiological responses varied between lines. Further correlation analysis indicated that the physiological bases of drought resistance and drought recovery are definitely different, and that maintaining higher chlorophyll content (r = 0.874*** and Fv/Fm (r = 0.626* under drought stress contributes to drought recovery. Our results suggest that both drought resistance and recovery are key determinants of plant drought adaptation, and that drought recovery may play a more important role than previously thought. In addition, leaf water potential, chlorophyll content and Fv/Fm could be used as efficient reference indicators in the selection of drought-adaptive genotypes.

  5. Holocene moisture variations over the arid central Asia revealed by a comprehensive sand-dune record from the central Tian Shan, NW China

    Science.gov (United States)

    Long, Hao; Shen, Ji; Chen, Jianhui; Tsukamoto, Sumiko; Yang, Linhai; Cheng, Hongyi; Frechen, Manfred

    2017-10-01

    Arid central Asia (ACA) is one of the largest arid (desert) areas in the world, and its climate is dominated by the westerlies. In this study, we examined sand dune evolution from the Bayanbulak Basin in the Tian Shan (Xinjiang, NW China), aiming to infer the Holocene moisture history of the ACA. Combined with stratigraphic observation and environmental proxies analysis (grain size, magnetic susceptibility and total organic content), large numbers of luminescence ages from multiple sites (eight sections, 79 samples) were applied to reconstruct the evolution of the sand dune accumulation in the study basin. The overall results imply very dry conditions characterized by sand dune accumulation at ∼12-6.5 ka, a wet interval between ∼6.5 and 0.8 ka when soil formation occurred, and decreased moisture during the last 0.8 ka. This moisture variation pattern is generally consistent with that inferred from many lacustrine records in the core zone of ACA, suggesting a widespread dry period in the early-to-middle Holocene and relatively wet middle-to-late Holocene. Thus, the moisture history derived from the current sand dune system contrasts with that in Asian monsoon areas, which are characterized by a strong monsoon (high precipitation) in the early and mid-Holocene and a weak monsoon (low precipitation and dry climate) during the late Holocene. Our results strongly suggest that the winter solar insolation and the external boundary conditions such as atmospheric CO2 concentration, ice sheets, and meltwater fluxes, have been major influential factors triggering the Holocene moisture evolution in the core zone of ACA.

  6. Response patterns of phytoplankton growth to variations in resuspension in the German Bight revealed by daily MERIS data in 2003 and 2004

    Directory of Open Access Journals (Sweden)

    Jian Su

    2015-10-01

    Full Text Available Chlorophyll (chl a concentration in coastal seas exhibits variability on various spatial and temporal scales. Resuspension of particulate matter can somewhat limit algal growth, but can also enhance productivity because of the intrusion of nutrient-rich pore water from sediments or bottom water layers into the whole water column. This study investigates whether characteristic changes in net phytoplankton growth can be directly linked to resuspension events within the German Bight. Satellite-derived chl a were used to derive spatial patterns of net rates of chl a increase/decrease (NR in 2003 and 2004. Spatial correlations between NR and mean water column irradiance were analysed. High correlations in space and time were found in most areas of the German Bight (R2 > 0.4, suggesting a tight coupling between light availability and algal growth during spring. These correlations were reduced within a distinct zone in the transition between shallow coastal areas and deeper offshore waters. In summer and autumn, a mismatch was found between phytoplankton blooms (chl a > 6 mg m−3 and spring-tidal induced resuspension events as indicated by bottom velocity, suggesting that there is no phytoplankton resuspension during spring tides. It is instead proposed here that frequent and recurrent spring-tidal resuspension events enhance algal growth by supplying remineralized nutrients. This hypothesis is corroborated by a lag correlation analysis between resuspension events and in-situ measured nutrient concentrations. This study outlines seasonally different patterns in phytoplankton productivity in response to variations in resuspension, which can serve as a reference for modelling coastal ecosystem dynamics.

  7. Analysis of the spatial-temporal variation characteristics of vegetative drought and its relationship with meteorological factors in China from 1982 to 2010.

    Science.gov (United States)

    Shen, Qiu; Liang, Liang; Luo, Xiang; Li, Yanjun; Zhang, Lianpeng

    2017-08-25

    Drought is a complex natural phenomenon that can cause reduced water supplies and can consequently have substantial effects on agriculture and socioeconomic activities. The objective of this study was to gain a better understanding of the spatial-temporal variation characteristics of vegetative drought and its relationship with meteorological factors in China. The Vegetation Condition Index (VCI) dataset calculated from NOAA/AVHRR images from 1982 to 2010 was used to analyse the spatial-temporal variation characteristics of vegetative drought in China. This study also examined the trends in meteorological factors and their influences on drought using monitoring data collected from 686 national ground meteorological stations. The results showed that the VCI appeared to slowly rise in China from 1982 to 2010. From 1982 to 1999, the VCI rose slowly. Then, around 2000, the VCI exhibited a severe fluctuation before it entered into a relatively stable stage. Drought frequencies in China were higher, showing a spatial distribution feature of "higher in the north and lower in the south". Based on the different levels of drought, the frequencies of mild and moderate drought in four geographical areas were higher, and the frequency of severe drought was higher only in ecologically vulnerable areas, such as the Tarim Basin and the Qaidam Basin. Drought was mainly influenced by meteorological factors, which differed regionally. In the northern region, the main influential factor was sunshine duration, while the other factors showed minimal effects. In the southern region and Tibetan Plateau, the main influential factors were sunshine duration and temperature. In the northwestern region, the main influential factors were wind velocity and station atmospheric pressure.

  8. Comparative Molecular and Morphological Variation Analysis of Siderastrea (Anthozoa, Scleractinia) Reveals the Presence of Siderastrea stellata in the Gulf of Mexico.

    Science.gov (United States)

    García, Norberto A Colín; Campos, Jorge E; Musi, José L Tello; Forsman, Zac H; Muñoz, Jorge L Montero; Reyes, Alejandro Monsalvo; González, Jesús E Arias

    2017-02-01

    The genus Siderastrea exhibits high levels of morphological variability. Some of its species share similar morphological characteristics with congeners, making their identification difficult. Siderastrea stellata has been reported as an intermediary of S. siderea and S. radians in the Brazilian reef ecosystem. In an earlier study conducted in Mexico, we detected Siderastrea colonies with morphological features that were not consistent with some siderastreid species previously reported in the Gulf of Mexico. Thus, we performed a combined morphological and molecular analysis to identify Siderastrea species boundaries from the Gulf of Mexico. Some colonies presented high morphologic variability, with characteristics that corresponded to Siderastrea stellata. Molecular analysis, using the nuclear ITS and ITS2 region, corroborated the morphological results, revealing low genetic variability between S. radians and S. stellata. Since the ITS sequences did not distinguish between Siderastrea species, we used the ITS2 region to differentiate S. stellata from S. radians. This is the first report of Siderastrea stellata and its variability in the Gulf of Mexico that is supported by morphological and molecular analyses.

  9. Revealed variations of air quality in industrial development over a remote plateau of Southwest China: an application of atmospheric visibility data

    Science.gov (United States)

    Zhao, Tianliang; Liu, Di; Zheng, Xiaobo; Yang, Lexin; Gu, Xiaoping; Hu, Jun; Shu, Zhuozhi; Chang, Jiacheng; Wu, Xiasheng

    2017-12-01

    Since the 1980s, an industrial development has bloomed in China including the Yunnan-Guizhou Plateau (YGP), a remote region in Southwest China. To analyze the regional variations in air quality over YGP during the industrial development, we adopt the equivalent visibility by excluding the influence of natural factors on the observed visibility based on the meteorological data observed at 203 sites over YGP from 1980 to 2010 in this study. The YGP air quality exhibits the tremendous spatial differences in a general distribution from western good to eastern poor air quality. A similar pattern shifts seasonally in the spatial distribution with a typical seasonality of air quality over YGP between summertime low air pollution and wintertime high air pollution. The increasing and decreasing trends in visibility are mostly concentrated, respectively, in the YGP regions with high and low visibility, displaying the phenomenon of polarization in air quality change over YGP during 1980-2010. The regional mean visibility of the YGP presents a significant declining trend with change rate of -1.5 km decade-1 for air quality deterioration. The seasonal differences in visibility between summer (33.6 km) and winter (25.2 km) became obscure with the interannual change trends of visibility with stronger declines (-2.29 km decade-1) in summer and weaker decreases (-0.89 km decade-1) in winter over 1980-2010, which lead to a indistinct seasonality of air quality change over YGP. The remote YGP had experienced more frequent haze pollution, especially in the eastern plateau over 31 years. In accompany of increasing energy consumption in the industrial development, population growth is an important factor influencing the interannual change of YGP air quality. The distinct spatial distribution in the YGP terrain exerts an impact on poor air quality in lower flatlands harbored by mountainous topography with good air quality. Declined monsoon winds could meteorologically drive the air

  10. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Directory of Open Access Journals (Sweden)

    Catherine Mooney

    Full Text Available MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  11. Clumped Isotope Thermometry Reveals Variations in Soil Carbonate Seasonal Biases Over >4 km of Relief in the Semi-Arid Andes of Central Chile

    Science.gov (United States)

    Burgener, L. K.; Huntington, K. W.; Hoke, G. D.; Schauer, A. J.; Ringham, M. C.; Latorre Hidalgo, C.; Díaz, F.

    2015-12-01

    The application of carbonate clumped isotope thermometry to soil carbonates has the potential to shed new light on questions regarding terrestrial paleoclimate. In order to better utilize this paleoclimate tool, outstanding questions regarding seasonal biases in soil carbonate formation and the relationship between soil carbonate formation temperatures (T(Δ47)) and surface temperatures must be resolved. We address these questions by comparing C, O, and clumped isotope data from Holocene/modern soil carbonates to modern meteorological data. The data were collected along a 170 km transect with >4 km of relief in central Chile (~30°S). Previous studies have suggested that soil carbonates should record a warm season bias and form in isotopic equilibrium with soil water and soil CO2. We identify two discrete climate zones separated by the local winter snow line (~3200 m). Below this boundary, precipitation falls as rain and soil carbonate T(Δ47) values at depths >40 cm resemble summer soil temperatures; at higher elevations, precipitation falls as snow and T(Δ47) values resemble mean annual soil temperatures. Soil carbonates from the highest sample site (4700 m), which is devoid of vegetation and located near perennial snow fields, yield anomalous δ18O, δ13C, and T(Δ47) values, indicative of kinetic isotope effects that we attribute to cryogenic carbonate formation. Our results suggest that soil carbonates from depths temperature and precipitation, and should not be used as paleotemperature proxies. These findings (1) highlight the role of soil moisture in modulating soil carbonate formation and the resulting T(Δ47) values, (2) underscore the importance of understanding past soil moisture conditions when attempting to reconstruct paleotemperatures using carbonate clumped isotope thermometry, and (3) suggest that soil carbonates from high elevation or high latitude sites may form under non-equilibrium conditions.

  12. The gene expression profile of resistant and susceptible Bombyx mori strains reveals cypovirus-associated variations in host gene transcript levels.

    Science.gov (United States)

    Guo, Rui; Wang, Simei; Xue, Renyu; Cao, Guangli; Hu, Xiaolong; Huang, Moli; Zhang, Yangqi; Lu, Yahong; Zhu, Liyuan; Chen, Fei; Liang, Zi; Kuang, Sulan; Gong, Chengliang

    2015-06-01

    High-throughput paired-end RNA sequencing (RNA-Seq) was performed to investigate the gene expression profile of a susceptible Bombyx mori strain, Lan5, and a resistant B. mori strain, Ou17, which were both orally infected with B. mori cypovirus (BmCPV) in the midgut. There were 330 and 218 up-regulated genes, while there were 147 and 260 down-regulated genes in the Lan5 and Ou17 strains, respectively. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment for differentially expressed genes (DEGs) were carried out. Moreover, gene interaction network (STRING) analyses were performed to analyze the relationships among the shared DEGs. Some of these genes were related and formed a large network, in which the genes for B. mori cuticular protein RR-2 motif 123 (BmCPR123) and the gene for B. mori DNA replication licensing factor Mcm2-like (BmMCM2) were key genes among the common up-regulated DEGs, whereas the gene for B. mori heat shock protein 20.1 (Bmhsp20.1) was the central gene among the shared down-regulated DEGs between Lan5 vs Lan5-CPV and Ou17 vs Ou17-CPV. These findings established a comprehensive database of genes that are differentially expressed in response to BmCPV infection between silkworm strains that differed in resistance to BmCPV and implied that these DEGs might be involved in B. mori immune responses against BmCPV infection.

