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Sample records for causing natural variation

  1. Genetic Interactions Between Transcription Factors Cause Natural Variation in Yeast

    PubMed Central

    Gerke, Justin; Lorenz, Kim; Cohen, Barak

    2016-01-01

    Our understanding of the genetic basis of phenotypic diversity is limited by the paucity of examples in which multiple, interacting loci have been identified. We show that natural variation in the efficiency of sporulation, the program in yeast that initiates the sexual phase of the life cycle, between oak tree and vineyard strains is due to allelic variation between four nucleotide changes in three transcription factors: IME1, RME1, and RSF1. Furthermore, we identified that selection has shaped quantitative variation in yeast sporulation between strains. These results illustrate how genetic interactions between transcription factors are a major source of phenotypic diversity within species. PMID:19164747

  2. 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

  3. 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

  4. 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…

  5. A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. III. Variations in Genetic Structure and Their Causes between Drosophila melanogaster and Its Sibling Species Drosophila simulans

    PubMed Central

    Choudhary, M.; Singh, Rama S.

    1987-01-01

    The natural populations of Drosophila melanogaster and Drosophila simulans were compared for their genetic structure. A total of 114 gene-protein loci were studied in four mainland (from Europe and Africa) and an island (Seychelle) populations of D. simulans and the results were compared with those obtained on the same set of homologous loci in fifteen worldwide populations of D. melanogaster. The main results are as follows: (1) D. melanogaster shows a significantly higher proportion of loci polymorphic than D. simulans (52% vs. 39%, P<0.05), (2) both species have similar mean heterozygosity and mean number of alleles per locus, (3) the two species share some highly polymorphic loci but they do not share loci that show high geographic differentiation, and (4) D. simulans shows significantly less geographic differentiation than D. melanogaster. The differences in genetic differentiation between the two species are limited to loci located on the X and second chromosomes only; loci on the third chromosome show similar level of geographic differentiation in both species. These two species have previously been shown to differ in their pattern of variation for chromosomal polymorphisms, quantitative and physiological characters, two-dimensional electrophoretic (2DE) proteins, middle repetitive DNA and mitochondrial DNA. Variation in niche-widths and/or genetic "strategies" of adaptation appear to be the main causes of differences in the genetic structure of these two species. PMID:17246411

  6. Causes of 142Nd Variation in Earth

    NASA Astrophysics Data System (ADS)

    Boyet, M.; Bouvier, A.; Gannoun, A.; Carlson, R.

    2015-12-01

    Variability of the 142Nd/144Nd ratio can reflect Sm/Nd fractionation during the lifetime of 146Sm, i.e. the first 500 Ma of Solar System history1 and nucleosynthetic heterogeneity inherited from the solar nebula. Deciphering the message carried by 142Nd variability requires a detailed examination of the data for Earth and meteorites. The elevated 142Nd/144Nd in terrestrial samples relative to average chondrites suggests that all terrestrial rocks sampled by volcanism over the Earth's history come from a geochemical reservoir characterized by a superchondritic Sm/Nd ratio. The chemical compliment to this reservoir, however, has never been seen, so it either was lost during Earth's accretion2,3, or is preserved in a deep hidden reservoir 1,4. These models are based on a comparison of Earth rocks and O-chondrites because they do not show any variation in stable Sm and Nd isotopic composition compared to Earth6-8. The first analyzed E-chondrites with terrestrial 142Nd/144Nd showed 144Sm excesses that reflect an excess p-process contribution. Although 142Nd is mainly produced by s-process, there is a direct p-process component estimated to be lower than 4 %. We will present new Sm and Nd isotopic data on meteoritic materials. CAIs show deficits in both r- and p-process isotopes that would lead to elevated 142Nd, yet the bulk C-chondrites in which they are contained show excesses in r-process isotopes and hence 142Nd/144Nd lower than terrestrial. The new E-chondrites data do not confirm the 142Nd-144Sm correlation observed in bulk chondrites In light of these results and using 146Sm-142Nd isochrons for constraining the bulk 142Nd/144Nd ratio of planetary bodies, we will discuss the 142Nd signature of terrestrial samples (from Hadean to present). 1Boyet & Carlson, Science 2005; 2O'Neill & Palme, Phil. Trans. R. Soc 2008; 3Caro et al. Nature 2008; 4Andreasen et al. EPSL 2008; 6Andreasen & Sharma, Science 2006; 7Carlson et al., Science 2007; 8Gannoun et al. PNAS 2011.

  7. 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. PMID:26927960

  8. DNA methylation contributes to natural human variation

    PubMed Central

    Heyn, Holger; Moran, Sebastian; Hernando-Herraez, Irene; Sayols, Sergi; Gomez, Antonio; Sandoval, Juan; Monk, Dave; Hata, Kenichiro; Marques-Bonet, Tomas; Wang, Liewei; Esteller, Manel

    2013-01-01

    DNA methylation patterns are important for establishing cell, tissue, and organism phenotypes, but little is known about their contribution to natural human variation. To determine their contribution to variability, we have generated genome-scale DNA methylation profiles of three human populations (Caucasian-American, African-American, and Han Chinese-American) and examined the differentially methylated CpG sites. The distinctly methylated genes identified suggest an influence of DNA methylation on phenotype differences, such as susceptibility to certain diseases and pathogens, and response to drugs and environmental agents. DNA methylation differences can be partially traced back to genetic variation, suggesting that differentially methylated CpG sites serve as evolutionarily established mediators between the genetic code and phenotypic variability. Notably, one-third of the DNA methylation differences were not associated with any genetic variation, suggesting that variation in population-specific sites takes place at the genetic and epigenetic levels, highlighting the contribution of epigenetic modification to natural human variation. PMID:23908385

  9. 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

  10. Fetal Circulatory Variation in an Acute Incident Causing Bradycardia

    PubMed Central

    Olgan, Safak; Sakinci, Mehmet; Dogan, Nasuh Utku; Cagliyan, Erkan; Altunyurt, Sabahattin

    2014-01-01

    Umbilical artery\\vein, middle cerebral artery, and ductus venosus Doppler velocimetry were performed at 33 weeks of gestation in the settings of an intrauterine growth restricted fetus during a heart rate deceleration. Interestingly, we recorded a sudden onset redistribution of fetal blood flow with fetal bradycardia. Spontaneous normalization of waveforms was observed once fetal heart rate returned to normal. Our case provides evidence to circulatory variation of a human fetus resulting from an acute incident causing bradycardia. PMID:25580322

  11. 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

  12. 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.

  13. 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.

  14. Numerical studies of HF Doppler variations caused by ionospheric disturbances

    NASA Astrophysics Data System (ADS)

    Takefu, M.; Hiroshige, N.

    HF Doppler variations caused by ionospheric disturbances are studied using an ionosphere model containing sinusoidal traveling electron density fluctuations. The present study uses a more realistic ionosphere model and a more accurate numerical method than previous works using corrugated specular reflector models. The study gives a clue to estimate the TID-associated fluctuations of ionospheric electron density by means of HF Doppler measurements. It is shown that some kinds of characteristic HF Doppler traces result depending on the wavelength of the disturbance and its traveling direction. Numerical results suggest that more or less 5 percent of the background electron density can explain most of the quasi-periodic variations on the observed HF Doppler records.

  15. 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

  16. Contextual dissonance effects: nature and causes.

    PubMed

    Rosenberg, M

    1977-08-01

    Contextual consonance or dissonance refers to the concordance of, or the discrepancy between, the individual's social characteristics and those of the population by which he is surrounded. Although a number of advantageous consequences have been shown to issue from contextual dissonance, self-esteem is not one of them. This article seeks to account for the deleterious effect of contextual dissonance on self-esteem by examining the nature of dissonant communications environments, dissonant cultural environments, and dissonant comparison reference groups. PMID:887692

  17. 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.

  18. Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

    PubMed Central

    Joseph, Bindu; Corwin, Jason A; Li, Baohua; Atwell, Suzi; Kliebenstein, Daniel J

    2013-01-01

    Understanding genome to phenotype linkages has been greatly enabled by genomic sequencing. However, most genome analysis is typically confined to the nuclear genome. We conducted a metabolomic QTL analysis on a reciprocal RIL population structured to examine how variation in the organelle genomes affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation was a central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation in metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural variation. DOI: http://dx.doi.org/10.7554/eLife.00776.001 PMID:24150750

  19. The control of natural variation in cytosine methylation in Arabidopsis.

    PubMed Central

    Riddle, Nicole C; Richards, Eric J

    2002-01-01

    We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA gene repeats at the two nucleolus organizer regions (NOR). Our findings indicate that natural variation in NOR methylation results from a combination of genetic and epigenetic mechanisms. Genetic variation in rRNA gene copy number and trans-acting modifier loci account for some of the natural variation in NOR methylation. Our results also suggest that divergence and inheritance of epigenetic information, independent of changes in underlying nucleotide sequence, may play an important role in maintaining natural variation in cytosine methylation. PMID:12242246

  20. Investigating causes of regional variations in atmospheric carbon dioxide concentrations

    NASA Astrophysics Data System (ADS)

    Corbin, Katherine D.

    focused on the impacts of land-cover heterogeneity and the effects of agricultural production on regional variations of atmospheric CO2 concentrations. Including sub-grid scale land cover heterogeneity improved simulated atmospheric CO2 concentrations by ˜ 1 ppm. Implementing a crop-phenology model that explicitly simulated corn and soybeans into a coupled ecosystem-atmosphere model dramatically improved CO2 fluxes and concentrations over the mid-continent, with reductions in CO2 concentration root mean square errors of nearly 50% (over 10 ppm at some locations). Both the model and observations showed concentrations as low as 340 ppm over central Iowa, and a regional gradient of over 30 ppm in ˜ 200 km occurred due to a combination of fluxes and meteorology. Since corn and soybeans have such a significant impact on both carbon fluxes and atmospheric concentrations, it is essential to model these crops accurately. In addition to biological surface fluxes, surface emissions due to fossil fuel combustion also cause variability in regional atmospheric CO2 concentrations. Using high-resolution fossil fuel emissions caused differences of over 10 ppm near the surface; and including temporal variability in the emissions impacted regional CO2 concentrations on monthly timescales, causing seasonal differences of more than 20 ppm in some locations. Using coarse spatial distributions and unaccounting for temporal variability in fossil fuel emissions created biases in the atmospheric CO2 concentrations and thus may cause significant errors in source and sink estimates from atmospheric inversions.

  1. 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

  2. [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

  3. 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.

  4. 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.

  5. Seasonal and clonal variations in technological and thermal properties of raw Hevea natural rubber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was undertaken over a ten-month period, under the environmental conditions within the state of Mato Grosso, Brazil, to evaluate the causes of variation in technological and thermal properties of raw natural rubber from different clones of Hevea brasiliensis (GT 1, PR 255, FX 3864 and RRIM...

  6. 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.

  7. 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...

  8. 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

  9. 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

  10. 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

  11. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    DOE PAGESBeta

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

    2016-06-08

    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 basedmore » 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. BWAmem 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.« less

  12. Community study of the causes of "natural" sudden death.

    PubMed Central

    Thomas, A. C.; Knapman, P. A.; Krikler, D. M.; Davies, M. J.

    1988-01-01

    Three hundred and fifty cases of "natural" sudden death within six hours of onset of symptoms in people ranging in age from 18 to 69 years in Wandsworth were studied using a detailed necropsy protocol to determine the cause of death. Sudden death occurred in 28 (8%) Asians and blacks, but because of the small number they were excluded from the study, leaving 322 cases. Ischaemic heart disease accounted for 189 (59%) of the 322 sudden deaths (155 (65%) men; 34 (41%) women) and no proportional increase in instantaneous compared with non-instantaneous sudden death was found. Non-ischaemic cardiac disease was the cause of sudden death in 24 cases (7.5%). Non-cardiac disease included pulmonary emboli, aortic aneurysms, and intracerebral haemorrhage and caused 89 (27.6%) deaths. Alcohol was the cause of nine deaths (2.8%) and in 11 (3.4%) cases (six men and five women) no cause of death was found. This study shows that although ischaemic heart disease is the single largest cause of sudden natural death there are other major causes. Images p1456-a PMID:3147014

  13. Independent FLC Mutations as Causes of Flowering-Time Variation in Arabidopsis thaliana and Capsella rubella

    PubMed Central

    Guo, Ya-Long; Todesco, Marco; Hagmann, Jörg; Das, Sandip; Weigel, Detlef

    2012-01-01

    Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering-time variation in A. thaliana. Here we document flowering time under different conditions in 20 C. rubella accessions from across the species’ range. Similar to A. thaliana, vernalization, long photoperiods and elevated ambient temperature generally promote flowering. In this collection of C. rubella accessions, we did not find any obvious loss-of-function FRI alleles. Using mapping-by-sequencing with two strains that have contrasting flowering behaviors, we identified a splice-site mutation in FLC as the likely cause of early flowering in accession 1408. However, other similarly early C. rubella accessions did not share this mutation. We conclude that the genetic basis of flowering-time variation in C. rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C. grandiflora a few tens of thousands of years ago. PMID:22865739

  14. What causes intraspecific variation in resting metabolic rate and what are its ecological consequences?

    PubMed Central

    Burton, T.; Killen, S. S.; Armstrong, J. D.; Metcalfe, N. B.

    2011-01-01

    Individual differences in the energy cost of self-maintenance (resting metabolic rate, RMR) are substantial and the focus of an emerging research area. These differences may influence fitness because self-maintenance is considered as a life-history component along with growth and reproduction. In this review, we ask why do some individuals have two to three times the ‘maintenance costs’ of conspecifics, and what are the fitness consequences? Using evidence from a range of species, we demonstrate that diverse factors, such as genotypes, maternal effects, early developmental conditions and personality differences contribute to variation in individual RMR. We review evidence that RMR is linked with fitness, showing correlations with traits such as growth and survival. However, these relationships are modulated by environmental conditions (e.g. food supply), suggesting that the fitness consequences of a given RMR may be context-dependent. Then, using empirical examples, we discuss broad-scale reasons why variation in RMR might persist in natural populations, including the role of both spatial and temporal variation in selection pressures and trans-generational effects. To conclude, we discuss experimental approaches that will enable more rigorous examination of the causes and consequences of individual variation in this key physiological trait. PMID:21957133

  15. 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.

  16. The Variation in Teachers' Grading Practices: Causes and Consequences.

    ERIC Educational Resources Information Center

    Bonesronning, Hans

    1999-01-01

    Discusses causes and consequences of teachers' grading practices, which vary greatly among Norwegian uppersecondary schools. Introduces an alternative to easy grading, in which rent-seeking students allocate time to affect the teacher's grading. Shows that teacher's grading is systematically associated with teacher characteristics. Hard grading…

  17. 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

  18. Human and nature-caused hazards: the affect heuristic causes biased decisions.

    PubMed

    Siegrist, Michael; Sütterlin, Bernadette

    2014-08-01

    People are more concerned about the negative consequences of human hazards compared with natural hazards. Results of four experiments show that the same negative outcome (e.g., number of birds killed by an oil spill) was more negatively evaluated when caused by humans than when caused by nature. Results further show that when identical risk information was provided, participants evaluated nuclear power more negatively compared with solar power. The affect associated with the hazard per se influenced the interpretation of the new information. Furthermore, the affect experienced in the situation fully mediated the evaluation of the negative outcomes of a hazard. People's reliance on the affect heuristic is a challenge for acceptance of cost-benefit analyses because equally negative outcomes are differently evaluated depending on the cause. Symbolically significant information and the affect evoked by this information may result in biased and riskier decisions. PMID:24576178

  19. 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.

  20. 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

  1. Heterochrony underpins natural variation in Cardamine hirsuta leaf form.

    PubMed

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

    2015-08-18

    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

  2. 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

  3. Spatial variation of sediment deposition in the Hudson River - a detailed inventory and potential causes (Invited)

    NASA Astrophysics Data System (ADS)

    Nitsche, F. O.; Kenna, T. C.

    2010-12-01

    Sediment deposition in urban estuaries is controlled by the interaction of human modifications and natural factors that include tides, fresh water inputs, bed morphology, sediment supply, and hydrodynamics. A key element of managing these estuaries is detailed understanding of sediment deposition and its driving processes. Using a combination of geophysical and geochemical analysis we establish a detailed inventory of 20 century deposition for most of the mud-dominated sections of the Hudson River. These data show variations between different segments of the Hudson River as well as strong local variations within each section, with depositional settings ranging from erosional to those accumulating at ~10 mm/year. Our work indicates that 170,000 - 250,000 metric tons of sediment are deposited annually in the areas studied, which is a significant portion of the estimated total annual sediment load of ~700,000 - 800,000 metric tons. This also suggests that some of the accumulated sediments are re-mobilized, e.g. during major storms. The observed patterns of deposition/erosion are primarily caused by natural conditions, but, in some parts, they are strongly influenced by human modifications of the estuary, such as dredging. In addition to improving our understanding of the sediment dynamic of the Hudson River, the observed distribution of sediment deposition is also an indicator for the occurrence of contaminants including heavy metals and PCB’s and thus a valuable tool for management decisions.

  4. The causes and consequences of seasonal variation in COPD exacerbations.

    PubMed

    Donaldson, Gavin C; Wedzicha, Jadwiga A

    2014-01-01

    The time of year when patients experience exacerbations of chronic obstructive pulmonary disease is a much-overlooked feature of the disease. The higher incidence of exacerbations in winter has important consequences for patients in terms of increased morbidity and mortality. The seasonality also imposes a considerable burden on already-overloaded health care services, with both primary care consultations and hospital admissions increasing in number. The seasonality of exacerbations varies with latitude, and is greater in more temperate climates, where there may be less protection from outdoor and indoor cold exposure. The precise causes of the seasonality are unknown, but thought to be partly due to the increased prevalence of respiratory viral infections circulating in cold, damp conditions. Increased susceptibility to viral infection may also be a mechanism mediated through increased airway inflammation or possibly reduced vitamin D levels. The seasonality of exacerbations informs us about the triggers of exacerbations and suggests possible strategies to reduce their number. PMID:25336941

  5. The causes and consequences of seasonal variation in COPD exacerbations

    PubMed Central

    Donaldson, Gavin C; Wedzicha, Jadwiga A

    2014-01-01

    The time of year when patients experience exacerbations of chronic obstructive pulmonary disease is a much-overlooked feature of the disease. The higher incidence of exacerbations in winter has important consequences for patients in terms of increased morbidity and mortality. The seasonality also imposes a considerable burden on already-overloaded health care services, with both primary care consultations and hospital admissions increasing in number. The seasonality of exacerbations varies with latitude, and is greater in more temperate climates, where there may be less protection from outdoor and indoor cold exposure. The precise causes of the seasonality are unknown, but thought to be partly due to the increased prevalence of respiratory viral infections circulating in cold, damp conditions. Increased susceptibility to viral infection may also be a mechanism mediated through increased airway inflammation or possibly reduced vitamin D levels. The seasonality of exacerbations informs us about the triggers of exacerbations and suggests possible strategies to reduce their number. PMID:25336941

  6. 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

  7. 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

  8. 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.

  9. Scheme for precise correction of orbit variation caused by dipole error field of insertion device

    NASA Astrophysics Data System (ADS)

    Nakatani, T.; Agui, A.; Aoyagi, H.; Matsushita, T.; Takao, M.; Takeuchi, M.; Yoshigoe, A.; Tanaka, H.

    2005-05-01

    We developed a scheme for precisely correcting the orbit variation caused by a dipole error field of an insertion device (ID) in a storage ring and investigated its performance. The key point for achieving the precise correction is to extract the variation of the beam orbit caused by the change of the ID error field from the observed variation. We periodically change parameters such as the gap and phase of the specified ID with a mirror-symmetric pattern over the measurement period to modulate the variation. The orbit variation is measured using conventional wide-frequency-band detectors and then the induced variation is extracted precisely through averaging and filtering procedures. Furthermore, the mirror-symmetric pattern enables us to independently extract the orbit variations caused by a static error field and by a dynamic one, e.g., an error field induced by the dynamical change of the ID gap or phase parameter. We built a time synchronization measurement system with a sampling rate of 100Hz and applied the scheme to the correction of the orbit variation caused by the error field of an APPLE-2-type undulator installed in the SPring-8 storage ring. The result shows that the developed scheme markedly improves the correction performance and suppresses the orbit variation caused by the ID error field down to the order of submicron. This scheme is applicable not only to the correction of the orbit variation caused by a special ID, the gap or phase of which is periodically changed during an experiment, but also to the correction of the orbit variation caused by a conventional ID which is used with a fixed gap and phase.

  10. Natural Selection VS. Random Drift: Evidence from Temporal Variation in Allele Frequencies in Nature

    PubMed Central

    Mueller, Laurence D.; Barr, Lorraine G.; Ayala, Francisco J.

    1985-01-01

    We have obtained monthly samples of two species, Drosophila pseudoobscura and Drosophila persimilis, in a natural population from Napa County, California. In each species, about 300 genes have been assayed by electrophoresis for each of seven enzyme loci in each monthly sample from March 1972 to June 1975. Using statistical methods developed for the purpose, we have examined whether the allele frequencies at different loci vary in a correlated fashion. The methods used do not detect natural selection when it is deterministic (e.g., overdominance or directional selection), but only when alleles at different loci vary simultaneously in response to the same environmental variations. Moreover, only relatively large fitness differences (of the order of 15%) are detectable. We have found strong evidence of correlated allele frequency variation in 13–20% of the cases examined. We interpret this as evidence that natural selection plays a major role in the evolution of protein polymorphisms in nature. PMID:4054608

  11. 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.

  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. 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. PMID:12374055

  14. 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

  15. 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

  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. 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. PMID:25568456

  18. Transformation of Natural Genetic Variation into Haemophilus Influenzae Genomes

    PubMed Central

    Mell, Joshua Chang; Shumilina, Svetlana; Hall, Ira M.; Redfield, Rosemary J.

    2011-01-01

    Many bacteria are able to efficiently bind and take up double-stranded DNA fragments, and the resulting natural transformation shapes bacterial genomes, transmits antibiotic resistance, and allows escape from immune surveillance. The genomes of many competent pathogens show evidence of extensive historical recombination between lineages, but the actual recombination events have not been well characterized. We used DNA from a clinical isolate of Haemophilus influenzae to transform competent cells of a laboratory strain. To identify which of the ∼40,000 polymorphic differences had recombined into the genomes of four transformed clones, their genomes and their donor and recipient parents were deep sequenced to high coverage. Each clone was found to contain ∼1000 donor polymorphisms in 3–6 contiguous runs (8.1±4.5 kb in length) that collectively comprised ∼1–3% of each transformed chromosome. Seven donor-specific insertions and deletions were also acquired as parts of larger donor segments, but the presence of other structural variation flanking 12 of 32 recombination breakpoints suggested that these often disrupt the progress of recombination events. This is the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, connecting experimental studies of transformation with the high levels of natural genetic variation found in isolates of the same species. PMID:21829353

  19. 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." PMID:10160463

  20. 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

  1. 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.

  2. 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. PMID:22773086

  3. 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

  4. Genomic Variation in Natural Populations of Drosophila melanogaster

    PubMed Central

    Langley, Charles H.; Stevens, Kristian; Cardeno, Charis; Lee, Yuh Chwen G.; Schrider, Daniel R.; Pool, John E.; Langley, Sasha A.; Suarez, Charlyn; Corbett-Detig, Russell B.; Kolaczkowski, Bryan; Fang, Shu; Nista, Phillip M.; Holloway, Alisha K.; Kern, Andrew D.; Dewey, Colin N.; Song, Yun S.; Hahn, Matthew W.; Begun, David J.

    2012-01-01

    This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere- and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 5′- and 3′-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species. PMID:22673804

  5. Dynamics and distribution of natural and human-caused hypoxia

    NASA Astrophysics Data System (ADS)

    Rabalais, N. N.; Díaz, R. J.; Levin, L. A.; Turner, R. E.; Gilbert, D.; Zhang, J.

    2010-02-01

    Water masses can become undersaturated with oxygen when natural processes alone or in combination with anthropogenic processes produce enough organic carbon that is aerobically decomposed faster than the rate of oxygen re-aeration. The dominant natural processes usually involved are photosynthetic carbon production and microbial respiration. The re-supply rate is indirectly related to its isolation from the surface layer. Hypoxic water masses (<2 mg L-1, or approximately 30% saturation) can form, therefore, under "natural" conditions, and are more likely to occur in marine systems when the water residence time is extended, water exchange and ventilation are minimal, stratification occurs, and where carbon production and export to the bottom layer are relatively high. Hypoxia has occurred through geological time and naturally occurs in oxygen minimum zones, deep basins, eastern boundary upwelling systems, and fjords. Hypoxia development and continuation in many areas of the world's coastal ocean is accelerated by human activities, especially where nutrient loading increased in the Anthropocene. This higher loading set in motion a cascading set of events related to eutrophication. The formation of hypoxic areas has been exacerbated by any combination of interactions that increase primary production and accumulation of organic carbon leading to increased respiratory demand for oxygen below a seasonal or permanent pycnocline. Nutrient loading is likely to increase further as population growth and resource intensification rises, especially with increased dependency on crops using fertilizers, burning of fossil fuels, urbanization, and waste water generation. It is likely that the occurrence and persistence of hypoxia will be even more widespread and have more impacts than presently observed. Global climate change will further complicate the causative factors in both natural and human-caused hypoxia. The likelihood of strengthened stratification alone, from increased

  6. 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.

  7. 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

  8. 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

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

    PubMed

    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

  10. 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

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

    PubMed Central

    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

  12. Extensive Cotransformation of Natural Variation into Chromosomes of Naturally Competent Haemophilus influenzae

    PubMed Central

    Mell, Joshua Chang; Lee, Jae Yun; Firme, Marlo; Sinha, Sunita; Redfield, Rosemary J.

    2014-01-01

    Naturally competent bacterial species actively take up environmental DNA and can incorporate it into their chromosomes by homologous recombination. This can bring genetic variation from environmental DNA to recipient chromosomes, often in multiple long “donor” segments. Here, we report the results of genome sequencing 96 colonies of a laboratory Haemophilus influenzae strain, which had been experimentally transformed by DNA from a diverged clinical isolate. Donor segments averaged 6.9 kb (spanning several genes) and were clustered into recombination tracts of ~19.5 kb. Individual colonies had replaced from 0.1 to 3.2% of their chromosomes, and ~1/3 of all donor-specific single-nucleotide variants were present in at least one recombinant. We found that nucleotide divergence did not obviously limit the locations of recombination tracts, although there were small but significant reductions in divergence at recombination breakpoints. Although indels occasionally transformed as parts of longer recombination tracts, they were common at breakpoints, suggesting that indels typically block progression of strand exchange. Some colonies had recombination tracts in which variant positions contained mixtures of both donor and recipient alleles. These tracts were clustered around the origin of replication and were interpreted as the result of heteroduplex segregation in the original transformed cell. Finally, a pilot experiment demonstrated the utility of natural transformation for genetically dissecting natural phenotypic variation. We discuss our results in the context of the potential to merge experimental and population genetic approaches, giving a more holistic understanding of bacterial gene transfer. PMID:24569039

  13. Extensive cotransformation of natural variation into chromosomes of naturally competent Haemophilus influenzae.

    PubMed

    Mell, Joshua Chang; Lee, Jae Yun; Firme, Marlo; Sinha, Sunita; Redfield, Rosemary J

    2014-04-01

    Naturally competent bacterial species actively take up environmental DNA and can incorporate it into their chromosomes by homologous recombination. This can bring genetic variation from environmental DNA to recipient chromosomes, often in multiple long "donor" segments. Here, we report the results of genome sequencing 96 colonies of a laboratory Haemophilus influenzae strain, which had been experimentally transformed by DNA from a diverged clinical isolate. Donor segments averaged 6.9 kb (spanning several genes) and were clustered into recombination tracts of ~19.5 kb. Individual colonies had replaced from 0.1 to 3.2% of their chromosomes, and ~1/3 of all donor-specific single-nucleotide variants were present in at least one recombinant. We found that nucleotide divergence did not obviously limit the locations of recombination tracts, although there were small but significant reductions in divergence at recombination breakpoints. Although indels occasionally transformed as parts of longer recombination tracts, they were common at breakpoints, suggesting that indels typically block progression of strand exchange. Some colonies had recombination tracts in which variant positions contained mixtures of both donor and recipient alleles. These tracts were clustered around the origin of replication and were interpreted as the result of heteroduplex segregation in the original transformed cell. Finally, a pilot experiment demonstrated the utility of natural transformation for genetically dissecting natural phenotypic variation. We discuss our results in the context of the potential to merge experimental and population genetic approaches, giving a more holistic understanding of bacterial gene transfer. PMID:24569039

  14. Length of human pregnancy and contributors to its natural variation

    PubMed Central

    Jukic, A.M.; Baird, D.D.; Weinberg, C.R.; McConnaughey, D.R.; Wilcox, A.J.

    2013-01-01

    STUDY QUESTION How variable is the length of human pregnancy, and are early hormonal events related to gestational length? SUMMARY ANSWER Among natural conceptions where the date of conception (ovulation) is known, the variation in pregnancy length spanned 37 days, even after excluding women with complications or preterm births. WHAT IS KNOWN ALREADY Previous studies of length of gestation have either estimated gestational age by last menstrual period (LMP) or ultrasound (both imperfect measures) or included pregnancies conceived through assisted reproductive technology. STUDY DESIGN, SIZE, DURATION The Early Pregnancy Study was a prospective cohort study (1982–85) that followed 130 singleton pregnancies from unassisted conception to birth, with detailed hormonal measurements through the conception cycle; 125 of these pregnancies were included in this analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS We calculated the length of gestation beginning at conception (ovulation) in 125 naturally conceived, singleton live births. Ovulation, implantation and corpus luteum (CL) rescue pattern were identified with urinary hormone measurements. We accounted for events that artificially shorten the natural length of gestation (Cesarean delivery or labor induction, i.e. ‘censoring’) using Kaplan–Meier curves and proportional hazards models. We examined hormonal and other factors in relation to length of gestation. We did not have ultrasound information to compare with our gold standard measure. MAIN RESULTS AND THE ROLE OF CHANCE The median time from ovulation to birth was 268 days (38 weeks, 2 days). Even after excluding six preterm births, the gestational length range was 37 days. The coefficient of variation was higher when measured by LMP (4.9%) than by ovulation (3.7%), reflecting the variability of time of ovulation. Conceptions that took longer to implant also took longer from implantation to delivery (P = 0.02). CL rescue pattern (reflecting ovarian response to

  15. 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...

