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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 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

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

    PubMed

    Briga, Michael; Verhulst, Simon

    2015-11-01

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

  7. 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.

  8. 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.

  9. Modeling Natural Variation through Distribution

    ERIC Educational Resources Information Center

    Lehrer, Richard; Schauble, Leona

    2004-01-01

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

  10. 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.

  11. 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

  12. 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.

  13. [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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Helium isotopic abundance variation in nature

    SciTech Connect

    Holden, N.E.

    1993-08-01

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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. [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).

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Natural allelic variations in highly polyploidy Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  17. 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

  18. 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

  19. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  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. 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.

  15. 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.

  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. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Genomic variation in natural populations of Drosophila melanogaster.

    PubMed

    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

    2012-10-01

    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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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).

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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…

  10. 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

  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. Mining and harnessing natural variation - a little MAGIC

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  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. 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

  19. 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.

  20. 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.

  1. 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

  2. Seasonal variation in natural recharge of coastal aquifers

    NASA Astrophysics Data System (ADS)

    Mollema, Pauline N.; Antonellini, Marco

    2013-06-01

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

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

    SciTech Connect

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

    2008-11-15

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

  4. 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

  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. 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

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  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. 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.

  3. 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

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

    PubMed Central

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

    2016-01-01

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

  5. Natural 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 (...

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

    2017-02-11

    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.

  8. 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

  9. 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.

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

    PubMed

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

    2010-08-01

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

  11. [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.

  12. 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

  13. 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

  14. 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.

  15. 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

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

    ERIC Educational Resources Information Center

    Chafel, Judith A.; Neitzel, Carin

    2005-01-01

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

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

    ERIC Educational Resources Information Center

    Belford, Susan; Gibbs, Margaret

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

  18. 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...

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. Analysis of Natural Variation in Bermudagrass (Cynodon dactylon) Reveals Physiological Responses Underlying Drought Tolerance

    PubMed Central

    Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

    2012-01-01

    Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H2O2) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H2O2 content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system. PMID:23285294

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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

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

    PubMed

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

    2014-01-01

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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  5. 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

  6. [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.

  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. 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.

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

    PubMed Central

    Aronov, Dmitriy; Fee, Michale S.

    2012-01-01

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

  10. 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

  11. 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.

  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. 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

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

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

    PubMed Central

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

    2012-01-01

    Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs) that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories. PMID:23185390

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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…

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  18. 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.

  19. 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%.

  20. 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

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

    PubMed Central

    Klitzman, Robert

    2013-01-01

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

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

    PubMed 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. 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.

  4. 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

  5. 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.

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

    ERIC Educational Resources Information Center

    Allen, Breon G.; And Others

    1994-01-01

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

  7. 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

  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. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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

  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. 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.

  3. 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

  4. 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.

  5. 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.

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

    USGS Publications Warehouse

    Garcia, V.; Conway, C.J.

    2009-01-01

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

  7. 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.

  8. Daily variations in ambulance calls for selected causes in Arkhangelsk, Russia: potential role of excessive alcohol consumption on weekends

    PubMed Central

    Drachev, Sergei N.; Unguryanu, Tatiana N.; Grjibovski, Andrej M.

    2012-01-01

    Objective To assess daily variations in ambulance calls for cardiovascular diseases (CVDs), mental and behavioral disorders, and external causes in Arkhangelsk, Northwest Russia, in 2000–2008. Study design A population-based study. Methods Data about all ambulance calls during the years 2000–2008 were obtained from the Arkhangelsk ambulance station. Information about patient's gender, age, doctor's diagnosis according to International Classification of Diseases, 10th revision, and the date of call were recorded. Pearson's Chi-squared tests were used for comparing proportions of ambulance calls across the week for CVDs (I00-99), mental and behavioral disorders (F00-F99), and external causes (S00-T98, V01-Y98). The ratio of incidence of ambulance calls on Saturday, Sunday, and Monday versus the rest of week was also calculated. Results There is a significant daily variation (p < 0.001) in calls for CVDs in men and women aged 18–59 and women aged 60 years and older, with increased numbers of calls on weekends and Mondays varying between 2 and 3% excess calls. For mental and behavioral disorders, a similar pattern was found in the age group of 18–59 year-olds. Ratios for the number of calls during weekends and Mondays vs. the rest of the week were 1.05 (95% CI: 1.02–1.08) among women and 1.02 (95% CI: 1.00–1.05) among men. For external causes, a significant variation and an increase in ambulance calls during Saturdays, Sundays, and Mondays from 4 to 17% excess calls was observed for both age and gender groups. Conclusions The observed daily variations in ambulance calls with an increased number of calls on weekends and Mondays for CVDs, mental and behavioral disorders, and external causes may be associated with excessive alcohol consumption on the weekends. Further research using data on individual levels of alcohol consumption are warranted. PMID:23130353

  9. 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).

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2004-09-01

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

  3. 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.

  4. 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.

  5. 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

  6. Apparent Transition in the Human Height Distribution Caused by Age-Dependent Variation during Puberty Period

    NASA Astrophysics Data System (ADS)

    Iwata, Takaki; Yamazaki, Yoshihiro; Kuninaka, Hiroto

    2013-08-01

    In this study, we examine the validity of the transition of the human height distribution from the log-normal distribution to the normal distribution during puberty, as suggested in an earlier study [Kuninaka et al.: J. Phys. Soc. Jpn. 78 (2009) 125001]. Our data analysis reveals that, in late puberty, the variation in height decreases as children grow. Thus, the classification of a height dataset by age at this stage leads us to analyze a mixture of distributions with larger means and smaller variations. This mixture distribution has a negative skewness and is consequently closer to the normal distribution than to the log-normal distribution. The opposite case occurs in early puberty and the mixture distribution is positively skewed, which resembles the log-normal distribution rather than the normal distribution. Thus, this scenario mimics the transition during puberty. Additionally, our scenario is realized through a numerical simulation based on a statistical model. The present study does not support the transition suggested by the earlier study.

  7. 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.

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

    USGS Publications Warehouse

    Risley, John C.

    1997-01-01

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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. [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.

  14. 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.

  15. 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.

  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. 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

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Miura, T.; Shimura, M.

    1980-03-01

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

  5. 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.

  6. Genetic and environmental causes of variation in perceived loneliness in young people.

    PubMed

    Waaktaar, Trine; Torgersen, Svenn

    2012-07-01

    Loneliness is prevalent in adolescence, despite the widespread expectation directed to young people to start building close relationships beyond the nuclear family. The aim of the present study was to explore the causal genetic and environmental structure behind variability in adolescents' perceived loneliness. Seven national cohorts (ages 12-18 years) of Norwegian twins reared together (1,394 twin pairs) participated. Perceived loneliness was measured with five items from the UCLA Loneliness Scale. Data were collected from mothers, fathers, and twins' self ratings by means of a posted questionnaire. Biometric analyses were applied, testing the causal architecture of loneliness within a psychometric model with one common latent factor in addition to specific genetic and environmental sources influencing the scores of each informant. The results showed a heritability (h(2)) of 75% on the latent perceived loneliness factor, and nonshared environmental effects (e(2)) explaining the remaining 25% of the latent factor variance. There were also significant rater-specific genetic and nonshared environmental effects. No shared environmental effects were found in the model, and there were no sex differences in the estimates. This study showed that variation in perceived loneliness in adolescents is highly genetic. Additional genetic and nonshared environmental etiological sources are to some extent represented in the scores of the specific rater.

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

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Fleming, Eric L.

    2007-01-01

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

  8. 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.

  9. 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.

  10. 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'.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  18. Variations of electric field and electric resistivity of air caused by dust motion

    NASA Astrophysics Data System (ADS)

    Seran, E.; Godefroy, M.; Renno, N.; Elliott, H.

    2013-08-01

    report results of a field campaign conducted in the Nevada desert with a suite of electric field instruments consisting of a field mill (FM) and a short dipole antenna (SDA). Furthermore, we show that a combination of the measurements of these two instruments allows the estimation of the electric resistivity of air, an important quantity that is extremely difficult to measure near the Earth's surface. The electric resistivity of air is found to vary between 1.5 · 1013 and 6 · 1013 Ω m and to correlate with changes in electric field. Vertical DC electric fields with amplitudes up to 6 kV m-1 were observed to correspond to clouds of dust blowing through the measurement site. Enhanced DC and AC electric fields are measured during periods when horizontal wind speed exceeds 7 m s-1, or around twice the background value. We suggest that low-frequency emissions, below ~200 Hz, are generated by the motion of electrically charged particles in the vicinity of the SDA electrode and propose a simple model to reproduce the observed spectra. According to this model, the spectral response is controlled by three parameters, (i) the speed of the charged particles, (ii) the charge concentration, and (iii) the minimum distance between the particle and the electrode. In order to explain the electric fields measured with the FM sensors at different heights, we developed a multilayer model that relates the electric field to the charge distribution. For example, a nonlinear variation of the electric field observed by the FM sensors below 50 cm is simulated by a near-surface layer of tens of centimeters that is filled with electrically charged particles that carry a predominantly negative charge in the vicinity of the soil. The charge concentration inside this layer is estimated to vary between 1012 and 5 · 1013 electrons m-3.

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

    PubMed Central

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

    2016-01-01

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

  20. 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.

  1. A mobile tool about causes and distribution of dramatic natural phenomena

    NASA Astrophysics Data System (ADS)

    Boppidi, Ravikanth Reddy

    Most Research suggests that tablet computers could aid the study of many scientific concepts that are difficult to grasp, such as places, time and statistics. These occur especially in the study of geology, chemistry, biology and so on. Tapping the technology will soon become critical career training for future generations. Teaching through mobile is more interactive and helps students to grasp quickly. In this thesis an interactive mobile tool is developed which explains about the causes and distribution of natural disasters like Earthquakes, Tsunami, Tropical Cyclones, Volcanic Eruptions and Tornadoes. The application shows the places of disasters on an interactive map and it also contains YouTube embedded videos, which explain the disasters visually. The advantage of this tool is, it can be deployed onto major mobile operating systems like Android and IOS. The application's user interface (UI) is made very responsive using D3 JavaScript, JQuery, Java Script, HTML, CSS so that it can adapt to mobiles, tablets, and desktop screens.

  2. Assessment of infrastructure functional damages caused by natural-technological disasters

    NASA Astrophysics Data System (ADS)

    Massabò, Marco; Trasforini, Eva; Traverso, Stefania; Rudari, Roberto; De Angeli, Silvia; Cecinati, Francesca; Cerruti, Valentina

    2013-04-01

    The assessment of infrastructure damages caused by technological disaster poses several challenges, from gathering needed information on the territorial system to the definition of functionality curves for infrastructures elements (such as, buildings, road school) that are exposed to both natural and technological event. Moreover, areas affected by natural or natech (technological disasters triggered by natural events) disasters have often very large extensions and a rapid survey of them to gather all the needed information is a very difficult task, for many reasons, not least the difficult access to the existing databases and resources. We use multispectral optical imagery with other geographical and unconventional data to identify and characterize exposed elements. Our efforts in the virtual survey and during the investigation steps have different aims: to identify the vulnerability of infrastructures, buildings or activities; to execute calculations of exposition to risk; to estimate physical and functional damages. Subsequently, we apply specific algorithms to estimate values of acting forces and physical and functional damages. The updated picture of target areas in terms of risk-prone people, infrastructures and their connections is very important. It is possible to develop algorithms providing values of systemic functionality for each network element. The methodology is here applied to a natech disaster, arising from the combination of a flood event (specifically, the January 2010 flooding of Drin and Buna rivers, with a worsening in the road safety levels in the Shkoder area) with and the subsequent overturning of a truck transporting hazardous material. The accident causes the loss of containment and the total material release. Once the release has taken place, the evolution will depend on the physical state of the substance spilled (liquid, gas or dust). As a specific case we consider the rupture of a trucks transporting liquid fuels such as gasoline

  3. Genetic variation in plant volatile emission does not result in differential attraction of natural enemies in the field.

    PubMed

    Wason, Elizabeth L; Hunter, Mark D

    2014-02-01

    Volatile organic chemical (VOC) emission by plants may serve as an adaptive plant defense by attracting the natural enemies of herbivores. For plant VOC emission to evolve as an adaptive defense, plants must show genetic variability for the trait. To date, such variability has been investigated primarily in agricultural systems, yet relatively little is known about genetic variation in VOCs emitted by natural populations of native plants. Here, we investigate intraspecific variation in constitutive and herbivore-induced plant VOC emission using the native common milkweed plant (Asclepias syriaca) and its monarch caterpillar herbivore (Danaus plexippus) in complementary field and common garden greenhouse experiments. In addition, we used a common garden field experiment to gauge natural enemy attraction to milkweed VOCs induced by monarch damage. We found evidence of genetic variation in the total constitutive and induced concentrations of VOCs and the composition of VOC blends emitted by milkweed plants. However, all milkweed genotypes responded similarly to induction by monarchs in terms of their relative change in VOC concentration and blend. Natural enemies attacked decoy caterpillars more frequently on damaged than on undamaged milkweed, and natural enemy visitation was associated with higher total VOC concentrations and with VOC blend. Thus, we present evidence that induced VOCs emitted by milkweed may function as a defense against herbivores. However, plant genotypes were equally attractive to natural enemies. Although milkweed genotypes diverge phenotypically in their VOC concentrations and blends, they converge into similar phenotypes with regard to magnitude of induction and enemy attraction.

  4. Causes of atmospheric CO2 variations over the last glacial-interglacial cycle

    NASA Astrophysics Data System (ADS)

    Kemppinen, K. M.; Holden, P.; Edwards, N.; Ridgwell, A. J.; Friend, A. D.; Wolff, E.

    2013-12-01

    During glacial-interglacial cycles, atmospheric CO2 increases by about 100 ppmv during brief interglacials. Despite years of research, the causes of this change are still not entirely understood. Here we attempt to explain the change in CO2 using, for the first time, an ensemble of coupled climate-carbon cycle simulations designed to consider the processes that are thought to contribute to variability of atmospheric CO2 on glacial/interglacial timescales. We begin by running the ensemble to equilibrium with Last Glacial Maximum (LGM; 21 kyr BP) forcings. By comparing the simulations with ice core data, we find that a small subset of the ensemble produces plausible atmospheric CO2 concentrations and climate. We build emulators of the full model with respect to atmospheric CO2, and perform sensitivity analyses on them to quantify the contributions of atmospheric, sea ice, ocean, and vegetation processes to variability in atmospheric CO2 under glacial forcings. We find that the variability is dominated by a few key parameters. We also use singular vector decomposition to investigate the parameter interactions required for achieving plausible CO2 at the LGM. This work is ongoing, and if plausible states are found, a transient ensemble will be run over the last glacial-interglacial cycle (126 kyr) using the associated parameter sets. This experiment will be the first of its kind as it allows simulated atmospheric CO2 to feedback to the physical climate model in an unconstrained manner.

  5. Factors affecting seasonal variation of membrane filtration resistance caused by Chlorella algae.

    PubMed

    Babel, Sandhya; Takizawa, Satoshi; Ozaki, Hiroaki

    2002-03-01

    A seasonal fluctuation pattern was observed in membrane filtration resistance by Chlorella algae cultured in open ponds in the tropical environment. In order to investigate the causes of this phenomenon, Chlorella was cultivated under controlled conditions and the cake resistance was measured by batch filtration in dead-end mode. The filtration resistance was found to be a function of environmental conditions. Algae could grow favourably and offered low specific cake resistance (R,s) on the order of 10(11) m/g for the culture temperature from 28 degrees C to 35 degrees C. The algal growth was inhibited and the specific cake resistance increased to the order of 10(12) m/g below or above this optimum temperature range. Strong solar radiation, coupled with high temperatures, also inhibited the growth of algae and resulted in higher specific cake resistance. The specific cake resistance of algae cultured at different temperatures increased with the amount of the extracellular organic matter (EOM) extracted by 0.1 N NaOH. Hence EOM, rather than bacteria present in the mono-algal culture, was considered to be the primary factor affecting the cake resistance. The specific cake resistance increased drastically after actively growing cells were stored in nutrient-free water under dark conditions. However, the resistance was slightly decreased when the algal cells were stored in NSIII nutrient media in a dark room, indicating the effect of nutrient availability on the change of the specific cake resistance under the light-limiting conditions. EOM extracted from the cells kept in the nutrient-free water contained less sugar than the fresh culture, whereas the EOM extracted from the cells stored in the NSIII media contained more sugar. The molecular distribution of the EOM shifted from below 1,000 kDa before storage to more than 2,000 kDa after storage in both the nutrient-free and NSIII media.

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

    PubMed

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

    2006-02-01

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

  7. The AT-hook motif-encoding gene METABOLIC NETWORK MODULATOR 1 underlies natural variation in Arabidopsis primary metabolism

    PubMed Central

    Li, Baohua; Kliebenstein, Daniel J.

    2014-01-01

    Regulation of primary metabolism is a central mechanism by which plants coordinate their various responses to biotic and abiotic challenge. To identify genes responsible for natural variation in primary metabolism, we focused on cloning a locus from Arabidopsis thaliana that influences the level of TCA cycle metabolites in planta. We found that the Met.V.67 locus was controlled by natural variation in METABOLIC NETWORK MODULATOR 1 (MNM1), which encoded an AT-hook motif-containing protein that was unique to the Brassicales lineage. MNM1 had wide ranging effects on plant metabolism and displayed a tissue expression pattern that was suggestive of a function in sink tissues. Natural variation within MNM1 had differential effects during a diurnal time course, and this temporal dependency was supported by analysis of T-DNA insertion and over-expression lines for MNM1. Thus, the cloning of a natural variation locus specifically associated with primary metabolism allowed us to identify MNM1 as a lineage-specific modulator of primary metabolism, suggesting that the regulation of primary metabolism can change during evolution. PMID:25202318

  8. Effects of a Changing Climate on Seasonal Variation in Natural Recharge of Unconfined Coastal Aquifers

    NASA Astrophysics Data System (ADS)

    Antonellini, Marco; Nella Mollema, Pauline

    2013-04-01

    Irregular rainfall patterns throughout the year result in the discontinuous natural recharge of coastal aquifers, which has an effect on the size of freshwater lenses present in sandy deposits. The thickness of the freshwater lenses is important in the context of farmland salinization and coastal ecosystems survival. This study presents numerical models that simulate continuous and discontinuous recharge in sandy coastal aquifers and the thickness of resulting fresh water lenses under current and future climate scenarios. Temperature data for the period 1960-1990 from LOCCLIM FAO and from the IPCC SRES A1b scenario for 2070-2100, have been used to calculate the potential evapotranspiration. Potential recharge was defined as the difference between the precipitation and potential evapotranspiration in twelve locations around the world: Ameland (The Netherlands), Auckland and Wellington (New Zealand), Hong Kong, Ravenna (Italy), Mekong (Vietnam), Mumbai (India), New Jersey (USA), Nile Delta (Egypt), Kobe and Tokyo (Japan), and Singapore. These locations have shallow coastal aquifers along low lying coasts and comparable aquifer structure, which is the result of similar sediment supply and deposition in the Holocene as well as by the sea level changes from the last ice age to the present time. Particular attention has been paid to temporal variations of natural recharge that can vary from continuous recharge throughout the year to discontinuous recharge. The most dramatic reduction in the magnitude of potential annual recharge by the end of this century will occur at lower latitudes (Mumbai, Singapore, Hong Kong and Mekong). The most pronounced change in length of the dry period occurs for Kobe (Japan) and Singapore even though the total annual amount of recharge remains practically the same. The Influence of variable recharge on the size of freshwater lenses surrounded by saline water is simulated with the SEAWAT model. Models where the recharge is applied

  9. Toward Understanding The B[e] Phenomenon. VI. Nature and Spectral Variations of HD 85567.

    NASA Astrophysics Data System (ADS)

    Khokhlov, S. A.; Miroshnichenko, A. S.; Mennickent, R.; Cabezas, M.; Zhanabaev, Z. Zh.; Reichart, D. E.; Ivarsen, K. M.; Haislip, J. B.; Nysewander, M. C.; LaCluyze, A. P.

