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Sample records for causing natural variation

  1. Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana

    PubMed Central

    Vlad, Daniela; Rappaport, Fabrice; Simon, Matthieu; Loudet, Olivier

    2010-01-01

    A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 × Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent—but still functional—combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation

  2. Variations of Hydrogen in the Thermosphere: Nature and Causes

    NASA Astrophysics Data System (ADS)

    Burns, A. G.; Wang, W.; Qian, L.; Crowley, G.; Thayer, J. P.

    2015-12-01

    Neutral hydrogen plays an important role in determining the state of the plasmasphere and its response to forcing from geomagnetic storms. Hydrogen's solar cycle variation is counterintuitive: there is more hydrogen at solar minimum at 300 km that there is at solar maximum. Similarly there is more hydrogen in winter than in summer and hydrogen density maximizes in the morning. In this presentation we describe these variations and consider some possible causes for them.

  3. Natural variation in Drosophila stressed locomotion meets or exceeds variation caused by hsp70 mutation: analysis of behavior and performance.

    PubMed

    Bettencourt, Brian R; Drohan, Brian W; Ireland, Andrea T; Santhanam, Mahalakshmi; Smrtic, Mary Beth; Sullivan, Erin M

    2009-05-01

    Thermotolerance involves more than life or death. Investigating the complexity of this trait will aid identification of its genetic contributors. We examined variation in thermally stressed walking behavior and performance in natural Drosophila melanogaster strains and strains mutant for the heat shock protein Hsp70, to determine which aspects of locomotion are affected by heat shock and genotype. We developed software for the large-scale capture, analysis, and visualization of locomotion, and determined: (1) Heat shock and thermal pretreatment significantly and differentially impact fly locomotor behavior and performance. (2) Stressed locomotion traits vary extensively among natural strains. (3) Interactions among treatments, strains, and traits are substantial and often counterintuitive. (4) Hsp70 overexpressing flies are faster and more basally thermoprotected in performance than Hsp70 null flies, but null flies are more unidirectional. (5) Natural variation in most stressed locomotion traits exceeds that caused by Hsp70 mutation, reveals uncoupling between thermoprotection of behavior and performance, and suggests significant genetic variation for trait-specific modifiers of thermotolerance.

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

    NASA Astrophysics Data System (ADS)

    Baker, Paul A.; Fritz, Sherilyn C.

    2015-09-01

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

  5. Natural diversity in flowering responses of Arabidopsis thaliana caused by variation in a tandem gene array.

    PubMed

    Rosloski, Sarah Marie; Jali, Sathya Sheela; Balasubramanian, Sureshkumar; Weigel, Detlef; Grbic, Vojislava

    2010-09-01

    Tandemly arrayed genes that belong to gene families characterize genomes of many organisms. Gene duplication and subsequent relaxation of selection can lead to the establishment of paralogous cluster members that may evolve along different trajectories. Here, we report on the structural variation in MADS AFFECTING FLOWERING 2 (MAF2) gene, one member of the tandemly duplicated cluster of MADS-box-containing transcription factors in Arabidopsis thaliana. The altered gene structure at the MAF2 locus is present as a moderate-frequency polymorphism in Arabidopsis and leads to the extensive diversity in transcript patterns due to alternative splicing. Rearrangements at the MAF2 locus are associated with an early flowering phenotype in BC(5) lines. The lack of suppression of flowering time in a MAF2-insertion line expressing the MAF2-specific artificial miRNA suggests that these MAF2 variants are behaving as loss-of-function alleles. The variation in gene architecture is also associated with segregation distortion, which may have facilitated the spread and the establishment of the corresponding alleles throughout the Eurasian range of the A. thaliana population.

  6. Variations Among Inner City Elementary Schools: An Investigation into the Nature and Causes of Their Differences.

    ERIC Educational Resources Information Center

    Doll, Russell C.

    The investigation in this study of inner-city elementary schools identified two main causes for successful learning environments. The strongest influence was thought to be the principal. An analysis of "problem oriented schools" showed that successful principals were prone to act independently of bureaucratic directives, and that they heeded…

  7. Natural variation in plep-1 causes male-male copulatory behavior in C. elegans

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Briga, Michael; Verhulst, Simon

    2015-11-01

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

  9. Natural variation of potato allene oxide synthase 2 causes differential levels of jasmonates and pathogen resistance in Arabidopsis

    PubMed Central

    Pajerowska-Mukhtar, Karolina M.; Mukhtar, M. Shahid; Guex, Nicolas; Halim, Vincentius A.; Rosahl, Sabine; Somssich, Imre E.

    2008-01-01

    Natural variation of plant pathogen resistance is often quantitative. This type of resistance can be genetically dissected in quantitative resistance loci (QRL). To unravel the molecular basis of QRL in potato (Solanum tuberosum), we employed the model plant Arabidopsis thaliana for functional analysis of natural variants of potato allene oxide synthase 2 (StAOS2). StAOS2 is a candidate gene for QRL on potato chromosome XI against the oömycete Phytophthora infestans causing late blight, and the bacterium Erwinia carotovora ssp. atroseptica causing stem black leg and tuber soft rot, both devastating diseases in potato cultivation. StAOS2 encodes a cytochrome P450 enzyme that is essential for biosynthesis of the defense signaling molecule jasmonic acid. Allele non-specific dsRNAi-mediated silencing of StAOS2 in potato drastically reduced jasmonic acid production and compromised quantitative late blight resistance. Five natural StAOS2 alleles were expressed in the null Arabidopsis aos mutant under control of the Arabidopsis AOS promoter and tested for differential complementation phenotypes. The aos mutant phenotypes evaluated were lack of jasmonates, male sterility and susceptibility to Erwinia carotovora ssp. carotovora. StAOS2 alleles that were associated with increased disease resistance in potato complemented all aos mutant phenotypes better than StAOS2 alleles associated with increased susceptibility. First structure models of ‘quantitative resistant’ versus ‘quantitative susceptible’ StAOS2 alleles suggested potential mechanisms for their differential activity. Our results demonstrate how a candidate gene approach in combination with using the homologous Arabidopsis mutant as functional reporter can help to dissect the molecular basis of complex traits in non model crop plants. Electronic supplementary material The online version of this article (doi:10.1007/s00425-008-0737-x) contains supplementary material, which is available to authorized users

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

    PubMed

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

    2011-02-01

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

  11. Genetic structure and natural variation associated with host of origin in Penicillium expansum strains causing blue mould.

    PubMed

    Sanzani, S M; Montemurro, C; Di Rienzo, V; Solfrizzo, M; Ippolito, A

    2013-07-15

    Blue mould, caused by Penicillium expansum, is one of the most economically damaging postharvest diseases of pome fruits, although it may affect a wider host range, including sweet cherries and table grapes. Several reports on the role of mycotoxins in plant pathogenesis have been published, but few focussed on the influence of mycotoxins on the variation in host preference amongst producing fungi. In the present study the influence of the host on P. expansum pathogenicity/virulence was investigated, focussing mainly on the relationship with patulin production. Three P. expansum strain groups, originating from apples, sweet cherries, and table grapes (7 strains per host) were grown on their hosts of isolation and on artificial media derived from them. Strains within each P. expansum group proved to be more aggressive and produced more patulin than the other two groups under evaluation when grown on the host from which they originated. Table grape strains were the most aggressive (81% disease incidence) and strongest patulin producers (up to 554μg/g). The difference in aggressiveness amongst strains was appreciable only in the presence of a living host, suggesting that the complex pathogen-host interaction significantly influenced the ability of P. expansum to cause the disease. Incidence/severity of the disease and patulin production proved to be positively correlated, supporting the role of patulin as virulence/pathogenicity factor. The existence of genetic variation amongst isolates was confirmed by the High Resolution Melting method that was set up herein, which permitted discrimination of P. expansum from other species (P. chrysogenum and P. crustosum) and, within the same species, amongst the host of origin. Host effect on toxin production appeared to be exerted at a transcriptional level.

  12. 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…

  13. 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…

  14. Precipitation drives global variation in natural selection.

    PubMed

    Siepielski, Adam M; Morrissey, Michael B; Buoro, Mathieu; Carlson, Stephanie M; Caruso, Christina M; Clegg, Sonya M; Coulson, Tim; DiBattista, Joseph; Gotanda, Kiyoko M; Francis, Clinton D; Hereford, Joe; Kingsolver, Joel G; Augustine, Kate E; Kruuk, Loeske E B; Martin, Ryan A; Sheldon, Ben C; Sletvold, Nina; Svensson, Erik I; Wade, Michael J; MacColl, Andrew D C

    2017-03-03

    Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation-natural selection-are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By showing that selection was influenced by climate variation, our results indicate that climate change may cause widespread alterations in selection regimes, potentially shifting evolutionary trajectories at a global scale.

  15. Promoter difference of LcFT1 is a leading cause of natural variation of flowering timing in different litchi cultivars (Litchi chinensis Sonn.).

    PubMed

    Ding, Feng; Zhang, Shuwei; Chen, Houbin; Su, Zuanxian; Zhang, Rong; Xiao, Qiusheng; Li, Hongli

    2015-12-01

    Litchi (Litchi chinensis) is an important subtropical evergreen fruit crop with high commercial value due to its high nutritional values and favorable tastes. However, irregular bearing attributed to unstable flowering is a major ongoing problem for litchi producers. There is a need to better understand the genetic and molecular mechanisms underlying the reproductive process in litchi. In a previous study, our laboratory had analyzed the transcriptome of litchi leaves before and after low-temperature treatment with RNA-seq technology. Herein, we demonstrated that litchi flowering was induced by low-temperature and identified two FLOWERING LOCUS T (FT) homologue genes named LcFT1 and LcFT2, respectively. We found that low-temperature could only induce LcFT1 expression in leaves, but could not induce LcFT2 expression. Heterologous expression of LcFT1 in transgenic tobacco and Arabidopsis plants induced their precocious flowering. These results indicate that LcFT1 plays a pivotal role in litchi floral induction by low-temperature. In addition, we found that two types of LcFT1 promoter existed in different litchi cultivars. The LcFT1 promoters in the early-flowering cultivars belonged to one type whereas LcFT1 promoters in the late-flowering belonged to another one. LcFT1 promoter in the early-flowering cultivars was more sensitive to low-temperature than that of the late-flowering cultivars was, which may be caused by the different cis-acting elements, including MYC, MYB, ABRE, and WRKY cis-acting elements, which were found to be present in the LcFT1 promoter sequences of the early-flowering cultivars. This difference may be responsible for the different requirements of low-temperature for floral induction in the early- and late-flowering cultivars of litchi. Taken together, the difference in LcFT1 promoter sequences may be one of the leading cause for the natural variation of flowering timing in different litchi cultivars. Our study has provided valuable genetic

  16. Morphogenetic origin of natural variation.

    PubMed

    Cherdantsev, Vladimir G; Scobeyeva, Victoria A

    2012-09-01

    We studied individual pathways of gastrulation in two related amphibian species making an emphasis on the developmental dynamics of normal variation in the geometry of gastrulation movements. Analyzing the variation dynamics, we show that the linear succession of developmental stages is a secondary phenomenon disguising self-oscillations that lie at the heart of the dorsal blastopore lip morphogenesis. Characteristic features of the equations derived to describe the oscillations are, first, their dependence only on the movement geometry and, second, including of the dynamics of spatial variance directly into the movement equations, making it clear that the reasons for variability of morphogenesis are the same that for morphogenesis itself. The equations describing morphogenetic oscillations are mathematically similar to those describing natural selection in that the system tends to minimize its variance, individual or within-individual one, but the spatially uniform state turns to be unstable. Comparing of the dynamics of natural developmental variation in gastrulation in two frog species shows that, depending on the mechanics and geometry mass cell movements, different types of gastrulation movements have different proportions of the between- to within-individual differences, which strongly influences the choice of characters subject to evolution. Instead of being a source of constraints imposed on externally guided evolutionary trends, morphogenesis becomes a driving force of the adaptively silent, but directional evolution of the developing systems, which seems to be the only possible way of originating of the evolutionary novelties, both in evolution and ontogeny of the biological structures.

  17. Extreme genomic variation in a natural population.

    PubMed

    Small, Kerrin S; Brudno, Michael; Hill, Matthew M; Sidow, Arend

    2007-03-27

    Whole-genome sequence data from samples of natural populations provide fertile grounds for analyses of intraspecific variation and tests of population genetic theory. We show that the urochordate Ciona savignyi, one of the species of ocean-dwelling broadcast spawners commonly known as sea squirts, exhibits the highest rates of single-nucleotide and structural polymorphism ever comprehensively quantified in a multicellular organism. We demonstrate that the cause for the extreme heterozygosity is a large effective population size, and, consistent with prediction by the neutral theory, we find evidence of strong purifying selection. These results constitute in-depth insight into the dynamics of highly polymorphic genomes and provide important empirical support of population genetic theory as it pertains to population size, heterozygosity, and natural selection.

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

    PubMed

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

    2012-12-01

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

  19. 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.

  20. Genetic engineering compared to natural genetic variations.

    PubMed

    Arber, Werner

    2010-11-30

    By comparing strategies of genetic alterations introduced in genetic engineering with spontaneously occurring genetic variation, we have come to conclude that both processes depend on several distinct and specific molecular mechanisms. These mechanisms can be attributed, with regard to their evolutionary impact, to three different strategies of genetic variation. These are local nucleotide sequence changes, intragenomic rearrangement of DNA segments and the acquisition of a foreign DNA segment by horizontal gene transfer. Both the strategies followed in genetic engineering and the amounts of DNA sequences thereby involved are identical to, or at least very comparable with, those involved in natural genetic variation. Therefore, conjectural risks of genetic engineering must be of the same order as those for natural biological evolution and for conventional breeding methods. These risks are known to be quite low. There is no scientific reason to assume special long-term risks for GM crops. For future agricultural developments, a road map is designed that can be expected to lead, by a combination of genetic engineering and conventional plant breeding, to crops that can insure food security and eliminate malnutrition and hunger for the entire human population on our planet. Public-private partnerships should be formed with the mission to reach the set goals in the coming decades.

  1. Intraocular pressure variations: causes and clinical significance.

    PubMed

    Sit, Arthur J

    2014-12-01

    Reduction of intraocular pressure (IOP) is the only known effective treatment for glaucoma. However, IOP is a highly variable and dynamic parameter, undergoing virtually constant changes from numerous factors, including body position and circadian rhythms. Despite this variability, evidence for the efficacy of IOP reduction in glaucoma is based on studies designed to assess mean IOP and not IOP variations. Post hoc analysis of data from major clinical trials has suggested that IOP variations may be an independent risk factor for the development of glaucoma or glaucomatous progression, at least in some patients, but the evidence is incomplete and further studies are required. In the interim, judicious selection of existing therapies can help to minimize IOP variations. In general, therapies that improve outflow instead of suppressing aqueous humor production result in more stable IOP. However, new technology to allow better monitoring of IOP, ideally in a continuous 24-hour manner, is required to fully understand the role of IOP variations in glaucoma. Copyright © 2014 Canadian Ophthalmological Society. Published by Elsevier Inc. All rights reserved.

  2. The nature of solar brightness variations

    NASA Astrophysics Data System (ADS)

    Shapiro, A. I.; Solanki, S. K.; Krivova, N. A.; Cameron, R. H.; Yeo, K. L.; Schmutz, W. K.

    2017-09-01

    Determining the sources of solar brightness variations1,2, often referred to as solar noise3, is important because solar noise limits the detection of solar oscillations3, is one of the drivers of the Earth's climate system4,5 and is a prototype of stellar variability6,7—an important limiting factor for the detection of extrasolar planets. Here, we model the magnetic contribution to solar brightness variability using high-cadence8,9 observations from the Solar Dynamics Observatory (SDO) and the Spectral And Total Irradiance REconstruction (SATIRE)10,11 model. The brightness variations caused by the constantly evolving cellular granulation pattern on the solar surface were computed with the Max Planck Institute for Solar System Research (MPS)/University of Chicago Radiative Magnetohydrodynamics (MURaM)12 code. We found that the surface magnetic field and granulation can together precisely explain solar noise (that is, solar variability excluding oscillations) on timescales from minutes to decades, accounting for all timescales that have so far been resolved or covered by irradiance measurements. We demonstrate that no other sources of variability are required to explain the data. Recent measurements of Sun-like stars by the COnvection ROtation and planetary Transits (CoRoT)13 and Kepler14 missions uncovered brightness variations similar to that of the Sun, but with a much wider variety of patterns15. Our finding that solar brightness variations can be replicated in detail with just two well-known sources will greatly simplify future modelling of existing CoRoT and Kepler as well as anticipated Transiting Exoplanet Survey Satellite16 and PLAnetary Transits and Oscillations of stars (PLATO)17 data.

  3. Variation in pollination: causes and consequences for plant reproduction.

    PubMed

    Richards, Shane A; Williams, Neal M; Harder, Lawrence D

    2009-09-01

    Pollen dispersal by animals varies extensively because of differences in pollinator visitation rates among plants, dissimilar pollination by the various pollinators that visit individual plants, and stochastic variation in deposition as an individual pollinator disperses a plant's pollen to subsequently visited recipient flowers. Such variation reduces expected female and male success if seed production decelerates with increasing pollen receipt, because less than average receipt diminishes mean seed production more than copious pollination increases it (Jensen's inequality). We report empirical studies of the nature and magnitude of pollen dispersal variance, which provide the basis for a numerical model of the consequences of dispersal for expected seed production. Model fitting revealed that dispersal of Brassica napus pollen by bumblebees and especially butterflies exhibited much more variation than is expected of a binomial process and was best modeled as a beta-binomial process with a constant mean. Overdispersion arose primarily during pollen dispersal by individual insects, since differences between individuals of the same pollinator type were limited. Our model revealed variance limitation as a previously unrecognized, substantial, and ubiquitous component of pollen limitation of seed production. Variance limitation should select for floral traits that increase pollinator visitation, reduce dispersal variance, or reduce the postpollination nonlinearities that cause Jensen's inequality.

  4. Comprehensive profiling and natural variation of flavonoids in rice.

    PubMed

    Dong, Xuekui; Chen, Wei; Wang, Wensheng; Zhang, Hongyan; Liu, Xianqing; Luo, Jie

    2014-09-01

    Flavonoids constitute a major group of plant phenolic compounds. While extensively studied in Arabidopsis, profiling and naturally occurring variation of these compounds in rice (Oryza sativa), the monocot model plant, are less reported. Using a collection of rice germplasm, comprehensive profiling and natural variation of flavonoids were presented in this report. Application of a widely targeted metabolomics method facilitated the simultaneous identification and quantification of more than 90 flavonoids using liquid chromatography tandem mass spectrometry (LC-MS/MS). Comparing flavonoid contents in various tissues during different developmental stages revealed tissue-specific accumulation of most flavonoids. Further investigation indicated that flavone mono-C-glycosides, malonylated flavonoid O-hexosides, and some flavonoid O-glycosides accumulated at significantly higher levels in indica than in japonica, while the opposite was observed for aromatic acylated flavone C-hexosyl-O-hexosides. In contrast to the highly differential accumulation between the two subspecies, relatively small variations within subspecies were detected for most flavonoids. Besides, an association analysis between flavonoid accumulation and its biosynthetic gene sequence polymorphisms disclosed that natural variation of flavonoids was probably caused by sequence polymorphisms in the coding region of flavonoid biosynthetic genes. Our work paves the way for future dissection of biosynthesis and regulation of flavonoid pathway in rice.

  5. River pollution caused by natural stone industry

    NASA Astrophysics Data System (ADS)

    Oktriani, Ani; Darmajanti, Linda; Soesilo, Tri Edhi Budhi

    2017-03-01

    The natural stone industry is classified as small industry. Current wastewater treatment still causes pollution in the river. This thesis aims to analyze the performance of wastewater treatment in natural stones industry. The data was collected from water quality test (parameters: temperature, pH, DO, and TSS). The wastewater treatment performance was in a slightly higher position compared to the 2nd class quality standards of Government Regulation No. 82/2001. The parameter that exceeded quality standards was the concentration of TSS, which was up to 240.8 mg/l. The high concentration of TSS was affected by the absence of sludge management schedule, which resulted in non-optimal precipitation. Besides that, the design of sedimentation basin was still not adapted with wastewater debit. Referring to the results, this study suggests the government of Cirebon District to provide wastewater treatment development through the village staff. Furthermore, the government also needs to give strict punishment to business owner who does not treat waste correctly and does not have a business license. Moreover, the sale value of sludge as byproduct of wastewater treatment needs to be increased.

  6. Natural variation in learning and memory.

    PubMed

    Mery, Frederic

    2013-02-01

    Learning is widespread in the animal kingdom. From the small nematode worm Caenorhabditis elegans to humans, learning appears to play a central role in adaptation to local spatial and temporal environmental conditions. Though the neurobiological mechanisms of learning and memory have been intensively studied, the function and adaptive significance of learning has only recently received interest. Using learning, animals may progressively adjust their behavior in response to new environmental conditions, suggesting benefits of learning on animal performance, at least in the short term. How does learning affect the overall fitness of an animal? What are the fitness benefits and costs of learning? How can we explain the natural variation in learning ability observed between individuals, between populations of the same species or between closely related species? What are the ecological circumstances that favor the evolution of learning? There are all emerging questions that are central to a better understanding of the evolution of cognition and animal adaptation. Here I review the recent evidence showing that learning and memory are molded by an animal's lifestyle within its ecological niche.

  7. Species conservation and natural variation among populations [Chapter 5

    Treesearch

    Leonard F. Ruggiero; Michael K. Schwartz; Keith B. Aubry; Charles J. Krebs; Amanda Stanley; Steven W. Buskirk

    2000-01-01

    In conservation planning, the importance of natural variation is often given inadequate consideration. However, ignoring the implications of variation within species may result in conservation strategies that jeopardize, rather than conserve, target species (see Grieg 1979; Turcek 1951; Storfer 1999). Natural variation in the traits of individuals and populations is...

  8. Analyses of natural variation indicates that the absence of RPS4/RRS1 and amino acid change in RPS4 cause loss of their functions and resistance to pathogens.

    PubMed

    Narusaka, Mari; Iuchi, Satoshi; Narusaka, Yoshihiro

    2017-03-04

    A pair of Arabidopsis thaliana resistance proteins, RPS4 and RRS1, recognizes the cognate Avr effector from the bacterial pathogens Pseudomonas syringae pv. tomato expressing avrRps4 (Pst-avrRps4), Ralstonia solanacearum, and the fungal pathogen Colletotrichum higginsianum and leads to defense signaling activation against the pathogens. In the present study, we analyzed 14 A. thaliana accessions for natural variation in Pst-avrRps4 and C. higginsianum susceptibility, and found new compatible and incompatible Arabidopsis-pathogen interactions. We first found that A. thaliana accession Cvi-0 is susceptible to Pst-avrRps4. Interestingly, the genome sequence assembly indicated that Cvi-0 lost both RPS4 and RRS1, but not RPS4B and RRS1B, compared to the reference genome sequence from A. thaliana accession Col-0. On the other hand, the natural variation analysis of RPS4 alleles from various Arabidopsis accessions revealed that one amino-acid change, Y950H, is responsible for the loss of resistance to Pst-avrRps4 and C. higginsianum in RLD-0. Our data indicate that the amino acid change, Y950H, in RPS4 resulted in the loss of both RPS4 and RRS1 functions and resistance to pathogens.

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

    PubMed

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

    2015-07-07

    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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Is biotic resistance enhanced by natural variation in diversity?

    USGS Publications Warehouse

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

    2017-01-01

    Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the underlying processes by dissecting how biotic resistance to new invaders may be shaped by the same environmental influences that determine diversity and other community properties.In grasslands with heterogeneous soils, we added invaders and removed competitors to analyze the causes of invasion resistance. Abiotic resistance was measured using invader success in the absence of the resident community. Biotic resistance was measured as the reduction in invader success in the presence of the resident community.Invaders were most successful where biotic resistance was lowest and abiotic resistance was highest, confirming the dominant role of biotic resistance. Contrary to theory, though, biotic resistance was highest where both species richness and functional diversity were lowest. In the multivariate framework of a structural equation model, biotic resistance was independent of community diversity, and was highest where fertile soils led to high community biomass.Seed predation slightly augmented biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results.We conclude that in natural systems, diversity may be correlated with invasibility and yet have little effect on biotic resistance to invasion. More generally, the environmental causes of variation in diversity should be considered when examining the potential functional consequences of diversity.

  15. The nature of genetic variation among viruses.

    PubMed

    Purcell, R H; Miller, R H

    1991-01-01

    Genetic variation among viruses may seem unimportant and academic--related only to pedagogical classification of things--but accurate determination of genetic relationships can have important implications, from characterizing the molecular basis of attenuation of viral vaccines to furthering knowledge about origins of viruses and even of life itself. It can even help to establish priority in the discovery of viruses when properly applied. The purpose of this brief review is to demonstrate how viruses change and what implications these changes can have on the delicate balance between the viral parasite and its host. Examples will be drawn from the hepatitis viruses when possible.

  16. 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. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

  17. Exploiting genomics and natural genetic variation to decode macrophage enhancers

    PubMed Central

    Romanoski, Casey E.; Link, Verena M.; Heinz, Sven; Glass, Christopher K.

    2015-01-01

    The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease. PMID:26298065

  18. Variation in gene expression within and among natural populations.

    PubMed

    Oleksiak, Marjorie F; Churchill, Gary A; Crawford, Douglas L

    2002-10-01

    Evolution may depend more strongly on variation in gene expression than on differences between variant forms of proteins. Regions of DNA that affect gene expression are highly variable, containing 0.6% polymorphic sites. These naturally occurring polymorphic nucleotides can alter in vivo transcription rates. Thus, one might expect substantial variation in gene expression between individuals. But the natural variation in mRNA expression for a large number of genes has not been measured. Here we report microarray studies addressing the variation in gene expression within and between natural populations of teleost fish of the genus Fundulus. We observed statistically significant differences in expression between individuals within the same population for approximately 18% of 907 genes. Expression typically differed by a factor of 1.5, and often more than 2.0. Differences between populations increased the variation. Much of the variation between populations was a positive function of the variation within populations and thus is most parsimoniously described as random. Some genes showed unexpected patterns of expression--changes unrelated to evolutionary distance. These data suggest that substantial natural variation exists in gene expression and that this quantitative variation is important in evolution.

  19. [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).

  20. Does natural variation in diversity affect biotic resistance?

    USGS Publications Warehouse

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

    2015-01-01

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

  1. Observed decadal variations in surface solar radiation and their causes

    NASA Astrophysics Data System (ADS)

    Ohmura, Atsumu

    2009-05-01

    Long-term variations of global solar irradiance at the Earth's surface from the beginning of the observations to 2005 are analyzed for more than 400 sites. Further, likely causes for the variations, an estimation of the magnitudes of aerosol direct and indirect effects, and the temperature sensitivity of the climate system due to radiation changes are evaluated. The record of observed global radiation begins with an increasing phase from 1920s to late 1940s/early 1960s. This brightening period (first brightening phase) is followed by the decreasing trend lasting to late 1980s, known as the global dimming, which finally translates into the second brightening phase in many regions of the world. These decadal variations are to great extent caused by aerosol and cloud fluctuations. The total aerosol effect as well as its direct and indirect effects were evaluated mainly on the basis of the observations. To meet this goal, simultaneous observations of global solar radiation and zenith transmittance are necessary. Five such regions/sites in Europe and Japan satisfy these conditions. By using the 20-year dimming phase from 1960 to 1980 and the 15-year brightening phase from 1990 to 2005, it was found that the aerosol direct and indirect effects played about an equal weight in changing global solar radiation. The temperature sensitivity due to radiation change is estimated at 0.05 to 0.06 K/(W m-2). The first brightening phase lasting to 1940s/early 1960s does not show a compatibility with the variation of transmittance of the atmosphere and originated probably from a different cause.

  2. 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.

  3. Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.

    PubMed

    Roux, Fabrice; Colomé-Tatché, Maria; Edelist, Cécile; Wardenaar, René; Guerche, Philippe; Hospital, Frédéric; Colot, Vincent; Jansen, Ritsert C; Johannes, Frank

    2011-08-01

    We extensively phenotyped 6000 Arabidopsis plants with experimentally perturbed DNA methylomes as well as a diverse panel of natural accessions in a common garden. We found that alterations in DNA methylation not only caused heritable phenotypic diversity but also produced heritability patterns closely resembling those of the natural accessions. Our findings indicate that epigenetically induced and naturally occurring variation in complex traits share part of their polygenic architecture and may offer complementary adaptation routes in ecological settings.

  4. 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.

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

    PubMed

    Takahashi, Kazuo H

    2013-03-01

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

  6. The Power of Natural Variation for Model Organism Biology.

    PubMed

    Gasch, Audrey P; Payseur, Bret A; Pool, John E

    2016-03-01

    Genetic background effects have long been recognized and, in some cases studied, but they are often viewed as a nuisance by molecular biologists. We suggest that genetic variation currently represents a critical frontier for molecular studies. Human genetics has seen a surge of interest in genetic variation and its contributions to disease, but insights into disease mechanisms are difficult since information about gene function is lacking. By contrast, model organism genetics has excelled at revealing molecular mechanisms of cellular processes, but often de-emphasizes genetic variation and its functional consequences. We argue that model organism biology would benefit from incorporating natural variation, both to capture how well laboratory lines exemplify the species they represent and to inform on molecular processes and their variability. Such a synthesis would also greatly expand the relevance of model systems for studies of complex trait variation, including disease.

  7. 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.

  8. The effect of variation in naturalness on phonetic perceptual identification

    NASA Astrophysics Data System (ADS)

    Remez, Robert E.; Yang, Cynthia Y.; Piorkowski, Rebecca L.; Wissig, Stephanie; Batchelder, Abigail; Nam, Heddy

    2002-05-01

    The relation between apparent naturalness and phonetic identification was assessed in six perceptual tests. A seven-step place-of-articulation series spanning [da] to [ga] was created with speech synthesis approximating the spectra of natural samples. The sensitivity of perceivers to this realization of a place contrast was assessed by estimating the cumulative d' across the series in identification tests. Four variants of this series differing in apparent naturalness were produced by altering the synthesis source function while preserving the center frequency and bandwidth of the formants, and by replicating the gross spectrotemporal patterns with time-varying sinusoids. In addition to calibrating perceivers' sensitivity to the place contrast over variation in naturalness, we conducted a naturalness tournament composed of items drawn from the five test series. A correlation of the findings of the naturalness tournament with the measures of phonetic sensitivity offers an index of the effect of variation in naturalness on phonetic perception. This study can resolve the dispute between the classic premise that intelligibility and naturalness are orthogonal attributes of speech perception, and the more recent premise entailed by episodically based accounts of perceptual categorization, that novel instances are identified by virtue of auditory similarity to prior exemplars. [Research supported by NIDCD.

  9. Natural allelic variations in highly polyploidy Saccharum complex

    USDA-ARS?s Scientific Manuscript database

    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...

  10. 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

  11. Geographic and molecular variation in a natural plant transgene.

    PubMed

    Vallenback, Pernilla; Bengtsson, Bengt O; Ghatnekar, Lena

    2010-03-01

    A PCR based survey of Festuca ovina plants from populations around the southern part of the Baltic Sea demonstrates both geographic and molecular variation in the enzyme gene PgiC2, horizontally transferred from a Poa-species. Our results show that PgiC2-a natural functional nuclear transgene-is not a local ephemeral phenomenon but is present in a very large number of individuals. We find also that its frequency is geographically variable and that it appears in more than one molecular form. The chloroplast variation in the region does not indicate any distinct subdivision due to different colonization routes after the last glaciation. Our data illustrate the geographic and molecular variation that may occur in natural populations with a polymorphic, unfixed transgene affected by diverse kinds of mutational and evolutionary processes.

  12. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    DOE PAGES

    Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.; ...

    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. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

  13. 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.

  14. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    PubMed Central

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

    2016-01-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  16. Natural transformation and phase variation modulation in Neisseria meningitidis.

    PubMed

    Alexander, Heather L; Richardson, Anthony R; Stojiljkovic, Igor

    2004-05-01

    Neisseria meningitidis has evolved the ability to control the expression-state of numerous genes by phase variation. It has been proposed that the process aids this human pathogen in coping with the diversity of microenvironments and host immune systems. Therefore, increased frequencies of phase variation may augment the organism's adaptability and virulence. In this study, we found that DNA derived from various neisserial co-colonizers of the human nasopharynx increased N. meningitidis switching frequencies, indicating that heterologous neisserial DNA modulates phase variation in a transformation-dependent manner. In order to determine whether the effect of heterologous DNA was specific to the Hb receptor, HmbR, we constructed a Universal Rates of Switching cassette (UROS). With this cassette, we demonstrated that heterologous DNA positively affects phase variation throughout the meningococcal genome, as UROS phase variation frequencies were also increased in the presence of neisserial DNA. Overexpressing components of the neisserial mismatch repair system partially alleviated DNA-induced changes in phase variation frequencies, thus implicating mismatch repair titration as a cause of these transformation-dependent increases in switching. The DNA-dependent effect on phase variation was transient and may serve as a mechanism for meningococcal genetic variability that avoids the fitness costs encountered by global mutators.

