Science.gov

Sample records for causing natural variation

  1. Natural courtship song variation caused by an intronic retroelement in an ion channel gene.

    PubMed

    Ding, Yun; Berrocal, Augusto; Morita, Tomoko; Longden, Kit D; Stern, David L

    2016-08-18

    Animal species display enormous variation for innate behaviours, but little is known about how this diversity arose. Here, using an unbiased genetic approach, we map a courtship song difference between wild isolates of Drosophila simulans and Drosophila mauritiana to a 966 base pair region within the slowpoke (slo) locus, which encodes a calcium-activated potassium channel. Using the reciprocal hemizygosity test, we confirm that slo is the causal locus and resolve the causal mutation to the evolutionarily recent insertion of a retroelement in a slo intron within D. simulans. Targeted deletion of this retroelement reverts the song phenotype and alters slo splicing. Like many ion channel genes, slo is expressed widely in the nervous system and influences a variety of behaviours; slo-null males sing little song with severely disrupted features. By contrast, the natural variant of slo alters a specific component of courtship song, illustrating that regulatory evolution of a highly pleiotropic ion channel gene can cause modular changes in behaviour. PMID:27509856

  2. Causes of natural variation in fitness: evidence from studies of Drosophila populations.

    PubMed

    Charlesworth, Brian

    2015-02-10

    DNA sequencing has revealed high levels of variability within most species. Statistical methods based on population genetics theory have been applied to the resulting data and suggest that most mutations affecting functionally important sequences are deleterious but subject to very weak selection. Quantitative genetic studies have provided information on the extent of genetic variation within populations in traits related to fitness and the rate at which variability in these traits arises by mutation. This paper attempts to combine the available information from applications of the two approaches to populations of the fruitfly Drosophila in order to estimate some important parameters of genetic variation, using a simple population genetics model of mutational effects on fitness components. Analyses based on this model suggest the existence of a class of mutations with much larger fitness effects than those inferred from sequence variability and that contribute most of the standing variation in fitness within a population caused by the input of mildly deleterious mutations. However, deleterious mutations explain only part of this standing variation, and other processes such as balancing selection appear to make a large contribution to genetic variation in fitness components in Drosophila.

  3. Causes of natural variation in fitness: Evidence from studies of Drosophila populations

    PubMed Central

    Charlesworth, Brian

    2015-01-01

    DNA sequencing has revealed high levels of variability within most species. Statistical methods based on population genetics theory have been applied to the resulting data and suggest that most mutations affecting functionally important sequences are deleterious but subject to very weak selection. Quantitative genetic studies have provided information on the extent of genetic variation within populations in traits related to fitness and the rate at which variability in these traits arises by mutation. This paper attempts to combine the available information from applications of the two approaches to populations of the fruitfly Drosophila in order to estimate some important parameters of genetic variation, using a simple population genetics model of mutational effects on fitness components. Analyses based on this model suggest the existence of a class of mutations with much larger fitness effects than those inferred from sequence variability and that contribute most of the standing variation in fitness within a population caused by the input of mildly deleterious mutations. However, deleterious mutations explain only part of this standing variation, and other processes such as balancing selection appear to make a large contribution to genetic variation in fitness components in Drosophila. PMID:25572964

  4. Nature and causes of Quaternary climate variation of tropical South America

    NASA Astrophysics Data System (ADS)

    Baker, Paul A.; Fritz, Sherilyn C.

    2015-09-01

    This selective review of the Quaternary paleoclimate of the South American summer monsoon (SASM) domain presents viewpoints regarding a range of key issues in the field, many of which are unresolved and some of which are controversial. (1) El Niño-Southern Oscillation variability, while the most important global-scale mode of interannual climate variation, is insufficient to explain most of the variation of tropical South American climate observed in both the instrumental and the paleoclimate records. (2) Significant climate variation in tropical South America occurs on seasonal to orbital (i.e. multi-millennial) time scales as a result of sea-surface temperature (SST) variation and ocean-atmosphere interactions of the tropical Atlantic. (3) Decadal-scale climate variability, linked with this tropical Atlantic variability, has been a persistent characteristic of climate in tropical South America for at least the past half millennium, and likely, far beyond. (4) Centennial-to-millennial climate events in tropical South America were of longer duration and, perhaps, larger amplitude than any observed in the instrumental period, which is little more than a century long in tropical South America. These were superimposed upon both precession-paced insolation changes that caused significant variation in SASM precipitation and eccentricity-paced global glacial boundary conditions that caused significant changes in the tropical South American moisture balance. As a result, river sediment and water discharge increased and decreased across tropical South America, lake levels rose and fell, paleolakes arose and disappeared on the Altiplano, glaciers waxed and waned in the tropical Andes, and the tropical rainforest underwent significant changes in composition and extent. To further evaluate climate forcing over the last glacial cycle (˜125 ka), we developed a climate forcing model that combines summer insolation forcing and a proxy for North Atlantic SST forcing to

  5. Natural Variation in plep-1 Causes Male-Male Copulatory Behavior in C. elegans.

    PubMed

    Noble, Luke M; Chang, Audrey S; McNelis, Daniel; Kramer, Max; Yen, Mimi; Nicodemus, Jasmine P; Riccardi, David D; Ammerman, Patrick; Phillips, Matthew; Islam, Tangirul; Rockman, Matthew V

    2015-10-19

    In sexual species, gametes have to find and recognize one another. Signaling is thus central to sexual reproduction and involves a rapidly evolving interplay of shared and divergent interests [1-4]. Among Caenorhabditis nematodes, three species have evolved self-fertilization, changing the balance of intersexual relations [5]. Males in these androdioecious species are rare, and the evolutionary interests of hermaphrodites dominate. Signaling has shifted accordingly, with females losing behavioral responses to males [6, 7] and males losing competitive abilities [8, 9]. Males in these species also show variable same-sex and autocopulatory mating behaviors [6, 10]. These behaviors could have evolved by relaxed selection on male function, accumulation of sexually antagonistic alleles that benefit hermaphrodites and harm males [5, 11], or neither of these, because androdioecy also reduces the ability of populations to respond to selection [12-14]. We have identified the genetic cause of a male-male mating behavior exhibited by geographically dispersed C. elegans isolates, wherein males mate with and deposit copulatory plugs on one another's excretory pores. We find a single locus of major effect that is explained by segregation of a loss-of-function mutation in an uncharacterized gene, plep-1, expressed in the excretory cell in both sexes. Males homozygous for the plep-1 mutation have excretory pores that are attractive or receptive to copulatory behavior of other males. Excretory pore plugs are injurious and hermaphrodite activity is compromised in plep-1 mutants, so the allele might be unconditionally deleterious, persisting in the population because the species' androdioecious mating system limits the reach of selection. PMID:26455306

  6. What can long-lived mutants tell us about mechanisms causing aging and lifespan variation in natural environments?

    PubMed

    Briga, Michael; Verhulst, Simon

    2015-11-01

    Long-lived mutants of model organisms have brought remarkable progress in our understanding of aging mechanisms. However, long-lived mutants are usually maintained in optimal standardized laboratory environments (SLEs), and it is not obvious to what extent insights from long-lived mutants in SLEs can be generalized to more natural environments. To address this question, we reviewed experiments that compared the fitness and lifespan advantage of long-lived mutants relative to wild type controls in SLEs and more challenging environments in various model organisms such as yeast Saccharomyces cerevisiae, the nematode worm Caenorhabditis elegans, the fruitfly Drosophila melanogaster and the mouse Mus musculus. In competition experiments over multiple generations, the long-lived mutants had a lower fitness relative to wild type controls, and this disadvantage was the clearest when the environment included natural challenges such as limited food (N=6 studies). It is well known that most long-lived mutants have impaired reproduction, which provides one reason for the fitness disadvantage. However, based on 12 experiments, we found that the lifespan advantage of long-lived mutants is diminished in more challenging environments, often to the extent that the wild type controls outlive the long-lived mutants. Thus, it appears that information on aging mechanisms obtained from long-lived mutants in SLEs may be specific to such environments, because those same mechanisms do not extend lifespan in more natural environments. This suggests that different mechanisms cause variation in aging and lifespan in SLEs compared to natural populations.

  7. Natural variation in phosphorylation of photosystem II proteins in Arabidopsis thaliana: is it caused by genetic variation in the STN kinases?

    PubMed Central

    Flood, Pádraic J.; Yin, Lan; Herdean, Andrei; Harbinson, Jeremy; Aarts, Mark G. M.; Spetea, Cornelia

    2014-01-01

    Reversible phosphorylation of photosystem II (PSII) proteins is an important regulatory mechanism that can protect plants from changes in ambient light intensity and quality. We hypothesized that there is natural variation in this process in Arabidopsis (Arabidopsis thaliana), and that this results from genetic variation in the STN7 and STN8 kinase genes. To test this, Arabidopsis accessions of diverse geographical origins were exposed to two light regimes, and the levels of phospho-D1 and phospho-light harvesting complex II (LHCII) proteins were quantified by western blotting with anti-phosphothreonine antibodies. Accessions were classified as having high, moderate or low phosphorylation relative to Col-0. This variation could not be explained by the abundance of the substrates in thylakoid membranes. In genotypes with atrazine-resistant forms of the D1 protein, low D1 and LHCII protein phosphorylation was observed, which may be due to low PSII efficiency, resulting in reduced activation of the STN kinases. In the remaining genotypes, phospho-D1 levels correlated with STN8 protein abundance in high-light conditions. In growth light, D1 and LHCII phosphorylation correlated with longitude and in the case of LHCII phosphorylation also with temperature variability. This suggests a possible role of natural variation in PSII protein phosphorylation in the adaptation of Arabidopsis to diverse environments. PMID:24591726

  8. Salinity variations in the water resources fed by the Etnean volcanic aquifers (Sicily, Italy): natural vs. anthropogenic causes.

    PubMed

    D'Alessandro, Walter; Bellomo, Sergio; Bonfanti, Pietro; Brusca, Lorenzo; Longo, Manfredi

    2011-02-01

    In this paper, in an attempt to reveal possible changes connected to natural or anthropogenic causes, the main results of hydrogeochemical monitoring carried out at Mount Etna are evaluated. We report on the salinity contents of the groundwaters that flow in fractured volcanics, which make up the flanks of the volcano. These waters, analyzed for major ion chemistry, were sampled regularly from 1994 to 2004. Basing on nonparametric Sen's slope estimator, time series of groundwater composition reveal that the salinity of most of the Etnean aquifers increased by 0.5% to 3.5% each year during this period. This change in the water chemistry is clearly referable to the overexploitation of the aquifers. This increasing trend needs to be inverted urgently; otherwise, it will cause a shortage of water in the near future, because the maximum admissible concentration of salinity for drinking water will be exceeded. PMID:20198508

  9. Modeling Natural Variation through Distribution

    ERIC Educational Resources Information Center

    Lehrer, Richard; Schauble, Leona

    2004-01-01

    This design study tracks the development of student thinking about natural variation as late elementary grade students learned about distribution in the context of modeling plant growth at the population level. The data-modeling approach assisted children in coordinating their understanding of particular cases with an evolving notion of data as an…

  10. A Photometric Catalog of Herbig AE/BE Stars and Discussion of the Nature and Cause of the Variations of UX Orionis Stars

    NASA Astrophysics Data System (ADS)

    Herbst, W.; Shevchenko, V. S.

    1999-08-01

    the variations of some large-amplitude UXors involves variable obscuration by circumstellar dust clumps orbiting the star in a disk viewed nearly edge-on. However, there are problems in extending this model to the entire class, which lead us to propose an alternative mechanism, i.e., unsteady accretion. Evidence favoring the accretion model over the obscuration model is presented. It is suggested that the thermal instability mechanism responsible for outbursts in interacting binary system disks, and possibly FUors, may be the cause of the deep minima in UXors.

  11. [Natural forming causes of China population distribution].

    PubMed

    Fang, Yu; Ouyang, Zhi-Yun; Zheng, Hua; Xiao, Yi; Niu, Jun-Feng; Chen, Sheng-Bin; Lu, Fei

    2012-12-01

    The diverse natural environment in China causes the spatial heterogeneity of China population distribution. It is essential to understand the interrelations between the population distribution pattern and natural environment to enhance the understanding of the man-land relationship and the realization of the sustainable management for the population, resources, and environment. This paper analyzed the China population distribution by adopting the index of population density (PD) in combining with spatial statistic method and Lorenz curve, and discussed the effects of the natural factors on the population distribution and the interrelations between the population distribution and 16 indices including average annual precipitation (AAP), average annual temperature (AAT), average annual sunshine duration (AASD), precipitation variation (PV), temperature variation (TV), sunshine duration variation (SDV), relative humidity (RH), aridity index (AI), warmth index ( WI), > or = 5 degrees C annual accumulated temperature (AACT), average elevation (AE), relative height difference (RHD), surface roughness (SR), water system density (WSD), net primary productivity (NPP), and shortest distance to seashore (SDTS). There existed an obvious aggregation phenomenon in the population distribution in China. The PD was high in east China, medium in central China, and low in west China, presenting an obvious positive spatial association. The PD was significantly positively correlated with WSD, AAT, AAP, NPP, AACT, PV, RH, and WI, and significantly negatively correlated with RHD, AE, SDV, SR, and SDTS. The climate factors (AAT, WI, PV, and NPP), topography factors (SR and RHD), and water system factor (WSD) together determined the basic pattern of the population distribution in China. It was suggested that the monitoring of the eco-environment in the east China of high population density should be strengthened to avoid the eco-environmental degradation due to the expanding population, and

  12. Hidden genetic nature of epigenetic natural variation in plants.

    PubMed

    Pecinka, Ales; Abdelsamad, Ahmed; Vu, Giang T H

    2013-11-01

    Transcriptional gene silencing (TGS) is an epigenetic mechanism that suppresses the activity of repetitive DNA elements via accumulation of repressive chromatin marks. We discuss natural variation in TGS, with a particular focus on cases that affect the function of protein-coding genes and lead to developmental or physiological changes. Comparison of the examples described has revealed that most natural variation is associated with genetic determinants, such as gene rearrangements, inverted repeats, and transposon insertions that triggered TGS. Recent technical advances have enabled the study of epigenetic natural variation at a whole-genome scale and revealed patterns of inter- and intraspecific epigenetic variation. Future studies exploring non-model species may reveal species-specific evolutionary adaptations at the level of chromatin configuration.

  13. Darwin's finches: population variation and natural selection.

    PubMed Central

    Grant, P R; Grant, B R; Smith, J N; Abbott, I J; Abbott, L K

    1976-01-01

    Van Valen's model, which relates morphological variation to ecological variation in an adaptive scheme, was investigated with individually marked and measured Darwin's finches on two adjacent Galápagos islands, Santa Cruz and Daphne Major. Results show that environmental heterogeneity is correlated with large continuous, morphological variation: variation in bill dimensions of Geospiza fortis is greater on Santa Cruz than on Daphne, as is environmental heterogeneity. Within populations of this species, different phenotypes distribute themselves in different habitat patches, select foods of different sizes and hardness, and exploit them with efficiencies that are phenotype- (bill size) dependent. These data constitute indirect evidence that natural selection has a controlling influence over the level of phenotypic variation exhibited by a population. Further evidence is that phenotypes did not survive equally well during the study period; on Daphne island G. fortis was apparently subjected to directional selection on bill tip length and G. scandens to normalizing selection on body weight and bill depth. Other factors which may have contributed to the establishment of a difference in variation between Santa Cruz and Daphne populations are the founder effect, genetic drift, and assortative mating. Annual climatic unpredictability is considered a source of environmental heterogeneity which, through its effect upon food supply, favors large morphological variation. It is predicted that species of large individual size are more influenced by this than are small species, and consequently exhibit greater size-corrected variation. The prediction is tested with data from six Geospiza species, and found to be correct. PMID:1061123

  14. Gene Tree Discordance Causes Apparent Substitution Rate Variation.

    PubMed

    Mendes, Fábio K; Hahn, Matthew W

    2016-07-01

    Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide data sets, often due to incomplete lineage sorting (ILS). This apparent substitution rate variation is caused when substitutions that occur on discordant gene trees are analyzed in the context of a single, fixed species tree. Such substitutions have to be resolved by proposing multiple substitutions on the species tree, and we therefore refer to this phenomenon as Substitutions Produced by ILS (SPILS). We use simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa. Specific branches of the species trees are consistently, but erroneously, inferred to be longer or shorter, and we show that these branches can be predicted based on discordant tree topologies. Moreover, we observe that fixing a species tree topology when performing tests of positive selection increases the false positive rate, particularly for genes whose discordant topologies are most affected by SPILS. Finally, we use data from multiple Drosophila species to show that SPILS can be detected in nature. Although the effects of SPILS are modest per gene, it has the potential to affect substitution rate variation whenever high levels of ILS are present, particularly in rapid radiations. The problems outlined here have implications for character mapping of any type of trait, and for any biological process that causes discordance. We discuss possible solutions to these problems, and areas in which they are likely to have caused faulty inferences of convergence and accelerated evolution.

  15. Variation, natural selection, and information content--a simulation.

    PubMed

    Testa, Bernard; Bojarski, Andrzej J

    2007-10-01

    In Neo-Darwinism, variation and natural selection are the two evolutionary mechanisms that propel biological evolution. Variation implies changes in the gene pool of a population, enlarging the genetic variability from which natural selection can choose. But in the absence of natural selection, variation causes dissipation and randomization. Natural selection, in contrast, constrains this variability by decreasing the survival and fertility of the less-adapted organisms. The objective of this study is to propose a highly simplified simulation of variation and natural selection, and to relate the observed evolutionary changes in a population to its information content. The model involves an imaginary population of individuals. A quantifiable character allows the individuals to be categorized into bins. The distribution of bins (a histogram) was assumed to be Gaussian. The content of each bin was calculated after one to twelve cycles, each cycle spanning N generations (N being undefined). In a first study, selection was simulated in the absence of variation. This was modeled by assuming a differential fertility factor F that increased linearly from the lower bins (F<1.00) to the higher bins (F>1.00). The fertility factor was applied as a multiplication factor during each cycle. Several ranges of fertility were investigated. The resulting histograms became skewed to the right. In a second study, variation was simulated in the absence of selection. This was modeled by assuming that during each cycle each bin lost a fixed percentage of its content (variation factor Y) to its two adjacent bins. The resulting histograms became broader and flatter, while retaining their bilateral symmetry. Different values of Y were monitored. In a third study, various values of F and Y were combined. Our model allows the straightforward application of Shannon's equation and the calculation of a Shannon-entropy (SE) values for each histogram. Natural selection was, thus, shown to result in

  16. Occupational asthma caused by natural rubber latex.

    PubMed

    Vandenplas, O

    1995-11-01

    IgE-mediated sensitization in protein allergens of natural rubber latex (NRL) can induce immediate hypersensitivity reactions ranging from mild urticaria in life threatening anaphylaxis after cutaneous, mucosal or visceral exposure. Elutable allergens from NRL gloves absorb to the cornstarch powder particles, become airborne, and have the potential to cause respiratory reactions. Recent studies indicate that asthma is a frequent manifestation of NRL allergy among workers manufacturing NRL materials and among health-care providers using NRL workers. NRL-induced asthma should receive increasing attention as it can lead to permanent respiratory sequelae and occupational disability. The need for early and accurate diagnosis is outlined and the different diagnostic approaches are reviewed. Specific issues pertaining to the management of affected subjects and to the prevention of exposure to airborne NRL are discussed. Ares of future research should include: 1) further characterization of relevant NRL allergens; 2) development and validation of methods for quantitative assessment of allergen content in NRL devices and workplace environment; 3) evaluation of the natural history and risk factors of NRL-induced asthma; and 5) analysis of effectiveness and cost of preventive strategies. PMID:8620969

  17. Patterns and causes of geographic variation in bat echolocation pulses.

    PubMed

    Jiang, Tinglei; Wu, Hui; Feng, Jiang

    2015-05-01

    Evolutionary biologists have a long-standing interest in how acoustic signals in animals vary geographically, because divergent ecology and sensory perception play an important role in speciation. Geographic comparisons are valuable in determining the factors that influence divergence of acoustic signals. Bats are social mammals and they depend mainly on echolocation pulses to locate prey, to navigate and to communicate. Mounting evidence shows that geographic variation of bat echolocation pulses is common, with a mean 5-10 kHz differences in peak frequency, and a high level of individual variation may be nested in this geographical variation. However, understanding the geographic variation of echolocation pulses in bats is very difficult, because of differences in sample and statistical analysis techniques as well as the variety of factors shaping the vocal geographic evolution. Geographic differences in echolocation pulses of bats generally lack latitudinal, longitudinal and elevational patterns, and little is known about vocal dialects. Evidence is accumulating to support the fact that geographic variation in echolocation pulses of bats may be caused by genetic drift, cultural drift, ecological selection, sexual selection and social selection. Future studies could relate geographic differences in echolocation pulses to social adaptation, vocal learning strategies and patterns of dispersal. In addition, new statistical techniques and acoustic playback experiments may help to illustrate the causes and consequences of the geographic evolution of echolocation pulse in bats. PMID:25664901

  18. Rapid establishment of genetic incompatibility through natural epigenetic variation.

    PubMed

    Durand, Stéphanie; Bouché, Nicolas; Perez Strand, Elsa; Loudet, Olivier; Camilleri, Christine

    2012-02-21

    Epigenetic variation is currently being investigated with the aim of deciphering its importance in both adaptation and evolution [1]. In plants, epimutations can underlie heritable phenotypic diversity [2-4], and epigenetic mechanisms might contribute to reproductive barriers between [5] or within species [6]. The extent of epigenetic variation begins to be appreciated in Arabidopsis [7], but the origin of natural epialleles and their impact in the wild remain largely unknown. Here we show that a genetic incompatibility among Arabidopsis thaliana strains is related to the epigenetic control of a pair of duplicate genes involved in fitness: a transposition event results in a rearranged paralogous structure that causes DNA methylation and transcriptional silencing of the other copy. We further show that this natural, strain-specific epiallele is stable over numerous generations even after removal of the duplicated, rearranged gene copy through crosses. Finally, we provide evidence that the rearranged gene copy triggers de novo DNA methylation and silencing of the unlinked native gene by RNA-directed DNA methylation. Our findings suggest an important role of naturally occurring epialleles originating from structural variation in rapidly establishing genetic incompatibilities following gene duplication events.

  19. Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior

    PubMed Central

    Shorter, John; Couch, Charlene; Huang, Wen; Carbone, Mary Anna; Peiffer, Jason; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2015-01-01

    Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO2, and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics. PMID:26100892

  20. Slope instability caused by small variations in hydraulic conductivity

    USGS Publications Warehouse

    Reid, M.E.

    1997-01-01

    Variations in hydraulic conductivity can greatly modify hillslope ground-water flow fields, effective-stress fields, and slope stability. In materials with uniform texture, hydraulic conductivities can vary over one to two orders of magnitude, yet small variations can be difficult to determine. The destabilizing effects caused by small (one order of magnitude or less) hydraulic conductivity variations using ground-water flow modeling, finite-element deformation analysis, and limit-equilibrium analysis are examined here. Low hydraulic conductivity materials that impede downslope ground-water flow can create unstable areas with locally elevated pore-water pressures. The destabilizing effects of small hydraulic heterogeneities can be as great as those induced by typical variations in the frictional strength (approximately 4??-8??) of texturally similar materials. Common "worst-case" assumptions about ground-water flow, such as a completely saturated "hydrostatic" pore-pressure distribution, do not account for locally elevated pore-water pressures and may not provide a conservative slope stability analysis. In site characterization, special attention should be paid to any materials that might impede downslope ground-water flow and create unstable regions.

  1. Causes of snow instability variations at the basin scale

    NASA Astrophysics Data System (ADS)

    Reuter, Benjamin; Richter, Bettina; Schweizer, Jürg

    2016-04-01

    The alpine snow cover accumulates layers during characteristic meteorological events. The so formed stratigraphic features of the snowpack are known to influence avalanche release processes, such as failure initiation or crack propagation. Synoptic scale meteorological processes are altered by the underlying terrain, which causes micro-meteorological differences at smaller scales, such as the basin scale, for instance. Such micro-meteorological effects of complex snow surfaces were successfully modeled suggesting that the time is ripe to investigate their influence on snow instability. In other words, we aim at identifying the causes of spatial snow instability variations at the scale of a small basin. Over the past years we have compiled several field data sets for a small basin above Davos (Eastern Swiss Alps) covering 400 m by 400 m and consisting of snow penetration resistance profiles collected with the snow micro-penetrometer, terrain data and terrestrial laser scans. Each dataset holds about 150 vertical profiles sampled semi-randomly in the basin and captures the situation of a specific day, hence a particular avalanche situation. At those 150 point measurements the criteria for failure initiation and crack propagation were calculated and their spatial structure was analyzed. Eventually, we were able to model the distribution of snow instability in the basin by external drift kriging. We based the regression models on terrain and snow depth data. Slope aspect was the most prominent driver, but the number of significant covariates depended on the situation. Our results further suggest that the observed differences were caused by external influences possibly due to meteorological forcing as their residual autocorrelation ranges were shorter than the ones of the terrain. Repeating the geostatistical analysis with snow cover model output as covariate data, we were able to identify the causes of the snow instability patterns observed at the basin scale. The most

  2. Acid lakes from natural and anthropogenic causes

    SciTech Connect

    Patrick, R.; Binetti, V.P.; Halterman, S.G.

    1981-01-30

    Lakes may be acid because of natural ecological conditions or because of anthropogenic activities. Apparently there has been a recent increase in acidity of many lakes in the northeastern United States. Factors that may be contributing to this increase include the use by utilities of precipitators, sulfur scrubbers, and tall stacks; the use of petroleum; and methods of combustion of fossil fuels.

  3. Helium isotopic abundance variation in nature

    SciTech Connect

    Holden, N.E.

    1993-08-01

    The isotopic abundance of helium in nature has been reviewed. This atomic weight value is based on the value of helium in the atmosphere, which is invariant around the world and up to a distance of 100,000 feet. Helium does vary in natural gas, volcanic rocks and gases, ocean floor sediments, waters of various types and in radioactive minerals and ores due to {alpha} particle decay of radioactive nuclides.

  4. DNA methylation: A source of random variation in natural populations.

    PubMed

    Massicotte, Rachel; Whitelaw, Emma; Angers, Bernard

    2011-04-01

    Epigenetic processes (e.g., DNA methylation) have been proposed as potentially important evolutionary mechanisms. However, before drawing conclusions about their evolutionary relevance, we need to evaluate the independence of epigenetic variation from genetic variation, as well as the extent of methylation polymorphism in nature. We evaluated these in natural populations of a clonal fish, Chrosomus eos-neogaeus, for which genetically identical individuals may be found in distinct environments. A genomic survey confirms the genetic uniformity of individuals, whereas a substantial level of inter-individual variation results in DNA methylation. Survey of the methylation status of the CpG dinucleotides of a fragment of a retrotransposon confirmed a marked difference in epiallelic composition among tissues, as well as among individuals. This study provides further evidence of epigenetic variation in the absence of genetic variation and demonstrates that this process can be a source of random variation in natural populations. PMID:21266851

  5. [A brief history of the natural causes of human disease].

    PubMed

    Lips-Castro, Walter

    2015-01-01

    In the study of the causes of disease that have arisen during the development of humankind, one can distinguish three major perspectives: the natural, the supernatural, and the artificial. In this paper we distinguish the rational natural causes of disease from the irrational natural causes. Within the natural and rational causal approaches of disease, we can highlight the Egyptian theory of putrid intestinal materials called "wechdu", the humoral theory, the atomistic theory, the contagious theory, the cellular theory, the molecular (genetic) theory, and the ecogenetic theory. Regarding the irrational, esoteric, and mystic causal approaches to disease, we highlight the astrological, the alchemical, the iatrochemical, the iatromechanical, and others (irritability, solidism, brownism, and mesmerism).

  6. Does natural variation in diversity affect biotic resistance?

    USGS Publications Warehouse

    Harrison, Susan; Cornell, Howard; Grace, James B.

    2015-01-01

    Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the key underlying process by dissecting how community diversity is shaped by the same environmental gradients that determine biotic and abiotic resistance to new invaders. In grasslands on highly heterogeneous soils, we used addition of a recent invader, competitor removal and structural equation modelling (SEM) to analyse soil influences on community diversity, biotic and abiotic resistance and invader success. Biotic resistance, measured by reduction in invader success in the presence of the resident community, was negatively correlated with species richness and functional diversity. However, in the multivariate SEM framework, biotic resistance was independent of all forms of diversity and was positively affected by soil fertility via community biomass. Abiotic resistance, measured by invader success in the absence of the resident community, peaked on infertile soils with low biomass and high community diversity. Net invader success was determined by biotic resistance, consistent with this invader's better performance on infertile soils in unmanipulated conditions. Seed predation added slightly to biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results. Synthesis. In natural systems, diversity may be correlated with invasibility and yet have no effect on either biotic or abiotic resistance to invasion. More generally, the environmental causes of variation in diversity should not be overlooked when considering the potential functional consequences of diversity.

  7. Causes and significance of variation in mammalian basal metabolism.

    PubMed

    Raichlen, David A; Gordon, Adam D; Muchlinski, Magdalena N; Snodgrass, J Josh

    2010-02-01

    Mammalian basal metabolic rates (BMR) increase with body mass, whichs explains approximately 95% of the variation in BMR. However, at a given mass, there remains a large amount of variation in BMR. While many researchers suggest that the overall scaling of BMR with body mass is due to physiological constraints, variation at a given body mass may provide clues as to how selection acts on BMR. Here, we examine this variation in BMR in a broad sample of mammals and we test the hypothesis that, across mammals, body composition explains differences in BMR at a given body mass. Variation in BMR is strongly correlated with variation in muscle mass, and both of these variables are correlated with latitude and ambient temperature. These results suggest that selection alters BMR in response to thermoregulatory pressures, and that selection uses muscle mass as a means to generate this variation. PMID:19730868

  8. Natural variations in the geomagnetically trapped electron population

    NASA Technical Reports Server (NTRS)

    Vampola, A. L.

    1972-01-01

    Temporal variations in the trapped natural electron flux intensities and energy spectra are discussed and demonstrated using recent satellite data. These data are intended to acquaint the space systems engineer with the types of natural variations that may be encountered during a mission and to augment the models of the electron environment currently being used in space system design and orbit selection. An understanding of the temporal variations which may be encountered should prove helpful. Some of the variations demonstrated here which are not widely known include: (1) addition of very energetic electrons to the outer zone during moderate magnetic storms: (2) addition of energetic electrons to the inner zone during major magnetic storms; (3) inversions in the outer zone electron energy spectrum during the decay phase of a storm injection event and (4) occasional formation of multiple maxima in the flux vs altitude profile of moderately energetic electrons.

  9. [A brief history of the natural causes of human disease].

    PubMed

    Lips-Castro, Walter

    2015-01-01

    In the study of the causes of disease that have arisen during the development of humankind, one can distinguish three major perspectives: the natural, the supernatural, and the artificial. In this paper we distinguish the rational natural causes of disease from the irrational natural causes. Within the natural and rational causal approaches of disease, we can highlight the Egyptian theory of putrid intestinal materials called "wechdu", the humoral theory, the atomistic theory, the contagious theory, the cellular theory, the molecular (genetic) theory, and the ecogenetic theory. Regarding the irrational, esoteric, and mystic causal approaches to disease, we highlight the astrological, the alchemical, the iatrochemical, the iatromechanical, and others (irritability, solidism, brownism, and mesmerism). PMID:26581540

  10. Multiple capacitors for natural genetic variation in Drosophila melanogaster.

    PubMed

    Takahashi, Kazuo H

    2013-03-01

    Cryptic genetic variation (CGV) or a standing genetic variation that is not ordinarily expressed as a phenotype is released when the robustness of organisms is impaired under environmental or genetic perturbations. Evolutionary capacitors modulate the amount of genetic variation exposed to natural selection and hidden cryptically; they have a fundamental effect on the evolvability of traits on evolutionary timescales. In this study, I have demonstrated the effects of multiple genomic regions of Drosophila melanogaster on CGV in wing shape. I examined the effects of 61 genomic deficiencies on quantitative and qualitative natural genetic variation in the wing shape of D. melanogaster. I have identified 10 genomic deficiencies that do not encompass a known candidate evolutionary capacitor, Hsp90, exposing natural CGV differently depending on the location of the deficiencies in the genome. Furthermore, five genomic deficiencies uncovered qualitative CGV in wing morphology. These findings suggest that CGV in wing shape of wild-type D. melanogaster is regulated by multiple capacitors with divergent functions. Future analysis of genes encompassed by these genomic regions would help elucidate novel capacitor genes and better understand the general features of capacitors regarding natural genetic variation.

  11. Deuterium: Natural variations used as a biological tracer

    USGS Publications Warehouse

    Gleason, J.D.; Friedman, I.

    1970-01-01

    The suggestion is made that isotope tracing be carried out by monitoring the natural variations in deuterium concentrations. As an example, the natural variations in deuterium concentrations between food and water collected in Illinois and food and water collected in Colorado were used to determine the residence time of water in the blood and urine of rats. We observed not only a 51/2-day turnover time of water in the blood and urine, but also evidence for the influx of water vapor from the atmosphere through the lungs into the blood.

  12. Natural allelic variations in highly polyploidy Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as important sugar and biofuel crop are highly polypoid with complex genomes. A large amount of natural phenotypic variation exists in sugarcane germplasm. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic seq...

  13. Extensive Natural Epigenetic Variation at a De Novo Originated Gene

    PubMed Central

    Silveira, Amanda Bortolini; Trontin, Charlotte; Cortijo, Sandra; Barau, Joan; Del Bem, Luiz Eduardo Vieira; Loudet, Olivier; Colot, Vincent; Vincentz, Michel

    2013-01-01

    Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5′end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation. PMID:23593031

  14. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    PubMed Central

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  15. Natural Allelic Variations in Highly Polyploidy Saccharum Complex.

    PubMed

    Song, Jian; Yang, Xiping; Resende, Marcio F R; Neves, Leandro G; Todd, James; Zhang, Jisen; Comstock, Jack C; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

  16. Natural Allelic Variations in Highly Polyploidy Saccharum Complex.

    PubMed

    Song, Jian; Yang, Xiping; Resende, Marcio F R; Neves, Leandro G; Todd, James; Zhang, Jisen; Comstock, Jack C; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  17. Causes of forbush decreases and other cosmic ray variations

    NASA Technical Reports Server (NTRS)

    Barouch, E.; Burlaga, L. F.

    1974-01-01

    The relationship between neutron monitor variations and the intensity variations of the interplanetary magnetic field is studied, using Deep River data and IMP-series satellite data. In over 80% of the cases studied, identifiable depressions of the cosmic ray intensity are associated with magnetic field enhancements of several hours duration and intensity above 10 gamma. Conversely, each magnetic field enhancement has an identifiable effect (though not necessarily a marked depression) on the cosmic ray intensity. Long lasting Forbush decreases are found to be the consequence of the successive action of several such features. An explanation is presented and discussed.

  18. Genetic Architecture of Natural Variation in Thermal Responses of Arabidopsis.

    PubMed

    Sanchez-Bermejo, Eduardo; Zhu, Wangsheng; Tasset, Celine; Eimer, Hannes; Sureshkumar, Sridevi; Singh, Rupali; Sundaramoorthi, Vignesh; Colling, Luana; Balasubramanian, Sureshkumar

    2015-09-01

    Wild strains of Arabidopsis (Arabidopsis thaliana) exhibit extensive natural variation in a wide variety of traits, including response to environmental changes. Ambient temperature is one of the major external factors that modulates plant growth and development. Here, we analyze the genetic architecture of natural variation in thermal responses of Arabidopsis. Exploiting wild accessions and recombinant inbred lines, we reveal extensive phenotypic variation in response to ambient temperature in distinct developmental traits such as hypocotyl elongation, root elongation, and flowering time. We show that variation in thermal response differs between traits, suggesting that the individual phenotypes do not capture all the variation associated with thermal response. Genome-wide association studies and quantitative trait locus analyses reveal that multiple rare alleles contribute to the genetic architecture of variation in thermal response. We identify at least 20 genomic regions that are associated with variation in thermal response. Further characterizations of temperature sensitivity quantitative trait loci that are shared between traits reveal a role for the blue-light receptor CRYPTOCHROME2 (CRY2) in thermosensory growth responses. We show the accession Cape Verde Islands is less sensitive to changes in ambient temperature, and through transgenic analysis, we demonstrate that allelic variation at CRY2 underlies this temperature insensitivity across several traits. Transgenic analyses suggest that the allelic effects of CRY2 on thermal response are dependent on genetic background suggestive of the presence of modifiers. In addition, our results indicate that complex light and temperature interactions, in a background-dependent manner, govern growth responses in Arabidopsis. PMID:26195568

  19. Genetic variation in natural honeybee populations, Apis mellifera capensis

    NASA Astrophysics Data System (ADS)

    Hepburn, Randall; Neumann, Peter; Radloff, Sarah E.

    2004-09-01

    Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

  20. Nonconsumptive predator-driven mortality causes natural selection on prey.

    PubMed

    Siepielski, Adam M; Wang, Jason; Prince, Garrett

    2014-03-01

    Predators frequently exert natural selection through differential consumption of their prey. However, predators may also cause prey mortality through nonconsumptive effects, which could cause selection if different prey phenotypes are differentially susceptible to this nonconsumptive mortality. Here we present an experimental test of this hypothesis, which reveals that nonconsumptive mortality imposed by predatory dragonflies causes selection on their damselfly prey favoring increased activity levels. These results are consistent with other studies of predator-driven selection, however, they reveal that consumption alone is not the only mechanism by which predators can exert selection on prey. Uncovering this mechanism also suggests that prey defensive traits may represent adaptations to not only avoid being consumed, but also for dealing with other sources of mortality caused by predators. Demonstrating selection through both consumptive and nonconsumptive predator mortality provides us with insight into the diverse effects of predators as an evolutionary force.

  1. Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions

    PubMed Central

    Zan, Yanjun; Shen, Xia; Forsberg, Simon K. G.; Carlborg, Örjan

    2016-01-01

    An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant’s extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype. In total, 2669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. A total of 646 cis-eQTL-regulated genes that lacked detectable transcripts in some accessions was found, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA transcripts for these genes. This study thus provides new insights into the overall genetic regulation of global gene expression diversity in the leaf of natural A. thaliana accessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwide A. thaliana population. PMID:27226169

  2. Genetic variation in natural populations of Populus tremuloide

    SciTech Connect

    Cheliak, W.M.

    1980-01-01

    Vegetative reproduction results in a mosaic of clones throughout the extensive natural range of this species. An electrophoretic survey of 26 loci in 222 trees from seven natural populations in Alberta demonstrated great variability. Average observed population heterozygosity was 0.52 with an average of 2.3 alleles per locus; 84% of the loci were polymorphic. A model (for a finite population with neutral alleles) was developed to investigate the effects of partial vegetative reproduction on the amount of variation in a population. Results of the survey conformed to those predicted by the model for a population with a rate of sexual establishment greater than 1/N, where N is the population size. The model states that under these conditions, vegetative reproduction has no effect on the population. Therefore, the high level of observed variation is not an artifact of the mode of natural reproduction. These results support conclusions about high population variability based on phenotypic measurements and also suggest a genetic basis for this variation, rather than simply phenotypic plasticity.

  3. Heterochrony underpins natural variation in Cardamine hirsuta leaf form

    PubMed Central

    Cartolano, Maria; Pieper, Bjorn; Lempe, Janne; Tattersall, Alex; Huijser, Peter; Tresch, Achim; Darrah, Peter R.; Hay, Angela; Tsiantis, Miltos

    2015-01-01

    A key problem in biology is whether the same processes underlie morphological variation between and within species. Here, by using plant leaves as an example, we show that the causes of diversity at these two evolutionary scales can be divergent. Some species like the model plant Arabidopsis thaliana have simple leaves, whereas others like the A. thaliana relative Cardamine hirsuta bear complex leaves comprising leaflets. Previous work has shown that these interspecific differences result mostly from variation in local tissue growth and patterning. Now, by cloning and characterizing a quantitative trait locus (QTL) for C. hirsuta leaf shape, we find that a different process, age-dependent progression of leaf form, underlies variation in this trait within species. This QTL effect is caused by cis-regulatory variation in the floral repressor ChFLC, such that genotypes with low-expressing ChFLC alleles show both early flowering and accelerated age-dependent changes in leaf form, including faster leaflet production. We provide evidence that this mechanism coordinates leaf development with reproductive timing and may help to optimize resource allocation to the next generation. PMID:26243877

  4. Causes of evolutionary rate variation among protein sites

    PubMed Central

    Echave, Julian; Spielman, Stephanie J.; Wilke, Claus O.

    2016-01-01

    It has long been recognized that certain sites within a protein, such as sites in the protein core or catalytic residues in enzymes, are more conserved than are other sites. However, our understanding of rate variation among sites remains surprisingly limited. Recent progress to address this includes the development of a wide array of reliable methods to estimate site-specific substitution rates from sequence alignments. In addition, several molecular traits have been identified that correlate with site-specific rates, and novel mechanistic, biophysical models have been proposed to explain the observed correlations. Nonetheless, at best, current models explain approximately 60% of the observed variance, highlighting the limitations of current methods and models, and the need for new research directions. PMID:26781812

  5. Natural Variation of Model Mutant Phenotypes in Ciona intestinalis

    PubMed Central

    Brown, Euan R.; Leccia, Nicola I.; Squarzoni, Paola; Tarallo, Raffaella; Alfano, Christian; Caputi, Luigi; D'Ambrosio, Palmira; Daniele, Paola; D'Aniello, Enrico; D'Aniello, Salvatore; Maiella, Sylvie; Miraglia, Valentina; Russo, Monia Teresa; Sorrenti, Gerarda; Branno, Margherita; Cariello, Lucio; Cirino, Paola; Locascio, Annamaria; Spagnuolo, Antonietta; Zanetti, Laura; Ristoratore, Filomena

    2008-01-01

    Background The study of ascidians (Chordata, Tunicata) has made a considerable contribution to our understanding of the origin and evolution of basal chordates. To provide further information to support forward genetics in Ciona intestinalis, we used a combination of natural variation and neutral population genetics as an approach for the systematic identification of new mutations. In addition to the significance of developmental variation for phenotype-driven studies, this approach can encompass important implications in evolutionary and population biology. Methodology/Principal Findings Here, we report a preliminary survey for naturally occurring mutations in three geographically interconnected populations of C. intestinalis. The influence of historical, geographical and environmental factors on the distribution of abnormal phenotypes was assessed by means of 12 microsatellites. We identified 37 possible mutant loci with stereotyped defects in embryonic development that segregate in a way typical of recessive alleles. Local populations were found to differ in genetic organization and frequency distribution of phenotypic classes. Conclusions/Significance Natural genetic polymorphism of C. intestinalis constitutes a valuable source of phenotypes for studying embryonic development in ascidians. Correlating genetic structure and the occurrence of abnormal phenotypes is a crucial focus for understanding the selective forces that shape natural finite populations, and may provide insights of great importance into the evolutionary mechanisms that generate animal diversity. PMID:18523552

  6. Natural enemies drive geographic variation in plant defenses.

    PubMed

    Züst, Tobias; Heichinger, Christian; Grossniklaus, Ueli; Harrington, Richard; Kliebenstein, Daniel J; Turnbull, Lindsay A

    2012-10-01

    Plants defend themselves against attack by natural enemies, and these defenses vary widely across populations. However, whether communities of natural enemies are a sufficiently potent force to maintain polymorphisms in defensive traits is largely unknown. Here, we exploit the genetic resources of Arabidopsis thaliana, coupled with 39 years of field data on aphid abundance, to (i) demonstrate that geographic patterns in a polymorphic defense locus (GS-ELONG) are strongly correlated with changes in the relative abundance of two specialist aphids; and (ii) demonstrate differential selection by the two aphids on GS-ELONG, using a multigeneration selection experiment. We thereby show a causal link between variation in abundance of the two specialist aphids and the geographic pattern at GS-ELONG, which highlights the potency of natural enemies as selective forces.

  7. Causes of variation in biotic interaction strength and phenotypic selection along an altitudinal gradient.

    PubMed

    Mezquida, Eduardo T; Benkman, Craig W

    2014-06-01

    Understanding the causes of variation in biotic interaction strength and phenotypic selection remains one of the outstanding goals of evolutionary ecology. Here we examine the variation in strength of interactions between two seed predators, common crossbills (Loxia curvirostra) and European red squirrels (Sciurus vulgaris), and mountain pine (Pinus uncinata) at and below tree limit in the Pyrenees, and how this translates into phenotypic selection. Seed predation by crossbills increased whereas seed predation by squirrels decreased with increasing elevation and as the canopy became more open. Overall, seed predation by crossbills averaged about twice that by squirrels, and the intensity of selection exerted by crossbills averaged between 2.6 and 7.5 times greater than by squirrels. The higher levels of seed predation by crossbills than squirrels were related to the relatively open nature of most of the forests, and the higher intensity of selection exerted by crossbills resulted from their higher levels of seed predation. However, most of the differences in selection intensity between crossbills and squirrels were the result of habitat features having a greater effect on the foraging behavior of squirrels than of crossbills, causing selection to be much lower for squirrels than for crossbills. PMID:24593660

  8. The Spatial Variation of Polar Rain Electrons and its Cause

    NASA Technical Reports Server (NTRS)

    Fairfield, D. H.; Wing, S.; Ruohoniemi, J. M.; Newell, P. T.; Gosling, J. T.; Skoug, R. M.

    2007-01-01

    It is generally accepted that field aligned electrons in the solar wind can follow field lines connected to Earth and precipitate in the polar ionosphere where they are known as polar rain. Few-hundred eV, field-aligned electrons of the solar wind "strahl" carry the interplanetary heat flux moving out from the sun and these electrons precipitate in either the northern or southern hemisphere depending on the magnetic field direction. These electrons produce enhanced polar rain in one hemisphere or the other although weaker polar rain is usually produced in the opposite hemisphere by whatever electrons are moving in the opposite direction. Although much evidence exists for this simple free entry mechanism, it has also long been known that there are spatial variations in the energies and intensities of the precipitating electrons. The present work compares electron distribution functions measured by the ACE spacecraft in the solar wind with those measured by the DMSP spacecraft at 800 km altitude over the polar cap. It is found that shifting the DMSP distribution functions in energy by amounts ranging from 10's to a few hundred eV produces quite good agreement with simultaneous ACE measurements. Over most of the polar cap this DMSP energy shift must be positive to achieve this agreement, suggesting the electrons have been decelerated by a field aligned potential as they move from the solar wind to low altitudes. The largest shifts occur on the nightside and on the dawn or dusk side, with the latter depending on the plasma convection pattern which is controlled by the orientation of the IMF. Nearer the cusp the shift is smaller or even negative. Since more massive tailward flowing magnetosheath ions are unable io follow the field lines into the magnetotail like the electrons, a field aligned potential is expected to develop to exclude low energy electrons and prevent an excessive charge imbalance. Such a potential would also produce the deceleration of those electrons

  9. What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation?

    PubMed Central

    Alonso-Blanco, Carlos; Aarts, Mark G.M.; Bentsink, Leonie; Keurentjes, Joost J.B.; Reymond, Matthieu; Vreugdenhil, Dick; Koornneef, Maarten

    2009-01-01

    Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available. PMID:19574434

  10. Recent climatic variations, their causes and neogene perspectives

    SciTech Connect

    Miller, M.M.

    1985-01-01

    Secular trends during the Little Ice Age and the Holocene suggest that if natural climatic controls prevail, both minor and major Ice Ages could be in the offing, the lesser one within a few centuries and a greater one in upwards of 10,000 years. Over the past 15 years, low elevation glaciers have experienced accelerated down wastage and retreat, paralleled by notable increase in ice volume in some of the higher elevation cirques. Teleconnectional similarities with modern glacier behavior in Scandinavia, the southern Andes and New Zealand support global significance of the record. Comparative data on polar sea ice changes in historic time also reflect the general regime trends of terrestrial glacier ice. At time, stage and age intervals, British Columbia-Yukon-Alaska glacial stratigraphy and ocean core evidence have suggested longer-term intervals of glacial climate at approximately 10, 20 40-50, 100 and possible as much as 500 thousand years. In the absence of a plausible explanation of the last 10-15 years of warming either from the solar cycle or from air-sea interactions, the concern is that a global carbon dioxide control on the general circulation may have begun during the 1960s. Systematic glacier/climate studies and further critical tests of the sun-weather interaction should be continued throughout the remaining years of this century.

  11. Natural variations of lithium isotopes in a mammalian model.

    PubMed

    Balter, Vincent; Vigier, Nathalie

    2014-03-01

    Despite lithium's extensive clinical applications, the cellular and molecular basis for the therapeutic effects remains to be elucidated. The large difference in mass between the two lithium isotopes ((6)Li and (7)Li) has prompted biochemists to explore the metabolism of Li by using pure (6)Li and (7)Li labeled drugs. However, experiments were carried out at very high Li concentrations, which did not reflect natural conditions. In the present study, we consider, for the first time, the natural variations of the (7)Li/(6)Li ratio in the organs and body fluids of an animal model, sheep. Each organ seems to be characterized by a specific Li isotope composition. So far, the range of the (7)Li/(6)Li ratio in the sheep body, expressed as δ permil variations relative to the L-SVEC standard (δ(7)Li), is about 40‰, between muscles (∼40‰) and kidney (∼0‰). Relative to a dietary δ(7)Li value of ∼+17‰, serum, red blood cells, muscle, liver, brain and kidney have a (7)Li enrichment of -12‰, -14‰, +22‰, +5‰, -3‰ and -15‰, respectively. The Li isotope composition is likely to be fractionated during intestinal absorption, with a greater absorption of (6)Li relative to (7)Li. According to previous conclusions obtained with (6)Li and (7)Li labeled chemicals, (6)Li appears to diffuse into erythrocytes faster than does (7)Li. However, this does not hold for myocytes and hepatocytes, because these two tissues have a higher δ(7)Li level than serum. Purely diffusive isotopic fractionation would leave all organs (7)Li-depleted relative to the serum, which is not the case, suggesting that active, molecule-specific, isotopic fractionation occurs in the body. Our preliminary results suggest that natural Li isotope variations can shed light on its regulation in the body, being active or passive.

  12. Environmental and biomedical applications of natural metal stable isotope variations

    USGS Publications Warehouse

    Bullen, T.D.; Walczyk, T.

    2009-01-01

    etal stable isotopes are now being used to trace metal contaminants in the environment and as indicators of human systemic function where metals play a role. Stable isotope abundance variations provide information about metal sources and the processes affecting metals in complex natural systems, complementing information gained from surrogate tracers, such as metal abundance ratios or biochemical markers of metal metabolism. The science is still in its infancy, but the results of initial studies confirm that metal stable isotopes can provide a powerful tool for forensic and biomedical investigations.

  13. Genetic architecture of natural variation in visual senescence in Drosophila

    PubMed Central

    Carbone, Mary Anna; Yamamoto, Akihiko; Huang, Wen; Lyman, Rachel A.; Meadors, Tess Brune; Yamamoto, Ryoan; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2016-01-01

    Senescence, i.e., functional decline with age, is a major determinant of health span in a rapidly aging population, but the genetic basis of interindividual variation in senescence remains largely unknown. Visual decline and age-related eye disorders are common manifestations of senescence, but disentangling age-dependent visual decline in human populations is challenging due to inability to control genetic background and variation in histories of environmental exposures. We assessed the genetic basis of natural variation in visual senescence by measuring age-dependent decline in phototaxis using Drosophila melanogaster as a genetic model system. We quantified phototaxis at 1, 2, and 4 wk of age in the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and found an average decline in phototaxis with age. We observed significant genetic variation for phototaxis at each age and significant genetic variation in senescence of phototaxis that is only partly correlated with phototaxis. Genome-wide association analyses in the DGRP and a DGRP-derived outbred, advanced intercross population identified candidate genes and genetic networks associated with eye and nervous system development and function, including seven genes with human orthologs previously associated with eye diseases. Ninety percent of candidate genes were functionally validated with targeted RNAi-mediated suppression of gene expression. Absence of candidate genes previously implicated with longevity indicates physiological systems may undergo senescence independent of organismal life span. Furthermore, we show that genes that shape early developmental processes also contribute to senescence, demonstrating that senescence is part of a genetic continuum that acts throughout the life span. PMID:27791033

  14. Peromyscus mice as a model for studying natural variation

    PubMed Central

    Bedford, Nicole L; Hoekstra, Hopi E

    2015-01-01

    The deer mouse (genus Peromyscus) is the most abundant mammal in North America, and it occupies almost every type of terrestrial habitat. It is not surprising therefore that the natural history of Peromyscus is among the best studied of any small mammal. For decades, the deer mouse has contributed to our understanding of population genetics, disease ecology, longevity, endocrinology and behavior. Over a century's worth of detailed descriptive studies of Peromyscus in the wild, coupled with emerging genetic and genomic techniques, have now positioned these mice as model organisms for the study of natural variation and adaptation. Recent work, combining field observations and laboratory experiments, has lead to exciting advances in a number of fields—from evolution and genetics, to physiology and neurobiology. DOI: http://dx.doi.org/10.7554/eLife.06813.001 PMID:26083802

  15. Peromyscus mice as a model for studying natural variation.

    PubMed

    Bedford, Nicole L; Hoekstra, Hopi E

    2015-01-01

    The deer mouse (genus Peromyscus) is the most abundant mammal in North America, and it occupies almost every type of terrestrial habitat. It is not surprising therefore that the natural history of Peromyscus is among the best studied of any small mammal. For decades, the deer mouse has contributed to our understanding of population genetics, disease ecology, longevity, endocrinology and behavior. Over a century's worth of detailed descriptive studies of Peromyscus in the wild, coupled with emerging genetic and genomic techniques, have now positioned these mice as model organisms for the study of natural variation and adaptation. Recent work, combining field observations and laboratory experiments, has lead to exciting advances in a number of fields-from evolution and genetics, to physiology and neurobiology. PMID:26083802

  16. Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus.

    PubMed

    Chen, Jinhui; Xie, Jianbo; Chen, Beibei; Quan, Mingyang; Li, Ying; Li, Bailian; Zhang, Deqiang

    2016-10-01

    Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus. We used RNA-seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA-target pairs showed significant co-expression. Gene ontology (GO) term analysis showed that most of the genes in the co-regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single-SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA-target pairs associated with the same traits. Multi-SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co-expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis. PMID:27265357

  17. Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus.

    PubMed

    Chen, Jinhui; Xie, Jianbo; Chen, Beibei; Quan, Mingyang; Li, Ying; Li, Bailian; Zhang, Deqiang

    2016-10-01

    Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus. We used RNA-seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA-target pairs showed significant co-expression. Gene ontology (GO) term analysis showed that most of the genes in the co-regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single-SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA-target pairs associated with the same traits. Multi-SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co-expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis.

  18. Nature, nurture and evolution of intra-species variation in mosquito arbovirus transmission competence.

    PubMed

    Tabachnick, Walter J

    2013-01-11

    Mosquitoes vary in their competence or ability to transmit arthropod-borne viruses (arboviruses). Many arboviruses cause disease in humans and animals. Identifying the environmental and genetic causes of variation in mosquito competence for arboviruses is one of the great challenges in public health. Progress identifying genetic (nature) and environmental (nurture) factors influencing mosquito competence for arboviruses is reviewed. There is great complexity in the various traits that comprise mosquito competence. The complex interactions between environmental and genetic factors controlling these traits and the factors shaping variation in Nature are largely unknown. The norms of reaction of specific genes influencing competence, their distributions in natural populations and the effects of genetic polymorphism on phenotypic variation need to be determined. Mechanisms influencing competence are not likely due to natural selection because of the direct effects of the arbovirus on mosquito fitness. More likely the traits for mosquito competence for arboviruses are the effects of adaptations for other functions of these competence mechanisms. Determining these other functions is essential to understand the evolution and distributions of competence for arboviruses. This information is needed to assess risk from mosquito-borne disease, predict new mosquito-arbovirus systems, and provide novel strategies to mitigate mosquito-borne arbovirus transmission.

  19. Permeability damage to natural fractures caused by fracturing fluid polymers

    SciTech Connect

    Gall, B.L.; Sattler, A.R.; Maloney, D.R.; Raible, C.J.

    1988-04-01

    Formation damage studies using artificially fractured, low-permeability sandstone cores indicate that viscosified fracturing fluids can severely restrict gas flow through these types of narrow fractures. These studies were performed in support of the Department of Energy's Multiwell Experiment (MWX). Extensive geological and production evaluations at the MWX site indicate that the presence of a natural fracture system is largely responsible for unstimulated gas production. The laboratory formation damage studies were designed to examine changes in cracked core permeability to gas caused by fracturing fluid residues introduced into such narrow fractures during fluid leakoff. Polysaccharide polymers caused significant reduction (up to 95%) to gas flow through cracked cores. Polymer fracturing fluid gels used in this study included hydroxypropyl guar, hydroxyethyl cellulose, and xanthan gum. In contrast, polyacrylamide gels caused little or no reduction in gas flow through cracked cores after liquid cleanup. Other components of fracturing fluids (surfactants, breakers, etc.) caused less damage to gas flows. Other factors affecting gas flow through cracked cores were investigated, including the effects of net confining stress and non-Darcy flow parameters. Results are related to some of the problems observed during the stimulation program conducted for the MWX. 24 refs., 4 figs., 7 tabs.

  20. Natural causes of the tundra-taiga boundary.

    PubMed

    Sveinbjörnsson, Bjartmar; Hofgaard, Annika; Lloyd, Andrea

    2002-08-01

    The tundra-taiga interface is characterized by a change in tree cover or density, tree size and shape, tree growth, and reproduction. Generally, trees get denser, taller, and less damaged as one moves from the tundra into the taiga proper. The environmental covariates and possible mechanisms resulting in these patterns are addressed in the paper. Low seed rain density, lack of safe sites caused by microclimatic variation, low surface substrate moisture, and low soil nutrient availability may limit the density of the tree species. Tree growth may be limited by a short growing season and further diminished, by shoot and root damage reducing carbon and nutrient stores as well as by reducing carbon and nutrient uptake capacities. Positive and negative feedbacks of tree density on tree growth exist at treeline. Increased tree density leads to increased air temperature and decreased wind damage, but also to lower soil temperature, reduced nutrient availability, and greater nutrient competition.

  1. Natural epigenetic variation in bats and its role in evolution.

    PubMed

    Liu, Sen; Sun, Keping; Jiang, Tinglei; Feng, Jiang

    2015-01-01

    When facing the challenges of environmental change, such as habitat fragmentation, organisms have to adjust their phenotype to adapt to various environmental stresses. Recent studies show that epigenetic modifications could mediate environmentally induced phenotypic variation, and this epigenetic variance could be inherited by future generations, indicating that epigenetic processes have potential evolutionary effects. Bats living in diverse environments show geographic variations in phenotype, and the females usually have natal philopatry, presenting an opportunity to explore how environments shape epigenetic marks on the genome and the evolutionary potential of epigenetic variance in bat populations for adaptation. We have explored the natural epigenetic diversity and structure of female populations of the great roundleaf bat (Hipposideros armiger), the least horseshoe bat (Rhinolophus pusillus) and the eastern bent-winged bat (Miniopterus fuliginosus) using a methylation-sensitive amplified polymorphism technique. We have also estimated the effects of genetic variance and ecological variables on epigenetic diversification. All three bat species have a low level of genomic DNA methylation and extensive epigenetic diversity that exceeds the corresponding genetic variance. DNA sequence divergence, epigenetic drift and environmental variables contribute to the epigenetic diversities of each species. Environment-induced epigenetic variation may be inherited as a result of both mitosis and meiosis, and their potential roles in evolution for bat populations are also discussed in this review.

  2. Distribution of polychaete assemblage in relation to natural environmental variation and anthropogenic stress

    NASA Astrophysics Data System (ADS)

    Zan, Xiaoxiao; Zhang, Chongliang; Xu, Binduo; Xue, Ying; Ren, Yiping

    2015-08-01

    Polychaete are diverse species of the soft-bottom community, and are often used as indicators in environment monitoring programs. However, the effects of anthropogenic activities and natural environmental variation on polychaete assemblage are rarely addressed. The goals of this study are to identify the effects of natural environmental variation and anthropogenic stress on polychaete assemblage, and to explore the relationship between the polychaete assemblage structure and anthropogenic stress without considering the natural environmental variation. Based on the data collected from the surveys conducted in the tidal flat of Jiaozhou Bay, the relationship between polychaete assemblage structure and environmental variables was determined using multivariate statistical methods including hierarchical cluster analysis, multidimensional scaling (MDS) and canonical correspondence analysis (CCA). The results showed that the polychaete assemblage was dominated by two species, Amphictene japonica and Heteromastus filiformis, and could be divided into two subgroups characterized by high and low species abundance. CCA illustrated that the natural environmental variables including water temperature and the distance from coast had primary effects on the polychaete assemblage structure; while stress of contaminants, such as As and Hg, had the secondary influences; and stress from the aquacultured species, mainly Ruditapes philippinarum, had a limited effect. Colinearity between the natural environmental variables and anthropogenic stress variables caused a critical divergence in the interpretation of CCA results, which highlighted the risk of a lack of information in environment assessment. Glycinde gurjanovae, Sternaspis scutata and Eulalia bilineata may serve as the `contamination indicators', which need to be confirmed in future studies.

  3. Natural epigenetic variation in the female great roundleaf bat (Hipposideros armiger) populations.

    PubMed

    Liu, Sen; Sun, Keping; Jiang, Tinglei; Ho, Jennifer P; Liu, Bao; Feng, Jiang

    2012-08-01

    Epigenetic modifications are considered to have an important role in evolution. DNA methylation is one of the best studied epigenetic mechanisms and methylation variability is crucial for promoting phenotypic diversification of organisms in response to environmental variation. A critical first step in the assessment of the potential role of epigenetic variation in evolution is the identification of DNA methylation polymorphisms and their relationship with genetic variations in natural populations. However, empirical data is scant in animals, and particularly so in wild mammals. Bats are considered as bioindicators because of their sensitivity to environmental perturbations and they may present an opportunity to explore epigenetic variance in wild mammalian populations. Our study is the first to explore these questions in the female great roundleaf bat (Hipposideros armiger) populations using the methylation-sensitive amplified polymorphism (MSAP) technique. We obtained 868 MSAP sites using 18 primer combinations and found (1) a low genomic methylation level (21.3 % on average), but extensive DNA methylation polymorphism (90.2 %) at 5'-CCGG-3' sites; (2) epigenetic variation that is structured into distinct between- (29.8 %) and within- (71.2 %) population components, as does genetic variation; and (3) a significant correlation between epigenetic and genetic variations (P < 0.05). These results may also apply to other wild mammalian populations. The possible causes for the correlation between epigenetic and genetic variations are discussed.

  4. Natural hazards: causes and effects. Lesson 7-Drought.

    PubMed

    Perez, E; Thompson, P

    1996-01-01

    Drought has long been recognized as one of the most insidious causes of human misery. Today, it is the natural disaster that annually claims the most victims. Its ability to cause widespread misery is estimated to be increasing. While generally associated with semiarid climates, drought may occur in areas that normally enjoy adequate rainfall and moisture. In the broadest sense, any lack of water for the normal needs of agriculture, livestock, industry, or human population may be termed as a drought. The cause may be lack of supply, contamination of supply, inadequate storage or conveyance facilities, or abnormal demand. Drought is a condition of climatic dryness severe enough to reduce soil moisture and water below the minimums necessary for sustaining plant, animal, and human life. Drought usually is accompanied by hot, dry winds and may be followed by damaging floods. More socially relevant than technically correct is the definition used by Ari Toubo Eibrahim, the minister of agriculture in Niger, who has said that a drought is "Not as much water as the people need."

  5. Rhythmic TMS Causes Local Entrainment of Natural Oscillatory Signatures

    PubMed Central

    Thut, Gregor; Veniero, Domenica; Romei, Vincenzo; Miniussi, Carlo; Schyns, Philippe; Gross, Joachim

    2011-01-01

    Summary Background Neuronal elements underlying perception, cognition, and action exhibit distinct oscillatory phenomena, measured in humans by electro- or magnetoencephalography (EEG/MEG). So far, the correlative or causal nature of the link between brain oscillations and functions has remained elusive. A compelling demonstration of causality would primarily generate oscillatory signatures that are known to correlate with particular cognitive functions and then assess the behavioral consequences. Here, we provide the first direct evidence for causal entrainment of brain oscillations by transcranial magnetic stimulation (TMS) using concurrent EEG. Results We used rhythmic TMS bursts to directly interact with an MEG-identified parietal α-oscillator, activated by attention and linked to perception. With TMS bursts tuned to its preferred α-frequency (α-TMS), we confirmed the three main predictions of entrainment of a natural oscillator: (1) that α-oscillations are induced during α-TMS (reproducing an oscillatory signature of the stimulated parietal cortex), (2) that there is progressive enhancement of this α-activity (synchronizing the targeted, α-generator to the α-TMS train), and (3) that this depends on the pre-TMS phase of the background α-rhythm (entrainment of natural, ongoing α-oscillations). Control conditions testing different TMS burst profiles and TMS-EEG in a phantom head confirmed specificity of α-boosting to the case of synchronization between TMS train and neural oscillator. Conclusions The periodic electromagnetic force that is generated during rhythmic TMS can cause local entrainment of natural brain oscillations, emulating oscillatory signatures activated by cognitive tasks. This reveals a new mechanism of online TMS action on brain activity and can account for frequency-specific behavioral TMS effects at the level of biologically relevant rhythms. PMID:21723129

  6. The causes of variation in learning and behavior: why individual differences matter.

    PubMed

    Sauce, Bruno; Matzel, Louis D

    2013-01-01

    IN A SEMINAL PAPER WRITTEN FIVE DECADES AGO, CRONBACH DISCUSSED THE TWO HIGHLY DISTINCT APPROACHES TO SCIENTIFIC PSYCHOLOGY: experimental and correlational. Today, although these two approaches are fruitfully implemented and embraced across some fields of psychology, this synergy is largely absent from other areas, such as in the study of learning and behavior. Both Tolman and Hull, in a rare case of agreement, stated that the correlational approach held little promise for the understanding of behavior. Interestingly, this dismissal of the study of individual differences was absent in the biologically oriented branches of behavior analysis, namely, behavioral genetics and ethology. Here we propose that the distinction between "causation" and "causes of variation" (with its origins in the field of genetics) reveals the potential value of the correlational approach in understanding the full complexity of learning and behavior. Although the experimental approach can illuminate the causal variables that modulate learning, the analysis of individual differences can elucidate how much and in which way variables interact to support variations in learning in complex natural environments. For example, understanding that a past experience with a stimulus influences its "associability" provides little insight into how individual predispositions interact to modulate this influence on associability. In this "new" light, we discuss examples from studies of individual differences in animals' performance in the Morris water maze and from our own work on individual differences in general intelligence in mice. These studies illustrate that, opposed to what Underwood famously suggested, studies of individual differences can do much more to psychology than merely providing preliminary indications of cause-effect relationships. PMID:23847569

  7. Impact of natural genetic variation on gene expression dynamics.

    PubMed

    Ackermann, Marit; Sikora-Wohlfeld, Weronika; Beyer, Andreas

    2013-06-01

    DNA sequence variation causes changes in gene expression, which in turn has profound effects on cellular states. These variations affect tissue development and may ultimately lead to pathological phenotypes. A genetic locus containing a sequence variation that affects gene expression is called an "expression quantitative trait locus" (eQTL). Whereas the impact of cellular context on expression levels in general is well established, a lot less is known about the cell-state specificity of eQTL. Previous studies differed with respect to how "dynamic eQTL" were defined. Here, we propose a unified framework distinguishing static, conditional and dynamic eQTL and suggest strategies for mapping these eQTL classes. Further, we introduce a new approach to simultaneously infer eQTL from different cell types. By using murine mRNA expression data from four stages of hematopoiesis and 14 related cellular traits, we demonstrate that static, conditional and dynamic eQTL, although derived from the same expression data, represent functionally distinct types of eQTL. While static eQTL affect generic cellular processes, non-static eQTL are more often involved in hematopoiesis and immune response. Our analysis revealed substantial effects of individual genetic variation on cell type-specific expression regulation. Among a total number of 3,941 eQTL we detected 2,729 static eQTL, 1,187 eQTL were conditionally active in one or several cell types, and 70 eQTL affected expression changes during cell type transitions. We also found evidence for feedback control mechanisms reverting the effect of an eQTL specifically in certain cell types. Loci correlated with hematological traits were enriched for conditional eQTL, thus, demonstrating the importance of conditional eQTL for understanding molecular mechanisms underlying physiological trait variation. The classification proposed here has the potential to streamline and unify future analysis of conditional and dynamic eQTL as well as many

  8. Regional variations in burnout rates in a natural resources agency.

    PubMed

    Ihrke, Douglas M; Johnson, Theresa L

    2002-01-01

    This study explores employee burnout within and across the four administrative regions of the Natural Resource Conservation Service (NRCS) based on the hypothesis that burnout levels will vary systematically with workload levels. Approximately 1100 District Conservationists (DCs), the front-line operating officers of the NRCS, were surveyed. Results indicate significant variation in workload and burnout levels but no significant association between these two variables within and across regions. Further analysis revealed that a number of important variables help to explain burnout across regions including job design, functional unit cooperation, and adequate staffing. Within regions, the variables that explain burnout are under the categories of leadership, job design, human resource systems, and agency policy. The authors make use of the research findings to develop a set of organization development (OD) recommendations to help the agency deal with burnout within and across regions.

