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Sample records for rapid phenotypic divergence

  1. Phenotypic divergence along geographic gradients reveals potential for rapid adaptation of the White-nose Syndrome pathogen, Pseudogymnoascus destructans, in North America.

    Science.gov (United States)

    Forsythe, Adrian; Giglio, Victoria; Asa, Jonathan; Xu, Jianping

    2018-06-18

    White-nose Syndrome (WNS) is an ongoing epizootic affecting multiple species of North American bats, caused by epidermal infections of the psychrophilic filamentous fungus, Pseudogymnoascus destructans Since its introduction from Europe, WNS has spread rapidly across eastern North America and resulted in high mortality rates in bats. At present, the mechanisms behind its spread and the extent of its adaptation to different geographic and ecological niches remain unknown. The objective of this study was to examine the geographic patterns of phenotypic variation and the potential evidence for adaptation among strains representing broad geographic locations in eastern North America. The morphological features of these strains were evaluated on artificial medium, and the viability of asexual arthroconidia of representative strains were investigated after storage at high (23°C), moderate (14°C), and low (4°C) temperatures at different lengths of times. Our analyses identified evidence for a geographic pattern of colony morphology changes among the clonal descendants of the fungus, with trait values correlated with increased distance from the epicenter of WNS. Our genomic comparisons of three representative isolates revealed novel genetic polymorphisms and suggested potential candidate mutations that might be related to some of the phenotypic changes. These results show that even though this pathogen arrived in North America only recently and reproduces asexually, there has been substantial evolution and phenotypic diversification during its rapid clonal expansion. Importance The causal agent of White-nose Syndrome in bats is Pseudogymnoascus destructans , a filamentous fungus recently introduced from its native range in Europe. Infections caused by P. destructans have progressed across the eastern parts of Canada and the United States over the last ten years. It is not clear how the disease is spread as the pathogen is unable to grow above 23°C and ambient

  2. Phenotypic Divergence in the Reproductive Traits of Marbled ...

    African Journals Online (AJOL)

    Overall, the results indicated some level of phenotypic divergence of the fish ... divergence cannot be partitioned between fishing mortality, genetic .... female fish was estimated from the egg counts ..... that greatly improved the quality of the.

  3. Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

    Science.gov (United States)

    Funk, W Chris; Murphy, Melanie A

    2010-02-01

    Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

  4. An Exponential Regulator for Rapidity Divergences

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ye [Fermilab; Neill, Duff [MIT, Cambridge, CTP; Zhu, Hua Xing [MIT, Cambridge, CTP

    2016-04-01

    Finding an efficient and compelling regularization of soft and collinear degrees of freedom at the same invariant mass scale, but separated in rapidity is a persistent problem in high-energy factorization. In the course of a calculation, one encounters divergences unregulated by dimensional regularization, often called rapidity divergences. Once regulated, a general framework exists for their renormalization, the rapidity renormalization group (RRG), leading to fully resummed calculations of transverse momentum (to the jet axis) sensitive quantities. We examine how this regularization can be implemented via a multi-differential factorization of the soft-collinear phase-space, leading to an (in principle) alternative non-perturbative regularization of rapidity divergences. As an example, we examine the fully-differential factorization of a color singlet's momentum spectrum in a hadron-hadron collision at threshold. We show how this factorization acts as a mother theory to both traditional threshold and transverse momentum resummation, recovering the classical results for both resummations. Examining the refactorization of the transverse momentum beam functions in the threshold region, we show that one can directly calculate the rapidity renormalized function, while shedding light on the structure of joint resummation. Finally, we show how using modern bootstrap techniques, the transverse momentum spectrum is determined by an expansion about the threshold factorization, leading to a viable higher loop scheme for calculating the relevant anomalous dimensions for the transverse momentum spectrum.

  5. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence.

    Science.gov (United States)

    Kellom, Matthew; Raymond, Jason

    2016-01-01

    The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive "top-down" centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance.

  6. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence.

    Directory of Open Access Journals (Sweden)

    Matthew Kellom

    Full Text Available The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive "top-down" centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance.

  7. Morphological divergence and flow-induced phenotypic plasticity in a native fish from anthropogenically altered stream habitats.

    Science.gov (United States)

    Franssen, Nathan R; Stewart, Laura K; Schaefer, Jacob F

    2013-11-01

    Understanding population-level responses to human-induced changes to habitats can elucidate the evolutionary consequences of rapid habitat alteration. Reservoirs constructed on streams expose stream fishes to novel selective pressures in these habitats. Assessing the drivers of trait divergence facilitated by these habitats will help identify evolutionary and ecological consequences of reservoir habitats. We tested for morphological divergence in a stream fish that occupies both stream and reservoir habitats. To assess contributions of genetic-level differences and phenotypic plasticity induced by flow variation, we spawned and reared individuals from both habitats types in flow and no flow conditions. Body shape significantly and consistently diverged in reservoir habitats compared with streams; individuals from reservoirs were shallower bodied with smaller heads compared with individuals from streams. Significant population-level differences in morphology persisted in offspring but morphological variation compared with field-collected individuals was limited to the head region. Populations demonstrated dissimilar flow-induced phenotypic plasticity when reared under flow, but phenotypic plasticity in response to flow variation was an unlikely explanation for observed phenotypic divergence in the field. Our results, together with previous investigations, suggest the environmental conditions currently thought to drive morphological change in reservoirs (i.e., predation and flow regimes) may not be the sole drivers of phenotypic change.

  8. Speciation in rapidly diverging systems: lessons from Lake Malawi.

    Science.gov (United States)

    Danley, P D; Kocher, T D

    2001-05-01

    Rapid evolutionary radiations provide insight into the fundamental processes involved in species formation. Here we examine the diversification of one such group, the cichlid fishes of Lake Malawi, which have radiated from a single ancestor into more than 400 species over the past 700 000 years. The phylogenetic history of this group suggests: (i) that their divergence has proceeded in three major bursts of cladogenesis; and (ii) that different selective forces have dominated each cladogenic event. The first episode resulted in the divergence of two major lineages, the sand- and rock-dwellers, each adapted to a major benthic macrohabitat. Among the rock-dwellers, competition for trophic resources then drove a second burst of cladogenesis, which resulted in the differentiation of trophic morphology. The third episode of cladogenesis is associated with differentiation of male nuptial colouration, most likely in response to divergent sexual selection. We discuss models of speciation in relation to this observed pattern. We advocate a model, divergence with gene flow, which reconciles the disparate selective forces responsible for the diversification of this group and suggest that the nonadaptive nature of the tertiary episode has significantly contributed to the extraordinary species richness of this group.

  9. Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster.

    Science.gov (United States)

    Burke, Molly K; Barter, Thomas T; Cabral, Larry G; Kezos, James N; Phillips, Mark A; Rutledge, Grant A; Phung, Kevin H; Chen, Richard H; Nguyen, Huy D; Mueller, Laurence D; Rose, Michael R

    2016-09-01

    Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  10. Structure of rapidity divergences in multi-parton scattering soft factors

    Science.gov (United States)

    Vladimirov, Alexey

    2018-04-01

    We discuss the structure of rapidity divergences that are presented in the soft factors of transverse momentum dependent (TMD) factorization theorems. To provide the discussion on the most general level we consider soft factors for multi-parton scattering. We show that the rapidity divergences are result of the gluon exchanges with the distant transverse plane, and are structurally equivalent to the ultraviolet divergences. It allows to formulate and to prove the renormalization theorem for rapidity divergences. The proof is made with the help the conformal transformation which maps rapidity divergences to ultraviolet divergences. The theorem is the systematic form of the factorization of rapidity divergences, which is required for the definition of TMD parton distributions. In particular, the definition of multi parton distributions is presented. The equivalence of ultraviolet and rapidity divergences leads to the exact relation between soft and rapidity anomalous dimensions. Using this relation we derive the rapidity anomalous dimension at the three-loop order.

  11. Conductive solar wind models in rapidly diverging flow geometries

    International Nuclear Information System (INIS)

    Holzer, T.E.; Leer, E.

    1980-01-01

    A detailed parameter study of conductive models of the solar wind has been carried out, extending the previous similar studies of Durney (1972) and Durney and Hundhausen (1974) by considering collisionless inhibition of thermal conduction, rapidly diverging flow geometries, and the structure of solutions for the entire n 0 -T 0 plane (n 0 and T 0 are the coronal base density and temperature). Primary emphasis is placed on understanding the complex effects of the physical processes operative in conductive solar wind models. There are five points of particular interest that have arisen from the study: (1) neither collisionless inhibition of thermal conduction nor rapidly diverging flow geometries can significantly increase the solar wind speed at 1 AU; (2) there exists a firm upper limit on the coronal base temperature consistent with observed values of the coronal base pressure and solar wind mass flux density; (3) the principal effect of rapidly diverging flow geometries is a decrease in the solar wind mass flux density at 1 AU and an increase in the mass flux density at the coronal base; (4) collisionless inhibition of thermal conduction can lead to a solar wind flow speed that either increases or decreases with increasing coronal base density (n 0 ) and temperature (T 0 , depending on the region of the n 0 -T 0 plane considered; (5) there is a region of the n 0 -T/sub o/ plane at high coronal base densities where low-speed, high-mass-flux, transonic solar wind flows exist: a region not previously considered

  12. Adaptation to different climates results in divergent phenotypic ...

    Indian Academy of Sciences (India)

    The phenotypic plasticity of wing size and wing shape of Zaprionus indianus was ... C) in two natural populations living under different climates, equatorial and ... size and shape in an invasive drosophilid. J. Genet. 87, 209–217]. Introduction.

  13. Mechanisms by Which Phenotypic Plasticity Affects Adaptive Divergence and Ecological Speciation.

    Science.gov (United States)

    Nonaka, Etsuko; Svanbäck, Richard; Thibert-Plante, Xavier; Englund, Göran; Brännström, Åke

    2015-11-01

    Phenotypic plasticity is the ability of one genotype to produce different phenotypes depending on environmental conditions. Several conceptual models emphasize the role of plasticity in promoting reproductive isolation and, ultimately, speciation in populations that forage on two or more resources. These models predict that plasticity plays a critical role in the early stages of speciation, prior to genetic divergence, by facilitating fast phenotypic divergence. The ability to plastically express alternative phenotypes may, however, interfere with the early phase of the formation of reproductive barriers, especially in the absence of geographic barriers. Here, we quantitatively investigate mechanisms under which plasticity can influence progress toward adaptive genetic diversification and ecological speciation. We use a stochastic, individual-based model of a predator-prey system incorporating sexual reproduction and mate choice in the predator. Our results show that evolving plasticity promotes the evolution of reproductive isolation under diversifying environments when individuals are able to correctly select a more profitable habitat with respect to their phenotypes (i.e., adaptive habitat choice) and to assortatively mate with relatively similar phenotypes. On the other hand, plasticity facilitates the evolution of plastic generalists when individuals have a limited capacity for adaptive habitat choice. We conclude that plasticity can accelerate the evolution of a reproductive barrier toward adaptive diversification and ecological speciation through enhanced phenotypic differentiation between diverging phenotypes.

  14. Low genetic and phenotypic divergence in a contact zone between freshwater and marine sticklebacks: gene flow constrains adaptation

    DEFF Research Database (Denmark)

    Pedersen, Susanne Holst; Ferchaud, Anne-Laure; Bertelsen, Mia Smedegaard

    2017-01-01

    Background: Distinct hybrid zones and phenotypic and genomic divergence is often observed between marine and freshwater threespine sticklebacks (Gasterosteus aculeatus). Nevertheless, cases also exist where marinefreshwater divergence is diffuse despite seemingly similar environmental settings...

  15. Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.

    Science.gov (United States)

    Schwartz, Tonia S; Bronikowski, Anne M

    2013-02-01

    The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes. © 2012 Blackwell Publishing Ltd.

  16. Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana.

    Science.gov (United States)

    Tobler, Michael; Dewitt, Thomas J; Schlupp, Ingo; García de León, Francisco J; Herrmann, Roger; Feulner, Philine G D; Tiedemann, Ralph; Plath, Martin

    2008-10-01

    Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.

  17. Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus.

    Science.gov (United States)

    Brennan, Reid S; Galvez, Fernando; Whitehead, Andrew

    2015-04-15

    The killifish Fundulus heteroclitus is an estuarine species with broad physiological plasticity, enabling acclimation to diverse stressors. Previous work suggests that freshwater populations expanded their physiology to accommodate low salinity environments; however, it is unknown whether this compromises their tolerance to high salinity. We used a comparative approach to investigate the mechanisms of a derived freshwater phenotype and the fate of an ancestral euryhaline phenotype after invasion of a freshwater environment. We compared physiological and transcriptomic responses to high- and low-salinity stress in fresh and brackish water populations and found an enhanced plasticity to low salinity in the freshwater population coupled with a reduced ability to acclimate to high salinity. Transcriptomic data identified genes with a conserved common response, a conserved salinity-dependent response and responses associated with population divergence. Conserved common acclimation responses revealed stress responses and alterations in cell-cycle regulation as important mechanisms in the general osmotic response. Salinity-specific responses included the regulation of genes involved in ion transport, intracellular calcium, energetic processes and cellular remodeling. Genes diverged between populations were primarily those showing salinity-specific expression and included those regulating polyamine homeostasis and the cell cycle. Additionally, when populations were matched with their native salinity, expression patterns were consistent with the concept of 'transcriptomic resilience', suggesting local adaptation. These findings provide insight into the fate of a plastic phenotype after a shift in environmental salinity and help to reveal mechanisms allowing for euryhalinity. © 2015. Published by The Company of Biologists Ltd.

  18. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco.

    Directory of Open Access Journals (Sweden)

    Pau Aleixandre

    Full Text Available The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis, and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands

  19. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).

    Science.gov (United States)

    Aleixandre, Pau; Hernández Montoya, Julio; Milá, Borja

    2013-01-01

    The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving

  20. Rapid divergence of mussel populations despite incomplete barriers to dispersal.

    Science.gov (United States)

    Maas, Diede L; Prost, Stefan; Bi, Ke; Smith, Lydia L; Armstrong, Ellie E; Aji, Ludi P; Toha, Abdul Hamid A; Gillespie, Rosemary G; Becking, Leontine E

    2018-04-01

    Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range F ST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence. © 2018 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

  1. Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

    Science.gov (United States)

    Glinsky, Gennadi V

    2016-09-19

    Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of

  2. Complex patterns of genetic and phenotypic divergence in an island bird and the consequences for delimiting conservation units.

    Science.gov (United States)

    Phillimore, A B; Owens, I P F; Black, R A; Chittock, J; Burke, T; Clegg, S M

    2008-06-01

    Substantial phenotypic and genetic variation is often found below the species level and this may be useful in quantifying biodiversity and predicting future diversification. However, relatively few studies have tested whether different aspects of intraspecific variation show congruent patterns across populations. Here, we quantify several aspects of divergence between 13 insular populations of an island endemic bird, the Vanuatu white-eye (Zosterops flavifrons). The components of divergence studied are mitochondrial DNA (mtDNA), nuclear DNA microsatellites and morphology. These different aspects of divergence present subtly different scenarios. For instance, an mtDNA phylogenetic tree reveals a potential cryptic species on the most southerly island in Vanuatu and considerable divergence between at least two other major phylogroups. Microsatellite loci suggest that population genetic divergence between insular populations, both between and within phylogroups, is substantial, a result that is consistent with a low level of interisland gene flow. Finally, most populations were found to be strongly morphologically divergent, but no single population was morphologically diagnosable from all others. Taken together, our results show that, although many measures of divergence are concordant in this system, the number of divergent units identified varies widely depending on the characters considered and approach used. A continuum of divergence and a degree of discordance between different characters are both to be expected under simple models of evolution, but they present problems in terms of delimiting conservation units.

  3. Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein.

    Science.gov (United States)

    Hellberg, M E; Moy, G W; Vacquier, V D

    2000-03-01

    Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (> 25 nonsynonymous substitutions per site per 10(9) years). cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (Dn/Ds > 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism.

  4. Divergent plate motion drives rapid exhumation of (ultra)high pressure rocks

    Science.gov (United States)

    Liao, Jie; Malusà, Marco G.; Zhao, Liang; Baldwin, Suzanne L.; Fitzgerald, Paul G.; Gerya, Taras

    2018-06-01

    Exhumation of (ultra)high pressure [(U)HP] rocks by upper-plate divergent motion above an unbroken slab, first proposed in the Western Alps, has never been tested by numerical methods. We present 2D thermo-mechanical models incorporating subduction of a thinned continental margin beneath either a continental or oceanic upper plate, followed by upper-plate divergent motion away from the lower plate. Results demonstrate how divergent plate motion may trigger rapid exhumation of large volumes of (U)HP rocks directly to the Earth's surface, without the need for significant overburden removal by erosion. Model exhumation paths are fully consistent with natural examples for a wide range of upper-plate divergence rates. Exhumation rates are systematically higher than the divergent rate imposed to the upper plate, and the modeled size of exhumed (U)HP domes is invariant for different rates of upper-plate divergence. Major variations are instead predicted at depth for differing model scenarios, as larger amounts of divergent motion may allow mantle-wedge exhumation to shallow depth under the exhuming domes. The transient temperature increase, due to ascent of mantle-wedge material in the subduction channel, has a limited effect on exhumed continental (U)HP rocks already at the surface. We test two examples, the Cenozoic (U)HP terranes of the Western Alps (continental upper plate) and eastern Papua New Guinea (oceanic upper plate). The good fit between model predictions and the geologic record in these terranes encourages the application of these models globally to pre-Cenozoic (U)HP terranes where the geologic record of exhumation is only partly preserved.

  5. Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

    Directory of Open Access Journals (Sweden)

    Stiassny Melanie LJ

    2010-05-01

    Full Text Available Abstract Background It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood. Results We examined genetic and morphological divergence among populations of two narrowly endemic cichlid species, Teleogramma depressum and Lamprologus tigripictilis, from a 100 km stretch of the lower Congo River using both nDNA microsatellites and mtDNA markers along with coordinate-based morphological techniques. In L. tigripictilis, the strongest genetic break was concordant with measurable phenotypic divergence but no morphological disjunction was detected for T. depressum despite significant differentiation at mtDNA and nDNA microsatellite markers. Conclusions The genetic markers revealed patterns of philopatry and estimates of genetic isolation that are among the highest reported for any African cichlid species over a comparable geographic scale. We hypothesize that the high levels of philopatry observed are generated and maintained by the extreme hydrology of the lower Congo River.

  6. Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

    Science.gov (United States)

    Pressoir, G; Berthaud, J

    2004-02-01

    To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

  7. Global Gene Expression Differences in Joints of Mice with Divergent Post Traumatic Osteoarthritis Phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Kibui, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-07-28

    Osteoarthritis (OA) is a debilitating joint disease characterized by cartilage degradation which prompts pain, stiffness and swelling. Contributing factors include age, genetics, obesity, injury and overuse of joints. OA is defined by an acute phase and a chronic phase whereby inflammation and degeneration of articular cartilage and other tissues is followed by joint pain and limited mobility. Patients remain asymptomatic until substantial joint damage has occurred and therefore rely on long term surgical joint replacement and pain management as their sole treatment options. For this reason, there is an increasing need to identify early stage osteoarthritis biomarkers. Our study aimed to identify and characterize gene expression variances in 3 different mouse strains (STR/ort, C57BL/6 and MRL/MpJ) with different susceptibility to post traumatic osteoarthritis (PTOA). Through RNA sequence analysis of whole knee joint RNA, we identified differentially expressed genes associated with the initial stages of PTOA in relation to mice with divergent phenotypes. These results will help elucidate potential mechanisms responsible for PTOA outcomes.

  8. Rapid male-specific regulatory divergence and down regulation of spermatogenesis genes in Drosophila species hybrids.

    Directory of Open Access Journals (Sweden)

    Jennifer Ferguson

    Full Text Available In most crosses between closely related species of Drosophila, the male hybrids are sterile and show postmeiotic abnormalities. A series of gene expression studies using genomic approaches have found significant down regulation of postmeiotic spermatogenesis genes in sterile male hybrids. These results have led some to suggest a direct relationship between down regulation in gene expression and hybrid sterility. An alternative explanation to a cause-and-effect relationship between misregulation of gene expression and male sterility is rapid divergence of male sex regulatory elements leading to incompatible interactions in an interspecies hybrid genome. To test the effect of regulatory divergence in spermatogenesis gene expression, we isolated 35 fertile D. simulans strains with D. mauritiana introgressions in either the X, second or third chromosome. We analyzed gene expression in these fertile hybrid strains for a subset of spermatogenesis genes previously reported as significantly under expressed in sterile hybrids relative to D. simulans. We found that fertile autosomal introgressions can cause levels of gene down regulation similar to that of sterile hybrids. We also found that X chromosome heterospecific introgressions cause significantly less gene down regulation than autosomal introgressions. Our results provide evidence that rapid male sex gene regulatory divergence can explain misexpression of spermatogenesis genes in hybrids.

  9. Phenotypic plasticity in response to the social environment: effects of density and sex ratio on mating behaviour following ecotype divergence.

    Directory of Open Access Journals (Sweden)

    Kristina Karlsson

    Full Text Available The ability to express phenotypically plastic responses to environmental cues might be adaptive in changing environments. We studied phenotypic plasticity in mating behaviour as a response to population density and adult sex ratio in a freshwater isopod (Asellus aquaticus. A. aquaticus has recently diverged into two distinct ecotypes, inhabiting different lake habitats (reed Phragmites australis and stonewort Chara tomentosa, respectively. In field surveys, we found that these habitats differ markedly in isopod population densities and adult sex ratios. These spatially and temporally demographic differences are likely to affect mating behaviour. We performed behavioural experiments using animals from both the ancestral ecotype ("reed" isopods and from the novel ecotype ("stonewort" isopods population. We found that neither ecotype adjusted their behaviour in response to population density. However, the reed ecotype had a higher intrinsic mating propensity across densities. In contrast to the effects of density, we found ecotype differences in plasticity in response to sex ratio. The stonewort ecotype show pronounced phenotypic plasticity in mating propensity to adult sex ratio, whereas the reed ecotype showed a more canalised behaviour with respect to this demographic factor. We suggest that the lower overall mating propensity and the phenotypic plasticity in response to sex ratio have evolved in the novel stonewort ecotype following invasion of the novel habitat. Plasticity in mating behaviour may in turn have effects on the direction and intensity of sexual selection in the stonewort habitat, which may fuel further ecotype divergence.

  10. Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

    Science.gov (United States)

    Wong, Mark K L; Woodman, James D; Rowell, David M

    2017-07-01

    Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

  11. Phenotypically divergent classification of preweaned heifer calves for feed efficiency indexes and their correlations with heat production and thermography.

    Science.gov (United States)

    Leão, J M; Coelho, S G; Machado, F S; Azevedo, R A; Lima, J A M; Carneiro, J C; Lage, C F A; Ferreira, A L; Pereira, L G R; Tomich, T R; Campos, M M

    2018-03-07

    The aims of this study were (1) to assess if there is phenotypical divergence for feed efficiency (FE) during the preweaning phase; (2) if FE is correlated with heat production (HP) measured by the face mask method or (3) by surface skin temperature via thermography, and (4) whether these methods are applicable to preweaned calves. Holstein × Gyr heifer calves (n = 36, birth body weight = 32.4 ± 6.6 kg) were enrolled and on trial between 4 and 12 wk of age and were classified into 2 residual feed intake (RFI) and residual body weight gain (RG) groups: high efficiency (HE; RFI, n = 10; and RG, n = 9) and low efficiency (LE; RFI, n = 10; and RG, n = 8). Calves were fed milk (6 L/d) and solid feed (95% starter and 5% chopped Tifton 85 hay, as fed). Growth was monitored weekly and feed intake (milk and solid feed) daily, during the whole period. Gas exchanges (O 2 consumption and production of CO 2 and CH 4 ) were obtained using a face mask at 45 ± 5 d of age and HP was estimated. Maximum temperatures were measured at 7 sites with an infrared camera at 62 ± 7 d of age. There was divergence in RFI and RG. Respectively, HE and LE calves had RFI of -0.14 and 0.13 kg/d, and RG of 0.05 and -0.07 kg/d. Dry matter intake was 15% lower in HE-RFI compared with LE-RFI, but no differences were observed in average daily weight gain. Within the RG test, no differences were observed in dry matter intake or average daily gain. The HE-RFI calves consumed less O 2 (L/d) and produced less CO 2 (L/d). Heart rate and HP were lower for HE-RFI calves compared with LE-RFI. Residual feed intake was correlated with HP (r = 0.48), O 2 consumption (r = 0.48), CO 2 production (r = 0.48), and heart rate (r = 0.40). No differences were observed in HP and gas exchanges between RG groups. Methane production was null in both groups. Eye temperature measured by thermography was 0.5°C greater in HE-RG than LE-RG calves. Differences in skin temperature between HE and LE calves were not observed at

  12. Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

    Science.gov (United States)

    Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

    2012-03-01

    Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

  13. Development of rapid phenotypic system for the identification

    Indian Academy of Sciences (India)

    Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology. The diagnosis and surveillance of diseases is dependent, to a great extent, on laboratory services, which cannot function without effective reliable reagents and diagnostics. Despite the advancement in microbiology ...

  14. Divergent Label-free Cell Phenotypic Pharmacology of Ligands at the Overexpressed β2-Adrenergic Receptors

    Science.gov (United States)

    Ferrie, Ann M.; Sun, Haiyan; Zaytseva, Natalya; Fang, Ye

    2014-01-01

    We present subclone sensitive cell phenotypic pharmacology of ligands at the β2-adrenergic receptor (β2-AR) stably expressed in HEK-293 cells. The parental cell line was transfected with green fluorescent protein (GFP)-tagged β2-AR. Four stable subclones were established and used to profile a library of sixty-nine AR ligands. Dynamic mass redistribution (DMR) profiling resulted in a pharmacological activity map suggesting that HEK293 endogenously expresses functional Gi-coupled α2-AR and Gs-coupled β2-AR, and the label-free cell phenotypic activity of AR ligands are subclone dependent. Pathway deconvolution revealed that the DMR of epinephrine is originated mostly from the remodeling of actin microfilaments and adhesion complexes, to less extent from the microtubule networks and receptor trafficking, and certain agonists displayed different efficacy towards the cAMP-Epac pathway. We demonstrate that receptor signaling and ligand pharmacology is sensitive to the receptor expression level, and the organization of the receptor and its signaling circuitry.

  15. Novel mutation in Sjogren-Larsson syndrome is associated with divergent neurologic phenotypes.

    Science.gov (United States)

    Davis, Kathleen; Holden, Kenton R; S'Aulis, Dana; Amador, Claudia; Matheus, M Gisele; Rizzo, William B

    2013-10-01

    Sjögren-Larsson syndrome is an inherited disorder of lipid metabolism caused by mutations in the ALDH3A2 gene that codes for fatty aldehyde dehydrogenase, which results in accumulation of fatty aldehydes and alcohols and is characterized by ichthyosis, intellectual disability, and spastic diplegia/quadriplegia. The authors describe 2 unrelated Honduran patients who carried the same novel homozygous nonsense mutation (c.1309A>T, p.K437X) and ALDH3A2 DNA haplotype, but widely differed in disease severity. One patient exhibited spastic quadriplegia with unusual neuroregression, whereas the other patient had the usual static form of spastic diplegia with neurodevelopmental disabilities. Biochemical analyses showed a similar profound deficiency of fatty aldehyde dehydrogenase activity and impaired fatty alcohol metabolism in both patients' cultured fibroblasts. These results indicate that variation in the neurologic phenotype of Sjögren-Larsson syndrome is not strictly determined by the ALDH3A2 mutation or the biochemical defect as expressed in cultured fibroblasts, but by unidentified epigenetic/environmental factors, gene modifiers, or other mechanisms.

  16. Phenotypic divergence among west European populations of Reed Bunting Emberiza schoeniclus: the effects of migratory and foraging behaviours.

    Directory of Open Access Journals (Sweden)

    Júlio M Neto

    Full Text Available Divergent selection and local adaptation are responsible for many phenotypic differences between populations, potentially leading to speciation through the evolution of reproductive barriers. Here we evaluated the morphometric divergence among west European populations of Reed Bunting in order to determine the extent of local adaptation relative to two important selection pressures often associated with speciation in birds: migration and diet. We show that, as expected by theory, migratory E. s. schoeniclus had longer and more pointed wings and a slightly smaller body mass than the resident subspecies, with the exception of E. s. lusitanica, which despite having rounder wings was the smallest of all subspecies. Tail length, however, did not vary according to the expectation (shorter tails in migrants probably because it is strongly correlated with wing length and might take longer to evolve. E. s. witherbyi, which feed on insects hiding inside reed stems during the winter, had a very thick, stubby bill. In contrast, northern populations, which feed on seeds, had thinner bills. Despite being much smaller, the southern E. s. lusitanica had a significantly thicker, longer bill than migratory E. s. schoeniclus, whereas birds from the UK population had significantly shorter, thinner bills. Geometric morphometric analyses revealed that the southern subspecies have a more convex culmen than E. s. schoeniclus, and E. s. lusitanica differs from the nominate subspecies in bill shape to a greater extent than in linear bill measurements, especially in males. Birds with a more convex culmen are thought to exert a greater strength at the bill tip, which is in agreement with their feeding technique. Overall, the three subspecies occurring in Western Europe differ in a variety of traits following the patterns predicted from their migratory and foraging behaviours, strongly suggesting that these birds have became locally adapted through natural selection.

  17. Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs

    Directory of Open Access Journals (Sweden)

    Michael H. Kohn

    2008-01-01

    Full Text Available While it remains a matter of some debate, rapid sequence evolution of the coding sequences of duplicate genes is characteristic for early phases past duplication, but long established duplicates generally evolve under constraint, much like the rest of the coding genome. As for coding sequences, it may be possible to infer evolutionary rate, selection, and constraint via contrasts between duplicate gene divergence in the 5 prime regions and in the corresponding synonymous site divergence in the coding regions. Finding elevated rates for the 5 prime regions of duplicated genes, in addition to the coding regions, would enable statements regarding the early processes of duplicate gene evolution. Here, 1 kb of each of the 5 prime regulatory regions of Drosophila melanogaster duplicate gene pairs were mapped onto one another to isolate shared sequence blocks. Genetic distances within shared sequence blocks (d5’ were found to increase as a function of synonymous (dS, and to a lesser extend, amino-acid (dA site divergence between duplicates. The rate d5’/dS was found to rapidly decay from values > 1 in young duplicate pairs (dS 0.8. Such rapid rates of 5 prime evolution exceeding 1 (~neutral predominantly were found to occur in duplicate pairs with low amino-acid site divergence and that tended to be co-regulated when assayed on microarrays. Conceivably, functional redundancy and relaxation of selective constraint facilitates subsequent positive selection on the 5 prime regions of young duplicate genes. This might promote the evolution of new functions (neofunctionalization or division of labor among duplicate genes (subfunctionalization. In contrast, similar to the vast portion of the non-coding genome, the 5 prime regions of long-established gene duplicates appear to evolve under selective constraint, indicating that these long-established gene duplicates have assumed critical functions.

  18. Kainic Acid-Induced Post-Status Epilepticus Models of Temporal Lobe Epilepsy with Diverging Seizure Phenotype and Neuropathology

    Directory of Open Access Journals (Sweden)

    Daniele Bertoglio

    2017-11-01

    Full Text Available The aim of epilepsy models is to investigate disease ontogenesis and therapeutic interventions in a consistent and prospective manner. The kainic acid-induced status epilepticus (KASE rat model is a widely used, well-validated model for temporal lobe epilepsy (TLE. As we noted significant variability within the model between labs potentially related to the rat strain used, we aimed to describe two variants of this model with diverging seizure phenotype and neuropathology. In addition, we evaluated two different protocols to induce status epilepticus (SE. Wistar Han (Charles River, France and Sprague-Dawley (Harlan, The Netherlands rats were subjected to KASE using the Hellier kainic acid (KA and a modified injection scheme. Duration of SE and latent phase were characterized by video-electroencephalography (vEEG in a subgroup of animals, while animals were sacrificed 1 week (subacute phase and 12 weeks (chronic phase post-SE. In the 12 weeks post-SE groups, seizures were monitored with vEEG. Neuronal loss (neuronal nuclei, microglial activation (OX-42 and translocator protein, and neurodegeneration (Fluorojade C were assessed. First, the Hellier protocol caused very high mortality in WH/CR rats compared to SD/H animals. The modified protocol resulted in a similar SE severity for WH/CR and SD/H rats, but effectively improved survival rates. The latent phase was significantly shorter (p < 0.0001 in SD/H (median 8.3 days animals compared to WH/CR (median 15.4 days. During the chronic phase, SD/H rats had more seizures/day compared to WH/CR animals (p < 0.01. However, neuronal degeneration and cell loss were overall more extensive in WH/CR than in SD/H rats; microglia activation was similar between the two strains 1 week post-SE, but higher in WH/CR rats 12 weeks post-SE. These neuropathological differences may be more related to the distinct neurotoxic effects of KA in the two rat strains than being the outcome of seizure

  19. Kainic Acid-Induced Post-Status Epilepticus Models of Temporal Lobe Epilepsy with Diverging Seizure Phenotype and Neuropathology

    Science.gov (United States)

    Bertoglio, Daniele; Amhaoul, Halima; Van Eetveldt, Annemie; Houbrechts, Ruben; Van De Vijver, Sebastiaan; Ali, Idrish; Dedeurwaerdere, Stefanie

    2017-01-01

    The aim of epilepsy models is to investigate disease ontogenesis and therapeutic interventions in a consistent and prospective manner. The kainic acid-induced status epilepticus (KASE) rat model is a widely used, well-validated model for temporal lobe epilepsy (TLE). As we noted significant variability within the model between labs potentially related to the rat strain used, we aimed to describe two variants of this model with diverging seizure phenotype and neuropathology. In addition, we evaluated two different protocols to induce status epilepticus (SE). Wistar Han (Charles River, France) and Sprague-Dawley (Harlan, The Netherlands) rats were subjected to KASE using the Hellier kainic acid (KA) and a modified injection scheme. Duration of SE and latent phase were characterized by video-electroencephalography (vEEG) in a subgroup of animals, while animals were sacrificed 1 week (subacute phase) and 12 weeks (chronic phase) post-SE. In the 12 weeks post-SE groups, seizures were monitored with vEEG. Neuronal loss (neuronal nuclei), microglial activation (OX-42 and translocator protein), and neurodegeneration (Fluorojade C) were assessed. First, the Hellier protocol caused very high mortality in WH/CR rats compared to SD/H animals. The modified protocol resulted in a similar SE severity for WH/CR and SD/H rats, but effectively improved survival rates. The latent phase was significantly shorter (p < 0.0001) in SD/H (median 8.3 days) animals compared to WH/CR (median 15.4 days). During the chronic phase, SD/H rats had more seizures/day compared to WH/CR animals (p < 0.01). However, neuronal degeneration and cell loss were overall more extensive in WH/CR than in SD/H rats; microglia activation was similar between the two strains 1 week post-SE, but higher in WH/CR rats 12 weeks post-SE. These neuropathological differences may be more related to the distinct neurotoxic effects of KA in the two rat strains than being the outcome of seizure burden

  20. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates.

    Directory of Open Access Journals (Sweden)

    Kathleen Semple Delaney

    2010-09-01

    Full Text Available Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding.We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation.Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

  1. A new delirium phenotype with rapid high amplitude onset and nearly as rapid reversal: Central Coast Australia Delirium Intervention Study.

    Science.gov (United States)

    Regal, Paul J

    2015-01-01

    delirium phenotype selects for a rapid high amplitude critical decline in attention, executive function, IADL, and apathy that recovers almost as rapidly.

  2. Population Divergence in Venom Bioactivities of Elapid Snake Pseudonaja textilis: Role of Procoagulant Proteins in Rapid Rodent Prey Incapacitation

    Science.gov (United States)

    Skejić, Jure; Hodgson, Wayne C.

    2013-01-01

    This study looked at how toxic proteins in venoms of adult Australian eastern Brown snakes Pseudonaja textilis from South Australian and Queensland populations interact with physiological functions of the lab SD rat Rattus norvegicus. Circulatory collapse and incoagulable blood occurred instantly after injection of venom under the dorsal skin of anaesthetised and mechanically ventilated rats in an imitation of a P. textilis bite. Intravenous injection of purified P. textilis (Mackay, QLD) venom prothrombin activator proteins caused instant failure of circulation, testifying of high toxicity of these proteins and suggesting their role in rapid incapacitation of rodent prey. The hypothesis is further supported by circulatory collapse occurring instantly despite artificial respiration in envenomed rats and the finding of extremely high venom procoagulant potency in rat plasma. LC-MS and physiology assays revealed divergent venom composition and biological activity of South Australian (Barossa locality) and Queensland (Mackay locality) populations, which may be driven by selection for different prey. The Queensland venom of P. textilis was found to be more procoagulant and to exhibit predominately presynaptic neurotoxicity, while the South Australian venom contained diverse postsynaptic type II and III α-neurotoxins in addition to the presynaptic neurotoxins and caused significantly faster onset of neuromuscular blockade in the rat phrenic nerve-diaphragm preparation. LC-MS analysis found evidence of multiple coagulation factor X-like proteins in P. textilis venoms, including a match to P. textilis coagulation factor X isoform 2, previously known to be expressed only in the liver. PMID:23691135

  3. Population divergence in venom bioactivities of elapid snake Pseudonaja textilis: role of procoagulant proteins in rapid rodent prey incapacitation.

    Directory of Open Access Journals (Sweden)

    Jure Skejić

    Full Text Available This study looked at how toxic proteins in venoms of adult Australian eastern Brown snakes Pseudonaja textilis from South Australian and Queensland populations interact with physiological functions of the lab SD rat Rattus norvegicus. Circulatory collapse and incoagulable blood occurred instantly after injection of venom under the dorsal skin of anaesthetised and mechanically ventilated rats in an imitation of a P. textilis bite. Intravenous injection of purified P. textilis (Mackay, QLD venom prothrombin activator proteins caused instant failure of circulation, testifying of high toxicity of these proteins and suggesting their role in rapid incapacitation of rodent prey. The hypothesis is further supported by circulatory collapse occurring instantly despite artificial respiration in envenomed rats and the finding of extremely high venom procoagulant potency in rat plasma. LC-MS and physiology assays revealed divergent venom composition and biological activity of South Australian (Barossa locality and Queensland (Mackay locality populations, which may be driven by selection for different prey. The Queensland venom of P. textilis was found to be more procoagulant and to exhibit predominately presynaptic neurotoxicity, while the South Australian venom contained diverse postsynaptic type II and III α-neurotoxins in addition to the presynaptic neurotoxins and caused significantly faster onset of neuromuscular blockade in the rat phrenic nerve-diaphragm preparation. LC-MS analysis found evidence of multiple coagulation factor X-like proteins in P. textilis venoms, including a match to P. textilis coagulation factor X isoform 2, previously known to be expressed only in the liver.

  4. Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation.

    Science.gov (United States)

    Corl, Ammon; Davis, Alison R; Kuchta, Shawn R; Sinervo, Barry

    2010-03-02

    Polymorphism may play an important role in speciation because new species could originate from the distinctive morphs observed in polymorphic populations. However, much remains to be understood about the process by which morphs found new species. To detail the steps of this mode of speciation, we studied the geographic variation and evolutionary history of a throat color polymorphism that distinguishes the "rock-paper-scissors" mating strategies of the side-blotched lizard, Uta stansburiana. We found that the polymorphism is geographically widespread and has been maintained for millions of years. However, there are many populations with reduced numbers of throat color morphs. Phylogenetic reconstruction showed that the polymorphism is ancestral, but it has been independently lost eight times, often giving rise to morphologically distinct subspecies/species. Changes to the polymorphism likely involved selection because the allele for one particular male strategy, the "sneaker" morph, has been lost in all cases. Polymorphism loss was associated with accelerated evolution of male size, female size, and sexual dimorphism, which suggests that polymorphism loss can promote rapid divergence among populations and aid species formation.

  5. Finite Divergence

    DEFF Research Database (Denmark)

    Hansen, Michael Edberg; Pandya, P. K.; Chaochen, Zhou

    1995-01-01

    the framework of duration calculus. Axioms and proof rules are given. Patterns of occurrence of divergence are classified into dense divergence, accumulative divergence and discrete divergence by appropriate axioms. Induction rules are given for reasoning about discrete divergence...

  6. Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes.

    Science.gov (United States)

    Faber-Hammond, Joshua; Samanta, Manoj P; Whitchurch, Elizabeth A; Manning, Dustin; Sisneros, Joseph A; Coffin, Allison B

    2015-01-01

    Acoustic communication is essential for the reproductive success of the plainfin midshipman fish (Porichthys notatus). During the breeding season, type I males use acoustic cues to advertise nest location to potential mates, creating an audible signal that attracts reproductive females. Type II (sneaker) males also likely use this social acoustic signal to find breeding pairs from which to steal fertilizations. Estrogen-induced changes in the auditory system of breeding females are thought to enhance neural encoding of the advertisement call, and recent anatomical data suggest the saccule (the main auditory end organ) as one possible target for this seasonal modulation. Here we describe saccular transcriptomes from all three sexual phenotypes (females, type I and II males) collected during the breeding season as a first step in understanding the mechanisms underlying sexual phenotype-specific and seasonal differences in auditory function. We used RNA-Seq on the Ion Torrent platform to create a combined transcriptome dataset containing over 79,000 assembled transcripts representing almost 9,000 unique annotated genes. These identified genes include several with known inner ear function and multiple steroid hormone receptors. Transcripts most closely matched to published genomes of nile tilapia and large yellow croaker, inconsistent with the phylogenetic relationship between these species but consistent with the importance of acoustic communication in their life-history strategies. We then compared the RNA-Seq results from the saccules of reproductive females with a separate transcriptome from the non-reproductive female phenotype and found over 700 differentially expressed transcripts, including members of the Wnt and Notch signaling pathways that mediate cell proliferation and hair cell addition in the inner ear. These data constitute a valuable resource for furthering our understanding of the molecular basis for peripheral auditory function as well as a range of

  7. Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus, a Teleost with Divergent Sexual Phenotypes.

    Directory of Open Access Journals (Sweden)

    Joshua Faber-Hammond

    Full Text Available Acoustic communication is essential for the reproductive success of the plainfin midshipman fish (Porichthys notatus. During the breeding season, type I males use acoustic cues to advertise nest location to potential mates, creating an audible signal that attracts reproductive females. Type II (sneaker males also likely use this social acoustic signal to find breeding pairs from which to steal fertilizations. Estrogen-induced changes in the auditory system of breeding females are thought to enhance neural encoding of the advertisement call, and recent anatomical data suggest the saccule (the main auditory end organ as one possible target for this seasonal modulation. Here we describe saccular transcriptomes from all three sexual phenotypes (females, type I and II males collected during the breeding season as a first step in understanding the mechanisms underlying sexual phenotype-specific and seasonal differences in auditory function. We used RNA-Seq on the Ion Torrent platform to create a combined transcriptome dataset containing over 79,000 assembled transcripts representing almost 9,000 unique annotated genes. These identified genes include several with known inner ear function and multiple steroid hormone receptors. Transcripts most closely matched to published genomes of nile tilapia and large yellow croaker, inconsistent with the phylogenetic relationship between these species but consistent with the importance of acoustic communication in their life-history strategies. We then compared the RNA-Seq results from the saccules of reproductive females with a separate transcriptome from the non-reproductive female phenotype and found over 700 differentially expressed transcripts, including members of the Wnt and Notch signaling pathways that mediate cell proliferation and hair cell addition in the inner ear. These data constitute a valuable resource for furthering our understanding of the molecular basis for peripheral auditory function as well

  8. Phenotypic flexibility of traits related to energy acquisition in mice divergently selected for basal metabolic rate (BMR).

    Science.gov (United States)

    Ksiazek, Aneta; Czerniecki, Jan; Konarzewski, Marek

    2009-03-01

    Theoretical considerations suggest that one of the main factors determining phenotypic flexibility of the digestive system is the size (mass) of internal organs. To test this, we used mice from two lines selected for high and low levels of basal metabolic rate (BMR). Mice with higher BMRs also have larger internal organs and higher daily food consumption (C) under non-stressful conditions. We exposed animals from both lines to a sudden cold exposure by transferring them (without prior acclimation) from an ambient temperature of 23 degrees C to 5 degrees C. Cold exposure elicited a twofold increase in C and a 25% reduction of apparent digestive efficiency. For the same body mass-corrected C, small intestine, kidneys, heart and liver of cold-exposed low-BMR mice were smaller than those of the high-BMR line. Therefore, the internal organs of low-BMR animals were burdened with substantially higher metabolic loads (defined as C or digestible food intake per total mass of a particular organ). The mass-specific activity of citrate synthase (CS) in the liver and kidneys (but not heart) was also lower in the low-BMR mice. The magnitude of phenotypic flexibility of internal organ size and CS activity was strictly proportional to the organ mass (in the case of kidneys and liver, also mass-specific CS activity) prior to an increased energy demand. Thus, phenotypic flexibility had additive rather than multiplicative dynamics. Our results also suggest that variation in BMR positively correlates with the magnitude of an immediate spare capacity that fuels the initial response of internal organs to a sudden metabolic stress.

  9. Short communication: Cytokine profiles from blood mononuclear cells of dairy cows classified with divergent immune response phenotypes.

    Science.gov (United States)

    Martin, C E; Paibomesai, M A; Emam, S M; Gallienne, J; Hine, B C; Thompson-Crispi, K A; Mallard, B A

    2016-03-01

    Genetic selection for enhanced immune response has been shown to decrease disease occurrence in dairy cattle. Cows can be classified as high (H), average, or low responders based on antibody-mediated immune response (AMIR), predominated by type-2 cytokine production, and cell-mediated immune response (CMIR) through estimated breeding values for these traits. The purpose of this study was to identify in vitro tests that correlate with in vivo immune response phenotyping in dairy cattle. Blood mononuclear cells (BMC) isolated from cows classified as H-AMIR and H-CMIR through estimated breeding values for immune response traits were stimulated with concanavalin A (ConA; Sigma Aldrich, St. Louis, MO) and gene expression, cytokine production, and cell proliferation was determined at multiple time points. A repeated measures model, which included the effects of immune response group, parity, and stage of lactation, was used to compare differences between immune response phenotype groups. The H-AMIR cows produced more IL-4 protein than H-CMIR cows at 48 h; however, no difference in gene expression of type-2 transcription factor GATA3 or IL4 was noted. The BMC from H-CMIR cows had increased production of IFN-γ protein at 48, 72, and 96 h compared with H-AMIR animals. Further, H-CMIR cows had increased expression of the IFNG gene at 16, 24, and 48 h post-treatment with ConA, although expression of the type-1 transcription factor gene TBX21 did not differ between immune response groups. Although proliferation of BMC increased from 24 to 72 h after ConA stimulation, no differences were found between the immune response groups. Overall, stimulation of H-AMIR and H-CMIR bovine BMC with ConA resulted in distinct cytokine production profiles according to genetically defined groups. These distinct cytokine profiles could be used to define disease resistance phenotypes in dairy cows according to stimulation in vitro; however, other immune response phenotypes should be assessed

  10. The effects of hybridization on divergent venom phenotypes: Characterization of venom from Crotalus scutulatus scutulatus × Crotalus oreganus helleri hybrids.

    Science.gov (United States)

    Smith, Cara Francesca; Mackessy, Stephen P

    2016-09-15

    Hybridization between divergent species can be analyzed to elucidate expression patterns of distinct parental characteristics, as well as to provide information about the extent of reproductive isolation between species. A known hybrid cross between two rattlesnakes with highly divergent venom phenotypes provided the opportunity to examine occurrence of parental venom characteristics in the F1 hybrids as well as ontogenetic shifts in the expression of these characters as the hybrids aged. Although venom phenotypes of adult rattlesnake venoms are known for many species, the effect of hybridization on phenotype inheritance is not well understood, and effects of hybridization on venom ontogeny have not yet been investigated. The current study investigates both phenomena resulting from the hybridization of a male snake with type I degradative venom, Crotalus oreganus helleri (Southern Pacific Rattlesnake), and a female snake with type II highly toxic venom, Crotalus scutulatus scutulatus (Mojave Rattlesnake). SDS-PAGE, enzymology, Western blot and reversed phase HPLC (RP-HPLC) were used to characterize the venom of the C. o. helleri male, the C. s. scutulatus female and their two hybrid offspring as they aged. In general, Crotalus o. helleri × C. s. scutulatus hybrid venoms appeared to exhibit overlapping parental venom profiles, and several different enzyme activity patterns. Both hybrids expressed C. o. helleri father-specific myotoxins as well as C. s. scutulatus mother-specific Mojave toxin. Snake venom metalloprotease activity displayed apparent sex-influenced expression patterns, while hybrid serine protease activities were intermediate to parental activities. The C. s. scutulatus × C. o. helleri hybrid male's venom profile provided the strongest evidence that type I and type II venom characteristics are expressed simultaneously in hybrid venoms, as this snake contained distinctive characteristics of both parental species. However, the possibility of

  11. Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

    Science.gov (United States)

    Mascher, Martin; Gerlach, Nina; Gahrtz, Manfred; Bucher, Marcel; Scholz, Uwe; Dresselhaus, Thomas

    2014-01-01

    Maize (Zea mays) is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis). Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs). Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL) of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and mycorrhizal fungi.

  12. Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available Maize (Zea mays is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis. Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs. Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and

  13. Mice with missense and nonsense NF1 mutations display divergent phenotypes compared with human neurofibromatosis type I

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    Kairong Li

    2016-07-01

    Full Text Available Neurofibromatosis type 1 (NF1 is a common genetic disorder characterized by the occurrence of nerve sheath tumors and considerable clinical heterogeneity. Some translational studies have been limited by the lack of animal models available for assessing patient-specific mutations. In order to test therapeutic approaches that might restore function to the mutated gene or gene product, we developed mice harboring NF1 patient-specific mutations including a nonsense mutation (c.2041C>T; p.Arg681* and a missense mutation (c.2542G>C; p.Gly848Arg. The latter is associated with the development of multiple plexiform neurofibromas along spinal nerve roots. We demonstrate that the human nonsense NF1Arg681* and missense NF1Gly848Arg mutations have different effects on neurofibromin expression in the mouse and each recapitulates unique aspects of the NF1 phenotype, depending upon the genetic context when assessed in the homozygous state or when paired with a conditional knockout allele. Whereas the missense Nf1Gly848Arg mutation fails to produce an overt phenotype in the mouse, animals homozygous for the nonsense Nf1Arg681* mutation are not viable. Mice with one Nf1Arg681* allele in combination with a conditional floxed Nf1 allele and the DhhCre transgene (Nf14F/Arg681*; DhhCre display disorganized nonmyelinating axons and neurofibromas along the spinal column, which leads to compression of the spinal cord and paralysis. This model will be valuable for preclinical testing of novel nonsense suppression therapies using drugs to target in-frame point mutations that create premature termination codons in individuals with NF1.

  14. Rapid phenotyping of crop root systems in undisturbed field soils using X-ray computed tomography.

    Science.gov (United States)

    Pfeifer, Johannes; Kirchgessner, Norbert; Colombi, Tino; Walter, Achim

    2015-01-01

    X-ray computed tomography (CT) has become a powerful tool for root phenotyping. Compared to rather classical, destructive methods, CT encompasses various advantages. In pot experiments the growth and development of the same individual root can be followed over time and in addition the unaltered configuration of the 3D root system architecture (RSA) interacting with a real field soil matrix can be studied. Yet, the throughput, which is essential for a more widespread application of CT for basic research or breeding programs, suffers from the bottleneck of rapid and standardized segmentation methods to extract root structures. Using available methods, root segmentation is done to a large extent manually, as it requires a lot of interactive parameter optimization and interpretation and therefore needs a lot of time. Based on commercially available software, this paper presents a protocol that is faster, more standardized and more versatile compared to existing segmentation methods, particularly if used to analyse field samples collected in situ. To the knowledge of the authors this is the first study approaching to develop a comprehensive segmentation method suitable for comparatively large columns sampled in situ which contain complex, not necessarily connected root systems from multiple plants grown in undisturbed field soil. Root systems from several crops were sampled in situ and CT-volumes determined with the presented method were compared to root dry matter of washed root samples. A highly significant (P < 0.01) and strong correlation (R(2) = 0.84) was found, demonstrating the value of the presented method in the context of field research. Subsequent to segmentation, a method for the measurement of root thickness distribution has been used. Root thickness is a central RSA trait for various physiological research questions such as root growth in compacted soil or under oxygen deficient soil conditions, but hardly assessable in high throughput until today, due

  15. Growth perturbations in a phenotype with rapid fetal growth preceding preterm labor and term birth.

    Science.gov (United States)

    Lampl, Michelle; Kusanovic, Juan Pedro; Erez, Offer; Gotsch, Francesca; Espinoza, Jimmy; Goncalves, Luis; Lee, Wesley; Gomez, Ricardo; Nien, Jyh Kae; Frongillo, Edward A; Romero, Roberto

    2009-01-01

    The variability in fetal growth rates and gestation duration in humans is not well understood. Of interest are women presenting with an episode of preterm labor and subsequently delivering a term neonate, who is small relative to peers of similar gestational age. To further understand these relationships, fetal growth patterns predating an episode of preterm labor were investigated. Retrospective analysis of fetal biometry assessed by serial ultrasound in a prospectively studied sample of pregnancies in Santiago, Chile, tested the hypothesis that fetal growth patterns among uncomplicated pregnancies (n = 3,706) and those with an episode of preterm labor followed by term delivery (n = 184) were identical across the time intervals 16-22 weeks, 22-28 weeks, and 28-34 weeks in a multilevel mixed-effects regression. The hypothesis was not supported. Fetal weight growth rate was faster from 16 weeks among pregnancies with an episode of preterm labor (P < 0.05), declined across midgestation (22-28 weeks, P < 0.05), and rebounded between 28 and 34 weeks (P = 0.06). This was associated with perturbations in abdominal circumference growth and proportionately larger biparietal diameter from 22 gestational weeks (P = 0.03), greater femur (P = 0.01), biparietal diameter (P = 0.001) and head circumference (P = 0.02) dimensions relative to abdominal circumference across midgestation (22-28 weeks), followed by proportionately smaller femur diaphyseal length (P = 0.02) and biparietal diameter (P = 0.03) subsequently. A distinctive rapid growth phenotype characterized fetal growth preceding an episode of preterm labor among this sample of term-delivered neonates. Perturbations in abdominal circumference growth and patterns of proportionality suggest an altered growth strategy pre-dating the preterm labor episode.

  16. Rapid plant invasion in distinct climates involves different sources of phenotypic variation.

    Directory of Open Access Journals (Sweden)

    Arnaud Monty

    Full Text Available When exotic species spread over novel environments, their phenotype will depend on a combination of different processes, including phenotypic plasticity (PP, local adaptation (LA, environmental maternal effects (EME and genetic drift (GD. Few attempts have been made to simultaneously address the importance of those processes in plant invasion. The present study uses the well-documented invasion history of Senecio inaequidens (Asteraceae in southern France, where it was introduced at a single wool-processing site. It gradually invaded the Mediterranean coast and the Pyrenean Mountains, which have noticeably different climates. We used seeds from Pyrenean and Mediterranean populations, as well as populations from the first introduction area, to explore the phenotypic variation related to climatic variation. A reciprocal sowing experiment was performed with gardens under Mediterranean and Pyrenean climates. We analyzed climatic phenotypic variation in germination, growth, reproduction, leaf physiology and survival. Genetic structure in the studied invasion area was characterized using AFLP. We found consistent genetic differentiation in growth traits but no home-site advantage, so weak support for LA to climate. In contrast, genetic differentiation showed a relationship with colonization history. PP in response to climate was observed for most traits, and it played an important role in leaf trait variation. EME mediated by seed mass influenced all but leaf traits in a Pyrenean climate. Heavier, earlier-germinating seeds produced larger individuals that produced more flower heads throughout the growing season. However, in the Mediterranean garden, seed mass only influenced the germination rate. The results show that phenotypic variation in response to climate depends on various ecological and evolutionary processes associated with geographical zone and life history traits. Seeing the relative importance of EME and GD, we argue that a "local

  17. A deep learning and novelty detection framework for rapid phenotyping in high-content screening

    Science.gov (United States)

    Sommer, Christoph; Hoefler, Rudolf; Samwer, Matthias; Gerlich, Daniel W.