  16. 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

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

    PubMed Central

    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

  18. 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

  19. The Natural Variation of Seed Weight Is Mainly Controlled by Maternal Genotype in Rapeseed (Brassica napus L.)

    PubMed Central

    Shi, Jiaqin; Wang, Xinfa; Liu, Guihua; Wang, Hanzhong

    2015-01-01

    Seed weight is a very important and complex trait in rapeseed (Brassica napus L.). The seed weight of rapeseed shows great variation in its natural germplasm resources; however, the morphological, cytological and genetic causes of this variation have remained unclear. In the present study, nine highly pure inbred rapeseed lines with large seed weight variation and different genetic backgrounds were selected for morphological, cytological and genetic studies on seed weight. The results showed the following: (1) Seed weight showed an extremely significant correlation and coordinated variation with seed size (including seed diameter, seed surface area and seed volume), but it showed no significant correlation with bulk density, which suggests that seed weight is determined by size rather than bulk density. (2) Seed weight showed a higher correlation with the cell numbers of seed coats and cotyledons than the cell sizes of seed coats and cotyledons, which suggests that cell number is more tightly correlated with final seed weight. (3) Seed weight was mainly controlled by the maternal genotype, with little or no xenia and cytoplasmic effects. This is the first report on the morphological and cytological causes of seed weight natural variation in rapeseed. We concluded that the natural variation of seed weight is mainly controlled by maternal genotype. This finding lays a foundation for genetic and breeding studies of seed weight in rapeseed and opens a new field of research on the regulation of seed traits in plants. PMID:25915862

  20. Historical variation of structural novelty in a natural product library.

    PubMed

    Kong, De-Xin; Guo, Ming-Yue; Xiao, Zhi-Hong; Chen, Ling-Ling; Zhang, Hong-Yu

    2011-11-01

    To evaluate the potential of natural products as novel structure suppliers, a historical analysis was performed on the structural novelty of a natural product library, viz., the Chapman & Hall/CRC Dictionary of Natural Products. The results show that although the unexplored natural product universe is still ample, it is more and more difficult to find novel agents from nature, with the discovery probability of novel structures and scaffolds being lower than 50% in the near future, which mainly results from the intrinsic redundancy of natural products and, thus, is unlikely to be reversed merely through technical progresses. PMID:22083910

  1. 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

  2. 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

  3. Photocentric variability of quasars caused by variations in their inner structure: consequences for Gaia measurements

    NASA Astrophysics Data System (ADS)

    Popović, L. Č.; Jovanović, P.; Stalevski, M.; Anton, S.; Andrei, A. H.; Kovačević, J.; Baes, M.

    2012-02-01

    Context. We study the photocenter position variability caused by variations in the quasar inner structure. We consider the variability in the accretion disk emissivity and torus structure variability caused by the different illumination by the central source. We discuss the possible detection of these effects by Gaia. Observations of the photocenter variability in two AGNs, SDSS J121855+020002 and SDSS J162011+1724327 have been reported and discussed. Aims: For variations in the quasar inner structure, we explore how much this effect can affect the position determination and whether it can (or not) be detected with the Gaia mission. Methods: We use models of (a) a relativistic disk, including the perturbation that can increase the brightness of part of the disk, and consequently offset the photocenter position, and (b) a dusty torus that absorbs and re-emits the incoming radiation from the accretion disk (central continuum source). We estimate the value of the photocenter offset caused by these two effects. Results: We found that perturbations in the inner structure can cause a significant offset to the photocenter. This offset depends on the characteristics of both the perturbation and accretion disk and on the structure of the torus. In the case of the two considered QSOs, the observed photocenter offsets cannot be explained by variations in the accretion disk and other effects should be considered. We discuss the possibility of exploding stars very close to the AGN source, and also that there are two variable sources at the center of these two AGNs that may indicate a binary supermassive black hole system on a kpc (pc) scale. Conclusions: The Gaia mission seems to be very promising, not only for astrometry, but also for exploring the inner structure of AGNs. We conclude that variations in the quasar inner structure can affect the observed photocenter (by up to several mas). There is a chance to observe such an effect in the case of bright and low-redshift QSOs.

  4. 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

  5. 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…

  6. Solastalgia: living with the environmental damage caused by natural disasters.

    PubMed

    Warsini, Sri; Mills, Jane; Usher, Kim

    2014-02-01

    Forced separation from one's home may trigger emotional distress. People who remain in their homes may experience emotional distress due to living in a severely damaged environment. These people experience a type of 'homesickness' similar to nostalgia because the land around them no longer resembles the home they knew and loved. What they lack is solace or comfort from their home; they long for the home environment to be the way it was before. "Solastalgia" is a term created to describe feelings which arise in people when an environment changes so much that it negatively affects an individual's quality of life. Such changed environments may include drought-stricken areas and open-cut mines. The aim of this article is to describe how solastalgia, originally conceptualized as the result of man-made environmental change, can be similarly applied to the survivors of natural disasters. Using volcanic eruptions as a case example, the authors argue that people who experience a natural disaster are likely to suffer from solastalgia for a number of reasons, which may include the loss of housing, livestock and farmland, and the ongoing danger of living in a disaster-prone area. These losses and fears challenge people's established sense of place and identity and can lead to feelings of helplessness and depression. PMID:24438454

  7. [Advances in congenital vertebral malformation caused by genomic copy number variation].

    PubMed

    Liu, Zhenlei; Wu, Nan; Wu, Zhihong; Zuo, Yuzhi; Qiu, Guixing

    2016-04-01

    Congenital vertebral malformation (CVM) is a congenital vertebral structural deformity caused by abnormal somitogenesis during embryonic development, of which the reason lies in gene mutation or abnormal regulation of the genes that coordinate somitogenesis during embryonic period. ICVAS had proposed a new classification algorithm for CVM, which facilitated exploration for its genetic etiology. Genomic Copy Number Variation (CNV) is a kind of DNA mutation, which is important for human evolution, phenotype polymorphism and diseases. Series of advances have been made on genetic causes of CVM, especially on CVM caused by CNV. CNVs of chromosome 16p11.2, 10q24.31, 17p11.2, 20p11, 22q11.2 and a few other regions are associated with CVM, indicating that gene dosage may play important roles in the development of the spinal cord. PMID:27029207

  8. 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

  9. 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.

  10. 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

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

    PubMed

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

    2012-08-01

    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

  12. 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.

  13. Sampling variation caused by A/D cards due to external trigger.

    PubMed

    Jaw, F S; Lin, C W; Wang, C Y

    1995-11-01

    In electrophysiological recording, a microcomputer-based analog-to-digital (A/D) card is an indispensable instrument for signal acquisition and analysis. In our studies, evoked responses sampled by our A/D card showed variation among different cycles. If several cycles had been averaged, the resultant waveform would have a smaller peak amplitude and a longer duration. To explain this phenomenon, a simulated sampling model of compound action potential was proposed. Our experimental data agreed very well with the prediction of the simulated model. The long and varied delay time between the external trigger and the first sampling in each cycle by our A/D card might be the main cause of such variation. This problem could not be solved by any post-sampled programming. Hence, for those electrophysiological laboratories which sampled evoked responses, to buy a new A/D card might be the most straightforward solution to the problem. PMID:8750100

  14. Temporal Variation in Natural Methane Seep Rate Due to Tides, Coal Oil Point Area, California

    NASA Astrophysics Data System (ADS)

    Boles, J. R.; Clark, J. F.; Leifer, I.; Washburn, L.

    2001-12-01

    Two large steel tents (each 30m by 30m) open at the bottom to the sea floor, capture about 16,800 m{3{ day -1 (594 MCF) of primarily methane from a large natural hydrocarbon seep, occurring a kilometer offshore in 67m of water. Hourly monitoring for 9 months shows the tidal forcing causes the flow rate to vary by 4-7% around the mean. These results are the first quantitative documentation of the effect of tides on natural gas seepage in relatively deep water. High tide correlates with reduced flow, low tide correlates with increased flow. The correlation indicates that each meter increase of sea height results in a decrease of 10 to 15 m3 hr-1 or 1.5 to 2.2% of the hourly flow rate. The observed cahnges are best accounted for by a pore activation mechanism, whereby gas is released from small pores at low pressure but is inhibited at higher pressure. Pressure dependent gas solubility changes are a less likely cause of flow variation. Our study implies that sea level differences, on a tidal time scale, can significantly change the gas seepage rate from sediments. Lower sea level in the last hundred thousand years would presumably allow higher gas loss from the sediment, assuming sufficient gas present, due to reduced hudrostatic pressure at the sediment-sea interface. The magnitude of this long term change cannot be extrapolated from our tidal data.

  15. 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. PMID:26830772

  16. Spatial patterns of variation due to natural selection in humans

    PubMed Central

    Novembre, John; Di Rienzo, Anna

    2013-01-01

    Empowered by technology and sampling efforts designed to facilitate genome-wide association mapping, human geneticists are now studying the geography of genetic variation with unprecedented detail. With high genomic coverage and geographic resolution, these studies are identifying loci with spatial signatures of selection, such as extreme levels of differentiation and correlations with environmental variables. Collectively, patterns at these loci are beginning to provide novel insights into the process of human adaptation. Here we review the challenges of these studies and emerging results, including how human population structure has influenced the response to novel selective pressures. PMID:19823195

  17. 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....

  18. 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.

  19. 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

  20. The causes of stemflow variation in three semi-arid growing species of northeastern Mexico

    NASA Astrophysics Data System (ADS)

    Návar, José

    1993-05-01

    This study was conducted to determine the role of some plant parameters on stemflow generation. Stemflow measurements in individual shrubs of three semi-arid growing species ( Diospyrus texana, Acacia farnesiana and Prosopis laevigata) were carried out under natural and simulated rainfall conditions in northeastern Mexico. Stemflow coefficients for individual shrubs were developed. The analysis of variance showed a significant difference among the species for both natural and simulated rainfall conditions. The multiple linear models suggested that the number of branches and position on the canopy, instead of total projected branch area, controls stemflow. There were also suggestions that bark roughness, leaf and twig position may also explain some of the interspecific stemflow variation. This contribution was suggested by an introduced funnelling ratio.

  1. 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

  2. Hydrological mass variations caused by extreme weather conditions in Aisa measured by GRACE TVG data

    NASA Astrophysics Data System (ADS)

    Zhang, Z.; Chao, B. F.

    2012-12-01

    Droughts, excessive rain, snowstorm, and flooding caused by extreme weather conditions, which occurred frequently in China during the last several years, are primarily associated with hydrological mass variations. The dual-satellite mission of GRACE (Gravity Recovery And Climate Experiment) launched in 2002 has enabled measurement of the Earth's (tiny) time-variable gravity (TVG), providing new and precise information about mass transport on or in the Earth, especially short periodic hydrological mass variations. In this study, we examine terrestrial water storage (TWS) changes in Chongqing (great drought occurred in 2006 summer), south China (snowstorm occurred in early 2008) and Thailand (flood occurred in 2011) using GRACE RL05 (RL04) time-variable gravity (TVG) data and predications from major climate and land surface models, including the National Centers for Environmental Prediction (NCEP) and European Centre for Medium-Range Weather Forecasts (ECWMF) reanalysis climate model and the global land data assimilation system (GLDAS) and river gauge data. The results demonstrate the unique potential of GRACE measurements in monitoring large-scale hydrological mass variation events and in evaluating advanced climate and land surface models.

  3. 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

  4. 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

  5. Variation in natural head position and establishing corrected head position.

    PubMed

    Barbera, A L; Sampson, W J; Townsend, G C

    2014-06-01

    Corrected head position (CHP) has been simulated by using the Frankfurt horizontal (FH) for over 100 years but FH varies between individuals. Because CHP is biologically relevant for orthodontic diagnosis and treatment planning, orthognathic surgical planning, and art, this study examined relationships between head position and selected cephalometric planes. Natural head position cephalograms of Aboriginal Australians and two contemporary samples from private orthodontic practices were analysed. Each sample comprised 40 individuals (20 males and 20 females). The Aboriginal Australian sample comprised longitudinal data (T1 early adolescent, T2 late adolescent, and T3 adult), enabling examination of natural head position (NHP) reproducibility over a period of approximately 8 years. Results of reproducibility differences revealed an absolute mean=2.9°, range=-7.9° to 8.2°, and standard deviation=3.6°. Stable basicranial line (SBL), neutral horizontal axis (NHA), FH, palatal plane (P plane), and Krogman-Walker plane (KW plane) demonstrated near parallelism and their mean angulations from the true horizontal (HOR) ranged between -4.6° and 2.4°. While NHP is not consistently reproducible at the individual level, the combined use of multiple planes such as SBL, P plane, and KW plane enables a more consistent CHP to be achieved. PMID:24785580

  6. 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

  7. Natural variation and genetic covariance in adult hippocampal neurogenesis

    SciTech Connect

    Kempermann, Gerd; Chesler, Elissa J; Lu, Lu; Williams, Robert; Gage, Fred

    2006-01-01

    Adult hippocampal neurogenesis is highly variable and heritable among laboratory strains of mice. Adult neurogenesis is also remarkably plastic and can be modulated by environment and activity. Here, we provide a systematic quantitative analysis of adult hippocampal neurogenesis in two large genetic reference panels of recombinant inbred strains (BXD and AXB?BXA, n ? 52 strains). We combined data on variation in neurogenesis with a new transcriptome database to extract a set of 190 genes with expression patterns that are also highly variable and that covary with rates of (i) cell proliferation, (ii) cell survival, or the numbers of surviving (iii) new neurons, and (iv) astrocytes. Expression of a subset of these neurogenesis-associated transcripts was controlled in cis across the BXD set. These self-modulating genes are particularly interesting candidates to control neurogenesis. Among these were musashi (Msi1h) and prominin1?CD133 (Prom1), both of which are linked to stem-cell maintenance and division. Twelve neurogenesis-associated transcripts had significant cis-acting quantitative trait loci, and, of these, six had plausible biological association with adult neurogenesis (Prom1, Ssbp2, Kcnq2, Ndufs2, Camk4, and Kcnj9). Only one cis- cting candidate was linked to both neurogenesis and gliogenesis, Rapgef6, a downstream target of ras signaling. The use of genetic reference panels coupled with phenotyping and global transcriptome profiling thus allowed insight into the complexity of the genetic control of adult neurogenesis.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. Intraspecific variation influences natural settlement of eastern oysters.

    PubMed

    Smee, Delbert L; Overath, R Deborah; Johnson, Keith D; Sanchez, James A

    2013-11-01

    As populations decline, their intraspecific diversity also diminishes. Population decline may be exacerbated if a decrease in intraspecific diversity also reduces important ecological functions that maintain population numbers. Oyster reefs are severely overharvested, declining by ~85 % worldwide. We tested how increasing within-species diversity of eastern oysters (Crassostrea virginica) using transplants would affect recruitment of oyster larvae, a key function necessary to maintain future populations. If harvesting reduces population numbers, within-species diversity, and connectivity, then oysters may lose the ability to adapt to changing environmental conditions as well as incur lower levels of recruitment that may hasten their decline. Results from laboratory and field studies indicated that oyster larvae use chemical cues from adult oysters and not from associated fouling communities to select settlement sites. To test how increasing within-species diversity of oysters affected recruitment, we collected oysters from three distinct bay systems in Texas, USA, and compared natural settlement in treatments where all oysters were from a single bay to a mixture of all three bays. Significantly greater recruitment occurred in mixed treatments in 2010, 2011, and 2012 even though oyster recruitment varied by order of magnitude during this time. The net biodiversity effect was positive in all 3 years, indicating that increased recruitment in mixed treatments can be greater than the additive effect of the single bay treatments. Losing intraspecific diversity may reduce recruitment and lead to further declines in oyster populations, illustrating the need for understanding how intraspecific diversity influences ecological functions. PMID:23543216

  13. The dynamic nature of alignment and variations in normal knees.

    PubMed

    Deep, K; Eachempati, K K; Apsingi, S

    2015-04-01

    The restoration of knee alignment is an important goal during total knee arthroplasty (TKA). In the past surgeons aimed to restore neutral limb alignment during surgery. However, previous studies have demonstrated alignment to be dynamic, varying depending on the position of the limb and the degree of weight-bearing, and between patients. We used a validated computer navigation system to measure the femorotibial mechanical angle (FTMA) in 264 knees in 77 male and 55 female healthy volunteers aged 18 to 35 years (mean 26.2). We found the mean supine alignment to be a varus angle of 1.2° (standard deviation (sd) 4), with few patients having neutral alignment. FTMA differs significantly between males and females (with a mean varus of 1.7° (sd 4) and 0.4° (sd 3.9), respectively; p = 0.008). It changes significantly with posture, the knee hyperextending by a mean of 5.6°, and coronal plane alignment becoming more varus by 2.2° (sd 3.6) on standing compared with supine. Knee alignment is different in different individuals and is dynamic in nature, changing with different postures. This may have implications for the assessment of alignment in TKA, which is achieved in non-weight-bearing conditions and which may not represent the situation observed during weight-bearing. PMID:25820888

  14. 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

  15. Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis

    PubMed Central

    Poupin, Nathalie; Mariotti, François; Huneau, Jean-François; Hermier, Dominique; Fouillet, Hélène

    2014-01-01

    Body tissues are generally 15N-enriched over the diet, with a discrimination factor (Δ15N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ15N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ15N system, by explicitly linking the sizes and Δ15N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to 15N accumulation in tissues, (ii) the Δ15N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ15N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ15N, and (v) Δ15N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ15N measurements. This work provides proof of concept that Δ15N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such

  16. Natural variation for lifespan and stress response in the nematode Caenorhabditis remanei.

    PubMed

    Reynolds, Rose M; Phillips, Patrick C

    2013-01-01

    Genetic approaches (e.g. mutation, RNA interference) in model organisms, particularly the nematode Caenorhabditis elegans, have yielded a wealth of information on cellular processes that can influence lifespan. Although longevity mutants discovered in the lab are instructive of cellular physiology, lab studies might miss important genes that influence health and longevity in the wild. C. elegans has relatively low natural genetic variation and high levels of linkage disequilibrium, and thus is not optimal for studying natural variation in longevity. In contrast, its close relative C. remanei possesses very high levels of molecular genetic variation and low levels of linkage disequilibrium. To determine whether C. remanei may be a good model system for the study of natural genetic variation in aging, we evaluated levels of quantitative genetic variation for longevity and resistance to oxidative, heat and UV stress. Heritability (and the coefficient of additive genetic variation) was high for oxidative and heat stress resistance, low (but significant) for longevity, and essentially zero for UV stress response. Our results suggest that C. remanei may be a powerful system for studying natural genetic variation for longevity and oxidative and heat stress response, as well as an informative model for the study of functional relationships between longevity and stress response. PMID:23658604

  17. Does infectious disease cause global variation in the frequency of intrastate armed conflict and civil war?

    PubMed

    Letendre, Kenneth; Fincher, Corey L; Thornhill, Randy

    2010-08-01

    Geographic and cross-national variation in the frequency of intrastate armed conflict and civil war is a subject of great interest. Previous theory on this variation has focused on the influence on human behaviour of climate, resource competition, national wealth, and cultural characteristics. We present the parasite-stress model of intrastate conflict, which unites previous work on the correlates of intrastate conflict by linking frequency of the outbreak of such conflict, including civil war, to the intensity of infectious disease across countries of the world. High intensity of infectious disease leads to the emergence of xenophobic and ethnocentric cultural norms. These cultures suffer greater poverty and deprivation due to the morbidity and mortality caused by disease, and as a result of decreased investment in public health and welfare. Resource competition among xenophobic and ethnocentric groups within a nation leads to increased frequency of civil war. We present support for the parasite-stress model with regression analyses. We find support for a direct effect of infectious disease on intrastate armed conflict, and support for an indirect effect of infectious disease on the incidence of civil war via its negative effect on national wealth. We consider the entanglements of feedback of conflict into further reduced wealth and increased incidence of disease, and discuss implications for international warfare and global patterns of wealth and imperialism. PMID:20377573

  18. An analytical model for Doppler frequency variations of ionospheric HF sounding caused by SSC

    NASA Astrophysics Data System (ADS)

    Pilipenko, V.; Fedorov, E.; Yumoto, K.; Ikeda, A.; Sun, T. R.

    2010-10-01

    A theoretical model to interpret the deviations of the Doppler sounding radio frequency during the SSC is proposed. The Doppler response is composed from long-period deviation with time scale ˜10 min and short-lived (˜1 min) positive spike. For the interpretation of this spike, the variations of Doppler velocity induced by compressional and Alfvén waves are theoretically estimated on the basis of the thin ionosphere approximation. The analytical model developed goes beyond the older numerical model which has been in use thus far to explain certain facets of the correlation between geomagnetic variations and HF Doppler shifts. This new model provides the possibility to easily estimate the Doppler frequency response to either Alfvén or compresssional modes for extraordinary and ordinary radio waves. A theoretical estimate indicates that, for the same amplitude of the ground magnetic disturbances, a large-scale compressional mode produces a larger ionospheric response than an Alfvén mode. The plasma vertical displacement caused by the ULF inductive electric field is shown to be the dominating effect. The magnitudes and waveforms of the simultaneously detected ionospheric and magnetic responses on SSC at a low-latitude site in Japan fit the considered model.

  19. 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.

  20. 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

    2016-05-01

    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.

  1. Temporal variation in natural methane seep rate due to tides, Coal Oil Point area, California

    NASA Astrophysics Data System (ADS)

    Boles, J. R.; Clark, J. F.; Leifer, I.; Washburn, L.

    2001-11-01

    Two large steel tents (each 30 m by 30 m), open at the bottom to the seafloor, capture ˜16,800 m3 d-1 (594 MCF) of primarily methane from a large natural hydrocarbon seep, occurring a kilometer offshore in 67 m of water. The gas is piped to shore where it is metered and processed. The seep flow rate was monitored hourly for 9 months. Our results show that the tidal forcing causes the flow rate to vary by 4-7% around the mean. These results are the first quantitative documentation of the effect of tides on natural gas seepage in relatively deep water. Time series analyses of the 9 month record clearly show four principal tidal components with periods of 12.0, 12.4, 23.9, and 25.8 hours. High tide correlates with reduced flow, and low tide correlates with increased flow. The correlation indicates that each meter increase of sea height results in a decrease of 10-15 m3 hr-1 or 1.5-2.2% of the hourly flow rate. The observed changes are best accounted for by a pore activation model, whereby gas is released from small pores at low pressures but is inhibited at higher pressure. Pressure-dependent gas solubility changes are a less likely cause of flow variation. Our study implies that sea level differences, on a tidal timescale, can significantly change the gas seepage rate from sediments. Lower sea level in the last hundred thousand years would presumably allow higher gas loss from the sediment, assuming sufficient gas present, because of reduced hydrostatic pressure at the sediment-sea interface. The magnitude of this long-term change cannot be extrapolated from our tidal data.

  2. 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

  3. Apparent pollution of groundwater caused by natural formation of chloroform in forest soils

    NASA Astrophysics Data System (ADS)

    Jacobsen, O.; Laier, T.; Albers, C. N.; Hunkeler, D.

    2011-12-01

    Halogenated compounds are known to be formed in natural environments. Many of these compounds are similar to industrially produced compounds and are toxic or carcinogenic. High concentration of chloroform in groundwater is usually attributed to anthropogenic input, but we have found that the groundwater beneath some pristine areas contained chloroform exceeding 1 μg/L. We investigated four coniferous forests over a period of several years in order to measure the net-formation of chloroform. Field measurements of atmospheric and soil air concentrations of chloroform were monitored. Analyses of soil air at 40 cm depth in different parts of the forests and adjacent areas revealed an extremely large variation in chloroform concentration exceeding two orders of magnitude. Up to 100 ppbv was found in soil air under the spruce forest, to be compared to an ambient atmospheric concentration of 0.02 ppbv. The concentration of chloroform in soil air showed seasonal variation similar to that of CO2. Chloroform formation during incubation of undisturbed top-soil samples was found to be largest in soils from dense conifers stands with well-developed humus layers, while low chloroform formation occurred in soils from beech forest and agricultural grassland. We suggest that the mechanism behind the formation of chloroform is an unspecific chlorination of organic matter, caused by microbial activity in the soil. The aquifers are in fluvio-glacial sands with few layers of silt and a groundwater table from 4 to 7 m below the surface. In the shallowest parts of the aquifer, the groundwater has chloroform concentrations of 0.1 to 5 μg/L, and the groundwater is oxic with an age from 5 to 45 years using CFC-dating. Analyses of oxic groundwater > 40 years showed that it still contained chloroform at concentrations of 1 μg/L. Stable carbon isotopic analyses of chloroform from the uppermost groundwater in different parts of the forests and from soil water showed values from δ13C = -13

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Sex, death, and genetic variation: natural and sexual selection on cricket song

    PubMed Central

    Gray, D. A.; Cade, W. H.

    1999-01-01

    Male field crickets, Gryllus integer, in Texas, USA, produce a trilled calling song that attracts female crickets, resulting in enhanced mating success. Gravid female parasitoid flies, Ormia ochracea, are also attracted to male cricket calling song, resulting in the death of the male within about seven days. Using playbacks of field-cricket calling song in the natural habitat, we show that both female crickets and female parasitoid flies prefer male calling song with average numbers of pulses per trill. Thus female crickets exert stabilizing sexual selection, whereas flies exert disruptive natural selection on male song. Disruptive natural selection will promote genetic variation and population divergence. Stabilizing sexual selection will reduce genetic variation and maintain population cohesiveness. These forces may balance and together maintain the observed high levels of genetic variation (ca. 40%) in male calling song.

  12. 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

  13. A variational justification of the assumed natural strain formulation of finite elements

    NASA Technical Reports Server (NTRS)

    Militello, Carmelo; Felippa, Carlos A.

    1991-01-01

    The objective is to study the assumed natural strain (ANS) formulation of finite elements from a variational standpoint. The study is based on two hybrid extensions of the Reissner-type functional that uses strains and displacements as independent fields. One of the forms is a genuine variational principle that contains an independent boundary traction field, whereas the other one represents a restricted variational principle. Two procedures for element level elimination of the strain field are discussed, and one of them is shown to be equivalent to the inclusion of incompatible displacement modes. Also, the 4-node C(exp 0) plate bending quadrilateral element is used to illustrate applications of this theory.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Peculiarities of electric and magnetic tipper variations caused by meteorological disturbances in the atmosphere

    NASA Astrophysics Data System (ADS)

    Adushkin, V. V.; Spivak, A. A.

    2016-01-01

    We present the results of the analysis of experimental data of synchronous observations of variations in the electric and magnetic fields as well as acoustic oscillations in the surface zone of the Earth compared with variations in the meteorological parameters. We demonstrate the synchronous variations in these fields and atmospheric parameters. We revealed, for the first time, not only synchronous but also advancing manifestations of the geomagnetic field perturbations. We introduce a new parameter: the inverse magnetic tipper whose variations during atmospheric perturbations are clearly manifested compared with the variations in the magnetic tipper.

  19. 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.

  20. Dose variations caused by setup errors in intracranial stereotactic radiotherapy: a PRESAGE study.

    PubMed

    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 1.5mm and 1°, respectively, generated a passing ratio of 62.2%. Translation shift of 0.7mm 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 0.7mm and 0.5° alter the dose distribution. The geometrical displacements affect dose delivery to

  1. 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

  2. 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

  3. 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

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

    PubMed Central

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

    2014-01-01

    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. PMID:24963002

  5. 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. PMID:24963002

  6. 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.

  7. 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

  8. 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).

  9. 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

  10. 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.

  11. Genomic Analysis of QTLs and Genes Altering Natural Variation in Stochastic Noise

    PubMed Central

    Maloof, Julin N.; Kliebenstein, Daniel J.

    2011-01-01

    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. Potassium Retention under Salt Stress Is Associated with Natural Variation in Salinity Tolerance among Arabidopsis Accessions

    PubMed Central

    Sun, Yanling; Kong, Xiangpei; Li, Cuiling; Liu, Yongxiu; Ding, Zhaojun

    2015-01-01

    Plants are exposed to various environmental stresses during their life cycle such as salt, drought and cold. Natural variation mediated plant growth adaptation has been employed as an effective approach in response to the diverse environmental cues such as salt stress. However, the molecular mechanism underlying this process is not well understood. In the present study, a collection of 82 Arabidopsis thaliana accessions (ecotypes) was screened with a view to identify variation for salinity tolerance. Seven accessions showed a higher level of tolerance than Col-0. The young seedlings of the tolerant accessions demonstrated a higher K+ content and a lower Na+/K+ ratio when exposed to salinity stress, but its Na+ content was the same as that of Col-0. The K+ transporter genes AtHAK5, AtCHX17 and AtKUP1 were up-regulated significantly in almost all the tolerant accessions, even in the absence of salinity stress. There was little genetic variation or positive transcriptional variation between the selections and Col-0 with respect to Na+-related transporter genes, as AtSOS genes, AtNHX1 and AtHKT1;1. In addition, under salinity stress, these selections accumulated higher compatible solutes and lower reactive oxygen species than did Col-0. Taken together, our results showed that natural variation in salinity tolerance of Arabidopsis seems to have been achieved by the strong capacity of K+ retention. PMID:25993093

  14. Long-term variations in natural, terrestrial VOC emissions: 1000-1990 AD

    NASA Astrophysics Data System (ADS)

    Acosta, J. C.; Struthers, H.; Zorita, E.; Ekman, A. M.; Riipinen, I.

    2012-12-01

    Natural vegetation emits large amounts of volatile organic compounds (e.g. monoterpenes and isoprene) into the atmosphere. Estimates of the total global source of biogenic volatile organic compounds (BVOCs) in the past millennium range between 1050 and 1100 Tg yr-1 (Adams et al. 2001). BVOCs have multiple impacts on atmospheric chemistry, for example they are believed to affect ozone formation, decrease the oxidizing capacity of the troposphere and substantially alter the concentrations of tropospheric aerosol in continental regions (Seinfeld et al., 1998). Organic compounds constitute 20-90% of the submicron aerosol mass, depending on location. Most of this contribution is secondary, meaning that the emitted VOCs are oxidized in the atmosphere followed by gas-to-particle conversion of the oxidation products (Jimenez et al., 2009). BVOCs emitted by vegetation are the dominant source of secondary organic aerosol (SOA) in the atmosphere (Guenther et al., 1995). Estimates on the present-day organic aerosol budgets are improving rapidly, but it is unclear how the organic aerosol fraction has evolved in the past. Such information is, however, needed for accurate estimates on the climate forcing caused by aerosols. Understanding the factors that have governed BVOC emissions in the past is a prerequisite for completing this task. We evaluate the variability of global fluxes of isoprene, monoterpenes and sesquiterpenes over the last millennium using the Model of Emissions of Gases and Aerosols from Nature (MEGAN) (Guenther et al., 2006). MEGAN estimates the emission activity of BVOCs using meteorological (Air temperature, solar radiation, soil moisture) and landcover (Plant Functional Types (PFTs) and Leaf Area Index (LAI)) inputs. The model is driven off-line using meteorological fields from existing Max Planck Institute Earth System Model (MPI-ESM) (Jungclaus et al. 2010) millennium simulations, and reconstructions of the global changes PFTs and LAI (Kaplan et al., 2010

  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. 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

  19. 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

  20. Assessment of Genetically Modified Soybean in Relation to Natural Variation in the Soybean Seed Metabolome

    PubMed Central

    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 and equivalence with respect to conventional crops. Untargeted metabolomics has the ability to profile diverse classes of metabolites and thus could be an adjunct for GM crop substantial equivalence assessment. 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. PMID:24170158

  1. The Myth of Community Differences as the Cause of Variations Among IRBs

    PubMed Central

    Klitzman, Robert

    2013-01-01

    Background Although variations among institutional review boards (IRBs) have been documented for 30 years, they continue, raising crucial questions as to why they persist as well as how IRBs view and respond to these variations. Methods In-depth, 2-hour interviews were conducted with 46 IRB chairs, administrators, and members. The leadership of 60 U.S. IRBs were contacted (every fourth one in the list of the top 240 institutions by NIH funding). IRB leaders from 34 of these institutions were interviewed (response rate = 55%). Results The interviewees suggest that differences often persist because IRBs think these are legitimate, and regulations permit variations due to differing “community values.” Yet, these variations frequently appear to stem more from differences in institutional and subjective personality factors, and from “more eyes” examining protocols, trying to foresee all potential future logistical problems, than from the values of the communities from which research participants are drawn. However, IRBs generally appear to defend these variations as reflecting underlying differences in community norms. Conclusions These data pose critical questions for policy and practice. Attitudinal changes and education among IRBs, principal investigators (PIs), policymakers, and others and research concerning these issues are needed. PMID:25285236

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

    PubMed

    Gooding, R H

    1996-07-01

    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

  3. 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

  4. Analysis of natural variation reveals neurogenetic networks for Drosophila olfactory behavior.

    PubMed

    Swarup, Shilpa; Huang, Wen; Mackay, Trudy F C; Anholt, Robert R H

    2013-01-15

    Understanding the relationship between genetic variation and phenotypic variation for quantitative traits is necessary for predicting responses to natural and artificial selection and disease risk in human populations, but is challenging because of large sample sizes required to detect and validate loci with small effects. Here, we used the inbred, sequenced, wild-derived lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to perform three complementary genome-wide association (GWA) studies for natural variation in olfactory behavior. The first GWA focused on single nucleotide polymorphisms (SNPs) associated with mean differences in olfactory behavior in the DGRP, the second was an extreme quantitative trait locus GWA on an outbred advanced intercross population derived from extreme DGRP lines, and the third was for SNPs affecting the variance among DGRP lines. No individual SNP in any analysis was associated with variation in olfactory behavior by using a strict threshold accounting for multiple tests, and no SNP overlapped among the analyses. However, combining the top SNPs from all three analyses revealed a statistically enriched network of genes involved in cellular signaling and neural development. We used mutational and gene expression analyses to validate both candidate genes and network connectivity at a high rate. The lack of replication between the GWA analyses, small marginal SNP effects, and convergence on common cellular networks were likely attributable to epistasis. These results suggest that fully understanding the genotype-phenotype relationship requires a paradigm shift from a focus on single SNPs to pathway associations. PMID:23277560

  5. 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.