  9. The global tobacco disease pandemic: nature, causes, and cures.

    PubMed

    Warner, K E; Mackay, J

    2006-01-01

    Tobacco use kills 5 million citizens globally every year. The World Health Organization (WHO) projects that the number of deaths will double just 15 years from now. Tobacco will then constitute the leading cause of death in the developing world, as it already is in developed countries today. This paper describes the nature and extent of the tobacco pandemic, characteristics of the global tobacco industry, and national and international efforts to diminish the toll of tobacco. The review includes examination of the economic and political strategies employed by the multinational tobacco industry to increase cigarette consumption, as well as the policies that governments have adopted to combat smoking. The most promising development is the new Framework Convention on Tobacco Control, WHO's first-ever international health treaty. While aggressive tobacco control policies can and will diminish the toll of tobacco, the prospects for the foreseeable future appear grim. PMID:19153895

  10. The global tobacco disease pandemic: nature, causes, and cures.

    PubMed

    Warner, K E; Mackay, J

    2006-01-01

    Tobacco use kills 5 million citizens globally every year. The World Health Organization (WHO) projects that the number of deaths will double just 15 years from now. Tobacco will then constitute the leading cause of death in the developing world, as it already is in developed countries today. This paper describes the nature and extent of the tobacco pandemic, characteristics of the global tobacco industry, and national and international efforts to diminish the toll of tobacco. The review includes examination of the economic and political strategies employed by the multinational tobacco industry to increase cigarette consumption, as well as the policies that governments have adopted to combat smoking. The most promising development is the new Framework Convention on Tobacco Control, WHO's first-ever international health treaty. While aggressive tobacco control policies can and will diminish the toll of tobacco, the prospects for the foreseeable future appear grim.

  11. FRIGIDA-Independent Variation in Flowering Time of Natural Arabidopsis thaliana Accessions

    PubMed Central

    Werner, Jonathan D.; Borevitz, Justin O.; Uhlenhaut, N. Henriette; Ecker, Joseph R.; Chory, Joanne; Weigel, Detlef

    2005-01-01

    FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) are two genes that, unless plants are vernalized, greatly delay flowering time in Arabidopsis thaliana. Natural loss-of-function mutations in FRI cause the early flowering growth habits of many A. thaliana accessions. To quantify the variation among wild accessions due to FRI, and to identify additional genetic loci in wild accessions that influence flowering time, we surveyed the flowering times of 145 accessions in long-day photoperiods, with and without a 30-day vernalization treatment, and genotyped them for two common natural lesions in FRI. FRI is disrupted in at least 84 of the accessions, accounting for only ∼40% of the flowering-time variation in long days. During efforts to dissect the causes for variation that are independent of known dysfunctional FRI alleles, we found new loss-of-function alleles in FLC, as well as late-flowering alleles that do not map to FRI or FLC. An FLC nonsense mutation was found in the early flowering Van-0 accession, which has otherwise functional FRI. In contrast, Lz-0 flowers late because of high levels of FLC expression, even though it has a deletion in FRI. Finally, eXtreme array mapping identified genomic regions linked to the vernalization-independent, late-flowering habit of Bur-0, which has an alternatively spliced FLC allele that behaves as a null allele. PMID:15911588

  12. Extensive Natural Variation in Arabidopsis Seed Mucilage Structure

    PubMed Central

    Voiniciuc, Cătălin; Zimmermann, Eva; Schmidt, Maximilian Heinrich-Wilhelm; Günl, Markus; Fu, Lanbao; North, Helen M.; Usadel, Björn

    2016-01-01

    Hydrated Arabidopsis thaliana seeds are coated by a gelatinous layer called mucilage, which is mainly composed of cell wall polysaccharides. Since mucilage is rich in pectin, its architecture can be visualized with the ruthenium red (RR) dye. We screened the seeds of around 280 Arabidopsis natural accessions for variation in mucilage structure, and identified a large number of novel variants that differed from the Col-0 wild-type. Most of the accessions released smaller RR-stained capsules compared to the Col-0 reference. By biochemically characterizing the phenotypes of 25 of these accessions in greater detail, we discovered that distinct changes in polysaccharide structure resulted in gelatinous coatings with a deceptively similar appearance. Monosaccharide composition analysis of total mucilage extracts revealed a remarkable variation (from 50 to 200% of Col-0 levels) in the content of galactose and mannose, which are important subunits of heteromannan. In addition, most of the natural variants had altered Pontamine Fast Scarlet 4B staining of cellulose and significantly reduced birefringence of crystalline structures. This indicates that the production or organization of cellulose may be affected by the presence of different amounts of hemicellulose. Although, the accessions described in this study were primarily collected from Western Europe, they form five different phenotypic classes based on the combined results of our experiments. This suggests that polymorphisms at multiple loci are likely responsible for the observed mucilage structure. The transcription of MUCILAGE-RELATED10 (MUCI10), which encodes a key enzyme for galactoglucomannan synthesis, was severely reduced in multiple variants that phenocopied the muci10-1 insertion mutant. Although, we could not pinpoint any causal polymorphisms in this gene, constitutive expression of fluorescently-tagged MUCI10 proteins complemented the mucilage defects of a muci10-like accession. This leads us to

  13. Natural and anthropogenic variations in methane sources during the past two millennia.

    PubMed

    Sapart, C J; Monteil, G; Prokopiou, M; van de Wal, R S W; Kaplan, J O; Sperlich, P; Krumhardt, K M; van der Veen, C; Houweling, S; Krol, M C; Blunier, T; Sowers, T; Martinerie, P; Witrant, E; Dahl-Jensen, D; Röckmann, T

    2012-10-01

    Methane is an important greenhouse gas that is emitted from multiple natural and anthropogenic sources. Atmospheric methane concentrations have varied on a number of timescales in the past, but what has caused these variations is not always well understood. The different sources and sinks of methane have specific isotopic signatures, and the isotopic composition of methane can therefore help to identify the environmental drivers of variations in atmospheric methane concentrations. Here we present high-resolution carbon isotope data (δ(13)C content) for methane from two ice cores from Greenland for the past two millennia. We find that the δ(13)C content underwent pronounced centennial-scale variations between 100 BC and AD 1600. With the help of two-box model calculations, we show that the centennial-scale variations in isotope ratios can be attributed to changes in pyrogenic and biogenic sources. We find correlations between these source changes and both natural climate variability--such as the Medieval Climate Anomaly and the Little Ice Age--and changes in human population and land use, such as the decline of the Roman empire and the Han dynasty, and the population expansion during the medieval period.

  14. Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.

    PubMed

    Lasky, Jesse R; Des Marais, David L; Lowry, David B; Povolotskaya, Inna; McKay, John K; Richards, James H; Keitt, Timothy H; Juenger, Thomas E

    2014-09-01

    Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients.

  15. Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

    PubMed Central

    Lasky, Jesse R.; Des Marais, David L.; Lowry, David B.; Povolotskaya, Inna; McKay, John K.; Richards, James H.; Keitt, Timothy H.; Juenger, Thomas E.

    2014-01-01

    Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, “eSR”) to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, “eGEI”). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients. PMID:24850899

  16. Natural and anthropogenic variations in methane sources during the past two millennia.

    PubMed

    Sapart, C J; Monteil, G; Prokopiou, M; van de Wal, R S W; Kaplan, J O; Sperlich, P; Krumhardt, K M; van der Veen, C; Houweling, S; Krol, M C; Blunier, T; Sowers, T; Martinerie, P; Witrant, E; Dahl-Jensen, D; Röckmann, T

    2012-10-01

    Methane is an important greenhouse gas that is emitted from multiple natural and anthropogenic sources. Atmospheric methane concentrations have varied on a number of timescales in the past, but what has caused these variations is not always well understood. The different sources and sinks of methane have specific isotopic signatures, and the isotopic composition of methane can therefore help to identify the environmental drivers of variations in atmospheric methane concentrations. Here we present high-resolution carbon isotope data (δ(13)C content) for methane from two ice cores from Greenland for the past two millennia. We find that the δ(13)C content underwent pronounced centennial-scale variations between 100 BC and AD 1600. With the help of two-box model calculations, we show that the centennial-scale variations in isotope ratios can be attributed to changes in pyrogenic and biogenic sources. We find correlations between these source changes and both natural climate variability--such as the Medieval Climate Anomaly and the Little Ice Age--and changes in human population and land use, such as the decline of the Roman empire and the Han dynasty, and the population expansion during the medieval period. PMID:23038470

  17. How natural infection by Nosema ceranae causes honeybee colony collapse.

    PubMed

    Higes, Mariano; Martín-Hernández, Raquel; Botías, Cristina; Bailón, Encarna Garrido; González-Porto, Amelia V; Barrios, Laura; Del Nozal, M Jesús; Bernal, José L; Jiménez, Juan J; Palencia, Pilar García; Meana, Aránzazu

    2008-10-01

    In recent years, honeybees (Apis mellifera) have been strangely disappearing from their hives, and strong colonies have suddenly become weak and died. The precise aetiology underlying the disappearance of the bees remains a mystery. However, during the same period, Nosema ceranae, a microsporidium of the Asian bee Apis cerana, seems to have colonized A. mellifera, and it's now frequently detected all over the world in both healthy and weak honeybee colonies. For first time, we show that natural N. ceranae infection can cause the sudden collapse of bee colonies, establishing a direct correlation between N. ceranae infection and the death of honeybee colonies under field conditions. Signs of colony weakness were not evident until the queen could no longer replace the loss of the infected bees. The long asymptomatic incubation period can explain the absence of evident symptoms prior to colony collapse. Furthermore, our results demonstrate that healthy colonies near to an infected one can also become infected, and that N. ceranae infection can be controlled with a specific antibiotic, fumagillin. Moreover, the administration of 120 mg of fumagillin has proven to eliminate the infection, but it cannot avoid reinfection after 6 months. We provide Koch's postulates between N. ceranae infection and a syndrome with a long incubation period involving continuous death of adult bees, non-stop brood rearing by the bees and colony loss in winter or early spring despite the presence of sufficient remaining pollen and honey.

  18. Regional Variation in Causes of Injuries among Terrorism Victims for Mass Casualty Events

    PubMed Central

    Regens, James L.; Schultheiss, Amy; Mould, Nick

    2015-01-01

    The efficient allocation of medical resources to prepare for and respond to mass casualty events (MCEs) attributable to intentional acts of terrorism is a major challenge confronting disaster planners and emergency personnel. This research article examines variation in regional patterns in the causes of injures associated with 77,258 successful terrorist attacks that occurred between 1970 and 2013 involving the use of explosives, firearms, and/or incendiaries. The objective of this research is to estimate regional variation in the use of different conventional weapons in successful terrorist attacks in each world region on variation in injury cause distributions. Indeed, we find that the distributions of the number of injuries attributable to specific weapons types (i.e., by cause) vary greatly among the 13 world regions identified within the Global Terrorism Database. PMID:26347857

  19. Regional Variation in Causes of Injuries among Terrorism Victims for Mass Casualty Events.

    PubMed

    Regens, James L; Schultheiss, Amy; Mould, Nick

    2015-01-01

    The efficient allocation of medical resources to prepare for and respond to mass casualty events (MCEs) attributable to intentional acts of terrorism is a major challenge confronting disaster planners and emergency personnel. This research article examines variation in regional patterns in the causes of injures associated with 77,258 successful terrorist attacks that occurred between 1970 and 2013 involving the use of explosives, firearms, and/or incendiaries. The objective of this research is to estimate regional variation in the use of different conventional weapons in successful terrorist attacks in each world region on variation in injury cause distributions. Indeed, we find that the distributions of the number of injuries attributable to specific weapons types (i.e., by cause) vary greatly among the 13 world regions identified within the Global Terrorism Database.

  20. Causes and consequences of intra-specific variation in vertebral number

    PubMed Central

    Tibblin, Petter; Berggren, Hanna; Nordahl, Oscar; Larsson, Per; Forsman, Anders

    2016-01-01

    Intraspecific variation in vertebral number is taxonomically widespread. Much scientific attention has been directed towards understanding patterns of variation in vertebral number among individuals and between populations, particularly across large spatial scales and in structured environments. However, the relative role of genes, plasticity, selection, and drift as drivers of individual variation and population differentiation remains unknown for most systems. Here, we report on patterns, causes and consequences of variation in vertebral number among and within sympatric subpopulations of pike (Esox lucius). Vertebral number differed among subpopulations, and common garden experiments indicated that this reflected genetic differences. A QST-FST comparison suggested that population differences represented local adaptations driven by divergent selection. Associations with fitness traits further indicated that vertebral counts were influenced both by stabilizing and directional selection within populations. Overall, our study enhances the understanding of adaptive variation, which is critical for the maintenance of intraspecific diversity and species conservation. PMID:27210072

  1. Natural variation in chemosensation: lessons from an island nematode.

    PubMed

    McGaughran, Angela; Morgan, Katy; Sommer, Ralf J

    2013-12-01

    All organisms must interact with their environment, responding in behavioral, chemical, and other ways to various stimuli throughout their life cycles. Characterizing traits that directly represent an organism's ability to sense and react to their environment provides useful insight into the evolution of life-history strategies. One such trait for the nematode Pristionchus pacificus, chemosensation, is involved in navigation to beetle hosts. Essential for the survival of the nematode, chemosensory behavior may be subject to variation as nematodes discriminate among chemical cues to complete their life cycle. We examine this hypothesis using natural isolates of P. pacificus from La Réunion Island. We select strains from a variety of La Réunion beetle hosts and geographic locations and examine their chemoattraction response toward organic compounds, beetle washes, and live beetles. We find that nematodes show significant differences in their response to various chemicals and are able to chemotax to live beetles in a novel assay. Further, strains can discriminate among different cues, showing more similar responses toward beetle washes than to organic compounds in cluster analyses. However, we find that variance in chemoattraction response is not significantly associated with temperature, location, or beetle host. Rather, strains show a more concerted response toward compounds they most likely directly encounter in the wild. We suggest that divergence in odor-guided behavior in P. pacificus may therefore have an important ecological component. PMID:24455150

  2. A subalpine forb's response to natural and experimental climate variation

    NASA Astrophysics Data System (ADS)

    Panetta, A. M.; Harte, J.; Stanton, M.

    2010-12-01

    In light of both molecular and ecological evidence that evolutionary change can happen over short time scales, many now acknowledge that adaptation could play an important role in species-level responses to climate change. Working out of the Rocky Mountain Biological Laboratory (RMBL) (http://www.rmbl.org/rockymountainbiolab/), we test the hypothesis that adaptation plays a role in a montane forb’s response to both experimental warming and climatic variation across elevations. Our focal organism, Androsace septentrionalis (Primulaceae, Figure 1), is a locally abundant, short-lived, highly selfing forb that spans a natural elevation gradient of 2500m to 4811m. Our study sites include six populations, two at high (3733m), mid (3186m), and low (2933) elevation sites. One of our mid-elevation populations is located in RMBL’s Warming Meadow, a series of five heated and five control plots. Since 1991, the Warming Meadow has yielded control and heated plot data on vegetation productivity, phenology, community structure, soil microclimate, and biogeochemistry. Over the past three years, we have marked, monitored, and collected seed from A. septentrionalis across both warmed and natural field sites. Here, we highlight how A. septentrionalis’ life history, morphology, and phenology vary across high, mid and low elevation, and we discuss how these results inform our hypotheses about adaptation in response to experimental warming. We also document the effects of twenty years of experimental warming on A. septentrionalis abundance, distribution, phenology, and fitness. Finally, we discuss two ongoing experiments that will help us determine: 1) how selection varies across heated and control plots and across moisture gradients within each plot: 2) whether or not we can detect adaptation in response to twenty years of experimental warming: and 3) what roles are played by plastic and genetic responses to different climatic regimes. By combining the cumulative results of a

  3. Comparative genomics reveals multiple causes of variation in mycotoxin production among Fusarium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Collectively, species of Fusarium produce a structurally diverse array of mycotoxins and other secondary metabolites (SMs), but individual species contribute to only a fraction of this diversity. To elucidate causes of variation in SM production among species, we are examining the distribution and e...

  4. Associations between DNA Sequence Variation and Variation in Expression of the Adh Gene in Natural Populations of Drosophila Melanogaster

    PubMed Central

    Laurie, C. C.; Bridgham, J. T.; Choudhary, M.

    1991-01-01

    A large part of the genetic variation in alcohol dehydrogenase (ADH) activity level in natural populations of Drosophila melanogaster is associated with segregation of an amino acid replacement polymorphism at nucleotide 1490, which generates a difference in electrophoretic mobility. Part of the allozymic difference in activity level is due to a catalytic efficiency difference, which is also caused by the amino acid replacement, and part is due to a difference in the concentration of ADH protein. A previous site-directed in vitro mutagenesis experiment clearly demonstrated that the amino acid replacement has no effect on the concentration of ADH protein, nor does a strongly associated silent polymorphism at nucleotide 1443. Here we analyze associations between polymorphisms within the Adh gene and variation in ADH protein level for a number of chromosomes derived from natural populations. A sequence length polymorphism within the first intron of the distal (adult) transcript, &1, is in strong linkage disequilibrium with the amino acid replacement. Among a sample of 46 isochromosomal lines analyzed, all but one of the 14 Fast lines have &1 and all but one of the 32 Slow lines lack &1. The exceptional Fast line has an unusually low level of ADH protein (typical of Slow lines) and the exceptional Slow line has an unusually high level (typical of Fast lines). These results suggest that the &1 polymorphism may be responsible for the average difference in ADH protein between the allozymic classes. A previous experiment localized the effect on ADH protein to a 2.3-kb restriction fragment. DNA sequences of this fragment from several alleles of each allozymic type indicate that no other polymorphisms within this region are as closely associated with the ADH protein level difference as the &1 polymorphism. PMID:1683848

  5. Natural Attributes and Agricultural Implications of Somatic Genome Variation.

    PubMed

    Li, Xiu-Qing

    2016-01-01

    This article proposes the concept of genome network, describes different variations of the somatic genome network, and reviews the agricultural implications of such variations. All genetic materials in a cell constitute the genome network of the cell and can jointly influence the cell's function and fate. The somatic genome of a plant is the genome network of cells in somatic tissues and of nonreproductive cells in pollen and ovules. Somatic genome variation (SGV, approximately equivalent to somagenetic variation) occurs at multiple levels, including stoichiometric, ploidy, and sequence variations. For a multicellular organism, the term "somatic genome variation" covers both the variation in part of the organism and the generation of new genotype individuals through somatic means from a sexually produced original genotype. For unicellular organisms, genome variation in somatic nuclei occurs at the whole organism level because there is only a single cell per individual. Growth, development and evolution of living organisms require both stability and instability of their genomes. Somatic genome variation displays many more attributes than genetic mutation and has strong implications for agriculture. PMID:26636317

  6. A joint history of the nature of genetic variation and the nature of schizophrenia.

    PubMed

    Kendler, K S

    2015-02-01

    This essay traces the history of concepts of genetic variation and schizophrenia from Darwin and Mendel to the present. For Darwin, the important form of genetic variation for evolution is continuous in nature and small in effect. Biometricians led by Pearson agreed and developed statistical genetic approaches utilizing trait correlations in relatives. Mendel studied discontinuous traits and subsequent Mendelians, led by Bateson, assumed that important genetic variation was large in effect producing discontinuous phenotypes. Although biometricians studied 'insanity', schizophrenia genetics under Kraepelin and Rüdin utilized Mendelian approaches congruent with their anatomical-clinical disease model of dementia praecox. Fisher showed, assuming many genes of small effect, Mendelian and Biometrical models were consilient. Echoing prior conflicts, psychiatric genetics since then has utilized both biometrical models, largely in twins, and Mendelian models, based on advancing molecular techniques. In 1968, Gottesman proposed a polygenic model for schizophrenia based on a threshold version of Fisher's theory. Since then, rigorous studies of the schizophrenia spectrum suggest that genetic risk for schizophrenia is more likely continuous than categorical. The last 5 years has seen increasingly convincing evidence from genome-wide association study (GWAS) and sequencing that genetic risk for schizophrenia is largely polygenic, and congruent with Fisher's and Gottesman's models. The gap between biometrical and molecular Mendelian models for schizophrenia has largely closed. The efforts to ground a categorical biomedical model of schizophrenia in Mendelian genetics have failed. The genetic risk for schizophrenia is widely distributed in human populations so that we all carry some degree of risk.

  7. Satellite-based studies of maize yield spatial variations and their causes in China

    NASA Astrophysics Data System (ADS)

    Zhao, Y.

    2013-12-01

    Maize production in China has been expanding significantly in the past two decades, but yield has become relatively stagnant in the past few years, and needs to be improved to meet increasing demand. Multiple studies found that the gap between potential and actual yield of maize is as large as 40% to 60% of yield potential. Although a few major causes of yield gap have been qualitatively identified with surveys, there has not been spatial analysis aimed at quantifying relative importance of specific biophysical and socio-economic causes, information which would be useful for targeting interventions. This study analyzes the causes of yield variation at field and village level in Quzhou county of North China Plain (NCP). We combine remote sensing and crop modeling to estimate yields in 2009-2012, and identify fields that are consistently high or low yielding. To establish the relationship between yield and potential factors, we gather data on those factors through a household survey. We select targeted survey fields such that not only both extremes of yield distribution but also all soil texture categories in the county is covered. Our survey assesses management and biophysical factors as well as social factors such as farmers' access to agronomic knowledge, which is approximated by distance to the closest demonstration plot or 'Science and technology backyard'. Our survey covers 10 townships, 53 villages and 180 fields. Three to ten farmers are surveyed depending on the amount of variation present among sub pixels of each field. According to survey results, we extract the amount of variation within as well as between villages and or soil type. The higher within village or within field variation, the higher importance of management factors. Factors such as soil type and access to knowledge are more represented by between village variation. Through regression and analysis of variance, we gain more quantitative and thorough understanding of causes to yield variation at

  8. Natural Variation and Copulatory Plug Formation in Caenorhabditis Elegans

    PubMed Central

    Hodgkin, J.; Doniach, T.

    1997-01-01

    Most of the available natural isolates of the nematode Caenorhabditis elegans have been examined and compared with the standard laboratory wild type (Bristol N2). Molecular markers, in particular transposon restriction fragment length polymorphisms, were used to assign these isolates to 22 different races, for which brood size and spontaneous male frequency were determined. Several distinctive traits were observed in some of these races. One example is mab-23, in a race from Vancouver, which leads to severe distortion of male genitalia and prevents male mating. Another is gro-1, segregating in a Californian race, which is associated with slow growth, heat resistance and longevity. Many races differ from N2 in carrying a dominant allele at the plg-1 locus, causing copulatory plug formation by males. Properties and possible advantages of the plugging trait have been investigated. The dominant plg-1 allele does not lead to increased male mating efficiency, but males from a Stanford race (CB4855), in which the plugging trait was first observed, are much more virile than N2 males. Crosses between N2 and CB4855 indicate that the higher virility is due to multiple factors. Size differences between N2 and CB4855 are associated with factors mapping to LGV and LGX. PMID:9136008

  9. Temporal variation of frictional strength in an earthquake swarm in NE Japan caused by fluid migration

    NASA Astrophysics Data System (ADS)

    Yoshida, Keisuke; Hasegawa, Akira; Yoshida, Takeyoshi

    2016-08-01

    Temporal variations of the fault frictional strength was investigated based on the diversity of focal mechanisms in the source area of the Yamagata-Fukushima border earthquake swarm, a significant earthquake swarm that occurred in central Tohoku, NE Japan, which started just after the 2011 M9.0 Tohoku-Oki earthquake. The focal mechanisms of events in this swarm activity were determined using P wave polarity data as well as short-period (1.5-2.5 Hz) waveform data from the direct P wave. The stress field in the source area of this swarm was estimated by applying stress tensor inversions to these focal mechanism data. Based on the estimated stress field, and under the assumption of uniform stress, we calculated relative frictional strengths for individual focal mechanisms. The calculated relative frictional strengths vary over a wide range, but their average value exhibits a characteristic temporal variation, which is at first small, but steadily increases with time for 100 to 150 days, and then becomes approximately constant. We confirmed this characteristic temporal variation of the average relative frictional strength by assuming the stress to be nonuniform. Similar temporal variations of the average relative frictional strength are obtained for even these cases, confirming the variation. The most likely cause for the observed temporal variation of the average relative frictional strength is the temporal variation of the pore fluid pressure in the source area of the swarm, facilitated by the Tohoku-Oki earthquake and the subsequent fluid diffusion.

  10. Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster.

    PubMed

    Jiang, Pengyao; Ludwig, Michael Z; Kreitman, Martin; Reinitz, John

    2015-09-01

    The evolution of canalized traits is a central question in evolutionary biology. Natural variation in highly conserved traits can provide clues about their evolutionary potential. Here we investigate natural variation in a conserved trait-even-skipped (eve) expression at the cellular blastoderm stage of embryonic development in Drosophila melanogaster. Expression of the pair-rule gene eve was quantitatively measured in three inbred lines derived from a natural population of D. melanogaster. One line showed marked differences in the spacing, amplitude and timing of formation of the characteristic seven-striped pattern over a 50-min period prior to the onset of gastrulation. Stripe 5 amplitude and the width of the interstripe between stripes 4 and 5 were both reduced in this line, while the interstripe distance between stripes 3 and 4 was increased. Engrailed expression in stage 10 embryos revealed a statistically significant increase in the length of parasegment 6 and a decrease in the length of parasegments 8 and 9. These changes are larger than those previously reported between D. melanogaster and D. pseudoobscura, two species that are thought to have diverged from a common ancestor over 25 million years ago. This line harbors a rare 448 bp deletion in the first intron of knirps (kni). This finding suggested that reduced Kni levels caused the deviant eve expression, and indeed we observed lower levels of Kni protein at early cycle 14A in L2 compared to the other two lines. A second of the three lines displayed an approximately 20% greater level of expression for all seven eve stripes. The three lines are each viable and fertile, and none display a segmentation defect as adults, suggesting that early-acting variation in eve expression is ameliorated by developmental buffering mechanisms acting later in development. Canalization of the segmentation pathway may reduce the fitness consequences of genetic variation, thus allowing the persistence of mutations with

  11. Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways.

    PubMed

    Singh, Kapil Dev; Roschitzki, Bernd; Snoek, L Basten; Grossmann, Jonas; Zheng, Xue; Elvin, Mark; Kamkina, Polina; Schrimpf, Sabine P; Poulin, Gino B; Kammenga, Jan E; Hengartner, Michael O

    2016-01-01

    Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch, and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains N2 (Bristol) and CB4856 (Hawaii) to enable quantitative trait locus (QTL) mapping. About half of the cases from the 44 genes tested showed a statistically significant change in protein abundance between various strains, most of these were however very weak (below 1.3-fold change). We detected a distant QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels. PMID:26985669

  12. Nature of Random Variation in the Nutrient Composition of Meals

    PubMed Central

    Balintfy, Joseph L.; Prekopa, Andras

    1966-01-01

    The mathematical formulation of nutrient variation in meals in presented by means of random vectors. The primary sources of nutrient variation in unit portions of menu items are identified and expressed in terms of random food-nutrient, random portion size and random ingredient composition variations. A secondary source of nutrient variation can be traced to the random selection process of combining menu items into individual meals from multiple choice menus. The separate as well as the joint effect of these sources on the total variation of the nutrient content of meals is described with the aid of variance-covariance matrices. The investigation is concluded with the formulation of multivariate probability statements concerning the adequacy of the nutrient content of meals relative to the distribution of the nutrient requirements over a given population. PMID:5971545

  13. Natural variation in the temperature range permissive for vernalization in accessions of Arabidopsis thaliana.

    PubMed

    Wollenberg, Amanda C; Amasino, Richard M

    2012-12-01

    Vernalization is an acceleration of flowering in response to chilling, and is normally studied in the laboratory at near-freezing (2-4 °C) temperatures. Many vernalization-requiring species, such as Arabidopsis thaliana, are found in a range of habitats with varying winter temperatures. Natural variation in the temperature range that elicits a vernalization response in Arabidopsis has not been fully explored. We characterized the effect of intermediate temperatures (7-19 °C) on 15 accessions and the well-studied reference line Col-FRI. Although progressively warmer temperatures are gradually less effective at activating expression of the vernalization-specific gene VERNALIZATION-INSENSITIVE 3 (VIN3) and in accelerating flowering, there is substantial natural variation in the upper threshold (T(max) ) of the flowering-time response. VIN3 is required for the T(max) (13 °C) response of Col-FRI. Surprisingly, even 16 °C treatment caused induction of VIN3 in six tested lines, despite the ineffectiveness of this temperature in accelerating flowering for two of them. Finally, we present evidence that mild acceleration of flowering by 19 °C exposure may counterbalance the flowering time delay caused by non-inductive photoperiods in at least one accession, creating an appearance of photoperiod insensitivity.

  14. Regional variation of natural peatland pool biogeochemistry and carbon concentrations

    NASA Astrophysics Data System (ADS)

    Turner, Ed; Billett, Mike; Chapman, Pippa; Baird, Andy; Dinsmore, Kerry; Holden, Joseph

    2015-04-01

    Natural open-water pools are a common feature of northern peatlands. They are characterised by low primary production, low pH, and often high concentrations of dissolved organic carbon (DOC). Peatland pools are also sources of atmospheric CH4, and thus have the potential to play an important role in global radiative forcing. Pool environmental variables, particularly water chemistry, vegetation community and physical characteristics, have the potential to exert strong controls on C cycling in pools; however, to our knowledge, no existing studies have addressed the potential variation in pool biogeochemistry and physical characteristics on a regional basis. A total of 66 peatland pools were studied across three regions of the UK (northern Scotland, south-west Scotland, and Northern Ireland) over the period September - October 2013. Vegetation communities, mean depth and basic water chemistry (pH, electrical conductivity and dissolved oxygen) were measured in situ. Water samples were taken for analysis of DOC, POC, DIC, CH4diss, CO2diss(dissolved CO2 and CH4),total N and P, and Cl-, SO42- and NO3-. To evaluate the composition of DOC, UV absorption was measured at 665, 470, 465, 436, 400, 360, 265, 254 nm. We show that many pool variables are significantly different between regions, including DOC, POC and CH4diss. The higher ratio of absorbance at 465 to absorbance at 665nm (E4/E6) for pools in Northern Ireland indicates DOC was sourced from less humified peat, which has implications for the bioavailability and mineralisation of organic carbon. Anion concentrations were significantly higher in the pools in northern Scotland than elsewhere, most likely due to a marine influence. SO42- is a CH4 electron acceptor and thus concentrations may influence methanogenesis. Hierarchical cluster analysis shows clear grouping of the individual pools within each region. PCA analysis showed that pools in SW Scotland were strongly associated with greater vegetative cover (Sphagnum

  15. A joint history of the nature of genetic variation and the nature of schizophrenia.

    PubMed

    Kendler, K S

    2015-02-01

    This essay traces the history of concepts of genetic variation and schizophrenia from Darwin and Mendel to the present. For Darwin, the important form of genetic variation for evolution is continuous in nature and small in effect. Biometricians led by Pearson agreed and developed statistical genetic approaches utilizing trait correlations in relatives. Mendel studied discontinuous traits and subsequent Mendelians, led by Bateson, assumed that important genetic variation was large in effect producing discontinuous phenotypes. Although biometricians studied 'insanity', schizophrenia genetics under Kraepelin and Rüdin utilized Mendelian approaches congruent with their anatomical-clinical disease model of dementia praecox. Fisher showed, assuming many genes of small effect, Mendelian and Biometrical models were consilient. Echoing prior conflicts, psychiatric genetics since then has utilized both biometrical models, largely in twins, and Mendelian models, based on advancing molecular techniques. In 1968, Gottesman proposed a polygenic model for schizophrenia based on a threshold version of Fisher's theory. Since then, rigorous studies of the schizophrenia spectrum suggest that genetic risk for schizophrenia is more likely continuous than categorical. The last 5 years has seen increasingly convincing evidence from genome-wide association study (GWAS) and sequencing that genetic risk for schizophrenia is largely polygenic, and congruent with Fisher's and Gottesman's models. The gap between biometrical and molecular Mendelian models for schizophrenia has largely closed. The efforts to ground a categorical biomedical model of schizophrenia in Mendelian genetics have failed. The genetic risk for schizophrenia is widely distributed in human populations so that we all carry some degree of risk. PMID:25134695

  16. Time variations of geopotential, gravity and vertical crustul deformations: nature and unity of cyclicities

    NASA Astrophysics Data System (ADS)

    Barkin, Yu. V.

    2003-04-01

    TIME VARIATIONS OF GEOPOTENTIAL, GRAVITY AND VERTICAL CRUSTAL DEFORMATIONS: NATURE AND UNITY OF CYCLICITIES Yu.V.Barkin Sternberg Astronomical Institute, Moscow, Russia, barkin@sai.msu.ru Gravitational action of the Moon and the Sun on the Earth generates very big additional mechanical forces and moments of the interaction of its neighboring shells (liquid core, mantle and another layers) and produces cyclic perturbations of the tensional state of the shells, their deformations, small relative translational displacements and small relative rotational oscillations of the shells, redistribution of the plastic and fluid masses and others. These additional forces and moments of the cyclic celestial-mechanical nature produce deformations of the all layers of the Earth and organize and control practically all natural processes. In given report we analyze these forces and moments caused by the Moon attraction. We have shown that they are conditionally periodic functions of time with definite basis of frequencies, which are some combinations of the frequencies of perturbations in the Moon orbital motion. Very important conclusion follows from our approach - natural processes are controlled and dictated by pointed mechanism and are subjected by cyclic variations with general for all processes base of frequencies. The fundamental basis of frequencies was established in result of theoretical study of the gravitational interaction of the Earth’s core and mantle with the Moon and the Sun and in result of analysis of observed variations of the many natural processes [1]. Predicted periods of variations of the natural processes were conformed by last results of the spectral analysis of gravity at Moscow fidicial station and by similar studies of the Earth rotation, vertical crustul deformations [2]. In particular periods, amplitudes (in a few microGal) and phases for about 20 harmonics of gravity variations were discovered in result of spectral analysis of the absolute

  17. Individual variation in prey selection by sea otters: Patterns, causes and implications

    USGS Publications Warehouse

    Estes, J.A.; Riedman, M.L.; Staedler, M.M.; Tinker, M.T.; Lyon, B.E.

    2003-01-01

    1. Longitudinal records of prey selection by 10 adult female sea otters on the Monterey Peninsula, California, from 1983 to 1990 demonstrate extreme inter-individual variation in diet. Variation in prey availability cannot explain these differences as the data were obtained from a common spatial-temporal area. 2. Individual dietary patterns persisted throughout our study, thus indicating that they are life-long characteristics. 3. Individual dietary patterns in sea otters appear to be transmitted along matrilines, probably by way of learning during the period of mother-young association. 4. Efficient utilization of different prey types probably requires radically different sensory/motor skills, each of which is difficult to acquire and all of which may exceed the learning and performance capacities of any single individual. This would explain the absence of generalists and inertia against switching, but not the existence of alternative specialists. 5. Such individual variation might arise in a constant environment from frequency-dependent effects, whereby the relative benefit of a given prey specialization depends on the number of other individuals utilizing that prey. Additionally, many of the sea otter's prey fluctuate substantially in abundance through time. This temporal variation, in conjunction with matrilineal transmission of foraging skills, may act to mediate the temporal dynamics of prey specializations. 6. Regardless of the exact cause, such extreme individual variation in diet has broad ramifications for population and community ecology. 7. The published literature indicates that similar patterns occur in many other species.

  18. Metabolic variation in natural populations of wild yeast

    PubMed Central

    Samani, Pedram; Low-Decarie, Etienne; McKelvey, Kyra; Bell, Thomas; Burt, Austin; Koufopanou, Vassiliki; Landry, Christian R; Bell, Graham

    2015-01-01

    Ecological diversification depends on the extent of genetic variation and on the pattern of covariation with respect to ecological opportunities. We investigated the pattern of utilization of carbon substrates in wild populations of budding yeast Saccharomyces paradoxus. All isolates grew well on a core diet of about 10 substrates, and most were also able to grow on a much larger ancillary diet comprising most of the 190 substrates we tested. There was substantial genetic variation within each population for some substrates. We found geographical variation of substrate use at continental, regional, and local scales. Isolates from Europe and North America could be distinguished on the basis of the pattern of yield across substrates. Two geographical races at the North American sites also differed in the pattern of substrate utilization. Substrate utilization patterns were also geographically correlated at local spatial scales. Pairwise genetic correlations between substrates were predominantly positive, reflecting overall variation in metabolic performance, but there was a consistent negative correlation between categories of substrates in two cases: between the core diet and the ancillary diet, and between pentose and hexose sugars. Such negative correlations in the utilization of substrate from different categories may indicate either intrinsic physiological trade-offs for the uptake and utilization of substrates from different categories, or the accumulation of conditionally neutral mutations. Divergence in substrate use accompanies genetic divergence at all spatial scales in S. paradoxus and may contribute to race formation and speciation. PMID:25691993

  19. Segmenting Words from Natural Speech: Subsegmental Variation in Segmental Cues

    ERIC Educational Resources Information Center

    Rytting, C. Anton; Brew, Chris; Fosler-Lussier, Eric

    2010-01-01

    Most computational models of word segmentation are trained and tested on transcripts of speech, rather than the speech itself, and assume that speech is converted into a sequence of symbols prior to word segmentation. We present a way of representing speech corpora that avoids this assumption, and preserves acoustic variation present in speech. We…

  20. Natural Variation in the Thermotolerance of Neural Function and Behavior due to a cGMP-Dependent Protein Kinase

    PubMed Central

    Dawson-Scully, Ken; Armstrong, Gary A.B.; Kent, Clement; Robertson, R. Meldrum; Sokolowski, Marla B.

    2007-01-01

    Although it is acknowledged that genetic variation contributes to individual differences in thermotolerance, the specific genes and pathways involved and how they are modulated by the environment remain poorly understood. We link natural variation in the thermotolerance of neural function and behavior in Drosophila melanogaster to the foraging gene (for, which encodes a cGMP-dependent protein kinase (PKG)) as well as to its downstream target, protein phosphatase 2A (PP2A). Genetic and pharmacological manipulations revealed that reduced PKG (or PP2A) activity caused increased thermotolerance of synaptic transmission at the larval neuromuscular junction. Like synaptic transmission, feeding movements were preserved at higher temperatures in larvae with lower PKG levels. In a comparative assay, pharmacological manipulations altering thermotolerance in a central circuit of Locusta migratoria demonstrated conservation of this neuroprotective pathway. In this circuit, either the inhibition of PKG or PP2A induced robust thermotolerance of neural function. We suggest that PKG and therefore the polymorphism associated with the allelic variation in for may provide populations with natural variation in heat stress tolerance. for's function in behavior is conserved across most organisms, including ants, bees, nematodes, and mammals. PKG's role in thermotolerance may also apply to these and other species. Natural variation in thermotolerance arising from genes involved in the PKG pathway could impact the evolution of thermotolerance in natural populations. PMID:17712421

  1. Changes in antigenic nature of lymphocytes caused by common viruses.

    PubMed

    Thompson, E; Lewis, C M; Pegrum, G D

    1973-12-22

    Healthy human lymphocytes were incubated in the presence of influenza A2/Singapore/57, herpes simplex type 1, or adenovirus type 2. After two days the cultures were inactivated by irradiation. Fresh lymphocytes taken from the same donor were then found to react to the virus-treated cells in short-term cultures. We suggest that this reactivity is due to a change in the surface characteristics of the lymphocytes brought about by the presence of the virus. This may account for anomalous reactions in mixed lymphocyte cultures, and a similar effect in vivo might cause accelerated graft rejection.

  2. Variations of iron flux and organic carbon remineralization in a subterranean estuary caused by interannual variations in recharge

    USGS Publications Warehouse

    Roy, Moutusi; Martin, Jonathan B.; Cable, Jaye E.; Smith, Christopher G.

    2013-01-01

    We determine the inter-annual variations in diagenetic reaction rates of sedimentary iron (Fe ) in an east Florida subterranean estuary and evaluate the connection between metal fluxes and recharge to the coastal aquifer. Over the three-year study period (from 2004 to 2007), the amount of Fe-oxides reduced at the study site decreased from 192 g/yr to 153 g/yr and associated organic carbon (OC) remineralization decreased from 48 g/yr to 38 g/yr. These reductions occurred although the Fe-oxide reduction rates remained constant around 1 mg/cm2/yr. These results suggest that changes in flow rates of submarine groundwater discharge (SGD) related to changes in precipitation may be important to fluxes of the diagenetic reaction products. Rainfall at a weather station approximately 5 km from the field area decreased from 12.6 cm/month to 8.4 cm/month from 2004 to 2007. Monthly potential evapotranspiration (PET) calculated from Thornthwaite’s method indicated potential evapotranspiration cycled from about 3 cm/month in the winter to about 15 cm/month in the summer so that net annual recharge to the aquifer decreased from 40 cm in 2004 to -10 cm in 2007. Simultaneously, with the decrease in recharge of groundwater, freshwater SGD decreased by around 20% and caused the originally 25 m wide freshwater seepage face to decrease in width by about 5 m. The smaller seepage face reduced the area under which Fe-oxides were undergoing reductive dissolution. Consequently, the observed decrease in Fe flux is controlled by hydrology of the subterranean estuary. These results point out the need to better understand linkages between temporal variations in diagenetic reactions and changes in flow within subterranean estuaries in order to accurately constrain their contribution to oceanic fluxes of solutes from subterranean estuaries.

  3. Rare cause of natural death in forensic setting: hemophagocytic syndrome.

    PubMed

    Ondruschka, B; Habeck, J-O; Hädrich, C; Dreßler, J; Bayer, R

    2016-05-01

    We report about the case of a sudden unexpected death of a 25-year-old male suffering from infectious disease. An autopsy was ordered with no final premortem diagnosis. Microscopic and microbiological examination revealed a pneumococcal bronchopneumonia and hemophagocytic lesions in the bone marrow. After integrating clinical and autopsy reports as well as additional postmortem investigations, the cause of death was found to be infectious-triggered hemophagocytic syndrome (HPS) with a final cytokine storm. This seems to be the first reported fatal case of a reactive form of HPS associated to Streptococcus pneumoniae to the best of our knowledge. HPS is a dangerous hyperinflammation with highly characteristic, but nonspecific, laboratory findings and symptoms. Autopsies in such cases must be carefully performed and include systematic tissue sampling done by an experienced pathologist. PMID:26718840

  4. Variation in predator species abundance can cause variable selection pressure on warning signaling prey

    PubMed Central

    Valkonen, Janne K; Nokelainen, Ossi; Niskanen, Martti; Kilpimaa, Janne; Björklund, Mats; Mappes, Johanna

    2012-01-01

    Predation pressure is expected to drive visual warning signals to evolve toward conspicuousness. However, coloration of defended species varies tremendously and can at certain instances be considered as more camouflaged rather than conspicuous. Recent theoretical studies suggest that the variation in signal conspicuousness can be caused by variation (within or between species) in predators' willingness to attack defended prey or by the broadness of the predators' signal generalization. If some of the predator species are capable of coping with the secondary defenses of their prey, selection can favor reduced prey signal conspicuousness via reduced detectability or recognition. In this study, we combine data collected during three large-scale field experiments to assess whether variation in avian predator species (red kite, black kite, common buzzard, short-toed eagle, and booted eagle) affects the predation pressure on warningly and non-warningly colored artificial snakes. Predation pressure varied among locations and interestingly, if common buzzards were abundant, there were disadvantages to snakes possessing warning signaling. Our results indicate that predator community can have important consequences on the evolution of warning signals. Predators that ignore the warning signal and defense can be the key for the maintenance of variation in warning signal architecture and maintenance of inconspicuous signaling. PMID:22957197

  5. Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria.

    PubMed

    Wintermans, Paul C A; Bakker, Peter A H M; Pieterse, Corné M J

    2016-04-01

    The plant growth-promoting rhizobacterium (PGPR) Pseudomonas simiae WCS417r stimulates lateral root formation and increases shoot growth in Arabidopsis thaliana (Arabidopsis). These plant growth-stimulating effects are partly caused by volatile organic compounds (VOCs) produced by the bacterium. Here, we performed a genome-wide association (GWA) study on natural genetic variation in Arabidopsis for the ability to profit from rhizobacteria-mediated plant growth-promotion. To this end, 302 Arabidopsis accessions were tested for root architecture characteristics and shoot fresh weight in response to exposure to WCS417r. Although virtually all Arabidopsis accessions tested responded positively to WCS417r, there was a large variation between accessions in the increase in shoot fresh weight, the extra number of lateral roots formed, and the effect on primary root length. Correlation analyses revealed that the bacterially-mediated increase in shoot fresh weight is related to alterations in root architecture. GWA mapping for WCS417r-stimulated changes in root and shoot growth characteristics revealed 10 genetic loci highly associated with the responsiveness of Arabidopsis to the plant growth-promoting activity of WCS417r. Several of the underlying candidate genes have been implicated in important plant growth-related processes. These results demonstrate that plants possess natural genetic variation for the capacity to profit from the plant growth-promoting function of a beneficial rhizobacterium in their rhizosphere. This knowledge is a promising starting point for sustainable breeding strategies for future crops that are better able to maximize profitable functions from their root microbiome.

  6. Turbulent nature of refractive-index variations in biological tissue

    NASA Astrophysics Data System (ADS)

    Schmitt, J. M.; Kumar, G.

    1996-08-01

    Phase-contrast microscopy shows that the structure of the refractive-index inhomogeneities in a variety of mammalian tissues resembles that of frozen turbulence. Viewed over a range of scales, the spectrum of index variations exhibits a power-law behavior for spatial frequencies spanning at least a decade (5-50 mu m-1 ) and has an outer scale in the range of 4-10 mu m , above which correlations are no longer seen. The observed structure function fits the classical Kolmogorov model of turbulence. These observations are fundamental to understanding light propagation in tissue and may provide clues about how tissues develop and organize.

  7. Local force variations caused by isoelectric impurities: Method of determination from first principles

    NASA Astrophysics Data System (ADS)

    Kunc, K.

    1983-02-01

    It is shown how the variation of lattice dynamical force constants caused by substitutional isoelectronic impurities can be evaluated ab initio. The approach, illustrated on the example of Al in GaAs, is based on local density functional and uses ionic pseudopotentials of Al, Ga, As as the only input; Hellmann-Feynman theorem is applied in order to extract from self-consistent electronic charge densities the forces acting on atoms in periodic patterns in which entire planes of impurities are displaced. The defect-induced variations of inter planar force constants are converted into the inter atomic ones, which can be compared with those determined by phenomenological models from the measured local mode frequencies. A method is presented which allows to account for the effect of relaxation without requiring an explicit determination of the latter. Particular problems resulting from dealing with entire plane of defects are discussed and an estimate for relaxation is given.

  8. Mining and harnessing natural variation - a little MAGIC

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As has been frequently noted, exotic germplasm ( lines unadapted to local conditions) can be sources of very beneficial genes. The trouble is that it's often difficult to identify these genes. We propose an approach in which mutations can be used to uncover useful variants of natural genes....

  9. Natural variation in folate levels among tomato (Solanum lycopersicum) accessions.

    PubMed

    Upadhyaya, Pallawi; Tyagi, Kamal; Sarma, Supriya; Tamboli, Vajir; Sreelakshmi, Yellamaraju; Sharma, Rameshwar

    2017-02-15

    Folate content was estimated in tomato (Solanum lycopersicum) accessions using microbiological assay (MA) and by LC-MS. The MA revealed that in red-ripe fruits folate levels ranged from 4 to 60μg/100g fresh weight. The LC-MS estimation of red-ripe fruits detected three folate forms, 5-CH3-THF, 5-CHO-THF, 5,10-CH(+)THF and folate levels ranged from 14 to 46μg/100g fresh weight. In mature green and red ripe fruit, 5-CH3-THF was the most abundant folate form. Comparison of LC-MS with MA revealed that MA inaccurately estimates folate levels. The accumulation of folate forms and their distribution varied among accessions. The single nucleotide polymorphism was examined in the key genes of the folate pathway to understand its linkage with folate levels. Despite the significant variation in folate levels among tomato accessions, little polymorphism was found in folate biosynthesis genes. Our results indicate that variation in folate level is governed by a more complex regulation at cellular homeostasis level. PMID:27664678

  10. On the Cause of Eastern Equatorial Pacific Ocean T-S Variations Associated with El Nino

    NASA Technical Reports Server (NTRS)

    Wang, Ou; Fukumori, Ichiro; Lee, Tong; Cheng, Benny

    2004-01-01

    The nature of observed variations in temperature-salinity (T-S) relationship between El Nino and non-El Nino years in the pycnocline of the eastern equatorial Pacific Ocean (NINO3 region, 5(deg)S-5(deg)N, 150(deg)W-90(deg)W) is investigated using an ocean general circulation model. The origin of the subject water mass is identified using the adjoint of a simulated passive tracer. The higher salinity during El Nino is attributed to larger convergence of saltier water from the Southern Hemisphere and smaller convergence of fresher water from the Northern Hemisphere.

  11. Reaction wood – a key cause of variation in cell wall recalcitrance in willow

    PubMed Central

    2012-01-01

    Background The recalcitrance of lignocellulosic cell wall biomass to deconstruction varies greatly in angiosperms, yet the source of this variation remains unclear. Here, in eight genotypes of short rotation coppice willow (Salix sp.) variability of the reaction wood (RW) response and the impact of this variation on cell wall recalcitrance to enzymatic saccharification was considered. Results A pot trial was designed to test if the ‘RW response’ varies between willow genotypes and contributes to the differences observed in cell wall recalcitrance to enzymatic saccharification in field-grown trees. Biomass composition was measured via wet chemistry and used with glucose release yields from enzymatic saccharification to determine cell wall recalcitrance. The levels of glucose release found for pot-grown control trees showed no significant correlation with glucose release from mature field-grown trees. However, when a RW phenotype was induced in pot-grown trees, glucose release was strongly correlated with that for mature field-grown trees. Field studies revealed a 5-fold increase in glucose release from a genotype grown at a site exposed to high wind speeds (a potentially high RW inducing environment) when compared with the same genotype grown at a more sheltered site. Conclusions Our findings provide evidence for a new concept concerning variation in the recalcitrance to enzymatic hydrolysis of the stem biomass of different, field-grown willow genotypes (and potentially other angiosperms). Specifically, that genotypic differences in the ability to produce a response to RW inducing conditions (a ‘RW response’) indicate that this RW response is a primary determinant of the variation observed in cell wall glucan accessibility. The identification of the importance of this RW response trait in willows, is likely to be valuable in selective breeding strategies in willow (and other angiosperm) biofuel crops and, with further work to dissect the nature of RW

  12. Monitoring natural and anthropogenic induced variations in water availability across Africa

    NASA Astrophysics Data System (ADS)

    Ahmed, M.; Sultan, M.; Wahr, J. M.; Yan, E.

    2014-12-01

    Africa, the second-driest continent in the world after Australia, is one of the most vulnerable continents to climate change. Understanding the impacts of climatic and anthropogenic factors on Africa's hydrologic systems is vital for the assessment and utilization of Africa's water resources. In this study, we utilize the Gravity Recovery and Climate Experiment (GRACE) and land surface models (LSM; GLDAS and CLM4.5) in conjunction with other readily-available temporal climatic and remote sensing, geological and hydrological datasets for monitoring the spatial and temporal trends in Terrestrial Water Storage (TWS) over a time period of 10 years (01/2003-12/2012) over the African continent and to investigate the nature (e.g., climatic and/or human pressures-related) of, and the controlling factors causing, these variations. Spatial and temporal (i.e., time series analysis) correlations of the trends extracted from GRACE-derived (TWSGRACE) and LSM-derived (TWSLSM) TWS indicate the following: (1) Large (≥ 90 % by area) sectors of Africa are undergoing statistically significant TWSGRACE and TWSLSM variations due to natural and anthropogenic causes; (2) a general correspondence between TWSGRACE and TWSLSM over areas (e.g., Niger and Mozambique NE basins in eastern and western Africa) largely controlled by natural (i.e., increase/decrease in precipitation and/or temperature) causes; (3) discrepancies are observed over areas that witnessed extensive anthropogenic effects measured by TWSGRACE but unaccounted for by TWSLSM. Examples include: (a) strong (compared to that observed by TWSLSM) negative TWSGRACE trends were observed over areas that witnessed heavy groundwater extraction (e.g., Western, Desert, Egypt); (b) strong (compared to that observed by TWSLSM) positive TWSGRACE over Lake Volta reservoir; and (c) strong (compared to that observed by TWSLSM) negative trends over areas undergoing heavy deforestation (e.g., northern and NW Congo Basin); (4) additional

  13. Causes and consequences of variation in leaf mass per area (LMA): a meta-analysis.

    PubMed

    Poorter, Hendrik; Niinemets, Ulo; Poorter, Lourens; Wright, Ian J; Villar, Rafael

    2009-01-01

    Here, we analysed a wide range of literature data on the leaf dry mass per unit area (LMA). In nature, LMA varies more than 100-fold among species. Part of this variation (c. 35%) can be ascribed to differences between functional groups, with evergreen species having the highest LMA, but most of the variation is within groups or biomes. When grown in the same controlled environment, leaf succulents and woody evergreen, perennial or slow-growing species have inherently high LMA. Within most of the functional groups studied, high-LMA species show higher leaf tissue densities. However, differences between evergreen and deciduous species result from larger volumes per area (thickness). Response curves constructed from experiments under controlled conditions showed that LMA varied strongly with light, temperature and submergence, moderately with CO2 concentration and nutrient and water stress, and marginally under most other conditions. Functional groups differed in the plasticity of LMA to these gradients. The physiological regulation is still unclear, but the consequences of variation in LMA and the suite of traits interconnected with it are strong. This trait complex is an important factor determining the fitness of species in their environment and affects various ecosystem processes.

  14. Physiological variation of retinal layer thickness is not caused by hydration: a randomised trial.

    PubMed

    Balk, Lisanne J; Oberwahrenbrock, Timm; Uitdehaag, Bernard M J; Petzold, Axel

    2014-09-15

    There is evidence for physiological variation of retinal thicknesses as determined by optical coherence tomography (OCT). We tested if such changes could be explained by hydration and would exceed what may be expected from normal ageing. Subjects (n=26) of a previous study were re-assessed and were randomised to 3 groups of a hydration escalation trial (no hydration, 1× hydration, 2× hydration). Automated retinal layer segmentations were performed for the macular retinal nerve fibre layer (RNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL) and outer nuclear layer (ONL). The averaged volumes were calculated for the central foveola, 3 mm and 6 mm circles of the ETDRS grid. Following oral hydration there were no significant differences of retinal layer thicknesses between the three randomised groups in any of the ETDRS regions at any time-point. Ageing related changes were significant over an 18 month period for the GCL. The negative outcome of this trial implies that, until the causes for the observed variation are resolved, investigators may need to accept, and include into trial power calculations, a small degree of variation (<1%) of quantitative SD-OCT imaging either due to human physiology or instrument/software related factors.

  15. Causes and consequences of spatial variation in sex ratios in a declining bird species.

    PubMed

    Morrison, Catriona A; Robinson, Robert A; Clark, Jacquie A; Gill, Jennifer A

    2016-09-01

    Male-biased sex ratios occur in many bird species, particularly in those with small or declining populations, but the causes of these skews and their consequences for local population demography are rarely known. Within-species variation in sex ratios can help to identify the demographic and behavioural processes associated with such biases. Small populations may be more likely to have skewed sex ratios if sex differences in survival, recruitment or dispersal vary with local abundance. Analyses of species with highly variable local abundances can help to identify these mechanisms and the implications for spatial variation in demography. Many migratory bird species are currently undergoing rapid and severe declines in abundance in parts of their breeding ranges and thus have sufficient spatial variation in abundance to explore the extent of sex ratio biases, their causes and implications. Using national-scale bird ringing data for one such species (willow warbler, Phylloscopus trochilus), we show that sex ratios vary greatly across Britain and that male-biased sites are more frequent in areas of low abundance, which are now widespread across much of south and east England. These sex ratio biases are sufficient to impact local productivity, as the relative number of juveniles caught at survey sites declines significantly with increasing sex ratio skew. Sex differences in survival could influence this sex ratio variation, but we find little evidence for sex differences in survival increasing with sex ratio skew. In addition, sex ratios have become male-biased over the last two decades, but there are no such trends in adult survival rates for males or females. This suggests that lower female recruitment into low abundance sites is contributing to these skews. These findings suggest that male-biased sex ratios in small and declining populations can arise through local-scale sex differences in survival and dispersal, with females recruiting disproportionately into larger

  16. Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast

    PubMed Central

    Hu, Wen; Suo, Fang; Du, Li-Lin

    2015-01-01

    Although the fission yeast Schizosaccharomyces pombe is a well-established model organism, studies of natural trait variations in this species remain limited. To assess the feasibility of segregant-pool-based mapping of phenotype-causing genes in natural strains of fission yeast, we investigated the cause of a maltose utilization defect (Mal-) of the S. pombe strain CBS5557 (originally known as Schizosaccharomyces malidevorans). Analyzing the genome sequence of CBS5557 revealed 955 nonconservative missense substitutions, and 61 potential loss-of-function variants including 47 frameshift indels, 13 early stop codons, and 1 splice site mutation. As a side benefit, our analysis confirmed 146 sequence errors in the reference genome and improved annotations of 27 genes. We applied bulk segregant analysis to map the causal locus of the Mal- phenotype. Through sequencing the segregant pools derived from a cross between CBS5557 and the laboratory strain, we located the locus to within a 2.23-Mb chromosome I inversion found in most S. pombe isolates including CBS5557. To map genes within the inversion region that occupies 18% of the genome, we created a laboratory strain containing the same inversion. Analyzing segregants from a cross between CBS5557 and the inversion-containing laboratory strain narrowed down the locus to a 200-kb interval and led us to identify agl1, which suffers a 5-bp deletion in CBS5557, as the causal gene. Interestingly, loss of agl1 through a 34-kb deletion underlies the Mal- phenotype of another S. pombe strain CGMCC2.1628. This work adapts and validates the bulk segregant analysis method for uncovering trait-gene relationship in natural fission yeast strains. PMID:26615217

  17. Stress Variation Caused by the Terrestrial Water Storage Inferred from GRACE Data

    NASA Astrophysics Data System (ADS)

    Yi, H.; Wen, L.

    2014-12-01

    We estimate stress variation caused by the terrestrial water storage (TWS) change from 2003 to 2013. We first infer the TWS change from the monthly gravity field change in the Gravity Recovery and Climate Experiment (GRACE). We then estimate the stress change at the Earth's surface caused by elastic loading of mass change associated with the inferred TWS change.The monthly spherical harmonics of the GRACE gravity solutions are processed using a decorrelation filter and Gaussian smoothing, to suppress the noise in high degree and order, following the approach of Swenson and Wahr [2006] and Chen et al. [2007]. The gravity variation associated with the glacial isostatic adjustment (GIA) is further removed from the GRACE solutions based on a geodynamical model by Paulson et al. [2007]. The inferred TWS changes exhibit a trend of increase from 2003 to 2013 in Amazon basin, southern Africa, the northern United State America (USA) and Queen Maud Land of Antarctica, and a trend of decrease in the same period in central Argentina, southern Chile, northern India, northern Iran, Alaska of the USA, Greenland and Marie Byrd Land of Antarctica.Surface stress variation due to the TWS loading is calculated, assuming an incompressible and self-gravitating Earth, with an elastic crust and a viscoelastic mantle overlying an inviscid core based on PREM model. We will present the geographical distribution of the stress variation caused by the TWS loading and discuss its possible implications. Chen, J. L., C. R. Wilson, B. D. Tapley, and S. Grand (2007), GRACE detects coseismic and postseismic deformation from the Sumatra-Andaman earthquake, Geophys Res Lett, 34(13), doi:10.1029/2007GL030356. Paulson, A., S. J. Zhong, and J. Wahr (2007), Inference of mantle viscosity from GRACE and relative sea level data, Geophys J Int, 171(2), 497-508, doi:10.1111/j.1365-246X.2007.03556.x. Swenson, S., and J. Wahr (2006), Post-processing removal of correlated errors in GRACE data, Geophys Res Lett, 33

  18. Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster.

    PubMed

    Arif, Saad; Murat, Sophie; Almudi, Isabel; Nunes, Maria D S; Bortolamiol-Becet, Diane; McGregor, Naomi S; Currie, James M S; Hughes, Harri; Ronshaugen, Matthew; Sucena, Élio; Lai, Eric C; Schlötterer, Christian; McGregor, Alistair P

    2013-03-18

    Identifying the genetic mechanisms underlying phenotypic change is essential to understanding how gene regulatory networks and ultimately the genotype-to-phenotype map evolve. It is recognized that microRNAs (miRNAs) have the potential to facilitate evolutionary change [1-3]; however, there are no known examples of natural morphological variation caused by evolutionary changes in miRNA expression. Therefore, the contribution of miRNAs to evolutionary change remains unknown [1, 4]. Drosophila melanogaster subgroup species display a portion of trichome-free cuticle on the femur of the second leg called the "naked valley." It was previously shown that Ultrabithorax (Ubx) is involved in naked valley variation between D. melanogaster and D. simulans [5, 6]. However, naked valley size also varies among populations of D. melanogaster, ranging from 1,000 up to 30,000 μm(2). We investigated the genetic basis of intraspecific differences in the naked valley in D. melanogaster and found that neither Ubx nor shavenbaby (svb) [7, 8] contributes to this morphological difference. Instead, we show that changes in mir-92a expression underlie the evolution of naked valley size in D. melanogaster through repression of shavenoid (sha) [9]. Therefore, our results reveal a novel mechanism for morphological evolution and suggest that modulation of the expression of miRNAs potentially plays a prominent role in generating organismal diversity.

  19. The Latitudinal and Longitudinal Variations of the Thermospheric Density Caused by Aurora Heating

    NASA Astrophysics Data System (ADS)

    Xu, J.; Wang, W.; Smith, A. K.; Jiang, G.; Yuan, W.

    2015-12-01

    We use thermospheric mass densities measured by the accelerometers on satellites of GRACE at ~480 km and CHAMP at ~380 km from 2002-2010 to study the longitudinal and latitudinal distribution of the diurnally averaged thermospheric mass density. The result shows that there are strong longitude variations in the diurnally averaged thermospheric mass density. These variations are global and have the similar characteristics at the two heights under geomagnetically quiet conditions (Ap<10). The largest relative longitudinal changes of the diurnally averaged thermospheric mass density occur at high latitudes from October to February in the Northern Hemisphere and from March to September in the Southern Hemisphere. The positive density peaks locate always near the magnetic poles. The high density regions extend toward lower latitudes and even into the opposite hemisphere. This extension appears to be tilted westward, but mostly is confined to the longitudes where the magnetic poles are located. Thus, the relative longitudinal changes of the diurnally averaged thermospheric mass density have strong seasonal variations and show an annual oscillation at high and middle latitudes but a semiannual oscillation around the equator. Our results suggest that heating of the magnetospheric origin in the auroral region is most likely the cause of these observed longitudinal and latitudinal structures. Our results also show that the relative longitude variation of the diurnally averaged thermospheric mass density is hemispherically asymmetric and more pronounced in the Southern Hemisphere. To check how deep the auroral heating can affect the atmosphere, we analyze the diurnally averaged temperature observed by TIMED/SABER and MIPAS. Results indicate that there are similar structure in the lower thermosphere and the impact of auroral heating on the thermodynamics of the neutral atmosphere can penetrate down to about 105 km under geomagnetically quiet conditions.

  20. Precipitation over two Southern Hemisphere locations: Long-term variation linked to natural and anthropogenic forcings

    NASA Astrophysics Data System (ADS)

    Heredia, Teresita; Elias, Ana G.