  13. High sequence variations in the region containing genes encoding a cellular morphogenesis protein and the repressor of sexual development help to reveal origins of Aspergillus oryzae.

    Science.gov (United States)

    Chang, Perng-Kuang; Scharfenstein, Leslie L; Solorzano, Cesar D; Abbas, Hamed K; Hua, Sui-Sheng T; Jones, Walker A; Zablotowicz, Robert M

    2015-05-04

    Aspergillus oryzae and Aspergillus flavus are closely related fungal species. The A. flavus morphotype that produces numerous small sclerotia (S strain) and aflatoxin has a unique 1.5 kb deletion in the norB-cypA region of the aflatoxin gene cluster (i.e. the S genotype). Phylogenetic studies have indicated that an isolate of the nonaflatoxigenic A. flavus with the S genotype is the ancestor of A. oryzae. Genome sequence comparison between A. flavus NRRL3357, which produces large sclerotia (L strain), and S-strain A. flavus 70S identified a region (samA-rosA) that was highly variable in the two morphotypes. A third type of samA-rosA region was found in A. oryzae RIB40. The three samA-rosA types were later revealed to be commonly present in A. flavus L-strain populations. Of the 182 L-strain A. flavus field isolates examined, 46%, 15% and 39% had the samA-rosA type of NRRL3357, 70S and RIB40, respectively. The three types also were found in 18 S-strain A. flavus isolates with different proportions. For A. oryzae, however, the majority (80%) of the 16 strains examined had the RIB40 type and none had the NRRL3357 type. The results suggested that A. oryzae strains in the current culture collections were mostly derived from the samA-rosA/RIB40 lineage of the nonaflatoxigenic A. flavus with the S genotype. Published by Elsevier B.V.

  14. A synthesis of Plio-Pleistocene leaf wax biomarker records of hydrological variation in East Africa and their relationship with hominin evolution

    Science.gov (United States)

    Lupien, R.; Russell, J. M.; Campisano, C. J.; Feibel, C. S.; Deino, A. L.; Kingston, J.; Potts, R.; Cohen, A. S.

    2017-12-01

    Climate change is thought to play a critical role in human evolution. However, the mechanisms behind this relationship are difficult to test due to a lack of long, high-quality paleoclimate records from hominin fossil locales. We improve the understanding of this relationship by examining Plio-Pleistocene lake sediment cores from East Africa that were drilled by the Hominin Sites and Paleolakes Drilling Project, an international effort to study the environment in which our hominin ancestors evolved and dispersed. We have analyzed organic geochemical signals of climate from drill cores from Ethiopia and Kenya spanning the Pliocene to recent time (from north to south: paleolake Hadar, Lake Turkana, Lake Baringo, and paleolake Koora). Specifically, we analyzed the hydrogen isotopic composition of terrestrial leaf waxes, which records changes in regional atmospheric circulation and hydrology. We reconstructed quantitative records of rainfall amount at each of the study sites, which host sediment spanning different geologic times and regions. By compiling these records, we test hominin evolutionary hypotheses as well as crucial questions about climate trend and variability. We find that there is a gradual or step-wise enrichment in δDwax, signifying a trend from a wet to dry climate, from the Pliocene to the Pleistocene, perhaps implying an influence of global temperature, ice sheet extent, and/or atmospheric greenhouse gas concentrations on East African climate. However, the shift is small relative to the amplitude of orbital-scale isotopic variations. The records indicate a strong influence of eccentricity-modulated orbital precession, and imply that local insolation effects are the likely cause of East African precipitation. Several of the intervals of high isotopic variability coincide with key hominin fossil or technological transitions, suggesting that climate variability plays a key role in hominin evolution.

  15. Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources

    Directory of Open Access Journals (Sweden)

    Xiaoqing Rong-Mullins

    2018-02-01

    . Hence, the complement to 4NQO resistance was poor growth on nonfermentable carbon sources, which in turn varied depending on the allele of Yrr1 expressed in the isogenic yeast. The oxidation state of the yeast affected the 4NQO toxicity by altering the reactive oxygen species (ROS generated by cellular metabolism. The integration of RNA-Seq and ChIP-Seq elucidated how Yrr1 regulates global gene transcription in response to 4NQO and how various Yrr1 alleles confer differential resistance to 4NQO. This study provides guidance for further investigation into how Yrr1 regulates cellular responses to 4NQO, as well as transcriptomic resources for further analysis of transcription factor variation on carbon source utilization.

  16. The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms.

    Science.gov (United States)

    Ma, Ji; Yang, Bingxian; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Wang, Xumin

    2013-10-10

    Mahonia bealei (Berberidaceae) is a frequently-used traditional Chinese medicinal plant with efficient anti-inflammatory ability. This plant is one of the sources of berberine, a new cholesterol-lowering drug with anti-diabetic activity. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of M. bealei. The complete cp genome of M. bealei is 164,792 bp in length, and has a typical structure with large (LSC 73,052 bp) and small (SSC 18,591 bp) single-copy regions separated by a pair of inverted repeats (IRs 36,501 bp) of large size. The Mahonia cp genome contains 111 unique genes and 39 genes are duplicated in the IR regions. The gene order and content of M. bealei are almost unarranged which is consistent with the hypothesis that large IRs stabilize cp genome and reduce gene loss-and-gain probabilities during evolutionary process. A large IR expansion of over 12 kb has occurred in M. bealei, 15 genes (rps19, rpl22, rps3, rpl16, rpl14, rps8, infA, rpl36, rps11, petD, petB, psbH, psbN, psbT and psbB) have expanded to have an additional copy in the IRs. The IR expansion rearrangement occurred via a double-strand DNA break and subsequence repair, which is different from the ordinary gene conversion mechanism. Repeat analysis identified 39 direct/inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Analysis also revealed 75 simple sequence repeat (SSR) loci and almost all are composed of A or T, contributing to a distinct bias in base composition. Comparison of protein-coding sequences with ESTs reveals 9 putative RNA edits and 5 of them resulted in non-synonymous modifications in rpoC1, rps2, rps19 and ycf1. Phylogenetic analysis using maximum parsimony (MP) and maximum likelihood (ML) was performed on a dataset composed of 65 protein-coding genes from 25 taxa, which yields an identical tree topology as previous plastid-based trees, and provides strong support for the sister relationship between Ranunculaceae and Berberidaceae

  17. Changes in host-mycorrhiza relationships revealed by stable isotopes after naturally-induced thinning of the stand: case study on Tuber aestivum.

    Science.gov (United States)

    Gavrichkova, Olga; Lauteri, Marco; Ciolfi, Marco; Chiocchini, Francesca; Paris, Pierluigi; Pisanelli, Andrea; Portarena, Silvia; Brugnoli, Enrico

    2016-04-01

    Terrestrial plants overcome nutrients and water limitations by forming mutualistic associations with mycorrhizal fungi. Fungi, in return, take advantage from the carbohydrates supplied by the host. Some mycorrhizal fruit bodies, like that of Tuber spp., have a peculiar gastronomic value with many efforts being undertaken to predict and enhance their productivity. However, many issues of truffle-producing mycorrhizal ecology are still poorly understood, in particular optimal conditions favoring fruit formation, potential host plants and host-mycorrhiza relationships. In this study, we tested the applicability of stable isotope measurements under natural abundance to identify the plants which likely host the mycorrhiza of Tuber aestivum and to characterize host-mycorrhizal nutrient, water and carbohydrate exchange under plant natural growing conditions and with the change of the forest cover after naturally occurred thinning. For these purposes, sampling of the fruit bodies of T. aestivum was performed during the growing season 2011 in a mixed broadleaved-coniferous forest in central Italy (initially the site was a manmade pine plantation). Nine truffle-producing parcels were identified with five being composed of the original Pinus pinaster -dominated vegetation and four in which pine was replaced by broadleaf species after both wind-induced thinning and natural dieback of pine trees. Seasonal variation of δ13C, δ15N and δ18O were analyzed in the fungal material, in the surrounding soil and in the plant material of the potential host species (xylem water in the trunk, branches and leaves, recently assimilated carbohydrates in phloem and leaves). The results showed a possibility of the identification of the mycorrhizal host species applying isotope analyses, with mycorrhiza receiving most part of the carbohydrates from the pine in pine-dominated parcels. Interestingly, in thinned parcels, the truffle bodies maintained isotope composition similar to bodies gathered

  18. Diurnal Variation of Rainfall Associated with Tropical Depression in South China and its Relationship to Land-Sea Contrast and Topography

    Directory of Open Access Journals (Sweden)

    Yuchun Zhao

    2013-12-01

    Full Text Available Convective precipitation associated with tropical depression (TD is one primary type of post-flooding season rainfall in South China (SC. Observations of the Tropical Rainfall Measuring Mission (TRMM satellite have shown specific diurnal features of convective rainfall in South China, which is somewhat different from that in other seasons or regions of China. Convective precipitation is usually organized into a rainfall band along the southeastern coast of South China in the early morning hours. The rainfall band develops and intensifies quickly in the morning, then moves inland in the afternoon and, finally, diminishes at night. The daily convective rainfall along the coast is much more than that in the inland region, and heavy rainfall is often found along the coast. A long-duration heavy rainfall event associated with tropical depression “Fitow” during the period from 28 August to 6 September 2001, is selected in this study to explore the diurnal feature of convective rainfall and its formation mechanism. Modeling results of the 10-day heavy rainfall event are compared with both rain-gauge observation and satellite-retrieved rainfall. Total precipitation and its spatial distribution, as well as diurnal variations are reasonably simulated and agree well with observations. Further analysis reveals that the development and movement of convective precipitation is mainly related to the land and sea breezes. The anomalous height-latitudinal circulation in the morning-to-noon hours is completely reversed in the afternoon-to-late-evening hours, with the convective rainfall swinging back and forth, following its updraft branch. Sensitivity experiments show that the afternoon convective rainfall in the inland region of SC is caused by the diurnal variation of solar radiation forcing. The mountain range along the coast and the complex topography in the inland region of SC plays a critical role in the enhancement of diurnal convective rainfall

  19. Revealing the relationship between the photocatalytic property and structure characteristic of reduced TiO2 by hydrogen and carbon monoxide treatment.

    Science.gov (United States)

    Liu, Yunpeng; Li, Yuhang; Yang, Siyuan; Lin, Yuan; Zuo, Jianliang; Liang, Hong; Peng, Feng

    2018-06-04

    The hydrogenation (reduction) has been considered as an effective method to improve the photocatalytic activity of TiO2, however, the underlying relationship between structure and photocatalytic performance has still not been adequately unveiled so far. Herein, to obtain insight into the effect of structure on photocatalytic activity, two types of reduced TiO2 were prepared by CO (CO-TiO2) and H2 (H-TiO2), respectively. For H-TiO2, Ti-H bonds and oxygen vacancies are formed on the surface of H-TiO2, resulting in a more disorder surface lattice. However, for CO-TiO2, the more Ti-OH bonds are formed on the surface and the more bulk oxygen vacancies are introduced, the disorder layer of CO-TiO2 is relatively thin owing to the most of surface vacancies repaired by Ti-OH bonds. Under the simulated solar irradiation, the photocatalytic H2 evolution rate of CO-TiO2 reaches 7.17 mmol g-1 h-1, which is 4.14 and 1.50 times those of TiO2 and H-TiO2, respectively. The photocatalytic degradation rate constant of methyl orange on CO-TiO2 is 2.45 and 6.39 times those on H-TiO2 and TiO2. The superior photocatalytic activity of CO-TiO2 is attributed to the effective separation and transfer of the photo-generated electron-hole pairs, due to the synergistic effects of oxygen vacancies and surface Ti-OH bonds. This study reveals the relation between the photocatalytic property and structure, and provides a new method to prepare highly active TiO2 for H2 production and environmental treatment. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Structure-activity relationships for flavone interactions with amyloid β reveal a novel anti-aggregatory and neuroprotective effect of 2',3',4'-trihydroxyflavone (2-D08).