  17. Exploiting natural variation to identify insect-resistance genes.

    PubMed

    Broekgaarden, Colette; Snoeren, Tjeerd A L; Dicke, Marcel; Vosman, Ben

    2011-10-01

    Herbivorous insects are widespread and often serious constraints to crop production. The use of insect-resistant crops is a very effective way to control insect pests in agriculture, and the development of such crops can be greatly enhanced by knowledge on plant resistance mechanisms and the genes involved. Plants have evolved diverse ways to cope with insect attack that has resulted in natural variation for resistance towards herbivorous insects. Studying the molecular genetics and transcriptional background of this variation has facilitated the identification of resistance genes and processes that lead to resistance against insects. With the development of new technologies, molecular studies are not restricted to model plants anymore. This review addresses the need to exploit natural variation in resistance towards insects to increase our knowledge on resistance mechanisms and the genes involved. We will discuss how this knowledge can be exploited in breeding programmes to provide sustainable crop protection against insect pests. Additionally, we discuss the current status of genetic research on insect-resistance genes. We conclude that insect-resistance mechanisms are still unclear at the molecular level and that exploiting natural variation with novel technologies will contribute greatly to the development of insect-resistant crop varieties.

  18. Cryptic genetic variation in natural populations: a predictive framework.

    PubMed

    Ledón-Rettig, Cris C; Pfennig, David W; Chunco, Amanda J; Dworkin, Ian

    2014-11-01

    Understanding how populations respond to rapid environmental change is critical both for preserving biodiversity and for human health. An increasing number of studies have shown that genetic variation that has no discernable effect under common ecological conditions can become amplified under stressful or novel conditions, suggesting that environmental change per se can provide the raw materials for adaptation. Indeed, the release of such hidden, or "cryptic," genetic variants has been increasingly viewed as playing a general and important role in allowing populations to respond to rapid environmental change. However, additional studies have suggested that there is a balance between cryptic genetic variants that are potentially adaptive in future environments and genetic variants that are deleterious. In this article, we begin by discussing how population and environmental parameters-such as effective population size and the historical frequency and strength of selection under inducing conditions-influence relative amounts of cryptic genetic variation among populations and the overall phenotypic effects of such variation. The amount and distribution of cryptic genetic variation will, in turn, determine the likelihood that cryptic variants, once expressed, will be adaptive or maladaptive during environmental transitions. We then present specific approaches for measuring these parameters in natural populations. Finally, we discuss one natural system that will be conducive to testing whether populations that vary in these parameters harbor different amounts, or types, of cryptic genetic variation. Generally, teasing apart how population and environmental parameters influence the accumulation of cryptic genetic variation will help us to understand how populations endure and adapt (or fail to adapt) to natural environmental change and anthropogenic disturbance.

  19. Contribution of transcriptional regulation to natural variations in Arabidopsis

    PubMed Central

    Chen, Wenqiong J; Chang, Sherman H; Hudson, Matthew E; Kwan, Wai-King; Li, Jingqiu; Estes, Bram; Knoll, Daniel; Shi, Liang; Zhu, Tong

    2005-01-01

    Background Genetic control of gene transcription is a key component in genome evolution. To understand the transcriptional basis of natural variation, we have studied genome-wide variations in transcription and characterized the genetic variations in regulatory elements among Arabidopsis accessions. Results Among five accessions (Col-0, C24, Ler, WS-2, and NO-0) 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis. Two-way ANOVA analysis has identified 60 genes whose mRNA levels differed in different accession backgrounds in an organ-dependent manner. Most of these genes were involved in stress responses and late stages of plant development, such as seed development. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession. Conclusion Genes that show substantial genetic variation in mRNA level are those with functions in signal transduction, transcription and stress response, suggesting the existence of variations in the regulatory mechanisms for these genes among different accessions. This is in contrast to those genes with significant polymorphisms in the coding regions identified by genomic hybridization, which include genes encoding transposon-related proteins, kinases and disease-resistance proteins. While relatively fewer sequence variations were detected on average in the coding regions of these genes, a number of differences were identified from the upstream regions, several of which alter potential cis-regulatory elements. Our results suggest that nucleotide polymorphisms in regulatory elements of genes encoding controlling factors could be primary targets of natural selection and a driving force behind the evolution of Arabidopsis accessions. PMID

  20. 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.

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

    PubMed

    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.

  2. Natural variation in innate immunity of a pioneer species.

    PubMed

    Holub, Eric B

    2007-08-01

    By 2010, we will have detailed knowledge about the genome of Arabidopsis thaliana from a Linnean-like effort by an international research community to identify nearly all of the genes in the species and to classify the products that these genes encode according to a primary function in a generic plant cell. To know the wild species, however, we will require knowledge of which genes provide the raw material for phenotypic variation and natural selection, and consequently affect the adaptability of individual plants and local populations across their geographic range, and ultimately survival of the species. Natural variation in innate immunity will be at the forefront of this exciting research frontier as a model for the molecular ecology of plant-microbe interactions.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. Natural diversity in daily rhythms of gene expression contributes to phenotypic variation

    PubMed Central

    de Montaigu, Amaury; Giakountis, Antonis; Rubin, Matthew; Tóth, Réka; Cremer, Frédéric; Sokolova, Vladislava; Porri, Aimone; Reymond, Matthieu; Weinig, Cynthia; Coupland, George

    2015-01-01

    Daily rhythms of gene expression provide a benefit to most organisms by ensuring that biological processes are activated at the optimal time of day. Although temporal patterns of expression control plant traits of agricultural importance, how natural genetic variation modifies these patterns during the day and how precisely these patterns influence phenotypes is poorly understood. The circadian clock regulates the timing of gene expression, and natural variation in circadian rhythms has been described, but circadian rhythms are measured in artificial continuous conditions that do not reflect the complexity of biologically relevant day/night cycles. By studying transcriptional rhythms of the evening-expressed gene GIGANTEA (GI) at high temporal resolution and during day/night cycles, we show that natural variation in the timing of GI expression occurs mostly under long days in 77 Arabidopsis accessions. This variation is explained by natural alleles that alter light sensitivity of GI, specifically in the evening, and that act at least partly independent of circadian rhythms. Natural alleles induce precise changes in the temporal waveform of GI expression, and these changes have detectable effects on PHYTOCHROME INTERACTING FACTOR 4 expression and growth. Our findings provide a paradigm for how natural alleles act within day/night cycles to precisely modify temporal gene expression waveforms and cause phenotypic diversity. Such alleles could confer an advantage by adjusting the activity of temporally regulated processes without severely disrupting the circadian system. PMID:25548158

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

    PubMed

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

    2014-03-01

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

  9. Causes, natural history, and incidence of salivary stones and obstructions.

    PubMed

    Harrison, John D

    2009-12-01

    Uncertainty about the causes and natural history of salivary stones (sialoliths) and other obstructions is being dispelled by clinical and experimental research. Sialoliths are now shown to be secondary to chronic obstructive sialadenitis. Microscopic stones (sialomicroliths) accumulate during secretory inactivity in normal salivary glands and produce atrophic foci by obstruction. Microbes ascend the main salivary duct during secretory inactivity and proliferate in atrophic foci and cause spreading inflammation, leading to inflammatory swelling and fibrosis that can compress large ducts. This leads to stagnation of secretory material rich in calcium that precipitates onto degenerating cellular membranes to form a sialolith.

  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. Natural variations of lithium isotopes in a mammalian model.

    PubMed

    Balter, Vincent; Vigier, Nathalie

    2014-03-01

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

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

    USGS Publications Warehouse

    Bullen, T.D.; Walczyk, T.

    2009-01-01

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

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

    PubMed Central

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

    2009-01-01

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

  14. 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. © 2014 Society for Risk Analysis.

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

    PubMed

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

    2016-10-25

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

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

    PubMed Central

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

    2016-01-01

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

  17. 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

  18. Transformation of natural genetic variation into Haemophilus influenzae genomes.

    PubMed

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

    2011-07-01

    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.

  19. Natural variation in herbivore-induced volatiles in Arabidopsis thaliana

    PubMed Central

    Snoeren, Tjeerd A. L.; Broekgaarden, Colette; Mumm, Roland; Dicke, Marcel; Bouwmeester, Harro J.

    2010-01-01

    To study whether natural variation in Arabidopsis thaliana could be used to dissect the genetic basis of responses to herbivory in terms of induced volatile emissions, nine accessions were characterized upon herbivory by biting-chewing Pieris rapae caterpillars or after treatment with the phytohormone jasmonic acid (JA). Analysis of 73 compounds in the headspace showed quantitative differences in the emission rates of several individual compounds among the accessions. Moreover, variation in the emission of volatile compounds after JA treatment was reflected in the behaviour of the parasitoid Diadegma semiclausum when they were offered the headspace volatiles of several combinations of accessions in two-choice experiments. Accessions also differ in transcript levels of genes that are associated with the emission of plant volatiles. The genes BSMT1 and Cyp72A13 could be connected to the emission of methyl salicylate and (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene (TMTT), respectively. Overall, Arabidopsis showed interesting phenotypic variations with respect to the volatile blend emitted in response to herbivory that can be exploited to identify genes and alleles that underlie this important plant trait. PMID:20488836

  20. 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.

  1. 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.

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

    PubMed

    Tabachnick, Walter J

    2013-01-11

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

  3. Nature, Nurture and Evolution of Intra-Species Variation in Mosquito Arbovirus Transmission Competence

    PubMed Central

    Tabachnick, Walter J.

    2013-01-01

    Mosquitoes vary in their competence or ability to transmit arthropod-borne viruses (arboviruses). Many arboviruses cause disease in humans and animals. Identifying the environmental and genetic causes of variation in mosquito competence for arboviruses is one of the great challenges in public health. Progress identifying genetic (nature) and environmental (nurture) factors influencing mosquito competence for arboviruses is reviewed. There is great complexity in the various traits that comprise mosquito competence. The complex interactions between environmental and genetic factors controlling these traits and the factors shaping variation in Nature are largely unknown. The norms of reaction of specific genes influencing competence, their distributions in natural populations and the effects of genetic polymorphism on phenotypic variation need to be determined. Mechanisms influencing competence are not likely due to natural selection because of the direct effects of the arbovirus on mosquito fitness. More likely the traits for mosquito competence for arboviruses are the effects of adaptations for other functions of these competence mechanisms. Determining these other functions is essential to understand the evolution and distributions of competence for arboviruses. This information is needed to assess risk from mosquito-borne disease, predict new mosquito-arbovirus systems, and provide novel strategies to mitigate mosquito-borne arbovirus transmission. PMID:23343982

  4. 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. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Natural Variation of Molecular and Morphological Gibberellin Responses1[OPEN

    PubMed Central

    Herman, Dorota; Kojima, Mikiko; Van Daele, Twiggy; Sakakibara, Hitoshi

    2017-01-01

    Although phytohormones such as gibberellins are essential for many conserved aspects of plant physiology and development, plants vary greatly in their responses to these regulatory compounds. Here, we use genetic perturbation of endogenous gibberellin levels to probe the extent of intraspecific variation in gibberellin responses in natural accessions of Arabidopsis (Arabidopsis thaliana). We find that these accessions vary greatly in their ability to buffer the effects of overexpression of GA20ox1, encoding a rate-limiting enzyme for gibberellin biosynthesis, with substantial differences in bioactive gibberellin concentrations as well as transcriptomes and growth trajectories. These findings demonstrate a surprising level of flexibility in the wiring of regulatory networks underlying hormone metabolism and signaling. PMID:27879393

  10. Independent natural genetic variation of punishment- versus relief-memory

    PubMed Central

    Appel, Mirjam; Kocabey, Samet; Savage, Sinead; König, Christian

    2016-01-01

    A painful event establishes two opponent memories: cues that are associated with pain onset are remembered negatively, whereas cues that coincide with the relief at pain offset acquire positive valence. Such punishment- versus relief-memories are conserved across species, including humans, and the balance between them is critical for adaptive behaviour with respect to pain and trauma. In the fruit fly, Drosophila melanogaster as a study case, we found that both punishment- and relief-memories display natural variation across wild-derived inbred strains, but they do not covary, suggesting a considerable level of dissociation in their genetic effectors. This provokes the question whether there may be heritable inter-individual differences in the balance between these opponent memories in man, with potential psycho-clinical implications. PMID:28003518

  11. Deep intronic variations may cause mild hemophilia A.

    PubMed

    Castaman, G; Giacomelli, S H; Mancuso, M E; D'Andrea, G; Santacroce, R; Sanna, S; Santagostino, E; Mannucci, P M; Goodeve, A; Rodeghiero, F

    2011-08-01

    In about 10% of patients with mild hemophilia A, no candidate gene mutations are apparent after complete gene sequencing. To analyze factor VIII gene (F8) mRNA for mutations in five families with mild hemophilia A with no apparent genomic mutation and a reduced response to desmopressin. In four cases, mRNA studies revealed the presence of an abnormal mRNA transcript in addition to normal F8 mRNA. Sequencing of the abnormal transcripts revealed complex abnormalities, which allowed the identification of three different intronic variations (c.2113+1152delA, c.5587-93C>T and c.5999-277G>A) at the DNA level, absent from 387 normal alleles. By in silico analysis, c.2113+1152delA and c.5587-93C>T were strongly predicted to result in the generation of new splice sites with the introduction of premature termination codons, while c.5999-277G>A was predicted to generate a new protein with 30 additional amino acids. However, these predictions were not homogeneous across the different mutations and programs used. The detrimental effect of two mutations was also confirmed by in vitro expression studies. These changes were also identified in related female carriers and in other mild HA patients not included in the original study. No mRNA abnormality was identified in the remaining patient. Although rare, deep intronic variations may be responsible for mild hemophilia A where no other F8 mutations have been identified and may be associated with a reduced biologic response to desmopressin. F8 mRNA analysis is a useful tool for the identification of deep intronic variation not detectable by standard DNA sequencing. © 2011 International Society on Thrombosis and Haemostasis.

  12. 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

  13. 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

  14. Exploiting budding yeast natural variation for industrial processes.

    PubMed

    Cubillos, Francisco A

    2016-11-01

    For the last two decades, the natural variation of the yeast Saccharomyces cerevisiae has been massively exploited with the aim of understanding ecological and evolutionary processes. As a result, many new genetic variants have been uncovered, providing a large catalogue of alleles underlying complex traits. These alleles represent a rich genetic resource with the potential to provide new strains that can cope with the growing demands of industrial fermentation processes. When surveyed in detail, several of these variants have proven useful in wine and beer industries by improving nitrogen utilisation, fermentation kinetics, ethanol production, sulphite resistance and aroma production. Here, I illustrate how allele-specific expression and polymorphisms within the coding region of GDB1 underlie fermentation kinetic differences in synthetic wine must. Nevertheless, the genetic basis of how GDB1 variants and other natural alleles interact in foreign genetic backgrounds remains unclear. Further studies in large sets of strains, recombinant hybrids and multiple parental pairs will broaden our knowledge of the molecular and genetic basis of trait adaptation for utilisation in applied and industrial processes.

  15. Causes of evolutionary rate variation among protein sites

    PubMed Central

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

    2016-01-01

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

  16. 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.

  17. 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. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

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

    PubMed Central

    Kendler, KS

    2014-01-01

    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. …Variations, as Darwin and most breeders recognized, were of two types. There were sports, large discontinuous variations, relatively rare … [and] there were the less

  19. 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

  20. 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

  1. 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

    2014-04-16

    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.

  2. 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

  3. 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.

  4. 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

  5. A conformal variational approach for helices in nature

    NASA Astrophysics Data System (ADS)

    Barros, Manuel; Ferrández, Angel

    2009-10-01

    We propose a two step variational principle to describe helical structures in nature. The first one is governed by an energy action which is a linear function in both curvature and torsion allowing to describe nonclosed structures including elliptical, spherical, and conical helices. These appear as rhumb lines in right cylinders constructed over plane curves. The model is completed with a conformal alternative which, in particular, gives a description of closed structures. The energy action is linear in the curvatures when computed in a conformal spherical metric. Now, helices appear as making a constant angle with a Villarceau flow and so they are loxodromes in surfaces which are stereographic projections of Hopf tubes, in particular, anchor rings, revolution tori, and Dupin cyclides. The model satisfies the requirements of simplicity and beauty as reflected in the three main principles that head its construction: least action, topological, and quantization. According to the latter, the main entities and quantities associated with the model should not be multiplied unnecessarily but they are quantized. In this sense, a quantization principle, a la Dirac, is obtained for closed structures and also for the critical levels of energy.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2012-10-04

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

  9. The 1001 Arabidopsis DNA Methylomes: An Important Resource for Studying Natural Genetic, Epigenetic, and Phenotypic Variation.

    PubMed

    Lang, Zhaobo; Xie, Shaojun; Zhu, Jian-Kang

    2016-11-01

    Intraspecific phenotypic diversity is controlled by natural genetic and epigenetic variation. Kawakatsu et al. recently sequenced the DNA methylomes of a global collection of over 1000 Arabidopsis accessions, and have thereby provided a comprehensive resource for studying natural genetic and epigenetic variation as well as the association of such variation with phenotypic diversity.

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

    PubMed

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

    2008-10-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  13. Short stature caused by a natural growth hormone antagonist.

    PubMed

    Chihara, K; Takahashi, Y; Kaji, H; Goji, K; Okimura, Y; Abe, H

    1998-01-01

    Severe short stature in a male child due to a single mutation in the GH-1 gene was first reported in 1996 by Takahashi et al. [N Engl J Med 1996;334:432-436]. This missense mutation was predicted to convert codon 77 from arginine (R) to cysteine (C). The child's chronological age was 4 years and 11 months, and his bone age 2 years and 6 months, i.e., equal to only 51% of his chronological age. Body proportions were normal except for the prominent forehead and saddle nose. Pituitary size was normal on magnetic resonance imaging examinations. Serum IGF-1, IGFBP-3 and GHBP were all decreased or at the lower limit of the normal range. Nocturnal urinary growth hormone (GH) excretion was high. Isoelectric focusing analysis revealed the presence of an abnormal GH peak in addition to the normal one. The R77C mutant GH possessed a 6 times greater affinity to GHBP than the wild-type GH, and inhibited tyrosine phosphorylation in IM-9 cells 10 times more potently than the wild-type GH, showing an antagonistic or a dominant negative action. In agreement with the antagonistic property of the mutant GH exhibited, the child did not show any increase in serum IGF-1 levels after exogenous hGH administration. It should be noted that the child in this study is not a typical case of Kowarski syndrome in which endogenous GH is found to be simply bioinactive, as in the patient we recently described elsewhere. Therefore, this patient's condition should be categorized as a new syndrome of short stature caused by a natural GH antagonist.

  14. 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

  15. 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

  16. Exploiting induced and natural epigenetic variation for crop improvement.

    PubMed

    Springer, Nathan M; Schmitz, Robert J

    2017-09-01

    Plant breeding has traditionally relied on combining the genetic diversity present within a species to develop combinations of alleles that provide desired traits. Epigenetic diversity may provide additional sources of variation within a species that could be captured or created for crop improvement. It will be important to understand the sources of epigenetic variation and the stability of newly formed epigenetic variants over generations to fully use the potential of epigenetic variation to improve crops. The development and application of methods for widespread epigenome profiling and engineering may generate new avenues for using the full potential of epigenetics in crop improvement.

  17. 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

  18. A review of the established and suspected causes of variations in human sex ratio at birth.

    PubMed

    James, William H; Grech, Victor

    2017-03-24

    The human sex ratio (proportion male) at birth (SRB) varies with many variables. Some of this variation has an established proximate cause. For instance, low SRB (more females) at birth are associated with various forms of stressful events or circumstances during or prior to pregnancy. These low SRB are almost certainly mainly caused by maternal-stress-induced male foetal loss. Other types of SRB variation are thought to be caused by hormonal variation in either or both parents around the time of conception. One or other of these two types of proximate cause seems to be responsible for most of the established variation of SRB. This will be illustrated here in respect of some selected forms of SRB variation. It seems likely that a clarification of the hormonal causes of SRB variation will also help explain the striking (apparent) inconsistencies in the results of reported tests of the influential Trivers-Willard hypothesis. It is further proposed that an appreciation of the evidence that parental hormones influence SRB may enhance understanding of several important pathologies (hepatitis B, toxoplasmosis, testicular cancer, prostate cancer and autism).

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

    Treesearch

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

    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...

  20. 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

  1. 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…

  2. Investigating Variation, Teacher's Edition. Probing the Natural World/3.

    ERIC Educational Resources Information Center

    Florida State Univ., Tallahassee. Dept. of Science Education.

    The teacher's edition for the unit entitled "Investigating Variation" in Intermediate Science Curriculum Study Level III, provides numerous suggestions for teaching specific activities included in the unit. The unit is aimed at selected aspects of measurement and analysis. The chapters included are "The Road…

  3. Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

    PubMed Central

    Knights, Andrew J.; Abreu-Goodger, Cei; van de Bunt, Martijn; Guerra-Assunção, José Afonso; Bartonicek, Nenad; van Dongen, Stijn; Mägi, Reedik; Nisbet, James; Barrett, Amy; Rantalainen, Mattias; Nica, Alexandra C.; Quail, Michael A.; Small, Kerrin S.; Glass, Daniel; Enright, Anton J.; Winn, John; Deloukas, Panos; Dermitzakis, Emmanouil T.; McCarthy, Mark I.; Spector, Timothy D.; Durbin, Richard; Lindgren, Cecilia M.

    2012-01-01

    Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population. PMID:22589741

  4. Accidental introductions of natural enemies: causes and implications

    USDA-ARS?s Scientific Manuscript database

    Accidental introductions of natural enemies, including parasitoid and predatory groups, may exceed species introduced intentionally. Several factors favor this: a general surge in international trade; lack of surveillance for species that are not associated with live plants or animals; inability to ...

  5. The causes of variation in tree seedling traits: the roles of environmental selection versus chance.

    PubMed

    Marks, Christian O

    2007-02-01

    A key aspect of biodiversity is the great quantitative variation in functional traits observed among species. One perspective asserts that trait values should converge on a single optimum value in a particular selective environment, and consequently trait variation would reflect differences in selective environment, and evolutionary outcomes would be predictable. An alternative perspective asserts that there are likely multiple alternative optima within a particular selective environment, and consequently different lineages would evolve toward different optima due to chance. Because there is evidence for both of these perspectives, there is a long-standing controversy over the relative importance of convergence due to environmental selection versus divergence due to chance in shaping trait variation. Here, I use a model of tree seedling growth and survival to distinguish trait variation associated with multiple alternative optima from variation associated with environmental differences. I show that variation in whole plant traits is best explained by environmental differences, whereas in organ level traits variation is more affected by alternative optima. Consequently, I predict that in nature variation in organ level traits is most closely related to phylogeny, whereas variation in whole plant traits is most closely related to ecology.

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

    NASA Astrophysics Data System (ADS)

    Barkin, Yu. V.

    2003-04-01

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

  7. Genetic Variation in Odorant Receptors Contributes to Variation in Olfactory Behavior in a Natural Population of Drosophila melanogaster

    PubMed Central

    Richgels, P. K.

    2012-01-01

    Chemoreception is a principle modality by which organisms gain information from their environment, and extensive variation in odor-mediated behavior has been documented within and among species. To examine the mechanisms by which sensory systems mediate these responses, we ask to what extent variation in Drosophila melanogaster odorant receptor genes contributes to variation in odor-mediated behavior. Significant differences in behavioral responses to structurally similar odorants, methyl hexanoate and ethyl hexanoate, were found in a natural population. Polymorphisms in 3 genomic regions (Or22a/Or22b, Or35a, and Or47a) were identified and associated with variation in behavior to these esters. Overall similarity in association profiles for both odorants was observed, except for Or47a in which polymorphisms were associated solely with variation in responses to ethyl hexanoate. Our analyses were then extended to examine polymorphisms in 3 odorant receptors previously reported to contribute to variation in olfactory behavior for the chemically distinct odorants benzaldehyde and acetophenone. Two Or10a polymorphisms were associated with variation in response to ethyl hexanoate. Finally, differences in Or35a and Or47a expression were associated with variation in responses to ethyl hexanoate. These results demonstrate that the genetic variation at the peripheral sensory stage plays a role in mediating differences in odor-mediated behavior. PMID:22038943

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed 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

  10. Mining and harnessing natural variation - a little MAGIC

    USDA-ARS?s Scientific Manuscript database

    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....

  11. 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.

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

    PubMed

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

    2017-02-15

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

  13. A global health problem caused by arsenic from natural sources.

    PubMed

    Ng, Jack C; Wang, Jianping; Shraim, Amjad

    2003-09-01

    Arsenic is a carcinogen to both humans and animals. Arsenicals have been associated with cancers of the skin, lung, and bladder. Clinical manifestations of chronic arsenic poisoning include non-cancer end point of hyper- and hypo-pigmentation, keratosis, hypertension, cardiovascular diseases and diabetes. Epidemiological evidence indicates that arsenic concentration exceeding 50 microg l(-1) in the drinking water is not public health protective. The current WHO recommended guideline value for arsenic in drinking water is 10 microg l(-1), whereas many developing countries are still having a value of 50 microg l(-1). It has been estimated that tens of millions of people are at risk exposing to excessive levels of arsenic from both contaminated water and arsenic-bearing coal from natural sources. The global health implication and possible intervention strategies were also discussed in this review article.

  14. Variation in genomic methylation in natural populations of chinese white poplar.

    PubMed

    Ma, Kaifeng; Song, Yuepeng; Yang, Xiaohui; Zhang, Zhiyi; Zhang, Deqiang

    2013-01-01

    It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST  = 0.159) were assessed by Shannon's diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5'-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.

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

    PubMed

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

    2016-04-01

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

  16. The nature of flow distortions caused by rotor blade wakes

    NASA Technical Reports Server (NTRS)

    Lakshminarayana, B.

    1976-01-01

    The distortion caused by wakes of rotor blades is one of the least understood phenomena in turbomachinery. An attempt is made to predict the decay characteristics of the defect in axial and tangential velocity components, and the decay of the maximum radial velocity inside the rotor wake using the momentum integral analysis. The predictions agree well with the experimental data taken at the exit of an axial flow fan operating at zero incidence. The measurements are carried out with a three sensor hot wire probe. The wake width is found to grow linearly with distance downstream and the defect in tangential velocity inside the rotor wake decays fastest of the three components. An empirical expression is also provided for the axial velocity profile of a rotor wake.

  17. Natural variations in the rhenium isotopic composition of meteorites

    NASA Astrophysics Data System (ADS)

    Liu, R.; Hu, L.; Humayun, M.

    2017-03-01

    Rhenium is an important element with which to test hypotheses of isotope variation. Historically, it has been difficult to precisely correct the instrumental mass bias in thermal ionization mass spectrometry. We used W as an internal standard to correct mass bias on the MC-ICP-MS, and obtained the first precise δ187Re values ( ±0.02‰, 2SE) for iron meteorites and chondritic metal. Relative to metal from H chondrites, IVB irons are systematically higher in δ187Re by 0.14 ‰. δ187Re for other irons are similar to H chondritic metal, although some individual samples show significant isotope fractionation. Since 185Re has a high neutron capture cross section, the effect of galactic cosmic-ray (GCR) irradiation on δ187Re was examined using correlations with Pt isotopes. The pre-GCR irradiation δ187Re for IVB irons is lower, but the difference in δ187Re between IVB irons and other meteoritic metal remains. Nuclear volume-dependent fractionation for Re is about the right magnitude near the melting point of iron, but because of the refractory and compatible character of Re, a compelling explanation in terms of mass-dependent fractionation is elusive. The magnitude of a nucleosynthetic s-process deficit for Re estimated from Mo and Ru isotopes is essentially unresolvable. Since thermal processing reduced nucleosynthetic effects in Pd, it is conceivable that Re isotopic variations larger than those in Mo and Ru may be present in IVBs since Re is more refractory than Mo and Ru. Thus, the Re isotopic difference between IVBs and other irons or chondritic metal remains unexplained.

  18. Erros in Site Index Determination Caused by Tree Age Variation in Even-Aged Oak Stands

    Treesearch

    Robert A. McQuilkin

    1975-01-01

    Age deviations of individual trees in even-aged oak stands in Missouri caused variations in the height growth patterns and site index estimates of these younger or older trees. A correction factor for site index estimates on these age-deviant trees is given.

  19. Linkage Disequilibrium in Natural Populations of DROSOPHILA MELANOGASTER. Seasonal Variation

    PubMed Central

    Langley, Charles H.; Ito, Kazuko; Voelker, Robert A.

    1977-01-01

    Linkage disequilibrium among ten polymorphic allozyme loci and polymorphic inversions on chromosomes 2 and 3 in a natural population of Drosophila melanogaster was examined early and late in the annual season. Similar to previous studies, little linkage disequilibrium was observed among allozymes. The two significant cases that were observed in the first sample behaved in a contradictory way. One declined much more rapidly than expected due simply to recombination; the other declined slowly as expected. There was little change in allozyme or inversion frequencies during the season. PMID:407131

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

    NASA Astrophysics Data System (ADS)

    Zhao, Y.

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Yoshida, Keisuke; Hasegawa, Akira; Yoshida, Takeyoshi

    2016-08-01

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

  2. Scale-dependent variation in forest structures in naturally dynamic boreal forest landscapes

    NASA Astrophysics Data System (ADS)

    Kulha, Niko; Pasanen, Leena; De Grandpré, Louis; Kuuluvainen, Timo; Aakala, Tuomas

    2017-04-01

    Natural forest structures vary at multiple spatial scales. This variation reflects the occurrence of driving factors, such as disturbances and variation in soil or topography. To explore and understand the linkages of forest structural characteristics and factors driving their variation, we need to recognize how the structural characteristics vary in relation to spatial scale. This can be achieved by identifying scale-dependent features in forest structure within unmanaged forest landscapes. By identifying these features and examining their relationship with potential driving factors, we can better understand the dynamics of forest structural development. Here, we examine the spatial variation in forest structures at multiple spatial scales, utilizing data from old-growth boreal forests in two regions with contrasting disturbance regimes: northern Finland and north-eastern Québec, Canada ( 67° 45'N, 29° 36'E, 49° 39'N, 67° 55'W, respectively). The three landscapes (4 km2 each) in Finland are dominated by Pinus sylvestris and Picea abies, whereas the two landscapes in Québec are dominated by Abies balsamea and Picea mariana. Québec's forests are a subject to cyclic outbreaks of the eastern spruce budworm, causing extensive mortality especially in A. balsamea-dominated stands. In the Finnish landscapes, gap- to patch-scale disturbances due to tree senescence, fungi and wind, as well as infrequent surface fires in areas dominated by P. sylvestris, prevail. Owing to the differences in the species compositions and the disturbance regimes, we expect differing scales of variation between the landscapes. To quantify patterns of variation, we visually interpret stereopairs of recent aerial photographs. From the photographs, we collect information on forest canopy coverage, species composition and dead wood. For the interpretation, each 4 km2 plot is divided into 0.1ha square cells (4096 per plot). Interpretations are validated against field observations and compiled

  3. [Medico-biological effect of natural electromagnetic variations].

    PubMed

    Oraevskiĭ, V N; Kuleshova, V P; Gurfinkel', Iu F; Guseva, A V; Rapoport, S I

    1998-01-01

    Emergency ambulance statistical data accumulated in Moscow during March 1983-October 1984 have been analyzed. Diurnal numbers of urgent hospitalization of patients in connection with suicides, mental disorders, myocardial infarction, defects of cerebrum vessels and arterial and venous diseases have been examined. Intensity and duration of planetary geomagnetic storms were used as magnetic activity indices. Comparison of geomagnetic and medical data rows has shown that at least 75% of magnetic storms caused increase in hospitalization of patients with the above-mentioned diseases on 30-80% at average. The dependence of the value of biotropic effect on the duration of effect and intensity of magnetic storm is observed.

  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. 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.

  6. Unused natural variation can lift yield barriers in plant breeding.

    PubMed

    Gur, Amit; Zamir, Dani

    2004-10-01

    Natural biodiversity is an underexploited sustainable resource that can enrich the genetic basis of cultivated plants with novel alleles that improve productivity and adaptation. We evaluated the progress in breeding for increased tomato (Solanum lycopersicum) yield using genotypes carrying a pyramid of three independent yield-promoting genomic regions introduced from the drought-tolerant green-fruited wild species Solanum pennellii. Yield of hybrids parented by the pyramided genotypes was more than 50% higher than that of a control market leader variety under both wet and dry field conditions that received 10% of the irrigation water. This demonstration of the breaking of agricultural yield barriers provides the rationale for implementing similar strategies for other agricultural organisms that are important for global food security.