    2017-01-01

    We report the results of high-resolution (R ∼ 80,000) spectroscopic observations of the emission-line object HD 85567, which has been classified as an FS CMa type object or a pre-main-sequence star. The main goal is to put more constraints on the object’s fundamental parameters, as well as on its nature and evolutionary state. Absorption lines in the spectrum of HD 85567 were found to be similar to those of mid-B-type dwarfs and correspond to the following fundamental parameters: Teff = 15,000 ± 500 K, v\\sin i=31+/- 3 km s‑1, and {log} g∼ 4.0. The interstellar extinction, AV = 0.50 ± 0.02 mag, was measured using the strengths of some diffuse interstellar bands. We also obtained UBV(RI)c images of a 10‧ × 10‧ region around the object. Photometry of projectionally close stars was used to derive an interstellar extinction law in this direction and resulted in a distance of 1300 ± 100 pc to the object and a luminosity of log L/L⊙ = 3.3 ± 0.2. We found no significant radial velocity variations of the absorption lines in the spectra of HD 85567 obtained during two-month-long periods of time in 2012 and 2015. Our analysis of the spectroscopic and photometric data available for the star led us to a conclusion that it cannot be a pre-main-sequence Herbig Ae/Be star. We argue that the circumstellar gas and dust were produced during the object’s evolution as most likely a binary system, which contains an undetected secondary component and is unlikely to be a merger product. This paper is partly based on observations obtained at the 1.5 m telescope of the Cerro Tololo Interamerican Observatory under CNTAC proposal 2012A–016.

  10. Linking Dynamic Phenotyping with Metabolite Analysis to Study Natural Variation in Drought Responses of Brachypodium distachyon

    PubMed Central

    Fisher, Lorraine H. C.; Han, Jiwan; Corke, Fiona M. K.; Akinyemi, Aderemi; Didion, Thomas; Nielsen, Klaus K.; Doonan, John H.; Mur, Luis A. J.; Bosch, Maurice

    2016-01-01

    Drought is an important environmental stress limiting the productivity of major crops worldwide. Understanding drought tolerance and possible mechanisms for improving drought resistance is therefore a prerequisite to develop drought-tolerant crops that produce significant yields with reduced amounts of water. Brachypodium distachyon (Brachypodium) is a key model species for cereals, forage grasses, and energy grasses. In this study, initial screening of a Brachypodium germplasm collection consisting of 138 different ecotypes exposed to progressive drought, highlighted the natural variation in morphology, biomass accumulation, and responses to drought stress. A core set of ten ecotypes, classified as being either tolerant, susceptible or intermediate, in response to drought stress, were exposed to mild or severe (respectively, 15 and 0% soil water content) drought stress and phenomic parameters linked to growth and color changes were assessed. When exposed to severe drought stress, phenotypic data and metabolite profiling combined with multivariate analysis revealed a remarkable consistency in separating the selected ecotypes into their different pre-defined drought tolerance groups. Increases in several metabolites, including for the phytohormones jasmonic acid and salicylic acid, and TCA-cycle intermediates, were positively correlated with biomass yield and with reduced yellow pixel counts; suggestive of delayed senescence, both key target traits for crop improvement to drought stress. While metabolite analysis also separated ecotypes into the distinct tolerance groupings after exposure to mild drought stress, similar analysis of the phenotypic data failed to do so, confirming the value of metabolomics to investigate early responses to drought stress. The results highlight the potential of combining the analyses of phenotypic and metabolic responses to identify key mechanisms and markers associated with drought tolerance in both the Brachypodium model plant as

  11. Determination of oxygen diffusion rates in magnetite from natural isotopic variations

    NASA Astrophysics Data System (ADS)

    Sharp, Z. D.

    1991-06-01

    The oxygen isotope compositions of magnetite grains, hosted in a calcite marble from the Bancroft terrane of the Ontario Grenville province, vary systematically with grain size. The δ18O values of magnetite and corresponding closure temperatures (Tc) based on Δcalcite-magnetite range from δ18O = 2.6‰, Tc = 505 °C for a grain radius of 0.075 mm, to δ18O = 5.5‰ Tc = 660 °C for a grain radius of 1.15 mm. The δ18O of the calcite is constant within a scale of 100 μm at a value of 12.3‰. The observed isotopic variations can be fit to the diffusion model of Dodson by the method of least squares (r = 0.98) to yield an activation energy (Q) = 211 (±20) kJ/mole and a pre-exponential factor (Do) = 4.3 (+3.3, -1.9) x 10-7 cm2/s for a cooling rate of 4 °C/m.y. The activation energy estimate is independent of the assumed cooling rate, but the calculated pre-exponential factor varies as follows: Do (cm2/s) = (dT/dt) x (-1.08 x 10-7). (Note: dT/dt is in °C/m.y.) The activation energy is identical to an experimental determination by Giletti and Hess, but the pre-exponential factor is 100 times lower. The difference is attributed to the water-rich conditions in the experiments and the absence of fluid in the slowly cooled marbles investigated in this study. The strong dependence of diffusion rate on water presence, or fH2O, may be used as a sensor for water-rich fluids during cooling in natural systems.

  12. Natural variation among Arabidopsis accessions reveals malic acid as a key mediator of Nickel (Ni) tolerance.

    PubMed

    Agrawal, Bhavana; Lakshmanan, Venkatachalam; Kaushik, Shail; Bais, Harsh P

    2012-08-01

    Plants have evolved various mechanisms for detoxification that are specific to the plant species as well as the metal ion chemical properties. Malic acid, which is commonly found in plants, participates in a number of physiological processes including metal chelation. Using natural variation among Arabidopsis accessions, we investigated the function of malic acid in Nickel (Ni) tolerance and detoxification. The Ni-induced production of reactive oxygen species was found to be modulated by intracellular malic acid, indicating its crucial role in Ni detoxification. Ni tolerance in Arabidopsis may actively involve malic acid and/or complexes of Ni and malic acid. Investigation of malic acid content in roots among tolerant ecotypes suggested that a complex of Ni and malic acid may be involved in translocation of Ni from roots to leaves. The exudation of malic acid from roots in response to Ni treatment in either susceptible or tolerant plant species was found to be partially dependent on AtALMT1 expression. A lower concentration of Ni (10 µM) treatment induced AtALMT1 expression in the Ni-tolerant Arabidopsis ecotypes. We found that the ecotype Santa Clara (S.C.) not only tolerated Ni but also accumulated more Ni in leaves compared to other ecotypes. Thus, the ecotype S.C. can be used as a model system to delineate the biochemical and genetic basis of Ni tolerance, accumulation, and detoxification in plants. The evolution of Ni hyperaccumulators, which are found in serpentine soils, is an interesting corollary to the fact that S.C. is also native to serpentine soils.

  13. Natural Genetic Variation in the Caenorhabditis elegans Response to Pseudomonas aeruginosa

    PubMed Central

    Martin, Natalia; Singh, Jogender; Aballay, Alejandro

    2017-01-01

    Caenorhabditis elegans responds to pathogenic microorganisms by activating its innate immune system, which consists of physical barriers, behavioral responses, and microbial killing mechanisms. We examined whether natural variation plays a role in the response of C. elegans to Pseudomonas aeruginosa using two C. elegans strains that carry the same allele of npr-1, a gene that encodes a G-protein-coupled receptor related to mammalian neuropeptide Y receptors, but that differ in their genetic backgrounds. Strains carrying an allele for the NPR-1 215F isoform have been shown to exhibit lack of pathogen avoidance behavior and deficient immune response toward P. aeruginosa relative to the wild-type (N2) strain. We found that the wild isolate from Germany RC301, which carries the allele for NPR-1 215F, shows an enhanced resistance to P. aeruginosa infection when compared with strain DA650, which also carries NPR-1 215F but in an N2 background. Using a whole-genome sequencing single-nucleotide polymorphism (WGS-SNP) mapping strategy, we determined that the resistance to P. aeruginosa infection maps to a region on chromosome V. Furthermore, we demonstrated that the mechanism for the enhanced resistance to P. aeruginosa infection relies exclusively on strong P. aeruginosa avoidance behavior, and does not involve the main immune, stress, and lifespan extension pathways in C. elegans. Our findings underscore the importance of pathogen-specific behavioral immune defense in the wild, which seems to be favored over the more energy-costly mechanism of activation of physiological cellular defenses. PMID:28179390

  14. Natural variations of copper and sulfur stable isotopes in blood of hepatocellular carcinoma patients.

    PubMed

    Balter, Vincent; Nogueira da Costa, Andre; Bondanese, Victor Paky; Jaouen, Klervia; Lamboux, Aline; Sangrajrang, Suleeporn; Vincent, Nicolas; Fourel, François; Télouk, Philippe; Gigou, Michelle; Lécuyer, Christophe; Srivatanakul, Petcharin; Bréchot, Christian; Albarède, Francis; Hainaut, Pierre

    2015-01-27

    The widespread hypoxic conditions of the tumor microenvironment can impair the metabolism of bioessential elements such as copper and sulfur, notably by changing their redox state and, as a consequence, their ability to bind specific molecules. Because competing redox state is known to drive isotopic fractionation, we have used here the stable isotope compositions of copper ((65)Cu/(63)Cu) and sulfur ((34)S/(32)S) in the blood of patients with hepatocellular carcinoma (HCC) as a tool to explore the cancer-driven copper and sulfur imbalances. We report that copper is (63)Cu-enriched by ∼0.4‰ and sulfur is (32)S-enriched by ∼1.5‰ in the blood of patients compared with that of control subjects. As expected, HCC patients have more copper in red blood cells and serum compared with control subjects. However, the isotopic signature of this blood extra copper burden is not in favor of a dietary origin but rather suggests a reallocation in the body of copper bound to cysteine-rich proteins such as metallothioneins. The magnitude of the sulfur isotope effect is similar in red blood cells and serum of HCC patients, implying that sulfur fractionation is systemic. The (32)S-enrichment of sulfur in the blood of HCC patients is compatible with the notion that sulfur partly originates from tumor-derived sulfides. The measurement of natural variations of stable isotope compositions, using techniques developed in the field of Earth sciences, can provide new means to detect and quantify cancer metabolic changes and provide insights into underlying mechanisms.

  15. Natural Genetic Variation in the Caenorhabditis elegans Response to Pseudomonas aeruginosa.

    PubMed

    Martin, Natalia; Singh, Jogender; Aballay, Alejandro

    2017-02-07

    Caenorhabditis elegans responds to pathogenic microorganisms by activating its innate immune system, which consists of physical barriers, behavioral responses, and microbial killing mechanisms. We examined whether natural variation plays a role in the response of C. elegans to Pseudomonas aeruginosa using two C. elegans strains that carry the same allele of npr-1, a gene that encodes a G-protein-coupled receptor related to mammalian neuropeptide Y receptors, but that differ in their genetic backgrounds. Strains carrying an allele for the NPR-1 215F isoform have been shown to exhibit lack of pathogen avoidance behavior and deficient immune response towards P. aeruginosa relative to the wild-type (N2) strain. We found that the wild isolate from Germany RC301, which carries the allele for NPR-1 215F, shows an enhanced resistance to P. aeruginosa infection when compared with strain DA650, which also carries NPR-1 215F but in an N2 background. Using a whole-genome sequencing single-nucleotide polymorphism (WGS-SNP) mapping strategy, we determined that the resistance to P. aeruginosa infection maps to a region on chromosome V. Furthermore, we demonstrated that the mechanism for the enhanced resistance to P. aeruginosa infection relies exclusively on strong P. aeruginosa avoidance behavior and does not involve the main immune, stress and lifespan extension pathways in C. elegans Our findings underscore the importance of pathogen-specific behavioral immune defense in the wild, which seems to be favored over the more energy-costly mechanism of activation of physiological cellular defenses.

  16. Natural variations of copper and sulfur stable isotopes in blood of hepatocellular carcinoma patients

    NASA Astrophysics Data System (ADS)

    Balter, Vincent; Nogueira da Costa, Andre; Paky Bondanese, Victor; Jaouen, Klervia; Lamboux, Aline; Sangrajrang, Suleeporn; Vincent, Nicolas; Fourel, François; Télouk, Philippe; Gigou, Michelle; Lécuyer, Christophe; Srivatanakul, Petcharin; Bréchot, Christian; Albarède, Francis; Hainaut, Pierre

    2015-01-01

    The widespread hypoxic conditions of the tumor microenvironment can impair the metabolism of bioessential elements such as copper and sulfur, notably by changing their redox state and, as a consequence, their ability to bind specific molecules. Because competing redox state is known to drive isotopic fractionation, we have used here the stable isotope compositions of copper (65Cu/63Cu) and sulfur (34S/32S) in the blood of patients with hepatocellular carcinoma (HCC) as a tool to explore the cancer-driven copper and sulfur imbalances. We report that copper is 63Cu-enriched by ∼0.4‰ and sulfur is 32S-enriched by ∼1.5‰ in the blood of patients compared with that of control subjects. As expected, HCC patients have more copper in red blood cells and serum compared with control subjects. However, the isotopic signature of this blood extra copper burden is not in favor of a dietary origin but rather suggests a reallocation in the body of copper bound to cysteine-rich proteins such as metallothioneins. The magnitude of the sulfur isotope effect is similar in red blood cells and serum of HCC patients, implying that sulfur fractionation is systemic. The 32S-enrichment of sulfur in the blood of HCC patients is compatible with the notion that sulfur partly originates from tumor-derived sulfides. The measurement of natural variations of stable isotope compositions, using techniques developed in the field of Earth sciences, can provide new means to detect and quantify cancer metabolic changes and provide insights into underlying mechanisms.

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

    NASA Astrophysics Data System (ADS)

    Kim, J. G.; Liu, H.

    2007-10-01

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

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

    PubMed Central

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

    2016-01-01

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

  19. Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes

    PubMed Central

    Härtl, Katja; Denton, Alisandra; Franz-Oberdorf, Katrin; Hoffmann, Thomas; Spornraft, Melanie; Usadel, Björn; Schwab, Wilfried

    2017-01-01

    Strawberry fruits (Fragaria vesca) are valued for their sweet fruity flavor, juicy texture, and characteristic red color caused by anthocyanin pigments. To gain a deeper insight into the regulation of anthocyanin biosynthesis, we performed comparative metabolite profiling and transcriptome analyses of one red-fruited and two natural white-fruited strawberry varieties in two tissues and three ripening stages. Developing fruit of the three genotypes showed a distinctive pattern of polyphenol accumulation already in green receptacle and achenes. Global analysis of the transcriptomes revealed that the ripening process in the white-fruited varieties is already affected at an early developmental stage. Key polyphenol genes showed considerably lower transcript levels in the receptacle and achenes of both white genotypes, compared to the red genotype. The expression of the anthocyanidin glucosyltransferase gene and a glutathione S-transferase, putatively involved in the vacuolar transport of the anthocyanins, seemed to be critical for anthocyanin formation. A bHLH transcription factor is among the differentially expressed genes as well. Furthermore, genes associated with flavor formation and fruit softening appear to be coordinately regulated and seem to interact with the polyphenol biosynthesis pathway. This study provides new information about polyphenol biosynthesis regulators in strawberry, and reveals genes unknown to affect anthocyanin formation. PMID:28327625

  20. A man-induced landslide in Lower Austria: natural conditions versus man-made causes

    NASA Astrophysics Data System (ADS)

    Kittel, Roland; Ottner, Franz; Damm, Bodo; Terhorst, Birgit

    2010-05-01

    In many cases, composition and characteristics of hillslope sediments are of particular importance related to landslide research in low mountain areas. The interaction of geologic, geomorphologic, and hydrologic factors determines the susceptibility for mass movements, which is affected by human impact as well. The present study aims to investigate factors that control mass movements and natural and anthropogenic impacts. On March 8th 2009, a landslide of 30.000 to 50.000 m³ occurred that destroyed a large part of a sports ground in the village of Hintersdorf, municipality of St. Andrä-Wördern (Lower Austria). As a result of extensive water supply ground liquefaction was initiated and the slide mass moved in form of a mud flow about 200 m down slope. As a consequence a small forest area and a fishpond were destroyed and an adjacent road was damaged. Closely to the event, first studies started and showed that the Hintersdorf landslide was triggered by extensive water saturation combined with hydrostatic pressure inside the slide mass. Heavy and long-lasting rainfalls and the start of snowmelt caused strong seepage and soil water saturation. Furthermore, insufficient ground drainage and overflow of a small retention pond intensified the unfavourable impact on soil-mechanical stability. Further studies included archive data analyse, field survey, as well as laboratory analyse and showed that high landslide susceptibility at the Hintersdorf landslide site was caused by a bundle of factors that control the process: The sports ground was built nearby the head of a trough valley that collects interflow and surface run-off from the surrounding slopes. The Flysch bedrock is covered extensively by clayey slope deposits. Furthermore, in the area of the valley head a waste deposit was operated up to the 1980's that resulted in a thick waste filling there. The Hintersdorf sports ground was constructed in 1984 on top of the waste body. Preliminary results show that hillslope

  1. A high-definition view of functional genetic variation from natural yeast genomes.

    PubMed

    Bergström, Anders; Simpson, Jared T; Salinas, Francisco; Barré, Benjamin; Parts, Leopold; Zia, Amin; Nguyen Ba, Alex N; Moses, Alan M; Louis, Edward J; Mustonen, Ville; Warringer, Jonas; Durbin, Richard; Liti, Gianni

    2014-04-01

    The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.

  2. A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

    PubMed Central

    Bergström, Anders; Simpson, Jared T.; Salinas, Francisco; Barré, Benjamin; Parts, Leopold; Zia, Amin; Nguyen Ba, Alex N.; Moses, Alan M.; Louis, Edward J.; Mustonen, Ville; Warringer, Jonas; Durbin, Richard; Liti, Gianni

    2014-01-01

    The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies. PMID:24425782

  3. Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster.

    PubMed

    Dembeck, Lauren M; Böröczky, Katalin; Huang, Wen; Schal, Coby; Anholt, Robert R H; Mackay, Trudy F C

    2015-11-14

    Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition.

  4. Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size.