    Science.gov (United States)

    Marsh, Dylan T; Das, Sukanya; Ridell, Jessica; Smid, Scott D

    2017-07-15

    Naturally-occurring flavonoids have well documented anti-aggregatory and neuroprotective properties against the hallmark toxic protein in Alzheimer's disease, amyloid β (Aβ). However the extensive diversity of flavonoids has limited the insight into the precise structure-activity relationships that confer such bioactive properties against the Aβ protein. In the present study we have characterised the Aβ binding properties, anti-aggregatory and neuroprotective effects of a discreet set of flavones, including the recently described novel protein sumoylation inhibitor 2',3',4'-trihydroxyflavone (2-D08). Quercetin, transilitin, jaceosidin, nobiletin and 2-D08 were incubated with human Aβ 1-42 for 48h in vitro and effects on Aβ fibrillisation kinetics and morphology measured using Thioflavin T (ThT) and electron microscopy respectively, in addition to effects on neuronal PC12 cell viability. Of the flavones studied, only quercetin, transilitin and 2-D08 significantly inhibited Aβ 1-42 aggregation and toxicity in PC12 cells. Of those, 2-D08 was the most effective inhibitor. The strong anti-amyloid activity of 2-D08 indicates that extensive hydroxylation in the B ring is the most important determinant of activity against β amyloid within the flavone scaffold. The lack of efficacy of jaceosidin and nobiletin indicate that extension of B ring hydroxylation with methoxyl groups result in an incremental loss of anti-fibrillar and neuroprotective activity, highlighting the constraint to vicinal hydroxyl groups in the B ring for effective inhibition of aggregation. These findings reveal further structural insights into anti-amyloid bioactivity of flavonoids in addition to a novel and efficacious anti-aggregatory and neuroprotective effect of the semi-synthetic flavone and sumoylation inhibitor 2',3',4'-trihydroxyflavone (2-D08). Such modified flavones may facilitate drug development targeting multiple pathways in neurodegenerative disease. Crown Copyright © 2017

  1. Can variation in hypothalamic-pituitary-adrenal (HPA-axis activity explain the relationship between depression and cognition in bipolar patients?

    Directory of Open Access Journals (Sweden)

    Marieke J van der Werf-Eldering

    Full Text Available Dysregulation of the hypothalamic-pituitary-adrenal (HPA axis is thought to be associated with more mood symptoms and worse cognitive functioning. This study examined whether variation in HPA axis activity underlies the association between mood symptoms and cognitive functioning.In 65 bipolar patients cognitive functioning was measured in domains of psychomotor speed, speed of information processing, attentional switching, verbal memory, visual memory, executive functioning and an overall mean score. Severity of depression was assessed by the Inventory of Depressive Symptomatology-self rating version. Saliva cortisol measurements were performed to calculate HPA axis indicators: cortisol awakening response, diurnal slope, the evening cortisol level and the cortisol suppression on the dexamethasone suppression test. Regression analyses of depressive symptoms and cognitive functioning on each HPA axis indicator were performed. In addition we calculated percentages explanation of the association between depressive symptoms and cognition by HPA axis indicators. Depressive symptoms were associated with dysfunction in psychomotor speed, attentional switching and the mean score, as well as with attenuation in diurnal slope value. No association was found between HPA axis activity and cognitive functioning and HPA axis activity did not explain the associations between depressive symptoms and cognition.As our study is the first one in this field specific for bipolar patients and changes in HPA-axis activity did not seem to explain the association between severity of depressive symptoms and cognitive functioning in bipolar patients, future studies are needed to evaluate other factors that might explain this relationship.

  2. Serum and synovial fluid C-reactive protein level variations in dogs with degenerative joint disease and their relationships with physiological parameters.

    Science.gov (United States)

    Boal, S; Miguel Carreira, L

    2015-09-01

    Degenerative joint disease (DJD) is a progressive, chronic joint disease with an inflammatory component promoting an acute phase protein (APP) response. C-reactive protein (CRP) is one of the most important APPs, used as an inflammation marker in human, but not veterinary medicine. The study was developed in a sample of 48 dogs (n = 48) with DJD and aimed to: 1) identify and quantify the synovial fluid CRP (SFCRP) in these specimens using a validated ELISA test for serum CRP (SCRP) detection and quantification; and 2) to study the possible relationship between SCRP and SFCRP levels variations in DJD patients evaluating the influence of some physical parameters such as gender, body weight, pain level, DJD grade, and the physical activity (PA) of the patients. Statistical analysis considered the results significant for p values <0.05. Our study showed that it is possible to detect and quantify SFCRP levels in DJD patients using a previously validated canine SCRP ELISA test, allowing us to point out a preliminary reference value for SFCRP in patients with DJD. Although, individuals with DJD presents SCRP values within the normal reference range and the SFCRP levels were always lower. Obesity, pain, and the DJD grade presented by the patients are conditions which seem to influence the SCRP levels but not the SFCRP.

  3. 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

    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......: We found that none of the symptoms and objective markers of respiratory disease were significantly associated with the GST null polymorphisms. An increasing number of positive alleles of the GSTM1 polymorphism tended to be associated lower prevalence of wheeze, cough, and high forced expiratory...

  4. Identification of a R2R3-MYB gene regulating anthocyanin biosynthesis and relationships between its variation and flower color difference in lotus (Nelumbo Adans.

    Directory of Open Access Journals (Sweden)

    Shan-Shan Sun

    2016-09-01

    Full Text Available The lotus (Nelumbonaceae: Nelumbo Adans. is a highly desired ornamental plant, comprising only two extant species, the sacred lotus (N. nucifera Gaerten. with red flowers and the American lotus (N. lutea Willd. with yellow flowers. Flower color is the most obvious difference of two species. To better understand the mechanism of flower color differentiation, the content of anthocyanins and the expression levels of four key structural genes (e.g., DFR, ANS, UFGT and GST were analyzed in two species. Our results revealed that anthocyanins were detected in red flowers, not yellow flowers. Expression analysis showed that no transcripts of GST gene and low expression level of three UFGT genes were detected in yellow flowers. In addition, three regulatory genes (NnMYB5, NnbHLH1 and NnTTG1 were isolated from red flowers and showed a high similarity to corresponding regulatory genes of other species. Sequence analysis of MYB5, bHLH1 and TTG1 in two species revealed striking differences in coding region and promoter region of MYB5 gene. Population analysis identified three MYB5 variants in Nelumbo: a functional allele existed in red flowers and two inactive forms existed in yellow flowers. This result revealed that there was an association between allelic variation in MYB5 gene and flower color difference. Yeast two-hybrid experiments showed that NnMYB5 interacts with NnbHLH1, NlbHLH1 and NnTTG1, and NnTTG1 also interacts with NnbHLH1 and NlbHLH1. The over-expression of NnMYB5 led to anthocyanin accumulation in immature seeds and flower stalks and up-regulation of expression of TT19 in Arabidopsis. Therefore, NnMYB5 is a transcription activator of anthocyanin synthesis. This study helps to elucidate the function of NnMYB5 and will contribute to clarify the mechanism of flower coloration and genetic engineering of flower color in lotus.

  5. Serological and virological survey of hepatitis E virus (HEV) in animal reservoirs from Uruguay reveals elevated prevalences and a very close phylogenetic relationship between swine and human strains.

    Science.gov (United States)

    Mirazo, Santiago; Gardinali, Noemí R; Cecilia, D'Albora; Verger, Lorenzo; Ottonelli, Florencia; Ramos, Natalia; Castro, Gustavo; Pinto, Marcelo A; Ré, Viviana; Pisano, Belén; Lozano, Alejandra; de Oliveira, Jaqueline Mendes; Arbiza, Juan

    2018-01-01

    Hepatitis E virus (HEV) infection is an issue of public health concern in high-income and non-endemic countries. Increasing evidence supports the hypothesis of a zoonotic route as the main mode of infection in this epidemiological setting, since the transmission of genotypes HEV-3 and HEV-4 from reservoirs to humans has been demonstrated. In America, studies have confirmed the circulation of HEV in pig herds but the zoonotic role of wild boars has never been evaluated. Uruguay has a high burden of HEV- associated acute hepatitis, and a close phylogenetic relationship was observed among human HEV-3 strains and European isolates detected in swine. However in this context, swine herds have never been surveyed. Herein is reported a survey of HEV in swine herds, pigs at slaughter-house and free-living wild boar populations. Two-hundred and twenty sera and 150 liver tissue samples from domestic pigs, and 140 sera from wild boars were tested for HEV by ELISA and PCR-based approaches. All tested swine farms resulted seropositive with an overall rate of 46.8%. In turn, 22.1% of the wild boars had anti-HEV antibodies. HEV RNA was detected in 16.6% and 9.3% of liver samples from slaughter-age pigs and adult wild boars sera, respectively. Three strains from domestic pig were also amplified by nested-PCR approaches. By contrast, none of the positive samples obtained from wild boars could be confirmed by nested-PCR. Phylogenetic analysis revealed a very high nucleotide identity among swine strains and sequences obtained from humans in Uruguay. Results showed that HEV is widely distributed among swine herds in Uruguay. Additionally, this study evidences for the first time in the American continent that wild boar populations are a reservoir for HEV, though its zoonotic role remains to be elucidated. Altogether, data presented here suggest a high zoonotic risk of HEV transmission from swine to humans. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Indian Academy of Sciences (India)

    there are a few reports on the genetic evaluation of tung tree germplasm. .... bES, Enshi in Hubei province; SN, Suining in Sichuan province. Journal of Genetics Vol. 94, Online Resources e6 ... gene diversity. Journal of Genetics Vol. 94, Online Resources e7 .... Pan Y., Pan L., Chen L., Zhang L. L., Nevo E. and Peng J. H..

  7. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

    Directory of Open Access Journals (Sweden)

    Dawn B. Goldsmith

    2015-06-01

    Full Text Available Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS site in the summer (September and winter (March of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years.

  8. Relationship between ureB Sequence Diversity, Urease Activity and Genotypic Variations of Different Helicobacter pylori Strains in Patients with Gastric Disorders.

    Science.gov (United States)

    Ghalehnoei, Hossein; Ahmadzadeh, Alireza; Farzi, Nastaran; Alebouyeh, Masoud; Aghdaei, Hamid Asadzadeh; Azimzadeh, Pendram; Molaei, Mahsa; Zali, Mohammad Reza

    2016-01-01

    Association of the severity of Helicobacter pylori induced diseases with virulence entity of the colonized strains was proven in some studies. Urease has been demonstrated as a potent virulence factor for H. pylori. The main aim of this study was investigation of the relationships of ureB sequence diversity, urease activity and virulence genotypes of different H. pylori strains with histopathological changes of gastric tissue in infected patients suffering from different gastric disorders. Analysis of the virulence genotypes in the isolated strains indicated significant associations between the presence of severe active gastritis and cagA+ (P = 0.039) or cagA/iceA1 genotypes (P = 0.026), and intestinal metaplasia and vacA m1 (P = 0.008) or vacA s1/m2 (P = 0.001) genotypes. Our results showed a 2.4-fold increased risk of peptic ulcer (95% CI: 0.483-11.93), compared with gastritis, in the infected patients who had dupA positive strains; however this association was not statistically significant. The results of urease activity showed a significant mean difference between the isolated strains from patients with PUD and NUD (P = 0.034). This activity was relatively higher among patients with intestinal metaplasia. Also a significant association was found between the lack of cagA and increased urease activity among the isolated strains (P = 0.036). While the greatest sequence variation of ureB was detected in a strain from a patient with intestinal metaplasia, the sole determined amino acid change in UreB sequence (Ala201Thr, 30%), showed no influence on urease activity. In conclusion, the supposed role of H. pylori urease to form peptic ulcer and advancing of intestinal metaplasia was postulated in this study. Higher urease activity in the colonizing H. pylori strains that present specific virulence factors was indicated as a risk factor for promotion of histopathological changes of gastric tissue that advance gastric malignancy.

  9. Personal exposure to PM2.5, black smoke and NO2 in Copenhagen: relationship to bedroom and outdoor concentrations covering seasonal variation.