  7. Regional variations in the nature of the incoming plate and its implication to the subduction zone

    NASA Astrophysics Data System (ADS)

    Fujie, Gou; Kodaira, Shuichi; Obana, Koichiro; Kaiho, Yuka; Sato, Takeshi; Yamamoto, Yojiro; Takahashi, Tsutomu; Miura, Seiichi; Yamada, Tomoaki

    2017-04-01

    The megathrust earthquakes like the 2011 Tohoku earthquake are caused by the interaction between the overlying plate and the subducting oceanic plate, indicating that the properties of the subducing oceanic plate, such as their geometry, thermal state, lithology, and water content, have a potential to controll the megathrust earthquakes. Of these properties, water content (degree of hydration) is highly influential because water transported by the incoming plate lowers the temperature of the subduction zone, promotes forearc metamorphism. Moreover, the presence of water and hydrated materials like serpentine can affect interplate seismic coupling on the plate interface. Accordingly, the regional variations in the degree of the hydration within the incoming plate might have strong influences on the regional variations in the interplate earthquakes. To reveal the regional variations in the nature of the incoming oceanic plate and its evolution owing to bending-related faulting near the trench axis, we conducted extensive controlled-source seismic surveys in the trench-outer rise region off northeastern Japan arc. We confirmed the systematic changes in seismic velocities owing to the bending-realated faulting, suggesting the water content within the incoming oceanic plate increases toward the trench accompanied by the development of bending-related fractures. In addition, we found along-trench variations in the seismic structure of the incoming oceanic plate; lower seismic velocities and higher Vp/Vs ration around the ancient fracture zones associated with ridge propagation. This observation suggests that the ancient scar on the oceanic plate influences along-trench variations in the current water amount transported by the oceanic plate. If we extend the ancient fracture zone toward the forearc region, it corresponds to an area of weak interplate coupling, characterized by low Vp and high Vp/Vs ratio around the depth of the plate interface. Our observations suggest

  8. 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

  9. Natural variation for a hybrid incompatibility between two species of Mimulus.

    PubMed

    Sweigart, Andrea L; Mason, Amanda R; Willis, John H

    2007-01-01

    Understanding the process by which hybrid incompatibility alleles become established in natural populations remains a major challenge to evolutionary biology. Previously, we discovered a two-locus Dobzhansky-Muller incompatibility that causes severe hybrid male sterility between two inbred lines of the incompletely isolated wildflower species, Mimulus guttatus and M. nasutus. An interspecific cross between these two inbred lines revealed that the M. guttatus (IM62) allele at hybrid male sterility 1 (hms1) acts dominantly in combination with recessive M. nasutus (SF5) alleles at hybrid male sterility 2 (hms2) to cause nearly complete hybrid male sterility. In this report, we extend these genetic analyses to investigate intraspecific variation for the hms1-hms2 incompatibility in natural populations of M. nasutus and M. guttatus, performing a series of interspecific crosses between individuals collected from a variety of geographic locales. Our results suggest that hms2 incompatibility alleles are common and geographically widespread within M. nasutus, but absent or rare in M. guttatus. In contrast, the hms1 locus is polymorphic within M. guttatus and the incompatibility allele appears to be extremely geographically restricted. We found evidence for the presence of the hms1 incompatibility allele in only two M. guttatus populations that exist within a few kilometers of each other. The restricted distribution of the hms1 incompatibility allele might currently limit the potential for the hms1-hms2 incompatibility to act as a species barrier between sympatric populations of M. guttatus and M. nasutus. Extensive sampling within a single M. guttatus population revealed that the hms1 locus is polymorphic and that the incompatibility allele appears to segregate at intermediate frequency, a pattern that is consistent with either genetic drift or natural selection.

  10. Seasonal variation in natural recharge of coastal aquifers

    NASA Astrophysics Data System (ADS)

    Mollema, Pauline N.; Antonellini, Marco

    2013-06-01

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

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

    SciTech Connect

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

    2008-11-15

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

  12. 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. ©2015 The British Editorial Society of Bone & Joint Surgery.

  13. Evolution of mir-92a Underlies Natural Morphological Variation in Drosophila melanogaster

    PubMed Central

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

    2013-01-01

    Summary Identifying the genetic mechanisms underlying phenotypic change is essential to understanding how gene regulatory networks and ultimately the genotype-to-phenotype map evolve. It is recognized that microRNAs (miRNAs) have the potential to facilitate evolutionary change [1–3]; however, there are no known examples of natural morphological variation caused by evolutionary changes in miRNA expression. Therefore, the contribution of miRNAs to evolutionary change remains unknown [1, 4]. Drosophila melanogaster subgroup species display a portion of trichome-free cuticle on the femur of the second leg called the “naked valley.” It was previously shown that Ultrabithorax (Ubx) is involved in naked valley variation between D. melanogaster and D. simulans [5, 6]. However, naked valley size also varies among populations of D. melanogaster, ranging from 1,000 up to 30,000 μm2. We investigated the genetic basis of intraspecific differences in the naked valley in D. melanogaster and found that neither Ubx nor shavenbaby (svb) [7, 8] contributes to this morphological difference. Instead, we show that changes in mir-92a expression underlie the evolution of naked valley size in D. melanogaster through repression of shavenoid (sha) [9]. Therefore, our results reveal a novel mechanism for morphological evolution and suggest that modulation of the expression of miRNAs potentially plays a prominent role in generating organismal diversity. PMID:23453955

  14. 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

  15. Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2.

    PubMed

    Makarevitch, Irina; Stupar, Robert M; Iniguez, A Leonardo; Haun, William J; Barbazuk, W Brad; Kaeppler, Shawn M; Springer, Nathan M

    2007-10-01

    The contribution of epigenetic alterations to natural variation for gene transcription levels remains unclear. In this study, we investigated the functional targets of the maize chromomethylase ZMET2 in multiple inbred lines to determine whether epigenetic changes conditioned by this chromomethylase are conserved or variable within the species. Gene expression microarrays were hybridized with RNA samples from the inbred lines B73 and Mo17 and from near-isogenic derivatives containing the loss-of-function allele zmet2-m1. A set of 126 genes that displayed statistically significant differential expression in zmet2 mutants relative to wild-type plants in at least one of the two genetic backgrounds was identified. Analysis of the transcript levels in both wild-type and mutant individuals revealed that only 10% of these genes were affected in zmet2 mutants in both B73 and Mo17 genetic backgrounds. Over 80% of the genes with expression patterns affected by zmet2 mutations display variation for gene expression between wild-type B73 and Mo17 plants. Further analysis was performed for 7 genes that were transcriptionally silent in wild-type B73, but expressed in B73 zmet2-m1, wild-type Mo17, and Mo17 zmet2-m1 lines. Mapping experiments confirmed that the expression differences in wild-type B73 relative to Mo17 inbreds for these genes were caused by cis-acting regulatory variation. Methylation-sensitive PCR and bisulfite sequencing demonstrated that for 5 of these genes the CpNpG methylation in the wild-type B73 genetic background was substantially decreased in the B73 zmet2-m1 mutant and in wild-type Mo17. A survey of eight maize inbreds reveals that each of these 5 genes exhibit transcriptionally silent and methylated states in some inbred lines and unmethylated, expressed states in other inbreds, providing evidence for natural variation in epigenetic states for some maize genes.

  16. Extensive Natural Intraspecific Variation in Stoichiometric (C:N:P) Composition in Two Terrestrial Insect Species

    PubMed Central

    Bertram, S. M.; Bowen, M.; Kyle, M.; Schade, J. D.

    2008-01-01

    Heterotrophic organisms must obtain essential elements in sufficient quantities from their food. Because plants naturally exhibit extensive variation in their elemental content, it is important to quantify the within-species stoichiometric variation of consumers. If extensive stoichiometric variation exists, it may help explain consumer variation in life-history strategy and fitness. To date, however, research on stoichiometric variation has focused on interspecific differences and assumed minimal intraspecific differences. Here this assumption is tested. Natural variation is quantified in body stoichiometry of two terrestrial insects: the generalist field cricket, Gryllus texensis Cade and Otte (Orthoptera: Gryllidae) and a specialist curculionid weevil, Sabinia setosa (Le Conte) (Coleoptera: Curculionidae). Both species exhibited extensive intraspecific stoichiometric variation. Cricket body nitrogen content ranged from 8–12% and there was a four-fold difference in body phosphorus content, ranging from 0.32–1.27%. Body size explained half this stoichiometric variation, with larger individuals containing less nitrogen and phosphorus. Weevils exhibited an almost three-fold difference in body phosphorus content, ranging from 0.38–0.97%. Overall, the variation observed within each of these species is comparable to the variation previously observed across almost all terrestrial insect species. PMID:20298114

  17. Variation in tumor natural history contributes to racial disparities in breast cancer stage at diagnosis.

    PubMed

    Batina, Nataliya G; Trentham-Dietz, Amy; Gangnon, Ronald E; Sprague, Brian L; Rosenberg, Marjorie A; Stout, Natasha K; Fryback, Dennis G; Alagoz, Oguzhan

    2013-04-01

    Black women tend to be diagnosed with breast cancer at a more advanced stage than whites and subsequently experience elevated breast cancer mortality. We sought to determine whether there are racial differences in tumor natural history that contribute to these disparities. We used the University of Wisconsin Breast Cancer Simulation Model, a validated member of the National Cancer Institute's Cancer Intervention and Surveillance Modeling Network, to evaluate the contribution of racial differences in tumor natural history to observed disparities in breast cancer incidence. We fit eight natural history parameters in race-specific models by calibrating to the observed race- and stage-specific 1975-2000 U.S. incidence rates, while accounting for known racial variation in population structure, underlying risk of breast cancer, screening mammography utilization, and mortality from other causes. The best fit models indicated that a number of natural history parameters must vary between blacks and whites to reproduce the observed stage-specific incidence patterns. The mean of the tumor growth rate parameter was 63.6 % higher for blacks than whites (0.18, SE 0.04 vs. 0.11, SE 0.02). The fraction of tumors considered highly aggressive based on their tendency to metastasize at a small size was 2.2 times greater among blacks than whites (0.41, SE 0.009 vs. 0.019, SE 0.008). Based on our simulation model, breast tumors in blacks grow faster and are more likely to metastasize earlier than tumors in whites. These differences suggest that targeted prevention and detection strategies that go beyond equalizing access to mammography may be needed to eliminate breast cancer disparities.

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

    PubMed Central

    Ristova, Daniela; Busch, Wolfgang

    2014-01-01

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

  19. 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

  20. Natural isotopic signatures of variations in body nitrogen fluxes: a compartmental model analysis.

    PubMed

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

    2014-10-01

    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

  1. Sex-ratio drive in Drosophila simulans: variation in segregation ratio of X chromosomes from a natural population.

    PubMed

    Montchamp-Moreau, Catherine; Cazemajor, Michel

    2002-11-01

    The sex-ratio trait that exists in a dozen Drosophila species is a case of naturally occurring X chromosome drive that causes males to produce female-biased progeny. Autosomal and Y polymorphism for suppressors are known to cause variation in drive expression, but the X chromosome polymorphism has never been thoroughly investigated. We characterized 41 X chromosomes from a natural population of Drosophila simulans that had been transferred to a suppressor-free genetic background. We found two clear-cut groups of chromosomes, sex-ratio and standard. The sex-ratio X chromosomes differed in their segregation ratio (81-96% females in the progeny), the less powerful drivers being less stable in their expression. A sib analysis, using a moderate driver, indicated that within-X variation in drive expression depended on genetic (autosomal) or epigenetic factors and that the age of the males also affected the trait. The other X chromosomes produced equal or roughly equal sex ratios, but again with significant variation. The continuous pattern of variation observed within both groups suggested that, in addition to a major sex-ratio gene, many X-linked loci of small effect modify the segregation ratio of this chromosome and are maintained in a polymorphic state. This was also supported by the frequency distribution of sex ratios produced by recombinant X chromosomes.

  2. Genetic Diversity in Cytokines Associated with Immune Variation and Resistance to Multiple Pathogens in a Natural Rodent Population

    PubMed Central

    Turner, Andrew K.; Begon, Mike; Jackson, Joseph A.; Bradley, Janette E.; Paterson, Steve

    2011-01-01

    Pathogens are believed to drive genetic diversity at host loci involved in immunity to infectious disease. To date, studies exploring the genetic basis of pathogen resistance in the wild have focussed almost exclusively on genes of the Major Histocompatibility Complex (MHC); the role of genetic variation elsewhere in the genome as a basis for variation in pathogen resistance has rarely been explored in natural populations. Cytokines are signalling molecules with a role in many immunological and physiological processes. Here we use a natural population of field voles (Microtus agrestis) to examine how genetic diversity at a suite of cytokine and other immune loci impacts the immune response phenotype and resistance to several endemic pathogen species. By using linear models to first control for a range of non-genetic factors, we demonstrate strong effects of genetic variation at cytokine loci both on host immunological parameters and on resistance to multiple pathogens. These effects were primarily localized to three cytokine genes (Interleukin 1 beta (Il1b), Il2, and Il12b), rather than to other cytokines tested, or to membrane-bound, non-cytokine immune loci. The observed genetic effects were as great as for other intrinsic factors such as sex and body weight. Our results demonstrate that genetic diversity at cytokine loci is a novel and important source of individual variation in immune function and pathogen resistance in natural populations. The products of these loci are therefore likely to affect interactions between pathogens and help determine survival and reproductive success in natural populations. Our study also highlights the utility of wild rodents as a model of ecological immunology, to better understand the causes and consequences of variation in immune function in natural populations including humans. PMID:22039363

  3. The cause of parasitic infection in natural populations of Daphnia (Crustacea: Cladocera): the role of host genetics.

    PubMed Central

    Little, T J; Ebert, D

    2000-01-01

    Disease patterns in nature may be determined by genetic variation for resistance or by factors, genetic or environmental, which influence the host-parasite encounter rate. Elucidating the cause of natural infection patterns has been a major pursuit of parasitologists, but it also matters for evolutionary biologists because host resistance genes must influence the expression of disease if parasite-mediated selection is to occur. We used a model system in order to disentangle the strict genetic component from other causes of infection in the wild. Using the crustacean Daphnia magna and its sterilizing bacterial parasite Pasteuria ramosa, we tested whether genetic variation for resistance, as determined under controlled conditions, accounted for the distribution of infections within natural populations. Specifically, we compared whether the clonally produced great-granddaughters of those individuals that were infected in field samples (but were subsequently 'cured' with antibiotics) were more susceptible than were the great-granddaughters of those individuals that were healthy in field samples. High doses of parasite spores led to increased infection in all four study populations, indicating the importance of encounter rate. Host genetics appeared to be irrelevant to natural infection patterns in one population. However, in three other populations hosts that were healthy in the field had greater genetic-based resistance than hosts that were infected in the field, unambiguously showing the effect of host genetic factors on the expression of disease in the wild. PMID:11416906

  4. The effects of oil spills on marine fish: Implications of spatial variation in natural mortality.

    PubMed

    Langangen, Ø; Olsen, E; Stige, L C; Ohlberger, J; Yaragina, N A; Vikebø, F B; Bogstad, B; Stenseth, N C; Hjermann, D Ø

    2017-04-04

    The effects of oil spills on marine biological systems are of great concern, especially in regions with high biological production of harvested resources such as in the Northeastern Atlantic. The scientific studies of the impact of oil spills on fish stocks tend to ignore that spatial patterns of natural mortality may influence the magnitude of the impact over time. Here, we first illustrate how spatial variation in natural mortality may affect the population impact by considering a thought experiment. Second, we consider an empirically based example of Northeast Arctic cod to extend the concept to a realistic setting. Finally, we present a scenario-based investigation of how the degree of spatial variation in natural mortality affects the impact over a gradient of oil spill sizes. Including the effects of spatial variations in natural mortality tends to widen the impact distribution, hence increasing the probability of both high and low impact events.

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

    USGS Publications Warehouse

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

    2003-01-01

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

  6. Critical dimension variation caused by wrinkle in extreme ultra-violet pellicle for 3-nm node

    NASA Astrophysics Data System (ADS)

    Kim, Guk-Jin; Kim, In-Seon; Lee, Sung-Gyu; Yeung, Michael; Kim, Min-Su; Park, Jin-Goo; Oh, Hye-Keun

    2017-10-01

    Extreme ultraviolet (EUV) pellicles help in the protection of EUV masks from defects, contaminants, and particles during the exposure process. However, a single-stack EUV pellicle can be easily deformed during the exposure process; therefore, multi-stack pellicles have been proposed to minimize the deformation of an EUV pellicle. However, wrinkles can be formed in an EUV pellicle due to extremely thin thickness. In this study, we investigated the impact of these wrinkles on the transmission and critical dimension (CD) variation for the 5- and 3-nm nodes. The 5- and 3-nm nodes can be used by conventional and high numerical aperture (NA) systems, respectively. The variation in the transmission and the allowable local tilt angle of the wrinkle as a function of the wrinkle height and periodicity were calculated. A change in transmission of 2.2% resulted in a 0.2 nm variation in the CD for the anamorphic NA system (3-nm node), whereas a transmission variation of 1.6% caused a 0.2 nm CD variation in the isomorphic NA system (5-nm node).

  7. 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

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

    PubMed

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

    2014-05-27

    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.

  9. Spatial variation in larval concentrations as a cause of spatial variation in settlement for the barnacle, Balanus glandula.

    PubMed

    Gaines, Steven; Brown, Stephen; Roughgarden, Jonathan

    1985-09-01

    Settlement rates of the high intertidal barnacle, Balanus glandula, were monitored at three sites in the rocky intertidal zone in Central California simultaneously with measurements of larval concentrations in the adjacent water column. In both 1983 and 1984, settlement rates onto vacant substrate differed among the sites by nearly two orders of magnitude. For all sampling dates, this spatial variation in settlement mirrored the spatial distribution of Balanus glandula cyprid concentration in the water column. A perfect rank correlation was found between cyprid concentrations near a site and subsequent settlement. A noteworthy observation was that the sites switched rank in their settlement rates from 1983 to 1984. This change in settlement rankings matched a switch in rankings for cyprid concentrations.Settlement itself appears to be an important cause of the spatial pattern of cyprid concentrations. Comparing the rates of settlement to estimates of the number of cyprids available at a site suggests that settlement causes a large drain on the cyprid population as a water mass passes over successive sites. No consistent spatial patterns were found in the distribution of other major plankton groups (calanoid copepods) that are similar in size to Balanus cyprids but do not settle.The large differences in settlement rates among these sites were previously shown to be a leading cause of large differences in the structure of benthic barnacle populations. The close correspondence shown here between these large differences in settlement and differences in larval concentrations suggests that nearshore oceanic processes affecting larval arrival contribute to the control of benthic community structure.

  10. 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

  11. 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

  12. In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

    PubMed Central

    Hicks, Kiley A.; Howe, Dana K.; Leung, Aubrey; Denver, Dee R.; Estes, Suzanne

    2012-01-01

    We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives. PMID:22952781

  13. 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

  14. Variations of iron flux and organic carbon remineralization in a subterranean estuary caused by inter-annual variations in recharge

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

    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 years study period (from 2004 to 2007), the amount of Fe-oxides reduced at the study site decreased from 192 to 153 g/yr and associated organic carbon (OC) remineralization decreased from 48 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 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.

  15. 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.

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

    PubMed

    Grunert, Steffen; Labudde, Dirk

    2015-01-01

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

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

    PubMed Central

    Labudde, Dirk

    2015-01-01

    The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations. PMID:26180540

  18. Temporal Variations of Solar UV Spectral Irradiance Caused by Solar Rotation and Active Region Evolution

    NASA Technical Reports Server (NTRS)

    Donnelly, R. F.; Heath, D. F.; Lean, J. L.; Rottman, G. J.

    1984-01-01

    Variations in the solar 100 to 400 nm UV spectral irradiance caused by solar rotation and active region evolution, are discussed as a function of UV wavelength, CMD dependence, and in relation to the temporal variations in the total solar irradiance, 10.7 cm radio flux, sunspot number and Ca K plage data. Active region radiation at cm wavelengths includes a component proportional to the magnetic field. Active region evolution involves a more rapid growth, peak and decay of sunspots and their strong magnetic fields than the Ca K plages and their related UV enhancements. Major plages often last a rotation or more longer than the active region's sunspots. Large active regions, including those associated with major dips in the total solar irradiance, tend to produce the strongest peaks in 10.7 cm and sunspot numbers on their first rotation, while the Ca K plages and UV enhancements peak on the next rotation and decay more slowly on subsequent rotations. Differences in CMD dependencies cause temporal differences including the stronger presence of 13 day variations in the UV flux.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. Natural allelic variation defines a role for ATMYC1: trichome cell fate determination.

    PubMed

    Symonds, V Vaughan; Hatlestad, Greg; Lloyd, Alan M

    2011-06-01

    The molecular nature of biological variation is not well understood. Indeed, many questions persist regarding the types of molecular changes and the classes of genes that underlie morphological variation within and among species. Here we have taken a candidate gene approach based on previous mapping results to identify the gene and ultimately a polymorphism that underlies a trichome density QTL in Arabidopsis thaliana. Our results show that natural allelic variation in the transcription factor ATMYC1 alters trichome density in A. thaliana; this is the first reported function for ATMYC1. Using site-directed mutagenesis and yeast two-hybrid experiments, we demonstrate that a single amino acid replacement in ATMYC1, discovered in four ecotypes, eliminates known protein-protein interactions in the trichome initiation pathway. Additionally, in a broad screen for molecular variation at ATMYC1, including 72 A. thaliana ecotypes, a high-frequency block of variation was detected that results in >10% amino acid replacement within one of the eight exons of the gene. This sequence variation harbors a strong signal of divergent selection but has no measurable effect on trichome density. Homologs of ATMYC1 are pleiotropic, however, so this block of variation may be the result of natural selection having acted on another trait, while maintaining the trichome density role of the gene. These results show that ATMYC1 is an important source of variation for epidermal traits in A. thaliana and indicate that the transcription factors that make up the TTG1 genetic pathway generally may be important sources of epidermal variation in plants.

  4. Variation in genotype and higher virulence of a strain of Sporothrix schenckii causing disseminated cutaneous sporotrichosis.

    PubMed

    Zhang, Zhenying; Liu, Xiaoming; Lv, Xuelian; Lin, Jingrong

    2011-12-01

    Sporotrichosis is usually a localized, lymphocutaneous disease, but its disseminated type was rarely reported. The main objective of this study was to identify specific DNA sequence variation and virulence of a strain of Sporothrix schenckii isolated from the lesion of disseminated cutaneous sporotrichosis. We confirmed this strain to be S. schenckii by(®) tubulin and chitin synthase gene sequence analysis in addition to the routine mycological and partial ITS and NTS sequencing. We found a 10-bp deletion in the ribosomal NTS region of this strain, in reference to the sequence of control strains isolated from fixed cutaneous sporotrichosis. After inoculated into immunosuppressed mice, this strain caused more extensive system involvement and showed stronger virulence than the control strain isolated from a fixed cutaneous sporotrichosis. Our study thus suggests that different clinical manifestation of sporotrichosis may be associated with variation in genotype and virulence of the strain, independent of effects due to the immune status of the host.

  5. 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

  6. Natural selection on individual variation in tolerance of gastrointestinal nematode infection.

    PubMed

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

    2014-07-01

    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.

  7. 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

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

    PubMed

    Reinhardt, Klaus

    2010-01-01

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

  9. 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.

  10. Natural variation in a single amino acid substitution underlies physiological responses to topoisomerase II poisons.

    PubMed

    Zdraljevic, Stefan; Strand, Christine; Seidel, Hannah S; Cook, Daniel E; Doench, John G; Andersen, Erik C

    2017-07-01

    Many chemotherapeutic drugs are differentially effective from one patient to the next. Understanding the causes of this variability is a critical step towards the development of personalized treatments and improvements to existing medications. Here, we investigate sensitivity to a group of anti-neoplastic drugs that target topoisomerase II using the model organism Caenorhabditis elegans. We show that wild strains of C. elegans vary in their sensitivity to these drugs, and we use an unbiased genetic approach to demonstrate that this natural variation is explained by a methionine-to-glutamine substitution in topoisomerase II (TOP-2). The presence of a non-polar methionine at this residue increases hydrophobic interactions between TOP-2 and its poison etoposide, as compared to a polar glutamine. We hypothesize that this stabilizing interaction results in increased genomic instability in strains that contain a methionine residue. The residue affected by this substitution is conserved from yeast to humans and is one of the few differences between the two human topoisomerase II isoforms (methionine in hTOPIIα and glutamine in hTOPIIβ). We go on to show that this amino acid difference between the two human topoisomerase isoforms influences cytotoxicity of topoisomerase II poisons in human cell lines. These results explain why hTOPIIα and hTOPIIβ are differentially affected by various poisons and demonstrate the utility of C. elegans in understanding the genetics of drug responses.

  11. Temporal analysis of natural variation for the rate of leaf production and its relationship with flowering initiation in Arabidopsis thaliana

    PubMed Central

    Méndez-Vigo, Belén; de Andrés, M. Teresa; Ramiro, Mercedes; Martínez-Zapater, José M.; Alonso-Blanco, Carlos

    2010-01-01

    Vegetative growth and flowering initiation are two crucial developmental processes in the life cycle of annual plants that are closely associated. The timing of both processes affects several presumed adaptive traits, such as flowering time (FT), total leaf number (TLN), or the rate of leaf production (RLP). However, the interactions among these complex processes and traits, and their mechanistic bases, remain largely unknown. To determine the genetic relationships between them, the natural genetic variation between A. thaliana accessions Fei-0 and Ler has been studied using a new population of 222 Ler×Fei-0 recombinant inbred lines. Temporal analysis of the parental development under a short day photoperiod distinguishes two vegetative phases differing in their RLP. QTL mapping of RLP in consecutive time intervals of vegetative development indicates that Ler/Fei-0 variation is caused by 10 loci whose small to moderate effects mainly display two different temporal patterns. Further comparative QTL analyses show that most of the genomic regions affecting FT or TLN also alter RLP. In addition, the partially independent genetic bases observed for FT and TLN appear determined by several genomic regions with two different patterns of phenotypic effects: regions with a larger effect on FT than TLN, and vice versa. The distinct temporal and pleiotropic patterns of QTL effects suggest that natural variation for flowering time is caused by different genetic mechanisms involved in vegetative and/or reproductive phase changes, most of them interacting with the control of leaf production rate. Thus, natural selection might contribute to maintain this genetic variation due to its phenotypic effects not only on the timing of flowering initiation but also on the rate of vegetative growth. PMID:20190039

  12. On the nature of the radial velocity variability of Aldebaran - A search for spectral line bisector variations

    NASA Astrophysics Data System (ADS)

    Hatzes, Artie P.; Cochran, William D.

    1998-02-01

    The shape of the Ti I 6303.8-A spectral line of Aldebaran as measured by the line bisector was investigated using high signal-to-noise ratio, high-resolution data. The goal of this study was to understand the nature of the 643-d period in the radial velocity for this star reported by Hatzes & Cochran. Variations in the line bisector with the radial velocity period would provide strong evidence in support of rotational modulation or stellar pulsations as the cause of the 643-d period. A lack of any bisector variability at this period would support the planet hypothesis. Variations in the line asymmetries are found with a period of 49.93 d. These variations are uncorrelated with the 643-d period found previously in the radial velocity measurements. It is demonstrated that this 50-d period is consistent with an m = 4 non-radial sectoral g-mode oscillation. The lack of spectral variability with the radial velocity period of 643 d may provide strong evidence in support of the hypothesis that this variability stems from the reflex motion of the central star due to a planetary companion having a mass of 11 Jupiter masses. However, this long-period variability may still be the result of a low-order (m = 2) pulsation mode as these would cause bisector variations of less than the error measurement.

  13. 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

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

    PubMed

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

    2009-01-01

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

  15. Dry-wet variations and cause analysis in Northeast China at multi-time scales

    NASA Astrophysics Data System (ADS)

    Hu, Qi; Pan, Feifei; Pan, Xuebiao; Hu, Liting; Wang, Xiaoxiao; Yang, Pengyu; Wei, Pei; Pan, Zhihua

    2017-07-01

    Global warming has caused unevenly distributed changes in precipitation and evapotranspiration, which has and will certainly impact on the wet-dry variations. Based on daily meteorological data collected at 91 weather stations in Northeast China (NEC), the spatiotemporal characteristics of dry and wet climatic variables (precipitation, crop reference evapotranspiration (ET0), and humid index (HI)) are analyzed, and the probable reasons causing the changes in these variables are discussed during the period of 1961-2014. Precipitation showed non-significant trend over the period of 1961-2014, while ET0 showed a significant decreasing trend, which led to climate wetting in NEC. The period of 2001-2012 exhibited smaller semiarid area and larger humid area compared to the period of 1961-1980, indicating NEC has experienced wetting process at decadal scale. ET0 was most sensitive to relative humidity, and wind speed was the second most sensitive variable. Sunshine hours and temperature were found to be less influential to ET0 in the study area. The changes in wind speed in the recent 54 years have caused the greatest influence on ET0, followed by temperature. For each month, wind speed was the most significant variable causing ET0 reduction in all months except July. Temperature, as a dominant factor, made a positive contribution to ET0 in February and March, as well as sunshine hours in June and July, and relative humidity in August and September. In summary, NEC has experienced noticeable climate wetting due to the significantly decreasing ET0, and the decrease in wind speed was the biggest contributor for the ET0 reduction. Although agricultural drought crisis is expected to be partly alleviated, regional water resources management and planning in Northeast China should consider the potential water shortage and water conflict in the future because of spatiotemporal dry-wet variations in NEC.

  16. Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus

    PubMed Central

    Oleksiak, Marjorie F; Roach, Jennifer L; Crawford, Douglas L

    2006-01-01

    Individual variation in gene expression is important for evolutionary adaptation1,2 and susceptibility to diseases and pathologies3,4. In this study, we address the functional importance of this variation by comparing cardiac metabolism to patterns of mRNA expression using microarrays. There is extensive variation in both cardiac metabolism and the expression of metabolic genes among individuals of the teleost fish Fundulus heteroclitus from natural outbred populations raised in a common environment: metabolism differed among individuals by a factor of more than 2, and expression levels of 94% of genes were significantly different (P < 0.01) between individuals in a population. This unexpectedly high variation in metabolic gene expression explains much of the variation in metabolism, suggesting that it is biologically relevant. The patterns of gene expression that are most important in explaining cardiac metabolism differ between groups of individuals. Apparently, the variation in metabolism seems to be related to different patterns of gene expression in the different groups of individuals. The magnitude of differences in gene expression in these groups is not important; large changes in expression have no greater predictive value than small changes. These data suggest that variation in physiological performance is related to the subtle variation in gene expression and that this relationship differs among individuals. PMID:15568023

  17. Variants of Rab GTPase-Effector Binding Protein-2 Cause Variation in the Collateral Circulation and Severity of Stroke.

    PubMed

    Lucitti, Jennifer L; Sealock, Robert; Buckley, Brian K; Zhang, Hua; Xiao, Lin; Dudley, Andrew C; Faber, James E

    2016-12-01

    The extent (number and diameter) of collateral vessels varies widely and is a major determinant, along with arteriogenesis (collateral remodeling), of variation in severity of tissue injury after large artery occlusion. Differences in genetic background underlie the majority of the variation in collateral extent in mice, through alterations in collaterogenesis (embryonic collateral formation). In brain and other tissues, ≈80% of the variation in collateral extent among different mouse strains has been linked to a region on chromosome 7. We recently used congenic (CNG) fine mapping of C57BL/6 (B6, high extent) and BALB/cByJ (BC, low extent) mice to narrow the region to a 737 Kb locus, Dce1. Herein, we report the causal gene. We used additional CNG mapping and knockout mice to narrow the number of candidate genes. Subsequent inspection identified a nonsynonymous single nucleotide polymorphism between B6 and BC within Rabep2 (rs33080487). We then created B6 mice with the BC single nucleotide polymorphism at this locus plus 3 other lines for predicted alteration or knockout of Rabep2 using gene editing. The single amino acid change caused by rs33080487 accounted for the difference in collateral extent and infarct volume between B6 and BC mice attributable to Dce1. Mechanistically, variants of Rabep2 altered collaterogenesis during embryogenesis but had no effect on angiogenesis examined in vivo and in vitro. Rabep2 deficiency altered endosome trafficking known to be involved in VEGF-A→VEGFR2 signaling required for collaterogenesis. Naturally occurring variants of Rabep2 are major determinants of variation in collateral extent and stroke severity in mice. © 2016 American Heart Association, Inc.