    2017-01-01

    Supervised machine learning is a powerful and widely used method for analyzing high-content screening data. Despite its accuracy, efficiency, and versatility, supervised machine learning has drawbacks, most notably its dependence on a priori knowledge of expected phenotypes and time-consuming classifier training. We provide a solution to these limitations with CellCognition Explorer, a generic novelty detection and deep learning framework. Application to several large-scale screening data sets on nuclear and mitotic cell morphologies demonstrates that CellCognition Explorer enables discovery of rare phenotypes without user training, which has broad implications for improved assay development in high-content screening. PMID:28954863

  18. Phylogenetic influences on leaf trait integration in Pelargonium (Geraniaceae): convergence, divergence, and historical adaptation to a rapidly changing climate.

    Science.gov (United States)

    Jones, Cynthia S; Martínez-Cabrera, Hugo I; Nicotra, Adrienne B; Mocko, Kerri; Marais, Elizabeth M; Schlichting, Carl D

    2013-07-01

    Trait integration may improve prediction of species and lineage responses to future climate change more than individual traits alone, particularly when analyses incorporate effects of phylogenetic relationships. The South African genus Pelargonium contains divergent major clades that have radiated along the same seasonal aridity gradient, presenting the opportunity to ask whether patterns of evolution in mean leaf trait values are achieved through the same set of coordinated changes among traits in each clade. Seven leaf traits were measured on field-collected leaves from one-third of the species (98) of the genus. Trait relationships were examined using phylogenetic regression within major clades. Disparity analysis determined whether the course of trait evolution paralleled historical climate change events. Divergence in mean trait values between sister clades A1 and A2 was consistent with expectations for leaves differing in longevity, despite strong similarity between clades in trait interactions. No traits in either clade exhibited significant relationships with multivariate climate axes, with one exception. Species in clades C and A2 included in this study occupied similar environments. These clades had similar values of individual trait means, except for δ(13)C, but they exhibited distinctive patterns of trait integration. Differing present-day patterns of trait integration are consistent with interpretations of adaptive responses to the prevailing climate at the time of each clade's origin. These differing patterns of integration are likely to exert strong effects on clade-level responses to future climate change in the winter rainfall region of South Africa.

  19. Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data

    OpenAIRE

    Chang, Jonathan; Chang, Jonathan

    2015-01-01

    1. Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic datasets has not kept pace. 2. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image-based landmarking. 3. We find that crowdsourced workers perform similarly to experienced morphologists on the same digitization tasks. We also demonstrate the speed and accuracy of our method on seven families of ray-f...

  20. Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes.

    Science.gov (United States)

    Steppan, Scott; Adkins, Ronald; Anderson, Joel

    2004-08-01

    The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.

  1. Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals

    Science.gov (United States)

    Raia, P.; Carotenuto, F.; Passaro, F.; Piras, P.; Fulgione, D.; Werdelin, L.; Saarinen, J.; Fortelius, M.

    2013-01-01

    A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation. PMID:23173207

  2. The Expression of TALEN before Fertilization Provides a Rapid Knock-Out Phenotype in Xenopus laevis Founder Embryos.

    Science.gov (United States)

    Miyamoto, Kei; Suzuki, Ken-Ichi T; Suzuki, Miyuki; Sakane, Yuto; Sakuma, Tetsushi; Herberg, Sarah; Simeone, Angela; Simpson, David; Jullien, Jerome; Yamamoto, Takashi; Gurdon, J B

    2015-01-01

    Recent advances in genome editing using programmable nucleases have revolutionized gene targeting in various organisms. Successful gene knock-out has been shown in Xenopus, a widely used model organism, although a system enabling less mosaic knock-out in founder embryos (F0) needs to be explored in order to judge phenotypes in the F0 generation. Here, we injected modified highly active transcription activator-like effector nuclease (TALEN) mRNA to oocytes at the germinal vesicle (GV) stage, followed by in vitro maturation and intracytoplasmic sperm injection, to achieve a full knock-out in F0 embryos. Unlike conventional injection methods to fertilized embryos, the injection of TALEN mRNA into GV oocytes allows expression of nucleases before fertilization, enabling them to work from an earlier stage. Using this procedure, most of developed embryos showed full knock-out phenotypes of the pigmentation gene tyrosinase and/or embryonic lethal gene pax6 in the founder generation. In addition, our method permitted a large 1 kb deletion. Thus, we describe nearly complete gene knock-out phenotypes in Xenopus laevis F0 embryos. The presented method will help to accelerate the production of knock-out frogs since we can bypass an extra generation of about 1 year in Xenopus laevis. Meantime, our method provides a unique opportunity to rapidly test the developmental effects of disrupting those genes that do not permit growth to an adult able to reproduce. In addition, the protocol shown here is considerably less invasive than the previously used host transfer since our protocol does not require surgery. The experimental scheme presented is potentially applicable to other organisms such as mammals and fish to resolve common issues of mosaicism in founders.

  3. Rapid divergence of histones in Hydrozoa (Cnidaria) and evolution of a novel histone involved in DNA damage response in hydra.

    Science.gov (United States)

    Reddy, Puli Chandramouli; Ubhe, Suyog; Sirwani, Neha; Lohokare, Rasika; Galande, Sanjeev

    2017-08-01

    Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra. Here, we report identification of the complete repertoire of histone-coding genes in the Hydra magnipapillata genome. Hydra histones were classified based on their copy numbers, gene structure and other characteristic features. Genomic organization of canonical histone genes revealed the presence of H2A-H2B and H3-H4 paired clusters in high frequency and also a cluster with all core histones along with H1. Phylogenetic analysis of identified members of H2A and H2B histones suggested rapid expansion of these groups in Hydrozoa resulting in the appearance of unique subtypes. Amino acid sequence level comparisons of H2A and H2B forms with bilaterian counterparts suggest the possibility of a highly mobile nature of nucleosomes in hydra. Absolute quantitation of transcripts confirmed the high copy number of histones and supported the canonical nature of H2A. Furthermore, functional characterization of H2A.X.1 and a unique variant H2A.X.2 in the gastric region suggest their role in the maintenance of genome integrity and differentiation processes. These findings provide insights into the evolution of histones and their variants in hydra. Copyright © 2017 Elsevier GmbH. All rights reserved.

  4. Acute Viral Respiratory Infection Rapidly Induces a CD8+ T Cell Exhaustion-like Phenotype.

    Science.gov (United States)

    Erickson, John J; Lu, Pengcheng; Wen, Sherry; Hastings, Andrew K; Gilchuk, Pavlo; Joyce, Sebastian; Shyr, Yu; Williams, John V

    2015-11-01

    Acute viral infections typically generate functional effector CD8(+) T cells (TCD8) that aid in pathogen clearance. However, during acute viral lower respiratory infection, lung TCD8 are functionally impaired and do not optimally control viral replication. T cells also become unresponsive to Ag during chronic infections and cancer via signaling by inhibitory receptors such as programmed cell death-1 (PD-1). PD-1 also contributes to TCD8 impairment during viral lower respiratory infection, but how it regulates TCD8 impairment and the connection between this state and T cell exhaustion during chronic infections are unknown. In this study, we show that PD-1 operates in a cell-intrinsic manner to impair lung TCD8. In light of this, we compared global gene expression profiles of impaired epitope-specific lung TCD8 to functional spleen TCD8 in the same human metapneumovirus-infected mice. These two populations differentially regulate hundreds of genes, including the upregulation of numerous inhibitory receptors by lung TCD8. We then compared the gene expression of TCD8 during human metapneumovirus infection to those in acute or chronic lymphocytic choriomeningitis virus infection. We find that the immunophenotype of lung TCD8 more closely resembles T cell exhaustion late into chronic infection than do functional effector T cells arising early in acute infection. Finally, we demonstrate that trafficking to the infected lung alone is insufficient for TCD8 impairment or inhibitory receptor upregulation, but that viral Ag-induced TCR signaling is also required. Our results indicate that viral Ag in infected lungs rapidly induces an exhaustion-like state in lung TCD8 characterized by progressive functional impairment and upregulation of numerous inhibitory receptors. Copyright © 2015 by The American Association of Immunologists, Inc.

  5. Active PI3K pathway causes an invasive phenotype which can be reversed or promoted by blocking the pathway at divergent nodes.

    Directory of Open Access Journals (Sweden)

    Jeffrey J Wallin

    Full Text Available The PTEN/PI3K pathway is commonly mutated in cancer and therefore represents an attractive target for therapeutic intervention. To investigate the primary phenotypes mediated by increased pathway signaling in a clean, patient-relevant context, an activating PIK3CA mutation (H1047R was knocked-in to an endogenous allele of the MCF10A non-tumorigenic human breast epithelial cell line. Introduction of an endogenously mutated PIK3CA allele resulted in a marked epithelial-mesenchymal transition (EMT and invasive phenotype, compared to isogenic wild-type cells. The invasive phenotype was linked to enhanced PIP(3 production via a S6K-IRS positive feedback mechanism. Moreover, potent and selective inhibitors of PI3K were highly effective in reversing this phenotype, which is optimally revealed in 3-dimensional cell culture. In contrast, inhibition of Akt or mTOR exacerbated the invasive phenotype. Our results suggest that invasion is a core phenotype mediated by increased PTEN/PI3K pathway activity and that therapeutic agents targeting different nodes of the PI3K pathway may have dramatic differences in their ability to reverse or promote cancer metastasis.

  6. Functional characterizations of venom phenotypes in the eastern diamondback rattlesnake (Crotalus adamanteus) and evidence for expression-driven divergence in toxic activities among populations

    Science.gov (United States)

    Margres, Mark J.; Walls, Robert; Suntravat, Montamas; Lucena, Sara; Sánchez, Elda E.; Rokyta, Darin R.

    2016-01-01

    Phenotypes frequently vary across and within species. The connection between specific phenotypic effects and function, however, is less understood despite being essential to our understanding of the adaptive process. Snake venoms are ideal for identifying functionally important phenotypic variation because venom variation is common, and venoms can be functionally characterized through simple assays and toxicity measurements. Previous work with the eastern diamondback rattlesnake (Crotalus adamanteus) used multivariate statistical approaches to identify six unique venom phenotypes. We functionally characterized hemolytic, gelatinase, fibrinogenolytic, and coagulant activity for all six phenotypes, as well as one additional venom, to determine if the statistically significant differences in toxin expression levels previously documented corresponded to differences in venom activity. In general, statistical differences in toxin expression predicted the identified functional differences, or lack thereof, in toxic activity, demonstrating that the statistical approach used to characterize C. adamanteus venoms was a fair representation of biologically meaningful differences. Minor differences in activity not accounted for by the statistical model may be the result of amino-acid differences and/or post-translational modifications, but overall we were able to link variation in protein expression levels to variation in function as predicted by multivariate statistical approaches. PMID:27179420

  7. Diverging Cohesion?

    DEFF Research Database (Denmark)

    Charron, Nicholas

    2016-01-01

    – which we define here as a combination of impartial bureaucratic practices, corruption and the rule of law – limits, and in some cases reverses the tendency towards greater divergence linked to trade. Countries with high levels of state capacity – that is, those that have greater government effectiveness......, stronger rule of law and lower corruption – experience lower levels of divergence, as they have the mechanisms to counterbalance the strong centripetal forces linked to openness. This claim is tested on countries that have experienced relatively high levels of increases in levels of economic and political......Why do increases in globalisation in the face of European expansion lead to sharp levels of regional divergences in wealth in some countries but not in others? The central crux of this paper is that convergence/divergence trends in European states are conditioned by ‘state capacity’. State capacity...

  8. The Clinical Phenotype of Idiopathic Rapid Eye Movement Sleep Behavior Disorder at Presentation: A Study in 203 Consecutive Patients.

    Science.gov (United States)

    Fernández-Arcos, Ana; Iranzo, Alex; Serradell, Mónica; Gaig, Carles; Santamaria, Joan

    2016-01-01

    To describe the clinical phenotype of idiopathic rapid eye movement (REM) sleep behavior disorder (IRBD) at presentation in a sleep center. Clinical history review of 203 consecutive patients with IRBD identified between 1990 and 2014. IRBD was diagnosed by clinical history plus video-polysomnographic demonstration of REM sleep with increased electromyographic activity linked to abnormal behaviors. Patients were 80% men with median age at IRBD diagnosis of 68 y (range, 50-85 y). In addition to the already known clinical picture of IRBD, other important features were apparent: 44% of the patients were not aware of their dream-enactment behaviors and 70% reported good sleep quality. In most of these cases bed partners were essential to convince patients to seek medical help. In 11% IRBD was elicited only after specific questioning when patients consulted for other reasons. Seven percent did not recall unpleasant dreams. Leaving the bed occurred occasionally in 24% of subjects in whom dementia with Lewy bodies often developed eventually. For the correct diagnosis of IRBD, video-polysomnography had to be repeated in 16% because of insufficient REM sleep or electromyographic artifacts from coexistent apneas. Some subjects with comorbid obstructive sleep apnea reported partial improvement of RBD symptoms following continuous positive airway pressure therapy. Lack of therapy with clonazepam resulted in an increased risk of sleep related injuries. Synucleinopathy was frequently diagnosed, even in patients with mild severity or uncommon IRBD presentations (e.g., patients who reported sleeping well, onset triggered by a life event, nocturnal ambulation) indicating that the development of a neurodegenerative disease is independent of the clinical presentation of IRBD. We report the largest IRBD cohort observed in a single center to date and highlight frequent features that were not reported or not sufficiently emphasized in previous publications. Physicians should be aware of

  9. Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus) - towards understanding gene function and regulatory evolution in an ecological model system for rapid phenotypic diversification.

    Science.gov (United States)

    Kratochwil, Claudius F; Sefton, Maggie M; Liang, Yipeng; Meyer, Axel

    2017-11-23

    The Midas cichlid species complex (Amphilophus spp.) is widely known among evolutionary biologists as a model system for sympatric speciation and adaptive phenotypic divergence within extremely short periods of time (a few hundred generations). The repeated parallel evolution of adaptive phenotypes in this radiation, combined with their near genetic identity, makes them an excellent model for studying phenotypic diversification. While many ecological and evolutionary studies have been performed on Midas cichlids, the molecular basis of specific phenotypes, particularly adaptations, and their underlying coding and cis-regulatory changes have not yet been studied thoroughly. For the first time in any New World cichlid, we use Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus). By adapting existing microinjection protocols, we established an effective protocol for transgenesis in Midas cichlids. Embryos were injected with a Tol2 plasmid construct that drives enhanced green fluorescent protein (eGFP) expression under the control of the ubiquitin promoter. The transgene was successfully integrated into the germline, driving strong ubiquitous expression of eGFP in the first transgenic Midas cichlid line. Additionally, we show transient expression of two further transgenic constructs, ubiquitin::tdTomato and mitfa::eGFP. Transgenesis in Midas cichlids will facilitate further investigation of the genetic basis of species-specific traits, many of which are adaptations. Transgenesis is a versatile tool not only for studying regulatory elements such as promoters and enhancers, but also for testing gene function through overexpression of allelic gene variants. As such, it is an important first step in establishing the Midas cichlid as a powerful model for studying adaptive coding and non-coding changes in an ecological and evolutionary context.

  10. Rapid Cellular Phenotyping of Human Pluripotent Stem Cell-Derived Cardiomyocytes using a Genetically Encoded Fluorescent Voltage Sensor

    Directory of Open Access Journals (Sweden)

    Jordan S. Leyton-Mange

    2014-02-01

    Full Text Available In addition to their promise in regenerative medicine, pluripotent stem cells have proved to be faithful models of many human diseases. In particular, patient-specific stem cell-derived cardiomyocytes recapitulate key features of several life-threatening cardiac arrhythmia syndromes. For both modeling and regenerative approaches, phenotyping of stem cell-derived tissues is critical. Cellular phenotyping has largely relied upon expression of lineage markers rather than physiologic attributes. This is especially true for cardiomyocytes, in part because electrophysiological recordings are labor intensive. Likewise, most optical voltage indicators suffer from phototoxicity, which damages cells and degrades signal quality. Here we present the use of a genetically encoded fluorescent voltage indicator, ArcLight, which we demonstrate can faithfully report transmembrane potentials in human stem cell-derived cardiomyocytes. We demonstrate the application of this fluorescent sensor in high-throughput, serial phenotyping of differentiating cardiomyocyte populations and in screening for drug-induced cardiotoxicity.

  11. Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation.

    Science.gov (United States)

    Gao, Lexuan; Geng, Yupeng; Li, Bo; Chen, Jiakuan; Yang, Ji

    2010-11-01

    Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome-wide methylation profiling using methylation-sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome-wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors. © 2010 Blackwell Publishing Ltd.

  12. Rapid-throughput skeletal phenotyping of 100 knockout mice identifies 9 new genes that determine bone strength.

    Directory of Open Access Journals (Sweden)

    J H Duncan Bassett

    Full Text Available Osteoporosis is a common polygenic disease and global healthcare priority but its genetic basis remains largely unknown. We report a high-throughput multi-parameter phenotype screen to identify functionally significant skeletal phenotypes in mice generated by the Wellcome Trust Sanger Institute Mouse Genetics Project and discover novel genes that may be involved in the pathogenesis of osteoporosis. The integrated use of primary phenotype data with quantitative x-ray microradiography, micro-computed tomography, statistical approaches and biomechanical testing in 100 unselected knockout mouse strains identified nine new genetic determinants of bone mass and strength. These nine new genes include five whose deletion results in low bone mass and four whose deletion results in high bone mass. None of the nine genes have been implicated previously in skeletal disorders and detailed analysis of the biomechanical consequences of their deletion revealed a novel functional classification of bone structure and strength. The organ-specific and disease-focused strategy described in this study can be applied to any biological system or tractable polygenic disease, thus providing a general basis to define gene function in a system-specific manner. Application of the approach to diseases affecting other physiological systems will help to realize the full potential of the International Mouse Phenotyping Consortium.

  13. Eficiência produtiva de cultivares de arroz com divergência fenotípica Production efficiency of rice cultivars with phenotypic diversity

    Directory of Open Access Journals (Sweden)

    Cleber M. Guimarães

    2008-10-01

    Full Text Available O objetivo do trabalho foi avaliar, fenotipicamente, as cultivares de arroz tradicionais Guarani e Caiapó, e as modernas, CIRAD L(-141, Maravilha, BR IRGA 409 e Metica 1, por meio da associação entre os vários componentes da produtividade de grãos, para prover base de seleção genética em populações de plantas. O estudo foi conduzido na estação chuvosa do ano agrícola de 2003-2004, na área experimental da Embrapa Arroz e Feijão, em Santo Antônio de Goiás, GO. Em condições de sequeiro, com suplementação hídrica, as cultivares de arroz de terras altas CIRAD L(-141, Guarani, Caiapó e Maravilha, apresentaram maiores índices de colheita e menores percentagens de esterilidade de espiguetas que as de arroz irrigado BR IRGA 409 e Metica 1. Concluiu-se que a maior produção de biomassa pelas cultivares de arroz irrigado não se refletiu na produtividade de grãos. A CIRAD L(-141 por apresentar alta área foliar, panículas densas com alto número de grãos e um comportamento intermediário em todos os componentes avaliados, como índice de colheita, massa dos grãos, fertilidade de perfilhos, perfilhamento, esterilidade de espiguetas e taxa de crescimento, produziu 12,5% a mais que a segunda mais produtiva. O aumento do índice de colheita e da massa dos grãos e a redução da esterilidade das espiguetas devido às suas altas correlações com a produtividade, são considerados prioritários em programas de melhoramento de arroz que visem obter cultivares mais produtivas.The objective of this study was to phenotypically evaluate the traditional rice cultivars Guarani and Caiapó, and the modern rice cultivars CIRAD L(-141, Maravilha, BR IRGA 409, and Metica 1 through association among various yield components to establish a genetic selection base in plant population. The study was conducted during the rainy season of 2003-2004, at the Embrapa Rice & Beans experimental station, in Santo Antônio de Goiás, Goiás, Brazil. With

  14. Rapid adaptation to a novel light environment: The importance of ontogeny and phenotypic plasticity in shaping the visual system of Nicaraguan Midas cichlid fish (Amphilophus citrinellus spp.).

    Science.gov (United States)

    Härer, Andreas; Torres-Dowdall, Julián; Meyer, Axel

    2017-10-01

    Colonization of novel habitats is typically challenging to organisms. In the initial stage after colonization, approximation to fitness optima in the new environment can occur by selection acting on standing genetic variation, modification of developmental patterns or phenotypic plasticity. Midas cichlids have recently colonized crater Lake Apoyo from great Lake Nicaragua. The photic environment of crater Lake Apoyo is shifted towards shorter wavelengths compared to great Lake Nicaragua and Midas cichlids from both lakes differ in visual sensitivity. We investigated the contribution of ontogeny and phenotypic plasticity in shaping the visual system of Midas cichlids after colonizing this novel photic environment. To this end, we measured cone opsin expression both during development and after experimental exposure to different light treatments. Midas cichlids from both lakes undergo ontogenetic changes in cone opsin expression, but visual sensitivity is consistently shifted towards shorter wavelengths in crater lake fish, which leads to a paedomorphic retention of their visual phenotype. This shift might be mediated by lower levels of thyroid hormone in crater lake Midas cichlids (measured indirectly as dio2 and dio3 gene expression). Exposing fish to different light treatments revealed that cone opsin expression is phenotypically plastic in both species during early development, with short and long wavelength light slowing or accelerating ontogenetic changes, respectively. Notably, this plastic response was maintained into adulthood only in the derived crater lake Midas cichlids. We conclude that the rapid evolution of Midas cichlids' visual system after colonizing crater Lake Apoyo was mediated by a shift in visual sensitivity during ontogeny and was further aided by phenotypic plasticity during development. © 2017 John Wiley & Sons Ltd.

  15. The expanding spectrum of neurological phenotypes in children with ATP1A3 mutations, Alternating Hemiplegia of Childhood, Rapid-onset Dystonia-Parkinsonism, CAPOS and beyond.

    Science.gov (United States)

    Sweney, Matthew T; Newcomb, Tara M; Swoboda, Kathryn J

    2015-01-01

    ATP1A3 mutations have now been recognized in infants and children presenting with a diverse group of neurological phenotypes, including Rapid-onset Dystonia-Parkinsonism (RDP), Alternating Hemiplegia of Childhood (AHC), and most recently, Cerebellar ataxia, Areflexia, Pes cavus, Optic atrophy, and Sensorineural hearing loss (CAPOS) syndrome. Existing literature on ATP1A3-related disorders in the pediatric population were reviewed, with attention to clinical features and associated genotypes among those with RDP, AHC, or CAPOS syndrome phenotypes. While classically defined phenotypes associated with AHC, RDP, and CAPOS syndromes are distinct, common elements among ATP1A3-related neurological disorders include characteristic episodic neurological symptoms and signs that vary in severity, duration, and frequency of occurrence. Affected children typically present in the context of an acute onset of paroxysmal, episodic neurological symptoms ranging from oculomotor abnormalities, hypotonia, paralysis, dystonia, ataxia, seizure-like episodes, or encephalopathy. Neurodevelopmental delays or persistence of dystonia, chorea, or ataxia after resolution of an initial episode are common, providing important clues for diagnosis. The phenotypic spectrum of ATP1A3-related neurological disorders continues to expand beyond the distinct yet overlapping phenotypes in patients with AHC, RDP, and CAPOS syndromes. ATP1A3 mutation analysis is appropriate to consider in the diagnostic algorithm for any child presenting with episodic or fluctuating ataxia, weakness or dystonia whether they manifest persistence of neurological symptoms between episodes. Additional work is needed to better identify and classify affected patients and develop targeted treatment approaches. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Rapid and sensitive phenotypic marker detection on breast cancer cells using surface-enhanced Raman scattering (SERS) imaging.

    Science.gov (United States)

    Lee, Sangyeop; Chon, Hyangah; Lee, Jiyoung; Ko, Juhui; Chung, Bong Hyun; Lim, Dong Woo; Choo, Jaebum

    2014-01-15

    We report a surface-enhanced Raman scattering (SERS)-based cellular imaging technique to detect and quantify breast cancer phenotypic markers expressed on cell surfaces. This technique involves the synthesis of SERS nano tags consisting of silica-encapsulated hollow gold nanospheres (SEHGNs) conjugated with specific antibodies. Hollow gold nanospheres (HGNs) enhance SERS signal intensity of individual particles by localizing surface electromagnetic fields through pinholes in the hollow particle structures. This capacity to enhance imaging at the level of single molecules permits the use of HGNs to detect specific biological markers expressed in living cancer cells. In addition, silica encapsulation greatly enhances the stability of nanoparticles. Here we applied a SERS-based imaging technique using SEHGNs in the multiplex imaging of three breast cancer cell phenotypes. Expression of epidermal growth factor (EGF), ErbB2, and insulin-like growth factor-1 (IGF-1) receptors were assessed in the MDA-MB-468, KPL4 and SK-BR-3 human breast cancer cell lines. SERS imaging technology described here can be used to test the phenotype of a cancer cell and quantify proteins expressed on the cell surface simultaneously. Based on results, this technique may enable an earlier diagnosis of breast cancer than is currently possible and offer guidance in treatment. © 2013 Elsevier B.V. All rights reserved.

  17. Convergence from divergence

    Science.gov (United States)

    Costin, Ovidiu; Dunne, Gerald V.

    2018-01-01

    We show how to convert divergent series, which typically occur in many applications in physics, into rapidly convergent inverse factorial series. This can be interpreted physically as a novel resummation of perturbative series. Being convergent, these new series allow rigorous extrapolation from an asymptotic region with a large parameter, to the opposite region where the parameter is small. We illustrate the method with various physical examples, and discuss how these convergent series relate to standard methods such as Borel summation, and also how they incorporate the physical Stokes phenomenon. We comment on the relation of these results to Dyson’s physical argument for the divergence of perturbation theory. This approach also leads naturally to a wide class of relations between bosonic and fermionic partition functions, and Klein-Gordon and Dirac determinants.

  18. Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles.

    Science.gov (United States)

    Li, Yang I; Kong, Lesheng; Ponting, Chris P; Haerty, Wilfried

    2013-01-01

    Sequencing of vertebrate genomes permits changes in distinct protein families, including gene gains and losses, to be ascribed to lineage-specific phenotypes. A prominent example of this is the large-scale duplication of beta-keratin genes in the ancestors of birds, which was crucial to the subsequent evolution of their beaks, claws, and feathers. Evidence suggests that the shell of Pseudomys nelsoni contains at least 16 beta-keratins proteins, but it is unknown whether this is a complete set and whether their corresponding genes are orthologous to avian beak, claw, or feather beta-keratin genes. To address these issues and to better understand the evolution of the turtle shell at a molecular level, we surveyed the diversity of beta-keratin genes from the genome assemblies of three turtles, Chrysemys picta, Pelodiscus sinensis, and Chelonia mydas, which together represent over 160 Myr of chelonian evolution. For these three turtles, we found 200 beta-keratins, which indicate that, as for birds, a large expansion of beta-keratin genes in turtles occurred concomitantly with the evolution of a unique phenotype, namely, their plastron and carapace. Phylogenetic reconstruction of beta-keratin gene evolution suggests that separate waves of gene duplication within a single genomic location gave rise to scales, claws, and feathers in birds, and independently the scutes of the shell in turtles.

  19. Estimation of phenotypic divergence and powdery mildew ...

    African Journals Online (AJOL)

    user

    2011-03-14

    Mar 14, 2011 ... fruit size which varied from 16.3 to 25.2 cm/fruit. Fruit color was also quite variable, the skin color of the collected genotypes was mainly dark green and light green, but two collections CSC-45 and CSC-71 had white skinned fruits. The flesh color of the cucumber was either white or cream in the collections.

  20. Estimation of phenotypic divergence and powdery mildew ...

    African Journals Online (AJOL)

    When the 30 populations were plotted on the first two principal components, accounting for 46% of the total variation, five clusters were identified, accounting for ... powdery mildew resistance can assist geneticists and breeders to identify populations with desirable characteristics for inclusion in variety breeding programs.

  1. Divergence of iron metabolism in wild Malaysian yeast.

    Science.gov (United States)

    Lee, Hana N; Mostovoy, Yulia; Hsu, Tiffany Y; Chang, Amanda H; Brem, Rachel B

    2013-12-09

    Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.

  2. Rapid eye movements during sleep in mice: High trait-like stability qualifies rapid eye movement density for characterization of phenotypic variation in sleep patterns of rodents

    Directory of Open Access Journals (Sweden)

    Fulda Stephany

    2011-11-01

    Full Text Available Abstract Background In humans, rapid eye movements (REM density during REM sleep plays a prominent role in psychiatric diseases. Especially in depression, an increased REM density is a vulnerability marker for depression. In clinical practice and research measurement of REM density is highly standardized. In basic animal research, almost no tools are available to obtain and systematically evaluate eye movement data, although, this would create increased comparability between human and animal sleep studies. Methods We obtained standardized electroencephalographic (EEG, electromyographic (EMG and electrooculographic (EOG signals from freely behaving mice. EOG electrodes were bilaterally and chronically implanted with placement of the electrodes directly between the musculus rectus superior and musculus rectus lateralis. After recovery, EEG, EMG and EOG signals were obtained for four days. Subsequent to the implantation process, we developed and validated an Eye Movement scoring in Mice Algorithm (EMMA to detect REM as singularities of the EOG signal, based on wavelet methodology. Results The distribution of wakefulness, non-REM (NREM sleep and rapid eye movement (REM sleep was typical of nocturnal rodents with small amounts of wakefulness and large amounts of NREM sleep during the light period and reversed proportions during the dark period. REM sleep was distributed correspondingly. REM density was significantly higher during REM sleep than NREM sleep. REM bursts were detected more often at the end of the dark period than the beginning of the light period. During REM sleep REM density showed an ultradian course, and during NREM sleep REM density peaked at the beginning of the dark period. Concerning individual eye movements, REM duration was longer and amplitude was lower during REM sleep than NREM sleep. The majority of single REM and REM bursts were associated with micro-arousals during NREM sleep, but not during REM sleep. Conclusions Sleep

  3. Memory phenotype CD4 T cells undergoing rapid, nonburst-like, cytokine-driven proliferation can be distinguished from antigen-experienced memory cells.

    Directory of Open Access Journals (Sweden)

    Souheil-Antoine Younes

    2011-10-01

    Full Text Available Memory phenotype (CD44(bright, CD25(negative CD4 spleen and lymph node T cells (MP cells proliferate rapidly in normal or germ-free donors, with BrdU uptake rates of 6% to 10% per day and Ki-67 positivity of 18% to 35%. The rapid proliferation of MP cells stands in contrast to the much slower proliferation of lymphocytic choriomeningitis virus (LCMV-specific memory cells that divide at rates ranging from <1% to 2% per day over the period from 15 to 60 days after LCMV infection. Anti-MHC class II antibodies fail to inhibit the in situ proliferation of MP cells, implying a non-T-cell receptor (TCR-driven proliferation. Such proliferation is partially inhibited by anti-IL-7Rα antibody. The sequence diversity of TCRβ CDR3 gene segments is comparable among the proliferating and quiescent MP cells from conventional and germ-free mice, implying that the majority of proliferating MP cells have not recently derived from a small cohort of cells that expand through multiple continuous rounds of cell division. We propose that MP cells constitute a diverse cell population, containing a subpopulation of slowly dividing authentic antigen-primed memory cells and a majority population of rapidly proliferating cells that did not arise from naïve cells through conventional antigen-driven clonal expansion.

  4. Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata.

    Science.gov (United States)

    Yao, Qiu-Yang; Xia, En-Hua; Liu, Fei-Hu; Gao, Li-Zhi

    2015-02-15

    WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Rapid mutation of Spirulina platensis by a new mutagenesis system of atmospheric and room temperature plasmas (ARTP and generation of a mutant library with diverse phenotypes.

    Directory of Open Access Journals (Sweden)

    Mingyue Fang

    Full Text Available In this paper, we aimed to improve the carbohydrate productivity of Spirulina platensis by generating mutants with increased carbohydrate content and growth rate. ARTP was used as a new mutagenesis tool to generate a mutant library of S. platensis with diverse phenotypes. Protocol for rapid mutation of S. platensis by 60 s treatment with helium driven ARTP and high throughput screening method of the mutants using the 96-well microplate and microplate reader was established. A mutant library of 62 mutants was then constructed and ideal mutants were selected out. The characteristics of the mutants after the mutagenesis inclined to be stable after around 9(th subculture, where the total mutation frequency and positive mutation frequency in terms of specific growth rate reached 45% and 25%, respectively. The mutants in mutant library showed diverse phenotypes in terms of cell growth rate, carbohydrate content and flocculation intensity. The positive mutation frequency in terms of cellular carbohydrate content with the increase by more than 20% percent than the wild strain was 32.3%. Compared with the wild strain, the representative mutants 3-A10 and 3-B2 showed 40.3% and 78.0% increase in carbohydrate content, respectively, while the mutant 4-B3 showed 10.5% increase in specific growth rate. The carbohydrate contents of the representative mutants were stable during different subcultures, indicating high genetic stability. ARTP was demonstrated to be an effective and non-GMO mutagenesis tool to generate the mutant library for multicellular microalgae.

  6. Rapid accumulation of HIV-1 thymidine analogue mutations and phenotypic impact following prolonged viral failure on zidovudine-based first-line ART in sub-Saharan Africa.

    Science.gov (United States)

    Goodall, Ruth L; Dunn, David T; Nkurunziza, Peter; Mugarura, Lincoln; Pattery, Theresa; Munderi, Paula; Kityo, Cissy; Gilks, Charles; Kaleebu, Pontiano; Pillay, Deenan; Gupta, Ravindra K

    2017-05-01

    Lack of viral load monitoring of ART is known to be associated with slower switch from a failing regimen and thereby higher prevalence of MDR HIV-1. Many countries have continued to use thymidine analogue drugs despite recommendations to use tenofovir in combination with a cytosine analogue and NNRTI as first-line ART. The effect of accumulated thymidine analogue mutations (TAMs) on phenotypic resistance over time has been poorly characterized in the African setting. A retrospective analysis of individuals with ongoing viral failure between weeks 48 and 96 in the NORA (Nevirapine OR Abacavir) study was conducted. We analysed 36 genotype pairs from weeks 48 and 96 of first-line ART (14 treated with zidovudine/lamivudine/nevirapine and 22 treated with zidovudine/lamivudine/abacavir). Phenotypic drug resistance was assessed using the Antivirogram assay (v. 2.5.01, Janssen Diagnostics). At 96 weeks, extensive TAMs (≥3 mutations) were present in 50% and 73% of nevirapine- and abacavir-treated patients, respectively. The mean (SE) number of TAMs accumulating between week 48 and week 96 was 1.50 (0.37) in nevirapine-treated participants and 1.82 (0.26) in abacavir-treated participants. Overall, zidovudine susceptibility of viruses was reduced between week 48 [geometric mean fold change (FC) 1.3] and week 96 (3.4, P  =   0.01). There was a small reduction in tenofovir susceptibility (FC 0.7 and 1.0, respectively, P  =   0.18). Ongoing viral failure with zidovudine-containing first-line ART is associated with rapidly increasing drug resistance that could be mitigated with effective viral load monitoring. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

  7. Rapid identification of ascomycetous yeasts from clinical specimens by a molecular method based on flow cytometry and comparison with identifications from phenotypic assays.

    Science.gov (United States)

    Page, Brent T; Shields, Christine E; Merz, William G; Kurtzman, Cletus P

    2006-09-01

    This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of Candida dubliniensis, 1 of C. bovina, 1 of C. palmioleophila, and 1 of C. bracarensis. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.

  8. String perturbation theory diverges

    International Nuclear Information System (INIS)

    Gross, D.J.; Periwal, V.

    1988-01-01

    We prove that perturbation theory for the bosonic string diverges for arbitrary values of the coupling constant and is not Borel summable. This divergence is independent of the existence of the infinities that occur in the theory due to the presence of tachyons and dilaton tadpoles. We discuss the physical implications of such a divergence

  9. A field evaluation of the Hardy TB MODS Kit™ for the rapid phenotypic diagnosis of tuberculosis and multi-drug resistant tuberculosis.

    Directory of Open Access Journals (Sweden)

    Laura Martin

    Full Text Available Even though the WHO-endorsed, non-commercial MODS assay offers rapid, reliable TB liquid culture and phenotypic drug susceptibility testing (DST at lower cost than any other diagnostic, uptake has been patchy. In part this reflects misperceptions about in-house assay quality assurance, but user convenience of one-stop procurement is also important. A commercial MODS kit was developed by Hardy Diagnostics (Santa Maria, CA, USA with PATH (Seattle, WA, USA to facilitate procurement, simplify procedures through readymade media, and enhance safety with a sealing silicone plate lid. Here we report the results from a large-scale field evaluation of the MODS kit in a government service laboratory.2446 sputum samples were cultured in parallel in Lowenstein-Jensen (LJ, conventional MODS and in the MODS kit. MODS kit DST was compared with conventional MODS (direct DST and proportion method (indirect DST. 778 samples (31.8% were Mycobacterium tuberculosis culture-positive. Compared to conventional MODS the sensitivity, specificity, positive, and negative predictive values (95% confidence intervals of the MODS Kit were 99.3% (98.3-99.8%, 98.3% (97.5-98.8%, 95.8% (94.0-97.1%, and 99.7% (99.3-99.9%. Median (interquartile ranges time to culture-positivity (and rifampicin and isoniazid DST was 10 (9-13 days for conventional MODS and 8.5 (7-11 for MODS Kit (p<0.01. Direct rifampicin and isoniazid DST in MODS kit was almost universally concordant with conventional MODS (97.9% agreement, 665/679 evaluable samples and reference indirect DST (97.9% agreement, 687/702 evaluable samples.MODS kit delivers performance indistinguishable from conventional MODS and offers a convenient, affordable alternative with enhanced safety from the sealing silicone lid. The availability in the marketplace of this platform, which conforms to European standards (CE-marked, readily repurposed for second-line DST in the near future, provides a fresh opportunity for improving equity of

  10. Sex chromosome turnover contributes to genomic divergence between incipient stickleback species.

    Directory of Open Access Journals (Sweden)

    Kohta Yoshida

    2014-03-01

    Full Text Available Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.

  11. The Patchwork Divergence Theorem

    OpenAIRE

    Dray, Tevian; Hellaby, Charles

    1994-01-01

    The divergence theorem in its usual form applies only to suitably smooth vector fields. For vector fields which are merely piecewise smooth, as is natural at a boundary between regions with different physical properties, one must patch together the divergence theorem applied separately in each region. We give an elegant derivation of the resulting "patchwork divergence theorem" which is independent of the metric signature in either region, and which is thus valid if the signature changes. (PA...

  12. Divergent Cumulative Cultural Evolution

    OpenAIRE

    Marriott, Chris; Chebib, Jobran

    2016-01-01

    Divergent cumulative cultural evolution occurs when the cultural evolutionary trajectory diverges from the biological evolutionary trajectory. We consider the conditions under which divergent cumulative cultural evolution can occur. We hypothesize that two conditions are necessary. First that genetic and cultural information are stored separately in the agent. Second cultural information must be transferred horizontally between agents of different generations. We implement a model with these ...

  13. IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.

    Directory of Open Access Journals (Sweden)

    N Lance Hepler

    2014-09-01

    Full Text Available Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals--a cure and a vaccine--remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab, determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license, documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.

  14. On infrared divergences

    International Nuclear Information System (INIS)

    Parisi, G.

    1979-01-01

    The structure of infrared divergences is studied in superrenormalizable interactions. It is conjectured that there is an extension of the Bogoliubov-Parasiuk-Hepp theorem which copes also with infrared divergences. The consequences of this conjecture on the singularities of the Borel transform in a massless asymptotic free field theory are discussed. The application of these ideas to gauge theories is briefly discussed. (Auth.)

  15. Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids.

    Science.gov (United States)

    Astudillo-Clavijo, Viviana; Arbour, Jessica H; López-Fernández, Hernán

    2015-05-01

    Simpson envisaged a conceptual model of adaptive radiation in which lineages diversify into "adaptive zones" within a macroevolutionary adaptive landscape. However, only a handful of studies have empirically investigated this adaptive landscape and its consequences for our interpretation of the underlying mechanisms of phenotypic evolution. In fish radiations the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification given the implications of locomotion for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general. We use multivariate ordination, models of phenotypic evolution and posterior predictive approaches to investigate the macroevolutionary adaptive landscape and test for evidence of early divergence of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by selection towards at least two distinct adaptive peaks and the early divergence of modern morphological disparity. One adaptive peak included the benthic and epibenthic invertivores and was characterized by fishes with deep, laterally compressed bodies that optimize precise, slow-swimming manoeuvres. The second adaptive peak resulted from a shift in adaptive optima in the species-rich ram-feeding/rheophilic Crenicichla-Teleocichla clade and was characterized by species with streamlined bodies that optimize fast starts and rapid manoeuvres. Evolutionary models and posterior predictive approaches favoured an early shift to a new adaptive peak over decreasing rates of evolution as the underlying process driving the early divergence of locomotor phenotypes. The influence of multiple adaptive peaks on the divergence of locomotor phenotypes in Geophagini is compatible with the expectations of an ecologically driven

  16. Sympatric and allopatric divergence of MHC genes in threespine stickleback.

    Directory of Open Access Journals (Sweden)

    Blake Matthews

    2010-06-01

    Full Text Available Parasites can strongly affect the evolution of their hosts, but their effects on host diversification are less clear. In theory, contrasting parasite communities in different foraging habitats could generate divergent selection on hosts and promote ecological speciation. Immune systems are costly to maintain, adaptable, and an important component of individual fitness. As a result, immune system genes, such as those of the Major Histocompatibility Complex (MHC, can change rapidly in response to parasite-mediated selection. In threespine stickleback (Gasterosteus aculeatus, as well as in other vertebrates, MHC genes have been linked with female mating preference, suggesting that divergent selection acting on MHC genes might influence speciation. Here, we examined genetic variation at MHC Class II loci of sticklebacks from two lakes with a limnetic and benthic species pair, and two lakes with a single species. In both lakes with species pairs, limnetics and benthics differed in their composition of MHC alleles, and limnetics had fewer MHC alleles per individual than benthics. Similar to the limnetics, the allopatric population with a pelagic phenotype had few MHC alleles per individual, suggesting a correlation between MHC genotype and foraging habitat. Using a simulation model we show that the diversity and composition of MHC alleles in a sympatric species pair depends on the amount of assortative mating and on the strength of parasite-mediated selection in adjacent foraging habitats. Our results indicate parallel divergence in the number of MHC alleles between sympatric stickleback species, possibly resulting from the contrasting parasite communities in littoral and pelagic habitats of lakes.

  17. Quantum skew divergence

    Energy Technology Data Exchange (ETDEWEB)

    Audenaert, Koenraad M. R., E-mail: koenraad.audenaert@rhul.ac.uk [Department of Mathematics, Royal Holloway University of London, Egham TW20 0EX, United Kingdom and Department of Physics and Astronomy, University of Ghent, S9, Krijgslaan 281, B-9000 Ghent (Belgium)

    2014-11-15

    In this paper, we study the quantum generalisation of the skew divergence, which is a dissimilarity measure between distributions introduced by Lee in the context of natural language processing. We provide an in-depth study of the quantum skew divergence, including its relation to other state distinguishability measures. Finally, we present a number of important applications: new continuity inequalities for the quantum Jensen-Shannon divergence and the Holevo information, and a new and short proof of Bravyi's Small Incremental Mixing conjecture.

  18. Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Logue Kyle

    2013-02-01

    Full Text Available Abstract Background Members of the Anopheles punctulatus group (AP group are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence have evolved. Methods DNA sequences of 14 mitochondrial (mt genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species. Results Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species. Conclusion Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.

  19. Development of rapid phenotypic system for the identification of Gram-negative oxidase-positive bacilli in resource-limited settings.

    Science.gov (United States)

    Kazmi, Mahmooda; Khan, Adnan; Kazmi, Shahana Urooj

    2013-06-01

    Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology. The diagnosis and surveillance of diseases is dependent, to a great extent, on laboratory services, which cannot function without effective reliable reagents and diagnostics. Despite the advancement in microbiology diagnosis globally, resourcelimited countries still struggle to provide an acceptable diagnosis quality which helps in clinical disease management and improve their mortality and morbidity data. During this study an indigenous product, Quick Test Strip (QTS) NE, was developed for the rapid identification of biochemically slower group of Gram-negative oxidase-positive bacilli that covers 19 different bacterial genera. Some of the members belonging to these groups are well-established human pathogens, e.g. various species of Vibrio, Pseudomonas, Burkholderia, Aeromonas, Achromobacter and Stenotrophomonas. This study also evaluates the performance of QTS-NE by comparing with genotypic characterization methods. A total of 232 clinical and reference bacterial isolates were tested by three different methods. QTSNE provides 100 percent concordant results with other rapid identification and molecular characterization methods and confirms the potential to be used in clinical diagnosis.

  20. Converging or Diverging Lens?

    Science.gov (United States)

    Branca, Mario

    2013-01-01

    Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

  1. Sexual imprinting on ecologically divergent traits leads to sexual isolation in sticklebacks.

    Science.gov (United States)

    Kozak, Genevieve M; Head, Megan L; Boughman, Janette W

    2011-09-07

    During sexual imprinting, offspring learn parental phenotypes and then select mates who are similar to their parents. Imprinting has been thought to contribute to the process of speciation in only a few rare cases; this is despite imprinting's potential to generate assortative mating and solve the problem of recombination in ecological speciation. If offspring imprint on parental traits under divergent selection, these traits will then be involved in both adaptation and mate preference. Such 'magic traits' easily generate sexual isolation and facilitate speciation. In this study, we show that imprinting occurs in two ecologically divergent stickleback species (benthics and limnetics: Gasterosteus spp.). Cross-fostered females preferred mates of their foster father's species. Furthermore, imprinting is essential for sexual isolation between species; isolation was reduced when females were raised without fathers. Daughters imprinted on father odour and colour during a critical period early in development. These traits have diverged between the species owing to differences in ecology. Therefore, we provide the first evidence that imprinting links ecological adaptation to sexual isolation between species. Our results suggest that imprinting may facilitate the evolution of sexual isolation during ecological speciation, may be especially important in cases of rapid diversification, and thus play an integral role in the generation of biodiversity.

  2. Local divergence and curvature divergence in first order optics

    Science.gov (United States)

    Mafusire, Cosmas; Krüger, Tjaart P. J.

    2018-06-01

    The far-field divergence of a light beam propagating through a first order optical system is presented as a square root of the sum of the squares of the local divergence and the curvature divergence. The local divergence is defined as the ratio of the beam parameter product to the beam width whilst the curvature divergence is a ratio of the space-angular moment also to the beam width. It is established that the beam’s focusing parameter can be defined as a ratio of the local divergence to the curvature divergence. The relationships between the two divergences and other second moment-based beam parameters are presented. Their various mathematical properties are presented such as their evolution through first order systems. The efficacy of the model in the analysis of high power continuous wave laser-based welding systems is briefly discussed.

  3. A rapid phenotypic assay for detection of acyclovir-resistant varicella-zoster virus with mutations in the thymidine kinase open reading frame.

    Science.gov (United States)

    Sahli, R; Andrei, G; Estrade, C; Snoeck, R; Meylan, P R

    2000-04-01

    Susceptibility assays by cell culture methods are time-consuming and are particularly difficult to perform with varicella-zoster virus (VZV). To overcome this limitation, we have adapted a functional test of the viral thymidine kinase (TK) in TK-deficient (tdk mutant) bacteria to detect ACV-resistant VZV in clinical samples. After PCR amplification, the complete viral TK open reading frame (ORF) is purified from PCR primers, digested with two restriction enzymes, and ligated in an oriented fashion into a bacterial expression vector. The ligation products are then used to transform tdk mutant bacteria. After transformation, an aliquot of the bacteria is plated onto a plate with minimal medium containing (i) ampicillin to select for plasmids carrying the viral TK ORF and (ii) isopropyl beta-D-thiogalactopyranoside (IPTG) to induce its expression. An identical aliquot of bacteria is also plated onto a medium containing, in addition to the components described above, 5-fluorodeoxyuridine (FUdR). Compared to the number of transformants on FUdR-free medium, the number of colonies carrying TK derived from susceptible strains was reduced by 86%, on average, in the presence of FUdR. In contrast, the number of transformants carrying TK from resistant strains with a mutant TK were reduced by only 4%, on average, on FUdR-containing plates. We have assessed the validity of this assay with cell culture isolates and several clinical samples including two cerebrospinal fluid samples from which no virus could be isolated. This colony reduction assay allowed the correct identification of the TK phenotype of each VZV isolate tested and can be completed within 3 days of receipt of the sample.

  4. When can stress facilitate divergence by altering time to flowering?

    OpenAIRE

    Jordan, Crispin Y.; Ally, Dilara; Hodgins, Kathryn A.

    2015-01-01

    Abstract Stressors and heterogeneity are ubiquitous features of natural environments, and theory suggests that when environmental qualities alter flowering schedules through phenotypic plasticity, assortative mating can result that promotes evolutionary divergence. Therefore, it is important to determine whether common ecological stressors induce similar changes in flowering time. We review previous studies to determine whether two important stressors, water restriction and herbivory, induce ...

  5. Regularization of divergent integrals

    OpenAIRE

    Felder, Giovanni; Kazhdan, David

    2016-01-01

    We study the Hadamard finite part of divergent integrals of differential forms with singularities on submanifolds. We give formulae for the dependence of the finite part on the choice of regularization and express them in terms of a suitable local residue map. The cases where the submanifold is a complex hypersurface in a complex manifold and where it is a boundary component of a manifold with boundary, arising in string perturbation theory, are treated in more detail.

  6. Phenotypic divergence in reproductive traits of the marbled ...

    African Journals Online (AJOL)

    Malindi and Watamu) and their adjacent reserves that allow regulated fishing. ... Results showed significant differences in fecundity between sites (F = 3.742, P = 0.004) with higher mean (± SD) fecundity for fish in the parks (110,128 ± 75,492) and ...

  7. Behavioural divergence, interfertility and speciation: a review.

    Science.gov (United States)

    Pillay, Neville; Rymer, Tasmin L

    2012-11-01

    Behavioural compatibility between mates is fundamental for maintaining species boundaries and is achieved through appropriate communication between males and females. A breakdown in communication will lead to behavioural divergence and reduced interfertility. In this review, we summarise the current knowledge on male signals and female perception of these signals, integrating the literature from several taxa. We advocate that signaller-perceiver coevolution, which is usually under strong stabilising selection to enable mating, forms the basis of species-specific mate recognition systems. The mechanisms (phylogeny, geography, ecology, biology) shaping signaller-perceiver systems are briefly discussed to demonstrate the factors underpinning the evolution of signaller-perceiver couplings. Since divergence and diversification of communication systems is driven by changes in the mechanical properties of sensory pathways and morphology of sensory organs, we highlight signal modalities (auditory, olfactory, visual, tactile) and their importance in communication, particularly in mate selection. Next, using available examples and generating a stylised model, we suggest how disruption (biological, ecological, stochastic) of signaller-perceiver systems drives behavioural divergence and consequently results in reduced interfertility and speciation. Future studies should adopt an integrative approach, combining multiple parameters (phylogeny, adaptive utility of communication systems, genetics and biomechanical/biochemical properties of signals and perception) to explore how disruption of signaller-perceiver systems results in behavioural divergence and reduced interfertility. Finally, we question the impact that rapid environmental change will have on disruption of communication systems, potentially interfering with signaller-perceiver couplings. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Contemporary parallel diversification, antipredator adaptations and phenotypic integration in an aquatic isopod.

    Directory of Open Access Journals (Sweden)

    Fabrice Eroukhmanoff

    2009-07-01

    Full Text Available It is increasingly being recognized that predation can be a strong diversifying agent promoting ecological divergence. Adaptations against different predatory regimes can emerge over short periods of time and include many different traits. We studied antipredator adaptations in two ecotypes of an isopod (Asellus aquaticus that have, diverged in parallel in two Swedish lakes over the last two decades. We quantified differences in escape speed, morphology and behavior for isopods from different ecotypes present in these lakes. Isopods from the source habitat (reed coexist with mainly invertebrate predators. They are more stream-profiled and have higher escape speeds than isopods in the newly colonized stonewort habitat, which has higher density of fish predators. Stonewort isopods also show more cautious behaviors and had higher levels of phenotypic integration between coloration and morphological traits than the reed isopods. Colonization of a novel habitat with a different predation regime has thus strengthened the correlations between pigmentation and morphology and weakened escape performance. The strong signature of parallelism for these phenotypic traits indicates that divergence is likely to be adaptive and is likely to have been driven by differences in predatory regimes. Furthermore, our results indicate that physical performance, behavior and morphology can change rapidly and in concert as new habitats are colonized.

  9. Divergent Perturbation Series

    International Nuclear Information System (INIS)

    Suslov, I.M.

    2005-01-01

    Various perturbation series are factorially divergent. The behavior of their high-order terms can be determined by Lipatov's method, which involves the use of instanton configurations of appropriate functional integrals. When the Lipatov asymptotic form is known and several lowest order terms of the perturbation series are found by direct calculation of diagrams, one can gain insight into the behavior of the remaining terms of the series, which can be resummed to solve various strong-coupling problems in a certain approximation. This approach is demonstrated by determining the Gell-Mann-Low functions in φ 4 theory, QED, and QCD with arbitrary coupling constants. An overview of the mathematical theory of divergent series is presented, and interpretation of perturbation series is discussed. Explicit derivations of the Lipatov asymptotic form are presented for some basic problems in theoretical physics. A solution is proposed to the problem of renormalon contributions, which hampered progress in this field in the late 1970s. Practical perturbation-series summation schemes are described both for a coupling constant of order unity and in the strong-coupling limit. An interpretation of the Borel integral is given for 'non-Borel-summable' series. Higher order corrections to the Lipatov asymptotic form are discussed

  10. Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence?

    Directory of Open Access Journals (Sweden)

    Runemark Anna

    2010-09-01

    Full Text Available Abstract Background Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. Results Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s ST for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that

  11. Adaptive divergence in resistance to herbivores in Datura stramonium

    Directory of Open Access Journals (Sweden)

    Guillermo Castillo

    2015-11-01

    Full Text Available Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations of Datura stramonium, we compared the degree of phenotypic differentiation (PST of leaf resistance traits (trichome density, atropine and scopolamine concentration against neutral genetic differentiation (FST at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher than FST across the range of trait heritability values. In contrast, genetic differentiation in trichome density was different from FST only when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits in D. stramonium.