  6. 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

  7. 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 ...

  8. 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

  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. 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

  11. 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.

  12. 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.

    2016-01-01

    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.

  13. 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.

  14. Natural Variation in MAM Within and Between Populations of Arabidopsis lyrata Determines Glucosinolate Phenotype

    PubMed Central

    Heidel, Andrew J.; Clauss, Maria J.; Kroymann, Juergen; Savolainen, Outi; Mitchell-Olds, Thomas

    2006-01-01

    The genetic variation that underlies the glucosinolate phenotype of Arabidopsis lyrata ssp. petraea was investigated between and within populations. A candidate glucosinolate biosynthetic locus (MAM, containing methylthioalkylmalate synthase genes) was mapped in A. lyrata to a location on linkage group 6 corresponding to the homologous location for MAM in A. thaliana. In A. thaliana MAM is responsible for side chain elongation in aliphatic glucosinolates, and the MAM phenotype can be characterized by the ratios of long- to short-chain glucosinolates. A quantitative trait loci (QTL) analysis of glucosinolate ratios in an A. lyrata interpopulation cross found one QTL at MAM. Additional QTL were identified for total indolic glucosinolates and for the ratio of aliphatic to indolic glucosinolates. MAM was then used as the candidate gene for a within-population cosegregation analysis in a natural A. lyrata population from Germany. Extensive variation in microsatellite markers at MAM was found and this variation cosegregated with the same glucosinolate ratios as in the QTL study. The combined results indicate that both between- and within-population genetic variation in the MAM region determines phenotypic variation in glucosinolate side chains in A. lyrata. PMID:16702431

  15. An Estimate of Changes in the Sun's Total Irradiance Caused by UV Irradiance Variations from 1874 to 1988

    NASA Technical Reports Server (NTRS)

    Lean, J.

    1990-01-01

    Enhanced emission from bright solar faculae is a source of significant variation in the sun's total irradiance. Relative to the emission from the quiet sun, facular emission is known to be considerably greater at UV wavelengths than at visible wavelengths. Determining the spectral dependence of facular emission is of interest for the physical insight this may provide to the origin of the sun's irradiance variations. It is also of interest because solar radiation at lambda less than 300 nm is almost totally absorbed in the Earth's atmosphere. Depending on the magnitude of the UV irradiance variations, changes in the sun's irradiance that penetrates to the Earth's surface may not be equivalent to total irradiance variations measured above the Earth's atmosphere. Using an empirical model of total irradiance variations which accounts separately for changes caused by bright faculae from those associated with dark sunspots, the contribution of UV irradiance variations to changes in the sun's total irradiance is estimated during solar cycles 12 to 21.

  16. 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

  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. 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.

  19. 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

  20. 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

  1. 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

  2. Intraspecific variation in testis asymmetry in birds: evidence for naturally occurring compensation

    PubMed Central

    Calhim, Sara; Birkhead, Tim R.

    2009-01-01

    In many taxa, the left and right testes often differ in size. The compensation hypothesis states that one testis of the pair serves as a ‘back-up’ for any reduced function in the other and provides a mechanism to explain intraspecific variation in degree and direction of gonad asymmetry. Although testis asymmetry is common in birds, evidence for natural testis compensation is unknown. Using a novel quantitative approach that can be applied to any bilateral organ or structure, we show that testis compensation occurs naturally in birds and can be complete when one testis fails to develop. Owing to a recurrent risk of testis impairment and an evolutionary trade-off between natural and sexual selections acting on the arrangement of internal organs in species with abdominal and/or seasonal testes, compensation adds an important, but neglected, dimension to measures of male reproductive investment. PMID:19324740

  3. Inadvertent Dural Puncture during Caudal Approach by the Introducer Needle for Epidural Adhesiolysis Caused by Anatomical Variation

    PubMed Central

    Kim, Si Gon; Kim, Do Wan; Lee, Yeon Ju

    2013-01-01

    There have been reports of abnormalities in the lumbosacral region involving a lower-than-normal termination of the dural sac, which is caused by disease or anatomical variation. Inadvertent dural puncture or other unexpected complications can occur during caudal epidural block or adhesiolysis in patients with these variations, but only a small number of case reports have described this issue. We report a case of dural puncture by the introducer needle before attempting caudal epidural adhesiolysis, which occurred even though the needle was not advanced upward after penetrating the sacrococcygeal ligament. Dural puncture was caused by a morphological abnormality in the lumbosacral region, with no pathological condition; the dural sac terminal was located more distally than normal. However, dural puncture could have been prevented if we had checked for such an abnormality in the magnetic resonance imaging (MRI) taken before the procedure. PMID:23614088

  4. 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. PMID:25594359

  5. 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

  6. 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

  7. 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

  8. 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. PMID:25488978

  9. Natural variation in the molecular stress network correlates with a behavioural syndrome.

    PubMed

    Aubin-Horth, Nadia; Deschênes, Marilou; Cloutier, Sophie

    2012-01-01

    In several species, individuals from the same population behave differently from each other. A functional link between variation in personality traits and the stress response has been suggested by studies in artificial selection lines in fish, birds and mammals. The aim of this study was to test whether the expression of genes involved in the stress response co-varies with personality traits in a natural population. Four personality traits, excreted cortisol level and brain expression of six candidate genes (CRF, CRF-R2, POMC1, GR1, GR2, MR) were measured in non-stressed wild-caught threespine sticklebacks (Gasterosteus aculeatus). We found correlations between variation in personality traits and variation in the expression of genes involved in the stress response. Aggressiveness was negatively correlated with cortisol levels. Boldness and aggressiveness formed a behavioural syndrome and were both positively correlated with brain expression of glucocorticoid receptors (GR1 and GR2). Boldness and exploration were positively correlated with expression of POMC1 but not with each other. Our results are compatible with a model that suggests that the aggressiveness-boldness behavioural syndrome could be the consequence of a physiological pleiotropic effect of glucocorticoid receptors, which are involved in the stress response and behaviour variation. PMID:22155114

  10. Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy.

    PubMed

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

    2016-08-01

    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

  11. Variation in Base-Substitution Mutation in Experimental and Natural Lineages of Caenorhabditis Nematodes

    PubMed Central

    Denver, Dee R.; Wilhelm, Larry J.; Howe, Dana K.; Gafner, Kristin; Dolan, Peter C.; Baer, Charles F.

    2012-01-01

    Variation among lineages in the mutation process has the potential to impact diverse biological processes ranging from susceptibilities to genetic disease to the mode and tempo of molecular evolution. The combination of high-throughput DNA sequencing (HTS) with mutation-accumulation (MA) experiments has provided a powerful approach to genome-wide mutation analysis, though insights into mutational variation have been limited by the vast evolutionary distances among the few species analyzed. We performed a HTS analysis of MA lines derived from four Caenorhabditis nematode natural genotypes: C. elegans N2 and PB306 and C. briggsae HK104 and PB800. Total mutation rates did not differ among the four sets of MA lines. A mutational bias toward G:C→A:T transitions and G:C→T:A transversions was observed in all four sets of MA lines. Chromosome-specific rates were mostly stable, though there was some evidence for a slightly elevated X chromosome mutation rate in PB306. Rates were homogeneous among functional coding sequence types and across autosomal cores, arms, and tips. Mutation spectra were similar among the four MA line sets but differed significantly when compared with patterns of natural base-substitution polymorphism for 13/14 comparisons performed. Our findings show that base-substitution mutation processes in these closely related animal lineages are mostly stable but differ from natural polymorphism patterns in these two species. PMID:22436997

  12. [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

  13. 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

  14. From sequence to function: Insights from natural variation in budding yeasts☆

    PubMed Central

    Nieduszynski, Conrad A.; Liti, Gianni

    2011-01-01

    Background Natural variation offers a powerful approach for assigning function to DNA sequence—a pressing challenge in the age of high throughput sequencing technologies. Scope of Review Here we review comparative genomic approaches that are bridging the sequence–function and genotype–phenotype gaps. Reverse genomic approaches aim to analyse sequence to assign function, whereas forward genomic approaches start from a phenotype and aim to identify the underlying genotype responsible. Major Conclusions Comparative genomic approaches, pioneered in budding yeasts, have resulted in dramatic improvements in our understanding of the function of both genes and regulatory sequences. Analogous studies in other systems, including humans, demonstrate the ubiquity of comparative genomic approaches. Recently, forward genomic approaches, exploiting natural variation within yeast populations, have started to offer powerful insights into how genotype influences phenotype and even the ability to predict phenotypes. General Significance Comparative genomic experiments are defining the fundamental rules that govern complex traits in natural populations from yeast to humans. This article is part of a Special Issue entitled Systems Biology of Microorganisms. PMID:21320572

  15. Natural Changes in Brain Temperature Underlie Variations in Song Tempo during a Mating Behavior

    PubMed Central

    Aronov, Dmitriy; Fee, Michale S.

    2012-01-01

    The song of a male zebra finch is a stereotyped motor sequence whose tempo varies with social context – whether or not the song is directed at a female bird – as well as with the time of day. The neural mechanisms underlying these changes in tempo are unknown. Here we show that brain temperature recorded in freely behaving male finches exhibits a global increase in response to the presentation of a female bird. This increase strongly correlates with, and largely explains, the faster tempo of songs directed at a female compared to songs produced in social isolation. Furthermore, we find that the observed diurnal variations in song tempo are also explained by natural variations in brain temperature. Our findings suggest that brain temperature is an important variable that can influence the dynamics of activity in neural circuits, as well as the temporal features of behaviors that some of these circuits generate. PMID:23112858

  16. 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.

  17. 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

  18. Implications for risk assessment of host factors causing large pharmacokinetic variations

    SciTech Connect

    Vesell, E.S.

    1985-12-01

    Normal human subjects vary widely in their capacity to eliminate many drugs and environmental chemicals. These variations range in magnitude from fourfold to fortyfold depending on the drug and the population studied. Pharmacogenetics deals with only one of many host factors responsible for these large pharmacokinetic differences. Age, sex, diet and exposure to other drugs and chemicals, including oral contraceptives, ethanol and cigarette smoking, can alter the genetically determined rate at which a particular subject eliminates drugs and environmental chemicals. These elimination rates, therefore, are dynamic and change even in the same subject with time and condition. Regulatory legislation has only recently begun to recognize this very broad spectrum of human susceptibility and the existence of multiple special subgroups of particularly sensitive subjects. In setting standards for environmental chemicals, EPA and NIOSH have attempted to protect the most sensitive humans and should be encouraged to continue this policy. For some drugs and environmental chemicals, the commonly used safety factor of 100 may be too low; for these chemicals large, interindividual pharmacokinetic variations produced by pharmacogenetic and other host factors may make a safety factor of 400 or 500 more adequate.

  19. What Causes the Inter-solar-cycle Variation of Total Solar Irradiance?

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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.

  20. Interannual variation of freshwater transport and its causes in the Korea Strait: A modeling study

    NASA Astrophysics Data System (ADS)

    Kim, Chang-Sin; Cho, Yang-Ki; Seo, Gwang-Ho; Choi, Byoung-Ju; Jung, Kyung Tae; Lee, Byeong-Gweon

    2014-04-01

    The variability of freshwater transport in the Korea Strait (FTKS) affects the circulation and ecosystem of the East/Japan Sea. Numerical simulations using realistic surface forcing, Changjiang River discharge (CRD), and open boundary values were performed to quantify the interannual variation of FTKS and to investigate its underlying physical processes. The simulated salinity and volume transport, which determine the variability of FTKS, were verified by comparing with observations. Salinity played a more important role than volume transport in inducing the interannual variation of FTKS. FTKS has a positive correlation with CRD, difference between precipitation and evaporation (P-E), southeasterly wind, and freshwater transport in the Taiwan Strait (FTTS). FTKS has its best correlation (0.62) with FTTS. The correlations with CRD (0.25) and P-E (0.37) are weaker, probably due to wind stress. The southeasterly wind that drives Changjiang diluted water toward the Korea Strait by Ekman flow in the East China Sea has good correlation (0.51) with FTKS. The vertical structures of FTKS and its variability are more effectively affected by CRD and P-E in the surface layer, FTTS in the middle layer, and the wind in the subsurface layer.

  1. Variations of annual and seasonal runoff in Guangdong Province, south China: spatiotemporal patterns and possible causes

    NASA Astrophysics Data System (ADS)

    Zhang, Qiang; Xiao, Mingzhong; Singh, Vijay P.; Xu, Chong-Yu; Li, Jianfeng

    2015-06-01

    In this study, we thoroughly analyzed spatial and temporal distributions of runoff and their relation with precipitation changes based on monthly runoff dataset at 25 hydrological stations and monthly precipitation at 127 stations in Guangdong Province, south China. Trends of the runoff and precipitation are detected using Mann-Kendall trend test technique. Correlations between runoff and precipitation are tested using Spearman's and Pearson's correlation coefficients. The results indicate that: (1) annual maximum monthly runoff is mainly in decreasing tendency and significant increasing annual minimum monthly runoff is observed in the northern and eastern Guangdong Province. In addition, annual mean runoff is observed to be increasing at the stations located in the West and North Rivers and the coastal region; (2) analysis of seasonal runoff variations indicates increasing runoff in spring, autumn and winter. Wherein, significant increase of runoff is found at 8 stations and only 3 stations are dominated by decreasing runoff in winter; (3) runoff changes of the Guangdong Province are mainly the results of precipitation changes. The Guangdong Province is wetter in winter, spring and autumn. Summer is coming to be drier as reflected by decreasing runoff in the season; (4) both precipitation change and water reservoirs also play important roles in the increasing of annual minimum monthly streamflow. Seasonal shifts of runoff variations may pose new challenges for the water resources management under the influences of climate changes and intensifying human activities.

  2. Oscillations in the power spectra of motor unit signals caused by refractoriness variations

    NASA Astrophysics Data System (ADS)

    Hu, X. L.; Tong, K. Y.; Hung, L. K.

    2004-09-01

    The refractory period of a motor unit is an important mechanism that regulates the motor unit firing, and its variation has been found in many physiological cases. In this study, a new observation that an increase in the motor unit refractoriness results in an enhancement of oscillations, or ripple effects, in the motor unit output power density spectra (PDS) has been identified and studied. The effects of the refractoriness variation on the PDS of motor unit firing were investigated on three levels: theoretical modeling, simulation and electromyographic (EMG) experimentation on human subjects. Both theoretical modeling and simulation showed the enhanced oscillations, ripple effects, in MUAPT PDS, given the increase in the refractoriness. It was also found that the extent of the increment in output PDS oscillation could be related to the motor unit size and the mean firing rate of the stimulation. A needle EMG experiment on biceps brachii muscles of five healthy human subjects was carried out during isometric contraction at 20% maximum voluntary contraction (MVC) for 20 s with a fatigue effort proceeded by MVC. The increased oscillations in the PDS of the real MUAPTs were observed with the rising of the motor unit refractoriness due to fatigue. The study gives new information for EMG spectra interpretation, and also provides a potential method for accessing neuromuscular transmission failure (NTF) due to fatigue during voluntary contraction.

  3. 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

  4. 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

  5. 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.

  6. 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…

  7. 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.

  8. Proximate causes of the variation of the human sex ratio at birth.

    PubMed

    James, William H

    2015-12-01

    There is evidence that the human sex ratio (proportion males at birth) is the result of two processes. First, the sexes of zygotes (from which the primary sex ratio would be calculated) are thought to be partially controlled by the hormone levels of both parents around the time of conception. Second, this primary sex ratio is apparently modified downwards by male-sex-selective spontaneous abortion caused by high levels of maternal stress-induced adrenal androgens, thus yielding the sex ratio at birth (the secondary sex ratio). Since maternal stress is one cause of spontaneous abortion (and of other forms of reproductive sub-optimality), and since some forms of pharmacological treatment of maternal stress are deleterious to the foetus, best practice would suggest non-pharmacological treatment (e.g. psychotherapy, hypnosis or massage) for pregnant women who have a previous history of spontaneous abortion, preterm birth or low-birth-weight infants. PMID:26549774

  9. Natural variation in symbiotic nitrogen-fixing Rhizobium and Frankia spp.

    PubMed

    Lie, T A; Akkermans, A D; van Egeraat, A W

    1984-01-01

    A description is given of the natural variation in nitrogen-fixing Rhizobium and Frankia spp. strains and the ability to form root nodules on compatible host plants. Arguments are given for the hypothesis that co-evolution has taken place through mutual interaction of host plants and indigenous Rhizobium and Frankia populations in the soil leading to most efficient symbiotic associations. The significance of root nodules as selective enrichment cultures of particular strains in natural and cultivated soils is exemplified by Rhizobium leguminosarum on various ecotypes of Pisum sativum and with Frankia sp. on various actinorhizal plants, in particular Alnus spp., in different geographic regions. The importance of a host-dependent distribution of Rhizobium and Frankia spp. for agriculture and forestry is discussed. PMID:6397130

  10. 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

  11. 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. PMID:27012286

  12. Unraveling functional significance of natural variations of a human galectin by glycodendrimersomes with programmable glycan surface

    PubMed Central

    Zhang, Shaodong; Moussodia, Ralph-Olivier; Vértesy, Sabine; André, Sabine; Klein, Michael L.; Gabius, Hans-Joachim; Percec, Virgil

    2015-01-01

    Surface-presented glycans (complex carbohydrates) are docking sites for adhesion/growth-regulatory galectins within cell–cell/matrix interactions. Alteration of the linker length in human galectin-8 and single-site mutation (F19Y) are used herein to illustrate the potential of glycodendrimersomes with programmable glycan displays as a model system to reveal the functional impact of natural sequence variations in trans recognition. Extension of the linker length slightly reduces lectin capacity as agglutinin and slows down aggregate formation at low ligand surface density. The mutant protein is considerably less active as agglutinin and less sensitive to low-level ligand presentation. The present results suggest that mimicking glycan complexity and microdomain occurrence on the glycodendrimersome surface can provide key insights into mechanisms to accomplish natural selectivity and specificity of lectins in structural and topological terms. PMID:25902539

  13. 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.

  14. Evaporation in the Atacama Desert: An empirical study of spatio-temporal variations and their causes

    NASA Astrophysics Data System (ADS)

    Houston, John

    2006-11-01

    SummaryThe Atacama Desert is hyper-arid, and areas where adequate moisture exists for evaporation are spatially highly restricted. Nevertheless, water resources exist and their evaluation requires knowledge of this elusive but important component of the hydrological cycle. Evaporation may occur in four typical areas: rivers and associated riparian zones, localized springs, large playas and extensive areas of bare soil after infrequent precipitation events. Transpiration is locally possible where moisture is sufficiently close to the surface to allow phreatophytes or scarce grass cover to grow, but virtually no information is available for quantification. Pan evaporation data from 11 stations for the period 1977-1991 is analyzed and complemented by analysis of an evaporation study conducted in the Salar de Atacama during 1987/1988. The results show that pan evaporation, and hence maximum potential evaporation may be considered largely a function of maximum temperature and elevation as well as density of the evaporating fluid. Actual evaporation is limited by available moisture and diminishes rapidly as the level of soil moisture saturation drops below the soil surface, extinguishing at ca. 2 m depth. Evaporation is greatest during the summer, but at higher elevations convective cloudiness develops during January and February reducing evaporating rates at a time when significant precipitation may occur. Inter-annual variations in pan evaporation are considerable and weakly correlated with ENSO, but variations in actual evaporation are damped by comparison. Regression equations are developed which have widespread applicability and may be used to estimate evaporation in areas where no site-specific data exists.

  15. 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.

  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%. PMID:25123485

  17. 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

  18. Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.

    PubMed

    Gunnarsson, Ulrika; Hellström, Anders R; Tixier-Boichard, Michele; Minvielle, Francis; Bed'hom, Bertrand; Ito, Shin'ichi; Jensen, Per; Rattink, Annemieke; Vereijken, Addie; Andersson, Leif

    2007-02-01

    S*S (Silver), S*N (wild type/gold), and S*AL (sex-linked imperfect albinism) form a series of alleles at the S (Silver) locus on chicken (Gallus gallus) chromosome Z. Similarly, sex-linked imperfect albinism (AL*A) is the bottom recessive allele at the orthologous AL locus in Japanese quail (Coturnix japonica). The solute carrier family 45, member 2, protein (SLC45A2), previously denoted membrane-associated transporter protein (MATP), has an important role in vesicle sorting in the melanocytes. Here we report five SLC45A2 mutations. The 106delT mutation in the chicken S*AL allele results in a frameshift and a premature stop codon and the corresponding mRNA appears to be degraded by nonsense-mediated mRNA decay. A splice-site mutation in the Japanese quail AL*A allele causes in-frame skipping of exon 4. Two independent missense mutations (Tyr277Cys and Leu347Met) were associated with the Silver allele in chicken. The functional significance of the former mutation, associated only with Silver in White Leghorn, is unclear. Ala72Asp was associated with the cinnamon allele (AL*C) in the Japanese quail. The most interesting feature concerning the SLC45A2 variants documented in this study is the specific inhibition of expression of red pheomelanin in Silver chickens. This phenotypic effect cannot be explained on the basis of the current, incomplete, understanding of SLC45A2 function. It is an enigma why recessive null mutations at this locus cause an almost complete absence of both eumelanin and pheomelanin whereas some missense mutations are dominant and cause a specific inhibition of pheomelanin production. PMID:17151254

  19. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis.

    PubMed

    Méndez-Vigo, Belén; Savic, Marija; Ausín, Israel; Ramiro, Mercedes; Martín, Beatriz; Picó, F Xavier; Alonso-Blanco, Carlos

    2016-02-01

    The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors. PMID:26173848

  20. 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. PMID:15306284

  1. Natural variation in a polyamine transporter determines paraquat tolerance in Arabidopsis

    PubMed Central

    Fujita, Miki; Fujita, Yasunari; Iuchi, Satoshi; Yamada, Kohji; Kobayashi, Yuriko; Urano, Kaoru; Kobayashi, Masatomo; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

    2012-01-01

    Polyamines (PAs) are ubiquitous, polycationic compounds that are essential for the growth and survival of all organisms. Although the PA-uptake system plays a key role in mammalian cancer and in plant survival, the underlying molecular mechanisms are not well understood. Here, we identified an Arabidopsis L-type amino acid transporter (LAT) family transporter, named RMV1 (resistant to methyl viologen 1), responsible for uptake of PA and its analog paraquat (PQ). The natural variation in PQ tolerance was determined in 22 Arabidopsis thaliana accessions based on the polymorphic variation of RMV1. An RMV1-GFP fusion protein localized to the plasma membrane in transformed cells. The Arabidopsis rmv1 mutant was highly resistant to PQ because of the reduction of PQ uptake activity. Uptake studies indicated that RMV1 mediates proton gradient-driven PQ transport. RMV1 overexpressing plants were hypersensitive to PA and PQ and showed elevated PA/PQ uptake activity, supporting the notion that PQ enters plant cells via a carrier system that inherently functions in PA transport. Furthermore, we demonstrated that polymorphic variation in RMV1 controls PA/PQ uptake activity. Our identification of a molecular entity for PA/PQ uptake and sensitivity provides an important clue for our understanding of the mechanism and biological significance of PA uptake. PMID:22492932

  2. Natural variation involving deletion alleles of FRIGIDA modulate temperature-sensitive flowering responses in Arabidopsis thaliana.

    PubMed

    Sanchez-Bermejo, Eduardo; Balasubramanian, Sureshkumar

    2016-06-01

    Ambient temperature is one of the major environmental factors that modulate plant growth and development. There is extensive natural genetic variation in thermal responses of plants exemplified by the variation exhibited by the accessions of Arabidopsis thaliana. In this work we have studied the enhanced temperature response in hypocotyl elongation and flowering shown by the Tsu-0 accession in long days. Genetic mapping in the Col-0 × Tsu-0 recombinant inbred line (RIL) population identified several QTLs for thermal response including three major effect loci encompassing candidate genes FRIGIDA (FRI), FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). We confirm and validate these QTLs. We show that the Tsu-0 FRI allele, which is the same as FRI-Ler is associated with late flowering but only at lower temperatures in long days. Using transgenic lines and accessions, we show that the FRI-Ler allele confers temperature-sensitive late flowering confirming a role for FRI in photoperiod-dependent thermal response. Through quantitative complementation with heterogeneous inbred families, we further show that cis-regulatory variation at FT contributes to the observed hypersensitivity of Tsu-0 to ambient temperature. Overall our results suggest that multiple loci that interact epistatically govern photoperiod-dependent thermal responses of A. thaliana. PMID:26662639

  3. Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans.

    PubMed

    Kamkina, Polina; Snoek, L Basten; Grossmann, Jonas; Volkers, Rita J M; Sterken, Mark G; Daube, Michael; Roschitzki, Bernd; Fortes, Claudia; Schlapbach, Ralph; Roth, Alexander; von Mering, Christian; Hengartner, Michael O; Schrimpf, Sabine P; Kammenga, Jan E

    2016-05-01

    Natural genetic variation is the raw material of evolution and influences disease development and progression. An important question is how this genetic variation translates into variation in protein abundance. To analyze the effects of the genetic background on gene and protein expression in the nematode Caenorhabditis elegans, we quantitatively compared the two genetically highly divergent wild-type strains N2 and CB4856. Gene expression was analyzed by microarray assays, and proteins were quantified using stable isotope labeling by amino acids in cell culture. Among all transcribed genes, we found 1,532 genes to be differentially transcribed between the two wild types. Of the total 3,238 quantified proteins, 129 proteins were significantly differentially expressed between N2 and CB4856. The differentially expressed proteins were enriched for genes that function in insulin-signaling and stress-response pathways, underlining strong divergence of these pathways in nematodes. The protein abundance of the two wild-type strains correlates more strongly than protein abundance versus transcript abundance within each wild type. Our findings indicate that in C. elegans only a fraction of the changes in protein abundance can be explained by the changes in mRNA abundance. These findings corroborate with the observations made across species. PMID:26944343

  4. 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.

  5. 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. PMID:23185390

  6. The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae

    PubMed Central

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

    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. PMID:23185390

  7. Thromboelastometry in veal calves to detect hemostatic variations caused by low doses of dexamethasone treatment

    PubMed Central

    2013-01-01

    Background The illegal administration of hormones, steroids, β-agonists and other anabolic agents to productive livestock in the European Union continues, despite the long-term ban on their use and despite the measures provided under the directives to monitor certain substances and residues thereof in the interest of protecting consumer health and animal wellbeing. Often administered in low doses in the form of a drug cocktail, these compounds escape detection by common analytical techniques. The aim of this study was to determine whether low-dose dexamethasone administration (0.4 mg orally per day, for 20 days) in white-meat calves produced variations in blood coagulation, as measured by thromboelastometry. A second aim was to determine whether such variations could be valid in detecting illicit low-dose dexamethasone treatment. Results The study population was 42 Friesian calves kept under controlled conditions until 6 months of age. The calves were subdivided into 2 groups: a control group (group A, n = 28) and a group treated with dexamethasone (group B, n = 14) for 20 days beginning at 5 months of age. When compared against the age-matched control group, the dexamethasone-treated calves showed a significant increase in alpha angle, maximum clot firmness and a significant decrease in clot formation time on all thromboelastometric profiles (P < 0.05). The clotting time was significantly decreased on the in-TEM® profile but increased on the ex-TEM® and fib-TEM® profiles (P <0.05). The Receiver Operating Characteristic curves, plotted for the Maximum Clot Elasticity (MCE), had a cut-off value ≥488.23 mm for in-TEM® MCE [Se 85.7%, (95% CI 57.2-98.2); Sp 100% 96.43% (95% CI 81.7-99.9] and a cut-off value ≥63.94 mm for fib-TEM® MCE [Se 92.8 (95% CI 66.1-99.8); Sp 89.3% (95% CI 71.8-97.7)]. In order to increase the sensitivity of the test two parameters (in-TEM® and fib-TEM® MCE) were used as two parallel tests; subsequently, the

  8. Natural variation in floral nectar proteins of two Nicotiana attenuata accessions

    PubMed Central

    2013-01-01

    Background Floral nectar (FN) contains not only energy-rich compounds to attract pollinators, but also defense chemicals and several proteins. However, proteomic analysis of FN has been hampered by the lack of publically available sequence information from nectar-producing plants. Here we used next-generation sequencing and advanced proteomics to profile FN proteins in the opportunistic outcrossing wild tobacco, Nicotiana attenuata. Results We constructed a transcriptome database of N. attenuata and characterized its nectar proteome using LC-MS/MS. The FN proteins of N. attenuata included nectarins, sugar-cleaving enzymes (glucosidase, galactosidase, and xylosidase), RNases, pathogen-related proteins, and lipid transfer proteins. Natural variation in FN proteins of eleven N. attenuata accessions revealed a negative relationship between the accumulation of two abundant proteins, nectarin1b and nectarin5. In addition, microarray analysis of nectary tissues revealed that protein accumulation in FN is not simply correlated with the accumulation of transcripts encoding FN proteins and identified a group of genes that were specifically expressed in the nectary. Conclusions Natural variation of identified FN proteins in the ecological model plant N. attenuata suggests that nectar chemistry may have a complex function in plant-pollinator-microbe interactions. PMID:23848992

  9. 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

  10. Alteration of Arabidopsis SLAC1 promoter and its association with natural variation in drought tolerance.

    PubMed

    Imai, Hiroe; Noda, Yusaku; Tamaoki, Masanori

    2015-01-01

    Natural variation for drought tolerance is a major issue in adaptation and geographic distribution of terrestrial plants. Despite the importance, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We analyzed the intraspecific drought tolerance variation between 2 accessions of Arabidopsis thaliana, Columbia (Col)-0 and Wassilewskija (Ws)-2. Measurement of weight loss in detached seedlings demonstrated a clear difference between drought-tolerant Col-0 and drought-sensitive Ws-2. They also differed in their stomatal response under drought condition. Using a quantitative genetic approach, we found a significant quantitative locus on chromosome 1. Surveying in the locus, we extrapolated that the SLAC1 gene, which is associated with stomatal closure, was likely responsible for the difference of drought tolerance. Comparison of their nucleotide and amino acid sequences revealed that there were few differences in regions encoding SLAC1 protein but was a large deletion in SLAC1 promoter of Ws-2. Histochemical GUS staining showed that the SLAC1 expressed dominantly in guard cells of Col-0, but did less in guard cells of Ws-2. Quantitative PCR analysis also showed that transcript level of SLAC1 in guard cells was higher in Col-0 than in Ws-2. The SLAC1 transcription analyses indicate low accumulation of SLAC1 in guard cells of Ws-2. When taken together, our results suggest that the low drought tolerance of Ws-2 was associated with the deletion of the promoter region of Ws-2 SLAC1. PMID:25695335

  11. 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

  12. Cyclone Tolerance in New World Arecaceae: Biogeographic Variation and Abiotic Natural Selection

    PubMed Central

    Griffith, M. Patrick; Noblick, Larry R.; Dowe, John L.; Husby, Chad E.; Calonje, Michael A.