  18. 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.

  19. 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.

  20. Natural population die-offs: causes and consequences for terrestrial mammals.

    PubMed

    Ameca Y Juárez, Eric I; Mace, Georgina M; Cowlishaw, Guy; Pettorelli, Nathalie

    2012-05-01

    Extreme changes in the environment can generate high mortalities in wildlife populations. When these mortalities are attributable to extreme natural events, they are referred to as natural population die-offs. Despite growing reports of such die-offs, a consensus on how to define them has not emerged. Furthermore, although anthropogenically caused extreme events are predicted to occur at a higher frequency and intensity compared with natural events, an integrative synthesis assessing their significance for wildlife population viability is lacking. These issues hamper the ability to identify populations most at risk. Here, we propose a functional definition of natural population die-offs, an assessment of extrinsic and intrinsic processes shaping these die-offs, and a framework for assessing the vulnerability of terrestrial mammals to natural and anthropogenically caused extreme events.

  1. 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

  2. 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.

  3. Natural variation of rice blast resistance gene Pi-d2

    USDA-ARS?s Scientific Manuscript database

    Studying natural variation of rice resistance (R) genes in cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of rice R gene Pi-d2 in 35 rice accessions of subgroups, aus (AUS), indica (IND), temperate japonica (...

  4. 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

  5. Use of natural variation to identify loci associated with relevant agronomic phenotypic traits

    USDA-ARS?s Scientific Manuscript database

    Analysis of natural allelic variation is a useful discovery tool to identify novel alleles in genes and pathways that are consistent with agronomic productivity and environmental stability. Switchgrass, a native perennial North American prairie grass and emerging biofuel feedstock species, is divide...

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2010-06-01

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

  8. Natural genetic variation in cuticular hydrocarbon expression in male and female Drosophila melanogaster.

    PubMed

    Foley, Brad; Chenoweth, Stephen F; Nuzhdin, Sergey V; Blows, Mark W

    2007-03-01

    Cuticular hydrocarbons (CHCs) act as contact pheromones in Drosophila melanogaster and are an important component of several ecological traits. Segregating genetic variation in the expression of CHCs at the population level in D. melanogaster is likely to be important for mate choice and climatic adaptation; however, this variation has never been characterized. Using a panel of recombinant inbred lines (RILs) derived from a natural population, we found significant between-line variation for nearly all CHCs in both sexes. We identified 25 QTL in females and 15 QTL in males that pleiotropically influence CHC expression. There was no evidence of colocalization of QTL for homologous traits across the sexes, indicating that sexual dimorphism and low intersex genetic correlations between homologous CHCs are a consequence of largely independent genetic control. This is consistent with a pattern of divergent sexual and natural selection between the sexes.

  9. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana

    PubMed Central

    Balasubramanian, Sureshkumar; Sureshkumar, Sridevi; Agrawal, Mitesh; Michael, Todd P.; Wessinger, Carrie; Maloof, Julin N.; Clark, Richard; Warthmann, Norman; Chory, Joanne; Weigel, Detlef

    2006-01-01

    Light plays an important role in modulating seedling growth and flowering time1. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a FRIGIDA-dependent latitudinal cline that is stronger than the one reported for FLOWERING LOCUS C, which together with FRIGIDA explains a large portion of the variation in A. thaliana flowering time2. In a genome-wide scan for association of 65 loci with latitude, there was an excess of significant p-values, indicative of population structure. Nevertheless, PHYC was the most strongly associated locus across 163 strains, suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work, together with previous findings3–6, suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response. PMID:16732287

  10. 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.

  11. Natural variation in stomatal abundance of Arabidopsis thaliana includes cryptic diversity for different developmental processes

    PubMed Central

    Delgado, Dolores; Alonso-Blanco, Carlos; Fenoll, Carmen; Mena, Montaña

    2011-01-01

    Background and Aims Current understanding of stomatal development in Arabidopsis thaliana is based on mutations producing aberrant, often lethal phenotypes. The aim was to discover if naturally occurring viable phenotypes would be useful for studying stomatal development in a species that enables further molecular analysis. Methods Natural variation in stomatal abundance of A. thaliana was explored in two collections comprising 62 wild accessions by surveying adaxial epidermal cell-type proportion (stomatal index) and density (stomatal and pavement cell density) traits in cotyledons and first leaves. Organ size variation was studied in a subset of accessions. For all traits, maternal effects derived from different laboratory environments were evaluated. In four selected accessions, distinct stomatal initiation processes were quantitatively analysed. Key Results and Conclusions Substantial genetic variation was found for all six stomatal abundance-related traits, which were weakly or not affected by laboratory maternal environments. Correlation analyses revealed overall relationships among all traits. Within each organ, stomatal density highly correlated with the other traits, suggesting common genetic bases. Each trait correlated between organs, supporting supra-organ control of stomatal abundance. Clustering analyses identified accessions with uncommon phenotypic patterns, suggesting differences among genetic programmes controlling the various traits. Variation was also found in organ size, which negatively correlated with cell densities in both organs and with stomatal index in the cotyledon. Relative proportions of primary and satellite lineages varied among the accessions analysed, indicating that distinct developmental components contribute to natural diversity in stomatal abundance. Accessions with similar stomatal indices showed different lineage class ratios, revealing hidden developmental phenotypes and showing that genetic determinants of primary and

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

    PubMed

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

    2016-04-01

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

  13. 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

  14. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    SciTech Connect

    Song, Jian; Yang, Xiping; Resende, Jr., 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 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. 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. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

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

    PubMed

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

    2011-09-01

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

  16. Natural Variation in the Strength and Direction of Male Mating Preferences for Female Pheromones in Drosophila melanogaster

    PubMed Central

    Pischedda, Alison; Shahandeh, Michael P.; Cochrane, Wesley G.; Cochrane, Veronica A.; Turner, Thomas L.

    2014-01-01

    Many animal species communicate using chemical signals. In Drosophila, cuticular hydrocarbons (CHCs) are involved in species and sexual identification, and have long been thought to act as stimulatory pheromones as well. However, a previous study reported that D. melanogaster males were more attracted to females that were lacking CHCs. This surprising result is consistent with several evolutionary hypotheses but is at odds with other work demonstrating that female CHCs are attractive to males. Here, we investigated natural variation in male preferences for female pheromones using transgenic flies that cannot produce CHCs. By perfuming females with CHCs and performing mate choice tests, we found that some male genotypes prefer females with pheromones, some have no apparent preference, and at least one male genotype prefers females without pheromones. This variation provides an excellent opportunity to further investigate the mechanistic causes and evolutionary implications of divergent pheromone preferences in D. melanogaster males. PMID:24489930

  17. Natural variation in the strength and direction of male mating preferences for female pheromones in Drosophila melanogaster.

    PubMed

    Pischedda, Alison; Shahandeh, Michael P; Cochrane, Wesley G; Cochrane, Veronica A; Turner, Thomas L

    2014-01-01

    Many animal species communicate using chemical signals. In Drosophila, cuticular hydrocarbons (CHCs) are involved in species and sexual identification, and have long been thought to act as stimulatory pheromones as well. However, a previous study reported that D. melanogaster males were more attracted to females that were lacking CHCs. This surprising result is consistent with several evolutionary hypotheses but is at odds with other work demonstrating that female CHCs are attractive to males. Here, we investigated natural variation in male preferences for female pheromones using transgenic flies that cannot produce CHCs. By perfuming females with CHCs and performing mate choice tests, we found that some male genotypes prefer females with pheromones, some have no apparent preference, and at least one male genotype prefers females without pheromones. This variation provides an excellent opportunity to further investigate the mechanistic causes and evolutionary implications of divergent pheromone preferences in D. melanogaster males.

  18. 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.

  19. Seasonal variations of all-cause and cause-specific mortality by age, gender, and socioeconomic condition in urban and rural areas of Bangladesh

    PubMed Central

    2011-01-01

    Background Mortality exhibits seasonal variations, which to a certain extent can be considered as mid-to long-term influences of meteorological conditions. In addition to atmospheric effects, the seasonal pattern of mortality is shaped by non-atmospheric determinants such as environmental conditions or socioeconomic status. Understanding the influence of season and other factors is essential when seeking to implement effective public health measures. The pressures of climate change make an understanding of the interdependencies between season, climate and health especially important. Methods This study investigated daily death counts collected within the Sample Vital Registration System (VSRS) established by the Bangladesh Bureau of Statistics (BBS). The sample was stratified by location (urban vs. rural), gender and socioeconomic status. Furthermore, seasonality was analyzed for all-cause mortality, and several cause-specific mortalities. Daily deviation from average mortality was calculated and seasonal fluctuations were elaborated using non parametric spline smoothing. A seasonality index for each year of life was calculated in order to assess the age-dependency of seasonal effects. Results We found distinctive seasonal variations of mortality with generally higher levels during the cold season. To some extent, a rudimentary secondary summer maximum could be observed. The degree and shape of seasonality changed with the cause of death as well as with location, gender, and SES and was strongly age-dependent. Urban areas were seen to be facing an increased summer mortality peak, particularly in terms of cardiovascular mortality. Generally, children and the elderly faced stronger seasonal effects than youths and young adults. Conclusion This study clearly demonstrated the complex and dynamic nature of seasonal impacts on mortality. The modifying effect of spatial and population characteristics were highlighted. While tropical regions have been, and still are

  20. A behavioral ecology approach to traffic accidents: interspecific variation in causes of traffic casualties among birds.

    PubMed

    Møller, Anders Pape; Erritzøe, Helga; Erritzøe, Johannes

    2011-04-01

    Birds and other animals are frequently killed by cars, causing the death of many million individuals per year. Why some species are killed more often than others has never been investigated. In this work hypothesized that risk taking behavior may affect the probability of certain kinds of individuals being killed disproportionately often. Furthermore, behavior of individuals on roads, abundance, habitat preferences, breeding sociality, and health status may all potentially affect the risk of being killed on roads. We used information on the abundance of road kills and the abundance in the surrounding environment of 50 species of birds obtained during regular censuses in 2001-2006 in a rural site in Denmark to test these predictions. The frequency of road kills increased linearly with abundance, while the proportion of individuals sitting on the road or flying low across the road only explained little additional variation in frequency of road casualties. After having accounted for abundance, we found that species with a short flight distance and hence taking greater risks when approached by a potential cause of danger were killed disproportionately often. In addition, solitary species, species with a high prevalence of Plasmodium infection, and species with a large bursa of Fabricius for their body size had a high susceptibility to being killed by cars. These findings suggest that a range of different factors indicative of risk-taking behavior, visual acuity and health status cause certain bird species to be susceptible to casualties due to cars.

  1. What Causes Partial F1 Hybrid Viability? Incomplete Penetrance versus Genetic Variation

    PubMed Central

    López-Fernández, Hernán; Bolnick, Daniel I.

    2007-01-01

    Background Interspecific hybrid crosses often produce offspring with reduced but non-zero survivorship. In this paper we ask why such partial inviability occurs. This partial inviability could arise from incomplete penetrance of lethal Dobzhansky-Muller incompatibilities (DMIs) shared by all members of a hybrid cross. Alternatively, siblings may differ with respect to the presence or number of DMIs, leading to genotype-dependent variation in viability and hence non-Mendelian segregation of parental alleles in surviving F1 hybrids. Methodology/Principal Findings We used amplified fragment length polymorphisms (AFLPs) to test for segregation distortion in one hybrid cross between green and longear sunfish (Lepomis cyanellus and L. megalotis). Hybrids showed partial viability, and twice as much segregation distortion (36.8%) of AFLPs as an intraspecific control cross (18.8%). Incomplete penetrance of DMIs, which should cause genotype-independent mortality, is insufficient to explain the observed segregation distortion. Conclusions/Significance We conclude that F1 hybrid sunfish are polymorphic for DMIs, either due to sex-linked DMI loci (causing Haldane's Rule), or polymorphic autosomal DMI loci. Because few AFLP markers were sex-linked (2%), the most parsimonious conclusion is that parents may have been heterozygous for loci causing hybrid inviability. PMID:18074018

  2. Variations in the Prevalence of Obesity Among European Countries, and a Consideration of Possible Causes.

    PubMed

    Blundell, John E; Baker, Jennifer Lyn; Boyland, Emma; Blaak, Ellen; Charzewska, Jadwiga; de Henauw, Stefaan; Frühbeck, Gema; Gonzalez-Gross, Marcela; Hebebrand, Johannes; Holm, Lotte; Kriaucioniene, Vilma; Lissner, Lauren; Oppert, Jean-Michel; Schindler, Karin; Silva, Analiza Mónica; Woodward, Euan

    2017-01-01

    Over the last 10 years the prevalence of obesity across the European continent has in general been rising. With the exception of a few countries where a levelling-off can be perceived, albeit at a high level, this upward trend seems likely to continue. However, considerable country to country variation is noticeable, with the proportion of people with obesity varying by 10% or more. This variation is intriguing and suggests the existence of different profiles of risk or protection factors operating in different countries. The identification of such protection factors could indicate suitable targets for interventions to help manage the obesity epidemic in Europe. This report is the output of a 2-day workshop on the 'Diversity of Obesity in Europe'. The workshop included 14 delegates from 12 different European countries. This report contains the contributions and discussions of the materials and viewpoints provided by these 14 experts; it is not the output of a single mind. However, such is the nature of scientific analysis regarding obesity that it is possible that a different set of 14 experts may have come to a different set of conclusions. Therefore the report should not be seen as a definitive statement of a stable situation. Rather it is a focus for discussion and comment, and a vehicle to drive forward further understanding and management of obesity in Europe. © 2017 The Author(s) Published by S. Karger GmbH, Freiburg.

  3. 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

  4. The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish.

    PubMed

    Passow, Courtney N; Henpita, Chathurika; Shaw, Jennifer H; Quackenbush, Corey R; Warren, Wesley C; Schartl, Manfred; Arias-Rodriguez, Lenin; Kelley, Joanna L; Tobler, Michael

    2017-09-19

    The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common garden and exposure experiments to establish cause and effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems. We studied two evolutionarily independent population pairs of an extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulfide (H2 S)-rich springs and adjacent nontoxic habitats, and assessed genome-wide expression patterns of wild-caught and common-garden raised individuals exposed to different concentrations of H2 S. We found that 7.7% of genes that were differentially expressed between sulfidic and nonsulfidic ecotypes remained differentially expressed in the laboratory, indicating that sources of selection other than H2 S - or plastic responses to other environmental factors - contribute substantially to gene expression patterns observed in the wild. Concordantly differentially expressed genes in the wild and the laboratory were primarily associated with H2 S detoxification, sulfur processing, and metabolic physiology. While shared ancestral plasticity played a minor role in shaping gene expression variation observed in nature, we documented evidence for evolved population differences in the constitutive expression as well as the H2 S-inducibility of candidate genes. Mechanisms underlying gene expression variation also varied substantially across the two ecotype pairs. These results provide a springboard for studying evolutionary modifications of gene regulatory mechanisms that underlie expression variation in locally adapted populations. This article is protected by copyright. All rights reserved. This article is protected by copyright

  5. Endogenous Abscisic Acid as a Key Switch for Natural Variation in Flooding-Induced Shoot Elongation1[W][OA

    PubMed Central

    Chen, Xin; Pierik, Ronald; Peeters, Anton J.M.; Poorter, Hendrik; Visser, Eric J.W.; Huber, Heidrun; de Kroon, Hans; Voesenek, Laurentius A.C.J.

    2010-01-01

    Elongation of leaves and stem is a key trait for survival of terrestrial plants during shallow but prolonged floods that completely submerge the shoot. However, natural floods at different locations vary strongly in duration and depth, and, therefore, populations from these locations are subjected to different selection pressure, leading to intraspecific variation. Here, we identified the signal transduction component that causes response variation in shoot elongation among two accessions of the wetland plant Rumex palustris. These accessions differed 2-fold in petiole elongation rates upon submergence, with fast elongation found in a population from a river floodplain and slow elongation in plants from a lake bank. Fast petiole elongation under water consumes carbohydrates and depends on the (inter)action of the plant hormones ethylene, abscisic acid, and gibberellic acid. We found that carbohydrate levels and dynamics in shoots did not differ between the fast and slow elongating plants, but that the level of ethylene-regulated abscisic acid in petioles, and hence gibberellic acid responsiveness of these petioles explained the difference in shoot elongation upon submergence. Since this is the exact signal transduction level that also explains the variation in flooding-induced shoot elongation among plant species (namely, R. palustris and Rumex acetosa), we suggest that natural selection results in similar modification of regulatory pathways within and between species. PMID:20699400

  6. CaGLK2 regulates natural variation of chlorophyll content and fruit color in pepper fruit.

    PubMed

    Brand, Arnon; Borovsky, Yelena; Hill, Theresa; Rahman, Khalis Afnan Abdul; Bellalou, Aharon; Van Deynze, Allen; Paran, Ilan

    2014-10-01

    We provide multiple evidences that CaGLK2 underlies a quantitative trait locus controlling natural variation in chlorophyll content and immature fruit color of pepper via modulating chloroplast compartment size. Pepper fruit quality is attributed to a variety of traits, affecting visual appearance, flavor, chemical composition and nutritional value. Among the quality traits, fruit color is of primary importance because the pigments that confer color are associated with nutrition, health and flavor. Although gene models have been proposed for qualitative aspects of fruit color, large natural variation in quantitative pigment content and fruit color exists in pepper. However, its genetic basis is largely unknown which hampers its utilization for plant improvement. We studied the role of GLK2, a GOLDEN2-like transcription factor that regulates chloroplast development in controlling natural variation for chlorophyll content and immature fruit color of pepper. The role of GLK2 in regulating fruit development has been studied previously in tomato using ectopic expression and the uniform ripening mutant analyses. However, pepper provides a unique opportunity to further study the function of this gene because of the wide natural variation of fruit colors in this species. Segregation, sequencing and expression analyses indicated that pepper GLK2 (CaGLK2) corresponds to the recently reported pc10 QTL that controls chloroplast development and chlorophyll content in pepper. CaGLK2 exerts its effect on chloroplast compartment size predominantly during immature fruit development. We show that the genetic background, sequence variation and expression pattern confer a complex and multi-level regulation of CaGLK2 and fruit color in Capsicum. The positive effect on fruit quality predominantly at the green stage conferred by CaGLK2 can be utilized to breed green pepper varieties with improved nutritional values and taste.

  7. 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

  8. Perceiving the causes of coarticulatory acoustic variation: consonant voicing and vowel pitch.

    PubMed

    Pardo, J S; Fowler, C A

    1997-10-01

    Coarticulatory acoustic variation is presumed to be caused by temporally overlapping linguistically significant gestures of the vocal tract. The complex acoustic consequences of such gestures can be hypothesized to specify them without recourse to context-sensitive representations of phonetic segments. When the consequences of separate gestures converge on a common acoustic dimension (e.g., fundamental frequency), perceptual parsing of the acoustic consequences of overlapping spoken gestures, rather than associations of acoustic features, is required to resolve the distinct gestural events. Direct tests of this theory were conducted. These tests revealed mutual influences of (1) fundamental frequency during a vowel on prior consonant perception, and (2) consonant identity on following vowel stress and pitch perception. The results of these converging tests lead to the conclusion that speech perception involves a process in which acoustic information for coarticulated gestures is parsed from the stream of speech.

  9. 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.

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

    PubMed

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

    2010-04-01

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

  11. Natural Variation of Plant Metabolism: Genetic Mechanisms, Interpretive Caveats, and Evolutionary and Mechanistic Insights1

    PubMed Central

    Soltis, Nicole E.; Kliebenstein, Daniel J.

    2015-01-01

    Combining quantitative genetics studies with metabolomics/metabolic profiling platforms, genomics, and transcriptomics is creating significant progress in identifying the causal genes controlling natural variation in metabolite accumulations and profiles. In this review, we discuss key mechanistic and evolutionary insights that are arising from these studies. This includes the potential role of transport and other processes in leading to a separation of the site of mechanistic causation and metabolic consequence. A reilluminated observation is the potential for genomic variation in the organelle to alter phenotypic variation alone and in epistatic interaction with the nuclear genetic variation. These studies are also highlighting new aspects of metabolic pleiotropy both in terms of the breadth of loci altering metabolic variation as well as the potential for broader effects on plant defense regulation of the metabolic variation than has previously been predicted. We also illustrate caveats that can be overlooked when translating quantitative genetics descriptors such as heritability and per-locus r2 to mechanistic or evolutionary interpretations. PMID:26272883

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

    PubMed

    Kovalenko, E E; Kruzhkova, Iu I

    2013-01-01

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

  13. The value of postmortem computed tomography in paediatric natural cause of death: a Dutch observational study.

    PubMed

    van Rijn, Rick R; Beek, Erik J; van de Putte, Elise M; Teeuw, Arianne H; Nikkels, Peter G J; Duijst, Wilma L J M; Nievelstein, Rutger-Jan A

    2017-07-05

    Postmortem CT is a relatively new field of interest within paediatric radiology. This paper focusses on its value in cases of unexpected natural death. We report on an observational Dutch study regarding the value of postmortem CT in children with an assumed natural unexpected death because postmortem CT is part of the Dutch NODO (additional investigations of cause of death) procedure. We included consecutive children who fulfilled criteria for the NODO procedure and were therefore referred to one of the centres for the procedure. Postmortem CT was performed in all cases and skeletal survey was performed in all children ages <5 years. The cause of death was defined in a consensus meeting. We included a total of 54 children (30 boys, median age 1.1 years, and 24 girls, median age 0.8 years). A definitive cause of death was established in 38 cases. In 7 cases the cause of death could be identified on postmortem CT. In 7 cases imaging findings were clinically relevant but did not lead to a cause of death. In the remaining 40 cases postmortem CT did not add to the diagnostic workup. Our study shows that in a group of children who unexpectedly died of an assumed natural cause of death and in whom a cause of death was found at autopsy, postmortem CT detected the cause of death in a minority of cases (12.9%). In the majority of cases (74.1%) postmortem CT did not add value in diagnosing the cause of death.

  14. Geographic Variation of Plant Circadian Clock Function in Natural and Agricultural Settings.

    PubMed

    Greenham, Kathleen; Lou, Ping; Puzey, Joshua R; Kumar, Ganesh; Arnevik, Cindy; Farid, Hany; Willis, John H; McClung, C Robertson

    2017-02-01

    The increasing demand for improved agricultural production will require more efficient breeding for traits that maintain yield under heterogeneous environments. The internal circadian oscillator is essential for perceiving and coordinating environmental cues such as day length, temperature, and abiotic stress responses within physiological processes. To investigate the contribution of the circadian clock to local adaptability, we have analyzed circadian period by leaf movement in natural populations of Mimulus guttatus and domesticated cultivars of Glycine max. We detected consistent variation in circadian period along a latitudinal gradient in annual populations of the wild plant and the selectively bred crop, and this provides novel evidence of natural and artificial selection for circadian performance. These findings provide new support that the circadian clock acts as a central regulator of plant adaptability and further highlight the potential of applying circadian clock gene variation to marker-assisted breeding programs in crops.

  15. 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

  16. 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.

  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 Nature, Causes and Effects of School Violence in South African High Schools

    ERIC Educational Resources Information Center

    Ncontsa, Vusumzi Nelson; Shumba, Almon

    2013-01-01

    We sought to investigate the nature, causes and effects of school violence in four South African high schools. A purposive sample of five principals, 80 learners and 20 educators was selected from the four schools used in the study. A sequential mixed method approach was used in this study; both questionnaires and interviews were used. The design…

  19. 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...

  20. 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…

  1. 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…

  2. 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…

  3. Inter-well scale natural fracture geometry and permeability variations in low-deformation carbonate rocks

    NASA Astrophysics Data System (ADS)

    Bisdom, K.; Bertotti, G.; Bezerra, F. H.

    2017-04-01

    Regional natural fracture networks often show variations on a scale below that captured by seismic reflection data. This variability is not considered in most reservoir models, but likely impacts uncertainties in permeability. We quantify this uncertainty using a database of 13,000 fractures in nine outcrops digitised in the carbonate Jandaíra Formation (Potiguar basin, Brazil). Distance between outcrops is on average 11 km, with a minimum of 300 m, which is comparable to the distance between wells in naturally fractured reservoirs. In between outcrops, significant variations exist in orientation, intensity, length and topology. Using discrete fracture-matrix flow models, we model the permeability of each deterministic pattern and find that small changes in geometry and topology result in permeability variations that are not captured by connectivity-based analyses such as percolation probabilities, particularly when the matrix is permeable. The permeability variations associated with subseismic-scale fracture variability are not captured in conventional stochastic models, but can be captured using deterministic outcrop models with flow through discrete fractures. The deterministic models provide a permeability range associated with subseismic fracture variability, that can be assigned to grid cells of fractured reservoir flow models, as an alternative to assuming constant permeability in the absence of subseismic-scale deformation.

  4. 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. Copyright © 2016 by the Genetics Society of America.

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

    PubMed Central

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

    2012-01-01

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

  6. 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. © 2015 John Wiley & Sons Ltd.

  7. 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.

  8. 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

  9. A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population

    PubMed Central

    Tunlid, Anders; Ghatnekar, Lena

    2015-01-01

    Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked ‘native’ PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats. PMID:26674953

  10. Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus.

    PubMed

    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.

  11. A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster

    PubMed Central

    Nolte, Viola; Tobler, Raymond; Stöbe, Petra; Futschik, Andreas; Schlötterer, Christian

    2013-01-01

    Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome. PMID:23754958

  12. A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population.

    PubMed

    Prentice, Honor C; Li, Yuan; Lönn, Mikael; Tunlid, Anders; Ghatnekar, Lena

    2015-12-22

    Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked 'native' PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats.

  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. Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae).

    PubMed

    Chester, Michael; Gallagher, Joseph P; Symonds, V Vaughan; Cruz da Silva, Ana Veruska; Mavrodiev, Evgeny V; Leitch, Andrew R; Soltis, Pamela S; Soltis, Douglas E

    2012-01-24

    Polyploidy, or whole genome duplication, has played a major role in the evolution of many eukaryotic lineages. Although the prevalence of polyploidy in plants is well documented, the molecular and cytological consequences are understood largely from newly formed polyploids (neopolyploids) that have been grown experimentally. Classical cytological and molecular cytogenetic studies both have shown that experimental neoallopolyploids often have meiotic irregularities, producing chromosomally variable gametes and progeny; however, little is known about the extent or duration of chromosomal variation in natural neoallopolyploid populations. We report the results of a molecular cytogenetic study on natural populations of a neoallopolyploid, Tragopogon miscellus, which formed multiple times in the past 80 y. Using genomic and fluorescence in situ hybridization, we uncovered massive and repeated patterns of chromosomal variation in all populations. No population was fixed for a particular karyotype; 76% of the individuals showed intergenomic translocations, and 69% were aneuploid for one or more chromosomes. Importantly, 85% of plants exhibiting aneuploidy still had the expected chromosome number, mostly through reciprocal monosomy-trisomy of homeologous chromosomes (1:3 copies) or nullisomy-tetrasomy (0:4 copies). The extensive chromosomal variation still present after ca. 40 generations in this biennial species suggests that substantial and prolonged chromosomal instability might be common in natural populations after whole genome duplication. A protracted period of genome instability in neoallopolyploids may increase opportunities for alterations to genome structure, losses of coding and noncoding DNA, and changes in gene expression.

  15. Odorant Receptor Polymorphisms and Natural Variation in Olfactory Behavior in Drosophila melanogaster

    PubMed Central

    Rollmann, Stephanie M.; Wang, Ping; Date, Priya; West, Steven A.; Mackay, Trudy F. C.; Anholt, Robert R. H.

    2010-01-01

    Animals perceive and discriminate among a vast array of sensory cues in their environment. Both genetic and environmental factors contribute to individual variation in behavioral responses to these cues. Here, we asked to what extent sequence variants in six Drosophila melanogaster odorant receptor (Or) genes are associated with variation in behavioral responses to benzaldehyde by sequencing alleles from a natural population. Sequence analyses showed signatures of deviations from neutrality for Or42b and Or85f, and linkage disequilibrium analyses showed a history of extensive recombination between polymorphic markers for all six Or genes. We identified polymorphisms in Or10a, Or43a, and Or67b that were significantly associated with variation in response to benzaldehyde. To verify these associations, we repeated the analyses with an independent set of behavioral measurements of responses to a structurally similar odorant, acetophenone. Association profiles for both odorants were similar with many polymorphisms and haplotypes associated with variation in responsiveness to both odorants. Some polymorphisms, however, were associated with one, but not the other odorant. We also observed a correspondence between behavioral response to benzaldehyde and differences in Or10a and Or43a expression. These results illustrate that sequence variants that arise during the evolution of odorant receptor genes can contribute to individual variation in olfactory behavior and give rise to subtle shifts in olfactory perception. PMID:20628035

  16. Comparison of seasonal variation between anthropogenic and natural emission inventory and Satellite observation in Southeast Asia

    NASA Astrophysics Data System (ADS)

    Kurata, G.; Lalitaporn, P.

    2012-12-01

    Since the economic growth of the countries in Southeast Asia is significantly rapid, the emission of air pollutant from the anthropogenic activity, such as industry, power generation and transportation is rapidly increasing. Moreover, biomass burning due to unsuitable agricultural management, deforestation and expansion of farmland are discharging large amount of pollutants, such as Carbon monoxide, volatile organic compound and particulate matter. Especially, the particulate matter from biomass burning causes the serious haze pollution in surrounding area in Southeast Asia. Furthermore, the biomass fuel used for cooking at residential sector discharges harmful pollutants including a particulate matter, and causes the adverse health impact to people on indoor and outdoor. In this study, we evaluated the spatial distribution and the seasonal variation of emission inventory for Southeast Asia region by comparing with satellite observation data in order to improve the accuracy of the impact assessment of air pollution by regional atmospheric chemistry transport model (WRF and CMAQ). As an emission inventory data, we used our original regional emission inventory for Southeast Asia region developed from detail transportation and industry data sets as well as a several existing emission inventories. As satellite observation data, the vertical column density of NO2, Particulate matter and Carbon monoxide obtained by various satellite, such as GOME, GOME2, SCIAMACY, OMI and so on. As a result of comparisons between satellite observation and emission inventories from 1996 to 2011, in the case of anthropogenic emission, seasonal variation was comparatively well in agreement with the seasonal variation of satellite data. However, the uncertainty of the seasonal variation was large on several large cities. In the case of emission from biomass burning, the seasonal variation was clear, but inter-annual variation was also large due to large scale climate condition.

  17. Variation in natural selection for growth and phlorotannins in the brown alga Fucus vesiculosus.

    PubMed

    Jormalainen, V; Honkanen, T

    2004-07-01

    Directional selection for plant traits associated with resistance to herbivory tends to eliminate genetic variation in such traits. On the other hand, balancing selection arising from trade-offs between resistance and growth or spatially variable selection acts against the elimination of genetic variation. We explore both the amount of genetic variation and variability of natural selection for growth and concentration of phenolic secondary compounds, phlorotannins, in the brown alga Fucus vesiculosus. We measured variation in selection at two growing depths and two levels of nutrient availability in algae that had faced two kinds of past growing environments. Genetic variation was low for growth but high for phlorotannins. The form and strength of selection for both focal traits depended on the past growing environment of the algae. We found strong directional selection for growth rate in algae previously subjected to higher ultraviolet radiation, but not in algae previously subjected to higher nutrient availability. Stabilizing selection for growth occurred especially in the deep growing environment. Selection for phlorotannins was generally weak, but in some past-environment-current-environment combinations we detected either directional selection against phlorotannins or stabilizing selection. Thus, phlorotannins are not selectively neutral but affect the fitness of F. vesiculosus. In particular, there may be a fitness cost of producing phlorotannins, but the realization of such a cost varies from one environment to another. Genetic correlations between selective environments were high for growth but nonexistent for phlorotannins, emphasizing the high phenotypic plasticity of phlorotannin production. The highly heterogeneous selection, including directional, stabilizing, and spatially variable selection as well as temporal change in selection due to responses to past environmental conditions, probably maintains a high amount of genetic variation in phlorotannins

  18. 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.