  12. Urbanization Is Associated with Divergence in Pace-of-Life in Great Tits

    Directory of Open Access Journals (Sweden)

    Anne Charmantier

    2017-05-01

    Full Text Available As an extension of the classic life history theory, the recently highlighted pace-of-life syndrome hypothesis predicts the coevolution of behavioral, physiological and life-history traits. For instance, bolder and shyer individuals do not only differ in personality profiles, but also in neuro-endocrinology and breeding patterns. While theory predicts that bolder (i.e., proactive, more aggressive individuals should colonize more rapidly urbanized habitats than shyer (i.e., reactive, less aggressive individuals, it is also predicted that across generations, adaptive selection processes could favor shyer individuals that are more sensitive to novel environmental cues. Here we compared two personality traits (handling aggression, exploration score in a novel environment, one physiological trait related to stress response (breath rate and four breeding traits (lay date, clutch size, hatching success and fledging success in a rural and an urban study population of Mediterranean great tits Parus major. Mixed models revealed strong phenotypic divergence between forest and city in most traits explored, in particular in personality, whereby urban great tits were more reactive to stress and faster explorers compared to rural birds (yet not more aggressive. Urban birds also laid smaller broods earlier in spring compared to their rural conspecifics, and city broods resulted in lower hatching success yet interestingly fledging success was similar. Nest-box centered measures of anthropogenic (artificial light, pedestrians, and cars perturbation and resource abundance allowed us to go beyond the classical forest/city comparison by exploring the phenotypic variation across an urbanization gradient. This revealed that high urbanization in nest-box surroundings was associated overall with earlier breeding and smaller clutches, but also with faster breath rate, although these trends showed strong annual variation. Ongoing rapid urbanization and non-random gene flow

  13. Evolution of molecular phenotypes under stabilizing selection

    International Nuclear Information System (INIS)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes. (paper)

  14. Genetic Divergence between Freshwater and Marine Morphs of Alewife (Alosa pseudoharengus): A ‘Next-Generation’ Sequencing Analysis

    Science.gov (United States)

    Czesny, Sergiusz; Epifanio, John; Michalak, Pawel

    2012-01-01

    Alewife Alosa pseudoharengus, a small clupeid fish native to Atlantic Ocean, has recently (∼150 years ago) invaded the North American Great Lakes and despite challenges of freshwater environment its populations exploded and disrupted local food web structures. This range expansion has been accompanied by dramatic changes at all levels of organization. Growth rates, size at maturation, or fecundity are only a few of the most distinct morphological and life history traits that contrast the two alewife morphs. A question arises to what extent these rapidly evolving differences between marine and freshwater varieties result from regulatory (including phenotypic plasticity) or structural mutations. To gain insights into expression changes and sequence divergence between marine and freshwater alewives, we sequenced transcriptomes of individuals from Lake Michigan and Atlantic Ocean. Population specific single nucleotide polymorphisms were rare but interestingly occurred in sequences of genes that also tended to show large differences in expression. Our results show that the striking phenotypic divergence between anadromous and lake alewives can be attributed to massive regulatory modifications rather than coding changes. PMID:22438868

  15. Adaptive evolution of molecular phenotypes

    International Nuclear Information System (INIS)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-01-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak. (paper)

  16. Quadratic divergences and dimensional regularisation

    International Nuclear Information System (INIS)

    Jack, I.; Jones, D.R.T.

    1990-01-01

    We present a detailed analysis of quadratic and quartic divergences in dimensionally regulated renormalisable theories. We perform explicit three-loop calculations for a general theory of scalars and fermions. We find that the higher-order quartic divergences are related to the lower-order ones by the renormalisation group β-functions. (orig.)

  17. Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

    Science.gov (United States)

    Baillie, Shauna M.; Muir, Andrew M.; Hansen, Michael J.; Krueger, Charles C.; Bentzen, Paul

    2016-01-01

    BackgroundAdaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycushthat considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing.ResultsFour putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments.ConclusionWe provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake

  18. divergence, pseudogenes, and

    Indian Academy of Sciences (India)

    Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evolution. Concerted evolution leads to intragenomic uniformity of repeats ...

  19. Linear energy divergences in Coulomb gauge QCD

    OpenAIRE

    Andrasi, A.

    2011-01-01

    The structure of linear energy divergences is analysed on the example of one graph to 3-loop order. Such dangerous divergences do cancel when all graphs are added, but next to leading divergences do not cancel out.

  20. Neuroanatomical phenotypes in mental illness: identifying convergent and divergent cortical phenotypes across autism, ADHD and schizophrenia.

    Science.gov (United States)

    Park, Min Tae M; Raznahan, Armin; Shaw, Philip; Gogtay, Nitin; Lerch, Jason P; Chakravarty, M Mallar

    2018-05-01

    There is evidence suggesting neuropsychiatric disorders share genomic, cognitive and clinical features. Here, we ask if autism-spectrum disorders (ASD), attention-deficit/hyperactivity disorder (ADHD) and schizophrenia share neuroanatomical variations. First, we used measures of cortical anatomy to estimate spatial overlap of neuroanatomical variation using univariate methods. Next, we developed a novel methodology to determine whether cortical deficits specifically target or are "enriched" within functional resting-state networks. We found cortical anomalies were preferentially enriched across functional networks rather than clustering spatially. Specifically, cortical thickness showed significant enrichment between patients with ASD and those with ADHD in the default mode network, between patients with ASD and those with schizophrenia in the frontoparietal and limbic networks, and between patients with ADHD and those with schizophrenia in the ventral attention network. Networks enriched in cortical thickness anomalies were also strongly represented in functional MRI results (Neurosynth; r = 0.64, p = 0.032). We did not account for variable symptom dimensions and severity in patient populations, and our cross-sectional design prevented longitudinal analyses of developmental trajectories. These findings suggest that common deficits across neuropsychiatric disorders cannot simply be characterized as arising out of local changes in cortical grey matter, but rather as entities of both local and systemic alterations targeting brain networks.

  1. Divergent synthesis and optoelectronic properties of oligodiacetylene building blocks

    NARCIS (Netherlands)

    Pilzak, G.S.; Lagen, van B.; Sudhölter, E.J.R.; Zuilhof, H.

    2008-01-01

    A new and divergent synthetic route to oligodiacetylene (ODA) building blocks has been developed via Sonogashira reactions under a reductive atmosphere. These central building blocks provide a new way for rapid preparation of long ODAs. In addition, we report on their optoelectronic properties which

  2. Eco-evo-devo in the Study of Adaptive Divergence: Examples from Threespine Stickleback (Gasterosteus aculeatus).

    Science.gov (United States)

    Jamniczky, Heather A; Barry, Tegan N; Rogers, Sean M

    2015-07-01

    The tight fit between form and function in organisms suggests the influence of adaptive evolution in biomechanics; however, the prevalence of adaptive traits, the mechanisms by which they arise and the corresponding responses to selection are subjects of extensive debate. We used three-dimensional microcomputed tomography and geometric morphometrics to characterize the structure of phenotypic covariance within the G. aculeatus trophic apparatus and its supporting structures in wild and controlled crosses of fish from two different localities. Our results reveal that while the structure of phenotypic covariance is conserved in marine and freshwater forms, it may be disrupted in the progeny of artificial crosses or during rapid adaptive divergence events. We discuss these results within the context of integrating covariance structure with quantitative genetics, toward establishing predictive links between genes, development, biomechanics, and the environment. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  3. Boiling flow through diverging microchannel

    Indian Academy of Sciences (India)

    such systems, for small pressure drop penalty and with good flow stability. .... ied the effect of divergence angle on mean and transient pressure/temperature distribution and .... supplying a fixed voltage and current using a power source meter.

  4. Atmospheric horizontal divergence and diffusion

    International Nuclear Information System (INIS)

    Castans, M.

    1981-01-01

    The action of horizontal divergence on diffusion near the ground is established through.a very simple flow model. The shape of the well-known Pasquill-Gifford-Turner curves, that apparently take account in some way of divergence, is justified. The possibility of explaining the discre--pancies between the conventional straight line model and experimental results, mainly under low-wind-speed satable conditions, is considered. Some hints for further research are made. (auth.)

  5. Extensive behavioural divergence following colonisation of the freshwater environment in threespine sticklebacks.

    Directory of Open Access Journals (Sweden)

    Carole Di-Poi

    Full Text Available Colonisation of novel environments means facing new ecological challenges often resulting in the evolution of striking divergence in phenotypes. However, little is known about behavioural divergence following colonisation, despite the predicted importance of the role of behavioural phenotype-environment associations in adaptive divergence. We studied the threespine stickleback (Gasterosteus aculeatus, a model system for postglacial colonisation of freshwater habitats largely differing in ecological conditions from the ones faced by the descendants of the marine ancestor. We found that common-environment reared freshwater juveniles were less social, more active and more aggressive than their marine counterparts. This behavioural divergence could represent the result of natural selection that acted on individuals following freshwater colonisation, with predation as a key selection agent. Alternatively, the behavioural profile of freshwater juveniles could represent the characteristics of individuals that preferentially invaded freshwater after the glacial retreat, drawn from the standing variation present in the marine population.

  6. Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

    Directory of Open Access Journals (Sweden)

    Abiyad eBaig

    2015-11-01

    Full Text Available Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN and cpn60 did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70, of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.

  7. Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.

    Directory of Open Access Journals (Sweden)

    Min Ni

    2013-09-01

    Full Text Available Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistance and enables rapid adaptive evolution. We report here that sexual reproduction generates phenotypic and genotypic diversity in the human pathogenic yeast Cryptococcus neoformans, which is globally distributed and commonly infects individuals with compromised immunity, such as HIV/AIDS patients, causing life-threatening meningoencephalitis. C. neoformans has a defined a-α opposite sexual cycle; however, >99% of isolates are of the α mating type. Interestingly, α cells can undergo α-α unisexual reproduction, even involving genotypically identical cells. A central question is: Why would cells mate with themselves given that sex is costly and typically serves to admix preexisting genetic diversity from genetically divergent parents? In this study, we demonstrate that α-α unisexual reproduction frequently generates phenotypic diversity, and the majority of these variant progeny are aneuploid. Aneuploidy is responsible for the observed phenotypic changes, as chromosome loss restoring euploidy results in a wild-type phenotype. Other genetic changes, including diploidization, chromosome length polymorphisms, SNPs, and indels, were also generated. Phenotypic/genotypic changes were not observed following asexual mitotic reproduction. Aneuploidy was also detected in progeny from a-α opposite-sex congenic mating; thus, both homothallic and heterothallic sexual reproduction can generate phenotypic diversity de novo. Our study suggests that the ability to undergo unisexual reproduction may be an evolutionary strategy for eukaryotic microbial pathogens, enabling de novo genotypic and phenotypic plasticity and facilitating rapid adaptation to novel environments.

  8. Male sex interspecies divergence and down regulation of expression of spermatogenesis genes in Drosophila sterile hybrids.

    Science.gov (United States)

    Sundararajan, Vignesh; Civetta, Alberto

    2011-01-01

    Male sex genes have shown a pattern of rapid interspecies divergence at both the coding and gene expression level. A common outcome from crosses between closely-related species is hybrid male sterility. Phenotypic and genetic studies in Drosophila sterile hybrid males have shown that spermatogenesis arrest is postmeiotic with few exceptions, and that most misregulated genes are involved in late stages of spermatogenesis. Comparative studies of gene regulation in sterile hybrids and parental species have mainly used microarrays providing a whole genome representation of regulatory problems in sterile hybrids. Real-time PCR studies can reject or reveal differences not observed in microarray assays. Moreover, differences in gene expression between samples can be dependant on the source of RNA (e.g., whole body vs. tissue). Here we survey expression in D. simulans, D. mauritiana and both intra and interspecies hybrids using a real-time PCR approach for eight genes expressed at the four main stages of sperm development. We find that all genes show a trend toward under expression in the testes of sterile hybrids relative to parental species with only the two proliferation genes (bam and bgcn) and the two meiotic class genes (can and sa) showing significant down regulation. The observed pattern of down regulation for the genes tested can not fully explain hybrid male sterility. We discuss the down regulation of spermatogenesis genes in hybrids between closely-related species within the contest of rapid divergence experienced by the male genome, hybrid sterility and possible allometric changes due to subtle testes-specific developmental abnormalities.

  9. String loop divergences and effective lagrangians

    International Nuclear Information System (INIS)

    Fischler, W.; Klebanov, I.; Susskind, L.

    1988-01-01

    We isolate logarithmic divergences from bosonic string amplitudes on a disc. These divergences are compared with 'tadpole' divergences in the effective field theory, with a covariant cosmological term implied by the counting of string coupling constants. We find an inconsistency between the two. This might be a problem in eliminating divergences from the bosonic string. (orig.)

  10. MAIT cells launch a rapid, robust and distinct hyperinflammatory response to bacterial superantigens and quickly acquire an anergic phenotype that impedes their cognate antimicrobial function: Defining a novel mechanism of superantigen-induced immunopathology and immunosuppression.

    Directory of Open Access Journals (Sweden)

    Christopher R Shaler

    2017-06-01

    Full Text Available Superantigens (SAgs are potent exotoxins secreted by Staphylococcus aureus and Streptococcus pyogenes. They target a large fraction of T cell pools to set in motion a "cytokine storm" with severe and sometimes life-threatening consequences typically encountered in toxic shock syndrome (TSS. Given the rapidity with which TSS develops, designing timely and truly targeted therapies for this syndrome requires identification of key mediators of the cytokine storm's initial wave. Equally important, early host responses to SAgs can be accompanied or followed by a state of immunosuppression, which in turn jeopardizes the host's ability to combat and clear infections. Unlike in mouse models, the mechanisms underlying SAg-associated immunosuppression in humans are ill-defined. In this work, we have identified a population of innate-like T cells, called mucosa-associated invariant T (MAIT cells, as the most powerful source of pro-inflammatory cytokines after exposure to SAgs. We have utilized primary human peripheral blood and hepatic mononuclear cells, mouse MAIT hybridoma lines, HLA-DR4-transgenic mice, MAIThighHLA-DR4+ bone marrow chimeras, and humanized NOD-scid IL-2Rγnull mice to demonstrate for the first time that: i mouse and human MAIT cells are hyperresponsive to SAgs, typified by staphylococcal enterotoxin B (SEB; ii the human MAIT cell response to SEB is rapid and far greater in magnitude than that launched by unfractionated conventional T, invariant natural killer T (iNKT or γδ T cells, and is characterized by production of interferon (IFN-γ, tumor necrosis factor (TNF-α and interleukin (IL-2, but not IL-17A; iii high-affinity MHC class II interaction with SAgs, but not MHC-related protein 1 (MR1 participation, is required for MAIT cell activation; iv MAIT cell responses to SEB can occur in a T cell receptor (TCR Vβ-specific manner but are largely contributed by IL-12 and IL-18; v as MAIT cells are primed by SAgs, they also begin to

  11. Molecular initiating events of the intersex phenotype: Low-dose exposure to 17α-ethinylestradiol rapidly regulates molecular networks associated with gonad differentiation in the adult fathead minnow testis

    International Nuclear Information System (INIS)

    Feswick, April; Loughery, Jennifer R.; Isaacs, Meghan A.; Munkittrick, Kelly R.; Martyniuk, Christopher J.

    2016-01-01

    testis, despite the fact that dmrt1 itself was not different in expression from control males. Transcriptional networks involving forkhead box L2 (foxl2) (transcript involved in ovarian follicle development) were increased in expression in the testis. Noteworthy was that a gene network associated to granulosa cell development was increased over 100%, suggesting that this transcriptome network may be important for monitoring estrogenic exposures. Other cell processes rapidly downregulated by EE2 at the transcript level included glucose homeostasis, response to heavy metal, amino acid catabolism, and the cyclooxygenase pathway. Conversely, lymphocyte chemotaxis, intermediate filament polymerization, glucocorticoid metabolism, carbohydrate utilization, and anterior/posterior axis specification were increased. These data provide new insight into the transcriptional responses that are perturbed prior to gonadal remodeling and intersex following exposure to estrogens. These data demonstrate that low concentrations of EE2 (1) rapidly suppresses male hormone production, (2) down-regulate molecular networks related to male sex differentiation, and (3) induce transcriptional networks related to granulosa cell development in the adult testis. These responses are hypothesized to be key molecular initiating events that occur prior to the development of the intersex phenotype following estrogenic exposures.

  12. Molecular initiating events of the intersex phenotype: Low-dose exposure to 17α-ethinylestradiol rapidly regulates molecular networks associated with gonad differentiation in the adult fathead minnow testis

    Energy Technology Data Exchange (ETDEWEB)

    Feswick, April; Loughery, Jennifer R.; Isaacs, Meghan A.; Munkittrick, Kelly R.; Martyniuk, Christopher J., E-mail: cmartyni@yahoo.ca

    2016-12-15

    testis, despite the fact that dmrt1 itself was not different in expression from control males. Transcriptional networks involving forkhead box L2 (foxl2) (transcript involved in ovarian follicle development) were increased in expression in the testis. Noteworthy was that a gene network associated to granulosa cell development was increased over 100%, suggesting that this transcriptome network may be important for monitoring estrogenic exposures. Other cell processes rapidly downregulated by EE2 at the transcript level included glucose homeostasis, response to heavy metal, amino acid catabolism, and the cyclooxygenase pathway. Conversely, lymphocyte chemotaxis, intermediate filament polymerization, glucocorticoid metabolism, carbohydrate utilization, and anterior/posterior axis specification were increased. These data provide new insight into the transcriptional responses that are perturbed prior to gonadal remodeling and intersex following exposure to estrogens. These data demonstrate that low concentrations of EE2 (1) rapidly suppresses male hormone production, (2) down-regulate molecular networks related to male sex differentiation, and (3) induce transcriptional networks related to granulosa cell development in the adult testis. These responses are hypothesized to be key molecular initiating events that occur prior to the development of the intersex phenotype following estrogenic exposures.

  13. Semantic search during divergent thinking.

    Science.gov (United States)

    Hass, Richard W

    2017-09-01

    Divergent thinking, as a method of examining creative cognition, has not been adequately analyzed in the context of modern cognitive theories. This article casts divergent thinking responding in the context of theories of memory search. First, it was argued that divergent thinking tasks are similar to semantic fluency tasks, but are more constrained, and less well structured. Next, response time distributions from 54 participants were analyzed for temporal and semantic clustering. Participants responded to two prompts from the alternative uses test: uses for a brick and uses for a bottle, for two minutes each. Participants' cumulative response curves were negatively accelerating, in line with theories of search of associative memory. However, results of analyses of semantic and temporal clustering suggested that clustering is less evident in alternative uses responding compared to semantic fluency tasks. This suggests either that divergent thinking responding does not involve an exhaustive search through a clustered memory trace, but rather that the process is more exploratory, yielding fewer overall responses that tend to drift away from close associates of the divergent thinking prompt. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis

    Directory of Open Access Journals (Sweden)

    Ornelas Juan

    2011-02-01

    Full Text Available Abstract Background Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. Results Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma, and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. Conclusions Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the

  15. Evolution of cichlid vision via trans-regulatory divergence

    Directory of Open Access Journals (Sweden)

    O’Quin Kelly E

    2012-12-01

    Full Text Available Abstract Background Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision. Results We identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73% occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can. Conclusions Combined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the

  16. Hyperreal Numbers for Infinite Divergent Series

    OpenAIRE

    Bartlett, Jonathan

    2018-01-01

    Treating divergent series properly has been an ongoing issue in mathematics. However, many of the problems in divergent series stem from the fact that divergent series were discovered prior to having a number system which could handle them. The infinities that resulted from divergent series led to contradictions within the real number system, but these contradictions are largely alleviated with the hyperreal number system. Hyperreal numbers provide a framework for dealing with divergent serie...

  17. Chained Kullback-Leibler Divergences

    Science.gov (United States)

    Pavlichin, Dmitri S.; Weissman, Tsachy

    2017-01-01

    We define and characterize the “chained” Kullback-Leibler divergence minw D(p‖w) + D(w‖q) minimized over all intermediate distributions w and the analogous k-fold chained K-L divergence min D(p‖wk−1) + … + D(w2‖w1) + D(w1‖q) minimized over the entire path (w1,…,wk−1). This quantity arises in a large deviations analysis of a Markov chain on the set of types – the Wright-Fisher model of neutral genetic drift: a population with allele distribution q produces offspring with allele distribution w, which then produce offspring with allele distribution p, and so on. The chained divergences enjoy some of the same properties as the K-L divergence (like joint convexity in the arguments) and appear in k-step versions of some of the same settings as the K-L divergence (like information projections and a conditional limit theorem). We further characterize the optimal k-step “path” of distributions appearing in the definition and apply our findings in a large deviations analysis of the Wright-Fisher process. We make a connection to information geometry via the previously studied continuum limit, where the number of steps tends to infinity, and the limiting path is a geodesic in the Fisher information metric. Finally, we offer a thermodynamic interpretation of the chained divergence (as the rate of operation of an appropriately defined Maxwell’s demon) and we state some natural extensions and applications (a k-step mutual information and k-step maximum likelihood inference). We release code for computing the objects we study. PMID:29130024

  18. When can stress facilitate divergence by altering time to flowering?

    Science.gov (United States)

    Jordan, Crispin Y; Ally, Dilara; Hodgins, Kathryn A

    2015-12-01

    Stressors and heterogeneity are ubiquitous features of natural environments, and theory suggests that when environmental qualities alter flowering schedules through phenotypic plasticity, assortative mating can result that promotes evolutionary divergence. Therefore, it is important to determine whether common ecological stressors induce similar changes in flowering time. We review previous studies to determine whether two important stressors, water restriction and herbivory, induce consistent flowering time responses among species; for example, how often do water restriction and herbivory both delay flowering? We focus on the direction of change in flowering time, which affects the potential for divergence in heterogeneous environments. We also tested whether these stressors influenced time to flowering and nonphenology traits using Mimulus guttatus. The literature review suggests that water restriction has variable effects on flowering time, whereas herbivory delays flowering with exceptional consistency. In the Mimulus experiment, low water and herbivory advanced and delayed flowering, respectively. Overall, our results temper theoretical predictions for evolutionary divergence due to habitat-induced changes in flowering time; in particular, we discuss how accounting for variation in the direction of change in flowering time can either increase or decrease the potential for divergence. In addition, we caution against adaptive interpretations of stress-induced phenology shifts.

  19. Niche divergence facilitated by fine-scale ecological partitioning in a recent cichlid fish adaptive radiation.

    Science.gov (United States)

    Ford, Antonia G P; Rüber, Lukas; Newton, Jason; Dasmahapatra, Kanchon K; Balarin, John D; Bruun, Kristoffer; Day, Julia J

    2016-12-01

    Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype-environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large-scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  20. The Relationship between Subthreshold Autistic Traits, Ambiguous Figure Perception and Divergent Thinking

    Science.gov (United States)

    Best, Catherine; Arora, Shruti; Porter, Fiona; Doherty, Martin

    2015-01-01

    This research investigates the paradox of creativity in autism. That is, whether people with subclinical autistic traits have cognitive styles conducive to creativity or whether they are disadvantaged by the implied cognitive and behavioural rigidity of the autism phenotype. The relationship between divergent thinking (a cognitive component of…

  1. On Hölder Projective Divergences

    KAUST Repository

    Nielsen, Frank

    2017-03-16

    We describe a framework to build distances by measuring the tightness of inequalities and introduce the notion of proper statistical divergences and improper pseudo-divergences. We then consider the Holder ordinary and reverse inequalities and present two novel classes of Holder divergences and pseudo-divergences that both encapsulate the special case of the Cauchy-Schwarz divergence. We report closed-form formulas for those statistical dissimilarities when considering distributions belonging to the same exponential family provided that the natural parameter space is a cone (e.g., multivariate Gaussians) or affine (e.g., categorical distributions). Those new classes of Holder distances are invariant to rescaling and thus do not require distributions to be normalized. Finally, we show how to compute statistical Holder centroids with respect to those divergences and carry out center-based clustering toy experiments on a set of Gaussian distributions which demonstrate empirically that symmetrized Holder divergences outperform the symmetric Cauchy-Schwarz divergence.

  2. On Hölder Projective Divergences

    KAUST Repository

    Nielsen, Frank; Sun, Ke; Marchand-Maillet, Stephane

    2017-01-01

    We describe a framework to build distances by measuring the tightness of inequalities and introduce the notion of proper statistical divergences and improper pseudo-divergences. We then consider the Holder ordinary and reverse inequalities and present two novel classes of Holder divergences and pseudo-divergences that both encapsulate the special case of the Cauchy-Schwarz divergence. We report closed-form formulas for those statistical dissimilarities when considering distributions belonging to the same exponential family provided that the natural parameter space is a cone (e.g., multivariate Gaussians) or affine (e.g., categorical distributions). Those new classes of Holder distances are invariant to rescaling and thus do not require distributions to be normalized. Finally, we show how to compute statistical Holder centroids with respect to those divergences and carry out center-based clustering toy experiments on a set of Gaussian distributions which demonstrate empirically that symmetrized Holder divergences outperform the symmetric Cauchy-Schwarz divergence.

  3. Genetic Divergence in Sugarcane Genotypes

    OpenAIRE

    Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad

    2012-01-01

    To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

  4. Computer recognition of divergences in Feynman graphs

    Energy Technology Data Exchange (ETDEWEB)

    Calmet, J

    1973-05-01

    The program described recognizes whether or not a graph is divergent. It determines the kind of the divergences found: vacuum polarizations, electron self energies and vertices. it does not consider infrared divergences. The programming language used is REDUCE. A LISP version is also available. The nature of the divergences and their counter terms was extensively used to write down this program, therefore it is limited to the case of quantum electrodynamics. (auth)

  5. Genetic divergence of tomato subsamples

    Directory of Open Access Journals (Sweden)

    André Pugnal Mattedi

    2014-02-01

    Full Text Available Understanding the genetic variability of a species is crucial for the progress of a genetic breeding program and requires characterization and evaluation of germplasm. This study aimed to characterize and evaluate 101 tomato subsamples of the Salad group (fresh market and two commercial controls, one of the Salad group (cv. Fanny and another of the Santa Cruz group (cv. Santa Clara. Four experiments were conducted in a randomized block design with three replications and five plants per plot. The joint analysis of variance was performed and characteristics with significant complex interaction between control and experiment were excluded. Subsequently, the multicollinearity diagnostic test was carried out and characteristics that contributed to severe multicollinearity were excluded. The relative importance of each characteristics for genetic divergence was calculated by the Singh's method (Singh, 1981, and the less important ones were excluded according to Garcia (1998. Results showed large genetic divergence among the subsamples for morphological, agronomic and organoleptic characteristics, indicating potential for genetic improvement. The characteristics total soluble solids, mean number of good fruits per plant, endocarp thickness, mean mass of marketable fruit per plant, total acidity, mean number of unmarketable fruit per plant, internode diameter, internode length, main stem thickness and leaf width contributed little to the genetic divergence between the subsamples and may be excluded in future studies.

  6. Divergent Host Plant Adaptation Drives the Evolution of Sexual Isolation in the Grasshopper Hesperotettix viridis (Orthoptera: Acrididae) in the Absence of Reinforcement

    Science.gov (United States)

    The beginning stages of lineage divergence can be difficult to detect, as correlations between altered genotypic and phenotypic attributes are often weak early in the process. Shifts in host plant use and divergence in mating signals can lead to sexual isolation and ultimately speciation. To underst...

  7. The relationship between intraspecific assortative mating and reproductive isolation between divergent populations

    Directory of Open Access Journals (Sweden)

    Daniel I. BOLNICK, Mark KIRKPATRICK

    2012-06-01

    Full Text Available The term 'assortative mating' has been applied to describe two very different phenomena: (1 the tendency for individuals to choose phenotypically similar mates from among conspecifics; or (2 the tendency to prefer conspecific over hete- rospecific mates (behavioral reproductive isolation. Both forms of assortative mating are widespread in nature, but the relationship between these behaviors remains unclear. Namely, it is plausible that a preference for phenotypically similar conspecifics incidentally reduces the probability of mating with phenotypically divergent heterospecifics. We present a model to calculate how the level of reproductive isolation depends on intraspecific assortative mating and the phenotypic divergence between species. For empirically reasonable levels of intraspecific assortment on a single trait axis, we show that strong reproductive isolation requires very substantial phenotypic divergence. We illustrate this point by applying our model to empirical data from threespine stickleback Gasterosteus aculeatus and Darwin’s Finches (Geospiza spp. We conclude that typical levels of intraspecific assortment cannot generally be extrapolated to explain levels of interspecific reproductive isolation. Instead, reproductive isolation between species likely arises from different mate choice behaviors, or multivariate assortative mating [Current Zoology 58 (3: 481–489, 2012].

  8. Statistical inference based on divergence measures

    CERN Document Server

    Pardo, Leandro

    2005-01-01

    The idea of using functionals of Information Theory, such as entropies or divergences, in statistical inference is not new. However, in spite of the fact that divergence statistics have become a very good alternative to the classical likelihood ratio test and the Pearson-type statistic in discrete models, many statisticians remain unaware of this powerful approach.Statistical Inference Based on Divergence Measures explores classical problems of statistical inference, such as estimation and hypothesis testing, on the basis of measures of entropy and divergence. The first two chapters form an overview, from a statistical perspective, of the most important measures of entropy and divergence and study their properties. The author then examines the statistical analysis of discrete multivariate data with emphasis is on problems in contingency tables and loglinear models using phi-divergence test statistics as well as minimum phi-divergence estimators. The final chapter looks at testing in general populations, prese...

  9. Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus.

    Science.gov (United States)

    Horton, Daniel L; Banyard, Ashley C; Marston, Denise A; Wise, Emma; Selden, David; Nunez, Alejandro; Hicks, Daniel; Lembo, Tiziana; Cleaveland, Sarah; Peel, Alison J; Kuzmin, Ivan V; Rupprecht, Charles E; Fooks, Anthony R

    2014-05-01

    In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya.

  10. Ultraviolet divergences and supersymmetric theories

    International Nuclear Information System (INIS)

    Sagnotti, A.

    1984-09-01

    This article is closely related to the one by Ferrara in these same Proceedings. It deals with what is perhaps the most fascinating property of supersymmetric theories, their improved ultraviolet behavior. My aim here is to present a survey of the state of the art as of August, 1984, and a somewhat more detailed discussion of the breakdown of the superspace power-counting beyond N = 2 superfields. A method is also described for simplifying divergence calculations that uses the locality of subtracted Feynman integrals. 74 references

  11. Ultraviolet divergences of Einstein gravity

    International Nuclear Information System (INIS)

    Goroff, M.H.

    1986-01-01

    The author discuss a two-loop calculation showing that the S matrix of Einstein's theory of gravity contains nonrenormalizable ultraviolet divergences in four dimension. The author discusses the calculation in both background field and normal field theory. The author describes a new method for dealing with ghost fields in gauge theories by combining them with suitable extensions of the gauge fields in higher dimensions. The author shows how using subtracted integrals in the calculation of higher loop graphs simplifies the calculation in the background field method by eliminating the need for mixed counterterms. Finally, the author makes some remarks about the implications of the result for supergravity theories

  12. Ground state energies from converging and diverging power series expansions

    International Nuclear Information System (INIS)

    Lisowski, C.; Norris, S.; Pelphrey, R.; Stefanovich, E.; Su, Q.; Grobe, R.

    2016-01-01

    It is often assumed that bound states of quantum mechanical systems are intrinsically non-perturbative in nature and therefore any power series expansion methods should be inapplicable to predict the energies for attractive potentials. However, if the spatial domain of the Schrödinger Hamiltonian for attractive one-dimensional potentials is confined to a finite length L, the usual Rayleigh–Schrödinger perturbation theory can converge rapidly and is perfectly accurate in the weak-binding region where the ground state’s spatial extension is comparable to L. Once the binding strength is so strong that the ground state’s extension is less than L, the power expansion becomes divergent, consistent with the expectation that bound states are non-perturbative. However, we propose a new truncated Borel-like summation technique that can recover the bound state energy from the diverging sum. We also show that perturbation theory becomes divergent in the vicinity of an avoided-level crossing. Here the same numerical summation technique can be applied to reproduce the energies from the diverging perturbative sums.

  13. Ground state energies from converging and diverging power series expansions

    Energy Technology Data Exchange (ETDEWEB)

    Lisowski, C.; Norris, S.; Pelphrey, R.; Stefanovich, E., E-mail: eugene-stefanovich@usa.net; Su, Q.; Grobe, R.

    2016-10-15

    It is often assumed that bound states of quantum mechanical systems are intrinsically non-perturbative in nature and therefore any power series expansion methods should be inapplicable to predict the energies for attractive potentials. However, if the spatial domain of the Schrödinger Hamiltonian for attractive one-dimensional potentials is confined to a finite length L, the usual Rayleigh–Schrödinger perturbation theory can converge rapidly and is perfectly accurate in the weak-binding region where the ground state’s spatial extension is comparable to L. Once the binding strength is so strong that the ground state’s extension is less than L, the power expansion becomes divergent, consistent with the expectation that bound states are non-perturbative. However, we propose a new truncated Borel-like summation technique that can recover the bound state energy from the diverging sum. We also show that perturbation theory becomes divergent in the vicinity of an avoided-level crossing. Here the same numerical summation technique can be applied to reproduce the energies from the diverging perturbative sums.

  14. Gene duplication and divergence affecting drug content in Cannabis sativa.

    Science.gov (United States)

    Weiblen, George D; Wenger, Jonathan P; Craft, Kathleen J; ElSohly, Mahmoud A; Mehmedic, Zlatko; Treiber, Erin L; Marks, M David

    2015-12-01

    Cannabis sativa is an economically important source of durable fibers, nutritious seeds, and psychoactive drugs but few economic plants are so poorly understood genetically. Marijuana and hemp were crossed to evaluate competing models of cannabinoid inheritance and to explain the predominance of tetrahydrocannabinolic acid (THCA) in marijuana compared with cannabidiolic acid (CBDA) in hemp. Individuals in the resulting F2 population were assessed for differential expression of cannabinoid synthase genes and were used in linkage mapping. Genetic markers associated with divergent cannabinoid phenotypes were identified. Although phenotypic segregation and a major quantitative trait locus (QTL) for the THCA/CBDA ratio were consistent with a simple model of codominant alleles at a single locus, the diversity of THCA and CBDA synthase sequences observed in the mapping population, the position of enzyme coding loci on the map, and patterns of expression suggest multiple linked loci. Phylogenetic analysis further suggests a history of duplication and divergence affecting drug content. Marijuana is distinguished from hemp by a nonfunctional CBDA synthase that appears to have been positively selected to enhance psychoactivity. An unlinked QTL for cannabinoid quantity may also have played a role in the recent escalation of drug potency. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  15. Divergent thinking and constructing episodic simulations.

    Science.gov (United States)

    Addis, Donna Rose; Pan, Ling; Musicaro, Regina; Schacter, Daniel L

    2016-01-01

    Divergent thinking likely plays an important role in simulating autobiographical events. We investigated whether divergent thinking is differentially associated with the ability to construct detailed imagined future and imagined past events as opposed to recalling past events. We also examined whether age differences in divergent thinking might underlie the reduced episodic detail generated by older adults. The richness of episodic detail comprising autobiographical events in young and older adults was assessed using the Autobiographical Interview. Divergent thinking abilities were measured using the Alternative Uses Task. Divergent thinking was significantly associated with the amount of episodic detail for imagined future events. Moreover, while age was significantly associated with imagined episodic detail, this effect was strongly related to age-related changes in episodic retrieval rather than divergent thinking.

  16. Divergent unprotected peptide macrocyclisation by palladium-mediated cysteine arylation.

    Science.gov (United States)

    Rojas, Anthony J; Zhang, Chi; Vinogradova, Ekaterina V; Buchwald, Nathan H; Reilly, John; Pentelute, Bradley L; Buchwald, Stephen L

    2017-06-01

    Macrocyclic peptides are important therapeutic candidates due to their improved physicochemical properties in comparison to their linear counterparts. Here we detail a method for a divergent macrocyclisation of unprotected peptides by crosslinking two cysteine residues with bis-palladium organometallic reagents. These synthetic intermediates are prepared in a single step from commercially available aryl bis-halides. Two bioactive linear peptides with cysteine residues at i , i + 4 and i , i + 7 positions, respectively, were cyclised to introduce a diverse array of aryl and bi-aryl linkers. These two series of macrocyclic peptides displayed similar linker-dependent lipophilicity, phospholipid affinity, and unique volume of distributions. Additionally, one of the bioactive peptides showed target binding affinity that was predominantly affected by the length of the linker. Collectively, this divergent strategy allowed rapid and convenient access to various aryl linkers, enabling the systematic evaluation of the effect of appending unit on the medicinal properties of macrocyclic peptides.

  17. Convergent evolution and divergent selection: lizards at the White Sands ecotone.

    Science.gov (United States)

    Rosenblum, Erica Bree

    2006-01-01

    Ecological transition zones, where organismal phenotypes result from a delicate balance between selection and migration, highlight the interplay of local adaptation and gene flow. Here, I study the response of an entire species assemblage to natural selection across a common ecotone. Three lizard species, distributed along a dramatic environmental gradient in substrate color, display convergent adaptation of blanched coloration on the gypsum dunes of White Sands National Monument. I investigate the role of gene flow in modulating phenotypic response to selection by quantifying color variation and genetic variation across the ecotone. I find species differences in degree of background matching and in genetic connectivity of populations across the ecotone. Differences among species in phenotypic response to selection scale precisely to levels of genetic isolation. Species with higher levels of gene flow across the ecotone exhibit less dramatic responses to selection. Results also reveal a strong signal of ecologically mediated divergence for White Sands lizards. For all species, phenotypic variation is better explained by habitat similarity than genetic similarity. Convergent evolution of blanched coloration at White Sands clearly reflects the action of strong divergent selection; however, adaptive response appears to be modulated by gene flow and demographic history and can be predicted by divergence-with-gene-flow models.

  18. ABO blood group phenotype frequency estimation using molecular phenotyping in rhesus and cynomolgus macaques.

    Science.gov (United States)

    Kanthaswamy, S; Ng, J; Oldt, R F; Valdivia, L; Houghton, P; Smith, D G

    2017-11-01

    A much larger sample (N = 2369) was used to evaluate a previously reported distribution of the A, AB and B blood group phenotypes in rhesus and cynomolgus macaques from six different regional populations. These samples, acquired from 15 different breeding and research facilities in the United States, were analyzed using a real-time quantitative polymerase chain reaction (qPCR) assay that targets single nucleotide polymorphisms (SNPs) responsible for the macaque A, B and AB phenotypes. The frequency distributions of blood group phenotypes of the two species differ significantly from each other and significant regional differentiation within the geographic ranges of each species was also observed. The B blood group phenotype was prevalent in rhesus macaques, especially those from India, while the frequencies of the A, B and AB phenotypes varied significantly among cynomolgus macaques from different geographic regions. The Mauritian cynomolgus macaques, despite having originated in Indonesia, showed significant (P ≪ .01) divergence from the Indonesian animals at the ABO blood group locus. Most Mauritian animals belonged to the B blood group while the Indonesian animals were mostly A. The close similarity in blood group frequency distributions between the Chinese rhesus and Indochinese cynomolgus macaques demonstrates that the introgression between these two species extends beyond the zone of intergradation in Indochina. This study underscores the importance of ABO blood group phenotyping of the domestic supply of macaques and their biospecimens. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  19. Genetic divergence analysis in pumpkin

    International Nuclear Information System (INIS)

    Quamruzzaman, A.M.; Moniruzzaman, M.

    2013-01-01

    Genetic divergence among 18 punpkin genotypes was estimated using Mahalanohis's 1) statistic. Altogether lour clusters were formed where cluster I contained the highest number of genotypes (8) and cluster II contained the lowest (I). The highest intra-cluster distance was observed h.ir cluster I (0.83 I) and the lowest for clustcr IV (0.65 I). The highest inter-cluster distance was observed between cluster I and 11(24.346). Cluster II recorded the highest mean for fruit number/plant, TSS, fruit yield and niinitnuiii III cavity length and cavity diameter. Cluster III had the second highest mean for fruit diameter, fruit number/plant, individual unit weight, fruit yield and the fewest number of days to 1st Female flowering, earliness being a desirable trait. These crosses may produce new recombinants with desirable traits. (author)

  20. Divergence operator and related inequalities

    CERN Document Server

    Acosta, Gabriel

    2017-01-01

    This Brief is mainly devoted to two classical and related results: the existence of a right inverse of the divergence operator and the so-called Korn Inequalities. It is well known that both results are fundamental tools in the analysis of some classic differential equations, particularly in those arising in fluid dynamics and elasticity. Several connections between these two topics and improved Poincaré inequalities are extensively treated. From simple key ideas the book is growing smoothly in complexity. Beginning with the study of these problems on star-shaped domains the arguments are extended first to John domains and then to Hölder α domains where the need of weighted spaces arises naturally. In this fashion, the authors succeed in presenting in an unified and concise way several classic and recent developments in the field. These features certainly makes this Brief useful for students, post-graduate students, and researchers as well.

  1. Ramanujan summation of divergent series

    CERN Document Server

    Candelpergher, Bernard

    2017-01-01

    The aim of this monograph is to give a detailed exposition of the summation method that Ramanujan uses in Chapter VI of his second Notebook. This method, presented by Ramanujan as an application of the Euler-MacLaurin formula, is here extended using a difference equation in a space of analytic functions. This provides simple proofs of theorems on the summation of some divergent series. Several examples and applications are given. For numerical evaluation, a formula in terms of convergent series is provided by the use of Newton interpolation. The relation with other summation processes such as those of Borel and Euler is also studied. Finally, in the last chapter, a purely algebraic theory is developed that unifies all these summation processes. This monograph is aimed at graduate students and researchers who have a basic knowledge of analytic function theory.

  2. Beam divergence scaling in neutral beam injectors

    International Nuclear Information System (INIS)

    Holmes, A.J.T.

    1976-01-01

    One of the main considerations in the design of neutral beam injectors is to monimize the divergence of the primary ion beam and hence maximize the beam transport and minimize the input of thermal gas. Experimental measurements of the divergence of a cylindrical ion beam are presented and these measurements are used to analyze the major components of ion beam divergence, namely: space charge expansion, gas-ion scattering, emittance and optical aberrations. The implication of these divergence components in the design of a neutral beam injector system is discussed and a method of maximizing the beam current is described for a given area of source plasma

  3. Guises and disguises of quadratic divergences

    Energy Technology Data Exchange (ETDEWEB)

    Cherchiglia, A.L., E-mail: adriano@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Vieira, A.R., E-mail: arvieira@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Hiller, Brigitte, E-mail: brigitte@teor.fis.uc.pt [Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, 3004-516 Coimbra (Portugal); Baêta Scarpelli, A.P., E-mail: scarpelli.apbs@dpf.gov.br [Setor Técnico-Científico, Departamento de Polícia Federal, Rua Hugo D’Antola, 95 - Lapa, São Paulo (Brazil); Sampaio, Marcos, E-mail: marcos.sampaio@durham.ac.uk [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Centre for Particle Theory, Department of Mathematical Sciences, Durham University, South Road Durham DH1 3LE (United Kingdom)

    2014-12-15

    In this contribution, we present a new perspective on the control of quadratic divergences in quantum field theory, in general, and in the Higgs naturalness problem, in particular. Our discussion is essentially based on an approach where UV divergences are parameterized, after being reduced to basic divergent integrals (BDI) in one internal momentum, as functions of a cutoff and a renormalization group scale λ. We illustrate our proposal with well-known examples, such as the gluon vacuum self energy of QCD and the Higgs decay in two photons within this approach. We also discuss frameworks in effective low-energy QCD models, where quadratic divergences are indeed fundamental.

  4. Divergence Palsy due to Divalproex and Oxcarbazepine.

    Science.gov (United States)

    Bouffard, Marc Albert; Caplan, Louis R; Torun, Nurhan

    This case series is the first to describe divergence palsy as an adverse effect of antiepileptic drug use. Diplopia is a common adverse effect of antiepileptic drugs, but no explanatory motility deficit has ever been reported. We present 2 patients, 1 on oxcarbazepine and 1 on divalproex, each with a normal examination result between spells and divergency palsy when symptomatic. Discontinuation of the antiepileptic medication led to resolution of the episodes in both cases. Rechallenge with the offending agent after washout in one patient resulted in recurrence of diplopia and divergence palsy, both resolving after subsequent withdrawal of the antiepileptic. Antiepileptic drugs may cause divergence palsy.

  5. Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks.

    Directory of Open Access Journals (Sweden)

    Mark Ravinet

    Full Text Available Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L. forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean FST = 0.12, we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an

  6. k-Means Clustering with Hölder Divergences

    KAUST Repository

    Nielsen, Frank; Sun, Ke; Marchand-Maillet, Sté phane

    2017-01-01

    We introduced two novel classes of Hölder divergences and Hölder pseudo-divergences that are both invariant to rescaling, and that both encapsulate the Cauchy-Schwarz divergence and the skew Bhattacharyya divergences. We review the elementary concepts of those parametric divergences, and perform a clustering analysis on two synthetic datasets. It is shown experimentally that the symmetrized Hölder divergences consistently outperform significantly the Cauchy-Schwarz divergence in clustering tasks.

  7. k-Means Clustering with Hölder Divergences

    KAUST Repository

    Nielsen, Frank

    2017-10-24

    We introduced two novel classes of Hölder divergences and Hölder pseudo-divergences that are both invariant to rescaling, and that both encapsulate the Cauchy-Schwarz divergence and the skew Bhattacharyya divergences. We review the elementary concepts of those parametric divergences, and perform a clustering analysis on two synthetic datasets. It is shown experimentally that the symmetrized Hölder divergences consistently outperform significantly the Cauchy-Schwarz divergence in clustering tasks.

  8. Asthma phenotypes in childhood.

    Science.gov (United States)

    Reddy, Monica B; Covar, Ronina A

    2016-04-01

    This review describes the literature over the past 18 months that evaluated childhood asthma phenotypes, highlighting the key aspects of these studies, and comparing these studies to previous ones in this area. Recent studies on asthma phenotypes have identified new phenotypes on the basis of statistical analyses (using cluster analysis and latent class analysis methodology) and have evaluated the outcomes and associated risk factors of previously established early childhood asthma phenotypes that are based on asthma onset and patterns of wheezing illness. There have also been investigations focusing on immunologic, physiologic, and genetic correlates of various phenotypes, as well as identification of subphenotypes of severe childhood asthma. Childhood asthma remains a heterogeneous condition, and investigations into these various presentations, risk factors, and outcomes are important since they can offer therapeutic and prognostic relevance. Further investigation into the immunopathology and genetic basis underlying childhood phenotypes is important so therapy can be tailored accordingly.

  9. Lexicographic presentation of grammatical divergence in Sesotho ...

    African Journals Online (AJOL)

    Relying on existing insights from the field of theoretical lexicography this article gives an innovative application to the relation of divergence by introducing the notion of grammatical divergence. In bilingual dictionaries with English and Sesotho sa Leboa as language pair lexicographers are confronted with a real challenge ...

  10. Divergent Thinking and Age-Related Changes

    Science.gov (United States)

    Palmiero, Massimiliano; Di Giacomo, Dina; Passafiume, Domenico

    2014-01-01

    Aging can affect cognition in different ways. The extent to which aging affects divergent thinking is unclear. In this study, younger and older adults were compared at the performance on the Torrance Test of Creative Thinking in visual and verbal form. Results showed that older adults can think divergently as younger participants, although they…

  11. Differential Survival between Visual Environments Supports a Role of Divergent Sensory Drive in Cichlid Fish Speciation.

    Science.gov (United States)

    Maan, Martine E; Seehausen, Ole; Groothuis, Ton G G

    2017-01-01

    Identifying the selective forces that initiate ecological speciation is a major challenge in evolutionary biology. Sensory drive has been implicated in speciation in various taxa, largely based on phenotype-environment correlations and signatures of selection in sensory genes. Here, we present a reciprocal transplant experiment revealing species differences in performance in alternative visual environments, consistent with speciation by divergent sensory drive. The closely related cichlids Pundamilia pundamilia and Pundamilia nyererei inhabit different visual environments in Lake Victoria and show associated differences in visual system properties. Mimicking the two light environments in the laboratory, we find a substantial reduction in survival of both species when reared in the other species' visual environment. This implies that the observed differences in Pundamilia color vision are indeed adaptive and substantiates the implicit assumption in sensory drive speciation models that divergent environmental selection is strong enough to drive divergence in sensory properties.

  12. Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species.

    Directory of Open Access Journals (Sweden)

    Gizem Kalay

    2010-11-01

    Full Text Available cis-regulatory DNA sequences known as enhancers control gene expression in space and time. They are central to metazoan development and are often responsible for changes in gene regulation that contribute to phenotypic evolution. Here, we examine the sequence, function, and genomic location of enhancers controlling tissue- and cell-type specific expression of the yellow gene in six Drosophila species. yellow is required for the production of dark pigment, and its expression has evolved largely in concert with divergent pigment patterns. Using Drosophila melanogaster as a transgenic host, we examined the expression of reporter genes in which either 5' intergenic or intronic sequences of yellow from each species controlled the expression of Green Fluorescent Protein. Surprisingly, we found that sequences controlling expression in the wing veins, as well as sequences controlling expression in epidermal cells of the abdomen, thorax, and wing, were located in different genomic regions in different species. By contrast, sequences controlling expression in bristle-associated cells were located in the intron of all species. Differences in the precise pattern of spatial expression within the developing epidermis of D. melanogaster transformants usually correlated with adult pigmentation in the species from which the cis-regulatory sequences were derived, which is consistent with cis-regulatory evolution affecting yellow expression playing a central role in Drosophila pigmentation divergence. Sequence comparisons among species favored a model in which sequential nucleotide substitutions were responsible for the observed changes in cis-regulatory architecture. Taken together, these data demonstrate frequent changes in yellow cis-regulatory architecture among Drosophila species. Similar analyses of other genes, combining in vivo functional tests of enhancer activity with in silico comparative genomics, are needed to determine whether the pattern of

  13. Clinical phenotypes of asthma

    NARCIS (Netherlands)

    Bel, Elisabeth H.

    2004-01-01

    PURPOSE OF REVIEW: Asthma is a phenotypically heterogeneous disorder and, over the years, many different clinical subtypes of asthma have been described. A precise definition of asthma phenotypes is now becoming more and more important, not only for a better understanding of pathophysiologic

  14. Genetic divergence of common bean cultivars.

    Science.gov (United States)

    Veloso, J S; Silva, W; Pinheiro, L R; Dos Santos, J B; Fonseca, N S; Euzebio, M P

    2015-09-22

    The aim of this study was to evaluate genetic divergence in the 'Carioca' (beige with brown stripes) common bean cultivar used by different institutions and in 16 other common bean cultivars used in the Rede Cooperativa de Pesquisa de Feijão (Cooperative Network of Common Bean Research), by using simple sequence repeats associated with agronomic traits that are highly distributed in the common bean genome. We evaluated 22 polymorphic loci using bulks containing DNA from 30 plants. There was genetic divergence among the Carioca cultivar provided by the institutions. Nevertheless, there was lower divergence among them than among the other cultivars. The cultivar used by Instituto Agronômico do Paraná was the most divergent in relation to the Carioca samples. The least divergence was observed among the samples used by Universidade Federal de Lavras and by Embrapa Arroz e Feijão. Of all the cultivars, 'CNFP 10104' and 'BRSMG Realce' showed the greatest dissimilarity. The cultivars were separated in two groups of greatest similarity using the Structure software. Genetic variation among cultivars was greater than the variation within or between the groups formed. This fact, together with the high estimate of heterozygosity observed and the genetic divergence of the samples of the Carioca cultivar in relation to the original provided by Instituto Agronômico de Campinas, indicates a mixture of cultivars. The high divergence among cultivars provides potential for the utilization of this genetic variability in plant breeding.

  15. The estimation of genetic divergence

    Science.gov (United States)

    Holmquist, R.; Conroy, T.

    1981-01-01

    Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.

  16. Divergence, recombination and retention of functionality during protein evolution

    Directory of Open Access Journals (Sweden)

    Xu Yanlong O

    2005-09-01

    Full Text Available Abstract We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models of proteins and ligands (or substrates. These simulations include thermodynamic features of protein stability and population dynamics. We refer to this approach as 'ab initio evolution' to emphasise the fact that the equilibrium details of fitness distributions arise from the physical principles of the system and not from any preconceived notions or arbitrary mathematical distributions. Here, we present results on the retention of functionality in homologous recombinants following population divergence. A central result is that protein structure characteristics can strongly influence recombinant functionality. Exceptional structures with many sequence options evolve quickly and tend to retain functionality -- even in highly diverged recombinants. By contrast, the more common structures with fewer sequence options evolve more slowly, but the fitness of recombinants drops off rapidly as homologous proteins diverge. These results have implications for understanding viral evolution, speciation and directed evolutionary experiments. Our analysis of the divergence process can also guide improved methods for accurately approximating folding probabilities in more complex but realistic systems.

  17. Verbal and visual divergent thinking in aging.

    Science.gov (United States)

    Palmiero, Massimiliano; Nori, Raffaella; Piccardi, Laura

    2017-04-01

    According to the peak and decline model divergent thinking declines at a specific age (in or after middle age). However, if divergent thinking declines steadily in aging still has to be clarified. In order to explore the age-related changes in verbal and visual divergent thinking, in the present study a sample of 159 participants was divided in five age groups: young adults (18-35 years), middle-aged adults (36-55), young old (56-74), old (75-85) and the oldest-old (86-98). Two divergent thinking tasks were administered: the alternative uses for cardboard boxes, aimed at assessing verbal ideational fluency, flexibility and originality; the completion drawing task, aimed at assessing visual ideational fluency, flexibility and originality. Results showed that after peaking in the young adult group (20-35 years) all components of verbal and visual divergent thinking stabilized in the middle-aged adult group (36-55 years) and then started declining in the young old group (56-75). Interestingly, all components were found to be preserved after declining. Yet, verbal and visual divergent thinking were found at the same extent across age groups, with the exception of visual ideational fluency, that was higher in the young old group, the old group and the oldest-old group than verbal ideational fluency. These results support the idea that divergent thinking does not decline steadily in the elderly. Given that older people can preserve to some extent verbal and visual divergent thinking, these findings have important implications for active aging, that is, divergent thinking might be fostered in aging in order to prevent the cognitive decline.

  18. Redundancy and divergence in the amyloid precursor protein family.

    Science.gov (United States)

    Shariati, S Ali M; De Strooper, Bart

    2013-06-27

    Gene duplication provides genetic material required for functional diversification. An interesting example is the amyloid precursor protein (APP) protein family. The APP gene family has experienced both expansion and contraction during evolution. The three mammalian members have been studied quite extensively in combined knock out models. The underlying assumption is that APP, amyloid precursor like protein 1 and 2 (APLP1, APLP2) are functionally redundant. This assumption is primarily supported by the similarities in biochemical processing of APP and APLPs and on the fact that the different APP genes appear to genetically interact at the level of the phenotype in combined knockout mice. However, unique features in each member of the APP family possibly contribute to specification of their function. In the current review, we discuss the evolution and the biology of the APP protein family with special attention to the distinct properties of each homologue. We propose that the functions of APP, APLP1 and APLP2 have diverged after duplication to contribute distinctly to different neuronal events. Our analysis reveals that APLP2 is significantly diverged from APP and APLP1. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  19. Rapid evolution of the intersexual genetic correlation for fitness in Drosophila melanogaster.