    2016-03-01

    The precipitation over Tucuman (26.8°S, 65.2°W), Argentina, and Sidney (33.8°S, 151.2°E), Australia, present similar long-term variation patterns. In this work anthropogenic and solar forcings are analyzed as possible drivers of this behavior. Due to the nature of the processes that lead to precipitation, the discernment between solar and anthropogenic effects, and the link between precipitation and solar activity are highly complex and hard to detect. The aim of this work is to convey the importance of recognizing and quantifying the different forcing acting on precipitation which sometimes are not exposed by a statistical analysis. Annual mean precipitation time series together with solar and geomagnetic activity indices and atmospheric CO2 are analyzed. In order to survey the role of different forcing on precipitation variation we used wavelet and regression analysis with CO2, Rz and aa as independent variables acting as anthropogenic, solar and geomagnetic activity forcing respectively. In the long-term, all of them, considered separately, would induce a similar mean increase in precipitation. The increasing concentration of greenhouse gases, which is thought to be the main factor causing the global warming, is expected to induce an increasing trend of ∼0.8 mm/year, according to some authors. In our case, we obtain a much smaller value: ∼0.15 mm/year which in addition, is similar to the expected forcing from Rz or aa. The wavelet analysis yield significant results for the quasi-decadal and longer-term variations only in the case of Sydney. Significant correlations at time-scales longer than 22 years are also obtained through the regression analysis for Sydney. Although Tucuman do not present significant results, there is a clear similar behavior in the long-term trend. In spite of the fact that the present analysis do not allow us to determine the "true" forcing of the overall increasing trend observed in precipitation, it points out not only

  1. Natural variation in embryo mechanics: gastrulation in Xenopus laevis is highly robust to variation in tissue stiffness

    PubMed Central

    von Dassow, Michelangelo; Davidson, Lance A.

    2009-01-01

    How sensitive is morphogenesis to the mechanical properties of embryos? To estimate an upper bound on the sensitivity of early morphogenetic movements to tissue mechanical properties, we assessed natural variability in the apparent stiffness among gastrula-stage Xenopus laevis embryos. We adapted micro-aspiration methods to make repeated, non-destructive measurements of apparent tissue stiffness in whole embryos. Stiffness varied by close to a factor of 2 among embryos within a single clutch. Variation between clutches was of similar magnitude. On the other hand, the direction of change in stiffness over the course of gastrulation was the same in all embryos and in all clutches. Neither pH nor salinity – two environmental factors we predicted could affect variability in nature – affected tissue stiffness. Our results indicate that gastrulation in X. laevis is robust to at least two-fold variation in tissue stiffness. PMID:19097119

  2. Seasonal variation in natural recharge of coastal aquifers

    NASA Astrophysics Data System (ADS)

    Mollema, Pauline N.; Antonellini, Marco

    2013-06-01

    Many coastal zones around the world have irregular precipitation throughout the year. This results in discontinuous natural recharge of coastal aquifers, which affects the size of freshwater lenses present in sandy deposits. Temperature data for the period 1960-1990 from LocClim (local climate estimator) and those obtained from the Intergovernmental Panel on Climate Change (IPCC) SRES A1b scenario for 2070-2100, have been used to calculate the potential evapotranspiration with the Thornthwaite method. Potential recharge (difference between precipitation and potential evapotranspiration) was defined at 12 locations: Ameland (The Netherlands), Auckland and Wellington (New Zealand); Hong Kong (China); Ravenna (Italy), Mekong (Vietnam), Mumbai (India), New Jersey (USA), Nile Delta (Egypt), Kobe and Tokyo (Japan), and Singapore. The influence of variable/discontinuous recharge on the size of freshwater lenses was simulated with the SEAWAT model. The discrepancy between models with continuous and with discontinuous recharge is relatively small in areas where the total annual recharge is low (258-616 mm/year); but in places with Monsoon-dominated climate (e.g. Mumbai, with recharge up to 1,686 mm/year), the difference in freshwater-lens thickness between the discontinuous and the continuous model is larger (up to 5 m) and thus important to consider in numerical models that estimate freshwater availability.

  3. Natural mercury isotope variation in coal deposits and organic soils

    SciTech Connect

    Abir, Biswas; Joel D. Blum; Bridget A. Bergquist; Gerald J. Keeler; Zhouqing Xie

    2008-11-15

    There is a need to distinguish among sources of Hg to the atmosphere in order to more fully understand global Hg pollution. In this study we investigate whether coal deposits within the United States, China, and Russia-Kazakhstan, which are three of the five greatest coal-producing regions, have diagnostic Hg isotopic fingerprints that can be used to discriminate among Hg sources. We also investigate the Hg isotopic composition of modern organic soil horizons developed in areas distant from point sources of Hg in North America. Mercury stored in coal deposits displays a wide range of both mass dependent fractionation and mass independent fractionation. {delta}{sup 202}Hg varies in coals by 3{per_thousand} and {Delta}{sup 201}Hg varies by 0.9{per_thousand}. Combining these two Hg isotope signals results in what may be a unique isotopic 'fingerprint' for many coal deposits. Mass independent fractionation of mercury has been demonstrated to occur during photochemical reactions of mercury. This suggests that Hg found in most coal deposits was subjected to photochemical reduction near the Earth's surface prior to deposition. The similarity in MDF and MIF of modern organic soils and coals from North America suggests that Hg deposition from coal may have imprinted an isotopic signature on soils. This research offers a new tool for characterizing mercury inputs from natural and anthropogenic sources to the atmosphere and provides new insights into the geochemistry of mercury in coal and soils. 35 refs., 2 figs., 1 tab.

  4. The genetic basis of natural variation in mushroom body size in Drosophila melanogaster

    PubMed Central

    Zwarts, Liesbeth; Vanden Broeck, Lies; Cappuyns, Elisa; Ayroles, Julien F.; Magwire, Michael M.; Vulsteke, Veerle; Clements, Jason; Mackay, Trudy F. C.; Callaerts, Patrick

    2015-01-01

    Genetic variation in brain size may provide the basis for the evolution of the brain and complex behaviours. The genetic substrate and the selective pressures acting on brain size are poorly understood. Here we use the Drosophila Genetic Reference Panel to map polymorphic variants affecting natural variation in mushroom body morphology. We identify 139 genes and 39 transcription factors and confirm effects on development and adult plasticity. We show correlations between morphology and aggression, sleep and lifespan. We propose that natural variation in adult brain size is controlled by interaction of the environment with gene networks controlling development and plasticity. PMID:26656654

  5. Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.

    PubMed

    Maddamsetti, Rohan; Hatcher, Philip J; Cruveiller, Stéphane; Médigue, Claudine; Barrick, Jeffrey E; Lenski, Richard E

    2015-11-01

    Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this hypothesis. In particular, the extent of synonymous variation across genes in that experiment does not reflect the variation observed in natural isolates of E. coli. Instead, gene length alone predicts with high accuracy the prevalence of synonymous changes in the experimental populations. We hypothesize that patterns of synonymous variation in natural E. coli populations are instead caused by differences across genomic regions in their effective population size that, in turn, reflect different histories of recombination, horizontal gene transfer, selection, and population structure.

  6. Natural Variation of Root Traits: From Development to Nutrient Uptake1

    PubMed Central

    Ristova, Daniela; Busch, Wolfgang

    2014-01-01

    The root system has a crucial role for plant growth and productivity. Due to the challenges of heterogeneous soil environments, diverse environmental signals are integrated into root developmental decisions. While root growth and growth responses are genetically determined, there is substantial natural variation for these traits. Studying the genetic basis of the natural variation of root growth traits can not only shed light on their evolution and ecological relevance but also can be used to map the genes and their alleles responsible for the regulation of these traits. Analysis of root phenotypes has revealed growth strategies and root growth responses to a variety of environmental stimuli, as well as the extent of natural variation of a variety of root traits including ion content, cellular properties, and root system architectures. Linkage and association mapping approaches have uncovered causal genes underlying the variation of these traits. PMID:25104725

  7. A new insight into the nature of seasonal variations in coordinate time series of GPS sites located near active faults

    NASA Astrophysics Data System (ADS)

    Trofimenko, Sergey V.; Bykov, Victor G.; Shestakov, Nikolay V.; Grib, Nikolay N.; Takahashi, Hiroaki

    2016-09-01

    This study provides new insights into the nature of seasonal variations in coordinate time series of GPS sites located near active faults and methods of their modeling. Monthly averaged coordinate time series were analyzed for several pairs of collocated GPS sites situated near the active fault intersection area, in close proximity to the central part of the northern boundary of the Amurian plate and the vicinity of the San Andreas Fault zone. It is concluded that the observed seasonal variations are best described by a breather function which is one of the solutions of the well-known sine-Gordon equation. The obtained results suggest that, in this case, the source of seasonal variations may be caused by the appearance of solitary strain waves in the fault intersection system, which may be qualitatively treated as standing waves of compression-extension of the geological medium. Based on statistical testing, the limits of applicability of the suggested model have been established.

  8. Amino acid repeats cause extraordinary coding sequence variation in the social amoeba Dictyostelium discoideum.

    PubMed

    Scala, Clea; Tian, Xiangjun; Mehdiabadi, Natasha J; Smith, Margaret H; Saxer, Gerda; Stephens, Katie; Buzombo, Prince; Strassmann, Joan E; Queller, David C

    2012-01-01

    Protein sequences are normally the most conserved elements of genomes owing to purifying selection to maintain their functions. We document an extraordinary amount of within-species protein sequence variation in the model eukaryote Dictyostelium discoideum stemming from triplet DNA repeats coding for long strings of single amino acids. D. discoideum has a very large number of such strings, many of which are polyglutamine repeats, the same sequence that causes various human neurological disorders in humans, like Huntington's disease. We show here that D. discoideum coding repeat loci are highly variable among individuals, making D. discoideum a candidate for the most variable proteome. The coding repeat loci are not significantly less variable than similar non-coding triplet repeats. This pattern is consistent with these amino-acid repeats being largely non-functional sequences evolving primarily by mutation and drift. PMID:23029418

  9. Genetic variation in 5-hydroxytryptamine transporter expression causes adaptive changes in 5-HT₄ receptor levels.

    PubMed

    Jennings, Katie Ann; Licht, Cecilie Löe; Bruce, Aynsley; Lesch, Klaus-Peter; Knudsen, Gitte Moos; Sharp, Trevor

    2012-09-01

    Genetic variation in 5-HT transporter (5-HTT) expression is a key risk factor for psychiatric disorder and has been linked to changes in the expression of certain 5-HT receptor subtypes. This study investigated the effect of variation in 5-HTT expression on 5-HT₄ receptor levels in both 5-HTT knockout (KO) and overexpressing (OE) mice using autoradiography with the selective 5-HT₄ receptor radioligand, [³H]SB207145. Compared to wild-type (5-HTT⁺/⁺) controls, homozygous 5-HTT KO mice (5-HTT⁻/⁻) had reduced 5-HT₄ receptor binding site density in all brain regions examined (35-65% of 5-HTT⁺/⁺). In contrast, the density of 5-HT₄ receptor binding sites was not significantly different between heterozygous 5-HTT KO mice (5-HTT⁻/⁺) and 5-HTT⁺/⁺ mice. The 5-HT synthesis inhibitor p-chlorophenylalanine (250 mg/kg twice daily for 3 d) abolished the difference in 5-HT₄ binding between 5-HTT⁻/⁻ and 5-HTT⁺/⁺ mice in all brain regions. Compared to wild-type (WT) littermate controls, 5-HTT OE mice had increased 5-HT₄ binding density across all brain regions, except amygdala (118-164% of WT) and this difference between genotypes was reduced by the 5-HTT inhibitor, fluoxetine (20 mg/kg twice daily, 3 d). Together, these findings suggest that variation in 5-HTT expression causes adaptive changes in 5-HT₄ receptor levels which are directly linked to alterations in 5-HT availability.

  10. Capacitor mismatch caused by oxide thickness variations in submicron I. C. processes

    SciTech Connect

    Tom Zimmerman

    1999-05-04

    Chip design in submicron processes will present new challenges and problems which were not present in designs with larger dimension processes. One effect in the newer processes is the field oxide thickness variation due to interconnect density variations. This effect becomes much more extreme for the smaller dimension processes. Large density discontinuities can cause lower yield and will also result in capacitor value mismatch over substantial distances from the edges of a large array when using poly/metal capacitors. If good matching in this type of large area capacitor array is required, the only way to achieve this is to guarantee nearly constant metal/ poly density for at least 1500 microns (this distance will likely depend on the process) around the edges of the array. If the array boundary is close to the chip edge, then dummy capacitors should be placed up to the chip edge, and another layout with similar density must be placed as close as possible to the relevant edges of the chip in the reticle. When using a standard MOSIS reticle size, this may entail placing dummy chip layouts around the chips of interest in order to guarantee that identical density exists for the required distance outside of any chip�s borders.

  11. Natural variations in xenobiotic-metabolizing enzymes: developing tools for coral monitoring

    NASA Astrophysics Data System (ADS)

    Rougée, L. R. A.; Richmond, R. H.; Collier, A. C.

    2014-06-01

    The continued deterioration of coral reefs worldwide demonstrates the need to develop diagnostic tools for corals that go beyond general ecological monitoring and can identify specific stressors at sublethal levels. Cellular diagnostics present an approach to defining indicators (biomarkers) that have the potential to reflect the impact of stress at the cellular level, allowing for the detection of intracellular changes in corals prior to outright mortality. Detoxification enzymes, which may be readily induced or inhibited by environmental stressors, present such a set of indicators. However, in order to apply these diagnostic tools for the detection of stress, a detailed understanding of their normal, homeostatic levels within healthy corals must first be established. Herein, we present molecular and biochemical evidence for the expression and activity of major Phase I detoxification enzymes cytochrome P450 (CYP450), CYP2E1, and CYP450 reductase, as well as the Phase II enzymes UDP, glucuronosyltransferase (UGT), β-glucuronidase, glutathione- S-transferase (GST), and arylsulfatase C (ASC) in the coral Pocillopora damicornis. Additionally, we characterized enzyme expression and activity variations over a reproductive cycle within a coral's life history to determine natural endogenous changes devoid of stress exposure. Significant changes in enzyme activity over the coral's natural lunar reproductive cycle were observed for CYP2E1 and CYP450 reductase as well as UGT and GST, while β-glucuronidase and ASC did not fluctuate significantly. The data represent a baseline description of `health' for the expression and activity of these enzymes that can be used toward understanding the impact of environmental stressors on corals. Such knowledge can be applied to address causes of coral reef ecosystem decline and to monitor effectiveness of mitigation strategies. Achieving a better understanding of cause-and-effect relationships between putative stressors and biological

  12. Understanding natural cause: children's explanations of how objects and their properties originate.

    PubMed

    Gelman, S A; Kremer, K E

    1991-04-01

    An understanding of natural cause includes the realization that events can occur independently of human activity or intentions. It also often entails realizing that causal mechanisms can be nonobservable or nonobvious. The present research investigated to what extent children ages 4-7 have developed a concept of natural cause. Study 1 examined children's understandings of object origins (e.g., how the sun began); Study 2 probed children's causal understandings of object behaviors and properties (e.g., why rabbits hop and have long ears). In both studies, children by age 4 were sensitive to the natural kind-artifact distinction in their explanations. They mentioned human intervention for human-made artifacts but rarely for naturally occurring things. Moreover, subjects at all ages were able to identify specific kinds of natural cause, including intrinsic causes (such as growth) and inborn nature. Finally, subjects understood the link between nonobvious, internal parts and self-generated activity (e.g., that bones are important for the flight of a bird). Altogether, these results suggest that even preschool children realize that natural causes exist. They contradict Piaget's characterization of young children as artificialistic (believing that naturally occurring things are created by people) and as focused on observable properties.

  13. Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus.

    PubMed

    Grunert, Steffen; Labudde, Dirk

    2015-01-01

    The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations.

  14. [Individual variation in the development of the common toad, Bufo bufo (Anura, Bufonidae): 3. Limitations of individual variation and their causes].

    PubMed

    Kovalenko, E E; Kruzhkova, Iu I

    2013-01-01

    The results of studies on the axial skeleton of the common toad (a model species) have been used to analyze factual limitations of individual variations. The results show that the states of the studied characters do not freely combine with each other but are subject to certain morphogenetic limitations. The causes of most these limitations have been revealed during the study. Classification of the main factors limiting individual variation in the course of development is presented.

  15. Genetic variation and causes of genotype-environment interaction in the body size of blue tit (Parus caeruleus).

    PubMed Central

    Merilä, J; Fry, J D

    1998-01-01

    In several studies of natural populations of birds, the heritability of body size estimated by parent-offspring regression has been lower when offspring have developed in poor feeding regimens than when they developed in good feeding regimens. This has led to the suggestion that adaptation under poor regimens may be constrained by lack of genetic variation. We examined the influence of environmental conditions on expression of genetic variation in body size of nestling blue tits (Parus caeruleus) by raising full sibs in artificially reduced and enlarged broods, corresponding to good and poor feeding regimens, respectively. Individuals grown in the poor regimen attained smaller body size than their sibs grown in the good regimen. However, there was among-family variation in response to the treatments--i.e., genotype-environment interactions (GEIs). Partitioning the GEI variance into contributions attributable to (1) differences in the among-family genetic variance between the treatments and (2) imperfect correlation of genotypic values across treatments identified the latter as the main cause of the GEI. Parent-offspring regressions were not significantly different when offspring were reared in the good environment (h2 = 0.75) vs. when they were reared in the poor environment (h2 = 0.63). Thus, there was little evidence that genetic variance in body size was lower under the poor conditions than under the good conditions. These results do not support the view that the genetic potential for adaptation to poor feeding conditions is less than that for adaptation to good conditions, but they do suggest that different genotypes may be favored under the different conditions. PMID:9539438

  16. Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

    PubMed Central

    Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

    2016-01-01

    Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact

  17. Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster.

    PubMed

    Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

    2016-01-01

    Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact

  18. Genetic analysis of natural variations in the architecture of Arabidopsis thaliana vegetative leaves.

    PubMed Central

    Pérez-Pérez, José Manuel; Serrano-Cartagena, José; Micol, José Luis

    2002-01-01

    To ascertain whether intraspecific variability might be a source of information as regards the genetic controls underlying plant leaf morphogenesis, we analyzed variations in the architecture of vegetative leaves in a large sample of Arabidopsis thaliana natural races. A total of 188 accessions from the Arabidopsis Information Service collection were grown and qualitatively classified into 14 phenotypic classes, which were defined according to petiole length, marginal configuration, and overall lamina shape. Accessions displaying extreme and opposite variations in the above-mentioned leaf architectural traits were crossed and their F(2) progeny was found to be not classifiable into discrete phenotypic classes. Furthermore, the leaf trait-based classification was not correlated with estimates on the genetic distances between the accessions being crossed, calculated after determining variations in repeat number at 22 microsatellite loci. Since these results suggested that intraspecific variability in A. thaliana leaf morphology arises from an accumulation of mutations at quantitative trait loci (QTL), we studied a mapping population of recombinant inbred lines (RILs) derived from a Landsberg erecta-0 x Columbia-4 cross. A total of 100 RILs were grown and the third and seventh leaves of 15 individuals from each RIL were collected and morphometrically analyzed. We identified a total of 16 and 13 QTL harboring naturally occurring alleles that contribute to natural variations in the architecture of juvenile and adult leaves, respectively. Our QTL mapping results confirmed the multifactorial nature of the observed natural variations in leaf architecture. PMID:12399398

  19. Magnetic field variation caused by rotational speed change in a magnetohydrodynamic dynamo.

    PubMed

    Miyagoshi, Takehiro; Hamano, Yozo

    2013-09-20

    We have performed numerical magnetohydrodynamic dynamo simulations in a spherical shell with rotational speed or length-of-day (LOD) variation, which is motivated by correlations between geomagnetic field and climatic variations with ice and non-ice ages. The results show that LOD variation leads to magnetic field variation whose amplitude is considerably larger than that of LOD variation. The heat flux at the outer sphere and the zonal flow also change. The mechanism of the magnetic field variation due to LOD variation is also found. The keys are changes of dynamo activity and Joule heating.

  20. Intraseasonal variation in survival and probable causes of mortality in greater sage-grouse Centrocercus urophasianus

    USGS Publications Warehouse

    Blomberg, Erik J.; Gibson, Daniel; Sedinger, James S.; Casazza, Michael L.; Coates, Peter S.

    2013-01-01

    The mortality process is a key component of avian population dynamics, and understanding factors that affect mortality is central to grouse conservation. Populations of greater sage-grouse Centrocercus urophasianus have declined across their range in western North America. We studied cause-specific mortality of radio-marked sage-grouse in Eureka County, Nevada, USA, during two seasons, nesting (2008-2012) and fall (2008-2010), when survival was known to be lower compared to other times of the year. We used known-fate and cumulative incidence function models to estimate weekly survival rates and cumulative risk of cause-specific mortalities, respectively. These methods allowed us to account for temporal variation in sample size and staggered entry of marked individuals into the sample to obtain robust estimates of survival and cause-specific mortality. We monitored 376 individual sage-grouse during the course of our study, and investigated 87 deaths. Predation was the major source of mortality, and accounted for 90% of all mortalities during our study. During the nesting season (1 April - 31 May), the cumulative risk of predation by raptors (0.10; 95% CI: 0.05-0.16) and mammals (0.08; 95% CI: 0.03-013) was relatively equal. In the fall (15 August - 31 October), the cumulative risk of mammal predation was greater (M(mam) = 0.12; 95% CI: 0.04-0.19) than either predation by raptors (M(rap) = 0.05; 95% CI: 0.00-0.10) or hunting harvest (M(hunt) = 0.02; 95% CI: 0.0-0.06). During both seasons, we observed relatively few additional sources of mortality (e.g. collision) and observed no evidence of disease-related mortality (e.g. West Nile Virus). In general, we found little evidence for intraseasonal temporal variation in survival, suggesting that the nesting and fall seasons represent biologically meaningful time intervals with respect to sage-grouse survival.

  1. The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length.

    PubMed

    Cook, Daniel E; Zdraljevic, Stefan; Tanny, Robyn E; Seo, Beomseok; Riccardi, David D; Noble, Luke M; Rockman, Matthew V; Alkema, Mark J; Braendle, Christian; Kammenga, Jan E; Wang, John; Kruglyak, Leonid; Félix, Marie-Anne; Lee, Junho; Andersen, Erik C

    2016-09-01

    Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans.

  2. The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length.

    PubMed

    Cook, Daniel E; Zdraljevic, Stefan; Tanny, Robyn E; Seo, Beomseok; Riccardi, David D; Noble, Luke M; Rockman, Matthew V; Alkema, Mark J; Braendle, Christian; Kammenga, Jan E; Wang, John; Kruglyak, Leonid; Félix, Marie-Anne; Lee, Junho; Andersen, Erik C

    2016-09-01

    Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans. PMID:27449056

  3. Enzyme Variability in the DROSOPHILA WILLISTONI Group. IV. Genic Variation in Natural Populations of DROSOPHILA WILLISTONI

    PubMed Central

    Ayala, Francisco J.; Powell, Jeffrey R.; Tracey, Martin L.; Mourão, Celso A.; Pérez-Salas, Santiago

    1972-01-01

    We describe allelic variation at 28 gene loci in natural populations of D. willistoni. Seventy samples were studied from localities extending from Mexico and Florida, through Central America, the West Indies, and tropical South America, down to South Brazil. At least several hundred, and often several thousand, genomes were sampled for each locus. We have discovered a great deal of genetic variation. On the average, 58% loci are polymorphic in a given population. (A locus is considered polymorphic when the frequency of the most common allele is no greater than 0.95). An individual fly is heterozygous, on the average, at 18.4% loci.—Concerning the pattern of the variation, the most remarkable finding is the similarity of the configuration of allelic frequencies from locality to locality throughout the distribution of the species. Our observations support the conclusion that balancing natural selection is the major factor responsible for the considerable genetic variation observed in D. willistoni. PMID:5013890

  4. The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

    PubMed Central

    Cook, Daniel E.; Zdraljevic, Stefan; Tanny, Robyn E.; Seo, Beomseok; Riccardi, David D.; Noble, Luke M.; Rockman, Matthew V.; Alkema, Mark J.; Braendle, Christian; Kammenga, Jan E.; Wang, John; Kruglyak, Leonid; Félix, Marie-Anne; Lee, Junho; Andersen, Erik C.

    2016-01-01

    Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans. PMID:27449056

  5. Natural Selection on Individual Variation in Tolerance of Gastrointestinal Nematode Infection

    PubMed Central

    Hayward, Adam D.; Nussey, Daniel H.; Wilson, Alastair J.; Berenos, Camillo; Pilkington, Jill G.; Watt, Kathryn A.; Pemberton, Josephine M.; Graham, Andrea L.

    2014-01-01

    Hosts may mitigate the impact of parasites by two broad strategies: resistance, which limits parasite burden, and tolerance, which limits the fitness or health cost of increasing parasite burden. The degree and causes of variation in both resistance and tolerance are expected to influence host–parasite evolutionary and epidemiological dynamics and inform disease management, yet very little empirical work has addressed tolerance in wild vertebrates. Here, we applied random regression models to longitudinal data from an unmanaged population of Soay sheep to estimate individual tolerance, defined as the rate of decline in body weight with increasing burden of highly prevalent gastrointestinal nematode parasites. On average, individuals lost weight as parasite burden increased, but whereas some lost weight slowly as burden increased (exhibiting high tolerance), other individuals lost weight significantly more rapidly (exhibiting low tolerance). We then investigated associations between tolerance and fitness using selection gradients that accounted for selection on correlated traits, including body weight. We found evidence for positive phenotypic selection on tolerance: on average, individuals who lost weight more slowly with increasing parasite burden had higher lifetime breeding success. This variation did not have an additive genetic basis. These results reveal that selection on tolerance operates under natural conditions. They also support theoretical predictions for the erosion of additive genetic variance of traits under strong directional selection and fixation of genes conferring tolerance. Our findings provide the first evidence of selection on individual tolerance of infection in animals and suggest practical applications in animal and human disease management in the face of highly prevalent parasites. PMID:25072883

  6. Chronological Variations of Children Poisoning Causes in Zahedan, South of Iran

    PubMed Central

    Sadeghi-Bojd, Simin; Khajeh, Ali

    2014-01-01

    Background: Poisoning is a common pediatric emergency among children and adolescents in the Emergency Department of Zahedan University of Medical Sciences hospital. Objectives: The aim of this study was comparing the characteristics and variations of pediatric poisoning between two retrospective studies (1998 and 2008). We hypothesized that the epidemiology of pediatric patients admitted for poisoning is related to variations of environmental agents and drug usage. Patients and Methods: Records of 170 patients from 1998 and 147 from 2008 with acute poisoning were retrospectively evaluated and compared. Results: Poisoning mostly occurred in children younger than five years old via oral route (72.94%-87%) and by single exposure (94.12%-96.6%). It was also noted that 86.8%-90% of cases were accidentally poisoned. Drugs were the most common poisoning agents in both studies (52.94% and 37.41%, respectively) and analgesics-antipyretics were the most common poisoning drugs. Drug poisoning was more common among children under five years old in both the studies. Neurological signs including lethargy and coma were the main presenting signs. About 80%-95% of cases were referred to the hospital within three hours of poisoning and supportive-symptomatic therapy was provided to them; charcoal/naloxone was administered for most of the patients (26.2% in 2008 and 21% in 1998). Mortality rate due to drug poisoning was 3-4 cases in both studies; but, non-drug poisoning mortality rate was higher. Conclusions: Preventable accidental poisoning is a significant cause of morbidity in children in developing countries. The study provided information on evolving trends and the need for increasing awareness about potential toxins as well as appropriate storage of toxins in the house to reduce the occurrence of accidental poisoning. PMID:25632384

  7. Natural selection and genital variation: a role for the environment, parasites and sperm ageing?

    PubMed

    Reinhardt, Klaus

    2010-01-01

    Male genitalia are more variable between species (and populations) than other organs, and are more morphologically complex in polygamous compared to monogamous species. Therefore, sexual selection has been put forward as the major explanation of genital variation and complexity, in particular cryptic female choice for male copulatory courtship. As cryptic female choice is based on differences between males it is somewhat paradoxical that there is such low within-species variation in male genitalia that they are a prime morphological identification character for animal species. Processes other than sexual selection may also lead to genitalia variation but they have recently become neglected. Here I focus on pleiotropy and natural selection and provide examples how they link genitalia morphology with genital environments. Pleiotropy appears to be important because most studies that specifically tested for pleiotropic effects on genital morphology found them. Natural selection likely favours certain genital morphology over others in various environments, as well as by reducing re-infection with sexually transmitted diseases or reducing the likelihood of fertilisation with aged sperm. Both pleiotropy and natural selection differ locally and between species so may contribute to local variation in genitalia and sometimes variation between monogamous and polygamous species. Furthermore, the multitude of genital environments will lead to a multitude of genital functions via natural selection and pleiotropy, and may also contribute to explaining the complexity of genitalia.

  8. Natural Variation Identifies Multiple Loci Controlling Petal Shape and Size in Arabidopsis thaliana

    PubMed Central

    Abraham, Mary C.; Metheetrairut, Chanatip; Irish, Vivian F.

    2013-01-01

    Natural variation in organ morphologies can have adaptive significance and contribute to speciation. However, the underlying allelic differences responsible for variation in organ size and shape remain poorly understood. We have utilized natural phenotypic variation in three Arabidopsis thaliana ecotypes to examine the genetic basis for quantitative variation in petal length, width, area, and shape. We identified 23 loci responsible for such variation, many of which appear to correspond to genes not previously implicated in controlling organ morphology. These analyses also demonstrated that allelic differences at distinct loci can independently affect petal length, width, area or shape, suggesting that these traits behave as independent modules. We also showed that ERECTA (ER), encoding a leucine-rich repeat (LRR) receptor-like serine-threonine kinase, is a major effect locus determining petal shape. Allelic variation at the ER locus was associated with differences in petal cell proliferation and concomitant effects on petal shape. ER has been previously shown to be required for regulating cell division and expansion in other contexts; the ER receptor-like kinase functioning to also control organ-specific proliferation patterns suggests that allelic variation in common signaling components may nonetheless have been a key factor in morphological diversification. PMID:23418598

  9. Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana

    PubMed Central

    Yu, Zheng; Haberer, Georg; Matthes, Michaela; Rattei, Thomas; Mayer, Klaus F. X.; Gierl, Alfons; Torres-Ruiz, Ramon A.

    2010-01-01

    Polyploidy, the presence of more than two complete sets of chromosomes in an organism, has significantly shaped the genomes of angiosperms during evolution. Two forms of polyploidy are often considered: allopolyploidy, which originates from interspecies hybrids, and autopolyploidy, which originates from intraspecies genome duplication events. Besides affecting genome organization, polyploidy generates other genetic effects. Synthetic allopolyploid plants exhibit considerable transcriptome alterations, part of which are likely caused by the reunion of previously diverged regulatory hierarchies. In contrast, autopolyploids have relatively uniform genomes, suggesting lower alteration of gene expression. To evaluate the impact of intraspecies genome duplication on the transcriptome, we generated a series of unique Arabidopsis thaliana autotetraploids by using different ecotypes. A. thaliana autotetraploids show transcriptome alterations that strongly depend on their parental genome composition and include changed expression of both new genes and gene groups previously described from allopolyploid Arabidopsis. Alterations in gene expression are stable, nonstochastic, developmentally specific, and associated with changes in DNA methylation. We propose that Arabidopsis possesses an inherent and heritable ability to sense and respond to elevated, yet balanced chromosome numbers. The impact of natural variation on alteration of autotetraploid gene expression stresses its potential importance in the evolution and breeding of plants. PMID:20876110

  10. Whole Earth Telescope observations of V471 Tauri - The nature of the white dwarf variations

    NASA Technical Reports Server (NTRS)

    Clemens, J. C.; Nather, R. E.; Winget, D. E.; Robinson, E. L.; Wood, M. A.; Claver, C. F.; Provencal, J.; Kleinman, S. J.; Bradley, P. A.; Frueh, M. L.

    1992-01-01

    Time-series photometric observations of the binary star V471 Tauri were conducted using the Whole Earth Telescope observing network. The purpose was to determine the mechanism responsible for causing the 555 and 277 s periodic luminosity variations exhibited by the white dwarf in this binary. Previous observers have proposed that either g-mode pulsations or rotation of an accreting magnetic white dwarf could cause the variations, but were unable to decide which was the correct model. The present observations have answered this question. Learning the cause of the white dwarf variations has been possible because of the discovery of a periodic signal at 562 s in the Johnson U-band flux of the binary. By identifying this signal as reprocessed radiation and using its phase to infer the phase of the shorter wavelength radiation which produces it, made it possible to compare the phase of the 555 s U-band variations to the phase of the X-ray variations. It was found that U-band maximum coincides with X-ray minimum. From this result it was concluded that the magnetic rotator model accurately describes the variations observed, but that models involving g-mode pulsations do not.

  11. Groundwater resources and quality variations caused by gravel mining in coastal streams

    NASA Astrophysics Data System (ADS)

    Mas-Pla, J.; Montaner, J.; Solà, J.

    1999-03-01

    We study the effects of gravel mining on the aquifer-river system in the Baix Fluvià area (NE Spain). Field data show that instream mining has caused a decline of the water-table head of the unconfined aquifer along the Fluvià river. Further, dredging in its lowermost reaches reduces its stage and decreases its slope to zero, which facilitates mixing with sea-water, and thus salty-water intrusion from the river into the aquifer. A dimensionless solution of the Boussinesq's equation is derived to estimate the water-table shape and the amount of groundwater lost as runoff for any given decline of the river stage. A flow and solute transport finite-element model is also used to calculate groundwater loses for the Fluvià case. We find that results of the general analytical solution are consistent with those of the numerical model, which reproduces the actual layered aquifer and a more appropriate domain geometry. Finally, the observed chloride distribution and time evolution are broadly reproduced using the numerical model. It shows that significant chloride plumes develop after the cone of depression of the nearby wells reaches the river. However, a natural clean-up takes place in the absence of pumping when the natural water gradient turns completely towards the river.

  12. Patient health causes substantial portion of geographic variation in Medicare costs.

    PubMed

    Collado, Megan

    2013-10-01

    Key findings. (1) Substantial geographic variation exists in Medicare costs, but to determine the source and extent of this variation requires proper accounting for population health differences. (2) While physician practice patterns likely affect Medicare geographic cost variations, population health explains at least 75 to 85 percent of the variations—more than previously estimated. (3) Policy strategies should consider the magnitude of the impact of beneficiary health status on Medicare costs in order to address geographic variation.

  13. Natural variation in flavonol accumulation in Arabidopsis is determined by the flavonol glucosyltransferase BGLU6.

    PubMed

    Ishihara, Hirofumi; Tohge, Takayuki; Viehöver, Prisca; Fernie, Alisdair R; Weisshaar, Bernd; Stracke, Ralf

    2016-03-01

    Flavonols are colourless secondary metabolites, primarily regarded as UV-protection pigments that are deposited in plants in their glycosylated forms. The glycosylation of flavonols is mainly catalysed by UDP-sugar-dependent glycosyltransferases (UGTs). Although the structures of flavonol glycosides accumulating in Arabidopsis thaliana are known, many genes involved in the flavonol glycosylation pathway are yet to be discovered. The flavonol glycoside profiles of seedlings from 81 naturally occurring A. thaliana accessions were screened using high performance thin layer chromatography. A qualitative variation in flavonol 3-O-gentiobioside 7-O-rhamnoside (F3GG7R) content was identified. Ler × Col-0 recombinant inbred line mapping and whole genome association mapping led to the identification of a glycoside hydrolase family 1-type gene, At1g60270/BGLU6, that encodes a homolog of acyl-glucose-dependent glucosyltransferases involved in the glycosylation of anthocyanins, possibly localized in the cytoplasm, and that is co-expressed with genes linked to phenylpropanoid biosynthesis. A causal single nucleotide polymorphism introducing a premature stop codon in non-producer accessions was found to be absent in the producers. Several other naturally occurring loss-of-function alleles were also identified. Two independent bglu6 T-DNA insertion mutants from the producer accessions showed loss of F3GG7R. Furthermore, bglu6 mutant lines complemented with the genomic Ler BGLU6 gene confirmed that BGLU6 is essential for production of F3GGR7. We have thus identified an accession-specific gene that causes a qualitative difference in flavonol glycoside accumulation in A. thaliana strains. This gene encodes a flavonol 3-O-glucoside: 6″-O-glucosyltransferase that does not belong to the large canonical family of flavonol glycosyltransferases that use UDP-conjugates as the activated sugar donor substrate. PMID:26717955

  14. Natural variation in flavonol accumulation in Arabidopsis is determined by the flavonol glucosyltransferase BGLU6

    PubMed Central

    Ishihara, Hirofumi; Tohge, Takayuki; Viehöver, Prisca; Fernie, Alisdair R.; Weisshaar, Bernd; Stracke, Ralf

    2016-01-01

    Flavonols are colourless secondary metabolites, primarily regarded as UV-protection pigments that are deposited in plants in their glycosylated forms. The glycosylation of flavonols is mainly catalysed by UDP-sugar-dependent glycosyltransferases (UGTs). Although the structures of flavonol glycosides accumulating in Arabidopsis thaliana are known, many genes involved in the flavonol glycosylation pathway are yet to be discovered. The flavonol glycoside profiles of seedlings from 81 naturally occurring A. thaliana accessions were screened using high performance thin layer chromatography. A qualitative variation in flavonol 3-O-gentiobioside 7-O-rhamnoside (F3GG7R) content was identified. Ler × Col-0 recombinant inbred line mapping and whole genome association mapping led to the identification of a glycoside hydrolase family 1-type gene, At1g60270/BGLU6, that encodes a homolog of acyl-glucose-dependent glucosyltransferases involved in the glycosylation of anthocyanins, possibly localized in the cytoplasm, and that is co-expressed with genes linked to phenylpropanoid biosynthesis. A causal single nucleotide polymorphism introducing a premature stop codon in non-producer accessions was found to be absent in the producers. Several other naturally occurring loss-of-function alleles were also identified. Two independent bglu6 T-DNA insertion mutants from the producer accessions showed loss of F3GG7R. Furthermore, bglu6 mutant lines complemented with the genomic Ler BGLU6 gene confirmed that BGLU6 is essential for production of F3GGR7. We have thus identified an accession-specific gene that causes a qualitative difference in flavonol glycoside accumulation in A. thaliana strains. This gene encodes a flavonol 3-O-glucoside: 6″-O-glucosyltransferase that does not belong to the large canonical family of flavonol glycosyltransferases that use UDP-conjugates as the activated sugar donor substrate. PMID:26717955

  15. Factors causing variations of lead and cadmium accumulation of feral pigeons (Columba livia).

    PubMed

    Nam, Dong-Ha; Lee, Doo-Pyo; Koo, Tae-Hoe

    2004-07-01

    In order to understand the factors causing variation of lead and cadmium accumulation in tissues of feral pigeons in Seoul and Ansan, Korea, we investigated their age, food items (crop and gizzard contents) as well as environmental factors such as soil, atmosphere, and local traffic density. The results indicate that concentrations of Pb and Cd were highly increased in the order of eggs < chicks < adults. In food analysis, supplementary foods (rice, small stones, domestic scraps, cements, hairs, Styrofoam, etc.) could be considered as factors considering the Pb concentration differences. Concentrations of Cd in foodstuffs, the proportion of crop contents as their major foods could have an influence on the difference of Cd levels from a nutritional viewpoint. The Pb levels in gizzard contents and soil had an effect on the tissue accumulations, these were associated with the volume of vehicular traffic. However, we could not find any differences of Cd concentrations in gizzard contents and soil, although there were significantly different Cd accumulations in target organs of adult pigeons between the study areas. The Pb and Cd levels in tissues did not correspond to atmospheric metal levels.

  16. Assessment of cross-sensor NDVI-variations caused by spectral band characteristics

    NASA Astrophysics Data System (ADS)

    Heinzel, V.; Franke, J.; Menz, G.

    2006-08-01

    Remote sensing-based vegetation indices are widely used for vegetation monitoring applications. The NDVI is the most commonly used indicator for spatial and temporal vegetation dynamics. For long term or multitemporal observations, the combined use of multisensoral NDVI data is necessary. However, due to different sensor characteristics NDVIvariations occur. The sensor geometry, like viewing- and solar angle, atmospherical conditions, topography and spatial or radiometric resolution influence the data. This study contributes to another important factor, the spectral characteristics of different sensors, in particular the relative spectral response (RSR) functions. In order to analyze the NDVI variations caused by different RSR functions, the multispectral bands of Landsat 5 TM, QuickBird, Aster and SPOT 5 were simulated by the use of hyperspectral data of the airborne HyMap sensor. The observed NDVI differences showed a non-linear but systematic NDVI offset between the sensors. Results indicate that the NDVI differences decrease significantly after cross-calibration. A gradual cross-sensor calibration of NDVI taking first spectral characteristics into account is essential. Residual factors could be calibrated in a second step. Such an inter-calibration is desirable for multisensoral NDVI- analyses to ensure the comparability of achieved results.

  17. An interpretation of induced electric currents in long pipelines caused by natural geomagnetic sources of the upper atmosphere

    USGS Publications Warehouse

    Campbell, W.H.

    1986-01-01

    Electric currents in long pipelines can contribute to corrosion effects that limit the pipe's lifetime. One cause of such electric currents is the geomagnetic field variations that have sources in the Earth's upper atmosphere. Knowledge of the general behavior of the sources allows a prediction of the occurrence times, favorable locations for the pipeline effects, and long-term projections of corrosion contributions. The source spectral characteristics, the Earth's conductivity profile, and a corrosion-frequency dependence limit the period range of the natural field changes that affect the pipe. The corrosion contribution by induced currents from geomagnetic sources should be evaluated for pipelines that are located at high and at equatorial latitudes. At midlatitude locations, the times of these natural current maxima should be avoided for the necessary accurate monitoring of the pipe-to-soil potential. ?? 1986 D. Reidel Publishing Company.

  18. Natural variation in photosynthetic capacity, growth, and yield in 64 field-grown wheat genotypes.

    PubMed

    Driever, S M; Lawson, T; Andralojc, P J; Raines, C A; Parry, M A J

    2014-09-01

    Increasing photosynthesis in wheat has been identified as an approach to enhance crop yield, with manipulation of key genes involved in electron transport and the Calvin cycle as one avenue currently being explored. However, natural variation in photosynthetic capacity is a currently unexploited genetic resource for potential crop improvement. Using gas-exchange analysis and protein analysis, the existing natural variation in photosynthetic capacity in a diverse panel of 64 elite wheat cultivars grown in the field was examined relative to growth traits, including biomass and harvest index. Significant variations in photosynthetic capacity, biomass, and yield were observed, although no consistent correlation was found between photosynthetic capacity of the flag leaf and grain yield when all cultivars were compared. The majority of the variation in photosynthesis could be explained by components related to maximum capacity and operational rates of CO2 assimilation, and to CO2 diffusion. Cluster analysis revealed that cultivars may have been bred unintentionally for desirable traits at the expense of photosynthetic capacity. These findings suggest that there is significant underutilized photosynthetic capacity among existing wheat varieties. Our observations are discussed in the context of exploiting existing natural variation in physiological processes for the improvement of photosynthesis in wheat.

  19. Spatiotemporal variation in linear natural selection on body color in wild guppies (Poecilia reticulata).

    PubMed

    Weese, Dylan J; Gordon, Swanne P; Hendry, Andrew P; Kinnison, Michael T

    2010-06-01

    We conducted 10 mark-recapture experiments in natural populations of Trinidadian guppies to test hypotheses concerning the role of viability selection in geographic patterns of male color variation. Previous work has reported that male guppies are more colorful in low-predation sites than in high-predation sites. This pattern of phenotypic variation has been theorized to reflect differences in the balance between natural (viability) selection that disfavors bright male color (owing to predation) and sexual selection that favors bright color (owing to female choice). Our results support the prediction that male color is disfavored by viability selection in both predation regimes. However, it does not support the prediction that viability selection against male color is weaker in low-predation experiments. Instead, some of the most intense bouts of selection against color occurred in low-predation experiments. Our results illustrate considerable spatiotemporal variation in selection among experiments, but such variation was not generally correlated with local patterns of color diversity. More complex selective interactions, possibly including the indirect effects of predators on variation in mating behavior, as well as other environmental factors, might be required to more fully explain patterns of secondary sexual trait variation in this system.

  20. Can exploiting natural genetic variation in leaf photosynthesis contribute to increasing rice productivity? A simulation analysis.

    PubMed

    Gu, Junfei; Yin, Xinyou; Stomph, Tjeerd-Jan; Struik, Paul C

    2014-01-01

    Rice productivity can be limited by available photosynthetic assimilates from leaves. However, the lack of significant correlation between crop yield and leaf photosynthetic rate (A) is noted frequently. Engineering for improved leaf photosynthesis has been argued to yield little increase in crop productivity because of complicated constraints and feedback mechanisms when moving up from leaf to crop level. Here we examined the extent to which natural genetic variation in A can contribute to increasing rice productivity. Using the mechanistic model GECROS, we analysed the impact of genetic variation in A on crop biomass production, based on the quantitative trait loci for various photosynthetic components within a rice introgression line population. We showed that genetic variation in A of 25% can be scaled up equally to crop level, resulting in an increase in biomass of 22-29% across different locations and years. This was probably because the genetic variation in A resulted not only from Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase)-limited photosynthesis but also from electron transport-limited photosynthesis; as a result, photosynthetic rates could be improved for both light-saturated and light-limited leaves in the canopy. Rice productivity could be significantly improved by mining the natural variation in existing germ-plasm, especially the variation in parameters determining light-limited photosynthesis.

  1. Variation in infectivity and aggressiveness in space and time in wild host-pathogen systems – causes and consequences

    PubMed Central

    Tack, Ayco JM; Thrall, Peter H; Barrett, Luke G; Burdon, Jeremy J; Laine, Anna-Liisa

    2012-01-01

    Variation in host resistance and in the ability of pathogens to infect and grow (i.e. pathogenicity) is important as it provides the raw material for antagonistic (co)evolution, and therefore underlies risks of disease spread, disease evolution, and host shifts. Moreover, the distribution of this variation in space and time may inform us about the mode of coevolutionary selection (arms race vs. fluctuating selection dynamics) and the relative roles of GxG interactions, gene flow, selection and genetic drift in shaping coevolutionary processes. While variation in host resistance has recently been reviewed, little is known about overall patterns in the frequency and scale of variation in pathogenicity, particularly in natural systems. Using 48 studies from 30 distinct host-pathogen systems, this review demonstrates that variation in pathogenicity is ubiquitous across multiple spatial and temporal scales. Quantitative analysis of a subset of extensively studied plant-pathogen systemsshows that the magnitude of within-population variation in pathogenicity is large relative to among-population variation, and that the distribution of pathogenicity partly mirrors the distribution of host resistance. At least part of the variation in pathogenicity found at a given spatial scale is adaptive, as evidenced by studies that have examined local adaptation at scales ranging from single hosts through metapopulations to entire continents, and – to a lesser extent - by comparisons of pathogenicity with neutral genetic variation. Together these results support coevolutionary selection through fluctuating selection dynamics. We end by outlining several promising directions for future research. PMID:22905782

  2. Variation in infectivity and aggressiveness in space and time in wild host-pathogen systems: causes and consequences.

    PubMed

    Tack, A J M; Thrall, P H; Barrett, L G; Burdon, J J; Laine, A-L

    2012-10-01

    Variation in host resistance and in the ability of pathogens to infect and grow (i.e. pathogenicity) is important as it provides the raw material for antagonistic (co)evolution and therefore underlies risks of disease spread, disease evolution and host shifts. Moreover, the distribution of this variation in space and time may inform us about the mode of coevolutionary selection (arms race vs. fluctuating selection dynamics) and the relative roles of G × G interactions, gene flow, selection and genetic drift in shaping coevolutionary processes. Although variation in host resistance has recently been reviewed, little is known about overall patterns in the frequency and scale of variation in pathogenicity, particularly in natural systems. Using 48 studies from 30 distinct host-pathogen systems, this review demonstrates that variation in pathogenicity is ubiquitous across multiple spatial and temporal scales. Quantitative analysis of a subset of extensively studied plant-pathogen systems shows that the magnitude of within-population variation in pathogenicity is large relative to among-population variation and that the distribution of pathogenicity partly mirrors the distribution of host resistance. At least part of the variation in pathogenicity found at a given spatial scale is adaptive, as evidenced by studies that have examined local adaptation at scales ranging from single hosts through metapopulations to entire continents and - to a lesser extent - by comparisons of pathogenicity with neutral genetic variation. Together, these results support coevolutionary selection through fluctuating selection dynamics. We end by outlining several promising directions for future research.

  3. Dose variations caused by setup errors in intracranial stereotactic radiotherapy: A PRESAGE study

    SciTech Connect

    Teng, Kieyin; Gagliardi, Frank; Alqathami, Mamdooh; Ackerly, Trevor; Geso, Moshi

    2014-01-01

    Stereotactic radiotherapy (SRT) requires tight margins around the tumor, thus producing a steep dose gradient between the tumor and the surrounding healthy tissue. Any setup errors might become clinically significant. To date, no study has been performed to evaluate the dosimetric variations caused by setup errors with a 3-dimensional dosimeter, the PRESAGE. This research aimed to evaluate the potential effect that setup errors have on the dose distribution of intracranial SRT. Computed tomography (CT) simulation of a CIRS radiosurgery head phantom was performed with 1.25-mm slice thickness. An ideal treatment plan was generated using Brainlab iPlan. A PRESAGE was made for every treatment with and without errors. A prescan using the optical CT scanner was carried out. Before treatment, the phantom was imaged using Brainlab ExacTrac. Actual radiotherapy treatments with and without errors were carried out with the Novalis treatment machine. Postscan was performed with an optical CT scanner to analyze the dose irradiation. The dose variation between treatments with and without errors was determined using a 3-dimensional gamma analysis. Errors are clinically insignificant when the passing ratio of the gamma analysis is 95% and above. Errors were clinically significant when the setup errors exceeded a 0.7-mm translation and a 0.5° rotation. The results showed that a 3-mm translation shift in the superior-inferior (SI), right-left (RL), and anterior-posterior (AP) directions and 2° couch rotation produced a passing ratio of 53.1%. Translational and rotational errors of 1.5 mm and 1°, respectively, generated a passing ratio of 62.2%. Translation shift of 0.7 mm in the directions of SI, RL, and AP and a 0.5° couch rotation produced a passing ratio of 96.2%. Preventing the occurrences of setup errors in intracranial SRT treatment is extremely important as errors greater than 0.7 mm and 0.5° alter the dose distribution. The geometrical displacements affect dose delivery

  4. Interstellar dust as a possible cause of the 22-year climatic variation

    NASA Astrophysics Data System (ADS)

    Shumilov, O.; Kasatkina, E.; Krapiec, M.

    It is generally believed that the low-frequency variability of climatic parameters seems to be connected to solar cycles. The main periodicities are: 11-year (Schwabe), 22-year (Hale), 33-year (Bruckner) and 80-100 (Gleissberg) cycles. The main heliophysical factors acting on climate are solar irradiance, intensity of solar and galactic cosmic rays relativistic particles with energies > 500 MeV) changing the cloud cover of the atmosphere and UVB-radiation. The 11-year and 80-90 solar cycles are apparent in solar radiation and galactic cosmic ray trends. At the same time the bidecadal Hale cycle, related to a reversal of solar magnetic field direction is rather weak in either solar radiation or galactic cosmic ray variation. Besides nobody can identify any physical mechanisms by which a reversal in solar magnetic field could influence climate. However, the 22-year cycle has been identified in practically all regional climatic (droughts, rainfall, tree growth) and temperature records all over the world. We discuss here one a possible cause of bidecadal periodicity in climatic records. A potential reason of this phenomenon seems to be a variation of stardust flux inside of the Solar System. The most recent observations by the DUST experiment on board the Ulysses spacecraft have shown that the solar magnetic field has lost its protective power during the last change of its polarity (the recent solar maximum), and stardust level inside of the Solar System was trebled [Landgraf et al., JGR, 108(A10), 2003]. The periodic increase of stardust inside the Solar System seems to influence the amount of extraterrestrial material that rains down to the Earth and consequently the Earth's atmosphere and climate through the alteration of atmospheric transparency and albedo. This material (interstellar dust and/or cometary matter) may also provide nucleation sites and thereby influence precipitation. It is now our purpose to investigate farther Arctic tree- ring records and to

  5. The atomic weight and isotopic composition of boron and their variation in nature

    SciTech Connect

    Holden, N.E.

    1993-08-01

    The boron isotopic composition and atomic weight value and their variation in nature are reviewed. Questions are raised about the previously recommended value and the uncertainty for the atomic weight. The problem of what constitutes an acceptable range for normal material and what should then be considered geologically exceptional is discussed. Recent measurements make some previous decisions in need of re-evaluation.

  6. Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness

    PubMed Central

    Kerwin, Rachel; Feusier, Julie; Corwin, Jason; Rubin, Matthew; Lin, Catherine; Muok, Alise; Larson, Brandon; Li, Baohua; Joseph, Bindu; Francisco, Marta; Copeland, Daniel; Weinig, Cynthia; Kliebenstein, Daniel J

    2015-01-01

    Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana. DOI: http://dx.doi.org/10.7554/eLife.05604.001 PMID:25867014

  7. The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster.

    PubMed

    Hunter, Chad M; Huang, Wen; Mackay, Trudy F C; Singh, Nadia D

    2016-04-01

    Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait.

  8. The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster

    PubMed Central

    Hunter, Chad M.; Huang, Wen; Mackay, Trudy F. C.; Singh, Nadia D.

    2016-01-01

    Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait. PMID:27035832

  9. Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Gordon, Sean

    2013-03-01

    Sean Gordon of the USDA on "Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  10. The Problem in ERP Determination Caused by the Variation of ERP

    NASA Astrophysics Data System (ADS)

    Zhu, S. Y.; Xu, B. X.; Zhang, H.

    The earth rotation parameters (ERP) vary with time, their variation is significant even in the time interval of one observing session. At present, it is impossible to determine their instantaneous values. Therefore, the determination of ERP will be contaminated by the variation of themselves. This error in ERP determination depends on two factors: (1) the amplitude of variation; (2) the coefficients in the observing equation (i.e. the observing geometry).

  11. Genomic analysis of QTLs and genes altering natural variation in stochastic noise.

    PubMed

    Jimenez-Gomez, Jose M; Corwin, Jason A; Joseph, Bindu; Maloof, Julin N; Kliebenstein, Daniel J

    2011-09-01

    Quantitative genetic analysis has long been used to study how natural variation of genotype can influence an organism's phenotype. While most studies have focused on genetic determinants of phenotypic average, it is rapidly becoming understood that stochastic noise is genetically determined. However, it is not known how many traits display genetic control of stochastic noise nor how broadly these stochastic loci are distributed within the genome. Understanding these questions is critical to our understanding of quantitative traits and how they relate to the underlying causal loci, especially since stochastic noise may be directly influenced by underlying changes in the wiring of regulatory networks. We identified QTLs controlling natural variation in stochastic noise of glucosinolates, plant defense metabolites, as well as QTLs for stochastic noise of related transcripts. These loci included stochastic noise QTLs unique for either transcript or metabolite variation. Validation of these loci showed that genetic polymorphism within the regulatory network alters stochastic noise independent of effects on corresponding average levels. We examined this phenomenon more globally, using transcriptomic datasets, and found that the Arabidopsis transcriptome exhibits significant, heritable differences in stochastic noise. Further analysis allowed us to identify QTLs that control genomic stochastic noise. Some genomic QTL were in common with those altering average transcript abundance, while others were unique to stochastic noise. Using a single isogenic population, we confirmed that natural variation at ELF3 alters stochastic noise in the circadian clock and metabolism. Since polymorphisms controlling stochastic noise in genomic phenotypes exist within wild germplasm for naturally selected phenotypes, this suggests that analysis of Arabidopsis evolution should account for genetic control of stochastic variance and average phenotypes. It remains to be determined if natural

  12. Genetic Architecture of Natural Variation in Thermal Responses of Arabidopsis1[OPEN

    PubMed Central

    Sanchez-Bermejo, Eduardo; Zhu, Wangsheng; Tasset, Celine; Eimer, Hannes; Sureshkumar, Sridevi; Singh, Rupali; Sundaramoorthi, Vignesh; Colling, Luana; Balasubramanian, Sureshkumar

    2015-01-01

    Wild strains of Arabidopsis (Arabidopsis thaliana) exhibit extensive natural variation in a wide variety of traits, including response to environmental changes. Ambient temperature is one of the major external factors that modulates plant growth and development. Here, we analyze the genetic architecture of natural variation in thermal responses of Arabidopsis. Exploiting wild accessions and recombinant inbred lines, we reveal extensive phenotypic variation in response to ambient temperature in distinct developmental traits such as hypocotyl elongation, root elongation, and flowering time. We show that variation in thermal response differs between traits, suggesting that the individual phenotypes do not capture all the variation associated with thermal response. Genome-wide association studies and quantitative trait locus analyses reveal that multiple rare alleles contribute to the genetic architecture of variation in thermal response. We identify at least 20 genomic regions that are associated with variation in thermal response. Further characterizations of temperature sensitivity quantitative trait loci that are shared between traits reveal a role for the blue-light receptor CRYPTOCHROME2 (CRY2) in thermosensory growth responses. We show the accession Cape Verde Islands is less sensitive to changes in ambient temperature, and through transgenic analysis, we demonstrate that allelic variation at CRY2 underlies this temperature insensitivity across several traits. Transgenic analyses suggest that the allelic effects of CRY2 on thermal response are dependent on genetic background suggestive of the presence of modifiers. In addition, our results indicate that complex light and temperature interactions, in a background-dependent manner, govern growth responses in Arabidopsis. PMID:26195568

  13. Spatial variations in natural background radiation: absorbed dose rates in air in Colorado.

    PubMed

    Stone, J M; Whicker, R D; Ibrahim, S A; Whicker, F W

    1999-05-01

    Large and small-scale spatial variations in natural ambient background radiation dose rates in Colorado were investigated at 1,150 specific locations with particular attention to 40 of the more populated areas along the Front Range of the Rocky Mountains. Total dose rates (including cosmic and terrestrial components) in Front Range communities below 2,000 m elevation averaged 135 nGy h(-1). Terrestrial dose rates had a coefficient of variation of 17%. Communities above 2,000 m had a mean total dose rate of 196 nGy h(-1), and a terrestrial dose rate coefficient of variation of 17%. Across all Front Range communities, the coefficient of variation for terrestrial dose rates was 22%. Within individual communities, coefficient of variation values for terrestrial dose rates ranged from 3 to 21%. Smaller-scale spatial variability (to within a few meters) was relatively small (coefficient of variation values generally ranged from 3 to 7%). A significant linear relationship (r2 = 0.83) between the size of area surveyed (km2) and coefficient of variation value for terrestrial dose rates was found. West of the Continental Divide, the terrestrial component accounted for roughly 60% of total measured dose rates, while east of the Continental Divide, where enriched granitic source rocks and associated soils are prevalent, the terrestrial component generally accounted for two-thirds or more of total dose rates. PMID:10201565

  14. An investigation of the potential causes for the seasonal and annual variations in indoor radon concentrations.

    PubMed

    Barazza, F; Gfeller, W; Palacios, M; Murith, C

    2015-11-01

    Indoor radon concentrations exhibit strong variations on short and long timescales. Besides human influences, meteorological factors significantly affect the radon concentrations indoors as well as outdoors. In this article, long-term measurements showing strong annual variations are presented, which take a very similar course in different buildings located in largely separated regions in Switzerland. Also, seasonal variations can be very significant. In general, variations in indoor radon levels can primarily be attributed to human influences. On the other hand, specific weather conditions can have a significant impact on indoor radon levels. In order to further investigate the connection between indoor radon levels and meteorological factors, a measuring campaign has been started in two buildings located in two different regions in Switzerland exhibiting different climatic characteristics. Preliminary results of these investigations are presented, which provide evidence for correlations between indoor radon levels and in particular outdoor temperatures, contributing to seasonal and annual as well as short-term variations in indoor radon concentrations.

  15. PERSPECTIVES ON LARGE-SCALE NATURAL RESOURCES SURVEYS WHEN CAUSE-EFFECT IS A POTENTIAL ISSUE

    EPA Science Inventory

    Our objective is to present a perspective on large-scale natural resource monitoring when cause-effect is a potential issue. We believe that the approach of designing a survey to meet traditional commodity production and resource state descriptive objectives is too restrictive an...

  16. Young Children's Ideas about the Nature, Causes, Justification, and Alleviation of Poverty

    ERIC Educational Resources Information Center

    Chafel, Judith A.; Neitzel, Carin

    2005-01-01

    Sixty-four 8-year-old boys and girls from urban and rural settings and representing different races and socioeconomic status backgrounds responded to questions about the nature, causes, justification, and alleviation of poverty. Much of what the children said indicated that they had not yet internalized prevailing adult norms and values about the…

  17. Subject Reaction to Human-Caused and Naturally-Occurring Radioactive Threat.

    ERIC Educational Resources Information Center

    Belford, Susan; Gibbs, Margaret

    While research has shown that people are adversely psychologically affected by knowledge that their communities have been toxically contaminated, it has been suggested that those who see a disaster as naturally occurring tend to be less adversely affected than those who see a disaster as caused by human acts. To examine this issue, questionnaires…

  18. Sensitivity of benzene natural attenuation to variations in kinetic and transport parameters in Liwa Aquifer, UAE.

    PubMed

    Mohamed, Mohamed M; Saleh, Nawal E; Sherif, Mohsen M

    2010-04-01

    Dissolved benzene was detected in the shallow unconfined Liwa aquifer (UAE). This aquifer represents the main freshwater source for a nearby residence camp area. A finite element model is used to simulate the fate, transport, and attenuation of the dissolved benzene plume to help decision makers assess natural attenuation as a viable remediation option. Sensitivity of benzene attenuation to uncertainties in the estimation of some of the kinetic and transport parameters is studied. It was found that natural attenuation is more sensitive to microbial growth rate and half saturation coefficients of both benzene and oxygen than initial biomass concentration and dispersivity coefficients. Increasing microbial growth rate by fourfold increased natural attenuation effectiveness after 40 years by 10%; while decreasing it by fourfold decreased natural attenuation effectiveness by 77%. On the other hand, increasing half saturation coefficient by fourfold decreased natural attenuation effectiveness by 46% in 40 years. Decreasing the same parameter fourfold caused natural attenuation effectiveness to increase by 9%.

  19. Sq and EEJ—A Review on the Daily Variation of the Geomagnetic Field Caused by Ionospheric Dynamo Currents

    NASA Astrophysics Data System (ADS)

    Yamazaki, Y.; Maute, A.

    2016-09-01

    A record of the geomagnetic field on the ground sometimes shows smooth daily variations on the order of a few tens of nano teslas. These daily variations, commonly known as Sq, are caused by electric currents of several μA/m2 flowing on the sunlit side of the E-region ionosphere at about 90-150 km heights. We review advances in our understanding of the geomagnetic daily variation and its source ionospheric currents during the past 75 years. Observations and existing theories are first outlined as background knowledge for the non-specialist. Data analysis methods, such as spherical harmonic analysis, are then described in detail. Various aspects of the geomagnetic daily variation are discussed and interpreted using these results. Finally, remaining issues are highlighted to provide possible directions for future work.

  20. Proximate causes of adaptive growth rates: growth efficiency variation among latitudinal populations of Rana temporaria.

    PubMed

    Lindgren, B; Laurila, A

    2005-07-01

    In ectothermic organisms, declining season length and lower temperature towards higher latitudes often select for latitudinal variation in growth and development. However, the energetic mechanisms underlying this adaptive variation are largely unknown. We investigated growth, food intake and growth efficiency of Rana temporaria tadpoles from eight populations along a 1500 km latitudinal gradient across Sweden. To gain an insight into the mechanisms of adaptation at organ level, we also examined variation in tadpole gut length. The tadpoles were raised at two temperatures (16 and 20 degrees C) in a laboratory common garden experiment. We found increased growth rate towards higher latitudes, regardless of temperature treatment. This increase in growth was not because of a higher food intake rate, but populations from higher latitudes had higher growth efficiency, i.e. they were more efficient at converting ingested food into body mass. Low temperature reduced growth efficiency most strongly in southern populations. Relative gut length increased with latitude, and tadpoles at low temperature tended to have longer guts. However, variation in gut length was not the sole adaptive explanation for increased growth efficiency as latitude and body length still explained significant amounts of variation in growth efficiency. Hence, additional energetic adaptations are probably involved in growth efficiency variation along the latitudinal gradient.

  1. Interfamily variation in amphibian early life-history traits: raw material for natural selection?

    PubMed Central

    Hopkins, Gareth R; Gall, Brian G; French, Susannah S; Brodie, Edmund D

    2012-01-01

    The embryonic development and time to hatching of eggs can be highly adaptive in some species, and thus under selective pressure. In this study, we examined the underlying interfamily variation in hatching timing and embryonic development in a population of an oviparous amphibian, the rough-skinned newt (Taricha granulosa). We found significant, high variability in degree of embryonic development and hatching timing among eggs from different females. Patterns of variation were present regardless of temperature. We also could not explain the differences among families by morphological traits of the females or their eggs. This study suggests that the variation necessary for natural selection to act upon is present in the early life history of this amphibian. PMID:22957168

  2. Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana.

    PubMed

    Sánchez-Bermejo, Eduardo; Castrillo, Gabriel; del Llano, Bárbara; Navarro, Cristina; Zarco-Fernández, Sonia; Martinez-Herrera, Dannys Jorge; Leo-del Puerto, Yolanda; Muñoz, Riansares; Cámara, Carmen; Paz-Ares, Javier; Alonso-Blanco, Carlos; Leyva, Antonio

    2014-01-01

    The enormous amount of environmental arsenic was a major factor in determining the biochemistry of incipient life forms early in the Earth's history. The most abundant chemical form in the reducing atmosphere was arsenite, which forced organisms to evolve strategies to manage this chemical species. Following the great oxygenation event, arsenite oxidized to arsenate and the action of arsenate reductases became a central survival requirement. The identity of a biologically relevant arsenate reductase in plants nonetheless continues to be debated. Here we identify a quantitative trait locus that encodes a novel arsenate reductase critical for arsenic tolerance in plants. Functional analyses indicate that several non-additive polymorphisms affect protein structure and account for the natural variation in arsenate reductase activity in Arabidopsis thaliana accessions. This study shows that arsenate reductases are an essential component for natural plant variation in As(V) tolerance. PMID:25099865

  3. Discriminating Natural Variation from Legacies of Disturbance in Semi-Arid Forests, Southwestern USA

    NASA Astrophysics Data System (ADS)

    Swetnam, T. L.; Lynch, A. M.; Falk, D. A.; Yool, S. R.; Guertin, D. P.