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

    PubMed Central

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

    2015-01-01

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

  20. Regional variations in mortality and causes of death in Israel, 2009-2013.

    PubMed

    Gordon, Ethel-Sherry; Haklai, Ziona; Meron, Jill; Aburbeh, Miriam; Salz, Inbal Weiss; Applbaum, Yael; Goldberger, Nehama F

    2017-08-01

    Regional variations in mortality can be used to study and assess differences in disease prevalence and factors leading to disease and mortality from different causes. To enable this comparison, it is important to standardize the mortality data to adjust for the effects of regional population differences in age, nationality and country of origin. Standardized mortality ratios (SMR) were calculated for the districts and sub-districts in Israel, for total mortality by gender as well as for leading causes of death and selected specific causes. Correlations were assessed between these SMRs, regional disease risk factors and socio-economic characteristics. Implications for health policy were then examined. Total mortality in the Northern District of Israel was not significantly different from the national average; but the Haifa, Tel Aviv, and Southern districts were significantly higher and the Jerusalem, Central, Judea and Samaria districts were lower. Cancer SMR was significantly lower in Jerusalem and not significantly higher in any region. Heart disease and diabetes SMRs were significantly higher in many sub-districts in the north of the country and lower in the south. SMRs for septicemia, influenza/pneumonia, and for cerebrovascular disease were higher in the south. Septicemia was also significantly higher in Tel Aviv and lower in the North, Haifa and Jerusalem districts. SMRs for accidents, particularly for motor vehicle accidents were significantly higher in the peripheral Zefat and Be'er Sheva sub-districts. The SMR, adjusted for age and ethnicity, is a good method for identifying districts that differ significantly from the national average. Some of the regional differences may be attributed to differences in the completion of death certificates. This needs to be addressed by efforts to improve reporting of causes of death, by educating physicians. The relatively low differences found after adjustment, show that factors associated with ethnicity may affect

  1. Hypervariable genomic variation to reconstruct the natural history of populations: lessons from the big cats.

    PubMed

    Menotti-Raymond, M; O'Brien, S J

    1995-09-01

    The extent and nature of variation in hypervariable regions DNA have been used in the past as a means to infer the natural histories of populations. We review the interpretation of the extent of genetic diversity for minisatellite DNA in the cheetah to estimate the timing of a population bottleneck in the species and the potential application of a second class of hypervariable DNA, microsatellite DNA, as a molecular tool to examine the natural histories of felid populations. A calibration curve relating the degree of allele fragment sharing in individuals to relatedness in a captive pedigree of cheetahs is presented. This measurement has important applications for management of potential matings in captive management situations.

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

    PubMed Central

    Calhim, Sara; Birkhead, Tim R.

    2009-01-01

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

  3. Natural and sexual selection act on different axes of variation in avian plumage color

    PubMed Central

    Dunn, Peter O.; Armenta, Jessica K.; Whittingham, Linda A.

    2015-01-01

    The bright colors of birds are often attributed to sexual selection on males, but in many species both sexes are colorful and it has been long debated whether sexual selection can also explain this variation. We show that most evolutionary transitions in color have been toward similar plumage in both sexes, and the color of both sexes (for example, bright or dull) was associated with indices of natural selection (for example, habitat type), whereas sexual differences in color were primarily associated with indices of sexual selection on males (for example, polygyny and large testes size). Debate about the evolution of bird coloration can be resolved by recognizing that both natural and sexual selection have been influential, but they have generally acted on two different axes: sexual selection on an axis of sexual differences and natural selection on both sexes for the type of color (for example, bright or dull). PMID:26601146

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

    SciTech Connect

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

    2012-05-09

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

  5. 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

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

    PubMed

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

    2013-08-01

    Cuttlebone is a natural marine cellular material possessing the exceptional mechanical properties of high compressive strength, high porosity and high permeability. This combination of properties is exceedingly desirable in biomedical applications, such as bone tissue scaffolds. In light of recent studies, which converted raw cuttlebone into hydroxyapatite tissue scaffolds, the impact of morphological variations in the microstructure of this natural cellular material on the effective mechanical properties is explored in this paper. Two extensions of the finite element-based homogenization method are employed to account for deviations from the assumption of periodicity. Firstly, a representative volume element (RVE) of cuttlebone is systematically varied to reflect the large range of microstructural configurations possibly among different cuttlefish species. The homogenization results reveal the critical importance of pillar formation and aspect ratio (height/width of RVE) on the effective bulk and shear moduli of cuttlebone. Secondly, multi-cell analysis domains (or multiple RVE domains) permit the introduction of random variations across neighboring cells. Such random variations decrease the bulk modulus whilst displaying minimal impact on the shear modulus. Increasing the average size of random variations increases the effect on bulk modulus. Also, the results converge rapidly as the size of the analysis domain is increased, meaning that a relatively small multi-cell domain can provide a reasonable approximation of the effective properties for a given set of random variation parameters. These results have important implications for the proposed use of raw cuttlebone as an engineering material. They also highlight some potential for biomimetic design capabilities for materials inspired by the cuttlebone microstructure, which may be applicable in biomedical applications such as bone tissue scaffolds. Copyright © 2013 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2011-10-01

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

  8. Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

    PubMed Central

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

    2011-01-01

    A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries of genetic variation, like allele frequencies, are also correlated with recombination rate and whether these correlations can be explained solely by negative selection against deleterious mutations or whether positive selection acting on favorable alleles is also required. Here we attempt to address these questions by analyzing three different genome-wide resequencing datasets from European individuals. We document several significant correlations between different genomic features. In particular, we find that average minor allele frequency and diversity are reduced in regions of low recombination and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations. However, models with strong positive selection on nonsynonymous mutations and little negative selection predict a stronger negative correlation between neutral diversity and nonsynonymous divergence than observed in the actual data, supporting the importance of negative, rather than positive, selection throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations. PMID:22022285

  9. Transformer sound level caused by core magnetostriction and winding stress displacement variation

    NASA Astrophysics Data System (ADS)

    Hsu, Chang-Hung; Huang, Yi-Mei; Hsieh, Min-Fu; Fu, Chao-Ming; Adireddy, Shiva; Chrisey, Douglas B.

    2017-05-01

    Magnetostriction caused by the exciting variation of the magnetic core and the current conducted by the winding wired to the core has a significant result impact on a power transformer. This paper presents the sound of a factory transformer before on-site delivery for no-load tests. This paper also discusses the winding characteristics from the transformer full-load tests. The simulation and the measurement for several transformers with capacities ranging from 15 to 60 MVA and high voltage 132kV to low voltage 33 kV are performed. This study compares the sound levels for transformers by no-load test (core/magnetostriction) and full-load test (winding/displacement ɛ ). The difference between the simulated and the measured sound levels is about 3dB. The results show that the sound level depends on several parameters, including winding displacement, capacity, mass of the core and windings. Comparative results of magnetic induction of cores and the electromagnetic force of windings for no-load and full-load conditions are examined.

  10. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Chew, Gina; Walczyk, Thomas

    2013-04-02

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

  13. Natural allelic variation of the IL-21 receptor modulates ischemic stroke infarct volume.

    PubMed

    Lee, Han Kyu; Keum, Sehoon; Sheng, Huaxin; Warner, David S; Lo, Donald C; Marchuk, Douglas A

    2016-08-01

    Risk for ischemic stroke has a strong genetic basis, but heritable factors also contribute to the extent of damage after a stroke has occurred. We previously identified a locus on distal mouse chromosome 7 that contributes over 50% of the variation in postischemic cerebral infarct volume observed between inbred strains. Here, we used ancestral haplotype analysis to fine-map this locus to 12 candidate genes. The gene encoding the IL-21 receptor (Il21r) showed a marked difference in strain-specific transcription levels and coding variants in neonatal and adult cortical tissue. Collateral vessel connections were moderately reduced in Il21r-deficient mice, and cerebral infarct volume increased 2.3-fold, suggesting that Il21r modulates both collateral vessel anatomy and innate neuroprotection. In brain slice explants, oxygen deprivation (OD) activated apoptotic pathways and increased neuronal cell death in IL-21 receptor-deficient (IL-21R-deficient) mice compared with control animals. We determined that the neuroprotective effects of IL-21R arose from signaling through JAK/STAT pathways and upregulation of caspase 3. Thus, natural genetic variation in murine Il21r influences neuronal cell viability after ischemia by modulating receptor function and downstream signal transduction. The identification of neuroprotective genes based on naturally occurring allelic variations has the potential to inform the development of drug targets for ischemic stroke treatment.

  14. Natural allelic variation of the IL-21 receptor modulates ischemic stroke infarct volume

    PubMed Central

    Lee, Han Kyu; Keum, Sehoon; Sheng, Huaxin; Warner, David S.; Lo, Donald C.

    2016-01-01

    Risk for ischemic stroke has a strong genetic basis, but heritable factors also contribute to the extent of damage after a stroke has occurred. We previously identified a locus on distal mouse chromosome 7 that contributes over 50% of the variation in postischemic cerebral infarct volume observed between inbred strains. Here, we used ancestral haplotype analysis to fine-map this locus to 12 candidate genes. The gene encoding the IL-21 receptor (Il21r) showed a marked difference in strain-specific transcription levels and coding variants in neonatal and adult cortical tissue. Collateral vessel connections were moderately reduced in Il21r-deficient mice, and cerebral infarct volume increased 2.3-fold, suggesting that Il21r modulates both collateral vessel anatomy and innate neuroprotection. In brain slice explants, oxygen deprivation (OD) activated apoptotic pathways and increased neuronal cell death in IL-21 receptor–deficient (IL-21R–deficient) mice compared with control animals. We determined that the neuroprotective effects of IL-21R arose from signaling through JAK/STAT pathways and upregulation of caspase 3. Thus, natural genetic variation in murine Il21r influences neuronal cell viability after ischemia by modulating receptor function and downstream signal transduction. The identification of neuroprotective genes based on naturally occurring allelic variations has the potential to inform the development of drug targets for ischemic stroke treatment. PMID:27400126

  15. Natural variation in a testosterone-mediated trade-off between mating effort and parental effort.

    PubMed

    McGlothlin, Joel W; Jawor, Jodie M; Ketterson, Ellen D

    2007-12-01

    Male birds frequently face a trade-off between acquiring mates and caring for offspring. Hormone manipulation studies indicate that testosterone often mediates this trade-off, increasing mating effort while decreasing parental effort. Little is known, however, about individual covariation between testosterone and relevant behavior on which selection might act. Using wild, male dark-eyed juncos (Junco hyemalis), we measured individual variation in testosterone levels before and after standardized injections of gonadotropin-releasing hormone (GnRH). The GnRH challenges have been shown to produce short-term testosterone increases that are similar to those produced naturally in response to social stimuli, repeatable in magnitude, and greater in males with more attractive ornaments. We correlated these testosterone increases with behavioral measures of mating and parental effort (aggressive response to a simulated territorial intrusion and nestling feeding, respectively). Males that showed higher postchallenge testosterone displayed more territorial behavior, and males that produced higher testosterone increases above initial levels displayed reduced parental behavior. Initial testosterone levels were positively but nonsignificantly correlated with aggression but did not predict parental behavior. These relationships suggest that natural variation in testosterone, specifically the production of short-term increases, may underlie individual variation in the mating effort/parental effort trade-off. We discuss the implications of these results for the evolution of hormonally mediated trade-offs.

  16. Analysis of natural variation of the potato tuber proteome reveals novel candidate genes for tuber bruising.

    PubMed

    Urbany, Claude; Colby, Thomas; Stich, Benjamin; Schmidt, Lysann; Schmidt, Jürgen; Gebhardt, Christiane

    2012-02-03

    Potato (Solanum tuberosum) presents a challenging organism for the genetic and molecular dissection of complex traits due to its tetraploidy and high heterozygosity. One such complex trait of high agronomic interest is the tuber susceptibility to bruising upon mechanical impact, which involves an enzymatic browning reaction. We have compared the tuber proteome of two groups of 10 potato cultivars differing in bruising susceptibility to (i) identify de novo proteins that contribute to bruising, based on differential protein expression, and (ii) validate these proteins by combining proteomics with association genetics. The comparison of 20 potato varieties yields insight into the high natural variation of tuber protein patterns due to genetic background. Seven genes or gene families were found that were both differentially expressed on the protein level between groups and for which DNA polymorphisms were associated with the investigated traits. A putative class III lipase was identified as a novel factor contributing to the natural variation of bruising. Additionally, tuber proteome changes triggered by mechanical impact, within and between groups, were monitored over time. Differentially expressed proteins were found, notably lipases, patatins, and annexins, showing remarkable time-dependent protein variation.

  17. 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.

  18. 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

  19. Genic and nongenic contributions to natural variation of quantitative traits in maize.

    PubMed

    Li, Xianran; Zhu, Chengsong; Yeh, Cheng-Ting; Wu, Wei; Takacs, Elizabeth M; Petsch, Katherine A; Tian, Feng; Bai, Guihua; Buckler, Edward S; Muehlbauer, Gary J; Timmermans, Marja C P; Scanlon, Michael J; Schnable, Patrick S; Yu, Jianming

    2012-12-01

    The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene-targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%-59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions.

  20. 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.

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

    PubMed Central

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

    2002-01-01

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

  2. 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

  3. 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

  4. Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance.

    PubMed

    Lewis, Jeffrey A; Elkon, Isaac M; McGee, Mick A; Higbee, Alan J; Gasch, Audrey P

    2010-12-01

    Ethanol production from lignocellulosic biomass holds promise as an alternative fuel. However, industrial stresses, including ethanol stress, limit microbial fermentation and thus prevent cost competitiveness with fossil fuels. To identify novel engineering targets for increased ethanol tolerance, we took advantage of natural diversity in wild Saccharomyces cerevisiae strains. We previously showed that an S288c-derived lab strain cannot acquire higher ethanol tolerance after a mild ethanol pretreatment, which is distinct from other stresses. Here, we measured acquired ethanol tolerance in a large panel of wild strains and show that most strains can acquire higher tolerance after pretreatment. We exploited this major phenotypic difference to address the mechanism of acquired ethanol tolerance, by comparing the global gene expression response to 5% ethanol in S288c and two wild strains. Hundreds of genes showed variation in ethanol-dependent gene expression across strains. Computational analysis identified several transcription factor modules and known coregulated genes as differentially expressed, implicating genetic variation in the ethanol signaling pathway. We used this information to identify genes required for acquisition of ethanol tolerance in wild strains, including new genes and processes not previously linked to ethanol tolerance, and four genes that increase ethanol tolerance when overexpressed. Our approach shows that comparative genomics across natural isolates can quickly identify genes for industrial engineering while expanding our understanding of natural diversity.

  5. [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.

  6. Exploiting Natural Variation in Saccharomyces cerevisiae to Identify Genes for Increased Ethanol Resistance

    PubMed Central

    Lewis, Jeffrey A.; Elkon, Isaac M.; McGee, Mick A.; Higbee, Alan J.; Gasch, Audrey P.

    2010-01-01

    Ethanol production from lignocellulosic biomass holds promise as an alternative fuel. However, industrial stresses, including ethanol stress, limit microbial fermentation and thus prevent cost competitiveness with fossil fuels. To identify novel engineering targets for increased ethanol tolerance, we took advantage of natural diversity in wild Saccharomyces cerevisiae strains. We previously showed that an S288c-derived lab strain cannot acquire higher ethanol tolerance after a mild ethanol pretreatment, which is distinct from other stresses. Here, we measured acquired ethanol tolerance in a large panel of wild strains and show that most strains can acquire higher tolerance after pretreatment. We exploited this major phenotypic difference to address the mechanism of acquired ethanol tolerance, by comparing the global gene expression response to 5% ethanol in S288c and two wild strains. Hundreds of genes showed variation in ethanol-dependent gene expression across strains. Computational analysis identified several transcription factor modules and known coregulated genes as differentially expressed, implicating genetic variation in the ethanol signaling pathway. We used this information to identify genes required for acquisition of ethanol tolerance in wild strains, including new genes and processes not previously linked to ethanol tolerance, and four genes that increase ethanol tolerance when overexpressed. Our approach shows that comparative genomics across natural isolates can quickly identify genes for industrial engineering while expanding our understanding of natural diversity. PMID:20855568

  7. Natural abundance variations in stable isotopes and their potential uses in animal physiological ecology.

    PubMed

    Gannes, L Z; Martínez del Rio, C; Koch, P

    1998-03-01

    Chemical, biological, and physical processes lead to distinctive "isotopic signatures" in biological materials that allow tracing of the origins of organic substances. Isotopic variation has been extensively used by plant physiological ecologists and by paleontologists, and recently ecologists have adopted the use of stable isotopes to measure ecosystem patterns and processes. To date, animal physiological ecologists have made minimal use of naturally occurring stable isotopes as tracers. Here we provide a review of the current and potential uses of naturally occurring stable isotopes in animal physiological ecology. We outline the physical and biological processes that lead to variation in isotopic abundance in plants and animals. We summarize current uses in animal physiological ecology (diet reconstruction and animal movement patterns), and suggest areas of research where the use of stable isotopes can be fruitful (protein balance and turnover and the allocation of dietary nutrients). We argue that animal physiological ecologists can benefit from including the measurement of naturally occurring stable isotopes in their battery of techniques. We also argue that animal physiologists can make an important contribution to the emerging field of stable isotopes in biology by testing experimentally the plethora of assumptions upon which the techniques rely.

  8. 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

  9. 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

  10. Natural changes in brain temperature underlie variations in song tempo during a mating behavior.

    PubMed

    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.

  11. 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.

  12. The consequence of natural selection on genetic variation in the mouse.

    PubMed

    Reuveni, Eli; Birney, Ewan; Gross, Cornelius T

    2010-04-01

    Laboratory mouse strains are known to have emerged from recent interbreeding between individuals of Mus musculus isolated populations. As a result of this breeding history, the collection of polymorphisms observed between laboratory mouse strains is likely to harbor the effects of natural selection between reproductively isolated populations. Until now no study has systematically investigated the consequences of this breeding history on gene evolution. Here we have used a novel, unbiased evolutionary approach to predict the founder origin of laboratory mouse strains and to assess the balance between ancient and newly emerged mutations in the founder subspecies. Our results confirm a contribution from at least four distinct subspecies. Additionally, our method allowed us to identify regions of relaxed selective constraint among laboratory mouse strains. This unique structure of variation is likely to have significant consequences on the use of mouse to find genes underlying phenotypic variation.

  13. Variation in Y Chromosome Segregation in Natural Populations of Drosophila melanogaster

    PubMed Central

    Clark, Andrew 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. PMID:3104134

  14. External cavity diode laser with frequency drift following natural variation in air pressure.

    PubMed

    Takamizawa, Akifumi; Yanagimachi, Shinya; Ikegami, Takeshi; Kawabata, Ryuzo

    2015-06-20

    A compact and mechanically very robust external cavity diode laser was made by removing any position adjusters such as precision screws and piezo actuators, taking advantage of a cat's eye retroreflector insensitive to misalignment. Under free-running operation during 150 h, the frequency drift followed natural variation in air pressure with a ratio of -66.6±0.1  MHz/hPa in a range between 1001.5 and 1013.6 hPa. The ratio was in good agreement with that estimated from variation in the effective cavity length derived from the relation between the pressure and the refractive index of air. These results indicate that an external cavity diode laser with predictable frequency drift was successfully created.

  15. Natural variation in Drosophila melanogaster diapause due to the insulin-regulated PI3-kinase

    PubMed Central

    Williams, Karen D.; Busto, Macarena; Suster, Maximiliano L.; So, Anthony K.-C.; Ben-Shahar, Yehuda; Leevers, Sally J.; Sokolowski, Marla B.

    2006-01-01

    This study links natural variation in a Drosophila melanogaster overwintering strategy, diapause, to the insulin-regulated phosphatidylinositol 3-kinase (PI3-kinase) gene, Dp110. Variation in diapause, a reproductive arrest, was associated with Dp110 by using Dp110 deletions and genomic rescue fragments in transgenic flies. Deletions of Dp110 increased the proportion of individuals in diapause, whereas expression of Dp110 in the nervous system, but not including the visual system, decreased it. The roles of phosphatidylinositol 3-kinase for both diapause in D. melanogaster and dauer formation in Caenorhabditis elegans suggest a conserved role for this kinase in both reproductive and developmental arrests in response to environmental stresses. PMID:17043223

  16. Investigating Natural Variation in Drosophila Courtship Song by the Evolve and Resequence Approach

    PubMed Central

    Turner, Thomas L.; Miller, Paige M.

    2012-01-01

    A primary goal of population genetics is to determine the genetic basis of natural trait variation. We could significantly advance this goal by developing comprehensive genome-wide approaches to link genotype and phenotype in model organisms. Here we combine artificial selection with population-based resequencing to investigate the genetic basis of variation in the interpulse interval (IPI) of Drosophila melanogaster courtship song. We performed divergent selection on replicate populations for only 14 generations, but had considerable power to differentiate alleles that evolved due to selection from those that evolved stochastically. We identified a large number of variants that changed frequency in response to selection for this simple behavior, and they are highly underrepresented on the X chromosome. Though our power was adequate using this experimental technique, the ability to differentiate causal variants from those affected by linked selection requires further development. PMID:22466043

  17. Egg discrimination along a gradient of natural variation in eggshell coloration

    PubMed Central

    Grim, Tomáš; Igic, Branislav; Samaš, Peter; López, Analía V.; Shawkey, Matthew D.; Hauber, Mark E.

    2017-01-01

    Accurate recognition of salient cues is critical for adaptive responses, but the underlying sensory and cognitive processes are often poorly understood. For example, hosts of avian brood parasites have long been assumed to reject foreign eggs from their nests based on the total degree of dissimilarity in colour to their own eggs, regardless of the foreign eggs' colours. We tested hosts' responses to gradients of natural (blue-green to brown) and artificial (green to purple) egg colours, and demonstrate that hosts base rejection decisions on both the direction and degree of colour dissimilarity along the natural, but not artificial, gradient of egg colours. Hosts rejected brown eggs and accepted blue-green eggs along the natural egg colour gradient, irrespective of the total perceived dissimilarity from their own egg's colour. By contrast, their responses did not vary along the artificial colour gradient. Our results demonstrate that egg recognition is specifically tuned to the natural gradient of avian eggshell colour and suggest a novel decision rule. These results highlight the importance of considering sensory reception and decision rules when studying perception, and illustrate that our understanding of recognition processes benefits from examining natural variation in phenotypes. PMID:28179521

  18. The effects of natural variation in background radioactivity on humans, animals and other organisms.

    PubMed

    Møller, Anders P; Mousseau, Timothy A

    2013-02-01

    Natural levels of radioactivity on the Earth vary by more than a thousand-fold; this spatial heterogeneity may suffice to create heterogeneous effects on physiology, mutation and selection. We review the literature on the relationship between variation in natural levels of radioactivity and evolution. First, we consider the effects of natural levels of radiation on mutations, DNA repair and genetics. A total of 46 studies with 373 effect size estimates revealed a small, but highly significant mean effect that was independent of adjustment for publication bias. Second, we found different mean effect sizes when studies were based on broad categories like physiology, immunology and disease frequency; mean weighted effect sizes were larger for studies of plants than animals, and larger in studies conducted in areas with higher levels of radiation. Third, these negative effects of radiation on mutations, immunology and life history are inconsistent with a general role of hormetic positive effects of radiation on living organisms. Fourth, we reviewed studies of radiation resistance among taxa. These studies suggest that current levels of natural radioactivity may affect mutational input and thereby the genetic constitution and composition of natural populations. Susceptibility to radiation varied among taxa, and several studies provided evidence of differences in susceptibility among populations or strains. Crucially, however, these studies are few and scattered, suggesting that a concerted effort to address this lack of research should be made. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

  19. Hazards caused by natural and anthropogenic changes of catchment area in karst

    NASA Astrophysics Data System (ADS)

    Bonacci, O.

    2004-11-01

    Determination of the catchment area is the starting point in most hydrological analyses. It serves as a basis for many hydrological and water resources management calculations. The catchment boundaries and areas in karst regions are often fragmented and not accurately known. They can change over time due to natural and anthropogenic causes. Natural and man-made processes cause changes of catchment area on different time and space scales. Human intervention, especially construction of dams and reservoirs, as well as interbasin water transfer through long tunnels and pipelines can introduce instantaneous, definite and hazardous change. This paper presents seven examples of natural and anthropogenic factors which influenced changes of catchment area in the Dinaric karst: 1) Closing of the Obod Estavelle in the Fatniceko polje; 2) Operation of the Zakucac hydroelectric power plant on the Cetina River; 3) Problems caused by Salakovac Reservoir; 4) Catastrophic flooding in the Cetinje Polje; 5) Regulation and canalization of the Trebišnjica River; 6) Building of the underground hydroelectric power plant Ombla; 7) An earthquake in Southern Croatia and Western Herzegovina.

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2011-12-14

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

  2. Mapping the natural variation in whole bone stiffness and strength across skeletal sites

    PubMed Central

    Schlecht, Stephen H.; Bigelow, Erin M.R.; Jepsen, Karl J.

    2016-01-01

    Traits of the skeletal system are coordinately adjusted to establish mechanical homeostasis in response to genetic and environmental factors. Prior work demonstrated that this `complex adaptive' process is not perfect, revealing a two-fold difference in whole bone stiffness of the tibia across a population. Robustness (specifically, total cross-sectional area relative to length) varies widely across skeletal sites and between sexes. However, it is unknown whether the natural variation in whole bone stiffness and strength also varies across skeletal sites and between men and women. We tested the hypotheses that: 1) all major long bones of the appendicular skeleton demonstrate inherent, systemic constraints in the degree to which morphological and compositional traits can be adjusted for a given robustness; and 2) these traits covary in a predictable manner independent of body size and robustness. We assessed the functional relationships among robustness, cortical area (Ct.Ar), cortical tissue mineral density (Ct.TMD), and bone strength index (BSI) across the long bones of the upper and lower limbs of 115 adult men and women. All bones showed a significant (p < 0.001) positive regression between BSI and robustness after adjusting for body size, with slender bones being 1.7–2.3 times less stiff and strong in men and 1.3–2.8 times less stiff and strong in women compared to robust bones. Our findings are the first to document the natural inter-individual variation in whole bone stiffness and strength that exist within populations and that is predictable based on skeletal robustness for all major long bones. Documenting and further understanding this natural variation in strength may be critical for differentially diagnosing and treating skeletal fragility. PMID:24999223

  3. The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatus

    PubMed Central

    Flagel, Lex E.; Willis, John H.; Vision, Todd J.

    2013-01-01

    Major unresolved questions in evolutionary genetics include determining the contributions of different mutational sources to the total pool of genetic variation in a species, and understanding how these different forms of genetic variation interact with natural selection. Recent work has shown that structural variants (SVs) (insertions, deletions, inversions, and transpositions) are a major source of genetic variation, often outnumbering single nucleotide variants in terms of total bases affected. Despite the near ubiquity of SVs, major questions about their interaction with natural selection remain. For example, how does the allele frequency spectrum of SVs differ when compared with single nucleotide variants? How often do SVs affect genes, and what are the consequences? To begin to address these questions, we have systematically identified and characterized a large set of submicroscopic insertion and deletion (indel) variants (between 1 and 200 kb in length) among ten inbred lines from a single natural population of the plant species Mimulus guttatus. After extensive computational filtering, we focused on a set of 4,142 high-confidence indels that showed an experimental validation rate of 73%. All but one of these indels were less than 200 kb. Although the largest were generally at lower frequencies in the population, a surprising number of large indels are at intermediate frequencies. Although indels overlapping with genes were much rarer than expected by chance, approximately 600 genes were affected by an indel. Nucleotide-binding site leucine-rich repeat (NBS–LRR) defense response genes were the most enriched among the gene families affected. Most indels associated with genes were rare and appeared to be under purifying selection, though we do find four high-frequency derived insertion alleles that show signatures of recent positive selection. PMID:24336482

  4. The standing pool of genomic structural variation in a natural population of Mimulus guttatus.

    PubMed

    Flagel, Lex E; Willis, John H; Vision, Todd J

    2014-01-01

    Major unresolved questions in evolutionary genetics include determining the contributions of different mutational sources to the total pool of genetic variation in a species, and understanding how these different forms of genetic variation interact with natural selection. Recent work has shown that structural variants (SVs) (insertions, deletions, inversions, and transpositions) are a major source of genetic variation, often outnumbering single nucleotide variants in terms of total bases affected. Despite the near ubiquity of SVs, major questions about their interaction with natural selection remain. For example, how does the allele frequency spectrum of SVs differ when compared with single nucleotide variants? How often do SVs affect genes, and what are the consequences? To begin to address these questions, we have systematically identified and characterized a large set of submicroscopic insertion and deletion (indel) variants (between 1 and 200 kb in length) among ten inbred lines from a single natural population of the plant species Mimulus guttatus. After extensive computational filtering, we focused on a set of 4,142 high-confidence indels that showed an experimental validation rate of 73%. All but one of these indels were less than 200 kb. Although the largest were generally at lower frequencies in the population, a surprising number of large indels are at intermediate frequencies. Although indels overlapping with genes were much rarer than expected by chance, approximately 600 genes were affected by an indel. Nucleotide-binding site leucine-rich repeat (NBS-LRR) defense response genes were the most enriched among the gene families affected. Most indels associated with genes were rare and appeared to be under purifying selection, though we do find four high-frequency derived insertion alleles that show signatures of recent positive selection.

  5. Mapping the natural variation in whole bone stiffness and strength across skeletal sites.

    PubMed

    Schlecht, Stephen H; Bigelow, Erin M R; Jepsen, Karl J

    2014-10-01

    Traits of the skeletal system are coordinately adjusted to establish mechanical homeostasis in response to genetic and environmental factors. Prior work demonstrated that this 'complex adaptive' process is not perfect, revealing a two-fold difference in whole bone stiffness of the tibia across a population. Robustness (specifically, total cross-sectional area relative to length) varies widely across skeletal sites and between sexes. However, it is unknown whether the natural variation in whole bone stiffness and strength also varies across skeletal sites and between men and women. We tested the hypotheses that: 1) all major long bones of the appendicular skeleton demonstrate inherent, systemic constraints in the degree to which morphological and compositional traits can be adjusted for a given robustness; and 2) these traits covary in a predictable manner independent of body size and robustness. We assessed the functional relationships among robustness, cortical area (Ct.Ar), cortical tissue mineral density (Ct.TMD), and bone strength index (BSI) across the long bones of the upper and lower limbs of 115 adult men and women. All bones showed a significant (p<0.001) positive regression between BSI and robustness after adjusting for body size, with slender bones being 1.7-2.3 times less stiff and strong in men and 1.3-2.8 times less stiff and strong in women compared to robust bones. Our findings are the first to document the natural inter-individual variation in whole bone stiffness and strength that exist within populations and that is predictable based on skeletal robustness for all major long bones. Documenting and further understanding this natural variation in strength may be critical for differentially diagnosing and treating skeletal fragility. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. 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.

  7. A General Model to Account for Enzyme Variation in Natural Populations

    PubMed Central

    Gillespie, John H.; Langley, Charles H.

    1974-01-01

    Approximate conditions for genetic polymorphism in temporally and spatially varying environments are presented for loci which are intermediate at the level of fitness or at the level of gene function. The conditions suggest that polymorphism will be more likely in more variable environments while unlikely in constant environments. Biochemical evidence is presented to justify the assumption of heterozygote intermediacy. Observations on natural populations are cited which substantiate the claim that allozymic polymorphism is primarily due to selection acting on environmental variation in gene function. PMID:4838763

  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. Natural variation in populations of persistently colonizing bacteria affect human host cell phenotype.

    PubMed

    Aras, Rahul A; Lee, Yongchan; Kim, Sung-Kook; Israel, Dawn; Peek, Richard M; Blaser, Martin J

    2003-08-15

    The highly diverse bacterium Helicobacter pylori, which persistently colonizes the human stomach, provides models to study the role of genome plasticity in host adaptation. Within H. pylori populations from 2 colonized individuals, intragenomic recombination between cagA DNA repeat sequences leads to deletion or duplication of tyrosine phosphorylation sites in the CagA protein, which is injected by a type IV secretion system into host cells. Experimental coculture of gastric epithelial cells with the strains containing these naturally occurring CagA phosphorylation site variants induced markedly divergent host cell morphologic responses. Mutants were constructed in which a phosphorylation site was either added or deleted in the expressed CagA protein; coculture studies confirmed that the naturally occurring differences in CagA phosphorylation are responsible for the observed phenotypic variation. These findings indicate that within an individual host, intragenomic recombination between H. pylori repetitive DNA produces strain variants differing in their signals to host cells.

  10. Natural variation of macrophage activation as disease-relevant phenotype predictive of inflammation and cancer survival.

    PubMed

    Buscher, Konrad; Ehinger, Erik; Gupta, Pritha; Pramod, Akula Bala; Wolf, Dennis; Tweet, George; Pan, Calvin; Mills, Charles D; Lusis, Aldons J; Ley, Klaus

    2017-07-24

    Although mouse models exist for many immune-based diseases, the clinical translation remains challenging. Most basic and translational studies utilize only a single inbred mouse strain. However, basal and diseased immune states in humans show vast inter-individual variability. Here, focusing on macrophage responses to lipopolysaccharide (LPS), we use the hybrid mouse diversity panel (HMDP) of 83 inbred strains as a surrogate for human natural immune variation. Since conventional bioinformatics fail to analyse a population spectrum, we highlight how gene signatures for LPS responsiveness can be derived based on an Interleukin-12β and arginase expression ratio. Compared to published signatures, these gene markers are more robust to identify susceptibility or resilience to several macrophage-related disorders in humans, including survival prediction across many tumours. This study highlights natural activation diversity as a disease-relevant dimension in macrophage biology, and suggests the HMDP as a viable tool to increase translatability of mouse data to clinical settings.