    Science.gov (United States)

    Sørensen, Mette; Loft, Steffen; Andersen, Helle Vibeke; Raaschou-Nielsen, Ole; Skovgaard, Lene Theil; Knudsen, Lisbeth E; Nielsen, Ivan V; Hertel, Ole

    2005-09-01

    Epidemiological studies have found negative associations between human health and particulate matter in urban air. In most studies outdoor monitoring of urban background has been used to assess exposure. In a field study, personal exposure as well as bedroom, front door and background 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 tobacco smoke (ETS) and burning of candles was collected by questionnaires. The personal exposure, the bedroom concentration and the front door concentration was set as outcome variable in separate models and analysed by mixed effect model regression methodology, regarding subject levels as a random 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 and the front door concentrations, and not the background concentration, were significantly associated to the personal exposure. The bedroom concentration was the strongest predictor of all three pollution measurements. The association between the bedroom and front door concentrations was significant for all 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 concentration was dependent upon the "season", with a stronger association in the warm season compared with the cold season, and for PM(2.5) and BS the same tendency was seen. Time exposed to

  10. Using an Explicit Emission Tagging Method in Global Modeling of Source-Receptor Relationships for Black Carbon in the Arctic: Variations, Sources and Transport Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hailong; Rasch, Philip J.; Easter, Richard C.; Singh, Balwinder; Zhang, Rudong; Ma, Po-Lun; Qian, Yun; Ghan, Steven J.; Beagley, Nathaniel

    2014-11-27

    We introduce an explicit emission tagging technique in the Community Atmosphere Model to quantify source-region-resolved characteristics of black carbon (BC), focusing on the Arctic. Explicit tagging of BC source regions without perturbing the emissions makes it straightforward to establish source-receptor relationships and transport pathways, providing a physically consistent and computationally efficient approach to produce a detailed characterization of the destiny of regional BC emissions and the potential for mitigation actions. Our analysis shows that the contributions of major source regions to the global BC burden are not proportional to the respective emissions due to strong region-dependent removal rates and lifetimes, while the contributions to BC direct radiative forcing show a near-linear dependence on their respective contributions to the burden. Distant sources contribute to BC in remote regions mostly in the mid- and upper troposphere, having much less impact on lower-level concentrations (and deposition) than on burden. Arctic BC concentrations, deposition and source contributions all have strong seasonal variations. Eastern Asia contributes the most to the wintertime Arctic burden. Northern Europe emissions are more important to both surface concentration and deposition in winter than in summer. The largest contribution to Arctic BC in the summer is from Northern Asia. Although local emissions contribute less than 10% to the annual mean BC burden and deposition within the Arctic, the per-emission efficiency is much higher than for major non-Arctic sources. The interannual variability (1996-2005) due to meteorology is small in annual mean BC burden and radiative forcing but is significant in yearly seasonal means over the Arctic. When a slow aging treatment of BC is introduced, the increase of BC lifetime and burden is source-dependent. Global BC forcing-per-burden efficiency also increases primarily due to changes in BC vertical distributions. The

  11. Identification of drug resistance and immune-driven variations in hepatitis C virus (HCV) NS3/4A, NS5A and NS5B regions reveals a new approach toward personalized medicine.

    Science.gov (United States)

    Ikram, Aqsa; Obaid, Ayesha; Awan, Faryal Mehwish; Hanif, Rumeza; Naz, Anam; Paracha, Rehan Zafar; Ali, Amjad; Janjua, Hussnain Ahmed

    2017-01-01

    Cellular immune responses (T cell responses) during hepatitis C virus (HCV) infection are significant factors for determining the outcome of infection. HCV adapts to host immune responses by inducing mutations in its genome at specific sites that are important for HLA processing/presentation. Moreover, HCV also adapts to resist potential drugs that are used to restrict its replication, such as direct-acting antivirals (DAAs). Although DAAs have significantly reduced disease burden, resistance to these drugs is still a challenge for the treatment of HCV infection. Recently, drug resistance mutations (DRMs) observed in HCV proteins (NS3/4A, NS5A and NS5B) have heightened concern that the emergence of drug resistance may compromise the effectiveness of DAAs. Therefore, the NS3/4A, NS5A and NS5B drug resistance variations were investigated in this study, and their prevalence was examined in a large number of protein sequences from all HCV genotypes. Furthermore, potential CD4 + and CD8 + T cell epitopes were predicted and their overlap with genetic variations was explored. The findings revealed that many reported DRMs within NS3/4A, NS5A and NS5B are not drug-induced; rather, they are already present in HCV strains, as they were also detected in HCV-naïve patients. This study highlights several hot spots in which HLA and drug selective pressure overlap. Interestingly, these overlapping mutations were frequently observed among many HCV genotypes. This study implicates that knowledge of the host HLA type and HCV subtype/genotype can provide important information in defining personalized therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. The human cerebral cortex is neither one nor many: Neuronal distribution reveals two quantitatively different zones in the grey matter, three in the white matter, and explains local variations in cortical folding

    Directory of Open Access Journals (Sweden)

    Pedro F. M. Ribeiro

    2013-09-01

    Full Text Available The human prefrontal cortex has been considered different in several aspects and relatively enlarged compared to the rest of the cortical areas. Here we determine whether the white and gray matter of the prefrontal portion of the human cerebral cortex have similar or different cellular compositions relative to the rest of the cortical regions by applying the Isotropic Fractionator to analyze the distribution of neurons along the entire anteroposterior axis of the cortex, and its relationship with the degree of gyrification, number of neurons under the cortical surface, and other parameters. The prefrontal region shares with the remainder of the cerebral cortex (except for occipital cortex the same relationship between cortical volume and number of neurons. In contrast, both occipital and prefrontal areas vary from other cortical areas in their connectivity through the white matter, with a systematic reduction of cortical connectivity through the white matter and an increase of the mean axon caliber along the anteroposterior axis. These two parameters explain local differences in the distribution of neurons underneath the cortical surface. We also show that local variations in cortical folding are neither a function of local numbers of neurons nor of cortical thickness, but correlate with properties of the white matter, and are best explained by the folding of the white matter surface. Our results suggest that the human cerebral cortex is divided in two zones (occipital and non-occipital that differ in how neurons distributed across their grey matter volume and in three zones (prefrontal, occipital, and non-occipital that differ in how neurons are connected through the white matter. Thus, the human prefrontal cortex has the largest fraction of neuronal connectivity through the white matter and the smallest average axonal caliber in the white matter within the cortex, although its neuronal composition fits the pattern found for other, non

  13. Experiencing variation

    DEFF Research Database (Denmark)

    Kobayashi, Sofie; Berge, Maria; Grout, Brian William Wilson

    2017-01-01

    This study contributes towards a better understanding of learning dynamics in doctoral supervision by analysing how learning opportunities are created in the interaction between supervisors and PhD students, using the notion of experiencing variation as a key to learning. Empirically, we have based...... the study on four video-recorded sessions, with four different PhD students and their supervisors, all from life sciences. Our analysis revealed that learning opportunities in the supervision sessions concerned either the content matter of research (for instance, understanding soil structure......), or the research methods— more specifically how to produce valid results. Our results illustrate how supervisors and PhD students create a space of learning together in their particular discipline by varying critical aspects of their research in their discussions. Situations where more openended research issues...

  14. Anatomic variation of the deep venous system and its relationship with deep vein thrombosis found on the lower extremity venograms that were obtained after artificial joint replacements

    International Nuclear Information System (INIS)

    Lee, Min Sun; Lee, Jee Eun; Hwang, Ji Young; Shim, Sung Shine; Yoo, Jeong Hyun; Suh, Jeong Soo; Park, Jae Young

    2006-01-01

    We wanted to evaluate the anatomic variations, the number of valves and the presence of deep vein thrombosis (DVT) on the lower extremity venograms obtained after artificial joint replacements, and we also wanted to determine the correlation of the incidence of DVT with the above-mentioned factors and the operation sites. From January to June 2004, conventional ascending contrast venographies of the lower extremities were performed in 119 patients at 7-10 days after artificial joint replacement, and all the patients were asymptomatic. Total knee replacement was done for 152 cases and total hip replacement was done for 34 cases. On all the venographic images of 186 limbs, the anatomic variations were classified and the presence of DVT was evaluated; the number of valves in the superficial femoral vein (SFV) and calf veins was counted. The sites of DVT were classified as calf, thigh and pelvis. Statistically, chi square tests and Fischer's exact tests were performed to determine the correlation of the incidence of DVT with the anatomic variations, the numbers of valves and the operation sites. Theoretically, there are 9 types of anatomical variation in the deep vein system of the lower extremity that can be classified, but only 7 types were observed in this study. The most frequent type was the normal single SFV type and this was noted in 117 cases (63%), and the others were all variations (69 cases, 37%). There was a 22.2% incidence of DVT (69 cases) in the normal single SFV type and 26.4% (17 cases) in the other variations. No significant difference was noted in the incidences of DVT between the two groups. In addition, no significant statistical differences were noted for the incidences of DVT between the single or variant multiple veins in the SFV and the popliteal vein (PV) respectively, between the different groups with small or large numbers of valves in the thigh and calf, respectively, and also between the different operation sites of the hip or knee

  15. Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

    International Nuclear Information System (INIS)

    Pascal, Laura E; Liu, Alvin Y; Vêncio, Ricardo ZN; Page, Laura S; Liebeskind, Emily S; Shadle, Christina P; Troisch, Pamela; Marzolf, Bruz; True, Lawrence D; Hood, Leroy E

    2009-01-01

    Prostate cancer cells in primary tumors have been typed CD10 - /CD13 - /CD24 hi /CD26 + /CD38 lo /CD44 - /CD104 - . This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. CD26 + cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types

  16. High resolution isotope data and ensemble modelling reveal ecohydrological controls on catchment storage-discharge relationships and flux travel time distributions

    Science.gov (United States)

    Soulsby, C.; Kuppel, S.; Smith, A.; Tetzlaff, D.

    2017-12-01

    The dynamics of water storage in a catchment provides a fundamental insight into the interlinkages between input and output fluxes, and how these are affected by environmental change. Such dynamics also mediate, and help us understand, the fundamental difference of the rapid celerity of the rainfall-runoff (minutes to hours) response of catchments and the much slower velocity of water particles (months to decades) as they are transported through catchment systems. In this contribution we report an intensive, long-term (>10year), multi-scale isotope study in the Scottish Highlands that has sought to better understand these issues. We have integrated empirical data collection with diverse modelling approaches to quantify the dynamics and residence times of storage in different compartments of the hydrological system (vegetation canopies, soils, ground waters etc.) and their relationship between the magnitude and travel time distributions of output fluxes (stream flow, transpiration and evaporation). Use of conceptual, physically-based and probabilistic modelling approaches give broadly consistent perspectives on the storage-discharge relationships and the preferential selection of younger waters in runoff, evaporation and transpiration; while older waters predominate in groundwater. The work also highlighted the importance role vegetation plays in regulating fluxes in evaporation and transpiration and how this contributes to the differential ageing of water in mobile and bulk waters in the soil compartment. A separate case study shows how land use change can affect storage distributions in a catchment and radically change travel time distributions in output fluxes.

  17. Variation of milk urea in dairy cattle : a study on factors that affect the relationship between urea concentration in milk and urea excretion in urine

    NARCIS (Netherlands)

    Spek, J.W.

    2013-01-01

    The aim of this thesis was to increase the applicability of milk urea nitrogen concentration (MUN) as a predictor of urinary urea nitrogen excretion (UUN) by identifying and quantifying factors that can explain variation in MUN that is not related to UUN. A literature study was conducted in

  18. Genetic variation in carbon isotope discrimination and its relationship to growth under field conditions in full-sib families of Picea mariana

    Science.gov (United States)

    Lawrence B. Flanagan; Kurt H. Johnsen

    1995-01-01

    Measurements of the stable carbon isotope composition of leaf tissue were made on Picea mariana (Mill.) B.S.P. trees from four full-sib families grown on three different field sites at the Petawawa National Forestry Institute, Ontario, Canada. The four families chosen exhibited genetic variation for growth characteristics. Genetic...

  19. The Relationship of Economic Variations to Mortality and Fertility Patterns on the Navajo Reservation. Lake Powell Research Project Bulletin Number 20, April 1976.

    Science.gov (United States)

    Kunitz, Stephen J.

    Divided into three sections, this research bulletin presents: (1) a brief review of changes in the American Indian mortality and fertility rates, illustrating a transition process much like that experienced by developing nations; (2) an analysis of variations in the social and economic organization of different parts of the Navajo Reservation; (3)…

  20. Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe.

    Science.gov (United States)

    Gonzalez, P; Labarère, J

    1998-11-01

    A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The

  1. Sinonasal anatomical variations: their relationship with chronic rhinosinusitis and effect on the severity of disease-a computerized tomography assisted anatomical and clinical study.