    Science.gov (United States)

    Collet, Julie M; Fuentes, Sara; Hesketh, Jack; Hill, Mark S; Innocenti, Paolo; Morrow, Edward H; Fowler, Kevin; Reuter, Max

    2016-04-01

    Sexual antagonism (SA) arises when male and female phenotypes are under opposing selection, yet genetically correlated. Until resolved, antagonism limits evolution toward optimal sex-specific phenotypes. Despite its importance for sex-specific adaptation and existing theory, the dynamics of SA resolution are not well understood empirically. Here, we present data from Drosophila melanogaster, compatible with a resolution of SA. We compared two independent replicates of the "LHM " population in which SA had previously been described. Both had been maintained under identical, controlled conditions, and separated for around 200 generations. Although heritabilities of male and female fitness were similar, the intersexual genetic correlation differed significantly, being negative in one replicate (indicating SA) but close to zero in the other. Using population sequencing, we show that phenotypic differences were associated with population divergence in allele frequencies at nonrandom loci across the genome. Large frequency changes were more prevalent in the population without SA and were enriched at loci mapping to genes previously shown to have sexually antagonistic relationships between expression and fitness. Our data suggest that rapid evolution toward SA resolution has occurred in one of the populations and open avenues toward studying the genetics of SA and its resolution. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  20. Two New Measures of Fuzzy Divergence and Their Properties

    Directory of Open Access Journals (Sweden)

    Om Parkash

    2006-06-01

    Full Text Available Several measures of directed divergence and their corresponding measures of fuzzy divergence are available in the exiting literature. Two new measures of fuzzy divergence have been developed and their desirable properties have been discussed.

  1. Treatment of divergent expansions in scattering theory

    International Nuclear Information System (INIS)

    Gersten, A.; Malin, S.

    1978-01-01

    One of the biggest obstacles in applying quantum field theory to realistic scattering problems are the divergencies of pertubation expansions for large coupling constants and the divergencies of partial wave expansions for massless particles exchanges. There exist, however, methods of summation of the divergent expansions which can lead to significant application in physics. In this paper we treat the problem of summing such expansions using three methods: (i) a generalization of the Pade approximation to the multivariable case. The suggested definition is unique and preserves unitarity. (ii) The summation of divergent partial waves for arbitrary spins. (iii) A successful application of a series inversion to the 3 P 1 nucleon-nucleon phase shift up to 200 MeV. (orig./WL) [de

  2. Divergence and convergence in nutrition science

    NARCIS (Netherlands)

    Penders, Bart; Spruit, Shannon L.; Sikkema, Jan; Maat, Jan; Schuurbiers, Daan

    2015-01-01

    Nutrigenomics diverged from mainstream nutrition science, ideologically, instrumentally and culturally, due to the establishment of a protective niche. That protection is fading. This article chronicles a case in which convergence between nutrigenomics and nutrition science is pursued. Here we

  3. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

    KAUST Repository

    Huang, Chao-Li; Ho, Chuan-Wen; Chiang, Yu-Chung; Shigemoto, Yasumasa; Hsu, Tsai-Wen; Hwang, Chi-Chuan; Ge, Xue-Jun; Chen, Charles; Wu, Tai-Han; Chou, Chang-Hung; Huang, Hao-Jen; Gojobori, Takashi; Osada, Naoki; Chiang, Tzen-Yuh

    2014-01-01

    Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

  4. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

    KAUST Repository

    Huang, Chao-Li

    2014-11-11

    Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

  5. Decoding divergent series in nonparaxial optics.

    Science.gov (United States)

    Borghi, Riccardo; Gori, Franco; Guattari, Giorgio; Santarsiero, Massimo

    2011-03-15

    A theoretical analysis aimed at investigating the divergent character of perturbative series involved in the study of free-space nonparaxial propagation of vectorial optical beams is proposed. Our analysis predicts a factorial divergence for such series and provides a theoretical framework within which the results of recently published numerical experiments concerning nonparaxial propagation of vectorial Gaussian beams find a meaningful interpretation in terms of the decoding operated on such series by the Weniger transformation.

  6. Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors.

    Directory of Open Access Journals (Sweden)

    Thomas B Duguet

    2016-07-01

    Full Text Available Helminth parasites rely on fast-synaptic transmission in their neuromusculature to experience the outside world and respond to it. Acetylcholine plays a pivotal role in this and its receptors are targeted by a wide variety of both natural and synthetic compounds used in human health and for the control of parasitic disease. The model, Caenorhabditis elegans is characterized by a large number of acetylcholine receptor subunit genes, a feature shared across the nematodes. This dynamic family is characterized by both gene duplication and loss between species. The pentameric levamisole-sensitive acetylcholine receptor has been characterized from C. elegans, comprised of five different subunits. More recently, cognate receptors have been reconstituted from multiple parasitic nematodes that are found to vary in subunit composition. In order to understand the implications of receptor composition change and the origins of potentially novel drug targets, we investigated a specific example of subunit duplication based on analysis of genome data for 25 species from the 50 helminth genome initiative. We found multiple independent duplications of the unc-29, acetylcholine receptor subunit, where codon substitution rate analysis identified positive, directional selection acting on amino acid positions associated with subunit assembly. Characterization of four gene copies from a model parasitic nematode, Haemonchus contortus, demonstrated that each copy has acquired unique functional characteristics based on phenotype rescue of transgenic C. elegans and electrophysiology of receptors reconstituted in Xenopus oocytes. We found evidence that a specific incompatibility has evolved for two subunits co-expressed in muscle. We demonstrated that functional divergence of acetylcholine receptors, driven by directional selection, can occur more rapidly than previously thought and may be mediated by alteration of receptor assembly. This phenomenon is common among the

  7. Collinearity, convergence and cancelling infrared divergences

    International Nuclear Information System (INIS)

    Lavelle, Martin; McMullan, David

    2006-01-01

    The Lee-Nauenberg theorem is a fundamental quantum mechanical result which provides the standard theoretical response to the problem of collinear and infrared divergences. Its argument, that the divergences due to massless charged particles can be removed by summing over degenerate states, has been successfully applied to systems with final state degeneracies such as LEP processes. If there are massless particles in both the initial and final states, as will be the case at the LHC, the theorem requires the incorporation of disconnected diagrams which produce connected interference effects at the level of the cross-section. However, this aspect of the theory has never been fully tested in the calculation of a cross-section. We show through explicit examples that in such cases the theorem introduces a divergent series of diagrams and hence fails to cancel the infrared divergences. It is also demonstrated that the widespread practice of treating soft infrared divergences by the Bloch-Nordsieck method and handling collinear divergences by the Lee-Nauenberg method is not consistent in such cases

  8. COMPUTER APPROACHES TO WHEAT HIGH-THROUGHPUT PHENOTYPING

    Directory of Open Access Journals (Sweden)

    Afonnikov D.

    2012-08-01

    Full Text Available The growing need for rapid and accurate approaches for large-scale assessment of phenotypic characters in plants becomes more and more obvious in the studies looking into relationships between genotype and phenotype. This need is due to the advent of high throughput methods for analysis of genomes. Nowadays, any genetic experiment involves data on thousands and dozens of thousands of plants. Traditional ways of assessing most phenotypic characteristics (those with reliance on the eye, the touch, the ruler are little effective on samples of such sizes. Modern approaches seek to take advantage of automated phenotyping, which warrants a much more rapid data acquisition, higher accuracy of the assessment of phenotypic features, measurement of new parameters of these features and exclusion of human subjectivity from the process. Additionally, automation allows measurement data to be rapidly loaded into computer databases, which reduces data processing time.In this work, we present the WheatPGE information system designed to solve the problem of integration of genotypic and phenotypic data and parameters of the environment, as well as to analyze the relationships between the genotype and phenotype in wheat. The system is used to consolidate miscellaneous data on a plant for storing and processing various morphological traits and genotypes of wheat plants as well as data on various environmental factors. The system is available at www.wheatdb.org. Its potential in genetic experiments has been demonstrated in high-throughput phenotyping of wheat leaf pubescence.

  9. Divergent and nonuniform gene expression patterns in mouse brain

    Science.gov (United States)

    Morris, John A.; Royall, Joshua J.; Bertagnolli, Darren; Boe, Andrew F.; Burnell, Josh J.; Byrnes, Emi J.; Copeland, Cathy; Desta, Tsega; Fischer, Shanna R.; Goldy, Jeff; Glattfelder, Katie J.; Kidney, Jolene M.; Lemon, Tracy; Orta, Geralyn J.; Parry, Sheana E.; Pathak, Sayan D.; Pearson, Owen C.; Reding, Melissa; Shapouri, Sheila; Smith, Kimberly A.; Soden, Chad; Solan, Beth M.; Weller, John; Takahashi, Joseph S.; Overly, Caroline C.; Lein, Ed S.; Hawrylycz, Michael J.; Hohmann, John G.; Jones, Allan R.

    2010-01-01

    Considerable progress has been made in understanding variations in gene sequence and expression level associated with phenotype, yet how genetic diversity translates into complex phenotypic differences remains poorly understood. Here, we examine the relationship between genetic background and spatial patterns of gene expression across seven strains of mice, providing the most extensive cellular-resolution comparative analysis of gene expression in the mammalian brain to date. Using comprehensive brainwide anatomic coverage (more than 200 brain regions), we applied in situ hybridization to analyze the spatial expression patterns of 49 genes encoding well-known pharmaceutical drug targets. Remarkably, over 50% of the genes examined showed interstrain expression variation. In addition, the variability was nonuniformly distributed across strain and neuroanatomic region, suggesting certain organizing principles. First, the degree of expression variance among strains mirrors genealogic relationships. Second, expression pattern differences were concentrated in higher-order brain regions such as the cortex and hippocampus. Divergence in gene expression patterns across the brain could contribute significantly to variations in behavior and responses to neuroactive drugs in laboratory mouse strains and may help to explain individual differences in human responsiveness to neuroactive drugs. PMID:20956311

  10. Distinct subspecies or phenotypic plasticity? Genetic and morphological differentiation of mountain honey bees in East Africa.

    Science.gov (United States)

    Gruber, Karl; Schöning, Caspar; Otte, Marianne; Kinuthia, Wanja; Hasselmann, Martin

    2013-09-01

    Identifying the forces shaping intraspecific phenotypic and genotypic divergence are of key importance in evolutionary biology. Phenotypic divergence may result from local adaptation or, especially in species with strong gene flow, from pronounced phenotypic plasticity. Here, we examine morphological and genetic divergence among populations of the western honey bee Apis mellifera in the topographically heterogeneous East African region. The currently accepted "mountain refugia hypothesis" states that populations living in disjunct montane forests belong to a different lineage than those in savanna habitats surrounding these forests. We obtained microsatellite data, mitochondrial sequences, and morphometric data from worker honey bees collected from feral colonies in three montane forests and corresponding neighboring savanna regions in Kenya. Honey bee colonies from montane forests showed distinct worker morphology compared with colonies in savanna areas. Mitochondrial sequence data did not support the existence of the two currently accepted subspecies. Furthermore, analyses of the microsatellite data with a Bayesian clustering method did not support the existence of two source populations as it would be expected under the mountain refugia scenario. Our findings suggest that phenotypic plasticity rather than distinct ancestry is the leading cause behind the phenotypic divergence observed between montane forest and savanna honey bees. Our study thus corroborates the idea that high gene flow may select for increased plasticity.

  11. Convergent evolution of phenotypic integration and its alignment with morphological diversification in Caribbean Anolis ecomorphs.

    Science.gov (United States)

    Kolbe, Jason J; Revell, Liam J; Szekely, Brian; Brodie, Edmund D; Losos, Jonathan B

    2011-12-01

    The adaptive landscape and the G-matrix are keys concepts for understanding how quantitative characters evolve during adaptive radiation. In particular, whether the adaptive landscape can drive convergence of phenotypic integration (i.e., the pattern of phenotypic variation and covariation summarized in the P-matrix) is not well studied. We estimated and compared P for 19 morphological traits in eight species of Caribbean Anolis lizards, finding that similarity in P among species was not correlated with phylogenetic distance. However, greater similarity in P among ecologically similar Anolis species (i.e., the trunk-ground ecomorph) suggests the role of convergent natural selection. Despite this convergence and relatively deep phylogenetic divergence, a large portion of eigenstructure of P is retained among our eight focal species. We also analyzed P as an approximation of G to test for correspondence with the pattern of phenotypic divergence in 21 Caribbean Anolis species. These patterns of covariation were coincident, suggesting that either genetic constraint has influenced the pattern of among-species divergence or, alternatively, that the adaptive landscape has influenced both G and the pattern of phenotypic divergence among species. We provide evidence for convergent evolution of phenotypic integration for one class of Anolis ecomorph, revealing yet another important dimension of evolutionary convergence in this group. No Claim to original U.S. government works.

  12. Dissecting phenotypic variation among AIS patients

    International Nuclear Information System (INIS)

    Wang Minghua; Wang Jiucun; Zhang Zhen; Zhao Zhimin; Zhang Rongmei; Hu Xiaohua; Tan Tao; Luo Shijing; Luo Zewei

    2005-01-01

    We have created genital skin fibroblast cell lines directly from three patients in a Chinese family affected by androgen insensitivity syndrome (AIS). All patients in the family share an identical AR Arg 840 Cys mutant but show different disease phenotypes. By using the cell lines, we find that the mutation has not influenced a normal androgen-binding capacity at 37 deg C but has reduced the affinity for androgens and may cause thermolability of the androgen-receptor complex. The impaired nuclear trafficking of the androgen receptor in the cell lines is highly correlated with the severity of donors' disease phenotype. The transactivity of the mutant is substantially weakened and the extent of the reduced transactivity reflects severity of the donors' disease symptom. Our data reveal that although etiology of AIS is monogenic and the mutant may alter the major biological functions of its wild allele, the function of the mutant AR can also be influenced by the different genetic backgrounds and thus explains the divergent disease phenotypes

  13. Properties of classical and quantum Jensen-Shannon divergence

    NARCIS (Netherlands)

    J. Briët (Jop); P. Harremoës (Peter)

    2009-01-01

    htmlabstractJensen-Shannon divergence (JD) is a symmetrized and smoothed version of the most important divergence measure of information theory, Kullback divergence. As opposed to Kullback divergence it determines in a very direct way a metric; indeed, it is the square of a metric. We consider a

  14. Beam Angular Divergence Effects in Ion Implantation

    International Nuclear Information System (INIS)

    Horsky, T. N.; Hahto, S. K.; Bilbrough, D. G.; Jacobson, D. C.; Krull, W. A.; Goldberg, R. D.; Current, M. I.; Hamamoto, N.; Umisedo, S.

    2008-01-01

    An important difference between monomer ion beams and heavy molecular beams is a significant reduction in beam angular divergence and increased on-wafer angular accuracy for molecular beams. This advantage in beam quality stems from a reduction in space-charge effects within the beam. Such improved angular accuracy has been shown to have a significant impact on the quality and yield of transistor devices [1,12]. In this study, B 18 H x + beam current and angular divergence data collected on a hybrid scanned beam line that magnetically scans the beam across the wafer is presented. Angular divergence is kept below 0.5 deg from an effective boron energy of 200 eV to 3000 eV. Under these conditions, the beam current is shown analytically to be limited by space charge below about 1 keV, but by the matching of the beam emittance to the acceptance of the beam line above 1 keV. In addition, results of a beam transport model which includes variable space charge compensation are presented, in which a drift mode B 18 H x + beam is compared to an otherwise identical boron beam after deceleration. Deceleration is shown to introduce significant space-charge blow up resulting in a large on-wafer angular divergence. The divergence effects introduced by wafer charging are also discussed.

  15. Ion divergence in magnetically insulated diodes

    International Nuclear Information System (INIS)

    Slutz, S.A.; Lemke, R.W.; Pointon, T.D.; Desjarlais, M.P.; Johnson, D.J.; Mehlhorn, T.A.; Filuk, A.; Bailey, J.

    1995-01-01

    Magnetically insulated ion diodes are being developed to drive inertial confinement fusion. Ion beam microdivergence must be reduced to achieve the very high beam intensities required to achieve this goal. Three-dimensional particle-in-cell simulations indicate that instability induced fluctuations can produce significant ion divergence during acceleration. These simulations exhibit a fast growing mode early in time, which has been identified as the diocotron instability. The divergence generated by this mode is modest due to the relatively high frequency (>1GHz). Later, a low-frequency low-phase-velocity instability develops. This instability couples effectively to the ions, since the frequency is approximately the reciprocal of the ion transit time, and can generate unacceptably large ion divergences (>30 mrad). Linear stability theory reveals that this mode requires perturbations parallel to the applied magnetic field and is related to the modified two stream instability. Measurements of ion density fluctuations and energy-momentum correlations have confirmed that instabilities develop in ion diodes and contribute to the ion divergence. In addition, spectroscopic measurements indicate that the ions have a significant transverse temperature very close to the emission surface. Passive lithium fluoride (LiF) anodes have larger transverse beam temperatures than laser irradiated active sources. Calculations of source divergence expected from the roughness of LiF surfaces and the possible removal of this layer is presented

  16. Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ.

    Science.gov (United States)

    Resnyk, C W; Carré, W; Wang, X; Porter, T E; Simon, J; Le Bihan-Duval, E; Duclos, M J; Aggrey, S E; Cogburn, L A

    2017-08-16

    Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens. We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription in abdominal fat of juvenile [1-11 weeks of age (wk)] chickens divergently selected on bodyweight at two ages (8 and 36 wk). Further, a RNA sequencing analysis was completed on the same abdominal fat samples taken from high-growth (HG) and low-growth (LG) cockerels at 7 wk, the age with the greatest divergence in body weight (3.2-fold) and visceral fatness (19.6-fold). Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918 genes as the main effect of age. The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk. The HG chickens are fatter and over-express numerous genes that support higher rates of visceral adipogenesis and lipogenesis. In abdominal fat of LG chickens, we found higher expression of many genes involved in hemostasis, energy catabolism and endocrine signaling, which likely contribute to their leaner phenotype and slower growth. Many transcription factors and their direct target genes identified in HG and LG chickens could be involved in their divergence in adiposity and growth rate. The present analyses of the visceral fat transcriptome in

  17. The divergence theorem for divergence measure vectorfields on sets with fractal boundaries

    Czech Academy of Sciences Publication Activity Database

    Šilhavý, Miroslav

    2009-01-01

    Roč. 14, č. 5 (2009), s. 445-455 ISSN 1081-2865 Institutional research plan: CEZ:AV0Z10190503 Keywords : divergence measure vectorfields * fractal s * divergence theorem Subject RIV: BA - General Mathematics Impact factor: 1.065, year: 2009

  18. Vibhakti Divergence between Sanskrit and Hindi

    Science.gov (United States)

    Shukla, Preeti; Shukl, Devanand; Kulkarni, Amba

    Translation divergence at various levels between languages arises due to the different conventions followed by different languages for coding the information of grammatical relations. Though Sanskrit and Hindi belong to the same Indo-Aryan family and structurally as well as lexically Hindi inherits a lot from Sanskrit, yet divergences are observed at the level of function words such as vibhaktis. Pāṇini in his Aṣṭādhyāyī has assigned a default vibhakti to kārakas alongwith many scopes for exceptions. He handles these exceptions either by imposing a new kāraka role or by assigning a special vibhakti. However, these methods are not acceptable in Hindi in toto. Based on the nature of deviation, we propose seven cases of divergences in this paper.

  19. Multidimensionality of behavioural phenotypes in Atlantic cod, Gadus morhua.

    Science.gov (United States)

    Meager, Justin J; Fernö, Anders; Skjæraasen, Jon Egil; Järvi, Torbjörn; Rodewald, Petra; Sverdrup, Gisle; Winberg, Svante; Mayer, Ian

    2012-06-25

    Much of the inter-individual variation observed in animal behaviour is now attributed to the existence of behavioural phenotypes or animal personalities. Such phenotypes may be fundamental to fisheries and aquaculture, yet there have been few detailed studies of this phenomenon in exploited marine animals. We investigated the behavioural and neuroendocrine responses of Atlantic cod (Gadus morhua L.), to situations reflecting critical ecological challenges: predator attacks and territorial challenges. Both hatchery-reared and wild fish were tested and behavioural profiles were compared with baseline conditions. We then used an objective, multivariate approach, rather than assigning individuals along one-dimensional behavioural axes, to examine whether distinct behavioural phenotypes were present. Our results indicate that two distinct behavioural phenotypes were evident in fish from each background. In hatchery-reared fish, phenotypes displayed divergent locomotor activity, sheltering, brain monoamine concentrations and responses to competitive challenges. In wild fish, phenotypes were distinguished primarily by locomotor activity, sheltering and responsiveness to predator stimuli. Hatcheries presumably represent a more stressful social environment, and social behaviour and neuroendocrine responses were important in discerning behavioural phenotypes in hatchery fish, whereas antipredator responses were important in discerning phenotypes in wild fish that have previously encountered predators. In both fish types, behavioural and physiological traits that classified individuals into phenotypes were not the same as those that were correlated across situations. These results highlight the multidimensionality of animal personalities, and that the processes that regulate one suite of behavioural traits may be very different to the processes that regulate other behaviours. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Diverging expectations in buyer-seller relationships

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Christensen, Poul Rind; Damgaard, Torben

    2009-01-01

    Many firms assume that outsourcing partnerships may allow them to strengthen their overall competitiveness. Lured by its intuitive appeal, several enter into such partnerships, only to realize that they represent a marginal rather than a magical solution to their quest for increasing market...... performance. We explore the proposed impact of diverging relationship norms on relationship expectations using data from an ongoing field study of Danish buyers and Chinese suppliers. We link these diverging expectations to the business practices of Danish buyers and Chinese and their institutional contexts...

  1. Universal portfolios generated by the Bregman divergence

    Science.gov (United States)

    Tan, Choon Peng; Kuang, Kee Seng

    2017-04-01

    The Bregman divergence of two probability vectors is a stronger form of the f-divergence introduced by Csiszar. Two versions of the Bregman universal portfolio are presented by exploiting the mean-value theorem. The explicit form of the Bregman universal portfolio generated by a function of a convex polynomial is derived and studied empirically. This portfolio can be regarded as another generalized of the well-known Helmbold portfolio. By running the portfolios on selected stock-price data sets from the local stock exchange, it is shown that it is possible to increase the wealth of the investor by using the portfolios in investment.

  2. Pollinator Competition as a Driver of Floral Divergence: An Experimental Test.

    Directory of Open Access Journals (Sweden)

    Ethan J Temeles

    Full Text Available Optimal foraging models of floral divergence predict that competition between two different types of pollinators will result in partitioning, increased assortative mating, and divergence of two floral phenotypes. We tested these predictions in a tropical plant-pollinator system using sexes of purple-throated carib hummingbirds (Anthracothorax jugularis as the pollinators, red and yellow inflorescence morphs of Heliconia caribaea as the plants, and fluorescent dyes as pollen analogs in an enclosed outdoor garden. When foraging alone, males exhibited a significant preference for the yellow morph of H. caribaea, whereas females exhibited no preference. In competition, males maintained their preference for the yellow morph and through aggression caused females to over-visit the red morph, resulting in resource partitioning. Competition significantly increased within-morph dye transfer (assortative mating relative to non-competitive environments. Competition and partitioning of color morphs by sexes of purple-throated caribs also resulted in selection for floral divergence as measured by dye deposition on stigmas. Red and yellow morphs did not differ significantly in dye deposition in the competition trials, but differences in dye deposition and preferences for morphs when sexes of purple-throated caribs foraged alone implied fixation of one or the other color morph in the absence of competition. Competition also resulted in selection for divergence in corolla length, with the red morph experiencing directional selection for longer corollas and the yellow morph experiencing stabilizing selection on corolla length. Our results thus support predictions of foraging models of floral divergence and indicate that pollinator competition is a viable mechanism for divergence in floral traits of plants.

  3. The spatial patterns of directional phenotypic selection.

    Science.gov (United States)

    Siepielski, Adam M; Gotanda, Kiyoko M; Morrissey, Michael B; Diamond, Sarah E; DiBattista, Joseph D; Carlson, Stephanie M

    2013-11-01

    Local adaptation, adaptive population divergence and speciation are often expected to result from populations evolving in response to spatial variation in selection. Yet, we lack a comprehensive understanding of the major features that characterise the spatial patterns of selection, namely the extent of variation among populations in the strength and direction of selection. Here, we analyse a data set of spatially replicated studies of directional phenotypic selection from natural populations. The data set includes 60 studies, consisting of 3937 estimates of selection across an average of five populations. We performed meta-analyses to explore features characterising spatial variation in directional selection. We found that selection tends to vary mainly in strength and less in direction among populations. Although differences in the direction of selection occur among populations they do so where selection is often weakest, which may limit the potential for ongoing adaptive population divergence. Overall, we also found that spatial variation in selection appears comparable to temporal (annual) variation in selection within populations; however, several deficiencies in available data currently complicate this comparison. We discuss future research needs to further advance our understanding of spatial variation in selection. © 2013 John Wiley & Sons Ltd/CNRS.

  4. The spatial patterns of directional phenotypic selection

    KAUST Repository

    Siepielski, Adam M.

    2013-09-12

    Local adaptation, adaptive population divergence and speciation are often expected to result from populations evolving in response to spatial variation in selection. Yet, we lack a comprehensive understanding of the major features that characterise the spatial patterns of selection, namely the extent of variation among populations in the strength and direction of selection. Here, we analyse a data set of spatially replicated studies of directional phenotypic selection from natural populations. The data set includes 60 studies, consisting of 3937 estimates of selection across an average of five populations. We performed meta-analyses to explore features characterising spatial variation in directional selection. We found that selection tends to vary mainly in strength and less in direction among populations. Although differences in the direction of selection occur among populations they do so where selection is often weakest, which may limit the potential for ongoing adaptive population divergence. Overall, we also found that spatial variation in selection appears comparable to temporal (annual) variation in selection within populations; however, several deficiencies in available data currently complicate this comparison. We discuss future research needs to further advance our understanding of spatial variation in selection. © 2013 John Wiley & Sons Ltd/CNRS.

  5. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Directory of Open Access Journals (Sweden)

    George L Sutphin

    2016-11-01

    Full Text Available The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  6. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning

    Science.gov (United States)

    Sutphin, George L.; Mahoney, J. Matthew; Sheppard, Keith; Walton, David O.; Korstanje, Ron

    2016-01-01

    The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species—humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/. PMID:27812085

  7. Design and testing of low-divergence elliptical-jet nozzles

    Energy Technology Data Exchange (ETDEWEB)

    Rouly, Etienne; Warkentin, Andrew; Bauer, Robert [Dalhousie University, Halifax (China)

    2015-05-15

    A novel approach was developed to design and fabricate nozzles to produce high-pressure low-divergence fluid jets. Rapid-prototype fabrication allowed for myriad experiments investigating effects of different geometric characteristics of nozzle internal geometry on jet divergence angle and fluid distribution. Nozzle apertures were elliptical in shape with aspect ratios between 1.00 and 2.45. The resulting nozzle designs were tested and the lowest elliptical jet divergence angle was 0.4 degrees. Nozzle pressures and flowrates ranged from 0.32 to 4.45 MPa and 13.6 to 37.9 LPM, respectively. CimCool CimTech 310 machining fluid was used in all experiments at a Brix concentration of 6.6 percent.

  8. Advanced phenotyping and phenotype data analysis for the plant growth and development study

    Directory of Open Access Journals (Sweden)

    Md. Matiur eRahaman

    2015-08-01

    Full Text Available Due to increase in the consumption of food, feed, fuel and to ensure global food security for rapidly growing human population, there is need to breed high yielding crops that can adapt to future climate. To solve these global issues, novel approaches are required to provide quantitative phenotypes to elucidate the genetic basis of agriculturally import traits and to screen germplasm with super performance in function under resource-limited environment. At present, plant phenomics has offered and integrated suite technologies for understanding the complete set of phenotypes of plants, towards the progression of the full characteristics of plants with whole sequenced genomes. In this aspect, high-throughput phenotyping platforms have been developed that enables to capture extensive and intensive phenotype data from non-destructive imaging over time. These developments advance our view on plant growth and performance with responses to the changing climate and environment. In this paper, we present a brief review on currently developed high-throughput plant phenotyping infrastructures based on imaging techniques and corresponding principles for phenotype data analysis.

  9. COPD: Definition and Phenotypes

    DEFF Research Database (Denmark)

    Vestbo, J.

    2014-01-01

    particles or gases. Exacerbations and comorbidities contribute to the overall severity in individual patients. The evolution of this definition and the diagnostic criteria currently in use are discussed. COPD is increasingly divided in subgroups or phenotypes based on specific features and association...

  10. Phenotypic Resistance to Antibiotics

    Directory of Open Access Journals (Sweden)

    Jose L. Martinez

    2013-04-01

    Full Text Available The development of antibiotic resistance is usually associated with genetic changes, either to the acquisition of resistance genes, or to mutations in elements relevant for the activity of the antibiotic. However, in some situations resistance can be achieved without any genetic alteration; this is called phenotypic resistance. Non-inherited resistance is associated to specific processes such as growth in biofilms, a stationary growth phase or persistence. These situations might occur during infection but they are not usually considered in classical susceptibility tests at the clinical microbiology laboratories. Recent work has also shown that the susceptibility to antibiotics is highly dependent on the bacterial metabolism and that global metabolic regulators can modulate this phenotype. This modulation includes situations in which bacteria can be more resistant or more susceptible to antibiotics. Understanding these processes will thus help in establishing novel therapeutic approaches based on the actual susceptibility shown by bacteria during infection, which might differ from that determined in the laboratory. In this review, we discuss different examples of phenotypic resistance and the mechanisms that regulate the crosstalk between bacterial metabolism and the susceptibility to antibiotics. Finally, information on strategies currently under development for diminishing the phenotypic resistance to antibiotics of bacterial pathogens is presented.

  11. Divergence in function and expression of the NOD26-like intrinsic proteins in plants

    Directory of Open Access Journals (Sweden)

    Feng Ying

    2009-07-01

    Full Text Available Abstract Background NOD26-like intrinsic proteins (NIPs that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further investigate the evolutionary mechanisms being responsible for the functional diversification of the NIP genes. To better understand this process, a comprehensive analysis including the phylogenetic, positive selection, functional divergence, and transcriptional analysis was carried out. Results The origination of NIPs could be dated back to the primitive land plants, and their diversification would be no younger than the emergence time of the moss P. patens. The rapid proliferation of NIPs in plants may be primarily attributed to the segmental chromosome duplication produced by polyploidy and tandem duplications. The maximum likelihood analysis revealed that NIPs should have experienced strong selective pressure for adaptive evolution after gene duplication and/or speciation, prompting the formation of distinct NIP groups. Functional divergence analysis at the amino acid level has provided strong statistical evidence for shifted evolutionary rate and/or radical change of the physiochemical properties of amino acids after gene duplication, and DIVERGE2 has identified the critical amino acid sites that are thought to be responsible for the divergence for further investigation. The expression of plant NIPs displays a distinct tissue-, cell-type-, and developmental specific pattern, and their responses to various stress treatments are quite different also. The differences in organization of cis-acting regulatory elements in the promoter regions may partially explain their distinction in expression. Conclusion A number of analyses both at the DNA and amino acid sequence levels have provided strong evidences that plant NIPs have

  12. Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

    Science.gov (United States)

    Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

    2013-07-01

    Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

  13. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow.

    Science.gov (United States)

    Sachdeva, Himani; Barton, Nicholas H

    2017-06-01

    Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  14. Phenotypic differentiation is associated with divergent sexual selection among closely related barn swallow populations

    Czech Academy of Sciences Publication Activity Database

    Wilkins, M. R.; Karaardic, H.; Vortman, Y.; Parchman, T. L.; Albrecht, Tomáš; Petrželková, Adéla; Özkan, L.; Pap, P. L.; Hubbard, J. K.; Hund, A. K.; Safran, R. J.

    2016-01-01

    Roč. 29, č. 12 (2016), s. 2410-2421 ISSN 1010-061X R&D Projects: GA MŠk(CZ) LH14045 Institutional support: RVO:68081766 Keywords : birds * natural selection * population genetics * sexual selection & conflicts * speciation Subject RIV: EG - Zoology Impact factor: 2.792, year: 2016

  15. Prion protein amyloidosis with divergent phenotype associated with two novel nonsense mutations in PRNP

    NARCIS (Netherlands)

    Jansen, Casper; Parchi, Piero; Capellari, Sabina; Vermeij, Ad J.; Corrado, Patrizia; Baas, Frank; Strammiello, Rosaria; van Gool, Willem A.; van Swieten, John C.; Rozemuller, Annemieke J. M.

    2010-01-01

    Stop codon mutations in the gene encoding the prion protein (PRNP) are very rare and have thus far only been described in two patients with prion protein cerebral amyloid angiopathy (PrP-CAA). In this report, we describe the clinical, histopathological and pathological prion protein (PrPSc)

  16. Stora's fine notion of divergent amplitudes

    Directory of Open Access Journals (Sweden)

    Joseph C. Várilly

    2016-11-01

    Full Text Available Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  17. Taming infrared divergences in the effective potential

    Energy Technology Data Exchange (ETDEWEB)

    Elias-Miro, J. [IFAE, Univ. Autonoma de Barcelona (Spain); Universitat Autonoma de Barcelona (Spain). Dept. de Fisica; Espinosa, J.R. [IFAE, Univ. Autonoma de Barcelona (Spain); ICREA, Institucio Catalana de Recerca i Estudis Avancats, Barcelona (Spain); Konstandin, T. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2014-06-15

    The Higgs effective potential in the Standard Model (SM), calculated perturbatively, generically suffers from infrared (IR) divergences when the (field-dependent) tree-level mass of the Goldstone bosons goes to zero. Such divergences can affect both the potential and its first derivative and become worse with increasing loop order. In this paper we show that these IR divergences are spurious, we perform a simple resummation of all IR-problematic terms known (up to three loops) and explain how to extend the resummation to cure all such divergences to any order. The method is of general applicability and would work in scenarios other than the SM. Our discussion has some bearing on a scenario recently proposed as a mechanism for gauge mediation of scale breaking in the ultraviolet, in which it is claimed that the low-energy Higgs potential is non-standard. We argue that all non-decoupling effects from the heavy sector can be absorbed in the renormalization of low-energy parameters leading to a SM-like effective theory.

  18. Bounding the bias of contrastive divergence learning

    DEFF Research Database (Denmark)

    Fischer, Anja; Igel, Christian

    2011-01-01

    Optimization based on k-step contrastive divergence (CD) has become a common way to train restricted Boltzmann machines (RBMs). The k-step CD is a biased estimator of the log-likelihood gradient relying on Gibbs sampling. We derive a new upper bound for this bias. Its magnitude depends on k...

  19. Hamiltonian representation of divergence-free fields

    International Nuclear Information System (INIS)

    Boozer, A.H.

    1984-11-01

    Globally divergence-free fields, such as the magnetic field and the vorticity, can be described by a two degree of freedom Hamiltonian. The Hamiltonian function provides a complete topological description of the field lines. The formulation also separates the dissipative and inertial time scale evolution of the magnetic and the vorticity fields

  20. Viewpoint Environmental Slogans: Memes with Diverging ...

    African Journals Online (AJOL)

    Environmental slogans can be seen as memes, i.e. cultural constructs that, not unlike genes, replicate themselves from one generation to the next. Memes may, however, be divergently interpreted and some memes can even have unwanted side-effects. We wanted to find out how supporters of an environmental ...

  1. The divergence theorem for unbounded vector fields

    OpenAIRE

    De Pauw, Thierry; Pfeffer, Washek F.

    2007-01-01

    In the context of Lebesgue integration, we derive the divergence theorem for unbounded vector. elds that can have singularities at every point of a compact set whose Minkowski content of codimension greater than two is. nite. The resulting integration by parts theorem is applied to removable sets of holomorphic and harmonic functions.

  2. Divergent Priors and well Behaved Bayes Factors

    NARCIS (Netherlands)

    R.W. Strachan (Rodney); H.K. van Dijk (Herman)

    2011-01-01

    textabstractDivergent priors are improper when defined on unbounded supports. Bartlett's paradox has been taken to imply that using improper priors results in ill-defined Bayes factors, preventing model comparison by posterior probabilities. However many improper priors have attractive properties

  3. The Harmonic Series Diverges Again and Again

    Science.gov (United States)

    Kifowit, Steven J.; Stamps, Terra A.

    2006-01-01

    The harmonic series is one of the most celebrated infinite series of mathematics. A quick glance at a variety of modern calculus textbooks reveals that there are two very popular proofs of the divergence of the harmonic series. In this article, the authors survey these popular proofs along with many other proofs that are equally simple and…

  4. Design of a divergence and alignment indicator

    International Nuclear Information System (INIS)

    Brenizer, J.S. Jr.; Raine, D.A.; Gao, J.; Chen, J.

    1996-01-01

    The divergence and alignment indicator (DAI) is an extension of the ASTM E803 L/D thermal neutron radiography L/D device that allows the user to determine both the beam centerline and the beam divergence. The DAI was made using aluminium plate and rods, and incorporated cadmium wire for contrast. Circular symmetry was utilized to simplify manufacture. The DAI was placed with the five posts against the film cassette or radioscopic imaging device in the physical center of the beam. The DAI was perpendicular to the selected beam radius when the front and back center Cd wire images overlap. The degree of misalignment was indicated by their image positions. After the DAI was aligned, analysis of the cadmium wire ''+'' image spacing yielded the beam divergence. The DAI was tested in a neutron beam which has an L/D of 30 but a small degree of divergence. The DAI was also imaged using an X-ray source. The point source predictions of Cd wire image locations showed good agreement with those measured from the X-ray radiograph. The neutron radiographic locations could be predicted using the point source equations, even though the neutron beam was a complex distributed source. (orig.)

  5. Enhancing Divergent Search through Extinction Events

    DEFF Research Database (Denmark)

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    for the capacity to evolve. This hypothesis is tested through experiments in two evolutionary robotics domains. The results show that combining extinction events with divergent search increases evolvability, while combining them with convergent search offers no similar benefit. The conclusion is that extinction...

  6. Taming infrared divergences in the effective potential

    International Nuclear Information System (INIS)

    Elias-Miro, J.; Konstandin, T.

    2014-06-01

    The Higgs effective potential in the Standard Model (SM), calculated perturbatively, generically suffers from infrared (IR) divergences when the (field-dependent) tree-level mass of the Goldstone bosons goes to zero. Such divergences can affect both the potential and its first derivative and become worse with increasing loop order. In this paper we show that these IR divergences are spurious, we perform a simple resummation of all IR-problematic terms known (up to three loops) and explain how to extend the resummation to cure all such divergences to any order. The method is of general applicability and would work in scenarios other than the SM. Our discussion has some bearing on a scenario recently proposed as a mechanism for gauge mediation of scale breaking in the ultraviolet, in which it is claimed that the low-energy Higgs potential is non-standard. We argue that all non-decoupling effects from the heavy sector can be absorbed in the renormalization of low-energy parameters leading to a SM-like effective theory.

  7. Phenotypic Covariation and Morphological Diversification in the Ruminant Skull.

    Science.gov (United States)

    Haber, Annat

    2016-05-01

    Differences among clades in their diversification patterns result from a combination of extrinsic and intrinsic factors. In this study, I examined the role of intrinsic factors in the morphological diversification of ruminants, in general, and in the differences between bovids and cervids, in particular. Using skull morphology, which embodies many of the adaptations that distinguish bovids and cervids, I examined 132 of the 200 extant ruminant species. As a proxy for intrinsic constraints, I quantified different aspects of the phenotypic covariation structure within species and compared them with the among-species divergence patterns, using phylogenetic comparative methods. My results show that for most species, divergence is well aligned with their phenotypic covariance matrix and that those that are better aligned have diverged further away from their ancestor. Bovids have dispersed into a wider range of directions in morphospace than cervids, and their overall disparity is higher. This difference is best explained by the lower eccentricity of bovids' within-species covariance matrices. These results are consistent with the role of intrinsic constraints in determining amount, range, and direction of dispersion and demonstrate that intrinsic constraints can influence macroevolutionary patterns even as the covariance structure evolves.

  8. A Rapid Aeroelasticity Optimization Method Based on the Stiffness characteristics

    OpenAIRE

    Yuan, Zhe; Huo, Shihui; Ren, Jianting

    2018-01-01

    A rapid aeroelasticity optimization method based on the stiffness characteristics was proposed in the present study. Large time expense in static aeroelasticity analysis based on traditional time domain aeroelasticity method is solved. Elastic axis location and torsional stiffness are discussed firstly. Both torsional stiffness and the distance between stiffness center and aerodynamic center have a direct impact on divergent velocity. The divergent velocity can be adjusted by changing the cor...

  9. Trophic divergence despite morphological convergence in a continental radiation of snakes.

    Science.gov (United States)

    Grundler, Michael C; Rabosky, Daniel L

    2014-07-22

    Ecological and phenotypic convergence is a potential outcome of adaptive radiation in response to ecological opportunity. However, a number of factors may limit convergence during evolutionary radiations, including interregional differences in biogeographic history and clade-specific constraints on form and function. Here, we demonstrate that a single clade of terrestrial snakes from Australia--the oxyuranine elapids--exhibits widespread morphological convergence with a phylogenetically diverse and distantly related assemblage of snakes from North America. Australian elapids have evolved nearly the full spectrum of phenotypic modalities that occurs among North American snakes. Much of the convergence appears to involve the recurrent evolution of stereotyped morphologies associated with foraging mode, locomotion and habitat use. By contrast, analysis of snake diets indicates striking divergence in feeding ecology between these faunas, partially reflecting regional differences in ecological allometry between Australia and North America. Widespread phenotypic convergence with the North American snake fauna coupled with divergence in feeding ecology are clear examples of how independent continental radiations may converge along some ecological axes yet differ profoundly along others. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  10. Ecological explanations to island gigantism: dietary niche divergence, predation, and size in an endemic lizard.

    Science.gov (United States)

    Runemark, Anna; Sagonas, Kostas; Svensson, Erik I

    2015-08-01

    Although rapid evolution of body size on islands has long been known, the ecological mechanisms behind this island phenomenon remain poorly understood. Diet is an important selective pressure for morphological divergence. Here we investigate if selection for novel diets has contributed to the multiple independent cases of island gigantism in the Skyros wall lizard (Podarcis gaigeae) and if diet, predation, or both factors best explain island gigantism. We combined data on body size, shape, bite force, and realized and available diets to address this. Several lines of evidence suggest that diet has contributed to the island gigantism. The larger islet lizards have relatively wider heads and higher bite performance in relation to mainland lizards than would be expected from size differences alone. The proportions of consumed and available hard prey are higher on islets than mainland localities, and lizard body size is significantly correlated with the proportion of hard prey. Furthermore, the main axis of divergence in head shape is significantly correlated with dietary divergence. Finally, a model with only diet and one including diet and predation regime explain body size divergence equally well. Our results suggest that diet is an important ecological factor behind insular body size divergence, but could be consistent with an additional role for predation.

  11. Thrust characteristics of a series of convergent-divergent exhaust nozzles at subsonic and supersonic flight speeds

    Science.gov (United States)

    Fradenburgh, Evan A; Gorton, Gerald C; Beke, Andrew

    1954-01-01

    An experimental investigation of a series of four convergent-divergent exhaust nozzles was conducted in the Lewis 8-by-6 foot supersonic wind tunnel at Mach numbers of 0.1, 0.6, 1.6, and 2.0 over a range of nozzle pressure ratios. The thrust characteristics of these nozzles were determined by a pressure-integration technique. From a thrust standpoint, a nozzle designed to give uniform parallel flow at the exit had no advantage over the simple geometric design with conical convergent and divergent sections. The rapid-divergent nozzles might be competitive with the more gradual-divergent nozzles since the relatively short length of these nozzles would be advantageous from a weight standpoint and might result in smaller thrust losses due to friction. The thrusts, with friction losses neglected, were predicted satisfactorily by one-dimensional theory for the nozzles with relatively gradual divergence. The thrusts of the rapid-divergent designs were several percentages below the theoretical values at the design pressure ratio or above, while at low pressure ratios there was a considerable effect of free-stream Mach number, with thrusts considerably above theoretical values at subsonic speeds and somewhat above theoretical values at supersonic speeds. This Mach numb effect appeared to be related to the variation of the model base pressure with free-stream Mach number.

  12. Cancellation of soft and collinear divergences in noncommutative QED

    International Nuclear Information System (INIS)

    Mirza, B.; Zarei, M.

    2006-01-01

    In this paper, we investigate the behavior of noncommutative IR divergences and will also discuss their cancellation in the physical cross sections. The commutative IR (soft) divergences existing in the nonplanar diagrams will be examined in order to prove an all-order cancellation of these divergences using the Weinberg's method. In noncommutative QED, collinear divergences due to triple photon splitting vertex, were encountered, which are shown to be canceled out by the noncommutative version of KLN theorem. This guarantees that there is no mixing between the Collinear, soft divergences and noncommutative IR divergences

  13. Phenotypic Approaches to Drought in Cassava: Review

    Directory of Open Access Journals (Sweden)

    Emmanuel eOkogbenin

    2013-05-01

    Full Text Available Cassava is an important crop in Africa, Asia, Latin America and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12 - 18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance

  14. Environmental change, phenotypic plasticity, and genetic compensation.

    Science.gov (United States)

    Grether, Gregory F

    2005-10-01

    When a species encounters novel environmental conditions, some phenotypic characters may develop differently than in the ancestral environment. Most environmental perturbations of development are likely to reduce fitness, and thus selection would usually be expected to favor genetic changes that restore the ancestral phenotype. I propose the term "genetic compensation" to refer to this form of adaptive evolution. Genetic compensation is a subset of genetic accommodation and the reverse of genetic assimilation. When genetic compensation has occurred along a spatial environmental gradient, the mean trait values of populations in different environments may be more similar in the field than when representatives of the same populations are raised in a common environment (i.e., countergradient variation). If compensation is complete, genetic divergence between populations may be cryptic, that is, not detectable in the field. Here I apply the concept of genetic compensation to three examples involving carotenoid-based sexual coloration and then use these and other examples to discuss the concept in a broader context. I show that genetic compensation may lead to a cryptic form of reproductive isolation between populations evolving in different environments, may explain some puzzling cases in which heritable traits exposed to strong directional selection fail to show the expected evolutionary response, and may complicate efforts to monitor populations for signs of environmental deterioration.

  15. Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis.

    Science.gov (United States)

    Lee, Jessica J Y; Gottlieb, Michael M; Lever, Jake; Jones, Steven J M; Blau, Nenad; van Karnebeek, Clara D M; Wasserman, Wyeth W

    2018-05-01

    Phenomics is the comprehensive study of phenotypes at every level of biology: from metabolites to organisms. With high throughput technologies increasing the scope of biological discoveries, the field of phenomics has been developing rapid and precise methods to collect, catalog, and analyze phenotypes. Such methods have allowed phenotypic data to be widely used in medical applications, from assisting clinical diagnoses to prioritizing genomic diagnoses. To channel the benefits of phenomics into the field of inborn errors of metabolism (IEM), we have recently launched IEMbase, an expert-curated knowledgebase of IEM and their disease-characterizing phenotypes. While our efforts with IEMbase have realized benefits, taking full advantage of phenomics requires a comprehensive curation of IEM phenotypes in core phenomics projects, which is dependent upon contributions from the IEM clinical and research community. Here, we assess the inclusion of IEM biochemical phenotypes in a core phenomics project, the Human Phenotype Ontology. We then demonstrate the utility of biochemical phenotypes using a text-based phenomics method to predict gene-disease relationships, showing that the prediction of IEM genes is significantly better using biochemical rather than clinical profiles. The findings herein provide a motivating goal for the IEM community to expand the computationally accessible descriptions of biochemical phenotypes associated with IEM in phenomics resources.

  16. Evolutionary divergence in sexual signals: Insights from within and among barn swallow populations

    Science.gov (United States)

    Wilkins, Matthew Reed

    A wealth of studies across diverse animal groups indicate the importance of sexual selection in shaping phenotypes within and across breeding populations. In recent decades, much research has focused on how divergent sexual selection pressures among populations may lead to speciation. For my first dissertation chapter, I performed a literature review on the causes and consequences of evolutionary divergence in acoustic signals and developed the acoustic window conceptual framework for understanding the contributions of selection, genetic drift, and evolutionary constraint to signal divergence. Further, I found that sexual selection explains acoustic differences between recently diverged populations of the best-studied taxa. However, the relative contributions of ecological selection, sexual selection, and drift to acoustic divergence have not typically been considered within the same study systems. The remainder of my dissertation used the Northern Hemisphere-distributed barn swallow ( Hirundo rustica) species complex as a model system to study sender-receiver dynamics, intra- and intersexual selection pressures, and visual and acoustic signal interactions at the local scale, and signal divergence across populations at the global scale. From song recordings taken across 19 sampling sites, spanning five of six described subspecies, I demonstrated considerable conservation in song structure. However, temporal traits were highly divergent across subspecies, and in particular, the speed of the terminal trill of songs. In a detailed study of the multimodal communication system of the barn swallow (including visual and acoustic traits), I demonstrated that males and females use different types of signals to mediate competition and mate choice. One of the only exceptions to this rule was trill rate, which was also implicated in song divergence across populations. In order to test the function of trill rate in communication, I performed a two-year playback study within the

  17. Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system, Lake Mývatn, Iceland.

    Science.gov (United States)

    Millet, Antoine; Kristjánsson, Bjarni K; Einarsson, Arni; Räsänen, Katja

    2013-09-01

    Eco-evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments - favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow.

  18. A phenome database (NEAUHLFPD) designed and constructed for broiler lines divergently selected for abdominal fat content.

    Science.gov (United States)

    Li, Min; Dong, Xiang-yu; Liang, Hao; Leng, Li; Zhang, Hui; Wang, Shou-zhi; Li, Hui; Du, Zhi-Qiang

    2017-05-20

    Effective management and analysis of precisely recorded phenotypic traits are important components of the selection and breeding of superior livestocks. Over two decades, we divergently selected chicken lines for abdominal fat content at Northeast Agricultural University (Northeast Agricultural University High and Low Fat, NEAUHLF), and collected large volume of phenotypic data related to the investigation on molecular genetic basis of adipose tissue deposition in broilers. To effectively and systematically store, manage and analyze phenotypic data, we built the NEAUHLF Phenome Database (NEAUHLFPD). NEAUHLFPD included the following phenotypic records: pedigree (generations 1-19) and 29 phenotypes, such as body sizes and weights, carcass traits and their corresponding rates. The design and construction strategy of NEAUHLFPD were executed as follows: (1) Framework design. We used Apache as our web server, MySQL and Navicat as database management tools, and PHP as the HTML-embedded language to create dynamic interactive website. (2) Structural components. On the main interface, detailed introduction on the composition, function, and the index buttons of the basic structure of the database could be found. The functional modules of NEAUHLFPD had two main components: the first module referred to the physical storage space for phenotypic data, in which functional manipulation on data can be realized, such as data indexing, filtering, range-setting, searching, etc.; the second module related to the calculation of basic descriptive statistics, where data filtered from the database can be used for the computation of basic statistical parameters and the simultaneous conditional sorting. NEAUHLFPD could be used to effectively store and manage not only phenotypic, but also genotypic and genomics data, which can facilitate further investigation on the molecular genetic basis of chicken adipose tissue growth and development, and expedite the selection and breeding of broilers

  19. Endemic infrared divergences in QED3 at finite temperature

    International Nuclear Information System (INIS)

    Lo, Pok Man; Swanson, Eric S.

    2011-01-01

    We demonstrate that massless QED in three dimensions contains endemic infrared divergences. It is argued that these divergences do not affect observables; furthermore, it is possible to choose a gauge that renders the theory finite.

  20. Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms.

    Science.gov (United States)

    Rokyta, Darin R; Margres, Mark J; Calvin, Kate

    2015-09-09

    Protein expression is a major link in the genotype-phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms. Copyright © 2015 Rokyta et al.

  1. Divergent Geophysical Evolution of Vesta and Ceres

    Science.gov (United States)

    Raymond, C. A.; Ermakov, A.; Castillo, J. C.; Fu, R. R.; McSween, H. Y., Jr.; McCord, T. B.; Park, R. S.; Russell, C. T.; De Sanctis, M. C.; Jaumann, R.; Konopliv, A. S.

    2017-12-01

    The Dawn mission explored two massive protoplanets in the main asteroid belt, Vesta and Ceres, that are fossils from the earliest epoch of solar system formation. Dawn's data provide evidence that these bodies formed very early, within the first few million years after CAIs, yet they followed divergent evolutionary paths. Vesta formed globally homogeneous distribution of minerals across the surface indicates that Ceres' interior experienced pervasive alteration. Topography and morphology of the surface reveals smoother, apparently resurfaced areas, generally at lower elevation, and rougher areas with greater relief. Local morphology such as crater floor deposits, isolated mountains, and enigmatic bright areas indicate recently active processes on Ceres, likely driven by brine cryovolcanism. Causes of the divergent evolution of these bodies include their accretionary environment, timing of accretion and size. Acknowledgements: Part of this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.

  2. PUBLIC INTEGRITY AND THE DIVERGENCE FROM IT

    Directory of Open Access Journals (Sweden)

    Simona‐Roxana ULMAN

    2013-12-01

    Full Text Available Public Integrity is one of the public sector’s essential objectives to attain. In contradiction, as a divergence from it, corruption is one of the persistent problems of the societies over years and it affects the credibility of public institutions and its ambassadors in front of the citizens and of the other related countries. All nations complain of corruption and, as it is observed in the Corruption Perception Index 2012, no country has a maximum score which shows that a country is totally clean. In this context, the study of the most important elements of the public integrity concept, the identification of what causes the divergence from it and the solutions detection become a relevant option for economic literature. In this context, the main objective of this paper is to emphasize the public integrity concept and its main aspects and to make a comparison between countries to achieve a large perspective of the world’s public integrity juncture.

  3. Flow over convergent and divergent wall riblets

    Energy Technology Data Exchange (ETDEWEB)

    Koeltzsch, K.; Dinkelacker, A.; Grundmann, R. [Institut fuer Luft- und Raumfahrttechnik, Technische Universitaet Dresden, 36460 Merkers (Germany)

    2002-08-01

    Fast swimming sharks have small riblets on their skin, which are assumed to improve the swimming performance of the fish. Fluid dynamic experiments in water as well as in air confirm this assumption. With riblet surfaces as compared to smooth surfaces, drag reductions up to about 10% were measured. The overall riblet pattern on sharks shows parallel riblets directed from head to tail, but besides this overall pattern fast swimming sharks have also small areas with converging riblets and others with diverging riblets. In the present study the velocity field over convergent and divergent riblet patterns is investigated by hot-wire measurements in turbulent pipe flow. Significant changes in the near wall velocity field were found. (orig.)

  4. Gluon mass generation without seagull divergences

    International Nuclear Information System (INIS)

    Aguilar, Arlene C.; Papavassiliou, Joannis

    2010-01-01

    Dynamical gluon mass generation has been traditionally plagued with seagull divergences, and all regularization procedures proposed over the years yield finite but scheme-dependent gluon masses. In this work we show how such divergences can be eliminated completely by virtue of a characteristic identity, valid in dimensional regularization. The ability to trigger the aforementioned identity hinges crucially on the particular Ansatz employed for the three-gluon vertex entering into the Schwinger-Dyson equation governing the gluon propagator. The use of the appropriate three-gluon vertex brings about an additional advantage: one obtains two separate (but coupled) integral equations, one for the effective charge and one for the gluon mass. This system of integral equations has a unique solution, which unambiguously determines these two quantities. Most notably, the effective charge freezes in the infrared, and the gluon mass displays power-law running in the ultraviolet, in agreement with earlier considerations.

  5. Increasing interpersonal trust through divergent thinking

    Directory of Open Access Journals (Sweden)

    Roberta eSellaro

    2014-06-01

    Full Text Available Interpersonal trust is an essential ingredient of many social relationships but how stable is it actually, and how is it controlled? There is evidence that the degree of trust into others might be rather volatile and can be affected by manipulations like drawing attention to personal interdependence or independence. Here we investigated whether the degree of interpersonal trust can be biased by inducing either a more integrative or a more cognitive-control mode by means of a creativity task requiring divergent or convergent thinking, respectively. Participants then performed the Trust Game, which provides an index of interpersonal trust by assessing the money units one participant (the trustor transfers to another participant (the trustee. As expected, participants transferred significantly more money to the trustee after engaging in divergent thinking as compared to convergent thinking. This observation provides support for the idea that interpersonal trust is controlled by domain-general (i.e., not socially dedicated cognitive states.