    2014-12-01

    Characterizing differences in existing vegetation driven by natural variation versus disturbance legacies could become a critical component of applied forest management practice with important implications for monitoring ecologic succession and eco-hydrological interactions within the critical zone. Here we characterize variations in aerial LiDAR derived forest structure at individual tree scale in Arizona and New Mexico. Differences in structure result from both topographic and climatological variations and from natural and human related disturbances. We chose a priori undisturbed and disturbed sites that included preservation, development, logging and wildfire as exemplars. We compare two topographic indices, the topographic position index (TPI) and topographic wetness index (TWI), to two local indicators of spatial association (LISA): the Getis-Ord Gi and Anselin's Moran I. We found TPI and TWI correlate well to positive z-scores (tall trees in tall neighborhoods) in undisturbed areas and that disturbed areas are clearly defined by negative z-scores, in some cases better than what is visible from traditional orthophotography and existing GIS maps. These LISA methods also serve as a robust technique for creating like-clustered stands, i.e. common stands used in forest inventory monitoring. This research provides a significant advancement in the ability to (1) quantity variation in forest structure across topographically complex landscapes, (2) identify and map previously unrecorded disturbance locations, and (3) quantify the different impacts of disturbance within the perimeter of a stand or event at ecologically relevant scale.

  4. Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage.

    PubMed

    Wilschut, Rutger A; Oplaat, Carla; Snoek, L Basten; Kirschner, Jan; Verhoeven, Koen J F

    2016-04-01

    Epigenetic variation has been proposed to contribute to the success of asexual plants, either as a contributor to phenotypic plasticity or by enabling transient adaptation via selection on transgenerationally stable, but reversible, epialleles. While recent studies in experimental plant populations have shown the potential for epigenetic mechanisms to contribute to adaptive phenotypes, it remains unknown whether heritable variation in ecologically relevant traits is at least partially epigenetically determined in natural populations. Here, we tested the hypothesis that DNA methylation variation contributes to heritable differences in flowering time within a single widespread apomictic clonal lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic clone members of the same apomictic lineage collected from different field sites showed heritable differences in flowering time, which was correlated with inherited differences in methylation-sensitive AFLP marker profiles. Differences in flowering between apomictic clone members were significantly reduced after in vivo demethylation using the DNA methyltransferase inhibitor zebularine. This synchronization of flowering times suggests that flowering time divergence within an apomictic lineage was mediated by differences in DNA methylation. While the underlying basis of the methylation polymorphism at functional flowering time-affecting loci remains to be demonstrated, our study shows that epigenetic variation contributes to heritable phenotypic divergence in ecologically relevant traits in natural plant populations. This result also suggests that epigenetic mechanisms can facilitate adaptive divergence within genetically uniform asexual lineages. PMID:26615058

  5. Natural variation in germination responses of Arabidopsis to seasonal cues and their associated physiological mechanisms

    PubMed Central

    Barua, Deepak; Butler, Colleen; Tisdale, Tracy E.; Donohue, Kathleen

    2012-01-01

    Background and Aims Despite the intense interest in phenological adaptation to environmental change, the fundamental character of natural variation in germination is almost entirely unknown. Specifically, it is not known whether different genotypes within a species are germination specialists to particular conditions, nor is it known what physiological mechanisms of germination regulation vary in natural populations and how they are associated with responses to particular environmental factors. Methods We used a set of recombinant inbred genotypes of Arabidopsis thaliana, in which linkage disequilibrium has been disrupted over seven generations, to test for genetic variation and covariation in germination responses to distinct environmental factors. We then examined physiological mechanisms associated with those responses, including seed-coat permeability and sensitivity to the phytohormones gibberellic acid (GA) and abscisic acid (ABA). Key Results Genetic variation for germination was environment-dependent, but no evidence for specialization of germination to different conditions was found. Hormonal sensitivities also exhibited significant genetic variation, but seed-coat properties did not. GA sensitivity was associated with germination responses to multiple environmental factors, but seed-coat permeability and ABA sensitivity were associated with specific germination responses, suggesting that an evolutionary change in GA sensitivity could affect germination in multiple environments, but that of ABA sensitivity may affect germination under more restricted conditions. Conclusions The physiological mechanisms of germination responses to specific environmental factors therefore can influence the ability to adapt to diverse seasonal environments encountered during colonization of new habitats or with future predicted climate change. PMID:22012958

  6. Tuning up mind's pattern to nature's own idea: Eddington's early twenties case for variational derivatives

    NASA Astrophysics Data System (ADS)

    Smadja, Ivahn

    This paper sets out to show how Eddington's early twenties case for variational derivatives significantly bears witness to a steady and consistent shift in focus from a resolute striving for objectivity towards "selective subjectivism" and structuralism. While framing his so-called "Hamiltonian derivatives" along the lines of previously available variational methods allowing to derive gravitational field equations from an action principle, Eddington assigned them a theoretical function of his own devising in The Mathematical Theory of Relativity (1923). I make clear that two stages should be marked out in Eddington's train of thought if the meaning of such variational derivatives is to be adequately assessed. As far as they were originally intended to embody the mind's collusion with nature by linking atomicity of matter with atomicity of action, variational derivatives were at first assigned a dual role requiring of them not only to express mind's craving for permanence but also to tune up mind's privileged pattern to "Nature's own idea". Whereas at a later stage, as affine field theory would provide a framework for world-building, such "Hamiltonian differentiation" would grow out of tune through gauge-invariance and, by disregarding how mathematical theory might precisely come into contact with actual world, would be turned into a mere heuristic device for structural knowledge.

  7. Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage.

    PubMed

    Wilschut, Rutger A; Oplaat, Carla; Snoek, L Basten; Kirschner, Jan; Verhoeven, Koen J F

    2016-04-01

    Epigenetic variation has been proposed to contribute to the success of asexual plants, either as a contributor to phenotypic plasticity or by enabling transient adaptation via selection on transgenerationally stable, but reversible, epialleles. While recent studies in experimental plant populations have shown the potential for epigenetic mechanisms to contribute to adaptive phenotypes, it remains unknown whether heritable variation in ecologically relevant traits is at least partially epigenetically determined in natural populations. Here, we tested the hypothesis that DNA methylation variation contributes to heritable differences in flowering time within a single widespread apomictic clonal lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic clone members of the same apomictic lineage collected from different field sites showed heritable differences in flowering time, which was correlated with inherited differences in methylation-sensitive AFLP marker profiles. Differences in flowering between apomictic clone members were significantly reduced after in vivo demethylation using the DNA methyltransferase inhibitor zebularine. This synchronization of flowering times suggests that flowering time divergence within an apomictic lineage was mediated by differences in DNA methylation. While the underlying basis of the methylation polymorphism at functional flowering time-affecting loci remains to be demonstrated, our study shows that epigenetic variation contributes to heritable phenotypic divergence in ecologically relevant traits in natural plant populations. This result also suggests that epigenetic mechanisms can facilitate adaptive divergence within genetically uniform asexual lineages.

  8. Genetic and Sequence Analysis of Genes Controlling Natural Variation of Seed-Coat and Flower Colors in Soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The soybean exhibits natural variation in flower and seed-coat colors via the deposition of various anthocyanin pigments in the respective tissues. Although pigmentation in seeds or flowers has been well dissected at molecular level in several plant species, the genes controlling natural variation ...

  9. Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus

    PubMed Central

    Raman, Harsh; Raman, Rosy; Kilian, Andrzej; Detering, Frank; Carling, Jason; Coombes, Neil; Diffey, Simon; Kadkol, Gururaj; Edwards, David; McCully, Margaret; Ruperao, Pradeep; Parkin, Isobel A. P.; Batley, Jacqueline; Luckett, David J.; Wratten, Neil

    2014-01-01

    Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified. PMID:25006804

  10. Naturally occurring variation in tadpole morphology and performance linked to predator regime

    PubMed Central

    Johnson, James B; Saenz, Daniel; Adams, Cory K; Hibbitts, Toby J

    2015-01-01

    Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic variations in the population and result in the evolution of reproductive barriers (ecological speciation) or phenotypic plasticity. We evaluated morphology and swimming performance in field collected Bronze Frog larvae (Lithobates clamitans) in ponds dominated by predatory fish and those dominated by invertebrate predators. Based on previous experimental findings, we hypothesized that tadpoles from fish-dominated ponds would have small bodies, long tails, and large tail muscles and that these features would facilitate fast-start speed. We also expected to see increased tail fin depth (i.e., the tail-lure morphology) in tadpoles from invertebrate-dominated ponds. Our results support our expectations with respect to morphology in affecting swimming performance of tadpoles in fish-dominated ponds. Furthermore, it is likely that divergent natural selection is playing a role in the diversification on morphology and locomotor performance in this system. PMID:26357533

  11. A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster.

    PubMed

    Bastide, Héloïse; Betancourt, Andrea; Nolte, Viola; Tobler, Raymond; Stöbe, Petra; Futschik, Andreas; Schlötterer, Christian

    2013-06-01

    Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome.

  12. Genetic variation in arthropod vectors of disease-causing organisms: obstacles and opportunities.

    PubMed Central

    Gooding, R H

    1996-01-01

    An overview of the genetic variation in arthropods that transmit pathogens to vertebrates is presented, emphasizing the genetics of vector-pathogen relationships and the biochemical genetics of vectors. Vector-pathogen interactions are reviewed briefly as a prelude to a discussion of the genetics of susceptibility and refractoriness in vectors. Susceptibility to pathogens is controlled by maternally inherited factors, sex-linked dominant alleles, and dominant and recessive autosomal genes. There is widespread interpopulation (including intercolony) and temporal variation in susceptibility to pathogens. The amount of biochemical genetic variation in vectors is similar to that found in other invertebrates. However, the amount varies widely among species, among populations within species, and temporally within populations. Biochemical genetic studies show that there is considerable genetic structuring of many vectors at the local, regional, and global levels. It is argued that genetic variation in vectors is critical in understanding vector-pathogen interactions and that genetic variation in vectors creates both obstacles to and opportunities for application of genetic techniques to the control of vectors. PMID:8809462

  13. Variation of Slope-Area Relationship Caused by a Catastrophic Landslide

    NASA Astrophysics Data System (ADS)

    Tseng, Chih-Ming; Lin, Ching-Weei; Dalla Fontana, Giancarlo; Tarolli, Paolo

    2013-04-01

    In August 2009, in Taiwan, Typhoon Morakot with a maximum rainfall of over 2,900 mm, induced over 23,000 landslides in mountainous area throughout southern Taiwan. One large scale deep-seated landslide, the Hsiaolin landslide, with an area of about 250 ha, buried the entire village causing 397 casualties, the disappearance of 53 people, and the destruction of over 100 houses (Lin et al., 2011; Tsou et al., 2011). The LiDAR-derived 2 m resolution DEMs before and after Typhoon Morakot was utilized in this study to perform the relation between slope and contributing area. Montgomery and Foufoula-Georgiou (1993), among other authors (eg. Tarolli and Dalla Fontana, 2009) suggested a partitioning of the landscape into drainage and slope regimes that include hillslopes, unchanneled valleys, debris flow-dominated channels, and alluvial channels. These regimes are based on the different patterns of slope-area relation in a loglog diagram. In the analyzed study area a significantly variation of slope-area diagram after the deep-seated landslide has been observed. Sediment mass produced by deep-seated landslide with approximately 2.7x107 m3 (Wu et al., 2011) depleted from hillslope, nearly 90 m deepest failure depth resulted in outward extend of upstream catchment boundary. Huge amount of sediment mass was transported downward also formed significant deposition in debris flow channel and alluvial channel, respectively. These phenomenon also reflects patterns in slope-area diagram. The contributing area related to hillslope-to-valley transition tends to migrate from 20 m2 to 50 m2, that means hillslope length become longer due to outward development of upstream catchment boundary. The local slope of debris flow channel, and alluvial channel section of the diagram, become gentler due to sediment depositions after the landslide. These high resolution analysis pre and post a major event, represent a strategic tool for a directly quantification of the processes that affected and

  14. Crosstalk in a KID Array Caused by the Thickness Variation of Superconducting Metal

    NASA Astrophysics Data System (ADS)

    Adane, A.; Boucher, C.; Coiffard, G.; Leclercq, S.; Schuster, K. F.; Goupy, J.; Calvo, M.; Hoarau, C.; Monfardini, A.

    2016-07-01

    The work presented in this paper is focused on the improvement of the kinetic detectors used on NIKA2 instrument (New IRAM KID array 2). Based on the simulation and low temperature measurements, it aims at showing how the variations of the superconducting metal corrupt the frequency comb of the kinetic Inductance detectors (KID) in the frequency range (between 1 and 3 GHz), i.e., how the superconducting metal inhomogeneity induces the resonance-to-resonance cross-coupling which deteriorates the homogeneity of the resonance quality factor and the frequency resonance separation. Solutions are then proposed to fight against the effect of these metallic variations when designing the KID array.

  15. Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory.

    PubMed

    Herrera, C M; Bazaga, P

    2011-04-01

    Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions.

  16. The cause of complexity in nature: An analytical and computational approach

    NASA Astrophysics Data System (ADS)

    Mainzer, Klaus

    2012-09-01

    This work is going to present the cause of complexity in nature from an analytical and computational point of view. The cause of complex pattern formation is explained by the local activity of cells in complex systems which are analytically modeled by nonlinear reaction-diffusion equations in physics, chemistry, biology and brain research. There are not only rigorous analytical criteria of local activity and the edge of chaos, but also constructive procedures to visualize them by computer simulations. In technology, the question arises whether these criteria and procedures can be used to construct artificial life and artificial minds.

  17. Genetic variation in natural and translocated populations of the endangered Delmarva fox squirrel (Sciurus niger cinereus)

    USGS Publications Warehouse

    Lance, S.L.; Maldonado, J.E.; Bocetti, C.I.; Pattee, O.H.; Ballou, J.D.; Fleischer, R.C.

    2003-01-01

    The Delmarva fox squirrel, Sciurus niger cinereus, is a federally listed endangered subspecies whose range has been reduced by 90%. In an attempt to increase both population size and range, translocation sites were established beginning in the 1960's by moving squirrels from the natural range to sites outside the current range. Although translocations have served as the primary component of the DFS recovery program, there has been very little post-release examination of the genetics of the translocation sites. In this study, we developed ten microsatellite loci, screened the three polymorphic loci, and sequenced a 330 bp fragment of the mitochondrial control region in order to assess levels of genetic variation in natural and translocated regions of Delmarva fox squirrels and to compare them to Southeastern fox squirrels (S. n. niger). Although we found low levels of microsatellite polymorphism, there were no differences in heterozygosity between natural and translocated regions, or between Delmarva and Southeastern fox squirrels. We found high levels of polymorphism in the mitochondrial control region. Our patterns of haplotype diversity suggest incomplete lineage sorting of the two subspecies. In general, our data suggest that the current levels of genetic variation in the translocated sites are representative of those found in the natural population, and we encourage the continued use of translocations as a major component of Delmarva fox squirrel recovery.

  18. Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae)

    PubMed Central

    Chester, M; Riley, R K; Soltis, P S; Soltis, D E

    2015-01-01

    Cytological studies have shown many newly formed allopolyploids (neoallopolyploids) exhibit chromosomal variation as a result of meiotic irregularities, but few naturally occurring neoallopolyploids have been examined. Little is known about how long chromosomal variation may persist and how it might influence the establishment and evolution of allopolyploids in nature. In this study we assess chromosomal composition in a natural neoallotetraploid, Tragopogon mirus, and compare it with T. miscellus, which is an allotetraploid of similar age (~40 generations old). We also assess whether parental gene losses in T. mirus correlate with entire or partial chromosome losses. Of 37 T. mirus individuals that were karyotyped, 23 (62%) were chromosomally additive of the parents, whereas the remaining 14 individuals (38%) had aneuploid compositions. The proportion of additive versus aneuploid individuals differed from that found previously in T. miscellus, in which aneuploidy was more common (69% Fisher's exact test, P=0.0033). Deviations from parental chromosome additivity within T. mirus individuals also did not reach the levels observed in T. miscellus, but similar compensated changes were observed. The loss of T. dubius-derived genes in two T. mirus individuals did not correlate with any chromosomal changes, indicating a role for smaller-scale genetic alterations. Overall, these data for T. mirus provide a second example of prolonged chromosomal instability in natural neoallopolyploid populations. PMID:25370212

  19. Evolutionary causes and consequences of consistent individual variation in cooperative behaviour

    PubMed Central

    Bergmüller, Ralph; Schürch, Roger; Hamilton, Ian M.

    2010-01-01

    Behaviour is typically regarded as among the most flexible of animal phenotypic traits. In particular, expression of cooperative behaviour is often assumed to be conditional upon the behaviours of others. This flexibility is a key component of many hypothesized mechanisms favouring the evolution of cooperative behaviour. However, evidence shows that cooperative behaviours are often less flexible than expected and that, in many species, individuals show consistent differences in the amount and type of cooperative and non-cooperative behaviours displayed. This phenomenon is known as ‘animal personality’ or a ‘behavioural syndrome’. Animal personality is evolutionarily relevant, as it typically shows heritable variation and can entail fitness consequences, and hence, is subject to evolutionary change. Here, we review the empirical evidence for individual variation in cooperative behaviour across taxa, we examine the evolutionary processes that have been invoked to explain the existence of individual variation in cooperative behaviour and we discuss the consequences of consistent individual differences on the evolutionary stability of cooperation. We highlight that consistent individual variation in cooperativeness can both stabilize or disrupt cooperation in populations. We conclude that recognizing the existence of consistent individual differences in cooperativeness is essential for an understanding of the evolution and prevalence of cooperation. PMID:20679117

  20. Cyclic Combustion Variations in Dual Fuel Partially Premixed Pilot-Ignited Natural Gas Engines

    SciTech Connect

    Srinivasan, K. K.; Krishnan, S. R.; Qi, Y.

    2012-05-09

    Dual fuel pilot ignited natural gas engines are identified as an efficient and viable alternative to conventional diesel engines. This paper examines cyclic combustion fluctuations in conventional dual fuel and in dual fuel partially premixed low temperature combustion (LTC). Conventional dual fueling with 95% (energy basis) natural gas (NG) substitution reduces NOx emissions by almost 90%t relative to straight diesel operation; however, this is accompanied by 98% increase in HC emissions, 10 percentage points reduction in fuel conversion efficiency (FCE) and 12 percentage points increase in COVimep. Dual fuel LTC is achieved by injection of a small amount of diesel fuel (2-3 percent on an energy basis) to ignite a premixed natural gas₋air mixture to attain very low NOx emissions (less than 0.2 g/kWh). Cyclic variations in both combustion modes were analyzed by observing the cyclic fluctuations in start of combustion (SOC), peak cylinder pressures (Pmax), combustion phasing (Ca50), and the separation between the diesel injection event and Ca50 (termed "relative combustion phasing" ). For conventional dual fueling, as % NG increases, Pmax decreases, SOC and Ca50 are delayed, and cyclic variations increase. For dual fuel LTC, as diesel injection timing is advanced from 20° to 60° BTDC, the relative combustion phasing is identified as an important combustion parameter along with SoC, Pmax, and CaPmax. For both combustion modes, cyclic variations were characterized by alternating slow and fast burn cycles, especially at high %NG and advanced injection timings. Finally, heat release return maps were analyzed to demonstrate thermal management strategies as an effective tool to mitigate cyclic combustion variations, especially in dual fuel LTC.

  1. Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila

    PubMed Central

    Najarro, Michael A.; Hackett, Jennifer L.; Smith, Brittny R.; Highfill, Chad A.; King, Elizabeth G.; Long, Anthony D.; Macdonald, Stuart J.

    2015-01-01

    Natural populations exhibit a great deal of interindividual genetic variation in the response to toxins, exemplified by the variable clinical efficacy of pharmaceutical drugs in humans, and the evolution of pesticide resistant insects. Such variation can result from several phenomena, including variable metabolic detoxification of the xenobiotic, and differential sensitivity of the molecular target of the toxin. Our goal is to genetically dissect variation in the response to xenobiotics, and characterize naturally-segregating polymorphisms that modulate toxicity. Here, we use the Drosophila Synthetic Population Resource (DSPR), a multiparent advanced intercross panel of recombinant inbred lines, to identify QTL (Quantitative Trait Loci) underlying xenobiotic resistance, and employ caffeine as a model toxic compound. Phenotyping over 1,700 genotypes led to the identification of ten QTL, each explaining 4.5–14.4% of the broad-sense heritability for caffeine resistance. Four QTL harbor members of the cytochrome P450 family of detoxification enzymes, which represent strong a priori candidate genes. The case is especially strong for Cyp12d1, with multiple lines of evidence indicating the gene causally impacts caffeine resistance. Cyp12d1 is implicated by QTL mapped in both panels of DSPR RILs, is significantly upregulated in the presence of caffeine, and RNAi knockdown robustly decreases caffeine tolerance. Furthermore, copy number variation at Cyp12d1 is strongly associated with phenotype in the DSPR, with a trend in the same direction observed in the DGRP (Drosophila Genetic Reference Panel). No additional plausible causative polymorphisms were observed in a full genomewide association study in the DGRP, or in analyses restricted to QTL regions mapped in the DSPR. Just as in human populations, replicating modest-effect, naturally-segregating causative variants in an association study framework in flies will likely require very large sample sizes. PMID:26619284

  2. Bioinspired lightweight cellular materials--understanding effects of natural variation on mechanical properties.

    PubMed

    Cadman, Joseph; Chang, Che-Cheng; Chen, Junning; Chen, Yuhang; Zhou, Shiwei; Li, Wei; Li, Qing

    2013-08-01

    Cuttlebone is a natural marine cellular material possessing the exceptional mechanical properties of high compressive strength, high porosity and high permeability. This combination of properties is exceedingly desirable in biomedical applications, such as bone tissue scaffolds. In light of recent studies, which converted raw cuttlebone into hydroxyapatite tissue scaffolds, the impact of morphological variations in the microstructure of this natural cellular material on the effective mechanical properties is explored in this paper. Two extensions of the finite element-based homogenization method are employed to account for deviations from the assumption of periodicity. Firstly, a representative volume element (RVE) of cuttlebone is systematically varied to reflect the large range of microstructural configurations possibly among different cuttlefish species. The homogenization results reveal the critical importance of pillar formation and aspect ratio (height/width of RVE) on the effective bulk and shear moduli of cuttlebone. Secondly, multi-cell analysis domains (or multiple RVE domains) permit the introduction of random variations across neighboring cells. Such random variations decrease the bulk modulus whilst displaying minimal impact on the shear modulus. Increasing the average size of random variations increases the effect on bulk modulus. Also, the results converge rapidly as the size of the analysis domain is increased, meaning that a relatively small multi-cell domain can provide a reasonable approximation of the effective properties for a given set of random variation parameters. These results have important implications for the proposed use of raw cuttlebone as an engineering material. They also highlight some potential for biomimetic design capabilities for materials inspired by the cuttlebone microstructure, which may be applicable in biomedical applications such as bone tissue scaffolds. PMID:23706194

  3. Natural variation reveals that intracellular distribution of ELF3 protein is associated with function in the circadian clock

    PubMed Central

    Anwer, Muhammad Usman; Boikoglou, Eleni; Herrero, Eva; Hallstein, Marc; Davis, Amanda Melaragno; Velikkakam James, Geo; Nagy, Ferenc; Davis, Seth Jon

    2014-01-01

    Natural selection of variants within the Arabidopsis thaliana circadian clock can be attributed to adaptation to varying environments. To define a basis for such variation, we examined clock speed in a reporter-modified Bay-0 x Shakdara recombinant inbred line and localized heritable variation. Extensive variation led us to identify EARLY FLOWERING3 (ELF3) as a major quantitative trait locus (QTL). The causal nucleotide polymorphism caused a short-period phenotype under light and severely dampened rhythm generation in darkness, and entrainment alterations resulted. We found that ELF3-Sha protein failed to properly localize to the nucleus, and its ability to accumulate in darkness was compromised. Evidence was provided that the ELF3-Sha allele originated in Central Asia. Collectively, we showed that ELF3 protein plays a vital role in defining its light-repressor action in the circadian clock and that its functional abilities are largely dependent on its cellular localization. DOI: http://dx.doi.org/10.7554/eLife.02206.001 PMID:24867215

  4. From Ends to Causes (and Back Again) by Metaphor: The Paradox of Natural Selection

    NASA Astrophysics Data System (ADS)

    Blancke, Stefaan; Schellens, Tammy; Soetaert, Ronald; Van Keer, Hilde; Braeckman, Johan

    2014-04-01

    Natural selection is one of the most famous metaphors in the history of science. Charles Darwin used the metaphor and the underlying analogy to frame his ideas about evolution and its main driving mechanism into a full-fledged theory. Because the metaphor turned out to be such a powerful epistemic tool, Darwin naturally assumed that he could also employ it as an educational tool to inform his contemporaries about his findings. Moreover, by using the metaphor Darwin was able to bring his theory in accordance with both the dominant philosophy of science in his time and the respected tradition of natural theology. However, as he introduced his theory of evolution by natural selection in On the origin of species in 1859, the metaphor also turned out to have a serious downside. Because of its intentional overtones, his contemporaries systematically misunderstood his metaphor not as a natural mechanism causing evolution to occur but as an agent who works towards particular ends. The difference in success between natural selection as an epistemic tool and its failure as an educational tool is labelled as a paradox. We explain the paradox from a cognitive perspective and discuss the implications for teaching evolution.

  5. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome.

    PubMed

    Lohmueller, Kirk E; Albrechtsen, Anders; Li, Yingrui; Kim, Su Yeon; Korneliussen, Thorfinn; Vinckenbosch, Nicolas; Tian, Geng; Huerta-Sanchez, Emilia; Feder, Alison F; Grarup, Niels; Jørgensen, Torben; Jiang, Tao; Witte, Daniel R; Sandbæk, Annelli; Hellmann, Ines; Lauritzen, Torsten; Hansen, Torben; Pedersen, Oluf; Wang, Jun; Nielsen, Rasmus

    2011-10-01

    A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries of genetic variation, like allele frequencies, are also correlated with recombination rate and whether these correlations can be explained solely by negative selection against deleterious mutations or whether positive selection acting on favorable alleles is also required. Here we attempt to address these questions by analyzing three different genome-wide resequencing datasets from European individuals. We document several significant correlations between different genomic features. In particular, we find that average minor allele frequency and diversity are reduced in regions of low recombination and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations. However, models with strong positive selection on nonsynonymous mutations and little negative selection predict a stronger negative correlation between neutral diversity and nonsynonymous divergence than observed in the actual data, supporting the importance of negative, rather than positive, selection throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations.

  6. Dispersion of the Geomagnetic Field Caused by Secular Variation: Constraints From Sediment Cores From Around Antarctica

    NASA Astrophysics Data System (ADS)

    Acton, G.; Jovane, L.; Verosub, K. L.; Sagnotti, L.; Ohneiser, C.; Strada, E.; Florindo, F.; Wilson, G. S.

    2010-12-01

    The angular dispersion of the virtual geomagnetic pole (VGP) measured over time and at many sites around the globe provides a measure of spatial variability in geodynamo processes. For example, longitudinal and latitudinal variations in dispersion may imply lateral differences in the boundary conditions at the core-mantle interface. Latitudinal variations in dispersion may also provide constraints on the size of dipole wobble and zonal non-dipole components. Furthermore, changes in dispersion across high latitudes may be indicative of changes in outer core flow regimes across the tangent cylinder. The spatial variation of dispersion, particularly the latitudinal variation, thus has the potential to be a powerful constraint on geodynamo models. Currently, estimates of the latitudinal variation in dispersion are based on volcanic data sets that give ambiguous results, with some studies finding an increase in dispersion with latitude and others finding virtually no change with latitude. The ambiguity arises mainly from the sparseness of data from high latitudes and from the difficulty in dealing with excursional VGPs in volcanic data sets. To improve the dispersion estimates at high latitudes, we use paleomagnetic data obtained from sedimentary ocean drill cores from several sites from around Antarctica, including ODP Leg 178 Sites 1095, 1096, and 1098 cored off the Antarctic Peninsula, and ANDRILL Site AND-2A and Eltanin Core 27-21 from the Ross Sea. Unlike volcanic units, sedimentary sections can provide continuous paleomagnetic records that capture both short and long term geomagnetic field variability. This allows us to examine not only the size of dispersion but changes in dispersion that occur over time. Such records also make it possible to investigate the amount of time it takes to average paleosecular variation and to use that information to estimate the duration of sedimentation at other sites. As with volcanics, a variety of issues, including sedimentation

  7. Measurement of isotope abundance variations in nature by gravimetric spiking isotope dilution analysis (GS-IDA).

    PubMed

    Chew, Gina; Walczyk, Thomas

    2013-04-01

    Subtle variations in the isotopic composition of elements carry unique information about physical and chemical processes in nature and are now exploited widely in diverse areas of research. Reliable measurement of natural isotope abundance variations is among the biggest challenges in inorganic mass spectrometry as they are highly sensitive to methodological bias. For decades, double spiking of the sample with a mix of two stable isotopes has been considered the reference technique for measuring such variations both by multicollector-inductively coupled plasma mass spectrometry (MC-ICPMS) and multicollector-thermal ionization mass spectrometry (MC-TIMS). However, this technique can only be applied to elements having at least four stable isotopes. Here we present a novel approach that requires measurement of three isotope signals only and which is more robust than the conventional double spiking technique. This became possible by gravimetric mixing of the sample with an isotopic spike in different proportions and by applying principles of isotope dilution for data analysis (GS-IDA). The potential and principle use of the technique is demonstrated for Mg in human urine using MC-TIMS for isotopic analysis. Mg is an element inaccessible to double spiking methods as it consists of three stable isotopes only and shows great potential for metabolically induced isotope effects waiting to be explored.

  8. Genetic Architecture of Natural Variation of Telomere Length in Arabidopsis thaliana

    PubMed Central

    Fulcher, Nick; Teubenbacher, Astrid; Kerdaffrec, Envel; Farlow, Ashley; Nordborg, Magnus; Riha, Karel

    2015-01-01

    Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis, however, are not well understood. To investigate the extent of natural variation of telomere length in Arabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere-mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTL. QTL detected in the Ler-2/Cvi-0 population were examined using near isogenic lines that confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in A. thaliana, identifies a network of QTL that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation. PMID:25488978

  9. Dissecting the genetic control of natural variation in salt tolerance of Arabidopsis thaliana accessions

    PubMed Central

    Katori, Taku; Ikeda, Akiro; Iuchi, Satoshi; Kobayashi, Masatomo; Shinozaki, Kazuo; Maehashi, Kenji; Sakata, Yoichi; Tanaka, Shigeo; Taji, Teruaki

    2010-01-01

    Many accessions (ecotypes) of Arabidopsis have been collected. Although few differences exist among their nucleotide sequences, these subtle differences induce large genetic variation in phenotypic traits such as stress tolerance and flowering time. To understand the natural variability in salt tolerance, large-scale soil pot experiments were performed to evaluate salt tolerance among 350 Arabidopsis thaliana accessions. The evaluation revealed a wide variation in the salt tolerance among accessions. Several accessions, including Bu-5, Bur-0, Ll-1, Wl-0, and Zu-0, exhibited marked stress tolerance compared with a salt-sensitive experimental accession, Col-0. The salt-tolerant accessions were also evaluated by agar plate assays. The data obtained by the large-scale assay correlated well with the results of a salt acclimation (SA) assay, in which plants were transferred to high-salinity medium following placement on moderate-salinity medium for 7 d. Genetic analyses indicated that the salt tolerance without SA is a quantitative trait under polygenic control, whereas salt tolerance with SA is regulated by a single gene located on chromosome 5 that is common among the markedly salt-tolerant accessions. These results provide important information for understanding the mechanisms underlying natural variation of salt tolerance in Arabidopsis. PMID:20080827

  10. Genetic architecture of natural variation of telomere length in Arabidopsis thaliana.

    PubMed

    Fulcher, Nick; Teubenbacher, Astrid; Kerdaffrec, Envel; Farlow, Ashley; Nordborg, Magnus; Riha, Karel

    2015-02-01

    Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis, however, are not well understood. To investigate the extent of natural variation of telomere length in Arabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere-mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTL. QTL detected in the Ler-2/Cvi-0 population were examined using near isogenic lines that confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in A. thaliana, identifies a network of QTL that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation.

  11. Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis

    PubMed Central

    Jensen, Lea M.; Jepsen, Henriette S. K.; Halkier, Barbara A.; Kliebenstein, Daniel J.; Burow, Meike

    2015-01-01

    Naturally variable regulatory networks control different biological processes including reproduction and defense. This variation within regulatory networks enables plants to optimize defense and reproduction in different environments. In this study we investigate the ability of two enzyme-encoding genes in the glucosinolate pathway, AOP2 and AOP3, to affect glucosinolate accumulation and flowering time. We have introduced the two highly similar enzymes into two different AOPnull accessions, Col-0 and Cph-0, and found that the genes differ in their ability to affect glucosinolate levels and flowering time across the accessions. This indicated that the different glucosinolates produced by AOP2 and AOP3 serve specific regulatory roles in controlling these phenotypes. While the changes in glucosinolate levels were similar in both accessions, the effect on flowering time was dependent on the genetic background pointing to natural variation in cross-talk between defense chemistry and onset of flowering. This variation likely reflects an adaptation to survival in different environments. PMID:26442014

  12. Natural variation in leaf morphology results from mutation of a novel KNOX gene.

    PubMed

    Kimura, Seisuke; Koenig, Daniel; Kang, Julie; Yoong, Fei Yian; Sinha, Neelima

    2008-05-01

    Striking diversity in size, arrangement, and complexity of leaves can sometimes be seen in closely related species. One such variation is found between wild tomato species collected by Charles Darwin from the Galapagos Islands [1-5]. Here, we show that a single-nucleotide deletion in the promoter of the PETROSELINUM (PTS) [3] gene upregulates the gene product in leaves and is responsible for the natural variation in leaf shape in the Galapagean tomatoes. PTS encodes a novel KNOTTED1-LIKE HOMEOBOX (KNOX) gene that lacks a homeodomain. We also showed that the tomato classical mutant bipinnata (bip) [6], which recapitulates the Pts phenotype, results from the loss of function of a BEL-LIKE HOMEODOMAIN (BELL) gene, BIP. We used bimolecular fluorescence complementation and two-hybrid competition assays to show that PTS represses KNOX1 protein interactions with BIP, as well as subsequent nuclear localization of this transcriptional complex. We suggest that natural variation in leaf shape can be created with a rheostat-like mechanism that alters the KNOX1 protein interaction network specifically during leaf development. This subtle change in interaction between transcription factors leaves essential KNOX1 function in the shoot apical meristem intact and appears to be a facile way to alter leaf morphology during evolution.

  13. A Focus on Natural Variation for Abiotic Constraints Response in the Model Species Arabidopsis thaliana

    PubMed Central

    Lefebvre, Valérie; Kiani, Seifollah Poormohammad; Durand-Tardif, Mylène

    2009-01-01

    Plants are particularly subject to environmental stress, as they cannot move from unfavourable surroundings. As a consequence they have to react in situ. In any case, plants have to sense the stress, then the signal has to be transduced to engage the appropriate response. Stress response is effected by regulating genes, by turning on molecular mechanisms to protect the whole organism and its components and/or to repair damage. Reactions vary depending on the type of stress and its intensity, but some are commonly turned on because some responses to different abiotic stresses are shared. In addition, there are multiple ways for plants to respond to environmental stress, depending on the species and life strategy, but also multiple ways within a species depending on plant variety or ecotype. It is regularly accepted that populations of a single species originating from diverse geographic origins and/or that have been subjected to different selective pressure, have evolved retaining the best alleles for completing their life cycle. Therefore, the study of natural variation in response to abiotic stress, can help unravel key genes and alleles for plants to cope with their unfavourable physical and chemical surroundings. This review is focusing on Arabidopsis thaliana which has been largely adopted by the global scientific community as a model organism. Also, tools and data that facilitate investigation of natural variation and abiotic stress encountered in the wild are set out. Characterization of accessions, QTLs detection and cloning of alleles responsible for variation are presented. PMID:20111677

  14. [Trends of food poisonings caused by natural toxins in Japan, 1989-2011].

    PubMed

    Toda, Miou; Uneyama, Chikako; Toyofuku, Hajime; Morikawa, Kaoru

    2012-01-01

    In order to reduce the health risk associated with food poisonings caused by natural toxins, it is necessary to implement risk management strategies based on previous poisoning data and risk factors. In present study, we statistically analyzed natural toxin food poisoning (NTFP) data published by the Ministry of Health, Labour and Welfare from 1989 to 2010 in Japan and reviewed the trends of NTFP for each natural toxin hazard. Since 1989, the number of incidents of NTFP in each year has not been reduced. Prevention and control are needed to reduce the risk of NTFP. The major site for all hazards was "at home". This result suggested that consumer education is critically important to inform about NTFP occurrence, preventive measures and emergency treatments. Furthermore, countermeasures for NTFPs which have never occurred in the past in Japan should be considered, because of the increasing variety of imported foods and changes resulting from the inerease of sea temperature with global warming.

  15. Midtarsal break variation in modern humans: Functional causes, skeletal correlates, and paleontological implications.

    PubMed

    DeSilva, J M; Bonne-Annee, R; Swanson, Z; Gill, C M; Sobel, M; Uy, J; Gill, S V

    2015-04-01

    The midtarsal break was once treated as a dichotomous, non-overlapping trait present in the foot of non-human primates and absent in humans. Recent work indicates that there is considerable variation in human midfoot dorsiflexion, with some overlap with the ape foot. These findings have called into question the uniqueness of the human lateral midfoot, and the use of osteological features in fossil hominins to characterize the midfoot of our extinct ancestors. Here, we present data on plantar pressure and pedal mechanics in a large sample of adults and children (n = 671) to test functional hypotheses concerning variation in midfoot flexibility. Lateral midfoot peak plantar pressure correlates with both sagittal plane flexion at the lateral tarsometatarsal joint, and dorsiflexion at the hallucal metatarsophalangeal joint. The latter finding suggests that midfoot laxity may compromise hallucal propulsion. Multiple regression statistics indicate that a low arch and pronation of the foot explain 40% of variation in midfoot peak plantar pressure, independent of age and BMI. MRI scans on a small subset of study participants (n = 19) reveals that curvature of the base of the 4th metatarsal correlates with lateral midfoot plantar pressure and that specific anatomies of foot bones do indeed reflect relative midfoot flexibility. However, while the shape of the base of the 4th metatarsal may reliably reflect midfoot mobility in individual hominins, given the wide range of overlapping variation in midfoot flexibility in both apes and humans, we caution against generalizing foot function in extinct hominin species until larger fossils samples are available.

  16. What constitutes a nesting attempt? Variation in criteria causes bias and hinders comparisons across studies

    USGS Publications Warehouse

    Garcia, V.; Conway, C.J.

    2009-01-01

    Because reliable estimates of nesting success are very important to avian studies, the definition of a "successful nest" and the use of different analytical methods to estimate success have received much attention. By contrast, variation in the criteria used to determine whether an occupied site that did not produce offspring contained a nesting attempt is a source of bias that has been largely ignored. This problem is especially severe in studies that deal with species whose nest contents are relatively inaccessible because observers cannot determine whether or not an egg was laid for a large proportion of occupied sites. Burrowing Owls (Athene cunicularia) often lay their eggs ???3 m below ground, so past Burrowing Owl studies have used a variety of criteria to determine whether a nesting attempt was initiated. We searched the literature to document the extent of that variation and examined how that variation influenced estimates of daily nest survival. We found 13 different sets of criteria used by previous authors and applied each criterion to our data set of 1,300 occupied burrows. We found significant variation in estimates of daily nest survival depending on the criteria used. Moreover, differences in daily nest survival among populations were apparent using some sets of criteria but not others. These inconsistencies may lead to incorrect conclusions and invalidate comparisons of the productivity and relative site quality among populations. We encourage future authors working on cavity-, canopy-, or burrow-nesting birds to provide specific details on the criteria they used to identify a nesting attempt. ?? 2009 by The American Ornithologists' Union. All rights reserved.

  17. Disentangling the causes of intrainflorescence variation in floral traits and fecundity in the hermaphrodite Silene acutifolia.

    PubMed

    Buide, M Luisa

    2008-04-01

    Inflorescence architecture directly determines variations in floral traits and fecundity. Disentangling these patterns of variation is crucial to understanding intraplant variation, which sometimes is directly attributed to competition for resources with developing fruits. The dichasial cymes of Silene acutifolia were experimentally manipulated in the field to analyze whether the declines in petal size, ovule number, fruit set, and seed/ovule ratio along the inflorescence are constrained by ontogenetic development or are phenotypically plastic in response to environmental changes. At the same time, the level of pollen deficit was measured on different positions of the dichasia. The results showed clearly that all measured variables were more influenced by architecture than by resource competition with developing fruits; the removal of central (basal) and primary lateral flowers in the dichasia did not increase either the measures of floral characters or fecundity. On the other hand, although most of the decline in fecundity was due to architectural effects, there was also a pollen limitation, dependent to some degree on inflorescence position, which was probably due to lower pollen availability in the population when secondary flowers are in the female phase.

  18. Variations in anatomy at the suprascapular notch possibly causing suprascapular nerve entrapment: an anatomical study.

    PubMed

    Bayramoğlu, A; Demiryürek, D; Tüccar, E; Erbil, M; Aldur, M M; Tetik, O; Doral, M N

    2003-11-01

    The purpose of the study was to determine anatomical variations at the suprascapular notch for better understanding of possible predisposing factors for suprascapular nerve entrapment. We dissected 32 shoulders of 16 cadavers between the ages of 39 and 74 years. We observed abnormally oriented superior fibers of the subscapularis muscle in five shoulders of the 16 cadavers, which were covering the entire anterior surface of the suprascapular notch and significantly reducing the available space for the suprascapular nerve. We also detected anterior coracoscapular ligament in six of the 32 shoulders, and calcified superior transverse scapular ligament in four of the shoulders. In this study, we classified the variations for the superior transverse scapular ligament. In conclusion, knowing the anatomical variations in detail along the course of the suprascapular nerve might be important for better understanding of location and source of the entrapment syndrome, especially for individuals who are involved in violent overhead sports activities such as volleyball and baseball. To our knowledge, close relationship of subscapularis muscle with the suprascapular nerve as a possible risk factor for suprascapular nerve entrapment has not been mentioned previously.

  19. Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.

    PubMed

    Flowers, Jonathan M; Hazzouri, Khaled M; Pham, Gina M; Rosas, Ulises; Bahmani, Tayebeh; Khraiwesh, Basel; Nelson, David R; Jijakli, Kenan; Abdrabu, Rasha; Harris, Elizabeth H; Lefebvre, Paul A; Hom, Erik F Y; Salehi-Ashtiani, Kourosh; Purugganan, Michael D

    2015-09-01

    We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.

  20. [Variation trends of natural vegetation net primary productivity in China under climate change scenario].

    PubMed

    Zhao, Dong-sheng; Wu, Shao-hong; Yin, Yun-he

    2011-04-01

    Based on the widely used Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ) for climate change study, and according to the features of natural environment in China, the operation mechanism of the model was adjusted, and the parameters were modified. With the modified LPJ model and taking 1961-1990 as baseline period, the responses of natural vegetation net primary productivity (NPP) in China to climate change in 1991-2080 were simulated under the Special Report on Emissions Scenarios (SRES) B2 scenario. In 1961-1990, the total NPP of natural vegetation in China was about 3.06 Pg C a(-1); in 1961-2080, the total NPP showed a fluctuant decreasing trend, with an accelerated decreasing rate. Under the condition of slight precipitation change, the increase of mean air temperature would have definite adverse impact on the NPP. Spatially, the NPP decreased from southeast coast to northwest inland, and this pattern would have less variation under climate change. In eastern China with higher NPP, especially in Northeast China, east of North China, and Loess Plateau, the NPP would mainly have a decreasing trend; while in western China with lower NPP, especially in the Tibetan Plateau and Tarim Basin, the NPP would be increased. With the intensive climate change, such a variation trend of NPP would be more obvious. PMID:21774310

  1. Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy1[OPEN

    PubMed Central

    Xiang, Yong; Song, Baoxing; Née, Guillaume; Kramer, Katharina; Soppe, Wim J.J.

    2016-01-01

    Seed dormancy controls the timing of germination, which regulates the adaptation of plants to their environment and influences agricultural production. The time of germination is under strong natural selection and shows variation within species due to local adaptation. The identification of genes underlying dormancy quantitative trait loci is a major scientific challenge, which is relevant for agricultural and ecological goals. In this study, we describe the identification of the DELAY OF GERMINATION18 (DOG18) quantitative trait locus, which was identified as a factor in natural variation for seed dormancy in Arabidopsis (Arabidopsis thaliana). DOG18 encodes a member of the clade A of the type 2C protein phosphatases family, which we previously identified as the REDUCED DORMANCY5 (RDO5) gene. DOG18/RDO5 shows a relatively high frequency of loss-of-function alleles in natural accessions restricted to northwestern Europe. The loss of dormancy in these loss-of-function alleles can be compensated for by genetic factors like DOG1 and DOG6, and by environmental factors such as low temperature. RDO5 does not have detectable phosphatase activity. Analysis of the phosphoproteome in dry and imbibed seeds revealed a general decrease in protein phosphorylation during seed imbibition that is enhanced in the rdo5 mutant. We conclude that RDO5 acts as a pseudophosphatase that inhibits dephosphorylation during seed imbibition. PMID:27288362

  2. Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments.

    PubMed Central

    Weinig, Cynthia; Ungerer, Mark C; Dorn, Lisa A; Kane, Nolan C; Toyonaga, Yuko; Halldorsdottir, Solveig S; Mackay, Trudy F C; Purugganan, Michael D; Schmitt, Johanna

    2002-01-01

    Molecular biologists are rapidly characterizing the genetic basis of flowering in model species such as Arabidopsis thaliana. However, it is not clear how the developmental pathways identified in controlled environments contribute to variation in reproductive timing in natural ecological settings. Here we report the first study of quantitative trait loci (QTL) for date of bolting (the transition from vegetative to reproductive growth) in A. thaliana in natural seasonal field environments and compare the results with those obtained under typical growth-chamber conditions. Two QTL specific to long days in the chamber were expressed only in spring-germinating cohorts in the field, and two loci specific to short days in the chamber were expressed only in fall-germinating cohorts, suggesting differential involvement of the photoperiod pathway in different seasonal environments. However, several other photoperiod-specific QTL with large effects in controlled conditions were undetectable in natural environments, indicating that expression of allelic variation at these loci was overridden by environmental factors specific to the field. Moreover, a substantial number of QTL with major effects on bolting date in one or more field environments were undetectable under controlled environment conditions. These novel loci suggest the involvement of additional genes in the transition to flowering under ecologically relevant conditions. PMID:12524356

  3. [Variation trends of natural vegetation net primary productivity in China under climate change scenario].

    PubMed

    Zhao, Dong-sheng; Wu, Shao-hong; Yin, Yun-he

    2011-04-01

    Based on the widely used Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ) for climate change study, and according to the features of natural environment in China, the operation mechanism of the model was adjusted, and the parameters were modified. With the modified LPJ model and taking 1961-1990 as baseline period, the responses of natural vegetation net primary productivity (NPP) in China to climate change in 1991-2080 were simulated under the Special Report on Emissions Scenarios (SRES) B2 scenario. In 1961-1990, the total NPP of natural vegetation in China was about 3.06 Pg C a(-1); in 1961-2080, the total NPP showed a fluctuant decreasing trend, with an accelerated decreasing rate. Under the condition of slight precipitation change, the increase of mean air temperature would have definite adverse impact on the NPP. Spatially, the NPP decreased from southeast coast to northwest inland, and this pattern would have less variation under climate change. In eastern China with higher NPP, especially in Northeast China, east of North China, and Loess Plateau, the NPP would mainly have a decreasing trend; while in western China with lower NPP, especially in the Tibetan Plateau and Tarim Basin, the NPP would be increased. With the intensive climate change, such a variation trend of NPP would be more obvious.

  4. Investigating natural variation in Drosophila courtship song by the evolve and resequence approach.

    PubMed

    Turner, Thomas L; Miller, Paige M

    2012-06-01

    A primary goal of population genetics is to determine the genetic basis of natural trait variation. We could significantly advance this goal by developing comprehensive genome-wide approaches to link genotype and phenotype in model organisms. Here we combine artificial selection with population-based resequencing to investigate the genetic basis of variation in the interpulse interval (IPI) of Drosophila melanogaster courtship song. We performed divergent selection on replicate populations for only 14 generations, but had considerable power to differentiate alleles that evolved due to selection from those that evolved stochastically. We identified a large number of variants that changed frequency in response to selection for this simple behavior, and they are highly underrepresented on the X chromosome. Though our power was adequate using this experimental technique, the ability to differentiate causal variants from those affected by linked selection requires further development.

  5. Variation in Y chromosome segregation in natural populations of Drosophila melanogaster

    SciTech Connect

    Clark, A.G.

    1987-01-01

    Functional variation among Y chromosomes in natural populations of Drosophila melanogaster was assayed by a segregation study. A total of 36 Y chromosomes was extracted and ten generations of replacement backcrossing yielded stocks with Y chromosomes in two different genetic backgrounds. Eleven of the Y chromosomes were from diverse geographic origins, and the remaining 25 were from locally captured flies. Segregation of sexes in adult offspring was scored for the four possible crosses among the two backgrounds with each Y chromosome. Although the design confounds meiotic drive and effects on viability, statistical partitioning of these effects reveals significant variation among lines in Y chromosome segregation. Results are discussed in regards to models of Y-linked segregation and viability effects, which suggest that Y-linked adaptive polymorphism is unlikely.

  6. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.

    PubMed

    Chen, Wei; Gao, Yanqiang; Xie, Weibo; Gong, Liang; Lu, Kai; Wang, Wensheng; Li, Yang; Liu, Xianqing; Zhang, Hongyan; Dong, Huaxia; Zhang, Wan; Zhang, Lejing; Yu, Sibin; Wang, Gongwei; Lian, Xingming; Luo, Jie

    2014-07-01

    Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

  7. Natural variation of folate content and composition in spinach (Spinacia oleracea) germplasm.

    PubMed

    Shohag, M J I; Wei, Yan-yan; Yu, Ning; Zhang, Jie; Wang, Kai; Patring, Johan; He, Zhen-li; Yang, Xiao-e

    2011-12-14

    Breeding to increase folate levels in edible parts of plants, termed folate biofortification, is an economical approach to fight against folate deficiency in humans, especially in the developing world. Germplasm with elevated folates are a useful genetic source for both breeding and direct use. Spinach is one of the well-know vegetables that contains a relatively high amount of folate. Currently, little is known about how much folate, and their composition varies in different spinach accessions. The aim of this study was to investigate natural variation in the folate content and composition of spinach genotypes grown under controlled environmental conditions. The folate content and composition in 67 spinach accessions were collected from the United States Department of Agriculture (USDA) and Asian Vegetable Research and Development Center (AVRDC) germplasm collections according to their origin, grown under control conditions to screen for natural diversity. Folates were extracted by a monoenzyme treatment and analyzed by a validated liquid chromatography (LC) method. The total folate content ranged from 54.1 to 173.2 μg/100 g of fresh weight, with 3.2-fold variation, and was accession-dependent. Four spinach accessions (PI 499372, NSL 6095, PI 261787, and TOT7337-B) have been identified as enriched folate content over 150 μg/100 g of fresh weight. The folate forms found were H(4)-folate, 5-CH(3)-H(4)-folate, and 5-HCO-H(4)-folate, and 10-CHO-folic acid also varied among different accessions and was responsible for variation in the total folate content. The major folate vitamer was represented by 5-CH(3)-H(4)-folate, which on average accounted for up to 52% of the total folate pool. The large variation in the total folate content and composition in diverse spinach accessions demonstrates the great genetic potential of diverse genotypes to be exploited by plant breeders.

  8. Modelling natural grass production and its spatio-temporal variations in a semiarid Mediterranean watershed

    NASA Astrophysics Data System (ADS)

    Schnabel, Susanne; Lozano-Parra, Javier; Maneta-López, Marco

    2014-05-01

    Natural grasses are found in semiarid rangelands with disperse tree cover of part of the Iberian Peninsula and constitute a resource with high ecologic and economic value worth, being an important source of food for livestock, playing a significant role in the hydrologic cycle, controlling the soil thermal regime, and are a key factor in reducing soil erosion and degradation. However, increasing pressure on the resources, changes in land use as well as possible climate variations threaten the sustainability of natural grasses. Despite of their importance, the spatio-temporal variations of pasture production over whole watersheds are poorly known. In this sense, previous studies by other authors have indicated its dependence on a balance of positive and negative effects brought about by the main limiting factors: water, light, nutrients and space. Nevertheless, the specific weight of each factor is not clear because they are highly variable due to climate characteristics and the structure of these agroforestry systems. We have used a physical spatially-distributed ecohydrologic model to investigate the specific weight of factors that contribute to pasture production in a semiarid watershed of 99.5 ha in western Spain. This model couples a two layer (canopy and understory) vertical local closure energy balance scheme, a hydrologic model and a carbon uptake and vegetation growth component, and it was run using a synthetic daily climate dataset generated by a stochastic weather generator, which reproduced the range of climatic variations observed under mediterranean current climate. The modelling results reproduced satisfactorily the seasonality effects of climate as precipitation and temperatures, as well as annual and inter-annual variations of pasture production. Spatial variations of pasture production were largely controlled by topographic and tree effects, showing medium-low values depending of considered areas. These low values require introduction of feed to

  9. Neutron moderation in the Oklo natural reactor and the time variation of α

    NASA Astrophysics Data System (ADS)

    Lamoreaux, S. K.; Torgerson, J. R.

    2004-06-01

    In previous analyses of the Oklo (Gabon) natural reactor to test for a possible time variation of the fine-structure constant α, a Maxwell-Boltzmann low energy neutron spectrum was assumed. We present here an analysis where a more realistic spectrum is employed and show that the most recent isotopic analysis of samples implies a decrease in α, over the last 2×109 years since the reactor was operating, of (αpast-αnow)/α⩾4.5×10-8 (6σ confidence). Issues regarding the interpretation of the shifts of the low energy neutron absorption resonances are discussed.

  10. Fast Oxidation Processes in a Naturally Reduced Aquifer Zone Caused by Dissolved Oxygen

    NASA Astrophysics Data System (ADS)

    Davis, J. A.; Jemison, N. E.; Williams, K. H.; Hobson, C.; Bush, R. P.

    2014-12-01

    The occurrence of naturally reduced zones is quite common in alluvial aquifers in the western U.S.A. due to the burial of woody debris in flood plains. The naturally reduced zones are heterogeneously dispersed in such aquifers and are characterized by high concentrations of organic carbon and reduced phases, including iron sulfides and reduced forms of metals, including uranium(IV). The persistence of high concentrations of dissolved uranium(VI) at uranium-contaminated aquifers on the Colorado Plateau has been attributed to slow oxidation of insoluble uranium(IV) mineral phases that are found in association with these natural reducing zones, although there is little understanding of the relative importance of various potential oxidants. Three field experiments were conducted within an alluvial aquifer adjacent to the Colorado River near Rifle, CO wherein groundwater associated with naturally reduced zones was pumped into a gas-impermeable tank, mixed with a conservative tracer (Br-), bubbled with a gas phase composed of 97% O2 and 3% CO2, and then returned to the subsurface in the same well from which it was withdrawn. Within minutes of re-injection of the oxygenated groundwater, dissolved uranium(VI) concentrations increased from less than 1 μM to greater than 2.5 μM, demonstrating that oxygen can be an important oxidant for uranium in these field systems if supplied to the naturally reduced zones. Small concentrations of nitrate were also observed in the previously nitrate-free groundwater, and Fe(II) decreased to the detection limit. These results contrast with other laboratory and field results in which oxygen was introduced to systems containing high concentrations of mackinawite (FeS) rather than the more crystalline iron sulfides found in aged, naturally reduced zones. The flux of oxygen to the naturally reduced zones in the alluvial aquifers occurs mainly through interactions between groundwater and gas phases at the water table, and seasonal variations

  11. Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences

    PubMed Central

    Puritz, Jonathan B.; Gold, John R.; Portnoy, David S.

    2016-01-01

    Conservation and management of exploited species depends on accurate knowledge of how genetic variation is partitioned across a fishery, especially as it relates to recruitment. Using double-digest restriction-site associated DNA sequencing, we surveyed variation in 7,382 single nucleotide polymorphisms (SNPs) in red snapper (Lutjanus campechanus) young-of-the-year (YOY) sampled at six localities and in adults sampled at two localities in the northern Gulf of Mexico. Significant genetic heterogeneity was detected between the two adult samples, separated by ~600 km, and at spatial scales less than five kilometers among samples of  YOY. Genetic differences between YOY samples and between YOY samples and adult samples were not associated with geographic distance, and a genome scan revealed no evidence of loci under selection. Estimates of the effective number of breeders, allelic richness, and relatedness within YOY samples were not consistent with sweepstakes recruitment. Instead, the data demonstrate, at least within one recruitment season, that multiple pulses of recruits originate from distinct groups of spawning adults, even at small spatial scales. For exploited species with this type of recruitment pattern, protection of spawning adults over wide geographic areas may be critical for ensuring productivity and stability of the fishery by maintaining larval supply and connectivity. PMID:27782185

  12. WHAT CAUSES THE INTER-SOLAR-CYCLE VARIATION OF TOTAL SOLAR IRRADIANCE?

    SciTech Connect

    Xiang, N. B.; Kong, D. F.

    2015-12-15

    The Physikalisch Meteorologisches Observatorium Davos total solar irradiance (TSI), Active Cavity Radiometer Irradiance Monitoring TSI, and Royal Meteorological Institute of Belgium TSI are three typical TSI composites. Magnetic Plage Strength Index (MPSI) and Mount Wilson Sunspot Index (MWSI) should indicate the weak and strong magnetic field activity on the solar full disk, respectively. Cross-correlation (CC) analysis of MWSI with three TSI composites shows that TSI should be weakly correlated with MWSI, and not be in phase with MWSI at timescales of solar cycles. The wavelet coherence (WTC) and partial wavelet coherence (PWC) of TSI with MWSI indicate that the inter-solar-cycle variation of TSI is also not related to solar strong magnetic field activity, which is represented by MWSI. However, CC analysis of MPSI with three TSI composites indicates that TSI should be moderately correlated and accurately in phase with MPSI at timescales of solar cycles, and that the statistical significance test indicates that the correlation coefficient of three TSI composites with MPSI is statistically significantly higher than that of three TSI composites with MWSI. Furthermore, the cross wavelet transform (XWT) and WTC of TSI with MPSI show that the TSI is highly related and actually in phase with MPSI at a timescale of a solar cycle as well. Consequently, the CC analysis, XWT, and WTC indicate that the solar weak magnetic activity on the full disk, which is represented by MPSI, dominates the inter-solar-cycle variation of TSI.

  13. Identifying variations in thinking about the nature of science: A phenomenographic study

    NASA Astrophysics Data System (ADS)

    Keiser, Jonathan Charles

    It is hard to imagine how one can be scientifically literate without understanding what science is about. One of the central elements of science education reform efforts over the last twenty years has been ensuring that students have a deep understanding of the nature of science (Abd-El-Khalick et al., 2008). However, research suggests these efforts have done little to improve students' understanding of the nature of science (Sutherland et al., 2007). Much of the current research is aimed at evaluating the correctness of students' conceptions or classifying conceptions according to philosophical positions (Bell et al., 2003; Khishfe 2008). This study attempts to build off that work by using an emergent phenomenographic research approach to identify variations in high school chemistry students' thinking about the nature of science, using open-ended written response data from a six-item questionnaire that probes the following aspects of the nature of science: (1) Purpose of science; (2) Tentativeness of scientific knowledge and the nature of theories; (3) Creativity & imagination; (4) Aim & structure of experiments. This analysis yielded 39 primary level codes, which were then collapsed based on similarity into 14 categories of description. These categories reflect a wide range of understanding about science. Further analysis highlighted relationships between the categories and suggests two different orientations toward the nature of science. Some high school students orient their thinking about science in terms of an activity driven to prove or make certain, characterized by a collection of facts, whereas other students orient their thinking about science in terms of a finding out activity that results in discovering new information. The results of this study reveal more nuanced conceptions within these four aspects of the nature of science. Implications for science education and future research are discussed.

  14. Unit-based incident reporting and root cause analysis: variation at three hospital unit types

    PubMed Central

    Wagner, Cordula; Merten, Hanneke; Zwaan, Laura; Lubberding, Sanne; Timmermans, Danielle; Smits, Marleen

    2016-01-01

    Objectives To minimise adverse events in healthcare, various large-scale incident reporting and learning systems have been developed worldwide. Nevertheless, learning from patient safety incidents is going slowly. Local, unit-based reporting systems can help to get faster and more detailed insight into unit-specific safety issues. The aim of our study was to gain insight into types and causes of patient safety incidents in hospital units and to explore differences between unit types. Design Prospective observational study. Setting 10 emergency medicine units, 10 internal medicine units and 10 general surgery units in 20 hospitals in the Netherlands participated. Patient safety incidents were reported by healthcare providers. Reports were analysed with root cause analysis. The results were compared between the 3 unit types. Results A total of 2028 incidents were reported in an average reporting period of 8 weeks per unit. More than half had some consequences for patients, such as a prolonged hospital stay or longer waiting time, and a small number resulted in patient harm. Significant differences in incident types and causes were found between unit types. Emergency units reported more incidents related to collaboration, whereas surgical and internal medicine units reported more incidents related to medication use. The distribution of root causes of surgical and emergency medicine units showed more mutual similarities than those of internal medicine units. Conclusions Comparable incidents and causes have been found in all units, but there were also differences between units and unit types. Unit-based incident reporting gives specific information and therefore makes improvements easier. We conclude that unit-based incident reporting has an added value besides hospital-wide or national reporting systems that already exist in various countries. PMID:27329443

  15. Molecular basis of natural variation and environmental control of trichome patterning.

    PubMed

    Hauser, Marie-Theres

    2014-01-01

    Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

  16. Natural genetic variation for morphological and molecular determinants of plant growth and yield.

    PubMed

    Nunes-Nesi, Adriano; Nascimento, Vitor de Laia; de Oliveira Silva, Franklin Magnum; Zsögön, Agustin; Araújo, Wagner L; Sulpice, Ronan

    2016-05-01

    The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes.

  17. Molecular basis of natural variation and environmental control of trichome patterning

    PubMed Central

    Hauser, Marie-Theres

    2014-01-01

    Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

  18. Learning about natural variation of odor mixtures enhances categorization in early olfactory processing.

    PubMed

    Locatelli, Fernando F; Fernandez, Patricia C; Smith, Brian H

    2016-09-01

    Natural odors are typically mixtures of several chemical components. Mixtures vary in composition among odor objects that have the same meaning. Therefore a central 'categorization' problem for an animal as it makes decisions about odors in natural contexts is to correctly identify odor variants that have the same meaning and avoid variants that have a different meaning. We propose that identified mechanisms of associative and non-associative plasticity in early sensory processing in the insect antennal lobe and mammalian olfactory bulb are central to solving this problem. Accordingly, this plasticity should work to improve categorization of odors that have the opposite meanings in relation to important events. Using synthetic mixtures designed to mimic natural odor variation among flowers, we studied how honey bees learn about and generalize among floral odors associated with food. We behaviorally conditioned honey bees on a difficult odor discrimination problem using synthetic mixtures that mimic natural variation among snapdragon flowers. We then used calcium imaging to measure responses of projection neurons of the antennal lobe, which is the first synaptic relay of olfactory sensory information in the brain, to study how ensembles of projection neurons change as a result of behavioral conditioning. We show how these ensembles become 'tuned' through plasticity to improve categorization of odors that have the different meanings. We argue that this tuning allows more efficient use of the immense coding space of the antennal lobe and olfactory bulb to solve the categorization problem. Our data point to the need for a better understanding of the 'statistics' of the odor space.

  19. Learning about natural variation of odor mixtures enhances categorization in early olfactory processing.

    PubMed

    Locatelli, Fernando F; Fernandez, Patricia C; Smith, Brian H

    2016-09-01

    Natural odors are typically mixtures of several chemical components. Mixtures vary in composition among odor objects that have the same meaning. Therefore a central 'categorization' problem for an animal as it makes decisions about odors in natural contexts is to correctly identify odor variants that have the same meaning and avoid variants that have a different meaning. We propose that identified mechanisms of associative and non-associative plasticity in early sensory processing in the insect antennal lobe and mammalian olfactory bulb are central to solving this problem. Accordingly, this plasticity should work to improve categorization of odors that have the opposite meanings in relation to important events. Using synthetic mixtures designed to mimic natural odor variation among flowers, we studied how honey bees learn about and generalize among floral odors associated with food. We behaviorally conditioned honey bees on a difficult odor discrimination problem using synthetic mixtures that mimic natural variation among snapdragon flowers. We then used calcium imaging to measure responses of projection neurons of the antennal lobe, which is the first synaptic relay of olfactory sensory information in the brain, to study how ensembles of projection neurons change as a result of behavioral conditioning. We show how these ensembles become 'tuned' through plasticity to improve categorization of odors that have the different meanings. We argue that this tuning allows more efficient use of the immense coding space of the antennal lobe and olfactory bulb to solve the categorization problem. Our data point to the need for a better understanding of the 'statistics' of the odor space. PMID:27412003

  20. Color variations of AR coatings caused by a leached layer on the substrate.

    PubMed

    Guenther, K H

    1981-01-01

    Color differences of AR-coated prisms were found to be due to a surface layer with a refractive index of n = 1.46 and a geometrical thickness of ~41 nra on the glass substrate (BaK4, n = 1.5688). The existence of this layer is demonstrated by reflection spectroscopy measurements together with numerical calculations of the spectral reflectance of both the uncoated and coated substrates. Auger electron spectroscopy depth profiling analyses reveal that the Ba content of the glass had been leached out completely in the layer. The leaching process was caused by an improper cleaning agent used with the uncoated prisms in the optical shop. In addition to its inherent optical interference effect, the leached substrate surface seems to influence the condensation and growth of the first layer of AR coatings deposited onto it thus causing additional changes of the spectral characteristics of the coating.

  1. [Pyrimidal syndrome and anatomical variations as a cause of insidious sciatic pain].

    PubMed

    Ortiz Sánchez, V E; Charco Roca, L M; Soria Quiles, A; Zafrilla Disla, E; Hernandez Mira, F

    2014-11-01

    The case is presented of a 42 year old woman who had been suffering a loss of strength in her left leg for six years. After an extensive diagnostic study, the pain was classified as of functional origin by a diagnosis of exclusion. Since then, the patient has tried all kind of drug treatments and conservative techniques without improvement. After an exhaustive study with inconclusive results, the case was discussed with the Orthopaedics Department, who performed an exploratory surgery, in which compression of the sciatic nerve due to an anatomical variation of the piriformis muscle was observed. Part of the muscle was resected during surgery and the sciatic nerve was freed, after which the patient experienced a great improvement.