    Science.gov (United States)

    Kaygusuz, Ahmet; Haksever, Mehmet; Akduman, Davut; Aslan, Sündüs; Sayar, Zeynep

    2014-09-01

    The anatomy of the sinonasal area has a very wide rage of anatomical variations. The significance of these anatomical variations in pathogenesis of rhinosinusitis, which is the commonest disease in the region, is still unclear. The aims of the study were to compare the rate of sinonasal anatomical variations with development and severity of chronic rhinosinusitis patients. CT scan of paranasal sinuses images of 99 individuals were retrospectively reviewed. 65 cases of chronic rhinosinusitis (study group) who had undergone endoscopic sinus surgery were compared with 34 cases without chronic rhinosinusitis (control group). Also in study group Lund-Mackay score of the sinus disease were calculated and compared to the rate of related anatomical variations. There were 74 (74.7 %) males and 25 (25.2 %) females with ages ranging from 13 to 70 years (mean 32.2 years). The anatomical variations recorded were: Septal deviation 47 (72.3) in study and 25 (73.5 %) in control group, concha bullosa 27 (41.5 %) in study and 18 (52.9 %) in control group, overpneumatized ethmoid bulla 17 (26.1 %) in study and 14 (41.1 %) in control group, pneumatized uncinate 3 (4.6 %) in study and 3 (8.8 %) in control group, agger nasi 42 (64.6 %) in study and 19 (55.8 %) in control group, paradoxical middle turbinates 9 (13.8 %) in study and 4 (11.7 %) in control group, Onodi cell 6 (9.2 %) in study and 2 (5.8 %) in control group, Haller's cells (infraorbital ethmoid cell) 9 (13.8 %) in study and 7 (20.5 %) in control group. None of these results were statistically significant between study and control group (p > 0.05). Lund-Mackay score (which was assumed to show the severity of the disease) of the maxillary, ethmoid and frontal sinus were calculated and compared to rate of septal deviation, concha bullosa, agger nasi cells. No significant correlation was conducted (p > 0.05). The results of study showed no statistically significant correlation between sinonasal anatomical

  2. Genetic variation in transpiration efficiency and relationships between whole plant and leaf gas exchange measurements in Saccharum spp. and related germplasm.

    Science.gov (United States)

    Jackson, Phillip; Basnayake, Jaya; Inman-Bamber, Geoff; Lakshmanan, Prakash; Natarajan, Sijesh; Stokes, Chris

    2016-02-01

    Fifty-one genotypes of sugarcane (Saccharum spp.) or closely related germplasm were evaluated in a pot experiment to examine genetic variation in transpiration efficiency. Significant variation in whole plant transpiration efficiency was observed, with the difference between lowest and highest genotypes being about 40% of the mean. Leaf gas exchange measurements were made across a wide range of conditions. There was significant genetic variation in intrinsic transpiration efficiency at a leaf level as measured by leaf internal CO2 (Ci) levels. Significant genetic variation in Ci was also observed within subsets of data representing narrow ranges of stomatal conductance. Ci had a low broad sense heritability (Hb = 0.11) on the basis of single measurements made at particular dates, because of high error variation and genotype × date interaction, but broad sense heritability for mean Ci across all dates was high (Hb = 0.81) because of the large number of measurements taken at different dates. Ci levels among genotypes at mid-range levels of conductance had a strong genetic correlation (-0.92 ± 0.30) with whole plant transpiration efficiency but genetic correlations between Ci and whole plant transpiration efficiency were weaker or not significant at higher and lower levels of conductance. Reduced Ci levels at any given level of conductance may result in improved yields in water-limited environments without trade-offs in rates of water use and growth. Targeted selection and improvement of lowered Ci per unit conductance via breeding may provide longer-term benefits for water-limited environments but the challenge will be to identify a low-cost screening methodology. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  3. Comparative expression analysis reveals lineage relationships between human and murine gliomas and a dominance of glial signatures during tumor propagation in vitro.

    Science.gov (United States)

    Henriquez, Nico V; Forshew, Tim; Tatevossian, Ruth; Ellis, Matthew; Richard-Loendt, Angela; Rogers, Hazel; Jacques, Thomas S; Reitboeck, Pablo Garcia; Pearce, Kerra; Sheer, Denise; Grundy, Richard G; Brandner, Sebastian

    2013-09-15

    Brain tumors are thought to originate from stem/progenitor cell populations that acquire specific genetic mutations. Although current preclinical models have relevance to human pathogenesis, most do not recapitulate the histogenesis of the human disease. Recently, a large series of human gliomas and medulloblastomas were analyzed for genetic signatures of prognosis and therapeutic response. Using a mouse model system that generates three distinct types of intrinsic brain tumors, we correlated RNA and protein expression levels with human brain tumors. A combination of genetic mutations and cellular environment during tumor propagation defined the incidence and phenotype of intrinsic murine tumors. Importantly, in vitro passage of cancer stem cells uniformly promoted a glial expression profile in culture and in brain tumors. Gene expression profiling revealed that experimental gliomas corresponded to distinct subclasses of human glioblastoma, whereas experimental supratentorial primitive neuroectodermal tumors (sPNET) correspond to atypical teratoid/rhabdoid tumor (AT/RT), a rare childhood tumor. ©2013 AACR.

  4. Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation

    Directory of Open Access Journals (Sweden)

    Cánovas Fernando G

    2011-12-01

    Full Text Available Abstract Background Understanding the processes driving speciation in marine ecosystems remained a challenge until recently, due to the unclear nature of dispersal boundaries. However, recent evidence for marine adaptive radiations and ecological speciation, as well as previously undetected patterns of cryptic speciation is overturning this view. Here, we use multi-gene phylogenetics to infer the family-level evolutionary history of Fucaceae (intertidal brown algae of the northern Pacific and Atlantic in order to investigate recent and unique patterns of radiative speciation in the genus Fucus in the Atlantic, in contrast with the mainly monospecific extant genera. Results We developed a set of markers from 13 protein coding genes based on polymorphic cDNA from EST libraries, which provided novel resolution allowing estimation of ancestral character states and a detailed reconstruction of the recent radiative history. Phylogenetic reconstructions yielded similar topologies and revealed four independent trans-Arctic colonization events by Fucaceae lineages, two of which also involved transitions from hermaphroditism to dioecy associated with Atlantic invasions. More recently, reversion of dioecious ancestral lineages towards hermaphroditism has occurred in the genus Fucus, particularly coinciding with colonization of more extreme habitats. Novel lineages in the genus Fucus were also revealed in association with southern habitats. These most recent speciation events occurred during the Pleistocene glaciations and coincided with a shift towards selfing mating systems, generally southward shifts in distribution, and invasion of novel habitats. Conclusions Diversification of the family occurred in the Late-Mid Miocene, with at least four independent trans-Artic lineage crossings coincident with two reproductive mode transitions. The genus Fucus arose in the Pliocene but radiated within a relatively short time frame about 2.5 million years ago

  5. Relationship Between the Menstrual Cycle and Timing of Ovulation Revealed by New Protocols: Analysis of Data from a Self-Tracking Health App.

    Science.gov (United States)

    Sohda, Satoshi; Suzuki, Kenta; Igari, Ichiro

    2017-11-27

    There are many mobile phone apps aimed at helping women map their ovulation and menstrual cycles and facilitating successful conception (or avoiding pregnancy). These apps usually ask users to input various biological features and have accumulated the menstrual cycle data of a vast number of women. The purpose of our study was to clarify how the data obtained from a self-tracking health app for female mobile phone users can be used to improve the accuracy of prediction of the date of next ovulation. Using the data of 7043 women who had reliable menstrual and ovulation records out of 8,000,000 users of a mobile phone app of a health care service, we analyzed the relationship between the menstrual cycle length, follicular phase length, and luteal phase length. Then we fitted a linear function to the relationship between the length of the menstrual cycle and timing of ovulation and compared it with the existing calendar-based methods. The correlation between the length of the menstrual cycle and the length of the follicular phase was stronger than the correlation between the length of the menstrual cycle and the length of the luteal phase, and there was a positive correlation between the lengths of past and future menstrual cycles. A strong positive correlation was also found between the mean length of past cycles and the length of the follicular phase. The correlation between the mean cycle length and the luteal phase length was also statistically significant. In most of the subjects, our method (ie, the calendar-based method based on the optimized function) outperformed the Ogino method of predicting the next ovulation date. Our method also outperformed the ovulation date prediction method that assumes the middle day of a mean menstrual cycle as the date of the next ovulation. The large number of subjects allowed us to capture the relationships between the lengths of the menstrual cycle, follicular phase, and luteal phase in more detail than previous studies. We

  6. Theta band activity in response to emotional expressions and its relationship with gamma band activity as revealed by MEG and advanced beamformer source imaging

    Directory of Open Access Journals (Sweden)

    Qian eLuo

    2014-02-01

    Full Text Available Neuronal oscillations in the theta and gamma bands have been shown to be important for cognition. Here we examined the temporal and spatial relationship between the two frequency bands in emotional processing using Magnetoencephalography and an advanced dynamic beamformer source imaging method called Synthetic Aperture Magnetometry. We found that areas including the amygdala, visual and frontal cortex showed significant event-related synchronization (ERS in both bands, suggesting a functional association of neuronal oscillations in the same areas in the two bands. However, while the temporal profile in both bands was similar in the amygdala, the peak in gamma band power was much earlier within both visual and frontal areas. Our results do not support a traditional view that the localizations of lower and higher frequencies are spatially distinct. Instead, they suggest that in emotional processing, neuronal oscillations in the gamma and theta bands may reflect, at least in visual and frontal cortex either different but related functional processes or, perhaps more probably, different computational components of the same functional process.

  7. Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers

    Directory of Open Access Journals (Sweden)

    Mariën J

    2008-03-01

    Full Text Available Abstract Background In recent years, several new hypotheses on phylogenetic relations among arthropods have been proposed on the basis of DNA sequences. One of the challenged hypotheses is the monophyly of hexapods. This discussion originated from analyses based on mitochondrial DNA datasets that, due to an unusual positioning of Collembola, suggested that the hexapod body plan evolved at least twice. Here, we re-evaluate the position of Collembola using ribosomal protein gene sequences. Results In total 48 ribosomal proteins were obtained for the collembolan Folsomia candida. These 48 sequences were aligned with sequence data on 35 other ecdysozoans. Each ribosomal protein gene was available for 25% to 86% of the taxa. However, the total sequence information was unequally distributed over the taxa and ranged between 4% and 100%. A concatenated dataset was constructed (5034 inferred amino acids in length, of which ~66% of the positions were filled. Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda. Conclusion Although ribosomal proteins in general may not evolve independently, they once more appear highly valuable for phylogenetic reconstruction. Our analyses clearly suggest that Hexapoda is monophyletic. This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships. Caution is needed when applying mitochondrial markers in deep phylogeny.

  8. Revealing pancrustacean relationships: phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers.

    Science.gov (United States)

    Timmermans, M J T N; Roelofs, D; Mariën, J; van Straalen, N M

    2008-03-12

    In recent years, several new hypotheses on phylogenetic relations among arthropods have been proposed on the basis of DNA sequences. One of the challenged hypotheses is the monophyly of hexapods. This discussion originated from analyses based on mitochondrial DNA datasets that, due to an unusual positioning of Collembola, suggested that the hexapod body plan evolved at least twice. Here, we re-evaluate the position of Collembola using ribosomal protein gene sequences. In total 48 ribosomal proteins were obtained for the collembolan Folsomia candida. These 48 sequences were aligned with sequence data on 35 other ecdysozoans. Each ribosomal protein gene was available for 25% to 86% of the taxa. However, the total sequence information was unequally distributed over the taxa and ranged between 4% and 100%. A concatenated dataset was constructed (5034 inferred amino acids in length), of which ~66% of the positions were filled. Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda. Although ribosomal proteins in general may not evolve independently, they once more appear highly valuable for phylogenetic reconstruction. Our analyses clearly suggest that Hexapoda is monophyletic. This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships. Caution is needed when applying mitochondrial markers in deep phylogeny.

  9. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

    Directory of Open Access Journals (Sweden)

    Hyun-Seob Song

    2015-03-01

    Full Text Available Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

  10. Structural and biochemical analysis of a unique phosphatase from Bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase.

    Directory of Open Access Journals (Sweden)

    Robert J Gruninger

    Full Text Available Bdellovibrio bacteriovorus is an unusual δ-proteobacterium that invades and preys on other Gram-negative bacteria and is of potential interest as a whole cell therapeutic against pathogens of man, animals and crops. PTPs (protein tyrosine phosphatases are an important class of enzyme involved in desphosphorylating a variety of substrates, often with implications in cell signaling. The B. bacteriovorus open reading frame Bd1204 is predicted to encode a PTP of unknown function. Bd1204 is both structurally and mechanistically related to the PTP-like phytase (PTPLP class of enzymes and possesses a number of unique properties not observed in any other PTPLPs characterized to date. Bd1204 does not display catalytic activity against some common protein tyrosine phosphatase substrates but is highly specific for hydrolysis of phosphomonoester bonds of inositol hexakisphosphate. The structure reveals that Bd1204 has the smallest and least electropositive active site of all characterized PTPLPs to date yet possesses a unique substrate specificity characterized by a strict preference for inositol hexakisphosphate. These two active site features are believed to be the most significant contributors to the specificity of phytate degrading enzymes. We speculate that Bd1204 may be involved in phosphate acquisition outside of prey.