  6. High temperature phase transitions without infrared divergences

    International Nuclear Information System (INIS)

    Tetradis, N.; Wetterich, C.

    1993-09-01

    The most commonly used method for the study of high temperature phase transitions is based on the perturbative evaluation of the temperature dependent effective potential. This method becomes unreliable in the case of a second order or weakly first order phase transition, due to the appearance of infrared divergences. These divergences can be controlled through the method of the effective average action which employs renormalization group ideas. We report on the study of the high temperature phase transition for the N-component φ 4 theory. A detailed quantitative picture of the second order phase transition is presented, including the critical exponents for the behaviour in the vicinity of the critical temperature. An independent check of the results is obtained in the large N limit, and contact with the perturbative approach is established through the study of the Schwinger-Dyson equations. (orig.)

  7. COMPARATIVE FINANCIAL STATEMENTS. CONVERGENCE VERSUS DIVERGENCE

    Directory of Open Access Journals (Sweden)

    Nicolae ECOBICI

    2010-09-01

    Full Text Available In this paper I compared the Romanian financial statements with the US GAAP financial statements in terms of two criteria: first the reference period and secondly the shape, structure and content of financial statements. Nowadays the two accounting systems, the French and Anglo-Saxon, tend to harmonize. I will present the convergences and the divergences between the financial statements of Romania, subject to OMFP 3055/2009, in parallel with the Anglo-Saxon accounting system.

  8. Divergent Effects of Dendritic Cells on Pancreatitis

    Science.gov (United States)

    2015-09-01

    role of dendritic cells in pancreatitis. Dendritic cells are professional antigen presenting cells which initiate innate and adaptive immune... Lymphoid -tissue-specific homing of bone- marrow-derived dendritic cells . Blood. 113:6638–6647. http://dx.doi .org/10.1182/blood-2009-02-204321 Dapito...Award Number: W81XWH-12-1-0313 TITLE: Divergent Effects of Dendritic Cells on Pancreatitis PRINCIPAL INVESTIGATOR: Dr. George Miller

  9. Initial States: IR and Collinear Divergences

    International Nuclear Information System (INIS)

    Lavelle, Martin; McMullan, David

    2007-01-01

    The standard approach to the infra-red problem is to use the Bloch-Nordsieck trick to handle soft divergences and the Lee-Nauenberg (LN) theorem for collinear singularities. We show that this is inconsistent in the presence of massless initial particles. Furthermore, we show that using the LN theorem with such initial states introduces a non-convergent infinite series of diagrams at any fixed order in perturbation theory

  10. Carnot efficiency at divergent power output

    Science.gov (United States)

    Polettini, Matteo; Esposito, Massimiliano

    2017-05-01

    The widely debated feasibility of thermodynamic machines achieving Carnot efficiency at finite power has been convincingly dismissed. Yet, the common wisdom that efficiency can only be optimal in the limit of infinitely slow processes overlooks the dual scenario of infinitely fast processes. We corroborate that efficient engines at divergent power output are not theoretically impossible, framing our claims within the theory of Stochastic Thermodynamics. We inspect the case of an electronic quantum dot coupled to three particle reservoirs to illustrate the physical rationale.

  11. Fast algorithms for computing phylogenetic divergence time.

    Science.gov (United States)

    Crosby, Ralph W; Williams, Tiffani L

    2017-12-06

    The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet scale well to studies with hundreds of taxa and thousands of DNA base pairs. For example a study of 349 primate taxa was estimated to require over 9 months of processing time. In this work, we present a new algorithm, AncestralAge, that significantly improves the performance of the divergence time process. As part of AncestralAge, we demonstrate a new method for the computation of phylogenetic likelihood and our experiments show a 90% improvement in likelihood computation time on the aforementioned dataset of 349 primates taxa with over 60,000 DNA base pairs. Additionally, we show that our new method for the computation of the Bayesian prior on node ages reduces the running time for this computation on the 349 taxa dataset by 99%. Through the use of these new algorithms we open up the ability to perform divergence time inference on large phylogenetic studies.

  12. Two families of astrophysical diverging lens models

    Science.gov (United States)

    Er, Xinzhong; Rogers, Adam

    2018-03-01

    In the standard gravitational lensing scenario, rays from a background source are bent in the direction of a foreground lensing mass distribution. Diverging lens behaviour produces deflections in the opposite sense to gravitational lensing, and is also of astrophysical interest. In fact, diverging lensing due to compact distributions of plasma has been proposed as an explanation for the extreme scattering events that produce frequency-dependent dimming of extragalactic radio sources, and may also be related to the refractive radio wave phenomena observed to affect the flux density of pulsars. In this work we study the behaviour of two families of astrophysical diverging lenses in the geometric optics limit, the power law, and the exponential plasma lenses. Generally, the members of these model families show distinct behaviour in terms of image formation and magnification, however the inclusion of a finite core for certain power-law lenses can produce a caustic and critical curve morphology that is similar to the well-studied Gaussian plasma lens. Both model families can produce dual radial critical curves, a novel distinction from the tangential distortion usually produced by gravitational (converging) lenses. The deflection angle and magnification of a plasma lens vary with the observational frequency, producing wavelength-dependent magnifications that alter the amplitudes and the shape of the light curves. Thus, multiwavelength observations can be used to physically constrain the distribution of the electron density in such lenses.

  13. New genes as drivers of phenotypic evolution

    Science.gov (United States)

    Chen, Sidi; Krinsky, Benjamin H.; Long, Manyuan

    2014-01-01

    During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution. PMID:23949544

  14. The direct Flow parametric Proof of Gauss' Divergence Theorem revisited

    DEFF Research Database (Denmark)

    Markvorsen, Steen

    The standard proof of the divergence theorem in undergraduate calculus courses covers the theorem for static domains between two graph surfaces. We show that within first year undergraduate curriculum, the flow proof of the dynamic version of the divergence theorem - which is usually considered...... we apply the key instrumental concepts and verify the various steps towards this alternative proof of the divergence theorem....

  15. Comparative genomics and repetitive sequence divergence in the species of diploid Nicotiana section Alatae.

    Science.gov (United States)

    Lim, K Yoong; Kovarik, Ales; Matyasek, Roman; Chase, Mark W; Knapp, Sandra; McCarthy, Elizabeth; Clarkson, James J; Leitch, Andrew R

    2006-12-01

    Combining phylogenetic reconstructions of species relationships with comparative genomic approaches is a powerful way to decipher evolutionary events associated with genome divergence. Here, we reconstruct the history of karyotype and tandem repeat evolution in species of diploid Nicotiana section Alatae. By analysis of plastid DNA, we resolved two clades with high bootstrap support, one containing N. alata, N. langsdorffii, N. forgetiana and N. bonariensis (called the n = 9 group) and another containing N. plumbaginifolia and N. longiflora (called the n = 10 group). Despite little plastid DNA sequence divergence, we observed, via fluorescent in situ hybridization, substantial chromosomal repatterning, including altered chromosome numbers, structure and distribution of repeats. Effort was focussed on 35S and 5S nuclear ribosomal DNA (rDNA) and the HRS60 satellite family of tandem repeats comprising the elements HRS60, NP3R and NP4R. We compared divergence of these repeats in diploids and polyploids of Nicotiana. There are dramatic shifts in the distribution of the satellite repeats and complete replacement of intergenic spacers (IGSs) of 35S rDNA associated with divergence of the species in section Alatae. We suggest that sequence homogenization has replaced HRS60 family repeats at sub-telomeric regions, but that this process may not occur, or occurs more slowly, when the repeats are found at intercalary locations. Sequence homogenization acts more rapidly (at least two orders of magnitude) on 35S rDNA than 5S rDNA and sub-telomeric satellite sequences. This rapid rate of divergence is analogous to that found in polyploid species, and is therefore, in plants, not only associated with polyploidy.

  16. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)

    DEFF Research Database (Denmark)

    Jacobsen, Magnus W.; Hansen, Michael Møller; Orlando, Ludovic

    2012-01-01

    colonized Denmark following the last glacial maximum, Bayesian Serial SimCoal analysis showed consistency with a scenario of long-term stability, resulting from a rapid initial sixfold population expansion. The findings illustrate the utility of mitogenome data for resolving recent intraspecific divergence...

  17. Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

    Directory of Open Access Journals (Sweden)

    Wang Xiao-Wei

    2012-10-01

    Full Text Available Abstract Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the transcriptomes of two invasive whiteflies species, Middle East Asia Minor 1 (MEAM1 and Mediterranean (MED, respectively. Results More than 16 million reads of 74 base pairs in length were obtained for the Asia II 3 species using the Illumina sequencing platform. These reads were assembled into 52,535 distinct sequences (mean size: 466 bp and 16,596 sequences were annotated with an E-value above 10-5. Protein family comparisons revealed obvious diversification among the transcriptomes of these species suggesting species-specific adaptations during whitefly evolution. On the contrary, substantial conservation of the whitefly transcriptomes was also evident, despite their differences. The overall divergence of coding sequences between the orthologous gene pairs of Asia II 3 and MEAM1 is 1.73%, which is comparable to the average divergence of Asia II 3 and MED transcriptomes (1.84% and much higher than that of MEAM1 and MED (0.83%. This is consistent with the previous phylogenetic analyses and crossing experiments suggesting these are distinct species. We also identified hundreds of highly diverged genes and compiled sequence identify data into gene functional groups and found the most divergent gene classes are Cytochrome P450, Glutathione metabolism and Oxidative phosphorylation. These results strongly suggest that the divergence of genes related to metabolism might be the driving force of the MEAM1 and Asia II 3 differentiation. We also analyzed single nucleotide polymorphisms within the orthologous gene pairs of indigenous and invasive whiteflies which are helpful for

  18. Variational divergence in wave scattering theory with Kirchhoffean trial functions

    Science.gov (United States)

    Bird, J. F.

    1986-01-01

    In a recent study of variational improvement of the Kirchhoff approximation for electromagnetic scattering by rough surfaces, a key ingredient in the variational principle was found to diverge for important configurations (e.g., backscatter) if the polarization had any vertical component. The cause and a cure of this divergence are discussed here. The divergence is demonstrated to occur for arbitrary perfectly conducting scatterers and its universal characterstics are determined, by means of a general divergence criterion that is derived. A variational cure for the divergence is prescribed, and it is tested successfully on a standard scattering model.

  19. No boundaries: genomes, organisms, and ecological interactions responsible for divergence and reproductive isolation.

    Science.gov (United States)

    Etges, William J

    2014-01-01

    Revealing the genetic basis of traits that cause reproductive isolation, particularly premating or sexual isolation, usually involves the same challenges as most attempts at genotype-phenotype mapping and so requires knowledge of how these traits are expressed in different individuals, populations, and environments, particularly under natural conditions. Genetic dissection of speciation phenotypes thus requires understanding of the internal and external contexts in which underlying genetic elements are expressed. Gene expression is a product of complex interacting factors internal and external to the organism including developmental programs, the genetic background including nuclear-cytotype interactions, epistatic relationships, interactions among individuals or social effects, stochasticity, and prevailing variation in ecological conditions. Understanding of genomic divergence associated with reproductive isolation will be facilitated by functional expression analysis of annotated genomes in organisms with well-studied evolutionary histories, phylogenetic affinities, and known patterns of ecological variation throughout their life cycles. I review progress and prospects for understanding the pervasive role of host plant use on genetic and phenotypic expression of reproductive isolating mechanisms in cactophilic Drosophila mojavensis and suggest how this system can be used as a model for revealing the genetic basis for species formation in organisms where speciation phenotypes are under the joint influences of genetic and environmental factors. © The American Genetic Association. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Neurogenomics and the role of a large mutational target on rapid behavioral change.

    Science.gov (United States)

    Stanley, Craig E; Kulathinal, Rob J

    2016-11-08

    Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage. However, unlike other rapidly evolving functional systems such as sperm-egg interactions and immune defense, the genetic basis of rapid behavioral change remains elusive. Here we propose that the rapid divergence and widespread novelty of innate and adaptive behavior is primarily a function of its genomic architecture. Specifically, we hypothesize that the broad diversity of behavioral phenotypes present at micro- and macroevolutionary scales is promoted by a disproportionately large mutational target of neurogenic genes. We present evidence that these large neuro-behavioral targets are significant and ubiquitous in animal genomes and suggest that behavior's novelty and rapid emergence are driven by a number of factors including more selection on a larger pool of variants, a greater role of phenotypic plasticity, and/or unique molecular features present in large genes. We briefly discuss the origins of these large neurogenic genes, as they relate to the remarkable diversity of metazoan behaviors, and highlight key consequences on both behavioral traits and neurogenic disease across, respectively, evolutionary and ontogenetic time scales. Current approaches to studying the genetic mechanisms underlying rapid phenotypic change primarily focus on identifying signatures of Darwinian selection in protein-coding regions. In contrast

  1. The Eurozone Dynamic Cohesion: Convergence or Divergence

    Directory of Open Access Journals (Sweden)

    Antonin Rusek

    2013-08-01

    Full Text Available The long term economic dynamics of the Eurozone’s original 12 countries (Greece, Italy, Spain, Portugal, Ireland, Germany, Netherlands, Luxembourg, Belgium, Austria, Finland, France is analyzed and compared. It is today increasingly recognized that the diverging competitiveness between the Eurozone members is at the root of the current crisis. But the competitiveness dynamics and its impact on the crucial fiscal and financial variables during the common currency existence is seldom analyzed and compared, especially as far as the different groups of countries (and/or different areas within the Eurozone are concerned.

  2. Diverging patterns with endogenous labor migration.

    Science.gov (United States)

    Reichlin, P; Rustichini, A

    1998-05-05

    "The standard neoclassical model cannot explain persistent migration flows and lack of cross-country convergence when capital and labor are mobile. Here we present a model where both phenomena may take place.... Our model is based on the Arrow-Romer approach to endogenous growth theory. We single out the importance of a (however weak) scale effect from the size of the workforce.... The main conclusion of this simple model is that lack of convergence, or even divergence, among countries is possible, even with perfect capital mobility and labor mobility." excerpt

  3. Projection Pursuit Through ϕ-Divergence Minimisation

    Directory of Open Access Journals (Sweden)

    Jacques Touboul

    2010-06-01

    Full Text Available In his 1985 article (“Projection pursuit”, Huber demonstrates the interest of his method to estimate a density from a data set in a simple given case. He considers the factorization of density through a Gaussian component and some residual density. Huber’s work is based on maximizing Kullback–Leibler divergence. Our proposal leads to a new algorithm. Furthermore, we will also consider the case when the density to be factorized is estimated from an i.i.d. sample. We will then propose a test for the factorization of the estimated density. Applications include a new test of fit pertaining to the elliptical copulas.

  4. Divergence-based tests for model diagnostic

    Czech Academy of Sciences Publication Activity Database

    Hobza, Tomáš; Esteban, M. D.; Morales, D.; Marhuenda, Y.

    2008-01-01

    Roč. 78, č. 13 (2008), s. 1702-1710 ISSN 0167-7152 R&D Projects: GA MŠk 1M0572 Grant - others:Instituto Nacional de Estadistica (ES) MTM2006-05693 Institutional research plan: CEZ:AV0Z10750506 Keywords : goodness of fit * devergence statistics * GLM * model checking * bootstrap Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.445, year: 2008 http://library.utia.cas.cz/separaty/2008/SI/hobza-divergence-based%20tests%20for%20model%20diagnostic.pdf

  5. Diverging expectations in buyer-seller relationships

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Christensen, Poul Rind; Damgaard, Torben

    2009-01-01

    Many firms assume that outsourcing partnerships may allow them to strengthen their overall competitiveness. Lured by its intuitive appeal, several enter into such partnerships, only to realize that they represent a marginal rather than a magical solution to their quest for increasing market...... SMEs. We discuss four relational expectations derived from the B2B literature on relational norms for addressing these divergences: Quality, frequency and scope of communication, role specifications and coordination of work nature of planning horizons, and trustworthiness and link these to relationship...

  6. Metabolic Rate and Climatic Fluctuations Shape Continental Wide Pattern of Genetic Divergence and Biodiversity in Fishes

    Science.gov (United States)

    April, Julien; Hanner, Robert H.; Mayden, Richard L.; Bernatchez, Louis

    2013-01-01

    Taxonomically exhaustive and continent wide patterns of genetic divergence within and between species have rarely been described and the underlying evolutionary causes shaping biodiversity distribution remain contentious. Here, we show that geographic patterns of intraspecific and interspecific genetic divergence among nearly all of the North American freshwater fish species (>750 species) support a dual role involving both the late Pliocene-Pleistocene climatic fluctuations and metabolic rate in determining latitudinal gradients of genetic divergence and very likely influencing speciation rates. Results indicate that the recurrent glacial cycles caused global reduction in intraspecific diversity, interspecific genetic divergence, and species richness at higher latitudes. At the opposite, longer geographic isolation, higher metabolic rate increasing substitution rate and possibly the rapid accumulation of genetic incompatibilities, led to an increasing biodiversity towards lower latitudes. This indicates that both intrinsic and extrinsic factors similarly affect micro and macro evolutionary processes shaping global patterns of biodiversity distribution. These results also indicate that factors favouring allopatric speciation are the main drivers underlying the diversification of North American freshwater fishes. PMID:23922969

  7. Cryptic lineage diversity, body size divergence, and sympatry in a species complex of Australian lizards (Gehyra).

    Science.gov (United States)

    Moritz, Craig C; Pratt, Renae C; Bank, Sarah; Bourke, Gayleen; Bragg, Jason G; Doughty, Paul; Keogh, J Scott; Laver, Rebecca J; Potter, Sally; Teasdale, Luisa C; Tedeschi, Leonardo G; Oliver, Paul M

    2018-01-01

    Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia-Gehyra nana and close relatives-we combine mtDNA phylogeography, exon-capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north-west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  8. Divergence in cryptic leaf colour provides local camouflage in an alpine plant.

    Science.gov (United States)

    Niu, Yang; Chen, Zhe; Stevens, Martin; Sun, Hang

    2017-10-11

    The efficacy of camouflage through background matching is highly environment-dependent, often resulting in intraspecific colour divergence in animals to optimize crypsis in different visual environments. This phenomenon is largely unexplored in plants, although several lines of evidence suggest they do use crypsis to avoid damage by herbivores. Using Corydalis hemidicentra, an alpine plant with cryptic leaf colour, we quantified background matching between leaves and surrounding rocks in five populations based on an approximate model of their butterfly enemy's colour perception. We also investigated the pigment basis of leaf colour variation and the association between feeding risk and camouflage efficacy. We show that plants exhibit remarkable colour divergence between populations, consistent with differences in rock appearances. Leaf colour varies because of a different quantitative combination of two basic pigments-chlorophyll and anthocyanin-plus different air spaces. As expected, leaf colours are better matched against their native backgrounds than against foreign ones in the eyes of the butterfly. Furthermore, improved crypsis tends to be associated with a higher level of feeding risk. These results suggest that divergent cryptic leaf colour may have evolved to optimize local camouflage in various visual environments, extending our understanding of colour evolution and intraspecific phenotype diversity in plants. © 2017 The Author(s).

  9. Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana.

    Science.gov (United States)

    Park, Briton; Rutter, Matthew T; Fenster, Charles B; Symonds, V Vaughan; Ungerer, Mark C; Townsend, Jeffrey P

    2017-08-01

    Mutations are crucial to evolution, providing the ultimate source of variation on which natural selection acts. Due to their key role, the distribution of mutational effects on quantitative traits is a key component to any inference regarding historical selection on phenotypic traits. In this paper, we expand on a previously developed test for selection that could be conducted assuming a Gaussian mutation effect distribution by developing approaches to also incorporate any of a family of heavy-tailed Laplace distributions of mutational effects. We apply the test to detect directional natural selection on five traits along the divergence of Columbia and Landsberg lineages of Arabidopsis thaliana , constituting the first test for natural selection in any organism using quantitative trait locus and mutation accumulation data to quantify the intensity of directional selection on a phenotypic trait. We demonstrate that the results of the test for selection can depend on the mutation effect distribution specified. Using the distributions exhibiting the best fit to mutation accumulation data, we infer that natural directional selection caused divergence in the rosette diameter and trichome density traits of the Columbia and Landsberg lineages. Copyright © 2017 by the Genetics Society of America.

  10. From metabolome to phenotype

    DEFF Research Database (Denmark)

    Khakimov, Bekzod; Rasmussen, Morten Arendt; Kannangara, Rubini Maya

    2017-01-01

    for ideal vegetable protein production and for augmented β-glucan production. Seeds from three barley lines (Bomi, lys3.a and lys5.f) were sampled eight times during grain filling and analysed for metabolites using gas chromatography-mass spectrometry (GC-MS). The lys3.a mutation disrupts a regulator gene...... their successful application to link genetic and environmental factors with the seed phenotype of unique and agro-economically important barley models for optimal vegetable protein and dietary fibre production......., causing an increase in proteins rich in the essential amino acid lysine, while lys5.f carries a mutation in an ADP-glucose transporter gene leading to a significant increase in production of mixed-linkage β-glucan at the expense of α-glucan. Unique metabolic patterns associated with the tricarboxylic acid...

  11. Deep Learning for Plant Phenotyping

    OpenAIRE

    Mori, Matteo

    2016-01-01

    Plant Phenotyping is an emerging science which provides us the knowledge to better understand plants. Indeed, the study of the link between genetic background and environment in which plants develop can help us to determine cures for plants’ sicknesses and new ways to improve yields using limited resources. In this regard, one of the main aspects of Plant Phenotyping that were studied in the past, was Root Phenotyping, which is based on the study of the root architectures. In particular, toda...

  12. Phenotype ontologies and cross-species analysis for translational research.

    Directory of Open Access Journals (Sweden)

    Peter N Robinson

    2014-04-01

    Full Text Available The use of model organisms as tools for the investigation of human genetic variation has significantly and rapidly advanced our understanding of the aetiologies underlying hereditary traits. However, while equivalences in the DNA sequence of two species may be readily inferred through evolutionary models, the identification of equivalence in the phenotypic consequences resulting from comparable genetic variation is far from straightforward, limiting the value of the modelling paradigm. In this review, we provide an overview of the emerging statistical and computational approaches to objectively identify phenotypic equivalence between human and model organisms with examples from the vertebrate models, mouse and zebrafish. Firstly, we discuss enrichment approaches, which deem the most frequent phenotype among the orthologues of a set of genes associated with a common human phenotype as the orthologous phenotype, or phenolog, in the model species. Secondly, we introduce and discuss computational reasoning approaches to identify phenotypic equivalences made possible through the development of intra- and interspecies ontologies. Finally, we consider the particular challenges involved in modelling neuropsychiatric disorders, which illustrate many of the remaining difficulties in developing comprehensive and unequivocal interspecies phenotype mappings.

  13. Integration of curated databases to identify genotype-phenotype associations

    Directory of Open Access Journals (Sweden)

    Li Jianrong

    2006-10-01

    Full Text Available Abstract Background The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on the molecules encoded by its genome. However, the link between molecular composition (i.e. genotype and phenotype for microbes is not obvious. While there have been several studies that address this challenge, none have yet proposed a large-scale method integrating curated biological information. Here we utilize a systematic approach to discover genotype-phenotype associations that combines phenotypic information from a biomedical informatics database, GIDEON, with the molecular information contained in National Center for Biotechnology Information's Clusters of Orthologous Groups database (NCBI COGs. Results Integrating the information in the two databases, we are able to correlate the presence or absence of a given protein in a microbe with its phenotype as measured by certain morphological characteristics or survival in a particular growth media. With a 0.8 correlation score threshold, 66% of the associations found were confirmed by the literature and at a 0.9 correlation threshold, 86% were positively verified. Conclusion Our results suggest possible phenotypic manifestations for proteins biochemically associated with sugar metabolism and electron transport. Moreover, we believe our approach can be extended to linking pathogenic phenotypes with functionally related proteins.

  14. Holstein-Friesian calves selected for divergence in residual feed intake during growth exhibited significant but reduced residual feed intake divergence in their first lactation.

    Science.gov (United States)

    Macdonald, K A; Pryce, J E; Spelman, R J; Davis, S R; Wales, W J; Waghorn, G C; Williams, Y J; Marett, L C; Hayes, B J

    2014-03-01

    Residual feed intake (RFI), as a measure of feed conversion during growth, was estimated for around 2,000 growing Holstein-Friesian heifer calves aged 6 to 9 mo in New Zealand and Australia, and individuals from the most and least efficient deciles (low and high RFI phenotypes) were retained. These animals (78 New Zealand cows, 105 Australian cows) were reevaluated during their first lactation to determine if divergence for RFI observed during growth was maintained during lactation. Mean daily body weight (BW) gain during assessment as calves had been 0.86 and 1.15 kg for the respective countries, and the divergence in RFI between most and least efficient deciles for growth was 21% (1.39 and 1.42 kg of dry matter, for New Zealand and Australia, respectively). At the commencement of evaluation during lactation, the cows were aged 26 to 29 mo. All were fed alfalfa and grass cubes; it was the sole diet in New Zealand, whereas 6 kg of crushed wheat/d was also fed in Australia. Measurements of RFI during lactation occurred for 34 to 37 d with measurements of milk production (daily), milk composition (2 to 3 times per week), BW and BW change (1 to 3 times per week), as well as body condition score (BCS). Daily milk production averaged 13.8 kg for New Zealand cows and 20.0 kg in Australia. No statistically significant differences were observed between calf RFI decile groups for dry matter intake, milk production, BW change, or BCS; however a significant difference was noted between groups for lactating RFI. Residual feed intake was about 3% lower for lactating cows identified as most efficient as growing calves, and no negative effects on production were observed. These results support the hypothesis that calves divergent for RFI during growth are also divergent for RFI when lactating. The causes for this reduced divergence need to be investigated to ensure that genetic selection programs based on low RFI (better efficiency) are robust. Copyright © 2014 American Dairy

  15. World health inequality: convergence, divergence, and development.

    Science.gov (United States)

    Clark, Rob

    2011-02-01

    Recent studies characterize the last half of the twentieth century as an era of cross-national health convergence, with some attributing welfare gains in the developing world to economic growth. In this study, I examine the extent to which welfare outcomes have actually converged and the extent to which economic development is responsible for the observed trends. Drawing from estimates covering 195 nations during the 1955-2005 period, I find that life expectancy averages converged during this time, but that infant mortality rates continuously diverged. I develop a narrative that implicates economic development in these contrasting trends, suggesting that health outcomes follow a "welfare Kuznets curve." Among poor countries, economic development improves life expectancy more than it reduces infant mortality, whereas the situation is reversed among wealthier nations. In this way, development has contributed to both convergence in life expectancy and divergence in infant mortality. Drawing from 674 observations across 163 countries during the 1980-2005 period, I find that the positive effect of GDP PC on life expectancy attenuates at higher levels of development, while the negative effect of GDP PC on infant mortality grows stronger. Copyright © 2010 Elsevier Ltd. All rights reserved.

  16. Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis

    NARCIS (Netherlands)

    Lee, Jessica J. Y.; Gottlieb, Michael M.; Lever, Jake; Jones, Steven J. M.; Blau, Nenad; van Karnebeek, Clara D. M.; Wasserman, Wyeth W.

    2018-01-01

    Phenomics is the comprehensive study of phenotypes at every level of biology: from metabolites to organisms. With high throughput technologies increasing the scope of biological discoveries, the field of phenomics has been developing rapid and precise methods to collect, catalog, and analyze

  17. Unexpected Functional Divergence of Bat Influenza Virus NS1 Proteins.

    Science.gov (United States)

    Turkington, Hannah L; Juozapaitis, Mindaugas; Tsolakos, Nikos; Corrales-Aguilar, Eugenia; Schwemmle, Martin; Hale, Benjamin G

    2018-03-01

    Recently, two influenza A virus (FLUAV) genomes were identified in Central and South American bats. These sequences exhibit notable divergence from classical FLUAV counterparts, and functionally, bat FLUAV glycoproteins lack canonical receptor binding and destroying activity. Nevertheless, other features that distinguish these viruses from classical FLUAVs have yet to be explored. Here, we studied the viral nonstructural protein NS1, a virulence factor that modulates host signaling to promote efficient propagation. Like all FLUAV NS1 proteins, bat FLUAV NS1s bind double-stranded RNA and act as interferon antagonists. Unexpectedly, we found that bat FLUAV NS1s are unique in being unable to bind host p85β, a regulatory subunit of the cellular metabolism-regulating enzyme, phosphoinositide 3-kinase (PI3K). Furthermore, neither bat FLUAV NS1 alone nor infection with a chimeric bat FLUAV efficiently activates Akt, a PI3K effector. Structure-guided mutagenesis revealed that the bat FLUAV NS1-p85β interaction can be reengineered (in a strain-specific manner) by changing two to four NS1 residues (96L, 99M, 100I, and 145T), thereby creating a hydrophobic patch. Notably, ameliorated p85β-binding is insufficient for bat FLUAV NS1 to activate PI3K, and a chimeric bat FLUAV expressing NS1 with engineered hydrophobic patch mutations exhibits cell-type-dependent, but species-independent, propagation phenotypes. We hypothesize that bat FLUAV hijacking of PI3K in the natural bat host has been selected against, perhaps because genes in this metabolic pathway were differentially shaped by evolution to suit the unique energy use strategies of this flying mammal. These data expand our understanding of the enigmatic functional divergence between bat FLUAVs and classical mammalian and avian FLUAVs. IMPORTANCE The potential for novel influenza A viruses to establish infections in humans from animals is a source of continuous concern due to possible severe outbreaks or pandemics. The

  18. Quantifying in situ phenotypic variability in the hydraulic properties of four tree species across their distribution range in Europe

    NARCIS (Netherlands)

    González-Muñoz, N.; Sterck, F.; Torres-Ruiz, J.M.; Petit, G.; Cochard, H.; Arx, von G.; Lintunen, A.; Caldeira, M.C.; Capdeville, G.; Copini, P.; Gebauer, R.; Grönlund, L.; Hölttä, T.; Lobo-do-Vale, R.; Peltoniemi, M.; Stritih, A.; Urban, J.; Delzon, S.

    2018-01-01

    Many studies have reported that hydraulic properties vary considerably between tree species, but little is known about their intraspecific variation and, therefore, their capacity to adapt to a warmer and drier climate. Here, we quantify phenotypic divergence and clinal variation for embolism

  19. Phenotypic differentiation of species from Aspergillus section Flavi on neutral red desiccated coconut agar

    DEFF Research Database (Denmark)

    Atanda, O. O.; Adetunji, M. C.; Ezekiel, C. N.

    2014-01-01

    In order to facilitate easy and rapid identification of aflatoxin-producing Aspergillus species, the phenotypic traits of Aspergillus section Flavi isolates were examined on neutral red desiccated coconut agar (NRDCA). Phenotype variations in colony morphology and the relationship between colour...

  20. Genetic architecture and phenotypic plasticity of thermally-regulated traits in an eruptive species, Dendroctonus ponderosae

    Science.gov (United States)

    Barbara J. Bentz; Ryan B. Bracewell; Karen E. Mock; Michael E. Pfrender

    2011-01-01

    Phenotypic plasticity in thermally-regulated traits enables close tracking of changing environmental conditions, and can thereby enhance the potential for rapid population increase, a hallmark of outbreak insect species. In a changing climate, exposure to conditions that exceed the capacity of existing phenotypic plasticity may occur. Combining information on genetic...

  1. Divergent thermal specialisation of two South African entomopathogenic nematodes

    Directory of Open Access Journals (Sweden)

    Matthew P. Hill

    2015-07-01

    Full Text Available Thermal physiology of entomopathogenic nematodes (EPN is a critical aspect of field performance and fitness. Thermal limits for survival and activity, and the ability of these limits to adjust (i.e., show phenotypic flexibility depending on recent thermal history, are generally poorly established, especially for non-model nematode species. Here we report the acute thermal limits for survival, and the thermal acclimation-related plasticity thereof for two key endemic South African EPN species, Steinernema yirgalemense and Heterorhabditis zealandica. Results including LT50 indicate S. yirgalemense (LT50 = 40.8 ± 0.3 °C has greater high temperature tolerance than H. zealandica (LT50 = 36.7 ± 0.2 °C, but S. yirgalemense (LT50 = −2.4 ± 0 °C has poorer low temperature tolerance in comparison to H. zealandica (LT50 = −9.7 ± 0.3 °C, suggesting these two EPN species occupy divergent thermal niches to one another.Acclimation had both negative and positive effects on temperature stress survival of both species, although the overall variation meant that many of these effects were non-significant. There was no indication of a consistent loss of plasticity with improved basal thermal tolerance for either species at upper lethal temperatures. At lower temperatures measured for H. zealandica, the 5 °C acclimation lowered survival until below −12.5 °C, where after it increased survival. Such results indicate that the thermal niche breadth of EPN species can differ significantly depending on recent thermal conditions, and should be characterized across a broad range of species to understand the evolution of thermal limits to performance and survival in this group.

  2. Divergent thermal specialisation of two South African entomopathogenic nematodes.

    Science.gov (United States)

    Hill, Matthew P; Malan, Antoinette P; Terblanche, John S

    2015-01-01

    Thermal physiology of entomopathogenic nematodes (EPN) is a critical aspect of field performance and fitness. Thermal limits for survival and activity, and the ability of these limits to adjust (i.e., show phenotypic flexibility) depending on recent thermal history, are generally poorly established, especially for non-model nematode species. Here we report the acute thermal limits for survival, and the thermal acclimation-related plasticity thereof for two key endemic South African EPN species, Steinernema yirgalemense and Heterorhabditis zealandica. Results including LT50 indicate S. yirgalemense (LT50 = 40.8 ± 0.3 °C) has greater high temperature tolerance than H. zealandica (LT50 = 36.7 ± 0.2 °C), but S. yirgalemense (LT50 = -2.4 ± 0 °C) has poorer low temperature tolerance in comparison to H. zealandica (LT50 = -9.7 ± 0.3 °C), suggesting these two EPN species occupy divergent thermal niches to one another. Acclimation had both negative and positive effects on temperature stress survival of both species, although the overall variation meant that many of these effects were non-significant. There was no indication of a consistent loss of plasticity with improved basal thermal tolerance for either species at upper lethal temperatures. At lower temperatures measured for H. zealandica, the 5 °C acclimation lowered survival until below -12.5 °C, where after it increased survival. Such results indicate that the thermal niche breadth of EPN species can differ significantly depending on recent thermal conditions, and should be characterized across a broad range of species to understand the evolution of thermal limits to performance and survival in this group.

  3. Genetic divergence through joint analysis of morphoagronomic and molecular characters in accessions of Jatropha curcas.

    Science.gov (United States)

    Pestana-Caldas, C N; Silva, S A; Machado, E L; de Souza, D R; Cerqueira-Pereira, E C; Silva, M S

    2016-10-05

    The aim of this study was to investigate the genetic divergence between accessions of Jatropha curcas through joint analysis of morphoagronomic and molecular characters. To this end, we investigated 11 morphoagronomic characters and performed molecular genotyping, using 23 inter-simple sequence repeat (ISSR) primers in 46 accessions of J. curcas. We calculated the contribution of each character on divergence using analysis of variance. The grouping among accessions was performed using the Ward-MLM (modified location model) method, using morphoagronomic and molecular data, whereas the cophenetic correlation was obtained based on Gower's algorithm. There were significant differences in all growth-related characteristics: number of primary and secondary branches per plant, plant height, and stem diameter. For characters related to grain production, differences were found for number of fruit clusters per plant and number of inflorescence clusters per plant and average number of seeds per fruit. The greatest phenotypic variation was found in plant height (59.67- 222.33 cm), whereas the smallest variation was found in average number of seeds per fruit (0-2.90), followed by the number of fruit clusters per plant (0-8.67). In total, 94 polymorphic ISSR fragments were obtained. The genotypic grouping identified six groups, indicating that there is genetic divergence among the accessions. The most promising crossings for future hybridization were identified among accessions UFRB60 and UFVJC45, and UFRB61 and UFVJC18. In conclusion, the joint analysis of morphoagronomic characters and ISSR markers is an efficient method to assess the genetic divergence in J. curcas.

  4. Floral and mating system divergence in secondary sympatry: testing an alternative hypothesis to reinforcement in Clarkia

    Science.gov (United States)

    Briscoe Runquist, Ryan D.; Moeller, David A.

    2014-01-01

    Background and Aims Reproductive character displacement (RCD) is often an important signature of reinforcement when partially cross-compatible taxa meet in secondary sympatry. In this study, floral evolution is examined during the Holocene range expansion of Clarkia xantiana subsp. parviflora from eastern Pleistocene refugia to a western zone of sympatry with its sister taxon, subsp. xantiana. Floral divergence between the two taxa is greater in sympatry than allopatry. The goal was to test an alternative hypothesis to reinforcement – that floral divergence of sympatric genotypes is simply a by-product of adaptation to pollination environments that differ between the allopatric and sympatric portions of the subspecies' range. Methods Floral trait data from two common garden studies were used to examine floral divergence between sympatric and allopatric regions and among phylogeographically defined lineages. In natural populations of C. x. parviflora, the magnitude of pollen limitation and reproductive assurance were quantified across its west-to-east range. Potted sympatric and allopatric genotypes were also reciprocally translocated between geographical regions to distinguish between the effects of floral phenotype versus contrasting pollinator environments on reproductive ecology. Key Results Sympatric populations are considerably smaller flowered with reduced herkogamy. Pollen limitation and the reproductive assurance value of selfing are greater in sympatric than in allopatric populations. Most significantly, reciprocal translocation experiments showed these differences in reproductive ecology cannot be attributed to contrasting pollinator environments between the sympatric and allopatric regions, but instead reflect the effects of flower size on pollinator attraction. Conclusions Floral evolution occurred during the westward range expansion of parviflora, particularly in the zone of sympatry with xantiana. No evidence was found that strongly reduced flower

  5. Floral and mating system divergence in secondary sympatry: testing an alternative hypothesis to reinforcement in Clarkia.

    Science.gov (United States)

    Briscoe Runquist, Ryan D; Moeller, David A

    2014-01-01

    Reproductive character displacement (RCD) is often an important signature of reinforcement when partially cross-compatible taxa meet in secondary sympatry. In this study, floral evolution is examined during the Holocene range expansion of Clarkia xantiana subsp. parviflora from eastern Pleistocene refugia to a western zone of sympatry with its sister taxon, subsp. xantiana. Floral divergence between the two taxa is greater in sympatry than allopatry. The goal was to test an alternative hypothesis to reinforcement - that floral divergence of sympatric genotypes is simply a by-product of adaptation to pollination environments that differ between the allopatric and sympatric portions of the subspecies' range. Floral trait data from two common garden studies were used to examine floral divergence between sympatric and allopatric regions and among phylogeographically defined lineages. In natural populations of C. x. parviflora, the magnitude of pollen limitation and reproductive assurance were quantified across its west-to-east range. Potted sympatric and allopatric genotypes were also reciprocally translocated between geographical regions to distinguish between the effects of floral phenotype versus contrasting pollinator environments on reproductive ecology. Sympatric populations are considerably smaller flowered with reduced herkogamy. Pollen limitation and the reproductive assurance value of selfing are greater in sympatric than in allopatric populations. Most significantly, reciprocal translocation experiments showed these differences in reproductive ecology cannot be attributed to contrasting pollinator environments between the sympatric and allopatric regions, but instead reflect the effects of flower size on pollinator attraction. Floral evolution occurred during the westward range expansion of parviflora, particularly in the zone of sympatry with xantiana. No evidence was found that strongly reduced flower size in sympatric parviflora (and RCD between

  6. Growth divergence: a challenging opportunity for dendrochronology

    Science.gov (United States)

    Buras, Allan; Sass-Klaassen, Ute; Wilmking, Martin

    2017-04-01

    Dendrochronology is an essential cornerstone of paleoclimatology and the evaluation of climate change impacts on forest ecosystems. However, a growing body of literature indicates that the standard dendrochronological approach may too rigorously neglect individualistic tree-growth (e.g. Wilmking et al., 2004, Buras et al., 2016). Amongst others, these studies showed convincing evidence that individual trees of the same species sampled at one site expressed different long-term growth patterns and therefore differing climate-growth relationships. This phenomenon is commonly termed growth divergence (GD) and possibly weakens our ability to correctly estimate past climate variability as discussed in the context of the so-called divergence phenomenon (D'Arrigo et al., 2008). In this context, climate change may naturally select for trees on the stand-level which are better adapted to future conditions. Although GD has been reported for several sites, the standard dendrochronological approach yet does not consider the existence of GD. A possible reason for this methodological persistence is the lack of detailed information on the frequency, magnitude, and impact of GD occurrence. To assess GD occurrence and related tree-individual variations in climate-growth response we conducted a global GD study by using 134 ring-width data representing 52 tree species and 16 genera distributed over 115 sites across 22 countries. Our analyses clearly reveal GD to be a common phenomenon as occurring in 85 % of all sites. GD was clearly related to the degree of tree-individual differences in climate-growth response. Respective transfer functions which appropriately accounted for GD by selection of tree-cohorts with a high share of long-term variance on average increased the precision and stability of tree-ring based climate reconstructions. Concluding, incorporation of GD assessments into the dendrochronological approach has a strong potential to improve the precision of our predictions

  7. Niche evolution and adaptive radiation: Testing the order of trait divergence

    Science.gov (United States)

    Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

    2006-01-01

    In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in

  8. A Separation between Divergence and Holevo Information for Ensembles

    OpenAIRE

    Jain, Rahul; Nayak, Ashwin; Su, Yi

    2007-01-01

    The notion of divergence information of an ensemble of probability distributions was introduced by Jain, Radhakrishnan, and Sen in the context of the ``substate theorem''. Since then, divergence has been recognized as a more natural measure of information in several situations in quantum and classical communication. We construct ensembles of probability distributions for which divergence information may be significantly smaller than the more standard Holevo information. As a result, we establ...

  9. Exact cancellation of quadratic divergences in top condensation models

    International Nuclear Information System (INIS)

    Blumhofer, A.

    1995-01-01

    We discuss the hierarchy problem and the corresponding quadratic divergences in the top mode Standard Model. Quadratic divergences appear at each order 1/N c since fermionic and bosonic contributions are of different order 1/N c . It is shown that the full dynamical system to all orders in 1/N c admits a solution, where the sum of all quadratic divergent contributions disappears. ((orig.))

  10. Plant Phenotype Characterization System

    Energy Technology Data Exchange (ETDEWEB)

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  11. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  12. Culturally divergent responses to mortality salience.

    Science.gov (United States)

    Ma-Kellams, Christine; Blascovich, Jim

    2011-08-01

    Two experiments compared the effects of death thoughts, or mortality salience, on European and Asian Americans. Research on terror management theory has demonstrated that in Western cultural groups, individuals typically employ self-protective strategies in the face of death-related thoughts. Given fundamental East-West differences in self-construal (i.e., the independent vs. interdependent self), we predicted that members of Eastern cultural groups would affirm other people, rather than defend and affirm the self, after encountering conditions of mortality salience. We primed European Americans and Asian Americans with either a death or a control prime and examined the effect of this manipulation on attitudes about a person who violates cultural norms (Study 1) and on attributions about the plight of an innocent victim (Study 2). Mortality salience promoted culturally divergent responses, leading European Americans to defend the self and Asian Americans to defend other people.

  13. Process model simulations of the divergence effect

    Science.gov (United States)

    Anchukaitis, K. J.; Evans, M. N.; D'Arrigo, R. D.; Smerdon, J. E.; Hughes, M. K.; Kaplan, A.; Vaganov, E. A.

    2007-12-01

    We explore the extent to which the Vaganov-Shashkin (VS) model of conifer tree-ring formation can explain evidence for changing relationships between climate and tree growth over recent decades. The VS model is driven by daily environmental forcing (temperature, soil moisture, and solar radiation), and simulates tree-ring growth cell-by-cell as a function of the most limiting environmental control. This simplified representation of tree physiology allows us to examine using a selection of case studies whether instances of divergence may be explained in terms of changes in limiting environmental dependencies or transient climate change. Identification of model-data differences permits further exploration of the effects of tree-ring standardization, atmospheric composition, and additional non-climatic factors.

  14. Hamiltonian mechanics and divergence-free fields

    International Nuclear Information System (INIS)

    Boozer, A.H.

    1986-08-01

    The field lines, or integral curves, of a divergence-free field in three dimensions are shown to be topologically equivalent to the trajectories of a Hamiltonian with two degrees of freedom. The consideration of fields that depend on a parameter allow the construction of a canonical perturbation theory which is valid even if the perturbation is large. If the parametric dependence of the magnetic, or the vorticity field is interpreted as time dependence, evolution equations are obtained which give Kelvin's theorem or the flux conservation theorem for ideal fluids and plasmas. The Hamiltonian methods prove especially useful for study of fields in which the field lines must be known throughout a volume of space

  15. Some Divergence Properties of Asset Price Models

    Directory of Open Access Journals (Sweden)

    Wolfgang Stummer

    2001-12-01

    Full Text Available Abstract: We consider asset price processes Xt which are weak solutions of one-dimensional stochastic differential equations of the form (equation (2 Such price models can be interpreted as non-lognormally-distributed generalizations of the geometric Brownian motion. We study properties of the Iα-divergence between the law of the solution Xt and the corresponding drift-less measure (the special case α=1 is the relative entropy. This will be applied to some context in statistical information theory as well as to arbitrage theory and contingent claim valuation. For instance, the seminal option pricing theorems of Black-Scholes and Merton appear as a special case.

  16. DIVERGING DISCOURSES ON THE SYR DARYA

    Directory of Open Access Journals (Sweden)

    Eelke Kraak

    2012-01-01

    Full Text Available The hydraulic mission of the Soviet Union has transformed Central Asia’s Syr Darya River into a governable entity. After the dissolution of the Soviet Union the river system disintegrated and conflict arose over the operation of the main dam and reservoir of the river: the Toktogul. Uzbekistan and Kyrgyzstan have widely different and diverging sanctioned discourses on how the dam should be operated and on the nature of the water itself. These discourses have had a significant impact on the hydro-politics of the river basin and the operation of the dam. The central argument of this paper is that both the decline of the Aral Sea, and the potential conflict between the states are driven by the same modernist governmentality of the river.

  17. Divergent clonal selection dominates medulloblastoma at recurrence

    Science.gov (United States)

    Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

    2016-01-01

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  18. A Δ11 desaturase gene genealogy reveals two divergent allelic classes within the European corn borer (Ostrinia nubilalis

    Directory of Open Access Journals (Sweden)

    Harrison Richard G

    2010-04-01

    Full Text Available Abstract Background Moth pheromone mating systems have been characterized at the molecular level, allowing evolutionary biologists to study how changes in protein sequence or gene expression affect pheromone phenotype, patterns of mating, and ultimately, the formation of barriers to gene exchange. Recent studies of Ostrinia pheromones have focused on the diversity of sex pheromone desaturases and their role in the specificity of pheromone production. Here we produce a Δ11 desaturase genealogy within Ostrinia nubilalis. We ask what has been the history of this gene, and whether this history suggests that changes in Δ11 desaturase have been involved in the divergence of the E and Z O. nubilalis pheromone strains. Results The Δ11 desaturase gene genealogy does not differentiate O. nubilalis pheromone strains. However, we find two distinct clades, separated by 2.9% sequence divergence, that do not sort with pheromone strain, geographic origin, or emergence time. We demonstrate that these clades do not represent gene duplicates, but rather allelic variation at a single gene locus. Conclusions Analyses of patterns of variation at the Δ11 desaturase gene in ECB suggest that this enzyme does not contribute to reproductive isolation between pheromone strains (E and Z. However, our genealogy reveals two deeply divergent allelic classes. Standing variation at loci that contribute to mate choice phenotypes may permit novel pheromone mating systems to arise in the presence of strong stabilizing selection.

  19. Meiotic Consequences of Genetic Divergence Across the Murine Pseudoautosomal Region.

    Science.gov (United States)

    Dumont, Beth L

    2017-03-01

    The production of haploid gametes during meiosis is dependent on the homology-driven processes of pairing, synapsis, and recombination. On the mammalian heterogametic sex chromosomes, these key meiotic activities are confined to the pseudoautosomal region (PAR), a short region of near-perfect sequence homology between the X and Y chromosomes. Despite its established importance for meiosis, the PAR is rapidly evolving, raising the question of how proper X / Y segregation is buffered against the accumulation of homology-disrupting mutations. Here, I investigate the interplay of PAR evolution and function in two interfertile house mouse subspecies characterized by structurally divergent PARs, Mus musculus domesticus and M. m. castaneus Using cytogenetic methods to visualize the sex chromosomes at meiosis, I show that intersubspecific F 1 hybrids harbor an increased frequency of pachytene spermatocytes with unsynapsed sex chromosomes. This high rate of asynapsis is due, in part, to the premature release of synaptic associations prior to completion of prophase I. Further, I show that when sex chromosomes do synapse in intersubspecific hybrids, recombination is reduced across the paired region. Together, these meiotic defects afflict ∼50% of spermatocytes from F 1 hybrids and lead to increased apoptosis in meiotically dividing cells. Despite flagrant disruption of the meiotic program, a subset of spermatocytes complete meiosis and intersubspecific F 1 males remain fertile. These findings cast light on the meiotic constraints that shape sex chromosome evolution and offer initial clues to resolve the paradox raised by the rapid evolution of this functionally significant locus. Copyright © 2017 by the Genetics Society of America.

  20. Neogene-dominated diversification in neotropical montane lichens: dating divergence events in the lichen-forming fungal genus Oropogon (Parmeliaceae).

    Science.gov (United States)

    Leavitt, Steven D; Esslinger, Theodore L; Lumbsch, H Thorsten

    2012-11-01

    Diversification in neotropical regions has been attributed to both Tertiary geological events and Pleistocene climatic fluctuations. However, the timing and processes driving speciation in these regions remain unexplored in many important groups. Here, we address the timing of diversification in the neotropical lichenized fungal genus Oropogon (Ascomycota) and assess traditional species boundaries. We analyzed sequence data from three loci to assess phenotypically circumscribed Oropogon species from the Oaxacan Highlands, Mexico. We provide a comparison of dated divergence estimates between concatenated gene trees and a calibrated multilocus species-tree using substitution rates for two DNA regions. We also compare estimates from a data set excluding ambiguously aligned regions and a data set including the hyper-variable regions in two ribosomal markers. Phylogenetic reconstructions were characterized by well-supported monophyletic clades corresponding to traditionally circumscribed species, with the exception of a single taxon. Divergence estimates indicate that most diversification of the sampled Oropogon species occurred throughout the Oligocene and Miocene, although diversification of a single closely related clade appears to have occurred during the late Pliocene and into the Pleistocene. Divergence estimates calculated from a data set with ambiguously aligned regions removed were much more recent than those from the full data set. Overall, our analyses place the majority of divergence events of Oropogon species from the Oaxacan Highlands within the Neogene and provide strong evidence that climatic changes during the Pleistocene were not a major factor driving speciation in the lichenized genus Oropogon in neotropical highlands.

  1. Phenotypic plasticity, costs of phenotypes, and costs of plasticity

    DEFF Research Database (Denmark)

    Callahan, Hilary S; Maughan, Heather; Steiner, Uli

    2008-01-01

    Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns...... of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both...... types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic...

  2. Recent rapid speciation and ecomorph divergence in Indo-Australian sea snakes. Molecular Evolution

    DEFF Research Database (Denmark)

    Sanders, Kate L.; Redsted Rasmussen, Arne; Mumpuni

    2013-01-01

    The viviparous sea snakes (Hydrophiinae) are a young radiation of at least 62 species that display spectacular morphological diversity and high levels of local sympatry. To shed light on the mechanisms underlying sea snake diversification, we investigated recent speciation and eco-morphological...

  3. Host imprints on bacterial genomes--rapid, divergent evolution in individual patients.

    Directory of Open Access Journals (Sweden)

    Jaroslaw Zdziarski

    Full Text Available Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.

  4. Deep Phenotyping: Deep Learning For Temporal Phenotype/Genotype Classification

    OpenAIRE

    Najafi, Mohammad; Namin, Sarah; Esmaeilzadeh, Mohammad; Brown, Tim; Borevitz, Justin

    2017-01-01

    High resolution and high throughput, genotype to phenotype studies in plants are underway to accelerate breeding of climate ready crops. Complex developmental phenotypes are observed by imaging a variety of accessions in different environment conditions, however extracting the genetically heritable traits is challenging. In the recent years, deep learning techniques and in particular Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs) and Long-Short Term Memories (LSTMs), h...

  5. Conformal anomaly and elimination of infrared divergences in curved spacetime

    International Nuclear Information System (INIS)

    Grib, A.A.; Nesteruk, A.V.; Pritomanov, S.A.

    1984-01-01

    The relation between the problem of eliminating the infrared divergences and the conformal anomaly of the regularized energy-momentum tensor is studied in homogeneous isotropic and anisotropic spacetime. It is shown that elimination of the infrared divergence by means of a cutoff or the introduction of a conformally invariant mass of the field leads to the absence of the conformal anomaly

  6. Performance analysis of alpha divergence in nonnegative matrix ...

    African Journals Online (AJOL)

    This is achieved by using a suitable cost function to determine the optimal factorization. Most work in this field has focused on the use of Euclidean and Kullback-Liebler (KL) divergence. This study looks into the use of α-divergence based non negative factorization in the context of single channel musical sound separation.

  7. Convergent and Divergent Thinking in the Context of Narrative Mysteries

    Science.gov (United States)

    Wenzel, William G.; Gerrig, Richard J.

    2015-01-01

    This project demonstrates how narrative mysteries provide a context in which readers engage in creative cognition. Drawing on the concepts of convergent and divergent thinking, we wrote stories that had either convergent or divergent outcomes. For example, one story had a character give his girlfriend a ring (a convergent outcome), whereas the…

  8. Transcriptome-wide patterns of divergence during allopatric evolution.

    Science.gov (United States)

    Pereira, Ricardo J; Barreto, Felipe S; Pierce, N Tessa; Carneiro, Miguel; Burton, Ronald S

    2016-04-01

    Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level. © 2016 John Wiley & Sons Ltd.

  9. Ultraviolet divergences in 1/N expansions of quantum field theories

    International Nuclear Information System (INIS)

    Rim, C.

    1984-01-01

    For asymptotically free theories, ultraviolet divergencies computed in 1/N expansion with dimensional regularization reduces to simple poles plus powers of Inelement of or finite terms. All divergences are determined by the two loop perturbative renormalization group functions. In an infrared free theory, however, element of = 0 becomes an essential singularity in the 1/N expansion

  10. Multiloop divergences in the closed bosonic string theory

    International Nuclear Information System (INIS)

    Gava, E.; Iengo, R.; Jayaraman, T.; Ramachandran, R.

    1985-12-01

    We discuss the structure of the divergences in the multiloop vacuum diagrams for the closed bosonic strings in the framework of the Polyakov covariant formalism. We find, by an explicit computation, that all the divergences in the theory may be interpreted as due to tadpole diagrams in which the dilation goes into the vacuum. (author)

  11. Evidence of multiple divergent mitochondrial lineages within the ...

    African Journals Online (AJOL)

    On this basis, the mitochondrial cytochrome c oxidase subunit 1 (COI) was used to reconstruct the phylogeny of Bicoxidens and reveal divergent lineages within the genus. Maximum likelihood and Bayesian inference analyses recovered a paraphyletic Bicoxidens phylogram with divergent lineages present in three species ...