  2. Metal accumulation in mosses across national boundaries: uncovering and ranking causes of spatial variation.

    PubMed

    Schröder, Winfried; Pesch, Roland; Englert, Cordula; Harmens, Harry; Suchara, Ivan; Zechmeister, Harald G; Thöni, Lotti; Mankovská, Blanka; Jeran, Zvonka; Grodzinska, Krystyna; Alber, Renate

    2008-01-01

    This study aimed at cross-border mapping metal loads in mosses in eight European countries in 1990, 1995, and 2000 and at investigating confounding factors. Geostatistics was used for mapping, indicating high local variances but clear spatial autocorrelations. Inference statistics identified differences of metal concentrations in mosses on both sides of the national borders. However, geostatistical analyses did not ascertain discontinuities of metal concentrations in mosses at national borders due to sample analysis in different laboratories applying a range of analytical techniques. Applying Classification and Regression Trees (CART) to the German moss data as an example, the local variation in metal concentrations in mosses were proved to depend mostly on different moss species, potential local emission sources, canopy drip and precipitation.

  3. The Decline in Living Kidney Donation in the United States: Random Variation or Cause for Concern?

    PubMed Central

    Rodrigue, James R.; Schold, Jesse D.; Mandelbrot, Didier A.

    2013-01-01

    The annual number of living kidney donors in the United States peaked at 6,647 in 2004. The preceding decade saw a 120% increase in living kidney donation. However, since 2004, living kidney donation has declined in all but one year, resulting in a 13% decline in the annual number of living kidney donors from 2004 to 2011. The proportional decline in living kidney donation has been more pronounced among men, blacks, younger adults, siblings, and parents. In this paper, we explore several possible explanations for the decline in living kidney donation, including an increase in medical unsuitability, an aging transplant patient population, financial disincentives, public policies, and shifting practice patterns, among others. We conclude that the decline in living donation is not merely reflective of random variation, but one that warrants action by transplant centers, the broader transplant community, and state and national governments. PMID:23759882

  4. The cause of the seasonal variation in the oxygen isotopic composition of precipitation along the western U.S. coast

    NASA Astrophysics Data System (ADS)

    Buenning, N. H.; Stott, L. D.; Yoshimura, K.; Berkelhammer, M. B.

    2012-12-01

    This study seeks to find the primary influence on the seasonal cycle of the oxygen isotopic composition of precipitation (δ18Op) along the western U.S. coast. Observed long-term mean seasonal variations of δ18Op from 16 different stations along the west coast are presented. The most robust features in the observations are high values in the summer and a drop in δ18Op during the winter, a feature observed at many mid-latitude locations. The Isotope-incorporated Global Spectral Model (IsoGSM) also simulates this wintertime drop in δ18Op along the west coast of the U.S. To better understand the cause of this seasonal variation, sensitivity experiments are performed with IsoGSM where individual oxygen isotope fractionation processes are turned off. These simulations reveal that the primary control on the seasonal variations is equilibrium oxygen isotopic fractionation during vapor condensation. There is almost no influence of the temperature dependence of equilibrium fractionation on the seasonal δ18Op cycle for both ocean evaporation and vapor condensation. Additional experiments (including tagging simulations) are performed to better understand why Rayleigh distillation causes the seasonal variation in δ18Op. Tagging results suggest no strong influence of seasonal moisture source variations on the seasonal δ18Op cycle, though the seasonal cycle of column-integrated water vapor δ18O values is in phase with the monthly shifts in moisture sources (in IsoGSM). The tagging simulations did however reveal that vertical oxygen isotope gradients and variations in condensation height cause the seasonal cycle in δ18Op. This results from seasonal changes in the polar jet, and subsequent changes to divergence and vertical velocities, which affects the uplift of moisture. These findings suggest that δ18Op in the western U.S. is a tracer of condensation height on seasonal timescales. The large influence of condensation height on δ18Op seasonality complicates

  5. Large-scale causes of variation in the serpentine vegetation of California

    USGS Publications Warehouse

    Grace, J.B.; Safford, H.D.; Harrison, S.

    2007-01-01

    Serpentine vegetation in California ranges from forest to shrubland and grassland, harbors many rare and endemic species, and is only moderately altered by invasive exotic species at the present time. To better understand the factors regulating the distribution of common/representative species, endemic/rare species, and the threat of exotics in this important flora, we analyzed broad-scale community patterns and environmental conditions in a geographically stratified set of samples from across the state. We considered three major classes of environmental influences: climate (especially precipitation), soils (especially the Mg2+/Ca2+ ratio), and the indirect influences of climate on soils. We used ordination to identify the major axes of variation in common species abundances, structural equation models to analyze the relationship of community axes and endemic and exotic species richness to the environment, and group analysis techniques to identify consistent groupings of species and characterize their properties. We found that community variation could be explained by a two-axis ordination. One axis ranged from conifer forest to grassland and was strongly related to precipitation. The second axis ranged from chaparral to grassland and had little relationship to current environmental conditions, suggesting a possible role for successional history. Precipitation and elevation were respectively the largest influences on endemic and exotic richness, followed by Mg 2+/Ca2+. The results also support the idea that long-term precipitation patterns have altered the Mg2+/Ca2+ ratio via selective leaching, resulting in indirect influences on endemics (positive) and exotics (negative) but not affecting the abundances of common species. We discuss implications of these findings for the conservation of the California serpentine flora. ?? 2007 Springer Science+Business Media B.V.

  6. Changes in the High-latitude Ocean as Possible Causes of Atmospheric CO2 Variations

    NASA Technical Reports Server (NTRS)

    Siegenthaler, U.

    1984-01-01

    Measurements on air enclosed in old polar ice have indicated that the atmospheric CO2 concentration was ca. 50 to 70 ppm lower in late glacial times than during the Holocene. Similar measurements performed on samples from a Greenland ice core, dating ca. 30,000 to 40,000 B.P., and have yielded evidence of several CO2 oscillations with an amplitude of ca. 50 ppm. Each change lasted on the order of a few centuries. A mechanism by which circulation changes in the high-latitude ocean could lead to rapid variations in atmospheric CO2 is proposed. In the Antarctic Ocean a slowing down of the vertical mixing would imply a smaller upward flux of sigma CO2 and nutrients. Assuming constant productivity, sigma CO2 and nutrients would be more completely used which would imply lower CO2 in these high-latitude surface waters. In areas with a warm surface, a slowing down of the circulation would not have a direct impact on CO2 because productivity would automatically decrease by the same factor as the upwelling rate of nutrients. Studies with a simple box model of the ocean-atmosphere system suggest that a suddent decrease by a factor of 2 of the water exchange between the surface and deep sea in high latitudes could lead to a CO2 decrease of ca. 40 to 50 ppm with a time constant of ca. 200 years. Deep-sea sediment studies indicate rapid changes in the high-latitude surface conditions of the North Atlantic and the Antarctic Oceans at the end of the last glaciation. Studies of carbon isotope ratios should help ascertain whether this proposed mechanism was indeed responsible for the CO2 variation.

  7. Some causes of inter-laboratory variation in the results of comet assay.

    PubMed

    Sirota, Nikolai P; Zhanataev, Aliy K; Kuznetsova, Elena A; Khizhnyak, Eugenii P; Anisina, Elena A; Durnev, Andrei D

    2014-08-01

    We performed an inter-laboratory study to determine the variation of comet assay results and to identify its possible reasons. An exchange of slides between Labs in different stages of the comet assay protocol was performed. Because identical slides, durations of alkali treatment and electrophoresis, and similar electric field strengths (2.0 V/cm and 2.14 V/cm) were used, we concluded that the observed inter-laboratory difference in the results is directly associated with the electrophoresis step. In Lab 1, mouse bone marrow cells were exposed to methyl methanesulfonate at concentrations of 10, 25 and 50 μM for 3 h at 37 °C. In Lab 2, cells the same as in Lab 1 were immobilized in LMA on slides and exposed to X-rays at doses of 3-8 Gy. We found that the transportation of slides after lysis or electrophoresis step, as well as different dyes used for scoring did not produce any significant effect on the results. No substantial difference in the data was also revealed when various software packages were used for image analysis. The temperature of the alkaline solution was shown to increase during electrophoresis and, besides, the temperature heterogeneity of the solution took place in the area of the platform, with a maximum in the middle of the chamber. The temperature heterogeneity could affect the rate of conversion of alkali labile sites into single stranded breaks. Thus, it was clearly indicated that real temperature variations during the alkali treatment and electrophoresis were an essential factor in the variability of the results between our Labs.

  8. Stratospheric Ozone Variations Caused by Solar Proton Events between 1963 and 2005

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Fleming, Eric L.

    2006-01-01

    Solar proton fluxes have been measured by satellites for over forty years (1963-2005). Several satellites, including the NASA Interplanetary Monitoring Platforms (1963-1993) and the NOAA Geostationary Operational Environmental Satellites (1994-2005), have been used to compile this long-term dataset. Some solar eruptions lead to solar proton events (SPEs) at the Earth, which typically last a few days. High energy solar protons associated with SPEs precipitate on the Earth's atmosphere and cause increases in odd hydrogen (HOx) and odd nitrogen (NOy) in the polar cap regions (greater than 60 degrees geomagnetic). The enhanced HOx leads to short-lived ozone depletion (days) due to the short lifetime of HOx constituents. The enhanced NOy leads to long-lived ozone changes because of the long lifetime of the NOy family in the stratosphere and lower mesosphere. Very large SPEs occurred in 1972, 1989, 2000, 2001, and 2003 and were predicted to cause maximum total ozone depletions of 1-3%, which lasted for several months to years past the events. These long-term ozone changes caused by SPES are discussed.

  9. The Effect of Cause of Death on Responses to the Bereaved: Suicide Compared to Accident and Natural Causes.

    ERIC Educational Resources Information Center

    Allen, Breon G.; And Others

    1994-01-01

    Examined impact of cause of death on responses to bereaved individual. Sixty adults listened to audiotape of recently bereaved widow. There were three versions of tape, each identical except for stated cause of death: suicide, accident, or heart attack. Found that respondents were more anxious after interaction than before. Perceptions of person…

  10. [Spatiotemporal variations of natural wetland CH4 emissions over China under future climate change].

    PubMed

    Liu, Jian-gong; Zhu, Qiu-an; Shen, Yan; Yang, Yan-zheng; Luo, Yun-peng; Peng, Chang-hui

    2015-11-01

    Based on a new process-based model, TRIPLEX-GHG, this paper analyzed the spatio-temporal variations of natural wetland CH4 emissions over China under different future climate change scenarios. When natural wetland distributions were fixed, the amount of CH4 emissions from natural wetland ecosystem over China would increase by 32.0%, 55.3% and 90.8% by the end of 21st century under three representative concentration pathways (RCPs) scenarios, RCP2. 6, RCP4.5 and RCP8.5, respectively, compared with the current level. Southern China would have higher CH4 emissions compared to that from central and northern China. Besides, there would be relatively low emission fluxes in western China while relatively high emission fluxes in eastern China. Spatially, the areas with relatively high CH4 emission fluxes would be concentrated in the middle-lower reaches of the Yangtze River, the Northeast and the coasts of the Pearl River. In the future, most natural wetlands would emit more CH4 for RCP4.5 and RCP8.5 than that of 2005. However, under RCP2.6 scenario, the increasing trend would be curbed and CH4 emissions (especially from the Qinghai-Tibet Plateau) begin to decrease in the late 21st century.

  11. Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach.

    PubMed

    Glinka, Sascha; Ometto, Lino; Mousset, Sylvain; Stephan, Wolfgang; De Lorenzo, David

    2003-11-01

    Demography and selection have been recognized for their important roles in shaping patterns of nucleotide variability. To investigate the relative effects of these forces in the genome of Drosophila melanogaster, we used a multi-locus scan (105 fragments) of X-linked DNA sequence variation in a putatively ancestral African and a derived European population. Surprisingly, we found evidence for a recent size expansion in the African population, i.e., a significant excess of singletons at a chromosome-wide level. In the European population, such an excess was not detected. In contrast to the African population, we found evidence for positive natural selection in the European sample: (i) a large number of loci with low levels of variation and (ii) a significant excess of derived variants at the low-variation loci that are fixed in the European sample but rare in the African population. These results are consistent with the hypothesis that the European population has experienced frequent selective sweeps in the recent past during its adaptation to new habitats. Our study shows the advantages of a genomic approach (over a locus-specific analysis) in disentangling demographic and selective forces.

  12. Natural variation in Pristionchus pacificus insect pheromone attraction involves the protein kinase EGL-4

    PubMed Central

    Hong, Ray L.; Witte, Hanh; Sommer, Ralf J.

    2008-01-01

    The geographical mosaic theory of coevolution predicts that different local species interactions will shape population traits, but little is known about the molecular factors involved in mediating the specificity of these interactions. Pristionchus nematodes associate with different scarab beetles around the world, with Pristionchus pacificus isolated primarily from the oriental beetle in Japan. In particular, the constituent populations of P. pacificus represent a rare opportunity to study multiple specialized interactions and the mechanisms that influence population traits at the genetic level. We identified a component of the cGMP signaling pathway to be involved in the natural variation for sensing the insect pheromone ETDA, using targeted introgression lines, exogenous cGMP treatment, and a null egl-4 allele. Our data strongly implicate egl-4 as one of several loci involved in behavioral variation in P. pacificus populations. That EGL-4 homologs have been independently implicated for behavioral variations in other invertebrate models suggests that EGL-4 may act as a modulator for interspecies behavioral repertoires across large phylogenetic distances. PMID:18509055

  13. The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae.

    PubMed

    Salinas, Francisco; Cubillos, Francisco A; Soto, Daniela; Garcia, Verónica; Bergström, Anders; Warringer, Jonas; Ganga, M Angélica; Louis, Edward J; Liti, Gianni; Martinez, Claudio

    2012-01-01

    Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs) that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories.

  14. On the Nature of Variations in Density and Composition within TATB-based Plastic Bonded Explosives

    SciTech Connect

    Kinney, J H; Willey, T M; Overturf, G

    2006-06-27

    Initiation of insensitive high explosives is affected by porosity in the 100 nm to micron size range. It is also recognized that as-pressed plastic bonded explosives (PBX) are heterogeneous in composition and density at much coarser length scale (10 microns-100 microns). However, variations in density and composition of these explosives have been poorly characterized. Here, we characterize the natural variations in composition and density of TATB-based PBX LX-17 with synchrotron radiation tomography and ultra small angle x-ray scattering. Large scale variations in composition occur as a result of binder enrichment at the prill particle boundaries. The pore fraction is twice as high in the prill particle as in the boundary. The pore distribution is bimodal, with small pores of 50-100 nm in radius and a broader distribution of pores in the 0.5-1.5 micron size range. The higher pore density within the prill particle is attributed to contact asperities between the crystallites that might inhibit complete consolidation and binder infiltration.

  15. Multiple natural enemies cause distance-dependent mortality at the seed-to-seedling transition.

    PubMed

    Fricke, Evan C; Tewksbury, Joshua J; Rogers, Haldre S

    2014-05-01

    Specialised natural enemies maintain forest diversity by reducing tree survival in a density- or distance-dependent manner. Fungal pathogens, insects and mammals are the enemy types most commonly hypothesised to cause this phenomenon. Still, their relative importance remains largely unknown, as robust manipulative experiments have generally targeted a single enemy type and life history stage. Here, we use fungicide, insecticide and physical exclosure treatments to isolate the impacts of each enemy type on two life history stages (germination and early seedling survival) in three tropical tree species. Distance dependence was evident for five of six species-stage combinations, with each enemy type causing distance dependence for at least one species stage and their importance varying widely between species and stages. Rather than implicating one enemy type as the primary agent of this phenomenon, our field experiments suggest that multiple agents acting at different life stages collectively contribute to this diversity-promoting mechanism.

  16. Glaciers. Attribution of global glacier mass loss to anthropogenic and natural causes.

    PubMed

    Marzeion, Ben; Cogley, J Graham; Richter, Kristin; Parkes, David

    2014-08-22

    The ongoing global glacier retreat is affecting human societies by causing sea-level rise, changing seasonal water availability, and increasing geohazards. Melting glaciers are an icon of anthropogenic climate change. However, glacier response times are typically decades or longer, which implies that the present-day glacier retreat is a mixed response to past and current natural climate variability and current anthropogenic forcing. Here we show that only 25 ± 35% of the global glacier mass loss during the period from 1851 to 2010 is attributable to anthropogenic causes. Nevertheless, the anthropogenic signal is detectable with high confidence in glacier mass balance observations during 1991 to 2010, and the anthropogenic fraction of global glacier mass loss during that period has increased to 69 ± 24%.

  17. Evolutionary causes and consequences of diversified CRISPR immune profiles in natural populations.

    PubMed

    England, Whitney E; Whitaker, Rachel J

    2013-12-01

    Host-pathogen co-evolution is a significant force which shapes the ecology and evolution of all types of organisms, and such interactions are driven by resistance and immunity mechanisms of the host. Diversity of resistance and immunity can affect the co-evolutionary trajectory of both host and pathogen. The microbial CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system is one host immunity mechanism which offers a tractable model for examining the dynamics of diversity in an immune system. In the present article, we review CRISPR variation observed in a variety of natural populations, examine the forces which can push CRISPRs towards high or low diversity, and investigate the consequences of various levels of diversity on microbial populations.

  18. Autism as a natural human variation: reflections on the claims of the neurodiversity movement.

    PubMed

    Jaarsma, Pier; Welin, Stellan

    2012-03-01

    Neurodiversity has remained a controversial concept over the last decade. In its broadest sense the concept of neurodiversity regards atypical neurological development as a normal human difference. The neurodiversity claim contains at least two different aspects. The first aspect is that autism, among other neurological conditions, is first and foremost a natural variation. The other aspect is about conferring rights and in particular value to the neurodiversity condition, demanding recognition and acceptance. Autism can be seen as a natural variation on par with for example homosexuality. The broad version of the neurodiversity claim, covering low-functioning as well as high-functioning autism, is problematic. Only a narrow conception of neurodiversity, referring exclusively to high-functioning autists, is reasonable. We will discuss the effects of DSM categorization and the medical model for high functioning autists. After a discussion of autism as a culture we will analyze various possible strategies for the neurodiversity movement to claim extra resources for autists as members of an underprivileged culture without being labelled disabled or as having a disorder. We will discuss their vulnerable status as a group and what obligation that confers on the majority of neurotypicals.

  19. Synthetic biology of metabolism: using natural variation to reverse engineer systems.

    PubMed

    Kliebenstein, Daniel J

    2014-06-01

    A goal of metabolic engineering is to take a plant and introduce new or modify existing pathways in a directed and predictable fashion. However, existing data does not provide the necessary level of information to allow for predictive models to be generated. One avenue to reverse engineer the necessary information is to study the genetic control of natural variation in plant primary and secondary metabolism. These studies are showing that any engineering model will have to incorporate information about 1000s of genes in both the nuclear and organellar genome to optimize the function of the introduced pathway. Further, these genes may interact in an unpredictable fashion complicating any engineering approach as it moves from the one or two gene manipulation to higher order stacking efforts. Finally, metabolic engineering may be influenced by a previously unrecognized potential for a plant to measure the metabolites within it. In combination, these observations from natural variation provide a beginning to help improve current efforts at metabolic engineering. PMID:24699221

  20. Autism as a natural human variation: reflections on the claims of the neurodiversity movement.

    PubMed

    Jaarsma, Pier; Welin, Stellan

    2012-03-01

    Neurodiversity has remained a controversial concept over the last decade. In its broadest sense the concept of neurodiversity regards atypical neurological development as a normal human difference. The neurodiversity claim contains at least two different aspects. The first aspect is that autism, among other neurological conditions, is first and foremost a natural variation. The other aspect is about conferring rights and in particular value to the neurodiversity condition, demanding recognition and acceptance. Autism can be seen as a natural variation on par with for example homosexuality. The broad version of the neurodiversity claim, covering low-functioning as well as high-functioning autism, is problematic. Only a narrow conception of neurodiversity, referring exclusively to high-functioning autists, is reasonable. We will discuss the effects of DSM categorization and the medical model for high functioning autists. After a discussion of autism as a culture we will analyze various possible strategies for the neurodiversity movement to claim extra resources for autists as members of an underprivileged culture without being labelled disabled or as having a disorder. We will discuss their vulnerable status as a group and what obligation that confers on the majority of neurotypicals. PMID:21311979

  1. Assessment of genetically modified soybean in relation to natural variation in the soybean seed metabolome.

    PubMed

    Clarke, Joseph D; Alexander, Danny C; Ward, Dennis P; Ryals, John A; Mitchell, Matthew W; Wulff, Jacob E; Guo, Lining

    2013-01-01

    Genetically modified (GM) crops currently constitute a significant and growing part of agriculture.An important aspect of GM crop adoption is to demonstrate safety; identifying differences in end points with respect to conventional crops is a part of the safety assessment process [corrected]. Untargeted metabolomics has the ability to profile diverse classes of metabolites and thus could be an adjunct for identification of differences between the GM crop and its conventional counterpart [corrected].To account for environmental effects and introgression of GM traits into diverse genetic backgrounds, we propose that the assessment for GM crop metabolic composition should be understood within the context of the natural variation for the crop. Using a non-targeted metabolomics platform, we profiled 169 metabolites and established their dynamic ranges from the seeds of 49 conventional soybean lines representing the current commercial genetic diversity. We further demonstrated that the metabolome of a GM line had no significant deviation from natural variation within the soybean metabolome, with the exception of changes in the targeted engineered pathway.

  2. Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several groups have reported on massive accumulation of total carotenoids in cassava storage root (CSR). Naturally occurring color variation associated with carotenoid accumulation was observed in cassava (Manihot esculenta Crantz) storage root of landraces from Amazon. Here carotenoid profiles from...

  3. Natural variation in steroid hormone profiles of male Timber Rattlesnakes, Crotalus horridus, in northwest Arkansas.

    PubMed

    Lind, Craig M; Beaupre, Steven J

    2014-09-15

    We describe the seasonal profile of circulating steroid hormones (testosterone and corticosterone) in relation to the breeding season in free ranging male Timber Rattlesnakes, Crotalus horridus, over the course of three active seasons. In addition, we examine variation in steroid concentrations across years and in relation to body condition. We found that seasonal profiles of plasma testosterone were different compared to other crotalines with similar mating patterns. Concentrations of testosterone were elevated above baseline in the three months leading up to the single late summer breeding season. Testosterone peaked in July at the onset of the breeding season and dropped to baseline during the peak months of breeding (August and September). Testosterone concentrations also varied annually. Although the exact cause of annual variation could not be established, our results indicate that weather patterns may have driven observed differences. Testosterone concentrations were positively related to body condition, indicating that testosterone production is modulated according to energetic status (particularly in the two months prior to the breeding season). Corticosterone did not vary seasonally or with any measured variable, a result similar to other studied crotalines. Our results highlight the importance of long-term descriptive studies of the regulatory mechanisms that underlie behavior and physiology in diverse taxa, as these mechanisms can vary greatly within and among populations and are valuable in elucidating the intrinsic and extrinsic sources of such variation.

  4. Natural allelic variations of xenobiotic-metabolizing enzymes affect sexual dimorphism in Oryzias latipes

    PubMed Central

    Katsumura, Takafumi; Oda, Shoji; Nakagome, Shigeki; Hanihara, Tsunehiko; Kataoka, Hiroshi; Mitani, Hiroshi; Kawamura, Shoji; Oota, Hiroki

    2014-01-01

    Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection. Interestingly, sexually selected traits show geographical variations within species despite strong directional selective pressures. This paradox has eluded many evolutionary biologists for some time, and several models have been proposed (e.g. ‘indicator model’ and ‘trade-off model’). However, disentangling which of these theories explains empirical patterns remains difficult, because genetic polymorphisms that cause variation in sexual differences are still unknown. In this study, we show that polymorphisms in cytochrome P450 (CYP) 1B1, which encodes a xenobiotic-metabolizing enzyme, are associated with geographical differences in sexual dimorphism in the anal fin morphology of medaka fish (Oryzias latipes). Biochemical assays and genetic cross experiments show that high- and low-activity CYP1B1 alleles enhanced and declined sex differences in anal fin shapes, respectively. Behavioural and phylogenetic analyses suggest maintenance of the high-activity allele by sexual selection, whereas the low-activity allele possibly has experienced positive selection due to by-product effects of CYP1B1 in inferred ancestral populations. The present data can elucidate evolutionary mechanisms behind genetic variations in sexual dimorphism and indicate trade-off interactions between two distinct mechanisms acting on the two alleles with pleiotropic effects of xenobiotic-metabolizing enzymes. PMID:25377463

  5. Natural allelic variations of xenobiotic-metabolizing enzymes affect sexual dimorphism in Oryzias latipes.

    PubMed

    Katsumura, Takafumi; Oda, Shoji; Nakagome, Shigeki; Hanihara, Tsunehiko; Kataoka, Hiroshi; Mitani, Hiroshi; Kawamura, Shoji; Oota, Hiroki

    2014-12-22

    Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection. Interestingly, sexually selected traits show geographical variations within species despite strong directional selective pressures. This paradox has eluded many evolutionary biologists for some time, and several models have been proposed (e.g. 'indicator model' and 'trade-off model'). However, disentangling which of these theories explains empirical patterns remains difficult, because genetic polymorphisms that cause variation in sexual differences are still unknown. In this study, we show that polymorphisms in cytochrome P450 (CYP) 1B1, which encodes a xenobiotic-metabolizing enzyme, are associated with geographical differences in sexual dimorphism in the anal fin morphology of medaka fish (Oryzias latipes). Biochemical assays and genetic cross experiments show that high- and low-activity CYP1B1 alleles enhanced and declined sex differences in anal fin shapes, respectively. Behavioural and phylogenetic analyses suggest maintenance of the high-activity allele by sexual selection, whereas the low-activity allele possibly has experienced positive selection due to by-product effects of CYP1B1 in inferred ancestral populations. The present data can elucidate evolutionary mechanisms behind genetic variations in sexual dimorphism and indicate trade-off interactions between two distinct mechanisms acting on the two alleles with pleiotropic effects of xenobiotic-metabolizing enzymes.

  6. Large-scale geographical variation confirms that climate change causes birds to lay earlier.

    PubMed

    Both, Christiaan; Artemyev, Aleksandr V; Blaauw, Bert; Cowie, Richard J; Dekhuijzen, Aarnoud J; Eeva, Tapio; Enemar, Anders; Gustafsson, Lars; Ivankina, Elena V; Järvinen, Antero; Metcalfe, Neil B; Nyholm, N Erik I; Potti, Jaime; Ravussin, Pierre-Alain; Sanz, Juan Jose; Silverin, Bengt; Slater, Fred M; Sokolov, Leonid V; Török, János; Winkel, Wolfgang; Wright, Jonathan; Zang, Herwig; Visser, Marcel E

    2004-08-22

    Advances in the phenology of organisms are often attributed to climate change, but alternatively, may reflect a publication bias towards advances and may be caused by environmental factors unrelated to climate change. Both factors are investigated using the breeding dates of 25 long-term studied populations of Ficedula flycatchers across Europe. Trends in spring temperature varied markedly between study sites, and across populations the advancement of laying date was stronger in areas where the spring temperatures increased more, giving support to the theory that climate change causally affects breeding date advancement.

  7. Causes, consequences, and perspectives in the variations of intestinal density of colonization of multidrug-resistant enterobacteria

    PubMed Central

    Ruppé, Etienne; Andremont, Antoine

    2013-01-01

    The intestinal microbiota is a complex environment that hosts 1013 to 1014 bacteria. Among these bacteria stand multidrug-resistant enterobacteria (MDRE), which intestinal densities can substantially vary, especially according to antibiotic exposure. The intestinal density of MDRE and their relative abundance (i.e., the proportion between the density of MDRE and the density of total enterobacteria) could play a major role in the infection process or patient-to-patient transmission. This review discusses the recent advances in understanding (i) what causes variations in the density or relative abundance of intestinal colonization, (ii) what are the clinical consequences of these variations, and (iii) what are the perspectives for maintaining these markers at low levels. PMID:23755045

  8. Stratospheric Ozone Variations Caused by Solar Proton Events between 1963 and the Present

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Fleming, Eric L.

    2007-01-01

    Solar proton fluxes have been measured by satellites for over forty years (1963-present). Several satellites, including the Interplanetary Monitoring Platforms (1963-1993) and the NOAA Geostationary Operational Environmental Satellites (1994-present), have been used to compile this long-term dataset. Some solar storms lead to solar proton events (SPEs) at the Earth, which typically last a few days. High energy solar protons associated with SPEs precipitate on the Earth's atmosphere and cause increases in odd hydrogen (HO(x)) and odd nitrogen (NO(y)) in the polar cap region (>60 degrees geomagnetic). The enhanced HO(x) leads to short-lived ozone depletion (-days) due to the short lifetime of HOx constituents. The enhanced NO(y) leads to long-lived ozone changes because of the long lifetime of the NO(y) family in the stratosphere and lower mesosphere. Very large SPEs occurred in 1972, 1989, 2000, 2001, and 2003 and were predicted to cause significant polar upper stratospheric ozone depletion (>10%), which lasted for several weeks past the events. Several satellite instruments (BUV, SBUV, SBUV/2, SAGE II, HALOE, SCIAMACHY, MIPAS, GOMOS, etc.) have measured ozone changes as a result of SPEs. The long-term influence of SPEs on ozone will be discussed in this presentation.

  9. The causes of variation in the presence of genetic covariance between sexual traits and preferences.

    PubMed

    Fowler-Finn, Kasey D; Rodríguez, Rafael L

    2016-05-01

    Mating traits and mate preferences often show patterns of tight correspondence across populations and species. These patterns of apparent coevolution may result from a genetic association between traits and preferences (i.e. trait-preference genetic covariance). We review the literature on trait-preference covariance to determine its prevalence and potential biological relevance. Of the 43 studies we identified, a surprising 63% detected covariance. We test multiple hypotheses for factors that may influence the likelihood of detecting this covariance. The main predictor was the presence of genetic variation in mate preferences, which is one of the three main conditions required for the establishment of covariance. In fact, 89% of the nine studies where heritability of preference was high detected covariance. Variables pertaining to the experimental methods and type of traits involved in different studies did not greatly influence the detection of trait-preference covariance. Trait-preference genetic covariance appears to be widespread and therefore represents an important and currently underappreciated factor in the coevolution of traits and preferences. PMID:25808899

  10. The causes of variation in the presence of genetic covariance between sexual traits and preferences.

    PubMed

    Fowler-Finn, Kasey D; Rodríguez, Rafael L

    2016-05-01

    Mating traits and mate preferences often show patterns of tight correspondence across populations and species. These patterns of apparent coevolution may result from a genetic association between traits and preferences (i.e. trait-preference genetic covariance). We review the literature on trait-preference covariance to determine its prevalence and potential biological relevance. Of the 43 studies we identified, a surprising 63% detected covariance. We test multiple hypotheses for factors that may influence the likelihood of detecting this covariance. The main predictor was the presence of genetic variation in mate preferences, which is one of the three main conditions required for the establishment of covariance. In fact, 89% of the nine studies where heritability of preference was high detected covariance. Variables pertaining to the experimental methods and type of traits involved in different studies did not greatly influence the detection of trait-preference covariance. Trait-preference genetic covariance appears to be widespread and therefore represents an important and currently underappreciated factor in the coevolution of traits and preferences.

  11. Epidemic seasonal infertility — a hypothesis for the cause of seasonal variation of births

    NASA Astrophysics Data System (ADS)

    Miura, T.; Shimura, M.

    1980-03-01

    A hypothesis is proposed to explain the seasonality of births and its variations, that some unrecognized epidemic infertile factors have existed seasonally. In that case, certain women born in a particular low birth rate season must be those who survived these infertile factors in very early stage of their fetal lives. Then in later years, when they become pregnant, they may possibly be immune or different in their susceptibility to these infertile factors. Therefore, mothers born in a particular low birth rate season would tend to bear babies more frequently in that season than the others. To examine this hypothesis, birth records in 1930 of two maternity hospitals in Tokyo were investigated. These years were chosen for a period when seasonality of birth was most prominent in Japan. First babies were excluded to eliminate disturbances by season of marriages and other possible non-biological factors. The results show that among 1038 mothers born in a low birthrate season, May July, 245 (23.6%) had babies in May July, while the other mothers had significantly less babies (19.0%, 819/4302, P<0.001) in the same season. This may imply that seasonality of birth may have been influenced by some immunogenic infertile factors epidemic in a particular season.

  12. Morphological variation in Staurastrum rotula (Zygnemaphyceae, Desmidiales) in the deepest natural Brazilian lake: essence or accident?

    PubMed

    Barbosa, L G; Araujo, G J M; Barbosa, F A R; Bicudo, C E M

    2014-05-01

    For many decades, polymorphism and its consequences have only been studied from the taxonomic point of view. Presently, interest has switched to the environmental causes of morphological variation and its consequences in the form and essence of the species. This study aimed at evaluating desmids morphological modifications of Staurastrum rotula Nordstedt during inter-annual succession patterns in two warm monomitic tropical lakes: Dom Helvécio (19°45'- 19°48'45″S, 42°33'45″W) and Carioca (19°45'20″S, 42°37'12″W). The effect of thermal stability and light and nutrients availability was based on samples collected monthly from January 2002 to December 2006 compared the morphological modifications. Results indicated that morphological variation, asexual reproduction, theratological forms, mucilaginous envelope and fungal infection were highest in Lake Dom Helvécio and coincided with the biomass increase of species with complex morphology between September and March (stratification period). The Zmix oscillation, wind and rainfall occurring at the end of the mixing period and beginning of the stratification were suggested as autochthonous and allochthonous disturbance agents, respectively, identified as inducers of asexual reproduction and consequently of the morphological variation. It was suggested that incidence of parasitism may act as a potential controlling agent for the Staurastrum rotula population size. It was concluded that morphological variation represents accidents in the original form, i.e. in the desmid species essence, promoting the existence of ecoforms, not of new infraspecific taxa. PMID:25166322

  13. Morphological variation in Staurastrum rotula (Zygnemaphyceae, Desmidiales) in the deepest natural Brazilian lake: essence or accident?

    PubMed

    Barbosa, L G; Araujo, G J M; Barbosa, F A R; Bicudo, C E M

    2014-05-01

    For many decades, polymorphism and its consequences have only been studied from the taxonomic point of view. Presently, interest has switched to the environmental causes of morphological variation and its consequences in the form and essence of the species. This study aimed at evaluating desmids morphological modifications of Staurastrum rotula Nordstedt during inter-annual succession patterns in two warm monomitic tropical lakes: Dom Helvécio (19°45'- 19°48'45″S, 42°33'45″W) and Carioca (19°45'20″S, 42°37'12″W). The effect of thermal stability and light and nutrients availability was based on samples collected monthly from January 2002 to December 2006 compared the morphological modifications. Results indicated that morphological variation, asexual reproduction, theratological forms, mucilaginous envelope and fungal infection were highest in Lake Dom Helvécio and coincided with the biomass increase of species with complex morphology between September and March (stratification period). The Zmix oscillation, wind and rainfall occurring at the end of the mixing period and beginning of the stratification were suggested as autochthonous and allochthonous disturbance agents, respectively, identified as inducers of asexual reproduction and consequently of the morphological variation. It was suggested that incidence of parasitism may act as a potential controlling agent for the Staurastrum rotula population size. It was concluded that morphological variation represents accidents in the original form, i.e. in the desmid species essence, promoting the existence of ecoforms, not of new infraspecific taxa.

  14. Using natural range of variation to set decision thresholds: a case study for great plains grasslands

    USGS Publications Warehouse

    Symstad, Amy J.; Jonas, Jayne L.; Edited by Guntenspergen, Glenn R.

    2014-01-01

    Natural range of variation (NRV) may be used to establish decision thresholds or action assessment points when ecological thresholds are either unknown or do not exist for attributes of interest in a managed ecosystem. The process for estimating NRV involves identifying spatial and temporal scales that adequately capture the heterogeneity of the ecosystem; compiling data for the attributes of interest via study of historic records, analysis and interpretation of proxy records, modeling, space-for-time substitutions, or analysis of long-term monitoring data; and quantifying the NRV from those data. At least 19 National Park Service (NPS) units in North America’s Great Plains are monitoring plant species richness and evenness as indicators of vegetation integrity in native grasslands, but little information on natural, temporal variability of these indicators is available. In this case study, we use six long-term vegetation monitoring datasets to quantify the temporal variability of these attributes in reference conditions for a variety of Great Plains grassland types, and then illustrate the implications of using different NRVs based on these quantities for setting management decision thresholds. Temporal variability of richness (as measured by the coefficient of variation, CV) is fairly consistent across the wide variety of conditions occurring in Colorado shortgrass prairie to Minnesota tallgrass sand savanna (CV 0.20–0.45) and generally less than that of production at the same sites. Temporal variability of evenness spans a greater range of CV than richness, and it is greater than that of production in some sites but less in other sites. This natural temporal variability may mask undesirable changes in Great Plains grasslands vegetation. Consequently, we suggest that managers consider using a relatively narrow NRV (interquartile range of all richness or evenness values observed in reference conditions) for designating a surveillance threshold, at which

  15. Pathogenic variation in isolates of Pseudomonas causing the brown blotch of cultivated mushroom, Agaricus bisporus

    PubMed Central

    Abou-Zeid, Mohamed A.

    2012-01-01

    Twenty seven bacterial isolates were isolated from superficial brown discolorations on the caps of cultivated Agaricus bisporus. After White Line Assay (WLA) and the assist of Biolog computer-identification system, isolates were divided into groups: (I) comprised ninteen bacterial isolates that positively responded to a Pseudomonas “reactans” reference strain (NCPPB1311) in WLA and were identified as Pseudomonas tolaasii, (II) comprised two isolates which were WLA+ towards the reference strain (JCM21583) of P. tolaasii and were proposed to be P. “reactans”. The third group comprised six isolates, two of which weakly responded to the strain of P. tolaasii and were identified as P. gingeri whereas the other four were WLA-and identified as P. fluorescens (three isolates) and P. marginalis (one isolate). Isolates of P. tolaasii showed high aggressiveness compared with those of P. “reactans” in pathogenicity tests. Cubes of 1 cm3 of A. bisporus turned brown and decreased in size when were inoculated with 10 µl of P. tolaasii suspension containing 108 CFU ml-1, whereas a similar concentration of P. “reactans” caused only light browning. Fifty µl of the same concentration of P. tolaasii isolates gave typical brown blotch symptoms on fresh mushroom sporophores whereas the two P. “reactans” isolates caused superficial light discoloration only after inoculation with 100 µl of the same concentration. Mixture from both bacterial suspensions increased the brown areas formed on the pileus. This is the first pathogenicity report of P. tolasii and P. “reactans” isolated from cultivated A. bisporus in Egypt. PMID:24031938

  16. The statistical significance test of regional climate change caused by land use and land cover variation in West China

    NASA Astrophysics Data System (ADS)

    Wang, H. J.; Shi, W. L.; Chen, X. H.

    2006-05-01

    The West Development Policy being implemented in China is causing significant land use and land cover (LULC) changes in West China. With the up-to-date satellite database of the Global Land Cover Characteristics Database (GLCCD) that characterizes the lower boundary conditions, the regional climate model RIEMS-TEA is used to simulate possible impacts of the significant LULC variation. The model was run for five continuous three-month periods from 1 June to 1 September of 1993, 1994, 1995, 1996, and 1997, and the results of the five groups are examined by means of a student t-test to identify the statistical significance of regional climate variation. The main results are: (1) The regional climate is affected by the LULC variation because the equilibrium of water and heat transfer in the air-vegetation interface is changed. (2) The integrated impact of the LULC variation on regional climate is not only limited to West China where the LULC varies, but also to some areas in the model domain where the LULC does not vary at all. (3) The East Asian monsoon system and its vertical structure are adjusted by the large scale LULC variation in western China, where the consequences axe the enhancement of the westward water vapor transfer from the east east and the relevant increase of wet-hydrostatic energy in the middle-upper atmospheric layers. (4) The ecological engineering in West China affects significantly the regional climate in Northwest China, North China and the middle-lower reaches of the Yangtze River; there are obvious effects in South, Northeast, and Southwest China, but minor effects in Tibet.

  17. [Temporal-spatial variations of reference evapotranspiration in Anhui Province and the quantification of the causes].

    PubMed

    Cao, Wen; Duan, Chun-feng; Yao, Yun; Yue, Wei

    2014-12-01

    In this paper, daily reference evapotranspiration (ET0) was computed with the recommended FAO-56 Penman-Monteith equation for Anhui Province using data collected 60 weather stations during 1961 to 2010 and its temporal-spatial variations were characterized. The determining factors in ET0 trends were inquired into through partial derivative quantification analysis for the study region. Results showed that the mean annual ET0 was 878.58 mm x a(-1) over the whole region during the study period. ET0 was the highest in summer and the lowest in winter. The mean annual ET0 decreased from the north to the south and from low altitude regions to high altitude regions. Both sunshine duration and wind speed were the dominant factors contributing to the interannual change of ET0, with less contribution from air temperature or relative humidity. The annual ET0 showed a general decline at a rate of -1.61 mm x a(-1) owing to a more negative contribution of sunshine duration and wind speed than a positive contribution of air temperature and relative humidity. ET0 increased insignificantly in spring and decreased slightly in both autumn and winter. However, it decreased significantly at a rate of -1.37 mm x a(-1) in summer. The main impacting factor was wind speed in spring, autumn and winter, but it was sunshine duration in summer. Great differences in the determining factors of the mean annual ET0 existed from area to area in Anhui Province. The wind speed was the determining factor for 36.7% of the whole stations distributing in the southern part of the area north to the Huaihe River and the area along the Huaihe River, while the sunshine duration was the determining factor for the other regions. PMID:25876416

  18. Genetic and environmental causes of variation in gestation length of Jersey crossbred cattle

    PubMed Central

    Kumar, Anshuman; Mandal, Ajoy; Gupta, A. K.; Ratwan, Poonam

    2016-01-01

    Aim: The objective of this study was to investigate the effect of genetic and non-genetic factors and estimate the genetic parameter for gestation length (GL) of Jersey crossbred cattle. Materials and Methods: The data included the 986 parturition records on Jersey crossbred cattle maintained at the Eastern Regional Station of ICAR-National Dairy Research Institute, Kalyani, West Bengal, India during 36 years (1978-2013). The data were analyzed applying mixed model least square technique considering the fixed effects of genetic group, season of calving, period of calving, parity of animal, birth weight, and sex of calf born from animal. The effect of sire was included as a random effect in the model. Results: The genetic group of animal, season of calving, parity of animal, and birth weight of calf born were found to be a significant source of variation in the GL, whereas the period of calving and sex of calf did not affect this trait. Cows with <50% and >62.5% Jersey inheritance had the shortest and longest GLs, respectively. Cows calved in summer and rainy season had shorter GL than those calved in the winter season. Older cows in 4th parity carried calves for longer days than the cows in 1st parity. The increase in calf birth weight significantly (p<0.01) contributed to a linear increase in GL value in this study. The heritability estimate of GL was 0.24±0.08. Conclusion: It can be concluded that selection for lower GL without distressing future growth of calf can be used to reduce calving difficulty, but a very small standard deviation of GL limits the benefit. Moreover, more accurate prediction of calving date will help in better management and health care of pregnant animals. PMID:27182128

  19. Chemical and microbial components of urban air PM cause seasonal variation of toxicological activity.

    PubMed

    Jalava, Pasi I; Happo, Mikko S; Huttunen, Kati; Sillanpää, Markus; Hillamo, Risto; Salonen, Raimo O; Hirvonen, Maija-Riitta

    2015-09-01

    The chemical and microbial composition of urban air particulate matter (PM) displays seasonal variation that may affect its harmfulness on human health. We studied the in vitro inflammatory and cellular metabolic activity/cytotoxicity of urban air particulate samples collected in four size-ranges (PM10-2.5, PM2.5-1, PM1-0.2, PM0.2) during four seasons in relatively clean urban environment in Helsinki, Finland. The composition of the same samples were analyzed, including ions, elements, PAH compounds and endotoxins. In addition, microbial contribution on the detected responses was studied by inhibiting the endotoxin-induced responses with Polymyxin B both in the PM samples and by two different bacterial strains representing Gram-positive and -negative bacteria. Macrophage cell line (RAW 264.7) was exposed to the size segregated particulate samples as well as to microbe samples for 24h and markers of inflammation and cytotoxicity were analyzed. The toxicological responses were dependent on the dose as well as size range of the particles, PM10-2.5 being the most potent and smaller size ranges having significantly smaller responses. Samples collected during spring and autumn had in most cases the highest inflammatory activity. Soil components and other non-exhaust particulate emissions from road traffic correlated with inflammatory responses in coarse particles. Instead, PAH-compounds and K(+) had negative associations with the particle-induced inflammatory responses in fine particles, suggesting the role of incomplete biomass combustion. Endotoxin content was the highest in PM10-2.5 samples and correspondingly, the largest decrease in the responses by Polymyxin B was seen with the very same samples. We found also that inhibitory effect of Polymyxin B was not completely specific for Gram-negative bacteria. Thus, in addition to endotoxin, also other microbial components may have a significant effect on the toxicological responses by ambient particulate matter.

  20. Variation of Natural Streamflow since 1470 in the Middle Yellow River, China

    PubMed Central

    Miao, Chi-Yuan; Ni, Jin-Ren

    2009-01-01

    Nowadays, as the available water resources throughout the World are becoming depleted, in order to manage and plan water resource better, more and more attention is being paid into the fluctuating characteristics of water discharges. However, the preexisting research was mainly focused on the last half century. In this paper, the natural streamflow observed since 1470 at the Sanmenxia station in the middle Yellow River basin was collected, and the methods of variation coefficient, moving average, Mann-Kendall test and wavelet transform were applied to analyze the dynamic characteristics of the streamflow. The results showed that, (1) between 1470 and 2007, the natural streamflow changed 200–919 × 108 m3, and water discharge varied moderately; (2) in the middle Yellow River basin, it appears that the most severe and most persistent droughts during circa 1868–1990, the periods of 1470s–1490s, 1920s–1930s and 1990s–2000s also presented the condition of sustained low flows; (3) the natural streamflow series shows increasing and decreasing trends during the periods of 1470–1880 and 1881–2007, respectively, but both trends are not significant at >95% confidence; in addition, it is still found the streamflow series shows abrupt changes circa 1845, 1935 and 1960, respectively; (4) within a 250-year scale, there are circa 11, 26, 67 and 120-year periods for natural streamflow at the Sanmenxia station, and the periodicity of the 120-year one is the strongest. The dynamic characteristics of natural streamflow is the comprehensive result by many influencing factors, such as precipitation, temperature, El Niño-Southern Oscillation, sunspots, human activity, etc. PMID:20049230

  1. Nature and results of treatment of war wounds caused by cluster bombs.

    PubMed

    Mitković, Milorad; Bumbasirević, Marko; Grubor, Predrag; Milenković, Sasa; Micić, Ivan; Stojiljković, Predrag; Kostić, Igor; Karaleić, Sasa; Stamenić, Sonja; Pavlović, Predrag; Stanojlović, Milos; Jovanović, Vladimir; Radovanović, Zoran; Cirić, Tamara; Kutlesić-Stojanović, Katarina; Mitković, Milan

    2013-01-01

    The aim of this study is to describe the nature of war wounds with fracture caused by cluster bombs and to suggest treatment options for such injuries. The nature of wounds caused by cluster bombs differs from those caused by conventional arms (they are more severe). The sides of the wounds are represented by conquasated soft tissues (such as fat and muscle) with thick dead tissues, ordinarily with a thickness of 0.5-4.5 cm. Another main characteristic of such injuries is the high percentage of amputations needed due to the high rate of neurovascular damage. This paper investigates the cases of 81 patients who sustained a total of 99 war wounds with fractures. The average age of the patients was 32.7 years while the youngest was 20 and the oldest, 77. According to The International Committee of the Red Cross (ICRC) classification of war wounds, 14 patients had grade I injuries, 48 patients grade II, and 29 patients, grade III. Mitkovic external fixation system, known also as the "War Fixator" was used for all fractures fixation. One protocol, which was a modification of the ICRC's protocol adapted to our specific conditions, was used throughout the study. For solving soft tissue defects, a rotator fasciocutan flap was the most frequently used. For solving of bones defect Mitkovic reconstructive external fixation device was used. All fractures we treated healed. We concluded that shortening the procedural time and being a very simple, immediate using of Mitkovic versatile external fixator ("War Fixator") is, leads to desirable results.

  2. Effects of walls temperature variation on double diffusive natural convection of Al2O3-water nanofluid in an enclosure

    NASA Astrophysics Data System (ADS)

    Sheikhzadeh, G. A.; Dastmalchi, M.; Khorasanizadeh, H.

    2013-12-01

    The effect of wall temperature variations on double diffusive natural convection of Al2O3-water nanofluid in a differentially heated square enclosure with constant temperature hot and cold vertical walls is studied numerically. Transport mechanisms of nanoparticles including Brownian diffusion and thermophoresis that cause heterogeneity are considered in non-homogeneous model. The hot and cold wall temperatures are varied, but the temperature difference between them is always maintained 5 °C. The thermophysical properties such as thermal conductivity, viscosity and density and thermophoresis diffusion and Brownian motion coefficients are considered variable with temperature and volume fraction of nanoparticles. The governing equations are discretized using the control volume method. The results show that nanoparticle transport mechanisms affect buoyancy force and cause formation of small vortexes near the top and bottom walls of the cavity and reduce the heat transfer. By increasing the temperature of the walls the effect of transport mechanisms decreases and due to enhanced convection the heat transfer rate increases.

  3. Variation in, and causes of, toxicity of cigarette butts to a cladoceran and microtox.

    PubMed

    Micevska, T; Warne, M St J; Pablo, F; Patra, R

    2006-02-01

    Cigarette butts are the most numerically frequent form of litter in the world. In Australia alone, 24-32 billion cigarette butts are littered annually. Despite this littering, few studies have been undertaken to explore the toxicity of cigarette butts in aquatic ecosystems. The acute toxicity of 19 filtered cigarette types to Ceriodaphnia cf. dubia (48-hr EC50 (immobilization)) and Vibrio fischeri (30-min EC50 (bioluminescence)) was determined using leachates from artificially smoked cigarette butts. There was a 2.9- and 8-fold difference in toxicity between the least and most toxic cigarette butts to C. cf. dubia and V. fischeri, respectively. Overall, C. cf. dubia was more inherently sensitive than V. fischeri by a factor of approximately 15.4, and the interspecies relationship between C. cf. dubia and V. fischeri was poor (R(2) = 0.07). This poor relationship indicates that toxicity data for cigarette butts for one species could not predict or model the toxicity of cigarette butts to the other species. However, the order of the toxicity of leachates can be predicted. It was determined that organic compounds caused the majority of toxicity in the cigarette butt leachates. Of the 14 organic compounds identified, nicotine and ethylphenol were suspected to be the main causative toxicants. There was a strong relationship between toxicity and tar content and between toxicity and nicotine content for two of the three brands of cigarettes (R(2 )> 0.70) for C. cf. dubia and one brand for V. fischeri. However, when the cigarettes were pooled, the relationship was weak (R(2) < 0.40) for both test species. Brand affected the toxicity to both species but more so for V. fischeri.

  4. Spatio-temporal distribution and natural variation of metabolites in citrus fruits.

    PubMed

    Wang, Shouchuang; Tu, Hong; Wan, Jian; Chen, Wei; Liu, Xianqing; Luo, Jie; Xu, Juan; Zhang, Hongyan

    2016-05-15

    To study the natural variation and spatio-temporal accumulation of citrus metabolites, liquid chromatography tandem mass spectrometry (LC-MS) based metabolome analysis was performed on four fruit tissues (flavedo, albedo, segment membrane and juice sacs) and different Citrus species (lemon, pummelo and grapefruit, sweet orange and mandarin). Using a non-targeted metabolomics approach, more than 2000 metabolite signals were detected, from which more than 54 metabolites, including amino acids, flavonoids and limonoids, were identified/annotated. Differential accumulation patterns of both primary metabolites and secondary metabolites in various tissues and species were revealed by our study. Further investigation indicated that flavedo accumulates more flavonoids while juice sacs contain more amino acids. Besides this, cluster analysis based on the levels of metabolites detected in 47 individual Citrus accessions clearly grouped them into four distinct clusters: pummelos and grapefruits, lemons, sweet oranges and mandarins, while the cluster of pummelos and grapefruits lay distinctly apart from the other three species.

  5. Ploidy-Regulated Variation in Biofilm-Related Phenotypes in Natural Isolates of Saccharomyces cerevisiae

    PubMed Central

    Hope, Elyse A.; Dunham, Maitreya J.

    2014-01-01

    The ability of yeast to form biofilms contributes to better survival under stressful conditions. We see the impact of yeast biofilms and “flocs” (clumps) in human health and industry, where forming clumps enables yeast to act as a natural filter in brewing and forming biofilms enables yeast to remain virulent in cases of fungal infection. Despite the importance of biofilms in yeast natural isolates, the majority of our knowledge about yeast biofilm genetics comes from work with a few tractable laboratory strains. A new collection of sequenced natural isolates from the Saccharomyces Genome Resequencing Project enabled us to examine the breadth of biofilm-related phenotypes in geographically, ecologically, and genetically diverse strains of Saccharomyces cerevisiae. We present a panel of 31 haploid and 24 diploid strains for which we have characterized six biofilm-related phenotypes: complex colony morphology, complex mat formation, flocculation, agar invasion, polystyrene adhesion, and psuedohyphal growth. Our results show that there is extensive phenotypic variation between and within strains, and that these six phenotypes are primarily uncorrelated or weakly correlated, with the notable exception of complex colony and complex mat formation. We also show that the phenotypic strength of these strains varies significantly depending on ploidy, and the diploid strains demonstrate both decreased and increased phenotypic strength with respect to their haploid counterparts. This is a more complex view of the impact of ploidy on biofilm-related phenotypes than previous work with laboratory strains has suggested, demonstrating the importance and enormous potential of working with natural isolates of yeast. PMID:25060625

  6. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

    PubMed Central

    Huang, Wen; Massouras, Andreas; Inoue, Yutaka; Peiffer, Jason; Ràmia, Miquel; Tarone, Aaron M.; Turlapati, Lavanya; Zichner, Thomas; Zhu, Dianhui; Lyman, Richard F.; Magwire, Michael M.; Blankenburg, Kerstin; Carbone, Mary Anna; Chang, Kyle; Ellis, Lisa L.; Fernandez, Sonia; Han, Yi; Highnam, Gareth; Hjelmen, Carl E.; Jack, John R.; Javaid, Mehwish; Jayaseelan, Joy; Kalra, Divya; Lee, Sandy; Lewis, Lora; Munidasa, Mala; Ongeri, Fiona; Patel, Shohba; Perales, Lora; Perez, Agapito; Pu, LingLing; Rollmann, Stephanie M.; Ruth, Robert; Saada, Nehad; Warner, Crystal; Williams, Aneisa; Wu, Yuan-Qing; Yamamoto, Akihiko; Zhang, Yiqing; Zhu, Yiming; Anholt, Robert R.H.; Korbel, Jan O.; Mittelman, David; Muzny, Donna M.; Gibbs, Richard A.; Barbadilla, Antonio; Johnston, J. Spencer; Stone, Eric A.; Richards, Stephen; Deplancke, Bart; Mackay, Trudy F.C.

    2014-01-01

    The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available. PMID:24714809

  7. Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa

    PubMed Central

    Xie, Qiguang; Lou, Ping; Hermand, Victor; Aman, Rashid; Park, Hee Jin; Yun, Dae-Jin; Kim, Woe Yeon; Salmela, Matti Juhani; Ewers, Brent E.; Weinig, Cynthia; Khan, Sarah L.; Schaible, D. Loring P.; McClung, C. Robertson

    2015-01-01

    GIGANTEA (GI) was originally identified by a late-flowering mutant in Arabidopsis, but subsequently has been shown to act in circadian period determination, light inhibition of hypocotyl elongation, and responses to multiple abiotic stresses, including tolerance to high salt and cold (freezing) temperature. Genetic mapping and analysis of families of heterogeneous inbred lines showed that natural variation in GI is responsible for a major quantitative trait locus in circadian period in Brassica rapa. We confirmed this conclusion by transgenic rescue of an Arabidopsis gi-201 loss of function mutant. The two B. rapa GI alleles each fully rescued the delayed flowering of Arabidopsis gi-201 but showed differential rescue of perturbations in red light inhibition of hypocotyl elongation and altered cold and salt tolerance. The B. rapa R500 GI allele, which failed to rescue the hypocotyl and abiotic stress phenotypes, disrupted circadian period determination in Arabidopsis. Analysis of chimeric B. rapa GI alleles identified the causal nucleotide polymorphism, which results in an amino acid substitution (S264A) between the two GI proteins. This polymorphism underlies variation in circadian period, cold and salt tolerance, and red light inhibition of hypocotyl elongation. Loss-of-function mutations of B. rapa GI confer delayed flowering, perturbed circadian rhythms in leaf movement, and increased freezing and increased salt tolerance, consistent with effects of similar mutations in Arabidopsis. Collectively, these data suggest that allelic variation of GI—and possibly of clock genes in general—offers an attractive target for molecular breeding for enhanced stress tolerance and potentially for improved crop yield. PMID:25775524

  8. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

    PubMed

    Huang, Wen; Massouras, Andreas; Inoue, Yutaka; Peiffer, Jason; Ràmia, Miquel; Tarone, Aaron M; Turlapati, Lavanya; Zichner, Thomas; Zhu, Dianhui; Lyman, Richard F; Magwire, Michael M; Blankenburg, Kerstin; Carbone, Mary Anna; Chang, Kyle; Ellis, Lisa L; Fernandez, Sonia; Han, Yi; Highnam, Gareth; Hjelmen, Carl E; Jack, John R; Javaid, Mehwish; Jayaseelan, Joy; Kalra, Divya; Lee, Sandy; Lewis, Lora; Munidasa, Mala; Ongeri, Fiona; Patel, Shohba; Perales, Lora; Perez, Agapito; Pu, LingLing; Rollmann, Stephanie M; Ruth, Robert; Saada, Nehad; Warner, Crystal; Williams, Aneisa; Wu, Yuan-Qing; Yamamoto, Akihiko; Zhang, Yiqing; Zhu, Yiming; Anholt, Robert R H; Korbel, Jan O; Mittelman, David; Muzny, Donna M; Gibbs, Richard A; Barbadilla, Antonio; Johnston, J Spencer; Stone, Eric A; Richards, Stephen; Deplancke, Bart; Mackay, Trudy F C

    2014-07-01

    The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.

  9. Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa.

    PubMed

    Xie, Qiguang; Lou, Ping; Hermand, Victor; Aman, Rashid; Park, Hee Jin; Yun, Dae-Jin; Kim, Woe Yeon; Salmela, Matti Juhani; Ewers, Brent E; Weinig, Cynthia; Khan, Sarah L; Schaible, D Loring P; McClung, C Robertson

    2015-03-24

    GIGANTEA (GI) was originally identified by a late-flowering mutant in Arabidopsis, but subsequently has been shown to act in circadian period determination, light inhibition of hypocotyl elongation, and responses to multiple abiotic stresses, including tolerance to high salt and cold (freezing) temperature. Genetic mapping and analysis of families of heterogeneous inbred lines showed that natural variation in GI is responsible for a major quantitative trait locus in circadian period in Brassica rapa. We confirmed this conclusion by transgenic rescue of an Arabidopsis gi-201 loss of function mutant. The two B. rapa GI alleles each fully rescued the delayed flowering of Arabidopsis gi-201 but showed differential rescue of perturbations in red light inhibition of hypocotyl elongation and altered cold and salt tolerance. The B. rapa R500 GI allele, which failed to rescue the hypocotyl and abiotic stress phenotypes, disrupted circadian period determination in Arabidopsis. Analysis of chimeric B. rapa GI alleles identified the causal nucleotide polymorphism, which results in an amino acid substitution (S264A) between the two GI proteins. This polymorphism underlies variation in circadian period, cold and salt tolerance, and red light inhibition of hypocotyl elongation. Loss-of-function mutations of B. rapa GI confer delayed flowering, perturbed circadian rhythms in leaf movement, and increased freezing and increased salt tolerance, consistent with effects of similar mutations in Arabidopsis. Collectively, these data suggest that allelic variation of GI-and possibly of clock genes in general-offers an attractive target for molecular breeding for enhanced stress tolerance and potentially for improved crop yield.

  10. Natural variation and gene regulatory basis for the responses of asparagus beans to soil drought.

    PubMed

    Xu, Pei; Moshelion, Menachem; Wu, XiaoHua; Halperin, Ofer; Wang, BaoGen; Luo, Jie; Wallach, Rony; Wu, Xinyi; Lu, Zhongfu; Li, Guojing

    2015-01-01

    Asparagus bean (Vigna unguiculata ssp. sesquipedalis) is the Asian subspecies of cowpea, a drought-resistant legume crop native to Africa. In order to explore the genetic variation of drought responses in asparagus bean, we conducted multi-year phenotyping of drought resistance traits across the Chinese asparagus bean mini-core. The phenotypic distribution indicated that the ssp. sesquipedalis subgene pool has maintained high natural variation in drought responses despite known domestic bottleneck. Thirty-nine SNP loci were found to show an association with drought resistance via a genome-wide association study (GWAS). Whole-plant water relations were compared among four genotypes by lysimetric assay. Apparent genotypic differences in transpiration patterns and the critical soil water threshold in relation to dehydration avoidance were observed, indicating a delicate adaptive mechanism for each genotype to its own climate. Microarray gene expression analyses revealed that known drought resistance pathways such as the ABA and phosphate lipid signaling pathways are conserved between different genotypes, while differential regulation of certain aquaporin genes and hormonal genes may be important for the genotypic differences. Our results suggest that divergent sensitivity to soil water content is an important mechanism configuring the genotypic specific responses to water deficit. The SNP markers identified provide useful resources for marker-assisted breeding. PMID:26579145

  11. Tuning polyelectrolyte multilayer structure by exploiting natural variation in fucoidan chemistry.

    PubMed

    Ho, Tracey T M; Bremmell, Kristen E; Krasowska, Marta; Stringer, Damien N; Thierry, Benjamin; Beattie, David A

    2015-03-21

    Fucoidan is a sulfated polysaccharide that is extracted primarily from seaweed. The polymer contains a natural variation in chemistry based upon the species of seaweed from which it is extracted. We have used two different fucoidans from two different seaweed species (Fucus vesiculosus - FV; and Undaria pinnatifida - UP) as polyanions for the formation of polysaccharide-based polyelectrolyte multilayers (PEMs), to determine if the chemistry of different fucoidans can be chosen to fine-tune the structure of the polymer film. Partially acetylated chitosan was chosen as the polycation for the work, and the presented data illustrate the effect of secondary hydrogen bonding interactions on PEM build-up and properties. Ellipsometry and quartz crystal microbalance with dissipation monitoring (QCM-D) measurements performed during film build-up enabled detailed measurements of layer thickness, adsorbed mass, and the dynamics of the multilayer formation process. High quality atomic force microscopy (AFM) images revealed the differences in morphology of the PEMs formed from the two fucoidans, and allowed for a more direct layer thickness measurement. X-ray photoelectron spectroscopy (XPS) confirmed the chemistry of the films, and an indication of the altered interactions between chitosan and fucoidan with variation in fucoidan type, but also with layer number. Distinct differences were observed between multilayers formed with the two fucoidans, with those constructed using UP having thinner, denser, less hydrated layers than those constructed using FV. These differences are discussed in the context of their varied chemistry, primarily their difference in molecular weight and degree of acetylation.

  12. Natural variation and gene regulatory basis for the responses of asparagus beans to soil drought.

    PubMed

    Xu, Pei; Moshelion, Menachem; Wu, XiaoHua; Halperin, Ofer; Wang, BaoGen; Luo, Jie; Wallach, Rony; Wu, Xinyi; Lu, Zhongfu; Li, Guojing

    2015-01-01

    Asparagus bean (Vigna unguiculata ssp. sesquipedalis) is the Asian subspecies of cowpea, a drought-resistant legume crop native to Africa. In order to explore the genetic variation of drought responses in asparagus bean, we conducted multi-year phenotyping of drought resistance traits across the Chinese asparagus bean mini-core. The phenotypic distribution indicated that the ssp. sesquipedalis subgene pool has maintained high natural variation in drought responses despite known domestic bottleneck. Thirty-nine SNP loci were found to show an association with drought resistance via a genome-wide association study (GWAS). Whole-plant water relations were compared among four genotypes by lysimetric assay. Apparent genotypic differences in transpiration patterns and the critical soil water threshold in relation to dehydration avoidance were observed, indicating a delicate adaptive mechanism for each genotype to its own climate. Microarray gene expression analyses revealed that known drought resistance pathways such as the ABA and phosphate lipid signaling pathways are conserved between different genotypes, while differential regulation of certain aquaporin genes and hormonal genes may be important for the genotypic differences. Our results suggest that divergent sensitivity to soil water content is an important mechanism configuring the genotypic specific responses to water deficit. The SNP markers identified provide useful resources for marker-assisted breeding.

  13. Natural variation and gene regulatory basis for the responses of asparagus beans to soil drought

    PubMed Central

    Xu, Pei; Moshelion, Menachem; Wu, XiaoHua; Halperin, Ofer; Wang, BaoGen; Luo, Jie; Wallach, Rony; Wu, Xinyi; Lu, Zhongfu; Li, Guojing

    2015-01-01

    Asparagus bean (Vigna unguiculata ssp. sesquipedalis) is the Asian subspecies of cowpea, a drought-resistant legume crop native to Africa. In order to explore the genetic variation of drought responses in asparagus bean, we conducted multi-year phenotyping of drought resistance traits across the Chinese asparagus bean mini-core. The phenotypic distribution indicated that the ssp. sesquipedalis subgene pool has maintained high natural variation in drought responses despite known domestic bottleneck. Thirty-nine SNP loci were found to show an association with drought resistance via a genome-wide association study (GWAS). Whole-plant water relations were compared among four genotypes by lysimetric assay. Apparent genotypic differences in transpiration patterns and the critical soil water threshold in relation to dehydration avoidance were observed, indicating a delicate adaptive mechanism for each genotype to its own climate. Microarray gene expression analyses revealed that known drought resistance pathways such as the ABA and phosphate lipid signaling pathways are conserved between different genotypes, while differential regulation of certain aquaporin genes and hormonal genes may be important for the genotypic differences. Our results suggest that divergent sensitivity to soil water content is an important mechanism configuring the genotypic specific responses to water deficit. The SNP markers identified provide useful resources for marker-assisted breeding. PMID:26579145

  14. Natural variation in epigenetic pathways affects the specification of female gamete precursors in Arabidopsis.

    PubMed

    Rodríguez-Leal, Daniel; León-Martínez, Gloria; Abad-Vivero, Ursula; Vielle-Calzada, Jean-Philippe

    2015-04-01

    In angiosperms, the transition to the female gametophytic phase relies on the specification of premeiotic gamete precursors from sporophytic cells in the ovule. In Arabidopsis thaliana, a single diploid cell is specified as the premeiotic female gamete precursor. Here, we show that ecotypes of Arabidopsis exhibit differences in megasporogenesis leading to phenotypes reminiscent of defects in dominant mutations that epigenetically affect the specification of female gamete precursors. Intraspecific hybridization and polyploidy exacerbate these defects, which segregate quantitatively in F2 populations derived from ecotypic hybrids, suggesting that multiple loci control cell specification at the onset of female meiosis. This variation in cell differentiation is influenced by the activity of ARGONAUTE9 (AGO9) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6), two genes involved in epigenetic silencing that control the specification of female gamete precursors. The pattern of transcriptional regulation and localization of AGO9 varies among ecotypes, and abnormal gamete precursors in ovules defective for RDR6 share identity with ectopic gamete precursors found in selected ecotypes. Our results indicate that differences in the epigenetic control of cell specification lead to natural phenotypic variation during megasporogenesis. We propose that this mechanism could be implicated in the emergence and evolution of the reproductive alternatives that prevail in flowering plants.