  11. 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. © 2016. Published by The Company of Biologists Ltd.

  12. 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

  13. The magnitude and selectivity of natural and multiple anthropogenic mortality causes in hunted brown bears.

    PubMed

    Bischof, Richard; Swenson, Jon E; Yoccoz, Nigel G; Mysterud, Atle; Gimenez, Olivier

    2009-05-01

    1. The population dynamic and evolutionary effects of harvesting are receiving growing attention among biologists. Cause-specific estimates of mortality are necessary to determine and compare the magnitude and selectivity of hunting and other types of mortalities. In addition to the logistic and financial constraints on longitudinal studies, they are complicated by the fact that nonhunting mortality in managed populations usually consists of a mix of natural and human-caused factors. 2. We used multistate capture-recapture (MCR) models to estimate cause-specific survival of brown bears (Ursus arctos) in two subpopulations in Sweden over a 23-year period. In our analysis, we distinguished between legal hunting and other sources of mortality, such as intraspecific predation, accidents, poaching, and damage control removals. We also tested whether a strong increase in harvest quotas after 1997 in one of the subpopulations affected vulnerability to legal hunting. 3. Although only a fraction of mortalities other than legal hunting could be considered natural, this group of causes showed a general pattern of demographic selectivity expected from natural mortality regimes in populations of long-lived species, namely greater vulnerability of young animals. On the other hand, demographic effects on hunting vulnerability were weak and inconsistent. Our findings support the assumption that hunting and other mortalities were additive. 4. As expected, an increase in hunting pressure coincided with a correspondingly large increase in vulnerability to hunting in the affected subpopulation. Because even unbiased harvest can lead to selective pressures on life-history traits, such as size at primiparity, increasing harvest quotas may not only affect population growth directly, but could also alter optimal life-history strategies in brown bears and other carnivores. 5. Legal hunting is the most conveniently assessed and the most easily managed cause of mortality in many wild

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

    PubMed

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

    2015-11-01

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

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

    PubMed

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

    2015-11-01

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

  16. 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.

  17. 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.

  18. Genetic variation in natural Melandrium album populations exposed to chronic ionizing radiation.

    PubMed

    Karimullina, Elina; Antonova, Elena V; Pozolotina, Vera N

    2016-11-01

    The effect of radiation pollution on genetic variation in natural populations of Melandrium album was investigated at the head part of the East-Ural Radioactive Trace (EURT) and background areas. The highest genetic differentiation estimated using F ST was revealed between compared pairs of the background and impact samples in populations of M. album. The highest rate of polymorphism was observed at the closest to nuclear accident, Impact-1 site. The unique alleles (Mdh-3(104), Pgi-2(106), Lap (105), Mdh-2(96), and Dia (94)) were discovered at the EURT. Individuals from chronically low-level irradiated sites were genetically closer than to plants from background sites using Nadhdh locus. The increase of the frequency of unique homozygous and heterozygous genotypes was identified in populations of M. album growing under chronic radiation exposure conditions. The largest contribution to the group of unique heterozygous genotypes at the EURT was made by three loci - Lap, Pgi-2, and Nadhdh; the main role in interpopulation differentiation of samples was made by the alleles Sod-2(115), Skdh (100), and Nadhdh (100). Our results provide evidence for the correlation between the increase of genetic variation other than the «genetic erosion» and chronic radiation exposure factor in natural plant populations.

  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. Differential Masking of Natural Genetic Variation by miR-9a in Drosophila.

    PubMed

    Cassidy, Justin J; Straughan, Alexander J; Carthew, Richard W

    2016-02-01

    Genetic variation is prevalent among individuals of the same species and yet the potential effects of genetic variation on developmental outcomes are frequently suppressed. Understanding the mechanisms that are responsible for this suppression is an important goal. Previously, we found that the microRNA miR-9a mitigates the impact of natural genetic variants that promote the development of scutellar bristles in adult Drosophila. Here we find that miR-9a does not affect the impact of genetic variants that inhibit the development of scutellar bristles. We show this using both directional and stabilizing selection in the laboratory. This specificity of action suggests that miR-9a does not interact with all functional classes of developmental genetic variants affecting sensory organ development. We also investigate the impact of miR-9a on a fitness trait, which is adult viability. At elevated physiological temperatures, miR-9a contributes to viability through masking genetic variants that hinder adult viability. We conclude that miR-9a activity in different developmental networks contributes to suppression of natural variants from perturbing development.

  1. Natural variation of male ornamental traits of the guppy, Poecilia reticulata.

    PubMed

    Tripathi, Namita; Hoffmann, Margarete; Dreyer, Christine

    2008-12-01

    Male ornamental traits of the guppy, Poecilia reticulata, provide an outstanding example of natural variation in sex-linked male-advantageous traits that are shaped by both sexual and environmental selection. A substantial fraction of the underlying genes is known to be genetically linked to the sex-determining region on the differentiating Y-chromosome. Intercrosses between parental populations originating from geographically distant locations in East Trinidad and Cumaná (Venezuela) were used to study segregation of ornamental traits in male progeny. In addition, we performed backcrosses to compare segregation of ornaments in presence or absence of prominent traits linked to the Y-chromosome. Another backcross strategy involving XY females from the laboratory strain zebrinus maculatus allowed studying additive and dominant effects of alleles on two different Y-chromosomes on pattern formation. For genetic mapping, we have previously developed nuclear SNP markers linked to expressed genes, including several genes known to be important for pattern formation in other species. Of these candidate genes 15 were placed on 11 different linkage groups. Our phenotypic and genotypic analysis of progeny from mapping crosses and backcrosses suggests several genetic mechanisms that enhance natural variation, namely, additive effects of codominant alleles, suppressive actions of dominant alleles, and a complex interplay between sex-linked and autosomal cofactors.

  2. 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.

  3. 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

  4. Natural and engineered coding variation in antidepressant-sensitive serotonin transporters.

    PubMed

    Ye, R; Blakely, R D

    2011-12-01

    The presynaptic serotonin (5-HT) transporter (SERT) is a key regulator of 5-HT signaling and is a major target for antidepressant medications and psychostimulants. In recent years, studies of natural and engineered genetic variation in SERT have provided new opportunities to understand structural dimensions of drug interactions and regulation of the transporter, to explore 5-HT contributions to antidepressant action, and to assess the impact of SERT-mediated 5-HT contributions to neuropsychiatric disorders. Here we review three examples from our recent studies where genetic changes in SERT, identified or engineered, have led to new models, findings, and theories that cast light on new dimensions of 5-HT action in the CNS and periphery. First, we review our work to identify specific residues through which SERT recognizes antagonists, and the conversion of this knowledge to the creation of mice lacking high-affinity antidepressant and cocaine sensitivity. Second, we discuss our studies of functional coding variation in SERT that exists in commonly used strains of inbred mice, and how this variation is beginning to reveal novel 5-HT-associated phenotypes. Third, we review our identification and functional characterization of multiple, hyperactive SERT coding variants in subjects with autism. Each of these activities has driven the development of new model systems that can be further exploited to understand the contribution of 5-HT signaling to risk for neuropsychiatric disorders and their treatment. Copyright © 2011. Published by Elsevier Ltd.

  5. A Photoreceptor Contributes to the Natural Variation of Diapause Induction in Daphnia magna.

    PubMed

    Roulin, Anne C; Bourgeois, Yann; Stiefel, Urs; Walser, Jean-Claude; Ebert, Dieter

    2016-12-01

    Diapause is an adaptation that allows organisms to survive harsh environmental conditions. In species occurring over broad habitat ranges, both the timing and the intensity of diapause induction can vary across populations, revealing patterns of local adaptation. Understanding the genetic architecture of this fitness-related trait would help clarify how populations adapt to their local environments. In the cyclical parthenogenetic crustacean Daphnia magna, diapause induction is a phenotypic plastic life history trait linked to sexual reproduction, as asexual females have the ability to switch to sexual reproduction and produce resting stages, their sole strategy for surviving habitat deterioration. We have previously shown that the induction of resting stage production correlates with changes in photoperiod that indicate the imminence of habitat deterioration and have identified a Quantitative Trait Locus (QTL) responsible for some of the variation in the induction of resting stages. Here, new data allows us to anchor the QTL to a large scaffold and then, using a combination of a new mapping panel, targeted association mapping and selection analysis in natural populations, to identify candidate genes within the QTL. Our results show that variation in a rhodopsin photoreceptor gene plays a significant role in the variation observed in resting stage induction. This finding provides a mechanistic explanation for the link between diapause and day-length perception that has been suggested in diverse arthropod taxa.

  6. 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.

  7. Natural variation and artificial selection in four genes determine grain shape in rice.

    PubMed

    Lu, Li; Shao, Di; Qiu, Xianjin; Sun, Liang; Yan, Wenhao; Zhou, Xiangchun; Yang, Lin; He, Yuqing; Yu, Sibin; Xing, Yongzhong

    2013-12-01

    The size of cultivated rice (Oryza sativa) grains has been altered by both domestication and artificial selection over the course of evolutionary history. Several quantitative trait loci (QTLs) for grain size have been cloned in the past 10 yr. To explore the natural variation in these QTLs, resequencing of grain width and weight 2 (GW2), grain size 5 (GS5) and QTL for seed width 5 (qSW5) and genotyping of grain size 3 (GS3) were performed in the germplasms of 127 varieties of rice (O. sativa) and 10-15 samples of wild rice (Oryza rufipogon). Ten, 10 and 15 haplotypes were observed for GW2, GS5 and qSW5. qSW5 and GS3 had the strongest effects on grain size, which have been widely utilized in rice production, whereas GW2 and GS5 showed more modest effects. GS5 showed small sequence variations in O. sativa germplasm and that of its progenitor O. rufipogon. qSW5 exhibited the highest level of nucleotide diversity. GW2 showed signs of purifying selection. The four grain size genes experienced different selection intensities depending on their genetic effects. In the indica population, linkage disequilibrium (LD) was detected among GS3, qSW5 and GS5. The substantial genetic variation in these four genes provides the flexibility needed to design various rice grain shapes. These findings provide insight into the evolutionary features of grain size genes in rice.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  9. Mechanisms causing variation in sexual size dimorphism in three sympatric, congeneric lizards.

    PubMed

    Manicom, Carryn; Alford, Ross; Schoener, Thomas W; Schwarzkopf, Lin

    2014-06-01

    Sexual differences in adult body size (sexual size dimorphism, or SSD) ultimately can be favored by selection because larger males are more likely to be successful competitors for females, because larger females bear larger clutches, or because intersexual size differences reduce resource competition. Natural selection during juvenile development can influence sexual dimorphism of adults, and selection on adults and juveniles may differ. Studies that address the relative contributions of adult body shape dimorphism and sexually dimorphic patterns of growth and maturity are particularly useful in understanding the evolution of size dimorphism, yet they are rare. We investigated three sympatric, congeneric lizard species with different degrees and directions of adult sexual dimorphism and compared their growth patterns, survival probabilities, and intersexual trophic niche differences. Different mechanisms, even within these closely related, sympatric species, acted on juvenile lizards to produce species differences in adult SSD. Both degree and direction of dimorphism resulted from differences between the sexes in either the duration of growth or the rate of growth, but not from differences in rates of survival or selection on juvenile growth rate. Species- and sex-specific trade-offs in the allocation of energy to growth and reproduction, as well as differential timing of maturation, thus caused the growth patterns of the sexes to diverge, producing SSD. The differences that we observed in the direction of SSD among these species is consistent with their different social systems, suggesting that differential selection on adult body size has been responsible for the observed species-specific differences in juvenile growth rates and maturational timing.

  10. A systems approach to model natural variation in reactive properties of bacterial ribosomes

    PubMed Central

    Jackson, Julius H; Schmidt, Thomas M; Herring, Patricia A

    2008-01-01

    Background Natural variation in protein output from translation in bacteria and archaea may be an organism-specific property of the ribosome. This paper adopts a systems approach to model the protein output as a measure of specific ribosome reactive properties in a ribosome-mediated translation apparatus. We use the steady-state assumption to define a transition state complex for the ribosome, coupled with mRNA, tRNA, amino acids and reaction factors, as a subsystem that allows a focus on the completed translational output as a measure of specific properties of the ribosome. Results In analogy to the steady-state reaction of an enzyme complex, we propose a steady-state translation complex for mRNA from any gene, and derive a maximum specific translation activity, Ta(max), as a property of the ribosomal reaction complex. Ta(max) has units of a-protein output per time per a-specific mRNA. A related property of the ribosome, T˜a(max⁡), has units of a-protein per time per total RNA with the relationship T˜a(max⁡) = ρa Ta(max), where ρa represents the fraction of total RNA committed to translation output of Pa from gene a message. Ta(max) as a ribosome property is analogous to kcat for a purified enzyme, and T˜a(max⁡) is analogous to enzyme specific activity in a crude extract. Conclusion Analogy to an enzyme reaction complex led us to a ribosome reaction model for measuring specific translation activity of a bacterial ribosome. We propose to use this model to design experimental tests of our hypothesis that specific translation activity is a ribosomal property that is subject to natural variation and natural selection much like Vmax and Km for any specific enzyme. PMID:18620602

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

    USGS Publications Warehouse

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Yamazaki, Y.; Maute, A.

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Yamazaki, Y.; Maute, A.

    2017-03-01

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

  14. Variation.

    ERIC Educational Resources Information Center

    Hamilton City Board of Education (Ontario).

    Suggestions for studying the topic of variation of individuals and objects (balls) to help develop elementary school students' measurement, comparison, classification, evaluation, and data collection and recording skills are made. General suggestions of variables that can be investigated are made for the study of human variation. Twelve specific…

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

    PubMed

    England, Whitney E; Whitaker, Rachel J

    2013-12-01

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

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

    PubMed

    Lindgren, B; Laurila, A

    2005-07-01

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

  17. 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%.

  18. Transcriptome-wide mining of the differentially expressed transcripts for natural variation of floral organ size in Physalis philadelphica

    PubMed Central

    He, Chaoying

    2012-01-01

    Natural phenotypic variation, a result of genetic variation, developed during evolution in response to environmental selections. Physalis philadelphica, known as tomatillo in the Solanaceae, is rich in floral and post-floral organ size diversity. However, its genetic variation is unknown. Here P. philadelphica was classified into three groups with large, intermediate, and small reproductive organ size, and a positive correlation was observed between floral organ and berry sizes. Through cDNA-amplified fragment length polymorphism (AFLP) analyses, 263 differentially expressed transcript-derived fragments (TDFs) were isolated from two accessions with different floral organ sizes. The genes encode various transcription factors, protein kinases, and enzymes, and they displayed multiple expression patterns during floral development, indicating a complexity in the genetic basis of phenotypic variation. Detailed expression analyses revealed that they were differentially expressed during floral and post-floral development, implying that they have roles in the development of flowers and fruits. Expression of three genes was further monitored in 26 accessions, and in particular the expression variation of Pp30, encoding an AP2-like transcription factor, correlates well with the observed phenotypic variations, which strongly supports an essential role for the gene in the natural variation of floral and post-floral organ size in Physalis. The results suggest that alteration in the expression pattern of a few key regulatory genes in the developmental process may be an important source of genetic variations that lead to natural variation in morphological traits. PMID:23081983

  19. Transcriptome-wide mining of the differentially expressed transcripts for natural variation of floral organ size in Physalis philadelphica.

    PubMed

    Wang, Li; Li, Zhichao; He, Chaoying

    2012-11-01

    Natural phenotypic variation, a result of genetic variation, developed during evolution in response to environmental selections. Physalis philadelphica, known as tomatillo in the Solanaceae, is rich in floral and post-floral organ size diversity. However, its genetic variation is unknown. Here P. philadelphica was classified into three groups with large, intermediate, and small reproductive organ size, and a positive correlation was observed between floral organ and berry sizes. Through cDNA-amplified fragment length polymorphism (AFLP) analyses, 263 differentially expressed transcript-derived fragments (TDFs) were isolated from two accessions with different floral organ sizes. The genes encode various transcription factors, protein kinases, and enzymes, and they displayed multiple expression patterns during floral development, indicating a complexity in the genetic basis of phenotypic variation. Detailed expression analyses revealed that they were differentially expressed during floral and post-floral development, implying that they have roles in the development of flowers and fruits. Expression of three genes was further monitored in 26 accessions, and in particular the expression variation of Pp30, encoding an AP2-like transcription factor, correlates well with the observed phenotypic variations, which strongly supports an essential role for the gene in the natural variation of floral and post-floral organ size in Physalis. The results suggest that alteration in the expression pattern of a few key regulatory genes in the developmental process may be an important source of genetic variations that lead to natural variation in morphological traits.

  20. Genetic variation of natural antibodies in milk of Dutch Holstein-Friesian cows.

    PubMed

    Ploegaert, T C W; Wijga, S; Tijhaar, E; van der Poel, J J; Lam, T J G M; Savelkoul, H F J; Parmentier, H K; van Arendonk, J A M

    2010-11-01

    Defense mechanisms of dairy cows against diseases partly rest on their naturally present disease resistance capacity. Natural antibodies (NAb) form a soluble part of the innate immune system, being defined as antibodies circulating in animals without prior intentional antigenic stimulation. Genetic selection on NAb titers in milk, therefore, might improve disease resistance. We estimated genetic parameters of NAb titers binding lipopolysaccharide, lipoteichoic acid (LTA), peptidoglycan, and keyhole limpet hemocyanin, and titers of the NAb isotypes IgG1, IgM, and IgA binding LTA in milk of Dutch Holstein-Friesian heifers. Natural antibody titers were measured in 1 milk sample from each of 1,939 Holstein-Friesian heifers and used for estimating genetic parameters of NAb titers. The data show that phenotypic variation exists among heifers in NAb titers binding lipopolysaccharide, LTA, peptidoglycan, and keyhole limpet hemocyanin, and the NAb isotypes IgG1, IgM, and IgA binding LTA in milk. High genetic correlations among NAb (ranging from 0.45 to 0.99) indicated a common genetic basis for the levels of different NAb in bovine milk. Intra-herd heritability estimates for NAb ranged from 0.10 to 0.53. The results indicated that NAb levels have potential for genetic selection. Copyright © 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  1. Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination

    PubMed Central

    Ziolkowski, Piotr A.; Underwood, Charles J.; Lambing, Christophe; Martinez-Garcia, Marina; Lawrence, Emma J.; Ziolkowska, Liliana; Griffin, Catherine; Choi, Kyuha; Franklin, F. Chris H.; Martienssen, Robert A.; Henderson, Ian R.

    2017-01-01

    During meiosis, homologous chromosomes undergo crossover recombination, which creates genetic diversity and balances homolog segregation. Despite these critical functions, crossover frequency varies extensively within and between species. Although natural crossover recombination modifier loci have been detected in plants, causal genes have remained elusive. Using natural Arabidopsis thaliana accessions, we identified two major recombination quantitative trait loci (rQTLs) that explain 56.9% of crossover variation in Col×Ler F2 populations. We mapped rQTL1 to semidominant polymorphisms in HEI10, which encodes a conserved ubiquitin E3 ligase that regulates crossovers. Null hei10 mutants are haploinsufficient, and, using genome-wide mapping and immunocytology, we show that transformation of additional HEI10 copies is sufficient to more than double euchromatic crossovers. However, heterochromatic centromeres remained recombination-suppressed. The strongest HEI10-mediated crossover increases occur in subtelomeric euchromatin, which is reminiscent of sex differences in Arabidopsis recombination. Our work reveals that HEI10 naturally limits Arabidopsis crossovers and has the potential to influence the response to selection. PMID:28223312

  2. 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

  3. 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

  4. 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…

  5. 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…

  6. Super-emitters in natural gas infrastructure are caused by abnormal process conditions

    PubMed Central

    Zavala-Araiza, Daniel; Alvarez, Ramón A; Lyon, David R.; Allen, David T.; Marchese, Anthony J.; Zimmerle, Daniel J.; Hamburg, Steven P.

    2017-01-01

    Effectively mitigating methane emissions from the natural gas supply chain requires addressing the disproportionate influence of high-emitting sources. Here we use a Monte Carlo simulation to aggregate methane emissions from all components on natural gas production sites in the Barnett Shale production region (Texas). Our total emission estimates are two-thirds of those derived from independent site-based measurements. Although some high-emitting operations occur by design (condensate flashing and liquid unloadings), they occur more than an order of magnitude less frequently than required to explain the reported frequency at which high site-based emissions are observed. We conclude that the occurrence of abnormal process conditions (for example, malfunctions upstream of the point of emissions; equipment issues) cause additional emissions that explain the gap between component-based and site-based emissions. Such abnormal conditions can cause a substantial proportion of a site's gas production to be emitted to the atmosphere and are the defining attribute of super-emitting sites. PMID:28091528

  7. Super-emitters in natural gas infrastructure are caused by abnormal process conditions

    NASA Astrophysics Data System (ADS)

    Zavala-Araiza, Daniel; Alvarez, Ramón A.; Lyon, David R.; Allen, David T.; Marchese, Anthony J.; Zimmerle, Daniel J.; Hamburg, Steven P.

    2017-01-01

    Effectively mitigating methane emissions from the natural gas supply chain requires addressing the disproportionate influence of high-emitting sources. Here we use a Monte Carlo simulation to aggregate methane emissions from all components on natural gas production sites in the Barnett Shale production region (Texas). Our total emission estimates are two-thirds of those derived from independent site-based measurements. Although some high-emitting operations occur by design (condensate flashing and liquid unloadings), they occur more than an order of magnitude less frequently than required to explain the reported frequency at which high site-based emissions are observed. We conclude that the occurrence of abnormal process conditions (for example, malfunctions upstream of the point of emissions; equipment issues) cause additional emissions that explain the gap between component-based and site-based emissions. Such abnormal conditions can cause a substantial proportion of a site's gas production to be emitted to the atmosphere and are the defining attribute of super-emitting sites.

  8. Super-emitters in natural gas infrastructure are caused by abnormal process conditions.

    PubMed

    Zavala-Araiza, Daniel; Alvarez, Ramón A; Lyon, David R; Allen, David T; Marchese, Anthony J; Zimmerle, Daniel J; Hamburg, Steven P

    2017-01-16

    Effectively mitigating methane emissions from the natural gas supply chain requires addressing the disproportionate influence of high-emitting sources. Here we use a Monte Carlo simulation to aggregate methane emissions from all components on natural gas production sites in the Barnett Shale production region (Texas). Our total emission estimates are two-thirds of those derived from independent site-based measurements. Although some high-emitting operations occur by design (condensate flashing and liquid unloadings), they occur more than an order of magnitude less frequently than required to explain the reported frequency at which high site-based emissions are observed. We conclude that the occurrence of abnormal process conditions (for example, malfunctions upstream of the point of emissions; equipment issues) cause additional emissions that explain the gap between component-based and site-based emissions. Such abnormal conditions can cause a substantial proportion of a site's gas production to be emitted to the atmosphere and are the defining attribute of super-emitting sites.

  9. Antimony Isotope Variations in Natural Systems Determined by MC-ICP-MS

    NASA Astrophysics Data System (ADS)

    Ludden, J.; Rouxel, O.; Fouquet, Y.

    2001-12-01

    Sb has two stable isotopes of mass 121 and 123 with average abundance of 57.362% and 42.638% respectively and to date no geochemical or cosmochemical investigations of the variations of these isotopes have been attempted. In fact, the development of Sb isotope measurements for biogeochemical studies is challenging as Sb isotopes have a low percentage mass differences (1.6%) precluding large mass fractionation and Sb is a trace element below 100 ng/g for most geological samples and below 100 ng/l for seawater. However, it is anticipated that the redox changes of Sb(V) and Sb(III) species as well as biological activity and Sb volatilization or transport in hydrothermal systems can produce significant isotope fractionation in natural systems. The isotopic analyses of Sb have been performed using a continuous flow hydride generation system coupled to a Micromass MC-ICP-MS and the instrumental mass fractionation is corrected using a standard-sample bracketing approach. Total Sb, as well as Sb(III) and Sb(V) aqueous species are chemically purified prior to HG-MC-ICP-MS analysis. Using this analytical scheme, the minimum Sb required per analysis is 10 ng and the estimated external precision of the 123Sb/121Sb isotope ratio is 0.4 ɛ -units (2σ ). The data are reported relative to our internal standards (MERCK elemental standard solution). The isotopic fractionation factors between the coexisting species Sb(III) and Sb(V) have been investigated both on-line and after chemical separation. For the kinetic reduction experiment of Sb(V), the reducing agent used was KI as classically used for Sb(V) reduction and we obtained an instantaneous fractionation factor of 8.6 ɛ -units. For off-line experiments, we separated Sb(III) from a partially oxidized Sb solution and obtained a fractionation factor ranging from 5 to 6 ɛ -units. Preliminary results on Sb isotopic composition of selected terrestrial materials including seawater, soils, sediments and hydrothermal sulfides have

  10. Natural variation in maternal care shapes adult social behavior in rats.

    PubMed

    Starr-Phillips, Emily J; Beery, Annaliese K

    2014-07-01

    Features of the early postnatal environment profoundly shape later physical and behavioral phenotypes. The amount of licking/grooming that rat dams direct towards their offspring has durable consequences, including behavioral and physiological dimensions of stress reactivity, cognition, and reproductive behavior. We examined how natural variation in maternal care alters social behavior in adult offspring and how this relates to anxiety behavior and oxytocin receptor density. Male and female offspring of mothers who received high levels of licking spent significantly more time in social contact with unfamiliar individuals than did offspring whose dams provided less grooming. Reduced anxiety behavior was associated with greater social interaction. No differences in oxytocin receptor binding assessed by (125) I-OVTA autoradiography were detected between groups. The present investigation characterizes a novel impact of maternal care on adult social interaction behavior, replicates anxiety behavior differences, and illustrates connections between social behavior and anxiety in adulthood across maternal treatment groups.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  12. 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

  13. Genetic variation detected by RAPD markers in natural populations of babassu palm (Attalea speciosa Mart.).

    PubMed

    Santos, M F; Damasceno-Silva, K J; Carvalhaes, M A; Lima, P S C

    2015-06-10

    The purpose of this study was to analyze the effects of management on the genetic structure of natural populations of Attalea speciosa in the State of Piauí, Brazil, using random-amplified polymorphic DNA (RAPD) markers. Three babassu populations under different management systems were selected. Polymerase chain reactions were performed for 20 RAPD primers. A total of 146 bands were generated, 141 of which were polymorphic (96.58%), with a variation of 4 and 12 loci and an average of 7 bands per primer. A dendrogram revealed a clear separation between the three populations (0.57). Data reliability and node consistency were verified by bootstrap values and the cophenetic correlation coefficient (88.15%). Coefficients of similarity between pairs of genotypes ranged from 0.26 to 0.86, with a mean of 0.57. Nei's genetic diversity index (HE) value of the population sampled in Teresina was 0.212, of Esperantina it was 0.195, and of José de Freitas it was 0.207. After the HE was decomposed, the complete diversity was found to be 0.3213. Genetic differentiation between populations was 0.362, and the estimation of gene flow between populations was low (0.879). Analysis of molecular variance revealed that 59.52% of the variation was contained within populations, and 40.48% was between populations. RAPD markers were effective for genetic diversity analysis within and between natural babassu populations, and exhibited a high level of polymorphism. Genetic diversity was the highest within populations; variability was lower in the managed populations than in the undisturbed populations.

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

    PubMed Central

    2014-01-01

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

  15. Natural Variation in Brachypodium Links Vernalization and Flowering Time Loci as Major Flowering Determinants1[OPEN

    PubMed Central

    Corke, Fiona M.K.; Opanowicz, Magdalena; Hernández-Pinzón, Inmaculada

    2017-01-01

    The domestication of plants is underscored by the selection of agriculturally favorable developmental traits, including flowering time, which resulted in the creation of varieties with altered growth habits. Research into the pathways underlying these growth habits in cereals has highlighted the role of three main flowering regulators: VERNALIZATION1 (VRN1), VRN2, and FLOWERING LOCUS T (FT). Previous reverse genetic studies suggested that the roles of VRN1 and FT are conserved in Brachypodium distachyon yet identified considerable ambiguity surrounding the role of VRN2. To investigate the natural diversity governing flowering time pathways in a nondomesticated grass, the reference B. distachyon accession Bd21 was crossed with the vernalization-dependent accession ABR6. Resequencing of ABR6 allowed the creation of a single-nucleotide polymorphism-based genetic map at the F4 stage of the mapping population. Flowering time was evaluated in F4:5 families in five environmental conditions, and three major loci were found to govern flowering time. Interestingly, two of these loci colocalize with the B. distachyon homologs of the major flowering pathway genes VRN2 and FT, whereas no linkage was observed at VRN1. Characterization of these candidates identified sequence and expression variation between the two parental genotypes, which may explain the contrasting growth habits. However, the identification of additional quantitative trait loci suggests that greater complexity underlies flowering time in this nondomesticated system. Studying the interaction of these regulators in B. distachyon provides insights into the evolutionary context of flowering time regulation in the Poaceae as well as elucidates the way humans have utilized the natural variation present in grasses to create modern temperate cereals. PMID:27650449

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2014-07-01

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

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

    PubMed

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

    2015-03-24

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  3. Natural variation for drought-response traits in the Mimulus guttatus species complex.

    PubMed

    Wu, Carrie A; Lowry, David B; Nutter, Laura I; Willis, John H

    2010-01-01

    Soil moisture is a key factor affecting plant abundance and distribution, both across and within species. In response to water limitation, plants have evolved numerous morphological, physiological, and phenological adaptations. In both well-watered and water-limited conditions, we identified considerable natural variation in drought-related whole-plant and leaf-level traits among closely related members of the Mimulus guttatus species complex that occupy a diversity of habitats in the field. The self-fertilizing Mimulus nasutus and serpentine-endemic Mimulus nudatus demonstrated the overall greatest tolerance to soil water limitation, exhibiting the smallest reduction in seed set relative to well-watered conditions. This may be due in part to early flowering, faster fruit development, and low stomatal density. In contrast, flowering of coastal M. guttatus was so delayed that it precluded any seed production in water-limited conditions. This range of phenotypic responses to soil water deficit in Mimulus, coupled with developing genomic resources, holds considerable promise for identifying genomic variation responsible for adaptive responses to soil water availability.

  4. Variations in normal color vision. V. Simulations of adaptation to natural color environments.

    PubMed

    Juricevic, Igor; Webster, Michael A

    2009-01-01

    Modern accounts of color appearance differ in whether they assume that the perceptual primaries (e.g., white and the unique hues of red, green, blue, and yellow) correspond to unique states determined by the spectral sensitivities of the observer or by the spectral statistics of the environment. We examined the interaction between observers and their environments by asking how color perception should vary if appearance depends on fixed responses in a set of color channels, when the sensitivities of these channels are adapted in plausible ways to different environments. Adaptation was modeled as gain changes in the cones and in multiple postreceptoral channels tuned to different directions in color-luminance space. Gains were adjusted so that the average channel responses were equated across two environments or for the same environment during different seasons, based on sets of natural outdoor scenes (Webster et al., 2007). Because of adaptation, even observers with a shared underlying physiology should perceive color in significantly and systematically different ways when they are exposed to and thus adapted by different contexts. These include differences in achromatic settings (owing to variations in the average chromaticity of locations) and differences in perceived hue (because of differences in scene contrasts). Modeling these changes provides a way of simulating how colors might be experienced by individuals in different color environments and provides a measure of how much color appearance might be modulated for a given observer by variations in the environment.

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

    PubMed Central

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

    2013-01-01

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

  6. Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish.

    PubMed

    Fraser, Dylan J; Debes, Paul V; Bernatchez, Louis; Hutchings, Jeffrey A

    2014-09-07

    Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

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

    PubMed

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

    2015-01-16

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

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

    PubMed

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

    2013-01-01

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

  9. 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.

  10. 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.