  11. Spatiotemporal relationships between growth and microtubule orientation as revealed in living root cells of Arabidopsis thaliana transformed with green-fluorescent-protein gene construct GFP-MBD

    Science.gov (United States)

    Granger, C. L.; Cyr, R. J.

    2001-01-01

    Arabidopsis thaliana plants were transformed with GFP-MBD (J. Marc et al., Plant Cell 10: 1927-1939, 1998) under the control of a constitutive (35S) or copper-inducible promoter. GFP-specific fluorescence distributions, levels, and persistence were determined and found to vary with age, tissue type, transgenic line, and individual plant. With the exception of an increased frequency of abnormal roots of 35S GFP-MBD plants grown on kanamycin-containing media, expression of GFP-MBD does not appear to affect plant phenotype. The number of leaves, branches, bolts, and siliques as well as overall height, leaf size, and seed set are similar between wild-type and transgenic plants as is the rate of root growth. Thus, we conclude that the transgenic plants can serve as a living model system in which the dynamic behavior of microtubules can be visualized. Confocal microscopy was used to simultaneously monitor growth and microtubule behavior within individual cells as they passed through the elongation zone of the Arabidopsis root. Generally, microtubules reoriented from transverse to oblique or longitudinal orientations as growth declined. Microtubule reorientation initiated at the ends of the cell did not necessarily occur simultaneously in adjacent neighboring cells and did not involve complete disintegration and repolymerization of microtubule arrays. Although growth rates correlated with microtubule reorientation, the two processes were not tightly coupled in terms of their temporal relationships, suggesting that other factor(s) may be involved in regulating both events. Additionally, microtubule orientation was more defined in cells whose growth was accelerating and less stringent in cells whose growth was decelerating, indicating that microtubule-orienting factor(s) may be sensitive to growth acceleration, rather than growth per se.

  12. Physical mapping of the split hand/split foot (SHSF) locus on chromosome 7 reveals a relationship between SHSF and the syndromic ectrodactylies

    Energy Technology Data Exchange (ETDEWEB)

    Poorkaj, P.; Nunes, M.E.; Geshuri, D. [Univ. of Washington, Seattle, WA (United States)] [and others

    1994-09-01

    Split hand/split foot (also knows as ectrodactyly) is a human developmental malformation characterized by missing digits and claw-like extremities. An autosomal dominant form of this disorder has been mapped to 7q21.3-q22.1 on the basis of SHSF-associated chromosomal rearrangements: this locus has been designated SHFD1. We have constructed a physical map of the SHFD1 region that consists of contiguous yeast artificial chromosome clones and spans approximately 8 Mb. Somatic cell hybrid and fluorescent in situ hybridization analyses were used to define SHSF-associated chromosomal breakpoints in fourteen patients. A critical interval of about 1 Mb was established for SHFD1 by analysis of six patients with deletions. Translocation and inversion breakpoints in seven other patients were found to localize within a 500-700 kb interval within the critical region. Several candidate genes including DLX5 and DLX6 (members of the Drosophilia Distal-less homeobox-containing gene family) localize to this region. At least four of these genes are expressed in the developing mouse limb bud. Of particular interest is the observation that 8 of the 14 patients studied have syndromic ectrodactyly, which is characterized by the association of SHSF with a variety of other anomalies including cleft lip/palate, ectodermal dysplasia, and renal anomalies. Thus, these data implicate a single gene or cluster of genes at the SHFD1 locus in a wide range of developmental processes and serve to establish a molecular genetic relationship between simple SHSF and a broad group of human birth defects.

  13. Sex and Relationships Education: A Comparison of Variation in Northern Ireland's and England's Policy-Making Processes

    Science.gov (United States)

    Wilkinson, Dana Cavender

    2017-01-01

    Despite Northern Ireland's deeply rooted religious history and the assumption that its citizens' sexual attitudes and behaviours are more reserved than their English counterparts, comprehensive school-based relationships and sexuality education (RSE) has been statutory for primary and post-primary pupils since 2007. The non-biological aspects of…

  14. Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative

    Science.gov (United States)

    Hertach, Thomas; Puissant, Stéphane; Gogala, Matija; Trilar, Tomi; Hagmann, Reto; Baur, Hannes; Kunz, Gernot; Wade, Elizabeth J.; Loader, Simon P.; Simon, Chris; Nagel, Peter

    2016-01-01

    Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive

  15. Patterns of altered neural synchrony in the default mode network in autism spectrum disorder revealed with magnetoencephalography (MEG): Relationship to clinical symptomatology.

    Science.gov (United States)

    Lajiness-O'Neill, Renée; Brennan, Jonathan R; Moran, John E; Richard, Annette E; Flores, Ana-Mercedes; Swick, Casey; Goodcase, Ryan; Andersen, Tiffany; McFarlane, Kaitlyn; Rusiniak, Kenneth; Kovelman, Ioulia; Wagley, Neelima; Ugolini, Maggie; Albright, Jeremy; Bowyer, Susan M

    2018-03-01

    Disrupted neural synchrony may be a primary electrophysiological abnormality in autism spectrum disorders (ASD), altering communication between discrete brain regions and contributing to abnormalities in patterns of connectivity within identified neural networks. Studies exploring brain dynamics to comprehensively characterize and link connectivity to large-scale cortical networks and clinical symptoms are lagging considerably. Patterns of neural coherence within the Default Mode Network (DMN) and Salience Network (SN) during resting state were investigated in 12 children with ASD (M Age  = 9.2) and 13 age and gender-matched neurotypicals (NT) (M Age  = 9.3) with magnetoencephalography. Coherence between 231 brain region pairs within four frequency bands (theta (4-7 Hz), alpha, (8-12 Hz), beta (13-30 Hz), and gamma (30-80 Hz)) was calculated. Relationships between neural coherence and social functioning were examined. ASD was characterized by lower synchronization across all frequencies, reaching clinical significance in the gamma band. Lower gamma synchrony between fronto-temporo-parietal regions was observed, partially consistent with diminished default mode network (DMN) connectivity. Lower gamma coherence in ASD was evident in cross-hemispheric connections between: angular with inferior/middle frontal; middle temporal with middle/inferior frontal; and within right-hemispheric connections between angular, middle temporal, and inferior/middle frontal cortices. Lower gamma coherence between left angular and left superior frontal, right inferior/middle frontal, and right precuneus and between right angular and inferior/middle frontal cortices was related to lower social/social-communication functioning. Results suggest a pattern of lower gamma band coherence in a subset of regions within the DMN in ASD (angular and middle temporal cortical areas) related to lower social/social-communicative functioning. Autism Res 2018, 11: 434-449. © 2017 International

  16. The relationship of glutathione-S-transferases copy number variation and indoor air pollution to symptoms and markers of respiratory disease.

    Science.gov (United States)

    Hersoug, Lars-Georg; Brasch-Andersen, Charlotte; Husemoen, Lise Lotte Nystrup; Sigsgaard, Torben; Linneberg, Allan

    2012-07-01

    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. 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. We conducted a population-based, cross-sectional study of 3471 persons aged 18-69 years. Information about exposure to indoor sources of PM and respiratory symptoms was obtained by a self-administered questionnaire. In addition, measurements of lung function (spirometry) and fractional exhaled nitric oxide were performed. Copy number variation of GSTM1 and GSTT1 was determined by polymerase chain reaction-based assays. We found that none of the symptoms and objective markers of respiratory disease were significantly associated with the GST null polymorphisms. An increasing number of positive alleles of the GSTM1 polymorphism tended to be associated lower prevalence of wheeze, cough, and high forced expiratory 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. In this adult population, GST copy number variations were not significantly associated with respiratory outcomes and did not modify the effects of self-reported exposure to indoor sources of PM on respiratory outcomes. © 2011 Blackwell Publishing Ltd.

  17. Orchestrating Proactive and Reactive Mechanisms for Filtering Distracting Information: Brain-Behavior Relationships Revealed by a Mixed-Design fMRI Study

    Science.gov (United States)

    Marini, Francesco; Demeter, Elise; Roberts, Kenneth C.; Chelazzi, Leonardo

    2016-01-01

    Given the information overload often imparted to human cognitive-processing systems, suppression of irrelevant and distracting information is essential for successful behavior. Using a hybrid block/event-related fMRI design, we characterized proactive and reactive brain mechanisms for filtering distracting stimuli. Participants performed a flanker task, discriminating the direction of a target arrow in the presence versus absence of congruent or incongruent flanking distracting arrows during either Pure blocks (distracters always absent) or Mixed blocks (distracters on 80% of trials). Each Mixed block had either 20% or 60% incongruent trials. Activations in the dorsal frontoparietal attention network during Mixed versus Pure blocks evidenced proactive (blockwise) recruitment of a distraction-filtering mechanism. Sustained activations in right middle frontal gyrus during 60% Incongruent blocks correlated positively with behavioral indices of distraction-filtering (slowing when distracters might occur) and negatively with distraction-related behavioral costs (incongruent vs congruent trials), suggesting a role in coordinating proactive filtering of potential distracters. Event-related analyses showed that incongruent trials elicited greater reactive activations in 20% (vs 60%) Incongruent blocks for counteracting distraction and conflict, including in the insula and anterior cingulate. Context-related effects in occipitoparietal cortex consisted of greater target-evoked activations for distracter-absent trials (central-target-only) in Mixed versus Pure blocks, suggesting enhanced attentional engagement. Functional-localizer analyses in V1/V2/V3 revealed less distracter-processing activity in 60% (vs 20%) Incongruent blocks, presumably reflecting tonic suppression by proactive filtering mechanisms. These results delineate brain mechanisms underlying proactive and reactive filtering of distraction and conflict, and how they are orchestrated depending on distraction

  18. Decadal Variation of the Relationship between Western Pacific Subtropical High and Summer Heatwaves in East China Modulated by Pacific Decadal Oscillation

    Science.gov (United States)

    Liu, Q.; Fu, C.; Zhou, T.

    2017-12-01

    This study investigates the relationship between Western Pacific Subtropical High (WPSH) and summer heatwaves over Eastern China in interannual scale during the period of 1959-2016. Based on surface daily maximum temperature of 654 monitoring stations over China and meteorological variables in reanalysis data, we calculate the number of heatwave days (NHD) (one heatwave day was defined as one day with its daily maximum temperature greater than 35 degrees centigrade) as well as WPSH index and then examine their interannual relationship. Although the high-NHD-related 850hPa horizontal wind structure was shared by that of high WPSH and decaying El Niño summer, a decadal oscillation emerges for the correlation between interannual WPSH and NHD after removing their interdecadal variability by Ensemble Empirical Mode Decomposition (EEMD) method. The correlation coefficient can reach up to as high as 0.69 and as low as 0.17 and assembles the Pacific Decadal Oscillation (PDO) pretty well. Compositing analysis demonstrates that unstable WPSH-NHD relationship is mainly attributed to the spatial structure distinction of WPSH and surface warming in the El Niño decaying summer of different PDO phases. In the El Niño decaying summer of positive PDO phases, remarkable enhanced warming over majority of Southeastern China matches well with the noticeable westward extension of WPSH, which seems to be forced by the cyclonic circulation anomaly over Japan. The warmer Pacific-Indian Ocean Warm Pool intensifies the Matsuno-Gill pattern over Maritime Continent, stimulating this cyclonic circulation anomaly via the northward propagation of Rossby wave. In the El Niño decaying summer of negative PDO phases, the cooler East China Sea enhances WPSH in North China and South China Sea, and thereby leads to a local cyclonic circulation anomaly over Eastern China, which would cause a large scope of cooling and out-of-phase WPSH-NHD relationship.

  19. Ecological variation in wealth–fertility relationships in Mongolia: the ‘central theoretical problem of sociobiology’ not a problem after all?