  15. Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data.

    PubMed

    Mönchgesang, Susann; Strehmel, Nadine; Schmidt, Stephan; Westphal, Lore; Taruttis, Franziska; Müller, Erik; Herklotz, Siska; Neumann, Steffen; Scheel, Dierk

    2016-01-01

    Many metabolomics studies focus on aboveground parts of the plant, while metabolism within roots and the chemical composition of the rhizosphere, as influenced by exudation, are not deeply investigated. In this study, we analysed exudate metabolic patterns of Arabidopsis thaliana and their variation in genetically diverse accessions. For this project, we used the 19 parental accessions of the Arabidopsis MAGIC collection. Plants were grown in a hydroponic system, their exudates were harvested before bolting and subjected to UPLC/ESI-QTOF-MS analysis. Metabolite profiles were analysed together with the genome sequence information. Our study uncovered distinct metabolite profiles for root exudates of the 19 accessions. Hierarchical clustering revealed similarities in the exudate metabolite profiles, which were partly reflected by the genetic distances. An association of metabolite absence with nonsense mutations was detected for the biosynthetic pathways of an indolic glucosinolate hydrolysis product, a hydroxycinnamic acid amine and a flavonoid triglycoside. Consequently, a direct link between metabolic phenotype and genotype was detected without using segregating populations. Moreover, genomics can help to identify biosynthetic enzymes in metabolomics experiments. Our study elucidates the chemical composition of the rhizosphere and its natural variation in A. thaliana, which is important for the attraction and shaping of microbial communities. PMID:27363486

  16. Natural Variation in Epigenetic Pathways Affects the Specification of Female Gamete Precursors in Arabidopsis[OPEN

    PubMed Central

    Rodríguez-Leal, Daniel; León-Martínez, Gloria; Abad-Vivero, Ursula; Vielle-Calzada, Jean-Philippe

    2015-01-01

    In angiosperms, the transition to the female gametophytic phase relies on the specification of premeiotic gamete precursors from sporophytic cells in the ovule. In Arabidopsis thaliana, a single diploid cell is specified as the premeiotic female gamete precursor. Here, we show that ecotypes of Arabidopsis exhibit differences in megasporogenesis leading to phenotypes reminiscent of defects in dominant mutations that epigenetically affect the specification of female gamete precursors. Intraspecific hybridization and polyploidy exacerbate these defects, which segregate quantitatively in F2 populations derived from ecotypic hybrids, suggesting that multiple loci control cell specification at the onset of female meiosis. This variation in cell differentiation is influenced by the activity of ARGONAUTE9 (AGO9) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6), two genes involved in epigenetic silencing that control the specification of female gamete precursors. The pattern of transcriptional regulation and localization of AGO9 varies among ecotypes, and abnormal gamete precursors in ovules defective for RDR6 share identity with ectopic gamete precursors found in selected ecotypes. Our results indicate that differences in the epigenetic control of cell specification lead to natural phenotypic variation during megasporogenesis. We propose that this mechanism could be implicated in the emergence and evolution of the reproductive alternatives that prevail in flowering plants. PMID:25829442

  17. Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data

    PubMed Central

    Mönchgesang, Susann; Strehmel, Nadine; Schmidt, Stephan; Westphal, Lore; Taruttis, Franziska; Müller, Erik; Herklotz, Siska; Neumann, Steffen; Scheel, Dierk

    2016-01-01

    Many metabolomics studies focus on aboveground parts of the plant, while metabolism within roots and the chemical composition of the rhizosphere, as influenced by exudation, are not deeply investigated. In this study, we analysed exudate metabolic patterns of Arabidopsis thaliana and their variation in genetically diverse accessions. For this project, we used the 19 parental accessions of the Arabidopsis MAGIC collection. Plants were grown in a hydroponic system, their exudates were harvested before bolting and subjected to UPLC/ESI-QTOF-MS analysis. Metabolite profiles were analysed together with the genome sequence information. Our study uncovered distinct metabolite profiles for root exudates of the 19 accessions. Hierarchical clustering revealed similarities in the exudate metabolite profiles, which were partly reflected by the genetic distances. An association of metabolite absence with nonsense mutations was detected for the biosynthetic pathways of an indolic glucosinolate hydrolysis product, a hydroxycinnamic acid amine and a flavonoid triglycoside. Consequently, a direct link between metabolic phenotype and genotype was detected without using segregating populations. Moreover, genomics can help to identify biosynthetic enzymes in metabolomics experiments. Our study elucidates the chemical composition of the rhizosphere and its natural variation in A. thaliana, which is important for the attraction and shaping of microbial communities. PMID:27363486

  18. Natural variation in epigenetic pathways affects the specification of female gamete precursors in Arabidopsis.

    PubMed

    Rodríguez-Leal, Daniel; León-Martínez, Gloria; Abad-Vivero, Ursula; Vielle-Calzada, Jean-Philippe

    2015-04-01

    In angiosperms, the transition to the female gametophytic phase relies on the specification of premeiotic gamete precursors from sporophytic cells in the ovule. In Arabidopsis thaliana, a single diploid cell is specified as the premeiotic female gamete precursor. Here, we show that ecotypes of Arabidopsis exhibit differences in megasporogenesis leading to phenotypes reminiscent of defects in dominant mutations that epigenetically affect the specification of female gamete precursors. Intraspecific hybridization and polyploidy exacerbate these defects, which segregate quantitatively in F2 populations derived from ecotypic hybrids, suggesting that multiple loci control cell specification at the onset of female meiosis. This variation in cell differentiation is influenced by the activity of ARGONAUTE9 (AGO9) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6), two genes involved in epigenetic silencing that control the specification of female gamete precursors. The pattern of transcriptional regulation and localization of AGO9 varies among ecotypes, and abnormal gamete precursors in ovules defective for RDR6 share identity with ectopic gamete precursors found in selected ecotypes. Our results indicate that differences in the epigenetic control of cell specification lead to natural phenotypic variation during megasporogenesis. We propose that this mechanism could be implicated in the emergence and evolution of the reproductive alternatives that prevail in flowering plants. PMID:25829442

  19. Genetic Mapping of Natural Variation in Schooling Tendency in the Threespine Stickleback

    PubMed Central

    Greenwood, Anna K.; Ardekani, Reza; McCann, Shaugnessy R.; Dubin, Matthew E.; Sullivan, Amy; Bensussen, Seth; Tavaré, Simon; Peichel, Catherine L.

    2015-01-01

    Although there is a heritable basis for many animal behaviors, the genetic architecture of behavioral variation in natural populations remains mostly unknown, particularly in vertebrates. We sought to identify the genetic basis for social affiliation in two populations of threespine sticklebacks (Gasterosteus aculeatus) that differ in their propensity to school. Marine sticklebacks from Japan school strongly whereas benthic sticklebacks from a lake in Canada are more solitary. Here, we expanded on our previous efforts to identify quantitative trait loci (QTL) for differences in schooling tendency. We tested fish multiple times in two assays that test different aspects of schooling tendency: 1) the model school assay, which presents fish with a school of eight model sticklebacks; and 2) the choice assay, in which fish are given a choice between the model school and a stationary artificial plant. We found low-to-moderate levels of repeatability, ranging from 0.1 to 0.5, in schooling phenotypes. To identify the genomic regions that contribute to differences in schooling tendency, we used QTL mapping in two types of crosses: benthic × marine backcrosses and an F2 intercross. We found two QTL for time spent with the school in the model school assay, and one QTL for number of approaches to the school in the choice assay. These QTL were on three different linkage groups, not previously linked to behavioral differences in sticklebacks. Our results highlight the importance of using multiple crosses and robust behavioral assays to uncover the genetic basis of behavioral variation in natural populations. PMID:25717151

  20. Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

    PubMed Central

    2014-01-01

    Background Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species. Results Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains. Conclusions The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains. PMID:24694239

  1. Variation of haemoglobin extinction coefficients can cause errors in the determination of haemoglobin concentration measured by near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Kim, J. G.; Liu, H.

    2007-10-01

    Near-infrared spectroscopy or imaging has been extensively applied to various biomedical applications since it can detect the concentrations of oxyhaemoglobin (HbO2), deoxyhaemoglobin (Hb) and total haemoglobin (Hbtotal) from deep tissues. To quantify concentrations of these haemoglobin derivatives, the extinction coefficient values of HbO2 and Hb have to be employed. However, it was not well recognized among researchers that small differences in extinction coefficients could cause significant errors in quantifying the concentrations of haemoglobin derivatives. In this study, we derived equations to estimate errors of haemoglobin derivatives caused by the variation of haemoglobin extinction coefficients. To prove our error analysis, we performed experiments using liquid-tissue phantoms containing 1% Intralipid in a phosphate-buffered saline solution. The gas intervention of pure oxygen was given in the solution to examine the oxygenation changes in the phantom, and 3 mL of human blood was added twice to show the changes in [Hbtotal]. The error calculation has shown that even a small variation (0.01 cm-1 mM-1) in extinction coefficients can produce appreciable relative errors in quantification of Δ[HbO2], Δ[Hb] and Δ[Hbtotal]. We have also observed that the error of Δ[Hbtotal] is not always larger than those of Δ[HbO2] and Δ[Hb]. This study concludes that we need to be aware of any variation in haemoglobin extinction coefficients, which could result from changes in temperature, and to utilize corresponding animal's haemoglobin extinction coefficients for the animal experiments, in order to obtain more accurate values of Δ[HbO2], Δ[Hb] and Δ[Hbtotal] from in vivo tissue measurements.

  2. Natural variation of 87Sr/86Sr in coral Porites from southern Taiwan

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Chiang, H.; Shen, C.; Lee, D.; Chen, Y.

    2009-12-01

    Monthly resolution 87Sr/86Sr records of living coral Porites heads, collected in Nanwan Bay, southernmost Taiwan (21o55’N, 120o47’E), were analyzed by a MC-ICP-MS at the Department of Geosciences, National Taiwan University. Between the time window of 1992 and 2002, 87Sr/86Sr ratios remained constant at 0.709176 in winter, while strong annual fluctuations between 0.709171 and 0.709203 were observed during the summer. No relationship is found between Sr/Ca and δ18O, which suggests that the effect of temperature and fresh water input are negligible to the observed summer fluctuations of 87Sr/86Sr in these corals. Furthermore, 87Sr/86Sr ratio in offshore water exhibits a significantly offset of 0.00002-0.00003, and which is positively correlated to the variations of the coral values of 0.70917-0.70918. If this is correct, there exists a source that is responsible for the low 87Sr/86Sr observed in the corals, alternatively, a biologically kinetic effect can also explain the data. In order to better constrain the causes of the observed 87Sr/86Sr variations in these corals, a 84Sr-86Sr double-spike method using TIMS is currently being set up, and the data will be presented in this meeting.

  3. Hydrophilic fraction of natural organic matter causing irreversible fouling of microfiltration and ultrafiltration membranes.

    PubMed

    Yamamura, Hiroshi; Okimoto, Kenji; Kimura, Katsuki; Watanabe, Yoshimasa

    2014-05-01

    Although membrane filtration is a promising technology in the field of drinking water treatment, persistent membrane fouling remains a major disadvantage. For more efficient operation, causative agents of membrane fouling need to be identified. Membrane fouling can be classified into physically reversible and irreversible fouling on basis of the removability of the foulants by physical cleaning. Four types of natural organic matter (NOM) in river water used as a source of drinking water were fractionated into hydrophobic and hydrophilic fractions, and their potential to develop irreversible membrane fouling was evaluated by a bench-scale filtration experiment together with spectroscopic and chromatographic analyses. In this study, only dissolved NOM was investigated without consideration of interactions of NOM fractions with particulate matter. Results demonstrated that despite identical total organic carbon (TOC), fouling development trends were significantly different between hydrophilic and hydrophobic fractions. The hydrophobic fractions did not increase membrane resistance, while the hydrophilic fractions caused severe loss of membrane permeability. These results were identical with the case when the calcium was added to hydrophobic and hydrophilic fractions. The largest difference in NOM characteristics between hydrophobic and hydrophilic fractions was the presence or absence of macromolecules; the primary constituent causing irreversible fouling was inferred to be "biopolymers", including carbohydrates and proteins. In addition, the results demonstrated that the extent of irreversible fouling was considerably different depending on the combination of membrane materials and NOM characteristics. Despite identical nominal pore size (0.1 μm), a polyvinylidene fluoride (PVDF) membrane was found to be more rapidly fouled than a PE membrane. This is probably explained by the generation of strong hydrogen bonding between hydroxyl groups of biopolymers and fluorine

  4. Hydrophilic fraction of natural organic matter causing irreversible fouling of microfiltration and ultrafiltration membranes.

    PubMed

    Yamamura, Hiroshi; Okimoto, Kenji; Kimura, Katsuki; Watanabe, Yoshimasa

    2014-05-01

    Although membrane filtration is a promising technology in the field of drinking water treatment, persistent membrane fouling remains a major disadvantage. For more efficient operation, causative agents of membrane fouling need to be identified. Membrane fouling can be classified into physically reversible and irreversible fouling on basis of the removability of the foulants by physical cleaning. Four types of natural organic matter (NOM) in river water used as a source of drinking water were fractionated into hydrophobic and hydrophilic fractions, and their potential to develop irreversible membrane fouling was evaluated by a bench-scale filtration experiment together with spectroscopic and chromatographic analyses. In this study, only dissolved NOM was investigated without consideration of interactions of NOM fractions with particulate matter. Results demonstrated that despite identical total organic carbon (TOC), fouling development trends were significantly different between hydrophilic and hydrophobic fractions. The hydrophobic fractions did not increase membrane resistance, while the hydrophilic fractions caused severe loss of membrane permeability. These results were identical with the case when the calcium was added to hydrophobic and hydrophilic fractions. The largest difference in NOM characteristics between hydrophobic and hydrophilic fractions was the presence or absence of macromolecules; the primary constituent causing irreversible fouling was inferred to be "biopolymers", including carbohydrates and proteins. In addition, the results demonstrated that the extent of irreversible fouling was considerably different depending on the combination of membrane materials and NOM characteristics. Despite identical nominal pore size (0.1 μm), a polyvinylidene fluoride (PVDF) membrane was found to be more rapidly fouled than a PE membrane. This is probably explained by the generation of strong hydrogen bonding between hydroxyl groups of biopolymers and fluorine

  5. Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates

    PubMed Central

    Micallef, Shirley A.; Shiaris, Michael P.; Colón-Carmona, Adán

    2009-01-01

    Plant species is considered to be one of the most important factors in shaping rhizobacterial communities, but specific plant–microbe interactions in the rhizosphere are still not fully understood. Arabidopsis thaliana, for which a large number of naturally occurring ecotype accessions exist, lacks mycorrhizal associations and is hence an ideal model for rhizobacterial studies. Eight Arabidopsis accessions were found to exert a marked selective influence on bacteria associated with their roots, as determined by terminal-restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA). Community differences in species composition and relative abundance were both significant (P <0.001). The eight distinct and reproducible accession-dependent community profiles also differed from control bulk soil. Root exudates of these variants were analysed by high performance liquid chromatography (HPLC) to try to establish whether the unique rhizobacterial assemblages among accessions could be attributed to plant-regulated chemical changes in the rhizosphere. Natural variation in root exudation patterns was clearly exhibited, suggesting that differences in exudation patterns among accessions could be influencing bacterial assemblages. Other factors such as root system architecture are also probably involved. Finally, to investigate the Arabidopsis rhizosphere further, the phylogenetic diversity of rhizobacteria from accession Cvi-0 is described. PMID:19342429

  6. Natural Genetic Variation Underlying Differences in Peromyscus Repetitive & Social/Aggressive Behaviors

    PubMed Central

    Shorter, Kimberly R.; Owen, Amy; Anderson, Vanessa; Hall-South, April C.; Hayford, Samantha; Cakora, Patricia; Crossland, Janet P.; Georgi, Velina R. M.; Perkins, Amy; Kelly, Sandra J.; Felder, Michael R.; Vrana, Paul B.

    2014-01-01

    Peromyscus maniculatus (BW) and P. polionotus (PO) are interfertile North American species that differ in many characteristics. For example, PO exhibit monogamy and BW animals are susceptible to repetitive behaviors and thus a model for neurobehavioral disorders such as Autism. We analyzed these two stocks as well as their hybrids, a BW YPO consomic line (previously shown to alter glucose homeostasis) and a natural P. maniculatus agouti variant (ANb = wide band agouti). We show that PO animals engage in far less repetitive behavior than BW animals, that this trait is dominant, and that trait distribution in both species is bi-modal. The ANb allele also reduces such behaviors, particularly in females. PO, F1, and ANb animals all dig significantly more than BW. Increased self-grooming is also a PO dominant trait, and there is a bimodal trait distribution in all groups except BW. The inter-stock differences in self-grooming are greater between males, and the consomic data suggest the Y chromosome plays a role. The monogamous PO animals engage in more social behavior than BW; hybrid animals exhibit intermediate levels. Surprisingly, ANb animals are also more social than BW animals, although ANb interactions led to aggressive interactions at higher levels than any other group. PO animals exhibited the lowest incidence of aggressive behaviors, while the hybrids exhibited BW levels. Thus this group exhibits natural, genetically tractable variation in several biomedically relevant traits. PMID:24407381

  7. Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

    PubMed Central

    Strauch, Renee C.; Svedin, Elisabeth; Dilkes, Brian; Chapple, Clint; Li, Xu

    2015-01-01

    Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. As an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite–gene associations led to the identification of N-malonyl-d-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5′-phosphate for its activity. This study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. It also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism. PMID:26324904

  8. Experimental evolution can unravel the complex causes of natural selection in clinical infections.

    PubMed

    Brockhurst, Michael A

    2015-06-01

    It is increasingly clear that rapid evolutionary dynamics are an important process in microbial ecology. Experimental evolution, wherein microbial evolution is observed in real-time, has revealed many instances of appreciable evolutionary change occurring on very short timescales of a few days or weeks in response to a variety of biotic and abiotic selection pressures. From clinical infections, including the chronic bacterial lung infections associated with cystic fibrosis that form a focus of my research, there is now abundant evidence suggesting that rapid evolution by infecting microbes contributes to host adaptation, treatment failure and worsening patient prognosis. However, disentangling the drivers of natural selection in complex infection environments is extremely challenging and limits our understanding of the selective pressures acting upon microbes in infections. Controlled evolution experiments can make a vital contribution to this by determining the causal links between predicted drivers of natural selection and the evolutionary responses of microbes. Integration of experimental evolution into studies of clinical infections is a key next step towards a better understanding of the causes and consequences of rapid microbial evolution in infections, and discovering how these evolutionary processes might be influenced to improve patient health.A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2015, can be viewed via this link: Michael A. Brockhurst https://www.youtube.com/watch?v=N1bodVSl27E.

  9. Experimental evolution can unravel the complex causes of natural selection in clinical infections.

    PubMed

    Brockhurst, Michael A

    2015-06-01

    It is increasingly clear that rapid evolutionary dynamics are an important process in microbial ecology. Experimental evolution, wherein microbial evolution is observed in real-time, has revealed many instances of appreciable evolutionary change occurring on very short timescales of a few days or weeks in response to a variety of biotic and abiotic selection pressures. From clinical infections, including the chronic bacterial lung infections associated with cystic fibrosis that form a focus of my research, there is now abundant evidence suggesting that rapid evolution by infecting microbes contributes to host adaptation, treatment failure and worsening patient prognosis. However, disentangling the drivers of natural selection in complex infection environments is extremely challenging and limits our understanding of the selective pressures acting upon microbes in infections. Controlled evolution experiments can make a vital contribution to this by determining the causal links between predicted drivers of natural selection and the evolutionary responses of microbes. Integration of experimental evolution into studies of clinical infections is a key next step towards a better understanding of the causes and consequences of rapid microbial evolution in infections, and discovering how these evolutionary processes might be influenced to improve patient health.A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2015, can be viewed via this link: Michael A. Brockhurst https://www.youtube.com/watch?v=N1bodVSl27E. PMID:25957311

  10. Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis.

    PubMed

    Dharanishanthi, Veeramuthu; Dasgupta, Modhumita Ghosh

    2016-10-01

    Natural genetic variation is randomly distributed and gene expression patterns vary widely in natural populations. These variations are an effect of multifactorial genetic perturbations resulting in different phenotypes. Genome-wide analysis can be used to comprehend the genetic basis governing this naturally occurring developmental variation. Secondary growth is a highly complex trait and systems genetics models are presently being applied to understand the molecular architecture of wood formation. In the present study, the natural variation in expression patterns of 18,987 transcripts expressed in the developing xylem tissues were documented across four phenotypes of Eucalyptus tereticornis with distinct holocellulose/klason lignin content. The differentially expressed genes across all the phenotypes were used to construct co-expression networks and sub-network 2 with 380 nodes and 17,711 edges was determined as the network of relevance, including 30 major cell wall biogenesis related transcripts with 2394 interactions and 10 families of transcription factors with 3360 interactions. EYE [EMBRYO YELLOW] was identified as major hub transcript with 173 degrees which interacted with known cell wall biogenesis genes. K-mean clustering was also performed for differentially expressed transcripts and two clusters discriminated the phenotypes based on their holocellulose/klason lignin content. The cluster based networks were enriched with GOs related to cell wall biogenesis and sugar metabolism. The networks developed in the present study enabled identification of critical regulators and novel transcripts whose expression variation could presumably govern the phenotypic variation in wood properties across E. tereticornis. PMID:27465117

  11. Identified Natural Hazards May Cause Adverse Impact on Sustainability of Desalination Plants in Red Sea

    NASA Astrophysics Data System (ADS)

    Aburizaiza, O. S.; Zaigham, N. A.; Nayyar, Z. A.; Mahar, G. A.; Siddique, A.; Eusufi, S. N.

    2011-12-01

    The Red Sea and its surrounding countries have harsh arid climatic conditions where fast growth of the socio-economic activities and rapid change of lifestyle have caused tremendous stress on water to the level of acute crisis. To meet the water demands, the Red Sea countries have adopted seawater desalination giving priority against their land-based resources. Saudi Arabia is the largest desalinated-water producers in the Red Sea and has practically no adequate backup plan in case of sudden unforeseen emergency. Out of about 3.64 million m3/day, Saudi Arabia is alone being desalinated about 3.29 m3/day seawater from Red Sea and more projects are in progress. Present integrated research study has identified some of natural and anthropogenic hazards, which may be major threats to the quality of the seawater as well as to the desalination plants themselves. Results of present study reveal that the submarine complex morphologic features may cause the isolation of Red Sea from any of the open sea, the increase in the seismicity trends, the active volcanism causing unique longitudinal as well as transverse deformations of the axial trough particularly in the southern part of the Red Sea, the consistently generating enormous hot-brine tectonic-factory all along the deeper parts of the Red Sea rifting trough and other related issues. Considering the identified odd conditions, the total dependence on seawater desalination may not be worthwhile for sustainable water management strategy and consequent socio-economic developments in future. It is recommended that the priority should also be given mainly in three main disciplines to meet the future water challenges - one, developing reliable backup water management; second, alternate options for the supplementary resources of water; and third, the development and immediate implementation of the water-use conservation strategy plan.

  12. Towards Better Understanding of GPS-based Ionospheric TEC Perturbations Caused by Natural Hazards

    NASA Astrophysics Data System (ADS)

    Komjathy, A.; Galvan, D. A.; Butala, M. D.; Stephens, P.; Mannucci, A. J.; Hickey, M. P.

    2011-12-01

    Natural hazards including earthquakes, volcanic eruptions, and tsunamis, have been significant threats to humans throughout recorded history. The Global Positioning System satellites have become primary sensors to measure signatures associated with such natural hazards. These signatures typically include GPS-derived seismic deformation measurements, co-seismic vertical displacements, and real-time GPS-derived ocean buoy positioning estimates. Another way to use GPS observables is to compute the ionospheric total electron content (TEC) to measure and monitor post-seismic ionospheric disturbances caused by earthquakes, volcano eruptions, and tsunamis. Recent advances in GPS data processing have demonstrated that ground-based GPS receivers are capable of detecting ionospheric TEC perturbations generated by surface Rayleigh, acoustic and gravity waves. There have been a number of papers published discussing TEC perturbations immediately following the Tohoku earthquake in Japan on March 11, 2011. Due to the dense GPS network in Japan (GEONET) and high earthquake magnitude, these reports are the clearest observations to date of the effect of a major earthquake and tsunami on the ionosphere near the epicenter. Most investigators have focused on the ionospheric response up to a few hours following the earthquake and tsunami. In our research we investigate the ionospheric TEC perturbations up to a few days before and after the event. We also address the impact of geomagnetic activity during March 11. We compare TEC perturbations on that day with other days showing similar geomagnetic activities. Initial results have revealed that the earthquake and tsunami generated TEC perturbations that were observable and detectable in the GEONET data for up to 24 hours following the Tohoku event. We will investigate optimized GPS processing techniques to derive high-precision TEC perturbations. The primary application involving the ionosphere will be the real-time monitoring of the

  13. Relations of Tualatin River water temperatures to natural and human-caused factors

    USGS Publications Warehouse

    Risley, John C.

    1997-01-01

    Aquatic research has long shown that the survival of cold-water fish, such as salmon and trout, decreases markedly as water temperatures increase above a critical threshold, particularly during sensitive life stages of the fish. In an effort to improve the overall health of aquatic ecosystems, the State of Oregon in 1996 adopted a maximum water-temperature standard of 17.8 degrees Celsius (68 degrees Fahrenheit), based on a 7-day moving average of daily maximum temperatures, for most water bodies in the State. Anthropogenic activities are not permitted to raise the temperature of a water body above this level. In the Tualatin River, a tributary of the Willamette River located in northwestern Oregon, water temperatures periodically surpass this threshold during the low-flow summer and fall months.An investigation by the U.S. Geological Survey quantified existing seasonal, diel, and spatial patterns of water temperatures in the main stem of the river, assessed the relation of water temperatures to natural climatic conditions and anthropogenic factors (such as wastewater-treatment-plant effluent and modification of riparian shading), and assessed the impact of various flow management practices on stream temperatures. Half-hourly temperature measurements were recorded at 13 monitoring sites from river mile (RM) 63.9 to RM 3.4 from May to November of 1994. Four synoptic water- temperature surveys also were conducted in the upstream and downstream vicinities of two wastewater-treatment-plant outfalls. Temperature and streamflow time-series data were used to calibrate two dynamic-flow heat-transfer models, DAFLOW-BLTM (RM 63.9-38.4) and CE-QUAL-W2 (RM 38.4-3.4). Simulations from the models provided a basis for approximating 'natural' historical temperature patterns, performing effluent and riparian-shading sensitivity analyses, and evaluating mitigation management scenarios under 1994 climatic conditions. Findings from the investigation included (1) under 'natural

  14. Natural sleep and its seasonal variations in three pre-industrial societies.

    PubMed

    Yetish, Gandhi; Kaplan, Hillard; Gurven, Michael; Wood, Brian; Pontzer, Herman; Manger, Paul R; Wilson, Charles; McGregor, Ronald; Siegel, Jerome M

    2015-11-01

    How did humans sleep before the modern era? Because the tools to measure sleep under natural conditions were developed long after the invention of the electric devices suspected of delaying and reducing sleep, we investigated sleep in three preindustrial societies [1-3]. We find that all three show similar sleep organization, suggesting that they express core human sleep patterns, most likely characteristic of pre-modern era Homo sapiens. Sleep periods, the times from onset to offset, averaged 6.9-8.5 hr, with sleep durations of 5.7-7.1 hr, amounts near the low end of those industrial societies [4-7]. There was a difference of nearly 1 hr between summer and winter sleep. Daily variation in sleep duration was strongly linked to time of onset, rather than offset. None of these groups began sleep near sunset, onset occurring, on average, 3.3 hr after sunset. Awakening was usually before sunrise. The sleep period consistently occurred during the nighttime period of falling environmental temperature, was not interrupted by extended periods of waking, and terminated, with vasoconstriction, near the nadir of daily ambient temperature. The daily cycle of temperature change, largely eliminated from modern sleep environments, may be a potent natural regulator of sleep. Light exposure was maximal in the morning and greatly decreased at noon, indicating that all three groups seek shade at midday and that light activation of the suprachiasmatic nucleus is maximal in the morning. Napping occurred on <7% of days in winter and <22% of days in summer. Mimicking aspects of the natural environment might be effective in treating certain modern sleep disorders.

  15. Temporal variations in natural attenuation of chlorinated aliphatic hydrocarbons in eutrophic river sediments impacted by a contaminated groundwater plume.

    PubMed

    Hamonts, Kelly; Kuhn, Thomas; Vos, Johan; Maesen, Miranda; Kalka, Harald; Smidt, Hauke; Springael, Dirk; Meckenstock, Rainer U; Dejonghe, Winnie

    2012-04-15

    Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. Biotransformation, sorption and dilution of CAHs in the impacted river sediments have been reported to reduce discharge, but the effect of temporal variations in environmental conditions on the occurrence and extent of those processes in river sediments is largely unknown. We monitored the reduction of CAH discharge into the Zenne River during a 21-month period. Despite a relatively stable influx of CAHs from the groundwater, the total reduction in CAH discharge from 120 to 20 cm depth in the river sediments, on average 74 ± 21%, showed moderate to large temporal variations, depending on the riverbed location. High organic carbon and anaerobic conditions in the river sediments allowed microbial reductive dechlorination of both chlorinated ethenes and chlorinated ethanes. δ(13)C values of the CAHs showed that this biotransformation was remarkably stable over time, despite fluctuating pore water temperatures. Daughter products of the CAHs, however, were not detected in stoichiometric amounts and suggested the co-occurrence of a physical process reducing the concentrations of CAHs in the riverbed. This process was the main process causing temporal variations in natural attenuation of the CAHs and was most likely dilution by surface water-mixing. However, higher spatial resolution monitoring of flow transients in the riverbed is required to prove dilution contributions due to dynamic surface water-groundwater flow exchanges. δ(13)C values and a site-specific isotope enrichment factor for reductive dechlorination of the main groundwater pollutant vinyl chloride (VC) allowed assessment of changes over time in the extent of both biotransformation and dilution of VC for different scenarios in which those processes either occurred consecutively or simultaneously between 120 and 20 cm depth in the riverbed. The extent of reductive dechlorination of VC ranged from 27

  16. Research of Ionospheric Total Electron Content Variations Caused by Powerful Radio Emission of `SURA' Facility on Network of Gnss - Receivers

    NASA Astrophysics Data System (ADS)

    Kogogin, Denis; Nasyrov, Igor; Grach, Savely; Shindin, Alexey; Zagretdinov, Renat; Shaimukhametov, Ramil; Kislichin, Alexander; Ryabova, Mariya

    Large-scale irregularities with scales of 5-50 km can be effectively studied using dual-frequency raying by signals of the Navstar (GPS) and GLONASS microwave satellite systems. During propagation through the heated region, such signals acquire an additional phase increment stipulated by the dispersion of radio waves in the ionospheric plasma and linearly related to the total electron content (TEC) on the propagation trajectory. In this work we present results of measurement of total electron content (TEC) variations in the F2 part of the ionosphere of the Earth caused by powerful radio emission of “Sura” facility carried out during several experimental companies from 2010 to 2013 years. Parameters of TEC-variations were obtained by dual - frequency global navigation satellite systems (GNSS) diagnostics. Registration of signal parameters from GNSS-transmitters was performed at spatially separated sites around the “Sura” facility: Vasilsursk (56(°) 08' N, 46(°) 05' E), Zelenodolsk (55(°) 52' N, 48(°) 33' E), Kazan (55(°) 48' N, 49(°) 08' E) and Yoshkar-Ola (56(°) 38'N, 47(°) 52'E). The initial data containing measurements of the phase L and pseudorange P for the operating frequencies f1 =1575.42 MHz and f2 = 1227.60 MHz are RINEX files. For a detail study of small TEC variations based on the initial dependence, the trend was removed by subtraction of the moving average with the use of the linear weight function. In the experiments radio path from GNSS satellite to Vasilsursk passed over the disturbed region of ionosphere, but radio paths to Zelenodolsk, to Kazan and to Yoshkar-Ola did not. However, TEC-variations correlated with pumping of ionosphere by ”Sura” facility were detected for three ground measurements sites, situated along the “Sura” facility geomagnetic longitude (Vasilsursk, Zelenodolsk, Kazan). Magnitudes of TEC-variations reached 0.15-0.3 TECU. Velocity of propagation of large-scale ionospheric disturbance stimulated by

  17. Topography caused by mantle density variations: observation-based estimates and models derived from tomography and lithosphere thickness

    NASA Astrophysics Data System (ADS)

    Steinberger, Bernhard

    2016-04-01

    Large-scale topography may be due to several causes, including (1) variations in crustal thickness and density structure, (2) oceanic lithosphere age differences, (3) subcrustal density variations in the continental lithosphere and (4) convective flow in the mantle beneath the lithosphere. The last contribution in particular may change with time and be responsible for continental inundations; distinguishing between these contributions is therefore important for linking Earth's history to its observed geological record. As a step towards this goal, this paper aims at such distinction for the present-day topography: the approach taken is deriving a `model' topography due to contributions (3) and (4), along with a model geoid, using a geodynamic mantle flow model. Both lithosphere thickness and density anomalies beneath the lithosphere are inferred from seismic tomography. Density anomalies within the continental lithosphere are uncertain, because they are probably due to variations in composition and temperature, making a simple scaling from seismic to density anomalies inappropriate. Therefore, we test a number of different assumptions regarding these. As a reality check, model topography is compared, in terms of both correlation and amplitude ratio, to `residual' topography, which follows from observed topography after subtracting contributions (1) and (2). The model geoid is compared to observations as well. Comparatively good agreement is found if there is either an excess density of ≈0.2 per cent in the lithosphere above ≈150 km depth, with anomalies below as inferred from tomography, or if the excess density is ≈0.4 per cent in the entire lithosphere. Further, a good fit is found for viscosity ≈1020 Pa s in the asthenosphere, increasing to ≈1023 Pa s in the lower mantle above D'. Results are quite dependent on which tomography models they are based on; for some recent ones, topography correlation is ≈0.6, many smaller scale features are matched

  18. Spatiotemporal variations in channel changes caused by cumulative factors in a meandering river: The lower Peixe River, Brazil

    NASA Astrophysics Data System (ADS)

    Morais, Eduardo S.; Rocha, Paulo C.; Hooke, Janet

    2016-11-01

    Channel changes in meandering rivers naturally exhibit complex behaviour, and understanding the river dynamics can be challenging in environments also subject to cumulative human impacts. Planform changes were analysed on four reaches of the lower course of the Peixe River, Brazil, at decadal scales over the period 1962-2008 from aerial photographs and satellite imagery, complemented by a historical map from 1907. Analysis of the spatial and temporal patterns of channel change mechanisms and morphometry of bends and of the sinuosity and morphodynamic variations of the reaches demonstrates major changes in planform characteristics. Sinuosity in all reaches decreased from ~ 2.6 to ~ 1.7, average wavelength of bends has increased from ~ 200 to ~ 500 m, and the planform has become much simpler. Changes have been progressive from downstream to upstream, with higher intensities of processes, particularly cutoffs first in downstream reaches then more recently in upstream reaches. It is suggested that channel changes represent a morphological adjustment to human interventions, such as reservoir construction and land use. However, evidence of the autogenic behaviour of meanders is highlighted in which the existence of compound meanders reveals control over the spatial variation in the reaches. The results suggest that geomorphic thresholds associated with the compound meander formation and the bend evolution should be considered, even in impacted meandering rivers, because they exert primary controls on the spatial-temporal adjustment of channels.

  19. Natural variation in cold tolerance in the nematode Pristionchus pacificus: the role of genotype and environment

    PubMed Central

    McGaughran, Angela; Sommer, Ralf J.

    2014-01-01

    ABSTRACT Low temperature is a primary determinant of growth and survival among organisms and almost all animals need to withstand temperature fluctuations in their surroundings. We used the hermaphroditic nematode Pristionchus pacificus to examine variation in cold tolerance in samples collected from 18 widespread locations. Samples were challenged by exposure to both direct and gradual low temperature after culture in the laboratory at 20°C. A short-term acclimation treatment was also applied to assess cold tolerance following a pre-exposure cold treatment. Finally, genotype-by-environment (G × E) analysis was performed on a subset of samples cultured at two additional temperatures (15°C and 25°C). P. pacificus displayed a high degree of natural variation in cold tolerance, corresponding to the presence of three distinct phenotypic classes among samples: cold tolerant, non-cold tolerant, cold tolerant plastic. Survival of gradual cold exposure was significantly higher than survival of direct exposure to low temperature and a cold exposure pre-treatment significantly enhanced cold tolerance in some samples. By focusing on a sub-set of well-sampled locations from tropical La Réunion Island, we found evidence of significant effects of genotype and environment on cold tolerance, and we also showed that, within the different Réunion locations sampled, all three phenotypic classes are generally well represented. Taken together, our results show that P. pacificus exhibits a highly plastic tolerance to cold exposure that may be partly driven by differential trait sensitivity in diverse environments. PMID:25150278

  20. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

    PubMed Central

    Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; Begun, David J.

    2016-01-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

  1. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster.

    PubMed

    Svetec, Nicolas; Cridland, Julie M; Zhao, Li; Begun, David J

    2016-03-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

  2. Natural-Scale Lava Flow Experiments on Video: Variations with Temperature, Slope, and Effusion Rate

    NASA Astrophysics Data System (ADS)

    Karson, J. A.; Wysocki, R.; Edwards, B. R.; Lev, E.

    2013-12-01

    Investigations of active basaltic lava flows and analog materials show that flow dynamics and final flow morphology are strongly determined by the rapidly evolving rheology of the lava crust which constrains the downslope advance of the lava flow. The non-dimensional factor Ψ (ratio of the time scale of crust formation to advective heat loss) provides a useful means of comparing different flows. The key parameters that control Ψ include the melt viscosity, temperature, effusion rate, and slope. Experimental lava flows, up to several meters long created in the Syracuse University Lava Project permit these variables to be investigated independently and in combination in volume-limited flows (<450 kg, 0.5 m3). Video results show lava is very sensitive to relatively small variations in these variables under experimental conditions. For example, experiments 1.1 Ga Keewenan basalt from the Mid-Continent Rift and 200 Ma basalt from the Palisades Sill show very different flow rates and flow morphologies for meter-scale flows on dry sand slopes between 5° and 20°, with all other variables held constant. Similar differences result from varying the effusion rate (~10-4m3s-1) or temperature (1050°-1250°C) on a constant slope. In addition, videos document the development of a wide range of reproducible lava flow structures found in natural lava flows including folds, shear zones, lava tubes, inflated lobes, break-outs, and bubbles (limu o'Pele), that provide additional information on lava crust development. New, continuous flow (cooling-limited) experiments show downslope variations under constant flow conditions.

  3. Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation

    PubMed Central

    Zhang, Han; Zhao, Yang-Yu; Song, Jing; Zhu, Qi-Ying; Yang, Hua; Zheng, Mei-Ling; Xuan, Zhao-Ling; Wei, Yuan; Chen, Yang; Yuan, Peng-Bo; Yu, Yang; Li, Da-Wei; Liang, Jun-Bin; Fan, Ling; Chen, Chong-Jian; Qiao, Jie

    2015-01-01

    Analyses of cell-free fetal DNA (cff-DNA) from maternal plasma using massively parallel sequencing enable the noninvasive detection of feto-placental chromosome aneuploidy; this technique has been widely used in clinics worldwide. Noninvasive prenatal tests (NIPT) based on cff-DNA have achieved very high accuracy; however, they suffer from maternal copy-number variations (CNV) that may cause false positives and false negatives. In this study, we developed an algorithm to exclude the effect of maternal CNV and refined the Z-score that is used to determine fetal aneuploidy. The simulation results showed that the algorithm is robust against variations of fetal concentration and maternal CNV size. We also introduced a method based on the discrepancy between feto-placental concentrations to help reduce the false-positive ratio. A total of 6615 pregnant women were enrolled in a prospective study to validate the accuracy of our method. All 106 fetuses with T21, 20 with T18, and three with T13 were tested using our method, with sensitivity of 100% and specificity of 99.97%. In the results, two cases with maternal duplications in chromosome 21, which were falsely predicted as T21 by the previous NIPT method, were correctly classified as normal by our algorithm, which demonstrated the effectiveness of our approach. PMID:26534864

  4. Immune activation is inversely related to, but does not cause variation in androgen levels in a cichlid fish species.

    PubMed

    Ros, Albert F H; Oliveira, Rui F; Dijkstra, Peter D; Groothuis, Ton G G

    2012-07-01

    Studies on birds and mammals indicate that sexual traits may signal superior health because active immunity, like inflammatory responses to infections, is suppressive to the production of androgens that facilitate the expression of these traits. Here we test this possible pathway for honest signaling in a teleost species, Sarotherodon galilaeus, by activating the immune system with sheep red blood cells (SRBC), which is a non-pathogenic T- and B-cell stimulating antigen. Two weeks after the start of treatment adult males injected with SRBC showed a significant increase in antibody production in comparison with control males. The variation in specific antibody production was negatively related with variation in both testosterone and 11-ketotestosterone levels. This suggests that investment in immune protection is incompatible with increased activity of the hypothalamic-pituitary-gonadal axis. However, opposite to our expectation no difference in androgen levels was found between placebo and SRBC treatment suggesting that immune activation did not cause androgen suppression in our studied species.

  5. Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation.

    PubMed

    Zhang, Han; Zhao, Yang-Yu; Song, Jing; Zhu, Qi-Ying; Yang, Hua; Zheng, Mei-Ling; Xuan, Zhao-Ling; Wei, Yuan; Chen, Yang; Yuan, Peng-Bo; Yu, Yang; Li, Da-Wei; Liang, Jun-Bin; Fan, Ling; Chen, Chong-Jian; Qiao, Jie

    2015-01-01

    Analyses of cell-free fetal DNA (cff-DNA) from maternal plasma using massively parallel sequencing enable the noninvasive detection of feto-placental chromosome aneuploidy; this technique has been widely used in clinics worldwide. Noninvasive prenatal tests (NIPT) based on cff-DNA have achieved very high accuracy; however, they suffer from maternal copy-number variations (CNV) that may cause false positives and false negatives. In this study, we developed an algorithm to exclude the effect of maternal CNV and refined the Z-score that is used to determine fetal aneuploidy. The simulation results showed that the algorithm is robust against variations of fetal concentration and maternal CNV size. We also introduced a method based on the discrepancy between feto-placental concentrations to help reduce the false-positive ratio. A total of 6615 pregnant women were enrolled in a prospective study to validate the accuracy of our method. All 106 fetuses with T21, 20 with T18, and three with T13 were tested using our method, with sensitivity of 100% and specificity of 99.97%. In the results, two cases with maternal duplications in chromosome 21, which were falsely predicted as T21 by the previous NIPT method, were correctly classified as normal by our algorithm, which demonstrated the effectiveness of our approach. PMID:26534864

  6. Fluvial filtering of land-to-ocean fluxes: from natural Holocene variations to Anthropocene

    NASA Astrophysics Data System (ADS)

    Meybeck, Michel; Vörösmarty, Charles

    2005-02-01

    The evolution of river systems and their related fluxes is considered at various time scales: ( i) over the last 18 000 years, under climatic variability control, ( ii) over the last 50 to 200 years (Anthropocene) due to direct human impacts. Natural Holocene variations in time and space depend on ( i) land-to-ocean connections (endorheism, glacial cover, exposure of continental shelf); ( ii) types of natural fluvial filters (e.g., wetlands, lakes, floodplains, estuaries). Anthropocene changes concern ( i) land-ocean connection (e.g., partial to total runoff reduction resulting from water management), ( ii) modification and removal of natural filters, ( iii) creation of new filters, particularly irrigated fields and reservoirs, ( iv) acceleration and/or development of material sources from human activities. The total river basin area directly affected by human activities is of the same order of magnitude ( >40 Mkm) as the total area affected over the last 18 000 years. A tentative analysis of 38 major river systems totaling 55 Mkm is proposed for several criteria: ( i) trajectories of Holocene evolution, ( ii) occurrence of natural fluvial filters, ( iii) present-day fluvial filters: most river basins are unique. Riverine fluxes per unit area are characterized by hot spots that exceed the world average by one order of magnitude. At the Anthropocene (i.e., since 1950), many riverine fluxes have globally increased (sodium, chloride, sulfate, nitrogen, phosphorous, heavy metals), others are stable (calcium, bicarbonate, sediments) or likely to decrease (dissolved silica). Future trajectories of river fluxes will depend on the balance between increased sources of material (e.g., soil erosion, pollution, fertilization), water abstraction for irrigation and the modification of fluvial filters, particularly the occurrence of reservoirs that already intercept half of the water and store at least 30% of river sediment fluxes. In some river systems, retention actually

  7. Using adult cloned trees grown under natural conditions to characterize BVOC emission variation

    NASA Astrophysics Data System (ADS)

    Persson, Ylva; Schurgers, Guy; Ekberg, Anna; Rinnan, Riikka; Holst, Thomas

    2015-04-01

    Biogenic Volatile Organic Compounds (BVOCs) are diverse chemical species produced and emitted from the vegetation as trace gases. BVOCs are commonly grouped into isoprene, monoterpenes and sesquiterpenes, where isoprene is mainly emitted by deciduous trees and monoterpenes and sesquiterpenes by coniferous trees. BVOCs are known to have a considerable impact on atmospheric chemistry and are precursors for secondary organic aerosol, which in turn are important for the aerosol feedback on the Earth's climate. Recently, Bäck et al. (2012) reported a high diversity of the chemical composition of emitted compounds from pine trees growing at the same stand due to genetic variation. This study here uses cloned trees growing naturally in a transect in Europe in order to exclude genetic variation and to assess emission variation between and within selected tree species grown at different climatic conditions. The International Phenological Garden (IPG) network, where cloned trees are used to monitor the long-term phenological observations of representative tree species for Europe provides a specific, cloned set of important tree species, which had been planted throughout Europe starting in 1957. This gives a unique opportunity to study the adaptation to various climatic conditions and field conditions in genetically identical plants in relation to BVOC emissions. During a field campaign in 2013 at the IPG site in Taastrup, Denmark (55°40' N, 12°18' E), seven trees were measured at three heights within the canopy. Measured trees were two English oaks (Quercus robur), one European beech (Fagus sylvatica) and four Norway spruces (Picea abies) of two provenances. For oak and one provenance of spruce, measurements were performed twice, both in June and in August in order to examine any emission pattern change with the progression of the summer. Measurements were performed using a gas-exchange cuvette of a photosynthesis system combined with BVOC adsorbent tubes, which were

  8. Pressure variation assisted fiber extraction and development of high performance natural fiber composites and nanocomposites

    NASA Astrophysics Data System (ADS)

    Markevicius, Gediminas

    It is believed, that due to the large surface areas provided by the nano scale materials, various composite properties could be enhanced when such particles are incorporated into a polymer matrix. There is also a trend of utilizing natural resources or reusing and recycling materials that are already available for the fabrication of the new composite materials. Cellulose is the most abundant natural polymer on the planet, and therefore it is not surprising to be of interest for composite fabrication. Basic structures of cellulose, comprised of long polysaccharide chains, are the building blocks of cellulose nano fibers. Nano fibers are further bound into micro fibrils and macro fibers. Theoretically pure cellulose nano fibers have tremendous strengths, and therefore are some of the most sought after nano particles. The fiber extraction however is a complex task. The ultrasound, which creates pressure variation in the medium, was employed to extract nano-size cellulose particles from microcrystalline cellulose (MCC). The length and the intensity of the cavitations were evaluated. Electron microscopy studies revealed that cellulose nanoparticles were successfully obtained from the MCC after ultrasound treatment of just 30 minutes. Structure of the fractionated cellulose was also analyzed with the help of X-ray diffraction, and its thermal properties were evaluated with the help of differential scanning calorimetry (DSC). Ultrasound treatment performed on the wheat straw, kenaf, and miscanthus particles altered fiber structure as a result of the cavitation. The micro fibers were generated from these materials after they were subjected to NaOH treatment followed by the ultrasound processing. The potential of larger than nano-sized natural fibers to be used for composite fabrication was also explored. The agricultural byproducts, such as wheat or rice straw, as well as other fast growing crops as miscanthus or kenaf, are comprised of three basic polymers. Just like in

  9. Spinal Cord Injury Caused by Stab Wounds: Incidence, Natural History, and Relevance for Future Research.

    PubMed

    McCaughey, Euan J; Purcell, Mariel; Barnett, Susan C; Allan, David B

    2016-08-01

    Spinal cord injury caused by stab wounds (SCISW) results from a partial or complete transection of the cord, and presents opportunities for interventional research. It is recognized that there is low incidence, but little is known about the natural history or the patient's suitability for long-term clinical outcome studies. This study aims to provide population-based evidence of the demographics of SCISW, and highlight the issues regarding the potential for future research. The database of the Queen Elizabeth National Spinal Injuries Unit (QENSIU), the sole center for treating SCI in Scotland, was reviewed between 1994 and 2013 to ascertain the incidence, demographics, functional recovery, and mortality rates for new SCISW. During this 20 year period, 35 patients with SCISW were admitted (97.1% male, mean age 30.0 years); 31.4% had a cervical injury, 60.0% had a thoracic injury, and 8.6% had a lumbar injury. All had a neurological examination, with 42.9% diagnosed as motor complete on admission and 77.1% discharged as motor incomplete. A total of 70.4% of patients with an American Spinal Injury Association Impairment Scale (AIS) level of A to C on admission had an improved AIS level on discharge. Nine (25.7%) patients have died since discharge, with mean life expectancy for these patients being 9.1 years after injury (20-65 years of age). Patients had higher levels of comorbidities, substance abuse, secondary events, and poor compliance compared with the general SCI population, which may have contributed to the high mortality rate observed post-discharge. The low incidence, heterogeneous nature, spontaneous recovery rate, and problematic follow-up makes those with penetrating stab injuries of the spinal cord a challenging patient group for SCI research.

  10. Natural variations in expression of regulatory and detoxification related genes under limiting phosphate and arsenate stress in Arabidopsis thaliana

    PubMed Central

    Shukla, Tapsi; Kumar, Smita; Khare, Ria; Tripathi, Rudra D.; Trivedi, Prabodh K.

    2015-01-01

    Abiotic stress including nutrient deficiency and heavy metal toxicity severely affects plant growth, development, and productivity. Genetic variations within and in between species are one of the important factors in establishing interactions and responses of plants with the environment. In the recent past, natural variations in Arabidopsis thaliana have been used to understand plant development and response toward different stresses at genetic level. Phosphorus deficiency negatively affects plant growth and metabolism and modulates expression of the genes involved in Pi homeostasis. Arsenate, As(V), a chemical analog of Pi, is taken up by the plants via phosphate transport system. Studies suggest that during Pi deficiency, enhanced As(V) uptake leads to increased toxicity in plants. Here, the natural variations in Arabidopsis have been utilized to study the As(V) stress response under limiting Pi condition. The primary root length was compared to identify differential response of three Arabidopsis accessions (Col-0, Sij-1, and Slavi-1) under limiting Pi and As(V) stress. To study the molecular mechanisms responsible for the differential response, comprehensive expression profiling of the genes involved in uptake, detoxification, and regulatory mechanisms was carried out. Analysis suggests genetic variation-dependent regulatory mechanisms may affect differential response of Arabidopsis natural variants toward As(V) stress under limiting Pi condition. Therefore, it is hypothesized that detailed analysis of the natural variations under multiple stress conditions might help in the better understanding of the biological processes involved in stress tolerance and adaptation. PMID:26557133

  11. Natural ferrihydrite as an agent for reducing turbidity caused by suspended clays.

    PubMed

    Rhoton, F E; Bigham, J M

    2009-01-01

    Biologically impaired waters are often caused by the turbidity associated with elevated suspended sediment concentrations. Turbidity can be reduced by the addition of positively charged compounds that coagulate negatively charged particles in suspension, causing them to flocculate. This research was conducted to determine the effectiveness of ferrihydrite, a poorly crystalline Fe oxide, as a flocculating agent for suspended clays similar to those found in high-turbidity waters of the Mississippi delta. Clay concentrations of 100 mg L(-1) from a Dubbs silt loam (fine silty, mixed, active, thermic Typic Hapludalfs), a Forestdale silty clay loam (fine, smectitic, thermic Typic Hapludalfs), and a Sharkey clay (very fine, smectitic, thermic Chromic Epiaquerts) were suspended in 0.0005 mol L(-1) CaCl(2) solutions at pH 5, 6, 7, or 8. Natural ferrihydrite with a zero point of charge at pH 5.8 was acquired from a drinking water treatment facility and mixed with the suspension at concentrations of 0, 10, 25, and 50 mg L(-1). After settling periods of 24 and 48 h, percent transmittance was measured at a wavelength of 420 nm using a 3-mL sample collected at a depth of 2 cm. The greatest reductions in turbidity after 24-h equilibration were recorded for the pH 5 suspensions of the Dubbs (31%) and Forestdale (37%) clays at a ferrihydrite concentration of 10 mg L(-1) and for the Sharkey clay at a ferrihydrite concentration of 25 mg L(-1) (relative to the 0 ferrihydrite treatment). Water clarity for all samples further increased after 48 h. These results indicate that the effectiveness of ferrihydrite, as a means of reducing turbidity associated with suspended clays, is greatest at pH values below its zero point of charge. PMID:19643754

  12. Novel or natural variation in ecohydrology-an example of smoldering combustion in the boreal forest

    NASA Astrophysics Data System (ADS)

    Johnson, E. A.; Martin, Y. E.

    2012-12-01

    Ecologists often implicitly assume that the physical environment has a potential for certain species composition unless dispersal is limited i.e. that species and their environment are in some sense co-evolved. Novel ecosystems imply that ecosystems are not generally novel in species composition. H.A Gleason in 1926 argued that vegetation was spatially and temporally variable in composition due to the differing contributions of the biotic and abiotic environments and thus all vegetation was in this sense novel. In the 1970's W.A. Watt and M.B. Davis show from pollen studies that vegetation composition changed often and quickly in the Pleistocene with no composition enduring for long periods. That is, there seem to be no modern analogues of past vegetation composition. Certainly ecosystems and their geophysical environments have recurrent patterns but also have major variations. To understand these patterns one must understand the processes that give rise to them. In this talk we will use the effect of the wildfire process of smoldering combustion on the vegetation of boreal and subalpine forests. We will accent the geophysical processes that affect the moisture content of the forest floor. Boreal forests consist mostly of coniferous trees which have relatively small branches to support individual needles and bundles of needles. This and the conical arrangement of branches make a transition from surface fires to crown fires relatively easy. This in part explains the predominance of crown fires (fire intensities > 4000 kWm-1). Boreal forests also have deeper organic layers (F &H soil layers) on the forest floor caused by slower decomposition. The loss of volatiles during decomposition explains the predominance of smoldering combustion in this layer during wildfires. The smoldering loss of the F layer and much of the H layer creates a habitat of more reliable water budget for survival of germinating tree seeds. Thus the amount of the F and H layers removed by

  13. Quantitative genetics of natural variation of behavior in Drosophila melanogaster: the possible role of the social environment on creating persistent patterns of group activity.

    PubMed

    Higgins, Laura A; Jones, Kelly M; Wayne, Marta L

    2005-07-01

    Using a set of nine effectively isogenic lines collected from nature in 1998, we observed unperturbed behaviors of mixed-sex groups of Drosophila melanogaster. We repeatedly scanned replicated groups of genetically identical individuals, five females and five males, and recorded the behavior of each individual (i.e., walking, feeding, grooming, flying, courting, mating, fighting, or resting). From these behaviors, we made a composite variable of activity for our quantitative genetic analysis. Genotypes differed in activity, explaining 14.41% of the variation in activity; 8.60% of the variation was explained by a significant genotype x sex interaction, which signifies genetic variation for sexual dimorphism in behavior. Phenotypic plasticity explained 11.13% of the variation in activity. Different genotypes and sexes within genotypes had different rank orders of the component behaviors that contribute to activity. We found no effect of common rearing environment. Instead, differences between replicate groups within genotype accounted for 19.47% variation in activity, and activity was significantly repeatable across scans. This emergent group behavior is likely caused by differences between groups of interacting individuals, even though individuals were genetically identical across groups. Thus, emergent group behavior explained almost as much variation in activity as the combined sources of genetic variation (23.01%), and this is an additional level on which selection could operate: individuals and groups. We discuss how differences among groups could change patterns of additive genetic variation available for evolution. Furthermore, because the behavior of an individual is influenced by conspecifics, genotype interactions between individuals could contribute to indirect selection. Finally, if we consider activity as a syndrome governing all component behaviors with strong genetic correlations among behaviors within an individual, then these component behaviors

  14. Genetic mapping of natural variation in a shade avoidance response: ELF3 is the candidate gene for a QTL in hypocotyl growth regulation

    PubMed Central

    Coluccio, M. Paula; Sanchez, Sabrina E.; Kasulin, Luciana; Yanovsky, Marcelo J.; Botto, Javier F.

    2011-01-01

    When plants become shaded by neighbouring plants, they perceive a decrease in the red/far-red (R/FR) ratio of the light environment, which provides an early and unambiguous warning of the presence of competing vegetation. The mechanistic bases of the natural genetic variation in response to shade signals remain largely unknown. This study demonstrates that a wide range of genetic variation for hypocotyl elongation in response to an FR pulse at the end of day (EOD), a light signal that simulates natural shade, exists between Arabidopsis accessions. A quantitative trait locus (QTL) mapping analysis was done in the Bayreuth×Shahdara recombinant inbred line population. EODINDEX1 is the most significant QTL identified in response to EOD. The Shahdara alleles at EODINDEX1 caused a reduced response to shade as a consequence of an impaired hypocotyl inhibition under white light, and an accelerated leaf movement rhythm, which correlated positively with the pattern of circadian expression of clock genes such as PRR7 and PRR9. Genetic and quantitative complementation analyses demonstrated that ELF3 is the most likely candidate gene underlying natural variation at EODINDEX1. In conclusion, ELF3 is proposed as a component of the shade avoidance signalling pathway responsible for the phenotypic differences between Arabidopsis populations in relation to adaptation in a changing light environment. PMID:20713464

  15. Use of natural pH variation to increase the flocculation of the marine microalgae Nannochloropsis oculata.

    PubMed

    Sales, Rafael; Abreu, Paulo Cesar

    2015-02-01

    Microalgae is largely used in aquaculture as feed. More recently, these microorganisms have been considered as an important feedstock for biodiesel production. However, the concentration of produced biomass represents a large parcel of production costs. In this study, we have evaluated the influence of natural pH variation of culture medium, caused by photosynthetic activity, on the flocculation of the marine microalgae Nannochloropsis oculata. Experiments were conducted with the same culture with different pH values (8.5 and 9.6), obtained after exposing the cells to different light conditions. For each pH value, different treatments were composed by adding 0, 5, 10, and 30 mM of NaOH and the flocculant Flopam® (FO4800 SH) at concentrations of 0, 0.5, 1, and 5 ppm. Higher flocculation efficiencies were obtained for the culture with pH 9.6 in comparison to 8.5 for the same NaOH and Flopam concentrations. Lower concentrations of base and flocculant were needed for flocculating the culture in higher pH, representing an economy of 20 % in the costs of crop harvesting.

  16. Use of natural pH variation to increase the flocculation of the marine microalgae Nannochloropsis oculata.

    PubMed

    Sales, Rafael; Abreu, Paulo Cesar

    2015-02-01

    Microalgae is largely used in aquaculture as feed. More recently, these microorganisms have been considered as an important feedstock for biodiesel production. However, the concentration of produced biomass represents a large parcel of production costs. In this study, we have evaluated the influence of natural pH variation of culture medium, caused by photosynthetic activity, on the flocculation of the marine microalgae Nannochloropsis oculata. Experiments were conducted with the same culture with different pH values (8.5 and 9.6), obtained after exposing the cells to different light conditions. For each pH value, different treatments were composed by adding 0, 5, 10, and 30 mM of NaOH and the flocculant Flopam® (FO4800 SH) at concentrations of 0, 0.5, 1, and 5 ppm. Higher flocculation efficiencies were obtained for the culture with pH 9.6 in comparison to 8.5 for the same NaOH and Flopam concentrations. Lower concentrations of base and flocculant were needed for flocculating the culture in higher pH, representing an economy of 20 % in the costs of crop harvesting. PMID:25432344

  17. Haptoglobin (HP) and Haptoglobin-related protein (HPR) copy number variation, natural selection, and trypanosomiasis.

    PubMed

    Hardwick, Robert J; Ménard, Anne; Sironi, Manuela; Milet, Jacqueline; Garcia, André; Sese, Claude; Yang, Fengtang; Fu, Beiyuan; Courtin, David; Hollox, Edward J

    2014-01-01

    Haptoglobin, coded by the HP gene, is a plasma protein that acts as a scavenger for free heme, and haptoglobin-related protein (coded by the HPR gene) forms part of the trypanolytic factor TLF-1, together with apolipoprotein L1 (ApoL1). We analyse the polymorphic small intragenic duplication of the HP gene, with alleles Hp1 and Hp2, in 52 populations, and find no evidence for natural selection either from extended haplotype analysis or from correlation with pathogen richness matrices. Using fiber-FISH, the paralog ratio test, and array-CGH data, we also confirm that the HPR gene is copy number variable, with duplication of the whole HPR gene at polymorphic frequencies in west and central Africa, up to an allele frequency of 15 %. The geographical distribution of the HPR duplication allele overlaps the region where the pathogen causing chronic human African trypanosomiasis, Trypanosoma brucei gambiense, is endemic. The HPR duplication has occurred on one SNP haplotype, but there is no strong evidence of extended homozygosity, a characteristic of recent natural selection. The HPR duplication shows a slight, non-significant undertransmission to human African trypanosomiasis-affected children of unaffected parents in the Democratic Republic of Congo. However, taken together with alleles of APOL1, there is an overall significant undertransmission of putative protective alleles to human African trypanosomiasis-affected children.

  18. Reproductive biology and pollination mechanisms of Epidendrum secundum (Orchidaceae). Floral variation: a consequence of natural hybridization?

    PubMed

    Pansarin, E R; Amaral, M C E

    2008-03-01

    The phenology, flower morphology, pollination mechanism and reproductive biology of Epidendrum secundum were studied in a semi-deciduous forest at the Serra do Japi (SJ), and in the Atlantic rain forest of Picinguaba, both natural reserves in the State of São Paulo, southeastern Brazil. E. secundum flowers all year round, with a flowering peak between September and January. This species is either a lithophytic or terrestrial herb in the SJ, whereas, in Picinguaba, it grows mainly in disturbed areas along roadsides. E. secundum is pollinated by several species of diurnal Lepidoptera at both study sites. In Picinguaba, where E. secundum is sympatric with E. fulgens and both share the same pollinators, pollen transference between these two species was recorded. E. secundum is self-compatible but pollinator-dependent. It is inter-compatible with E. fulgens, producing fertile seeds. In contrast to the population of the SJ, in the Picinguaba region, floral morphology is quite variable among plants and some individuals present flowers with characteristics in-between both sympatric species, suggesting that natural hybridization occasionally occurs. The anthropogenic perturbation is probably the cause of the occurrence of E. secundum in the Picinguaba region, enabling its contact with E. fulgens.

  19. Physical nature and timing variations of the eclipsing system V407 Pegasi

    SciTech Connect

    Lee, Jae Woo; Park, Jang-Ho; Hong, Kyeongsoo; Kim, Seung-Lee; Lee, Chung-Uk E-mail: pooh107162@kasi.re.kr E-mail: slkim@kasi.re.kr

    2014-04-01

    New multiband CCD photometry is presented for V407 Peg; the R {sub C} light curves are the first ever compiled. Our light curves, displaying a flat bottom at secondary minimum and an O'Connell effect, were simultaneously analyzed with the radial velocity (RV) curves given by Rucinski et al. The light changes of the system are best modeled using both a hot spot on the secondary star and a third light. The model also represents historical light curves. All available minimum epochs, including our six timing measurements, have been examined and they indicate that the eclipse timing variation is mainly caused by light asymmetries due to the spot activity detected in the light-curve synthesis. The hot spot may be produced as a result of the impact of the gas stream from the primary star. Our light and velocity solutions indicate that V407 Peg is a totally eclipsing A-type overcontact binary with values of q = 0.251, i = 87.°6, ΔT = 496 K, f = 61%, and l {sub 3} = 11∼16%. Individual masses and radii of both components are determined to be M {sub 1} = 1.72 M {sub ☉}, M {sub 2} = 0.43 M {sub ☉}, R {sub 1} = 2.15 R {sub ☉}, and R {sub 2} = 1.21 R {sub ☉}. These results are very different from previous ones, which is probably caused by the light curves with distorted and inclined eclipses used in those other analyses. The fact that there are no objects optically related to the system and that the seasonal RVs show a large discrepancy in systemic velocity indicates that the third light source most likely arises from a tertiary component orbiting the eclipsing pair.

  20. Physical Nature and Timing Variations of the Eclipsing System V407 Pegasi

    NASA Astrophysics Data System (ADS)

    Lee, Jae Woo; Park, Jang-Ho; Hong, Kyeongsoo; Kim, Seung-Lee; Lee, Chung-Uk

    2014-04-01

    New multiband CCD photometry is presented for V407 Peg; the R C light curves are the first ever compiled. Our light curves, displaying a flat bottom at secondary minimum and an O'Connell effect, were simultaneously analyzed with the radial velocity (RV) curves given by Rucinski et al. The light changes of the system are best modeled using both a hot spot on the secondary star and a third light. The model also represents historical light curves. All available minimum epochs, including our six timing measurements, have been examined and they indicate that the eclipse timing variation is mainly caused by light asymmetries due to the spot activity detected in the light-curve synthesis. The hot spot may be produced as a result of the impact of the gas stream from the primary star. Our light and velocity solutions indicate that V407 Peg is a totally eclipsing A-type overcontact binary with values of q = 0.251, i = 87.°6, ΔT = 496 K, f = 61%, and l 3 = 11~16%. Individual masses and radii of both components are determined to be M 1 = 1.72 M ⊙, M 2 = 0.43 M ⊙, R 1 = 2.15 R ⊙, and R 2 = 1.21 R ⊙. These results are very different from previous ones, which is probably caused by the light curves with distorted and inclined eclipses used in those other analyses. The fact that there are no objects optically related to the system and that the seasonal RVs show a large discrepancy in systemic velocity indicates that the third light source most likely arises from a tertiary component orbiting the eclipsing pair.