  11. Natural variation in an ABC transporter gene associated with seed size evolution in tomato species.

    PubMed

    Orsi, Cintia Hotta; Tanksley, Steven D

    2009-01-01

    Seed size is a key determinant of evolutionary fitness in plants and is a trait that often undergoes tremendous changes during crop domestication. Seed size is most often quantitatively inherited, and it has been shown that Sw4.1 is one of the most significant quantitative trait loci (QTLs) underlying the evolution of seed size in the genus Solanum-especially in species related to the cultivated tomato. Using a combination of genetic, developmental, molecular, and transgenic techniques, we have pinpointed the cause of the Sw4.1 QTL to a gene encoding an ABC transporter gene. This gene exerts its control on seed size, not through the maternal plant, but rather via gene expression in the developing zygote. Phenotypic effects of allelic variation at Sw4.1 are manifested early in seed development at stages corresponding to the rapid deposition of starch and lipids into the endospermic cells. Through synteny, we have identified the Arabidopsis Sw4.1 ortholog. Mutagenesis has revealed that this ortholog is associated with seed length variation and fatty acid deposition in seeds, raising the possibility that the ABC transporter may modulate seed size variation in other species. Transcription studies show that the ABC transporter gene is expressed not only in seeds, but also in other tissues (leaves and roots) and, thus, may perform functions in parts of the plants other than developing seeds. Cloning and characterization of the Sw4.1 QTL gives new insight into how plants change seed during evolution and may open future opportunities for modulating seed size in crop plants for human purposes.

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

    DOE PAGES

    Strauch, Renee C.; Svedin, Elisabeth; Dilkes, Brian; ...

    2015-08-31

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

  13. Neutrons reveal how nature uses structural themes and variation in biological regulation

    NASA Astrophysics Data System (ADS)

    Trewhella, Jill

    2006-11-01

    Healthy cellular function requires tight regulation of a multitude of bio-molecular interactions and processes, often in response to external stimuli. In achieving this regulation, nature uses a number of ‘second messengers’ that are released inside cells in response to first messengers, such as hormones that bind to the cell surface. Divalent calcium and cyclic nucleotides, like cAMP, are among nature's second messengers that bind to receptor proteins inside cells order to regulate the activities of various targets, including many protein kinases. Kinases are enzymes that catalyze the attachment of phosphate groups to proteins in order to modulate their functions. We have been using neutron contrast variation and small-angle solution scattering to study the interactions of the second messenger receptor proteins and their regulatory targets in order to understand the structural basis for these complex processes that use a number of common structural motifs to accomplish highly regulated function. Our most recent work has focused on the different isoforms of the cAMP-dependent protein kinase and the muscle regulatory complex troponin.

  14. Variation in performance of surfactant loading and resulting nitrate removal among four selected natural zeolites.

    PubMed

    Guan, Huade; Bestland, Erick; Zhu, Chuanyu; Zhu, Honglin; Albertsdottir, Dora; Hutson, John; Simmons, Craig T; Ginic-Markovic, Milena; Tao, Xian; Ellis, Amanda V

    2010-11-15

    Surfactant modified zeolites (SMZs) have the capacity to target various types of water contaminants at relatively low cost and thus are being increasingly considered for use in improving water quality. It is important to know the surfactant loading performance of a zeolite before it is put into application. In this work we compare the loading capacity of a surfactant, hexadecyltrimethylammonium bromide (HDTMA-Br), onto four natural zeolites obtained from specific locations in the USA, Croatia, China, and Australia. The surfactant loading is examined using thermogravimetric analysis (TGA), Fourier transform infrared (FT-IR) spectroscopy, and Raman spectroscopy. We then compare the resulting SMZs performance in removing nitrate from water. Results show that TGA is useful to determine the HDTMA loading capacity on natural zeolites. It is also useful to distinguish between a HDTMA bi-layer and a HDTMA mono-layer on the SMZ surface, which has not been previously reported in the literature. TGA results infer that HDTMA (bi-layer) loading decreases in the order of US zeolite>Croatian zeolite>Chinese zeolite>Australian zeolite. This order of loading explains variation in performance of nitrate removal between the four SMZs. The SMZs remove 8-18 times more nitrate than the raw zeolites. SMZs prepared from the selected US and Croatian zeolites were more efficient in nitrate removal than the two zeolites commercially obtained from Australia and China. Copyright © 2010 Elsevier B.V. All rights reserved.

  15. HIV-1 Tat and Viral Latency: What We Can Learn from Naturally Occurring Sequence Variations.

    PubMed

    Kamori, Doreen; Ueno, Takamasa

    2017-01-01

    Despite the effective use of antiretroviral therapy, the remainder of a latently HIV-1-infected reservoir mainly in the resting memory CD4(+) T lymphocyte subset has provided a great setback toward viral eradication. While host transcriptional silencing machinery is thought to play a dominant role in HIV-1 latency, HIV-1 protein such as Tat, may affect both the establishment and the reversal of latency. Indeed, mutational studies have demonstrated that insufficient Tat transactivation activity can result in impaired transcription of viral genes and the establishment of latency in cell culture experiments. Because Tat protein is one of highly variable proteins within HIV-1 proteome, it is conceivable that naturally occurring Tat mutations may differentially modulate Tat functions, thereby influencing the establishment and/or the reversal of viral latency in vivo. In this mini review, we summarize the recent findings of Tat naturally occurring polymorphisms associating with host immune responses and we highlight the implication of Tat sequence variations in relation to HIV latency.

  16. HIV-1 Tat and Viral Latency: What We Can Learn from Naturally Occurring Sequence Variations

    PubMed Central

    Kamori, Doreen; Ueno, Takamasa

    2017-01-01

    Despite the effective use of antiretroviral therapy, the remainder of a latently HIV-1-infected reservoir mainly in the resting memory CD4+ T lymphocyte subset has provided a great setback toward viral eradication. While host transcriptional silencing machinery is thought to play a dominant role in HIV-1 latency, HIV-1 protein such as Tat, may affect both the establishment and the reversal of latency. Indeed, mutational studies have demonstrated that insufficient Tat transactivation activity can result in impaired transcription of viral genes and the establishment of latency in cell culture experiments. Because Tat protein is one of highly variable proteins within HIV-1 proteome, it is conceivable that naturally occurring Tat mutations may differentially modulate Tat functions, thereby influencing the establishment and/or the reversal of viral latency in vivo. In this mini review, we summarize the recent findings of Tat naturally occurring polymorphisms associating with host immune responses and we highlight the implication of Tat sequence variations in relation to HIV latency. PMID:28194140

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  1. The Expanding Family of Natural Anion Channelrhodopsins Reveals Large Variations in Kinetics, Conductance, and Spectral Sensitivity

    PubMed Central

    Govorunova, Elena G.; Sineshchekov, Oleg A.; Rodarte, Elsa M.; Janz, Roger; Morelle, Olivier; Melkonian, Michael; Wong, Gane K.-S.; Spudich, John L.

    2017-01-01

    Natural anion channelrhodopsins (ACRs) discovered in the cryptophyte alga Guillardia theta generate large hyperpolarizing currents at membrane potentials above the Nernst equilibrium potential for Cl− and thus can be used as efficient inhibitory tools for optogenetics. We have identified and characterized new ACR homologs in different cryptophyte species, showing that all of them are anion-selective, and thus expanded this protein family to 20 functionally confirmed members. Sequence comparison of natural ACRs and engineered Cl−-conducting mutants of cation channelrhodopsins (CCRs) showed radical differences in their anion selectivity filters. In particular, the Glu90 residue in channelrhodopsin 2, which needed to be mutated to a neutral or alkaline residue to confer anion selectivity to CCRs, is nevertheless conserved in all of the ACRs identified. The new ACRs showed a large variation of the amplitude, kinetics, and spectral sensitivity of their photocurrents. A notable variant, designated “ZipACR”, is particularly promising for inhibitory optogenetics because of its combination of larger current amplitudes than those of previously reported ACRs and an unprecedentedly fast conductance cycle (current half-decay time 2–4 ms depending on voltage). ZipACR expressed in cultured mouse hippocampal neurons enabled precise photoinhibition of individual spikes in trains of up to 50 Hz frequency. PMID:28256618

  2. Inter-clinic variation in the chances of natural conception of subfertile couples.

    PubMed

    Tjon-Kon-Fat, R I; Lar, D N; Steyerberg, E W; Broekmans, F J; Hompes, P; Mol, B W J; Steures, P; Bossuyt, P M M; van der Veen, F; van der Steeg, J W; Eijkemans, M J C

    2013-05-01

    for female age, duration of subfertility, percentage of progressive motile sperm, primary/secondary subfertility and post-coital test (P < 0.001). Adjusted hazard ratios and EB estimates ranged from 0.50 to 2.21 and 0.58 to 1.53, respectively. Among the 21 clinics, there were 4 university hospitals, 10 non-university hospitals with an ACU and 7 non-university hospitals without an ACU. In the multivariable analysis, the type of clinic was not significant (P = 0.11). Calibration gave an average intercept of -0.25 (95% range: -1.04-0.53) and average slope of 0.81 (95% range: 0.03-1.60). Six clinics had a negative intercept that differed significantly from zero and three clinics had a negative or positive slope that differed significantly from one. A more extensive model including more predictors could give less variation in the differences between the clinics. Variation in work-up protocol between clinics could also have played a role. In fertility prediction research the Cox proportional hazards regression is the most widely used statistical model, but as the underlying assumptions have rarely been evaluated, this model could lead to biased outcomes. Our findings suggest that the synthesis model to predict natural conception is useful overall in clinical practice but in a minority of clinics the model is not well calibrated. Updating the synthesis model to include a center-specific baseline chance might improve the synthesis model for certain clinics. The study (on which this secondary data-analysis was based) was supported by grant 945/12/002 from ZonMW, the Netherlands Organization for Health Research and Development, The Hague, the Netherlands.

  3. Epilepsy-causing sequence variations in SIK1 disrupt synaptic activity response gene expression and affect neuronal morphology.

    PubMed

    Pröschel, Christoph; Hansen, Jeanne N; Ali, Adil; Tuttle, Emily; Lacagnina, Michelle; Buscaglia, Georgia; Halterman, Marc W; Paciorkowski, Alex R

    2017-02-01

    SIK1 syndrome is a newly described developmental epilepsy disorder caused by heterozygous mutations in the salt-inducible kinase SIK1. To better understand the pathophysiology of SIK1 syndrome, we studied the effects of SIK1 pathogenic sequence variations in human neurons. Primary human fetal cortical neurons were transfected with a lentiviral vector to overexpress wild-type and mutant SIK1 protein. We evaluated the transcriptional activity of known downstream gene targets in neurons expressing mutant SIK1 compared with wild type. We then assayed neuronal morphology by measuring neurite length, number and branching. Truncating SIK1 sequence variations were associated with abnormal MEF2C transcriptional activity and decreased MEF2C protein levels. Epilepsy-causing SIK1 sequence variations were associated with significantly decreased expression of ARC (activity-regulated cytoskeletal-associated) and other synaptic activity response element genes. Assay of mRNA levels for other MEF2C target genes NR4A1 (Nur77) and NRG1, found significantly, decreased the expression of these genes as well. The missense p.(Pro287Thr) SIK1 sequence variation was associated with abnormal neuronal morphology, with significant decreases in mean neurite length, mean number of neurites and a significant increase in proximal branches compared with wild type. Epilepsy-causing SIK1 sequence variations resulted in abnormalities in the MEF2C-ARC pathway of neuronal development and synapse activity response. This work provides the first insights into the mechanisms of pathogenesis in SIK1 syndrome, and extends the ARX-MEF2C pathway in the pathogenesis of developmental epilepsy.

  4. Natural Variation in Sensitivity to a Loss of Chloroplast Translation in Arabidopsis1[W][OPEN

    PubMed Central

    Parker, Nicole; Wang, Yixing; Meinke, David

    2014-01-01

    Mutations that eliminate chloroplast translation in Arabidopsis (Arabidopsis thaliana) result in embryo lethality. The stage of embryo arrest, however, can be influenced by genetic background. To identify genes responsible for improved growth in the absence of chloroplast translation, we examined seedling responses of different Arabidopsis accessions on spectinomycin, an inhibitor of chloroplast translation, and crossed the most tolerant accessions with embryo-defective mutants disrupted in chloroplast ribosomal proteins generated in a sensitive background. The results indicate that tolerance is mediated by ACC2, a duplicated nuclear gene that targets homomeric acetyl-coenzyme A carboxylase to plastids, where the multidomain protein can participate in fatty acid biosynthesis. In the presence of functional ACC2, tolerance is enhanced by a second locus that maps to chromosome 5 and heightened by additional genetic modifiers present in the most tolerant accessions. Notably, some of the most sensitive accessions contain nonsense mutations in ACC2, including the “Nossen” line used to generate several of the mutants studied here. Functional ACC2 protein is therefore not required for survival in natural environments, where heteromeric acetyl-coenzyme A carboxylase encoded in part by the chloroplast genome can function instead. This work highlights an interesting example of a tandem gene duplication in Arabidopsis, helps to explain the range of embryo phenotypes found in Arabidopsis mutants disrupted in essential chloroplast functions, addresses the nature of essential proteins encoded by the chloroplast genome, and underscores the value of using natural variation to study the relationship between chloroplast translation, plant metabolism, protein import, and plant development. PMID:25336520

  5. Natural variation in sensitivity to a loss of chloroplast translation in Arabidopsis.

    PubMed

    Parker, Nicole; Wang, Yixing; Meinke, David

    2014-12-01

    Mutations that eliminate chloroplast translation in Arabidopsis (Arabidopsis thaliana) result in embryo lethality. The stage of embryo arrest, however, can be influenced by genetic background. To identify genes responsible for improved growth in the absence of chloroplast translation, we examined seedling responses of different Arabidopsis accessions on spectinomycin, an inhibitor of chloroplast translation, and crossed the most tolerant accessions with embryo-defective mutants disrupted in chloroplast ribosomal proteins generated in a sensitive background. The results indicate that tolerance is mediated by ACC2, a duplicated nuclear gene that targets homomeric acetyl-coenzyme A carboxylase to plastids, where the multidomain protein can participate in fatty acid biosynthesis. In the presence of functional ACC2, tolerance is enhanced by a second locus that maps to chromosome 5 and heightened by additional genetic modifiers present in the most tolerant accessions. Notably, some of the most sensitive accessions contain nonsense mutations in ACC2, including the "Nossen" line used to generate several of the mutants studied here. Functional ACC2 protein is therefore not required for survival in natural environments, where heteromeric acetyl-coenzyme A carboxylase encoded in part by the chloroplast genome can function instead. This work highlights an interesting example of a tandem gene duplication in Arabidopsis, helps to explain the range of embryo phenotypes found in Arabidopsis mutants disrupted in essential chloroplast functions, addresses the nature of essential proteins encoded by the chloroplast genome, and underscores the value of using natural variation to study the relationship between chloroplast translation, plant metabolism, protein import, and plant development.

  6. Natural sleep and its seasonal variations in three pre-industrial societies.

    PubMed

    Yetish, Gandhi; Kaplan, Hillard; Gurven, Michael; Wood, Brian; Pontzer, Herman; Manger, Paul R; Wilson, Charles; McGregor, Ronald; Siegel, Jerome M

    2015-11-02

    How did humans sleep before the modern era? Because the tools to measure sleep under natural conditions were developed long after the invention of the electric devices suspected of delaying and reducing sleep, we investigated sleep in three preindustrial societies [1-3]. We find that all three show similar sleep organization, suggesting that they express core human sleep patterns, most likely characteristic of pre-modern era Homo sapiens. Sleep periods, the times from onset to offset, averaged 6.9-8.5 hr, with sleep durations of 5.7-7.1 hr, amounts near the low end of those industrial societies [4-7]. There was a difference of nearly 1 hr between summer and winter sleep. Daily variation in sleep duration was strongly linked to time of onset, rather than offset. None of these groups began sleep near sunset, onset occurring, on average, 3.3 hr after sunset. Awakening was usually before sunrise. The sleep period consistently occurred during the nighttime period of falling environmental temperature, was not interrupted by extended periods of waking, and terminated, with vasoconstriction, near the nadir of daily ambient temperature. The daily cycle of temperature change, largely eliminated from modern sleep environments, may be a potent natural regulator of sleep. Light exposure was maximal in the morning and greatly decreased at noon, indicating that all three groups seek shade at midday and that light activation of the suprachiasmatic nucleus is maximal in the morning. Napping occurred on <7% of days in winter and <22% of days in summer. Mimicking aspects of the natural environment might be effective in treating certain modern sleep disorders. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Natural variation of piRNA expression affects immunity to transposable elements

    PubMed Central

    Radion, Elizaveta; Mironova, Anastasia; Akulenko, Natalia; Abramov, Yuri; Morgunova, Valeriya; Kordyukova, Maria Y.; Olovnikov, Ivan

    2017-01-01

    In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon He

  8. 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. © 2015 Wiley Periodicals, Inc.

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

    USGS Publications Warehouse

    Garcia, V.; Conway, C.J.

    2009-01-01

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

  10. Finite-element models on spatiotemporal variations in intraplate seismicity caused by postglacial unloading and rebound: Implications for active normal faults in the Basin and Range Province

    NASA Astrophysics Data System (ADS)

    Karow, T.; Hampel, A.

    2007-12-01

    The actively extending Basin and Range Province was covered by numerous pluvial lakes and glaciers on several of the higher ranges during the Last Glacial Maximum (Osburn and Bevis, QSR, 2001). The largest lakes were Lake Bonneville and Lake Lahontan, located in the eastern and western parts of the Basin and Range Province, respectively. Regression of these lakes at the end of last glacial period caused significant isostatic rebound of the lithosphere (Bills et al., JGR, 1994; Bills et al., JGR, 2007). The rebound associated with the regression of Lake Bonneville has been shown, using two-dimensional numerical models, to affect the stress field of the lithosphere and to cause a slip rate increase on the Wasatch normal fault (Hetzel and Hampel, Nature 2005). Here we use three-dimensional finite-element models of normal fault arrays to investigate spatiotemporal variations in the regional stress field and in the rate of normal faulting caused by glacial-interglacial variations of the surface load. Our models indicate that regression of Lake Lahontan but also of smaller lakes and glaciers alter the regional stress field and hence may ultimately affect the intraplate seismicity. Paleoseismological data from faults in the east-central and northern Basin and Range Province seem to support the idea of an increase in seismicity after the Last Glacial Maximum (Friedrich el al., JGR, 2003; Stickney and Bartholomew, BSSA, 1987; Wesnousky et al., JGR, 2005).

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

    PubMed

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

    2014-05-01

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

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

    PubMed

    Brockhurst, Michael A

    2015-06-01

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

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

    NASA Technical Reports Server (NTRS)

    Militello, Carmelo; Felippa, Carlos A.

    1990-01-01

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

  14. Protective effect of natural flavonoids on rat peritoneal macrophages injury caused by asbestos fibers.

    PubMed

    Kostyuk, V A; Potapovich, A I; Speransky, S D; Maslova, G T

    1996-01-01

    Exposure of macrophages to asbestos fibers resulted in enhancement of the production of oxygen radicals, determined by a lucigenin enhanced chemiluminescence (LEC) assay, a formation of thiobarbituric acid reactive substances (TBARS), a LDH release into the incubation mixture, and a rapid lysis of the cells. Rutin (Rut) and quercetin (Qr) were effective in inhibiting LEC, TBARS formation, and reducing peritoneal macrophages injury caused by asbestos. The concentrations pre-treatment of antioxidants that were required to prevent the injury of peritoneal macrophages caused by asbestos by 50% (IC50) were 90 microM and 290 microM for Qr and Rut, respectively. Both flavonoids were found to be oxidized during exposure of peritoneal macrophages to asbestos and the oxidation was SOD sensitive. The efficacy of flavonoids as antioxidant agents as well as superoxide ion scavengers was also evaluated using appropriate model systems, and both quercetin and rutin were found to be effective in scavenging O2.-. These findings indicate that flavonoids are able to prevent the respiratory burst in rat peritoneal macrophages exposed to asbestos at the stage of activated oxygen species generation, mainly as superoxide scavengers. On the basis of this study it was concluded that natural flavonoids quercetin and rutin would be promising drug candidates for a prophylactic asbestos-induced disease.

  15. Relations of Tualatin River water temperatures to natural and human-caused factors

    USGS Publications Warehouse

    Risley, John C.

    1997-01-01

    Aquatic research has long shown that the survival of cold-water fish, such as salmon and trout, decreases markedly as water temperatures increase above a critical threshold, particularly during sensitive life stages of the fish. In an effort to improve the overall health of aquatic ecosystems, the State of Oregon in 1996 adopted a maximum water-temperature standard of 17.8 degrees Celsius (68 degrees Fahrenheit), based on a 7-day moving average of daily maximum temperatures, for most water bodies in the State. Anthropogenic activities are not permitted to raise the temperature of a water body above this level. In the Tualatin River, a tributary of the Willamette River located in northwestern Oregon, water temperatures periodically surpass this threshold during the low-flow summer and fall months.An investigation by the U.S. Geological Survey quantified existing seasonal, diel, and spatial patterns of water temperatures in the main stem of the river, assessed the relation of water temperatures to natural climatic conditions and anthropogenic factors (such as wastewater-treatment-plant effluent and modification of riparian shading), and assessed the impact of various flow management practices on stream temperatures. Half-hourly temperature measurements were recorded at 13 monitoring sites from river mile (RM) 63.9 to RM 3.4 from May to November of 1994. Four synoptic water- temperature surveys also were conducted in the upstream and downstream vicinities of two wastewater-treatment-plant outfalls. Temperature and streamflow time-series data were used to calibrate two dynamic-flow heat-transfer models, DAFLOW-BLTM (RM 63.9-38.4) and CE-QUAL-W2 (RM 38.4-3.4). Simulations from the models provided a basis for approximating 'natural' historical temperature patterns, performing effluent and riparian-shading sensitivity analyses, and evaluating mitigation management scenarios under 1994 climatic conditions. Findings from the investigation included (1) under 'natural

  16. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

    PubMed Central

    Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; Begun, David J.

    2016-01-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

  17. Nucleotide variation of the Est-6 gene region in natural populations of Drosophila melanogaster.

    PubMed Central

    Balakirev, Evgeniy S; Ayala, Francisco J

    2003-01-01

    We have investigated nucleotide polymorphism in the Est-6 gene region in four samples of Drosophila melanogaster derived from natural populations of East Africa (Zimbabwe), Europe (Spain), North America (California), and South America (Venezuela). There are two divergent sequence types in the North and South American samples, which are not perfectly (North America) or not at all (South America) associated with the Est-6 allozyme variation. Less pronounced or no sequence dimorphism occurs in the European and African samples, respectively. The level of nucleotide diversity is highest in the African sample, lower (and similar to each other) in the samples from Europe and North America, and lowest in the sample from South America. The extent of linkage disequilibrium is low in Africa (1.23% significant associations), but much higher in non-African populations (22.59, 21.45, and 37.68% in Europe, North America, and South America, respectively). Tests of neutrality with recombination are significant in non-African samples but not significant in the African sample. We propose that demographic history (bottleneck and admixture of genetically different populations) is the major factor shaping the nucleotide patterns in the Est-6 gene region. However, positive selection modifies the pattern: balanced selection creates elevated levels of nucleotide variation around functionally important (target) polymorphic sites (RsaI-/RsaI+ in the promoter region and F/S in the coding region) in both African and non-African samples; and directional selection, acting during the geographic expansion phase of D. melanogaster, creates an excess of very similar sequences (RsaI- and S allelic lineages, in the promoter and coding regions, respectively) in the non-African samples. PMID:14704175

  18. Fluvial filtering of land-to-ocean fluxes: from natural Holocene variations to Anthropocene

    NASA Astrophysics Data System (ADS)

    Meybeck, Michel; Vörösmarty, Charles

    2005-02-01

    The evolution of river systems and their related fluxes is considered at various time scales: ( i) over the last 18 000 years, under climatic variability control, ( ii) over the last 50 to 200 years (Anthropocene) due to direct human impacts. Natural Holocene variations in time and space depend on ( i) land-to-ocean connections (endorheism, glacial cover, exposure of continental shelf); ( ii) types of natural fluvial filters (e.g., wetlands, lakes, floodplains, estuaries). Anthropocene changes concern ( i) land-ocean connection (e.g., partial to total runoff reduction resulting from water management), ( ii) modification and removal of natural filters, ( iii) creation of new filters, particularly irrigated fields and reservoirs, ( iv) acceleration and/or development of material sources from human activities. The total river basin area directly affected by human activities is of the same order of magnitude ( >40 Mkm) as the total area affected over the last 18 000 years. A tentative analysis of 38 major river systems totaling 55 Mkm is proposed for several criteria: ( i) trajectories of Holocene evolution, ( ii) occurrence of natural fluvial filters, ( iii) present-day fluvial filters: most river basins are unique. Riverine fluxes per unit area are characterized by hot spots that exceed the world average by one order of magnitude. At the Anthropocene (i.e., since 1950), many riverine fluxes have globally increased (sodium, chloride, sulfate, nitrogen, phosphorous, heavy metals), others are stable (calcium, bicarbonate, sediments) or likely to decrease (dissolved silica). Future trajectories of river fluxes will depend on the balance between increased sources of material (e.g., soil erosion, pollution, fertilization), water abstraction for irrigation and the modification of fluvial filters, particularly the occurrence of reservoirs that already intercept half of the water and store at least 30% of river sediment fluxes. In some river systems, retention actually

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  20. Pressure variation assisted fiber extraction and development of high performance natural fiber composites and nanocomposites

    NASA Astrophysics Data System (ADS)

    Markevicius, Gediminas

    It is believed, that due to the large surface areas provided by the nano scale materials, various composite properties could be enhanced when such particles are incorporated into a polymer matrix. There is also a trend of utilizing natural resources or reusing and recycling materials that are already available for the fabrication of the new composite materials. Cellulose is the most abundant natural polymer on the planet, and therefore it is not surprising to be of interest for composite fabrication. Basic structures of cellulose, comprised of long polysaccharide chains, are the building blocks of cellulose nano fibers. Nano fibers are further bound into micro fibrils and macro fibers. Theoretically pure cellulose nano fibers have tremendous strengths, and therefore are some of the most sought after nano particles. The fiber extraction however is a complex task. The ultrasound, which creates pressure variation in the medium, was employed to extract nano-size cellulose particles from microcrystalline cellulose (MCC). The length and the intensity of the cavitations were evaluated. Electron microscopy studies revealed that cellulose nanoparticles were successfully obtained from the MCC after ultrasound treatment of just 30 minutes. Structure of the fractionated cellulose was also analyzed with the help of X-ray diffraction, and its thermal properties were evaluated with the help of differential scanning calorimetry (DSC). Ultrasound treatment performed on the wheat straw, kenaf, and miscanthus particles altered fiber structure as a result of the cavitation. The micro fibers were generated from these materials after they were subjected to NaOH treatment followed by the ultrasound processing. The potential of larger than nano-sized natural fibers to be used for composite fabrication was also explored. The agricultural byproducts, such as wheat or rice straw, as well as other fast growing crops as miscanthus or kenaf, are comprised of three basic polymers. Just like in

  1. Prospective study of the incidence, nature and causes of dispensing errors in community pharmacies.

    PubMed

    Ashcroft, Darren M; Quinlan, Paul; Blenkinsopp, Alison

    2005-05-01

    Each year over 600 million prescription items are dispensed in community pharmacies in England and Wales. Despite this, there is little published evidence relating to dispensing errors and near misses occurring in this setting. This study sought to determine their incidence, nature and causes. Prospective study over a 4-week period in 35 community pharmacies (9 independent pharmacies and 26 chain pharmacies) in the UK. Pharmacists recorded details of all incidents that occurred during the dispensing process, including information about: the stage at which the error was detected; who found the error; who made the error; type of error; reported cause of error and circumstances associated with the error. 125,395 prescribed items were dispensed during the study period and 330 incidents were recorded relating to 310 prescriptions. 280 (84.8%) incidents were classified as a near miss (rate per 10,000 items dispensed=22.33, 95%CI 19.79-25.10), while the remaining 50 (15.2%) were classified as dispensing errors (rate per 10,000 items dispensed=3.99, 95%CI 2.96-5.26). Selection errors were the most common types of incidents (199, 60.3%), followed by labeling (109, 33.0%) and bagging errors (22, 6.6%). Most of the incidents were caused either by misreading the prescription (90, 24.5%), similar drug names (62, 16.8%), selecting the previous drug or dose from the patient's medication record on the pharmacy computer (42, 11.4%) or similar packaging (28, 7.6%). This study has demonstrated that a wide range of medication errors occur in community pharmacies. On average, for every 10,000 items dispensed, there are around 22 near misses and four dispensing errors. Given the current plans for reporting adverse events in the NHS, greater insight into the likely incidence and nature of dispensing errors will be helpful in designing effective risk management strategies in primary care. Copyright (c) 2004 John Wiley & Sons, Ltd.

  2. Shifting patterns of natural variation in the nuclear genome of caenorhabditis elegans.

    PubMed

    Solorzano, Eleanne; Okamoto, Kazufusa; Datla, Pushpa; Sung, Way; Bergeron, R D; Thomas, W K

    2011-06-16

    Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2). The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.In both CB4856 and CB4858, based on a measure of the strength of selection (ka/ks), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, ka/ks values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, ka/ks values differ between chromosomes. The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the ka/ks ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.

  3. Shifting patterns of natural variation in the nuclear genome of caenorhabditis elegans

    PubMed Central

    2011-01-01

    Background Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2). Results The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison. In both CB4856 and CB4858, based on a measure of the strength of selection (ka/ks), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, ka/ks values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, ka/ks values differ between chromosomes. Conclusions The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the ka/ks ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome

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

    SciTech Connect

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

    2015-12-15

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

  5. 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.

  6. 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.

  7. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    1992-01-01

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

  10. Genome Size Variation in Central European Species of Cirsium (Compositae) and their Natural Hybrids

    PubMed Central

    BUREŠ, PETR; WANG, YI-FENG; HOROVÁ, LUCIE; SUDA, JAN

    2004-01-01

    • Background and Aims Nuclear DNA amounts of 12 diploid and one tetraploid taxa and 12 natural interspecific hybrids of Cirsium from 102 populations in the Czech Republic, Austria, Slovakia and Hungary were estimated. • Methods DAPI and PI flow cytometry were used. • Key Results 2C-values of diploid (2n = 34) species varied from 2·14 pg in C. heterophyllum to 3·60 pg in C. eriophorum (1·68-fold difference); the 2C value for the tetraploid C. vulgare was estimated at 5·54 pg. The DNA contents of hybrids were located between the values of their putative parents, although usually closer to the species with the smaller genome. Biennial species of Cirsium possessed larger nuclear DNA amounts than their perennial relatives. Genome size was negatively correlated with Ellenberg's indicator values for continentality and moisture and with eastern limits of distribution. A negative relationship was also detected between the genome size and the tendency to form natural interspecific hybrids. On the contrary, C-values positively corresponded with the spinyness (degree of spinosity). AT frequency ranged from 48·38 % in C. eriophorum to 51·75 % in C. arvense. Significant intraspecific DNA content variation in DAPI sessions was detected in C. acaule (probably due to the presence of B-chromosomes), and in tetraploid C. vulgare. Only the diploid level was confirmed for the Pannonian C. brachycephalum, generally considered to be tetraploid. In addition, triploidy was discovered for the first time in C. rivulare. • Conclusions Considerable differences in nuclear DNA content exist among Central European species of Cirsium on the diploid level. Perennial soft spiny Cirsium species of wet habitats and continental distributions generally have smaller genomes. The hybrids of diploid species remain diploid, and their DNA content is smaller than the mean of the parents. Species with smaller genomes produce interspecific hybrids more frequently. PMID:15292040

  11. Natural variations in expression of regulatory and detoxification related genes under limiting phosphate and arsenate stress in Arabidopsis thaliana

    PubMed Central

    Shukla, Tapsi; Kumar, Smita; Khare, Ria; Tripathi, Rudra D.; Trivedi, Prabodh K.

    2015-01-01

    Abiotic stress including nutrient deficiency and heavy metal toxicity severely affects plant growth, development, and productivity. Genetic variations within and in between species are one of the important factors in establishing interactions and responses of plants with the environment. In the recent past, natural variations in Arabidopsis thaliana have been used to understand plant development and response toward different stresses at genetic level. Phosphorus deficiency negatively affects plant growth and metabolism and modulates expression of the genes involved in Pi homeostasis. Arsenate, As(V), a chemical analog of Pi, is taken up by the plants via phosphate transport system. Studies suggest that during Pi deficiency, enhanced As(V) uptake leads to increased toxicity in plants. Here, the natural variations in Arabidopsis have been utilized to study the As(V) stress response under limiting Pi condition. The primary root length was compared to identify differential response of three Arabidopsis accessions (Col-0, Sij-1, and Slavi-1) under limiting Pi and As(V) stress. To study the molecular mechanisms responsible for the differential response, comprehensive expression profiling of the genes involved in uptake, detoxification, and regulatory mechanisms was carried out. Analysis suggests genetic variation-dependent regulatory mechanisms may affect differential response of Arabidopsis natural variants toward As(V) stress under limiting Pi condition. Therefore, it is hypothesized that detailed analysis of the natural variations under multiple stress conditions might help in the better understanding of the biological processes involved in stress tolerance and adaptation. PMID:26557133

  12. Perturbations of flows of incompressible nonlinearly viscous and viscoplastic fluids caused by variations in material functions

    NASA Astrophysics Data System (ADS)

    Georgievskii, D. V.