    Science.gov (United States)

    Alvergne, Alexandra; Lummaa, Virpi

    2014-01-01

    The negative wealth–fertility relationship brought about by market integration remains a puzzle to classic evolutionary models. Evolutionary ecologists have argued that this phenomenon results from both stronger trade-offs between reproductive and socioeconomic success in the highest social classes and the comparison of groups rather than individuals. Indeed, studies in contemporary low fertility settings have typically used aggregated samples that may mask positive wealth–fertility relationships. Furthermore, while much evidence attests to trade-offs between reproductive and socioeconomic success, few studies have explicitly tested the idea that such constraints are intensified by market integration. Using data from Mongolia, a post-socialist nation that underwent mass privatization, we examine wealth–fertility relationships over time and across a rural–urban gradient. Among post-reproductive women, reproductive fitness is the lowest in urban areas, but increases with wealth in all regions. After liberalization, a demographic–economic paradox emerges in urban areas: while educational attainment negatively impacts female fertility in all regions, education uniquely provides socioeconomic benefits in urban contexts. As market integration progresses, socio-economic returns to education increase and women who limit their reproduction to pursue education get wealthier. The results support the view that selection favoured mechanisms that respond to opportunities for status enhancement rather than fertility maximization. PMID:25320175

  20. Variation in the carbon and oxygen isotope composition of plant biomass and its relationship to water-use efficiency at the leaf- and ecosystem-scales in a northern Great Plains grassland.

    Science.gov (United States)

    Flanagan, Lawrence B; Farquhar, Graham D

    2014-02-01

    Measurements of the carbon (δ(13) Cm ) and oxygen (δ(18) Om ) isotope composition of C3 plant tissue provide important insights into controls on water-use efficiency. We investigated the causes of seasonal and inter-annual variability in water-use efficiency in a grassland near Lethbridge, Canada using stable isotope (leaf-scale) and eddy covariance measurements (ecosystem-scale). The positive relationship between δ(13) Cm and δ(18) Om values for samples collected during 1998-2001 indicated that variation in stomatal conductance and water stress-induced changes in the degree of stomatal limitation of net photosynthesis were the major controls on variation in δ(13) Cm and biomass production during this time. By comparison, the lack of a significant relationship between δ(13) Cm and δ(18) Om values during 2002, 2003 and 2006 demonstrated that water stress was not a significant limitation on photosynthesis and biomass production in these years. Water-use efficiency was higher in 2000 than 1999, consistent with expectations because of greater stomatal limitation of photosynthesis and lower leaf ci /ca during the drier conditions of 2000. Calculated values of leaf-scale water-use efficiency were 2-3 times higher than ecosystem-scale water-use efficiency, a difference that was likely due to carbon lost in root respiration and water lost during soil evaporation that was not accounted for by the stable isotope measurements. © 2013 John Wiley & Sons Ltd.

  1. Genetic variation in Hyperpolarization-activated cyclic nucleotide-gated (HCN channels and its relationship with neuroticism, cognition and risk of depression

    Directory of Open Access Journals (Sweden)

    Andrew Mark Mcintosh

    2012-07-01

    Full Text Available Hyperpolarization-activated cyclic nucleotide-gated (HCN channels are encoded by four genes (HCN1-4 and, through activation by cyclic AMP (cAMP, represent a point of convergence for several psychosis risk genes. On the basis of positive preliminary data, we sought to test whether genetic variation in HCN1-4 conferred risk of depression or cognitive impairment in the Generation Scotland: Scottish Family Health Study. HCN1, HCN2, HCN3 and HCN4 were genotyped for 43 haplotype-tagging SNPs and tested for association with DSM-IV depression, neuroticism and a battery of cognitive tests assessing cognitive ability, memory, verbal fluency and psychomotor performance. No association was found between any HCN channel gene SNP and risk of depression, neuroticism or on any cognitive measure. The current study does not support a genetic role for HCN channels in conferring risk of depression or cognitive impairment in human subjects within the Scottish population.

  2. Genetic variation of the GLUT10 glucose transporter (SLC2A10) and relationships to type 2 diabetes and intermediary traits

    DEFF Research Database (Denmark)

    Andersen, Gitte; Rose, Christian Schack; Hamid, Yasmin Hassan

    2003-01-01

    The SLC2A10 gene encodes the GLUT10 facilitative glucose transporter, which is expressed in high amounts in liver and pancreas. The gene is mapped to chromosome 20q12-q13.1, a region that has been shown to be linked to type 2 diabetes. The gene was examined in 61 Danish type 2 diabetic patients......, and a total of six variants (-27C-->T, Ala206Thr, Ala272Ala, IVS2 + 10G-->A, IVS4 + 18T-->G, and IVS4 + 26G-->A) were identified and investigated in an association study, which included 503 type 2 diabetic patients and 510 glucose-tolerant control subjects. None of the variants were associated with type 2...... substantially to the pathogenesis of type 2 diabetes in the examined study population. However, the codon 206 polymorphism may be related to the interindividual variation in fasting and oral glucose-induced serum insulin levels....

  3. Variation in NCB5OR: studies of relationships to type 2 diabetes, maturity-onset diabetes of the young, and gestational diabetes mellitus

    DEFF Research Database (Denmark)

    Andersen, Gitte; Wegner, Lise; Rose, Christian Schack

    2004-01-01

    candidate gene and examined the coding region of NCB5OR in 120 type 2 diabetic patients and 63 patients with maturity-onset diabetes of the young using denaturing high-performance liquid chromatography. We identified a total of 22 novel nucleotide variants. Three variants [IVS5+7del(CT), Gln187Arg, and His......223Arg] were genotyped in a case-control design comprising 1,246 subjects (717 type 2 diabetic patients and 529 subjects with normal glucose tolerance). In addition, four rare variants were investigated for cosegregation with diabetes in multiplex type 2 diabetic families. The IVS5+7del(CT) variant...... was associated with common late-onset type 2 diabetes; however, we failed to relate this variant to any diabetes-related quantitative traits among the 529 control subjects. Thus, variation in the coding region of NCB5OR is not a major contributor in the pathogenesis of nonautoimmune diabetes....

  4. The relationship between innovation and price variation process innovations and product; La Relacion entre innovacion y variacion de los precios innovaciones de proceso y de producto

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, X.; Miles-Touya, D.; Pazo, C.

    2012-07-01

    The aim of this study is to analyze the relationship between innovation and price changes, distinguishing between process and product innovations. The former directly affects production costs, the changes of which could be transferred to prices. The latter enables companies to differentiate their products vertically or horizontally and increases the consumers willingness to pay, which may lead companies to raise prices. The results show that firms that introduce product innovations are more likely to raise prices and firms that introduce process innovations are more likely to reduce them. The magnitudes of the effects are different. (Author)

  5. The Relationship of Throwing Arm Mechanics and Elbow Varus Torque: Within-Subject Variation for Professional Baseball Pitchers Across 82,000 Throws.

    Science.gov (United States)

    Camp, Christopher L; Tubbs, Travis G; Fleisig, Glenn S; Dines, Joshua S; Dines, David M; Altchek, David W; Dowling, Brittany

    2017-11-01

    Likely due to the high level of strain exerted across the elbow during the throwing motion, elbow injuries are on the rise in baseball. To identify at-risk athletes and guide postinjury return-to-throw programs, a better understanding of the variables that influence elbow varus torque is desired. To describe the within-subject relationship between elbow varus torque and arm slot and arm rotation in professional baseball pitchers. Descriptive laboratory study. A total of 81 professional pitchers performed 82,000 throws while wearing a motusBASEBALL sensor and sleeve. These throws represented a combination of throw types, such as warm-up/catch, structured long-toss, bullpen throwing from a mound, and live game activity. Variables recorded for each throw included arm slot (angle of the forearm relative to the ground at ball release), arm speed (maximal rotational velocity of the forearm), arm rotation (maximal external rotation of the throwing arm relative to the ground), and elbow varus torque. Linear mixed-effects models and likelihood ratio tests were used to estimate the relationship between elbow varus torque and arm slot, arm speed, and arm rotation within individual pitchers. All 3 metrics-arm slot (χ 2 = 428, P relationship with elbow varus torque. Within individual athletes, a 1-N.m increase in elbow varus torque was associated with a 13° decrease in arm slot, a 116 deg/s increase in arm speed, and an 8° increase in arm rotation. Elbow varus torque increased significantly as pitchers increased their arm rotation during the arm cocking phase, increased the rotational velocity of their arm during the arm acceleration phase of throwing, and decreased arm slot at ball release. Thus, shoulder flexibility, arm speed, and elbow varus torque (and likely injury risk) are interrelated and should be considered collectively when treating pitchers. It is well established that elbow varus torque is related to ulnar collateral ligament injuries in overhead throwers. This

  6. Seasonal variation in chromophoric dissolved organic matter and relationships among fluorescent components, absorption coefficients and dissolved organic carbon in the Bohai Sea, the Yellow Sea and the East China Sea

    Science.gov (United States)

    Zhu, Wen-Zhuo; Zhang, Hong-Hai; Zhang, Jing; Yang, Gui-Peng

    2018-04-01

    The absorption coefficient and fluorescent components of chromophoric dissolved organic matter (CDOM) in the Bohai Sea (BS), Yellow Sea (YS), and East China Sea (ECS) in spring and autumn were analyzed in this study. Excitation-emission matrices (EEMs) combined with parallel factor analysis (PARAFAC) identified three components, namely, humic-like C1, tyrosine-like C2 and tryptophan-like C3. The seasonal variations in the vertical patterns of the CDOM absorption coefficient (aCDOM(355)) and fluorescent components were influenced by the seasonal water mass except for the terrestrial input. The relationship between aCDOM(355) and dissolved organic matter (DOC) was attributed to their own mixing behavior. The correlation of the fluorescent components with DOC was disturbed by other non-conservative processes during the export of CDOM to the open ocean. The different chemical compositions and origins of DOC and CDOM led to variability in carbon-specific CDOM absorption (a*CDOM(355)) and fluorescent component ratios (ICn/IC1). The relationship between a*CDOM(355) and aCDOM(355) demonstrated that dissolved organic matter (DOM) in the BS, but not in the ECS, highly contributed non-absorbing DOC to the total DOC concentration. The photodegradation of dominant terrestrially derived CDOM in the ECS contributed to the positive relationship between a*CDOM(355) and ICn/IC1. By contrast, the abundant autochthonous CDOM in the YS was negatively correlated with ICn/IC1 in autumn. Our established box models showed that water exchange is a potentially important source of the aromatic components in the BS, YS, and ECS. Hence, the seasonal variations in water exchange might contribute to the variability of CDOM chemical composition in the BS, YS, and ECS, and significantly influence the structure and function of their ecosystems.

  7. Modelling the relationship between zooplankton biomass and environmental variations in the distribution of 210Po during a one year cycle in northwestern Mediterranean coastal waters.

    Science.gov (United States)

    Färber Lorda, Jaime; Tateda, Yutaka; Fowler, Scott W

    2017-08-01

    To clarify the relationship between zooplankton biomass and the environmental kinetics of the natural radionuclide 210 Po during a one-year period (October 1995 to November 1996) in northwestern Mediterranean coastal waters, a modelling analysis was applied. Using 210 Po concentrations in seawater and zooplankton, the 210 Po uptake rate constant from food for zooplankton was evaluated using a biokinetics calculation involving the uptake and the excretion rate constants between seawater and zooplankton. Using the transfer constants obtained, the 210 Po concentrations in zooplankton were reconstructed and validated by observed concentrations. The simulation results were in good agreement with the measured 210 Po concentrations in zooplankton. Assuming that 210 Po fecal excretion represents the majority of the excretion of 210 Po from zooplankton, the fecal matter associated 210 Po vertical flux was calculated, and compared with the observed vertical fluxes of 210 Po measured in sediment traps. The modelling evaluation showed that fecal pellet vertical transport could not fully explain the observed sinking fluxes of particulate organic matter at 150 m depth, suggesting that other sinking biodetrital aggregates are also important components of the plankton-derived vertical flux of 210 Po. The relationship between 210 Po concentration in seawater and that in rain and dry fallout and their potential effect on 210 Po concentrations in zooplankton at this location were also examined. A similar, but diphased trend between 210 Po in zooplankton and 210 Po in rain and dry fallout deposition rate was demonstrated. 210 Po concentrations in the dissolved phase of seawater tended to diminish as mean daily rainfall increased suggesting that rain inputs serve as a 210 Po dilution mechanism in seawater at this location. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Quantitative variation in water-use efficiency across water regimes and its relationship with circadian, vegetative, reproductive, and leaf gas-exchange traits.

