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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. 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

  5. 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…

  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. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  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. 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

  18. 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.

  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. 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.

  6. 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...

  7. 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

  8. 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...

  9. 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

  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

    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

  12. 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

  13. 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

  14. 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

  15. 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…

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  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. 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

  3. 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

  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. 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

  6. 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

  7. 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.

  8. 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

  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. 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

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

    PubMed

    Bedford, Nicole L; Hoekstra, Hopi E

    2015-01-01

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

  16. 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

  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. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  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. 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

  19. 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

  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. 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.

  3. 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

  4. [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

  5. 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.

  6. 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

  7. 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…

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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....

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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.

  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. 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

  8. 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.

  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. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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

  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. 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.

  2. 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.

  3. 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

  4. 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

  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. 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

  8. 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

  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. 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

  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. 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.

  14. 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.

  15. 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

  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. 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

  18. 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

  19. 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

  20. 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

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

    PubMed Central

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

    2012-01-01

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

  2. 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

  3. 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.

  4. 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).

  5. 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

  6. 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

  7. 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.

  8. 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

  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. 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…

  16. 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…

  17. 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...

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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 ...

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  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. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    PubMed Central

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

    2016-01-01

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

  15. 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

  16. 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

  17. 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

  18. 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

  19. [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

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-06-01

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

  10. 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…

  11. 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.

  12. 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

  13. 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

  14. 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

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

    PubMed

    Hauser, Marie-Theres

    2014-01-01

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

  16. Natural 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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...

  1. 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...

  2. 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

  3. 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

  4. 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.

  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. 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).

  7. 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

  8. 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.

  9. 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.

  10. [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