    2008-01-01

    Background and Aims Consistent abiotic factors can affect directional selection; cyclones are abiotic phenomena with near-discrete geographic limits. The current study investigates selective pressure of cyclones on plants at the species level, testing for possible natural selection. Methods New World Arecaceae (palms) are used as a model system, as plants with monopodial, unbranched arborescent form are most directly affected by the selective pressure of wind load. Living specimens of known provenance grown at a common site were affected by the same cyclone. Data on percentage mortality were compiled and analysed in biogeographic and phylogenetic contexts. Key Results Palms of cyclone-prone provenance exhibited a much lower (one order of magnitude) range in cyclone tolerance, and significantly lower (P < 0·001) mean percentage mortality than collections from cyclone-free areas. Palms of cyclone-free provenance had much greater variation in tolerance, and significantly greater mean percentage mortality. A test for serial independence recovered no significant phylogenetic autocorrelation of percentage mortality. Conclusions Variation in cyclone tolerance in New World Arecaceae correlates with biogeography, and is not confounded with phylogeny. These results suggest natural selection of cyclone tolerance in cyclone-prone areas. PMID:18669575

  13. 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

  14. 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.

  15. Natural variation in expression of genes associated with 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...

  16. 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...

  17. 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

  18. A general approximate method for the groundwater response problem caused by water level variation

    NASA Astrophysics Data System (ADS)

    Jiang, Qinghui; Tang, Yuehao

    2015-10-01

    The Boussinesq equation (BEQ) can be used to describe groundwater flow through an unconfined aquifer. Based on 1D BEQ, we present a general approximate method to predict the water table response in a semi-infinite aquifer system with a vertical or sloping boundary. A decomposition method is adopted by separating the original problem into a linear diffusion equation (DE) and two correction functions. The linear DE satisfies all the initial and boundary conditions, reflecting the basic characteristics of groundwater movement. The correction functions quantitatively measure the errors due to the degeneration from the original BEQ to a linear DE. As the correction functions must be linearized to obtain analytical solution forms, the proposed method is an approximate approach. In the case studies, we apply this method to four different situations of water level variation (i.e., constant, sudden, linear and periodic change) resting on vertical or sloping boundaries. The results are compared against numerical results, field data and other analytical solutions, which demonstrate that the proposed method has a good accuracy and versatility over a wide range of applications.

  19. 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

  20. Causes and consequences of the variation in the number of ovarian follicles in cattle.

    PubMed

    Evans, A C O; Mossa, F; Fair, T; Lonergan, P; Butler, S T; Zielak-Steciwko, A E; Smith, G W; Jimenez-Krassel, F; Folger, J K; Ireland, J L H; Ireland, J J

    2010-01-01

    In cattle we have noted that the antral follicle count (AFC, follicles > or = 3 mm in diameter) varies greatly among animals (from 5 to 50), is repeatable within animals, and is highly correlated with the total number of healthy follicles in ovaries. Also, animals with low AFC have higher serum concentrations of FSH and LH, but lower concentrations of Anti-Mullerian Hormone, progesterone and androgens than animals with high AFC. We have investigated the effect of maternal environment during gestation on their offspring AFC by restricting maternal nutrition to 60% of maintenance requirements (compared with 100% in controls) during the first third of gestation. Calves born to nutritionally restricted mothers had 60% lower AFC compared with calves born to mothers fed control diets. In other studies we have evidence to indicate that fertility may be compromised in animals with low AFC due to effects on oocytes, progesterone and the endometrium compared with animals with high AFC. To examine this directly we assessed AFC in post-partum dairy cows and found that cows with a high AFC had higher pregnancy rates, shorter calving to conception intervals and received fewer services during the breeding season compared with cows with a low AFC. In addition, the high variation in follicle numbers in adults may not only be reflective of reproductive disorders and suboptimal fertility, but there is evidence to indicate that it may be associated with alterations in the function of other non-reproductive systems (e.g. cardiovascular) that may have profound effects on the animal's health and welfare. PMID:21755688

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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. PMID:16328625

  6. Magnetospheric electric field variations caused by storm-time shock fronts

    NASA Astrophysics Data System (ADS)

    Kokorowski, M.; Bering, E. A.; Ruohoniemi, M.; Sample, J. G.; Holzworth, R. H.; Bale, S. D.; Blake, J. B.; Collier, A. B.; Hughes, A. R. W.; Lay, E. H.; Lin, R. P.; McCarthy, M. P.; Millan, R. M.; Moraal, H.; O'Brien, T. P.; Parks, G. K.; Pulupa, M.; Reddell, B. D.; Smith, D. M.; Stoker, P. H.; Woodger, L.

    2008-07-01

    On January 20, 2005 there was an X 7.1 solar flare at 0636 UT with an accompanied halo coronal mass ejection (CME). The resultant interplanetary shock impacted earth ˜36 h later. Near earth, the Advanced Composition Explorer (ACE) spacecraft observed two impulses with a staircase structure in density and pressure. The estimated earth-arrival times of these impulses were 1713 UT and 1845 UT on January 21, 2005. Three MINIature Spectrometer (MINIS) balloons were aloft on January 21st; one in the northern polar stratosphere and two in the southern polar stratosphere. MeV relativistic electron precipitation (REP) observed by all three balloons is coincident (<3 min) with the impulse arrivals and magnetospheric compression observed by both GOES 10 and 12. Balloon electric field data from the southern hemisphere show no signs of the impulse electric field directly reaching the ionosphere. Enhancement of the balloon-observed convection electric field by as much as 40 mV/m in less than 20 min during this time period is consistent with typical substorm growth. Precipitation-induced ionospheric conductivity enhancements are suggested to be (a) the result of both shock arrival and substorm activity and (b) the cause of rapid (<6 min) decreases in the observed electric field (by as much as 40 mV/m). There is poor agreement between peak cross polar cap potential in the northern hemisphere calculated from Super Dual Auroral Radar Network (SuperDARN) echoes and horizontal electric field at the MINIS balloon locations in the southern hemisphere. Possible reasons for this poor agreement include (a) a true lack of north-south conjugacy between measurement sites, (b) an invalid comparison between global (SuperDARN radar) and local (MINIS balloon) measurements and/or (c) radar absorption resulting from precipitation-induced D-region ionosphere density enhancements.

  7. Zonal concentration of some geophysical process intensity caused by tides and variations in the Earth's rotation velocity

    NASA Astrophysics Data System (ADS)

    Levin, B.; Domanski, A.; Sasorova, E.

    2014-01-01

    We analyzed what kind of fundamental physical phenomena can be responsible for the generation of the anomalous latitudinal zones of the seismic activity, and the hotspots, and some other geophysical processes. The assessment of tidal effect contribution to the earthquake preparation process is discussed. A disk model of the Earth's rotation was proposed. The model is acceptable for the homogeneous Earth and for the heterogeneous one. The disk model explains the nucleation of two maximums of the gradient of the moment of inertia over latitude with respect to the Equator. Effects of the variations in the Earth's rotation angular velocity were estimated and the possible features caused by the rotation velocity instability were described. The variations in the relative velocity of the Earth's rotation (dimensionless value ν ≈ (T - P)/P) are approximately equal upon the average to 10-8, where T is the observed length of day for the Earth, and P is the astronomical day. These variations lead to the occurrence of the additional energy estimated as 1020 J. The authors proposed the hypothesis of a pulsating geoid based on effects of the Earth's rotation features, and tidal forces, and conception of critical latitudes in the solid Earth. This hypothesis may highlight the phenomenon of zonal intensification of some geological processes in the solid Earth (the seismic activity, and hotspot location, and major ore deposit locations).

  8. 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.

  9. [Genomic variation of laboratory strains and natural populations of Drosophila melanogaster exposed to X-irradiation].

    PubMed

    Shokhanov, S O; Shcherbata, G R; Chernik, Ia I

    1997-01-01

    The spontaneous and X-ray-induced mutation rates and spectrums were estimated in laboratory strains and natural populations of Drosophila melanogaster from the Chernobyl meltdown area. Laboratory strains Oregon R and y2w alpha 4 were stable. In all natural populations, the spontaneous mutation rate was an order of magnitude higher (10(-3)) than in laboratory strains. Irradiation at a total dose of 3000 R was shown to induce genetic instability in the stable laboratory strain y2w alpha 4 and to increase the mutation rate and spectrum range in the unstable natural population P1. A high level of genetic instability was observed both in the first and second generations. Genetic analysis by means of classical genetic and molecular methods was performed; in crosses, a collection of spontaneous and induced mutants was used. The molecular genetic nature of mutations at the white and cut loci was analyzed by Southern blot-hybridization. Mutations at the white locus were shown to result both from transposition and recombination events; cut mutations were caused by deletions. PMID:9162688

  10. 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.

  11. 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. PMID:26775938

  12. Compounds of Natural Origin and Acupuncture for the Treatment of Diseases Caused by Estrogen Deficiency.

    PubMed

    Thakur, Abhishek; Mandal, Subhash C; Banerjee, Sugato

    2016-06-01

    A predominant number of diseases affecting women are related to female hormones. In most of the cases, these diseases are reported to be associated with menstrual problems. These diseases affect female reproductive organs such as the breast, uterus, and ovaries. Estrogen is the main hormone responsible for the menstrual cycle, so irregular menstruation is primarily due to a disturbance in estrogen levels. Estrogen imbalance leads to various pathological conditions in premenopausal women, such as endometriosis, breast cancer, colorectal cancer, prostate cancer, poly cysts, intrahepatic cholestasis of pregnancy, osteoporosis, cardiovascular diseases, obesity, etc. In this review, we discuss common drug targets and therapeutic strategies, including acupuncture and compounds of natural origin, for the treatment of diseases caused by estrogen deficiency. PMID:27342884

  13. 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

  14. N-representability and variational stability in natural orbital functional theory

    NASA Astrophysics Data System (ADS)

    Herbert, John M.; Harriman, John E.

    2003-06-01

    Several "reconstructive" proposals for density matrix functional theory are investigated, each of which expresses the two-electron density matrix, and therefore the electronic energy, as a functional of the natural orbitals and their occupation numbers. It is shown that for each of these functionals, half of the parallel-spin eigenvalues of the reconstructed two-electron density matrix are necessarily negative. Illustrative all-electron calculations for Be and LiH, in a variety of Gaussian basis sets, demonstrate that these spurious negative eigenvalues lower the electronic energy substantially. In spite of this, there is no indication that the variationally optimized energy diverges as the basis set approaches completeness, as has been suggested based on calculations with a small number of active orbitals. The apparent variational instability reported previously is attributed to qualitative differences between the minimal-basis and extended-basis potential curves, for certain functionals. However, we identify one functional that yields accurate LiH potential curves—comparable to full configuration interaction results—in both minimal and extended basis sets. Explicitly antisymmetric reconstructions are recommended as a remedy for the positivity problem.

  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. WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

    PubMed

    Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

    2013-01-01

    Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

  17. 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

  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. Natural Genetic Variation of Arabidopsis thaliana Is Geographically Structured in the Iberian Peninsula

    PubMed Central

    Picó, F. Xavier; Méndez-Vigo, Belén; Martínez-Zapater, José M.; Alonso-Blanco, Carlos

    2008-01-01

    To understand the demographic history of Arabidopsis thaliana within its native geographical range, we have studied its genetic structure in the Iberian Peninsula region. We have analyzed the amount and spatial distribution of A. thaliana genetic variation by genotyping 268 individuals sampled in 100 natural populations from the Iberian Peninsula. Analyses of 175 individuals from 7 of these populations, with 20 chloroplast and nuclear microsatellite loci and 109 common single nucleotide polymorphisms, show significant population differentiation and isolation by distance. In addition, analyses of one genotype from 100 populations detected significant isolation by distance over the entire Iberian Peninsula, as well as among six Iberian subregions. Analyses of these 100 genotypes with different model-based clustering algorithms inferred four genetic clusters, which show a clear-cut geographical differentiation pattern. On the other hand, clustering analysis of a worldwide sample showed a west–east Eurasian longitudinal spatial gradient of the commonest Iberian genetic cluster. These results indicate that A. thaliana genetic variation displays significant regional structure and consistently support the hypothesis that Iberia has been a glacial refugium for A. thaliana. Furthermore, the Iberian geographical structure indicates a complex regional population dynamics, suggesting that this region contained multiple Pleistocene refugia with a different contribution to the postglacial colonization of Europe. PMID:18716334

  20. Multielement stoichiometry in Quercus variabilis under natural phosphorus variation in subtropical China

    PubMed Central

    Zhou, Xuan; Sun, Xiao; Du, Baoming; Yin, Shan; Liu, Chunjiang

    2015-01-01

    Plant stoichiometry in relation to environmental factors has recently received increasing attention. However, regulations and variations of plant elements in different environments are not well understood. We investigated homeostasis and variation of macroelements (C, N, P, K, Ca, Mg, and S), essential microelements (Fe, Mn, and Zn) and non-essential elements (Al) in Quercus variabilis leaves at a range of natural P concentration from P-rich to P-deficient (typical subtropical conditions) soils. The results showed that element ratios were more stable (except for C:P and Mn:P) than individual element concentrations. Of the individual elements, protein-related elements (e.g. N, S, and Fe) were correlated with leaf P while non-protein elements (e.g. C, K, and Ca) were not. The degree of homeostasis indicated that macroelements (N, P, and Ca) concentrations were more variable than microelements (Mn, Zn, and Al) under a varying element concentration in soils. These results suggest that local P-rich geochemistry alters leaf element concentrations, but not element ratios, and that plants are capable of meeting their needs for elements in certain proportions to achieve optimal performance under varying elemental conditions. PMID:25592849

  1. 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

  2. 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

  3. 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

  4. Natural variation of the root morphological response to nitrate supply in Arabidopsis thaliana.

    PubMed

    De Pessemier, Jérôme; Chardon, Fabien; Juraniec, Michal; Delaplace, Pierre; Hermans, Christian

    2013-01-01

    Nitrogen fertilization increases crop yield but excessive nitrate use can be a major environmental problem due to soil leaching or greenhouse gas emission. Root traits have been seldom considered as selection criteria to improve Nitrogen Use Efficiency of crops, due to the difficulty of measuring root traits under field conditions. Nonetheless, learning about mechanisms of lateral root (LR) growth stimulation or repression by nitrate availability could help to redesign root system architecture (RSA), a strategy aimed at developing plants with a dense and profound root system and with higher N uptake efficiency. Here, we explored the genetic diversity provided by natural populations of the model species Arabidopsis thaliana to identify potentially adaptive differences in biomass production and root morphology in response to nitrate availability. A core collection of 24 accessions that maximizes the genetic diversity within the species and Col-0 (the reference accession) were grown vertically on agar medium at moderate (N+) nitrate level for 6 days and then transferred to the same condition or to low (N-) nitrate concentration for 7 days. There was a major nutritional effect on the shoot biomass and root to shoot biomass ratio. The variation of the root biomass and RSA traits (primary root length, LRs number, LR mean length, total LRs length and LR densities) was primarily genetically determined. Differences in RSA traits between accessions were somewhat more pronounced at N-. Some accessions produced almost no visible LRs (Pyl-1, N13) at N-, while other produced up to a dozen (Kn-0). Taken together our data illustrate that natural variation exists within Arabidopsis for the studied traits. The identification of RSA ideotypes in the N response will facilitate further analysis of quantitative traits for root morphology. PMID:22683348

  5. 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

  6. 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

  7. 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.

  8. 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

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

    SciTech Connect

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

    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

  10. Impact of natural variation in bacterial F17G adhesins on crystallization behaviour.

    PubMed

    Buts, Lieven; Wellens, Adinda; Van Molle, Inge; Wyns, Lode; Loris, Remy; Lahmann, Martina; Oscarson, Stefan; De Greve, Henri; Bouckaert, Julie

    2005-08-01

    Since the introduction of structural genomics, the protein has been recognized as the most important variable in crystallization. Recent strategies to modify a protein to improve crystal quality have included rationally engineered point mutations, truncations, deletions and fusions. Five naturally occurring variants, differing in 1-18 amino acids, of the 177-residue lectin domain of the F17G fimbrial adhesin were expressed and purified in identical ways. For four out of the five variants crystals were obtained, mostly in non-isomorphous space groups, with diffraction limits ranging between 2.4 and 1.1 A resolution. A comparative analysis of the crystal-packing contacts revealed that the variable amino acids are often involved in lattice contacts and a single amino-acid substitution can suffice to radically change crystal packing. A statistical approach proved reliable to estimate the compatibilities of the variant sequences with the observed crystal forms. In conclusion, natural variation, universally present within prokaryotic species, is a valuable genetic resource that can be favourably employed to enhance the crystallization success rate with considerably less effort than other strategies. PMID:16041081

  11. Natural Variation in Petal Color in Lycoris longituba Revealed by Anthocyanin Components

    PubMed Central

    He, Qiuling; Shen, Ye; Wang, Mingxiu; Huang, Minren; Yang, Ruizhen; Zhu, Shuijin; Wang, Liangsheng; Xu, Yanjun; Wu, Rongling

    2011-01-01

    Lycoris longituba is one of the species belonging to the Amaryllidaceae family. Despite its limited distribution, endemic to central eastern China, this species displays an exceptionally wide diversity of flower colors from purple, red, orange, to yellow, in nature. We study the natural variation of floral color in L. longituba by testing the components of water-soluble vacuolar pigments – anthocyanins – in its petals using high-performance liquid chromatography coupled with photodiode array detection and electrospray ionization mass spectrometry. Four anthocyanins were identified, cyanidin-3-sophoroside (Cy3So), cyanidin-3-xylosylglucoside (Cy3XyGlc), cyanidin-3-sambubioside (Cy3Sa), and pelargonidin-3-xylosylglucoside (Pg3XyGlc), which occur at various amounts in L. longituba petals of different colors. A multivariate analysis was used to explore the relationship between pigments and flower color. Anthocyanins have been thought to play a major role in acting as a UV screen that protects the plant's DNA from sunlight damage and attracting insects for the purpose of pollination. Thus, knowledge about the content and type of anthocyanins determining the petal coloration of Lycoris longituba will help to study the adaptive evolution of flowers and provide useful information for the ornamental breeding of this species. PMID:21829604

  12. 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

  13. Variations in the Nature of Triple Bonds: The N2, HCN, and HC2H Series.

    PubMed

    Xu, Lu T; Dunning, Thom H

    2016-07-01

    The inertness of molecular nitrogen and the reactivity of acetylene suggest there are significant variations in the nature of triple bonds. To understand these differences, we performed generalized valence bond as well as more accurate electronic structure calculations on three molecules with putative triple bonds: N2, HCN, and HC2H. The calculations predict that the triple bond in HC2H is quite different from the triple bond in N2, with HCN being an intermediate case but closer to N2 than HC2H. The triple bond in N2 is a traditional triple bond with the spins of the electrons in the bonding orbital pairs predominantly singlet coupled in the GVB wave function (92%). In HC2H, however, there is a substantial amount of residual CH(a(4)Σ(-)) fragment coupling in the triple bond at its equilibrium geometry with the contribution of the perfect pairing spin function dropping to 82% (77% in a full valence GVB calculation). This difference in the nature of the triple bond in N2 and HC2H may well be responsible for the differences in the reactivities of N2 and HC2H. PMID:27299373

  14. 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

  15. Population history and natural selection shape patterns of genetic variation in 132 genes.

    PubMed

    Akey, Joshua M; Eberle, Michael A; Rieder, Mark J; Carlson, Christopher S; Shriver, Mark D; Nickerson, Deborah A; Kruglyak, Leonid

    2004-10-01

    Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex disease genes. Although the signature that natural selection imparts on DNA sequence variation is difficult to disentangle from the effects of neutral processes such as population demographic history, selective and demographic forces can be distinguished by analyzing multiple loci dispersed throughout the genome. We studied the molecular evolution of 132 genes by comprehensively resequencing them in 24 African-Americans and 23 European-Americans. We developed a rigorous computational approach for taking into account multiple hypothesis tests and demographic history and found that while many apparent selective events can instead be explained by demography, there is also strong evidence for positive or balancing selection at eight genes in the European-American population, but none in the African-American population. Our results suggest that the migration of modern humans out of Africa into new environments was accompanied by genetic adaptations to emergent selective forces. In addition, a region containing four contiguous genes on Chromosome 7 showed striking evidence of a recent selective sweep in European-Americans. More generally, our results have important implications for mapping genes underlying complex human diseases. PMID:15361935

  16. 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

  17. A variational justification of the assumed natural strain formulation of finite elements. I - Variational principles. II - The C(0) four-node plate element

    NASA Technical Reports Server (NTRS)

    Militello, Carmelo; Felippa, Carlos A.

    1990-01-01

    The assumed natural strain formulation of finite elements is interpreted from a variational standpoint. The approach is based on hybrid extensions of the Reissner-type functional which uses the strains and displacements as independent fields. Consideration is restricted to linear elasticity. The four-node C(0) plate-bending quadrilateral is used as a specific example to illustrate the application of the present interpretation. A key finding is that any change in the strain-displacement interpolation from the variationally consistent interpolation must be associated in some way to the addition of incompatible displacement modes.

  18. Seasonal and spatial variations of diurnal variations of the VLF pulsed flux of the natural electromagnetic field recorded in middle latitudes

    NASA Astrophysics Data System (ADS)

    Naguslaeva, I. B.; Bashkuev, Yu. B.; Dembelov, M. G.

    2016-05-01

    A database of continuous measurements of the VLF pulsed flux of the natural electromagnetic field of the Earth (NEMFE) in southern Siberia during the period from March 31, 2008 to the present was created. Analysis of long-term continuous observations has shown that NEMFE diurnal variations have stable seasonal changes. A high interannual correlation coefficient of NEMFE diurnal variations for the same months in 2008-2014 was discovered. The analysis of data from spaced recorders has shown a high degree of spatial correlation, which indicates a single local mechanism of the NEMFE formation.

  19. Topography caused by mantle density variations: Observation-based estimates and models derived from tomography and lithosphere thickness

    NASA Astrophysics Data System (ADS)

    Steinberger, Bernhard

    2016-01-01

    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% in the lithosphere above ≈150 km depth, with anomalies below as inferred from tomography, or if the excess density is ≈0.4% in the entire lithosphere. Further, a good fit is found for viscosity ≈1020 Pas in the asthenosphere, increasing to ≈1023 Pas 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, topography

  20. 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

  1. 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. PMID:26480842

  2. 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

  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. The Holocene flood variability of rivers in the Lesser Caucasus region - natural and human causes

    NASA Astrophysics Data System (ADS)

    von Suchodoletz, Hans; Zielhofer, Christoph; Faust, Dominik

    2015-04-01

    Flooding constitutes a serious hazard for human civilisations. In order to predict future flooding it is necessary to understand the former dynamics of river systems, i.e. causes and triggers for changes of their flood variability during the past. Fluvial sediments are generally good archives for studying flood events at centennial and millennial time scales. However, due to the discontinuous and complex character of fluvial sequences these studies have to be comprehensive and must be compared with other palaeoenvironmental archives from the studied region. Floodplains in the Caucasus area are generally densely populated and regularly hit by strong inundations. This demonstrates the urgent need to understand the flood variability of rivers in this region. Accordingly, during the last years we comparatively studied Holocene fluvial sediments along several rivers in eastern Georgia that originate from the Lesser Caucasus Mountains. These sediments are naturally outcropped in numerous sections and were investigated with geomorphologic, stratigraphic, sedimentologic and geochronologic methods. Our investigations demonstrate that the flood variability of the investigated rivers showed a similar pattern during the first part of the Holocene that obviously followed climatically-controlled vegetation changes. More humid periods were characterized by geomorphic stability indicated by soil formation, whereas more arid periods showed geomorphic activity characterized by the accumulation of fluvial sediments. In difference, the late Holocene pattern of flood variability showed increasing differences between the rivers what indicates a dominant anthropogenic influence during that period. Altogether, it appeared that the natural pattern of flood variability of this region is similar to that of other semi-arid to semi-humid regions.

  5. 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. PMID:26825180

  6. 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

  7. 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

  8. 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

  9. 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. PMID:25599229

  10. 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.

  11. 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

  12. 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

  13. 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

  14. Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet

    PubMed Central

    Saïdou, Abdoul-Aziz; Mariac, Cédric; Luong, Vivianne; Pham, Jean-Louis; Bezançon, Gilles; Vigouroux, Yves

    2009-01-01

    The identification of genes selected during and after plant domestication is an important research topic to enhance knowledge on adaptative evolution. Adaptation to different climates was a key factor in the spread of domesticated crops. We conducted a study to identify genes responsible for these adaptations in pearl millet and developed an association framework to identify genetic variations associated with the phenotype in this species. A set of 90 inbred lines genotyped using microsatellite loci and AFLP markers was used. The population structure was assessed using two different Bayesian approaches that allow inbreeding or not. Association studies were performed using a linear mixed model considering both the population structure and familial relationships between inbred lines. We assessed the ability of the method to limit the number of false positive associations on the basis of the two different Bayesian methods, the number of populations considered and different morphological traits while also assessing the power of the methodology to detect given additive effects. Finally, we applied this methodology to a set of eight pearl millet genes homologous to cereal flowering pathway genes. We found significant associations between several polymorphisms of the pearl millet PHYC gene and flowering time, spike length, and stem diameter in the inbred line panel. To validate this association, we performed a second association analysis in a different set of pearl millet individuals from Niger. We confirmed a significant association between genetic variation in this gene and these characters. PMID:19433627

  15. Dynamics of Cytoplasmic Incompatibility and Mtdna Variation in Natural Drosophila Simulans Populations

    PubMed Central

    Turelli, M.; Hoffmann, A. A.; McKechnie, S. W.

    1992-01-01

    In Drosophila simulans a cytoplasmically transmitted microorganism causes reduced egg hatch when infected males mate with uninfected females. The infection is rapidly spreading northward in California. Data on a specific mtDNA restriction site length polymorphism show that changes in the frequency of mtDNA variants are associated with this spread. All infected flies possess the same mtDNA allele, whereas the uninfected flies are polymorphic. Given that both paternal inheritance of the infection and imperfect maternal transmission have been demonstrated, one might expect instead that both infected and uninfected flies would possess both mtDNA variants. Our data suggest that imperfect female transmission of the infection (and/or the loss of the infection among progeny) is more common in nature than paternal transmission. A simple model of intrapopulation dynamics, with empirically supported parameter values, adequately describes the joint frequencies of the mtDNA variants and incompatibility types. PMID:1468627

  16. 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.

  17. 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. PMID:14753645

  18. 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

  19. 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

  20. 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

  1. 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. PMID:18304195

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. Analysis of natural ground-water level variations for hydrogeologic conceptualization, Hanford Site, Washington

    NASA Astrophysics Data System (ADS)

    Nevulis, Richard H.; Davis, Donald R.; Sorooshian, Soroosh

    1989-07-01

    This study involves the analysis of groundwater level time series for the purpose of obtaining details for a conceptual hydrogeologic model at a time when conventional hydraulic stress testing was not feasible due to regulatory considerations. The study area is located in south central Washington in the Pasco Basin which was a candidate site for underground disposal of high-level radioactive nuclear wastes. Advantages of such passive methods of analysis may include relative simplicity, low cost, and avoidance of disturbances typically associated with stress testing of aquifers. Through this approach, natural and incidental man-made groundwater level variations, most of which are quite small, are examined by statistical and analytical methods in conjunction with hydrogeologic models to draw inferences on the hydrogeology. Vertical connectivity of the hydrostratigraphic units is also examined by analyzing groundwater level time series of five units at three piezometer nests. It is concluded that a combination of statistical/analytical approaches used in a complementary fashion can provide useful information about the hydrogeology of a given area. A meaningful analysis requires that there is (1) a source of influence on the groundwater levels, (2) a response to that influence, (3) a sufficiently long data record, and (4) measurement and analytical techniques which allow the detection and identification of the influence and response.

  7. Natural Selection Canalizes Expression Variation of Environmentally Induced Plasticity-Enabling Genes

    PubMed Central

    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.

    2014-01-01

    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

  8. Developing natural convection in a fluid layer with localized heating and large viscosity variation

    NASA Astrophysics Data System (ADS)

    Hickox, C. E.; Chu, Tze Yao

    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.

  9. 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

  10. 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.

  11. Natural Variation for Carbohydrate Content in Arabidopsis. Interaction with Complex Traits Dissected by Quantitative Genetics1

    PubMed Central

    Calenge, Fanny; Saliba-Colombani, Véra; Mahieu, Stéphanie; Loudet, Olivier; Daniel-Vedele, Françoise; Krapp, Anne

    2006-01-01

    Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 × Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes. PMID:16798941

  12. 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

  13. Nuclear genomic control of naturally occurring variation in mitochondrial function in Drosophila melanogaster

    PubMed Central

    2012-01-01

    Background Mitochondria are organelles found in nearly all eukaryotic cells that play a crucial role in cellular survival and function. Mitochondrial function is under the control of nuclear and mitochondrial genomes. While the latter has been the focus of most genetic research, we remain largely ignorant about the nuclear-encoded genomic control of inter-individual variability in mitochondrial function. Here, we used Drosophila melanogaster as our model organism to address this question. Results We quantified mitochondrial state 3 and state 4 respiration rates and P:O ratio in mitochondria isolated from the thoraces of 40 sequenced inbred lines of the Drosophila Genetic Reference Panel. We found significant within-population genetic variability for all mitochondrial traits. Hence, we performed genome-wide association mapping and identified 141 single nucleotide polymorphisms (SNPs) associated with differences in mitochondrial respiration and efficiency (P ≤1 × 10-5). Gene-centered regression models showed that 2–3 SNPs can explain 31, 13, and 18% of the phenotypic variation in state 3, state 4, and P:O ratio, respectively. Most of the genes tagged by the SNPs are involved in organ development, second messenger-mediated signaling pathways, and cytoskeleton remodeling. One of these genes, sallimus (sls), encodes a component of the muscle sarcomere. We confirmed the direct effect of sls on mitochondrial respiration using two viable mutants and their coisogenic wild-type strain. Furthermore, correlation network analysis revealed that sls functions as a transcriptional hub in a co-regulated module associated with mitochondrial respiration and is connected to CG7834, which is predicted to encode a protein with mitochondrial electron transfer flavoprotein activity. This latter finding was also verified in the sls mutants. Conclusions Our results provide novel insights into the genetic factors regulating natural variation in mitochondrial function in D

  14. 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

  15. Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in the LRR-KISS gene.