    Science.gov (United States)

    Edwards, Christine E; Ewers, Brent E; McClung, C Robertson; Lou, Ping; Weinig, Cynthia

    2012-05-01

    Drought limits light harvesting, resulting in lower plant growth and reproduction. One trait important for plant drought response is water-use efficiency (WUE). We investigated (1) how the joint genetic architecture of WUE, reproductive characters, and vegetative traits changed across drought and well-watered conditions, (2) whether traits with distinct developmental bases (e.g. leaf gas exchange versus reproduction) differed in the environmental sensitivity of their genetic architecture, and (3) whether quantitative variation in circadian period was related to drought response in Brassica rapa. Overall, WUE increased in drought, primarily because stomatal conductance, and thus water loss, declined more than carbon fixation. Genotypes with the highest WUE in drought expressed the lowest WUE in well-watered conditions, and had the largest vegetative and floral organs in both treatments. Thus, large changes in WUE enabled some genotypes to approach vegetative and reproductive trait optima across environments. The genetic architecture differed for gas-exchange and vegetative traits across drought and well-watered conditions, but not for floral traits. Correlations between circadian and leaf gas-exchange traits were significant but did not vary across treatments, indicating that circadian period affects physiological function regardless of water availability. These results suggest that WUE is important for drought tolerance in Brassica rapa and that artificial selection for increased WUE in drought will not result in maladaptive expression of other traits that are correlated with WUE.

  9. Spatial variation in the degradation rate of the pesticides isoproturon, azoxystrobin and diflufenican in soil and its relationship with chemical and microbial properties

    International Nuclear Information System (INIS)

    Bending, Gary D.; Lincoln, Suzanne D.; Edmondson, Rodney N.

    2006-01-01

    The extent of within field variability in the degradation rate of the pesticides isoproturon, azoxystrobin and diflufenican, and the role of intrinsic soil factors and technical errors in contributing to the variability, was investigated in sites on sandy-loam and clay-loam. At each site, 40 topsoil samples were taken from a 160x60 m area, and pesticides applied in the laboratory. Time to 25% dissipation (DT25) ranged between 13 and 61 weeks for diflufenican, 5.6 and 17.2 weeks for azoxystrobin, and 0.3 and 12.5 weeks for isoproturon. Variability in DT25 was higher in the sandy-loam in which there was also greatest variability in soil chemical and microbial properties. Technical error associated with pesticide extraction, analysis and lack of model fit during derivation of DT25 accounted for between 5.3 and 25.8% of the variability for isoproturon and azoxystrobin, but could account for almost all the variability for diflufenican. Azoxystrobin DT25, sorption and pH were significantly correlated. - Spatial variation determines risk assessment for pesticides in soil

  10. Variation of heavy metal and micro and macro element concentrations of bread and durum wheats and their relationship in grain of Turkish wheat cultivars.

    Science.gov (United States)

    Harmankaya, Mustafa; Ozcan, Mehmet Musa; Gezgin, Sait

    2012-09-01

    The 64 varieties displayed a large variation for all mineral elements, investigated Fe, Mn and Zn, ranging from 24.2 to 43.1 mg/kg, 27.6 to 64.8 mg/kg and 10.4 to 38.2 mg/kg, respectively. The mean Ca, K, Mg, Na, P and S concentrations in wheat rain varieties amounted to 378, 4,266, 1,183, 317, 3,513 and 1,542 mg/kg, respectively. Ca, K, Mg, Na, P and S contents of wheat varieties changed at the levels between 266 and 531 mg/kg, 3,029 and 5,566 mg/kg, 972 and 1,525 mg/kg, 277 and 368 mg/kg, 2,422 and 4,610 mg/kg and 1,241 to 2,052 mg/kg, respectively. The concentrations of Al, Cu, Fe, Mn and Zn of durum wheat samples were found at high levels. The mean Al, Cr, Mo, Ni, Cu, Fe, Mn and Zn concentrations in durum wheat varieties amounted to 10.93, 0.47, 0.72, 0.72, 5.37, 34.9, 37.28 and 20.88 mg/kg, respectively.

  11. Spatial variation in the degradation rate of the pesticides isoproturon, azoxystrobin and diflufenican in soil and its relationship with chemical and microbial properties

    Energy Technology Data Exchange (ETDEWEB)

    Bending, Gary D. [Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF (United Kingdom)]. E-mail: gary.bending@warwick.ac.uk; Lincoln, Suzanne D. [Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF (United Kingdom); Edmondson, Rodney N. [Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF (United Kingdom)

    2006-01-15

    The extent of within field variability in the degradation rate of the pesticides isoproturon, azoxystrobin and diflufenican, and the role of intrinsic soil factors and technical errors in contributing to the variability, was investigated in sites on sandy-loam and clay-loam. At each site, 40 topsoil samples were taken from a 160x60 m area, and pesticides applied in the laboratory. Time to 25% dissipation (DT25) ranged between 13 and 61 weeks for diflufenican, 5.6 and 17.2 weeks for azoxystrobin, and 0.3 and 12.5 weeks for isoproturon. Variability in DT25 was higher in the sandy-loam in which there was also greatest variability in soil chemical and microbial properties. Technical error associated with pesticide extraction, analysis and lack of model fit during derivation of DT25 accounted for between 5.3 and 25.8% of the variability for isoproturon and azoxystrobin, but could account for almost all the variability for diflufenican. Azoxystrobin DT25, sorption and pH were significantly correlated. - Spatial variation determines risk assessment for pesticides in soil.

  12. Modelling reveals endogenous osmotic adaptation of storage tissue water potential as an important driver determining different stem diameter variation patterns in the mangrove species Avicennia marina and Rhizophora stylosa.

    Science.gov (United States)

    Vandegehuchte, Maurits W; Guyot, Adrien; Hubeau, Michiel; De Swaef, Tom; Lockington, David A; Steppe, Kathy

    2014-09-01

    Stem diameter variations are mainly determined by the radial water transport between xylem and storage tissues. This radial transport results from the water potential difference between these tissues, which is influenced by both hydraulic and carbon related processes. Measurements have shown that when subjected to the same environmental conditions, the co-occurring mangrove species Avicennia marina and Rhizophora stylosa unexpectedly show a totally different pattern in daily stem diameter variation. Using in situ measurements of stem diameter variation, stem water potential and sap flow, a mechanistic flow and storage model based on the cohesion-tension theory was applied to assess the differences in osmotic storage water potential between Avicennia marina and Rhizophora stylosa. Both species, subjected to the same environmental conditions, showed a resembling daily pattern in simulated osmotic storage water potential. However, the osmotic storage water potential of R. stylosa started to decrease slightly after that of A. marina in the morning and increased again slightly later in the evening. This small shift in osmotic storage water potential likely underlaid the marked differences in daily stem diameter variation pattern between the two species. The results show that in addition to environmental dynamics, endogenous changes in the osmotic storage water potential must be taken into account in order to accurately predict stem diameter variations, and hence growth.

  13. Relationship between variations in the level of endogenous thiols and antioxidant activity of lipids and radiosensitivity of animals of different species

    International Nuclear Information System (INIS)

    Burlakova, E.B.; Graevskaya, B.M.; Ivanenko, G.F.; Shishkina, L.N.; AN SSSR, Moscow. Inst. Ehvolyutsionnoj Morfologii i Ehkologii Zhivotnykh)

    1978-01-01

    Initial levels of total and nonprotein sulfhydryl groups and antioxidant activity (AOA) of lipids of the spleen and liver are measured in animals of different species. Radiosensitivity of animals is assessed by the value of LDsub(50/30). No reliable correlation has been revealed between initial levels of endogenous thiols and AOA of lipids. There is a positive correlation between AOA of the spleen lipids and LDsub(50/30) as well as between the level of endogenous thiols and radioresistance of the animal species under study. It is likely that the level of endogenous thiols and AOA of lipids reflect various aspects of cellular metabolism which is responsible for radioresistance of the organism

  14. The interdecadal change in the intensity of interannual variation of spring precipitation over southern China and its relationship with the SST anomaly

    Science.gov (United States)

    Qiao, Y.; Xu, C.

    2017-12-01

    Based on the observed precipitation data from 756 China stations, ERA-interim reanalysis dataset, and HadISST dataset for 1979-2014, this paper investigates the intensity of interannual variation (IIV) of spring precipitation over southern China during 1979-2014 and related large-scale atmospheric and oceanic signal through empirical orthogonal function (EOF) method and other statistical analysis methods. The results show that the IIV of spring precipitation over South China (SC) was stronger during 1979-1994, which is related to the spring western Pacific (WP) sea surface temperature anomaly (SSTA) and the previous winter South Pacific tripole (SPT) pattern of SSTA. Anomalous cooler (warmer) WP SSTA triggers anomalous descending (ascending) motion and lower-level anticyclone (cyclone), which in turn induces anomalous ascent (descent) over SC through an anomalous vertical circulation. The SPT can influence the spring precipitation over SC by impacting WP SST. The stronger IIV of WP SST and SPT led to an intensified IIV of spring rainfall over SC. The IIV of spring precipitation over middle and lower reaches of the Yangtze River (YZR) was more intense during 1995-2006. The intensified interannual variability of spring rainfall over YZR is interrelated with the increase in the amplitude of the spring southern Indian Ocean dipole (SIOD) in early 1990s. During the positive (negative) SIOD, the western Pacific subtropical high (WPSH) is stronger (weaker), which is favorable (unfavorable) for the transportation of vapor from Pacific to YZR. At the same time, the pressure ridge over Siberia and East Asian trough is weaker (stronger), enhancing (weakening) the spring precipitation over YZR.

  15. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  16. Geographic variation in the relationships of temperature, salinity or sigma sub t versus plant nutrient concentrations in the world ocean. [silicic acid, nitrate, and phosphate concentration

    Science.gov (United States)

    Kamykowski, D.; Zentara, S. J.

    1985-01-01

    A NODC data set representing all regions of the world ocean was analyzed for temperature and sigma-t relationships with nitrate, phosphate or silicic acid. Six cubic regressions were for each ten degree square of latitude and longitude containing adequate data. World maps display the locations that allow the prediction of plant nutrient concentrations from temperature or sigma-t. Geographic coverage improves along the sequence: nitrate, phosphate, and silicic acid and is better for sigma-t than for temperature. Contour maps of the approximate temperature of sigma-t at which these nitrients are no longer measurable in a parcel of water are generated, based on a percentile analysis of the temperature or sigma-t at which less than a selected amount of plant nutrient occurs. Results are stored on magnetic tape in tabular form. The global potential to predict plant nutrient concentrations from remotely sensed temperature of sigma-t and to emphasize the latitudinally and longitudinally changing phytoplankton growth environment in present and past oceans is demonstrated.

  17. Hydroxypropyl-β-CD vs. its α-homologue for a 3D modified polyrotaxane network formation and properties: the relationship between modified CD and polymer revealed through comparison.

    Science.gov (United States)

    Li, Zhao; Zheng, Zhen; Su, Shan; Yu, Lin; Wang, Xinling

    2016-09-14

    The threading mechanism of the hydroxypropyl-cyclodextrin (Hy-CD)/tetrahedron-like poly(ethylene glycol) (tetra-PEG) based host-guest complex and the relationship between Hy-CD and poly(ethylene oxide) (PEO) in the three-dimensional modified polyrotaxane (PR) formed by the complex were revealed through the comparison between Hy-β-CD/tetra-PEG and Hy-α-CD/tetra-PEG based systems from the macroscopic material view to the microscopic molecular view. The complexation between Hy-CD and tetra-PEG in water experiences a threading-dethreading-rethreading process which is controlled by the intermolecular interaction intensity or molecular hindrance depending on the feed ratio of Hy-CD to tetra-PEG. In the 3D modified PR, the methyl group of the Hy part on one Hy-CD can insert into the cavity of the adjacent Hy-CD and interacts with both the interior surface of the cavity and the PEO segment within the cavity if the cavity of Hy-CD is large enough. The threaded Hy-CD in the PR straightens the chain of PEO and suppresses the segment motion of the PEO. With the decrease of the cavity size of Hy-CD, the degree of suppression on the segment motion of PEO increases. Hy-CD threaded on the PEO chain can also deform when the 3D modified PR is compressed, and the degree of deformation increases with the increase of the cavity size of Hy-CD. These results of the modified CD/PEG based complex system set it apart from the unmodified CD/PEG based one, and reveal the structure-property relationship of this new type of Hy-CD/tetra-PEG based 3D modified PR material.

  18. Interannual variation in the fine-mode MODIS aerosol optical depth and its relationship to the changes in sulfur dioxide emissions in China between 2000 and 2010

    Directory of Open Access Journals (Sweden)

    S. Itahashi

    2012-03-01

    Full Text Available Anthropogenic SO2 emissions increased alongside economic development in China at a rate of 12.7% yr−1 from 2000 to 2005.