    2007-06-01

    Material functions are necessary element of the constitutive relations determining any model of continuum. These functions can be defined as a collection of objects from which the operator of constitutive relations can be reconstructed completely. The material functions are found in test experiments and show the differences between a given medium and other media in the framework of the same model [1]. The "test experiment theory" is an important part of modern experimental mechanics. Just as in any experiment, from determining the viscosity coefficient by using the rotational viscosimeters to constructing the yield surface by using machines combined loading, the material functions are determined with an unavoidable error. For example, experimenters know that, in experiments with arbitrary accuracy, the moduli of elasticity can only be measured with an unimprovable tolerance of about 7%. Starting already from [2], the investigators' attention has been repeatedly drawn to the fact that it is necessary to take into account this tolerance in determining the material constants, functions, and functionals in problems of mechanics and especially in analyzing the stability of deformation processes. Mathematically, this means that problems of stability under perturbations of the initial data, external constantly acting forces, domain boundaries, etc. should be supplemented with the assumption that the material functions have unknown perturbations of a certain class [3]. The variations of material functions in the framework of the linearized stability theory were considered in [2, 4, 5]. In what follows, we study isotropic tensor functions in the most general case of scalar and tensor nonlinearity. These functions are assigned the meaning of constitutive relations between the stress and strain rate tensors in continuum. These constitutive relations contain scalar material functions of invariants on which, as follows from the above, some variations proportional to a small

  13. Haptoglobin (HP) and Haptoglobin-related protein (HPR) copy number variation, natural selection, and trypanosomiasis.

    PubMed

    Hardwick, Robert J; Ménard, Anne; Sironi, Manuela; Milet, Jacqueline; Garcia, André; Sese, Claude; Yang, Fengtang; Fu, Beiyuan; Courtin, David; Hollox, Edward J

    2014-01-01

    Haptoglobin, coded by the HP gene, is a plasma protein that acts as a scavenger for free heme, and haptoglobin-related protein (coded by the HPR gene) forms part of the trypanolytic factor TLF-1, together with apolipoprotein L1 (ApoL1). We analyse the polymorphic small intragenic duplication of the HP gene, with alleles Hp1 and Hp2, in 52 populations, and find no evidence for natural selection either from extended haplotype analysis or from correlation with pathogen richness matrices. Using fiber-FISH, the paralog ratio test, and array-CGH data, we also confirm that the HPR gene is copy number variable, with duplication of the whole HPR gene at polymorphic frequencies in west and central Africa, up to an allele frequency of 15 %. The geographical distribution of the HPR duplication allele overlaps the region where the pathogen causing chronic human African trypanosomiasis, Trypanosoma brucei gambiense, is endemic. The HPR duplication has occurred on one SNP haplotype, but there is no strong evidence of extended homozygosity, a characteristic of recent natural selection. The HPR duplication shows a slight, non-significant undertransmission to human African trypanosomiasis-affected children of unaffected parents in the Democratic Republic of Congo. However, taken together with alleles of APOL1, there is an overall significant undertransmission of putative protective alleles to human African trypanosomiasis-affected children.

  14. Reproductive biology and pollination mechanisms of Epidendrum secundum (Orchidaceae). Floral variation: a consequence of natural hybridization?

    PubMed

    Pansarin, E R; Amaral, M C E

    2008-03-01

    The phenology, flower morphology, pollination mechanism and reproductive biology of Epidendrum secundum were studied in a semi-deciduous forest at the Serra do Japi (SJ), and in the Atlantic rain forest of Picinguaba, both natural reserves in the State of São Paulo, southeastern Brazil. E. secundum flowers all year round, with a flowering peak between September and January. This species is either a lithophytic or terrestrial herb in the SJ, whereas, in Picinguaba, it grows mainly in disturbed areas along roadsides. E. secundum is pollinated by several species of diurnal Lepidoptera at both study sites. In Picinguaba, where E. secundum is sympatric with E. fulgens and both share the same pollinators, pollen transference between these two species was recorded. E. secundum is self-compatible but pollinator-dependent. It is inter-compatible with E. fulgens, producing fertile seeds. In contrast to the population of the SJ, in the Picinguaba region, floral morphology is quite variable among plants and some individuals present flowers with characteristics in-between both sympatric species, suggesting that natural hybridization occasionally occurs. The anthropogenic perturbation is probably the cause of the occurrence of E. secundum in the Picinguaba region, enabling its contact with E. fulgens.

  15. The decline in living kidney donation in the United States: random variation or cause for concern?

    PubMed

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

    2013-11-15

    The annual number of living kidney donors in the United States peaked at 6647 in 2004. The preceding decade saw a 120% increase in living kidney donation. However, since 2004, living kidney donation has declined in all but 1 year, resulting in a 13% decline in the annual number of living kidney donors from 2004 to 2011. The proportional decline in living kidney donation has been more pronounced among men, blacks, younger adults, siblings, and parents. In this article, we explore several possible explanations for the decline in living kidney donation, including an increase in medical unsuitability, an aging transplant patient population, financial disincentives, public policies, and shifting practice patterns, among others. We conclude that the decline in living donation is not merely reflective of random variation but one that warrants action by the transplant centers, the broader transplant community, and the state and national governments.

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

    PubMed

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

    2014-11-01

    The case is presented of a 42 year old woman who had been suffering a loss of strength in her left leg for six years. After an extensive diagnostic study, the pain was classified as of functional origin by a diagnosis of exclusion. Since then, the patient has tried all kind of drug treatments and conservative techniques without improvement. After an exhaustive study with inconclusive results, the case was discussed with the Orthopaedics Department, who performed an exploratory surgery, in which compression of the sciatic nerve due to an anatomical variation of the piriformis muscle was observed. Part of the muscle was resected during surgery and the sciatic nerve was freed, after which the patient experienced a great improvement. Copyright © 2013 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2008-01-01

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

  19. The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention

    PubMed Central

    Akhund-Zade, Jamilla; Bergland, Alan O.; Crowe, Sarah O.; Unckless, Robert L.

    2017-01-01

    Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A. Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention. PMID:28042107

  20. The genetic basis of natural variation for iron homeostasis in the maize IBM population.

    PubMed

    Benke, Andreas; Urbany, Claude; Marsian, Johanna; Shi, Rongli; Wirén, Nicolaus von; Stich, Benjamin

    2014-01-09

    Iron (Fe) deficiency symptoms in maize (Zea mays subsp. mays) express as leaf chlorosis, growth retardation, as well as yield reduction and are typically observed when plants grow in calcareous soils at alkaline pH. To improve our understanding of genotypical variability in the tolerance to Fe deficiency-induced chlorosis, the objectives of this study were to (i) determine the natural genetic variation of traits related to Fe homeostasis in the maize intermated B73 × Mo17 (IBM) population, (ii) to identify quantitative trait loci (QTLs) for these traits, and (iii) to analyze expression levels of genes known to be involved in Fe homeostasis as well as of candidate genes obtained from the QTL analysis. In hydroponically-grown maize, a total of 47 and 39 QTLs were detected for the traits recorded under limited and adequate supply of Fe, respectively. From the QTL results, we were able to identify new putative candidate genes involved in Fe homeostasis under a deficient or adequate Fe nutritional status, like Ferredoxin class gene, putative ferredoxin PETF, metal tolerance protein MTP4, and MTP8. Furthermore, our expression analysis of candidate genes suggested the importance of trans-acting regulation for 2'-deoxymugineic acid synthase 1 (DMAS1), nicotianamine synthase (NAS3, NAS1), formate dehydrogenase 1 (FDH1), methylthioribose-1-phosphate isomerase (IDI2), aspartate/tyrosine/aromatic aminotransferase (IDI4), and methylthioribose kinase (MTK).

  1. The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention.

    PubMed

    Akhund-Zade, Jamilla; Bergland, Alan O; Crowe, Sarah O; Unckless, Robert L

    2017-01-01

    Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention.

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

    NASA Astrophysics Data System (ADS)

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

    1989-07-01

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

  3. Ionic nature of burn-induced variation potential in wheat leaves.

    PubMed

    Katicheva, Lyubov; Sukhov, Vladimir; Akinchits, Elena; Vodeneev, Vladimir

    2014-08-01

    Variation potential (VP) in higher plants cells is a transitory depolarization of the plasma membrane occurring in response to external damage. The effects of VP on different physiological processes are actively studied, but little is known about their ionic nature, which limits the interpretation of VP-induced functional changes. It is thought that VP generation is based on transient inactivation of plasma membrane proton pumps and is not connected to passive ionic fluxes. To study burn-induced VP in wheat seedlings, we measured membrane electric potential and cell input resistance. Cell input resistance decreased during VP generation, indicating that ionic channels were activated. In addition, VP amplitude decreased when the extracellular calcium concentration was lowered. When anion channels were blocked by ethacrynic acid addition, the VP had poor depolarization speed and amplitude. A decrease in the chlorine gradient by extracellular chlorine concentration shift leads to lowering of the VP amplitude and depolarization speed. This result indicates the role of chlorine efflux in depolarization phase formation. The VP repolarization is connected to potassium ion efflux, that is confirmed by repolarization suppression under addition of the potassium channel blocker tetraethylammonium (TEA) and an increase in the extracellular potassium concentration. We also showed that the addition of a proton pump inhibitor leads to membrane potential depolarization and inhibition of VP generation. These results suggest that the VP may be formed not only by transient suppression of proton pumps but also by passive ionic fluxes through the membrane.

  4. Heterotaxy in Caenorhabditis: widespread natural variation in left–right arrangement of the major organs

    PubMed Central

    Callander, Davon C.; López-Santos, Agustín; Torres Cleuren, Yamila N.; Santure, Anna W.

    2016-01-01

    Although the arrangement of internal organs in most metazoans is profoundly left–right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristic Caenorhabditis species. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’. PMID:27821534

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

    PubMed

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

    2016-05-15

    To study the natural variation and spatio-temporal accumulation of citrus metabolites, liquid chromatography tandem mass spectrometry (LC-MS) based metabolome analysis was performed on four fruit tissues (flavedo, albedo, segment membrane and juice sacs) and different Citrus species (lemon, pummelo and grapefruit, sweet orange and mandarin). Using a non-targeted metabolomics approach, more than 2000 metabolite signals were detected, from which more than 54 metabolites, including amino acids, flavonoids and limonoids, were identified/annotated. Differential accumulation patterns of both primary metabolites and secondary metabolites in various tissues and species were revealed by our study. Further investigation indicated that flavedo accumulates more flavonoids while juice sacs contain more amino acids. Besides this, cluster analysis based on the levels of metabolites detected in 47 individual Citrus accessions clearly grouped them into four distinct clusters: pummelos and grapefruits, lemons, sweet oranges and mandarins, while the cluster of pummelos and grapefruits lay distinctly apart from the other three species. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Complex Genetics Control Natural Variation in Arabidopsis thaliana Resistance to Botrytis cinerea

    PubMed Central

    Rowe, Heather C.; Kliebenstein, Daniel J.

    2008-01-01

    The genetic architecture of plant defense against microbial pathogens may be influenced by pathogen lifestyle. While plant interactions with biotrophic pathogens are frequently controlled by the action of large-effect resistance genes that follow classic Mendelian inheritance, our study suggests that plant defense against the necrotrophic pathogen Botrytis cinerea is primarily quantitative and genetically complex. Few studies of quantitative resistance to necrotrophic pathogens have used large plant mapping populations to dissect the genetic structure of resistance. Using a large structured mapping population of Arabidopsis thaliana, we identified quantitative trait loci influencing plant response to B. cinerea, measured as expansion of necrotic lesions on leaves and accumulation of the antimicrobial compound camalexin. Testing multiple B. cinerea isolates, we identified 23 separate QTL in this population, ranging in isolate-specificity from being identified with a single isolate to controlling resistance against all isolates tested. We identified a set of QTL controlling accumulation of camalexin in response to pathogen infection that largely colocalized with lesion QTL. The identified resistance QTL appear to function in epistatic networks involving three or more loci. Detection of multilocus connections suggests that natural variation in specific signaling or response networks may control A. thaliana–B. cinerea interaction in this population. PMID:18845849

  7. Heterotaxy in Caenorhabditis: widespread natural variation in left-right arrangement of the major organs.

    PubMed

    Alcorn, Melissa R; Callander, Davon C; López-Santos, Agustín; Torres Cleuren, Yamila N; Birsoy, Bilge; Joshi, Pradeep M; Santure, Anna W; Rothman, Joel H

    2016-12-19

    Although the arrangement of internal organs in most metazoans is profoundly left-right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristic Caenorhabditis species. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

  8. Characterizing Male–Female Interactions Using Natural Genetic Variation in Drosophila melanogaster

    PubMed Central

    Reinhart, Michael; Carney, Tara; Clark, Andrew G.

    2015-01-01

    Drosophila melanogaster females commonly mate with multiple males establishing the opportunity for pre- and postcopulatory sexual selection. Traits impacting sexual selection can be affected by a complex interplay of the genotypes of the competing males, the genotype of the female, and compatibilities between the males and females. We scored males from 96 2nd and 94 3rd chromosome substitution lines for traits affecting reproductive success when mated with females from 3 different genetic backgrounds. The traits included male-induced female refractoriness, male remating ability, the proportion of offspring sired under competitive conditions and male-induced female fecundity. We observed significant effects of male line, female genetic background, and strong male by female interactions. Some males appeared to be “generalists” and performed consistently across the different females; other males appeared to be “specialists” and performed very well with a particular female and poorly with others. “Specialist” males did not, however, prefer to court those females with whom they had the highest reproductive fitness. Using 143 polymorphisms in male reproductive genes, we mapped several genes that had consistent effects across the different females including a derived, high fitness allele in Acp26Aa that may be the target of adaptive evolution. We also identified a polymorphism upstream of PebII that may interact with the female genetic background to affect male-induced refractoriness to remating. These results suggest that natural variation in PebII might contribute to the observed male–female interactions. PMID:25425680

  9. Multigenic Natural Variation Underlies Caenorhabditis elegans Olfactory Preference for the Bacterial Pathogen Serratia marcescens

    PubMed Central

    Glater, Elizabeth E.; Rockman, Matthew V.; Bargmann, Cornelia I.

    2013-01-01

    The nematode Caenorhabditis elegans can use olfaction to discriminate among different kinds of bacteria, its major food source. We asked how natural genetic variation contributes to choice behavior, focusing on differences in olfactory preference behavior between two wild-type C. elegans strains. The laboratory strain N2 strongly prefers the odor of Serratia marcescens, a soil bacterium that is pathogenic to C. elegans, to the odor of Escherichia coli, a commonly used laboratory food source. The divergent Hawaiian strain CB4856 has a weaker attraction to Serratia than the N2 strain, and this behavioral difference has a complex genetic basis. At least three quantitative trait loci (QTLs) from the CB4856 Hawaii strain (HW) with large effect sizes lead to reduced Serratia preference when introgressed into an N2 genetic background. These loci interact and have epistatic interactions with at least two antagonistic QTLs from HW that increase Serratia preference. The complex genetic architecture of this C. elegans trait is reminiscent of the architecture of mammalian metabolic and behavioral traits. PMID:24347628

  10. Natural variation in gestational cortisol is associated with patterns of growth in marmoset monkeys (Callithrix geoffroyi).

    PubMed

    Mustoe, Aaryn C; Birnie, Andrew K; Korgan, Austin C; Santo, Jonathan B; French, Jeffrey A

    2012-02-01

    High levels of prenatal cortisol have been previously reported to retard fetal growth. Although cortisol plays a pivotal role in prenatal maturation, heightened exposure to cortisol can result in lower body weights at birth, which have been shown to be associated with adult diseases like hypertension and cardiovascular disease. This study examines the relationship between natural variation in gestational cortisol and fetal and postnatal growth in marmoset monkeys. Urinary samples obtained during the mother's gestation were analyzed for cortisol. Marmoset body mass index (BMI) was measured from birth through 540 days in 30- or 60-day intervals. Multi-level modeling was used to test if marmoset growth over time was predicted by changes in gestational cortisol controlling for time, sex, litter, and litter size. The results show that offspring exposed to intra-uterine environments with elevated levels of cortisol had lower linear BMI rates of change shortly after birth than did offspring exposed to lower levels of cortisol, but exhibited a higher curvilinear growth rate during adolescence. Average daily change in gestational cortisol during the first trimester had a stronger relationship with postnatal growth than change during the third trimester. Higher exposure to cortisol during gestation does alter developmental trajectories, however there appears to be a catch-up period during later post-natal growth. These observations contribute to a larger discussion about the relationship of maternal glucocorticoids on offspring development and the possibility of an earlier vulnerable developmental window.

  11. Natural variation in gestational cortisol is associated with patterns of growth in marmoset monkeys (Callithrix geoffroyi)

    PubMed Central

    Mustoe, Aaryn C.; Birnie, Andrew K.; Korgan, Austin C.; Santo, Jonathan B.; French, Jeffrey A.

    2012-01-01

    High levels of prenatal cortisol have been previously reported to retard fetal growth. Although cortisol plays a pivotal role in prenatal maturation, heightened exposure to cortisol can result in lower body weights at birth, which have been shown to be associated with adult diseases like hypertension and cardiovascular disease. This study examines the relationship between natural variation in gestational cortisol and fetal and postnatal growth in marmoset monkeys. Urinary samples obtained during the mother’s gestation were analyzed for cortisol. Marmoset body mass index (BMI) was measured from birth through 540 days in 30- or 60-day intervals. Multi-level modeling was used to test if marmoset growth over time was predicted by changes in gestational cortisol controlling for time, sex, litter, and litter size. The results show that offspring exposed to intra-uterine environments with elevated levels of cortisol had lower linear BMI rates of change shortly after birth than did offspring exposed to lower levels of cortisol, but exhibited a higher curvilinear growth rate during adolescence. Average daily change in gestational cortisol during the first trimester had a stronger relationship with postnatal growth than change during the third trimester. Higher exposure to cortisol during gestation does alter developmental trajectories, however there appears to be a catch-up period during later post-natal growth. These observations contribute to a larger discussion about the relationship of maternal glucocorticoids on offspring development and the possibility of an earlier vulnerable developmental window. PMID:22212825

  12. Natural Variation in Gene Expression Between Wild and Weedy Populations of Helianthus annuus

    PubMed Central

    Lai, Zhao; Kane, Nolan C.; Zou, Yi; Rieseberg, Loren H.

    2008-01-01

    The molecular genetic changes underlying the transformation of wild plants into agricultural weeds are poorly understood. Here we use a sunflower cDNA microarray to detect variation in gene expression between two wild (non-weedy) Helianthus annuus populations from Utah and Kansas and four weedy H. annuus populations collected from agricultural fields in Utah, Kansas, Indiana, and California. When grown in a common growth chamber environment, populations differed substantially in their gene expression patterns, indicating extensive genetic differentiation. Overall, 165 uni-genes, representing ∼5% of total genes on the array, showed significant differential expression in one or more weedy populations when compared to both wild populations. This subset of genes is enriched for abiotic/biotic stimulus and stress response proteins, which may underlie niche transitions from the natural sites to agricultural fields for H. annuus. However, only a small proportion of the differentially expressed genes overlapped in multiple wild vs. weedy comparisons, indicating that most of the observed expression changes are due to local adaptation or neutral processes, as opposed to parallel genotypic adaptation to agricultural fields. These results are consistent with an earlier phylogeographic study suggesting that weedy sunflowers have evolved multiple times in different regions of the United States and further indicate that the evolution of weedy sunflowers has been accompanied by substantial gene expression divergence in different weedy populations. PMID:18689879

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

    USGS Publications Warehouse

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

    2007-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Siegenthaler, U.

    1984-01-01

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

  15. Seasonal variations in mortality caused by cardiovascular diseases in Norway and Ireland.

    PubMed

    Eng, H; Mercer, J B

    1998-04-01

    Seasonal variations in mortality resulting from cardiovascular diseases (CVD) have been demonstrated in many countries, with the highest levels observed during the coldest months of the year. We studied the seasonal changes in CVD mortality in Norway and the Republic of Ireland, two countries which are demographically quite similar, but climatically different; we also examined the relation between CVD mortality and air temperature. Registered monthly data for mortality from CVD for the period 1985-1995 were obtained from the Norwegian Central Bureau of Statistics and the Irish Central Statistics Office. Meteorological data were provided by the Norwegian Institute of Meteorology and Met Eireann, in Ireland. Monthly mortality ratio for both men and women aged 60 and older was calculated from the mortality date. Mean monthly air temperatures for the two countries were calculated from the meteorological data. For the 10-year period investigated, the lowest and highest monthly mortality ratios were on average found in August and January, respectively, and mean excess winter mortality, expressed as the difference between the August and January values for the entire 10-year period, was 22% (Norway) and 35% (Ireland). However, when the percentage difference in the months with the respective highest and lowest mortality ratios were calculated for each year, the average of these differences for each of the 10 individual years was 29% and 45%. Mortality ratio was found to increase much more steeply with decreasing air temperature in Ireland than in Norway. Although the seasonal variation between CVD mortality in both countries is similar, the different relation with climatic conditions may result from differences in housing standards, allowing outdoor temperatures to have a greater influence on indoor temperature in Ireland than in Norway.

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

    NASA Technical Reports Server (NTRS)

    Siegenthaler, U.

    1984-01-01

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

  17. The cryptoendolithic microbial environment in the Antarctic cold desert: temperature variations in nature

    NASA Technical Reports Server (NTRS)

    McKay, C. P.; Friedmann, E. I.

    1985-01-01

    In the Antarctic cold desert, cryptoendolithic microorganisms live under the surface of porous sandstone rocks. During the austral summer, the environment of the near-surface rock layers colonized by organisms is characterized by two kinds of temperature oscillations, both occurring across the freezing point. Low-frequency (diurnal) and large-amplitude (up to about 20 degrees C) oscillations on the sunlit surface of rocks result in a daily freeze-thaw cycle. This is a result of the diurnal changes in the sun altitude and angle with respect to the rock surface. The biological effect of this oscillation is the regulation of the onset and cessation of metabolic activity. The high-frequency (few minutes) oscillations occur only under certain weather conditions (sunny days with light winds) and are superimposed on the low-frequency oscillations. They are caused by the cooling effect of wind gusts on rock surfaces that are much warmer than ambient air temperatures. High-frequency oscillations result in a rapid freeze-thaw cycle on the surface, which, however, does not reach the microbial zone. These high-frequency freeze-thaw oscillations are probably the cause of the abiotic nature of the rock surface. Both oscillations seem to have an effect on rock weathering.

  18. The cryptoendolithic microbial environment in the Antarctic cold desert: temperature variations in nature.

    PubMed

    McKay, C P; Friedmann, E I

    1985-01-01

    In the Antarctic cold desert, cryptoendolithic microorganisms live under the surface of porous sandstone rocks. During the austral summer, the environment of the near-surface rock layers colonized by organisms is characterized by two kinds of temperature oscillations, both occurring across the freezing point. Low-frequency (diurnal) and large-amplitude (up to about 20 degrees C) oscillations on the sunlit surface of rocks result in a daily freeze-thaw cycle. This is a result of the diurnal changes in the sun altitude and angle with respect to the rock surface. The biological effect of this oscillation is the regulation of the onset and cessation of metabolic activity. The high-frequency (few minutes) oscillations occur only under certain weather conditions (sunny days with light winds) and are superimposed on the low-frequency oscillations. They are caused by the cooling effect of wind gusts on rock surfaces that are much warmer than ambient air temperatures. High-frequency oscillations result in a rapid freeze-thaw cycle on the surface, which, however, does not reach the microbial zone. These high-frequency freeze-thaw oscillations are probably the cause of the abiotic nature of the rock surface. Both oscillations seem to have an effect on rock weathering.

  19. The cryptoendolithic microbial environment in the Antarctic cold desert: temperature variations in nature

    NASA Technical Reports Server (NTRS)

    McKay, C. P.; Friedmann, E. I.

    1985-01-01

    In the Antarctic cold desert, cryptoendolithic microorganisms live under the surface of porous sandstone rocks. During the austral summer, the environment of the near-surface rock layers colonized by organisms is characterized by two kinds of temperature oscillations, both occurring across the freezing point. Low-frequency (diurnal) and large-amplitude (up to about 20 degrees C) oscillations on the sunlit surface of rocks result in a daily freeze-thaw cycle. This is a result of the diurnal changes in the sun altitude and angle with respect to the rock surface. The biological effect of this oscillation is the regulation of the onset and cessation of metabolic activity. The high-frequency (few minutes) oscillations occur only under certain weather conditions (sunny days with light winds) and are superimposed on the low-frequency oscillations. They are caused by the cooling effect of wind gusts on rock surfaces that are much warmer than ambient air temperatures. High-frequency oscillations result in a rapid freeze-thaw cycle on the surface, which, however, does not reach the microbial zone. These high-frequency freeze-thaw oscillations are probably the cause of the abiotic nature of the rock surface. Both oscillations seem to have an effect on rock weathering.

  20. 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.

  1. Spinal Cord Injury Caused by Stab Wounds: Incidence, Natural History, and Relevance for Future Research.

    PubMed

    McCaughey, Euan J; Purcell, Mariel; Barnett, Susan C; Allan, David B

    2016-08-01

    Spinal cord injury caused by stab wounds (SCISW) results from a partial or complete transection of the cord, and presents opportunities for interventional research. It is recognized that there is low incidence, but little is known about the natural history or the patient's suitability for long-term clinical outcome studies. This study aims to provide population-based evidence of the demographics of SCISW, and highlight the issues regarding the potential for future research. The database of the Queen Elizabeth National Spinal Injuries Unit (QENSIU), the sole center for treating SCI in Scotland, was reviewed between 1994 and 2013 to ascertain the incidence, demographics, functional recovery, and mortality rates for new SCISW. During this 20 year period, 35 patients with SCISW were admitted (97.1% male, mean age 30.0 years); 31.4% had a cervical injury, 60.0% had a thoracic injury, and 8.6% had a lumbar injury. All had a neurological examination, with 42.9% diagnosed as motor complete on admission and 77.1% discharged as motor incomplete. A total of 70.4% of patients with an American Spinal Injury Association Impairment Scale (AIS) level of A to C on admission had an improved AIS level on discharge. Nine (25.7%) patients have died since discharge, with mean life expectancy for these patients being 9.1 years after injury (20-65 years of age). Patients had higher levels of comorbidities, substance abuse, secondary events, and poor compliance compared with the general SCI population, which may have contributed to the high mortality rate observed post-discharge. The low incidence, heterogeneous nature, spontaneous recovery rate, and problematic follow-up makes those with penetrating stab injuries of the spinal cord a challenging patient group for SCI research.

  2. Physical nature and timing variations of the eclipsing system V407 Pegasi

    SciTech Connect

    Lee, Jae Woo; Park, Jang-Ho; Hong, Kyeongsoo; Kim, Seung-Lee; Lee, Chung-Uk E-mail: pooh107162@kasi.re.kr E-mail: slkim@kasi.re.kr

    2014-04-01

    New multiband CCD photometry is presented for V407 Peg; the R {sub C} light curves are the first ever compiled. Our light curves, displaying a flat bottom at secondary minimum and an O'Connell effect, were simultaneously analyzed with the radial velocity (RV) curves given by Rucinski et al. The light changes of the system are best modeled using both a hot spot on the secondary star and a third light. The model also represents historical light curves. All available minimum epochs, including our six timing measurements, have been examined and they indicate that the eclipse timing variation is mainly caused by light asymmetries due to the spot activity detected in the light-curve synthesis. The hot spot may be produced as a result of the impact of the gas stream from the primary star. Our light and velocity solutions indicate that V407 Peg is a totally eclipsing A-type overcontact binary with values of q = 0.251, i = 87.°6, ΔT = 496 K, f = 61%, and l {sub 3} = 11∼16%. Individual masses and radii of both components are determined to be M {sub 1} = 1.72 M {sub ☉}, M {sub 2} = 0.43 M {sub ☉}, R {sub 1} = 2.15 R {sub ☉}, and R {sub 2} = 1.21 R {sub ☉}. These results are very different from previous ones, which is probably caused by the light curves with distorted and inclined eclipses used in those other analyses. The fact that there are no objects optically related to the system and that the seasonal RVs show a large discrepancy in systemic velocity indicates that the third light source most likely arises from a tertiary component orbiting the eclipsing pair.

  3. Numerical simulation of scouring-deposition variations caused by rainfall-induced landslides in the upstream of Zengwun River, Taiwan

    NASA Astrophysics Data System (ADS)

    Lee, Ming-Hsi; Liao, Yi-Wen; Tsai, Kuang-Jung

    2017-04-01

    In recent years, the increasing sediment disasters of severe rainfall-induced landslides on human lives and lifeline facilities worldwide have advanced the necessity to find out both economically acceptable and useful techniques to predict the occurrence and destructive power of the disasters. In August 2009, Typhoon Morakot brought a large amount of rainfall with both high intensity and long duration to a vast area of Taiwan. Unfortunately, this resulted in a catastrophic landslide in watershed of Zengwun-River reservoir, southern Taiwan. Meanwhile, large amounts of landslides were formed in the upstream of Zengwun River. The major scope of this study is to apply numerical model to simulate the scouring-deposition variations caused by rainfall-induced landslides that occurred in the upstream of Zengwun River during Typhoon Morakot. This study proposed the relation diagrams of the intermediate diameter (d50), recurrence interval (T) and scouring-deposition depth (D), and applied the diagrams to understand the impacts of the scouring-deposition variations on the structures for water and soil conservation and their measurements. Based on the simulation of scouring-deposition variation at the Da-Bu dam and Da-Bang dam, this study also discussed the scouring-deposition variations of different sections under different scenarios (including flow rate, intermediate diameters and structures). In summary, the result suggested that the diagrams of the intermediate diameter, recurrence interval and scouring-deposition depth could be used as the reference for designing the check dams, ground sills and lateral constructions.

  4. Genetic variation in bank vole populations in natural and metal-contaminated areas.

    PubMed

    Mikowska, Magdalena; Gaura, Aneta; Sadowska, Edyta; Koteja, Paweł; Świergosz-Kowalewska, Renata

    2014-11-01

    The effects of isolation and heavy-metal pollution on genetic diversity in Myodes (=Clethrionomys) glareolus populations were studied. Isolation and pollution are considered to have important effects on biodiversity. Animals were collected from ten populations in isolated (island), mainland, and metal-polluted areas. Three populations were in areas near zinc and lead smelters; four were on islands in the relatively unpolluted Mazurian Lake District and in the Bieszczady Mountains; and three were in clean-mainland areas in the Mazurian Lake District, the Niepołomice Forest, and the Bieszczady Mountains. Cadmium and lead concentrations in liver and kidney were measured to assess the animals' exposure to metals. The metal concentrations were greater in animals from areas classed as polluted than in animals from the clean-mainland areas and islands. The genetic diversity of each population was analyzed using eight microsatellite markers. The results confirmed that isolation adversely affects genetic diversity in M. glareolus populations (giving low heterozygosity and poor allelic richness), but the effect of metal exposure on genetic diversity was not strong. Of the samples from polluted areas, only the Katowice population, which is exposed to high levels of metal pollution and is also isolated because of human activity, showed genetic variation parameters that were similar to those for the island populations. Nei's genetic distances indicated that the island populations were genetically distant from each other and from the other populations, and there were noticeable inbreeding effects that would have been caused by the isolation of these populations.

  5. 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

  6. Mutations in SLC45A2 Cause Plumage Color Variation in Chicken and Japanese Quail

    PubMed Central

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

    2007-01-01

    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

  7. Secular variations in composition of the solar wind - Evidence and causes

    NASA Technical Reports Server (NTRS)

    Kerridge, J. F.

    1980-01-01

    Variations in the composition of the regolith due to irradiation by the solar wind are examined by categorizing the exposure history recorded in each sample. The history can be defined by two parameters: the duration of solar wind exposure (maturity) and a measure of how long the exposure took place (antiquity). Three partially successful methods for determining antiquity are described: the regolith contains small amounts of unsupported, trapped radiogenic noble gases, the most common being Ar-40. Assuming relatively prompt outgassing of the lunar interior, the amount of Ar-40 implanted per unit time should be proportional to the lunar content of K-40, and thus should have decayed exponentially over the lifetime of the moon. Normalization to constant exposure duration is achieved by taking the ratio Ar-40/Ar-36 in trapped gas, Ar-36 being an efficiently trapped solar wind species. The second method involves the interaction between galactic cosmic rays and lunar material producing certain spallogenic nuclides which may be analyzed in terms of a cosmic ray exposure age. The third method deals with the fact that there is a general tendency for depth within a core to be related to time deposition; two variants of this method are presented.

  8. 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. © 2015 Cambridge Philosophical Society.