    PubMed

    Julkowska, Magdalena M; Klei, Karlijn; Fokkens, Like; Haring, Michel A; Schranz, M Eric; Testerink, Christa

    2016-04-01

    Natural variation among Arabidopsis accessions is an important genetic resource to identify mechanisms underlying plant development and stress tolerance. To evaluate the natural variation in salinity stress tolerance, two large-scale experiments were performed on two populations consisting of 160 Arabidopsis accessions each. Multiple traits, including projected rosette area, and fresh and dry weight were collected as an estimate for salinity tolerance. Our results reveal a correlation between rosette size under salt stress conditions and developmental differences between the accessions grown in control conditions, suggesting that in general larger plants were more salt tolerant. This correlation was less pronounced when plants were grown under severe salt stress conditions. Subsequent genome wide association study (GWAS) revealed associations with novel candidate genes for salinity tolerance such as LRR-KISS (At4g08850),flowering locus KH-domain containing protein and a DUF1639-containing protein Accessions with high LRR-KISS expression developed larger rosettes under salt stress conditions. Further characterization of allelic variation in candidate genes identified in this study will provide more insight into mechanisms of salt stress tolerance due to enhanced shoot growth. PMID:26873976

  16. Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in the LRR-KISS gene

    PubMed Central

    Julkowska, Magdalena M.; Klei, Karlijn; Fokkens, Like; Haring, Michel A.; Schranz, M. Eric; Testerink, Christa

    2016-01-01

    Natural variation among Arabidopsis accessions is an important genetic resource to identify mechanisms underlying plant development and stress tolerance. To evaluate the natural variation in salinity stress tolerance, two large-scale experiments were performed on two populations consisting of 160 Arabidopsis accessions each. Multiple traits, including projected rosette area, and fresh and dry weight were collected as an estimate for salinity tolerance. Our results reveal a correlation between rosette size under salt stress conditions and developmental differences between the accessions grown in control conditions, suggesting that in general larger plants were more salt tolerant. This correlation was less pronounced when plants were grown under severe salt stress conditions. Subsequent genome wide association study (GWAS) revealed associations with novel candidate genes for salinity tolerance such as LRR-KISS (At4g08850), flowering locus KH-domain containing protein and a DUF1639-containing protein. Accessions with high LRR-KISS expression developed larger rosettes under salt stress conditions. Further characterization of allelic variation in candidate genes identified in this study will provide more insight into mechanisms of salt stress tolerance due to enhanced shoot growth. PMID:26873976

  17. 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

  18. 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

  19. 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.

  20. Genetic variation for worm burdens in laying hens naturally infected with gastro-intestinal nematodes.

    PubMed

    Wongrak, K; Daş, G; von Borstel, U König; Gauly, M

    2015-01-01

    1. Genetic parameters were determined for the worm burden of the most common gastro-intestinal nematodes in two chicken genotypes after being exposed to free-range farming conditions for a laying period. 2. Seventeen-week-old hens of 2 brown genotypes, Lohmann Brown (LB) plus (n = 230) and LB classic (n = 230), were reared for a laying period and subjected to post-mortem parasitological examinations at 79 weeks (LB plus) or 88 weeks (LB classic) of age. 3. There was no significant difference in faecal egg counts between the genotypes. Almost all hens (>99%) were infected with at least one nematode species. Species-specific nematode prevalence ranged from 85.8% to 99.1% between the two genotypes. Heterakis gallinarum was the most prevalent nematode (98.5%), followed by Ascaridia galli (96.2%) and Capillaria spp. (86.1%). Capillaria spp. were composed of C. obsignata (79%), C. caudinflata (16%) and C. bursata (5%). 4. All phenotypic and genetic correlations among worm counts of different parasite species were positive in combined genotypes (rP ranged from 0.05 to 0.30 and rG ranged from 0.29 to 0.88). A strong genetic correlation (rG = 0.88 ± 0.34) between counts of A. galli and H. gallinarum was quantified. Heritability for total worm burden for LB plus and LB classic, respectively, were 0.55 ± 0.18 and 0.55 ± 0.34. Across both genotypes, the heritability of total worm burden was 0.56 ± 0.16. 5. In conclusion, there is a high variation attributable to genetic background of chickens in their responses to naturally acquired nematode infections. The high positive genetic correlation between counts of closely related worm species (e.g. A. galli and H. gallinarum) may indicate existence of similar genetically determined mechanism(s) in chickens for controlling these nematodes. PMID:25486507

  1. 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

  2. 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

  3. Natural genetic variation in the expression regulation of the chloroplast antioxidant system among Arabidopsis thaliana accessions.

    PubMed

    Juszczak, Ilona; Rudnik, Radoslaw; Pietzenuk, Björn; Baier, Margarete

    2012-09-01

    Photosynthesis is the predominant source of reactive oxygen species in light. In order to prevent the negative influence of reactive oxygen species (ROS) on cell functionality, chloroplasts have evolved a highly efficient antioxidant protection system. Here, we present the first study on natural variation in this system. Comparison of temperature and developmental responses in seven accessions of Arabidopsis thaliana from northern habitats showed that the regulation is widely genetically manifested, but hardly correlates with geographic parameters. Transcript, polysomal RNA (pRNA) and protein data showed that the ecotypes use different strategies to adjust the chloroplast antioxidative defense system, either by regulating transcript abundance or initiation of translation. Comparison of mRNA and pRNA levels showed that Col-0 invests more into transcript accumulation, while Van-0, WS and C24 regulates the chloroplast antioxidant protection system more on the level of pRNA. Nevertheless, both strategies of regulation led to the expression of chloroplast antioxidant enzymes at sufficient level to efficiently protect plants from ROS accumulation in Col-0, WS, C24 and Van-0. On the contrary, Cvi-0, Ms-0 and Kas-1 accumulated high amounts of ROS. The expression of copper/zinc superoxide dismutase (Csd2), ascorbate peroxidases and 2-Cys peroxiredoxins was higher in Cvi-0 on the transcriptional level, while Csd2, peroxiredoxin Q, type II peroxiredoxin E and glutathione peroxidase 1 were induced in Ms-0 on the mRNA level. Similar to Kas-1, in which mRNA levels were less than or similar to Col-0 gene, specific support for translation was observed in Ms-0, showing that the ecotypes use different strategies to adjust the antioxidant system. PMID:22339086

  4. Natural Variation of Heterokaryon Incompatibility Gene het-c in Podospora anserina Reveals Diversifying Selection

    PubMed Central

    Bastiaans, Eric; Debets, Alfons J.M.; Aanen, Duur K.; van Diepeningen, Anne D.; Saupe, Sven J.; Paoletti, Mathieu

    2014-01-01

    In filamentous fungi, allorecognition takes the form of heterokaryon incompatibility, a cell death reaction triggered when genetically distinct hyphae fuse. Heterokaryon incompatibility is controlled by specific loci termed het-loci. In this article, we analyzed the natural variation in one such fungal allorecognition determinant, the het-c heterokaryon incompatibility locus of the filamentous ascomycete Podospora anserina. The het-c locus determines an allogenic incompatibility reaction together with two unlinked loci termed het-d and het-e. Each het-c allele is incompatible with a specific subset of the het-d and het-e alleles. We analyzed variability at the het-c locus in a population of 110 individuals, and in additional isolates from various localities. We identified a total of 11 het-c alleles, which define 7 distinct incompatibility specificity classes in combination with the known het-d and het-e alleles. We found that the het-c allorecognition gene of P. anserina is under diversifying selection. We find a highly unequal allele distribution of het-c in the population, which contrasts with the more balanced distribution of functional groups of het-c based on their allorecognition function. One explanation for the observed het-c diversity in the population is its function in allorecognition. However, alleles that are most efficient in allorecognition are rare. An alternative and not exclusive explanation for the observed diversity is that het-c is involved in pathogen recognition. In Arabidopsis thaliana, a homolog of het-c is a pathogen effector target, supporting this hypothesis. We hypothesize that the het-c diversity in P. anserina results from both its functions in pathogen-defense, and allorecognition. PMID:24448643

  5. Natural variation of heterokaryon incompatibility gene het-c in Podospora anserina reveals diversifying selection.

    PubMed

    Bastiaans, Eric; Debets, Alfons J M; Aanen, Duur K; van Diepeningen, Anne D; Saupe, Sven J; Paoletti, Mathieu

    2014-04-01

    In filamentous fungi, allorecognition takes the form of heterokaryon incompatibility, a cell death reaction triggered when genetically distinct hyphae fuse. Heterokaryon incompatibility is controlled by specific loci termed het-loci. In this article, we analyzed the natural variation in one such fungal allorecognition determinant, the het-c heterokaryon incompatibility locus of the filamentous ascomycete Podospora anserina. The het-c locus determines an allogenic incompatibility reaction together with two unlinked loci termed het-d and het-e. Each het-c allele is incompatible with a specific subset of the het-d and het-e alleles. We analyzed variability at the het-c locus in a population of 110 individuals, and in additional isolates from various localities. We identified a total of 11 het-c alleles, which define 7 distinct incompatibility specificity classes in combination with the known het-d and het-e alleles. We found that the het-c allorecognition gene of P. anserina is under diversifying selection. We find a highly unequal allele distribution of het-c in the population, which contrasts with the more balanced distribution of functional groups of het-c based on their allorecognition function. One explanation for the observed het-c diversity in the population is its function in allorecognition. However, alleles that are most efficient in allorecognition are rare. An alternative and not exclusive explanation for the observed diversity is that het-c is involved in pathogen recognition. In Arabidopsis thaliana, a homolog of het-c is a pathogen effector target, supporting this hypothesis. We hypothesize that the het-c diversity in P. anserina results from both its functions in pathogen-defense, and allorecognition. PMID:24448643

  6. 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. PMID:25583489

  7. 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

  8. Short-term variation in sperm competition causes sperm-mediated epigenetic effects on early offspring performance in the zebrafish

    PubMed Central

    Zajitschek, Susanne; Hotzy, Cosima; Zajitschek, Felix; Immler, Simone

    2014-01-01

    The inheritance of non-genetic factors is increasingly seen to play a major role in ecology and evolution. While the causes and consequences of epigenetic effects transmitted from the mother to the offspring have received ample attention, much less is known about how variation in the condition of the father affects the offspring. Here, we manipulated the intensity of sperm competition experienced by male zebrafish Danio rerio to investigate the potential for sperm-mediated epigenetic effects over a relatively short period of time. We found that the rapid responses of males to varying intensity of sperm competition not only affected sperm traits as shown previously, but also the performance of the resulting offspring. We observed that males exposed to high intensity of sperm competition produced faster swimming and more motile sperm, and sired offspring that hatched over a narrower time frame but exhibited a lower survival rate than males exposed to low intensity of sperm competition. Our results provide striking evidence for short-term paternal effects and the possible fitness consequences of such sperm-mediated non-genetic factors not only for the resulting offspring but also for the female. PMID:24789902

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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…

  15. 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

  16. The criteria of natural disasters, caused by hydro-meteorological natural phenomena in winter period in different urban regions of Russia

    NASA Astrophysics Data System (ADS)

    Gavrilova, S.

    2012-04-01

    Russia is one of the most spread countries in the world and it has the big number of different types of natural phenomena, which can cause natural disaster. Unfortunately, nowadays the number of victims of natural hazards and their influence on technological systems doesn't decrease. There are many reasons of that situation - both geographical and human. One of the reasons is the fact that the criteria of which meteorological or hydrological conditions can cause an emergency situation are equal for the whole territory of Russia. And that's why many dangerous situations are underestimated. The analysis of the distribution of criteria in Russia shows that only temperature phenomena (such as frost or heat) have really space differentiation. The criteria of different natural disasters and hazards should depend on many factors - both social-economical and hydro-meteorological. Social-economical factors depend on human occupancy of territory, on the method of usage the land etc. So, it is clear, that in very populated areas (as big cities) the criteria should be different than in other areas. Hydro-meteorological factors deal with climatic and landscape conditions of the territories. The geographical zoning of Russia was conduct and clusters with equal parameters were determined. That means that in these areas the same hydro meteorological characteristics can be used for. The new criteria for the number of natural phenomena (such as hale, snowfalls etc) were found. The updated criteria was determined both by analyzing the factual reports on emergency situation, caused by natural phenomena in each cluster and the characteristics from meteorological stations. Updating criteria of natural disasters, taking into account different characteristics of the analyzing area can be wildly used in Russian ministry of emergency situation and Gydrometeorological services for predicting emergency situation for safety and sustainable development in different regions.* *The work was

  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. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. Wild rodents as a model to discover genes and pathways underlying natural variation in infectious disease susceptibility.

    PubMed

    Turner, Andrew K; Paterson, Steve

    2013-04-01

    Individuals vary in their susceptibility to infectious disease and it is now well established that host genetic factors form a major component of this variation. The discovery of genes underlying susceptibility has the potential to lead to improved disease control, through the identification and management of vulnerable individuals and the discovery of novel therapeutic targets. Laboratory rodents have proved invaluable for ascertaining the function of genes involved in immunity to infection. However, these captive animals experience conditions very different to the natural environment, lacking the genetic diversity and environmental pressures characteristic of natural populations, including those of humans. It has therefore often proved difficult to translate basic laboratory research to the real world. In order to further our understanding of the genetic basis of infectious disease resistance, and the evolutionary forces that drive variation in susceptibility, we propose that genetic research traditionally conducted on laboratory animals is expanded to the more ecologically valid arena of natural populations. In this article we highlight the potential of using wild rodents as a new resource for biomedical research, to link the functional genetic knowledge gained from laboratory rodents with the variation in infectious disease susceptibility observed in humans and other natural populations. © 2013 Blackwell Publishing Ltd. PMID:23550923

  4. 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. PMID:26678756

  5. 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.

  6. Geographic Variations in Hotspot Geochemistry Caused by 3D Dynamics and Melting of a Heterogeneous Mantle Plume

    NASA Astrophysics Data System (ADS)

    Bianco, T. A.; Ito, G.; van Hunen, J.; Ballmer, M.; Mahoney, J. J.

    2006-12-01

    Spatial variations in magma geochemistry among hotspot volcanoes hold clues to the dynamics and composition of the mantle feeding hotspot volcanism. We use a 3D geodynamic model of plume-lithosphere interaction to explore the causes of spatial patterns of magmatic volumes and compositions at intraplate hotspots. This study focuses on coupling between upper mantle flow, heat transfer, and melting of a heterogeneous (veined) plume. We assume multiple lithologies have different solidi, trace-element, and isotope composition. We use the Cartesian finite-element code, CITCOM, (Zhong and Watts, 2002) to simulate mantle convection with the extended Boussinesq approximation in a volume of upper mantle 400 km in thickness. A parameterized melting model is used to simulate melting of materials with different water contents (Katz et al., 2003). Melt depletion (F) for each lithology is calculated at finite element nodes as a function of temperature, pressure, and water content and is advected using particle tracers. We quantify the response of the geographic pattern of the volume and composition of magmas to different lithospheric thicknesses, and plume temperatures and viscosities, which together control the melting rates and sizes of the melting zones for the different lithologies. In the case of two-lithologies, preliminary results of a sluggishly convecting plume rising beneath thick lithosphere (60-100 km) predict that the melting zone of the least refractory "lithology 1" is wider than that of the more refractory "lithology 2". This leads to the prediction that on the surface, the isotope signature of lithology 1 is most prominent at the leading edge (i.e., upwind edge of plate motion) of the hotspot, whereas the isotope signature of lithology 2 is strongest at the hotspot center. This pattern will likely change for plumes convecting more vigorously or thinner lithosphere.

  7. 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.

  8. 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)

  9. Dynamic impact on a frozen support caused by natural and quasinatural oscillations of an ice plate

    NASA Astrophysics Data System (ADS)

    Greshilov, A. G.

    2016-01-01

    This paper presents the results of the numerical and analytical study of natural and quasinatural bending-gravitational oscillations of a circular elastic ice plate floating on the fluid surface and frozen onto a cylindrical vertical support. In the framework of the shallow water theory for bounded and unbounded reservoirs, the dependence of natural and quasinatural frequencies of geometrical parameters of the oscillation region is studied.

  10. Natural variation of histone modification and its impact on gene expression in the rat genome

    PubMed Central

    Rintisch, Carola; Heinig, Matthias; Bauerfeind, Anja; Schafer, Sebastian; Mieth, Christin; Patone, Giannino; Hummel, Oliver; Chen, Wei; Cook, Stuart; Cuppen, Edwin; Colomé-Tatché, Maria; Johannes, Frank; Jansen, Ritsert C.; Neil, Helen; Werner, Michel; Pravenec, Michal; Vingron, Martin; Hubner, Norbert

    2014-01-01

    Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype–phenotype relationships. PMID:24793478

  11. Natural variation of histone modification and its impact on gene expression in the rat genome.

    PubMed

    Rintisch, Carola; Heinig, Matthias; Bauerfeind, Anja; Schafer, Sebastian; Mieth, Christin; Patone, Giannino; Hummel, Oliver; Chen, Wei; Cook, Stuart; Cuppen, Edwin; Colomé-Tatché, Maria; Johannes, Frank; Jansen, Ritsert C; Neil, Helen; Werner, Michel; Pravenec, Michal; Vingron, Martin; Hubner, Norbert

    2014-06-01

    Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype-phenotype relationships. PMID:24793478

  12. 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,…

  13. Natural Variation in the Pto Pathogen Resistance Gene Within Species of Wild Tomato (Lycopersicon). I. Functional Analysis of Pto Alleles

    PubMed Central

    Rose, Laura E.; Langley, Charles H.; Bernal, Adriana J.; Michelmore, Richard W.

    2005-01-01

    Disease resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) in the cultivated tomato, Lycopersicon esculentum, and the closely related L. pimpinellifolium is triggered by the physical interaction between plant disease resistance protein, Pto, and the pathogen avirulence protein, AvrPto. To investigate the extent to which variation in the Pto gene is responsible for naturally occurring variation in resistance to Pst, we determined the resistance phenotype of 51 accessions from seven species of Lycopersicon to isogenic strains of Pst differing in the presence of avrPto. One-third of the plants displayed resistance specifically when the pathogen expressed AvrPto, consistent with a gene-for-gene interaction. To test whether this resistance in these species was conferred specifically by the Pto gene, alleles of Pto were amplified and sequenced from 49 individuals and a subset (16) of these alleles was tested in planta using Agrobacterium-mediated transient assays. Eleven alleles conferred a hypersensitive resistance response (HR) in the presence of AvrPto, while 5 did not. Ten amino acid substitutions associated with the absence of AvrPto recognition and HR were identified, none of which had been identified in previous structure-function studies. Additionally, 3 alleles encoding putative pseudogenes of Pto were isolated from two species of Lycopersicon. Therefore, a large proportion, but not all, of the natural variation in the reaction to strains of Pst expressing AvrPto can be attributed to sequence variation in the Pto gene. PMID:15944360

  14. 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

  15. 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

  16. 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,…

  17. 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

  18. 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...

  19. 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…

  20. Possible changes in natural Pc 1 pulsation activity caused by BART

    SciTech Connect

    Samadani, R.; Fraser-Smith, A.C.; Villard, O.G. Jr.

    1981-10-01

    In a previous preliminary study of the diurnal variation of Pc 1 pulsation activity at Stanford during four months in 1975, evidence was obtained for changes in the rate of occurrence of the pulsations around the times when service was started and terminated by the San Francisco Bay Area Rapid Transit (BART) system (Fraser-Smith et al., 1979). The present study extends this earlier work by analyzing Pc 1 pulsation data recorded at Stanford during 1976. Spectrograms of N--S geomagnetic activity were prepared for the complete year and 15-minute intervals containing Pc 1 pulsation activity were tabulated. The diurnal variations of the Pc 1 activity (as measured by these 15-minute intervals) for weekdays, during which BART was in operation, and weekends, during which BART was not normally in operation, were compared. Correlations of the observed differences with the BART schedule suggest once again that the ultralow-frequency electromagnetic noise produced by BART may be influencing the occurrence of Pc 1 pulsations along the Stanford geomagnetic meridian.

  1. 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.

  2. 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

  3. 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

  4. Patterned Ground in Wetlands of the Maya Lowlands: Anthropogenic and Natural Causes

    NASA Astrophysics Data System (ADS)

    Beach, T.; Beach, S. L.

    2004-12-01

    We use geological and archaeological evidence to understand the formation of patterned ground in perennial and seasonal wetlands in the karst depressions of Belize and Guatemala. Some scholars have argued that these features are the remnants of ancient Maya wetland fields, chinampas, on which intensive cultivation produced food that could begin to nourish the extremely high population of the Late Classic (A.D. 550-850). Others have argued that these were natural features or that they represent landscape manipulation for rising sea level in the Preclassic (1000 B.C. -A.D. 250). We present the evidence for ancient intensive agriculture and natural landscape formation with multiple proxies: excavated field and canal features, artifacts, pollen, soil stratigraphy, and water chemistry. Evidence thus far suggests that many regional depressions have Preclassic (1200 BC to AD 200) or earlier paleosols, buried from 1-2 m by eroded soils induced by Maya land use practices. These paleosols were buried by eroded sediments from uplands and by precipitation of gypsum from rising groundwater. The sedimentation occurred largely between the Preclassic and Late Classic, when ancient Maya farmers built canals in pre-existing low spots to reclaim these wetlands. Thus, stable natural processes, environmental change, and human manipulation have acted together to form patterned wetland ground over the later Holocene.

  5. 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.

  6. Natural variation and evolution of the avirulence genes in Magnaporthe oryzae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The avirulence genes in Magnaporthe oryzae are important determinants for the corresponding resistance genes in rice. In the present study, we analyzed DNA sequence variation of the five avirulence genes, AVR-Pita1, AVR-Pik, AVR-Piz(t), AVR-Pia and AVR-Pii in field blast isolates in order to unders...

  7. 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…

  8. 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...

  9. Variations in stress and immune responses of cattle: Natural deviations and nutritional influences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Given the importance of the innate immune response with regard to the overall health and survival of domestic livestock, the primary immunological focus of this manuscript is on variations that exist within the innate immune system, and efforts to selectively and precisely modulate this system in a ...

  10. 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.

  11. Genetic and Phenotypic Variation of FMDV During Serial Passages in a Natural Host

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foot-and-Mouth Disease Virus (FMDV) exhibits high mutation rates during replication that have been suggested to be of adaptive value. However, even though genetic variation in RNA viruses has been extensively examined during virus replication in a wide variety of in vitro cell cultures, very little ...

  12. 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…

  13. Sudden unexpected infant death: differentiating natural from abusive causes in the emergency department.

    PubMed

    Bechtel, Kirsten

    2012-10-01

    Sudden unexpected infant deaths (SUIDs) are deaths in infants younger than 12 months that occur suddenly, unexpectedly, and without obvious cause in the emergency department (ED). Sudden infant death syndrome, the leading cause of SUID in the United States, is much more common, but fatal child abuse and neglect have been sometimes mistaken for sudden infant death syndrome. The distinction between these 2 entities can only be made after a thorough investigation of the scene, interview of caregivers, and a complete forensic autopsy. Development of ED guidelines for the reporting and evaluation of SUID, in collaboration with the local medical examiner and child death review teams, will enable ED practitioners to collect important information in a compassionate manner that will be valuable to the investigating personnel. PMID:23034500

  14. 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

  15. PEP1 of Arabis alpina Is Encoded by Two Overlapping Genes That Contribute to Natural Genetic Variation in Perennial Flowering

    PubMed Central

    Albani, Maria C.; Castaings, Loren; Wötzel, Stefan; Mateos, Julieta L.; Wunder, Jörg; Wang, Renhou; Reymond, Mathieu; Coupland, George

    2012-01-01

    Higher plants exhibit a variety of different life histories. Annual plants live for less than a year and after flowering produce seeds and senesce. By contrast perennials live for many years, dividing their life cycle into episodes of vegetative growth and flowering. Environmental cues control key check points in both life histories. Genes controlling responses to these cues exhibit natural genetic variation that has been studied most in short-lived annuals. We characterize natural genetic variation conferring differences in the perennial life cycle of Arabis alpina. Previously the accession Pajares was shown to flower after prolonged exposure to cold (vernalization) and only for a limited period before returning to vegetative growth. We describe five accessions of A. alpina that do not require vernalization to flower and flower continuously. Genetic complementation showed that these accessions carry mutant alleles at PERPETUAL FLOWERING 1 (PEP1), which encodes a MADS box transcription factor orthologous to FLOWERING LOCUS C in the annual Arabidopsis thaliana. Each accession carries a different mutation at PEP1, suggesting that such variation has arisen independently many times. Characterization of these alleles demonstrated that in most accessions, including Pajares, the PEP1 locus contains a tandem arrangement of a full length and a partial PEP1 copy, which give rise to two full-length transcripts that are differentially expressed. This complexity contrasts with the single gene present in A. thaliana and might contribute to the more complex expression pattern of PEP1 that is associated with the perennial life-cycle. Our work demonstrates that natural accessions of A. alpina exhibit distinct life histories conferred by differences in PEP1 activity, and that continuous flowering forms have arisen multiple times by inactivation of the floral repressor PEP1. Similar phenotypic variation is found in other herbaceous perennial species, and our results provide a

  16. Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis

    PubMed Central

    Li, Dapeng; Baldwin, Ian T.; Gaquerel, Emmanuel

    2015-01-01

    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

  17. Slip rate variations on faults in the Basin-and-Range Province caused by regression of Late Pleistocene Lake Bonneville and Lake Lahontan

    NASA Astrophysics Data System (ADS)

    Karow, Tobias; Hampel, Andrea

    2010-12-01

    Late Pleistocene regression of two large pluvial lakes—Lake Bonneville and Lake Lahontan—caused considerable lithospheric rebound in the Basin-and-Range Province, USA. Here, we use finite-element models to show how lake growth and regression affect the temporal and spatial slip evolution on faults near the former lakes. Our results show that fluctuations in the volume of Lake Bonneville caused along-strike slip variations on the Wasatch normal fault, with a pronounced slip rate increase on its northern and central parts during lake regression. The response of normal and strike-slip faults near the ring-shaped Lake Lahontan depends on their location within the rebound area. Faults located in the centre of rebound show a slip rate increase during lake regression, whereas strike-slip faults at the periphery decelerate. All slip rate variations are caused by differential stress changes owing to changing lake levels, regardless of the individual fault response.

  18. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

    PubMed Central

    Krause, David J.; Whitaker, Rachel J.

    2015-01-01

    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. PMID:26316424

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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. PMID:26301428

  5. 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

  6. 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.

  7. Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation

    PubMed Central

    Nakagome, Shigeki; Mano, Shuhei; Kozlowski, Lukasz; Bujnicki, Janusz M.; Shibata, Hiroki; Fukumaki, Yasuaki; Kidd, Judith R.; Kidd, Kenneth K.; Kawamura, Shoji; Oota, Hiroki

    2012-01-01

    Risk alleles for complex diseases are widely spread throughout human populations. However, little is known about the geographic distribution and frequencies of risk alleles, which may contribute to differences in disease susceptibility and prevalence among populations. Here, we focus on Crohn's disease (CD) as a model for the evolutionary study of complex disease alleles. Recent genome-wide association studies and classical linkage analyses have identified more than 70 susceptible genomic regions for CD in Europeans, but only a few have been confirmed in non-European populations. Our analysis of eight European-specific susceptibility genes using HapMap data shows that at the NOD2 locus the CD-risk alleles are linked with a haplotype specific to CEU at a frequency that is significantly higher compared with the entire genome. We subsequently examined nine global populations and found that the CD-risk alleles spread through hitchhiking with a high-frequency haplotype (H1) exclusive to Europeans. To examine the neutrality of NOD2, we performed phylogenetic network analyses, coalescent simulation, protein structural prediction, characterization of mutation patterns, and estimations of population growth and time to most recent common ancestor (TMRCA). We found that while H1 was significantly prevalent in European populations, the H1 TMRCA predated human migration out of Africa. H1 is likely to have undergone negative selection because 1) the root of H1 genealogy is defined by a preexisting amino acid substitution that causes serious conformational changes to the NOD2 protein, 2) the haplotype has almost become extinct in Africa, and 3) the haplotype has not been affected by the recent European expansion reflected in the other haplotypes. Nevertheless, H1 has survived in European populations, suggesting that the haplotype is advantageous to this group. We propose that several CD-risk alleles, which destabilize and disrupt the NOD2 protein, have been maintained by natural

  8. 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

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

    PubMed

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

    2016-06-01

    Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes. PMID:26428711

  10. 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

  11. 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

  12. Chromosomal and environmental determinants of morphometric variation in natural populations of the malaria vector Anopheles funestus in Cameroon

    PubMed Central

    Ayala, Diego; Caro-Riaño, Harling; Dujardin, Jean-Pierre; Rahola, Nil; Simard, Frederic; Fontenille, Didier

    2013-01-01

    Anopheles funestus is one of the most proficient malaria vectors in the world, mainly because of its remarkable ability to populate a wide range of ecological settings across Africa. Its formidable environmental plasticity has been primarily associated to high amounts of genetic and inversion polymorphisms. However, very little is known about the morphological changes that this ecological adaptation entails. Here, we report on wing morphometric variations in karyotyped specimens of this species collected throughout a wide range of eco-geographical conditions in Cameroon (Central Africa). Our results revealed strong selection on mosquito wing traits. Variation of wing size was dependent on temperature and elevation (p<0.001), while wing shape did not exhibit a specific environmental pattern. On the other hand, we observed a significant correlation of wing shape variation (p<0.001), but not size (p>0.05), with regard to karyotype. This pattern was maintained across different environmental conditions. In conclusion, our findings cast strong evidence that change in morphometric traits are under natural selection and contribute to local adaptation in Anopheles funestus populations. Furthermore, the robust relation between chromosome polymorphisms and wing shape suggests new evolutionary hypotheses about the effect of chromosomal inversions on phenotypic variation in this malaria vector. PMID:21414420

  13. 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.

  14. Effects of natural attenuation processes on groundwater contamination caused by abandoned waste sites in Berlin

    NASA Astrophysics Data System (ADS)

    Kerndorff, Helmut; Kühn, Stephan; Minden, Thomas; Orlikowski, Dagmar; Struppe, Thomas

    2008-07-01

    The aim of this research project is to identify, characterize and quantify natural attenuation (NA) processes in groundwater affected by emissions of abandoned waste disposal sites in Berlin-Kladow/Gatow, Germany. It is part of the funding priority called KORA established by the Federal Ministry for Education and Research (BMBF) to explore the extent to which NA can be used for remedial purposes for varied forms of soil and groundwater contamination. Information on the emission behaviour of individual parameters is generated on the basis of hydrogeochemical comparison of 20 years old and new data. Using groundwater-modelling and CFC-analysis, information on the transport and retention of pollutants in groundwater is compiled. The microbial colonization of contaminated aquifers is characterized by molecular biological methods [polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE)] to differentiate between contaminated and not contaminated zones.

  15. The natural ocean acidification and fertilization event caused by the submarine eruption of El Hierro

    PubMed Central

    Santana-Casiano, J. M.; González-Dávila, M.; Fraile-Nuez, E.; de Armas, D.; González, A. G.; Domínguez-Yanes, J. F.; Escánez, J.