    PubMed

    Wang, Li; He, Lingli; Li, Jing; Zhao, Jing; Li, Zhichao; He, Chaoying

    2014-07-01

    The genetic basis of size variation in the reproductive organs of tomatillo (Physalis philadelphica) is unknown. Here we report that the expression levels of the gene Physalis Organ Size 1 (POS1) are positively associated with size variation in P. philadelphica reproductive organs such flowers, berries and seeds. POS1 knockdown results in smaller flowers and berries with smaller cells as compared with their wild-type counterparts. Conversely, POS1 overexpression promotes organ size without increasing the cell number. The first introns of the POS1 alleles from the large, intermediate and small tomatillo groups contain one, two and three 37-bp repeats, respectively. Furthermore, our results show that copy variation of repeats in the first intron of POS1 alleles results in differential expression of this gene. Thus, co-variation in tomatillo reproductive organ sizes can be attributed to the novel regulatory variation in POS1.

  5. Research of Ionospheric Total Electron Content Variations Caused by Powerful Radio Emission of `SURA' Facility on Network of Gnss - Receivers

    NASA Astrophysics Data System (ADS)

    Kogogin, Denis; Nasyrov, Igor; Grach, Savely; Shindin, Alexey; Zagretdinov, Renat; Shaimukhametov, Ramil; Kislichin, Alexander; Ryabova, Mariya

    Large-scale irregularities with scales of 5-50 km can be effectively studied using dual-frequency raying by signals of the Navstar (GPS) and GLONASS microwave satellite systems. During propagation through the heated region, such signals acquire an additional phase increment stipulated by the dispersion of radio waves in the ionospheric plasma and linearly related to the total electron content (TEC) on the propagation trajectory. In this work we present results of measurement of total electron content (TEC) variations in the F2 part of the ionosphere of the Earth caused by powerful radio emission of “Sura” facility carried out during several experimental companies from 2010 to 2013 years. Parameters of TEC-variations were obtained by dual - frequency global navigation satellite systems (GNSS) diagnostics. Registration of signal parameters from GNSS-transmitters was performed at spatially separated sites around the “Sura” facility: Vasilsursk (56(°) 08' N, 46(°) 05' E), Zelenodolsk (55(°) 52' N, 48(°) 33' E), Kazan (55(°) 48' N, 49(°) 08' E) and Yoshkar-Ola (56(°) 38'N, 47(°) 52'E). The initial data containing measurements of the phase L and pseudorange P for the operating frequencies f1 =1575.42 MHz and f2 = 1227.60 MHz are RINEX files. For a detail study of small TEC variations based on the initial dependence, the trend was removed by subtraction of the moving average with the use of the linear weight function. In the experiments radio path from GNSS satellite to Vasilsursk passed over the disturbed region of ionosphere, but radio paths to Zelenodolsk, to Kazan and to Yoshkar-Ola did not. However, TEC-variations correlated with pumping of ionosphere by ”Sura” facility were detected for three ground measurements sites, situated along the “Sura” facility geomagnetic longitude (Vasilsursk, Zelenodolsk, Kazan). Magnitudes of TEC-variations reached 0.15-0.3 TECU. Velocity of propagation of large-scale ionospheric disturbance stimulated by

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

    NASA Astrophysics Data System (ADS)

    Steinberger, Bernhard

    2016-04-01

    Large-scale topography may be due to several causes, including (1) variations in crustal thickness and density structure, (2) oceanic lithosphere age differences, (3) subcrustal density variations in the continental lithosphere and (4) convective flow in the mantle beneath the lithosphere. The last contribution in particular may change with time and be responsible for continental inundations; distinguishing between these contributions is therefore important for linking Earth's history to its observed geological record. As a step towards this goal, this paper aims at such distinction for the present-day topography: the approach taken is deriving a `model' topography due to contributions (3) and (4), along with a model geoid, using a geodynamic mantle flow model. Both lithosphere thickness and density anomalies beneath the lithosphere are inferred from seismic tomography. Density anomalies within the continental lithosphere are uncertain, because they are probably due to variations in composition and temperature, making a simple scaling from seismic to density anomalies inappropriate. Therefore, we test a number of different assumptions regarding these. As a reality check, model topography is compared, in terms of both correlation and amplitude ratio, to `residual' topography, which follows from observed topography after subtracting contributions (1) and (2). The model geoid is compared to observations as well. Comparatively good agreement is found if there is either an excess density of ≈0.2 per cent in the lithosphere above ≈150 km depth, with anomalies below as inferred from tomography, or if the excess density is ≈0.4 per cent in the entire lithosphere. Further, a good fit is found for viscosity ≈1020 Pa s in the asthenosphere, increasing to ≈1023 Pa s in the lower mantle above D'. Results are quite dependent on which tomography models they are based on; for some recent ones, topography correlation is ≈0.6, many smaller scale features are matched

  7. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa.

    PubMed

    Franks, Steven J; Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J; Lalchan, Rebecca; Jordan, Kevin P; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  8. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa

    PubMed Central

    Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J.; Lalchan, Rebecca; Jordan, Kevin P.; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  9. Untangling the nature of spatial variations of cold dust properties in star forming galaxies

    SciTech Connect

    Kirkpatrick, Allison; Calzetti, Daniela; Kennicutt, Robert; Galametz, Maud; Gordon, Karl; Groves, Brent; Tabatabaei, Fatemeh; Hunt, Leslie; Dale, Daniel; Hinz, Joannah

    2014-07-10

    We investigate the far-infrared (IR) dust emission for 20 local star forming galaxies from the Key Insights on Nearby Galaxies: A Far-IR Survey with Herschel (KINGFISH) sample. We model the far-IR/submillimeter spectral energy distribution (SED) using images from Spitzer Space Telescope and Herschel Space Observatory. We calculate the cold dust temperature (T{sub c} ) and emissivity (β) on a pixel by pixel basis (where each pixel ranges from 0.1 to 3 kpc{sup 2}) using a two-temperature modified blackbody fitting routine. Our fitting method allows us to investigate the resolved nature of temperature and emissivity variations by modeling from the galaxy centers to the outskirts (physical scales of ∼15-50 kpc, depending on the size of the galaxy). We fit each SED in two ways: (1) fit T{sub c} and β simultaneously, (2) hold β constant and fit T{sub c} . We compare T{sub c} and β with star formation rates (calculated from L{sub Hα} and L{sub 24μm}), the luminosity of the old stellar population (traced through L{sub 3.6μm}), and the dust mass surface density (traced by 500 μm luminosity, L{sub 500}). We find a significant trend between SFR/L{sub 500} and T{sub c} , implying that the flux of hard UV photons relative to the amount of dust is significantly contributing to the heating of the cold, or diffuse, dust component. We also see a trend between L{sub 3.6}/L{sub 500} and β, indicating that the old stellar population contributes to the heating at far-IR/submillimeter wavelengths. Finally, we find that when β is held constant, T{sub c} exhibits a strongly decreasing radial trend, illustrating that the shape of the far-IR SED is changing radially through a galaxy, thus confirming on a sample almost double in size the trends observed in Galametz et al.

  10. Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines

    PubMed Central

    Ulvestad, Marte; Overland, Indra

    2012-01-01

    This article develops a formal model for comparing the cost structure of the two main transport options for natural gas: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG. PMID:24683269

  11. Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines.

    PubMed

    Ulvestad, Marte; Overland, Indra

    2012-06-01

    THIS ARTICLE DEVELOPS A FORMAL MODEL FOR COMPARING THE COST STRUCTURE OF THE TWO MAIN TRANSPORT OPTIONS FOR NATURAL GAS: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG.

  12. Spatiotemporal variations in channel changes caused by cumulative factors in a meandering river: The lower Peixe River, Brazil

    NASA Astrophysics Data System (ADS)

    Morais, Eduardo S.; Rocha, Paulo C.; Hooke, Janet

    2016-11-01

    Channel changes in meandering rivers naturally exhibit complex behaviour, and understanding the river dynamics can be challenging in environments also subject to cumulative human impacts. Planform changes were analysed on four reaches of the lower course of the Peixe River, Brazil, at decadal scales over the period 1962-2008 from aerial photographs and satellite imagery, complemented by a historical map from 1907. Analysis of the spatial and temporal patterns of channel change mechanisms and morphometry of bends and of the sinuosity and morphodynamic variations of the reaches demonstrates major changes in planform characteristics. Sinuosity in all reaches decreased from 2.6 to 1.7, average wavelength of bends has increased from 200 to 500 m, and the planform has become much simpler. Changes have been progressive from downstream to upstream, with higher intensities of processes, particularly cutoffs first in downstream reaches then more recently in upstream reaches. It is suggested that channel changes represent a morphological adjustment to human interventions, such as reservoir construction and land use. However, evidence of the autogenic behaviour of meanders is highlighted in which the existence of compound meanders reveals control over the spatial variation in the reaches. The results suggest that geomorphic thresholds associated with the compound meander formation and the bend evolution should be considered, even in impacted meandering rivers, because they exert primary controls on the spatial-temporal adjustment of channels.

  13. Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation.

    PubMed

    Verhulst, Eveline C; Mateman, A Christa; Zwier, Mathijs V; Caro, Samuel P; Verhoeven, Koen J F; van Oers, Kees

    2016-04-01

    Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here, we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their DNA methylation levels at the dopamine receptor D4 (DRD4) gene. This D4 receptor is statistically associated with personality traits in both humans and nonhuman animals, including the great tit. Previous work in this songbird failed to detect functional genetic polymorphisms within DRD4 that could account for the gene-trait association. However, our observation supports the idea that DRD4 is functionally involved in exploratory behaviour but that its effects are mediated by DNA methylation. While the exact mechanism underlying the transgenerational consistency of DRD4 methylation remains to be elucidated, this study shows that epigenetic mechanisms are involved in shaping natural variation in personality traits. We outline how this first finding provides a basis for investigating the epigenetic contribution to personality traits in natural systems and its subsequent role for understanding the ecology and evolution of behavioural consistency.

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

    ERIC Educational Resources Information Center

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

    2014-01-01

    Natural selection is one of the most famous metaphors in the history of science. Charles Darwin used the metaphor and the underlying analogy to frame his ideas about evolution and its main driving mechanism into a full-fledged theory. Because the metaphor turned out to be such a powerful epistemic tool, Darwin naturally assumed that he could also…

  15. Variation in Type A Trichothecene Production and Trichothecene Biosynthetic Genes in Fusarium goolgardi from Natural Ecosystems of Australia

    PubMed Central

    Rocha, Liliana O.; Laurence, Matthew H.; Proctor, Robert H.; McCormick, Susan P.; Summerell, Brett A.; Liew, Edward C. Y.

    2015-01-01

    Fusarium goolgardi, isolated from the grass tree Xanthorrhoea glauca in natural ecosystems of Australia, is closely related to fusaria that produce a subgroup of trichothecene (type A) mycotoxins that lack a carbonyl group at carbon atom 8 (C-8). Mass spectrometric analysis revealed that F. goolgardi isolates produce type A trichothecenes, but exhibited one of two chemotypes. Some isolates (50%) produced multiple type A trichothecenes, including 4,15-diacetoxyscirpenol (DAS), neosolaniol (NEO), 8-acetylneosolaniol (Ac-NEO) and T-2 toxin (DAS-NEO-T2 chemotype). Other isolates (50%) produced only DAS (DAS chemotype). In the phylogenies inferred from DNA sequences of genes encoding the RNA polymerase II largest (RPB1) and second largest (RPB2) subunits as well as the trichothecene biosynthetic genes (TRI), F. goolgardi isolates were resolved as a monophyletic clade, distinct from other type A trichothecene-producing species. However, the relationships of F. goolgardi to the other species varied depending on whether phylogenies were inferred from RPB1 and RPB2, the 12-gene TRI cluster, the two-gene TRI1-TRI16 locus, or the single-gene TRI101 locus. Phylogenies based on different TRI loci resolved isolates with different chemotypes into distinct clades, even though only the TRI1-TRI16 locus is responsible for structural variation at C-8. Sequence analysis indicated that TRI1 and TRI16 are functional in F. goolgardi isolates with the DAS-NEO-T2 chemotype, but non-functional in isolates with DAS chemotype due to the presence of premature stop codons caused by a point mutation. PMID:26556373

  16. Annual Variation in Flowering Phenology, Pollination, Mating System, and Pollen Yield in Two Natural Populations of Schima wallichii (DC.) Korth

    PubMed Central

    Khanduri, Vinod Prasad; Sharma, C. M.; Kumar, K. S.; Ghildiyal, S. K.

    2013-01-01

    Background. Schima wallichii is a highly valuable tree of tropical forest in north-east Himalaya region that grows naturally in a wide range of altitudes between 750 and 2400 m asl with varying environments. Flowering phenology of tropical tree species at population level is generally ignored and therefore a detailed knowledge of flowering and fruiting patterns of important multipurpose tree species is critical to the successful management of forest genetic resources. Materials and Methods. The study was conducted at two different altitudes (i.e., 750 m and 900 m asl) in the tropical semideciduous forest of north-east Himalaya. The floral phenology including flowering synchrony in the populations, anthesis, anther dehiscence, stigma receptivity, pollinators visitation frequency, and mating system including index of self-incompatibility were worked out in Schima wallichii according to the ear-marked standard methods given by various scientists for each parameter. Results. The flowering period in Schima wallichii varied from 33 to 42 days with mean synchrony of 0.54 to 0.68 between the populations. The stigma was receptive up to 2.5 days only and showed slightly protandrous type of dichogamy. Average pollen production ranged between 6.90 × 107 pollen per tree in 2007 and 15.49 × 108 pollen per tree in 2011. A three-year masting cycle was noticed in this species. The frequency of visitation of honey bees was fairly high (5.2 ± 1.12 visits/flower/hour) as compared to other pollinators. The hand pollination revealed maximum fruit (74.2 ± 5.72%) and seed (70.8 ± 7.46%) settings. Conclusions. The variation in flowering phenology and pollen yield individually and annually along with temporal separation in anther dehiscence and pollinator's visitation cause pollen limited reproduction, which ultimately influences the reproductive success in Schima wallichii. PMID:24501577

  17. Observer variation in grading sacroiliac radiographs might be a cause of 'sacroiliitis' reported in certain disease states.

    PubMed Central

    Yazici, H; Turunç, M; Ozdoğan, H; Yurdakul, S; Akinci, A; Barnes, C G

    1987-01-01

    Radiological sacroiliitis in Behçet's syndrome (BS) has been a subject of controversy. We have examined pelvic radiographs of 38 patients with BS and 28 age and sex matched controls which we reported previously, and also 17 with ankylosing spondylitis (AS), 27 with non-renal familial Mediterranean fever (FMF), and 33 with primary osteoarthrosis (OA). Initially, five observers assessed radiographs on two different occasions according to the New York criteria for sacroiliitis in a blind protocol. Later, three of them examined the various possible abnormalities of the sacroiliac (SI) joints after training sessions. Although the inter- and intraobserver variation was quite high, all observers found the expected changes in patients with AS. The abnormalities detected in the other diseases were either mild, inconsistent, or both. Erosions were confined to patients with AS, and osteophytes and glenoid sulci to patients with OA. We conclude that high observer variation in interpreting a film of the anteroposterior (AP) view of the pelvis for sacroiliitis may be a major cause of reported 'sacroiliitis' in BS and FMF. PMID:3827336

  18. Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation.

    PubMed

    Zhang, Han; Zhao, Yang-Yu; Song, Jing; Zhu, Qi-Ying; Yang, Hua; Zheng, Mei-Ling; Xuan, Zhao-Ling; Wei, Yuan; Chen, Yang; Yuan, Peng-Bo; Yu, Yang; Li, Da-Wei; Liang, Jun-Bin; Fan, Ling; Chen, Chong-Jian; Qiao, Jie

    2015-11-04

    Analyses of cell-free fetal DNA (cff-DNA) from maternal plasma using massively parallel sequencing enable the noninvasive detection of feto-placental chromosome aneuploidy; this technique has been widely used in clinics worldwide. Noninvasive prenatal tests (NIPT) based on cff-DNA have achieved very high accuracy; however, they suffer from maternal copy-number variations (CNV) that may cause false positives and false negatives. In this study, we developed an algorithm to exclude the effect of maternal CNV and refined the Z-score that is used to determine fetal aneuploidy. The simulation results showed that the algorithm is robust against variations of fetal concentration and maternal CNV size. We also introduced a method based on the discrepancy between feto-placental concentrations to help reduce the false-positive ratio. A total of 6615 pregnant women were enrolled in a prospective study to validate the accuracy of our method. All 106 fetuses with T21, 20 with T18, and three with T13 were tested using our method, with sensitivity of 100% and specificity of 99.97%. In the results, two cases with maternal duplications in chromosome 21, which were falsely predicted as T21 by the previous NIPT method, were correctly classified as normal by our algorithm, which demonstrated the effectiveness of our approach.

  19. The Natural Variation in Lifespans of Single Yeast Cells Is Related to Variation in Cell Size, Ribosomal Protein, and Division Time

    PubMed Central

    Janssens, Georges E.

    2016-01-01

    There is a large variability in lifespans of individuals even if they are genetically identical and raised under the same environmental conditions. Our recent system wide study of replicative aging in baker’s yeast predicts that protein biogenesis is a driver of aging. Here, we address how the natural variation in replicative lifespan within wild-type populations of yeast cells correlates to three biogenesis-related parameters, namely cell size, ribosomal protein Rpl13A-GFP levels, and division times. Imaging wild type yeast cells in microfluidic devices we observe that in all cells and at all ages, the division times as well as the increase in cell size that single yeast undergo while aging negatively correlate to their lifespan. In the longer-lived cells Rpl13A-GFP levels also negatively correlate to lifespan. Interestingly however, at young ages in the population, ribosome concentration was lowest in the cells that increased the most in size and had shorter lifespans. The correlations between these molecular and cellular properties related to biogenesis and lifespan explain a small portion of the variation in lifespans of individual cells, consistent with the highly individual and multifactorial nature of aging. PMID:27907085

  20. The Natural Variation in Lifespans of Single Yeast Cells Is Related to Variation in Cell Size, Ribosomal Protein, and Division Time.

    PubMed

    Janssens, Georges E; Veenhoff, Liesbeth M

    2016-01-01

    There is a large variability in lifespans of individuals even if they are genetically identical and raised under the same environmental conditions. Our recent system wide study of replicative aging in baker's yeast predicts that protein biogenesis is a driver of aging. Here, we address how the natural variation in replicative lifespan within wild-type populations of yeast cells correlates to three biogenesis-related parameters, namely cell size, ribosomal protein Rpl13A-GFP levels, and division times. Imaging wild type yeast cells in microfluidic devices we observe that in all cells and at all ages, the division times as well as the increase in cell size that single yeast undergo while aging negatively correlate to their lifespan. In the longer-lived cells Rpl13A-GFP levels also negatively correlate to lifespan. Interestingly however, at young ages in the population, ribosome concentration was lowest in the cells that increased the most in size and had shorter lifespans. The correlations between these molecular and cellular properties related to biogenesis and lifespan explain a small portion of the variation in lifespans of individual cells, consistent with the highly individual and multifactorial nature of aging.