  12. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae

    Directory of Open Access Journals (Sweden)

    Ober Karen A

    2010-08-01

    Full Text Available Abstract Background Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. Results According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Conclusions Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

  13. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae).

    Science.gov (United States)

    Ober, Karen A; Heider, Thomas N

    2010-08-27

    Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

  14. Vorticity and divergence in the high-latitude upper thermosphere

    International Nuclear Information System (INIS)

    Thayer, J.P.; Killeen, T.L.

    1991-01-01

    Measurements made from the Dynamics Explorer-2 satellite in November 1981 through January 1982 and November 1982 through January 1983 have been analyzed to determine the divergence and vertical component of vorticity of the high-latitude neutral wind field in the upper thermosphere for quiet (kp≤6) geomagnetic conditions and for both northern (winter) and southern (summer) hemispheres in the polar thermosphere and provides insight into the relative strengths of the different sources of momentum and energy responsible for driving the winds. The principal findings from this work include the following: The mean neutral wind pattern is dominated by rotational flow rather than by divergent flow, with a typical vorticity: divergence ratio of ∼ 2:1 for active conditions and ∼ 4:1 for quiet conditions. Comparison of the divergence and vorticity patterns for quiet and active conditions indicates that the divergent component of the neutral flow intensifies more significantly with increasing geomagnetic activity than does the rotational component

  15. Escort entropies and divergences and related canonical distribution

    International Nuclear Information System (INIS)

    Bercher, J.-F.

    2011-01-01

    We discuss two families of two-parameter entropies and divergences, derived from the standard Renyi and Tsallis entropies and divergences. These divergences and entropies are found as divergences or entropies of escort distributions. Exploiting the nonnegativity of the divergences, we derive the expression of the canonical distribution associated to the new entropies and a observable given as an escort-mean value. We show that this canonical distribution extends, and smoothly connects, the results obtained in nonextensive thermodynamics for the standard and generalized mean value constraints. -- Highlights: → Two-parameter entropies are derived from q-entropies and escort distributions. → The related canonical distribution is derived. → This connects and extends known results in nonextensive statistics.

  16. One-loop divergences in the quantum theory of supergravity

    International Nuclear Information System (INIS)

    Nieuwenhuizen, P. van; Vermaseren, J.A.M.

    1976-01-01

    Supergravity does not lead to a finite quantum theory of gravitation when coupled to the spin 1, 1/2 matter multiplet. The S-matrix of photon-photon scattering diverges; its divergences are proportional to the square of the photon energy-momentum tensor, in agreement with electro-magnetic duality and chiral invariance. The graviton self-energy corrections are divergent in pure supergravity as well as in the coupled Maxwell-Einstein system and satisfy their Ward identity because the supersymmetry ghost field is commuting. The photon-graviton vertex corrections diverge, as expected from the non-invariance of the action under local scale transformations, and satisfy the equivalence principle at the quantum level. The photon self-energy is divergent. (Auth.)

  17. Active learning for noisy oracle via density power divergence.

    Science.gov (United States)

    Sogawa, Yasuhiro; Ueno, Tsuyoshi; Kawahara, Yoshinobu; Washio, Takashi

    2013-10-01

    The accuracy of active learning is critically influenced by the existence of noisy labels given by a noisy oracle. In this paper, we propose a novel pool-based active learning framework through robust measures based on density power divergence. By minimizing density power divergence, such as β-divergence and γ-divergence, one can estimate the model accurately even under the existence of noisy labels within data. Accordingly, we develop query selecting measures for pool-based active learning using these divergences. In addition, we propose an evaluation scheme for these measures based on asymptotic statistical analyses, which enables us to perform active learning by evaluating an estimation error directly. Experiments with benchmark datasets and real-world image datasets show that our active learning scheme performs better than several baseline methods. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Experimental studies of adaptation in Clarkia xantiana. III. Phenotypic selection across a subspecies border.

    Science.gov (United States)

    Anderson, Jill T; Eckhart, Vincent M; Geber, Monica A

    2015-09-01

    Sister taxa with distinct phenotypes often occupy contrasting environments in parapatric ranges, yet we generally do not know whether trait divergence reflects spatially varying selection. We conducted a reciprocal transplant experiment to test whether selection favors "native phenotypes" in two subspecies of Clarkia xantiana (Onagraceae), an annual plant in California. For four quantitative traits that differ between subspecies, we estimated phenotypic selection in subspecies' exclusive ranges and their contact zone in two consecutive years. We predicted that in the arid, pollinator-scarce eastern region, selection favors phenotypes of the native subspecies parviflora: small leaves, slow leaf growth, early flowering, and diminutive flowers. In the wetter, pollinator-rich, western range of subspecies xantiana, we expected selection for opposite phenotypes. We investigated pollinator contributions to selection by comparing naturally pollinated and pollen-supplemented individuals. For reproductive traits and for subspecies xantiana, selection generally matched expectations. The contact zone sometimes showed distinctive selection, and in ssp. parviflora selection sometimes favored nonnative phenotypes. Pollinators influenced selection on flowering time but not on flower size. Little temporal variation in selection occurred, possibly because of plastic trait responses across years. Though there were exceptions and some causes of selection remain obscure, phenotypic differentiation between subspecies appears to reflect spatially variable selection. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  19. PHENOTYPIC CORRELATIONS AND BODY WEIGHTS ...

    African Journals Online (AJOL)

    Dr Osondu

    Ethiopian Journal of Environmental Studies and Management Vol. 4 No.3 2011. PHENOTYPIC ... because of its high meat quality and acceptance by her populace. The meat is ... commands high price in the restaurants and markets than other ...

  20. Macrophage reaction against biomaterials in the mouse model - Phenotypes, functions and markers.

    Science.gov (United States)

    Klopfleisch, R

    2016-10-01

    The foreign body reaction (FBR) is a response of the host tissue against more or less degradation-resistant foreign macromolecular material. The reaction is divided into five different phases which involve most aspects of the innate and the adaptive immune system: protein adsorption, acute and chronic inflammation, foreign body giant cell formation and fibrosis. It is long known, that macrophages play a central role in all of these phases except for protein adsorption. Initially it was believed that the macrophage driven FBR has a complete negative effect on biocompatibility. Recent progress in biomaterial and macrophage research however describe macrophages as more than pure antigen phagocytosing and presenting cells and thus pro-inflammatory cells involved in biomaterial encapsulation and failure. Quite contrary, both, pro-inflammatory M1 macrophages, the diverse regulatory M2 macrophage subtypes and even foreign body giant cells (FBGC) are after necessary for integration of non-degradable biomaterials and degradation and replacement of degradable biomaterials. This review gives a comprehensive overview on the taxonomy of the currently known macrophage subtypes. Their diverging functions, metabolism and markers are summarized and the relevance of this more diverse macrophage picture for the design of biomaterials is shortly discussed. The view on role of macrophages in the foreign body reaction against biomaterials is rapidly changing. Despite the initial idea that macrophage are mainly involved in undesired degradation and biomaterial rejection it becomes now clear that they are nevertheless necessary for proper integration of non-degradable biomaterials and degradation of placeholder, degradable biomaterials. As a pathologist I experienced a lack on a good summary on the current taxonomy, functions and phenotypes of macrophages in my recent projects on the biocompatibility of biomaterials in the mouse model. The submitted review therefore intends to gives a

  1. Divergent mortality trends by ethnicity in Fiji.

    Science.gov (United States)

    Taylor, Richard; Carter, Karen; Naidu, Shivnay; Linhart, Christine; Azim, Syed; Rao, Chalapati; Lopez, Alan D

    2013-12-01

    To examine trends in infant mortality rate (IMR), adult mortality and life expectancy (LE) in the two major Fijian ethnic groups since 1975. Estimates of IMR, adult mortality (15-59 years) and LE by ethnicity are calculated from previously unreported Fiji Ministry of Health data and extracted from published sources. Over 1975-2008: IMR decreased from 33 to 20 deaths/1,000 live births in i-Taukei (Fiji Melanesians); and 38 to 18 in Fijians of Indian descent. Increased adult male mortality among i-Taukei and decline among Fijians of Indian descent led to an equal probability of dying in 2007 of 29%; while in female adults the probability trended upwards in i-Taukei to 25%, and declined in Fijians of Indian descent to 17%. Life expectancy in both ethnicities increased until 1985 (to 64 years for males; 68 for females) then forming a plateau in males of both ethnicities, and Fijian females of Indian descent, but declining in i-Taukei females to 66 years in 2007. Despite IMR declines over 1975-2008, LE for i-Taukei and Fijians of Indian descent has not increased since 1985, and has actually decreased in i-Taukei women, consistent with trends in adult mortality (15-59 years). Mortality analyses in Fiji that consider the entire population mask divergent trends in the major ethnic groups. This situation is most likely a consequence of non-communicable disease mortality, requiring further assessment and a strengthened response.

  2. On the divergences of inflationary superhorizon perturbations

    Energy Technology Data Exchange (ETDEWEB)

    Enqvist, K; Nurmi, S [Physics Department, University of Helsinki, PO Box 64, Helsinki, FIN-00014 (Finland); Podolsky, D; Rigopoulos, G I, E-mail: kari.enqvist@helsinki.fi, E-mail: sami.nurmi@helsinki.fi, E-mail: dmitry.podolsky@helsinki.fi, E-mail: gerasimos.rigopoulos@helsinki.fi [Helsinki Institute of Physics, University of Helsinki, PO Box 64, Helsinki, FIN-00014 (Finland)

    2008-04-15

    We discuss the infrared divergences that appear to plague cosmological perturbation theory. We show that, within the stochastic framework, they are regulated by eternal inflation so that the theory predicts finite fluctuations. Using the {Delta}N formalism to one loop, we demonstrate that the infrared modes can be absorbed into additive constants and the coefficients of the diagrammatic expansion for the connected parts of two-and three-point functions of the curvature perturbation. As a result, the use of any infrared cutoff below the scale of eternal inflation is permitted, provided that the background fields are appropriately redefined. The natural choice for the infrared cutoff would, of course, be the present horizon; other choices manifest themselves in the running of the correlators. We also demonstrate that it is possible to define observables that are renormalization-group-invariant. As an example, we derive a non-perturbative, infrared finite and renormalization point-independent relation between the two-point correlators of the curvature perturbation for the case of the free single field.

  3. Remarkable ancient divergences amongst neglected lorisiform primates

    Science.gov (United States)

    Nekaris, K. Anne‐Isola; Perkin, Andrew; Bearder, Simon K.; Pimley, Elizabeth R.; Schulze, Helga; Streicher, Ulrike; Nadler, Tilo; Kitchener, Andrew; Zischler, Hans; Zinner, Dietmar; Roos, Christian

    2015-01-01

    Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub‐Saharan Africa and South/South‐East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ∼80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group. © 2015 The Linnean Society of London PMID:26900177

  4. Divergence and adaptive evolution of the gibberellin oxidase genes in plants.

    Science.gov (United States)

    Huang, Yuan; Wang, Xi; Ge, Song; Rao, Guang-Yuan

    2015-09-29

    The important phytohormone gibberellins (GAs) play key roles in various developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis pathway, but their classification, evolutionary history and the forces driving the evolution of plant GAox genes remain poorly understood. This study provides the first large-scale evolutionary analysis of GAox genes in plants by using an extensive whole-genome dataset of 41 species, representing green algae, bryophytes, pteridophyte, and seed plants. We defined eight subfamilies under the GAox family, namely C19-GA2ox, C20-GA2ox, GA20ox,GA3ox, GAox-A, GAox-B, GAox-C and GAox-D. Of these, subfamilies GAox-A, GAox-B, GAox-C and GAox-D are described for the first time. On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants. We also detected the subfamily-specific motifs and potential sites of some GAox genes, which might have evolved under positive selection. GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection. Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.

  5. Rapid shallow breathing

    Science.gov (United States)

    Tachypnea; Breathing - rapid and shallow; Fast shallow breathing; Respiratory rate - rapid and shallow ... Shallow, rapid breathing has many possible medical causes, including: Asthma Blood clot in an artery in the ...

  6. [Mexican phenotype and genotype Vibrio cholerae 01].

    Science.gov (United States)

    Giono, S; Gutiérrez Cogno, L; Rodríguez Angeles, G; del Rio Zolezzi, A; Valdespino González, J L; Sepúlveda Amor, J

    1995-01-01

    This paper presents the phenotypical and genotypical characterization of 26922 Vibrio cholerae 01 strains isolated in Mexico from 1991 to 1993. All strains isolated were El Tor biovar. Strains were sensitive to antibiotics excluding furazolidone, streptomycin and sulfisoxasole to which we found resistance in 97% and we are using this characteristic as epidemiological markers. We detected a marked change in frequency of Inaba serotype from 1991, when it was dominant, with 99.5%, until 1992 when Ogawa serotype turned to be dominant with 95% of isolates. All Vibrio cholerae 01 strains, except one Ogawa strain, were to igenic, and V. choleraeno 01 were not toxigenic by ELISA, PCR and cell culture tests. Dominant ribotype was 5, but we found some strains with 6a pattern and two with ribotype 12. We are searching for ribotype 2 among hemolytic strains in order to learn if there is any relation to Gulf Coast strains prevalent in the USA, but until now we have not found any V. cholerae ribotype 2 in our isolates. Even if rapid tests are recommended for immediate diagnosis of cholera, it is necessary to continue bacterial isolation in order to have strains for phenotyping and genotyping studies that may support epidemiological analysis.

  7. Jensen divergence based on Fisher’s information

    International Nuclear Information System (INIS)

    Sánchez-Moreno, P; Zarzo, A; Dehesa, J S

    2012-01-01

    The measure of Jensen–Fisher divergence between probability distributions is introduced and its theoretical grounds set up. This quantity, in contrast to the remaining Jensen divergences, grasps the fluctuations of the probability distributions because it is controlled by the (local) Fisher information, which is a gradient functional of the distribution. So it is appropriate and informative when studying the similarity of distributions, mainly for those having oscillatory character. The new Jensen–Fisher divergence shares with the Jensen–Shannon divergence the following properties: non-negativity, additivity when applied to an arbitrary number of probability densities, symmetry under exchange of these densities, vanishing under certain conditions and definiteness even when these densities present non-common zeros. Moreover, the Jensen–Fisher divergence is shown to be expressed in terms of the relative Fisher information as the Jensen–Shannon divergence does in terms of the Kullback–Leibler or relative Shannon entropy. Finally, the Jensen–Shannon and Jensen–Fisher divergences are compared for the following three large, non-trivial and qualitatively different families of probability distributions: the sinusoidal, generalized gamma-like and Rakhmanov–Hermite distributions, which are closely related to the quantum-mechanical probability densities of numerous physical systems. (paper)

  8. Total Bregman Divergence and its Applications to Shape Retrieval.

    Science.gov (United States)

    Liu, Meizhu; Vemuri, Baba C; Amari, Shun-Ichi; Nielsen, Frank

    2010-01-01

    Shape database search is ubiquitous in the world of biometric systems, CAD systems etc. Shape data in these domains is experiencing an explosive growth and usually requires search of whole shape databases to retrieve the best matches with accuracy and efficiency for a variety of tasks. In this paper, we present a novel divergence measure between any two given points in [Formula: see text] or two distribution functions. This divergence measures the orthogonal distance between the tangent to the convex function (used in the definition of the divergence) at one of its input arguments and its second argument. This is in contrast to the ordinate distance taken in the usual definition of the Bregman class of divergences [4]. We use this orthogonal distance to redefine the Bregman class of divergences and develop a new theory for estimating the center of a set of vectors as well as probability distribution functions. The new class of divergences are dubbed the total Bregman divergence (TBD). We present the l 1 -norm based TBD center that is dubbed the t-center which is then used as a cluster center of a class of shapes The t-center is weighted mean and this weight is small for noise and outliers. We present a shape retrieval scheme using TBD and the t-center for representing the classes of shapes from the MPEG-7 database and compare the results with other state-of-the-art methods in literature.

  9. Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems

    Science.gov (United States)

    Furman, Benjamin L S; Evans, Ben J

    2018-01-01

    Abstract There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions. PMID:29608717

  10. Ecological divergence and evolutionary transition of resprouting types in Banksia attenuata.

    Science.gov (United States)

    He, Tianhua

    2014-08-01

    Resprouting is a key functional trait that allows plants to survive diverse disturbances. The fitness benefits associated with resprouting include a rapid return to adult growth, early flowering, and setting seed. The resprouting responses observed following fire are varied, as are the ecological outcomes. Understanding the ecological divergence and evolutionary pathways of different resprouting types and how the environment and genetics interact to drive such morphological evolution represents an important, but under-studied, topic. In the present study, microsatellite markers and microevolutionary approaches were used to better understand: (1) whether genetic differentiation is related to morphological divergence among resprouting types and if so, whether there are any specific genetic variations associated with morphological divergence and (2) the evolutionary pathway of the transitions between two resprouting types in Banksia attenuata (epicormic resprouting from aerial stems or branch; resprouting from a underground lignotuber). The results revealed an association between population genetic differentiation and the morphological divergence of postfire resprouting types in B. attenuata. A microsatellite allele has been shown to be associated with epicormic populations. Approximate Bayesian Computation analysis revealed a likely evolutionary transition from epicormic to lignotuberous resprouting in B. attenuata. It is concluded that the postfire resprouting type in B. attenuata is likely determined by the fire's characteristics. The differentiated expression of postfire resprouting types in different environments is likely a consequence of local genetic adaptation. The capacity to shift the postfire resprouting type to adapt to diverse fire regimes is most likely the key factor explaining why B. attenuata is the most widespread member of the Banksia genus.

  11. Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

    Directory of Open Access Journals (Sweden)

    Julianne M O'Reilly-Wapstra

    Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

  12. Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence.

    Science.gov (United States)

    Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

    2017-08-16

    Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae). Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation. Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances. Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations. © 2017 Botanical Society of America.

  13. Childhood asthma-predictive phenotype.

    Science.gov (United States)

    Guilbert, Theresa W; Mauger, David T; Lemanske, Robert F

    2014-01-01

    Wheezing is a fairly common symptom in early childhood, but only some of these toddlers will experience continued wheezing symptoms in later childhood. The definition of the asthma-predictive phenotype is in children with frequent, recurrent wheezing in early life who have risk factors associated with the continuation of asthma symptoms in later life. Several asthma-predictive phenotypes were developed retrospectively based on large, longitudinal cohort studies; however, it can be difficult to differentiate these phenotypes clinically as the expression of symptoms, and risk factors can change with time. Genetic, environmental, developmental, and host factors and their interactions may contribute to the development, severity, and persistence of the asthma phenotype over time. Key characteristics that distinguish the childhood asthma-predictive phenotype include the following: male sex; a history of wheezing, with lower respiratory tract infections; history of parental asthma; history of atopic dermatitis; eosinophilia; early sensitization to food or aeroallergens; or lower lung function in early life. Copyright © 2014 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  14. Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence.

    Science.gov (United States)

    Turner, Barbara; Paun, Ovidiu; Munzinger, Jérôme; Chase, Mark W; Samuel, Rosabelle

    2016-06-01

    Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low. Here we evaluate the usefulness of these data types to resolve phylogenetic relationships among closely related Diospyros species. Twenty-two closely related Diospyros species from New Caledonia were investigated using whole plastid genomes and nrDNA data from low-coverage next-generation sequencing (NGS). Phylogenetic trees were inferred using maximum parsimony, maximum likelihood and Bayesian inference on separate plastid and nrDNA and combined matrices. The plastid and nrDNA sequences were, singly and together, unable to provide well supported phylogenetic relationships among the closely related New Caledonian Diospyros species. In the nrDNA, a 6-fold greater percentage of parsimony-informative characters compared with plastid DNA was found, but the total number of informative sites was greater for the much larger plastid DNA genomes. Combining the plastid and nuclear data improved resolution. Plastid results showed a trend towards geographical clustering of accessions rather than following taxonomic species. In plant groups in which multiple plastid markers are not sufficiently informative, an investigation at the level of the entire plastid genome may also not be sufficient for detailed phylogenetic reconstruction. Sequencing of complete plastid genomes and nrDNA repeats seems to clarify some relationships among the New Caledonian Diospyros species, but the higher percentage of parsimony-informative characters in nrDNA compared with plastid DNA did not help to resolve the phylogenetic tree

  15. Interspecific genetic divergence in grey mullets from the Goa region

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Martins, M.; Naik, S.

    Genetic divergence and phylogenetic relationships among Mugil cephalus, Liza subviridis and Valamugil cunnesius were investigated by examining the electrophoretic patterns of ten enzymes and sarcoplasmic proteins. Among the 19 loci detected, eight...

  16. Role of mantle flow in Nubia-Somalia plate divergence

    Science.gov (United States)

    Stamps, D. S.; Iaffaldano, G.; Calais, E.

    2015-01-01

    Present-day continental extension along the East African Rift System (EARS) has often been attributed to diverging sublithospheric mantle flow associated with the African Superplume. This implies a degree of viscous coupling between mantle and lithosphere that remains poorly constrained. Recent advances in estimating present-day opening rates along the EARS from geodesy offer an opportunity to address this issue with geodynamic modeling of the mantle-lithosphere system. Here we use numerical models of the global mantle-plates coupled system to test the role of present-day mantle flow in Nubia-Somalia plate divergence across the EARS. The scenario yielding the best fit to geodetic observations is one where torques associated with gradients of gravitational potential energy stored in the African highlands are resisted by weak continental faults and mantle basal drag. These results suggest that shear tractions from diverging mantle flow play a minor role in present-day Nubia-Somalia divergence.

  17. Diverging diamond interchange performance evaluation (I-44 and Route 13)

    Science.gov (United States)

    2011-02-01

    Performance evaluation was conducted on the first diverging diamond interchange (DDI) or double : crossover interchange (DCD) constructed in the United States. This evaluation assessed traffic operations, safety and : public perceptions t...

  18. A divergence theorem for pseudo-Finsler spaces

    OpenAIRE

    Minguzzi, E.

    2015-01-01

    We study the divergence theorem on pseudo-Finsler spaces and obtain a completely Finslerian version for spaces having a vanishing mean Cartan torsion. This result helps to clarify the problem of energy-momentum conservation in Finsler gravity theories.

  19. Stora's fine notion of divergent amplitudes

    International Nuclear Information System (INIS)

    Várilly, Joseph C.; Gracia-Bondía, José M.

    2016-01-01

    Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  20. Principal Curves for Statistical Divergences and an Application to Finance

    Directory of Open Access Journals (Sweden)

    Ana Flávia P. Rodrigues

    2018-05-01

    Full Text Available This paper proposes a method for the beta pricing model under the consideration of non-Gaussian returns by means of a generalization of the mean-variance model and the use of principal curves to define a divergence model for the optimization of the pricing model. We rely on the q-exponential model so consider the properties of the divergences which are used to describe the statistical model and fully characterize the behavior of the assets. We derive the minimum divergence portfolio, which generalizes the Markowitz’s (mean-divergence approach and relying on the information geometrical aspects of the distributions the Capital Asset Pricing Model (CAPM is then derived under the geometrical characterization of the distributions which model the data, all by the consideration of principal curves approach. We discuss the possibility of integration of our model into an adaptive procedure that can be used for the search of optimum points on finance applications.

  1. NATO Technology: From Gap to Divergence? (Defense Horizons, July 2004)

    National Research Council Canada - National Science Library

    Daniel, Donald

    2004-01-01

    .... Over several decades, great disparities in the funding of defense research and technology by NATO members has produced a widening technological gap that threatens to become a divergence a condition...

  2. Camouflage target detection via hyperspectral imaging plus information divergence measurement

    Science.gov (United States)

    Chen, Yuheng; Chen, Xinhua; Zhou, Jiankang; Ji, Yiqun; Shen, Weimin

    2016-01-01

    Target detection is one of most important applications in remote sensing. Nowadays accurate camouflage target distinction is often resorted to spectral imaging technique due to its high-resolution spectral/spatial information acquisition ability as well as plenty of data processing methods. In this paper, hyper-spectral imaging technique together with spectral information divergence measure method is used to solve camouflage target detection problem. A self-developed visual-band hyper-spectral imaging device is adopted to collect data cubes of certain experimental scene before spectral information divergences are worked out so as to discriminate target camouflage and anomaly. Full-band information divergences are measured to evaluate target detection effect visually and quantitatively. Information divergence measurement is proved to be a low-cost and effective tool for target detection task and can be further developed to other target detection applications beyond spectral imaging technique.

  3. Tumor progression: analysis of the instability of the metastatic phenotype, sensitivity to radiation and chemotherapy

    International Nuclear Information System (INIS)

    Welch, D.R.

    1984-01-01

    The major complications for tumor therapy are 1) tumor spread (metastasis); 2) the mixed nature of tumors (heterogeneity); and 3) the capacity of tumors to evolve (progress). To study these tumor characteristics, the rat 13762NF mammary adenocarcinoma was cloned and studied for metastatic properties and sensitivities to therapy (chemotherapy, radiation and hyperthermia). The cell clones were heterogeneous and no correlation between metastatic potential and therapeutic sensitivities was observed. Further, these phenotypes were unstable during pasage in vitro; yet, the changes were clone dependent and reproducible using different cryoprotected cell stocks. To understand the phenotypic instability, subclones were isolated from low and high passage cell clones. The results demonstrated that 1) tumor cells are heterogeneous for multiple phenotypes; 2) tumor cells are unstable for multiple phenotypes; 3) the magnitude, direction and time of occurrence of phenotypic drift is clone dependent; 4) the sensitivity of cell clones to ionizing radiation (γ or heat) and chemotherapy agents is independent of their metastatic potential; 5) shifts in metastatic potential and sensitivity to therapy may occur simultaneously but are not linked; and 6) tumor cells independently diverge to form several subpopulations with unique phenotypic profiles

  4. Impact of urothelial carcinoma with divergent differentiation on tumor stage

    Directory of Open Access Journals (Sweden)

    S Chalise

    2016-03-01

    Full Text Available Background: Urinary bladder cancer is classified as urothelial or non-urothelial. Ninenty percent of bladder cancer are urothelial and has propensity for divergent differentiation. Squamous differentiation is associated with unfavourable prognostic features. The aim of this study is to determine the significance of urothelial carcinoma with divergent differentiation in relation to tumor stage and lymphovascular as well as perineural invasion in radical cystectomy and partial cystectomy specimen.Materials and methods: This prospective study was done among 51 patients who underwent radical cystectomy or partial cystectomy at Bhaktapur Cancer Hospital from 1st August 2013 to 31st December 2015. Received specimen was grossed following standard protocol and histopathological evaluation was done in relation to tumor type, depth of invasion, Lymphovascular and perineural invasion.Results: Pure urothelial carcinoma comprises 47.1% of cases. Among the divergent differentiation, urothelial carcinoma with squamous differentiation was the commonest one (39.2% followed by glandular differentiation (5.9%, sarcomatoid differentiation (3.9%, clear cell variant (2.0% and squamous along with sarcomatoid variant (2.0%. Statistical significant correlation was found between urothelial carcinoma with divergent differentiation and tumor stage (p<0.012. Statistically significant correlation was also found between urothelial carcinoma with divergent differentiation and lymphovascular invasion (p=0.012 as well as perineural invasion (p=0.037.Conclusion:  Most common divergent differentiation was squamous differentiation. Urothelial carcinoma with divergent differentiation was associated with higher stage and lymphovascular as well as perineural invasion. So it is mandatory to search for the divergent differentiation in urothelial carcinoma as this may be associated with unfavourable prognosis.

  5. The direct Flow parametric Proof of Gauss' Divergence Theorem revisited

    OpenAIRE

    Markvorsen, Steen

    2006-01-01

    The standard proof of the divergence theorem in undergraduate calculus courses covers the theorem for static domains between two graph surfaces. We show that within first year undergraduate curriculum, the flow proof of the dynamic version of the divergence theorem - which is usually considered only much later in more advanced math courses - is comprehensible with only a little extension of the first year curriculum. Moreover, it is more intuitive than the static proof. We support this intuit...

  6. Dimensional regularization and infrared divergences in quantum electrodynamics

    International Nuclear Information System (INIS)

    Marculescu, S.

    1979-01-01

    Dimensional continuation was devised as a powerful regularization method for ultraviolet divergences in quantum field theories. Recently it was clear, at least for quantum electrodynamics, that such a method could be employed for factorizing out infrared divergences from the on-shell S-matrix elements. This provides a renormalization scheme on the electron mass-shell without using a gauge violating ''photon mass''. (author)

  7. Diverging Trade Strategies in Latin America: An Analytical Framework

    OpenAIRE

    Aggarwal, Vinod K.; Espach, Ralph H.

    2003-01-01

    Although there is increasing divergence among the trade policies of various Latin American nations, overall the last twenty years have seen a dramatic shift away from protectionism towards liberalization. Focusing on case studies of four Latin American nations — Brazil, Mexico, Chile and Argentina — the authors use an analytical framework to explain the rationales behind divergent policies. The analytical approach used considers the combination of economic, political and strategic objectives ...

  8. Robust bounds on risk-sensitive functionals via Renyi divergence

    OpenAIRE

    Atar, Rami; Chowdhary, Kamaljit; Dupuis, Paul

    2013-01-01

    We extend the duality between exponential integrals and relative entropy to a variational formula for exponential integrals involving the Renyi divergence. This formula characterizes the dependence of risk-sensitive functionals and related quantities determined by tail behavior to perturbations in the underlying distributions, in terms of the Renyi divergence. The characterization gives rise to upper and lower bounds that are meaningful for all values of a large deviation scaling parameter, a...

  9. Neural Mechanisms of Episodic Retrieval Support Divergent Creative Thinking.

    Science.gov (United States)

    Madore, Kevin P; Thakral, Preston P; Beaty, Roger E; Addis, Donna Rose; Schacter, Daniel L

    2017-11-17

    Prior research has indicated that brain regions and networks that support semantic memory, top-down and bottom-up attention, and cognitive control are all involved in divergent creative thinking. Kernels of evidence suggest that neural processes supporting episodic memory-the retrieval of particular elements of prior experiences-may also be involved in divergent thinking, but such processes have typically been characterized as not very relevant for, or even a hindrance to, creative output. In the present study, we combine functional magnetic resonance imaging with an experimental manipulation to test formally, for the first time, episodic memory's involvement in divergent thinking. Following a manipulation that facilitates detailed episodic retrieval, we observed greater neural activity in the hippocampus and stronger connectivity between a core brain network linked to episodic processing and a frontoparietal brain network linked to cognitive control during divergent thinking relative to an object association control task that requires little divergent thinking. Stronger coupling following the retrieval manipulation extended to a subsequent resting-state scan. Neural effects of the episodic manipulation were consistent with behavioral effects of enhanced idea production on divergent thinking but not object association. The results indicate that conceptual frameworks should accommodate the idea that episodic retrieval can function as a component process of creative idea generation, and highlight how the brain flexibly utilizes the retrieval of episodic details for tasks beyond simple remembering. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone.

    Science.gov (United States)

    Cooke, Georgina M; Landguth, Erin L; Beheregaray, Luciano B

    2014-07-01

    Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual-based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  11. The hidden function of egg white antimicrobials: egg weight-dependent effects of avidin on avian embryo survival and hatchling phenotype

    Czech Academy of Sciences Publication Activity Database

    Krkavcová, E.; Kreisinger, J.; Hyánková, L.; Hyršl, P.; Javůrková, Veronika

    2018-01-01

    Roč. 7, č. 4 (2018), č. článku bio031518. ISSN 2046-6390 Keywords : biotin deficiency affects * growth-performance * binding protein * intraspecific variation * maternal testosterone * divergent selection * offspring phenotype * immune function * chi cken-embryo * precocial bird * Albumen * maternal effects * antimicrobials * Avidin-biotin complex * embryogenesis * plasma complement Impact factor: 2.095, year: 2016

  12. Divergent immunological responses following glutaraldehyde exposure

    International Nuclear Information System (INIS)

    Azadi, Shahla; Klink, Kimberly J.; Meade, B. Jean

    2004-01-01

    Although Glutaraldehyde (Glut) has been demonstrated to be a moderate contact sensitizer, numerous cases of occupational asthma related to Glut exposure have been reported. The purpose of these studies was to examine the dose-response relationship between Glut exposure and the development of T cell-mediated vs. IgE- mediated responses. Initial evaluation of the sensitization potential was conducted using the local lymph node assay (LLNA) at concentrations ranging from 0.75% to 2.5%. A concentration-dependent increase in lymphocyte proliferation was observed with EC3 values of 0.072% and 0.089% in CBA and BALB/c mice, respectively. The mouse ear swelling test (MEST) was used to evaluate the potential for Glut to elicit IgE (1/2 h post challenge) and contact hypersensitivity (24 and 48 h post challenge) responses. An immediate response was observed in animals induced and challenged with 2.5% Glut, whereas animals induced with 0.1% or 0.75% and challenged with 2.5% exhibited a delayed response 48 h post challenge. IgE-inducing potential was evaluated by phenotypic analysis of draining lymph node cells and measurement of total serum IgE levels. Only the 2.5% exposed group demonstrated a significant increase (P + B220 + cells and serum IgE. Following 3 days of dermal exposure, a significant increase in IL-4 mRNA in the draining lymph nodes was observed only in the 2.5% exposed group. These results indicate that the development of an immediate vs. a delayed hypersensitivity response following dermal exposure to Glut is at least in part mediated by the exposure concentration

  13. UAV-Based Thermal Imaging for High-Throughput Field Phenotyping of Black Poplar Response to Drought.

    Science.gov (United States)

    Ludovisi, Riccardo; Tauro, Flavia; Salvati, Riccardo; Khoury, Sacha; Mugnozza Scarascia, Giuseppe; Harfouche, Antoine

    2017-01-01

    Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby Populus nigra L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV)-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP) aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level) HTFP approach to investigate the response to drought of a full-sib F 2 partially inbred population (termed here 'POP6'), whose F 1 was obtained from an intraspecific P. nigra controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought) on a population of 4603 trees (503 genotypes) hosted in two adjacent experimental plots (1.67 ha) by conducting low-elevation (25 m) flights with an aerial drone and capturing 7836 thermal infrared (TIR) images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature ( T c ) was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype

  14. UAV-Based Thermal Imaging for High-Throughput Field Phenotyping of Black Poplar Response to Drought

    Directory of Open Access Journals (Sweden)

    Riccardo Ludovisi

    2017-09-01

    Full Text Available Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby Populus nigra L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level HTFP approach to investigate the response to drought of a full-sib F2 partially inbred population (termed here ‘POP6’, whose F1 was obtained from an intraspecific P. nigra controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought on a population of 4603 trees (503 genotypes hosted in two adjacent experimental plots (1.67 ha by conducting low-elevation (25 m flights with an aerial drone and capturing 7836 thermal infrared (TIR images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature (Tc was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype

  15. Divergent methylation pattern in adult stage between two forms of Tetranychus urticae (Acari: Tetranychidae).

    Science.gov (United States)

    Yang, Si-Xia; Guo, Chao; Zhao, Xiu-Ting; Sun, Jing-Tao; Hong, Xiao-Yue

    2017-02-19

    The two-spotted spider mite, Tetranychus urticae Koch has two forms: green form and red form. Understanding the molecular basis of how these two forms established without divergent genetic background is an intriguing area. As a well-known epigenetic process, DNA methylation has particularly important roles in gene regulation and developmental variation across diverse organisms that do not alter genetic background. Here, to investigate whether DNA methylation could be associated with different phenotypic consequences in the two forms of T. urticae, we surveyed the genome-wide cytosine methylation status and expression level of DNA methyltransferase 3 (Tudnmt3) throughout their entire life cycle. Methylation-sensitive amplification polymorphism (MSAP) analyses of 585 loci revealed variable methylation patterns in the different developmental stages. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between female adults of the two forms. The gene expression of Tudnmt3 was detected in all examined developmental stages, which was significantly different in the adult stage of the two forms. Together, our results reveal the epigenetic distance between the two forms of T. urticae, suggesting that DNA methylation might be implicated in different developmental demands, and contribute to different phenotypes in the adult stage of these two forms. © 2017 Institute of Zoology, Chinese Academy of Sciences.

  16. Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae).

    Science.gov (United States)

    Eckert, Andrew J; Shahi, Hurshbir; Datwyler, Shannon L; Neale, David B

    2012-08-01

    Plant populations arrayed across sharp environmental gradients are ideal systems for identifying the genetic basis of ecologically relevant phenotypes. A series of five uplifted marine terraces along the northern coast of California represents one such system where morphologically distinct populations of lodgepole pine (Pinus contorta) are distributed across sharp soil gradients ranging from fertile soils near the coast to podzolic soils ca. 5 km inland. A total of 92 trees was sampled across four coastal marine terraces (N = 10-46 trees/terrace) located in Mendocino County, California and sequenced for a set of 24 candidate genes for growth and responses to various soil chemistry variables. Statistical analyses relying on patterns of nucleotide diversity were employed to identify genes whose diversity patterns were inconsistent with three null models. Most genes displayed patterns of nucleotide diversity that were consistent with null models (N = 19) or with the presence of paralogs (N = 3). Two genes, however, were exceptional: an aluminum responsive ABC-transporter with F(ST) = 0.664 and an inorganic phosphate transporter characterized by divergent haplotypes segregating at intermediate frequencies in most populations. Spatially variable natural selection along gradients of aluminum and phosphate ion concentrations likely accounted for both outliers. These results shed light on some of the genetic components comprising the extended phenotype of this ecosystem, as well as highlight ecotones as fruitful study systems for the detection of adaptive genetic variants.

  17. The application of flexible unmanned aerial vehicle remote sensing for field-based crop phenotyping: Current status and perspectives

    Science.gov (United States)

    Phenotyping plays an important role in crop science research; the accurate and rapid acquisition of phenotypic information of plants or cells in different environments is helpful for exploring the inheritance and expression patterns of the genome to determine the association of genomic and phenotypi...

  18. Phenotypic spectrum of GABRA1

    DEFF Research Database (Denmark)

    Johannesen, Katrine; Marini, Carla; Pfeffer, Siona

    2016-01-01

    OBJECTIVE: To delineate phenotypic heterogeneity, we describe the clinical features of a cohort of patients with GABRA1 gene mutations. METHODS: Patients with GABRA1 mutations were ascertained through an international collaboration. Clinical, EEG, and genetic data were collected. Functional analy...

  19. Leaf segmentation in plant phenotyping

    NARCIS (Netherlands)

    Scharr, Hanno; Minervini, Massimo; French, Andrew P.; Klukas, Christian; Kramer, David M.; Liu, Xiaoming; Luengo, Imanol; Pape, Jean Michel; Polder, Gerrit; Vukadinovic, Danijela; Yin, Xi; Tsaftaris, Sotirios A.

    2016-01-01

    Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape

  20. Delineating SPTAN1 associated phenotypes

    DEFF Research Database (Denmark)

    Syrbe, Steffen; Harms, Frederike L; Parrini, Elena

    2017-01-01

    De novo in-frame deletions and duplications in the SPTAN1 gene, encoding the non-erythrocyte αII spectrin, have been associated with severe West syndrome with hypomyelination and pontocerebellar atrophy. We aimed at comprehensively delineating the phenotypic spectrum associated with SPTAN1 mutati...

  1. Interoperability between phenotype and anatomy ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

    2010-12-15

    Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

  2. Duplication of Dio3 genes in teleost fish and their divergent expression in skin during flatfish metamorphosis.

    Science.gov (United States)

    Alves, R N; Cardoso, J C R; Harboe, T; Martins, R S T; Manchado, M; Norberg, B; Power, D M

    2017-05-15

    Deiodinase 3 (Dio3) plays an essential role during early development in vertebrates by controlling tissue thyroid hormone (TH) availability. The Atlantic halibut (Hippoglossus hippoglossus) possesses duplicate dio3 genes (dio3a and dio3b). Expression analysis indicates that dio3b levels change in abocular skin during metamorphosis and this suggests that this enzyme is associated with the divergent development of larval skin to the juvenile phenotype. In larvae exposed to MMI, a chemical that inhibits TH production, expression of dio3b in ocular skin is significantly up-regulated suggesting that THs normally modulate this genes expression during this developmental event. The molecular basis for divergent dio3a and dio3b expression and responsiveness to MMI treatment is explained by the multiple conserved TREs in the proximal promoter region of teleost dio3b and their absence from the promoter of dio3a. We propose that the divergent expression of dio3 in ocular and abocular skin during halibut metamorphosis contributes to the asymmetric pigment development in response to THs. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation

    Directory of Open Access Journals (Sweden)

    Gregersen Finn

    2010-11-01

    Full Text Available Abstract Background Evaluating the limits of adaptation to temperature is important given the IPCC-predicted rise in global temperatures. The rate and scope of evolutionary adaptation can be limited by low genetic diversity, gene flow, and costs associated with adaptive change. Freshwater organisms are physically confined to lakes and rivers, and must therefore deal directly with climate variation and change. In this study, we take advantage of a system characterised by low genetic variation, small population size, gene flow and between-trait trade-offs to study how such conditions affect the ability of a freshwater fish to adapt to climate change. We test for genetically-based differences in developmental traits indicating local adaptation, by conducting a common-garden experiment using embryos and larvae from replicate pairs of sympatric grayling demes that spawn and develop in natural cold and warm water, respectively. These demes have common ancestors from a colonization event 22 generations ago. Consequently, we explore if diversification may occur under severely constraining conditions. Results We found evidence for divergence in ontogenetic rates. The divergence pattern followed adaptation predictions as cold-deme individuals displayed higher growth rates and yolk conversion efficiency than warm-deme individuals at the same temperature. The cold-deme embryos had a higher rate of muscle mass development. Most of the growth- and development differences occurred prior to hatch. The divergence was probably not caused by genetic drift as there was a strong degree of parallelism in the divergence pattern and because phenotypic differentiation (QST was larger than estimated genetic drift levels (microsatellite FST between demes from different temperature groups. We also document that these particular grayling populations cannot develop successfully at temperatures above 12°C, whereas other European populations can, and that increasing the

  4. Phenotypic and functional plasticity of cells of innate immunity: macrophages, mast cells and neutrophils

    DEFF Research Database (Denmark)

    Galli, Stephen J; Borregaard, Niels; Wynn, Thomas A

    2011-01-01

    Hematopoietic cells, including lymphoid and myeloid cells, can develop into phenotypically distinct 'subpopulations' with different functions. However, evidence indicates that some of these subpopulations can manifest substantial plasticity (that is, undergo changes in their phenotype and function......). Here we focus on the occurrence of phenotypically distinct subpopulations in three lineages of myeloid cells with important roles in innate and acquired immunity: macrophages, mast cells and neutrophils. Cytokine signals, epigenetic modifications and other microenvironmental factors can substantially...... and, in some cases, rapidly and reversibly alter the phenotype of these cells and influence their function. This suggests that regulation of the phenotype and function of differentiated hematopoietic cells by microenvironmental factors, including those generated during immune responses, represents...

  5. Phenotypic and functional plasticity of cells of innate immunity: macrophages, mast cells and neutrophils

    DEFF Research Database (Denmark)

    Galli, Stephen J; Borregaard, Niels; Wynn, Thomas A

    2011-01-01

    ). Here we focus on the occurrence of phenotypically distinct subpopulations in three lineages of myeloid cells with important roles in innate and acquired immunity: macrophages, mast cells and neutrophils. Cytokine signals, epigenetic modifications and other microenvironmental factors can substantially......Hematopoietic cells, including lymphoid and myeloid cells, can develop into phenotypically distinct 'subpopulations' with different functions. However, evidence indicates that some of these subpopulations can manifest substantial plasticity (that is, undergo changes in their phenotype and function...... and, in some cases, rapidly and reversibly alter the phenotype of these cells and influence their function. This suggests that regulation of the phenotype and function of differentiated hematopoietic cells by microenvironmental factors, including those generated during immune responses, represents...

  6. Individualized Hydrocodone Therapy Based on Phenotype, Pharmacogenetics, and Pharmacokinetic Dosing.

    Science.gov (United States)

    Linares, Oscar A; Fudin, Jeffrey; Daly, Annemarie L; Boston, Raymond C

    2015-12-01

    (1) To quantify hydrocodone (HC) and hydromorphone (HM) metabolite pharmacokinetics with pharmacogenetics in CYP2D6 ultra-rapid metabolizer (UM), extensive metabolizer (EM), and poor metabolizer (PM) metabolizer phenotypes. (2) To develop an HC phenotype-specific dosing strategy for HC that accounts for HM production using clinical pharmacokinetics integrated with pharmacogenetics for patient safety. In silico clinical trial simulation. Healthy white men and women without comorbidities or history of opioid, or any other drug or nutraceutical use, age 26.3±5.7 years (mean±SD; range, 19 to 36 y) and weight 71.9±16.8 kg (range, 50 to 108 kg). CYP2D6 phenotype-specific HC clinical pharmacokinetic parameter estimates and phenotype-specific percentages of HM formed from HC. PMs had lower indices of HC disposition compared with UMs and EMs. Clearance was reduced by nearly 60% and the t1/2 was increased by about 68% compared with EMs. The canonical order for HC clearance was UM>EM>PM. HC elimination mainly by the liver, represented by ke, was reduced about 70% in PM. However, HC's apparent Vd was not significantly different among UMs, EMs, and PM. The canonical order of predicted plasma HM concentrations was UM>EM>PM. For each of the CYP2D6 phenotypes, the mean predicted HM levels were within HM's therapeutic range, which indicates HC has significant phenotype-dependent pro-drug effects. Our results demonstrate that pharmacogenetics afford clinicians an opportunity to individualize HC dosing, while adding enhanced opportunity to account for its conversion to HM in the body.

  7. DAST in Flight Showing Diverging Wingtip Oscillations

    Science.gov (United States)

    1980-01-01

    normal stiffness. This was done because stiffness requires structural weight but ensures freedom from flutter-an uncontrolled, divergent oscillation of the structure, driven by aerodynamic forces and resulting in structural failure. The program used refined theoretical tools to predict at what speed flutter would occur. It then designed a high-response control system to counteract the motion and permit a much lighter wing structure. The wing had, in effect, 'electronic stiffness.' Flight research with this concept was extremely hazardous because an error in either the flutter prediction or control system implementation would result in wing structural failure and the loss of the vehicle. Because of this, flight demonstration of a sub-scale vehicle made sense from the standpoint of both safety and cost. The program anticipated structural failure during the course of the flight research. The Firebee II was a supersonic drone selected as the DAST testbed because its wing could be easily replaced, it used only tail-mounted control surfaces, and it was available as surplus from the U. S. Air Force. It was capable of 5-g turns (that is, turns producing acceleration equal to 5 times that of gravity). Langley outfitted a drone with an aeroelastic, supercritical research wing suitable for a Mach 0.98 cruise transport with a predicted flutter speed of Mach 0.95 at an altitude of 25,000 feet. Dryden and Langley, in conjunction with Boeing, designed and fabricated a digital flutter suppression system (FSS). Dryden developed an RPRV (remotely piloted research vehicle) flight control system; integrated the wing, FSS, and vehicle systems; and conducted the flight program. In addition to a digital flight control system and aeroelastic wings, each DAST drone had research equipment mounted in its nose and a mid-air retrieval system in its tail. The drones were originally launched from the NASA B-52 bomber and later from a DC-130. The DAST vehicle's flight was monitored from the sky by an F

  8. Rotational and divergent kinetic energy in the mesoscale model ALADIN

    Directory of Open Access Journals (Sweden)

    V. Blažica

    2013-03-01

    Full Text Available Kinetic energy spectra from the mesoscale numerical weather prediction (NWP model ALADIN with horizontal resolution 4.4 km are split into divergent and rotational components which are then compared at horizontal scales below 300 km and various vertical levels. It is shown that about 50% of kinetic energy in the free troposphere in ALADIN is divergent energy. The percentage increases towards 70% near the surface and in the upper troposphere towards 100 hPa. The maximal percentage of divergent energy is found at stratospheric levels around 100 hPa and at scales below 100 km which are not represented by the global models. At all levels, the divergent energy spectra are characterised by shallower slopes than the rotational energy spectra, and the difference increases as horizontal scales become larger. A very similar vertical distribution of divergent energy is obtained by using the standard ALADIN approach for the computation of spectra based on the extension zone and by applying detrending approach commonly used in mesoscale NWP community.

  9. Sufficient Statistics for Divergence and the Probability of Misclassification

    Science.gov (United States)

    Quirein, J.

    1972-01-01

    One particular aspect is considered of the feature selection problem which results from the transformation x=Bz, where B is a k by n matrix of rank k and k is or = to n. It is shown that in general, such a transformation results in a loss of information. In terms of the divergence, this is equivalent to the fact that the average divergence computed using the variable x is less than or equal to the average divergence computed using the variable z. A loss of information in terms of the probability of misclassification is shown to be equivalent to the fact that the probability of misclassification computed using variable x is greater than or equal to the probability of misclassification computed using variable z. First, the necessary facts relating k-dimensional and n-dimensional integrals are derived. Then the mentioned results about the divergence and probability of misclassification are derived. Finally it is shown that if no information is lost (in x = Bz) as measured by the divergence, then no information is lost as measured by the probability of misclassification.

  10. Concrete ensemble Kalman filters with rigorous catastrophic filter divergence.

    Science.gov (United States)

    Kelly, David; Majda, Andrew J; Tong, Xin T

    2015-08-25

    The ensemble Kalman filter and ensemble square root filters are data assimilation methods used to combine high-dimensional, nonlinear dynamical models with observed data. Ensemble methods are indispensable tools in science and engineering and have enjoyed great success in geophysical sciences, because they allow for computationally cheap low-ensemble-state approximation for extremely high-dimensional turbulent forecast models. From a theoretical perspective, the dynamical properties of these methods are poorly understood. One of the central mysteries is the numerical phenomenon known as catastrophic filter divergence, whereby ensemble-state estimates explode to machine infinity, despite the true state remaining in a bounded region. In this article we provide a breakthrough insight into the phenomenon, by introducing a simple and natural forecast model that transparently exhibits catastrophic filter divergence under all ensemble methods and a large set of initializations. For this model, catastrophic filter divergence is not an artifact of numerical instability, but rather a true dynamical property of the filter. The divergence is not only validated numerically but also proven rigorously. The model cleanly illustrates mechanisms that give rise to catastrophic divergence and confirms intuitive accounts of the phenomena given in past literature.

  11. Sandwiched Rényi divergence satisfies data processing inequality

    International Nuclear Information System (INIS)

    Beigi, Salman

    2013-01-01

    Sandwiched (quantum) α-Rényi divergence has been recently defined in the independent works of Wilde et al. [“Strong converse for the classical capacity of entanglement-breaking channels,” preprint http://arxiv.org/abs/arXiv:1306.1586 (2013)] and Müller-Lennert et al. [“On quantum Rényi entropies: a new definition, some properties and several conjectures,” preprint http://arxiv.org/abs/arXiv:1306.3142v1 (2013)]. This new quantum divergence has already found applications in quantum information theory. Here we further investigate properties of this new quantum divergence. In particular, we show that sandwiched α-Rényi divergence satisfies the data processing inequality for all values of α > 1. Moreover we prove that α-Holevo information, a variant of Holevo information defined in terms of sandwiched α-Rényi divergence, is super-additive. Our results are based on Hölder's inequality, the Riesz-Thorin theorem and ideas from the theory of complex interpolation. We also employ Sion's minimax theorem

  12. Ayahuasca enhances creative divergent thinking while decreasing conventional convergent thinking.

    Science.gov (United States)

    Kuypers, K P C; Riba, J; de la Fuente Revenga, M; Barker, S; Theunissen, E L; Ramaekers, J G

    2016-09-01

    Ayahuasca is a South American psychotropic plant tea traditionally used in Amazonian shamanism. The tea contains the psychedelic 5-HT2A receptor agonist N,N-dimethyltryptamine (DMT), plus β-carboline alkaloids with monoamine oxidase-inhibiting properties. Increasing evidence from anecdotal reports and open-label studies indicates that ayahuasca may have therapeutic effects in treatment of substance use disorders and depression. A recent study on the psychological effects of ayahuasca found that the tea reduces judgmental processing and inner reactivity, classic goals of mindfulness psychotherapy. Another psychological facet that could potentially be targeted by ayahuasca is creative divergent thinking. This mode of thinking can enhance and strengthen psychological flexibility by allowing individuals to generate new and effective cognitive, emotional, and behavioral strategies. The present study aimed to assess the potential effects of ayahuasca on creative thinking. We visited two spiritual ayahuasca workshops and invited participants to conduct creativity tests before and during the acute effects of ayahuasca. In total, 26 participants consented. Creativity tests included the "pattern/line meanings test" (PLMT) and the "picture concept test" (PCT), both assessing divergent thinking and the latter also assessing convergent thinking. While no significant effects were found for the PLMT, ayahuasca intake significantly modified divergent and convergent thinking as measured by the PCT. While convergent thinking decreased after intake, divergent thinking increased. The present data indicate that ayahuasca enhances creative divergent thinking. They suggest that ayahuasca increases psychological flexibility, which may facilitate psychotherapeutic interventions and support clinical trial initiatives.

  13. Automated phenotyping of permanent crops

    Science.gov (United States)

    McPeek, K. Thomas; Steddom, Karl; Zamudio, Joseph; Pant, Paras; Mullenbach, Tyler

    2017-05-01

    AGERpoint is defining a new technology space for the growers' industry by introducing novel applications for sensor technology and data analysis to growers of permanent crops. Serving data to a state-of-the-art analytics engine from a cutting edge sensor platform, a new paradigm in precision agriculture is being developed that allows growers to understand the unique needs of each tree, bush or vine in their operation. Autonomous aerial and terrestrial vehicles equipped with multiple varieties of remote sensing technologies give AGERpoint the ability to measure key morphological and spectral features of permanent crops. This work demonstrates how such phenotypic measurements combined with machine learning algorithms can be used to determine the variety of crops (e.g., almond and pecan trees). This phenotypic and varietal information represents the first step in enabling growers with the ability to tailor their management practices to individual plants and maximize their economic productivity.

  14. Phenotypic deconstruction of gene circuitry.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2013-06-01

    It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

  15. Phenotypic deconstruction of gene circuitry

    Science.gov (United States)

    Lomnitz, Jason G.; Savageau, Michael A.

    2013-06-01

    It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

  16. Rapid identification of genes controlling virulence and immunity in malaria parasites

    KAUST Repository

    Abkallo, Hussein M.; Martinelli, Axel; Inoue, Megumi; Ramaprasad, Abhinay; Xangsayarath, Phonepadith; Gitaka, Jesse; Tang, Jianxia; Yahata, Kazuhide; Zoungrana, Augustin; Mitaka, Hayato; Acharjee, Arita; Datta, Partha P.; Hunt, Paul; Carter, Richard; Kaneko, Osamu; Mustonen, Ville; Illingworth, Christopher J. R.; Pain, Arnab; Culleton, Richard

    2017-01-01

    Identifying the genetic determinants of phenotypes that impact disease severity is of fundamental importance for the design of new interventions against malaria. Here we present a rapid genome-wide approach capable of identifying multiple genetic

  17. Wine Expertise Predicts Taste Phenotype.

    Science.gov (United States)

    Hayes, John E; Pickering, Gary J

    2012-03-01

    Taste phenotypes have long been studied in relation to alcohol intake, dependence, and family history, with contradictory findings. However, on balance - with appropriate caveats about populations tested, outcomes measured and psychophysical methods used - an association between variation in taste responsiveness and some alcohol behaviors is supported. Recent work suggests super-tasting (operationalized via propylthiouracil (PROP) bitterness) not only associates with heightened response but also with more acute discrimination between stimuli. Here, we explore relationships between food and beverage adventurousness and taste phenotype. A convenience sample of wine drinkers (n=330) were recruited in Ontario and phenotyped for PROP bitterness via filter paper disk. They also filled out a short questionnaire regarding willingness to try new foods, alcoholic beverages and wines as well as level of wine involvement, which was used to classify them as a wine expert (n=110) or wine consumer (n=220). In univariate logisitic models, food adventurousness predicted trying new wines and beverages but not expertise. Likewise, wine expertise predicted willingness to try new wines and beverages but not foods. In separate multivariate logistic models, willingness to try new wines and beverages was predicted by expertise and food adventurousness but not PROP. However, mean PROP bitterness was higher among wine experts than wine consumers, and the conditional distribution functions differed between experts and consumers. In contrast, PROP means and distributions did not differ with food adventurousness. These data suggest individuals may self-select for specific professions based on sensory ability (i.e., an active gene-environment correlation) but phenotype does not explain willingness to try new stimuli.