    2013-01-01

    The shallow submarine eruption which took place in October 10th 2011, 1.8 km south of the island of El Hierro (Canary Islands) allowed the study of the abrupt changes in the physical-chemical properties of seawater caused by volcanic discharges. In order to monitor the evolution of these changes, seven oceanographic surveys were carried out over six months (November 2011-April 2012) from the beginning of the eruptive stage to the post-eruptive phase. Here, we present dramatic changes in the water column chemistry including large decreases in pH, striking effects on the carbonate system, decreases in the oxygen concentrations and enrichment of Fe(II) and nutrients. Our findings highlight that the same volcano which was responsible for the creation of a highly corrosive environment, affecting marine biota, has also provided the nutrients required for the rapid recuperation of the marine ecosystem. PMID:23355953

  16. 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

  17. 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

  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. Variation in cardiac glycoside content of monarch butterflies from natural populations in eastern North America.

    PubMed

    Brower, L P; McEvoy, P B; Williamson, K L; Flannery, M A

    1972-08-01

    A new spectrophotometric assay has been used to determine the gross concentration of cardiac glycoside in individual monarch butterflies. Adults sampled during the fall migration in four areas of eastern North America exhibited a wide variation in cardiac glycoside concentration. The correlation between spectrophotometrically measured concentrations and emetic dose determinations supports the existence of a broad palatability spectrum in wild monarch butterflies. The cardiac gylcoside concentration is greater in females than in males and is independent of the dry weight of the butterflies; contrary to prediction, both the concentration mean and variance decrease southward. The defensive advantage of incorporating cardiac glycosides may be balanced by detrimental effects on individual viability. PMID:5043141

  20. Natural variation in synthesis and catabolism genes influences dhurrin content in sorghum (Sorghum bicolor L. Moench)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cyanogenic glucosides are natural compounds found in over 1,000 species of angiosperms that produce HCN and are deemed undesirable for agricultural use. However, these compounds are important components of primary defensive mechanisms of many plant species. One of the best-studied cyanogenic glucos...

  1. The Natural Sciences in the University: Change and Variation over the 20th Century

    ERIC Educational Resources Information Center

    Gabler, Jay; Frank, David John

    2005-01-01

    The changing academic priorities of universities are often discussed but little investigated by social scientists: What accounts for the striking expansions and contractions in disciplinary fields over time? Focusing specifically on the natural sciences, this article articulates a global-institutional argument that holds that deep shifts in…

  2. Variable defect structures cause the magnetic low-temperature transition in natural monoclinic pyrrhotite

    NASA Astrophysics Data System (ADS)

    Koulialias, D.; Kind, J.; Charilaou, M.; Weidler, P. G.; Löffler, J. F.; Gehring, A. U.

    2016-02-01

    Non-stoichiometric monoclinic 4C pyrrhotite (Fe7S8) is a major magnetic remanence carrier in the Earth's crust and in extraterrestrial materials. Because of its low-temperature magnetic transition around 30 K also known as Besnus transition, which is considered to be an intrinsic property, this mineral phase is easily detectable in natural samples. Although the physical properties of pyrrhotite have intensively been studied, the mechanism behind the pronounced change in magnetization at the low-temperature transition is still debated. Here we report magnetization experiments on a pyrrhotite crystal (Fe6.6S8) that consists of a 4C and an incommensurate 5C* superstructure that are different in their defect structure. The occurrence of two superstructures is magnetically confirmed by symmetric inflection points in hysteresis measurements above the transition at about 30 K. The disappearance of the inflection points and the associated change of the hysteresis parameters indicate that the two superstructures become strongly coupled to form a unitary magnetic anisotropy system at the transition. From this it follows that the Besnus transition in monoclinic pyrrhotite is an extrinsic magnetic phenomenon with respect to the 4C superstructure and therefore the physics behind it is in fact different from that of the well-known Verwey transition.

  3. Natural and experimental evidence of viscerotropic infection caused by Leishmania tropica from North Sinai, Egypt.

    PubMed

    Doha, Said A; Shehata, Magdi G; Fahmy, Adel R; Samy, Abdallah M

    2014-08-01

    Cutaneous leishmaniasis (CL) is a neglected clinical form that is quite prevalent in Eastern North parts of the country in Sinai Peninsula. Leishmania tropica was identified by previous reports as the causative agent responsible for viscerotropic infections in-patients and experimental animals. Here, we reported the viscerotropic infections from naturally infected rodent Gerbillus pyramidum floweri collected from North-Sinai. Footpad and tail lesions, spleenomegaly, and malformed dark-colored spleen were the characteristic CL symptoms. The spleen of the rodent found positive to amastigote impression smear. ITS-1 DNA was sequenced and revealed 100% identity of the strain in the current study to the other L. tropica sequences identified from the patients with the suspected CL and inhabited the same study area. The current findings confirmed the susceptibility of gerbil to L. tropica, and raise the concerns for the role of rodents as accidental host suffering the infections. The susceptibility of wild and experimental rodents to the same L. tropica strain was also investigated; BALB/c and G. pyramidum were more susceptible to L. tropica (24.33 ± 4.37 and 25 ± 4.58 days post-infection, respectively). Similar viscerotropic pathologies were reported in experimental infection of only golden hamster (≈ 120 days post-infection), and G. p. floweri (≈ 160 days post-infection). PMID:25597157

  4. Insights into sexual reproduction in Aspergillus flavus from variation in experimental crosses and natural populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aspergillus flavus contaminates many important crops worldwide and is the major producer of aflatoxins, which are cancer-causing secondary metabolites. Biological control is the most effective means of reducing inoculum levels of detrimental aflatoxin-producing fungal pathogens in agricultural syst...

  5. Natural genetic variation in the lycopene epsilon cyclase gene can enhance provitamin A biofortification of maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dietary micronutrient deficiencies are a major source of morbidity and mortality worldwide. Vitamin A deficiency is particularly devastating, causing blindness or corneal afflictions in 40 million children each year, and putting an additional 140-250 million at risk for related vitamin A deficiency...

  6. Automatic segmentation and statistical shape modeling of the paranasal sinuses to estimate natural variations

    NASA Astrophysics Data System (ADS)

    Sinha, Ayushi; Leonard, Simon; Reiter, Austin; Ishii, Masaru; Taylor, Russell H.; Hager, Gregory D.

    2016-03-01

    We present an automatic segmentation and statistical shape modeling system for the paranasal sinuses which allows us to locate structures in and around the sinuses, as well as to observe the variability in these structures. This system involves deformably registering a given patient image to a manually segmented template image, and using the resulting deformation field to transfer labels from the template to the patient image. We use 3D snake splines to correct errors in this initial segmentation. Once we have several accurately segmented images, we build statistical shape models to observe the population mean and variance for each structure. These shape models are useful to us in several ways. Regular registration methods are insufficient to accurately register pre-operative computed tomography (CT) images with intra-operative endoscopy video of the sinuses. This is because of deformations that occur in structures containing erectile tissue. Our aim is to estimate these deformations using our shape models in order to improve video-CT registration, as well as to distinguish normal variations in anatomy from abnormal variations, and automatically detect and stage pathology. We can also compare the mean shapes and variances in different populations, such as different genders or ethnicities, in order to observe differences and similarities, as well as in different age groups in order to observe the developmental changes that occur in the sinuses.

  7. Exploring nitrogen remobilization for seed filling using natural variation in Arabidopsis thaliana.

    PubMed

    Masclaux-Daubresse, Céline; Chardon, Fabien

    2011-03-01

    Nineteen Arabidopsis accessions grown at low (LOW N) and high (HIGH N) nitrate supplies were labelled using (15)N to trace nitrogen remobilization to the seeds. Effects of genotype and nutrition were examined. Nitrate availability affected biomass and yield, and highly modified the nitrogen concentration in the dry remains. Surprisingly, variations of one-seed dry weight (DW(1S)) and harvest index (HI) were poorly affected by nutrition. Nitrogen harvest index (NHI) was highly correlated with HI and showed that nitrogen use efficiency (NUE) was increased at LOW N. Nitrogen remobilization efficiency (NRE), as (15)N partitioning in seeds ((15)NHI), was also higher at LOW N. The relative specific abundance (RSA) in seeds and whole plants indicated that the (14)NO(3) absorbed post-labelling was mainly allocated to the seeds (SEEDS) at LOW N, but to the dry remains (DR) at HIGH N. Nitrogen concentration (N%) in the DR was then 4-fold higher at HIGH N compared with LOW N, whilst N% in seeds was poorly modified. Although NHI and (15)NHI were highly correlated to HI, significant variations in NUE and NRE were identified using normalization to HI. New insights provided in this report are helpful for the comprehension of NUE and NRE concepts in Arabidopsis as well as in crops and especially in Brassica napus. PMID:21273332

  8. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

    PubMed Central

    Salinas, Francisco; de Boer, Carl G.; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F.; Martínez, Claudio; Cubillos, Francisco A.

    2016-01-01

    Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

  9. Exploring nitrogen remobilization for seed filling using natural variation in Arabidopsis thaliana

    PubMed Central

    Masclaux-Daubresse, Céline; Chardon, Fabien

    2011-01-01

    Nineteen Arabidopsis accessions grown at low (LOW N) and high (HIGH N) nitrate supplies were labelled using 15N to trace nitrogen remobilization to the seeds. Effects of genotype and nutrition were examined. Nitrate availability affected biomass and yield, and highly modified the nitrogen concentration in the dry remains. Surprisingly, variations of one-seed dry weight (DW1S) and harvest index (HI) were poorly affected by nutrition. Nitrogen harvest index (NHI) was highly correlated with HI and showed that nitrogen use efficiency (NUE) was increased at LOW N. Nitrogen remobilization efficiency (NRE), as 15N partitioning in seeds (15NHI), was also higher at LOW N. The relative specific abundance (RSA) in seeds and whole plants indicated that the 14NO3 absorbed post-labelling was mainly allocated to the seeds (SEEDS) at LOW N, but to the dry remains (DR) at HIGH N. Nitrogen concentration (N%) in the DR was then 4-fold higher at HIGH N compared with LOW N, whilst N% in seeds was poorly modified. Although NHI and 15NHI were highly correlated to HI, significant variations in NUE and NRE were identified using normalization to HI. New insights provided in this report are helpful for the comprehension of NUE and NRE concepts in Arabidopsis as well as in crops and especially in Brassica napus. PMID:21273332

  10. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast.

    PubMed

    Salinas, Francisco; de Boer, Carl G; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F; Martínez, Claudio; Cubillos, Francisco A

    2016-01-01

    Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

  11. Novel candidate genes influencing natural variation in potato tuber cold sweetening identified by comparative proteomics and association mapping

    PubMed Central

    2013-01-01

    Background Higher plants evolved various strategies to adapt to chilling conditions. Among other transcriptional and metabolic responses to cold temperatures plants accumulate a range of solutes including sugars. The accumulation of the reducing sugars glucose and fructose in mature potato tubers during exposure to cold temperatures is referred to as cold induced sweetening (CIS). The molecular basis of CIS in potato tubers is of interest not only in basic research on plant adaptation to environmental stress but also in applied research, since high amounts of reducing sugars affect negatively the quality of processed food products such as potato chips. CIS-tolerance varies considerably among potato cultivars. Our objective was to identify by an unbiased approach genes and cellular processes influencing natural variation of tuber sugar content before and during cold storage in potato cultivars used in breeding programs. We compared by two-dimensional polyacrylamide gel electrophoresis the tuber proteomes of cultivars highly diverse for CIS. DNA polymorphisms in genomic sequences encoding differentially expressed proteins were tested for association with tuber starch content, starch yield and processing quality. Results Pronounced natural variation of CIS was detected in tubers of a population of 40 tetraploid potato cultivars. Significant differences in protein expression were detected between CIS-tolerant and CIS-sensitive cultivars before the onset as well as during cold storage. Identifiable differential proteins corresponded to protease inhibitors, patatins, heat shock proteins, lipoxygenase, phospholipase A1 and leucine aminopeptidase (Lap). Association mapping based on single nucleotide polymorphisms supported a role of Lap in the natural variation of the quantitative traits tuber starch and sugar content. Conclusions The combination of comparative proteomics and association genetics led to the discovery of novel candidate genes for influencing the natural

  12. Natural Variation of 238U/235U in Geo- and Cosmochemistry

    NASA Astrophysics Data System (ADS)

    Weyer, S.; Brennecka, G.; Montoya Pino, C.; Noordmann, J.; Schauble, E. A.; Wadhwa, M.; Anbar, A. D.

    2009-12-01

    The ratio of the two primordial U isotopes has long been assumed to be invariant (i.e. 238U/235U = 137.88, [1]) in the Solar [1, 2]. Due to analytical improvements, small (‰-range) U isotope variations can now be detected in both terrestrial [3, 4, 5] and meteoritic materials [6]. Uranium isotope variations on Earth are produced by chemical reactions, analogous to stable isotope fractionation, although U has no stable isotopes. The range of U isotope variations observed thus far on Earth exceeds 1‰ and is mostly driven by nuclear field shift effects, which depend on nuclear volume rather than mass [7]. The strongest isotope fractionation appears to occur between oxidized and reduced U species (UVI and UIV). As a result, oxic environments (e.g., seawater) are enriched in the light U isotope, 235U, while anoxic sediments (e.g., from the Black Sea) are enriched in the heavy U isotope, 238U [4]. This redox-sensitive behavior of U isotope compositions makes the 238U/235U ratio promising for use as a paleo-redox proxy. In paleoceanography, 238U/235U ratios can be used to estimate the extent of seafloor anoxia. During periods of enhanced global ocean anoxia (e.g., during the mid-Cretaceous oceanic anoxic event OAE-2) heavy U was preferentially buried into anoxic sediments. Accordingly, sea water and all oceanic sinks became depleted in heavy U. We used this shift in U isotope compositions to estimate a three times enhancement of anoxic environments in the oceans during OAE-2 compared to today [8]. In meteoritic materials, 238U/235U variations may be produced by (1) chemical reactions (2) nucleosynthetic anomalies and/or (3) decay of the short-lived extant 247Cm (half life = 15.6 Ma) to 235U. We investigated the U isotope composition of calcium aluminum-rich inclusions (CAIs). The Pb-Pb ages of CAIs define the age of the Solar System, as they represent the first solids to condense from the cooling protoplanetary disk. The investigated CAIs from the Allende meteorite

  13. Natural variations in OsγTMT contribute to diversity of the α-tocopherol content in rice.

    PubMed

    Wang, Xiao-Qiang; Yoon, Min-Young; He, Qiang; Kim, Tae-Sung; Tong, Wei; Choi, Bu-Woong; Lee, Young-Sang; Park, Yong-Jin

    2015-12-01

    Tocopherols and tocotrienols, collectively known as tocochromanols, are lipid-soluble molecules that belong to the group of vitamin E compounds. Among them, α-tocopherol (αΤ) is one of the antioxidants with diverse functions and benefits for humans and animals. Thus, understanding the genetic basis of these traits would be valuable to improve nutritional quality by breeding in rice. Genome-wide association study (GWAS) has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. To discover the genes or QTLs underlying the naturally occurring variations of αΤ content in rice, we performed GWAS using 1.44 million high-quality single-nucleotide polymorphisms acquired from re-sequencing of 137 accessions from a diverse rice core collection. Thirteen candidate genes were found across 2-year phenotypic data, among which gamma-tocopherol methyltransferase (OsγTMT) was identified as the major factor responsible for the αΤ content among rice accessions. Nucleotide variations in the coding region of OsγTMT were significantly associated with the αΤ content variations, while nucleotide polymorphisms in the promoter region of OsγTMT also could partly demonstrate the correlation with αΤ content variations, according to our RNA expression analyses. This study provides useful information for genetic factors underlying αΤ content variations in rice, which will significantly contribute the research on αΤ biosynthesis mechanisms and αΤ improvement of rice. PMID:25990214

  14. Differences in monthly variation, cause, and place of injury between femoral neck and trochanteric fractures: 6-year survey (2008–2013) in Kyoto prefecture, Japan

    PubMed Central

    Horii, Motoyuki; Fujiwara, Hiroyoshi; Mikami, Yasuo; Ikeda, Takumi; Ueshima, Keiichiro; Ikoma, Kazuya; Shirai, Toshiharu; Nagae, Masateru; Oka, Yoshinobu; Sawada, Koshiro; Kuriyama, Nagato; Kubo, Toshikazu

    2016-01-01

    Summary Background The incidence of femoral neck and trochanteric fractures reportedly differ by age and regionality. We investigated differences in monthly variations of the occurrence of femoral neck and trochanteric fractures as well as place and cause of injury in the Kyoto prefecture over a 6-year period. Methods Fracture type (neck or trochanteric fracture), age, sex, place of injury, and cause of injury were surveyed among patients aged ≥ 65 years with hip fractures that occurred between 2008 and 2013 who were treated in 1 of 13 participating hospitals (5 in an urban area and 8 in a rural area). The proportion of sick beds in the participating hospitals was 24.7% (4,151/16,781). Monthly variations in the number of patients were investigated in urban and rural areas in addition to the entire Kyoto prefecture. Place of injury was classified as indoors or outdoors, and cause of injury was categorized as simple fall, accident, or uncertain. Results There were 2,826 patients with neck fractures (mean age, 82.1 years) and 3,305 patients with trochanteric fractures (mean age, 85.0 years). There were similarities in the monthly variation of the number of fractures in addition to the place and cause of injury between neck and trochanteric fractures. Indoors (approximately 74%) and simple falls (approximately 78%) were the primary place and cause of injury, respectively. The place of injury was not significantly different by fracture type with each age group. Significantly more patients with neck fracture had “uncertain” as the cause of injury than trochanteric fracture in all age groups. Conclusions Based on the results of the present study, the injury pattern might not have a great effect on the susceptibility difference between neck and trochanteric fractures. PMID:27252738

  15. The Causes of Self‐sterility in Natural Populations of the Relictual Angiosperm, Illicium floridanum (Illiciaceae)

    PubMed Central

    KOEHL, VERONICA; THIEN, LEONARD B.; HEIJ, ELIZABETH G.; SAGE, TAMMY L.

    2004-01-01

    • Background and Aims Illicium floridanum, a species belonging to the basal extant angiosperm taxon Illiciaceae, reportedly exhibits self‐incompatibility (SI). To date, the site and timing of SI within the carpel of this species remains unidentified. Thus, the objective of this research was to determine the cellular and temporal aspects of SI in I. floridanum. • Methods Following controlled application of cross‐ and self‐pollen in natural populations of I. floridanum, embryo sac development and temporal aspects of stigma receptivity, as well as pollen tube growth, fertilization, and embryo and endosperm development, were investigated with the aid of light and fluorescence microscopy. • Key Results Flowers of I. floridanum exhibited complete dichogamy whereby stigmas only supported cross‐ and self‐pollen tube growth prior to anther dehiscence. In contrast to earlier reports of SI in this species, a prezygotic SI resulting in rejection of self‐pollen tube growth at the stigma was absent and there were no significant differences between cross‐ versus self‐pollen germination and pollen tube growth within the style and ovary during the first 5 d after pollination. Structural development of the four‐celled embryo sac was not differentially influenced by pollen type as noted to occur in other angiosperms with late‐acting ovarian SI. The ovule micropyle and embryo sac were penetrated equally by cross‐ and self‐pollen tubes. In addition, there were no statistically significant differences in cross‐ versus self‐fertilization. A resting zygote and multicellular endosperm at a variety of developmental stages was present by 30 d after application of cross‐ or self‐pollen. • Conclusions In the clear absence of a prezygotic SI that was previously reported to result in differential self‐pollen tube growth at the stigma, self‐ sterility in I. floridanum is likely due to early‐acting inbreeding depression, although late‐acting post

  16. Simple applicable methods for assessing natural hazards caused by landslides and erosion processes in torrent catchments

    NASA Astrophysics Data System (ADS)

    Tilch, N.; Melzner, S.; Janda, C.; Koçiu, A.

    2009-04-01

    The present study for the "Bucklige Welt- Wechselland" area, a mountainous region of about 1300 km² in the eastern part of Austria, was conducted under the authority of the Austrian Service for Torrent and Avalanche Control (WLV). The ultimate ambition of this study was directed towards the improvement of regional expertise by developing susceptibility maps at catchment scale, which display the disposition towards the occurrence of the mentioned processes and their bed-load-potentials. These results about hazard potential should form the basis for further planning decisions (more detailed investigations, hazard zoning) of governmental authorities responsible for the study region. Past events within the study area have shown, that besides floods, also landslides and fluvial erosion have a significant hazardous potential through their contribution to enormous bed loads and debris flows. As the interaction of dispositional and triggering factors are expected to be very complex, this regional study was carried out within a close interdisciplinary collaboration of three project partners, focusing on the main project modules "Hydrology and Climatic Impacts" (Vienna University of Technology), "Land Use and Pedology" (The Research and Training Centre for Forests, Natural Hazards and Landscape in Innsbruck) and "Geology and Geomorphology" (Geological Survey of Austria). The work was conducted using generally available data (DEM, Geology, Land Use) and field data to a minor extent. The quality and scale of these available data sources restricted the development of methods to simple approaches, which could easily be applied in the future within other areas by regional experts. The developed methodology and outcomes of the module "geology and geomorphology" are introduced on the basis of the derived susceptibility maps showing "dominant processes" and "relative bed- load- potentials".

  17. Temporal variation of the earth's low-degree zonal gravitational field caused by atmospheric mass redistribution - 1980-1988

    NASA Technical Reports Server (NTRS)

    Chao, B. Fong; Au, Andrew Y.

    1991-01-01

    Temporal variations in the low-degree zonal harmonics of the earth's gravitational field have recently been observed by satellite laser ranging. A host of geophysical processes contribute to these variations. The present paper studies quantitatively a prime contributor, atmospheric mass redistribution, using ECMWF global surface pressure data for the period of 1980-1988. The annual and semiannual amplitudes and phases of the zonal J(l) coefficient with degree l = 2-6 with and without the oceanic inverted-barometer (IB) effect are computed to obtain the predicted effects on the orbit nodal residuals of Lageos and Starlette. These predicted values are then compared with observations. It is found that the atmospheric influence, combined with the hydrological influence agree well with the Lageos observation for the annual term. The corresponding match appears poorer for Starlette.

  18. Amplitude variations of whistler-mode signals caused by their interaction with energetic electrons of the magnetosphere

    NASA Technical Reports Server (NTRS)

    Bernard, L. C.

    1973-01-01

    Whistler mode waves that propagate through the magnetosphere exchange energy with energetic electrons by wave-particle interaction mechanisms. Using linear theory, a detailed investigation is presented of the resulting amplitude variations of the wave as it propagates. Arbitrary wave frequency and direction of propagation are considered. A general class of electron distributions that are nonseparable in particle energy and pitch-angle is proposed. It is found that the proposed distribution model is consistent with available whistler and particle observations. This model yields insignificant amplitude variation over a large frequency band, a feature commonly observed in whistler data. This feature implies a certain equilibrium between waves and particles in the magnetosphere over a wide spread of particle energy, and is relevant to plasma injection experiments and to monitoring the distribution of energetic electrons in the magnetosphere.

  19. Assessment of the Nature, Distribution and Causes of Land Subsidence in Central and Northern Saudi Arabia

    NASA Astrophysics Data System (ADS)

    Othman, A.; Sultan, M.; Al Harbi, H.; Youssef, A.; Ahmed, M.; Emil, M.; Zabramwi, Y.; Alzahrani, S.; Bahamil, A.; Chouinard, K.

    2014-12-01

    Numerous land subsidence events have been recently reported from central and northern parts of the Kingdom of Saudi Arabia in Hail, Al Qassim, Al Jowf, and Buraydah Provinces. In some cases, these incidences resulted in losses in life and property. In this study, an integrated (field, geologic, remote sensing) approach is applied to accomplish the following: (1) identify the spatial distribution and extent of areas affected by subsidence (TASK I), (2) identify the factor(s) causing such subsidence (TASK II), and (3) identify areas threatened by such phenomena across northern and central parts of the Kingdom using criteria extracted from TASK II (TASK III). A three-fold approach was applied: (1) visits were conducted to collect field observations from reported subsidence locations, (2) spatial correlations were implemented in a web-based GIS environment for the reported subsidence locations in relation to relevant co-registered static datasets (e.g., rock and soil types, geologic structures) and temporal datasets (e.g., groundwater extraction, landuse/landcover, distribution and magnitude of earthquakes), (3) subsidence rates were extracted applying the Small BAseline Subset (SBAS) radar interferometric technique and using European Remote Sensing satellite-1 (ERS-1), ERS-2, and the Environmental Satellite (Envisat) data sets. Our findings (from radar interferometric studies) indicate that the distribution of areas undergoing subsidence are consistent/correlate with: (1) reported subsidence locations, but reveal many additional unreported subsidence locations, (2) irrigated lands, especially those witnessing a progressive increase in agricultural activities with time; (3) outcrops of the Saq sandstone aquifer system, the main source for fresh groundwater in the Kingdom, (4) outcrops the Minjur limestone formation that are subject to karstification; and (5) urban centers lacking appropriate sewage and drainage systems.

  20. Length-of-day variations caused by El Nino-Southern Oscillation and Quasi-Biennial Oscillation

    NASA Technical Reports Server (NTRS)

    Chao, B. Fong

    1989-01-01

    Two prominent interannual atmospheric fluctuations, the El Nino-Southern Oscillation in the troposphere-ocean system and the Quasi-Biennial Oscillation in the equatorial stratosphere, account for most of the observed interannual length-of-day (LOD) variation from 1964 through 1987, with a relative contribution of about 2 to 1. Thus the atmosphere-LOD connection extends from seasonal and shorter periods to interannual periods up to about 10 years.

  1. Natural Genetic Variation of Freezing Tolerance in Arabidopsis[W][OA

    PubMed Central

    Hannah, Matthew A.; Wiese, Dana; Freund, Susanne; Fiehn, Oliver; Heyer, Arnd G.; Hincha, Dirk K.

    2006-01-01

    Low temperature is a primary determinant of plant growth and survival. Using accessions of Arabidopsis (Arabidopsis thaliana) originating from Scandinavia to the Cape Verde Islands, we show that freezing tolerance of natural accessions correlates with habitat winter temperatures, identifying low temperature as an important selective pressure for Arabidopsis. Combined metabolite and transcript profiling show that during cold exposure, global changes of transcripts, but not of metabolites, correlate with the ability of Arabidopsis to cold acclimate. There are, however, metabolites and transcripts, including several transcription factors, that correlate with freezing tolerance, indicating regulatory pathways that may be of primary importance for this trait. These data identify that enhanced freezing tolerance is associated with the down-regulation of photosynthesis and hormonal responses and the induction of flavonoid metabolism, provide evidence for naturally increased nonacclimated freezing tolerance due to the constitutive activation of the C-repeat binding factors pathway, and identify candidate transcriptional regulators that correlate with freezing tolerance. PMID:16844837

  2. Judgments of noticeable differences in sound fields of concert halls caused by intensity variations in early reflections.

    PubMed

    Okano, Toshiyuki

    2002-01-01

    In concert halls early reflections combine with the direct sound and with reverberation to determine the subjective rating of a room's acoustics. Of interest is how variations in the amplitudes of these early reflections are related to the subjectively just-noticeable differences (jnd) in several important acoustical parameters for their wide range encountered in existing halls. Investigated were four subjective parameters, apparent source width (ASW), loudness, intimacy and clarity, which are related to the physical measurements, [1-IACC(E3)], G, ITDG, and C80, defined mathematically in Beranek [Concert and Opera Halls: How They Sound (Acoustical Society of America, New York, 1996)]. Forty-eight types of sound fields were chosen in which to make variations in the amplitudes of early reflections and were reproduced electro-acoustically by multiple loudspeakers in an anechoic chamber. The results indicate that ASW and loudness are more sensitive to changes in the levels of early reflections, and were the primary parameters investigated. Although the number of subjects available with enough experience in listening classical music is limited and the measured jnd is an initial estimation, the jnd of [1-IACC(E3)] is measured as 0.065+/-0.015 in variations of sound field structures and the jnd of G was measured as 0.25+/-0.15 dB, which is consistent with the results of previous studies. PMID:11831797

  3. Judgments of noticeable differences in sound fields of concert halls caused by intensity variations in early reflections

    NASA Astrophysics Data System (ADS)

    Okano, Toshiyuki

    2002-01-01

    In concert halls early reflections combine with the direct sound and with reverberation to determine the subjective rating of a room's acoustics. Of interest is how variations in the amplitudes of these early reflections are related to the subjectively just-noticeable differences (jnd) in several important acoustical parameters for their wide range encountered in existing halls. Investigated were four subjective parameters, apparent source width (ASW), loudness, intimacy and clarity, which are related to the physical measurements, [1-IACCE3], G, ITDG, and C80, defined mathematically in Beranek [Concert and Opera Halls: How They Sound (Acoustical Society of America, New York, 1996)]. Forty-eight types of sound fields were chosen in which to make variations in the amplitudes of early reflections and were reproduced electro-acoustically by multiple loudspeakers in an anechoic chamber. The results indicate that ASW and loudness are more sensitive to changes in the levels of early reflections, and were the primary parameters investigated. Although the number of subjects available with enough experience in listening classical music is limited and the measured jnd is an initial estimation, the jnd of [1-IACCE3] is measured as 0.065+/-0.015 in variations of sound field structures and the jnd of G was measured as 0.25+/-0.15 dB, which is consistent with the results of previous studies.

  4. Variation in KRAS driver substitution distributions between tumor types is determined by both mutation and natural selection

    PubMed Central

    Ostrow, Sheli L.; Simon, Einav; Prinz, Elad; Bick, Tova; Shentzer, Talia; Nagawkar, Sima S.; Sabo, Edmond; Ben-Izhak, Ofer; Hershberg, Ruth; Hershkovitz, Dov

    2016-01-01

    Different tumor types vary greatly in their distribution of driver substitutions. Here, we analyzed how mutation and natural selection contribute to differences in the distribution of KRAS driver substitutions between lung, colon and pancreatic adenocarcinomas. We were able to demonstrate that both differences in mutation and differences in selection drive variation in the distribution of KRAS driver substitutions between tumor types. By accounting for the effects of mutation on the distribution of KRAS driver substitutions, we could identify specific KRAS driver substitutions that are more favored by selection in specific tumor types. Such driver substitutions likely improve fitness most when they occur within the context of the tumor type in which they are preferentially favored. Fitting with this, we found that driver substitutions that are more favored by natural selection in a specific type of tumor tend to associate with worse clinical outcomes specifically in that type of tumor. PMID:26902163

  5. Reappraisal of the limit on the variation in α implied by the Oklo natural fission reactors

    NASA Astrophysics Data System (ADS)

    Davis, Edward D.; Hamdan, Leila

    2015-07-01

    Background: A signature of many dynamical models of dark energy is that they admit variation in the fine structure constant α over cosmological time scales. Purpose: We reconsider the analysis of the sensitivity of neutron resonance energies Ei to changes in α with a view to resolving uncertainties that plague earlier treatments. Methods: We point out that with more appropriate choices of nuclear parameters, the standard estimate (from Damour and Dyson) of the sensitivity for resonances in Sm is increased by a factor of 2.5. We go on to identify and compute excitation, Coulomb, and deformation corrections. To this end, we use deformed Fermi density distributions fitted to the output of Hartree-Fock (HF) + BCS calculations (with both the SLy4 and SkM* Skyrme functionals), the energetics of the surface diffuseness of nuclei, and thermal properties of their deformation. We also invoke the eigenstate thermalization hypothesis, performing the requisite microcanonical averages with two phenomenological level densities which, via the leptodermous expansion of the level density parameter, include the effect of increased surface diffuseness. Theoretical uncertainties are assessed with the inter-model prescription of Dobaczewski et al. [J. Phys. G: Nucl. Part. Phys. 41, 074001 (2014), 10.1088/0954-3899/41/7/074001]. Results: The corrections diminish the revised Sm sensitivity but not by more than 25%. Subject to a weak and testable restriction on the change in mq/Λ (relative to the change in α ) since the time when the Oklo reactors were active (mq is the average of the u and d current quark masses, and Λ is the mass scale of quantum chromodynamics), we deduce that | αOklo-αnow|<1.1 × 10-8αnow (95% confidence level). The corresponding bound on the present-day time variation of α is tighter than the best limit to date from atomic clock experiments. Conclusions: The order of magnitude of our Oklo bound on changes in α is reliable. It is one order of magnitude lower

  6. The measurement of the ionospheric total content variations caused by a powerful radio emission of "Sura" facility on a network of GNSS-receivers

    NASA Astrophysics Data System (ADS)

    Nasyrov, I. A.; Kogogin, D. A.; Shindin, A. V.; Grach, S. M.; Zagretdinov, R. V.