  1. The cryptoendolithic microbial environment in the Antarctic cold desert: temperature variations in nature

    NASA Technical Reports Server (NTRS)

    McKay, C. P.; Friedmann, E. I.

    1985-01-01

    In the Antarctic cold desert, cryptoendolithic microorganisms live under the surface of porous sandstone rocks. During the austral summer, the environment of the near-surface rock layers colonized by organisms is characterized by two kinds of temperature oscillations, both occurring across the freezing point. Low-frequency (diurnal) and large-amplitude (up to about 20 degrees C) oscillations on the sunlit surface of rocks result in a daily freeze-thaw cycle. This is a result of the diurnal changes in the sun altitude and angle with respect to the rock surface. The biological effect of this oscillation is the regulation of the onset and cessation of metabolic activity. The high-frequency (few minutes) oscillations occur only under certain weather conditions (sunny days with light winds) and are superimposed on the low-frequency oscillations. They are caused by the cooling effect of wind gusts on rock surfaces that are much warmer than ambient air temperatures. High-frequency oscillations result in a rapid freeze-thaw cycle on the surface, which, however, does not reach the microbial zone. These high-frequency freeze-thaw oscillations are probably the cause of the abiotic nature of the rock surface. Both oscillations seem to have an effect on rock weathering.

  2. The cryptoendolithic microbial environment in the Antarctic cold desert: temperature variations in nature.

    PubMed

    McKay, C P; Friedmann, E I

    1985-01-01

    In the Antarctic cold desert, cryptoendolithic microorganisms live under the surface of porous sandstone rocks. During the austral summer, the environment of the near-surface rock layers colonized by organisms is characterized by two kinds of temperature oscillations, both occurring across the freezing point. Low-frequency (diurnal) and large-amplitude (up to about 20 degrees C) oscillations on the sunlit surface of rocks result in a daily freeze-thaw cycle. This is a result of the diurnal changes in the sun altitude and angle with respect to the rock surface. The biological effect of this oscillation is the regulation of the onset and cessation of metabolic activity. The high-frequency (few minutes) oscillations occur only under certain weather conditions (sunny days with light winds) and are superimposed on the low-frequency oscillations. They are caused by the cooling effect of wind gusts on rock surfaces that are much warmer than ambient air temperatures. High-frequency oscillations result in a rapid freeze-thaw cycle on the surface, which, however, does not reach the microbial zone. These high-frequency freeze-thaw oscillations are probably the cause of the abiotic nature of the rock surface. Both oscillations seem to have an effect on rock weathering.

  3. Natural variation in maternal sensitivity is reflected in maternal brain responses to infant stimuli.

    PubMed

    Elmadih, Alya; Wan, Ming Wai; Downey, Darragh; Elliott, Rebecca; Swain, James E; Abel, Kathryn M

    2016-10-01

    Increasing evidence suggests that discrete neural networks that mediate emotion processing are activated when mothers respond to infant's images or cries. Accumulating data also indicate that natural variation in maternal caregiving behavior is related to maternal oxytocin (OT) levels. However, brain activation to infant cues has not been studied comparing mothers at disparate ends of the "maternal sensitivity" spectrum. Based on observed mother-infant play interaction at 4-6 months postpartum in 80 antenatally recruited mothers, 15 mothers with the highest sensitivity (HSMs) and 15 mothers with the lowest sensitivity (LSMs) were followed at 7-9 months using functional magnetic resonance imaging (fMRI) to examine brain responses to viewing videos of their "own" versus an "unknown" infant in 3 affect states (neutral, happy, and sad). Plasma OT measurements were taken from mothers following play interactions with their infant. Compared with LSMs, HSMs showed significantly greater brain activation in right superior temporal gyrus (STG) in response to own versus unknown neutral infant and to own happy versus neutral control. Changes in brain activation were significantly negatively correlated with plasma OT responses in HSMs mothers. Conversely, compared with HSMs, LSMs showed no significant activation difference in response to own infant separately or in contrast to unknown infant. Activation of STG may index sensitive maternal response to own infant stimuli. Sensitive parenting may have its unique profile in relation to brain responses which can act as biomarkers for future intervention studies that enhance sensitivity of maternal care. (PsycINFO Database Record PMID:27513806

  4. Divergence of Eurosta solidaginis in response to host plant variation and natural enemies.

    PubMed

    Craig, Timothy P; Itami, Joanne K

    2011-03-01

    We tested the hypothesis that forest and prairie populations of the gall-inducing fly, Eurosta solidaginis, have diverged in response to variation in selection by its host plant Solidago altissima, and its natural enemies. A reciprocal cross infection design experiment demonstrated that fly populations from the prairie and forest biomes had higher survival on local biome plants compared to foreign biome host plants. Flies from each biome also had an oviposition preference for their local plants. Each fly population induced galls of the size and shape found in their local biome on host plants from both biomes indicating a genetic basis to the differences in gall morphology. Solidago altissima from the prairie and forest biomes retained significant morphological differences in the common garden indicating that they are genetically differentiated, possibly at the subspecies level. The populations are partially reproductively isolated as a result of a combination of prezygotic isolation due to host-associated assortative mating, and postzygotic isolation due to low hybrid survival. We conclude that E. solidaginis is undergoing diversifying selection to adapt to differences between prairie and forest habitats.

  5. Complex Genetics Control Natural Variation in Arabidopsis thaliana Resistance to Botrytis cinerea

    PubMed Central

    Rowe, Heather C.; Kliebenstein, Daniel J.

    2008-01-01

    The genetic architecture of plant defense against microbial pathogens may be influenced by pathogen lifestyle. While plant interactions with biotrophic pathogens are frequently controlled by the action of large-effect resistance genes that follow classic Mendelian inheritance, our study suggests that plant defense against the necrotrophic pathogen Botrytis cinerea is primarily quantitative and genetically complex. Few studies of quantitative resistance to necrotrophic pathogens have used large plant mapping populations to dissect the genetic structure of resistance. Using a large structured mapping population of Arabidopsis thaliana, we identified quantitative trait loci influencing plant response to B. cinerea, measured as expansion of necrotic lesions on leaves and accumulation of the antimicrobial compound camalexin. Testing multiple B. cinerea isolates, we identified 23 separate QTL in this population, ranging in isolate-specificity from being identified with a single isolate to controlling resistance against all isolates tested. We identified a set of QTL controlling accumulation of camalexin in response to pathogen infection that largely colocalized with lesion QTL. The identified resistance QTL appear to function in epistatic networks involving three or more loci. Detection of multilocus connections suggests that natural variation in specific signaling or response networks may control A. thaliana–B. cinerea interaction in this population. PMID:18845849

  6. Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes.

    PubMed

    Shaw, Joseph R; Hampton, Thomas H; King, Benjamin L; Whitehead, Andrew; Galvez, Fernando; Gross, Robert H; Keith, Nathan; Notch, Emily; Jung, Dawoon; Glaholt, Stephen P; Chen, Celia Y; Colbourne, John K; Stanton, Bruce A

    2014-11-01

    Many organisms survive fluctuating and extreme environmental conditions by manifesting multiple distinct phenotypes during adulthood by means of developmental processes that enable phenotypic plasticity. We report on the discovery of putative plasticity-enabling genes that are involved in transforming the gill of the euryhaline teleost fish, Fundulus heteroclitus, from its freshwater to its seawater gill-type, a process that alters both morphology and function. Gene expression that normally enables osmotic plasticity is inhibited by arsenic. Gene sets defined by antagonistic interactions between arsenic and salinity show reduced transcriptional variation among individual fish, suggesting unusually accurate and precise regulatory control of these genes, consistent with the hypothesis that they participate in a canalized developmental response. We observe that natural selection acts to preserve canalized gene expression in populations of killifish that are most tolerant to abrupt salinity change and that these populations show the least variability in their transcription of genes enabling plasticity of the gill. We found that genes participating in this highly canalized and conserved plasticity-enabling response had significantly fewer and less complex associations with transcriptional regulators than genes that respond only to arsenic or salinity. Collectively these findings, which are drawn from the relationships between environmental challenge, plasticity, and canalization among populations, suggest that the selective processes that facilitate phenotypic plasticity do so by targeting the regulatory networks that gives rise to the response. These findings also provide a generalized, conceptual framework of how genes might interact with the environment and evolve toward the development of plastic traits. PMID:25158801

  7. Natural variation in gene expression between wild and weedy populations of Helianthus annuus.

    PubMed

    Lai, Zhao; Kane, Nolan C; Zou, Yi; Rieseberg, Loren H

    2008-08-01

    The molecular genetic changes underlying the transformation of wild plants into agricultural weeds are poorly understood. Here we use a sunflower cDNA microarray to detect variation in gene expression between two wild (non-weedy) Helianthus annuus populations from Utah and Kansas and four weedy H. annuus populations collected from agricultural fields in Utah, Kansas, Indiana, and California. When grown in a common growth chamber environment, populations differed substantially in their gene expression patterns, indicating extensive genetic differentiation. Overall, 165 uni-genes, representing approximately 5% of total genes on the array, showed significant differential expression in one or more weedy populations when compared to both wild populations. This subset of genes is enriched for abiotic/biotic stimulus and stress response proteins, which may underlie niche transitions from the natural sites to agricultural fields for H. annuus. However, only a small proportion of the differentially expressed genes overlapped in multiple wild vs. weedy comparisons, indicating that most of the observed expression changes are due to local adaptation or neutral processes, as opposed to parallel genotypic adaptation to agricultural fields. These results are consistent with an earlier phylogeographic study suggesting that weedy sunflowers have evolved multiple times in different regions of the United States and further indicate that the evolution of weedy sunflowers has been accompanied by substantial gene expression divergence in different weedy populations.

  8. Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes.

    PubMed

    Shaw, Joseph R; Hampton, Thomas H; King, Benjamin L; Whitehead, Andrew; Galvez, Fernando; Gross, Robert H; Keith, Nathan; Notch, Emily; Jung, Dawoon; Glaholt, Stephen P; Chen, Celia Y; Colbourne, John K; Stanton, Bruce A

    2014-11-01

    Many organisms survive fluctuating and extreme environmental conditions by manifesting multiple distinct phenotypes during adulthood by means of developmental processes that enable phenotypic plasticity. We report on the discovery of putative plasticity-enabling genes that are involved in transforming the gill of the euryhaline teleost fish, Fundulus heteroclitus, from its freshwater to its seawater gill-type, a process that alters both morphology and function. Gene expression that normally enables osmotic plasticity is inhibited by arsenic. Gene sets defined by antagonistic interactions between arsenic and salinity show reduced transcriptional variation among individual fish, suggesting unusually accurate and precise regulatory control of these genes, consistent with the hypothesis that they participate in a canalized developmental response. We observe that natural selection acts to preserve canalized gene expression in populations of killifish that are most tolerant to abrupt salinity change and that these populations show the least variability in their transcription of genes enabling plasticity of the gill. We found that genes participating in this highly canalized and conserved plasticity-enabling response had significantly fewer and less complex associations with transcriptional regulators than genes that respond only to arsenic or salinity. Collectively these findings, which are drawn from the relationships between environmental challenge, plasticity, and canalization among populations, suggest that the selective processes that facilitate phenotypic plasticity do so by targeting the regulatory networks that gives rise to the response. These findings also provide a generalized, conceptual framework of how genes might interact with the environment and evolve toward the development of plastic traits.

  9. Developing natural convection in a fluid layer with localized heating and large viscosity variation

    SciTech Connect

    Hickox, C.E.; Chu, Tze Yao.

    1991-01-01

    Numerical simulations and laboratory experiments are used to elucidate aspects of transient natural convection in a magma chamber. The magma chamber is modeled as a horizontal fluid layer confined within an enclosure of square planform and heated from below by a strip heater centered on the lower boundary of the enclosure. The width of the strip heater and the depth of the fluid layer are one-fourth of the layer width. Corn syrup is used as the working fluid in order to approximate the large viscosity variation with temperature and the large Prandtl number typical of magma. The quiescent, uniform, fluid layer is subjected to instantaneous heating from the strip heater producing a transient flow which is dominated by two counter-rotating convective cells. Experimentally determined characteristics of the developing flow are compared with numerical simulations carried out with a finite element computer program. The results of numerical simulations are in essential agreement with experimental data. Differences between the numerical simulations and experimental measurements are conjectured to result from non-ideal effects present in the experiment which are difficult to represent accurately in a numerical simulation.

  10. Multigenic natural variation underlies Caenorhabditis elegans olfactory preference for the bacterial pathogen Serratia marcescens.

    PubMed

    Glater, Elizabeth E; Rockman, Matthew V; Bargmann, Cornelia I

    2014-02-19

    The nematode Caenorhabditis elegans can use olfaction to discriminate among different kinds of bacteria, its major food source. We asked how natural genetic variation contributes to choice behavior, focusing on differences in olfactory preference behavior between two wild-type C. elegans strains. The laboratory strain N2 strongly prefers the odor of Serratia marcescens, a soil bacterium that is pathogenic to C. elegans, to the odor of Escherichia coli, a commonly used laboratory food source. The divergent Hawaiian strain CB4856 has a weaker attraction to Serratia than the N2 strain, and this behavioral difference has a complex genetic basis. At least three quantitative trait loci (QTLs) from the CB4856 Hawaii strain (HW) with large effect sizes lead to reduced Serratia preference when introgressed into an N2 genetic background. These loci interact and have epistatic interactions with at least two antagonistic QTLs from HW that increase Serratia preference. The complex genetic architecture of this C. elegans trait is reminiscent of the architecture of mammalian metabolic and behavioral traits.

  11. A mobile tool about causes and distribution of dramatic natural phenomena

    NASA Astrophysics Data System (ADS)

    Boppidi, Ravikanth Reddy

    Most Research suggests that tablet computers could aid the study of many scientific concepts that are difficult to grasp, such as places, time and statistics. These occur especially in the study of geology, chemistry, biology and so on. Tapping the technology will soon become critical career training for future generations. Teaching through mobile is more interactive and helps students to grasp quickly. In this thesis an interactive mobile tool is developed which explains about the causes and distribution of natural disasters like Earthquakes, Tsunami, Tropical Cyclones, Volcanic Eruptions and Tornadoes. The application shows the places of disasters on an interactive map and it also contains YouTube embedded videos, which explain the disasters visually. The advantage of this tool is, it can be deployed onto major mobile operating systems like Android and IOS. The application's user interface (UI) is made very responsive using D3 JavaScript, JQuery, Java Script, HTML, CSS so that it can adapt to mobiles, tablets, and desktop screens.

  12. Tourist perceptions of degradation caused by coastal nature-based recreation.

    PubMed

    Priskin, Julianna

    2003-08-01

    Tourist perceptions of environmental degradation caused by nature-based tourism activities in a coastal environment were determined in the Central Coast Region of Western Australia. Structured surveys were administered to 702 visitors over two peak seasons. Visitors were required to indicate their perceptions on a Likert-type scale. Activities assessed were swimming, boating, fishing, diving and snorkelling, (wind)surfing, sandboarding, four-wheel driving, (bush)walking, camping, horseriding and sightseeing. Tourists had significantly variable demographic characteristics over two seasons and participated in different activities. However, perception of environmental degradation of individual activities did not vary significantly between seasons, except for fishing, four-wheel driving and sandboarding. The age, origin and level of education of visitors had more effect on perceptions than gender or income group. Participation in an activity affected perceptions only for those who went fishing, sandboarding, four-wheel driving and sightseeing. Visitor perceptions were comparable to 'real' impacts documented in the recreation ecology literature. The results of this research indicate a need for improved visitor education and interpretation facilities.

  13. Variation at the hepatic lipase and apolipoprotein AI/CIII/AIV loci is a major cause of genetically determined variation in plasma HDL cholesterol levels.

    PubMed Central

    Cohen, J C; Wang, Z; Grundy, S M; Stoesz, M R; Guerra, R

    1994-01-01

    Genetic factors have been shown to play an important role in determining interindividual variation in plasma HDL-C levels, but the specific genetic determinants of HDL cholesterol (HDL-C) levels have not been elucidated. In this study, the effects of variation in the genomic regions encoding hepatic lipase, apolipoprotein AI/CIII/AIV, and the cholesteryl ester transfer protein on plasma HDL-C levels were examined in 73 normotriglyceridemic, Caucasian nuclear families. Genetic factors accounted for 56.5 +/- 13% of the interindividual variation in plasma HDL-C levels. For each candidate gene, adjusted plasma HDL-C levels of sibling pairs who shared zero, one, or two parental alleles identical-by-descent were compared using sibling-pair linkage analysis. Allelic variation in the genes encoding hepatic lipase and apolipoprotein AI/CIII/AIV accounted for 25 and 22%, respectively, of the total interindividual variation in plasma HDL-C levels. In contrast, none of the variation in plasma HDL-C levels could be accounted for by allelic variation in the cholesteryl ester transfer protein. These findings indicate that a major fraction of the genetically determined variation in plasma HDL-C levels is conferred by allelic variation at the hepatic lipase and the apolipoprotein AI/CIII/AIV gene loci. PMID:7989594

  14. Assessment of infrastructure functional damages caused by natural-technological disasters

    NASA Astrophysics Data System (ADS)

    Massabò, Marco; Trasforini, Eva; Traverso, Stefania; Rudari, Roberto; De Angeli, Silvia; Cecinati, Francesca; Cerruti, Valentina

    2013-04-01

    The assessment of infrastructure damages caused by technological disaster poses several challenges, from gathering needed information on the territorial system to the definition of functionality curves for infrastructures elements (such as, buildings, road school) that are exposed to both natural and technological event. Moreover, areas affected by natural or natech (technological disasters triggered by natural events) disasters have often very large extensions and a rapid survey of them to gather all the needed information is a very difficult task, for many reasons, not least the difficult access to the existing databases and resources. We use multispectral optical imagery with other geographical and unconventional data to identify and characterize exposed elements. Our efforts in the virtual survey and during the investigation steps have different aims: to identify the vulnerability of infrastructures, buildings or activities; to execute calculations of exposition to risk; to estimate physical and functional damages. Subsequently, we apply specific algorithms to estimate values of acting forces and physical and functional damages. The updated picture of target areas in terms of risk-prone people, infrastructures and their connections is very important. It is possible to develop algorithms providing values of systemic functionality for each network element. The methodology is here applied to a natech disaster, arising from the combination of a flood event (specifically, the January 2010 flooding of Drin and Buna rivers, with a worsening in the road safety levels in the Shkoder area) with and the subsequent overturning of a truck transporting hazardous material. The accident causes the loss of containment and the total material release. Once the release has taken place, the evolution will depend on the physical state of the substance spilled (liquid, gas or dust). As a specific case we consider the rupture of a trucks transporting liquid fuels such as gasoline

  15. Natural variation of the Y chromosome suppresses sex ratio distortion and modulates testis-specific gene expression in Drosophila simulans.

    PubMed

    Branco, A T; Tao, Y; Hartl, D L; Lemos, B

    2013-07-01

    X-linked sex-ratio distorters that disrupt spermatogenesis can cause a deficiency in functional Y-bearing sperm and a female-biased sex ratio. Y-linked modifiers that restore a normal sex ratio might be abundant and favored when a X-linked distorter is present. Here we investigated natural variation of Y-linked suppressors of sex-ratio in the Winters systems and the ability of these chromosomes to modulate gene expression in Drosophila simulans. Seventy-eight Y chromosomes of worldwide origin were assayed for their resistance to the X-linked sex-ratio distorter gene Dox. Y chromosome diversity caused males to sire ∼63% to ∼98% female progeny. Genome-wide gene expression analysis revealed hundreds of genes differentially expressed between isogenic males with sensitive (high sex ratio) and resistant (low sex ratio) Y chromosomes from the same population. Although the expression of about 75% of all testis-specific genes remained unchanged across Y chromosomes, a subset of post-meiotic genes was upregulated by resistant Y chromosomes. Conversely, a set of accessory gland-specific genes and mitochondrial genes were downregulated in males with resistant Y chromosomes. The D. simulans Y chromosome also modulated gene expression in XXY females in which the Y-linked protein-coding genes are not transcribed. The data suggest that the Y chromosome might exert its regulatory functions through epigenetic mechanisms that do not require the expression of protein-coding genes. The gene network that modulates sex ratio distortion by the Y chromosome is poorly understood, other than that it might include interactions with mitochondria and enriched for genes expressed in post-meiotic stages of spermatogenesis.

  16. Genetic variation in plant volatile emission does not result in differential attraction of natural enemies in the field.

    PubMed

    Wason, Elizabeth L; Hunter, Mark D

    2014-02-01

    Volatile organic chemical (VOC) emission by plants may serve as an adaptive plant defense by attracting the natural enemies of herbivores. For plant VOC emission to evolve as an adaptive defense, plants must show genetic variability for the trait. To date, such variability has been investigated primarily in agricultural systems, yet relatively little is known about genetic variation in VOCs emitted by natural populations of native plants. Here, we investigate intraspecific variation in constitutive and herbivore-induced plant VOC emission using the native common milkweed plant (Asclepias syriaca) and its monarch caterpillar herbivore (Danaus plexippus) in complementary field and common garden greenhouse experiments. In addition, we used a common garden field experiment to gauge natural enemy attraction to milkweed VOCs induced by monarch damage. We found evidence of genetic variation in the total constitutive and induced concentrations of VOCs and the composition of VOC blends emitted by milkweed plants. However, all milkweed genotypes responded similarly to induction by monarchs in terms of their relative change in VOC concentration and blend. Natural enemies attacked decoy caterpillars more frequently on damaged than on undamaged milkweed, and natural enemy visitation was associated with higher total VOC concentrations and with VOC blend. Thus, we present evidence that induced VOCs emitted by milkweed may function as a defense against herbivores. However, plant genotypes were equally attractive to natural enemies. Although milkweed genotypes diverge phenotypically in their VOC concentrations and blends, they converge into similar phenotypes with regard to magnitude of induction and enemy attraction.

  17. Genetic variation in plant volatile emission does not result in differential attraction of natural enemies in the field.

    PubMed

    Wason, Elizabeth L; Hunter, Mark D

    2014-02-01

    Volatile organic chemical (VOC) emission by plants may serve as an adaptive plant defense by attracting the natural enemies of herbivores. For plant VOC emission to evolve as an adaptive defense, plants must show genetic variability for the trait. To date, such variability has been investigated primarily in agricultural systems, yet relatively little is known about genetic variation in VOCs emitted by natural populations of native plants. Here, we investigate intraspecific variation in constitutive and herbivore-induced plant VOC emission using the native common milkweed plant (Asclepias syriaca) and its monarch caterpillar herbivore (Danaus plexippus) in complementary field and common garden greenhouse experiments. In addition, we used a common garden field experiment to gauge natural enemy attraction to milkweed VOCs induced by monarch damage. We found evidence of genetic variation in the total constitutive and induced concentrations of VOCs and the composition of VOC blends emitted by milkweed plants. However, all milkweed genotypes responded similarly to induction by monarchs in terms of their relative change in VOC concentration and blend. Natural enemies attacked decoy caterpillars more frequently on damaged than on undamaged milkweed, and natural enemy visitation was associated with higher total VOC concentrations and with VOC blend. Thus, we present evidence that induced VOCs emitted by milkweed may function as a defense against herbivores. However, plant genotypes were equally attractive to natural enemies. Although milkweed genotypes diverge phenotypically in their VOC concentrations and blends, they converge into similar phenotypes with regard to magnitude of induction and enemy attraction. PMID:24096739

  18. Weathering and deterioration of volcanic tuff rocks used as natural building stone caused by moisture expansion

    NASA Astrophysics Data System (ADS)

    Wedekind, W.; Lopez-Doncel, R.; Dohrmann, R.; Siegesmund, S.

    2012-04-01

    Volcanic tuff rocks are one of the most frequently used natural building rocks. Tuff rocks show great assortment in composition, grain size, sorting and textures, however scaling, flaking and cracking mostly affect all of them. Diverse authors suggest, that the swelling ability of clay minerals provoke moisture expansion contributing for the weathering and deterioration of the rocks and finally for the construction. Fourteen building volcanic tuff rocks from Germany, Hungary and Mexico of different ages, with diverse compositions and weathering conditions were studied in order to determine the influence of the moisture content regarding their deterioration. Hydric (water saturated) and hygric (related to the relative humidity) wetting experiments realized on the tuffs show that the phenomenon of the expansion certainly can be related to the content on clay minerals, which were clearly identified by XRD analysis. The moisture contents also dependents on the porosity, principally effective porosity and the radii distribution of the pores, because more water can be adsorbed and transported into the rock. However, there are tuff samples, which show a moderate or none expansion, although they have an important amount of clay minerals. Petrographic and geochemical analysis show, that the presence of other phyillosilicate minerals, like muscovite (sericite) and biotite, plays likewise an important role during the moisture expansion. On the other hand we identified a tuff type rich in clay minerals, which shows important hygric expansion but it is not so clear by the hydric water immersion experiment, because this tuff contains a high amount of calcium carbonate, principally in the fine grained matrix causing dissolution of the matrix and crumbling of the non-soluble particles including the clay-silt fraction. In this case it seems to be that the dissolution of the carbonate matrix causes a secondary porosity, which accelerates and favors the expansion and in consequent

  19. The AT-hook motif-encoding gene METABOLIC NETWORK MODULATOR 1 underlies natural variation in Arabidopsis primary metabolism

    PubMed Central

    Li, Baohua; Kliebenstein, Daniel J.

    2014-01-01

    Regulation of primary metabolism is a central mechanism by which plants coordinate their various responses to biotic and abiotic challenge. To identify genes responsible for natural variation in primary metabolism, we focused on cloning a locus from Arabidopsis thaliana that influences the level of TCA cycle metabolites in planta. We found that the Met.V.67 locus was controlled by natural variation in METABOLIC NETWORK MODULATOR 1 (MNM1), which encoded an AT-hook motif-containing protein that was unique to the Brassicales lineage. MNM1 had wide ranging effects on plant metabolism and displayed a tissue expression pattern that was suggestive of a function in sink tissues. Natural variation within MNM1 had differential effects during a diurnal time course, and this temporal dependency was supported by analysis of T-DNA insertion and over-expression lines for MNM1. Thus, the cloning of a natural variation locus specifically associated with primary metabolism allowed us to identify MNM1 as a lineage-specific modulator of primary metabolism, suggesting that the regulation of primary metabolism can change during evolution. PMID:25202318

  20. O the Foundations of the Dynamical Theory of Fractured Porous Media and the Gravity Variations Caused by Dilatancies.

    NASA Astrophysics Data System (ADS)

    Sun, Yue-Feng

    This thesis investigates the dynamical theory of multiphase fractured porous media, by which the shear wave velocities can now be obtained that are in agreement with experiments, which were against the prediction of the Biot theory. The anisotropy, P and S wave velocities, and also waveforms can now be explicitly expressed as functions of structural, physical, and reservoir parameters such as porosity and pore fluid content, which are the key for the enhancement of seismic resolution and the determination of detailed subsurface structures and in-situ physical properties of subsurface materials, and so are essential for reservoir characterization and reservoir modeling. In addition, there generally exist 2 times A kinds of waves in an A-phase fractured porous medium, i.e., A kinds of P (compressional) waves and A kinds of S (shear) waves. The theory includes the Biot theory and the squirt mechanisms as special cases. The theory is developed using topological spaces and the principle of covariance. The basic theory of 3A -dimensional Riemannian manifold of an A-phase fractured porous medium is given. The equations governing the structural evolution and the interactions between physical properties and structural changes in space and time are also derived, which are needed to understand many new phenomena associated with structural aggregated systems in many fields such as the studies of multiphase structural media, non-Newtonian fluids, and condensed-matter physics. The thermo-dynamics of structural media is also discussed. The deformation, fracturing, and stress relaxation with or without fluid invasion cause dilatations of the fractured porous medium under a tectonic stress. The gravity change caused by these dilatancies has been formulated using the variational principle. The concept of mepicentroid is developed, which, differing from the concept of epicenter, is an essential concept for understanding the association of gravity variation in space and time with the

  1. Does Childbirth Cause Psychiatric Disorders? A Population-Based Study Paralleling a Natural Experiment

    PubMed Central

    Munk-Olsen, Trine; Agerbo, Esben

    2014-01-01

    Background: Childbirth is associated with increased risk of first-time psychiatric episodes, and an unwanted pregnancy has been suggested as a possible etiologic contributor. To what extent childbirth causes psychiatric episodes and whether a planned pregnancy reduces the risk of postpartum psychiatric episodes has not been established. Methods: We conducted a cohort study using data derived from Danish population registers, including all women having in vitro fertilization (IVF) treatment and their partners with recorded information in the IVF register covering fertility treatments in Denmark at all public and private treatment sites from January 1994 to December 2005. We compared parents and childless persons to examine whether childbirth is directly associated with onset of first-time psychiatric episodes, with incidence rate ratios (risk of first psychiatric inpatient or outpatient treatment) as the main outcome measures. Results: The incidence rate for any type of psychiatric disorder 0-90 days postpartum was 11.3 per 1000 person-years (95% confidence interval = 8.2-15.0), and 3.8 (3.4-4.3) among women not giving birth. IVF-treated mothers had an increased risk of a psychiatric episode postpartum, incidence rate ratio = 2.9 (2.0-4.2) compared with the risk of psychiatric episodes in childless women. Risk of psychiatric episodes from 90 days postpartum and onwards was decreased (incidence rate ratio = 0.9 [0.7-1.0]). Conclusions: Using a study design paralleling a natural experiment, our results showed that childbirth is associated with first-time psychiatric disorders in new mothers, indicating that a planned pregnancy does not reduce risks of or prevent postpartum psychiatric episodes. PMID:25322321

  2. The chicken as a natural model for extraintestinal infections caused by avian pathogenic Escherichia coli (APEC).

    PubMed

    Antão, Esther-Maria; Glodde, Susanne; Li, Ganwu; Sharifi, Reza; Homeier, Timo; Laturnus, Claudia; Diehl, Ines; Bethe, Astrid; Philipp, Hans-C; Preisinger, Rudolf; Wieler, Lothar H; Ewers, Christa

    2008-01-01

    E. coli infections in avian species have become an economic threat to the poultry industry worldwide. Several factors have been associated with the virulence of E. coli in avian hosts, but no specific virulence gene has been identified as being entirely responsible for the pathogenicity of avian pathogenic E. coli (APEC). Needless to say, the chicken would serve as the best model organism for unravelling the pathogenic mechanisms of APEC, an extraintestinal pathogen. Five-week-old white leghorn SPF chickens were infected intra-tracheally with a well characterized APEC field strain IMT5155 (O2:K1:H5) using different doses corresponding to the respective models of infection established, that is, the lung colonization model allowing re-isolation of bacteria only from the lung but not from other internal organs, and the systemic infection model. These two models represent the crucial steps in the pathogenesis of APEC infections, including the colonization of the lung epithelium and the spread of bacteria throughout the bloodstream. The read-out system includes a clinical score, pathomorphological changes and bacterial load determination. The lung colonization model has been established and described for the first time in this study, in addition to a comprehensive account of a systemic infection model which enables the study of severe extraintestinal pathogenic E. coli (ExPEC) infections. These in vivo models enable the application of various molecular approaches to study host-pathogen interactions more closely. The most important application of such genetic manipulation techniques is the identification of genes required for extraintestinal virulence, as well as host genes involved in immunity in vivo. The knowledge obtained from these studies serves the dual purpose of shedding light on the nature of virulence itself, as well as providing a route for rational attenuation of the pathogen for vaccine construction, a measure by which extraintestinal infections, including

  3. A look into the nature and causes of human errors in the intensive care unit*

    PubMed Central

    Donchin, Y; Gopher, D; Olin, M; Badihi, Y; Biesky, M; Sprung, C; Pizov, R; Cotev, S

    2003-01-01

    

Objectives: The purpose of this study was to investigate the nature and causes of human errors in the intensive care unit (ICU), adopting approaches proposed by human factors engineering. The basic assumption was that errors occur and follow a pattern that can be uncovered. Design: Concurrent incident study. Setting: Medical-surgical ICU of a university hospital. Measurements and main results: Two types of data were collected: errors reported by physicians and nurses immediately after an error discovery; and activity profiles based on 24-h records taken by observers with human engineering experience on a sample of patients. During the 4 months of data collection, a total of 554 human errors were reported by the medical staff. Errors were rated for severity and classified according to the body system and type of medical activity involved. There was an average of 178 activities per patient per day and an estimated number of 1.7 errors per patient per day. For the ICU as a whole, a severe or potentially detrimental error occurred on average twice a day. Physicians and nurses were about equal contributors to the number of errors, although nurses had many more activities per day. Conclusions: A significant number of dangerous human errors occur in the ICU. Many of these errors could be attributed to problems of communication between the physicians and nurses. Applying human factor engineering concepts to the study of the weak points of a specific ICU may help to reduce the number of errors. Errors should not be considered as an incurable disease, but rather as preventable phenomena. PMID:12679512

  4. Effects of a Changing Climate on Seasonal Variation in Natural Recharge of Unconfined Coastal Aquifers

    NASA Astrophysics Data System (ADS)

    Antonellini, Marco; Nella Mollema, Pauline

    2013-04-01

    Irregular rainfall patterns throughout the year result in the discontinuous natural recharge of coastal aquifers, which has an effect on the size of freshwater lenses present in sandy deposits. The thickness of the freshwater lenses is important in the context of farmland salinization and coastal ecosystems survival. This study presents numerical models that simulate continuous and discontinuous recharge in sandy coastal aquifers and the thickness of resulting fresh water lenses under current and future climate scenarios. Temperature data for the period 1960-1990 from LOCCLIM FAO and from the IPCC SRES A1b scenario for 2070-2100, have been used to calculate the potential evapotranspiration. Potential recharge was defined as the difference between the precipitation and potential evapotranspiration in twelve locations around the world: Ameland (The Netherlands), Auckland and Wellington (New Zealand), Hong Kong, Ravenna (Italy), Mekong (Vietnam), Mumbai (India), New Jersey (USA), Nile Delta (Egypt), Kobe and Tokyo (Japan), and Singapore. These locations have shallow coastal aquifers along low lying coasts and comparable aquifer structure, which is the result of similar sediment supply and deposition in the Holocene as well as by the sea level changes from the last ice age to the present time. Particular attention has been paid to temporal variations of natural recharge that can vary from continuous recharge throughout the year to discontinuous recharge. The most dramatic reduction in the magnitude of potential annual recharge by the end of this century will occur at lower latitudes (Mumbai, Singapore, Hong Kong and Mekong). The most pronounced change in length of the dry period occurs for Kobe (Japan) and Singapore even though the total annual amount of recharge remains practically the same. The Influence of variable recharge on the size of freshwater lenses surrounded by saline water is simulated with the SEAWAT model. Models where the recharge is applied

  5. High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

    PubMed Central

    2013-01-01

    Background Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is

  6. Natural selection and genetic variation for female resistance to harm from males.

    PubMed

    Linder, J E; Rice, W R

    2005-05-01

    The sexual conflict hypothesis predicts that males evolve traits that exploit the higher parental investment of females, which generates selection for females to counter-evolve resistance. In Drosophila melanogaster it is now established that males harm females and that there is genetic variation among males for the degree of this harm. Genetic variation among females for resistance to harm from males, and the corresponding strength of selection on this variation, however, have not been quantified previously. Here we carryout a genome-wide screen for female resistance to harm from males. We estimate that the cost of interactions with males depresses lifetime fecundity of females by 15% (95% CI: 8.2-22.0), that genetic variation for female resistance constitutes 17% of total genetic variation for female adult fitness, and that propensity to remate in response to persistent male courtship is a major factor contributing to genetic variation for female resistance.

  7. Natural variations of copper and sulfur stable isotopes in blood of hepatocellular carcinoma patients.

    PubMed

    Balter, Vincent; Nogueira da Costa, Andre; Bondanese, Victor Paky; Jaouen, Klervia; Lamboux, Aline; Sangrajrang, Suleeporn; Vincent, Nicolas; Fourel, François; Télouk, Philippe; Gigou, Michelle; Lécuyer, Christophe; Srivatanakul, Petcharin; Bréchot, Christian; Albarède, Francis; Hainaut, Pierre

    2015-01-27

    The widespread hypoxic conditions of the tumor microenvironment can impair the metabolism of bioessential elements such as copper and sulfur, notably by changing their redox state and, as a consequence, their ability to bind specific molecules. Because competing redox state is known to drive isotopic fractionation, we have used here the stable isotope compositions of copper ((65)Cu/(63)Cu) and sulfur ((34)S/(32)S) in the blood of patients with hepatocellular carcinoma (HCC) as a tool to explore the cancer-driven copper and sulfur imbalances. We report that copper is (63)Cu-enriched by ∼0.4‰ and sulfur is (32)S-enriched by ∼1.5‰ in the blood of patients compared with that of control subjects. As expected, HCC patients have more copper in red blood cells and serum compared with control subjects. However, the isotopic signature of this blood extra copper burden is not in favor of a dietary origin but rather suggests a reallocation in the body of copper bound to cysteine-rich proteins such as metallothioneins. The magnitude of the sulfur isotope effect is similar in red blood cells and serum of HCC patients, implying that sulfur fractionation is systemic. The (32)S-enrichment of sulfur in the blood of HCC patients is compatible with the notion that sulfur partly originates from tumor-derived sulfides. The measurement of natural variations of stable isotope compositions, using techniques developed in the field of Earth sciences, can provide new means to detect and quantify cancer metabolic changes and provide insights into underlying mechanisms.

  8. Natural variations of copper and sulfur stable isotopes in blood of hepatocellular carcinoma patients

    PubMed Central

    Balter, Vincent; Nogueira da Costa, Andre; Bondanese, Victor Paky; Jaouen, Klervia; Lamboux, Aline; Sangrajrang, Suleeporn; Vincent, Nicolas; Fourel, François; Télouk, Philippe; Gigou, Michelle; Lécuyer, Christophe; Srivatanakul, Petcharin; Bréchot, Christian; Albarède, Francis; Hainaut, Pierre

    2015-01-01

    The widespread hypoxic conditions of the tumor microenvironment can impair the metabolism of bioessential elements such as copper and sulfur, notably by changing their redox state and, as a consequence, their ability to bind specific molecules. Because competing redox state is known to drive isotopic fractionation, we have used here the stable isotope compositions of copper (65Cu/63Cu) and sulfur (34S/32S) in the blood of patients with hepatocellular carcinoma (HCC) as a tool to explore the cancer-driven copper and sulfur imbalances. We report that copper is 63Cu-enriched by ∼0.4‰ and sulfur is 32S-enriched by ∼1.5‰ in the blood of patients compared with that of control subjects. As expected, HCC patients have more copper in red blood cells and serum compared with control subjects. However, the isotopic signature of this blood extra copper burden is not in favor of a dietary origin but rather suggests a reallocation in the body of copper bound to cysteine-rich proteins such as metallothioneins. The magnitude of the sulfur isotope effect is similar in red blood cells and serum of HCC patients, implying that sulfur fractionation is systemic. The 32S-enrichment of sulfur in the blood of HCC patients is compatible with the notion that sulfur partly originates from tumor-derived sulfides. The measurement of natural variations of stable isotope compositions, using techniques developed in the field of Earth sciences, can provide new means to detect and quantify cancer metabolic changes and provide insights into underlying mechanisms. PMID:25583489

  9. Natural variation in early parental care correlates with social behaviors in adolescent prairie voles (Microtus ochrogaster)

    PubMed Central

    Perkeybile, Allison M.; Griffin, Luana L.; Bales, Karen L.

    2013-01-01

    Natural variation in early parental care may contribute to long-term changes in behavior in the offspring. Here we investigate the role of variable early care in biparental prairie voles (Microtus ochrogaster). Total amounts of parental care were initially quantified for 24 breeder pairs and pairs were ranked in relation to one another based on total contact. Consistency in key components of care suggested a trait-like quality to parental care. Based on this ranking, breeder pairs from the top (high-contact) and bottom (low-contact) quartiles were selected to produce high- and low-contact offspring to investigate adolescent behavior after varying early care. Parental care of subject offspring was again observed postnatally. Offspring of high-contact parents spent more time passively nursing and received more paternal non-huddling contact while low-contact offspring spent more time actively nursing and received more paternal huddling and pseudohuddling in the first postnatal days (PNDs). Low-contact offspring also displayed faster rates of development on a number of physical markers. Post-weaning, offspring were evaluated on anxiety-like behavior, social behavior and pre-pulse inhibition (PPI) to a tactile and an acoustic startle. High-contact offspring spent more time sniffing a juvenile and less time autogrooming. With an infant, high-contact offspring spent more time in non-huddling contact and less time autogrooming and retrieving than did low-contact offspring. Considering sexes separately, high-contact females spent more time sniffing a novel juvenile than low-contact females. High-contact males spent more time in non-huddling contact with an infant than low-contact males; while low-contact females retrieved infants more than high-contact females. In both measures of social behavior, high-contact males spent less time autogrooming than low-contact males. These results suggest a relationship between early-life care and differences in social behavior in

  10. Natural variations of copper and sulfur stable isotopes in blood of hepatocellular carcinoma patients

    NASA Astrophysics Data System (ADS)

    Balter, Vincent; Nogueira da Costa, Andre; Paky Bondanese, Victor; Jaouen, Klervia; Lamboux, Aline; Sangrajrang, Suleeporn; Vincent, Nicolas; Fourel, François; Télouk, Philippe; Gigou, Michelle; Lécuyer, Christophe; Srivatanakul, Petcharin; Bréchot, Christian; Albarède, Francis; Hainaut, Pierre

    2015-01-01

    The widespread hypoxic conditions of the tumor microenvironment can impair the metabolism of bioessential elements such as copper and sulfur, notably by changing their redox state and, as a consequence, their ability to bind specific molecules. Because competing redox state is known to drive isotopic fractionation, we have used here the stable isotope compositions of copper (65Cu/63Cu) and sulfur (34S/32S) in the blood of patients with hepatocellular carcinoma (HCC) as a tool to explore the cancer-driven copper and sulfur imbalances. We report that copper is 63Cu-enriched by ∼0.4‰ and sulfur is 32S-enriched by ∼1.5‰ in the blood of patients compared with that of control subjects. As expected, HCC patients have more copper in red blood cells and serum compared with control subjects. However, the isotopic signature of this blood extra copper burden is not in favor of a dietary origin but rather suggests a reallocation in the body of copper bound to cysteine-rich proteins such as metallothioneins. The magnitude of the sulfur isotope effect is similar in red blood cells and serum of HCC patients, implying that sulfur fractionation is systemic. The 32S-enrichment of sulfur in the blood of HCC patients is compatible with the notion that sulfur partly originates from tumor-derived sulfides. The measurement of natural variations of stable isotope compositions, using techniques developed in the field of Earth sciences, can provide new means to detect and quantify cancer metabolic changes and provide insights into underlying mechanisms.

  11. Genomic regulation of natural variation in cortical and noncortical brain volume

    PubMed Central

    Beatty, Jackson; Laughlin, Rick E

    2006-01-01

    Background The relative growth of the neocortex parallels the emergence of complex cognitive functions across species. To determine the regions of the mammalian genome responsible for natural variations in cortical volume, we conducted a complex trait analysis using 34 strains of recombinant inbred (Rl) strains of mice (BXD), as well as their two parental strains (C57BL/6J and DBA/2J). We measured both neocortical volume and total brain volume in 155 coronally sectioned mouse brains that were Nissl stained and embedded in celloidin. After correction for shrinkage, the measured cortical and noncortical brain volumes were entered into a multiple regression analysis, which removed the effects of body size and age from the measurements. Marker regression and interval mapping were computed using WebQTL. Results An ANOVA revealed that more than half of the variance of these regressed phenotypes is genetically determined. We then identified the regions of the genome regulating this heritability. We located genomic regions in which a linkage disequilibrium was present using WebQTL as both a mapping engine and genomic database. For neocortex, we found a genome-wide significant quantitative trait locus (QTL) on chromosome 11 (marker D11Mit19), as well as a suggestive QTL on chromosome 16 (marker D16Mit100). In contrast, for noncortex the effect of chromosome 11 was markedly reduced, and a significant QTL appeared on chromosome 19 (D19Mit22). Conclusion This classic pattern of double dissociation argues strongly for different genetic factors regulating relative cortical size, as opposed to brain volume more generally. It is likely, however, that the effects of proximal chromosome 11 extend beyond the neocortex strictly defined. An analysis of single nucleotide polymorphisms in these regions indicated that ciliary neurotrophic factor (Cntf) is quite possibly the gene underlying the noncortical QTL. Evidence for a candidate gene modulating neocortical volume was much weaker

  12. Natural variation in early parental care correlates with social behaviors in adolescent prairie voles (Microtus ochrogaster).

    PubMed

    Perkeybile, Allison M; Griffin, Luana L; Bales, Karen L

    2013-01-01

    Natural variation in early parental care may contribute to long-term changes in behavior in the offspring. Here we investigate the role of variable early care in biparental prairie voles (Microtus ochrogaster). Total amounts of parental care were initially quantified for 24 breeder pairs and pairs were ranked in relation to one another based on total contact. Consistency in key components of care suggested a trait-like quality to parental care. Based on this ranking, breeder pairs from the top (high-contact) and bottom (low-contact) quartiles were selected to produce high- and low-contact offspring to investigate adolescent behavior after varying early care. Parental care of subject offspring was again observed postnatally. Offspring of high-contact parents spent more time passively nursing and received more paternal non-huddling contact while low-contact offspring spent more time actively nursing and received more paternal huddling and pseudohuddling in the first postnatal days (PNDs). Low-contact offspring also displayed faster rates of development on a number of physical markers. Post-weaning, offspring were evaluated on anxiety-like behavior, social behavior and pre-pulse inhibition (PPI) to a tactile and an acoustic startle. High-contact offspring spent more time sniffing a juvenile and less time autogrooming. With an infant, high-contact offspring spent more time in non-huddling contact and less time autogrooming and retrieving than did low-contact offspring. Considering sexes separately, high-contact females spent more time sniffing a novel juvenile than low-contact females. High-contact males spent more time in non-huddling contact with an infant than low-contact males; while low-contact females retrieved infants more than high-contact females. In both measures of social behavior, high-contact males spent less time autogrooming than low-contact males. These results suggest a relationship between early-life care and differences in social behavior in

  13. A man-induced landslide in Lower Austria: natural conditions versus man-made causes

    NASA Astrophysics Data System (ADS)

    Kittel, Roland; Ottner, Franz; Damm, Bodo; Terhorst, Birgit

    2010-05-01

    In many cases, composition and characteristics of hillslope sediments are of particular importance related to landslide research in low mountain areas. The interaction of geologic, geomorphologic, and hydrologic factors determines the susceptibility for mass movements, which is affected by human impact as well. The present study aims to investigate factors that control mass movements and natural and anthropogenic impacts. On March 8th 2009, a landslide of 30.000 to 50.000 m³ occurred that destroyed a large part of a sports ground in the village of Hintersdorf, municipality of St. Andrä-Wördern (Lower Austria). As a result of extensive water supply ground liquefaction was initiated and the slide mass moved in form of a mud flow about 200 m down slope. As a consequence a small forest area and a fishpond were destroyed and an adjacent road was damaged. Closely to the event, first studies started and showed that the Hintersdorf landslide was triggered by extensive water saturation combined with hydrostatic pressure inside the slide mass. Heavy and long-lasting rainfalls and the start of snowmelt caused strong seepage and soil water saturation. Furthermore, insufficient ground drainage and overflow of a small retention pond intensified the unfavourable impact on soil-mechanical stability. Further studies included archive data analyse, field survey, as well as laboratory analyse and showed that high landslide susceptibility at the Hintersdorf landslide site was caused by a bundle of factors that control the process: The sports ground was built nearby the head of a trough valley that collects interflow and surface run-off from the surrounding slopes. The Flysch bedrock is covered extensively by clayey slope deposits. Furthermore, in the area of the valley head a waste deposit was operated up to the 1980's that resulted in a thick waste filling there. The Hintersdorf sports ground was constructed in 1984 on top of the waste body. Preliminary results show that hillslope

  14. The Nature, Extent, and Consequences of Genetic Variation in the opa Repeats of Notch in Drosophila

    PubMed Central

    Rice, Clinton; Beekman, Danielle; Liu, Liping; Erives, Albert

    2015-01-01

    Polyglutamine (pQ) tracts are abundant in proteins co-interacting on DNA. The lengths of these pQ tracts can modulate their interaction strengths. However, pQ tracts >40 residues are pathologically prone to amyloidogenic self-assembly. Here, we assess the extent and consequences of variation in the pQ-encoding opa repeats of Notch in Drosophila melanogaster. We use Sanger sequencing to genotype opa sequences (5′-CAX repeats), which have resisted assembly using short sequence reads. While most sampled lines carry the major allele opa31 encoding Q13HQ17 or the opa32 allele encoding Q13HQ18, many lines carry rare alleles encoding pQ tracts >32 residues: opa33a (Q14HQ18), opa33b (Q15HQ17), opa34 (Q16HQ17), opa35a1/opa35a2 (Q13HQ21), opa36 (Q13HQ22), and opa37 (Q13HQ23). Only one rare allele encodes a tract <31 residues: opa23 (Q13–Q10). This opa23 allele shortens the pQ tract while simultaneously eliminating the interrupting histidine. We introgressed these opa variant alleles into common backgrounds and measured the frequency of Notch-type phenotypes. Homozygotes for the short and long opa alleles have defects in embryonic survival and sensory bristle organ patterning, and sometimes show wing notching. Consistent with functional differences between Notch opa variants, we find that a scute inversion carrying the rare opa33b allele suppresses the bristle patterning defect caused by achaete/scute insufficiency, while an equivalent scute inversion carrying opa31 manifests the patterning defect. Our results demonstrate the existence of potent pQ variants of Notch and the need for long read genotyping of key repeat variables underlying gene regulatory networks. PMID:26362765

  15. Fault geometric complexity and how it may cause temporal slip-rate variation within an interacting fault system

    NASA Astrophysics Data System (ADS)

    Zielke, Olaf; Arrowsmith, Ramon

    2010-05-01

    Slip-rates along individual faults may differ as a function of measurement time scale. Short-term slip-rates may be higher than the long term rate and vice versa. For example, vertical slip-rates along the Wasatch Fault, Utah are 1.7+/-0.5 mm/yr since 6ka, <0.6 mm/yr since 130ka, and 0.5-0.7 mm/yr since 10Ma (Friedrich et al., 2003). Following conventional earthquake recurrence models like the characteristic earthquake model, this observation implies that the driving strain accumulation rates may have changed over the respective time scales as well. While potential explanations for such slip-rate variations may be found for example in the reorganization of plate tectonic motion or mantle flow dynamics, causing changes in the crustal velocity field over long spatial wavelengths, no single geophysical explanation exists. Temporal changes in earthquake rate (i.e., event clustering) due to elastic interactions within a complex fault system may present an alternative explanation that requires neither variations in strain accumulation rate or nor changes in fault constitutive behavior for frictional sliding. In the presented study, we explore this scenario and investigate how fault geometric complexity, fault segmentation and fault (segment) interaction affect the seismic behavior and slip-rate along individual faults while keeping tectonic stressing-rate and frictional behavior constant in time. For that, we used FIMozFric--a physics-based numerical earthquake simulator, based on Okada's (1992) formulations for internal displacements and strains due to shear and tensile faults in a half-space. Faults are divided into a large number of equal-sized fault patches which communicate via elastic interaction, allowing implementation of geometrically complex, non-planar faults. Each patch has assigned a static and dynamic friction coefficient. The difference between those values is a function of depth--corresponding to the temperature-dependence of velocity-weakening that is

  16. Genetic and Molecular Analyses of Natural Variation Indicate CBF2 as a Candidate Gene for Underlying a Freezing Tolerance Quantitative Trait Locus in Arabidopsis1[w

    PubMed Central

    Alonso-Blanco, Carlos; Gomez-Mena, Concepción; Llorente, Francisco; Koornneef, Maarten; Salinas, Julio; Martínez-Zapater, José M.

    2005-01-01

    Natural variation for freezing tolerance is a major component of adaptation and geographic distribution of plant species. However, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We have analyzed the intraspecific freezing tolerance variation existent between two geographically distant accessions of Arabidopsis (Arabidopsis thaliana), Cape Verde Islands (Cvi) and Landsberg erecta (Ler). They differed in their freezing tolerance before and after cold acclimation, as well as in the cold acclimation response in relation to photoperiod conditions. Using a quantitative genetic approach, we found that freezing tolerance differences after cold acclimation were determined by seven quantitative trait loci (QTL), named FREEZING TOLERANCE QTL 1 (FTQ1) to FTQ7. FTQ4 was the QTL with the largest effect detected in two photoperiod conditions, while five other FTQ loci behaved as photoperiod dependent. FTQ4 colocated with the tandem repeated genes C-REPEAT BINDING FACTOR 1 (CBF1), CBF2, and CBF3, which encode transcriptional activators involved in the cold acclimation response. The low freezing tolerance of FTQ4-Cvi alleles was associated with a deletion of the promoter region of Cvi CBF2, and with low RNA expression of CBF2 and of several CBF target genes. Genetic complementation of FTQ4-Cvi plants with a CBF2-Ler transgene suggests that such CBF2 allelic variation is the cause of CBF2 misexpression and the molecular basis of FTQ4. PMID:16244146

  17. Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana

    PubMed Central

    Chao, Dai-Yin; Silva, Adriano; Baxter, Ivan; Huang, Yu S.; Nordborg, Magnus; Danku, John; Lahner, Brett; Yakubova, Elena; Salt, David E.

    2012-01-01

    Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5–2 µg Cd g−1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids. PMID:22969436

  18. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa.

    PubMed

    Franks, Steven J; Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J; Lalchan, Rebecca; Jordan, Kevin P; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  19. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa

    PubMed Central

    Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J.; Lalchan, Rebecca; Jordan, Kevin P.; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  20. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa.

    PubMed

    Franks, Steven J; Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J; Lalchan, Rebecca; Jordan, Kevin P; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  1. A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

    PubMed Central

    Bergström, Anders; Simpson, Jared T.; Salinas, Francisco; Barré, Benjamin; Parts, Leopold; Zia, Amin; Nguyen Ba, Alex N.; Moses, Alan M.; Louis, Edward J.; Mustonen, Ville; Warringer, Jonas; Durbin, Richard; Liti, Gianni

    2014-01-01

    The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies. PMID:24425782

  2. Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

    PubMed Central

    Pignatta, Daniela; Erdmann, Robert M; Scheer, Elias; Picard, Colette L; Bell, George W; Gehring, Mary

    2014-01-01

    Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. DOI: http://dx.doi.org/10.7554/eLife.03198.001 PMID:24994762

  3. Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster.

    PubMed

    Dembeck, Lauren M; Böröczky, Katalin; Huang, Wen; Schal, Coby; Anholt, Robert R H; Mackay, Trudy F C

    2015-11-14

    Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition.

  4. Natural Variation in a Subtelomeric Region of Arabidopsis: Implications for the Genomic Dynamics of a Chromosome End

    PubMed Central

    Kuo, Hui-Fen; Olsen, Kenneth M.; Richards, Eric J.

    2006-01-01

    We investigated genome dynamics at a chromosome end in the model plant Arabidopsis thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric region of chromosome 1 north (∼3.5 kb), which represents the relatively simple organization of subtelomeric regions in this species. PCR fragment-length variation across the subtelomeric region indicated that the 1.4-kb distal region showed elevated structural variation relative to the centromere-proximal region. Examination of nucleotide sequences from this 1.4-kb region revealed diverse DNA rearrangements, including an inversion, several deletions, and an insertion of a retrotransposon LTR. The structures at the deletion and inversion breakpoints are characteristic of simple deletion-associated nonhomologous end-joining (NHEJ) events. There was strong linkage disequilibrium between the distal subtelomeric region and the proximal telomere, which contains degenerate and variant telomeric repeats. Variation in the proximal telomere was characterized by the expansion and deletion of blocks of repeats. Our sample of accessions documented two independent chromosome-healing events associated with terminal deletions of the subtelomeric region as well as the capture of a scrambled mitochondrial DNA segment in the proximal telomeric array. This natural variation study highlights the variety of genomic events that drive the fluidity of chromosome termini. PMID:16547105

  5. Nature and frequency of mutations in the [alpha]-galactosidase A gene that cause Fabry disease

    SciTech Connect

    Eng, C.M.; Resnick-Silverman, L.A.; Niehaus, D.J.; Astrin, K.H.; Desnick, R.J. )

    1993-12-01

    To determine the nature and frequency of the molecular lesions causing the classical and milder-variant Fabry phenotypes, and for precise carrier detection in Fabry families, the [alpha]-Gal A transcripts or genomic sequences from unrelated Fabry hemizygotes were analyzed. In patients with the classical phenotype, 18 new mutations were identified: N34S, C56G, W162R, R227Q, R227X, D264V, D266V, S297F, D313Y, G328A, W340X, E398X, IVS2+2, IVS5[delta]-2,3, 773[delta]2, 954[delta]5, 1016[delta]11, and 1123[delta]53. Unrelated asymptomatic or mildly affected patients with symptoms confined to the heart had a missense mutation, N215S, that expressed residual enzymatic activity. Related, moderately affected patients with late-onset cardiac and pulmonary manifestations had a small deletion, 1208[delta]3, that predicted the in-frame deletion of arginine 404 near the terminus of the 429 residue enzyme polypeptide. In addition, five small gene rearrangements involving exonic sequences were identified in unrelated classically affected patients. Two small deletions and one small duplication had short direct repeats at their respective breakpoint junctions and presumably resulted from slipped mispairing. A deletion occurred at a potential polymerase [alpha] arrest site, while the breakpoints of another deletion occurred at an inverted tetranucleotide repeat. Screening of unrelated Fabry patients with allele-specific oligonucleotides for seven mutations revealed that these were private, with the notable exception of N215S, R227Q, and R227X, which were each found in several unrelated families from different ethnic backgrounds. The CpG dinucleotide at codon 227 was the most common site of mutation, having been altered in 5% of the 148 unrelated Fabry alleles. These studies revealed that most [alpha]-Gal A lesions were private, that codon 227 was a mutational hot spot, and that certain mutations predicted a milder disease phenotype. 40 refs., 8 figs., 3 tabs.

  6. From Ends to Causes (and Back Again) by Metaphor: The Paradox of Natural Selection

    ERIC Educational Resources Information Center

    Blancke, Stefaan; Schellens, Tammy; Soetaert, Ronald; Van Keer, Hilde; Braeckman, Johan

    2014-01-01

    Natural selection is one of the most famous metaphors in the history of science. Charles Darwin used the metaphor and the underlying analogy to frame his ideas about evolution and its main driving mechanism into a full-fledged theory. Because the metaphor turned out to be such a powerful epistemic tool, Darwin naturally assumed that he could also…

  7. Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines

    PubMed Central

    Ulvestad, Marte; Overland, Indra

    2012-01-01

    This article develops a formal model for comparing the cost structure of the two main transport options for natural gas: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG. PMID:24683269

  8. Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines.

    PubMed

    Ulvestad, Marte; Overland, Indra

    2012-06-01

    THIS ARTICLE DEVELOPS A FORMAL MODEL FOR COMPARING THE COST STRUCTURE OF THE TWO MAIN TRANSPORT OPTIONS FOR NATURAL GAS: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG.

  9. Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines.

    PubMed

    Ulvestad, Marte; Overland, Indra

    2012-06-01

    THIS ARTICLE DEVELOPS A FORMAL MODEL FOR COMPARING THE COST STRUCTURE OF THE TWO MAIN TRANSPORT OPTIONS FOR NATURAL GAS: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG. PMID:24683269

  10. Genetic Basis for Spontaneous Hybrid Genome Doubling during Allopolyploid Speciation of Common Wheat Shown by Natural Variation Analyses of the Paternal Species

    PubMed Central

    Matsuoka, Yoshihiro; Nasuda, Shuhei; Ashida, Yasuyo; Nitta, Miyuki; Tsujimoto, Hisashi; Takumi, Shigeo; Kawahara, Taihachi

    2013-01-01

    The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome), namely Triticumturgidum L. (AABB genome) and Aegilopstauschii Coss. (DD genome). An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL) analysis showed that (1) production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2) first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3) six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii’s ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated that the

  11. Annual Variation in Flowering Phenology, Pollination, Mating System, and Pollen Yield in Two Natural Populations of Schima wallichii (DC.) Korth

    PubMed Central

    Khanduri, Vinod Prasad; Sharma, C. M.; Kumar, K. S.; Ghildiyal, S. K.

    2013-01-01

    Background. Schima wallichii is a highly valuable tree of tropical forest in north-east Himalaya region that grows naturally in a wide range of altitudes between 750 and 2400 m asl with varying environments. Flowering phenology of tropical tree species at population level is generally ignored and therefore a detailed knowledge of flowering and fruiting patterns of important multipurpose tree species is critical to the successful management of forest genetic resources. Materials and Methods. The study was conducted at two different altitudes (i.e., 750 m and 900 m asl) in the tropical semideciduous forest of north-east Himalaya. The floral phenology including flowering synchrony in the populations, anthesis, anther dehiscence, stigma receptivity, pollinators visitation frequency, and mating system including index of self-incompatibility were worked out in Schima wallichii according to the ear-marked standard methods given by various scientists for each parameter. Results. The flowering period in Schima wallichii varied from 33 to 42 days with mean synchrony of 0.54 to 0.68 between the populations. The stigma was receptive up to 2.5 days only and showed slightly protandrous type of dichogamy. Average pollen production ranged between 6.90 × 107 pollen per tree in 2007 and 15.49 × 108 pollen per tree in 2011. A three-year masting cycle was noticed in this species. The frequency of visitation of honey bees was fairly high (5.2 ± 1.12 visits/flower/hour) as compared to other pollinators. The hand pollination revealed maximum fruit (74.2 ± 5.72%) and seed (70.8 ± 7.46%) settings. Conclusions. The variation in flowering phenology and pollen yield individually and annually along with temporal separation in anther dehiscence and pollinator's visitation cause pollen limited reproduction, which ultimately influences the reproductive success in Schima wallichii. PMID:24501577

  12. Variation in type A trichothecene production and trichothecene biosynthetic genes in Fusarium goolgardi from natural ecosystems of Australia.

    PubMed

    Rocha, Liliana O; Laurence, Matthew H; Proctor, Robert H; McCormick, Susan P; Summerell, Brett A; Liew, Edward C Y

    2015-11-01

    Fusarium goolgardi, isolated from the grass tree Xanthorrhoea glauca in natural ecosystems of Australia, is closely related to fusaria that produce a subgroup of trichothecene (type A) mycotoxins that lack a carbonyl group at carbon atom 8 (C-8). Mass spectrometric analysis revealed that F. goolgardi isolates produce type A trichothecenes, but exhibited one of two chemotypes. Some isolates (50%) produced multiple type A trichothecenes, including 4,15-diacetoxyscirpenol (DAS), neosolaniol (NEO), 8-acetylneosolaniol (Ac-NEO) and T-2 toxin (DAS-NEO-T2 chemotype). Other isolates (50%) produced only DAS (DAS chemotype). In the phylogenies inferred from DNA sequences of genes encoding the RNA polymerase II largest (RPB1) and second largest (RPB2) subunits as well as the trichothecene biosynthetic genes (TRI), F. goolgardi isolates were resolved as a monophyletic clade, distinct from other type A trichothecene-producing species. However, the relationships of F. goolgardi to the other species varied depending on whether phylogenies were inferred from RPB1 and RPB2, the 12-gene TRI cluster, the two-gene TRI1-TRI16 locus, or the single-gene TRI101 locus. Phylogenies based on different TRI loci resolved isolates with different chemotypes into distinct clades, even though only the TRI1-TRI16 locus is responsible for structural variation at C-8. Sequence analysis indicated that TRI1 and TRI16 are functional in F. goolgardi isolates with the DAS-NEO-T2 chemotype, but non-functional in isolates with DAS chemotype due to the presence of premature stop codons caused by a point mutation. PMID:26556373

  13. Variation in Type A Trichothecene Production and Trichothecene Biosynthetic Genes in Fusarium goolgardi from Natural Ecosystems of Australia

    PubMed Central

    Rocha, Liliana O.; Laurence, Matthew H.; Proctor, Robert H.; McCormick, Susan P.; Summerell, Brett A.; Liew, Edward C. Y.

    2015-01-01

    Fusarium goolgardi, isolated from the grass tree Xanthorrhoea glauca in natural ecosystems of Australia, is closely related to fusaria that produce a subgroup of trichothecene (type A) mycotoxins that lack a carbonyl group at carbon atom 8 (C-8). Mass spectrometric analysis revealed that F. goolgardi isolates produce type A trichothecenes, but exhibited one of two chemotypes. Some isolates (50%) produced multiple type A trichothecenes, including 4,15-diacetoxyscirpenol (DAS), neosolaniol (NEO), 8-acetylneosolaniol (Ac-NEO) and T-2 toxin (DAS-NEO-T2 chemotype). Other isolates (50%) produced only DAS (DAS chemotype). In the phylogenies inferred from DNA sequences of genes encoding the RNA polymerase II largest (RPB1) and second largest (RPB2) subunits as well as the trichothecene biosynthetic genes (TRI), F. goolgardi isolates were resolved as a monophyletic clade, distinct from other type A trichothecene-producing species. However, the relationships of F. goolgardi to the other species varied depending on whether phylogenies were inferred from RPB1 and RPB2, the 12-gene TRI cluster, the two-gene TRI1-TRI16 locus, or the single-gene TRI101 locus. Phylogenies based on different TRI loci resolved isolates with different chemotypes into distinct clades, even though only the TRI1-TRI16 locus is responsible for structural variation at C-8. Sequence analysis indicated that TRI1 and TRI16 are functional in F. goolgardi isolates with the DAS-NEO-T2 chemotype, but non-functional in isolates with DAS chemotype due to the presence of premature stop codons caused by a point mutation. PMID:26556373

  14. Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation.

    PubMed

    Verhulst, Eveline C; Mateman, A Christa; Zwier, Mathijs V; Caro, Samuel P; Verhoeven, Koen J F; van Oers, Kees

    2016-04-01

    Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here, we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their DNA methylation levels at the dopamine receptor D4 (DRD4) gene. This D4 receptor is statistically associated with personality traits in both humans and nonhuman animals, including the great tit. Previous work in this songbird failed to detect functional genetic polymorphisms within DRD4 that could account for the gene-trait association. However, our observation supports the idea that DRD4 is functionally involved in exploratory behaviour but that its effects are mediated by DNA methylation. While the exact mechanism underlying the transgenerational consistency of DRD4 methylation remains to be elucidated, this study shows that epigenetic mechanisms are involved in shaping natural variation in personality traits. We outline how this first finding provides a basis for investigating the epigenetic contribution to personality traits in natural systems and its subsequent role for understanding the ecology and evolution of behavioural consistency.

  15. Untangling the nature of spatial variations of cold dust properties in star forming galaxies

    SciTech Connect

    Kirkpatrick, Allison; Calzetti, Daniela; Kennicutt, Robert; Galametz, Maud; Gordon, Karl; Groves, Brent; Tabatabaei, Fatemeh; Hunt, Leslie; Dale, Daniel; Hinz, Joannah

    2014-07-10

    We investigate the far-infrared (IR) dust emission for 20 local star forming galaxies from the Key Insights on Nearby Galaxies: A Far-IR Survey with Herschel (KINGFISH) sample. We model the far-IR/submillimeter spectral energy distribution (SED) using images from Spitzer Space Telescope and Herschel Space Observatory. We calculate the cold dust temperature (T{sub c} ) and emissivity (β) on a pixel by pixel basis (where each pixel ranges from 0.1 to 3 kpc{sup 2}) using a two-temperature modified blackbody fitting routine. Our fitting method allows us to investigate the resolved nature of temperature and emissivity variations by modeling from the galaxy centers to the outskirts (physical scales of ∼15-50 kpc, depending on the size of the galaxy). We fit each SED in two ways: (1) fit T{sub c} and β simultaneously, (2) hold β constant and fit T{sub c} . We compare T{sub c} and β with star formation rates (calculated from L{sub Hα} and L{sub 24μm}), the luminosity of the old stellar population (traced through L{sub 3.6μm}), and the dust mass surface density (traced by 500 μm luminosity, L{sub 500}). We find a significant trend between SFR/L{sub 500} and T{sub c} , implying that the flux of hard UV photons relative to the amount of dust is significantly contributing to the heating of the cold, or diffuse, dust component. We also see a trend between L{sub 3.6}/L{sub 500} and β, indicating that the old stellar population contributes to the heating at far-IR/submillimeter wavelengths. Finally, we find that when β is held constant, T{sub c} exhibits a strongly decreasing radial trend, illustrating that the shape of the far-IR SED is changing radially through a galaxy, thus confirming on a sample almost double in size the trends observed in Galametz et al.

  16. Variations in the relation between education and cause-specific mortality in 19 European populations: a test of the "fundamental causes" theory of social inequalities in health.

    PubMed

    Mackenbach, Johan P; Kulhánová, Ivana; Bopp, Matthias; Deboosere, Patrick; Eikemo, Terje A; Hoffmann, Rasmus; Kulik, Margarete C; Leinsalu, Mall; Martikainen, Pekka; Menvielle, Gwenn; Regidor, Enrique; Wojtyniak, Bogdan; Östergren, Olof; Lundberg, Olle

    2015-02-01

    Link and Phelan have proposed to explain the persistence of health inequalities from the fact that socioeconomic status is a "fundamental cause" which embodies an array of resources that can be used to avoid disease risks no matter what mechanisms are relevant at any given time. To test this theory we compared the magnitude of inequalities in mortality between more and less preventable causes of death in 19 European populations, and assessed whether inequalities in mortality from preventable causes are larger in countries with larger resource inequalities. We collected and harmonized mortality data by educational level on 19 national and regional populations from 16 European countries in the first decade of the 21st century. We calculated age-adjusted Relative Risks of mortality among men and women aged 30-79 for 24 causes of death, which were classified into four groups: amenable to behavior change, amenable to medical intervention, amenable to injury prevention, and non-preventable. Although an overwhelming majority of Relative Risks indicate higher mortality risks among the lower educated, the strength of the education-mortality relation is highly variable between causes of death and populations. Inequalities in mortality are generally larger for causes amenable to behavior change, medical intervention and injury prevention than for non-preventable causes. The contrast between preventable and non-preventable causes is large for causes amenable to behavior change, but absent for causes amenable to injury prevention among women. The contrast between preventable and non-preventable causes is larger in Central & Eastern Europe, where resource inequalities are substantial, than in the Nordic countries and continental Europe, where resource inequalities are relatively small, but they are absent or small in Southern Europe, where resource inequalities are also large. In conclusion, our results provide some further support for the theory of "fundamental causes". However

  17. Variations in the relation between education and cause-specific mortality in 19 European populations: a test of the "fundamental causes" theory of social inequalities in health.

    PubMed

    Mackenbach, Johan P; Kulhánová, Ivana; Bopp, Matthias; Deboosere, Patrick; Eikemo, Terje A; Hoffmann, Rasmus; Kulik, Margarete C; Leinsalu, Mall; Martikainen, Pekka; Menvielle, Gwenn; Regidor, Enrique; Wojtyniak, Bogdan; Östergren, Olof; Lundberg, Olle

    2015-02-01

    Link and Phelan have proposed to explain the persistence of health inequalities from the fact that socioeconomic status is a "fundamental cause" which embodies an array of resources that can be used to avoid disease risks no matter what mechanisms are relevant at any given time. To test this theory we compared the magnitude of inequalities in mortality between more and less preventable causes of death in 19 European populations, and assessed whether inequalities in mortality from preventable causes are larger in countries with larger resource inequalities. We collected and harmonized mortality data by educational level on 19 national and regional populations from 16 European countries in the first decade of the 21st century. We calculated age-adjusted Relative Risks of mortality among men and women aged 30-79 for 24 causes of death, which were classified into four groups: amenable to behavior change, amenable to medical intervention, amenable to injury prevention, and non-preventable. Although an overwhelming majority of Relative Risks indicate higher mortality risks among the lower educated, the strength of the education-mortality relation is highly variable between causes of death and populations. Inequalities in mortality are generally larger for causes amenable to behavior change, medical intervention and injury prevention than for non-preventable causes. The contrast between preventable and non-preventable causes is large for causes amenable to behavior change, but absent for causes amenable to injury prevention among women. The contrast between preventable and non-preventable causes is larger in Central & Eastern Europe, where resource inequalities are substantial, than in the Nordic countries and continental Europe, where resource inequalities are relatively small, but they are absent or small in Southern Europe, where resource inequalities are also large. In conclusion, our results provide some further support for the theory of "fundamental causes". However

  18. The Nature, Causes and Practices of Academic Dishonesty/Cheating in Higher Education: The Case of Hawassa University

    ERIC Educational Resources Information Center

    Bachore, Mebratu Mulatu

    2016-01-01

    The main objective of the study was to assess the perception of teachers and learners on the nature of practice, the type and the causes of academic cheating (dishonesty) in Hawassa University. The study was basically a survey which employed both qualitative and quantitative approaches to gather data. The subjects were 20 instructors and 60…

  19. ON THE VARIATION OF ZONAL GRAVITY COEFFICIENTS OF A GIANT PLANET CAUSED BY ITS DEEP ZONAL FLOWS

    SciTech Connect

    Kong Dali; Zhang Keke; Schubert, Gerald E-mail: kzhang@ex.ac.uk

    2012-04-01

    Rapidly rotating giant planets are usually marked by the existence of strong zonal flows at the cloud level. If the zonal flow is sufficiently deep and strong, it can produce hydrostatic-related gravitational anomalies through distortion of the planet's shape. This paper determines the zonal gravity coefficients, J{sub 2n}, n = 1, 2, 3, ..., via an analytical method taking into account rotation-induced shape changes by assuming that a planet has an effective uniform density and that the zonal flows arise from deep convection and extend along cylinders parallel to the rotation axis. Two different but related hydrostatic models are considered. When a giant planet is in rigid-body rotation, the exact solution of the problem using oblate spheroidal coordinates is derived, allowing us to compute the value of its zonal gravity coefficients J-bar{sub 2n}, n=1,2,3,..., without making any approximation. When the deep zonal flow is sufficiently strong, we develop a general perturbation theory for estimating the variation of the zonal gravity coefficients, {Delta}J{sub 2n}=J{sub 2n}-J-bar{sub 2n}, n=1,2,3,..., caused by the effect of the deep zonal flows for an arbitrarily rapidly rotating planet. Applying the general theory to Jupiter, we find that the deep zonal flow could contribute up to 0.3% of the J{sub 2} coefficient and 0.7% of J{sub 4}. It is also found that the shape-driven harmonics at the 10th zonal gravity coefficient become dominant, i.e., {Delta}J{sub 2n}>=J-bar{sub 2n} for n {>=} 5.

  20. Assessing the Genome-Wide Effect of Promoter Region Tandem Repeat Natural Variation on Gene Expression

    PubMed Central

    Elmore, Martha H.; Gibbons, John G.; Rokas, Antonis

    2012-01-01

    Copy number polymorphisms of nucleotide tandem repeat (TR) regions, such as microsatellites and minisatellites, are mutationally reversible and highly abundant in eukaryotic genomes. Studies linking TR polymorphism to phenotypic variation have led some to suggest that TR variation modulates and majorly contributes to phenotypic variation; however, studies in which the authors assess the genome-wide impact of TR variation on phenotype are lacking. To address this question, we quantified relationships between polymorphism levels in 143 genome-wide promoter region TRs across 16 isolates of the filamentous fungus Aspergillus flavus and its ecotype Aspergillus oryzae with expression levels of their downstream genes. We found that only 4.3% of relationships tested were significant; these findings were consistent with models in which TRs act as “tuning,” “volume,” or “optimality” “knobs” of phenotype but not with “switch” models. Furthermore, the promoter regions of differentially expressed genes between A. oryzae and A. flavus did not show TR enrichment, suggesting that genome-wide differences in molecular phenotype between the two species are not significantly associated with TRs. Although in some cases TR polymorphisms do contribute to transcript abundance variation, these results argue that at least in this case, TRs might not be major modulators of variation in phenotype. PMID:23275886

  1. Behavior Disorders after Severe Head Injury: Their Nature and Causes and Strategies for Management.

    ERIC Educational Resources Information Center

    Eames, Peter

    1988-01-01

    The article discusses the multifactorial causation of behavior disorders after head injury, arguing that management strategies must be based on an understanding of their general nature and on specific knowledge of the individual's history and injury. (DB)

  2. Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

    ERIC Educational Resources Information Center

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

  3. Genetic Variation Segregating in Natural Populations of Tribolium Castaneum Affecting Traits Observed in Hybrids with T. Freemani

    PubMed Central

    Wade, M. J.; Johnson, N. A.; Jones, R.; Siguel, V.; McNaughton, M.

    1997-01-01

    We investigated patterns of within-species genetic variation for traits observed in hybrids (hybrid numbers, hybrid sex ratios, and hybrid male deformities) between two species of flour beetles, Tribolium castaneum and T. freemani. We found genetic variation segregating among four natural populations of T. castaneum as well as within these populations. For some hybrid traits, we observed as much variation among populations 750 km apart as between populations on different continents, suggesting genetic differentiation at a local scale. Within natural populations, the variation segregating among sires is greater than that found in an earlier study for an outbred laboratory population and comparable to that observed between inbred lines derived from the outbred stock by eight generations of brother-sister mating. When sires from T. castaneum are mated to conspecific and heterospecific females, we do not observe a significant correlation at the level of the family mean between the intraspecific and interspecific phenotypes, suggesting the independence of the hybrid traits from comparable traits within species. We discuss our findings in relation to the evolutionary genetics of speciation and the expression of epistatic genetic variance in interspecific crosses. PMID:9383066

  4. Natural variation in odorant recognition among odorant-binding proteins in Drosophila melanogaster.

    PubMed

    Wang, Ping; Lyman, Richard F; Mackay, Trudy F C; Anholt, Robert R H

    2010-03-01

    Chemical recognition is essential for survival and reproduction. Adaptive evolution has resulted in diverse chemoreceptor families, in which polymorphisms contribute to individual variation in chemosensation. To gain insights into the genetic determinants of individual variation in odorant recognition, we measured olfactory responses to two structurally similar odorants in a population of wild-derived inbred lines of Drosophila melanogaster. Odorant-binding proteins (OBPs) are the first components of the insect olfactory system to encounter odorants. Previously four single-nucleotide polymorphisms (SNPs) in the Obp99 group were associated with variation in olfactory responses to benzaldehyde. Here, we identify six different SNPs that are associated with variation in responses to a structurally similar odorant, acetophenone, in the same Obp genes. Five SNPs are in coding regions of Obp99b and Obp99d and one SNP is in the 3'-untranslated region of Obp99a (A610G). We found that the 610G allele is associated with higher response scores to acetophenone than the 610A allele, but with lower expression of Obp99a, suggesting that binding of acetophenone to Opb99a might limit rather than facilitate access to odorant receptors. Our results show that overlapping sets of OBPs contribute to odorant recognition for structurally similar odorants, but that different SNPs are associated with odorant-specific individual variation. Thus, dual olfactory recognition where OBPs regulate odorant access to receptors may enhance olfactory discrimination. PMID:20026676

  5. Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster

    PubMed Central

    Dembeck, Lauren M; Böröczky, Katalin; Huang, Wen; Schal, Coby; Anholt, Robert R H; Mackay, Trudy F C

    2015-01-01

    Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition. DOI: http://dx.doi.org/10.7554/eLife.09861.001 PMID:26568309

  6. Diurnal and circadian variation of sleep and alertness in men vs. naturally cycling women.

    PubMed

    Boivin, Diane B; Shechter, Ari; Boudreau, Philippe; Begum, Esmot Ara; Ng Ying-Kin, Ng Mien Kwong

    2016-09-27

    This study quantifies sex differences in the diurnal and circadian variation of sleep and waking while controlling for menstrual cycle phase and hormonal contraceptive use. We compared the diurnal and circadian variation of sleep and alertness of 8 women studied during two phases of the menstrual cycle and 3 women studied during their midfollicular phase with that of 15 men. Participants underwent an ultradian sleep-wake cycle (USW) procedure consisting of 36 cycles of 60-min wake episodes alternating with 60-min nap opportunities. Core body temperature (CBT), salivary melatonin, subjective alertness, and polysomnographically recorded sleep were measured throughout this procedure. All analyzed measures showed a significant diurnal and circadian variation throughout the USW procedure. Compared with men, women demonstrated a significant phase advance of the CBT but not melatonin rhythms, as well as an advance in the diurnal and circadian variation of sleep measures and subjective alertness. Furthermore, women experienced an increased amplitude of the diurnal and circadian variation of alertness, mainly due to a larger decline in the nocturnal nadir. Our results indicate that women are likely initiating sleep at a later circadian phase than men, which may be one factor contributing to the increased susceptibility to sleep disturbances reported in women. Lower nighttime alertness is also observed, suggesting a physiological basis for a greater susceptibility to maladaptation to night shift work in women. PMID:27621470

  7. Genetic and Biochemical Basis of Enzyme Activity Variation in Natural Populations. I. Alcohol Dehydrogenase in DROSOPHILA MELANOGASTER

    PubMed Central

    McDonald, John F.; Ayala, Francisco J.

    1978-01-01

    Recent studies by various authors suggest that variation in gene regulation may be common in nature, and might be of great evolutionary consequence; but the ascertainment of variation in gene regulation has proven to be a difficult problem. In this study, we explore this problem by measuring alcohol dehydrogenase (ADH) activity in Drosophila melanogaster strains homozygous for various combinations of given second and third chromosomes sampled from a natural population. The structural locus (Adh) coding for ADH is on the second chromosome. The results show that: (1) there are genes, other than Adh, that affect the levels of ADH activity; (2) at least some of these "regulatory" genes are located on the third chromosome, and thus are not adjacent to the Adh locus; (3) variation exists in natural populations for such regulatory genes; (4) the effect of these regulatory genes varies as they interact with different second chromosomes; (5) third chromosomes with high-activity genes are either partially or completely dominant over chromosomes with low-activity genes; (6) the effects of the regulatory genes are pervasive throughout development; and (7) the third chromosome genes regulate the levels of ADH activity by affecting the number of ADH molecules in the flies. The results are consistent with the view that the evolution of regulatory genes may play an important role in adaptation. PMID:97168

  8. Learning to be different: Acquired skills, social learning, frequency dependence, and environmental variation can cause behaviourally mediated foraging specializations

    USGS Publications Warehouse

    Tinker, M.T.; Mangel, M.; Estes, J.A.

    2009-01-01

    Question: How does the ability to improve foraging skills by learning, and to transfer that learned knowledge, affect the development of intra-population foraging specializations? Features of the model: We use both a state-dependent life-history model implemented by stochastic dynamic programming (SDPM) and an individual-based model (IBM) to capture the dynamic nature of behavioural preferences in feeding. Variables in the SDPM include energy reserves, skill levels, energy and handling time per single prey item, metabolic rate, the rates at which skills are learned and forgotten, the effect of skills on handling time, and the relationship between energy reserves and fitness. Additional variables in the IBM include the probability of successful weaning, the logistic dynamics of the prey species with stochastic recruitment, the intensity of top-down control of prey by predators, the mean and variance in skill levels of new recruits, and the extent to which learned Information can be transmitted via matrilineal social learning. Key range of variables: We explore the effects of approaching the time horizon in the SDPM, changing the extent to which skills can improve with experience, increasing the rates of learning or forgetting of skills, changing whether the learning curve is constant, accelerating (T-shaped) or decelerating ('r'-shaped), changing both mean and maximum possible energy reserves, changing metabolic costs of foraging, and changing the rate of encounter with prey. Conclusions: The model results show that the following factors increase the degree of prey specialization observed in a predator population: (1) Experience handling a prey type can substantially improve foraging skills for that prey. (2) There is limited ability to retain complex learned skills for multiple prey types. (3) The learning curve for acquiring new foraging skills is accelerating, or J-shaped. (4) The metabolic costs of foraging are high relative to available energy reserves. (5

  9. Causes and prevention of corrosion in carbon steel natural gas coolers

    SciTech Connect

    Kotwica, D.J.; Minevski, L.

    1998-12-31

    Two case histories in which high pressure natural gas coolers had failed due to the presence of carbon dioxide are reviewed. CO{sub 2} along with CO and H{sub 2}S are acid gases usually present in natural gas feeds. Carbonic acid can form in aqueous condensate, lowering the pH and locally corroding mild steel tube metal. Stress corrosion cracking (SCC) can occur in tubing containing residual tensile stresses from welding or manufacturing. Bicarbonates and carbonates concentrated in condensate from CO{sub 2} and CO present in natural gas are required to produce SCC. Cathodic depolarizers such as oxygen in conjunction with the presence of carbonic acid will increase the corrosion rate of mild steel. Oxygen also increases the susceptibility of mild steel to carbonate SCC.

  10. Quartz-calcite oxygen isotope thermometry: A calibration based on natural isotopic variations

    NASA Astrophysics Data System (ADS)

    Sharp, Z. D.; Kirschner, D. L.

    1994-10-01

    An empirical calibration for the quartz-calcite thermometer was derived from measured Δ18O( qz- cc) values from greenschist-facies marbles, veins composed of cogenetic quartz and calcite and various low-grade metamorphic rocks. The Δ18O( qz- cc) values vary systematically with independently determined formation temperature and can be fit to the expression 1000 ln α( qz- cc) = 0.87(±0.06) × 10 6/ T2. In contrast, published results from direct-exchange experiments between calcite and quartz are 1000 ln α( qz- cc) = 0.38(±0.06) × 10 6/ T2, far smaller than in the present study. Application of the experimental mineral-water and especially the direct-exchange calibrations to natural samples, yields unreasonably low geological temperatures. It is difficult to envision a mechanism whereby the measured fractionations in greenschist-grade marbles can be reconciled with the very low temperature estimates obtained with the direct-exchange experimental calibration. Oxygen diffusion rates in quartz are too slow to explain the discrepancy. Postmetamorphic exchange could have occurred with a hydrothermal fluid, but it is unlikely that the δ18O( calcite) values of all samples would be shifted by an amount that would result in a linear relationship between 1000 ln α( qz- cc) and T-2. More likely, the discrepancy is due to a kinetic effect in the experiments. The very small fractionations observed in the direct-exchange experiments may have been caused by diffusion-related effects during recrystallization of the quartz and calcite. The problem of recrystallization is eliminated in mineral-CO 2 exchange experiments. Combined CO 2-calcite and CO 2-quartz glass experiments yield the expression 1000 ln α (qz-cc) = 0.78 ( 0¯.08) , in good agreement with the empirical calibration. The new empirical calibration yields reasonable temperature estimates for a wide range of samples and can be used for thermometry in rock types and over temperature intervals where other quantitative

  11. The nature of the optical variations of Seyfert galaxy 3C 120

    SciTech Connect

    Webb, J.R. Austin State Univ., TX )

    1990-01-01

    Results are presented from 61 years of optical observations of the Seyfert galaxy 3C 120. A previously published model of the 3C 120 light curve, derived from power spectrum analysis, is found to be valid for historical as well as current data. It is concluded that the optical variations of 3C 120 can be separated into a linear component, a sinusoidal component, and rapid, high-amplitude flares. Possible sources of the regular variations observed in 3C 120 are also suggested in the context of accretion models and other theoretical models. 15 refs.

  12. Design of a comprehensive biochemistry and molecular biology experiment: phase variation caused by recombinational regulation of bacterial gene expression.

    PubMed

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about Salmonella enterica serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation, antibody agglutination test, and PCR analysis. Phase variation was observed by baterial motility assay and identified by antibody agglutination test and PCR analysis. This comprehensive experiment can be performed to help students improve their ability to use the knowledge acquired in Biochemistry and Molecular Biology.

  13. Weekly variations of discharge and groundwater quality caused by intermittent water supply in an urbanized karst catchment

    NASA Astrophysics Data System (ADS)

    Grimmeisen, Felix; Zemann, Moritz; Goeppert, Nadine; Goldscheider, Nico

    2016-06-01

    Leaky sewerage and water distribution networks are an enormous problem throughout the world, specifically in developing countries and regions with water scarcity. Especially in many arid and semi-arid regions, intermittent water supply (IWS) is common practice to cope with water shortage. This study investigates the combined influence of urban activities, IWS and water losses on groundwater quality and discusses the implications for water management. In the city of As-Salt (Jordan), local water supply is mostly based on groundwater from the karst aquifer that underlies the city. Water is delivered to different supply zones for 24, 48 or 60 h each week with drinking water losses of around 50-60%. Fecal contamination in groundwater, mostly originating from the likewise leaky sewer system is a severe challenge for the local water supplier. In order to improve understanding of the local water cycle and contamination dynamics in the aquifer beneath the city, a down gradient spring and an observation well were chosen to identify contaminant occurrence and loads. Nitrate, Escherichia coli, spring discharge and the well water level were monitored for 2 years. Autocorrelation analyses of time series recorded during the dry season revealed weekly periodicity of spring discharge (45 ± 3.9 L s-1) and NO3-N concentrations (11.4 ± 0.8 mg L-1) along with weekly varying E. coli levels partly exceeding 2.420 MPN 100 mL-1. Cross-correlation analyses demonstrate a significant and inverse correlation of nitrate and discharge variations which points to a periodic dilution of contaminated groundwater by freshwater from the leaking IWS being the principal cause of the observed fluctuations. Contaminant inputs from leaking sewers appear to be rather constant. The results reveal the distinct impact of leaking clean IWS on the local groundwater and subsequently on the local water supply and therefore demonstrate the need for action regarding the mitigation of groundwater contamination and

  14. Examining the Nature and Perceived Causes of Indiscipline in Zimbabwean Secondary Schools

    ERIC Educational Resources Information Center

    Ametepee, Lawrence K.; Chitiyo, Morgan; Abu, Susan

    2009-01-01

    The problem of student indiscipline is an issue of concern for teachers and parents around the world. Teachers need to maintain student discipline and for them to do so it is important that they also understand the nature of discipline problems. This study, by Lawrence Kofi Ametepee, who is studying for a PhD in special education, Morgan Chitiyo,…

  15. HYDRODYNAMIC AND RADIATIVE MODELING OF TEMPORAL H{alpha} EMISSION V/R VARIATIONS CAUSED BY DISCONTINUOUS MASS TRANSFER IN BINARIES

    SciTech Connect

    Chadima, Pavel; Harmanec, Petr; Wolf, Marek; Firt, Roman; Ruzdjak, Domagoj; Bozic, Hrvoje; Koubsky, Pavel

    2011-07-15

    H{alpha} emission V/R variations caused by discontinuous mass transfer in interacting binaries with a rapidly rotating accreting star are modeled qualitatively for the first time. The program ZEUS-MP was used to create a non-linear three-dimensional hydrodynamical model of a development of a blob of gaseous material injected into an orbit around a star. It resulted in the formation of an elongated disk with a slow prograde revolution. The LTE radiative transfer program SHELLSPEC was used to calculate the H{alpha} profiles originating in the disk for several phases of its revolution. The profiles have the form of a double emission and exhibit V/R and radial velocity variations. However, these variations should be a temporal phenomenon since imposing a viscosity in the given model would lead to a circularization of the disk and fading-out of the given variations.

  16. Natural Selection and Evolution: Using Multimedia Slide Shows to Emphasize the Role of Genetic Variation

    ERIC Educational Resources Information Center

    Malone, Molly

    2012-01-01

    Most middle school students comprehend that organisms have adaptations that enable their survival and that successful adaptations prevail in a population over time. Yet they often miss that those bird beaks, moth-wing colors, or whatever traits are the result of random, normal genetic variations that just happen to confer a negative, neutral, or…

  17. Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast.

    PubMed

    Liti, Gianni; Haricharan, Svasti; Cubillos, Francisco A; Tierney, Anna L; Sharp, Sarah; Bertuch, Alison A; Parts, Leopold; Bailes, Elizabeth; Louis, Edward J

    2009-09-01

    In yeast, as in humans, telomere length varies among individuals and is controlled by multiple loci. In a quest to define the extent of variation in telomere length, we screened 112 wild-type Saccharomyces sensu stricto isolates. We found extensive telomere length variation in S. paradoxus isolates. This phenotype correlated with their geographic origin: European strains were observed to have extremely short telomeres (<150 bp), whereas American isolates had telomeres approximately three times as long (>400 bp). Insertions of a URA3 gene near telomeres allowed accurate analysis of individual telomere lengths and telomere position effect (TPE). Crossing the American and European strains resulted in F1 spores with a continuum of telomere lengths consistent with what would be predicted if many quantitative trait loci (QTLs) were involved in length maintenance. Variation in TPE is similarly quantitative but only weakly correlated with telomere length. Genotyping F1 segregants indicated several QTLs associated with telomere length and silencing variation. These QTLs include likely candidate genes but also map to regions where there are no known genes involved in telomeric properties. We detected transgressive segregation for both phenotypes. We validated by reciprocal hemizygosity that YKU80 and TLC1 are telomere-length QTLs in the two S. paradoxus subpopulations. Furthermore, we propose that sequence divergence within the Ku heterodimer generates negative epistasis within one of the allelic combinations (American-YKU70 and European-YKU80) resulting in very short telomeres. PMID:19763176

  18. Probing the Natural World, Volume 3A, Investigating Variation and Winds and Weather.

    ERIC Educational Resources Information Center

    Burkman, Ernest

    Included are two of the eight units of the Intermediate Science Curriculum Study materials designed for grade nine students. These are "investigating variation" and "winds and weather." Introductory notes to the student explain how the book is to be used. Each chapter starts with a short statement of a general problem, then concepts are developed…

  19. Assessment of the natural variation of low abundant metabolic proteins in soybean seeds using proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry, we investigated the distribution of the low abundant proteins that are involved in soybean seed development in four wild and twelve cultivated soybean genotypes. We found proteomic variation of these proteins within and...

  20. On the Nature of Syntactic Variation: Evidence from Complex Predicates and Complex Word-Formation.

    ERIC Educational Resources Information Center

    Snyder, William

    2001-01-01

    Provides evidence from child language acquisition and comparative syntax for existence of a syntactic parameter in the classical sense of Chomsky (1981), with simultaneous effects on syntactic argument structure. Implications are that syntax is subject to points of substantive parametric variation as envisioned in Chomsky, and the time course of…

  1. Naturally occurring continued fractions in the variation of Kepler's equation. [for guidance and trajectory optimization

    NASA Technical Reports Server (NTRS)

    Shepperd, Stanley W.

    1988-01-01

    A family of functions involving integrals of universal functions is introduced. These functions have some interesting mathematical properties including the fact that they may be expressed as Gaussian continued fractions. A unique method of performing the integration is demonstrated which indicates why these functions may be important in the variation of Kepler's equation.

  2. Natural Ferrihydrite as an Agent for Reducing Turbidity Caused by Suspended Clays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The turbidity of water can be reduced by the addition of positively charged compounds which coagulate negatively charged clay particles in suspension causing them to flocculate. This research was conducted to determine the effectiveness of the Fe oxide mineral ferrihydrite as a flocculating agent fo...

  3. The Nature, Extent and Causes of Abuse of Children with Disabilities in Schools in Botswana

    ERIC Educational Resources Information Center

    Shumba, Almon; Abosi, Okey C.

    2011-01-01

    Studies show that the exact number of children with disabilities in Botswana is unknown. A study on child abuse sought to determine: the forms of child abuse perpetrated on children with disabilities; the extent of child abuse; and the causes of child abuse of children with disabilities. A questionnaire on child abuse was adapted and used to…

  4. Possible causes of variation in acrylamide concentration in French fries prepared in food service establishments: an observational study.

    PubMed

    Sanny, M; Jinap, S; Bakker, E J; van Boekel, M A J S; Luning, P A

    2012-05-01

    Acrylamide is a probable human carcinogen, and its presence in a range of fried and oven-cooked foods has raised considerable health concern world-wide. Dietary intake studies observed significant variations in acrylamide concentrations, which complicate risk assessment and the establishment of effective control measures. The objective of this study was to obtain an insight into the actual variation in acrylamide concentrations in French fries prepared under typical conditions in a food service establishment (FSE). Besides acrylamide, frying time, frying temperature, and reducing sugars were measured and the actual practices at receiving, thawing and frying during French fries preparation were observed and recorded. The variation in the actual frying temperature contributed most to the variation in acrylamide concentrations, followed by the variation in actual frying time; no obvious effect of reducing sugars was found. The lack of standardised control of frying temperature and frying time (due to inadequate frying equipment) and the variable practices of food handlers seem to contribute most to the large variation and high acrylamide concentrations in French fries prepared in a restaurant type of FSE as compared to chain fast-food services, and institutional caterers. The obtained insights in this study can be used to develop dedicated control measures in FSE, which may contribute to a sustainable reduction in the acrylamide intake. PMID:26434272

  5. Possible causes of variation in acrylamide concentration in French fries prepared in food service establishments: an observational study.

    PubMed

    Sanny, M; Jinap, S; Bakker, E J; van Boekel, M A J S; Luning, P A

    2012-05-01

    Acrylamide is a probable human carcinogen, and its presence in a range of fried and oven-cooked foods has raised considerable health concern world-wide. Dietary intake studies observed significant variations in acrylamide concentrations, which complicate risk assessment and the establishment of effective control measures. The objective of this study was to obtain an insight into the actual variation in acrylamide concentrations in French fries prepared under typical conditions in a food service establishment (FSE). Besides acrylamide, frying time, frying temperature, and reducing sugars were measured and the actual practices at receiving, thawing and frying during French fries preparation were observed and recorded. The variation in the actual frying temperature contributed most to the variation in acrylamide concentrations, followed by the variation in actual frying time; no obvious effect of reducing sugars was found. The lack of standardised control of frying temperature and frying time (due to inadequate frying equipment) and the variable practices of food handlers seem to contribute most to the large variation and high acrylamide concentrations in French fries prepared in a restaurant type of FSE as compared to chain fast-food services, and institutional caterers. The obtained insights in this study can be used to develop dedicated control measures in FSE, which may contribute to a sustainable reduction in the acrylamide intake.

  6. Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis.

    PubMed

    Li, Dapeng; Baldwin, Ian T; Gaquerel, Emmanuel

    2015-07-28

    Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United States--including the well-characterized Utah 30th generation inbred accession--and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis. PMID:26170304

  7. Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis.

    PubMed

    Li, Dapeng; Baldwin, Ian T; Gaquerel, Emmanuel

    2015-07-28

    Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United States--including the well-characterized Utah 30th generation inbred accession--and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis.

  8. Nature and frequency of mutations in the argininosuccinate synthetase gene that cause classical citrullinemia.

    PubMed

    Kobayashi, K; Kakinoki, H; Fukushige, T; Shaheen, N; Terazono, H; Saheki, T

    1995-10-01

    Citrullinemia is an autosomal recessive disorder caused by a genetic deficiency of argininosuccinate synthetase (ASS). So far 20 mutations in ASS mRNA have been identified in human classical citrullinemia, including 14 single base changes causing missense mutations in the coding sequence of the enzyme, 4 mutations associated with an absence of exons 5, 6, 7, or 13 in mRNA, 1 mutation with a deletion of the first 7 bases in exon 16 (which is caused by abnormal splicing), and 1 mutation with an insertion of 37 bases between the exon 15 and 16 regions in mRNA. In order to identify the abnormality in the ASS gene causing the exon 7 and 13 deletion mutations and the 37-base insertion mutation between exons 15 and 16 in mRNA, and to establish a DNA diagnostic test, we isolated and sequenced the genomic DNA surrounding each exon. The absence of exon 7 or 13 in ASS mRNA resulted from abnormal splicing caused by a single base change in the intron region: IVS-6(-2) (a transition of A to G at the second nucleotide position within the 3' splice cleavage site of intron 6) and IVS-13(+5) (a transition of G to A at the fifth nucleotide position within the 5' splice cleavage site of intron 13), respectively. The IVS-6(-2) mutation resulted in the creation of an MspI restriction site. DNA diagnostic analysis of 33 Japanese alleles with classical citrullinemia showed that 19 alleles had the IVS-6(-2) mutation (over 50% of the mutated alleles in Japanese patients). It was thus confirmed that one mutation is predominant in Japan. This differs from the situation in the USA where there is far greater heterogeneity. The insertion mutation in mRNA on the other hand resulted from abnormal splicing caused by a 13-bp deletion at the splice-junction between exon 15 and intron 15. The deletion had a short direct repeat (CTCAGG) at the breakpoint junction and presumably resulted from slipped mispairing. PMID:7557970

  9. Methods for predicting peak discharge of floods caused by failure of natural and constructed earthen dams

    USGS Publications Warehouse

    Walder, J.S.; O'Connor, J. E.

    1997-01-01

    Floods from failures of natural and constructed dams constitute a widespread hazard to people and property. Expeditious means of assessing flood hazards are necessary, particularly in the case of natural dams, which may form suddenly and unexpectedly. We revise statistical relations (derived from data for past constructed and natural dam failures) between peak discharge (Q(p)) and water volume released (V(0)) or drop in lake level (d) but assert that such relations, even when cast into a dimensionless form, are of limited utility because they fail to portray the effect of breach-formation rate. We then analyze a simple, physically based model of dam-breach formation to show that the hydrograph at the breach depends primarily on a dimensionless parameter ?? = kV0/g1/2d7/2, where k is the mean erosion rate of the breach and g is acceleration due to gravity. The functional relationship between Q(p) and ?? takes asymptotically distinct forms depending on whether ?? << 1 (relatively slow breach formation or small lake volume) or ?? >> 1 (relatively fast breach formation or large lake volume). Theoretical predictions agree well with data from dam failures for which k, and thus ??, can be estimated. The theory thus provides a rapid means of predicting the plausible range of values of peak discharge at the breach in an earthen dam as long as the impounded water volume and the water depth at the dam face can be estimated.

  10. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes.

    PubMed

    Krause, David J; Whitaker, Rachel J

    2015-11-01

    Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.

  11. Cultural variation is part of human nature : Literary universals, context-sensitivity, and "shakespeare in the bush".

    PubMed

    Sugiyama, Michelle Scalise

    2003-12-01

    In 1966, Laura Bohannan wrote her classic essay challenging the supposition that great literary works speak to universal human concerns and conditions and, by extension, that human nature is the same everywhere. Her evidence: the Tiv of West Africa interpret Hamlet differently from Westerners. While Bohannan's essay implies that cognitive universality and cultural variation are mutually exclusive phenomena, adaptationist theory suggests otherwise. Adaptive problems ("the human condition") and cognitive adaptations ("human nature") are constant across cultures. What differs between cultures is habitat: owing to environmental variation, the means and information relevant to solving adaptive problems differ from place to place. Thus, we find differences between cultures not because human minds differ in design but largely because human habitats differ in resources and history. On this view, we would expect world literature to express both human universals and cultural particularities. Specifically, we should expect to find literary universality at the macro level (e.g., adaptive problems, cognitive adaptations) and literary variation at the micro level (e.g., local solutions to adaptive problems).

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

    PubMed

    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.

  13. Variation in Chemical Defense Among Natural Populations of Common Toad, Bufo bufo, Tadpoles: the Role of Environmental Factors.

    PubMed

    Bókony, Veronika; Móricz, Ágnes M; Tóth, Zsófia; Gál, Zoltán; Kurali, Anikó; Mikó, Zsanett; Pásztor, Katalin; Szederkényi, Márk; Tóth, Zoltán; Ujszegi, János; Üveges, Bálint; Krüzselyi, Dániel; Capon, Robert J; Hoi, Herbert; Hettyey, Attila

    2016-04-01

    Defensive toxins are widespread in nature, yet we know little about how various environmental factors shape the evolution of chemical defense, especially in vertebrates. In this study we investigated the natural variation in the amount and composition of bufadienolide toxins, and the relative importance of ecological factors in predicting that variation, in larvae of the common toad, Bufo bufo, an amphibian that produces toxins de novo. We found that tadpoles' toxin content varied markedly among populations, and the number of compounds per tadpole also differed between two geographical regions. The most consistent predictor of toxicity was the strength of competition, indicating that tadpoles produced more compounds and larger amounts of toxins when coexisting with more competitors. Additionally, tadpoles tended to contain larger concentrations of bufadienolides in ponds that were less prone to desiccation, suggesting that the costs of toxin production can only be afforded by tadpoles that do not need to drastically speed up their development. Interestingly, this trade-off was not alleviated by higher food abundance, as periphyton biomass had negligible effect on chemical defense. Even more surprisingly, we found no evidence that higher predation risk enhances chemical defenses, suggesting that low predictability of predation risk and high mortality cost of low toxicity might select for constitutive expression of chemical defense irrespective of the actual level of predation risk. Our findings highlight that the variation in chemical defense may be influenced by environmental heterogeneity in both the need for, and constraints on, toxicity as predicted by optimal defense theory.

  14. Variation in Chemical Defense Among Natural Populations of Common Toad, Bufo bufo, Tadpoles: the Role of Environmental Factors.

    PubMed

    Bókony, Veronika; Móricz, Ágnes M; Tóth, Zsófia; Gál, Zoltán; Kurali, Anikó; Mikó, Zsanett; Pásztor, Katalin; Szederkényi, Márk; Tóth, Zoltán; Ujszegi, János; Üveges, Bálint; Krüzselyi, Dániel; Capon, Robert J; Hoi, Herbert; Hettyey, Attila

    2016-04-01

    Defensive toxins are widespread in nature, yet we know little about how various environmental factors shape the evolution of chemical defense, especially in vertebrates. In this study we investigated the natural variation in the amount and composition of bufadienolide toxins, and the relative importance of ecological factors in predicting that variation, in larvae of the common toad, Bufo bufo, an amphibian that produces toxins de novo. We found that tadpoles' toxin content varied markedly among populations, and the number of compounds per tadpole also differed between two geographical regions. The most consistent predictor of toxicity was the strength of competition, indicating that tadpoles produced more compounds and larger amounts of toxins when coexisting with more competitors. Additionally, tadpoles tended to contain larger concentrations of bufadienolides in ponds that were less prone to desiccation, suggesting that the costs of toxin production can only be afforded by tadpoles that do not need to drastically speed up their development. Interestingly, this trade-off was not alleviated by higher food abundance, as periphyton biomass had negligible effect on chemical defense. Even more surprisingly, we found no evidence that higher predation risk enhances chemical defenses, suggesting that low predictability of predation risk and high mortality cost of low toxicity might select for constitutive expression of chemical defense irrespective of the actual level of predation risk. Our findings highlight that the variation in chemical defense may be influenced by environmental heterogeneity in both the need for, and constraints on, toxicity as predicted by optimal defense theory. PMID:27059330

  15. Modeling Modern Methane Emissions from Natural Wetlands. 2; Interannual Variations 1982-1993

    NASA Technical Reports Server (NTRS)

    Walter, Bernadette P.; Heimann, Martin; Mattews, Elaine; Hansen, James E. (Technical Monitor)

    2001-01-01

    A global run of a process-based methane model [Walter et al., this issue] is performed using high-frequency atmospheric forcing fields from ECMWF reanalyses of the period from 1982 to 1993. We calculate global annual methane emissions to be 260 Tg/ yr. 25% of methane emissions originate from wetlands north of 30 deg. N. Only 60% of the produced methane is emitted, while the rest is re-oxidized. A comparison of zonal integrals of simulated global wetland emissions and results obtained by an inverse modeling approach shows good agreement. In a test with data from two wetlands, the seasonality of simulated and observed methane emissions agrees well. The effects of sub-grid scale variations in model parameters and input data are examined. Modeled methane emissions show high regional, seasonal and interannual variability. Seasonal cycles of methane emissions are dominated by temperature in high latitude wetlands, and by changes in the water table in tropical wetlands. Sensitivity tests show that +/- 1 C changes in temperature lead to +/- 20 % changes in methane emissions from wetlands. Uniform changes of +/- 20% in precipitation alter methane emissions by about +/- 18%. Limitations in the model are analyzed. Simulated interannual variations in methane emissions from wetlands are compared to observed atmospheric growth rate anomalies. Our model simulation results suggest that contributions from other sources than wetlands and/or the sinks are more important in the tropics than north-of 30 deg. N. In higher northern latitudes, it seems that a large part, of the observed interannual variations can be explained by variations in wetland emissions. Our results also suggest that reduced wetland emissions played an important role in the observed negative methane growth rate anomaly in 1992.

  16. Population variation and natural selection on leaf traits in cork oak throughout its distribution range

    NASA Astrophysics Data System (ADS)

    Ramírez-Valiente, José Alberto; Valladares, Fernando; Sánchez-Gómez, David; Delgado, Antonio; Aranda, Ismael

    2014-07-01

    A central issue in evolutionary biology is the exploration of functional trait variation among populations and the extent to which this variation has adaptive value. It was recently proposed that specific leaf area (SLA), leaf nitrogen concentration per mass (Nmass) and water use efficiency in cork oak play an important role in adaptation to water availability in the environment. In order to investigate this hypothesis, we explored, first, whether there was population-level variation in cork oak (Quercus suber) for these functional traits throughout its distribution range; if this were the case, it would be consistent with the hypothesis that different rainfall patterns have led to ecotypic differentiation in this species. Second, we studied whether the population-level variation matched short-term selection on these traits under different water availability conditions using two fitness components: survival and growth. We found high population-level differentiation in SLA and Nmass, with populations from dry places exhibiting the lowest values for SLA and Nmass. Likewise, reduced SLA had fitness benefits in terms of growth for plants under dry conditions. However, contrary to our expectations, we did not find any pattern of association between functional traits and survival in nine-year-old saplings despite considerable drought during one year of the study period. These results together with findings from the literature suggest that early stages of development are the most critical period for this species. Most importantly, these findings suggest that cork oak saplings have a considerable potential to cope with dry conditions. This capacity to withstand aridity has important implications for conservation of cork oak woodlands under the ongoing climate change.

  17. Impurities and Electronic Property Variations of Natural MoS2 Crystal Surfaces.

    PubMed

    Addou, Rafik; McDonnell, Stephen; Barrera, Diego; Guo, Zaibing; Azcatl, Angelica; Wang, Jian; Zhu, Hui; Hinkle, Christopher L; Quevedo-Lopez, Manuel; Alshareef, Husam N; Colombo, Luigi; Hsu, Julia W P; Wallace, Robert M

    2015-09-22

    Room temperature X-ray photoelectron spectroscopy (XPS), inductively coupled plasma mass spectrometry (ICPMS), high resolution Rutherford backscattering spectrometry (HR-RBS), Kelvin probe method, and scanning tunneling microscopy (STM) are employed to study the properties of a freshly exfoliated surface of geological MoS2 crystals. Our findings reveal that the semiconductor 2H-MoS2 exhibits both n- and p-type behavior, and the work function as measured by the Kelvin probe is found to vary from 4.4 to 5.3 eV. The presence of impurities in parts-per-million (ppm) and a surface defect density of up to 8% of the total area could explain the variation of the Fermi level position. High resolution RBS data also show a large variation in the MoSx composition (1.8 < x < 2.05) at the surface. Thus, the variation in the conductivity, the work function, and stoichiometry across small areas of MoS2 will have to be controlled during crystal growth in order to provide high quality uniform materials for future device fabrication.

  18. THE ANTICORRELATED NATURE OF THE PRIMARY AND SECONDARY ECLIPSE TIMING VARIATIONS FOR THE KEPLER CONTACT BINARIES

    SciTech Connect

    Tran, K.; Rappaport, S.; Levine, A.; Borkovits, T.; Csizmadia, Sz.; Kalomeni, B. E-mail: aml@space.mit.edu E-mail: szilard.csizmadia@dlr.de

    2013-09-01

    We report a study of the eclipse timing variations in contact binary systems, using long-cadence lightcurves from the Kepler archive. As a first step, observed minus calculated (O - C) curves were produced for both the primary and secondary eclipses of some 2000 Kepler binaries. We find {approx}390 short-period binaries with O - C curves that exhibit (1) random walk-like variations or quasi-periodicities, with typical amplitudes of {+-}200-300 s, and (2) anticorrelations between the primary and secondary eclipse timing variations. We present a detailed analysis and results for 32 of these binaries with orbital periods in the range of 0.35 {+-} 0.05 days. The anticorrelations observed in their O - C curves cannot be explained by a model involving mass transfer, which, among other things, requires implausibly high rates of {approx}0.01 M{sub Sun} yr{sup -1}. We show that the anticorrelated behavior, the amplitude of the O - C delays, and the overall random walk-like behavior can be explained by the presence of a starspot that is continuously visible around the orbit and slowly changes its longitude on timescales of weeks to months. The quasi-periods of {approx}50-200 days observed in the O - C curves suggest values for k, the coefficient of the latitude dependence of the stellar differential rotation, of {approx}0.003-0.013.

  19. Natural allelic variations in glutathione peroxidase-1 affect its subcellular localization and function.

    PubMed

    Bera, Soumen; Weinberg, Frank; Ekoue, Dede N; Ansenberger-Fricano, Kristine; Mao, Mao; Bonini, Marcelo G; Diamond, Alan M

    2014-09-15

    Glutathione peroxidase 1 (GPx-1) has been implicated in the etiology of several common diseases due to the association between specific allelic variations and cancer risk. The most common among these variations are the codon 198 polymorphism that results in either a leucine or proline and the number of alanine repeat codons in the coding sequence. The molecular and biologic consequences of these variations remain to be characterized. Toward achieving this goal, we have examined the cellular location of GPx-1 encoded by allelic variants by ectopically expressing these genes in MCF-7 human breast carcinoma cells that produce undetectable levels of GPx-1, thus achieving exclusive expression in the same cellular environment. A differential distribution between the cytoplasm and mitochondria was observed, with the allele expressing the leucine-198 polymorphism and 7 alanine repeats being more cytoplasmically located than the other alleles examined. To assess whether the distribution of GPx-1 between the cytoplasm and mitochondria had a biologic consequence, we engineered derivative GPx-1 proteins that were targeted to the mitochondria by the addition of a mitochondria targeting sequence and expressed these proteins in MCF-7 cells. These cells were examined for their response to oxidative stress, energy metabolism, and impact on cancer-associated signaling molecules. The results obtained indicated that both primary GPx-1 sequence and cellular location have a profound impact on cellular biology and offer feasible hypotheses about how expression of distinct GPx-1 alleles can affect cancer risk. Cancer Res; 74(18); 5118-26. ©2014 AACR.

  20. Seasonal, synoptic and diurnal variation of atmospheric water-isotopologues in the boundary layer of Southwestern Germany caused by plant transpiration, cold-front passages and dewfall.

    NASA Astrophysics Data System (ADS)

    Christner, Emanuel; Dyroff, Christoph; Kohler, Martin; Zahn, Andreas; Gonzales, Yenny; Schneider, Matthias

    2013-04-01

    Atmospheric water is an enormously crucial trace gas. It is responsible for ~70 % of the natural greenhouse effect (Schmidt et al., JGR, 2010) and carries huge amounts of latent heat. The isotopic composition of water vapor is an elegant tracer for a better understanding and quantification of the extremely complex and variable hydrological cycle in Earth's atmosphere (evaporation, cloud condensation, rainout, re-evaporation, snow), which in turn is a prerequisite to improve climate modeling and predictions. As H216O, H218O and HDO differ in vapor pressure and mass, isotope fractionation occurs due to condensation, evaporation and diffusion processes. In contrast to that, plants are able to transpire water with almost no isotope fractionation. For that reason the ratio of isotopologue concentrations in the boundary layer (BL) provides, compared to humidity measurements alone, independent and additional constraints for quantifying the strength of evaporation and transpiration. Furthermore the isotope ratios contain information about transport history of an air mass and microphysical processes, that is not accessible by humidity measurements. Within the project MUSICA (MUlti-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water) a commercial Picarro Analyzer L2120-i is operated at Karlsruhe in Southwestern Germany, which is continuously measuring the isotopologues H216O, HDO and H218O of atmospheric water vapor since January 2012. A one year record of H216O, HDO and H218O shows clear seasonal, synoptic and diurnal characteristics and reveals the main driving processes affecting the isotopic composition of water vapor in the Middle European BL. Changes in continental plant transpiration and evaporation throughout the year lead to a slow seasonal HDO/H216O-variation, that cannot be explained by pure Rayleigh condensation. Furthermore, cold-front passages from NW lead to fast and pronounced depletion of the HDO/H216O-ratio within

  1. Natural variation in learning rate and memory dynamics in parasitoid wasps: opportunities for converging ecology and neuroscience

    PubMed Central

    Hoedjes, Katja M.; Kruidhof, H. Marjolein; Huigens, Martinus E.; Dicke, Marcel; Vet, Louise E. M.; Smid, Hans M.

    2011-01-01

    Although the neural and genetic pathways underlying learning and memory formation seem strikingly similar among species of distant animal phyla, several more subtle inter- and intraspecific differences become evident from studies on model organisms. The true significance of such variation can only be understood when integrating this with information on the ecological relevance. Here, we argue that parasitoid wasps provide an excellent opportunity for multi-disciplinary studies that integrate ultimate and proximate approaches. These insects display interspecific variation in learning rate and memory dynamics that reflects natural variation in a daunting foraging task that largely determines their fitness: finding the inconspicuous hosts to which they will assign their offspring to develop. We review bioassays used for oviposition learning, the ecological factors that are considered to underlie the observed differences in learning rate and memory dynamics, and the opportunities for convergence of ecology and neuroscience that are offered by using parasitoid wasps as model species. We advocate that variation in learning and memory traits has evolved to suit an insect's lifestyle within its ecological niche. PMID:21106587

  2. Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae)

    PubMed Central

    Brazzola, Gregory; Chèvre, Nathalie; Wedekind, Claus

    2014-01-01

    The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within Alpine whitefish. We sampled spawners from two species of different lakes, bred them in vitro in a full-factorial design each, and studied growth and mortality of embryos. Exposure to EE2 turned out to be toxic in all concentrations we tested (≥1 ng/L). It reduced embryo viability and slowed down embryogenesis. We found significant additive genetic variation in EE2-induced mortality in both species, that is, genotypes differed in their tolerance to estrogen pollution. We also found maternal effects on embryo development to be influenced by EE2, that is, some maternal sib groups were more susceptible to EE2 than others. In conclusion, the toxic effects of EE2 were strong, but both species demonstrated the kind of additive genetic variation that is necessary for an evolutionary response to this type of pollution. PMID:25553069

  3. Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae).

    PubMed

    Brazzola, Gregory; Chèvre, Nathalie; Wedekind, Claus

    2014-11-01

    The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within Alpine whitefish. We sampled spawners from two species of different lakes, bred them in vitro in a full-factorial design each, and studied growth and mortality of embryos. Exposure to EE2 turned out to be toxic in all concentrations we tested (≥1 ng/L). It reduced embryo viability and slowed down embryogenesis. We found significant additive genetic variation in EE2-induced mortality in both species, that is, genotypes differed in their tolerance to estrogen pollution. We also found maternal effects on embryo development to be influenced by EE2, that is, some maternal sib groups were more susceptible to EE2 than others. In conclusion, the toxic effects of EE2 were strong, but both species demonstrated the kind of additive genetic variation that is necessary for an evolutionary response to this type of pollution. PMID:25553069

  4. [Naturally caused imbalance of elements in the population of the Yamal Region (a review)].

    PubMed

    Lekhanova, E N; Kiriliuk, L I; Buganov, A A; Zakharina, T N; Bakhtina, E A; Lebedeva, I N

    2008-01-01

    The study has indicated that microelementosis in the natives and newcomers of Yamal is caused by the geochemical features of the region and supplemented by inadequate zinc intake. The region's waters differ in their hygienic standards and high levels of iron and the air is characterized by the latter's deficiency. Fe is ingested equally with water and foodstuffs while Cu and Zn are mainly with foods. The trace element status of the newcomers is considerably close to that in the natives of the North and associated with the chemical composition of the region's waters.

  5. Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species.

    PubMed

    Hasselman, Daniel J; Argo, Emily E; McBride, Meghan C; Bentzen, Paul; Schultz, Thomas F; Perez-Umphrey, Anna A; Palkovacs, Eric P

    2014-03-01

    Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry have received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites, we examined hybridization between sympatric populations of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) to test whether the frequency of hybridization and pattern of introgression have been impacted by the construction of a dam that isolated formerly anadromous populations of both species in a landlocked freshwater reservoir. The frequency of hybridization and pattern of introgression differed markedly between anadromous and landlocked populations. The rangewide frequency of hybridization among anadromous populations was generally 0-8%, whereas all landlocked individuals were hybrids. Although neutral introgression was observed among anadromous hybrids, directional introgression leading to increased prevalence of alewife genotypes was detected among landlocked hybrids. We demonstrate that habitat alteration can lead to hybrid swarm formation between divergent species that naturally occur sympatrically, and provide empirical evidence that reinforcement does not always sustain reproductive isolation under such circumstances.

  6. Assessment of occupational exposure to uranium by indirect methods needs information on natural background variations.

    PubMed

    Muikku, M; Heikkinen, T; Puhakainen, M; Rahola, T; Salonen, L

    2007-01-01

    Urine monitoring is the preferred method to determine exposure to soluble compounds of uranium in workplaces. The interpretation of uranium contents in workers bioassay samples requires knowledge on uranium excretion and its dependence on intake by diet. Exceptionally high concentrations of natural uranium in private drinking water sources have been measured in the granite areas of Southern Finland. Consequently, high concentrations of natural uranium have been observed in the urine and hair samples of people using water from their own drilled wells. Natural uranium content in urine and hair samples of family members, who use uranium-rich household water, have been analyzed by using ICP-MS. The uranium concentrations both in urine and hair samples of the study subjects were significantly higher than the world-wide average values. In addition, gammaspectrometric methods have been tested for determining uranium in hair samples. This method can be used only for samples with highly elevated uranium concentrations.

  7. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations.

    PubMed

    Schielzeth, Holger; Husby, Arild

    2014-07-01

    A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies. PMID:24689944

  8. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations.

    PubMed

    Schielzeth, Holger; Husby, Arild

    2014-07-01

    A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.

  9. Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii[OPEN

    PubMed Central

    Hazzouri, Khaled M.; Rosas, Ulises; Bahmani, Tayebeh; Nelson, David R.; Abdrabu, Rasha; Harris, Elizabeth H.; Salehi-Ashtiani, Kourosh; Purugganan, Michael D.

    2015-01-01

    We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits. PMID:26392080

  10. Seasonal variation of natural mortality factors of the guava psyllid Triozoida limbata.

    PubMed

    Semeão, A A; Martins, J C; Picanço, M C; Chediak, M; da Silva, E M; Silva, G A

    2012-12-01

    It is important to understand how components of the agroecosystem interfere with the attack of a pest species and their seasonality in order to use these components in IPM programs. This study focused on the evaluation of the seasonality of natural control factors associated with the guava psyllid Triozoida limbata (Enderlein) in Brazil. Life-table data were collected from an experimental guava orchard during four periods that roughly represented four seasons. Natural mortality was monitored daily through the immature stages, and the relative importance of each natural mortality factor and its seasonality was determined. Significant statistical differences were observed in the mortality during the four periods (P < 0.05). Several factors contributed to the mortality of T. limbata, including rainfall, physiological disturbance, the parasitoid Psyllaephagus sp. (Hymenoptera: Encyrtidae) and specific predators: syrphids, predatory wasps and other generalist predators. Depending on the location of nymphs (exposed or inside galls), the relative importance of the different natural mortality factors changed. The principal component analysis (PCA) showed some trends in the relationship of natural control agents and weather conditions. For example, the occurrence of predatory wasps was positively correlated with temperature and occurrence of winds; the occurrence of syrphids and Psyllaephagus sp. were negatively correlated with temperature and winds; and the occurrence of other generalist predators were negatively correlated with the occurrence of rainfall and photoperiod. The results showed the importance of natural mortality factors for the management of T. limbata and their changes through the different seasons which should be considered when implementing IPM programs in guava orchards. PMID:22677036

  11. Seasonal variation of natural mortality factors of the guava psyllid Triozoida limbata.

    PubMed

    Semeão, A A; Martins, J C; Picanço, M C; Chediak, M; da Silva, E M; Silva, G A

    2012-12-01

    It is important to understand how components of the agroecosystem interfere with the attack of a pest species and their seasonality in order to use these components in IPM programs. This study focused on the evaluation of the seasonality of natural control factors associated with the guava psyllid Triozoida limbata (Enderlein) in Brazil. Life-table data were collected from an experimental guava orchard during four periods that roughly represented four seasons. Natural mortality was monitored daily through the immature stages, and the relative importance of each natural mortality factor and its seasonality was determined. Significant statistical differences were observed in the mortality during the four periods (P < 0.05). Several factors contributed to the mortality of T. limbata, including rainfall, physiological disturbance, the parasitoid Psyllaephagus sp. (Hymenoptera: Encyrtidae) and specific predators: syrphids, predatory wasps and other generalist predators. Depending on the location of nymphs (exposed or inside galls), the relative importance of the different natural mortality factors changed. The principal component analysis (PCA) showed some trends in the relationship of natural control agents and weather conditions. For example, the occurrence of predatory wasps was positively correlated with temperature and occurrence of winds; the occurrence of syrphids and Psyllaephagus sp. were negatively correlated with temperature and winds; and the occurrence of other generalist predators were negatively correlated with the occurrence of rainfall and photoperiod. The results showed the importance of natural mortality factors for the management of T. limbata and their changes through the different seasons which should be considered when implementing IPM programs in guava orchards.

  12. The nature and causes of chronic obstructive pulmonary disease: A historical perspective

    PubMed Central

    Warren, C Peter W

    2009-01-01

    Chronic obstructive pulmonary disease (COPD) is the currently favoured name for the diseases formerly known as emphysema and bronchitis. COPD has been recognized for more than 200 years. Its cardinal symptoms are cough, phlegm and dyspnea, and its pathology is characterized by enlarged airspaces and obstructed airways. In the 19th century, the diagnosis of COPD depended on its symptoms and signs of a hyperinflated chest, and reduced expiratory breath sounds. The airflow obstruction evident on spirometry was identified in that century, but did not enter into clinical practice. Bronchitis, and the mechanical forces required to overcome its obstruction, was believed to be responsible for emphysema, although the inflammation present was recognized. The causes of bronchitis, and hence emphysema, included atmospheric and domestic air pollution, as well as dusty occupations. Cigarette smoking only became recognized as the dominant cause in the 20th century. The lessons learned of the risks for COPD in 19th-century Britain are very pertinent to the world today. PMID:19262908

  13. A new perspective on size hierarchies in nature: patterns, causes, and consequences.

    PubMed

    Buston, Peter M; Cant, Michael A

    2006-08-01

    Many plant and animal aggregations have size hierarchies within which a variety of sizes of individuals, from large to small, can be found. Size hierarchies are thought to indicate the existence of competition amongst individuals within the aggregation, but determining their exact cause is difficult. The key to understanding size hierarchies lies in first quantifying the pattern of size and growth of individuals. We conducted a quantitative investigation of pattern in the size hierarchy of the clown anemonefish Amphiprion percula, in Madang Lagoon, Papua New Guinea. Here, groups of A. percula occupy sea anemones (Heteractis magnifica) that provide protection from predators. Within each anemone there is a single group composed of a breeding pair and zero to four non-breeders. Within each group there is a single size hierarchy; the female is largest (rank 1), the male is second largest (rank 2), and the non-breeders get progressively smaller (ranks 3-6). We demonstrate that individuals adjacent in rank are separated by body size ratios whose distribution is significantly different from the distribution expected under a null model-the growth of individuals is regulated such that each dominant ends up being about 1.26 times the size of its immediate subordinate. We show that it is decisions about growth at the individual level that generate the size hierarchy at the group level, and thereby determine maximum group size and population size. This study provides a new perspective on the pattern, causes and consequences of size hierarchies.

  14. The Nature and Cause of Spectral Variability in LMC X-1

    NASA Technical Reports Server (NTRS)

    Ruhlen, L.; Smith, D. M.; Scank, J. H.

    2011-01-01

    We present the results of a long-term observation campaign of the extragalactic wind-accreting black-hole X-ray binary LMC X-1, using the Proportional Counter Array on the Rossi X-Ray Timing Explorer (RXTE). The observations show that LMC X-1's accretion disk exhibits an anomalous temperature-luminosity relation. We use deep archival RXTE observations to show that large movements across the temperature-luminosity space occupied by the system can take place on time scales as short as half an hour. These changes cannot be adequately explained by perturbations that propagate from the outer disk on a viscous timescale. We propose instead that the apparent disk variations reflect rapid fluctuations within the Compton up-scattering coronal material, which occults the inner parts of the disk. The expected relationship between the observed disk luminosity and apparent disk temperature derived from the variable occultation model is quantitatively shown to be in good agreement with the observations. Two other observations support this picture: an inverse correlation between the flux in the power-law spectral component and the fitted inner disk temperature, and a near-constant total photon flux, suggesting that the inner disk is not ejected when a lower temperature is observed.

  15. Destructive Interactions Between Mitigation Strategies and the Causes of Unexpected Failures in Natural Hazard Mitigation Systems

    NASA Astrophysics Data System (ADS)

    Day, S. J.; Fearnley, C. J.

    2013-12-01

    Large investments in the mitigation of natural hazards, using a variety of technology-based mitigation strategies, have proven to be surprisingly ineffective in some recent natural disasters. These failures reveal a need for a systematic classification of mitigation strategies; an understanding of the scientific uncertainties that affect the effectiveness of such strategies; and an understanding of how the different types of strategy within an overall mitigation system interact destructively to reduce the effectiveness of the overall mitigation system. We classify mitigation strategies into permanent, responsive and anticipatory. Permanent mitigation strategies such as flood and tsunami defenses or land use restrictions, are both costly and 'brittle': when they malfunction they can increase mortality. Such strategies critically depend on the accuracy of the estimates of expected hazard intensity in the hazard assessments that underpin their design. Responsive mitigation strategies such as tsunami and lahar warning systems rely on capacities to detect and quantify the hazard source events and to transmit warnings fast enough to enable at risk populations to decide and act effectively. Self-warning and voluntary evacuation is also usually a responsive mitigation strategy. Uncertainty in the nature and magnitude of the detected hazard source event is often the key scientific obstacle to responsive mitigation; public understanding of both the hazard and the warnings, to enable decision making, can also be a critical obstacle. Anticipatory mitigation strategies use interpretation of precursors to hazard source events and are used widely in mitigation of volcanic hazards. Their critical limitations are due to uncertainties in time, space and magnitude relationships between precursors and hazard events. Examples of destructive interaction between different mitigation strategies are provided by the Tohoku 2011 earthquake and tsunami; recent earthquakes that have impacted

  16. The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses.

    PubMed

    Caballero, Armando; Tenesa, Albert; Keightley, Peter D

    2015-12-01

    We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03-0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem.

  17. Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Copy number variations (CNV) are well known genomic variants, which often complicate structural and functional genomics studies. Here, we integrated the CNV region (CNVR) result detected from 1,682 Nellore cattle with the equivalent result derived from the Bovine HapMap samples. Through comparing CN...

  18. Economics of Scholarly Publishing: Exploring the Causes of Subscription Price Variations of Scholarly Journals in Business Subject-Specific Areas

    ERIC Educational Resources Information Center

    Liu, Lewis G.

    2011-01-01

    This empirical research investigates subscription price variations of scholarly journals in five business subject-specific areas using the semilogarithmic regression model. It has two main purposes. The first is to address the unsettled debate over whether or not and to what extent commercial publishers reap monopoly profits by overcharging…

  19. Variations in the Nature of Metal Adsorption on Ultrathin Al(2)O(3) Films

    SciTech Connect

    Bogicevic, A.; Jennison, D.R.

    1998-11-24

    First-principles density-functional calculations are used to study metal adsorption (Li, K, Y, Nb, Ru, Pd, Pt, Cu, Ag, Au, and Al at 1/3-4 monolayer coverages) atop 5 ~ A1203 films on Al(Ill). The oxide-metal bond is ionic at Iow coverages but, with interesting exceptions, caused by polari@i ,~-cE!vED at high coverages where the overlayer is metallic. Binding trends are explained in terms of s'imp e concepts. Increasing overlayer thickness can cause the adsorbate-oxide interface structure to than . %lEc o ~ 1998 and while some metals wet, most do not.

  20. Determining the Cause of a Header Failure in a Natural Gas Production Facility

    SciTech Connect

    Matthes, S.A.; Covino, B.S., Jr.; Bullard, S.J.; Ziomek-Moroz, M.; Holcomb, G.R.

    2007-03-01

    An investigation was made into the premature failure of a gas-header at the Rocky Mountain Oilfield Testing Center (RMOTC) natural gas production facility. A wide variety of possible failure mechanisms were considered: design of the header, deviation from normal pipe alloy composition, physical orientation of the header, gas composition and flow rate, type of corrosion, protectiveness of the interior oxide film, time of wetness, and erosion-corrosion. The failed header was examined using metallographic techniques, scanning electron microscopy, and microanalysis. A comparison of the failure site and an analogous site that had not failed, but exhibited similar metal thinning was also performed. From these studies it was concluded that failure resulted from erosion-corrosion, and that design elements of the header and orientation with respect to gas flow contributed to the mass loss at the failure point.