  18. From plant genomes to phenotypes

    OpenAIRE

    Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

    2017-01-01

    Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

  19. Quantitative complete tooth variation among east Asians and Native Americans: developmental biology as a tool for the assessment of human divergence.

    Science.gov (United States)

    Shields, E D

    1996-01-01

    The quantification of total tooth structure derived from X-rays of Vietnamese, Southern Chinese, Mongolians, Western Eskimos, and Peruvian pre-Inca (Huari Empire) populations was used to examine dental divergence and the morphogenetics of change. Multivariate derived distances between the samples helped identify a quasicontinuous web of ethnic groups with two binary clusters ensconced within the web. One cluster was composed of Mongolians, Western Eskimos, and pre-Inca, and the other group consisted of the Southern Chinese and Vietnamese. Mongolians entered the quasicontinuum from a divergent angle (externally influenced) from that of the Southeast Asians. The Chinese and pre-Inca formed the polar samples of the distance superstructure. The pre-Inca sample was the most isolated, its closest neighbor being the Western Eskimos. Univariate and multivariate analyses suggested that the pre-Inca, whose ancestors arrived in America perhaps approximately 30,000 years ago, was the least derived sample. Clearly, microevolutionary change occurred among the samples, but the dental phenotype was resistant to environmental developmental perturbations. An assessment of dental divergence and developmental biology suggested that the overall dental phenotype is a complex multigenic morphological character, and that the observed variation evolved through total genomic drift. The quantified dental phenotype is greater than its highly multigenic algorithm and its development homeostasis is tightly controlled, or canalized, by the deterministic organization of a complex nonlinear epigenetic milieu. The overall dental phenotype quantified here was selectively neutral and a good character to help reconstruct the sequence of human evolution, but if the outlying homeostatic threshold was or will be exceeded in antecedents and descendants, respectively, evolutionary saltation occurs.

  20. Early phenotypical diagnoses in Trembler-J mice model.

    Science.gov (United States)

    Rosso, Gonzalo; Cal, Karina; Canclini, Lucía; Damián, Juan Pablo; Ruiz, Paul; Rodríguez, Héctor; Sotelo, José Roberto; Vazquez, Cristina; Kun, Alejandra

    2010-06-30

    Pmp-22 mutant mice (Trembler-J: B6.D2-Pmp22/J), are used as a model to study Charcot-Marie-Tooth type 1A (CMT1A). The identification of individual genotypes is a routine in the management of the Tr(J) colony. The earliest phenotypic manifestation of the pmp-22 mutation is just about 20th postnatal days, when pups begin to tremble. In this study, a rapid and simple diagnostic method was developed by modifying the Tail Suspension Test (MTST) to determine the difference between the Tr(J) and the wild-type mice phenotype. The animal behavioral phenotypes generated during the test were consistent with the specific genotype of each animal. The MTST allowed us to infer the heterozygous genotype in early postnatal stages, at 11 days after birth. The motor impairment of Tr(J) mice was also analyzed by a Fixed Bar Test (FBT), which revealed the disease evolution according to age. The main advantages of MTST are its objectivity, simplicity, and from the viewpoint of animal welfare, it is a non-invasive technique that combined with his rapidity show its very well applicability for use from an early age in these mice. Copyright 2010 Elsevier B.V. All rights reserved.

  1. Discordant introgression in a rapidly expanding hybrid swarm

    Science.gov (United States)

    Ward, Jessica L.; Blum, Mike J.; Walters, David M.; Porter, Brady A.; Burkhead, Noel; Freeman, Byron

    2012-01-01

    The erosion of species boundaries can involve rapid evolutionary change. Consequently, many aspects of the process remain poorly understood, including the formation, expansion, and evolution of hybrid swarms. Biological invasions involving hybridization present exceptional opportunities to study the erosion of species boundaries because timelines of interactions and outcomes are frequently well known. Here, we examined clinal variation across codominant and maternally inherited genetic markers as well as phenotypic traits to characterize the expansion and evolution of a hybrid swarm between native Cyprinella venusta and invasive Cyprinella lutrensis minnows. Discordant introgression of phenotype, microsatellite multilocus genotype, and mtDNA haplotype indicates that the observable expansion of the C. venusta x C. lutrensis hybrid swarm is a false invasion front. Both parental and hybrid individuals closely resembling C. lutrensis are numerically dominant in the expansion wake, indicating that the non-native parental phenotype may be selectively favored. These findings show that cryptic introgression can extend beyond the phenotypic boundaries of hybrid swarms and that hybrid swarms likely expand more rapidly than can be documented from phenotypic variation alone. Similarly, dominance of a single parental phenotype following an introduction event may lead to instances of species erosion being mistaken for species displacement without hybridization.

  2. Phenotypic covariance at species' borders.

    Science.gov (United States)

    Caley, M Julian; Cripps, Edward; Game, Edward T

    2013-05-28

    Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

  3. A novel 3D imaging system for strawberry phenotyping

    Directory of Open Access Journals (Sweden)

    Joe Q. He

    2017-11-01

    Full Text Available Abstract Background Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. Results A low cost multi-view stereo (MVS imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. Conclusion This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique.

  4. A novel 3D imaging system for strawberry phenotyping.

    Science.gov (United States)

    He, Joe Q; Harrison, Richard J; Li, Bo

    2017-01-01

    Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. A low cost multi-view stereo (MVS) imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique.

  5. Two Stable Variants of Burkholderia pseudomallei Strain MSHR5848 Express Broadly Divergent in vitro Phenotypes Associated with their Virulence Differences

    Science.gov (United States)

    2016-11-21

    initial growth advantage when exposed to nutrient- rich niches such as the intestinal tract or infected lungs. For instance, type 1 preferentially...possible initial growth advantage of type 1 in nutrient- rich niches , the evolving bacterial adaptation and deregulation of the utilization of...conditions, eg., the macrophage environment (Fig. 10) and inhibitory chemicals (PM substrates, Table 7A, B and Table S- 2). Survival in a defined niche such

  6. Divergent regulation of CBF regulon on cold tolerance and plant phenotype in cassava overexpressing Arabidopsis CBF3 gene

    Directory of Open Access Journals (Sweden)

    Dong An

    2016-12-01

    Full Text Available Cassava is a tropical origin plant that is sensitive to chilling stress. In order to understand the CBF cold response pathway, a well-recognized regulatory mechanism in temperate plants, in cassava, overexpression of an Arabidopsis CBF3 gene is studied. This gene renders cassava increasingly tolerant to cold and drought stresses but is associated with retarded plant growth, leaf curling, reduced storage root yield, and reduced anthocyanin accumulation in a transcript abundance-dependent manner. Physiological analysis revealed that the transgenic cassava increased proline accumulation, reduced malondialdehyde production, and electrolyte leakage under cold stress. These transgenic lines also showed high relative water content when faced with drought. The expression of partial CBF-targeted genes in response to cold displayed temporal and spatial variations in the wild-type and transgenic plants: highly inducible in leaves and less altered in apical buds. In addition, anthocyanin accumulation was inhibited by downregulating the expression of genes involved in its biosynthesis and by interplaying between the CBF3 and the endogenous transcription factors. Thus, the heterologous CBF3 modulates the expression of stress-related genes and carries out a series of physiological adjustments under stressful conditions, showing a varied regulation pattern of CBF regulon from that of cassava CBFs.

  7. Assessment of host-associated genetic differentiation among phenotypically divergent populations of a coral-eating gastropod across the Caribbean.

    Directory of Open Access Journals (Sweden)

    Lyza Johnston

    Full Text Available Host-associated adaptation is emerging as a potential driver of population differentiation and speciation for marine organisms with major implications for ecosystem structure and function. Coralliophila abbreviata are corallivorous gastropods that live and feed on most of the reef-building corals in the tropical western Atlantic and Caribbean. Populations of C. abbreviata associated with the threatened acroporid corals, Acropora palmata and A. cervicornis, display different behavioral, morphological, demographic, and life-history characteristics than those that inhabit other coral host taxa, indicating that host-specific selective forces may be acting on C. abbreviata. Here, we used newly developed polymorphic microsatellite loci and mitochondrial cytochrome b sequence data to assess the population genetic structure, connectivity, and demographic history of C. abbreviata populations from three coral host taxa (A. palmata, Montastraea spp., Mycetophyllia spp. and six geographic locations across the Caribbean. Analysis of molecular variance provided some evidence of weak and possibly geographically variable host-associated differentiation but no evidence of differentiation among sampling locations or major oceanographic regions, suggesting high gene flow across the Caribbean. Phylogenetic network and bayesian clustering analyses supported a hypothesis of a single panmictic population as individuals failed to cluster by host or sampling location. Demographic analyses consistently supported a scenario of population expansion during the Pleistocene, a time of major carbonate reef development in the region. Although further study is needed to fully elucidate the interactive effects of host-associated selection and high gene flow in this system, our results have implications for local and regional community interactions and impact of predation on declining coral populations.

  8. Assessment of host-associated genetic differentiation among phenotypically divergent populations of a coral-eating gastropod across the Caribbean.

    Science.gov (United States)

    Johnston, Lyza; Miller, Margaret W; Baums, Iliana B

    2012-01-01

    Host-associated adaptation is emerging as a potential driver of population differentiation and speciation for marine organisms with major implications for ecosystem structure and function. Coralliophila abbreviata are corallivorous gastropods that live and feed on most of the reef-building corals in the tropical western Atlantic and Caribbean. Populations of C. abbreviata associated with the threatened acroporid corals, Acropora palmata and A. cervicornis, display different behavioral, morphological, demographic, and life-history characteristics than those that inhabit other coral host taxa, indicating that host-specific selective forces may be acting on C. abbreviata. Here, we used newly developed polymorphic microsatellite loci and mitochondrial cytochrome b sequence data to assess the population genetic structure, connectivity, and demographic history of C. abbreviata populations from three coral host taxa (A. palmata, Montastraea spp., Mycetophyllia spp.) and six geographic locations across the Caribbean. Analysis of molecular variance provided some evidence of weak and possibly geographically variable host-associated differentiation but no evidence of differentiation among sampling locations or major oceanographic regions, suggesting high gene flow across the Caribbean. Phylogenetic network and bayesian clustering analyses supported a hypothesis of a single panmictic population as individuals failed to cluster by host or sampling location. Demographic analyses consistently supported a scenario of population expansion during the Pleistocene, a time of major carbonate reef development in the region. Although further study is needed to fully elucidate the interactive effects of host-associated selection and high gene flow in this system, our results have implications for local and regional community interactions and impact of predation on declining coral populations.

  9. Phenotypes in defined genotypes including siblings with Usher syndrome.

    Science.gov (United States)

    Malm, Eva; Ponjavic, Vesna; Möller, Claes; Kimberling, William J; Andréasson, Sten

    2011-06-01

    To characterize visual function in defined genotypes including siblings with Usher syndrome. Thirteen patients with phenotypically different subtypes of Usher syndrome, including 3 families with affected siblings, were selected. Genetic analysis and ophthalmological examinations including visual fields, full-field electroretinography (ERG), multifocal electroretinography (mf ERG), and optical coherence tomography (OCT) were assessed. The patients' degree of visual handicap was evaluated by a questionnaire (ADL). Twelve of thirteen patients were genotyped as Usher 1B, 1D, 1F, 2A, 2C or 3A. In 12 of 13 patients examined with ERG the 30 Hz flickering light response revealed remaining cone function. In 3 of the patients with Usher type 1 mf ERG demonstrated a specific pattern, with a sharp distinction between the area with reduced function and the central area with remaining macular function and normal peak time. OCT demonstrated loss of foveal depression with distortion of the foveal architecture in the macula in all patients. The foveal thickness ranged from 159 to 384 µm and was not correlated to retinal function. Three siblings shared the same mutation for Usher 2C but in contrast to previous reports regarding this genotype, 1 of them diverged in phenotype with substantially normal visual fields, almost normal OCT and mf ERG findings, and only moderately reduced rod and cone function according to ERG. Evaluation of visual function comprising both the severity of the rod cone degeneration and the function in the macular region confirm phenotypical heterogeneity within siblings and between different genotypes of Usher syndrome.

  10. Phenotypic Changes in Different Spinach Varieties Grown and Selected under Organic Conditions

    Directory of Open Access Journals (Sweden)

    Nicolas Schermann

    2011-09-01

    Full Text Available Organic and low-input agriculture needs flexible varieties that can buffer environmental stress and adapt to the needs of farmers. We implemented an experiment to investigate the evolutionary capacities of a sample of spinach (Spinacia oleracea L. population varieties for a number of phenotypic traits. Three farmers cultivated, selected and multiplied one or several populations over two years on their farms. The third year, the versions of the varieties cultivated and selected by the different farmers were compared to the original seed lots they had been given. After two cycles of cultivation and on-farm mass selection, all the observed varieties showed significant phenotypic changes (differences between the original version and the version cultivated by farmers for morphological and phenological traits. When the divergence among versions within varieties was studied, the results show that the varieties conserved their identity, except for one variety, which evolved in such a way that it may now be considered two different varieties. The heterogeneity of the population varieties was assessed in comparison with a commercial F1 hybrid used as control, and we found no specific differences in phenotypic diversity between the hybrid and population varieties. The phenotypic changes shown by the population varieties in response to on-farm cultivation and selection could be useful for the development of specific adaptation. These results call into question the current European seed legislation and the requirements of phenotypic stability for conservation varieties.

  11. Computational Investigations in Rectangular Convergent and Divergent Ribbed Channels

    Science.gov (United States)

    Sivakumar, Karthikeyan; Kulasekharan, N.; Natarajan, E.

    2018-05-01

    Computational investigations on the rib turbulated flow inside a convergent and divergent rectangular channel with square ribs of different rib heights and different Reynolds numbers (Re=20,000, 40,000 and 60,000). The ribs were arranged in a staggered fashion between the upper and lower surfaces of the test section. Computational investigations are carried out using computational fluid dynamic software ANSYS Fluent 14.0. Suitable solver settings like turbulence models were identified from the literature and the boundary conditions for the simulations on a solution of independent grid. Computations were carried out for both convergent and divergent channels with 0 (smooth duct), 1.5, 3, 6, 9 and 12 mm rib heights, to identify the ribbed channel with optimal performance, assessed using a thermo hydraulic performance parameter. The convergent and divergent rectangular channels show higher Nu values than the standard correlation values.

  12. Frequencies of digits, divergence points, and Schmidt games

    International Nuclear Information System (INIS)

    Olsen, L.

    2009-01-01

    Sets of divergence points, i.e. numbers x (or tuples of numbers) for which the limiting frequency of a given string of N-adic digits of x fails to exist, have recently attracted huge interest in the literature. In this paper we consider sets of simultaneous divergence points, i.e. numbers x (or tuples of numbers) for which the limiting frequencies of all strings of N-adic digits of x fail to exist. We show that many natural sets of simultaneous divergence points are (α, β)-wining sets in the sense of the Schmidt game. As an application we obtain lower bounds for the Hausdorff dimension of these sets.

  13. Structure of UV divergences in maximally supersymmetric gauge theories

    Science.gov (United States)

    Kazakov, D. I.; Borlakov, A. T.; Tolkachev, D. M.; Vlasenko, D. E.

    2018-06-01

    We consider the UV divergences up to sub-subleading order for the four-point on-shell scattering amplitudes in D =8 supersymmetric Yang-Mills theory in the planar limit. We trace how the leading, subleading, etc divergences appear in all orders of perturbation theory. The structure of these divergences is typical for any local quantum field theory independently on renormalizability. We show how the generalized renormalization group equations allow one to evaluate the leading, subleading, etc. contributions in all orders of perturbation theory starting from one-, two-, etc. loop diagrams respectively. We focus then on subtraction scheme dependence of the results and show that in full analogy with renormalizable theories the scheme dependence can be absorbed into the redefinition of the couplings. The only difference is that the role of the couplings play dimensionless combinations like g2s2 or g2t2, where s and t are the Mandelstam variables.

  14. To be liked versus respected: Divergent goals in interracial interactions.

    Science.gov (United States)

    Bergsieker, Hilary B; Shelton, J Nicole; Richeson, Jennifer A

    2010-08-01

    Pervasive representations of Blacks and Latinos as unintelligent and of Whites as racist may give rise to divergent impression management goals in interracial interactions. We present studies showing that in interracial interactions racial minorities seek to be respected and seen as competent more than Whites do, whereas Whites seek to be liked and seen as moral more than racial minorities do. These divergent impression management goals are reflected in Whites' and racial minorities' self-report responses (Studies 1a, 1b, 2, and 4) and behaviors (Studies 3a and 3b). Divergent goals are observed in pre-existing relationships (Study 2), as well as in live interactions (Studies 3a, 3b, and 4), and are associated with higher levels of negative other-directed affect (Study 4). Implications of these goals for interracial communication and misunderstandings are discussed.

  15. Genetic divergence in sesame based on morphological and agronomic traits

    Directory of Open Access Journals (Sweden)

    Nair Helena Castro Arriel

    2007-01-01

    Full Text Available The evaluation of diversity in germplasm collections is important for both plant breeders and germplasmcurators to optimize the use of the variability available. Diversity can be estimated by different genetic markers. The purposeof this study was to estimate the genetic divergence of 30 morphological and agronomic traits in 108 sesame genotypes bymultivariate analysis. The Cole-Rodgers index was used to establish the dissimilarity matrices. The principal componentanalysis identified the traits that contributed most to the divergence and the genotypes were clustered by Tocher’s optimization.Despite the narrow genetic basis, the markers were efficient to characterize the genotypes and identify the most similar groupsor duplicate and divergent genotypes. Greatest variation was found for the traits number of capsules per plant and grain yield.

  16. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models.

    Science.gov (United States)

    McCormack, John E; Zellmer, Amanda J; Knowles, L Lacey

    2010-05-01

    The role of ecology in the origin of species has been the subject of long-standing interest to evolutionary biologists. New sources of spatially explicit ecological data allow for large-scale tests of whether speciation is associated with niche divergence or whether closely related species tend to be similar ecologically (niche conservatism). Because of the confounding effects of spatial autocorrelation of environmental variables, we generate null expectations for niche divergence for both an ecological-niche modeling and a multivariate approach to address the question: do allopatrically distributed taxa occupy similar niches? In a classic system for the study of niche evolution--the Aphelocoma jays--we show that there is little evidence for niche divergence among Mexican Jay (A. ultramarina) lineages in the process of speciation, contrary to previous results. In contrast, Aphelocoma species that exist in partial sympatry in some regions show evidence for niche divergence. Our approach is widely applicable to the many cases of allopatric lineages in the beginning stages of speciation. These results do not support an ecological speciation model for Mexican Jay lineages because, in most cases, the allopatric environments they occupy are not significantly more divergent than expected under a null model.

  17. Robust Covariance Estimators Based on Information Divergences and Riemannian Manifold

    Directory of Open Access Journals (Sweden)

    Xiaoqiang Hua

    2018-03-01

    Full Text Available This paper proposes a class of covariance estimators based on information divergences in heterogeneous environments. In particular, the problem of covariance estimation is reformulated on the Riemannian manifold of Hermitian positive-definite (HPD matrices. The means associated with information divergences are derived and used as the estimators. Without resorting to the complete knowledge of the probability distribution of the sample data, the geometry of the Riemannian manifold of HPD matrices is considered in mean estimators. Moreover, the robustness of mean estimators is analyzed using the influence function. Simulation results indicate the robustness and superiority of an adaptive normalized matched filter with our proposed estimators compared with the existing alternatives.

  18. Bubble Divergences: Sorting out Topology from Cell Structure

    Science.gov (United States)

    Bonzom, Valentin; Smerlak, Matteo

    2012-02-01

    We conclude our analysis of bubble divergences in the flat spinfoam model. In [arXiv:1008.1476] we showed that the divergence degree of an arbitrary two-complex Gamma can be evaluated exactly by means of twisted cohomology. Here, we specialize this result to the case where Gamma is the two-skeleton of the cell decomposition of a pseudomanifold, and sharpen it with a careful analysis of the cellular and topological structures involved. Moreover, we explain in detail how this approach reproduces all the previous powercounting results for the Boulatov-Ooguri (colored) tensor models, and sheds light on algebraic-topological aspects of Gurau's 1/N expansion.

  19. Zimmermann's forest formula, infrared divergences and the QCD beta function

    Directory of Open Access Journals (Sweden)

    Franz Herzog

    2018-01-01

    Full Text Available We review Zimmermann's forest formula, which solves Bogoliubov's recursive R-operation for the subtraction of ultraviolet divergences in perturbative Quantum Field Theory. We further discuss a generalisation of the R-operation which subtracts besides ultraviolet also Euclidean infrared divergences. This generalisation, which goes under the name of the R⁎-operation, can be used efficiently to compute renormalisation constants. We will discuss several results obtained by this method with focus on the QCD beta function at five loops as well as the application to hadronic Higgs boson decay rates at N4LO. This article summarizes a talk given at the Wolfhart Zimmermann Memorial Symposium.

  20. Divergence from factorizable distributions and matroid representations by partitions

    Czech Academy of Sciences Publication Activity Database

    Matúš, František

    2009-01-01

    Roč. 55, č. 12 (2009), s. 5375-5381 ISSN 0018-9448 R&D Projects: GA AV ČR IAA100750603; GA ČR GA201/04/0393 Institutional research plan: CEZ:AV0Z10750506 Keywords : Information divergence * relative entropy * Shannon entropy * exponential family * hierarchical model * log-linear model * contingency table * Gibbs distribution * matroid representation * secret sharing scheme * maximum likelihood. Subject RIV: BA - General Mathematics Impact factor: 2.357, year: 2009 http://library.utia.cas.cz/separaty/2009/MTR/matus-divergence from factorizable distributions and matroid representations by partitions.pdf

  1. O Cabimento dos Embargos de Divergência

    OpenAIRE

    LOURENCO, S. R.

    2012-01-01

    A presente pesquisa objetiva demonstrar os embargos de divergência com enfoque nos elementos processuais do cabimento de tal modalidade recursal em nosso ordenamento jurídico. Para tanto, investigaremos os aspectos gerais dos embargos de divergência, a partir da análise dos elementos históricos enquanto a criação do instituto, como também sua finalidade e classificação no ordenamento jurídico brasileiro. Após, analisaremos o requisito de admissibilidade do cabimento dos embargo...

  2. Ultraviolet divergences in higher dimensional supersymmetric Yang-Mills theories

    International Nuclear Information System (INIS)

    Howe, P.S.; Stelle, K.S.

    1984-01-01

    We determine the loop orders for the onset of allowed ultra-violet divergences in higher dimensional supersymmetric Yang-Mills theories. Cancellations are controlled by the non-renormalization theorems for the linearly realizable supersymmetries and by the requirement that counterterms display the full non-linear supersymmetries when the classical equations of motion are imposed. The first allowed divergences in the maximal super Yang-Mills theories occur at four loops in five dimensions, three loops in six dimensions and two loops in seven dimensions. (orig.)

  3. Asymptotic states and infrared divergences in gauge theories

    International Nuclear Information System (INIS)

    Butler, D.R.

    1981-01-01

    The gauge theories, Gravity and QCD are shown to be infrared finite to a non-trival order by a generalization of the coherent state approach. The asymptotic Hamiltonian operator is used, along with a mathematical theorem by Magnus, to specify a S-operator and to show cancellation of infrared divergences at the amplitude level. This procedure is exemplified in Gravity to third order and applied to QCD for leading order divergences to fifth order in the coupling constant. Dimensional regularization is used to isolate the infrared singularities in QCD. The sections on Gravity include a derivation of the infrared structure of the propagators for a massive particle and the graviton

  4. An ancient divergence among the bacteria. [methanogenic phylogeny

    Science.gov (United States)

    Balch, W. E.; Magrum, L. J.; Fox, G. E.; Wolfe, R. S.; Woese, C. R.

    1977-01-01

    The 16S ribosomal RNZs from two species of met methanogenic bacteria, the mesophile Methanobacterium ruminantium and the thermophile Methanobacterium thermoautotrophicum, have been characterized in terms of the oligonucleotides produced by digestion with T1 ribonuclease. These two organisms are found to be sufficiently related that they can be considered members of the same genus or family. However, they bear only slight resemblance to 'typical' Procaryotic genera; such as Escherichia, Bacillus and Anacystis. The divergence of the methanogenic bacteria from other bacteria may be the most ancient phylogenetic event yet detected - antedating considerably the divergence of the blue green algal line for example, from the main bacterial line.

  5. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Directory of Open Access Journals (Sweden)

    Borja Milá

    Full Text Available The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%, yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%, with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In

  6. Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation.

    Science.gov (United States)

    Lande, Russell

    2009-07-01

    Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.

  7. On the usage of divergence nudging in the DMI nowcasting system

    Science.gov (United States)

    Korsholm, Ulrik; Petersen, Claus; Hansen Sass, Bent; Woetmann Nielsen, Niels; Getreuer Jensen, David; Olsen, Bjarke Tobias; Vedel, Henrik

    2014-05-01

    DMI has recently proposed a new method for nudging radar reflectivity CAPPI products into their operational nowcasting system. The system is based on rapid update cycles (with hourly frequency) with the High Resolution Limited Area Model combined with surface and upper air analysis at each initial time. During the first 1.5 hours of a simulation the model dynamical state is nudged in accordance with the CAPPI product after which a free forecast is produced with a forecast length of 12 hours. The nudging method is based on the assumption that precipitation is forced by low level moisture convergence and an enhanced moisture source will lead to convective triggering of the model cloud scheme. If the model under-predicts precipitation before cut-off horizontal low level divergence is nudged towards an estimated value. These pseudo observations are calculated from the CAPPI product by assuming a specific vertical profile of the change in divergence field. The strength of the nudging is proportional to the difference between observed and modelled precipitation. When over-predicting, the low level moisture source is reduced, and in-cloud moisture is nudged towards environmental values. Results have been analysed in terms of the fractions skill score and the ability of the nudging method to position the precipitation cells correctly is discussed. The ability of the model to retain memory of the precipitation systems in the free forecast has also been investigated and examples of combining the nudging method with extrapolated reflectivity fields are also shown.

  8. Anthropogenic habitat disturbance and ecological divergence between incipient species of the malaria mosquito Anopheles gambiae.

    Science.gov (United States)

    Kamdem, Colince; Tene Fossog, Billy; Simard, Frédéric; Etouna, Joachim; Ndo, Cyrille; Kengne, Pierre; Boussès, Philippe; Etoa, François-Xavier; Awono-Ambene, Parfait; Fontenille, Didier; Antonio-Nkondjio, Christophe; Besansky, Nora J; Costantini, Carlo

    2012-01-01

    Anthropogenic habitat disturbance is a prime cause in the current trend of the Earth's reduction in biodiversity. Here we show that the human footprint on the Central African rainforest, which is resulting in deforestation and growth of densely populated urban agglomerates, is associated to ecological divergence and cryptic speciation leading to adaptive radiation within the major malaria mosquito Anopheles gambiae. In southern Cameroon, the frequency of two molecular forms--M and S--among which reproductive isolation is strong but still incomplete, was correlated to an index of urbanisation extracted from remotely sensed data, expressed as the proportion of built-up surface in each sampling unit. The two forms markedly segregated along an urbanisation gradient forming a bimodal cline of ∼6-km width: the S form was exclusive to the rural habitat, whereas only the M form was present in the core of densely urbanised settings, co-occurring at times in the same polluted larval habitats of the southern house mosquito Culex quinquefasciatus--a species association that was not historically recorded before. Our results indicate that when humans create novel habitats and ecological heterogeneities, they can provide evolutionary opportunities for rapid adaptive niche shifts associated with lineage divergence, whose consequences upon malaria transmission might be significant.

  9. Health transition in Brazil: regional variations and divergence/convergence in mortality.

    Science.gov (United States)

    Borges, Gabriel Mendes

    2017-08-21

    This study analyzes the main characteristics of the health transition in Brazil and its five major regions, using a framework that accounts for regional inequalities in mortality trends. The regional mortality divergence/convergence process is described and discussed by considering the specific contributions of age groups and causes of death in life expectancy variations. Results show that mortality change in Brazil has follow the epidemiologic transition theory to some extent during the period under analysis - for instance, the sharp decline in infant mortality in all regions (first from infectious and parasitic diseases and then from causes associated with the perinatal period) and the increase in the participation of chronic and degenerative diseases as the main cause of death. However, some features of Brazilian transition have not followed the linear and unidirectional pattern proposed by the epidemiologic transition theory, which helps to understand the periods of regional divergence in life expectancy, despite the long-term trends showing reducing regional inequalities. The emergence of HIV/AIDS, the persistence of relatively high levels of other infections and parasitic diseases, the regional differences in the unexpected mortality improvements from cardiovascular diseases, and the rapid and strong variations in mortality from external causes are some of the examples.

  10. Unmanned Aerial Vehicle Remote Sensing for Field-Based Crop Phenotyping: Current Status and Perspectives

    Directory of Open Access Journals (Sweden)

    Guijun Yang

    2017-06-01

    Full Text Available Phenotyping plays an important role in crop science research; the accurate and rapid acquisition of phenotypic information of plants or cells in different environments is helpful for exploring the inheritance and expression patterns of the genome to determine the association of genomic and phenotypic information to increase the crop yield. Traditional methods for acquiring crop traits, such as plant height, leaf color, leaf area index (LAI, chlorophyll content, biomass and yield, rely on manual sampling, which is time-consuming and laborious. Unmanned aerial vehicle remote sensing platforms (UAV-RSPs equipped with different sensors have recently become an important approach for fast and non-destructive high throughput phenotyping and have the advantage of flexible and convenient operation, on-demand access to data and high spatial resolution. UAV-RSPs are a powerful tool for studying phenomics and genomics. As the methods and applications for field phenotyping using UAVs to users who willing to derive phenotypic parameters from large fields and tests with the minimum effort on field work and getting highly reliable results are necessary, the current status and perspectives on the topic of UAV-RSPs for field-based phenotyping were reviewed based on the literature survey of crop phenotyping using UAV-RSPs in the Web of Science™ Core Collection database and cases study by NERCITA. The reference for the selection of UAV platforms and remote sensing sensors, the commonly adopted methods and typical applications for analyzing phenotypic traits by UAV-RSPs, and the challenge for crop phenotyping by UAV-RSPs were considered. The review can provide theoretical and technical support to promote the applications of UAV-RSPs for crop phenotyping.

  11. Knowledge-based analysis of phenotypes

    KAUST Repository

    Hoendorf, Robert

    2016-01-27

    Phenotypes are the observable characteristics of an organism, and they are widely recorded in biology and medicine. To facilitate data integration, ontologies that formally describe phenotypes are being developed in several domains. I will describe a formal framework to describe phenotypes. A formalized theory of phenotypes is not only useful for domain analysis, but can also be applied to assist in the diagnosis of rare genetic diseases, and I will show how our results on the ontology of phenotypes is now applied in biomedical research.

  12. Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

    Science.gov (United States)

    Ali, Sajid; Rodriguez-Algaba, Julian; Thach, Tine; Sørensen, Chris K.; Hansen, Jens G.; Lassen, Poul; Nazari, Kumarse; Hodson, David P.; Justesen, Annemarie F.; Hovmøller, Mogens S.

    2017-01-01

    We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009–2015 revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales. PMID:28676811

  13. Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Sinha Amit

    2012-06-01

    Full Text Available Abstract Background An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans. Results We have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance. Conclusion Our data set provides a catalog for future functional investigations and indicates novel insight

  14. Context-Dependent Functional Divergence of the Notch Ligands DLL1 and DLL4 In Vivo.

    Directory of Open Access Journals (Sweden)

    Kristina Preuße

    2015-06-01

    Full Text Available Notch signalling is a fundamental pathway that shapes the developing embryo and sustains adult tissues by direct communication between ligand and receptor molecules on adjacent cells. Among the ligands are two Delta paralogues, DLL1 and DLL4, that are conserved in mammals and share a similar structure and sequence. They activate the Notch receptor partly in overlapping expression domains where they fulfil redundant functions in some processes (e.g. maintenance of the crypt cell progenitor pool. In other processes, however, they appear to act differently (e.g. maintenance of foetal arterial identity raising the questions of how similar DLL1 and DLL4 really are and which mechanism causes the apparent context-dependent divergence. By analysing mice that conditionally overexpress DLL1 or DLL4 from the same genomic locus (Hprt and mice that express DLL4 instead of DLL1 from the endogenous Dll1 locus (Dll1Dll4ki, we found functional differences that are tissue-specific: while DLL1 and DLL4 act redundantly during the maintenance of retinal progenitors, their function varies in the presomitic mesoderm (PSM where somites form in a Notch-dependent process. In the anterior PSM, every cell expresses both Notch receptors and ligands, and DLL1 is the only activator of Notch while DLL4 is not endogenously expressed. Transgenic DLL4 cannot replace DLL1 during somitogenesis and in heterozygous Dll1Dll4ki/+ mice, the Dll1Dll4ki allele causes a dominant segmentation phenotype. Testing several aspects of the complex Notch signalling system in vitro, we found that both ligands have a similar trans-activation potential but that only DLL4 is an efficient cis-inhibitor of Notch signalling, causing a reduced net activation of Notch. These differential cis-inhibitory properties are likely to contribute to the functional divergence of DLL1 and DLL4.

  15. Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

    Directory of Open Access Journals (Sweden)

    Sajid Ali

    2017-06-01

    Full Text Available We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009–2015 revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales.

  16. Molecular evolution of the Bovini tribe (Bovidae, Bovinae: Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

    Directory of Open Access Journals (Sweden)

    McCulloch Alan

    2009-04-01

    Full Text Available Abstract Background If mutation within the coding region of the genome is largely not adaptive, the ratio of nonsynonymous (dN to synonymous substitutions (dS per site (dN/dS should be approximately equal among closely related species. Furthermore, dN/dS in divergence between species should be equivalent to dN/dS in polymorphisms. This hypothesis is of particular interest in closely related members of the Bovini tribe, because domestication has promoted rapid phenotypic divergence through strong artificial selection of some species while others remain undomesticated. We examined a number of genes that may be involved in milk production in Domestic cattle and a number of their wild relatives for evidence that domestication had affected molecular evolution. Elevated rates of dN/dS were further queried to determine if they were the result of positive selection, low effective population size (Ne or reduced selective constraint. Results We have found that the domestication process has contributed to higher dN/dS ratios in cattle, especially in the lineages leading to the Domestic cow (Bos taurus and Mithan (Bos frontalis and within some breeds of Domestic cow. However, the high rates of dN/dS polymorphism within B. taurus when compared to species divergence suggest that positive selection has not elevated evolutionary rates in these genes. Likewise, the low rate of dN/dS in Bison, which has undergone a recent population bottleneck, indicates a reduction in population size alone is not responsible for these observations. Conclusion The effect of selection depends on effective population size and the selection coefficient (Nes. Typically under domestication both selection pressure for traits important in fitness in the wild and Ne are reduced. Therefore, reduced selective constraint could be responsible for the observed elevated evolutionary ratios in domesticated species, especially in B. taurus and B. frontalis, which have the highest dN/dS in the

  17. NIH Mouse Metabolic Phenotyping Centers: the power of centralized phenotyping.

    Science.gov (United States)

    Laughlin, Maren R; Lloyd, K C Kent; Cline, Gary W; Wasserman, David H

    2012-10-01

    The Mouse Metabolic Phenotyping Centers (MMPCs) were founded in 2001 by the National Institutes of Health (NIH) to advance biomedical research by providing the scientific community with standardized, high-quality phenotyping services for mouse models of diabetes, obesity, and their complications. The intent is to allow researchers to take optimum advantage of the many new mouse models produced in labs and in high-throughput public efforts. The six MMPCs are located at universities around the country and perform complex metabolic tests in intact mice and hormone and analyte assays in tissues on a fee-for-service basis. Testing is subsidized by the NIH in order to reduce the barriers for mouse researchers. Although data derived from these tests belong to the researcher submitting mice or tissues, these data are archived after publication in a public database run by the MMPC Coordinating and Bioinformatics Unit. It is hoped that data from experiments performed in many mouse models of metabolic diseases, using standard protocols, will be useful in understanding the nature of these complex disorders. The current areas of expertise include energy balance and body composition, insulin action and secretion, whole-body and tissue carbohydrate and lipid metabolism, cardiovascular and renal function, and metabolic pathway kinetics. In addition to providing services, the MMPC staff provides expertise and advice to researchers, and works to develop and refine test protocols to best meet the community's needs in light of current scientific developments. Test technology is disseminated by publications and through annual courses.

  18. A Bystander Mechanism Explains the Specific Phenotype of a Broadly Expressed Misfolded Protein.

    Directory of Open Access Journals (Sweden)

    Lauren Klabonski

    2016-12-01

    Full Text Available Misfolded proteins in transgenic models of conformational diseases interfere with proteostasis machinery and compromise the function of many structurally and functionally unrelated metastable proteins. This collateral damage to cellular proteins has been termed 'bystander' mechanism. How a single misfolded protein overwhelms the proteostasis, and how broadly-expressed mutant proteins cause cell type-selective phenotypes in disease are open questions. We tested the gain-of-function mechanism of a R37C folding mutation in an endogenous IGF-like C.elegans protein DAF-28. DAF-28(R37C is broadly expressed, but only causes dysfunction in one specific neuron, ASI, leading to a distinct developmental phenotype. We find that this phenotype is caused by selective disruption of normal biogenesis of an unrelated endogenous protein, DAF-7/TGF-β. The combined deficiency of DAF-28 and DAF-7 biogenesis, but not of DAF-28 alone, explains the gain-of-function phenotype-deficient pro-growth signaling by the ASI neuron. Using functional, fluorescently-tagged protein, we find that, in animals with mutant DAF-28/IGF, the wild-type DAF-7/TGF-β is mislocalized to and accumulates in the proximal axon of the ASI neuron. Activation of two different branches of the unfolded protein response can modulate both the developmental phenotype and DAF-7 mislocalization in DAF-28(R37C animals, but appear to act through divergent mechanisms. Our finding that bystander targeting of TGF-β explains the phenotype caused by a folding mutation in an IGF-like protein suggests that, in conformational diseases, bystander misfolding may specify the distinct phenotypes caused by different folding mutations.

  19. Color change, phenotypic plasticity, and camouflage

    Directory of Open Access Journals (Sweden)

    Martin eStevens

    2016-05-01

    Full Text Available The ability to change appearance over a range of timescales is widespread in nature, existing in many invertebrate and vertebrate groups. This can include color change occurring in seconds, minutes, and hours, to longer term changes associated with phenotypic plasticity and development. A major function is for camouflage against predators because color change and plasticity enables animals to match their surroundings and potentially reduce the risk of predation. Recently, we published findings (Stevens et al. 2014a showing how shore crabs can change their appearance and better match the background to predator vision in the short term. This, coupled with a number of past studies, emphasizes the potential that animals have to modify their appearance for camouflage. However, the majority of studies on camouflage and color plasticity have focused on a small number of species capable of unusually rapid changes. There are many broad questions that remain about the nature, mechanisms, evolution, and adaptive value of color change and plasticity for concealment. Here, I discuss past work and outline six questions relating to color change and plasticity, as well as major avenues for future work.

  20. The Human Phenotype Ontology in 2017

    International Nuclear Information System (INIS)

    Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie

    2016-01-01

    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

  1. Phenotypic variability in Meesmann's dystrophy

    DEFF Research Database (Denmark)

    Ehlers, Niels; Hjortdal, Jesper; Nielsen, Kim

    2008-01-01

    symptoms often include blurred vision and ocular irritation. Typical cases may be entirely free of complaints. Intermittent pain episodes, such as occur in recurrent erosion syndrome, are not the rule. Genetic sequencing indicated a familial relationship with the originally described Meesmann family......'s dystrophy occurs worldwide. The largest family described is the original German one, now supplemented with a Danish branch. Despite the presence of an identical genetic defect, the clinical phenotype varies. This suggests that non-KRT12-related mechanisms are responsible for the variation....

  2. The thrifty phenotype hypothesis revisited

    DEFF Research Database (Denmark)

    Vaag, A A; Grunnet, L G; Arora, G P

    2012-01-01

    Twenty years ago, Hales and Barker along with their co-workers published some of their pioneering papers proposing the 'thrifty phenotype hypothesis' in Diabetologia (4;35:595-601 and 3;36:62-67). Their postulate that fetal programming could represent an important player in the origin of type 2...... of the underlying molecular mechanisms. Type 2 diabetes is a multiple-organ disease, and developmental programming, with its idea of organ plasticity, is a plausible hypothesis for a common basis for the widespread organ dysfunctions in type 2 diabetes and the metabolic syndrome. Only two among the 45 known type 2...

  3. Rapid Prototyping Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The ARDEC Rapid Prototyping (RP) Laboratory was established in December 1992 to provide low cost RP capabilities to the ARDEC engineering community. The Stratasys,...

  4. Rates of genomic divergence in humans, chimpanzees and their lice.

    Science.gov (United States)

    Johnson, Kevin P; Allen, Julie M; Olds, Brett P; Mugisha, Lawrence; Reed, David L; Paige, Ken N; Pittendrigh, Barry R

    2014-02-22

    The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.

  5. Micropolar Fluids Using B-spline Divergence Conforming Spaces

    KAUST Repository

    Sarmiento, Adel; Garcia, Daniel; Dalcin, Lisandro; Collier, Nathan; Calo, Victor M.

    2014-01-01

    The divergence free formulation was used to guarantee an accurate solution of the flow. This formulation was implemented using the framework PetIGA as a basis, using its parallel stuctures to achieve high scalability. The results of the square heat driven cavity test case are in good agreement with those reported earlier.

  6. Divergent apparent temperature sensitivity of terrestrial ecosystem respiration

    Science.gov (United States)

    Bing Song; Shuli Niu; Ruise Luo; Yiqi Luo; Jiquan Chen; Guirui Yu; Janusz Olejnik; Georg Wohlfahrt; Gerard Kiely; Ako Noormets; Leonardo Montagnani; Alessandro Cescatti; Vincenzo Magliulo; Beverly Elizabeth Law; Magnus Lund; Andrej Varlagin; Antonio Raschi; Matthias Peichl; Mats B. Nilsson; Lutz Merbold

    2014-01-01

    Recent studies revealed convergent temperature sensitivity of ecosystem respiration (Re) within aquatic ecosystems and between terrestrial and aquatic ecosystems. We do not know yet whether various terrestrial ecosystems have consistent or divergent temperature sensitivity. Here, we synthesized 163 eddy covariance flux sites across the world and...

  7. Gauge-invariance and infrared divergences in the luminosity distance

    Energy Technology Data Exchange (ETDEWEB)

    Biern, Sang Gyu; Yoo, Jaiyul, E-mail: sgbiern@physik.uzh.ch, E-mail: jyoo@physik.uzh.ch [Center for Theoretical Astrophysics and Cosmology, Institute for Computational Science, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich (Switzerland)

    2017-04-01

    Measurements of the luminosity distance have played a key role in discovering the late-time cosmic acceleration. However, when accounting for inhomogeneities in the Universe, its interpretation has been plagued with infrared divergences in its theoretical predictions, which are in some cases used to explain the cosmic acceleration without dark energy. The infrared divergences in most calculations are artificially removed by imposing an infrared cut-off scale. We show that a gauge-invariant calculation of the luminosity distance is devoid of such divergences and consistent with the equivalence principle, eliminating the need to impose a cut-off scale. We present proper numerical calculations of the luminosity distance using the gauge-invariant expression and demonstrate that the numerical results with an ad hoc cut-off scale in previous calculations have negligible systematic errors as long as the cut-off scale is larger than the horizon scale. We discuss the origin of infrared divergences and their cancellation in the luminosity distance.

  8. Mass generation and the problem of seagull divergences

    International Nuclear Information System (INIS)

    Figueiredo, C. T.; Aguilar, A. C.

    2016-01-01

    The gluon mass generation is a purely non-perturbative effect, and the natural framework to study it in the continuum are the Schwinger-Dyson equations (SDEs) of the theory. At the level of the SDEs the generation of such a mass is associated with the existence of infrared finite solutions for the gluon propagator. From the theoretical point of view, the dynamical gluon mass generation has been traditionally plagued with seagull divergences. In this work, we will review how such divergences can be eliminated completely by virtue of a characteristic identity, valid in dimensional regularization. As a pedagogical example, we will first discuss in the context of scalar QED how it is possible to eliminate all seagull divergences, by triggering the aforementioned special identity, which enforces the masslessness of the photon. Then, we will discuss what happens in QCD and present an Ansatz for the three gluon vertex, which completely eliminates all seagull divergences and at same time allows for the possibility of a dynamical gluon mass generation. (paper)

  9. Sand-mediated divergence between shallow reef communities on ...

    African Journals Online (AJOL)

    Sand-mediated divergence between shallow reef communities on horizontal and vertical substrata in the western Indian Ocean. SN Porter, GM Branch, KJ Sink. Abstract. Distinctions are rarely made between vertical and horizontal surfaces when assessing reef community composition, yet physical differences are expected ...

  10. Determining divergence times with a protein clock: update and reevaluation

    Science.gov (United States)

    Feng, D. F.; Cho, G.; Doolittle, R. F.; Bada, J. L. (Principal Investigator)

    1997-01-01

    A recent study of the divergence times of the major groups of organisms as gauged by amino acid sequence comparison has been expanded and the data have been reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substitution rate at different sites. Beyond that, the availability of complete genome sequences for several eubacteria and an archaebacterium has had a great impact on the interpretation of certain aspects of the data. Thus, the majority of the archaebacterial sequences are not consistent with currently accepted views of the Tree of Life which cluster the archaebacteria with eukaryotes. Instead, they are either outliers or mixed in with eubacterial orthologs. The simplest resolution of the problem is to postulate that many of these sequences were carried into eukaryotes by early eubacterial endosymbionts about 2 billion years ago, only very shortly after or even coincident with the divergence of eukaryotes and archaebacteria. The strong resemblances of these same enzymes among the major eubacterial groups suggest that the cyanobacteria and Gram-positive and Gram-negative eubacteria also diverged at about this same time, whereas the much greater differences between archaebacterial and eubacterial sequences indicate these two groups may have diverged between 3 and 4 billion years ago.

  11. Divergent Explanatory Production (DEP): The Relationship between Resilience and Creativity

    Science.gov (United States)

    Hernández, Óscar Sánchez; Méndez, Francisco Xavier; Garber, Judy

    2015-01-01

    Introduction: The aim of the study is to describe and analyze a new test and construct, Divergent Explanatory Production (DEP), defined as the ability to observe adverse situations from various points of view. At the theoretical level, it is a bridge between the reformulated model of learned helplessness (as a resilience model), and creative…

  12. Gauge-invariance and infrared divergences in the luminosity distance

    International Nuclear Information System (INIS)

    Biern, Sang Gyu; Yoo, Jaiyul

    2017-01-01

    Measurements of the luminosity distance have played a key role in discovering the late-time cosmic acceleration. However, when accounting for inhomogeneities in the Universe, its interpretation has been plagued with infrared divergences in its theoretical predictions, which are in some cases used to explain the cosmic acceleration without dark energy. The infrared divergences in most calculations are artificially removed by imposing an infrared cut-off scale. We show that a gauge-invariant calculation of the luminosity distance is devoid of such divergences and consistent with the equivalence principle, eliminating the need to impose a cut-off scale. We present proper numerical calculations of the luminosity distance using the gauge-invariant expression and demonstrate that the numerical results with an ad hoc cut-off scale in previous calculations have negligible systematic errors as long as the cut-off scale is larger than the horizon scale. We discuss the origin of infrared divergences and their cancellation in the luminosity distance.

  13. The equational theory of prebisimilarity over basic CCS with divergence

    NARCIS (Netherlands)

    Aceto, L.; Capobianco, S.; Ingólfsdóttir, A.; Luttik, B.

    2008-01-01

    This paper studies the equational theory of prebisimilarity, a bisimulation-based preorder introduced by Hennessy and Milner in the early 1980s, over basic CCS with the divergent process O. It is well known that prebisimilarity affords a finite ground-complete axiomatization over this language; this

  14. Stimulating Divergent Thinking in Junior High Career Education.

    Science.gov (United States)

    Ranke, Charlotte; Champoux, Ellen M.

    1981-01-01

    Describes a middle school career-oriented teaching unit with emphasis on teaching for divergent thinking. The unit provides hands-on opportunities for eighth-grade students to explore careers using the knowledge and skills developed in their home economics class. The careers are restaurant management, hospitality service, and interior design. (CT)

  15. Divergence time estimates of mammals from molecular clocks and ...

    Indian Academy of Sciences (India)

    Prakash

    2009-10-30

    Oct 30, 2009 ... In the last decade and a half, mammalian phylogeny and lineage divergence .... not the sudden availability of ecological niches following the KTB mass .... fish fauna, ostracods, and palynofossils (Singh et al. 2006;. Prasad et al. ... tendons and hence the functional adaptations of the animal during its life and ...

  16. Transcutaneous vagus nerve stimulation (tVNS) enhances divergent thinking.

    Science.gov (United States)

    Colzato, Lorenza S; Ritter, Simone M; Steenbergen, Laura

    2018-03-01

    Creativity is one of the most important cognitive skills in our complex and fast-changing world. Previous correlative evidence showed that gamma-aminobutyric acid (GABA) is involved in divergent but not convergent thinking. In the current study, a placebo/sham-controlled, randomized between-group design was used to test a causal relation between vagus nerve and creativity. We employed transcutaneous vagus nerve stimulation (tVNS), a novel non-invasive brain stimulation technique to stimulate afferent fibers of the vagus nerve and speculated to increase GABA levels, in 80 healthy young volunteers. Creative performance was assessed in terms of divergent thinking (Alternate Uses Task) and convergent thinking tasks (Remote Associates Test, Creative Problem Solving Task, Idea Selection Task). Results demonstrate active tVNS, compared to sham stimulation, enhanced divergent thinking. Bayesian analysis reported the data to be inconclusive regarding a possible effect of tVNS on convergent thinking. Therefore, our findings corroborate the idea that the vagus nerve is causally involved in creative performance. Even thought we did not directly measure GABA levels, our results suggest that GABA (likely to be increased in active tVNS condition) supports the ability to select among competing options in high selection demand (divergent thinking) but not in low selection demand (convergent thinking). Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. The loop expansion as a divergent-power-series expansion

    International Nuclear Information System (INIS)

    Murai, N.

    1981-01-01

    The loop expansion should be divergent, possibly an asymptotic one, in the Euclidean path integral formulation. This consideration is important in applications of the symmetric and mass-independent renormalization. The [1,1] Pade approximant is calculated in a PHI 4 model. Its classical vacua may be not truely stable for nonzero coupling constant. (author)

  18. An asymptotic formula of the divergent bilateral basic hypergeometric series

    OpenAIRE

    Morita, Takeshi

    2012-01-01

    We show an asymptotic formula of the divergent bilateral basic hypergeometric series ${}_1\\psi_0 (a;-;q,\\cdot)$ with using the $q$-Borel-Laplace method. We also give the limit $q\\to 1-0$ of our asymptotic formula.

  19. Navier–Stokes flow in converging–diverging distensible tubes

    Directory of Open Access Journals (Sweden)

    Taha Sochi

    2015-09-01

    Full Text Available We use a method based on the lubrication approximation in conjunction with a residual-based mass-continuity iterative solution scheme to compute the flow rate and pressure field in distensible converging–diverging tubes for Navier–Stokes fluids. We employ an analytical formula derived from a one-dimensional version of the Navier–Stokes equations to describe the underlying flow model that provides the residual function. This formula correlates the flow rate to the boundary pressures in straight cylindrical elastic tubes with constant-radius. We validate our findings by the convergence toward a final solution with fine discretization as well as by comparison to the Poiseuille-type flow in its convergence toward analytic solutions found earlier in rigid converging–diverging tubes. We also tested the method on limiting special cases of cylindrical elastic tubes with constant-radius where the numerical solutions converged to the expected analytical solutions. The distensible model has also been endorsed by its convergence toward the rigid Poiseuille-type model with increasing the tube wall stiffness. Lubrication-based one-dimensional finite element method was also used for verification. In this investigation five converging–diverging geometries are used for demonstration, validation and as prototypes for modeling converging–diverging geometries in general.

  20. Functional Analysis of HIV/AIDS Stigma: Consensus or Divergence?

    Science.gov (United States)

    Hosseinzadeh, Hassan; Hossain, Syeda Zakia

    2011-01-01

    Functional theory proposes that attitudes may serve a variety of purposes for individuals. This study aimed to determine whether stigmatized attitudes toward HIV/AIDS serve the same function for all (consensus function) or serve different functions for different individuals (divergence function) by assessing various aspects of HIV/AIDS stigma…

  1. Genetic Divergence in Ducks for Economic Traits | Kalita | Animal ...

    African Journals Online (AJOL)

    D2 Statistics was used to identify the genetic divergence in 4 groups of duck, namely Khaki Campbell (KC), Desi (D), Khaki Campbell x Desi (KC x D) and Desi x Khaki Campbell (D x KC) reared under rural conditions at the Siphajar, Darrang District, Assam, India. The study showed that both Khaki Campbell and Desi or ...

  2. Micropolar Fluids Using B-spline Divergence Conforming Spaces

    KAUST Repository

    Sarmiento, Adel

    2014-06-06

    We discretized the two-dimensional linear momentum, microrotation, energy and mass conservation equations from micropolar fluids theory, with the finite element method, creating divergence conforming spaces based on B-spline basis functions to obtain pointwise divergence free solutions [8]. Weak boundary conditions were imposed using Nitsche\\'s method for tangential conditions, while normal conditions were imposed strongly. Once the exact mass conservation was provided by the divergence free formulation, we focused on evaluating the differences between micropolar fluids and conventional fluids, to show the advantages of using the micropolar fluid model to capture the features of complex fluids. A square and an arc heat driven cavities were solved as test cases. A variation of the parameters of the model, along with the variation of Rayleigh number were performed for a better understanding of the system. The divergence free formulation was used to guarantee an accurate solution of the flow. This formulation was implemented using the framework PetIGA as a basis, using its parallel stuctures to achieve high scalability. The results of the square heat driven cavity test case are in good agreement with those reported earlier.

  3. The odd couple: Diverging paths in language policy and educational ...

    African Journals Online (AJOL)

    This paper examines the divergences between what educational policy calls for in South African schools with regard to language and learning and what takes place in schools. It argues that South African constitutional and education policy statements employ an idea of languages as bound entities and systems, and ...

  4. Analysis of growth characteristics in short-term divergently selected ...

    African Journals Online (AJOL)

    weeks of age body weight in divergent lines of Japanese quail. Growth curves for both sexes within each selection group resembled the general sigmoid shape of a typical growth curve. Gompertz model curves and the observed growth curves were ...

  5. Divergence-Free Wavelets on the Hypercube : General Boundary Conditions

    NARCIS (Netherlands)

    Stevenson, R.