    2016-02-01

    Observations of the perturbations of total electron content (TEC) caused by a powerful radio emission of "Sura" facility (Radio Physical Research Institute, N. Novgorod) were carried out during several experimental campaigns from March of 2010 to March 2013. In this paper the data of experimental measurements of TEC-variations conducted on March, 15, 2010 and on March, 12, 2013, are presented. 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 along the geomagnetic latitude: Vasilsursk (56 °08‧ N, 46 °05‧ E), Zelenodolsk (55 °52‧ N, 48 °33‧ E) and Kazan (55 °48‧ N, 49 °08‧ E). In the experiments radio path from GNSS satellite to Vasilsursk passed over the disturbed region of ionosphere, but radio paths to Zelenodolsk and to Kazan did not. However, TEC-variations correlated with pumping of ionosphere by "Sura" facility were detected for all up to three ground measurements sites. Magnitudes of TEC-variations reached up to ∼ 0.6 - 0.7 TECU. The speculation that a sharp gradient of the electron density formed at the border of the main lobe of "Sura" facility may cause the generation of IGW is presented.

  7. Genetic variation of the repeated MAL loci in natural populations of Saccharomyces cerevisiae and Saccharomyces paradoxus.

    PubMed

    Naumov, G I; Naumova, E S; Michels, C A

    1994-03-01

    In Saccharomyces cerevisiae, the gene functions required to ferment the disaccharide maltose are encoded by the MAL loci. Any one of five highly sequence homologous MAL loci identified in various S. cerevisiae strains (called MAL1, 2, 3, 4 and 6) is sufficient to ferment maltose. Each is a complex of three genes encoding maltose permease, maltase and a transcription activator. This family of loci maps to telomere-linked positions on different chromosomes and most natural strains contain more than one MAL locus. A number of naturally occurring, mutant alleles of MAL1 and MAL3 have been characterized which lack one or more of the gene functions encoded by the fully functional MAL loci. Loss of these gene functions appears to have resulted from mutation and/or rearrangement within the locus. Studies to date concentrated on the standard maltose fermenting strains of S. cerevisiae available from the Berkeley Yeast Stock Center collection. In this report we extend our genetic analysis of the MAL loci to a number of maltose fermenting and nonfermenting natural strains of S. cerevisiae and Saccharomyces paradoxus. No new MAL loci were discovered but several new mutant alleles of MAL1 were identified. The evolution of this gene family is discussed. PMID:8005435

  8. Natural variation in Fc glycosylation of HIV-specific antibodies impacts antiviral activity

    PubMed Central

    Ackerman, Margaret E.; Crispin, Max; Yu, Xiaojie; Baruah, Kavitha; Boesch, Austin W.; Harvey, David J.; Dugast, Anne-Sophie; Heizen, Erin L.; Ercan, Altan; Choi, Ickwon; Streeck, Hendrik; Nigrovic, Peter A.; Bailey-Kellogg, Chris; Scanlan, Chris; Alter, Galit

    2013-01-01

    While the induction of a neutralizing antibody response against HIV remains a daunting goal, data from both natural infection and vaccine-induced immune responses suggest that it may be possible to induce antibodies with enhanced Fc effector activity and improved antiviral control via vaccination. However, the specific features of naturally induced HIV-specific antibodies that allow for the potent recruitment of antiviral activity and the means by which these functions are regulated are poorly defined. Because antibody effector functions are critically dependent on antibody Fc domain glycosylation, we aimed to define the natural glycoforms associated with robust Fc-mediated antiviral activity. We demonstrate that spontaneous control of HIV and improved antiviral activity are associated with a dramatic shift in the global antibody-glycosylation profile toward agalactosylated glycoforms. HIV-specific antibodies exhibited an even greater frequency of agalactosylated, afucosylated, and asialylated glycans. These glycoforms were associated with enhanced Fc-mediated reduction of viral replication and enhanced Fc receptor binding and were consistent with transcriptional profiling of glycosyltransferases in peripheral B cells. These data suggest that B cell programs tune antibody glycosylation actively in an antigen-specific manner, potentially contributing to antiviral control during HIV infection. PMID:23563315

  9. Variation in oxygen isotope ratio of dissolved orthophosphate induced by uptake process in natural coral holobionts

    NASA Astrophysics Data System (ADS)

    Ferrera, Charissa M.; Miyajima, Toshihiro; Watanabe, Atsushi; Umezawa, Yu; Morimoto, Naoko; San Diego-McGlone, Maria Lourdes; Nadaoka, Kazuo

    2016-06-01

    A model incubation experiment using natural zooxanthellate corals was conducted to evaluate the influence of phosphate uptake by coral holobionts on oxygen isotope ratio of dissolved PO4 3- (δ18Op). Live coral samples of Acropora digitifera, Porites cylindrica, and Heliopora coerulea were collected from coral reefs around Ishigaki Island (Okinawa, Japan) and Bolinao (northern Luzon, Philippines) and incubated for 3-5 d after acclimatization under natural light conditions with elevated concentrations of PO4 3-. Phosphate uptake by corals behaved linearly with incubation time, with uptake rate depending on temperature. δ18Op usually increased with time toward the equilibrium value with respect to oxygen isotope exchange with ambient seawater, but sometimes became higher than equilibrium value at the end of incubation. The magnitude of the isotope effect associated with uptake depended on coral species; the greatest effect was in A. digitifera and the smallest in H. coerulea. However, it varied even within samples of a single coral species, which suggests multiple uptake processes with different isotope effects operating simultaneously with varying relative contributions in the coral holobionts used. In natural environments where concentrations of PO4 3- are much lower than those used during incubation, PO4 3- is presumably turned over much faster and the δ18Op easily altered by corals and other major primary producers. This should be taken into consideration when using δ18Op as an indicator of external PO4 3- sources in coastal ecosystems.

  10. Physically-based modeling of drag force caused by natural woody vegetation

    NASA Astrophysics Data System (ADS)

    Järvelä, J.; Aberle, J.

    2014-12-01

    Riparian areas and floodplains are characterized by woody vegetation, which is an essential feature to be accounted for in many hydro-environmental models. For applications including flood protection, river restoration and modelling of sediment processes, there is a need to improve the reliability of flow resistance estimates. Conventional methods such as the use of lumped resistance coefficients or simplistic cylinder-based drag force equations can result in significant errors, as these methods do not adequately address the effect of foliage and reconfiguration of flexible plant parts under flow action. To tackle the problem, physically-based methods relying on objective and measurable vegetation properties are advantageous for describing complex vegetation. We have conducted flume and towing tank investigations with living and artificial plants, both in arrays and with isolated plants, providing new insight into advanced parameterization of natural vegetation. The stem, leaf and total areas of the trees confirmed to be suitable characteristic dimensions for estimating flow resistance. Consequently, we propose the use of leaf area index and leaf-to-stem-area ratio to achieve better drag force estimates. Novel remote sensing techniques including laser scanning have become available for effective collection of the required data. The benefits of the proposed parameterization have been clearly demonstrated in our newest experimental studies, but it remains to be investigated to what extent the parameter values are species-specific and how they depend on local habitat conditions. The purpose of this contribution is to summarize developments in the estimation of vegetative drag force based on physically-based approaches as the latest research results are somewhat dispersed. In particular, concerning woody vegetation we seek to discuss three issues: 1) parameterization of reconfiguration with the Vogel exponent; 2) advantage of parameterizing plants with the leaf area

  11. Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures

    PubMed Central

    2012-01-01

    Background Biological systems respond to changes in both the Earth's magnetic and gravitational fields, but as experiments in space are expensive and infrequent, Earth-based simulation techniques are required. A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself. Results Using diamagnetic levitation, we exposed Arabidopsis thaliana in vitro callus cultures to five environments with different levels of effective gravity and magnetic field strengths. The environments included levitation, i.e. simulated μg* (close to 0 g* at B = 10.1 T), intermediate g* (0.1 g* at B = 14.7 T) and enhanced gravity levels (1.9 g* at B = 14.7 T and 2 g* at B = 10.1 T) plus an internal 1 g* control (B = 16.5 T). The asterisk denotes the presence of the background magnetic field, as opposed to the effective gravity environments in the absence of an applied magnetic field, created using a Random Position Machine (simulated μg) and a Large Diameter Centrifuge (2 g). Microarray analysis indicates that changes in the overall gene expression of cultured cells exposed to these unusual environments barely reach significance using an FDR algorithm. However, it was found that gravitational and magnetic fields produce synergistic variations in the steady state of the transcriptional profile of plants. Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies. Conclusions A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which

  12. Along-Arc Variation in Slab Surface Temperature Caused By 3D Material Circulation at the Plate Interface

    NASA Astrophysics Data System (ADS)

    Morishige, M.; Van Keken, P. E.

    2014-12-01

    In the northeast Japan arc, we can observe the along-arc variation of Quaternary volcano distribution, topography, seismic wave velocity, and Bouguer gravity anomaly whose characteristic wavelength is ~80 km. These observations may be related to 3D thermal structure in the mantle wedge and/or subducting Pacific slab. As a possible explanation of this, small-scale convection in the mantle wedge of thermal and chemical origin has been proposed so far. In this presentation, we will show another possible explanation for it. It is known mainly based on surface heat flow observation that the mantle wedge in this region is decoupled from the subducting Pacific slab down to ~80 km depth for geological time scale. We also observe that the down-dip limit of low angle thrust type earthquakes in this region is ~50 km depth. These suggest that in the northeast Japan arc, the mantle wedge and the slab decouples by brittle failure down to 50 km depth and by plastic deformation from 50 to 80 km depth. In order to test the effects of the plate interface on the thermal structure in this region, we construct 3D finite element models. The mantle flow is computed only in the mantle wedge, whereas temperature is computed for the whole model domain. We assume a thin, low viscosity layer just above the slab surface from 50 to 80 km depth to decouple the mantle wedge and the slab. We find that the along-arc variation in the slab surface temperature gradually develops with time. Its characteristic wavelength is ~100 km, which is comparable to or slightly higher than that observed. It arises because of the small-scale 3D circulation in the assumed low viscosity layer. The wavelength and the time of onset may depend on the viscosity and dimension of the low viscosity layer. Surface heat flow, on the other hand, does not show significant along-arc variation because forearc mantle is kept cold and hence rigid. These findings suggest that the observed along-arc variation in the northeast Japan

  13. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in Arabidopsis thaliana

    PubMed Central

    Seleznev, Andrei; Méndez-Vigo, Belén; Picó, F. Xavier; Sureshkumar, Sridevi; Sundaramoorthi, Vignesh; Bulach, Dieter; Powell, David; Seemann, Torsten; Alonso-Blanco, Carlos; Balasubramanian, Sureshkumar

    2015-01-01

    Plants are highly sensitive to environmental changes and even small variations in ambient temperature have severe consequences on their growth and development. Temperature affects multiple aspects of plant development, but the processes and mechanisms underlying thermo-sensitive growth responses are mostly unknown. Here we exploit natural variation in Arabidopsis thaliana to identify and characterize novel components and processes mediating thermo-sensitive growth responses in plants. Phenotypic screening of wild accessions identified several strains displaying pleiotropic growth defects, at cellular and organism levels, specifically at high ambient temperatures. Positional cloning and characterization of the underlying gene revealed that ICARUS1 (ICA1), which encodes a protein of the tRNAHis guanylyl transferase (Thg1) superfamily, is required for plant growth at high temperatures. Transcriptome and gene marker analyses together with DNA content measurements show that ICA1 loss-of-function results in down regulation of cell cycle associated genes at high temperatures, which is linked with a block in G2/M transition and endoreduplication. In addition, plants with mutations in ICA1 show enhanced sensitivity to DNA damage. Characterization of additional strains that carry lesions in ICA1, but display normal growth, shows that alternative splicing is likely to alleviate the deleterious effects of some natural mutations. Furthermore, analyses of worldwide and regional collections of natural accessions indicate that ICA1 loss-of-function has arisen several times independently, and that these occur at high frequency in some local populations. Overall our results suggest that ICA1-mediated-modulation of fundamental processes such as tRNAHis maturation, modify plant growth responses to temperature changes in a quantitative and reversible manner, in natural populations. PMID:25951176

  14. Identification of Genes Responsible for Natural Variation in Volatile Content Using Next-Generation Sequencing Technology.

    PubMed

    Amaya, Iraida; Pillet, Jeremy; Folta, Kevin M

    2016-01-01

    Identification of the genes controlling the variation of key traits remains a challenge for plant researchers and represents a goal for the development of functional markers and their implementation in marker-assisted crop breeding. As an example we describe the identification of volatile organic compounds (VOCs) that segregate as single locus or mayor quantitative trait loci (QTL) in strawberry F1 segregating populations. Next, we describe a fast and efficient method for RNA extraction in strawberry that yields high-quality RNA for downstream RNA-seq analysis. Finally, two alternative methods for analysis of global transcript expression in contrasting lines will be described in order to identify the candidate gene and genes with differential expression using RNA-seq. PMID:26577779

  15. Experimental approaches to studying the nature and impact of splicing variation in zebrafish.

    PubMed

    Keightley, M C; Markmiller, S; Love, C G; Rasko, J E J; Lieschke, G J; Heath, J K

    2016-01-01

    From a fixed number of genes carried in all cells, organisms create considerable diversity in cellular phenotype through differential regulation of gene expression. One prevalent source of transcriptome diversity is alternative pre-mRNA splicing, which is manifested in many different forms. Zebrafish models of splicing dysfunction due to mutated spliceosome components provide opportunity to link biochemical analyses of spliceosome structure and function with whole organism phenotypic outcomes. Drawing from experience with two zebrafish mutants: cephalophŏnus (a prpf8 mutant, isolated for defects in granulopoiesis) and caliban (a rnpc3 mutant, isolated for defects in digestive organ development), we describe the use of glycerol gradient sedimentation and native gel electrophoresis to resolve components of aberrant splicing complexes. We also describe how RNAseq can be employed to examine relatively rare alternative splicing events including intron retention. Such experimental approaches in zebrafish can promote understanding of how splicing variation and dysfunction contribute to phenotypic diversity and disease pathogenesis. PMID:27443930

  16. Patterns of Natural and Human-Caused Mortality Factors of a Rare Forest Carnivore, the Fisher (Pekania pennanti) in California.

    PubMed

    Gabriel, Mourad W; Woods, Leslie W; Wengert, Greta M; Stephenson, Nicole; Higley, J Mark; Thompson, Craig; Matthews, Sean M; Sweitzer, Rick A; Purcell, Kathryn; Barrett, Reginald H; Keller, Stefan M; Gaffney, Patricia; Jones, Megan; Poppenga, Robert; Foley, Janet E; Brown, Richard N; Clifford, Deana L; Sacks, Benjamin N

    2015-01-01

    Wildlife populations of conservation concern are limited in distribution, population size and persistence by various factors, including mortality. The fisher (Pekania pennanti), a North American mid-sized carnivore whose range in the western Pacific United States has retracted considerably in the past century, was proposed for threatened status protection in late 2014 under the United States Endangered Species Act by the United States Fish and Wildlife Service in its West Coast Distinct Population Segment. We investigated mortality in 167 fishers from two genetically and geographically distinct sub-populations in California within this West Coast Distinct Population Segment using a combination of gross necropsy, histology, toxicology and molecular methods. Overall, predation (70%), natural disease (16%), toxicant poisoning (10%) and, less commonly, vehicular strike (2%) and other anthropogenic causes (2%) were causes of mortality observed. We documented both an increase in mortality to (57% increase) and exposure (6%) from pesticides in fishers in just the past three years, highlighting further that toxicants from marijuana cultivation still pose a threat. Additionally, exposure to multiple rodenticides significantly increased the likelihood of mortality from rodenticide poisoning. Poisoning was significantly more common in male than female fishers and was 7 times more likely than disease to kill males. Based on necropsy findings, suspected causes of mortality based on field evidence alone tended to underestimate the frequency of disease-related mortalities. This study is the first comprehensive investigation of mortality causes of fishers and provides essential information to assist in the conservation of this species. PMID:26536481

  17. Patterns of Natural and Human-Caused Mortality Factors of a Rare Forest Carnivore, the Fisher (Pekania pennanti) in California

    PubMed Central

    Gabriel, Mourad W.; Stephenson, Nicole; Higley, J. Mark; Thompson, Craig; Matthews, Sean M.; Sweitzer, Rick A.; Purcell, Kathryn; Barrett, Reginald H.; Keller, Stefan M.; Gaffney, Patricia; Jones, Megan; Poppenga, Robert; Foley, Janet E.; Brown, Richard N.; Clifford, Deana L.; Sacks, Benjamin N.

    2015-01-01

    Wildlife populations of conservation concern are limited in distribution, population size and persistence by various factors, including mortality. The fisher (Pekania pennanti), a North American mid-sized carnivore whose range in the western Pacific United States has retracted considerably in the past century, was proposed for threatened status protection in late 2014 under the United States Endangered Species Act by the United States Fish and Wildlife Service in its West Coast Distinct Population Segment. We investigated mortality in 167 fishers from two genetically and geographically distinct sub-populations in California within this West Coast Distinct Population Segment using a combination of gross necropsy, histology, toxicology and molecular methods. Overall, predation (70%), natural disease (16%), toxicant poisoning (10%) and, less commonly, vehicular strike (2%) and other anthropogenic causes (2%) were causes of mortality observed. We documented both an increase in mortality to (57% increase) and exposure (6%) from pesticides in fishers in just the past three years, highlighting further that toxicants from marijuana cultivation still pose a threat. Additionally, exposure to multiple rodenticides significantly increased the likelihood of mortality from rodenticide poisoning. Poisoning was significantly more common in male than female fishers and was 7 times more likely than disease to kill males. Based on necropsy findings, suspected causes of mortality based on field evidence alone tended to underestimate the frequency of disease-related mortalities. This study is the first comprehensive investigation of mortality causes of fishers and provides essential information to assist in the conservation of this species. PMID:26536481

  18. Cooling rate variation in natural volcanic glasses from Tenerife, Canary Islands

    NASA Astrophysics Data System (ADS)

    Wilding, M.; Webb, Sharon; Dingwell, D.; Ablay, Giray; Marti, Joan

    1996-10-01

    Silicate melts form glasses in a variety of geological environments. The relaxation (equilibration) of the frozen glass structure provides a means of investigating the quench rates of natural glasses, and this cooling history provides an important constraint for models of melt dynamics. Phonolite glasses from the central volcanic edifice of Tenerife, Canary Islands indicate a range of five orders of magnitude cooling rate, determined by modeling the relaxation of the structure-dependent property, enthalpy ( H) across the glass transition. The relaxation of enthalpy is determined by heat capacity ( c p = Δ H/Δ T) measurement of natural glass samples by differential scanning calorimetry (DSC). Upon heating, the heat capacity curve in the vicinity of the glass transition has a geometry characteristic of the previous cooling rate. A series of thermal treatments applied to each individual sample results in a set of sample-specific parameters which are used to model the heat capacity curve of the naturally cooled glass. The cooling rate is then derived. The equivalence of shear and enthalpic relaxation enables the relaxation of enthalpy for these volcanic samples to be described by a general term for the evolution of fictive temperature. Quench rates for thirty-one glasses are calculated to be within the range 10°C s 1 to 7°C per day. The cooling rates quoted are linear approximations across the glass transition. Within different volcanic facies cooling rates depend on several factors. The most rapidly cooled glasses occur where samples lose heat by radiation from the surface. Our analyses indicate that in certain environments, a natural annealing process results in slow quench rates. This is interpreted as either a slow initial cooling process or the reheating of a glass to an annealing temperature within the glass transition interval. The latter results in relaxation to a lower temperature structure. Controls on these processes include the initial temperature and

  19. Allelic Variation in Cell Wall Candidate Genes Affecting Solid Wood Properties in Natural Populations and Land Races of Pinus radiata

    PubMed Central

    Dillon, S. K.; Nolan, M.; Li, W.; Bell, C.; Wu, H. X.; Southerton, S. G.

    2010-01-01

    Forest trees are ideally suited to association mapping due to their high levels of diversity and low genomic linkage disequilibrium. Using an association mapping approach, single-nucleotide polymorphism (SNP) markers influencing quantitative variation in wood quality were identified in a natural population of Pinus radiata. Of 149 sites examined, 10 demonstrated significant associations (P < 0.05, q < 0.1) with one or more traits after accounting for population structure and experimentwise error. Without accounting for marker interactions, phenotypic variation attributed to individual SNPs ranged from 2 to 6.5%. Undesirable negative correlations between wood quality and growth were not observed, indicating potential to break negative correlations by selecting for individual SNPs in breeding programs. Markers that yielded significant associations were reexamined in an Australian land race. SNPs from three genes (PAL1, PCBER, and SUSY) yielded significant associations. Importantly, associations with two of these genes validated associations with density previously observed in the discovery population. In both cases, decreased wood density was associated with the minor allele, suggesting that these SNPs may be under weak negative purifying selection for density in the natural populations. These results demonstrate the utility of LD mapping to detect associations, even when the power to detect SNPs with small effect is anticipated to be low. PMID:20498299

  20. A global conformance quality model. A new strategic tool for minimizing defects caused by variation, error, and complexity

    SciTech Connect

    Hinckley, C.M.

    1994-01-01

    The performance of Japanese products in the marketplace points to the dominant role of quality in product competition. Our focus is motivated by the tremendous pressure to improve conformance quality by reducing defects to previously unimaginable limits in the range of 1 to 10 parts per million. Toward this end, we have developed a new model of conformance quality that addresses each of the three principle defect sources: (1) Variation, (2) Human Error, and (3) Complexity. Although the role of variation in conformance quality is well documented, errors occur so infrequently that their significance is not well known. We have shown that statistical methods are not useful in characterizing and controlling errors, the most common source of defects. Excessive complexity is also a root source of defects, since it increases errors and variation defects. A missing link in the defining a global model has been the lack of a sound correlation between complexity and defects. We have used Design for Assembly (DFA) methods to quantify assembly complexity and have shown that assembly times can be described in terms of the Pareto distribution in a clear exception to the Central Limit Theorem. Within individual companies we have found defects to be highly correlated with DFA measures of complexity in broad studies covering tens of millions of assembly operations. Applying the global concepts, we predicted that Motorola`s Six Sigma method would only reduce defects by roughly a factor of two rather than orders of magnitude, a prediction confirmed by Motorola`s data. We have also shown that the potential defects rates of product concepts can be compared in the earliest stages of development. The global Conformance Quality Model has demonstrated that the best strategy for improvement depends upon the quality control strengths and weaknesses.

  1. Causes of variation in soil carbon predictions from CMIP5 Earth system models and comparison with observations

    NASA Astrophysics Data System (ADS)

    Todd-Brown, K. E. O.; Randerson, J. T.; Post, W. M.; Hoffman, F. M.; Tarnocai, C.; Schuur, E. A. G.; Allison, S. D.

    2012-10-01

    Stocks of soil organic carbon represent a large component of the carbon cycle that may participate in climate change feedbacks, particularly on decadal and century scales. For Earth system models (ESMs), the ability to accurately represent the global distribution of existing soil carbon stocks is a prerequisite for predicting future carbon-climate feedbacks. We compared soil carbon predictions from 16 ESMs to empirical data from the Harmonized World Soil Database (HWSD) and Northern Circumpolar Soil Carbon Database (NCSCD). Model estimates of global soil carbon stocks ranged from 510 to 3050 Pg C, compared to an estimate of 890-1660 Pg C from the HWSD. Model predictions for the high latitudes fell between 60 and 800 Pg C, compared to 380-620 Pg C from the NCSCD and 290 Pg C from the HWSD. This 5.3-fold variation in global soil carbon across models compared to a 3.4-fold variation in net primary productivity (NPP) and a 3.8-fold variation in global soil carbon turnover times. The spatial distribution of soil carbon predicted by the ESMs was not well correlated with the HWSD (Pearson's correlations < 0.4, RMSE 9.4 to 22.8 kg C m-2), although model-data agreement generally improved at the biome scale. There was poor agreement between the HWSD and NCSCD datasets in northern latitudes (Pearson's correlation = 0.33), indicating uncertainty in empirical estimates of soil carbon. We found that a reduced complexity model dependent on NPP and soil temperature explained most of the spatial variation in soil carbon predicted by most ESMs (R2 values between 0.73 and 0.93). This result suggests that differences in soil carbon predictions between ESMs are driven primarily by differences in predicted NPP and the parameterization of soil carbon responses to NPP and temperature not by structural differences between the models. Future work should focus on accurately representing these driving variables and modifying model structure to include additional processes.

  2. Ancestry variation and footprints of natural selection along the genome in Latin American populations

    PubMed Central

    Deng, Lian; Ruiz-Linares, Andrés; Xu, Shuhua; Wang, Sijia

    2016-01-01

    Latin American populations stem from the admixture of Europeans, Africans and Native Americans, which started over 400 years ago and had lasted for several centuries. Extreme deviation over the genome-wide average in ancestry estimations at certain genomic locations could reflect recent natural selection. We evaluated the distribution of ancestry estimations using 678 genome-wide microsatellite markers in 249 individuals from 13 admixed populations across Latin America. We found significant deviations in ancestry estimations including three locations with more than 3.5 times standard deviations from the genome-wide average: an excess of European ancestry at 1p36 and 14q32, and an excess of African ancestry at 6p22. Using simulations, we could show that at least the deviation at 6p22 was unlikely to result from genetic drift alone. By applying different linguistic groups as well as the most likely ancestral Native American populations as the ancestry, we showed that the choice of Native American ancestry could affect the local ancestry estimation. However, the signal at 6p22 consistently appeared in most of the analyses using various ancestral groups. This study provided important insights for recent natural selection in the context of the unique history of the New World and implications for disease mapping. PMID:26887503

  3. Ancestry variation and footprints of natural selection along the genome in Latin American populations.

    PubMed

    Deng, Lian; Ruiz-Linares, Andrés; Xu, Shuhua; Wang, Sijia

    2016-01-01

    Latin American populations stem from the admixture of Europeans, Africans and Native Americans, which started over 400 years ago and had lasted for several centuries. Extreme deviation over the genome-wide average in ancestry estimations at certain genomic locations could reflect recent natural selection. We evaluated the distribution of ancestry estimations using 678 genome-wide microsatellite markers in 249 individuals from 13 admixed populations across Latin America. We found significant deviations in ancestry estimations including three locations with more than 3.5 times standard deviations from the genome-wide average: an excess of European ancestry at 1p36 and 14q32, and an excess of African ancestry at 6p22. Using simulations, we could show that at least the deviation at 6p22 was unlikely to result from genetic drift alone. By applying different linguistic groups as well as the most likely ancestral Native American populations as the ancestry, we showed that the choice of Native American ancestry could affect the local ancestry estimation. However, the signal at 6p22 consistently appeared in most of the analyses using various ancestral groups. This study provided important insights for recent natural selection in the context of the unique history of the New World and implications for disease mapping. PMID:26887503

  4. Differentially expressed genes linked to natural variation in long-term memory formation in Cotesia parasitic wasps

    PubMed Central

    van Vugt, Joke J. F. A.; Hoedjes, Katja M.; van de Geest, Henri C.; Schijlen, Elio W. G. M.; Vet, Louise E. M.; Smid, Hans M.

    2015-01-01

    Even though learning and memory are universal traits in the Animal Kingdom, closely related species reveal substantial variation in learning rate and memory dynamics. To determine the genetic background of this natural variation, we studied two congeneric parasitic wasp species, Cotesia glomerata and C. rubecula, which lay their eggs in caterpillars of the large and small cabbage white butterfly. A successful egg laying event serves as an unconditioned stimulus (US) in a classical conditioning paradigm, where plant odors become associated with the encounter of a suitable host caterpillar. Depending on the host species, the number of conditioning trials and the parasitic wasp species, three different types of transcription-dependent long-term memory (LTM) and one type of transcription-independent, anesthesia-resistant memory (ARM) can be distinguished. To identify transcripts underlying these differences in memory formation, we isolated mRNA from parasitic wasp heads at three different time points between induction and consolidation of each of the four memory types, and for each sample three biological replicates, where after strand-specific paired-end 100 bp deep sequencing. Transcriptomes were assembled de novo and differential expression was determined for each memory type and time point after conditioning, compared to unconditioned wasps. Most differentially expressed (DE) genes and antisense transcripts were only DE in one of the LTM types. Among the DE genes that were DE in two or more LTM types, were many protein kinases and phosphatases, small GTPases, receptors and ion channels. Some genes were DE in opposing directions between any of the LTM memory types and ARM, suggesting that ARM in Cotesia requires the transcription of genes inhibiting LTM or vice versa. We discuss our findings in the context of neuronal functioning, including RNA splicing and transport, epigenetic regulation, neurotransmitter/peptide synthesis and antisense transcription. In

  5. Exploring the natural variation for seedling traits and their link with seed dimensions in tomato.

    PubMed

    Khan, Noorullah; Kazmi, Rashid H; Willems, Leo A J; van Heusden, Adriaan W; Ligterink, Wilco; Hilhorst, Henk W M

    2012-01-01

    The success of germination, growth and final yield of every crop depends to a large extent on the quality of the seeds used to grow the crop. Seed quality is defined as the viability and vigor attribute of a seed that enables the emergence and establishment of normal seedlings under a wide range of environments. We attempt to dissect the mechanisms involved in the acquisition of seed quality, through a combined approach of physiology and genetics. To achieve this goal we explored the genetic variation found in a RIL population of Solanum lycopersicum (cv. Moneymaker) x Solanum pimpinellifolium through extensive phenotyping of seed and seedling traits under both normal and nutrient stress conditions and root system architecture (RSA) traits under optimal conditions. We have identified 62 major QTLs on 21 different positions for seed, seedling and RSA traits in this population. We identified QTLs that were common across both conditions, as well as specific to stress conditions. Most of the QTLs identified for seedling traits co-located with seed size and seed weight QTLs and the positive alleles were mostly contributed by the S. lycopersicum parent. Co-location of QTLs for different traits might suggest that the same locus has pleiotropic effects on multiple traits due to a common mechanistic basis. We show that seed weight has a strong effect on seedling vigor and these results are of great importance for the isolation of the corresponding genes and elucidation of the underlying mechanisms. PMID:22952841

  6. Natural Variation in Skin Thickness Argues for Mechanical Stimulus Control by Force Instead of Displacement.

    PubMed

    Wang, Yuxiang; Marshall, Kara L; Baba, Yoshichika; Lumpkin, Ellen A; Gerling, Gregory J

    2013-01-01

    The neural response to touch stimuli is influenced by skin properties as well as the delivery of stimuli. Here, we compare stimuli controlled by displacement and force, and analyze the impact on firing rates of slowly adapting type I afferents as skin thickness and elasticity change. Uniaxial compression tests were used to measure the mechanical properties of mouse hind limb skin (n=5), resulting in a range of skin thickness measurements (211.6-530.6 μm) and hyper- and visco-elastic properties (average coefficient of variation=0.27).Values were integrated to an axisymmetric finite element model using an Ogden strain energy function. This calculated the propagation of surface loads to tactile end-organ locations, where maximum compressive stress and its rate were sampled and linearly regressed to firing rate. For the observed range of skin thickness, firing response was predicted under both force and displacement control of a ramp-and-hold stimulus. Over the ramp phase of stimulation, the variance in predicted firing rate was higher under displacement than under force control (22.2versus 4.9 Hz) with a similar trend in the sustained phase of stimulation (4.6versus1.3Hz). Given that skin thickness varies significantly between specimens, for human skin perhaps seven more so than for mice, the use of force control is predicted to decrease experimental variance in neurophysiological and psychophysical responses. PMID:24500653

  7. Natural Variation in Skin Thickness Argues for Mechanical Stimulus Control by Force Instead of Displacement

    PubMed Central

    Wang, Yuxiang; Marshall, Kara L.; Baba, Yoshichika; Lumpkin, Ellen A.; Gerling, Gregory J.

    2013-01-01

    The neural response to touch stimuli is influenced by skin properties as well as the delivery of stimuli. Here, we compare stimuli controlled by displacement and force, and analyze the impact on firing rates of slowly adapting type I afferents as skin thickness and elasticity change. Uniaxial compression tests were used to measure the mechanical properties of mouse hind limb skin (n=5), resulting in a range of skin thickness measurements (211.6–530.6 μm) and hyper- and visco-elastic properties (average coefficient of variation=0.27).Values were integrated to an axisymmetric finite element model using an Ogden strain energy function. This calculated the propagation of surface loads to tactile end-organ locations, where maximum compressive stress and its rate were sampled and linearly regressed to firing rate. For the observed range of skin thickness, firing response was predicted under both force and displacement control of a ramp-and-hold stimulus. Over the ramp phase of stimulation, the variance in predicted firing rate was higher under displacement than under force control (22.2versus 4.9 Hz) with a similar trend in the sustained phase of stimulation (4.6versus1.3Hz). Given that skin thickness varies significantly between specimens, for human skin perhaps seven more so than for mice, the use of force control is predicted to decrease experimental variance in neurophysiological and psychophysical responses. PMID:24500653

  8. Transcriptomic seasonal variations in a natural population of zebra mussel (Dreissena polymorpha).

    PubMed

    Navarro, Anna; Campos, Bruno; Barata, Carlos; Piña, Benjamin

    2013-06-01

    The zebra mussel Dreissena polymorpha is a Caspian Sea bivalve that colonized freshwater bodies worldwide during the XX century. To analyze the impact of seasonal and environmental variations on the physiology and metabolism of this invasive species, we developed a custom microarray using 4057 publicly available DNA sequences from Dreissena and other related genera. Transcriptome profiles were analyzed using half-body samples from a relatively clean site (Riba-Roja, low Ebro River, N.E. Spain), at three different stages of the annual cycle: Pre-spawning (February), spawning (June), and gonad resorption (September). Transcripts from a total of 745 unique sequences showed significant changes among these three groups of samples. Functional characterization of these transcripts based on their closest known homologues showed that genes involved in stress defense (oxidative and infection) were overrepresented in September, whereas genes related to reproductive functions were overrepresented in the spawning and pre-spawning periods. This transcriptomic information can help to identify developmental stages at which the organism is more vulnerable for future control strategies. These data will also contribute to the implementation of gene expression-based assays for pollution monitoring in water bodies harboring stable zebra mussel populations. PMID:23567168

  9. Comparative analysis of maize (Zea mays) crop performance: natural variation, incremental improvements and economic impacts.

    PubMed

    Leibman, Mark; Shryock, Jereme J; Clements, Michael J; Hall, Michael A; Loida, Paul J; McClerren, Amanda L; McKiness, Zoe P; Phillips, Jonathan R; Rice, Elena A; Stark, Steven B

    2014-09-01

    Grain yield from maize hybrids continues to improve through advances in breeding and biotechnology. Despite genetic improvements to hybrid maize, grain yield from distinct maize hybrids is expected to vary across growing locations due to numerous environmental factors. In this study, we examine across-location variation in grain yield among maize hybrids in three case studies. The three case studies examine hybrid improvement through breeding, introduction of an insect protection trait or introduction of a transcription factor trait associated with increased yield. In all cases, grain yield from each hybrid population had a Gaussian distribution. Across-location distributions of grain yield from each hybrid partially overlapped. The hybrid with a higher mean grain yield typically outperformed its comparator at most, but not all, of the growing locations (a 'win rate'). These results suggest that a broad set of environmental factors similarly impacts grain yields from both conventional- and biotechnology-derived maize hybrids and that grain yields among two or more hybrids should be compared with consideration given to both mean yield performance and the frequency of locations at which each hybrid 'wins' against its comparators. From an economic standpoint, growers recognize the value of genetically improved maize hybrids that outperform comparators in the majority of locations. Grower adoption of improved maize hybrids drives increases in average U.S. maize grain yields and contributes significant value to the economy. PMID:24851925

  10. Exploring the Natural Variation for Seedling Traits and Their Link with Seed Dimensions in Tomato

    PubMed Central

    Willems, Leo A. J.; van Heusden, Adriaan W.; Ligterink, Wilco; Hilhorst, Henk W. M.

    2012-01-01

    The success of germination, growth and final yield of every crop depends to a large extent on the quality of the seeds used to grow the crop. Seed quality is defined as the viability and vigor attribute of a seed that enables the emergence and establishment of normal seedlings under a wide range of environments. We attempt to dissect the mechanisms involved in the acquisition of seed quality, through a combined approach of physiology and genetics. To achieve this goal we explored the genetic variation found in a RIL population of Solanum lycopersicum (cv. Moneymaker) x Solanum pimpinellifolium through extensive phenotyping of seed and seedling traits under both normal and nutrient stress conditions and root system architecture (RSA) traits under optimal conditions. We have identified 62 major QTLs on 21 different positions for seed, seedling and RSA traits in this population. We identified QTLs that were common across both conditions, as well as specific to stress conditions. Most of the QTLs identified for seedling traits co-located with seed size and seed weight QTLs and the positive alleles were mostly contributed by the S. lycopersicum parent. Co-location of QTLs for different traits might suggest that the same locus has pleiotropic effects on multiple traits due to a common mechanistic basis. We show that seed weight has a strong effect on seedling vigor and these results are of great importance for the isolation of the corresponding genes and elucidation of the underlying mechanisms. PMID:22952841

  11. Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling.

    PubMed

    McGarrity, Sarah; Halldórsson, Haraldur; Palsson, Sirus; Johansson, Pär I; Rolfsson, Óttar

    2016-01-01

    High-throughput biochemical profiling has led to a requirement for advanced data interpretation techniques capable of integrating the analysis of gene, protein, and metabolic profiles to shed light on genotype-phenotype relationships. Herein, we consider the current state of knowledge of endothelial cell (EC) metabolism and its connections to cardiovascular disease (CVD) and explore the use of genome-scale metabolic models (GEMs) for integrating metabolic and genomic data. GEMs combine gene expression and metabolic data acting as frameworks for their analysis and, ultimately, afford mechanistic understanding of how genetic variation impacts metabolism. We demonstrate how GEMs can be used to investigate CVD-related genetic variation, drug resistance mechanisms, and novel metabolic pathways in ECs. The application of GEMs in personalized medicine is also highlighted. Particularly, we focus on the potential of GEMs to identify metabolic biomarkers of endothelial dysfunction and to discover methods of stratifying treatments for CVDs based on individual genetic markers. Recent advances in systems biology methodology, and how these methodologies can be applied to understand EC metabolism in both health and disease, are thus highlighted. PMID:27148541

  12. Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling

    PubMed Central

    McGarrity, Sarah; Halldórsson, Haraldur; Palsson, Sirus; Johansson, Pär I.; Rolfsson, Óttar

    2016-01-01

    High-throughput biochemical profiling has led to a requirement for advanced data interpretation techniques capable of integrating the analysis of gene, protein, and metabolic profiles to shed light on genotype–phenotype relationships. Herein, we consider the current state of knowledge of endothelial cell (EC) metabolism and its connections to cardiovascular disease (CVD) and explore the use of genome-scale metabolic models (GEMs) for integrating metabolic and genomic data. GEMs combine gene expression and metabolic data acting as frameworks for their analysis and, ultimately, afford mechanistic understanding of how genetic variation impacts metabolism. We demonstrate how GEMs can be used to investigate CVD-related genetic variation, drug resistance mechanisms, and novel metabolic pathways in ECs. The application of GEMs in personalized medicine is also highlighted. Particularly, we focus on the potential of GEMs to identify metabolic biomarkers of endothelial dysfunction and to discover methods of stratifying treatments for CVDs based on individual genetic markers. Recent advances in systems biology methodology, and how these methodologies can be applied to understand EC metabolism in both health and disease, are thus highlighted. PMID:27148541

  13. Natural variation in maternal care and cross-tissue patterns of oxytocin receptor gene methylation in rats.

    PubMed

    Beery, Annaliese K; McEwen, Lisa M; MacIsaac, Julia L; Francis, Darlene D; Kobor, Michael S

    2016-01-01

    This article is part of a Special Issue "Parental Care". Since the first report of maternal care effects on DNA methylation in rats, epigenetic modifications of the genome in response to life experience have become the subject of intense focus across many disciplines. Oxytocin receptor expression varies in response to early experience, and both oxytocin signaling and methylation status of the oxytocin receptor gene (Oxtr) in blood have been related to disordered social behavior. It is unknown whether Oxtr DNA methylation varies in response to early life experience, and whether currently employed peripheral measures of Oxtr methylation reflect variation in the brain. We examined the effects of early life rearing experience via natural variation in maternal licking and grooming during the first week of life on behavior, physiology, gene expression, and epigenetic regulation of Oxtr across blood and brain tissues (mononucleocytes, hippocampus, striatum, and hypothalamus). Rats reared by "high" licking-grooming (HL) and "low" licking-grooming (LL) rat dams exhibited differences across study outcomes: LL offspring were more active in behavioral arenas, exhibited lower body mass in adulthood, and showed reduced corticosterone responsivity to a stressor. Oxtr DNA methylation was significantly lower at multiple CpGs in the blood of LL versus HL males, but no differences were found in the brain. Across groups, Oxtr transcript levels in the hypothalamus were associated with reduced corticosterone secretion in response to stress, congruent with the role of oxytocin signaling in this region. Methylation of specific CpGs at a high or low level was consistent across tissues, especially within the brain. However, individual variation in DNA methylation relative to these global patterns was not consistent across tissues. These results suggest that blood Oxtr DNA methylation may reflect early experience of maternal care, and that Oxtr methylation across tissues is highly concordant

  14. Causes of variation in soil carbon simulations from CMIP5 Earth system models and comparison with observations

    NASA Astrophysics Data System (ADS)

    Todd-Brown, K. E. O.; Randerson, J. T.; Post, W. M.; Hoffman, F. M.; Tarnocai, C.; Schuur, E. A. G.; Allison, S. D.

    2013-03-01

    Stocks of soil organic carbon represent a large component of the carbon cycle that may participate in climate change feedbacks, particularly on decadal and centennial timescales. For Earth system models (ESMs), the ability to accurately represent the global distribution of existing soil carbon stocks is a prerequisite for accurately predicting future carbon-climate feedbacks. We compared soil carbon simulations from 11 model centers to empirical data from the Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). Model estimates of global soil carbon stocks ranged from 510 to 3040 Pg C, compared to an estimate of 1260 Pg C (with a 95% confidence interval of 890-1660 Pg C) from the HWSD. Model simulations for the high northern latitudes fell between 60 and 820 Pg C, compared to 500 Pg C (with a 95% confidence interval of 380-620 Pg C) for the NCSCD and 290 Pg C for the HWSD. Global soil carbon varied 5.9 fold across models in response to a 2.6-fold variation in global net primary productivity (NPP) and a 3.6-fold variation in global soil carbon turnover times. Model-data agreement was moderate at the biome level (R2 values ranged from 0.38 to 0.97 with a mean of 0.75); however, the spatial distribution of soil carbon simulated by the ESMs at the 1° scale was not well correlated with the HWSD (Pearson correlation coefficients less than 0.4 and root mean square errors from 9.4 to 20.8 kg C m-2). In northern latitudes where the two data sets overlapped, agreement between the HWSD and the NCSCD was poor (Pearson correlation coefficient 0.33), indicating uncertainty in empirical estimates of soil carbon. We found that a reduced complexity model dependent on NPP and soil temperature explained much of the 1° spatial variation in soil carbon within most ESMs (R2 values between 0.62 and 0.93 for 9 of 11 model centers). However, the same reduced complexity model only explained 10% of the spatial variation in HWSD soil carbon when

  15. Instrumental variables I: instrumental variables exploit natural variation in nonexperimental data to estimate causal relationships

    PubMed Central

    Rassen, Jeremy A.; Brookhart, M. Alan; Glynn, Robert J.; Mittleman, Murray A.; Schneeweiss, Sebastian

    2010-01-01

    The gold standard of study design for treatment evaluation is widely acknowledged to be the randomized controlled trial (RCT). Trials allow for the estimation of causal effect by randomly assigning participants either to an intervention or comparison group; through the assumption of “exchangeability” between groups, comparing the outcomes will yield an estimate of causal effect. In the many cases where RCTs are impractical or unethical, instrumental variable (IV) analysis offers a nonexperimental alternative based on many of the same principles. IV analysis relies on finding a naturally varying phenomenon, related to treatment but not to outcome except through the effect of treatment itself, and then using this phenomenon as a proxy for the confounded treatment variable. This article demonstrates how IV analysis arises from an analogous but potentially impossible RCT design, and outlines the assumptions necessary for valid estimation. It gives examples of instruments used in clinical epidemiology and concludes with an outline on estimation of effects. PMID:19356901

  16. Naturally occurring rhodopsin mutation in the dog causes retinal dysfunction and degeneration mimicking human dominant retinitis pigmentosa

    PubMed Central

    Kijas, James W.; Cideciyan, Artur V.; Aleman, Tomas S.; Pianta, Michael J.; Pearce-Kelling, Susan E.; Miller, Brian J.; Jacobson, Samuel G.; Aguirre, Gustavo D.; Acland, Gregory M.

    2002-01-01

    Rhodopsin is the G protein-coupled receptor that is activated by light and initiates the transduction cascade leading to night (rod) vision. Naturally occurring pathogenic rhodopsin (RHO) mutations have been previously identified only in humans and are a common cause of dominantly inherited blindness from retinal degeneration. We identified English Mastiff dogs with a naturally occurring dominant retinal degeneration and determined the cause to be a point mutation in the RHO gene (Thr4Arg). Dogs with this mutant allele manifest a retinal phenotype that closely mimics that in humans with RHO mutations. The phenotypic features shared by dog and man include a dramatically slowed time course of recovery of rod photoreceptor function after light exposure and a distinctive topographic pattern to the retinal degeneration. The canine disease offers opportunities to explore the basis of prolonged photoreceptor recovery after light in RHO mutations and determine whether there are links between the dysfunction and apoptotic retinal cell death. The RHO mutant dog also becomes the large animal needed for preclinical trials of therapies for a major subset of human retinopathies. PMID:11972042

  17. Natural and anthropogenic variations in atmospheric mercury deposition during the Holocene near Quelccaya Ice Cap, Peru

    NASA Astrophysics Data System (ADS)

    Beal, Samuel A.; Kelly, Meredith A.; Stroup, Justin S.; Jackson, Brian P.; Lowell, Thomas V.; Tapia, Pedro M.

    2014-04-01

    Mercury (Hg) is a toxic metal that is transported globally through the atmosphere. Emissions of Hg from mineral reservoirs and recycling between soil/biomass, oceans, and the atmosphere are fundamental to the global Hg cycle, yet past emissions from anthropogenic and natural sources are not fully constrained. We use a sediment core from Yanacocha, a headwater lake in southeastern Peru, to study the anthropogenic and natural controls on atmospheric Hg deposition during the Holocene. From 12.3 to 3.5 ka, Hg fluxes in the record are relatively constant (mean ± 1σ: 1.4 ± 0.6 µg m-2 a-1). Past Hg deposition does not correlate with changes in regional temperature and precipitation or with most large volcanic events that occurred regionally (~300-400 km from Yanacocha) and globally. In 1450 B.C. (3.4 ka), Hg fluxes abruptly increased and reached the Holocene-maximum flux (6.7 µg m-2 a-1) in 1200 B.C., concurrent with a ~100 year peak in Fe and chalcophile metals (As, Ag, Tl) and the presence of framboidal pyrite. Continuously elevated Hg fluxes from 1200 to 500 B.C. suggest a protracted mining-dust source near Yanacocha that is identical in timing to documented pre-Incan cinnabar mining in central Peru. During Incan and Colonial time (A.D. 1450-1650), Hg deposition remains elevated relative to background levels but lower relative to other Hg records from sediment cores in central Peru, indicating a limited spatial extent of preindustrial Hg emissions. Hg fluxes from A.D. 1980 to 2011 (4.0 ± 1.0 µg m-2 a-1) are 3.0 ± 1.5 times greater than preanthropogenic fluxes.

  18. Measurement of rRNA Variations in Natural Communities of Microorganisms on the Southeastern U.S. Continental Shelf †

    PubMed Central

    Kramer, Jonathan G.; Singleton, Fred L.

    1993-01-01

    The development of a clear understanding of the physiology of marine prokaryotes is complicated by the difficulties inherent in resolving the activity of various components of natural microbial communities. Application of appropriate molecular biological techniques offers a means of overcoming some of these problems. In this regard, we have used direct probing of bulk RNA purified from selective size fractions to examine variations in the rRNA content of heterotrophic communities and Synechococcus populations on the southeastern U.S. continental shelf. Heterotrophic communities in natural seawater cultures amended with selected substrates were examined. Synechococcus populations were isolated from the water column by differential filtration. The total cellular rRNA content of the target populations was assayed by probing RNA purified from these samples with an oligonucleotide complementing a universally conserved region in the eubacterial 16S rRNA (heterotrophs) or with a 1.5-kbp fragment encoding the Synechococcus sp. strain WH 7803 16S rRNA (cyanobacteria). The analyses revealed that heterotrophic bacteria responded to the addition of glucose and trace nutrients after a 6-h lag period. However, no response was detected after amino acids were added. The cellular rRNA content increased 48-fold before dropping to a value 20 times that detected before nutrients were added. Variations in the rRNA content from Synechococcus spp. followed a distinct diel pattern imposed by the phasing of cell division within the irradiance cycle. The results indicate that careful application of these appropriate molecular biological techniques can be of great use in discerning basic physiological characteristics of selected natural populations and the mechanisms which regulate growth at the subcellular level. Images PMID:16349009

  19. Exploiting natural variation of secondary metabolism identifies a gene controlling the glycosylation diversity of dihydroxybenzoic acids in Arabidopsis thaliana.

    PubMed

    Li, Xu; Svedin, Elisabeth; Mo, Huaping; Atwell, Susanna; Dilkes, Brian P; Chapple, Clint

    2014-11-01

    Plant secondary metabolism is an active research area because of the unique and important roles the specialized metabolites have in the interaction of plants with their biotic and abiotic environment, the diversity and complexity of the compounds and their importance to human medicine. Thousands of natural accessions of Arabidopsis thaliana characterized with increasing genomic precision are available, providing new opportunities to explore the biochemical and genetic mechanisms affecting variation in secondary metabolism within this model species. In this study, we focused on four aromatic metabolites that were differentially accumulated among 96 Arabidopsis natural accessions as revealed by leaf metabolic profiling. Using UV, mass spectrometry, and NMR data, we identified these four compounds as different dihydroxybenzoic acid (DHBA) glycosides, namely 2,5-dihydroxybenzoic acid (gentisic acid) 5-O-β-D-glucoside, 2,3-dihydroxybenzoic acid 3-O-β-D-glucoside, 2,5-dihydroxybenzoic acid 5-O-β-D-xyloside, and 2,3-dihydroxybenzoic acid 3-O-β-D-xyloside. Quantitative trait locus (QTL) mapping using recombinant inbred lines generated from C24 and Col-0 revealed a major-effect QTL controlling the relative proportion of xylosides vs. glucosides. Association mapping identified markers linked to a gene encoding a UDP glycosyltransferase gene. Analysis of Transfer DNA (T-DNA) knockout lines verified that this gene is required for DHBA xylosylation in planta and recombinant protein was able to xylosylate DHBA in vitro. This study demonstrates that exploiting natural variation of secondary metabolism is a powerful approach for gene function discovery. PMID:25173843

  20. Untangling Natural Seascape Variation from Marine Reserve Effects Using a Landscape Approach

    PubMed Central

    Huntington, Brittany E.; Karnauskas, Mandy; Babcock, Elizabeth A.; Lirman, Diego

    2010-01-01

    Distinguishing management effects from the inherent variability in a system is a key consideration in assessing reserve efficacy. Here, we demonstrate how seascape heterogeneity, defined as the spatial configuration and composition of coral reef habitats, can mask our ability to discern reserve effects. We then test the application of a landscape approach, utilizing advances in benthic habitat mapping and GIS techniques, to quantify this heterogeneity and alleviate the confounding influence during reserve assessment. Seascape metrics were quantified at multiple spatial scales using a combination of spatial image analysis and in situ surveys at 87 patch reef sites in Glover's Reef Lagoon, Belize, within and outside a marine reserve enforced since 1998. Patch reef sites were then clustered into classes sharing similar seascape attributes using metrics that correlated significantly to observed variations in both fish and coral communities. When the efficacy of the marine reserve was assessed without including landscape attributes, no reserve effects were detected in the diversity and abundance of fish and coral communities, despite 10 years of management protection. However, grouping sites based on landscape attributes revealed significant reserve effects between site classes. Fish had higher total biomass (1.5×) and commercially important biomass (1.75×) inside the reserve and coral cover was 1.8 times greater inside the reserve, though direction and degree of response varied by seascape class. Our findings show that the application of a landscape classification approach vastly improves our ability to evaluate the efficacy of marine reserves by controlling for confounding effects of seascape heterogeneity and suggests that landscape heterogeneity should be considered in future reserve design. PMID:20808833

  1. Tunicate pregnane X receptor (PXR) orthologs: transcript characterization and natural variation.

    PubMed

    Richter, Ingrid; Fidler, Andrew E

    2015-10-01

    Vertebrate pregnane X receptor (PXR, NR1I2), a ligand-activated nuclear receptor (NR), regulates expression of detoxification genes. Vertebrate PXR orthologs may adaptively evolve to bind deleterious/toxic xenobiotics typically encountered by organisms from their diet. Tunicates (phylum Chordata) are marine filter-feeders that form a sister clade to the Vertebrata. Genomes of two tunicate taxa, Ciona intestinalis and Botryllus schlosseri, encode at least two PXR orthologs (abbreviated VDR/PXRα and β). Here we report characterization of the transcript structures and sequence variation of three tunicate PXR orthologs: C. intestinalis VDR/PXRα and β, and B. schlosseri VDR/PXRα. The three predicted proteins consist of both DNA-binding (DBD) and ligand-binding (LBD) domains typical of NRs. The C. intestinalis VDR/PXRβ LBD may be significantly larger than that of the VDR/PXRα orthologs. In both tunicate taxa, the mRNAs were characterized by high frequencies of single nucleotide polymorphisms (SNPs, ca. 3 SNPs/100 base pairs). The majority of SNPs were synonymous and standard tests (Tajima's D, dN/dS ratios) indicated strong purifying selection. However, one base pair frameshift allelic variants were found in the C. intestinalis VDR/PXRα and β genes. The predicted proteins consisted of a DBD but lacked an LBD. The persistence of these variants may possibly reflect constitutive expression of detoxification genes as a selective advantage in the marine environment. These results provide a foundation for further investigations into the molecular evolution, population genetics and functioning of tunicate receptors involved in detection of marine bioactive compounds. PMID:25988373

  2. Extensive sequence variation in rice blast resistance gene Pi54 makes it broad spectrum in nature

    PubMed Central

    Thakur, Shallu; Singh, Pankaj K.; Das, Alok; Rathour, R.; Variar, M.; Prashanthi, S. K.; Singh, A. K.; Singh, U. D.; Chand, Duni; Singh, N. K.; Sharma, Tilak R.

    2015-01-01

    Rice blast resistant gene, Pi54 cloned from rice line, Tetep, is effective against diverse isolates of Magnaporthe oryzae. In this study, we prospected the allelic variants of the dominant blast resistance gene from a set of 92 rice lines to determine the nucleotide diversity, pattern of its molecular evolution, phylogenetic relationships and evolutionary dynamics, and to develop allele specific markers. High quality sequences were generated for homologs of Pi54 gene. Using comparative sequence analysis, InDels of variable sizes in all the alleles were observed. Profiling of the selected sites of SNP (Single Nucleotide Polymorphism) and amino acids (N sites ≥ 10) exhibited constant frequency distribution of mutational and substitutional sites between the resistance and susceptible rice lines, respectively. A total of 50 new haplotypes based on the nucleotide polymorphism was also identified. A unique haplotype (H_3) was found to be linked to all the resistant alleles isolated from indica rice lines. Unique leucine zipper and tyrosine sulfation sites were identified in the predicted Pi54 proteins. Selection signals were observed in entire coding sequence of resistance alleles, as compared to LRR domains for susceptible alleles. This is a maiden report of extensive variability of Pi54 alleles in different landraces and cultivated varieties, possibly, attributing broad-spectrum resistance to Magnaporthe oryzae. The sequence variation in two consensus region: 163 and 144 bp were used for the development of allele specific DNA markers. Validated markers can be used for the selection and identification of better allele(s) and their introgression in commercial rice cultivars employing marker assisted selection. PMID:26052332

  3. Untangling natural seascape variation from marine reserve effects using a landscape approach.

    PubMed

    Huntington, Brittany E; Karnauskas, Mandy; Babcock, Elizabeth A; Lirman, Diego

    2010-01-01

    Distinguishing management effects from the inherent variability in a system is a key consideration in assessing reserve efficacy. Here, we demonstrate how seascape heterogeneity, defined as the spatial configuration and composition of coral reef habitats, can mask our ability to discern reserve effects. We then test the application of a landscape approach, utilizing advances in benthic habitat mapping and GIS techniques, to quantify this heterogeneity and alleviate the confounding influence during reserve assessment. Seascape metrics were quantified at multiple spatial scales using a combination of spatial image analysis and in situ surveys at 87 patch reef sites in Glover's Reef Lagoon, Belize, within and outside a marine reserve enforced since 1998. Patch reef sites were then clustered into classes sharing similar seascape attributes using metrics that correlated significantly to observed variations in both fish and coral communities. When the efficacy of the marine reserve was assessed without including landscape attributes, no reserve effects were detected in the diversity and abundance of fish and coral communities, despite 10 years of management protection. However, grouping sites based on landscape attributes revealed significant reserve effects between site classes. Fish had higher total biomass (1.5x) and commercially important biomass (1.75x) inside the reserve and coral cover was 1.8 times greater inside the reserve, though direction and degree of response varied by seascape class. Our findings show that the application of a landscape classification approach vastly improves our ability to evaluate the efficacy of marine reserves by controlling for confounding effects of seascape heterogeneity and suggests that landscape heterogeneity should be considered in future reserve design. PMID:20808833

  4. Pilin-gene phase variation of Moraxella bovis is caused by an inversion of the pilin genes.

    PubMed Central

    Marrs, C F; Ruehl, W W; Schoolnik, G K; Falkow, S

    1988-01-01

    Moraxella bovis Epp63 can express either of two different pilin proteins, called alpha and beta. We have previously cloned and sequenced the beta-pilin gene and now report that DNAs isolated from bacteria expressing alpha pilin have hybridization patterns consistently different from those of bacteria expressing beta pilin. The phase variation between alpha- and beta-pilin gene expression appears to be associated with an inversion of about 2 kilobases of DNA, whose endpoints occur within the coding region of the expressed pilin gene. Comparisons of the beta-pilin gene sequence with those of well-studied bacterial inversion systems revealed a stretch of 58% sequence similarity (21 of 36 base pairs) between the left inverted repeat of the Salmonella typhimurium flagellar hin control region and the amino-terminal portion of the beta-pilin gene. Images PMID:2898471

  5. The dynamic nature of DNA methylation: a role in response to social and seasonal variation.

    PubMed

    Alvarado, Sebastian; Fernald, Russell D; Storey, Kenneth B; Szyf, Moshe

    2014-07-01

    An organism's ability to adapt to its environment depends on its ability to regulate and maintain tissue specific, temporal patterns of gene transcription in response to specific environmental cues. Epigenetic mechanisms are responsible for many of the intricacies of a gene's regulation that alter expression patterns without affecting the genetic sequence. In particular, DNA methylation has been shown to have an important role in regulating early development and in some human diseases. Within these domains, DNA methylation has been extensively characterized over the past 60 years, but the discovery of its role in regulating behavioral outcomes has led to renewed interest in its potential roles in animal behavior and phenotypic plasticity. The conservation of DNA methylation across the animal kingdom suggests a possible role in the plasticity of genomic responses to environmental cues in natural environments. Here, we review the historical context for the study of DNA methylation, its function and mechanisms, and provide examples of gene/environment interactions in response to social and seasonal cues. Finally, we discuss useful tools to interrogate and dissect the function of DNA methylation in non-model organisms. PMID:24813708

  6. Statistical evidence for the natural variation of the central Pacific El Niño

    NASA Astrophysics Data System (ADS)

    Kim, Jin-Soo; Kim, Kwang-Yul; Yeh, Sang-Wook

    2012-06-01

    Extensive studies claimed that the central equatorial Pacific (CP) El Niño has occurred more frequently and strongly than the eastern equatorial Pacific El Niño in recent years. To explain this phenomenon, spatial patterns and principal component time series from several sea surface temperature (SST) data sets in the tropical Pacific are analyzed for the period of 1951-2010. Cyclostationary empirical orthogonal function analysis separates two modes of SST variability, which explain about 50% and 10% of the total SST variability, respectively. Their spatial and temporal patterns are similar among the different SST data sets. The first mode captures the typical El Niño pattern, while the second mode is a dipole pattern in the tropical Pacific. The two modes are, by definition, uncorrelated over the analysis period but are in phase since the late 1990s; superposition of the two modes results in a significant warming in the CP region, which is a potential explanation for a more frequent occurrence of the CP El Niño in the recent decades. Similar analysis is conducted based on the 500 year data from the Geophysical Fluid Dynamics Laboratory Climate Model version 2.1 under the preindustrial condition. The result is generally consistent with the observations yielding occasional in-phase relationship between the two modes. Thus, it cannot be ruled out that a more frequent occurrence of the CP El Niño in recent years is a natural feature of the equatorial climate system.

  7. Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

    PubMed Central

    Shen, Xia; De Jonge, Jennifer; Forsberg, Simon K. G.; Pettersson, Mats E.; Sheng, Zheya; Hennig, Lars; Carlborg, Örjan

    2014-01-01

    As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel meth