  1. The Nature, Causes and Practices of Academic Dishonesty/Cheating in Higher Education: The Case of Hawassa University

    ERIC Educational Resources Information Center

    Bachore, Mebratu Mulatu

    2016-01-01

    The main objective of the study was to assess the perception of teachers and learners on the nature of practice, the type and the causes of academic cheating (dishonesty) in Hawassa University. The study was basically a survey which employed both qualitative and quantitative approaches to gather data. The subjects were 20 instructors and 60…

  2. Arsenic: Association of regional concentrations in drinking water with suicide and natural causes of death in Italy.

    PubMed

    Pompili, Maurizio; Vichi, Monica; Dinelli, Enrico; Erbuto, Denise; Pycha, Roger; Serafini, Gianluca; Giordano, Gloria; Valera, Paolo; Albanese, Stefano; Lima, Annamaria; De Vivo, Benedetto; Cicchella, Domenico; Rihmer, Zoltan; Fiorillo, Andrea; Amore, Mario; Girardi, Paolo; Baldessarini, Ross J

    2017-03-01

    Arsenic, as a toxin, may be associated with higher mortality rates, although its relationship to suicide is not clear. Given this uncertainty, we evaluated associations between local arsenic concentrations in tapwater and mortality in regions of Italy, to test the hypothesis that both natural-cause and suicide death rates would be higher with greater trace concentrations of arsenic. Arsenic concentrations in drinking-water samples from 145 sites were assayed by mass spectrometry, and correlated with local rates of mortality due to suicide and natural causes between 1980 and 2011, using weighted, least-squares univariate and multivariate regression modeling. Arsenic concentrations averaged 0.969 (CI: 0.543-1.396) µg/L, well below an accepted safe maximum of 10µg/L. Arsenic levels were negatively associated with corresponding suicide rates, consistently among both men and women in all three study-decades, whereas mortality from natural causes increased with arsenic levels. Contrary to an hypothesized greater risk of suicide with higher concentrations of arsenic, we found a negative association, suggesting a possible protective effect, whereas mortality from natural causes was increased, in accord with known toxic effects of arsenic. The unexpected inverse association between arsenic and suicide requires further study.

  3. Natural Variation in Odorant Recognition Among Odorant-Binding Proteins in Drosophila melanogaster

    PubMed Central

    Wang, Ping; Lyman, Richard F.; Mackay, Trudy F. C.; Anholt, Robert R. H.

    2010-01-01

    Chemical recognition is essential for survival and reproduction. Adaptive evolution has resulted in diverse chemoreceptor families, in which polymorphisms contribute to individual variation in chemosensation. To gain insights into the genetic determinants of individual variation in odorant recognition, we measured olfactory responses to two structurally similar odorants in a population of wild-derived inbred lines of Drosophila melanogaster. Odorant-binding proteins (OBPs) are the first components of the insect olfactory system to encounter odorants. Previously four single-nucleotide polymorphisms (SNPs) in the Obp99 group were associated with variation in olfactory responses to benzaldehyde. Here, we identify six different SNPs that are associated with variation in responses to a structurally similar odorant, acetophenone, in the same Obp genes. Five SNPs are in coding regions of Obp99b and Obp99d and one SNP is in the 3′-untranslated region of Obp99a (A610G). We found that the 610G allele is associated with higher response scores to acetophenone than the 610A allele, but with lower expression of Obp99a, suggesting that binding of acetophenone to Opb99a might limit rather than facilitate access to odorant receptors. Our results show that overlapping sets of OBPs contribute to odorant recognition for structurally similar odorants, but that different SNPs are associated with odorant-specific individual variation. Thus, dual olfactory recognition where OBPs regulate odorant access to receptors may enhance olfactory discrimination. PMID:20026676

  4. Diurnal and circadian variation of sleep and alertness in men vs. naturally cycling women.

    PubMed

    Boivin, Diane B; Shechter, Ari; Boudreau, Philippe; Begum, Esmot Ara; Ng Ying-Kin, Ng Mien Kwong

    2016-09-27

    This study quantifies sex differences in the diurnal and circadian variation of sleep and waking while controlling for menstrual cycle phase and hormonal contraceptive use. We compared the diurnal and circadian variation of sleep and alertness of 8 women studied during two phases of the menstrual cycle and 3 women studied during their midfollicular phase with that of 15 men. Participants underwent an ultradian sleep-wake cycle (USW) procedure consisting of 36 cycles of 60-min wake episodes alternating with 60-min nap opportunities. Core body temperature (CBT), salivary melatonin, subjective alertness, and polysomnographically recorded sleep were measured throughout this procedure. All analyzed measures showed a significant diurnal and circadian variation throughout the USW procedure. Compared with men, women demonstrated a significant phase advance of the CBT but not melatonin rhythms, as well as an advance in the diurnal and circadian variation of sleep measures and subjective alertness. Furthermore, women experienced an increased amplitude of the diurnal and circadian variation of alertness, mainly due to a larger decline in the nocturnal nadir. Our results indicate that women are likely initiating sleep at a later circadian phase than men, which may be one factor contributing to the increased susceptibility to sleep disturbances reported in women. Lower nighttime alertness is also observed, suggesting a physiological basis for a greater susceptibility to maladaptation to night shift work in women.

  5. Diurnal and circadian variation of sleep and alertness in men vs. naturally cycling women

    PubMed Central

    Boivin, Diane B.; Shechter, Ari; Boudreau, Philippe; Begum, Esmot Ara; Ng Ying-Kin, Ng Mien Kwong

    2016-01-01

    This study quantifies sex differences in the diurnal and circadian variation of sleep and waking while controlling for menstrual cycle phase and hormonal contraceptive use. We compared the diurnal and circadian variation of sleep and alertness of 8 women studied during two phases of the menstrual cycle and 3 women studied during their midfollicular phase with that of 15 men. Participants underwent an ultradian sleep–wake cycle (USW) procedure consisting of 36 cycles of 60-min wake episodes alternating with 60-min nap opportunities. Core body temperature (CBT), salivary melatonin, subjective alertness, and polysomnographically recorded sleep were measured throughout this procedure. All analyzed measures showed a significant diurnal and circadian variation throughout the USW procedure. Compared with men, women demonstrated a significant phase advance of the CBT but not melatonin rhythms, as well as an advance in the diurnal and circadian variation of sleep measures and subjective alertness. Furthermore, women experienced an increased amplitude of the diurnal and circadian variation of alertness, mainly due to a larger decline in the nocturnal nadir. Our results indicate that women are likely initiating sleep at a later circadian phase than men, which may be one factor contributing to the increased susceptibility to sleep disturbances reported in women. Lower nighttime alertness is also observed, suggesting a physiological basis for a greater susceptibility to maladaptation to night shift work in women. PMID:27621470

  6. Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster

    PubMed Central

    Dembeck, Lauren M; Böröczky, Katalin; Huang, Wen; Schal, Coby; Anholt, Robert R H; Mackay, Trudy F C

    2015-01-01

    Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition. DOI: http://dx.doi.org/10.7554/eLife.09861.001 PMID:26568309

  7. Genome-wide association implicates numerous genes and pleiotropy underlying ecological trait variation in natural populations of Populus trichocarpa

    SciTech Connect

    McKown, Athena; Klapste, Jaroslav; Guy, Robert; Geraldes, Armando; Porth, Ilga; Hannemann, Jan; Friedmann, Michael; Muchero, Wellington; Tuskan, Gerald A; Ehlting, Juergen; Cronk, Quentin; El-Kassaby, Yousry; Mansfield, Shawn; Douglas, Carl

    2014-01-01

    To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).

  8. Natural variation in the Pto pathogen resistance gene within species of wild tomato (Lycopersicon). I. Functional analysis of Pto alleles.

    PubMed

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

    2005-09-01

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

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

    PubMed Central

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

    2005-01-01

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

  10. Patterns of Naturally Occurring Restriction Map Variation, Dopa Decarboxylase Activity Variation and Linkage Disequilibrium in the Ddc Gene Region of Drosophila Melanogaster

    PubMed Central

    Aquadro, C. F.; Jennings-Jr, R. M.; Bland, M. M.; Laurie, C. C.; Langley, C. H.

    1992-01-01

    Forty-six second-chromosome lines of Drosophila melanogaster isolated from five natural populations were surveyed for restriction map variation in a 65-kb region surrounding the gene (Ddc) encoding dopa decarboxylase (DDC). Sixty-nine restriction sites were scored, 13 of which were polymorphic. Average heterozygosity per nucleotide was estimated to be 0.005. Eight large (0.7-5.0 kb) inserts, two small inserts (100 and 200 bp) and three small deletions (100-300 bp) were also observed across the 65-kb region. We see no evidence for a reduction in either nucleotide heterozygosity or insertion/deletion variation in the central 26-kb segment containing Ddc and a dense cluster of lethal complementation groups and transcripts (>/=9 genes) compared to that seen in the adjacent regions (totaling 39 kb) in which only a single gene and transcript has been detected, or to that observed for other gene regions in D. melanogaster. The distribution of restriction site variation shows no significant departure from that expected under an equilibrium neutral model. However insertions and deletions show a significant departure from neutrality in that they are too rare in frequency, consistent with them being deleterious on average. Significant linkage disequilibrium among variants exists across much of the 65-kb region. Lower regional rates of recombination combined with the influence of polymorphic chromosomal inversions, rather than epistatic selection among genes in the dense cluster, probably are sufficient explanations for the creation and/or maintenance of the linkage disequilibrium observed in the Ddc region. We have also assayed adult DDC enzyme activity in these same lines. Twofold variation in activity among lines is observed within our sample. Significant associations are observed between level of DDC enzyme activity and restriction map variants. Surprisingly, one line with a 5.0-kb insert within an intron and one line with a 1.5-kb insert near the 5' end of Ddc each show

  11. Description, seasonal morphological variation, and molecular identification of Paraxanthus barbiger megalopae obtained from the natural environment

    NASA Astrophysics Data System (ADS)

    Ampuero, David; Palma, Alvaro T.; Veliz, David; Pardo, Luis Miguel

    2010-06-01

    Larval identification represents a powerful tool for detailed studies on recruitment and population dynamics in marine invertebrates. However, intra-specific morphological variation can become a serious limitation for the correct identification at species level. High morphological variation can be expected in species with continuous breeding periods because larvae are exposed to seasonal fluctuations in physical and biological factors during their development in the plankton. We describe, for the first time, the megalopae of Paraxanthus barbiger, one of the most common and abundant brachyuran crabs along the coast of Chile. To validate larvae identification, the 16S rRNA gene was sequenced from both megalopae and adults, and was compared with sequences of three sympatric species. In addition, size, body shape, and appendage setation pattern variations were analyzed with a year-round sampling scheme. The results demonstrated high seasonal phenotypic plasticity in size. Despite these differences, certain conservative characteristics exist which can be very useful for identification at species level.

  12. The nature of the optical variations of Seyfert galaxy 3C 120

    SciTech Connect

    Webb, J.R. Austin State Univ., TX )

    1990-01-01

    Results are presented from 61 years of optical observations of the Seyfert galaxy 3C 120. A previously published model of the 3C 120 light curve, derived from power spectrum analysis, is found to be valid for historical as well as current data. It is concluded that the optical variations of 3C 120 can be separated into a linear component, a sinusoidal component, and rapid, high-amplitude flares. Possible sources of the regular variations observed in 3C 120 are also suggested in the context of accretion models and other theoretical models. 15 refs.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. Naturally occurring continued fractions in the variation of Kepler's equation. [for guidance and trajectory optimization

    NASA Technical Reports Server (NTRS)

    Shepperd, Stanley W.

    1988-01-01

    A family of functions involving integrals of universal functions is introduced. These functions have some interesting mathematical properties including the fact that they may be expressed as Gaussian continued fractions. A unique method of performing the integration is demonstrated which indicates why these functions may be important in the variation of Kepler's equation.

  15. Natural variation for gene expression responses to abiotic stress in maize.

    PubMed

    Waters, Amanda J; Makarevitch, Irina; Noshay, Jaclyn; Burghardt, Liana T; Hirsch, Candice N; Hirsch, Cory D; Springer, Nathan M

    2017-02-01

    Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels of expression in response to abiotic stress, which requires concerted action of both cis- and trans-regulatory features. In order to study the variability in transcriptome response to abiotic stress, RNA sequencing was performed using 14-day-old maize seedlings of inbreds B73, Mo17, Oh43, PH207 and B37 under control, cold and heat conditions. Large numbers of genes that responded differentially to stress between parental inbred lines were identified. RNA sequencing was also performed on similar tissues of the F1 hybrids produced by crossing B73 and each of the three other inbred lines. By evaluating allele-specific transcript abundance in the F1 hybrids, we were able to measure the abundance of cis- and trans-regulatory variation between genotypes for both steady-state and stress-responsive expression differences. Although examples of trans-regulatory variation were observed, cis-regulatory variation was more common for both steady-state and stress-responsive expression differences. The genes with cis-allelic variation for response to cold or heat stress provided an opportunity to study the basis for regulatory diversity.

  16. On the Nature of Syntactic Variation: Evidence from Complex Predicates and Complex Word-Formation.

    ERIC Educational Resources Information Center

    Snyder, William

    2001-01-01

    Provides evidence from child language acquisition and comparative syntax for existence of a syntactic parameter in the classical sense of Chomsky (1981), with simultaneous effects on syntactic argument structure. Implications are that syntax is subject to points of substantive parametric variation as envisioned in Chomsky, and the time course of…

  17. Natural Selection and Evolution: Using Multimedia Slide Shows to Emphasize the Role of Genetic Variation

    ERIC Educational Resources Information Center

    Malone, Molly

    2012-01-01

    Most middle school students comprehend that organisms have adaptations that enable their survival and that successful adaptations prevail in a population over time. Yet they often miss that those bird beaks, moth-wing colors, or whatever traits are the result of random, normal genetic variations that just happen to confer a negative, neutral, or…

  18. Assessment of the natural variation of low abundant metabolic proteins in soybean seeds using proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry, we investigated the distribution of the low abundant proteins that are involved in soybean seed development in four wild and twelve cultivated soybean genotypes. We found proteomic variation of these proteins within and...

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

    PubMed

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

    2015-07-28

    Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United States--including the well-characterized Utah 30th generation inbred accession--and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis.

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

    PubMed Central

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

    2012-01-01

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

  1. The Nature, Extent and Causes of Abuse of Children with Disabilities in Schools in Botswana

    ERIC Educational Resources Information Center

    Shumba, Almon; Abosi, Okey C.

    2011-01-01

    Studies show that the exact number of children with disabilities in Botswana is unknown. A study on child abuse sought to determine: the forms of child abuse perpetrated on children with disabilities; the extent of child abuse; and the causes of child abuse of children with disabilities. A questionnaire on child abuse was adapted and used to…

  2. Modeling Modern Methane Emissions from Natural Wetlands. 2; Interannual Variations 1982-1993

    NASA Technical Reports Server (NTRS)

    Walter, Bernadette P.; Heimann, Martin; Mattews, Elaine; Hansen, James E. (Technical Monitor)

    2001-01-01

    A global run of a process-based methane model [Walter et al., this issue] is performed using high-frequency atmospheric forcing fields from ECMWF reanalyses of the period from 1982 to 1993. We calculate global annual methane emissions to be 260 Tg/ yr. 25% of methane emissions originate from wetlands north of 30 deg. N. Only 60% of the produced methane is emitted, while the rest is re-oxidized. A comparison of zonal integrals of simulated global wetland emissions and results obtained by an inverse modeling approach shows good agreement. In a test with data from two wetlands, the seasonality of simulated and observed methane emissions agrees well. The effects of sub-grid scale variations in model parameters and input data are examined. Modeled methane emissions show high regional, seasonal and interannual variability. Seasonal cycles of methane emissions are dominated by temperature in high latitude wetlands, and by changes in the water table in tropical wetlands. Sensitivity tests show that +/- 1 C changes in temperature lead to +/- 20 % changes in methane emissions from wetlands. Uniform changes of +/- 20% in precipitation alter methane emissions by about +/- 18%. Limitations in the model are analyzed. Simulated interannual variations in methane emissions from wetlands are compared to observed atmospheric growth rate anomalies. Our model simulation results suggest that contributions from other sources than wetlands and/or the sinks are more important in the tropics than north-of 30 deg. N. In higher northern latitudes, it seems that a large part, of the observed interannual variations can be explained by variations in wetland emissions. Our results also suggest that reduced wetland emissions played an important role in the observed negative methane growth rate anomaly in 1992.

  3. Population variation and natural selection on leaf traits in cork oak throughout its distribution range

    NASA Astrophysics Data System (ADS)

    Ramírez-Valiente, José Alberto; Valladares, Fernando; Sánchez-Gómez, David; Delgado, Antonio; Aranda, Ismael

    2014-07-01

    A central issue in evolutionary biology is the exploration of functional trait variation among populations and the extent to which this variation has adaptive value. It was recently proposed that specific leaf area (SLA), leaf nitrogen concentration per mass (Nmass) and water use efficiency in cork oak play an important role in adaptation to water availability in the environment. In order to investigate this hypothesis, we explored, first, whether there was population-level variation in cork oak (Quercus suber) for these functional traits throughout its distribution range; if this were the case, it would be consistent with the hypothesis that different rainfall patterns have led to ecotypic differentiation in this species. Second, we studied whether the population-level variation matched short-term selection on these traits under different water availability conditions using two fitness components: survival and growth. We found high population-level differentiation in SLA and Nmass, with populations from dry places exhibiting the lowest values for SLA and Nmass. Likewise, reduced SLA had fitness benefits in terms of growth for plants under dry conditions. However, contrary to our expectations, we did not find any pattern of association between functional traits and survival in nine-year-old saplings despite considerable drought during one year of the study period. These results together with findings from the literature suggest that early stages of development are the most critical period for this species. Most importantly, these findings suggest that cork oak saplings have a considerable potential to cope with dry conditions. This capacity to withstand aridity has important implications for conservation of cork oak woodlands under the ongoing climate change.

  4. Electrophoretically detectable protein variation in natural populations of the lone star tick, Amblyomma americanum (Acari: Ixodidae).

    PubMed

    Hilburn, L R; Sattler, P W

    1986-08-01

    Nine populations of Amblyomma americanum (L.) were examined electrophoretically for variation of 21 enzymes. Only three enzymes were not polymorphic and the average heterozygosity per individual (h) for the species was 0.085 with a range of 0.077 to 0.110, comparing well with values in other arthropods. The average Nei identity value for pairwise comparisons among the nine populations was high, 0.994 +/- 0.004 (I +/- SD). These high identity values and the absence of geographic structuring of the protein variation suggest that this species is genetically homogeneous. Normal levels of genic variability within and a lack of divergence between populations were not predicted by models developed to describe these genetic characteristics on the basis of the heterogeneities encountered by parasites in their environment. An analysis of data from several different species of ticks suggests host mobility and abundance, as well as tick abundance and selectivity in choosing a host, are important parameters in determining genetic variation in these ectoparasites.

  5. THE ANTICORRELATED NATURE OF THE PRIMARY AND SECONDARY ECLIPSE TIMING VARIATIONS FOR THE KEPLER CONTACT BINARIES

    SciTech Connect

    Tran, K.; Rappaport, S.; Levine, A.; Borkovits, T.; Csizmadia, Sz.; Kalomeni, B. E-mail: aml@space.mit.edu E-mail: szilard.csizmadia@dlr.de

    2013-09-01

    We report a study of the eclipse timing variations in contact binary systems, using long-cadence lightcurves from the Kepler archive. As a first step, observed minus calculated (O - C) curves were produced for both the primary and secondary eclipses of some 2000 Kepler binaries. We find {approx}390 short-period binaries with O - C curves that exhibit (1) random walk-like variations or quasi-periodicities, with typical amplitudes of {+-}200-300 s, and (2) anticorrelations between the primary and secondary eclipse timing variations. We present a detailed analysis and results for 32 of these binaries with orbital periods in the range of 0.35 {+-} 0.05 days. The anticorrelations observed in their O - C curves cannot be explained by a model involving mass transfer, which, among other things, requires implausibly high rates of {approx}0.01 M{sub Sun} yr{sup -1}. We show that the anticorrelated behavior, the amplitude of the O - C delays, and the overall random walk-like behavior can be explained by the presence of a starspot that is continuously visible around the orbit and slowly changes its longitude on timescales of weeks to months. The quasi-periods of {approx}50-200 days observed in the O - C curves suggest values for k, the coefficient of the latitude dependence of the stellar differential rotation, of {approx}0.003-0.013.

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

    NASA Astrophysics Data System (ADS)

    Beach, T.; Beach, S. L.

    2004-12-01

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

  7. Modelling seasonal variations of natural radioactivity in soils: A case study in southern Italy

    NASA Astrophysics Data System (ADS)

    Guagliardi, Ilaria; Rovella, Natalia; Apollaro, Carmine; Bloise, Andrea; Rosa, Rosanna De; Scarciglia, Fabio; Buttafuoco, Gabriele

    2016-12-01

    The activity of natural radionuclides in soil has become an environmental concern for local public and national authorities because of the harmful effects of radiation exposure on human health. In this context, modelling and mapping the activity of natural radionuclides in soil is an important research topic. The study was aimed to model, in a spatial sense, the soil radioactivity in an urban and peri-urban soils area in southern Italy to analyse the seasonal influence on soil radioactivity. Measures of gamma radiation naturally emitted through the decay of radioactive isotopes (potassium, uranium and thorium) were analysed using a geostatistical approach to map the spatial distribution of soil radioactivity. The activity of three radionuclides was measured at 181 locations using a high-resolution ?-ray spectrometry. To take into account the influence of season, the measurements were carried out in summer and in winter. Activity data were analysed by using a geostatistical approach and zones of relatively high or low radioactivity were delineated. Among the main processes which influence natural radioactivity such as geology, geochemical, pedological, and ecological processes, results of this study showed a prominent control of radio-emission measurements by seasonal changes. Low natural radioactivity levels were measured in December associated with winter weather and moist soil conditions (due to high rainfall and low temperature), and higher activity values in July, when the soil was dry and no precipitations occurred.

  8. Cultural variation is part of human nature : Literary universals, context-sensitivity, and "shakespeare in the bush".

    PubMed

    Sugiyama, Michelle Scalise

    2003-12-01

    In 1966, Laura Bohannan wrote her classic essay challenging the supposition that great literary works speak to universal human concerns and conditions and, by extension, that human nature is the same everywhere. Her evidence: the Tiv of West Africa interpret Hamlet differently from Westerners. While Bohannan's essay implies that cognitive universality and cultural variation are mutually exclusive phenomena, adaptationist theory suggests otherwise. Adaptive problems ("the human condition") and cognitive adaptations ("human nature") are constant across cultures. What differs between cultures is habitat: owing to environmental variation, the means and information relevant to solving adaptive problems differ from place to place. Thus, we find differences between cultures not because human minds differ in design but largely because human habitats differ in resources and history. On this view, we would expect world literature to express both human universals and cultural particularities. Specifically, we should expect to find literary universality at the macro level (e.g., adaptive problems, cognitive adaptations) and literary variation at the micro level (e.g., local solutions to adaptive problems).

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

    PubMed

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

    2015-06-01

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

  10. eIF4E Resistance: Natural Variation Should Guide Gene Editing.

    PubMed

    Bastet, Anna; Robaglia, Christophe; Gallois, Jean-Luc

    2017-02-28

    eIF4E translation initiation factors have emerged as major susceptibility factors for RNA viruses. Natural eIF4E-based resistance alleles are found in many species and are mostly variants that maintain the translation function of the protein. eIF4E genes represent major targets for engineering viral resistance, and gene-editing technologies can be used to make up for the lack of natural resistance alleles in some crops, often by knocking out eIF4E susceptibility factors. However, we report here how redundancy among eIF4E genes can restrict the efficient use of knockout alleles in breeding. We therefore discuss how gene-editing technologies can be used to design de novo functional alleles, using knowledge about the natural evolution of eIF4E genes in different species, to drive resistance to viruses without affecting plant physiology.

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

    PubMed Central

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

    2012-01-01

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

  12. Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae).

    PubMed

    Brazzola, Gregory; Chèvre, Nathalie; Wedekind, Claus

    2014-11-01

    The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within Alpine whitefish. We sampled spawners from two species of different lakes, bred them in vitro in a full-factorial design each, and studied growth and mortality of embryos. Exposure to EE2 turned out to be toxic in all concentrations we tested (≥1 ng/L). It reduced embryo viability and slowed down embryogenesis. We found significant additive genetic variation in EE2-induced mortality in both species, that is, genotypes differed in their tolerance to estrogen pollution. We also found maternal effects on embryo development to be influenced by EE2, that is, some maternal sib groups were more susceptible to EE2 than others. In conclusion, the toxic effects of EE2 were strong, but both species demonstrated the kind of additive genetic variation that is necessary for an evolutionary response to this type of pollution.

  13. Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae)

    PubMed Central

    Brazzola, Gregory; Chèvre, Nathalie; Wedekind, Claus

    2014-01-01

    The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within Alpine whitefish. We sampled spawners from two species of different lakes, bred them in vitro in a full-factorial design each, and studied growth and mortality of embryos. Exposure to EE2 turned out to be toxic in all concentrations we tested (≥1 ng/L). It reduced embryo viability and slowed down embryogenesis. We found significant additive genetic variation in EE2-induced mortality in both species, that is, genotypes differed in their tolerance to estrogen pollution. We also found maternal effects on embryo development to be influenced by EE2, that is, some maternal sib groups were more susceptible to EE2 than others. In conclusion, the toxic effects of EE2 were strong, but both species demonstrated the kind of additive genetic variation that is necessary for an evolutionary response to this type of pollution. PMID:25553069

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

    PubMed Central

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

    2013-01-01

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

  15. Natural variation in learning rate and memory dynamics in parasitoid wasps: opportunities for converging ecology and neuroscience

    PubMed Central

    Hoedjes, Katja M.; Kruidhof, H. Marjolein; Huigens, Martinus E.; Dicke, Marcel; Vet, Louise E. M.; Smid, Hans M.

    2011-01-01

    Although the neural and genetic pathways underlying learning and memory formation seem strikingly similar among species of distant animal phyla, several more subtle inter- and intraspecific differences become evident from studies on model organisms. The true significance of such variation can only be understood when integrating this with information on the ecological relevance. Here, we argue that parasitoid wasps provide an excellent opportunity for multi-disciplinary studies that integrate ultimate and proximate approaches. These insects display interspecific variation in learning rate and memory dynamics that reflects natural variation in a daunting foraging task that largely determines their fitness: finding the inconspicuous hosts to which they will assign their offspring to develop. We review bioassays used for oviposition learning, the ecological factors that are considered to underlie the observed differences in learning rate and memory dynamics, and the opportunities for convergence of ecology and neuroscience that are offered by using parasitoid wasps as model species. We advocate that variation in learning and memory traits has evolved to suit an insect's lifestyle within its ecological niche. PMID:21106587

  16. Natural variation in learning rate and memory dynamics in parasitoid wasps: opportunities for converging ecology and neuroscience.

    PubMed

    Hoedjes, Katja M; Kruidhof, H Marjolein; Huigens, Martinus E; Dicke, Marcel; Vet, Louise E M; Smid, Hans M

    2011-03-22

    Although the neural and genetic pathways underlying learning and memory formation seem strikingly similar among species of distant animal phyla, several more subtle inter- and intraspecific differences become evident from studies on model organisms. The true significance of such variation can only be understood when integrating this with information on the ecological relevance. Here, we argue that parasitoid wasps provide an excellent opportunity for multi-disciplinary studies that integrate ultimate and proximate approaches. These insects display interspecific variation in learning rate and memory dynamics that reflects natural variation in a daunting foraging task that largely determines their fitness: finding the inconspicuous hosts to which they will assign their offspring to develop. We review bioassays used for oviposition learning, the ecological factors that are considered to underlie the observed differences in learning rate and memory dynamics, and the opportunities for convergence of ecology and neuroscience that are offered by using parasitoid wasps as model species. We advocate that variation in learning and memory traits has evolved to suit an insect's lifestyle within its ecological niche.

  17. Benthic community response to habitat variation: A case of study from a natural protected area, the Celestun coastal lagoon

    NASA Astrophysics Data System (ADS)

    Pech, Daniel; Ardisson, Pedro-Luis; Hernández-Guevara, Norma A.

    2007-12-01

    Little information currently exists on spatial and temporal benthic community variations in tropical coastal lagoons. Here, the benthic community response to habitat variation in the Celestun coastal lagoon, northwest Yucatan peninsula, was seasonally examined during the 1994-1995 climatic cycle into a grid of 12 sampling sites distributed along the salinity gradient of the lagoon. Habitat variation was assessed through physical factors associated both to the water column (e.g. salinity) and the bottom sediment (e.g. sand, silt and clay fractions). The benthic community response was assessed through species diversity measures and abundance. Under the influence of climatic seasonality, variations in habitat conditions followed by changes in the benthic community characteristics were expected. Results from two-way ANOVAs showed that for the period of study, Celestun lagoon was more heterogeneous along the spatial axis of variability than along the temporal one. Multiple regression analysis showed that salinity was spatially the main factor influencing the benthic community characteristics. Temporally, the sediment characteristics were observed to exert significant effects on the species diversity characteristics but not on abundance. Other variables assessed (dissolved oxygen, pH, temperature and water column transparency) exhibited no significant covariance with species diversity and abundance. Since generated from historical data, these results have the potential to be useful as a benchmark to the establishment of monitoring programs in the light of the increasing anthropogenic pressure on the natural resources of the lagoon and surrounding coastal area.

  18. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations.

    PubMed

    Schielzeth, Holger; Husby, Arild

    2014-07-01

    A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.

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

    PubMed Central

    Hazzouri, Khaled M.; Rosas, Ulises; Bahmani, Tayebeh; Nelson, David R.; Abdrabu, Rasha; Harris, Elizabeth H.; Salehi-Ashtiani, Kourosh; Purugganan, Michael D.

    2015-01-01

    We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits. PMID:26392080

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. Indy gene variation in natural populations confers fitness advantage and life span extension through transposon insertion.

    PubMed

    Zhu, Chen-Tseh; Chang, Chengyi; Reenan, Robert A; Helfand, Stephen L

    2014-01-01

    Natural selection acts to maximize reproductive fitness. However, antagonism between life span and reproductive success frequently poses a dilemma pitting the cost of fecundity against longevity. Here, we show that natural populations of Drosophila melanogaster harbor a Hoppel transposon insertion variant in the longevity gene Indy (I'm not dead yet), which confers both increased reproduction and longevity through metabolic changes. Heterozygosity for this natural long-lived variant has been maintained in isolates despite long-term inbreeding under laboratory conditions and advantageously confers increased fecundity. DNA sequences of variant chromosome isolates show evidence of selective sweep acting on the advantageous allele, suggesting that natural selection acts to maintain this variant. The transposon insertion also regulates Indy expression level, which has experimentally been shown to affect life span and fecundity. Thus, in the wild, evolution reaffirms that the mechanism of heterozygote advantage has acted upon the Indy gene to assure increased reproductive fitness and, coincidentally, longer life span through regulatory transposon mutagenesis.

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

    ERIC Educational Resources Information Center

    Gabler, Jay; Frank, David John

    2005-01-01

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

  3. The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses

    PubMed Central

    Caballero, Armando; Tenesa, Albert; Keightley, Peter D.

    2015-01-01

    We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03–0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem. PMID:26482794

  4. Drosophila melanogaster Natural Variation Affects Growth Dynamics of Infecting Listeria monocytogenes

    PubMed Central

    Hotson, Alejandra Guzmán; Schneider, David S.

    2015-01-01

    We find that in a Listeria monocytogenes/Drosophila melanogaster infection model, L. monocytogenes grows according to logistic kinetics, which means we can measure both a maximal growth rate and growth plateau for the microbe. Genetic variation of the host affects both of the pathogen growth parameters, and they can vary independently. Because growth rates and ceilings both correlate with host survival, both properties could drive evolution of the host. We find that growth rates and ceilings are sensitive to the initial infectious dose in a host genotype–dependent manner, implying that experimental results differ as we change the original challenge dose within a single strain of host. PMID:26438294

  5. Seasonal fluctuation in susceptibility to insecticides within natural populations of Drosophila melanogaster. II. Features of genetic variation in susceptibility to organophosphate insecticides within natural populations of D. melanogaster.

    PubMed

    Miyo, Takahiro; Oguma, Yuzuru; Charlesworth, Brian

    2006-08-01

    To elucidate genetic variation in susceptibility to organophosphate insecticides within natural populations of Drosophila melanogaster, we conducted an analysis of variance for mortality data sets of isofemale lines (10-286 lines) used in the previous studies. Susceptibility of isofemale lines to the three organophosphate insecticides was continuously distributed within each natural population, ranging from susceptible to resistant. Analysis of variance showed highly significant variation among isofemale lines in susceptibility to each insecticide for each natural population. Significant genetic variances in susceptibility to the three chemicals were estimated for the Katsunuma population; 0.0529-0.2722 for malathion, 0.0492-0.1603 for prothiophos, and 0.0469-0.1696 for fenitrothion. Contrary to the consistent seasonal tendency towards an increase in mean susceptibility in the fall, reported in the previous study, genetic variances in susceptibility to the three organophosphates did not change significantly in 1997 but tended to increase by 2- to 5-times in 1998. We tested whether both the observed situations, maintenance and increase in genetic variance in organophosphate resistance, can be generated under circumstances in which the levels of resistance to the three organophosphates tended to decrease, by conducting a simulation analysis, based on the hypothesis that resistant genotypes have lower fitnesses than susceptible ones under the density-independent condition. The simulation analysis generally explained the pattern in the mean susceptibility and genetic variances in susceptibility to the three organophosphates, observed in the Katsunuma population of D. melanogaster. It was suggested that the differences in the frequencies of resistance genes in the summer population could affect the patterns in genetic variance in organophosphate resistance in the fall population.

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

    PubMed

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

    2016-02-22

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

  7. Genetic basis of natural variation in body pigmentation in Drosophila melanogaster

    PubMed Central

    Dembeck, Lauren M; Huang, Wen; Carbone, Mary Anna; Mackay, Trudy F C

    2015-01-01

    Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at bab1, t and e affect variation in abdominal pigmentation in several populations of Drosophila melanogaster. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in bab1, t and e; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including bab1, t and e and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of Drosophila pigmentation is complex, with a few major genes and many other loci with smaller effects. PMID:26554300

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

    PubMed Central

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

    2016-01-01

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

  9. Genetics of Brazil nut (Bertholletia excelsa Humb. & Bonpl.: Lecythidaceae) : 1. Genetic variation in natural populations.

    PubMed

    Buckley, D P; O'Malley, D M; Apsit, V; Prance, G T; Bawa, K S

    1988-12-01

    We provide an estimate of genetic variation within and between two populations of Bertholletia excelsa (Brazil nut), a large canopy tree found in the rain forests of South America. Average heterozygosity is 0.190, and 54.3% of the sampled loci are polymorphic. The population structure deviates significantly from Hardy-Weinberg expectations for Fest2 and Pgm2 (F =0.405 and 0.443, respectively) in one population, and highly significantly (F=-0.341) for Gdh in the other population. Although allele frequencies of the two populations differ significantly for Aat2, Est5, Mdh1, and Mdh2B, Nei's coefficient of gene differentiation (Gst) indicates that the between-population component (Dst) of genic diversity represents only 3.75% of the size of the within-population component (Hs). The implications of these findings in terms of conservation genetics are that much of the genetic diversity of this species may be preserved within one or a few populations. However, such populations must be very large because it appears that the large amount of genetic variation in Brazil nut populations is maintained by extensive gene flow and bonds of mating over a large area. The genetic architecture of Bertholletia excelsa is similar to that expected for an extensively diploidized paleopolyploid species.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  11. Genetic basis of natural variation in body pigmentation in Drosophila melanogaster.

    PubMed

    Dembeck, Lauren M; Huang, Wen; Carbone, Mary Anna; Mackay, Trudy F C

    2015-01-01

    Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at bab1, t and e affect variation in abdominal pigmentation in several populations of Drosophila melanogaster. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in bab1, t and e; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including bab1, t and e and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of Drosophila pigmentation is complex, with a few major genes and many other loci with smaller effects.

  12. The Nature and Cause of Spectral Variability in LMC X-1

    NASA Technical Reports Server (NTRS)

    Ruhlen, L.; Smith, D. M.; Scank, J. H.

    2011-01-01

    We present the results of a long-term observation campaign of the extragalactic wind-accreting black-hole X-ray binary LMC X-1, using the Proportional Counter Array on the Rossi X-Ray Timing Explorer (RXTE). The observations show that LMC X-1's accretion disk exhibits an anomalous temperature-luminosity relation. We use deep archival RXTE observations to show that large movements across the temperature-luminosity space occupied by the system can take place on time scales as short as half an hour. These changes cannot be adequately explained by perturbations that propagate from the outer disk on a viscous timescale. We propose instead that the apparent disk variations reflect rapid fluctuations within the Compton up-scattering coronal material, which occults the inner parts of the disk. The expected relationship between the observed disk luminosity and apparent disk temperature derived from the variable occultation model is quantitatively shown to be in good agreement with the observations. Two other observations support this picture: an inverse correlation between the flux in the power-law spectral component and the fitted inner disk temperature, and a near-constant total photon flux, suggesting that the inner disk is not ejected when a lower temperature is observed.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  15. The nature and causes of chronic obstructive pulmonary disease: A historical perspective

    PubMed Central

    Warren, C Peter W

    2009-01-01

    Chronic obstructive pulmonary disease (COPD) is the currently favoured name for the diseases formerly known as emphysema and bronchitis. COPD has been recognized for more than 200 years. Its cardinal symptoms are cough, phlegm and dyspnea, and its pathology is characterized by enlarged airspaces and obstructed airways. In the 19th century, the diagnosis of COPD depended on its symptoms and signs of a hyperinflated chest, and reduced expiratory breath sounds. The airflow obstruction evident on spirometry was identified in that century, but did not enter into clinical practice. Bronchitis, and the mechanical forces required to overcome its obstruction, was believed to be responsible for emphysema, although the inflammation present was recognized. The causes of bronchitis, and hence emphysema, included atmospheric and domestic air pollution, as well as dusty occupations. Cigarette smoking only became recognized as the dominant cause in the 20th century. The lessons learned of the risks for COPD in 19th-century Britain are very pertinent to the world today. PMID:19262908

  16. Natural off-stoichiometry causes carrier doping in half-Heusler filled tetrahedral structures

    NASA Astrophysics Data System (ADS)

    Yu, Yonggang G.; Zhang, Xiuwen; Zunger, Alex

    2017-02-01

    The half-Heusler filled tetrahedral structures (FTSs) are zinc-blende-like compounds, where an additional atom is filling its previously empty interstitial site. The FTSs having 18 valence electrons per formula unit are an emerging family of functional materials, whose intrinsic doping trends underlying a wide range of electronic functionalities are yet to be understood. Interestingly, even pristine compounds without any attempt at impurity/chemical doping exhibit intriguing trends in the free carriers they exhibit. Applying the first principles theory of doping to a few prototype compounds in the AIVBXCIV and AIVBIXCV groups, we describe the key ingredients controlling the materials' propensity for both intrinsic and extrinsic doping: (a) The spontaneous deviations from 1:1:1 stoichiometry reflect predictable thermodynamic stability of specific competing phases. (b) Bulk ABC compounds containing 3 d elements in the B position (ZrNiSn and ZrCoSb) are predicted to be naturally 3 d rich. The B =3 d interstitials are the prevailing shallow donors, whereas the potential acceptors (e.g., Zr vacancy and Sn-on-Zr antisite) are ineffective electron killers, resulting in an overall uncompensated n -type character, even without any chemical doping. In these materials, the band edges are "natural impurity bands" due to non-Daltonian off-stoichiometry, such as B interstitials, not intrinsic bulk controlled states as in a perfect crystal. (c) Bulk ABC compounds containing 5 d elements in the B position (ZrPtSn, ZrIrSb, and TaIrGe) are predicted to be naturally C rich and A poor. This promotes the hole-producing C -on-A antisite defects rather than B -interstitial donors. The resultant p -type character (without chemical doping) therein is "latent" for C =Sn and Sb; however, as the C -on-A hole-producing acceptors are rather deep and p typeness is manifest only at high temperature or via impurity doping. In contrast, in TaIrGe (B =Ir , 5 d ) , the prevailing hole-producing Ge

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  18. Determining the Cause of a Header Failure in a Natural Gas Production Facility

    SciTech Connect

    Matthes, S.A.; Covino, B.S., Jr.; Bullard, S.J.; Ziomek-Moroz, M.; Holcomb, G.R.

    2007-03-01

    An investigation was made into the premature failure of a gas-header at the Rocky Mountain Oilfield Testing Center (RMOTC) natural gas production facility. A wide variety of possible failure mechanisms were considered: design of the header, deviation from normal pipe alloy composition, physical orientation of the header, gas composition and flow rate, type of corrosion, protectiveness of the interior oxide film, time of wetness, and erosion-corrosion. The failed header was examined using metallographic techniques, scanning electron microscopy, and microanalysis. A comparison of the failure site and an analogous site that had not failed, but exhibited similar metal thinning was also performed. From these studies it was concluded that failure resulted from erosion-corrosion, and that design elements of the header and orientation with respect to gas flow contributed to the mass loss at the failure point.

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

    PubMed Central

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

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Davis, Edward D.; Hamdan, Leila

    2015-07-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  4. Variations in the relation between education and cause-specific mortality in 19 European populations: a test of the "fundamental causes" theory of social inequalities in health.

    PubMed

    Mackenbach, Johan P; Kulhánová, Ivana; Bopp, Matthias; Deboosere, Patrick; Eikemo, Terje A; Hoffmann, Rasmus; Kulik, Margarete C; Leinsalu, Mall; Martikainen, Pekka; Menvielle, Gwenn; Regidor, Enrique; Wojtyniak, Bogdan; Östergren, Olof; Lundberg, Olle

    2015-02-01

    Link and Phelan have proposed to explain the persistence of health inequalities from the fact that socioeconomic status is a "fundamental cause" which embodies an array of resources that can be used to avoid disease risks no matter what mechanisms are relevant at any given time. To test this theory we compared the magnitude of inequalities in mortality between more and less preventable causes of death in 19 European populations, and assessed whether inequalities in mortality from preventable causes are larger in countries with larger resource inequalities. We collected and harmonized mortality data by educational level on 19 national and regional populations from 16 European countries in the first decade of the 21st century. We calculated age-adjusted Relative Risks of mortality among men and women aged 30-79 for 24 causes of death, which were classified into four groups: amenable to behavior change, amenable to medical intervention, amenable to injury prevention, and non-preventable. Although an overwhelming majority of Relative Risks indicate higher mortality risks among the lower educated, the strength of the education-mortality relation is highly variable between causes of death and populations. Inequalities in mortality are generally larger for causes amenable to behavior change, medical intervention and injury prevention than for non-preventable causes. The contrast between preventable and non-preventable causes is large for causes amenable to behavior change, but absent for causes amenable to injury prevention among women. The contrast between preventable and non-preventable causes is larger in Central & Eastern Europe, where resource inequalities are substantial, than in the Nordic countries and continental Europe, where resource inequalities are relatively small, but they are absent or small in Southern Europe, where resource inequalities are also large. In conclusion, our results provide some further support for the theory of "fundamental causes". However

  5. ON THE VARIATION OF ZONAL GRAVITY COEFFICIENTS OF A GIANT PLANET CAUSED BY ITS DEEP ZONAL FLOWS

    SciTech Connect

    Kong Dali; Zhang Keke; Schubert, Gerald E-mail: kzhang@ex.ac.uk

    2012-04-01

    Rapidly rotating giant planets are usually marked by the existence of strong zonal flows at the cloud level. If the zonal flow is sufficiently deep and strong, it can produce hydrostatic-related gravitational anomalies through distortion of the planet's shape. This paper determines the zonal gravity coefficients, J{sub 2n}, n = 1, 2, 3, ..., via an analytical method taking into account rotation-induced shape changes by assuming that a planet has an effective uniform density and that the zonal flows arise from deep convection and extend along cylinders parallel to the rotation axis. Two different but related hydrostatic models are considered. When a giant planet is in rigid-body rotation, the exact solution of the problem using oblate spheroidal coordinates is derived, allowing us to compute the value of its zonal gravity coefficients J-bar{sub 2n}, n=1,2,3,..., without making any approximation. When the deep zonal flow is sufficiently strong, we develop a general perturbation theory for estimating the variation of the zonal gravity coefficients, {Delta}J{sub 2n}=J{sub 2n}-J-bar{sub 2n}, n=1,2,3,..., caused by the effect of the deep zonal flows for an arbitrarily rapidly rotating planet. Applying the general theory to Jupiter, we find that the deep zonal flow could contribute up to 0.3% of the J{sub 2} coefficient and 0.7% of J{sub 4}. It is also found that the shape-driven harmonics at the 10th zonal gravity coefficient become dominant, i.e., {Delta}J{sub 2n}>=J-bar{sub 2n} for n {>=} 5.

  6. Tomographic inverse estimation of aquifer properties based on pressure variations caused by transient water-supply pumping

    NASA Astrophysics Data System (ADS)

    Vesselinov, V. V.; Harp, D. R.; Koch, R. J.; Birdsell, K. H.

    2008-12-01

    Groundwater pumping of water-supply wells frequently exhibits substantial temporal and spatial variability. Wells are typically operated periodically (on daily and seasonal temporal scales), and the total production is controlled by the water-supply demand,. The pumping causes temporal and spatial variability in the water levels around the pumping wells. During the wellfield operation, water-level data are collected from the production and nearby observation wells. Water level fluctuations are a result of the manner in which the pumping is conducted, aquifer heterogeneity, and variations in other influences such as recharge, poroelastic effects, etc. The variability in aquifer stresses due to pumping can provide valuable information about aquifer properties. The supply-well pumping can be viewed as a single prolonged pumping test extending over multiple pumping cycles and including multiple pumping and observation wells. Here we discuss water level and pumping production data acquired during water-supply production from the regional aquifer at Los Alamos, New Mexico. We have performed extensive interpretation of the data using analytical and numerical techniques. The analytical techniques are applied to provide (1) initial screening of the data for measurement errors, (2) identification of correlations between the pumping and water-level variability, and (3) estimation of the large-scale properties of the aquifer. The numerical models are applied to characterize the spatial heterogeneity of the aquifer using an approach based on tomographic inverse analysis. Our results demonstrate that there are large-scale features in the aquifer that appear to control the spatial propagation of transient pumping effects. The identified aquifer heterogeneities were not previously recognized and are expected to have important effects on the potential migration of contaminants in the regional aquifer.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-23

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

  9. Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens

    PubMed Central

    Wright, Dominic; Boije, Henrik; Meadows, Jennifer R. S.; Bed'hom, Bertrand; Gourichon, David; Vieaud, Agathe; Tixier-Boichard, Michèle; Rubin, Carl-Johan; Imsland, Freyja; Hallböök, Finn; Andersson, Leif

    2009-01-01

    Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less susceptible to frost lesions. Here we report that Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor. This must be the causative mutation since all other polymorphisms associated with the Pea-comb allele were excluded by genetic analysis. SOX5 controls cell fate and differentiation and is essential for skeletal development, chondrocyte differentiation, and extracellular matrix production. Immunostaining in early embryos demonstrated that Pea-comb is associated with ectopic expression of SOX5 in mesenchymal cells located just beneath the surface ectoderm where the comb and wattles will subsequently develop. The results imply that the duplication expansion interferes with the regulation of SOX5 expression during the differentiation of cells crucial for the development of comb and wattles. The study provides novel insight into the nature of mutations that contribute to phenotypic evolution and is the first description of a spontaneous and fully viable mutation in this developmentally important gene. PMID:19521496

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2014-08-01

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

  12. Optimal immunity meets natural variation: the evolutionary biology of host defence.

    PubMed

    Graham, A L

    2013-11-01

    This editorial introduces the seven articles that comprise the Parasite Immunology special issue on the Evolutionary Biology of Host Defence. The rationale for an evolutionary approach to immunoparasitology is briefly outlined, and then the articles are placed in that broader context. A central aim of each article is to explain the generation and maintenance of immunological heterogeneity among hosts in nature. The authors describe new tools and approaches that enable unprecedented insight into evolutionary and immunological processes in both the laboratory and the wild. The examples discussed include insects, birds and mammals (as hosts) and trypanosomes, apicomplexans and nematodes (as parasites).

  13. Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

    ERIC Educational Resources Information Center

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

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

    NASA Astrophysics Data System (ADS)

    Magdalena Santana-Casiano, J.; González-Dávila, Melchor; Fraile-Nuez, Eugenio

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Santana-Casiano, J.; Fraile-Nuez, E.; Gonzalez-Davila, M.

    2013-12-01

    The shallow submarine eruption which took place in October 10th 2011, 1.8 km south of the island of El Hierro (Canary Islands) allowed the study of the abrupt changes in the physical-chemical properties of seawater caused by volcanic discharges. In order to monitor the evolution of these changes, seven oceanographic surveys were carried out over six months (November 2011-April 2012) from the beginning of the eruptive stage to the post-eruptive phase. It was observed dramatic changes in the water column chemistry including large decreases in pH, striking effects on the carbonate system, decreases in the oxygen concentrations and enrichment of Fe(II) and nutrients. The findings highlight that the same volcano which was responsible for the creation of a highly corrosive environment, affecting marine biota, has also provided the nutrients required for the rapid recuperation of the marine ecosystem. In January 2013, a new project, the VULCANO project, was iniciated to study the post-eruptive phase in the submarine volcanic area.

  16. Natural variation in developmental life-history traits of the bacterium Myxococcus xanthus.

    PubMed

    Kraemer, Susanne A; Toups, Melissa A; Velicer, Gregory J

    2010-08-01

    The soil bacterium Myxococcus xanthus is a model for the study of cooperative microbial behaviours such as social motility and fruiting body formation. Several M. xanthus developmental traits that are frequently quantified for laboratory strains are likely to be significant components of fitness in natural populations, yet little is known about the degree to which such traits vary in the wild and may therefore be subject to natural selection. Here, we have tested whether several key M. xanthus developmental life-history traits have diverged significantly among strains both from globally distant origins and from within a sympatric, centimetre-scale population. The isolates examined here were found to vary considerably, in a heritable manner, in their rate of developmental aggregation and in both their rate and efficiency of spore production. Isolates also varied in the nutrient-concentration threshold triggering spore formation and in the heat resistance of spores. The large diversity of developmental phenotypes documented here leads to questions regarding the relative roles of selection and genetic drift in shaping the diversity of local soil populations with respect to these developmental traits. It also raises the question of whether fitness in the wild is largely determined by traits that are expressed independent of social context or by behaviours that are expressed only in genetically heterogeneous social groups.

  17. Variation in essential oil and bioactive compounds of Curcuma kwangsiensis collected from natural habitats.

    PubMed

    Zhang, Lanyue; Yang, Zhiwen; Huang, Zebin; Zhao, Mincong; Li, Penghui; Zhou, Wei; Zhang, Kun; Zheng, Xi; Lin, Li; Tang, Jian; Fang, Yanxiong; Du, Zhiyun

    2017-04-11

    The chemical compositions of essential oils (EOs) extracted from Curcuma kwangsiensis rhizomes collected from six natural habitats in China were evaluated using gas chromatography-mass spectrometry (GC-MS). Fifty-seven components were identified from the six Eos; their main constituents were 8,9-dehydro-9-formyl-cycloisolongifolene (2.37-42.59%), germacrone (6.53-22.20%), and L-camphor (0.19-6.12%). The six EOs exhibited different DPPH radical-scavenging activities (IC50 , 2.24-31.03 μg/mL), with the activity of most of the EOs being much higher than that of Trolox C (IC50 , 10.49 μg/mL) and BHT (IC50 , 54.13 μg/mL). Most EOs had potent antimicrobial effects against the tested bacteria and fungus. They also exhibited cytotoxicity in B16 (IC50 , 4.44-147.4 μg/mL) and LNCaP cells (IC50 , 73.94-429.25 μg/mL). The EOs showed excellent anti-inflammatory action by significantly downregulating the expression of pro-inflammatory cytokines, cyclooxygenase-2 and tumor necrosis factor-α. This study provides insight into relationship among growth location, phytoconstituents, and bioactivities; the results indicate the potential of C. kwangsiensis as natural nutrients, medicines, and others additives. This article is protected by copyright. All rights reserved.

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

    PubMed

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

    2016-02-18

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

  19. Acceptability of variations in question intonation in natural and synthesized American English

    NASA Astrophysics Data System (ADS)

    Syrdal, Ann K.; Jilka, Matthias

    2004-05-01

    In a previous study exploring American English question intonation, we found that some speakers deviated considerably from expected question prosody. In this study, we focus on listener-rated acceptability of the various prosodic patterns observed for yes/no and wh questions. A variety of intonational patterns realized in both question utterances recorded from five female and three male professional speakers and in questions synthesized from several TTS voices of both genders was presented to listeners. Subjects judged the acceptability of each utterance in the context of a dialogue between a travel agent and customer. We hypothesized that question utterances with the expected intonational features (phrase-final fall in wh questions, phrase-final rise in yes/no questions) would be rated as more acceptable than question utterances with deviating intonational features, and that this result would hold for both natural and synthetic speech conditions. In addition, following our previous results, we hypothesized that the unexpected intonation pattern of phrase-final falls for yes/no questions would be more acceptable for lower-pitched than for higher-pitched voices. We also varied the prominence of the interrogative pronouns in synthetic wh questions in order to see whether simulating their high intonational prominence in natural wh questions improved the acceptability of synthetic wh questions.

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

    PubMed Central

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

    2004-01-01

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

  1. Beta 2-adrenergic stimulation causes detachment of natural killer cells from cultured endothelium.

    PubMed

    Benschop, R J; Oostveen, F G; Heijnen, C J; Ballieux, R E

    1993-12-01

    Physical exercise, mental stress, or infusion of beta-adrenergic agonists result in an increase in the number of natural killer (NK) cells in the peripheral circulation. In view of the specific migration pattern of NK cells in vivo, it has been suggested that these cells may be released from the marginating pool in blood vessels. In the present report, the in vitro effect of catecholamines on the adhesion of NK cells to unstimulated human endothelial cells (EC) was characterized. Peripheral blood mononuclear cells were allowed to adhere to monolayers of EC, after which the adherent lymphocyte fraction was analyzed phenotypically by flow cytometry. NK cells were found to adhere preferentially to EC, a process that was reversed by the addition of various adrenergic agonists. Catecholamines selectively affected adhesion of NK cells and had no effect on T cell adhesion to EC, as was determined by the use of purified cell populations. Detachment of NK cells from EC could be achieved by short incubations (5 min) with epinephrine (EPI) and was concentration-dependent, with an ED50 of 2 x 10(-10)M. Using a panel of alpha- and beta-adrenergic agonists and antagonists, we show that the detachment of NK cells is mediated via beta 2-adrenergic receptors. In line with the lower affinity for beta 2-adrenergic receptors, norepinephrine was less effective than EPI in inducing detachment of NK cells from EC. Direct activation of adenylate-cyclase with forskolin gave similar results as observed with EPI, indicating that signaling through cAMP is necessary to induce detachment of NK cells from EC. The results of the present study lend support to the hypothesis that catecholamines, via beta 2-adrenergic receptors, can induce recruitment of NK cells from the marginating pool to the circulating pool, by changing the adhesive interactions between NK cells and EC.

  2. Arabidopsis thaliana natural variation reveals connections between UV radiation stress and plant pathogen-like defense responses.

    PubMed

    Piofczyk, Thomas; Jeena, Ganga; Pecinka, Ales

    2015-08-01

    UV radiation is a ubiquitous component of solar radiation that affects plant growth and development. Here we studied growth related traits of 345 Arabidopsis thaliana accessions in response to UV radiation stress. We analyzed the genetic basis of this natural variation by genome-wide association studies, which suggested a specific candidate genomic region. RNA-sequencing of three sensitive and three resistant accessions combined with mutant analysis revealed five large effect genes. Mutations in PHE ammonia lyase 1 (PAL1) and putative kinase At1g76360 rendered Arabidopsis hypersensitive to UV stress, while loss of function from putative methyltransferase At4g22530, novel plant snare 12 (NPSN12) and defense gene activated disease resistance 2 (ADR2) conferred higher UV stress resistance. Three sensitive accessions showed strong ADR2 transcriptional activation, accumulation of salicylic acid (SA) and dwarf growth upon UV stress, while these phenotypes were much less affected in resistant plants. The phenotype of sensitive accessions resembles autoimmune reactions due to overexpression of defense related genes, and suggests that natural variation in response to UV radiation stress is driven by pathogen-like responses in Arabidopsis.

  3. Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture[OPEN

    PubMed Central

    Herman, Dorota; Slabbinck, Bram; Van Daele, Twiggy; Maleux, Katrien

    2016-01-01

    Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under nonlethal drought conditions is lacking. Recent advances in genomics, phenomics, and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves. Although no major effect locus was found to be associated with growth in mild drought, the transcriptome analysis delivered further insight into the natural variation of transcriptional responses to mild drought in a specific tissue. Coexpression analysis indicated the presence of gene clusters that co-vary over different genetic backgrounds, among others a cluster of genes with important regulatory functions in the growth response to osmotic stress. It was found that the occurrence of a mild drought stress response in leaves can be inferred with high accuracy across accessions based on the expression profile of 283 genes. A genome-wide association study on the expression data revealed that trans regulation seems to be more important than cis regulation in the transcriptional response to environmental perturbations. PMID:27729396

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  5. Learning to be different: Acquired skills, social learning, frequency dependence, and environmental variation can cause behaviourally mediated foraging specializations

    USGS Publications Warehouse

    Tinker, M.T.; Mangel, M.; Estes, J.A.

    2009-01-01

    Question: How does the ability to improve foraging skills by learning, and to transfer that learned knowledge, affect the development of intra-population foraging specializations? Features of the model: We use both a state-dependent life-history model implemented by stochastic dynamic programming (SDPM) and an individual-based model (IBM) to capture the dynamic nature of behavioural preferences in feeding. Variables in the SDPM include energy reserves, skill levels, energy and handling time per single prey item, metabolic rate, the rates at which skills are learned and forgotten, the effect of skills on handling time, and the relationship between energy reserves and fitness. Additional variables in the IBM include the probability of successful weaning, the logistic dynamics of the prey species with stochastic recruitment, the intensity of top-down control of prey by predators, the mean and variance in skill levels of new recruits, and the extent to which learned Information can be transmitted via matrilineal social learning. Key range of variables: We explore the effects of approaching the time horizon in the SDPM, changing the extent to which skills can improve with experience, increasing the rates of learning or forgetting of skills, changing whether the learning curve is constant, accelerating (T-shaped) or decelerating ('r'-shaped), changing both mean and maximum possible energy reserves, changing metabolic costs of foraging, and changing the rate of encounter with prey. Conclusions: The model results show that the following factors increase the degree of prey specialization observed in a predator population: (1) Experience handling a prey type can substantially improve foraging skills for that prey. (2) There is limited ability to retain complex learned skills for multiple prey types. (3) The learning curve for acquiring new foraging skills is accelerating, or J-shaped. (4) The metabolic costs of foraging are high relative to available energy reserves. (5

  6. Patterns of cuticular hydrocarbon variation and genetic similarity between natural populations of Amblyomma cajennense (Acari: Ixodidae).

    PubMed

    Estrada-Peña, A; Guglielmone, A A; Mangold, A J; Castellá, J

    1993-10-01

    Gas chromatography has been used to analyze the variation in cuticular hydrocarbon patterns between several populations of Amblyomma cajennense. 88 compounds were detected and these could be divided into 17 groups of hydrocarbons. Heterozygosis in the populations ranges from 0% to 25.84%. Isomers for pentacosane, heptacosane and nonatriacontane are the most variable, with 13, 10 and 11 variants, respectively. Nei's genetic identity and genetic distance show that populations may be considered as regional variants of only one species: the results do not indicate the presence of sibling species. However, a relatively high genetic distance has been observed between several Cuban and continental populations, suggesting a long reproductive isolation. Gas chromatography of cuticular hydrocarbons is a good alternative to isozyme analysis for population studies, when collecting conditions do not allow the use of live ticks and only alcohol-preserved collections are available. The high number of compounds available for genetic studies will provide excellent markers for evaluating the extent of gene flow and migration of tick species.

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

    PubMed

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

    2014-09-01

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

  8. Elemental stoichiometry and compositions of weevil larvae and two acorn hosts under natural phosphorus variation

    PubMed Central

    Ji, Huawei; Du, Baoming; Liu, Chunjiang

    2017-01-01

    To understand how different trophic organisms in a parasite food chain adapt to the differences in soil nutrient conditions, we investigated stoichiometric variation and homeostasis of multiple elements in two acorn trees, Quercus variabilis and Quercus acutissima, and their parasite weevil larvae (Curculio davidi Fairmaire) at phosphorus (P)-deficient and P-rich sites in subtropical China where P-rich ores are scattered among dominant P-deficient soils. Results showed that elemental stoichiometry and compositions of both acorns and weevil larvae differed significantly between P-deficient and P-rich sites (p < 0.05), with the largest contribution of acorn and weevil larva P in distinguishing the stoichiometric compositions between the two site types. The two acorn species were statistically separated by their acorn elemental stoichiometry and compositions (p < 0.05), but no difference was observed on weevil larvae between the two acorn species. P was one of the few elements that were non strict homeostasis in both acorns and weevil larvae. These findings highlight the importance of both environmental influence in elemental stoichiometry and composition and physiological regulations of nutritional needs in organisms and provide possible stoichiometric responses of both plants and animals to P loading, a worldwide issue from excess release of P into the environment. PMID:28378822

  9. Essential oil variation among natural populations of Lavandula multifida L. (Lamiaceae).

    PubMed

    Chograni, Hnia; Zaouali, Yosr; Rajeb, Chayma; Boussaid, Mohamed

    2010-04-01

    Volatiles from twelve wild Tunisian populations of Lavandula multifida L. growing in different bioclimatic zones were assessed by GC (RI) and GC/MS. Thirty-six constituents, representing 83.48% of the total oil were identified. The major components at the species level were carvacrol (31.81%), beta-bisabolene (14.89%), and acrylic acid dodecyl ester (11.43%). These volatiles, together with alpha-pinene, were also the main compounds discriminating the populations. According to these dominant compounds, one chemotype was revealed, a carvacrol/beta-bisabolene/acrylic acid dodecyl ester chemotype. However, a significant variation among the populations was observed for the majority of the constituents. A high chemical-population structure, estimated both by principal component analysis (PCA) and unweighted pair group method with averaging (UPGMA) cluster analysis based on Euclidean distances, was observed. Both methods allowed separation of the populations in three groups defined rather by minor than by major compounds. The population groups were not strictly concordant with their bioclimatic or geographic location. Conservation strategies should concern all populations, because of their low size and their high level of destruction. Populations exhibiting particular compounds other than the major ones should be protected first.

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-01-01

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

  12. Relations of Naturally Occurring Variations in State Anxiety and Cognitive Functioning.

    PubMed

    Meissel, Emily E E; Salthouse, Timothy A

    2016-08-01

    Although effects of anxiety on cognitive performance have been extensively examined, anxiety-cognition relationships are often defined by between-person relationships. The current research investigated the effects of within-person variations in state anxiety on cognitive performance based on measures from three separate sessions in a sample of 1,769 healthy adults ranging from 18 to 99 years of age. Some of the adults in the sample exhibited a wide range of state anxiety across the three sessions, whereas others were fairly stable. Although one might have expected that cognitive performance would be low only on sessions in which the level of state anxiety was high, this pattern was not evident in any of five different cognitive abilities (vocabulary, memory, reasoning, spatial relations, or perceptual speed tasks). Instead, one's average level of anxiety was a more important determinant of cognitive performance than one's current level of state anxiety. Specifically, for memory and reasoning abilities, trait anxiety alone related to decreased cognitive function, regardless of state anxiety. For spatial relations and speed abilities, low state anxiety was related to decreased cognitive function in participants with high trait anxiety.

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

    NASA Astrophysics Data System (ADS)

    Järvelä, J.; Aberle, J.

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  17. Design of a comprehensive biochemistry and molecular biology experiment: phase variation caused by recombinational regulation of bacterial gene expression.

    PubMed

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about Salmonella enterica serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation, antibody agglutination test, and PCR analysis. Phase variation was observed by baterial motility assay and identified by antibody agglutination test and PCR analysis. This comprehensive experiment can be performed to help students improve their ability to use the knowledge acquired in Biochemistry and Molecular Biology.

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

    PubMed

    Richter, Ingrid; Fidler, Andrew E

    2015-10-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

    Kramer, Jonathan G.; Singleton, Fred L.

    1993-01-01

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

  1. Weekly variations of discharge and groundwater quality caused by intermittent water supply in an urbanized karst catchment

    NASA Astrophysics Data System (ADS)

    Grimmeisen, Felix; Zemann, Moritz; Goeppert, Nadine; Goldscheider, Nico

    2016-06-01

    Leaky sewerage and water distribution networks are an enormous problem throughout the world, specifically in developing countries and regions with water scarcity. Especially in many arid and semi-arid regions, intermittent water supply (IWS) is common practice to cope with water shortage. This study investigates the combined influence of urban activities, IWS and water losses on groundwater quality and discusses the implications for water management. In the city of As-Salt (Jordan), local water supply is mostly based on groundwater from the karst aquifer that underlies the city. Water is delivered to different supply zones for 24, 48 or 60 h each week with drinking water losses of around 50-60%. Fecal contamination in groundwater, mostly originating from the likewise leaky sewer system is a severe challenge for the local water supplier. In order to improve understanding of the local water cycle and contamination dynamics in the aquifer beneath the city, a down gradient spring and an observation well were chosen to identify contaminant occurrence and loads. Nitrate, Escherichia coli, spring discharge and the well water level were monitored for 2 years. Autocorrelation analyses of time series recorded during the dry season revealed weekly periodicity of spring discharge (45 ± 3.9 L s-1) and NO3-N concentrations (11.4 ± 0.8 mg L-1) along with weekly varying E. coli levels partly exceeding 2.420 MPN 100 mL-1. Cross-correlation analyses demonstrate a significant and inverse correlation of nitrate and discharge variations which points to a periodic dilution of contaminated groundwater by freshwater from the leaking IWS being the principal cause of the observed fluctuations. Contaminant inputs from leaking sewers appear to be rather constant. The results reveal the distinct impact of leaking clean IWS on the local groundwater and subsequently on the local water supply and therefore demonstrate the need for action regarding the mitigation of groundwater contamination and

  2. Optimum dose variation caused by post exposure bake temperature difference inside photoresist over different sublayers and thickness

    NASA Astrophysics Data System (ADS)

    Kang, Young-Min; An, Ilsin; Kim, Do Wan; Oh, Hye-Keun

    2008-03-01

    In principle, the dose should not be changed to make the same linewidth if a perfect anti-reflection coating (ARC) is used for all the sublayers underneath the resist. However, the optimum dose for different sublayers and thicknesses are different even though perfect ARC is used. The post exposure bake (PEB) process of a chemically amplified resist is one of the key processes to make very small features of semiconductor device. The photo-generated acid makes the deprotection of protected polymer, and this deprotection highly depends on the PEB temperature and time. The diffusion length of acid is also strongly dependent on PEB temperature and time. As the linewidth of the device decreases, smaller diffusion length is required to reduce the roughness of the line edge and width. One of the key factors to determine the deprotection and acid diffusion is the initial temperature rising and the final real temperature inside the resist. The unpredictable temperature rising to the pre-set temperature mainly causes the variation of linewidth and the optimum dose. In order to predict the accurate PEB temperature and time dependency of the linewidth and dose, the heat transfer from the hot plate to the resist on the top of the multiply stacked sublayers over the silicon wafer has to be known since the reaction and diffusion occur inside the resist, not on the top of the bare silicon wafer. We studied heat transfer from the hot plate to the top of the resist including conductivity and thickness of each sublayer. For this purpose, a novel numerical approach incorporated with analytic method was proposed to solve the heat conduction problem. The unknowns for temperature are located only at the interfaces between layers, so that it is fast and efficient. We calculated the time that is consumed for the resist to attain the prescribed PEB temperature for the different multi stacks and thicknesses. Calculation shows that the temperature rising is different and final temperature on

  3. HYDRODYNAMIC AND RADIATIVE MODELING OF TEMPORAL H{alpha} EMISSION V/R VARIATIONS CAUSED BY DISCONTINUOUS MASS TRANSFER IN BINARIES

    SciTech Connect

    Chadima, Pavel; Harmanec, Petr; Wolf, Marek; Firt, Roman; Ruzdjak, Domagoj; Bozic, Hrvoje; Koubsky, Pavel

    2011-07-15

    H{alpha} emission V/R variations caused by discontinuous mass transfer in interacting binaries with a rapidly rotating accreting star are modeled qualitatively for the first time. The program ZEUS-MP was used to create a non-linear three-dimensional hydrodynamical model of a development of a blob of gaseous material injected into an orbit around a star. It resulted in the formation of an elongated disk with a slow prograde revolution. The LTE radiative transfer program SHELLSPEC was used to calculate the H{alpha} profiles originating in the disk for several phases of its revolution. The profiles have the form of a double emission and exhibit V/R and radial velocity variations. However, these variations should be a temporal phenomenon since imposing a viscosity in the given model would lead to a circularization of the disk and fading-out of the given variations.

  4. Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs

    PubMed Central

    Cardoso, Catarina; Zhang, Yanxia; Jamil, Muhammad; Hepworth, Jo; Charnikhova, Tatsiana; Dimkpa, Stanley O. N.; Meharg, Caroline; Wright, Mark H.; Liu, Junwei; Meng, Xiangbing; Wang, Yonghong; Li, Jiayang; McCouch, Susan R.; Leyser, Ottoline; Price, Adam H.; Bouwmeester, Harro J.; Ruyter-Spira, Carolien

    2014-01-01

    Rice (Oryza sativa) cultivar Azucena—belonging to the Japonica subspecies—exudes high strigolactone (SL) levels and induces high germination of the root parasitic plant Striga hermonthica. Consistent with the fact that SLs also inhibit shoot branching, Azucena is a low-tillering variety. In contrast, Bala, an Indica cultivar, is a low-SL producer, stimulates less Striga germination, and is highly tillered. Using a Bala × Azucena F6 population, a major quantitative trait loci—qSLB1.1—for the exudation of SL, tillering, and induction of Striga germination was detected on chromosome 1. Sequence analysis of the corresponding locus revealed a rearrangement of a 51- to 59-kbp stretch between 28.9 and 29 Mbp in the Bala genome, resulting in the deletion of two cytochrome P450 genes—SLB1 and SLB2—with high homology to the Arabidopsis SL biosynthesis gene, MAX1. Both rice genes rescue the Arabidopsis max1-1 highly branched mutant phenotype and increase the production of the SL, ent-2′-epi-5-deoxystrigol, when overexpressed in Bala. Furthermore, analysis of this region in 367 cultivars of the publicly available Rice Diversity Panel population shows that the rearrangement at this locus is a recurrent natural trait associated with the Indica/Japonica divide in rice. PMID:24464483

  5. Natural variation of fecundity components in a widespread plant with dimorphic seeds

    NASA Astrophysics Data System (ADS)

    Braza, Rita; Arroyo, J.; García, M. B.

    2010-09-01

    The number and size of seeds are the basis of the quantity and quality components of female reproductive fitness in plants, playing a central role in the evolutionary ecology of life history diversification. In this study we show and analyze the natural variability of several fecundity variables (fruit set, seed production per fruit, seed size, total seed production per plant, and proportion of small seeds) in Plantago coronopus, a widespread, short-lived herb with dimorphic seeds. The structure of such variability was examined at the individual, population (eight locations with different environments within the same region), and life history levels (annual vs perennial), and correlated to soil fertility. There was no divergence associated to the life history for any of the variables studied. Total seed production (the quantity component of female fitness) was correlated with maternal resources, while the size of the large mucilaginous, basal seeds, and the proportion of the small apical seeds (quality component) were more associated to environmental resources. Thus, internal and external resources shape different fitness components, maximizing seed production, and fitting the size and proportion of different kind of seeds to local conditions irrespective of life history. P. coronopus illustrates the versatility of short-lived widespread plants to combine fecundity traits in a flexible manner, in order to increase fitness at each of the many possible habitats they occupy over heterogeneous environments.

  6. Epigenetic regulation of sex ratios may explain natural variation in self-fertilization rates

    PubMed Central

    Ellison, Amy; Rodríguez López, Carlos Marcelino; Moran, Paloma; Breen, James; Swain, Martin; Megias, Manuel; Hegarty, Matthew; Wilkinson, Mike; Pawluk, Rebecca; Consuegra, Sofia

    2015-01-01

    Self-fertilization (selfing) favours reproductive success when mate availability is low, but renders populations more vulnerable to environmental change by reducing genetic variability. A mixed-breeding strategy (alternating selfing and outcrossing) may allow species to balance these needs, but requires a system for regulating sexual identity. We explored the role of DNA methylation as a regulatory system for sex-ratio modulation in the mixed-mating fish Kryptolebias marmoratus. We found a significant interaction between sexual identity (male or hermaphrodite), temperature and methylation patterns when two selfing lines were exposed to different temperatures during development. We also identified several genes differentially methylated in males and hermaphrodites that represent candidates for the temperature-mediated sex regulation in K. marmoratus. We conclude that an epigenetic mechanism regulated by temperature modulates sexual identity in this selfing species, providing a potentially widespread mechanism by which environmental change may influence selfing rates. We also suggest that K. marmoratus, with naturally inbred populations, represents a good vertebrate model for epigenetic studies. PMID:26559950

  7. Natural variation of magnesium isotopes in mammal bones and teeth from two South African trophic chains

    NASA Astrophysics Data System (ADS)

    Martin, Jeremy E.; Vance, Derek; Balter, Vincent

    2014-04-01

    Isotopic fractionations accompanying element transfer through terrestrial ecosystems have the potential to shed light on ecological interactions between primary producers and consumers, but with the exception of carbon and nitrogen this potential has barely been exploited. Here, the magnesium stable isotope composition of bones and teeth of extant mammals from Kruger National Park (KNP) and Western Cape (WC), South Africa was measured for the first time. The nature of the geological substrate proves to be a major determinant of the ecosystem isotope baseline, as indicated by the lighter magnesium isotope ratios measured in WC mammals (ranging from -1.58‰ to -0.79‰) compared to those from KNP mammals (ranging from -1.01‰ to -0.04‰). Therefore, comparisons between the isotope signatures of taxa must be restricted to a pre-defined geographic area with a homogeneous substrate. In both parks, Mg shows slight enrichment in heavier isotopes from herbivores to carnivores. Plant remains trapped in the dentition of herbivores provide direct evidence of dietary source and, when available, were measured. In KNP only, δ26Mg of plant remains is systematically lighter than the values for herbivore teeth. These results invite further exploration of the variability of Mg isotopes in vertebrate ecosystems in order to test whether magnesium, a bio-essential element present in relatively large proportions in bone and teeth apatite, may serve as an additional trophic tracer to nitrogen, which is a constituent of collagen that rapidly degrades after burial.

  8. Variation in resource limitation of plant reproduction influences natural selection on floral traits of Asclepias syriaca.

    PubMed

    Caruso, Christina M; Remington, Davin L D; Ostergren, Kate E

    2005-11-01

    The availability of both pollen and resources can influence natural selection on floral traits, but their relative importance in shaping floral evolution is unclear. We experimentally manipulated pollinator and resource (fertilizer and water) availability in the perennial wildflower Asclepias syriaca L. Nine floral traits, one male fitness component (number of pollinia removed), and two female fitness components (number of pollinia inserted and number of fruits initiated) were measured for plants in each of three treatments (unmanipulated control, decreased pollinator access, and resource supplementation). Although decreasing pollinators' access to flowers did result in fewer pollinia inserted and removed, fruit set and phenotypic selection on floral traits via female and male fitness did not differ from the control. In contrast, resource supplementation increased fruit set, and phenotypic selection on seven out of nine floral traits was stronger via female than male fitness, consistent with the prediction that selection via female fitness would be greater when reproduction was less resource-limited. Our results support the hypothesis that abiotic resource availability can influence floral evolution by altering gender-specific selection.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  11. Possible causes of variation in acrylamide concentration in French fries prepared in food service establishments: an observational study.

    PubMed

    Sanny, M; Jinap, S; Bakker, E J; van Boekel, M A J S; Luning, P A

    2012-05-01

    Acrylamide is a probable human carcinogen, and its presence in a range of fried and oven-cooked foods has raised considerable health concern world-wide. Dietary intake studies observed significant variations in acrylamide concentrations, which complicate risk assessment and the establishment of effective control measures. The objective of this study was to obtain an insight into the actual variation in acrylamide concentrations in French fries prepared under typical conditions in a food service establishment (FSE). Besides acrylamide, frying time, frying temperature, and reducing sugars were measured and the actual practices at receiving, thawing and frying during French fries preparation were observed and recorded. The variation in the actual frying temperature contributed most to the variation in acrylamide concentrations, followed by the variation in actual frying time; no obvious effect of reducing sugars was found. The lack of standardised control of frying temperature and frying time (due to inadequate frying equipment) and the variable practices of food handlers seem to contribute most to the large variation and high acrylamide concentrations in French fries prepared in a restaurant type of FSE as compared to chain fast-food services, and institutional caterers. The obtained insights in this study can be used to develop dedicated control measures in FSE, which may contribute to a sustainable reduction in the acrylamide intake.

  12. Tracking Down the Causes of Recent Induced and Natural Intraplate Earthquakes with 3D Seismological Analyses in Northwest Germany

    NASA Astrophysics Data System (ADS)

    Uta, P.; Brandes, C.; Boennemann, C.; Plenefisch, T.; Winsemann, J.

    2015-12-01

    Northwest Germany is a typical low strain intraplate region with a low seismic activity. Nevertheless, 58 well documented earthquakes with magnitudes of 0.5 - 4.3 affected the area in the last 40 years. Most of the epicenters were located in the vicinity of active natural gas fields and some inside. Accordingly, the earthquakes were interpreted as a consequence of hydrocarbon recovery (e.g. Dahm et al. 2007, Bischoff et al. 2013) and classified as induced events in the bulletins of the Federal Institute for Geosciences and Natural Resources (BGR). The two major ones have magnitudes of 4.3 and 4.0. They are the strongest earthquakes ever recorded in Northern Germany. Consequently, these events raise the question whether the ongoing extraction itself can cause them or if other natural tectonic processes like glacial isostatic adjustment may considerably contribute to their initiation. Recent studies of Brandes et al. (2012) imply that lithospheric stress changes due to post glacial isostatic adjustment might be also a potential natural cause for earthquakes in Central Europe. In order to better analyse the earthquakes and to test this latter hypothesis we performed a relocalization of the events with the NonLinLoc (Lomax et al. 2000) program package and two differently scaled 3D P-wave velocity models. Depending on the station coverage for a distinct event, either a fine gridded local model (88 x 73 x 15 km, WEG-model, made available by the industry) or a coarse regional model (1600 x 1600 x 45 km, data from CRUST1.0, Laske et al. 2013) and for some cases a combination of both models was used for the relocalization. The results confirm the trend of the older routine analysis: The majority of the events are located at the margins of the natural gas fields, some of them are now located closer to them. Focal depths mostly vary between 3.5 km and 10 km. However, for some of the events, especially for the older events with relatively bad station coverage, the error bars

  13. Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)

    PubMed Central

    Vann, Laura; Kono, Thomas; Pyhäjärvi, Tanja

    2015-01-01

    The teosinte branched1(tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maize tb1 allele in teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in teosinte. We assessed the prevalence of the Hopscotch element across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Additionally, we calculated population genetic summaries using sequence data from a subset of individuals from four teosinte populations and collected phenotypic data using seed from a single teosinte population where Hopscotch was found segregating at high frequency. Genotyping results indicate the Hopscotch element is found in a number of teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on the tb1 locus, revealing a potential ecological role, but a greenhouse experiment does not detect a strong association between the Hopscotch and tillering in teosinte. Our findings suggest the role of Hopscotch differs between maize and teosinte. Future work should assess tb1 expression levels in teosinte with and without the Hopscotch and more comprehensively phenotype teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in teosinte. PMID:25909039

  14. Regional variation in the biogeochemical and physical characteristics of natural peatland pools.

    PubMed

    Turner, T Edward; Billett, Michael F; Baird, Andy J; Chapman, Pippa J; Dinsmore, Kerry J; Holden, Joseph

    2016-03-01

    Natural open-water pools are a common feature of northern peatlands and are known to be an important source of atmospheric methane (CH4). Pool environmental variables, particularly water chemistry, vegetation community and physical characteristics, have the potential to exert strong controls on carbon cycling in pools. A total of 66 peatland pools were studied across three regions of the UK (northern Scotland, south-west Scotland, and Northern Ireland). We found that within-region variability of pool water chemistry was low; however, for many pool variables measured there were significant differences between regions. PCA analysis showed that pools in SW Scotland were strongly associated with greater vegetative cover and shallower water depth which is likely to increase dissolved organic carbon (DOC) mineralisation rates, whereas pools in N Scotland were more open and deeper. Pool water DOC, particulate organic carbon and dissolved CH4 concentrations were significantly different between regions. Pools in Northern Ireland had the highest concentrations of DOC (mean=14.5 mg L(-1)) and CH4 (mean=20.6 μg C L(-1)). Chloride and sulphate concentrations were significantly higher in the pools in N Scotland (mean values 26.3 and 2.40 mg L(-1), respectively) than elsewhere, due to a stronger marine influence. The ratio of UV absorbance at 465 nm to absorbance at 665 nm for pools in Northern Ireland indicated that DOC was sourced from poorly humified peat, potentially increasing the bioavailability and mineralisation of organic carbon in pools compared to the pools elsewhere. This study, which specifically aims to address a lack of basic biogeochemical knowledge about pool water chemistry, clearly shows that peatland pools are highly regionally variable. This is likely to be a reflection of significant regional-scale differences in peatland C cycling.

  15. Salinity tolerance in soybean is modulated by natural variation in GmSALT3.

    PubMed

    Guan, Rongxia; Qu, Yue; Guo, Yong; Yu, Lili; Liu, Ying; Jiang, Jinghan; Chen, Jiangang; Ren, Yulong; Liu, Guangyu; Tian, Lei; Jin, Longguo; Liu, Zhangxiong; Hong, Huilong; Chang, Ruzhen; Gilliham, Matthew; Qiu, Lijuan

    2014-12-01

    The identification of genes that improve the salt tolerance of crops is essential for the effective utilization of saline soils for agriculture. Here, we use fine mapping in a soybean (Glycine max (L.) Merr.) population derived from the commercial cultivars Tiefeng 8 and 85-140 to identify GmSALT3 (salt tolerance-associated gene on chromosome 3), a dominant gene associated with limiting the accumulation of sodium ions (Na+) in shoots and a substantial enhancement in salt tolerance in soybean. GmSALT3 encodes a protein from the cation/H+ exchanger family that we localized to the endoplasmic reticulum and which is preferentially expressed in the salt-tolerant parent Tiefeng 8 within root cells associated with phloem and xylem. We identified in the salt-sensitive parent, 85-140, a 3.78-kb copia retrotransposon insertion in exon 3 of Gmsalt3 that truncates the transcript. By sequencing 31 soybean landraces and 22 wild soybean (Glycine soja) a total of nine haplotypes including two salt-tolerant haplotypes and seven salt-sensitive haplotypes were identified. By analysing the distribution of haplotypes among 172 Chinese soybean landraces and 57 wild soybean we found that haplotype 1 (H1, found in Tiefeng 8) was strongly associated with salt tolerance and is likely to be the ancestral allele. Alleles H2-H6, H8 and H9, which do not confer salinity tolerance, were acquired more recently. H1, unlike other alleles, has a wide geographical range including saline areas, which indicates it is maintained when required but its potent stress tolerance can be lost during natural selection and domestication. GmSALT3 is a gene associated with salt tolerance with great potential for soybean improvement.

  16. Topographic monitoring of a middle estuary mudflat, Humber estuary, UK--anthropogenic impacts and natural variation.

    PubMed

    Boyes, Suzanne J; Allen, James H

    2007-01-01

    Annual topographic surveys were carried out at the Saltend mudflat (Humber estuary, UK) between 1998 and 2006. These surveys formed part of an ongoing monitoring programme to examine the potential effects on the mudflat topography of the construction and operation of a waste water treatment works (WwTW) development by Yorkshire Water. Of particular concern was the potential disruption to the sedimentological regime within the special protection area (SPA) and candidate special area of conservation (cSAC) which could affect the invertebrate communities and ornithological functioning of the site. In addition to the development of the WwTW located to the extreme north-west of the site, a port extension removing 10ha of the Saltend intertidal mudflat (outside the SPA but immediately south east of the WwTW) also occurred between 1999 and 2006. Minimal change was noted across the site following the construction and operation of the WwTW between 1998 and 2000. However, the construction of the bund in closer proximity to the SPA and cSAC masked any potential impact the WwTW could have had across the site after 2000. Profiles and contour mapping indicate that significant mudflat accretion occurred in the immediate area of the bund, with a general increase recorded across the western section of the site since 2000. In contrast the alternations to channel planform and subsequent rapid accretion of the mudflat to the east of the jetty, being a significant distance from the developments, are attributed to natural cyclical changes.

  17. Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites

    PubMed Central

    Melamed, Daniel; Young, David L.; Miller, Christina R.; Fields, Stanley

    2015-01-01

    Many protein interactions are conserved among organisms despite changes in the amino acid sequences that comprise their contact sites, a property that has been used to infer the location of these sites from protein homology. In an inter-species complementation experiment, a sequence present in a homologue is substituted into a protein and tested for its ability to support function. Therefore, substitutions that inhibit function can identify interaction sites that changed over evolution. However, most of the sequence differences within a protein family remain unexplored because of the small-scale nature of these complementation approaches. Here we use existing high throughput mutational data on the in vivo function of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein, Pab1, to analyze its sites of interaction. Of 197 single amino acid differences in 52 Pab1 homologues, 17 reduce the function of Pab1 when substituted into the yeast protein. The majority of these deleterious mutations interfere with the binding of the RRM2 domain to eIF4G1 and eIF4G2, isoforms of a translation initiation factor. A large-scale mutational analysis of the RRM2 domain in a two-hybrid assay for eIF4G1 binding supports these findings and identifies peripheral residues that make a smaller contribution to eIF4G1 binding. Three single amino acid substitutions in yeast Pab1 corresponding to residues from the human orthologue are deleterious and eliminate binding to the yeast eIF4G isoforms. We create a triple mutant that carries these substitutions and other humanizing substitutions that collectively support a switch in binding specificity of RRM2 from the yeast eIF4G1 to its human orthologue. Finally, we map other deleterious substitutions in Pab1 to inter-domain (RRM2–RRM1) or protein-RNA (RRM2–poly(A)) interaction sites. Thus, the combined approach of large-scale mutational data and evolutionary conservation can be used to characterize interaction sites at single

  18. Natural variations in calcium isotope composition as a monitor of bone mineral balance in humans.

    NASA Astrophysics Data System (ADS)

    Skulan, J.; Anbar, A.; Thomas, B.; Smith, S.

    2004-12-01

    The skeleton is the largest reservoir of calcium in the human body and is responsible for the short term control of blood levels of this element. Accurate measurement of changes in bone calcium balance is critical to understanding how calcium metabolism responds to physiological and environmental changes and, more specifically, to diagnosing and evaluating the effectiveness of treatments for osteoporosis and other serious calcium-related disorders. It is very difficult to measure bone calcium balance using current techniques, however, because these techniques rely either on separate estimates of bone resorption and formation that are not quantitatively comparable, or on complex and expensive studies of calcium kinetics using administered isotopic tracers. This difficulty is even more apparent and more severe for measurements of short-term changes in bone calcium balance that do not produce detectable changes in bone mineral density. Calcium isotopes may provide a novel means of addressing this problem. The foundation of this isotope application is the ca. 1.3 per mil fractionation of calcium during bone formation, favoring light calcium in the bone. This fractionation results in a steady-state isotopic offset between calcium in bone and calcium in soft tissues, blood and urine. Perturbations to this steady state due to changes in the net formation or resorption of bone should be reflected in changes in the isotopic composition of soft tissues and fluids. Here we present evidence that easily detectable shifts in the natural calcium isotope composition of human urine rapidly reflect changes in bone calcium balance. Urine from subjects in a 17-week bed rest study was analyzed for calcium isotopic composition. Bed rest promotes net resorption of bone, shifting calcium from bone to soft tissues, blood and urine. The calcium isotope composition of patients in this study shifted toward lighter values during bed rest, consistent with net resorption of isotopically

  19. Natural and Human-Induced Variations in Accretion of the Roanoke Bay-head Delta

    NASA Astrophysics Data System (ADS)

    Jalowska, A.; McKee, B. A.; Rodriguez, A. B.

    2014-12-01

    Bay-head deltas (BHD), along with their adjacent floodplains serve as storage sites for lithogenic and organic material on millennial time scales and are biogeochemically active sites on daily to decadal time scales, contributing to global nutrient and carbon cycles. BHD host unique, highly diverse ecosystems such as the pristine swamp forest and hardwood bottomlands, of the Lower Roanoke River, NC. The global value of ecosystem services provided by wetlands within natural BHD is 2.5 to 2.8 mln 2007$/km2/year. BHD are very sensitive to changes in sedimentation and to changes in the rate of sea-level rise. Core descriptions, 14C geo-chronologies and grain-size analyses show that the Roanoke BHD in North Carolina, USA experienced two episodes of retreat in late Holocene. The first event occurred around ca 3500 cal. yr. BC and is recognized as a prominent flooding surface separating the delta plain environment, below, from interdistributary bay, above. Across the flooding surface rates of sediment accumulation decreased from 1.8-3.3 mm/year to 0.5-0.6 mm/year. That change was associated with increased sediment accommodation. Sedimentation rates were keeping up with the low rates of sea-level rise until 1600-1700 AD. During that time, the delta started to rapidly accrete and the interdistributary bay was buried with delta plain and prodelta sediment. This occurred in response to the low rates of sea-level rise at that time (-0.1 to 0.47 mm/year) and the release of large quantities of sediments associated with the initiation of agriculture by European settlers in the drainage basin. The second episode of retreat was initiated during the 19th century when the rate of sea-level rose to 2.1 mm/year. During that time, agricultural practices improved, decreasing the amount of sediments delivered to the mouth of the Roanoke River. Under these conditions, the delta started backstepping. Analyses of historical maps, aerial photography, and side-scan sonar data show that between

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

    PubMed

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

    2002-04-30

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

  1. Seasonal, synoptic and diurnal variation of atmospheric water-isotopologues in the boundary layer of Southwestern Germany caused by plant transpiration, cold-front passages and dewfall.

    NASA Astrophysics Data System (ADS)

    Christner, Emanuel; Dyroff, Christoph; Kohler, Martin; Zahn, Andreas; Gonzales, Yenny; Schneider, Matthias

    2013-04-01

    Atmospheric water is an enormously crucial trace gas. It is responsible for ~70 % of the natural greenhouse effect (Schmidt et al., JGR, 2010) and carries huge amounts of latent heat. The isotopic composition of water vapor is an elegant tracer for a better understanding and quantification of the extremely complex and variable hydrological cycle in Earth's atmosphere (evaporation, cloud condensation, rainout, re-evaporation, snow), which in turn is a prerequisite to improve climate modeling and predictions. As H216O, H218O and HDO differ in vapor pressure and mass, isotope fractionation occurs due to condensation, evaporation and diffusion processes. In contrast to that, plants are able to transpire water with almost no isotope fractionation. For that reason the ratio of isotopologue concentrations in the boundary layer (BL) provides, compared to humidity measurements alone, independent and additional constraints for quantifying the strength of evaporation and transpiration. Furthermore the isotope ratios contain information about transport history of an air mass and microphysical processes, that is not accessible by humidity measurements. Within the project MUSICA (MUlti-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water) a commercial Picarro Analyzer L2120-i is operated at Karlsruhe in Southwestern Germany, which is continuously measuring the isotopologues H216O, HDO and H218O of atmospheric water vapor since January 2012. A one year record of H216O, HDO and H218O shows clear seasonal, synoptic and diurnal characteristics and reveals the main driving processes affecting the isotopic composition of water vapor in the Middle European BL. Changes in continental plant transpiration and evaporation throughout the year lead to a slow seasonal HDO/H216O-variation, that cannot be explained by pure Rayleigh condensation. Furthermore, cold-front passages from NW lead to fast and pronounced depletion of the HDO/H216O-ratio within

  2. Groundwater capture processes under a seasonal variation in natural recharge and discharge

    NASA Astrophysics Data System (ADS)

    Maddock, Thomas, III.; Vionnet, Leticia Beatriz

    "Capture" is the increase in recharge and the decrease in discharge that occurs when pumping is imposed on an aquifer system that was in a previous state of approximate dynamic equilibrium. Regional groundwater models are usually used to calculate capture in a two-step procedure. A steady-state solution provides an initial-head configuration, a set of flows through the boundaries for the modeled region, and the initial basis for the capture calculation. The transient solutions provide the total change in flows through the boundaries. A difference between the transient and steady-state solutions renders the capture calculation. When seasonality is a modeling issue, the use of a single initial hydraulic head and a single set of boundary flows leads to miscalculations of capture. Instead, an initial condition for each season should be used. This approach may be accomplished by determining steady oscillatory solutions, which vary through the seasons but repeat from year to year. A regional groundwater model previously developed for a portion of the San Pedro River basin, Arizona, USA, is modified to illustrate the effect that different initial conditions have on transient solutions and on capture calculations. Résumé Les "prélèvements" sont constitués par l'augmentation de la recharge et par la diminution de l'écoulement qui se produit lorsqu'un pompage est imposéà un système aquifère qui était auparavant dans un état proche de l'équilibre dynamique. Les modèles régionaux de nappe sont en général utilisés pour calculer les prélèvements dans une procédure à deux étapes. Une solution en régime permanent donne la configuration piézométrique initiale, un jeu de conditions aux limites pour la région modélisée et les données de base pour le calcul des prélèvements. Les solutions transitoires donnent les modifications globales des conditions aux limites. Lorsque des variations saisonnières sont produites en sortie du modèle, le recours à une

  3. Variations in mitochondrial membrane potential correlate with malic acid production by natural isolates of Saccharomyces cerevisiae sake strains.

    PubMed

    Oba, Takahiro; Kusumoto, Kenichi; Kichise, Yuki; Izumoto, Eiji; Nakayama, Shunichi; Tashiro, Kosuke; Kuhara, Satoru; Kitagaki, Hiroshi

    2014-08-01

    Research on the relationship between mitochondrial membrane potential and fermentation profile is being intensely pursued because of the potential for developing advanced fermentation technologies. In the present study, we isolated naturally occurring strains of yeast from sake mash that produce high levels of malic acid and demonstrate that variations in mitochondrial mem