    2016-01-01

    On the n-dimensional hypercube, for given k∈N, wavelet Riesz bases are constructed for the subspace of divergence-free vector fields of the Sobolev space Hk((0,1)n)n with general homogeneous Dirichlet boundary conditions, including slip or no-slip boundary conditions. Both primal and suitable dual

  6. Factor analysis models via I-divergence optimization

    NARCIS (Netherlands)

    Finesso, L.; Spreij, P.

    2016-01-01

    Given a positive definite covariance matrix Σˆ of dimension n, we approximate it with a covariance of the form HH⊤+D, where H has a prescribed number k0 is diagonal. The quality of the approximation is gauged by the I-divergence between the zero mean normal laws with covariances

  7. ACE phenotyping in Gaucher disease.

    Science.gov (United States)

    Danilov, Sergei M; Tikhomirova, Victoria E; Metzger, Roman; Naperova, Irina A; Bukina, Tatiana M; Goker-Alpan, Ozlem; Tayebi, Nahid; Gayfullin, Nurshat M; Schwartz, David E; Samokhodskaya, Larisa M; Kost, Olga A; Sidransky, Ellen

    2018-04-01

    Gaucher disease is characterized by the activation of splenic and hepatic macrophages, accompanied by dramatically increased levels of angiotensin-converting enzyme (ACE). To evaluate the source of the elevated blood ACE, we performed complete ACE phenotyping using blood, spleen and liver samples from patients with Gaucher disease and controls. ACE phenotyping included 1) immunohistochemical staining for ACE; 2) measuring ACE activity with two substrates (HHL and ZPHL); 3) calculating the ratio of the rates of substrate hydrolysis (ZPHL/HHL ratio); 4) assessing the conformational fingerprint of ACE by evaluating the pattern of binding of monoclonal antibodies to 16 different ACE epitopes. We show that in patients with Gaucher disease, the dramatically increased levels of ACE originate from activated splenic and/or hepatic macrophages (Gaucher cells), and that both its conformational fingerprint and kinetic characteristics (ZPHL/HHL ratio) differ from controls and from patients with sarcoid granulomas. Furthermore, normal spleen was found to produce high levels of endogenous ACE inhibitors and a novel, tightly-bound 10-30 kDa ACE effector which is deficient in Gaucher spleen. The conformation of ACE is tissue-specific. In Gaucher disease, ACE produced by activated splenic macrophages differs from that in hepatic macrophages, as well as from macrophages and dendritic cells in sarcoid granulomas. The observed differences are likely due to altered ACE glycosylation or sialylation in these diseased organs. The conformational differences in ACE may serve as a specific biomarker for Gaucher disease. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Assessing carbon source-dependent phenotypic variability in Pseudomonas putida

    DEFF Research Database (Denmark)

    Nikel, Pablo Ivan; de Lorenzo, Victor

    2018-01-01

    capacity of single bacteria by means of fluorescence microscopy and flow cytometry, in combination with the analysis of the temporal takeoff of growth in single-cell cultures, is a simple and easy-to-implement approach. It can help to understand the link between macroscopic phenotypes (e.g., microbial......The soil bacterium Pseudomonas putida is rapidly becoming a platform of choice for applications that require a microbial host highly resistant to different types of stresses and elevated rates of reducing power regeneration. P. putida is capable of growing in a wide variety of carbon sources...

  9. Rapid Tooling via Stereolithography

    OpenAIRE

    Montgomery, Eva

    2006-01-01

    Approximately three years ago, composite stereolithography (SL) resins were introduced to the marketplace, offering performance features beyond what traditional SL resins could offer. In particular, the high heat deflection temperatures and high stiffness of these highly filled resins have opened the door to several new rapid prototyping (RP) applications, including wind tunnel test modelling and, more recently, rapid tooling.

  10. MSAP In Tiger Snakes: Island Populations Are Epigenetically More Divergent

    OpenAIRE

    Konate, Moumouni; Lopez, Carlos; Thomson, Vicki

    2017-01-01

    Research on changes in phenotypic plasticity within wild animal populations is centuries old, however far fewer studies have investigated the role that epigenetics play in the development or persistence of natural variation in response to environmental change. Tiger snakes (Notechis scutatus) are an ideal study organism to investigate the link between epigenetics and phenotypic responses to environmental change, as they live on a range of offshore islands with different environments and prey ...

  11. Of mice and men: divergence of gene expression patterns in kidney.

    Directory of Open Access Journals (Sweden)

    Lydie Cheval

    Full Text Available Since the development of methods for homologous gene recombination, mouse models have played a central role in research in renal pathophysiology. However, many published and unpublished results show that mice with genetic changes mimicking human pathogenic mutations do not display the human phenotype. These functional differences may stem from differences in gene expression between mouse and human kidneys. However, large scale comparison of gene expression networks revealed conservation of gene expression among a large panel of human and mouse tissues including kidneys. Because renal functions result from the spatial integration of elementary processes originating in the glomerulus and the successive segments constituting the nephron, we hypothesized that differences in gene expression profiles along the human and mouse nephron might account for different behaviors. Analysis of SAGE libraries generated from the glomerulus and seven anatomically defined nephron segments from human and mouse kidneys allowed us to identify 4644 pairs of gene orthologs expressed in either one or both species. Quantitative analysis shows that many transcripts are present at different levels in the two species. It also shows poor conservation of gene expression profiles, with less than 10% of the 4644 gene orthologs displaying a higher conservation of expression profiles than the neutral expectation (p<0.05. Accordingly, hierarchical clustering reveals a higher degree of conservation of gene expression patterns between functionally unrelated kidney structures within a given species than between cognate structures from the two species. Similar findings were obtained for sub-groups of genes with either kidney-specific or housekeeping functions. Conservation of gene expression at the scale of the whole organ and divergence at the level of its constituting sub-structures likely account for the fact that although kidneys assume the same global function in the two species

  12. Rapid improvement teams.

    Science.gov (United States)

    Alemi, F; Moore, S; Headrick, L; Neuhauser, D; Hekelman, F; Kizys, N

    1998-03-01

    Suggestions, most of which are supported by empirical studies, are provided on how total quality management (TQM) teams can be used to bring about faster organizationwide improvements. Ideas are offered on how to identify the right problem, have rapid meetings, plan rapidly, collect data rapidly, and make rapid whole-system changes. Suggestions for identifying the right problem include (1) postpone benchmarking when problems are obvious, (2) define the problem in terms of customer experience so as not to blame employees nor embed a solution in the problem statement, (3) communicate with the rest of the organization from the start, (4) state the problem from different perspectives, and (5) break large problems into smaller units. Suggestions for having rapid meetings include (1) choose a nonparticipating facilitator to expedite meetings, (2) meet with each team member before the team meeting, (3) postpone evaluation of ideas, and (4) rethink conclusions of a meeting before acting on them. Suggestions for rapid planning include reducing time spent on flowcharting by focusing on the future, not the present. Suggestions for rapid data collection include (1) sample patients for surveys, (2) rely on numerical estimates by process owners, and (3) plan for rapid data collection. Suggestions for rapid organizationwide implementation include (1) change membership on cross-functional teams, (2) get outside perspectives, (3) use unfolding storyboards, and (4) go beyond self-interest to motivate lasting change in the organization. Additional empirical investigations of time saved as a consequence of the strategies provided are needed. If organizations solve their problems rapidly, fewer unresolved problems may remain.

  13. Divergência genética em linhagens de melancia Genetic divergence in watermelon lines

    Directory of Open Access Journals (Sweden)

    Flávio de França Souza

    2005-06-01

    Full Text Available A divergência genética entre 31 genótipos de melancia foi avaliada por meio da análise de variáveis canônicas e de técnicas de agrupamento (Tocher e método hierárquico de Ward baseadas na distância generalizada de Mahalanobis (D²ii'. Trinta linhagens, obtidas a partir de acessos coletados no Nordeste brasileiro e a cultivar 'Crimson Sweet' foram avaliadas quanto ao número de dias para o aparecimento da primeira flor masculina e da primeira flor feminina (NDM e NDF; número do nó da primeira flor masculina e da primeira flor feminina (NGM e NGF; número de frutos por planta (NFP; comprimento de rama principal (CRP; peso médio de fruto (PMF; teor de sólidos solúveis (TSS; diâmetro transversal e longitudinal do fruto (DTF e DLF e espessura média de casca (EMC. O experimento foi realizado em delineamento de blocos ao acaso com três repetições, compostas por parcelas de sete plantas. As características que mais contribuíram para a divergência entre as linhagens foram número de frutos por planta, diâmetro longitudinal, teor de sólidos solúveis e peso médio de fruto. Foram formados três grupos por meio do método de otimização de Tocher, três por meio do método hierárquico de Ward e quatro grupos pela dispersão gráfica baseada nas duas primeiras variáveis canônicas. Neste caso, o grupo I compôs-se de sete linhagens de Pernambuco e uma da Bahia; o grupo II reuniu todas as 21 linhagens do Maranhão; os grupos III e IV foram compostos pela linhagem 97-0247.008 (Pernambuco e pela cultivar Crimson Sweet, respectivamente. As linhagens 87-019.021 e 87-019.022 foram as mais semelhantes, enquanto a linhagem 87-019.023 e 'Crimson Sweet' apresentaram maior dissimilaridade pela distância generalizada Mahalanobis (D²ii'. Os cruzamentos mais promissores serão aqueles realizados entre Crimson Sweet e as linhagens do grupo II. Cruzamentos entre Crimson Sweet e as linhagens do grupo I serão interessantes para a obtenção de

  14. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization.

    Science.gov (United States)

    Gimmler, Anna; Stoeck, Thorsten

    2015-08-01

    Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Rapid response systems.

    Science.gov (United States)

    Lyons, Patrick G; Edelson, Dana P; Churpek, Matthew M

    2018-07-01

    Rapid response systems are commonly employed by hospitals to identify and respond to deteriorating patients outside of the intensive care unit. Controversy exists about the benefits of rapid response systems. We aimed to review the current state of the rapid response literature, including evolving aspects of afferent (risk detection) and efferent (intervention) arms, outcome measurement, process improvement, and implementation. Articles written in English and published in PubMed. Rapid response systems are heterogeneous, with important differences among afferent and efferent arms. Clinically meaningful outcomes may include unexpected mortality, in-hospital cardiac arrest, length of stay, cost, and processes of care at end of life. Both positive and negative interventional studies have been published, although the two largest randomized trials involving rapid response systems - the Medical Early Response and Intervention Trial (MERIT) and the Effect of a Pediatric Early Warning System on All-Cause Mortality in Hospitalized Pediatric Patients (EPOCH) trial - did not find a mortality benefit with these systems, albeit with important limitations. Advances in monitoring technologies, risk assessment strategies, and behavioral ergonomics may offer opportunities for improvement. Rapid responses may improve some meaningful outcomes, although these findings remain controversial. These systems may also improve care for patients at the end of life. Rapid response systems are expected to continue evolving with novel developments in monitoring technologies, risk prediction informatics, and work in human factors. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Refined Phenotyping of Modic Changes

    Science.gov (United States)

    Määttä, Juhani H.; Karppinen, Jaro; Paananen, Markus; Bow, Cora; Luk, Keith D.K.; Cheung, Kenneth M.C.; Samartzis, Dino

    2016-01-01

    Abstract Low back pain (LBP) is the world's most disabling condition. Modic changes (MC) are vertebral bone marrow changes adjacent to the endplates as noted on magnetic resonance imaging. The associations of specific MC types and patterns with prolonged, severe LBP and disability remain speculative. This study assessed the relationship of prolonged, severe LBP and back-related disability, with the presence and morphology of lumbar MC in a large cross-sectional population-based study of Southern Chinese. We addressed the topographical and morphological dimensions of MC along with other magnetic resonance imaging phenotypes (eg, disc degeneration and displacement) on the basis of axial T1 and sagittal T2-weighted imaging of L1-S1. Prolonged severe LBP was defined as LBP lasting ≥30 days during the past year, and a visual analog scale severest pain intensity of at least 6/10. An Oswestry Disability Index score of 15% was regarded as significant disability. We also assessed subject demographics, occupation, and lifestyle factors. In total, 1142 subjects (63% females, mean age 53 years) were assessed. Of these, 282 (24.7%) had MC (7.1% type I, 17.6% type II). MC subjects were older (P = 0.003), had more frequent disc displacements (P disability. The strength of the associations increased with the number of MC. This large-scale study is the first to definitively note MC types and specific morphologies to be independently associated with prolonged severe LBP and back-related disability. This proposed refined MC phenotype may have direct implications in clinical decision-making as to the development and management of LBP. Understanding of these imaging biomarkers can lead to new preventative and personalized therapeutics related to LBP. PMID:27258491

  17. Development and evaluation of a phenotypic assay monitoring resistance formation to protease inhibitors in HIV-1-infected patients.

    Science.gov (United States)

    Gehringer, Heike; Von der Helm, Klaus; Seelmeir, Sigrid; Weissbrich, Benedikt; Eberle, Josef; Nitschko, Hans

    2003-05-01

    A novel phenotypic assay, based on recombinant expression of the HIV-1-protease was developed and evaluated; it monitors the formation of resistance to protease inhibitors. The HIV-1 protease-encoding region from the blood sample of patients was amplified, ligated into the expression vector pBD2, and recombinantly expressed in Escherichia coli TG1 cells. The resulting recombinant enzyme was purified by a newly developed one-step acid extraction protocol. The protease activity was determined in presence of five selected HIV protease inhibitors and the 50% inhibitory concentration (IC(50)) to the respective protease inhibitors determined. The degree of resistance was expressed in terms of x-fold increase in IC(50) compared to the IC(50) value of an HIV-1 wild type protease preparation. The established test system showed a reproducible recombinant expression of each individual patients' HIV-1 protease population. Samples of nine clinically well characterised HIV-1-infected patients with varying degrees of resistance were analysed. There was a good correlation between clinical parameters and the results obtained by this phenotypic assay. For the majority of patients a blind genotypic analysis of the patients' protease domain revealed a fair correlation to the results of the phenotypic assay. In a minority of patients our phenotypic results diverged from the genotypic ones. This novel phenotypic assay can be carried out within 8-10 days, and offers a significant advantage in time to the current employed phenotypic tests.

  18. Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants.

    Science.gov (United States)

    Reusch, Thorsten B H

    2014-01-01

    I summarize marine studies on plastic versus adaptive responses to global change. Due to the lack of time series, this review focuses largely on the potential for adaptive evolution in marine animals and plants. The approaches were mainly synchronic comparisons of phenotypically divergent populations, substituting spatial contrasts in temperature or CO2 environments for temporal changes, or in assessments of adaptive genetic diversity within populations for traits important under global change. The available literature is biased towards gastropods, crustaceans, cnidarians and macroalgae. Focal traits were mostly environmental tolerances, which correspond to phenotypic buffering, a plasticity type that maintains a functional phenotype despite external disturbance. Almost all studies address coastal species that are already today exposed to fluctuations in temperature, pH and oxygen levels. Recommendations for future research include (i) initiation and analyses of observational and experimental temporal studies encompassing diverse phenotypic traits (including diapausing cues, dispersal traits, reproductive timing, morphology) (ii) quantification of nongenetic trans-generational effects along with components of additive genetic variance (iii) adaptive changes in microbe-host associations under the holobiont model in response to global change (iv) evolution of plasticity patterns under increasingly fluctuating environments and extreme conditions and (v) joint consideration of demography and evolutionary adaptation in evolutionary rescue approaches.

  19. Dominant negative mutations of Caenorhabditis elegans daf-7 confer a novel developmental phenotype.

    Science.gov (United States)

    Crook, Matt; Grant, Warwick N

    2013-06-01

    TGF-β signaling pathways are involved in the control of development in every member of the animal kingdom. As such, TGF-β ligands are widely divergent yet retain a set of core conserved features, specifically, a pre-protein cleavage site and several conserved ligand domain residues, the disruption of which produces a dominant negative phenotype. We have extended these observations into an invertebrate system by creating a series of loss-of-function Caenorhabditis elegans daf-7 transgenes. When we tested these mutant transgenes in a daf-7/+ background, we saw a molting and excretory canal phenotype. Members of both pathways downstream of daf-4 were required for this phenotype. Our results show that the basic mechanisms of TGF-β function are conserved across the animal kingdom. A subset of our daf-7 mutations also produced an unexpected and novel phenotype. Epistasis experiments demonstrated that both daf-3/-5 and sma-4/-9 were downstream of our mutant daf-7 transgenes, which suggests not only a role for DAF-7 in the control of molting and the development of the excretory system but also that daf-7 and dbl-1 signaling may converge downstream of their shared Type II receptor, daf-4. Our approach may unveil new roles in development for other invertebrate TGF-β ligands. Copyright © 2013 Wiley Periodicals, Inc.

  20. The phenotypic variance gradient - a novel concept.

    Science.gov (United States)

    Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

    2014-11-01

    Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely "a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added". This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a "phenotypic variance gradient", are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization.

  1. Microarray analysis of subcutaneous adipose tissue from mature cows with divergent body weight gain after feed restriction and realimentation

    Directory of Open Access Journals (Sweden)

    H.C. Cunningham

    2018-02-01

    Full Text Available Body weight response to periods of feed restriction and realimentation is critical and relevant to the agricultural industry. The purpose of this study was to evaluate differentially expressed genes identified in subcutaneous adipose tissue collected from cows divergent in body weight (BW gain after feed restriction and realimentation. We compared adipose samples from cows with greater gain based on average daily gain (ADG during realimentation with samples from cows with lesser gain. Specifically, there were four comparisons including two comparing the high and low gain animals across each feeding period (feed restriction and realimentation and two that compared differences in feed restriction and realimentation across high or low gain classifications. Using microarray analysis, we provide a set of differentially expressed genes identified between the high and low gain at both periods of nutrient restriction and realimentation. These data identify multiple differentially expressed genes between these two phenotypes across both nutritional environments. Keywords: Beef cows, Subcutaneous fat, Transcriptome

  2. Clinical features of Friedreich's ataxia: classical and atypical phenotypes.

    Science.gov (United States)

    Parkinson, Michael H; Boesch, Sylvia; Nachbauer, Wolfgang; Mariotti, Caterina; Giunti, Paola

    2013-08-01

    One hundred and fifty years since Nikolaus Friedreich's first description of the degenerative ataxic syndrome which bears his name, his description remains at the core of the classical clinical phenotype of gait and limb ataxia, poor balance and coordination, leg weakness, sensory loss, areflexia, impaired walking, dysarthria, dysphagia, eye movement abnormalities, scoliosis, foot deformities, cardiomyopathy and diabetes. Onset is typically around puberty with slow progression and shortened life-span often related to cardiac complications. Inheritance is autosomal recessive with the vast majority of cases showing an unstable intronic GAA expansion in both alleles of the frataxin gene on chromosome 9q13. A small number of cases are caused by a compound heterozygous expansion with a point mutation or deletion. Understanding of the underlying molecular biology has enabled identification of atypical phenotypes with late onset, or atypical features such as retained reflexes. Late-onset cases tend to have slower progression and are associated with smaller GAA expansions. Early-onset cases tend to have more rapid progression and a higher frequency of non-neurological features such as diabetes, cardiomyopathy, scoliosis and pes cavus. Compound heterozygotes, including those with large deletions, often have atypical features. In this paper, we review the classical and atypical clinical phenotypes of Friedreich's ataxia. © 2013 International Society for Neurochemistry.

  3. Study of selected phenotype switching strategies in time varying environment

    Energy Technology Data Exchange (ETDEWEB)

    Horvath, Denis, E-mail: horvath.denis@gmail.com [Centre of Interdisciplinary Biosciences, Institute of Physics, Faculty of Science, P.J. Šafárik University in Košice, Jesenná 5, 040 01 Košice (Slovakia); Brutovsky, Branislav, E-mail: branislav.brutovsky@upjs.sk [Department of Biophysics, Institute of Physics, P.J. Šafárik University in Košice, Jesenná 5, 040 01 Košice (Slovakia)

    2016-03-22

    Population heterogeneity plays an important role across many research, as well as the real-world, problems. The population heterogeneity relates to the ability of a population to cope with an environment change (or uncertainty) preventing its extinction. However, this ability is not always desirable as can be exemplified by an intratumor heterogeneity which positively correlates with the development of resistance to therapy. Causation of population heterogeneity is therefore in biology and medicine an intensively studied topic. In this paper the evolution of a specific strategy of population diversification, the phenotype switching, is studied at a conceptual level. The presented simulation model studies evolution of a large population of asexual organisms in a time-varying environment represented by a stochastic Markov process. Each organism disposes with a stochastic or nonlinear deterministic switching strategy realized by discrete-time models with evolvable parameters. We demonstrate that under rapidly varying exogenous conditions organisms operate in the vicinity of the bet-hedging strategy, while the deterministic patterns become relevant as the environmental variations are less frequent. Statistical characterization of the steady state regimes of the populations is done using the Hellinger and Kullback–Leibler functional distances and the Hamming distance. - Highlights: • Relation between phenotype switching and environment is studied. • The Markov chain Monte Carlo based model is developed. • Stochastic and deterministic strategies of phenotype switching are utilized. • Statistical measures of the dynamic heterogeneity reveal universal properties. • The results extend to higher lattice dimensions.

  4. Study of selected phenotype switching strategies in time varying environment

    International Nuclear Information System (INIS)

    Horvath, Denis; Brutovsky, Branislav

    2016-01-01

    Population heterogeneity plays an important role across many research, as well as the real-world, problems. The population heterogeneity relates to the ability of a population to cope with an environment change (or uncertainty) preventing its extinction. However, this ability is not always desirable as can be exemplified by an intratumor heterogeneity which positively correlates with the development of resistance to therapy. Causation of population heterogeneity is therefore in biology and medicine an intensively studied topic. In this paper the evolution of a specific strategy of population diversification, the phenotype switching, is studied at a conceptual level. The presented simulation model studies evolution of a large population of asexual organisms in a time-varying environment represented by a stochastic Markov process. Each organism disposes with a stochastic or nonlinear deterministic switching strategy realized by discrete-time models with evolvable parameters. We demonstrate that under rapidly varying exogenous conditions organisms operate in the vicinity of the bet-hedging strategy, while the deterministic patterns become relevant as the environmental variations are less frequent. Statistical characterization of the steady state regimes of the populations is done using the Hellinger and Kullback–Leibler functional distances and the Hamming distance. - Highlights: • Relation between phenotype switching and environment is studied. • The Markov chain Monte Carlo based model is developed. • Stochastic and deterministic strategies of phenotype switching are utilized. • Statistical measures of the dynamic heterogeneity reveal universal properties. • The results extend to higher lattice dimensions.

  5. Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei

    Science.gov (United States)

    Dinh Thi, Vinh Ha; Coriton, Olivier; Le Clainche, Isabelle; Arnaud, Dominique; Gordon, Sean P.; Linc, Gabriella; Catalan, Pilar; Hasterok, Robert; Vogel, John P.; Jahier, Joseph; Chalhoub, Boulos

    2016-01-01

    Brachypodium hybridum (2n = 30) is a natural allopolyploid with highly divergent sub-genomes derived from two extant diploid species, B. distachyon (2n = 10) and B. stacei (2n = 20) that differ in chromosome evolution and number. We created synthetic B. hybridum allotetraploids by hybridizing various lines of B. distachyon and B. stacei. The initial amphihaploid F1 interspecific hybrids were obtained at low frequencies when B. distachyon was used as the maternal parent (0.15% or 0.245% depending on the line used) and were sterile. No hybrids were obtained from reciprocal crosses or when autotetraploids of the parental species were crossed. Colchicine treatment was used to double the genome of the F1 amphihaploid lines leading to allotetraploids. The genome-doubled F1 plants produced a few S1 (first selfed generation) seeds after self-pollination. S1 plants from one parental combination (Bd3-1×Bsta5) were fertile and gave rise to further generations whereas those of another parental combination (Bd21×ABR114) were sterile, illustrating the importance of the parental lineages crossed. The synthetic allotetraploids were stable and resembled the natural B. hybridum at the phenotypic, cytogenetic and genomic levels. The successful creation of synthetic B. hybridum offers the possibility to study changes in genome structure and regulation at the earliest stages of allopolyploid formation in comparison with the parental species and natural B. hybridum. PMID:27936041

  6. Genetic Divergence and Chemotype Diversity in the Fusarium Head Blight Pathogen Fusarium poae.

    Science.gov (United States)

    Vanheule, Adriaan; De Boevre, Marthe; Moretti, Antonio; Scauflaire, Jonathan; Munaut, Françoise; De Saeger, Sarah; Bekaert, Boris; Haesaert, Geert; Waalwijk, Cees; van der Lee, Theo; Audenaert, Kris

    2017-08-23

    Fusarium head blight is a disease caused by a complex of Fusarium species. F. poae is omnipresent throughout Europe in spite of its low virulence. In this study, we assessed a geographically diverse collection of F. poae isolates for its genetic diversity using AFLP (Amplified Fragment Length Polymorphism). Furthermore, studying the mating type locus and chromosomal insertions, we identified hallmarks of both sexual recombination and clonal spread of successful genotypes in the population. Despite the large genetic variation found, all F. poae isolates possess the nivalenol chemotype based on Tri7 sequence analysis. Nevertheless, Tri gene clusters showed two layers of genetic variability. Firstly, the Tri1 locus was highly variable with mostly synonymous mutations and mutations in introns pointing to a strong purifying selection pressure. Secondly, in a subset of isolates, the main trichothecene gene cluster was invaded by a transposable element between Tri5 and Tri6 . To investigate the impact of these variations on the phenotypic chemotype, mycotoxin production was assessed on artificial medium. Complex blends of type A and type B trichothecenes were produced but neither genetic variability in the Tri genes nor variability in the genome or geography accounted for the divergence in trichothecene production. In view of its complex chemotype, it will be of utmost interest to uncover the role of trichothecenes in virulence, spread and survival of F. poae .

  7. Parallel behavioral and morphological divergence in fence lizards on two college campuses

    Science.gov (United States)

    Howe, Stephen; Hynes, Stephanie; Hobbs, Brooke; Handal, Karina

    2018-01-01

    The spread of urban development has dramatically altered natural habitats, modifying community relationships, abiotic factors, and structural features. Animal populations living in these areas must perish, emigrate, or find ways to adjust to a suite of new selective pressures. Those that successfully inhabit the urban environment may make behavioral, physiological, and/or morphological adjustments that represent either evolutionary change and/or phenotypic plasticity. We tested for effects of urbanization on antipredator behavior and associated morphology across an urban-wild gradient in the western fence lizard (Sceloporus occidentalis) in two California counties, Santa Barbara and San Luis Obispo. We compared college campuses in both counties with adjacent rural habitats, conducting field trials that allowed us to characterize antipredator behavior in response to the acute stress of capture. We found notable divergence between campus and rural behavior, with campus lizards more frequently exhibiting diminished escape behavior, including tonic immobility, and lower sprint speeds. Furthermore, campus females had significantly shorter limbs, and while this did not explain variation in sprint speed, those with shorter limbs were more likely to show tonic immobility. We hypothesize that these parallel behavioral and morphological changes on both campuses reflect adjustment to a novel environment involving changes in predation and human presence. PMID:29444102

  8. Geographic divergence and colour change in response to visual backgrounds and illumination intensity in bearded dragons.

    Science.gov (United States)

    Cadena, Viviana; Smith, Kathleen R; Endler, John A; Stuart-Fox, Devi

    2017-03-15

    Animals may improve camouflage by both dynamic colour change and local evolutionary adaptation of colour but we have little understanding of their relative importance in colour-changing species. We tested for differences in colour change in response to background colour and light intensity in two populations of central bearded dragon lizards ( Pogona vitticeps ) representing the extremes in body coloration and geographical range. We found that bearded dragons change colour in response to various backgrounds and that colour change is affected by illumination intensity. Within-individual colour change was similar in magnitude in the two populations but varied between backgrounds. However, at the endpoints of colour change, each population showed greater similarity to backgrounds that were representative of the local habitat compared with the other population, indicating local adaptation to visual backgrounds. Our results suggest that even in species that change colour, both phenotypic plasticity and geographic divergence of coloration may contribute to improved camouflage. © 2017. Published by The Company of Biologists Ltd.

  9. Divergence is not enough: the use of ecological niche models for the validation of taxon boundaries.

    Science.gov (United States)

    Dagnino, D; Minuto, L; Casazza, G

    2017-11-01

    Delimiting taxon boundaries is crucial for any evolutionary research and conservation regulation. In order to avoid mistaken description of species, the approach of integrative taxonomy recommends considering multidisciplinary lines of evidence, including ecology. Unfortunately, ecological data are often difficult to quantify objectively. Here we test and discuss the potential use of ecological niche models for validating taxon boundaries, using three pairs of closely related plant taxa endemic to the south-western Alps as a case study. We also discuss the application of ecological niche models for species delimitation and the implementation of different approaches. Niche overlap, niche equivalency and niche similarity were assessed both in multidimensional environmental space and in geographic space to look for differences in the niche of three pairs of closely related plant taxa. We detected a high degree of niche differentiation between taxa although this result seems not due to differences in habitat selection. The different statistical tests gave contrasting outcomes between environmental and geographic spaces. According to our results, niche divergence does not seem to support taxon boundaries at species level, but may have had important consequences for local adaptation and in generating phenotypic diversity at intraspecific level. Environmental space analysis should be preferred to geographic space as it provides more clear results. Even if the different analyses widely disagree in their conclusions about taxon boundaries, our study suggests that ecological niche models may help taxonomists to reach a decision. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  10. Divergence of perturbation theory in large scale structures

    Science.gov (United States)

    Pajer, Enrico; van der Woude, Drian

    2018-05-01

    We make progress towards an analytical understanding of the regime of validity of perturbation theory for large scale structures and the nature of some non-perturbative corrections. We restrict ourselves to 1D gravitational collapse, for which exact solutions before shell crossing are known. We review the convergence of perturbation theory for the power spectrum, recently proven by McQuinn and White [1], and extend it to non-Gaussian initial conditions and the bispectrum. In contrast, we prove that perturbation theory diverges for the real space two-point correlation function and for the probability density function (PDF) of the density averaged in cells and all the cumulants derived from it. We attribute these divergences to the statistical averaging intrinsic to cosmological observables, which, even on very large and "perturbative" scales, gives non-vanishing weight to all extreme fluctuations. Finally, we discuss some general properties of non-perturbative effects in real space and Fourier space.

  11. Little evidence for dynamic divergences in ultraviscous molecular liquids

    DEFF Research Database (Denmark)

    Hecksher, Tina; Nielsen, Albena; Olsen, Niels Boye

    2008-01-01

    The physics of the ultraviscous liquid phase preceding glass formation continues to pose major problems that remain unsolved. It is actively debated, for instance, whether the marked increase of the relaxation time reflects an underlying phase transition to a state of infinite relaxation time....... To elucidate the empirical evidence for this intriguing scenario, some of the most accurate relaxationtime data available for any class of ultraviscous liquids-those obtained by dielectric relaxation experiments on organic liquids just above the glass transition-were compiled. Analysis of data for 42 liquids...... shows that there is no compelling evidence for the Vogel-Fulcher-Tammann (VFT) prediction that the relaxation time diverges at a finite temperature.We conclude that theories with a dynamic divergence of the VFT formlack a direct experimental basis....

  12. Convergence and divergence, a concept for explaining drug actions.

    Science.gov (United States)

    Watanabe, Takehiko; Kamisaki, Yoshinori; Timmerman, Henk

    2004-10-01

    For the teaching and/or learning about drug actions and for the discovery and development of new drugs, it is important to understand how drugs act on living bodies. So far, there has been no clear description on the general principle of drug action in pharmacology textbooks. We propose two principles to depict the action mechanism of drugs. The first is that most, if not all, drugs act on proteins at the molecular level, that is, enzymes, receptors, ion channels, and transporters. The second is that a drug may cause divergent or convergent responses, resulting in changes of a physiological or pathological function of the human body. The concept of divergence and convergence can be used to explain the complex individuality of drug actions.

  13. Divergent biparietal diameter growth rates in twin pregnancies.

    Science.gov (United States)

    Houlton, M C

    1977-05-01

    Twenty-eight twin pregnancies were monitored by serial ultrasonic cephalometry from 30 or 31 weeks' gestation. The rates of growth of the individual twins as determined by biparietal diameters were similar in 11 cases (39%) and divergent in 17 (61%). When the rates of growth were divergent, the lesser rate was always below the mean for singleton pregnancies, and the incidence of small-for-gestational-age babies was 18 of 34 (53%). It was apparent that the greater the difference in biparietal diameters within the 2 weeks preceding delivery, the higher the risk of a small-for-gestation-age baby being delivered. No comment could be made on the growth rate prior to 28 weeks except that at diagnosis there was little or no difference in biparietal diameters.

  14. Summation of Divergent Series and Zeldovich's Regularization Method

    International Nuclear Information System (INIS)

    Mur, V.D.; Pozdnyakov, S.G.; Popruzhenko, S.V.; Popov, V.S.

    2005-01-01

    A method for summing divergent series, including perturbation-theory series, is considered. This method is an analog of Zeldovich's regularization method in the theory of quasistationary states. It is shown that the method in question is more powerful than the well-known Abel and Borel methods, but that it is compatible with them (that is, it leads to the same value for the sum of a series). The constraints on the parameter domain that arise upon the removal of the regularization of divergent integrals by this method are discussed. The dynamical Stark shifts and widths of loosely bound s states in the field of a circularly polarized electromagnetic wave are calculated at various values of the Keldysh adiabaticity parameter and the multiquantum parameter

  15. Divergence-free MHD Simulations with the HERACLES Code

    Directory of Open Access Journals (Sweden)

    Vides J.

    2013-12-01

    Full Text Available Numerical simulations of the magnetohydrodynamics (MHD equations have played a significant role in plasma research over the years. The need of obtaining physical and stable solutions to these equations has led to the development of several schemes, all requiring to satisfy and preserve the divergence constraint of the magnetic field numerically. In this paper, we aim to show the importance of maintaining this constraint numerically. We investigate in particular the hyperbolic divergence cleaning technique applied to the ideal MHD equations on a collocated grid and compare it to the constrained transport technique that uses a staggered grid to maintain the property. The methods are implemented in the software HERACLES and several numerical tests are presented, where the robustness and accuracy of the different schemes can be directly compared.

  16. Relations between heat exchange and Rényi divergences

    Science.gov (United States)

    Wei, Bo-Bo

    2018-04-01

    In this work, we establish an exact relation which connects the heat exchange between two systems initialized in their thermodynamic equilibrium states at different temperatures and the Rényi divergences between the initial thermodynamic equilibrium state and the final nonequilibrium state of the total system. The relation tells us that the various moments of the heat statistics are determined by the Renyi divergences between the initial equilibrium state and the final nonequilibrium state of the global system. In particular the average heat exchange is quantified by the relative entropy between the initial equilibrium state and the final nonequilibrium state of the global system. The relation is applicable to both finite classical systems and finite quantum systems.

  17. Divergent series, summability and resurgence II simple and multiple summability

    CERN Document Server

    Loday-Richaud, Michèle

    2016-01-01

    Addressing the question how to “sum” a power series in one variable when it diverges, that is, how to attach to it analytic functions, the volume gives answers by presenting and comparing the various theories of k-summability and multisummability. These theories apply in particular to all solutions of ordinary differential equations. The volume includes applications, examples and revisits, from a cohomological point of view, the group of tangent-to-identity germs of diffeomorphisms of C studied in volume 1. With a view to applying the theories to solutions of differential equations, a detailed survey of linear ordinary differential equations is provided which includes Gevrey asymptotic expansions, Newton polygons, index theorems and Sibuya’s proof of the meromorphic classification theorem that characterizes the Stokes phenomenon for linear differential equations. This volume is the second of a series of three entitled Divergent Series, Summability and Resurgence. It is aimed at graduate students and res...

  18. Exopolysaccharide (EPS synthesis by Oenococcus oeni: from genes to phenotypes.

    Directory of Open Access Journals (Sweden)

    Maria Dimopoulou

    Full Text Available Oenococcus oeni is the bacterial species which drives malolactic fermentation in wine. The analysis of 50 genomic sequences of O. oeni (14 already available and 36 newly sequenced ones provided an inventory of the genes potentially involved in exopolysaccharide (EPS biosynthesis. The loci identified are: two gene clusters named eps1 and eps2, three isolated glycoside-hydrolase genes named dsrO, dsrV and levO, and three isolated glycosyltransferase genes named gtf, it3, it4. The isolated genes were present or absent depending on the strain and the eps gene clusters composition diverged from one strain to another. The soluble and capsular EPS production capacity of several strains was examined after growth in different culture media and the EPS structure was determined. Genotype to phenotype correlations showed that several EPS biosynthetic pathways were active and complementary in O. oeni. Can be distinguished: (i a Wzy-dependent synthetic pathway, allowing the production of heteropolysaccharides made of glucose, galactose and rhamnose, mainly in a capsular form, (ii a glucan synthase pathway (Gtf, involved in β-glucan synthesis in a free and a cell-associated form, giving a ropy phenotype to growth media and (iii homopolysaccharide synthesis from sucrose (α-glucan or β-fructan by glycoside-hydrolases of the GH70 and GH68 families. The eps gene distribution on the phylogenetic tree was examined. Fifty out of 50 studied genomes possessed several genes dedicated to EPS metabolism. This suggests that these polymers are important for the adaptation of O. oeni to its specific ecological niche, wine and possibly contribute to the technological performance of malolactic starters.

  19. Divergence of Cs-137 sources fluence used in brachytherapy

    International Nuclear Information System (INIS)

    Vianello, E.A.; Almeida, C.E. de

    1998-01-01

    In this work the experimental determination of correction factor for fluence divergence (kln) of linear Cs-137 sources CDCS J4, with Farmer ionization chamber model 2571 in a central and perpendicular plan to source axis, for distances range from 1 to 7 cm., has been presented. The experimental results were compared to calculating by Kondo and Randolph (1960) isotropic theory and Bielajew (1990) anisotropic theory. (Author)

  20. Real and metaphorical hunger: the case of The Divergent Trilogy

    OpenAIRE

    Paravano, Cristina

    2015-01-01

    The present contribution investigates how the issue of hunger becomes a means of expressing and communicating personal and social identity in Veronica Roth’s best seller trilogy Divergent (2011-13). Roth portrays a dystopian future developing a multifaceted concept of hunger, both real and figurative, and using food as a cultural metaphor. The trilogy is set in a post-apocalyptic Chicago, whose population is divided into five allegorical factions, according to a number of personal and social ...

  1. [Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

    Science.gov (United States)

    Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

    2014-10-01

    Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax.

  2. Existence and multiplicity of solutions for divergence type elliptic equations

    Directory of Open Access Journals (Sweden)

    Lin Zhao

    2011-03-01

    Full Text Available We establish the existence and multiplicity of weak solutions of a problem involving a uniformly convex elliptic operator in divergence form. We find one nontrivial solution by the mountain pass lemma, when the nonlinearity has a $(p-1$-superlinear growth at infinity, and two nontrivial solutions by minimization and mountain pass when the nonlinear term has a $(p-1$-sublinear growth at infinity.

  3. Infra-red divergences and Regge behaviour in QCD

    International Nuclear Information System (INIS)

    Jaroszewicz, T.

    1980-01-01

    We analyze high energy behaviour of multi-gluon exchange amplitudes in the leading-lns approximation in perturbation theory. Working in the Coulomb gauge and employing Ward identities we derive an integral equation for the n-gluon system in the exchange channel. We find that the Regge behaviour is associated with exponentiation of leading infrared divergences, and the position of the j-plane singularities is determined by the colour quantum numbers of the exchanged system. (author)

  4. Schroedinger propagation of initial discontinuities leads to divergence of moments

    International Nuclear Information System (INIS)

    Marchewka, A.; Schuss, Z.

    2009-01-01

    We show that the large phase expansion of the Schroedinger propagation of an initially discontinuous wave function leads to the divergence of average energy, momentum, and displacement, rendering them unphysical states. If initially discontinuous wave functions are considered to be approximations to continuous ones, the determinant of the spreading rate of these averages is the maximal gradient of the initial wave function. Therefore a dilemma arises between the inclusion of discontinuous wave functions in quantum mechanics and the requirement of finite moments.

  5. Schroedinger propagation of initial discontinuities leads to divergence of moments

    Energy Technology Data Exchange (ETDEWEB)

    Marchewka, A., E-mail: avi.marchewka@gmail.co [Ruppin Academic Center, Emek-Hefer 40250 (Israel); Schuss, Z., E-mail: schuss@post.tau.ac.i [Department of Mathematics, Tel-Aviv University, Ramat-Aviv, 69978 Tel-Aviv (Israel)

    2009-09-21

    We show that the large phase expansion of the Schroedinger propagation of an initially discontinuous wave function leads to the divergence of average energy, momentum, and displacement, rendering them unphysical states. If initially discontinuous wave functions are considered to be approximations to continuous ones, the determinant of the spreading rate of these averages is the maximal gradient of the initial wave function. Therefore a dilemma arises between the inclusion of discontinuous wave functions in quantum mechanics and the requirement of finite moments.

  6. Chloroplast Genome Evolution in Early Diverged Leptosporangiate Ferns

    OpenAIRE

    Kim, Hyoung Tae; Chung, Myong Gi; Kim, Ki-Joong

    2014-01-01

    In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. c...

  7. Revision of Drusinae subfamily (Trichoptera, Limnephilidae: divergence by paraproct and paramere: speciation in isolation by integration

    Directory of Open Access Journals (Sweden)

    Oláh, János

    2017-08-01

    Full Text Available In the last few years we have described over 70 new incipient sibling limnephild species applying the discovered Trichoptera speciation traits of the paraproct and paramere for species recognition and delimitation. In this revision on Drusinae subfamily, comprising 177 species, we have applied these subtle, but rapid and stable speciation traits and described 49 new sibling species from the “well studied” European mountain ranges. Discussing the theoretical background we have elaborated and adapted a new character state ranking system of phenomics to revise the long-neglected taxonomy of the Drusinae subfamily and synonymised the Cryptothrix, Monocentra, Metanoea, Leptodrusus, Anomalopterygella, Hadimina genera with the Drusus genus. These old genera of artificial constructs were established exclusively by divergences of secondary sexual traits known already to have only species level ranking value. According to our new character ranking system in the Drusinae subfamily, beside the Drusus genus, only the Ecclisopteryx genus has been retained having robust generic level divegences of paraproct loss and ancestral duplication of spine organising centre on the paramere pattern. Speciation trait function of the peg-packed surface on the paraproct head in Drusus genus moved to the gonopod apices and integrated into variously shaped stimulatory organ in the Ecclisopteryx genus. In the Drusus genus the ancestral divergence of the single spine organising centre has integrated 11 species groups with remarkably stable paramere spine pattern. Based upon ancestral divergences in the paraproct architecture we have differenciated 28 species complexes inside the 11 species groups. The delineation of the 163 mostly incipient siblings species, inside the 28 species complexes with 44 new Drusus species, was based primarily on the divergences of speciation trait, that is in the stimulatory head shape of the apical arms on the dorsal branches of the paraproct

  8. Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

    Directory of Open Access Journals (Sweden)

    Daly Michael J

    2005-10-01

    Full Text Available Abstract Background Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria. Results By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27 and Deinococcus megaplasmid (DR177. Conclusion After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of

  9. Cryptic Plutella species show deep divergence despite the capacity to hybridize.

    Science.gov (United States)

    Perry, Kym D; Baker, Gregory J; Powis, Kevin J; Kent, Joanne K; Ward, Christopher M; Baxter, Simon W

    2018-05-29

    .5% of P. xylostella. Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these Plutella species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact. Although P. australiana is a potential pest of brassicaceous crops, it is of secondary importance to P. xylostella.

  10. Genetic diversity in soybean genotypes using phenotypic characters and enzymatic markers.

    Science.gov (United States)

    Zambiazzi, E V; Bruzi, A T; Sales, A P; Borges, I M M; Guilherme, S R; Zuffo, A M; Lima, J G; Ribeiro, F O; Mendes, A E S; Godinho, S H M; Carvalho, M L M

    2017-09-21

    The objective of this study was to evaluate the genetic diversity of soybean cultivars by adopting phenotypic traits and enzymatic markers, the relative contribution of agronomic traits to diversity, as well as diversity between the level of technology used in soybean cultivars and genetic breeding programs in which cultivars were inserted. The experiments were conducted on the field at the Center for Scientific and Technological Development in crop-livestock production and the Electrophoresis Laboratory of Lavras Federal University. The agronomic traits adopted were grain yield, plant height, first legume insertion, plant lodging, the mass of one thousand seeds, and days for complete maturation, in which the Euclidean distance, grouped by Tocher and UPGMA criteria, was obtained. After electrophorese gels for enzymatic systems, dehydrogenase alcohol, esterase, superoxide dismutase, and peroxidase were performed. The genetic similarity estimative was also obtained between genotypes by the Jaccard coefficient with subsequent grouping by the UPGMA method. The formation of two groups was shown using phenotypic characters in the genetic diversity study and individually discriminating the cultivar 97R73 RR. The character with the greatest contribution to the genetic divergence was grain yield with contribution higher than 90.0%. To obtain six different groups, individually discriminating the cultivars CG 8166 RR, FPS Jupiter RR, and BRS MG 780 RR, enzymatic markers were used. Cultivars carrying the RR technology presented more divergence than conventional cultivars and IPRO cultivars.

  11. Socio-Cognitive Phenotypes Differentially Modulate Large-Scale Structural Covariance Networks.

    Science.gov (United States)

    Valk, Sofie L; Bernhardt, Boris C; Böckler, Anne; Trautwein, Fynn-Mathis; Kanske, Philipp; Singer, Tania

    2017-02-01

    Functional neuroimaging studies have suggested the existence of 2 largely distinct social cognition networks, one for theory of mind (taking others' cognitive perspective) and another for empathy (sharing others' affective states). To address whether these networks can also be dissociated at the level of brain structure, we combined behavioral phenotyping across multiple socio-cognitive tasks with 3-Tesla MRI cortical thickness and structural covariance analysis in 270 healthy adults, recruited across 2 sites. Regional thickness mapping only provided partial support for divergent substrates, highlighting that individual differences in empathy relate to left insular-opercular thickness while no correlation between thickness and mentalizing scores was found. Conversely, structural covariance analysis showed clearly divergent network modulations by socio-cognitive and -affective phenotypes. Specifically, individual differences in theory of mind related to structural integration between temporo-parietal and dorsomedial prefrontal regions while empathy modulated the strength of dorsal anterior insula networks. Findings were robust across both recruitment sites, suggesting generalizability. At the level of structural network embedding, our study provides a double dissociation between empathy and mentalizing. Moreover, our findings suggest that structural substrates of higher-order social cognition are reflected rather in interregional networks than in the the local anatomical markup of specific regions per se. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. A limit of the quantum Rényi divergence

    International Nuclear Information System (INIS)

    Datta, Nilanjana; Leditzky, Felix

    2014-01-01

    Recently, an interesting quantity called the quantum Rényi divergence (or ‘sandwiched’ Rényi relative entropy) was defined for pairs of positive semi-definite operators ρ and σ. It depends on a parameter α and acts as a parent quantity for other relative entropies which have important operational significance in quantum information theory: the quantum relative entropy and the min- and max-relative entropies. There is, however, another relative entropy, called the 0-relative Rényi entropy, which plays a key role in the analysis of various quantum information-processing tasks in the one-shot setting. We prove that the 0-relative Rényi entropy is obtainable from the quantum Rényi divergence only if ρ and σ have equal supports. This, along with existing results in the literature, suggests that it suffices to consider two essential parent quantities from which operationally relevant entropic quantities can be derived—the quantum Rényi divergence with parameter α ⩾ 1/2, and the α-relative Rényi entropy with α ∈ [0, 1). (paper)

  13. Infrared divergences for free quantum fields in cosmological spacetimes

    Science.gov (United States)

    Higuchi, Atsushi; Rendell, Nicola

    2018-06-01

    We investigate the nature of infrared divergences for the free graviton and inflaton two-point functions in flat Friedman–Lemaître–Robertson–Walker spacetime. These divergences arise because the momentum integral for these two-point functions diverges in the infrared. It is straightforward to see that the power of the momentum in the integrand can be increased by 2 in the infrared using large gauge transformations, which are sufficient for rendering these two-point functions infrared finite for slow-roll inflation. In other words, if the integrand of the momentum integral for these two-point functions behaves like , where p is the momentum, in the infrared, then it can be made to behave like by large gauge transformations. On the other hand, it is known that, if one smears these two-point functions in a gauge-invariant manner, the power of the momentum in the integrand is changed from to . This fact suggests that the power of the momentum in the integrand for these two-point functions can be increased by 4 using large gauge transformations. In this paper we show that this is indeed the case. Thus, the two-point functions for the graviton and inflaton fields can be made finite by large gauge transformations for a large class of potentials and states in single-field inflation.

  14. A vadose zone water fluxmeter with divergence control

    Science.gov (United States)

    Gee, G.W.; Ward, A.L.; Caldwell, T.G.; Ritter, J.C.

    2002-01-01

    Unsaturated water flux densities are needed to quantify water and contaminant transfer within the vadose zone. However, water flux densities are seldom measured directly and often are predicted with uncertainties of an order or magnitude or more. A water fluxmeter was designed, constructed, and tested to directly measure drainage fluxes in field soils. The fluxmeter was designed to minimize divergence. It concentrates flow into a narrow sensing region filled with a fiberglass wick. The wick applies suction, proportional to its length, and passively drains the meter. The meter can be installed in an augured borehole at almost any depth below the root zone. Water flux through the meter is measured with a self‐calibrating tipping bucket, with a sensitivity of ∼4 mL tip−1. For our meter this is equivalent to detection limit of ∼0.1 mm. Passive‐wick devices previously have not properly corrected for flow divergence. Laboratory measurements supported predictions of a two‐dimensional (2‐D) numerical model, which showed that control of the collector height H and knowledge of soil hydraulic properties are required for improving divergence control, particularly at fluxes below 1000 mm yr−1. The water fluxmeter is simple in concept, is inexpensive, and has the capability of providing continuous and reliable monitoring of unsaturated water fluxes ranging from less than 1 mm yr−1 to more than 1000 mm yr−1.

  15. Flutter and divergence instability of supported piezoelectric nanotubes conveying fluid

    Science.gov (United States)

    Bahaadini, Reza; Hosseini, Mohammad; Jamali, Behnam

    2018-01-01

    In this paper, divergence and flutter instabilities of supported piezoelectric nanotubes containing flowing fluid are investigated. To take the size effects into account, the nonlocal elasticity theory is implemented in conjunction with the Euler-Bernoulli beam theory incorporating surface stress effects. The Knudsen number is applied to investigate the slip boundary conditions between the flow and wall of nanotube. The nonlocal governing equations of nanotube are obtained using Newtonian method, including the influence of piezoelectric voltage, surface effects, Knudsen number and nonlocal parameter. Applying Galerkin approach to transform resulting equations into a set of eigenvalue equations under the simple-simple (S-S) and clamped-clamped (C-C) boundary conditions. The effects of the piezoelectric voltage, surface effects, Knudsen number, nonlocal parameter and boundary conditions on the divergence and flutter boundaries of nanotubes are discussed. It is observed that the fluid-conveying nanotubes with both ends supported lose their stability by divergence first and then by flutter with increase in fluid velocity. Results indicate the importance of using piezoelectric voltage, nonlocal parameter and Knudsen number in decrease of critical flow velocities of system. Moreover, the surface effects have a significant role on the eigenfrequencies and critical fluid velocity.

  16. Cellular basis of morphological variation and temperature-related plasticity in Drosophila melanogaster strains with divergent wing shapes.

    Science.gov (United States)

    Torquato, Libéria Souza; Mattos, Daniel; Matta, Bruna Palma; Bitner-Mathé, Blanche Christine

    2014-12-01

    Organ shape evolves through cross-generational changes in developmental patterns at cellular and/or tissue levels that ultimately alter tissue dimensions and final adult proportions. Here, we investigated the cellular basis of an artificially selected divergence in the outline shape of Drosophila melanogaster wings, by comparing flies with elongated or rounded wing shapes but with remarkably similar wing sizes. We also tested whether cellular plasticity in response to developmental temperature was altered by such selection. Results show that variation in cellular traits is associated with wing shape differences, and that cell number may play an important role in wing shape response to selection. Regarding the effects of developmental temperature, a size-related plastic response was observed, in that flies reared at 16 °C developed larger wings with larger and more numerous cells across all intervein regions relative to flies reared at 25 °C. Nevertheless, no conclusive indication of altered phenotypic plasticity was found between selection strains for any wing or cellular trait. We also described how cell area is distributed across different intervein regions. It follows that cell area tends to decrease along the anterior wing compartment and increase along the posterior one. Remarkably, such pattern was observed not only in the selected strains but also in the natural baseline population, suggesting that it might be canalized during development and was not altered by the intense program of artificial selection for divergent wing shapes.

  17. Cattle phenotypes can disguise their maternal ancestry.

    Science.gov (United States)

    Srirattana, Kanokwan; McCosker, Kieren; Schatz, Tim; St John, Justin C

    2017-06-26

    Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments. A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P cattle with a Bos taurus phenotype. The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.

  18. Phenotypic distance among assai palm’s mother plants (Euterpe oleracea Mart. from Eastern Amazon

    Directory of Open Access Journals (Sweden)

    Rosemiro Santos Galate

    2014-09-01

    Full Text Available The açai palm tree (Euterpe oleracea Mart. is native to the Amazonian estuary. Media revelation of the nutraceutical properties of açai palm has resulted in its introduction in the national and international markets, consequently increasing the açai palm crop area in the Amazon. Nevertheless, açai palm cultivation is performed in a rational manner, because of limited product extraction from the native açai palm varieties. The study aimed to conduct a preliminary estimate of genetic variability, parameters, and phenotypic divergence of parent açai palms. Data from 129 parent plants from northeast Pará was collected. Analysis of variance (ANOVA of 22 morphoagronomic traits was performed to estimate the genetic parameters. Divergence was estimated using standardized average euclidean distance by using unweighted pair group method with arithmetic mean (UPGMA and Tocher clustering methods. Significant variance was noted in 77.3% traits (ANOVA, p<0.01 and p<0.05; CVg/CVe ratio indicated that 72.3% traits may present genetic variability for use in breeding programs. The euclidean distance showed EO-070 and EO-072 parent plants (Combu Island as the least divergent, and EO-010 (Belém and EO-018 (Salinópolis as the most divergent. The clustering methods determined ten (Tocher and nine (UPGMA similar groups. The most dissimilar parent plants were EO-035 (Capitão Poço, EO- 109 (Combu Island, EO-019 (Salinópolis, and EO-010 (Belém (Tocher method, whereas even the EO-010 (Belém; EO-011 (São João de Pirabas; EO-017, EO-018, and EO-019 (Salinópolis; EO-062 and EO-109 (Combu Island plants showed dissimilarity. We concluded that the 129 mother plants have high phenotypic variability, indicating the possibility of their use in genetic breeding programs. Further, the divergent parent plants can be used in the production of genotypes with favorable characteristics.

  19. Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence.

    Science.gov (United States)

    Pereira, Ricardo J; Monahan, William B; Wake, David B

    2011-07-06

    Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI. By augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI. These results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.

  20. Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications

    International Nuclear Information System (INIS)

    Nugoli, Mélanie; Theillet, Charles; Chuchana, Paul; Vendrell, Julie; Orsetti, Béatrice; Ursule, Lisa; Nguyen, Catherine; Birnbaum, Daniel; Douzery, Emmanuel JP; Cohen, Pascale

    2003-01-01

    Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems. In this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution. MCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels. The analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved