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Sample records for gene flow shape

  1. Shaped Recess Flow Control

    Science.gov (United States)

    Shyam, Vikram (Inventor); Poinsatte, Philip (Inventor); Thurman, Douglas (Inventor)

    2017-01-01

    One or more embodiments of techniques or systems for shaped recess flow control are provided herein. A shaped recess or cavity can be formed on a surface associated with fluid flow. The shaped recess can be configured to create or induce fluid effects, temperature effects, or shedding effects that interact with a free stream or other structures. The shaped recess can be formed at an angle to a free stream flow and may be substantially "V" shaped. The shaped recess can be coupled with a cooling channel, for example. The shaped recess can be upstream or downstream from a cooling channel and aligned in a variety of manners. Due to the fluid effects, shedding effects, and temperature effects created by a shaped recess, lift-off or separation of cooling jets of cooling channels can be mitigated, thereby enhancing film cooling effectiveness.

  2. Some flows in shape optimization

    CERN Document Server

    Cardaliaguet, Pierre; 10.1007/s00205-006-0002-z

    2010-01-01

    Geometric flows related to shape optimization problems of Bernoulli type are investigated. The evolution law is the sum of a curvature term and a nonlocal term of Hele-Shaw type. We introduce generalized set solutions, the definition of which is widely inspired by viscosity solutions. The main result is an inclusion preservation principle for generalized solutions. As a consequence, we obtain existence, uniqueness and stability of solutions. Asymptotic behavior for the flow is discussed: we prove that the solutions converge to a generalized Bernoulli exterior free boundary problem.

  3. The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States.

    Science.gov (United States)

    Robinson, Stacie J; Samuel, Michael D; Lopez, Davin L; Shelton, Paul

    2012-09-01

    One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.

  4. Liquid Flow in Shaped Fiber Bundle

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yan; WANG Hua-ping; CHEN Yue-hua

    2006-01-01

    By computation and comparison of the critical spreading coefficient parameter, it was found that shaped fiber bundle is better for wetting. Liquid-air interface tension of liquid arising the shaped fiber bundle body is considered as one critical factor besides liquid viscosity, inertia force and liquid-fiber interface tension. Experimental result simulation demonstrated that the liquid-air interface tension is correlated with the geometric size of the liquid arising in body, φ0 (x) and which is affected by the cross sectional shape of fiber and the radius of single fiber. The shaped fiber bundle model is introduced to investigate liquid flow in fiber assembly. The model is generated based on a random function for stochastic forming of fibers in bundle and it is necessary to combine this fundamental model with physical explanation for investigation of liquid flow in fiber assembly.

  5. Thermoinduced plastic flow and shape memory effects

    Directory of Open Access Journals (Sweden)

    Xiao Heng

    2011-01-01

    Full Text Available We propose an enhanced form of thermocoupled J2-flow models of finite deformation elastoplasticity with temperature-dependent yielding and hardening behaviour. The thermomechanical constitutive structure of these models is rendered free and explicit in the rigorous sense of thermodynamic consistency. Namely, with a free energy function explicitly introduced in terms of almost any given form of the thermomechanical constitutive functions, the requirements from the second law are identically fulfilled with positive internal dissipation. We study the case when a dependence of yielding and hardening on temperature is given and demonstrate that thermosensitive yielding with anisotropic hardening may give rise to appreciable plastic flow either in a process of heating or in a cyclic process of heating/cooling, thus leading to the findings of one- and two-way thermoinduced plastic flow. We then show that such theoretical findings turn out to be the effects found in shape memory materials, such as one- and two-way memory effects. Thus, shape memory effects may be explained to be thermoinduced plastic flow resulting from thermosensitive yielding and hardening behaviour. These and other relevant facts may suggest that, from a phenomenological standpoint, thermocoupled elastoplastic J2-flow models with thermosensitive yielding and hardening may furnish natural, straightforward descriptions of thermomechanical behaviour of shape memory materials.

  6. Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus

    Directory of Open Access Journals (Sweden)

    Snell Howard L

    2009-12-01

    Full Text Available Abstract Background Marine iguanas (Amblyrhynchus cristatus inhabit the coastlines of large and small islands throughout the Galápagos archipelago, providing a rich system to study the spatial and temporal factors influencing the phylogeographic distribution and population structure of a species. Here, we analyze the microevolution of marine iguanas using the complete mitochondrial control region (CR as well as 13 microsatellite loci representing more than 1200 individuals from 13 islands. Results CR data show that marine iguanas occupy three general clades: one that is widely distributed across the northern archipelago, and likely spread from east to west by way of the South Equatorial current, a second that is found mostly on the older eastern and central islands, and a third that is limited to the younger northern and western islands. Generally, the CR haplotype distribution pattern supports the colonization of the archipelago from the older, eastern islands to the younger, western islands. However, there are also signatures of recurrent, historical gene flow between islands after population establishment. Bayesian cluster analysis of microsatellite genotypes indicates the existence of twenty distinct genetic clusters generally following a one-cluster-per-island pattern. However, two well-differentiated clusters were found on the easternmost island of San Cristóbal, while nine distinct and highly intermixed clusters were found on youngest, westernmost islands of Isabela and Fernandina. High mtDNA and microsatellite genetic diversity were observed for populations on Isabela and Fernandina that may be the result of a recent population expansion and founder events from multiple sources. Conclusions While a past genetic study based on pure FST analysis suggested that marine iguana populations display high levels of nuclear (but not mitochondrial gene flow due to male-biased dispersal, the results of our sex-biased dispersal tests and the

  7. The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

    Directory of Open Access Journals (Sweden)

    Schaefer H Martin

    2011-06-01

    Full Text Available Abstract Background While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes across its wide distributional range in Chile and Argentina. Results Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. Conclusions Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations.

  8. Genomics of local adaptation with gene flow.

    Science.gov (United States)

    Tigano, Anna; Friesen, Vicki L

    2016-05-01

    Gene flow is a fundamental evolutionary force in adaptation that is especially important to understand as humans are rapidly changing both the natural environment and natural levels of gene flow. Theory proposes a multifaceted role for gene flow in adaptation, but it focuses mainly on the disruptive effect that gene flow has on adaptation when selection is not strong enough to prevent the loss of locally adapted alleles. The role of gene flow in adaptation is now better understood due to the recent development of both genomic models of adaptive evolution and genomic techniques, which both point to the importance of genetic architecture in the origin and maintenance of adaptation with gene flow. In this review, we discuss three main topics on the genomics of adaptation with gene flow. First, we investigate selection on migration and gene flow. Second, we discuss the three potential sources of adaptive variation in relation to the role of gene flow in the origin of adaptation. Third, we explain how local adaptation is maintained despite gene flow: we provide a synthesis of recent genomic models of adaptation, discuss the genomic mechanisms and review empirical studies on the genomics of adaptation with gene flow. Despite predictions on the disruptive effect of gene flow in adaptation, an increasing number of studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow.

  9. Shape flows for spectral optimization problems

    CERN Document Server

    Bucur, Dorin; Stefanelli, Ulisse

    2011-01-01

    We consider a general formulation of gradient flow evolution for problems whose natural framework is the one of metric spaces. The applications we deal with are concerned with the evolution of {\\it capacitary measures} with respect to the $\\gamma$-convergence dissipation distance and with the evolution of domains in spectral optimization problems.

  10. Cortical Flow-Driven Shapes of Nonadherent Cells

    Science.gov (United States)

    Callan-Jones, A. C.; Ruprecht, V.; Wieser, S.; Heisenberg, C. P.; Voituriez, R.

    2016-01-01

    Nonadherent polarized cells have been observed to have a pearlike, elongated shape. Using a minimal model that describes the cell cortex as a thin layer of contractile active gel, we show that the anisotropy of active stresses, controlled by cortical viscosity and filament ordering, can account for this morphology. The predicted shapes can be determined from the flow pattern only; they prove to be independent of the mechanism at the origin of the cortical flow, and are only weakly sensitive to the cytoplasmic rheology. In the case of actin flows resulting from a contractile instability, we propose a phase diagram of three-dimensional cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate shapes, all of which have been observed in experiment.

  11. Computational Investigation of Flows in Diffusing S-shaped Intakes

    Directory of Open Access Journals (Sweden)

    R. Menzies

    2001-01-01

    Full Text Available This paper examines the flow in a diffusing s-shaped aircraft air intake using computational fluid dynamics (CFD simulations. Diffusing s-shaped ducts such as the RAE intake model 2129 (M2129 give rise to complex flow patterns that develop as a result of the offset between the intake cowl plane and engine face plane. Euler results compare favourably with experiment and previous calculations for a low mass flow case. For a high mass flow case a converged steady solution was not found and the problem was then simulated using an unsteady flow solver. A choked flow at the intake throat and complex shock reflection system, together with a highly unsteady flow downstream of the first bend, yielded results that did not compare well with previous experimental data. Previous work had also experienced this problem and a modification to the geometry to account for flow separation was required to obtain a steady flow.RANS results utilising a selection of turbulence models were more satisfactory. The low mass flow case showed good comparison with experiment and previous calculations. A problem of the low mass flow case is the prediction of secondary flow. It was found that the SST turbulence model best predicted this feature. Fully converged high mass flow results were obtained. Once more, SST results proved to match experiment and previous computations the best. Problems with the prediction of the flow in the cowl region of the duct were experienced with the S-A and k-w models. One of the main problems of turbulence closures in intake flows is the transition of the freestream from laminar to turbulent over the intake cowl region. It is likely that the improvement in this prediction using the SST turbulence model will lead to more satisfactory results for both high and low mass flow rates.

  12. Targeted gene flow for conservation.

    Science.gov (United States)

    Kelly, Ella; Phillips, Ben L

    2016-04-01

    Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre-adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species' range there may be long-standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens.

  13. Water flow and fin shape polymorphism in coral reef fishes.

    Science.gov (United States)

    Binning, Sandra A; Roche, Dominique G

    2015-03-01

    Water flow gradients have been linked to phenotypic differences and swimming performance across a variety of fish assemblages. However, the extent to which water motion shapes patterns of phenotypic divergence within species remains unknown. We tested the generality of the functional relationship between swimming morphology and water flow by exploring the extent of fin and body shape polymorphism in 12 widespread species from three families (Acanthuridae, Labridae, Pomacentridae) of pectoral-fin swimming (labriform) fishes living across localized wave exposure gradients. The pectoral fin shape of Labridae and Acanthuridae species was strongly related to wave exposure: individuals with more tapered, higher aspect ratio (AR) fins were found on windward reef crests, whereas individuals with rounder, lower AR fins were found on leeward, sheltered reefs. Three of seven Pomacentridae species showed similar trends, and pectoral fin shape was also strongly related to wave exposure in pomacentrids when fin aspect ratios of three species were compared across flow habitats at very small spatial scales (back lagoon). Unlike fin shape, there were no intraspecific differences in fish body fineless ratio across habitats or depths. Contrary to our predictions, there was no pattern relating species' abundances to polymorphism across habitats (i.e., abundance was not higher at sites where morphology is better adapted to the environment). This suggests that there are behavioral and/or physiological mechanisms enabling some species to persist across flow habitats in the absence of morphological differences. We suggest that functional relationships between swimming morphology and water flow not only structure species assemblages, but are yet another important variable contributing to phenotypic differences within species. The close links between fin shape polymorphism and local water flow conditions appear to be important for understanding species' distributions as well as patterns of

  14. Form, shape and function: segmented blood flow in the choriocapillaris

    Science.gov (United States)

    Zouache, M. A.; Eames, I.; Klettner, C. A.; Luthert, P. J.

    2016-10-01

    The development of fluid transport systems was a key event in the evolution of animals and plants. While within vertebrates branched geometries predominate, the choriocapillaris, which is the microvascular bed that is responsible for the maintenance of the outer retina, has evolved a planar topology. Here we examine the flow and mass transfer properties associated with this unusual geometry. We show that as a result of the form of the choriocapillaris, the blood flow is decomposed into a tessellation of functional vascular segments of various shapes delineated by separation surfaces across which there is no flow, and in the vicinity of which the transport of passive substances is diffusion-limited. The shape of each functional segment is determined by the distribution of arterioles and venules and their respective relative flow rates. We also show that, remarkably, the mass exchange with the outer retina is a function of the shape of each functional segment. In addition to introducing a novel framework in which the structure and function of the metabolite delivery system to the outer retina may be investigated in health and disease, the present work provides a general characterisation of the flow and transfers in multipole Hele-Shaw configurations.

  15. Blade Shape Optimization of Liquid Turbine Flow Sensor

    Institute of Scientific and Technical Information of China (English)

    郭素娜; 张涛; 孙立军; 杨振; 杨文量

    2016-01-01

    Based on the characteristic curve analysis, the method using 2D(K ) square difference of meter factor at different flow rates was developed to evaluate the performance of turbine flow sensor in this study. Then according to the distribution of entrance velocity, it was supposed that reducing the blade area near the tip could decrease the linearity error of a sensor. Therefore, the influence of different blade shape parameters on the performance of the sensor was investigated by combining computational fluid dynamics(CFD)simulation with experimental test. The experimental results showed that, for the liquid turbine flow sensor with a diameter of 10 mm, the linearity error was smallest, and the performance of sensor was optimal when blade shape parameter equaled 0.25.

  16. Gene flow from glyphosate-resistant crops.

    Science.gov (United States)

    Mallory-Smith, Carol; Zapiola, Maria

    2008-04-01

    Gene flow from transgenic glyphosate-resistant crops can result in the adventitious presence of the transgene, which may negatively impact markets. Gene flow can also produce glyphosate-resistant plants that may interfere with weed management systems. The objective of this article is to review the gene flow literature as it pertains to glyphosate-resistant crops. Gene flow is a natural phenomenon not unique to transgenic crops and can occur via pollen, seed and, in some cases, vegetative propagules. Gene flow via pollen can occur in all crops, even those that are considered to be self-pollinated, because all have low levels of outcrossing. Gene flow via seed or vegetative propagules occurs when they are moved naturally or by humans during crop production and commercialization. There are many factors that influence gene flow; therefore, it is difficult to prevent or predict. Gene flow via pollen and seed from glyphosate-resistant canola and creeping bentgrass fields has been documented. The adventitious presence of the transgene responsible for glyphosate resistance has been found in commercial seed lots of canola, corn and soybeans. In general, the glyphosate-resistant trait is not considered to provide an ecological advantage. However, regulators should consider the examples of gene flow from glyphosate-resistant crops when formulating rules for the release of crops with traits that could negatively impact the environment or human health.

  17. Flow and heat transfer of petal shaped double tube

    Science.gov (United States)

    Shakouchi, Toshihiko; Kawashima, Yuki; Tsujimoto, Koichi; Ando, Toshitake

    2014-06-01

    In this study, the flow and heat transfer characteristics of petal-shaped double tube with 6 petals are examined experimentally for a compact heat exchanger. As results, the heat transfer rate, Q, of the 6 petal shaped double tube (6-p tube) is much larger than that, Qp, of conventional circular double tube in all Reynolds number Rein,h (where, the reference length is hydraulic diameter) ranges. For example, at Rein,h =(0.5~1.0)× 104 it is about 4 times of Qp. The heat transfer enhancement of 6-p tube is by the increase of heat transfer area, wetting perimeter, and a highly fluctuating flow, and Q of the 6-p tube can be expressed by Q [kW/m] = 0.54Rein,h + 2245.

  18. Shape Evolution of Sandwitched Droplet in Microconfined Shear Flow

    CERN Document Server

    Chaudhury, Kaustav; Roy, Tamal; Chakraborty, Suman

    2015-01-01

    Droplets confined in a microfluidic channel often exhibit intriguing shapes, primarily attributable to complex hydrodynamic interactions over small scales. We show that effect of varied substrate wettability conditions may further complicate these interactions remarkably, and often non-trivially. Our studies reveal that the combined influence of substrate wettability and fluidic confinement eventually culminates towards influencing the droplet transients, distortion of the local shear flow field, as well as drop stabilization against breakup or detachment, allowing one to develop different regimes of shapes evolution that are fascinatingly distinct from the ones reported in earlier studies on drop breakup in micro-confined shear flows. We further demonstrate that combined consequences of wall effects and interfacial wettability characteristics can be exploited to pattern microfluidic substrates with pre-designed patches, bearing far-ranging scientific and technological consequences in several scientific and t...

  19. Quantitative control of organ shape by combinatorial gene activity.

    Directory of Open Access Journals (Sweden)

    Min-Long Cui

    Full Text Available The development of organs with particular shapes, like wings or flowers, depends on regional activity of transcription factors and signalling molecules. However, the mechanisms that link these molecular activities to the morphogenetic events underlying shape are poorly understood. Here we describe a combination of experimental and computational approaches that address this problem, applying them to a group of genes controlling flower shape in the Snapdragon (Antirrhinum. Four transcription factors are known to play a key role in the control of floral shape and asymmetry in Snapdragon. We use quantitative shape analysis of mutants for these factors to define principal components underlying flower shape variation. We show that each transcription factor has a specific effect on the shape and size of regions within the flower, shifting the position of the flower in shape space. These shifts are further analysed by generating double mutants and lines that express some of the genes ectopically. By integrating these observations with known gene expression patterns and interactions, we arrive at a combinatorial scheme for how regional effects on shape are genetically controlled. We evaluate our scheme by incorporating the proposed interactions into a generative model, where the developing flower is treated as a material sheet that grows according to how genes modify local polarities and growth rates. The petal shapes generated by the model show a good quantitative match with those observed experimentally for each petal in numerous genotypes, thus validating the hypothesised scheme. This article therefore shows how complex shapes can be accounted for by combinatorial effects of transcription factors on regional growth properties. This finding has implications not only for how shapes develop but also for how they may have evolved through tinkering with transcription factors and their targets.

  20. Traveling hairpin-shaped fluid vortices in plane Couette flow.

    Science.gov (United States)

    Deguchi, K; Nagata, M

    2010-11-01

    Traveling-wave solutions are discovered in plane Couette flow. They are obtained when the so-called steady hairpin vortex state found recently by Gibson [J. Fluid Mech. 638, 243 (2009)] and Itano and Generalis [Phys. Rev. Lett. 102, 114501 (2009)] is continued to sliding Couette flow geometry between two concentric cylinders by using the radius ratio as a homotopy parameter. It turns out that in the plane Couette flow geometry two traveling waves having the phase velocities with opposite signs are associated with their appearance from the steady hairpin vortex state, where the amplitude of the phase velocities increases gradually from zero as the Reynolds number is increased. The solutions obviously inherit the streaky structure of the hairpin vortex state, but shape preserving flow patterns propagate in the streamwise direction. Other striking features of the solution are asymmetric mean flow profiles and strong quasistreamwise vortices which occupy the vicinity of only the top or bottom moving boundary, depending on the sign of the phase velocity. Furthermore, we find that the pitchfork bifurcation associated with the appearance of the solution becomes imperfect when the flow is perturbed by a Poiseuille flow component.

  1. Computation of Hypersonic Flow about Maneuvering Vehicles with Changing Shapes

    Energy Technology Data Exchange (ETDEWEB)

    Ferencz, R M; Felker, F F; Castillo, V M

    2004-02-23

    Vehicles moving at hypersonic speeds have great importance to the National Security. Ballistic missile re-entry vehicles (RV's) travel at hypersonic speeds, as do missile defense intercept vehicles. Despite the importance of the problem, no computational analysis method is available to predict the aerodynamic environment of maneuvering hypersonic vehicles, and no analysis is available to predict the transient effects of their shape changes. The present state-of-the-art for hypersonic flow calculations typically still considers steady flow about fixed shapes. Additionally, with present computational methods, it is not possible to compute the entire transient structural and thermal loads for a re-entry vehicle. The objective of this research is to provide the required theoretical development and a computational analysis tool for calculating the hypersonic flow about maneuvering, deforming RV's. This key enabling technology will allow the development of a complete multi-mechanics simulation of the entire RV flight sequence, including important transient effects such as complex flight dynamics. This will allow the computation of the as-delivered state of the payload in both normal and unusual operational environments. This new analysis capability could also provide the ability to predict the nonlinear, transient behavior of endo-atmospheric missile interceptor vehicles to the input of advanced control systems. Due to the computational intensity of fluid dynamics for hypersonics, the usual approach for calculating the flow about a vehicle that is changing shape is to complete a series of steady calculations, each with a fixed shape. However, this quasi-steady approach is not adequate to resolve the frequencies characteristic of a vehicle's structural dynamics. Our approach is to include the effects of the unsteady body shape changes in the finite-volume method by allowing for arbitrary translation and deformation of the control volumes. Furthermore

  2. Effect of Flow Channel Shape on Performance in Reverse Electrodialysis

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Kilsung [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Kim, Deok Han; Kim, Daejoong [Sogang Univ., Seoul (Korea, Republic of)

    2017-05-15

    Reverse electrodialysis (RED), which generates electrical energy from the difference in concentration of two solutions, has been actively studied owing to its high potential and the increased interest in renewable energy resulting from the Paris Agreement on climate change. For RED commercialization, its power density needs to be maximized, and therefore various methods have been discussed. In this paper, the power density was measured using various flow shapes based on the aspect ratio, opening ratio, and number of distribution channels. We found that the power density is enhanced with a decrease in the aspect ratio and an increase in the opening ratio and number of distribution channels.

  3. Evaluation of nozzle shapes for an optical flow meter

    Science.gov (United States)

    Sheikholeslami, M. Z.; Patel, B. R.

    1992-05-01

    Numerical modeling is performed for turbulent flow in axisymmetric nozzles using Creare's computer program FLUENT/BFC. The primary objective of the project was to assist Spectron Development Laboratories in selecting an optimum nozzle shape for an optical flowmeter. The nozzle performance is evaluated for various length to diameter ratios, area contraction ratios, and Reynolds numbers. The computations have demonstrated that a cubic profile nozzle with length to diameter ratio of 1.6 and area contraction ratio of 6.2 can decrease the velocity profile non-uniformity from 15 percent at the entrance to 1 percent at the exit. The configuration is recommended for further investigation.

  4. Effect of Impeller Geometry and Tongue Shape on the Flow Field of Cross Flow Fans

    Institute of Scientific and Technical Information of China (English)

    M. Govardhan; G. Venkateswarlu

    2003-01-01

    Experiments were conducted to investigate the effect of impeller geometry and tongue shape on the flow field of cross flow fans.Three impellers (Ⅰ,Ⅱ,Ⅲ)having same outer diameter,but different radius ratio and blade angles were employed for the investigation. Each impeller was tested with two tongue shapes. Flow survey was carded out for each impeller and tongue shape at two flow coefficients, and for each flow coefficient at different circumferential positions. The flow is two-dimensional along the blade span except near the shrouds.The total pressure developed by the impellers in each case is found to be maximum at a circumferential position of around 270°. The total and static pressures at the inlet of impellers are more or less same regardless of impeller and tongue geometry, but they vary considerably at exit of the impellers. Impeller Ⅲ with tongue T2 develops higher total pressure and efficiency where as impeller Ⅱ with tongue T_2 develops minimum total pressure.Higher diffusion and smaller vortex size are the reasons for better performance of impeller Ⅲ with tongue T2.

  5. Effects of wave shape on sheet flow sediment transport

    Science.gov (United States)

    Hsu, T.-J.; Hanes, D.M.

    2004-01-01

    A two-phase model is implemented to study the effects of wave shape on the transport of coarse-grained sediment in the sheet flow regime. The model is based on balance equations for the average mass, momentum, and fluctuation energy for both the fluid and sediment phases. Model simulations indicate that the responses of the sheet flow, such as the velocity profiles, the instantaneous bed shear stress, the sediment flux, and the total amount of the mobilized sediment, cannot be fully parameterized by quasi-steady free-stream velocity and may be correlated with the magnitude of local horizontal pressure gradient (or free-stream acceleration). A net sediment flux in the direction of wave advance is obtained for both skewed and saw-tooth wave shapes typical of shoaled and breaking waves. The model further suggests that at critical values of the horizontal pressure gradient, there is a failure event within the bed that mobilizes more sediment into the mobile sheet and enhances the sediment flux. Preliminary attempts to parameterize the total bed shear stress and the total sediment flux appear promising. Copyright 2004 by the American Geophysical Union.

  6. The flow of gene expression.

    Science.gov (United States)

    Misteli, Tom

    2004-03-01

    Gene expression is a highly interconnected multistep process. A recent meeting in Iguazu Falls, Argentina, highlighted the need to uncover both the molecular details of each single step as well as the mechanisms of coordination among processes in order to fully understand the expression of genes.

  7. On Shape Dependence and RG Flow of Entanglement Entropy

    CERN Document Server

    Klebanov, Igor R; Pufu, Silviu S; Safdi, Benjamin R

    2012-01-01

    We use a mix of field theoretic and holographic techniques to elucidate various properties of quantum entanglement entropy. In (3+1)-dimensional conformal field theory we study the divergent terms in the entropy when the entangling surface has a conical or a wedge singularity. In (2+1)-dimensional field theory with a mass gap we calculate, for an arbitrary smooth entanglement contour, the expansion of the entropy in inverse odd powers of the mass. We show that the shape-dependent coefficients that arise are even powers of the extrinsic curvature and its derivatives. A useful dual construction of a (2+1)-dimensional theory, which allows us to exhibit these properties, is provided by the CGLP background. This smooth warped throat solution of 11-dimensional supergravity describes renormalization group flow from a conformal field theory in the UV to a gapped one in the IR. For this flow we calculate the recently introduced renormalized entanglement entropy and confirm that it is a monotonic function.

  8. Effect of particle shape and size on flow properties of lactose powders

    Institute of Scientific and Technical Information of China (English)

    Xiaowei Fu; Deborah Huck; Lisa Makein; Brian Armstrong; Ulf Willen; Tim Freeman

    2012-01-01

    The shape and size of particles are understood to affect the bulk behaviour of powders,though there are but few studies that present quantitative information on the relationship between particle shape and the flow properties of powder.This is due in part to the lack of techniques for rapidly determining both particle shape and the range of flow characteristics that describe the response of powders to the stress and shear experienced during their processing.This study presents data that quantifies the influence of particle shape/size of three different lactose powders on their respective flow and bulk characteristics.Two of the samples differ in size but have similar shapes; the third sample is more spherical but similar in size to one of the other two samples.The results demonstrate that in addition to particle size,particle shape significantly affect the flow characteristics of a powder over a wide range of stress conditions.

  9. Experimental and Numerical Analysis of Egg-Shaped Sewer Pipes Flow Performance

    Directory of Open Access Journals (Sweden)

    Manuel Regueiro-Picallo

    2016-12-01

    Full Text Available A Computational Fluid Dynamics (CFD model was developed to analyze the open-channel flow in a new set of egg-shaped pipes for small combined sewer systems. The egg-shaped cross-section was selected after studying several geometries under different flow conditions. Once the egg-shaped cross-section was defined, a real-scale physical model was built and a series of partial-full flow experiments were performed in order to validate the numerical simulations. Furthermore, the numerical velocity distributions were compared with an experimental formulation for analytic geometries, with comparison results indicating a satisfactory concordance. After the hydraulic performance of the egg-shaped pipe was analyzed, the numerical model was used to compare the average velocity and shear stress against an equivalent area circular pipe under low flow conditions. The proposed egg shape showed a better flow performance up to a filling ratio of h/H = 0.25.

  10. Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models

    Science.gov (United States)

    Leaf shape traits have long been a focus of many disciplines, but searching for complex genetic and environmental interactive mechanisms regulating leaf shape variation has not yet been well developed. The question of the respective roles of gene and environment and how they interplay to modulate l...

  11. Sex-biased gene flow among elk in the greater Yellowstone ecosystem

    Science.gov (United States)

    , Brian K. Hand; , Shanyuan Chen; , N. Anderson; , A. Beja-Pereira; Cross, Paul C.; , M. Ebinger; , H. Edwards; , R.A. Garrott; , M.D. Kardos; Kauffman, Matthew J.; , E.L. Landguth; , A. Middleton; , B. Scurlock; , P.J. White; , P. Zager; , M.K. Schwartz; , G. Luikart

    2014-01-01

    We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf = 46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel’s r = 0.274, P = 0.168). Large mitochondrial DNA genetic distances (e.g., FST > 0.2) between some of the geographically closest populations (<65 km) suggested behavioral factors and/or landscape features might shape female gene flow patterns. Given the strong sex-biased gene flow, future research and conservation efforts should consider the sexes separately when modeling corridors of gene flow or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female gene flow provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased gene flow likely to occur in many species

  12. Numerical Simulation of Capillary Flow in Fan-Shaped Asymmetric Interior Corner Under Microgravity

    Science.gov (United States)

    Yong-Qiang, Li; Wen-Hui, Cao; Ling, Liu

    2017-02-01

    Based on fluid mechanics theories, this research focuses on numerical simulation and analysis of capillary flow under microgravity in fan-shaped asymmetric interior corner. We analyze the effect the contact angle has on rising height in a fan-shaped asymmetric interior corner, and get the Concus-Finn condition the calculation of capillary flow needs to satisfy in fan-shaped asymmetric interior corner. Then we study the effect that different parameters of experimental medium and container configuration has on capillary flow in fan-shaped asymmetric interior corner when Concus-Finn condition is fulfilled. The conclusions of this paper has an important role in guiding the analytic solution of flow in a fan-shaped asymmetric interior corner under microgravity. We can also chose the appropriate experimental medium and design a container based on this paper.

  13. On the relation between gene flow theory and genetic gain

    Directory of Open Access Journals (Sweden)

    Woolliams John A

    2000-01-01

    Full Text Available Abstract In conventional gene flow theory the rate of genetic gain is calculated as the summed products of genetic selection differential and asymptotic proportion of genes deriving from sex-age groups. Recent studies have shown that asymptotic proportions of genes predicted from conventional gene flow theory may deviate considerably from true proportions. However, the rate of genetic gain predicted from conventional gene flow theory was accurate. The current note shows that the connection between asymptotic proportions of genes and rate of genetic gain that is embodied in conventional gene flow theory is invalid, even though genetic gain may be predicted correctly from it.

  14. Acoustic characteristics of the flow over different shapes of nozzle chevrons,

    Directory of Open Access Journals (Sweden)

    Daniel CRUNTEANU

    2013-09-01

    Full Text Available The objective of this paper is to present a comparison between different types of chevrons and their influence on the acoustic power level radiated by the flow over them. The comparison was performed using a two-dimensional simulation of the flow over four different shapes of chevrons resulting propagation of the acoustic waves for each shape. Acoustic characteristics were revealed studying the main flow parameters (pressure, velocity, kinetic energy in order to be able to discover the most efficient shape of chevron regarding the acoustic power level emitted.

  15. Reexamination of Hagen-Poiseuille flow: Shape dependence of the hydraulic resistance in microchannels

    DEFF Research Database (Denmark)

    Mortensen, Asger; Okkels, Fridolin; Bruus, Henrik

    2005-01-01

    We consider pressure-driven, steady-state Poiseuille flow in straight channels with various cross-sectional shapes: elliptic, rectangular, triangular, and harmonic-perturbed circles. A given shape is characterized by its perimeter P and area A which are combined into the dimensionless compactness...

  16. Sensitivity of the gradient oscillatory number to flow input waveform shapes.

    Science.gov (United States)

    Shimogonya, Yuji; Kumamaru, Hiroshige; Itoh, Kazuhiro

    2012-04-05

    The sensitivity of the gradient oscillatory number (GON), which is a potential hemodynamic indicator for cerebral aneurysm initiation, to flow input waveform shapes was examined by performing computational fluid dynamics (CFD) simulations of an anatomical model of a human internal carotid artery under three different waveform shape conditions. The local absolute variation (standard deviation) and relative variation (coefficient of variation) of the GON calculations for three waveform shapes were computed to quantify the variation in GON due to waveform shape changes. For all waveform shapes, an elevated GON was evident at a known aneurysm site, albeit occurring at additional sites. No significant differences were observed among the qualitative GON distributions derived using the three different waveform shapes. These results suggest that the GON is largely insensitive to the variability in flow input waveform shapes. The quantitative analysis revealed that GON displays an improved relative variation over a relatively high GON range. We therefore conclude that it is reasonable to use assumed flow input waveform shapes as a substitute for individual real waveform shapes for the detection of possible GON elevations of individual clinical cases in large-scale studies, where the higher values of GON are of primary interest.

  17. Flow simulation and shape optimization for aircraft design

    Science.gov (United States)

    Kroll, Norbert; Gauger, Nicolas R.; Brezillon, Joel; Dwight, Richard; Fazzolari, Antonio; Vollmer, Daniel; Becker, Klaus; Barnewitz, Holger; Schulz, Volker; Hazra, Subhendu

    2007-06-01

    Within the framework of the German aerospace research program, the CFD project MEGADESIGN was initiated. The main goal of the project is the development of efficient numerical methods for shape design and optimization. In order to meet the requirements of industrial implementations a co-operative effort has been set up which involves the German aircraft industry, the DLR, several universities and some small enterprises specialized in numerical optimization. This paper outlines the planned activities within MEGADESIGN, the status at the beginning of the project and it presents some early results achieved in the project.

  18. Imbibition in porous membranes of complex shape: quasi-stationary flow in thin rectangular segments.

    Science.gov (United States)

    Mendez, Sergio; Fenton, Erin M; Gallegos, Gil R; Petsev, Dimiter N; Sibbett, Scott S; Stone, Howard A; Zhang, Yi; López, Gabriel P

    2010-01-19

    The sustained liquid flow of a typical lateral flow assay can be mimicked by two-dimensional shaped, thin porous membranes, specifically rectangular membranes appended to circular sectors. In designing these fan-shaped devices, we have been aided by analytical equations and finite-element simulations. We show both mathematically and experimentally how a continuous increase in unwetted pore volume causes a deviation from traditional imbibition, and leads to quasi-stationary flow in the rectangular element. These results are both theoretically and practically important because they indicate how medical diagnostic test strips may be fabricated without incorporating an absorbent pad.

  19. Parachute gore shape and flow visualization during transient and steady-state conditions.

    Science.gov (United States)

    Dereng, V. G.

    1973-01-01

    Single parachute gore segments were tested in an experimental wind tunnel having a unique 'V' splitter plate test section with a glass panel on the near side and a grid of orifices for smoke injection on the back panel. The parachute gore shape and flow patterns were viewed in cross section during the inflation process and also during changing flow conditions as would occur with rapid reduction of payload weight. Observations of flow during inflation revealed a transient internal counterflow and the formation and degeneration of several trailing vortices. Gore shapes observed compared well with those of free flight.

  20. Effect of weld line shape on material flow during friction stir welding of aluminum and steel

    Science.gov (United States)

    Yasui, Toshiaki; Ando, Naoyuki; Morinaka, Shinpei; Mizushima, Hiroki; Fukumoto, Masahiro

    2014-08-01

    The effect of weld line shape on material flow during the friction stir welding of aluminum and steel was investigated. The material flow velocity was evaluated with simulated experiments using plasticine as the simulant material. The validity of the simulated experiments was verified by the marker material experiments on aluminum. The circumferential velocity of material around the probe increased with the depth from the weld surface. The effect is significant in cases where the advancing side is located on the outside of curve and those with higher curvature. Thus, there is an influence of weld line shape on material flow.

  1. RESEARCH ON THE MOTION CHARACTERISTICS OF FIBER SUSPENSIONS IN A WEDGE-SHAPED FLOW

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In this paper the motion of cylindrical particles in a wedge-shaped flow was studied. The velocity distribution of wedge-shaped flow was simulated first, then the Euler-Lagrange model used to calculate the motion of cylindrical particles. The evolution of particle location, velocity and orientation with time was examined. The trajectories of the particles with different particle Stokes number, rate of flow and initial particle orientation were drawn. The results indicate that the Stokes number and initial orientation are important parameters which affect the particle motion. The conclusions are helpful to the engineering applications.

  2. Coherent structures and flow topology of transitional separated-reattached flow over two and three dimensional geometrical shapes

    Science.gov (United States)

    Diabil, Hayder Azeez; Li, Xin Kai; Abdalla, Ibrahim Elrayah

    2017-09-01

    Large-scale organized motions (commonly referred to coherent structures) and flow topology of a transitional separated-reattached flow have been visualised and investigated using flow visualisation techniques. Two geometrical shapes including two-dimensional flat plate with rectangular leading edge and three-dimensional square cylinder are chosen to shed a light on the flow topology and present coherent structures of the flow over these shapes. For both geometries and in the early stage of the transition, two-dimensional Kelvin-Helmholtz rolls are formed downstream of the leading edge. They are observed to be twisting around the square cylinder while they stay flat in the case of the two-dimensional flat plate. For both geometrical shapes, the two-dimensional Kelvin-Helmholtz rolls move downstream of the leading edge and they are subjected to distortion to form three-dimensional hairpin structures. The flow topology in the flat plate is different from that in the square cylinder. For the flat plate, there is a merging process by a pairing of the Kelvin-Helmholtz rolls to form a large structure that breaks down directly into many hairpin structures. For the squire cylinder case, the Kelvin-Helmholtz roll evolves topologically to form a hairpin structure. In the squire cylinder case, the reattachment length is much shorter and a forming of the three-dimensional structures is closer to the leading edge than that in the flat plate case.

  3. Effect of angle of attack on the flow past a harbor seal vibrissa shaped cylinder

    Science.gov (United States)

    Kim, Hyo Ju; Yoon, Hyun Sik

    2016-11-01

    The present study considered the geometric disturbance inspired by a harbor seal vibrissa of which undulated surface structures are known as a detecting device to capture the water movement induced by prey fish. In addition, this vibrissa plays an important role to suppress vortex-induced vibration, which has been reported by the previous researches. The present study aims at finding the effect of the angle of attack (AOA) on flow characteristics around the harbor seal vibrissa shaped cylinder, since the flow direction facing the harbor seal vibrissa with the elliptic shape can be changed during the harbor seal's movements and surrounding conditions. Therefore, we considered a wide range of AOA varying from 0 to 90 degree. We carried out large eddy simulation (LES) to investigate the flow around inclined vibrissa shaped cylinder for the Reynolds number (Re) of 500 based hydraulic diameter of a harbor seal vibrissa shape. For comparison, the flow over the elliptic cylinder was also simulated according to AOA at the same Re. The vortical structures of both vibrissa shaped and elliptic cylinders have been compared to identify the fundamental mechanism making the difference flow quantities. This subject is supported by Korea Ministry of Environment (MOE) as "the Chemical Accident Prevention Technology Development Project.", National Research Foundation of Korea (NRF) Grant through GCRCSOP (No.20110030013) and (NRF-2015R1D1A3A01020867).

  4. Effects of texture component orientation on orientation flow visibility for 3-D shape perception.

    Science.gov (United States)

    Fowler, Michelle L; Li, Andrea

    2013-01-01

    In images of textured 3-D surfaces, orientation flows created by the texture components parallel to the surface slant play a critical role in conveying the surface slant and shape. This study examines the visibility of these orientation flows in complex patterns. Specifically, we examine the effect of orientation of neighboring texture components on orientation flow visibility. Complex plaids consisting of gratings equally spaced in orientation were mapped onto planar and curved surfaces. The visibility of the component that creates the orientation flows was quantified by measuring its contrast threshold (CT) while varying the combination of neighboring components present in the pattern. CTs were consistently lowest only when components closest in orientation to that of the orientation flows were subtracted from the pattern. This finding suggests that a previously reported frequency-selective cross-orientation suppression mechanism involved with the perception of 3-D shape from texture is affected by proximity in orientation of concurrent texture components.

  5. Effects of texture component orientation on orientation flow visibility for 3-D shape perception.

    Directory of Open Access Journals (Sweden)

    Michelle L Fowler

    Full Text Available In images of textured 3-D surfaces, orientation flows created by the texture components parallel to the surface slant play a critical role in conveying the surface slant and shape. This study examines the visibility of these orientation flows in complex patterns. Specifically, we examine the effect of orientation of neighboring texture components on orientation flow visibility. Complex plaids consisting of gratings equally spaced in orientation were mapped onto planar and curved surfaces. The visibility of the component that creates the orientation flows was quantified by measuring its contrast threshold (CT while varying the combination of neighboring components present in the pattern. CTs were consistently lowest only when components closest in orientation to that of the orientation flows were subtracted from the pattern. This finding suggests that a previously reported frequency-selective cross-orientation suppression mechanism involved with the perception of 3-D shape from texture is affected by proximity in orientation of concurrent texture components.

  6. Chemotaxis and flow disorder shape microbial dispersion in porous media

    Science.gov (United States)

    De Anna, Pietro; Yawata, Yutaka; Stocker, Roman; Juanes, Ruben

    2017-04-01

    Bacteria drive a plethora of natural processes in the subsurface, consuming organic matter and catalysing chemical reactions that are key to global elemental cycles. These macro-scale consequences result from the collective action of individual bacteria at the micro-scale, which are modulated by the highly heterogeneous subsurface environment, dominated by flow disorder and strong chemical gradients. Yet, despite the generally recognized importance of these microscale processes, microbe-host medium interaction at the pore scale remain poorly characterized and understood. Here, we introduce a microfluidic model system to directly image and quantify the role of cell motility on bacterial dispersion and residence time in confined, porous, media. Using the soil-dwelling bacterium Bacillus subtilis and the common amino acid serine as a resource, we observe that chemotaxis in highly disordered and confined physico-chemical environment affords bacteria an increase in their ability to persistently occupy the host medium. Our findings illustrate that the interplay between bacterial behaviour and pore-scale disorder in fluid velocity and nutrient concentration directly impacts the residence time, transport and bio-geo-chemical transformation rates of biota in the subsurface, and thus likely the processes they mediate.

  7. Effects of probe shape change on flow phenomena during Jovian entry

    Science.gov (United States)

    Tiwari, S. N.; Subramanian, S. V.

    1979-01-01

    The effects of probe shape change on the flow phenomena around a Jovian entry body is investigated. The initial body shapes considered are: 45-degree sphere cone, 35-degree hyperboloid, and 45-degree ellipsoid. The radiating shock-layer flow is assumed to be axisymmetric, inviscid, and in chemical and local thermodynamic equilibrium. The radiative transfer is calculated with an existing nongray radiation model that accounts for molecular band, atomic line, and continuum transitions. The results indicate that the shock-standoff distance, shock temperature and density, wall pressure distribution and radiative heating to the body are influenced significantly because of the probe shape change. The effect of shape change on radiative heating of the afterbody was considerably larger for the sphere cone and ellipsoid than for the hyperboloid. For the peak heating conditions, the net radiative heating to the body was found to be highest for the ellipsoid

  8. Effect of Jet Shape on Flow and Torque Characteristics of Pelton Turbine Runner

    Directory of Open Access Journals (Sweden)

    Vishal Gupta,

    2014-01-01

    Full Text Available In Pelton turbine, the energy carried by water is converted into kinetic energy by providing nozzle at the end of penstock. The shape of jet affects the force and torque on the bucket and runner of turbine. The nozzle of circular cross section is commonly used. In this paper attempt has been made to study the effect of four different jet shapes on the flow and torque characteristics of Pelton turbine runner through numerical simulation.

  9. Packing, alignment and flow of shape-anisotropic grains in a 3D silo experiment

    Science.gov (United States)

    Börzsönyi, Tamás; Somfai, Ellák; Szabó, Balázs; Wegner, Sandra; Mier, Pascal; Rose, Georg; Stannarius, Ralf

    2016-09-01

    Granular material flowing through bottlenecks, like the openings of silos, tend to clog and thus inhibit further flow. We study this phenomenon in a three-dimensional hopper for spherical and shape-anisotropic particles by means of x-ray tomography. The x-ray tomograms provide information on the bulk of the granular filling, and allows us to determine the particle positions and orientations inside the silo. In addition, it allows us to calculate local packing densities in different parts of the container. We find that in the flowing zone of the silo particles show a preferred orientation and thereby a higher order. Similarly to simple shear flows, the average orientation of the particles is not parallel to the streamlines but encloses a certain angle with it. In most parts of the hopper, the angular distribution of the particles did not reach the one corresponding to stationary shear flow, thus the average orientation angle in the hopper deviates more from the streamlines than in stationary shear flows. In the flowing parts of the silo, shear induced dilation is observed, which is more pronounced for elongated grains than for nearly spherical particles. The clogged state is characterized by a dome, i.e. the geometry of the layer of grains blocking the outflow. The shape of the dome depends on the particle shape.

  10. Numerical Simulation of Unsteady Flows and Shape Oscillations in Liquid Droplets Induced by Deployment Needle Retraction

    Science.gov (United States)

    Yan, Jin; Shaw, Benjamin D.

    2010-02-01

    Retractable opposed needles are often used in reduced-gravity droplet combustion experiments to deploy droplets prior to ignition. Needle retraction induces droplet shape oscillations and internal flows that can have important effects on subsequent droplet behaviors. In the present paper, the unsteady flows and droplet shape oscillations associated with deployment needle retraction are investigated using the commercial CFD software package Fluent. A volume-of-fluid method with a second-order upwind scheme and a dual time stepping solver is employed to solve the conservation equations in 2-d and 3-d simulations of droplets prior to ignition. A moving-mesh method is employed to model needle movements. Calculations indicate that rapid needle retraction causes ligament formation between a droplet and a needle, with ligament breakage sometimes resulting in the formation of satellite droplets. Needle retraction also induces droplet shape oscillations that rapidly decay, though significant internal flows are predicted to remain within droplets even after droplet shape oscillations have damped to low levels. The calculations indicate that the initial needle spacing can have important effects on droplet shape oscillations and internal flow characteristics. Comparison of model predictions and experimental data is favorable.

  11. Experimental Investigation on Cross Flow of Wedge-shaped Gap in the core of Prismatic VHTR

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jeong Hun; Park, Goon Cherl; Cho, Hyoung Kyu [Seoul National University, Seoul (Korea, Republic of); Yoon, Su Jong [Idaho National Laboratory, Idaho Falls (United States)

    2014-10-15

    The core of the PMR type reactor consists of assemblies of hexagonal graphite blocks. The graphite blocks have lots of advantages for neutron economy and high temperature structural integrity. The height and flat-to-flat width of fuel bock are 793 mm and 360 mm, respectively. Each block has 108 coolant channels of which the diameter is 16 mm. And there are gaps between blocks not only vertically but also horizontally for reloading of the fuel elements. The vertical gap induces the bypass flow and through the horizontal gap the cross flow is formed. Since the complicated flow distribution occurs by the bypass flow and cross flow, flow characteristics in the core of the PMR reactor cannot be treated as a simple pipe flow. The fuel zone of the PMR core consists of multiple layers of fuel blocks. The shape change of the fuel blocks could be caused by the thermal expansion and fast-neutron induced shrinkage. It could make different axial shrinkage of fuel block and this leads to wedge-shaped gaps between two stacked fuel blocks. The cross flow is often considered as a leakage flow through the horizontal gap between stacked fuel blocks and it complicates the flow distribution in the reactor core by connecting the coolant channel and the bypass gap. Moreover, the cross flow could lead to uneven coolant distribution and consequently cause superheating of individual fuel element zones with increased fission product release. Since the core cross flow has a negative impact on safety and efficiency of VHTR, core cross flow phenomena have to be investigated to improve the core thermal margin of VHTR. To develop the cross flow loss coefficient model for determination of the flow distribution for PMR core analysis codes, study on cross flow for PMR200 core is essential. In particular, to predict the amount of flow through the cross flow gap, obtaining accurate flow loss coefficient is important. In this study, the full-scale cross flow experimental facility was constructed to

  12. Wavefront shaping for imaging-based flow velocity measurements through distortions using a Fresnel guide star.

    Science.gov (United States)

    Koukourakis, Nektarios; Fregin, Bob; König, Jörg; Büttner, Lars; Czarske, Jürgen W

    2016-09-19

    Imaging-based flow measurement techniques, like particle image velocimetry (PIV), are vulnerable to time-varying distortions like refractive index inhomogeneities or fluctuating phase boundaries. Such distortions strongly increase the velocity error, as the position assignment of the tracer particles and the decrease of image contrast exhibit significant uncertainties. We demonstrate that wavefront shaping based on spatially distributed guide stars has the potential to significantly reduce the measurement uncertainty. Proof of concept experiments show an improvement by more than one order of magnitude. Possible applications for the wavefront shaping PIV range from measurements in jets and film flows to biomedical applications.

  13. Research on vibration characteristics of L-shaped plate using a mobility power flow approach

    Institute of Scientific and Technical Information of China (English)

    CHEN Xiao-li; SHENG Mei-ping

    2007-01-01

    L-shaped plates have become an important focuses in structural vibration research. To determine their vibration characteristics, this paper applied a mobility power flow method. Firstly, the L-shaped plate was divided into two substructures to simplify analysis. The coupled bending moment was then deduced by applying a continuous vibration property on the common edge. Next, the response on any point of the plate and the input and transmitted power flow formulas were calculated. Numerical simulations showed the distribution of the coupled bending moment and the response of the whole structure. The validity of this method was verified by the SEA approach.

  14. The curved shape of Caulobacter crescentus enhances surface colonization in flow

    Science.gov (United States)

    Persat, Alexandre; Stone, Howard A.; Gitai, Zemer

    2014-05-01

    Each bacterial species has a characteristic shape, but the benefits of specific morphologies remain largely unknown. To understand potential functions for cell shape, we focused on the curved bacterium Caulobacter crescentus. Paradoxically, C. crescentus curvature is robustly maintained in the wild but straight mutants have no known disadvantage in standard laboratory conditions. Here we demonstrate that cell curvature enhances C. crescentus surface colonization in flow. Imaging the formation of microcolonies at high spatial and temporal resolution indicates that flow causes curved cells to orient such that they arc over the surface, thereby decreasing the distance between the surface and polar adhesive pili, and orienting pili to face the surface. C. crescentus thus repurposes pilus retraction, typically used for surface motility, for surface attachment. The benefit provided by curvature is eliminated at high flow intensity, raising the possibility that diversity in curvature adapts related species for life in different flow environments.

  15. The curved shape of the bacterium Caulobacter crescentus enhances colonization of surfaces in flow

    Science.gov (United States)

    Persat, Alexandre; Gitai, Zemer; Stone, Howard

    2014-11-01

    Bacteria thrive in all types of fluid environments; flow is thus a ubiquitous aspect of their lives. Bacteria have evolved a variety of cellular components contributing to their growth in specific environments. However, cellular features that help them survive and develop in flow have been rarely characterized. Here, we show that Caulobacter crescentus may have evolved its curved shape to enhance the colonization of surfaces in flow. C. crescentus curvature is preserved in the wild but straight mutants have no known growth disadvantage in standard laboratory conditions. Leveraging microfluidics and single-cell imaging, we demonstrate that curvature enhances surface colonization in flow, promoting the formation of larger microcolonies. Cells attach to a surface from a single pole, so that flow affects their orientation. In flow, viscous forces generate a torque on the curved cell body, which reorients the cell in the direction of the flow. The curved cell appears to arc above the surface, optimally orienting its unattached pole towards the surface. This reduces the distance between the surface and the pole, thereby enhancing attachment of its progeny. Additionally, we show that curved shape enhances colony spreading across the direction of the flow, generating more robust biofilm compared to straight mutants.

  16. Thin-film flow in helically wound shallow channels of arbitrary cross-sectional shape

    Science.gov (United States)

    Arnold, D. J.; Stokes, Y. M.; Green, J. E. F.

    2017-01-01

    We consider the steady, gravity-driven flow of a thin film of viscous fluid down a helically wound shallow channel of arbitrary cross-sectional shape with arbitrary torsion and curvature. This extends our previous work [D. J. Arnold et al., "Thin-film flow in helically-wound rectangular channels of arbitrary torsion and curvature," J. Fluid Mech. 764, 76-94 (2015)] on channels of rectangular cross section. The Navier-Stokes equations are expressed in a novel, non-orthogonal coordinate system fitted to the channel bottom. By assuming that the channel depth is small compared to its width and that the fluid depth in the vertical direction is also small compared to its typical horizontal extent, we are able to solve for the velocity components and pressure analytically. Using these results, a differential equation for the free surface shape is obtained, which must in general be solved numerically. Motivated by the aim of understanding flows in static spiral particle separators used in mineral processing, we investigate the effect of cross-sectional shape on the secondary flow in the channel cross section. We show that the competition between gravity and inertia in non-rectangular channels is qualitatively similar to that in rectangular channels, but that the cross-sectional shape has a strong influence on the breakup of the secondary flow into multiple clockwise-rotating cells. This may be triggered by small changes to the channel geometry, such as one or more bumps in the channel bottom that are small relative to the fluid depth. In contrast to the secondary flow which is quite sensitive to small bumps in the channel bottom, the free-surface profile is relatively insensitive to these. The sensitivity of the flow to the channel geometry may have important implications for the design of efficient spiral particle separators.

  17. Bubble shape and breakage events in a vertical pipe at the boiler flow line

    Directory of Open Access Journals (Sweden)

    Fsadni Andrew

    2014-03-01

    Full Text Available The theoretical and experimental aspects concerning the typical bubble shape at the flow line of a standard domestic central heating system are investigated. This is done in support of the on-going research on two-phase flows in domestic central heating systems. Bubble nucleation and detachment at the primary heat exchanger wall of a domestic central heating boiler results in a bubbly two-phase flow in the system pipe work. Bubbly flow results in undesired cold spots at higher points in the system, consequently diminishing system performance. An experimental analysis was done on the bubble shape at the exit of the boiler through the application of photographic techniques. The results are presented in terms of the measured bubble aspect ratios at some principal system operating conditions. The dimensionless Eotvos and bubble Reynolds number were calculated and tabulated with the measured mean diameters. The data was subsequently correlated to the bubble shape regime diagram. Results suggest that most bubbles are quasi-spherical in shape with a noticeable elongation at lower bulk fluid Reynolds numbers.

  18. Bubble shape and breakage events in a vertical pipe at the boiler flow line

    Science.gov (United States)

    Fsadni, Andrew; Ge, Yunting

    2014-03-01

    The theoretical and experimental aspects concerning the typical bubble shape at the flow line of a standard domestic central heating system are investigated. This is done in support of the on-going research on two-phase flows in domestic central heating systems. Bubble nucleation and detachment at the primary heat exchanger wall of a domestic central heating boiler results in a bubbly two-phase flow in the system pipe work. Bubbly flow results in undesired cold spots at higher points in the system, consequently diminishing system performance. An experimental analysis was done on the bubble shape at the exit of the boiler through the application of photographic techniques. The results are presented in terms of the measured bubble aspect ratios at some principal system operating conditions. The dimensionless Eotvos and bubble Reynolds number were calculated and tabulated with the measured mean diameters. The data was subsequently correlated to the bubble shape regime diagram. Results suggest that most bubbles are quasi-spherical in shape with a noticeable elongation at lower bulk fluid Reynolds numbers.

  19. The Himalayas: barrier and conduit for gene flow.

    Science.gov (United States)

    Gayden, Tenzin; Perez, Annabel; Persad, Patrice J; Bukhari, Areej; Chennakrishnaiah, Shilpa; Simms, Tanya; Maloney, Trisha; Rodriguez, Kristina; Herrera, Rene J

    2013-06-01

    The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y-chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian-specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep-rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y-chromosome data indicate sex-biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia.

  20. Measurement of Size-dependent Dynamic Shape Factors of Quartz Particles in Two Flow Regimes

    Energy Technology Data Exchange (ETDEWEB)

    Alexander, Jennifer M.; Bell, David M.; Imre, D.; Kleiber, Paul; Grassian, Vicki H.; Zelenyuk, Alla

    2016-08-02

    Understanding and modeling the behavior of quartz dust particles, commonly found in the atmosphere, requires knowledge of many relevant particles properties, including particle shape. This study uses a single particle mass spectrometer, a differential mobility analyzer, and an aerosol particle mass analyzer to measure quartz aerosol particles mobility, aerodynamic, and volume equivalent diameters, mass, composition, effective density, and dynamic shape factor as a function of particle size, in both the free molecular and transition flow regimes. The results clearly demonstrate that dynamic shape factors can vary significantly as a function of particle size. For the quartz samples studied here, the dynamic shape factors increase with size, indicating that larger particles are significantly more aspherical than smaller particles. In addition, dynamic shape factors measured in the free-molecular (χv) and transition (χt) flow regimes can be significantly different, and these differences vary with the size of the quartz particles. For quartz, χv of small (d < 200 nm) particles is 1.25, while χv of larger particles (d ~ 440 nm) is 1.6, with a continuously increasing trend with particle size. In contrast χt, of small particles starts at 1.1 increasing slowly to 1.34 for 550 nm diameter particles. The multidimensional particle characterization approach used here goes beyond determination of average properties for each size, to provide additional information about how the particle dynamic shape factor may vary even for particles with the same mass and volume equivalent diameter.

  1. Modeling three-dimensional flow about ellipsoidal inhomogeneities with application to flow to a gravel-packed well and flow through lens-shaped inhomogeneities

    Science.gov (United States)

    Fitts, Charles R.

    1991-05-01

    Analytic functions are superimposed to model three-dimensional steady groundwater flow in regions containing one or more Inhomogeneities shaped like prolate or oblate ellipsoids of revolution. Each function and the sum of such functions are solutions of Laplace's equation, the governing differential equation for steady groundwater flow. The functions are implemented in a manner that provides exact continuity of flow across the entire boundary of each inhomogeneity. In general, continuity of head is provided at specified control points on the boundary and is approximated between control points. For the case of one inhomogeneity in a uniform flow field, it turns out that there is exact continuity of head across the entire surface of the inhomogeneity. The method is implemented in a computer program written by the author. Two applications are demonstrated: (1) flow to a gravel-packed well and (2) flow through a series of lens-shaped inhomogeneities. The examples demonstrate that the approximation of continuity of head can be made acceptable for many problems. A possible application of the technique would be testing various theories regarding contaminant migration and dispersion by simulating flow and chemical diffusion through large numbers of lens-shaped inhomogeneities.

  2. Transient flow model and pressure dynamic features of tree-shaped fractal re- servoirs

    Institute of Scientific and Technical Information of China (English)

    TAN Xiao-hua; LI Xiao-ping

    2014-01-01

    A transient flow model of tree-shaped fractal reservoirs is built by embedding a fracture network simulated by a tree-shaped fractal network into a matrix system. The model can be solved using the Laplace conversion method. The dimensionless bottom hole pressure can be obtained using the Stehfest numerical inversion method. The bi-logarithmic type curves for the tree-shaped fractal reservoirs are thus obtained. The pressure transient responses under different fractal factors are discussed. The factors with a primary effect on the inter-porosity flow regime include the initial branch numberN, the length ratioα, and the branch angleθ. The diameter ratioβ has a significant effect on the fracture radial flow, the inter-porosity and the total system radial flow regimes. The total branch levelM of the network mainly influences the total system radial flow regime. The model presented in this paper provides a new methodology for analyzing and predicting the pressure dynamic characteristics of naturally fractured reservoirs.

  3. Microcapillary flow behavior of magnetic nanofluids in the presence of plate shaped bentonite particles

    Science.gov (United States)

    Parmar, Mayur; Virpura, Hiral; Patel, Rajesh

    2013-04-01

    Plate shaped bentonite particles of size ˜600 nm and thickness ˜2 nm are dispersed in a magnetic nanofluid. Magnetic field dependent flow behavior of this composite suspension is studied using a horizontal microcapillary placed between the poles of an electromagnet. The plate shaped bentonite particle produces extra hindrance to the flow under the application of moderate magnetic field and produces an enhanced magnetoviscous effect. 75% volume concentration of bentonite produces eight times larger change in magnetic field dependent viscosity than does the pure magnetic nanofluid. Hindrance to the flow is due to the chain like structure of magnetic nanoparticles, tumbling and rotational motion of bentonite particles and interaction between magnetic and bentonite particles. The field-induced structures are also observed using an optical microscope. Results offer several advantages over the inverse MR effect as well as to study the motion of biological cells and tissues under the effect of magnetic field.

  4. Flow rate of polygonal grains through a bottleneck: Interplay between shape and size

    Directory of Open Access Journals (Sweden)

    Ezequiel Goldberg

    2015-11-01

    Full Text Available We report two-dimensional simulations of circular and polygonal grains passing through an aperture at the bottom of a silo. The mass flow rate for regular polygons is lower than for disks\\red{,} as observed by other authors. We show that both the exit velocity of the grains and the packing fraction are lower for polygons, which leads to the reduced flow rate. We point out the importance of the criteria used to define when two objects of different shape are considered to be of the same size. Depending on this criteria, the mass flow rate may vary significantly for some polygons. Moreover, the particle flow rate is non-trivially related to a combination of mass flow rate, particle shape and particle size. For some polygons, the particle flow rate may be lower or higher than that of the corresponding disks depending on the size comparison criteria. Received: 18 May 2015, Accepted: 30 October 2015; Edited by: F. Melo; Reviewed by: J.-N. Roux, Universite Parsi Est, Laboratoire Navier, Champs-sur-Marne, France; DOI: http://dx.doi.org/10.4279/PIP.070016 Cite as: E Goldberg, C M Carlevaro, L A Pugnaloni, Papers in Physics 7, 070016 (2015

  5. The role of different grain shapes in modifying intra-pore flow and transport phenomena

    Science.gov (United States)

    Chaudhary, K.; Cardenas, B.; Bennett, P.; Ketcham, R. A.

    2010-12-01

    Intra-pore (10 -100 µm) fluid flow and mass transport depend on pore geometry. This has implication on microbial and biogeochemical processes within pores and residual trapping of Supercritical CO2. Since effects of grain size and grain sorting are already known, we investigate the effect of grain shapes in modifying intra-pore fluid flow and mass transport both inside and between pores and stagnant zones. Numerical simulations are carried out by solving the Navier-Stokes equations on idealized 2-D domains representing grain shapes such as squares and circles. We conduct a sensitivity study by varying grain angularity and imposing different Reynolds numbers flows to analyze their influence on permeability and distribution of vortices, also known as recirculation zones. We observe that the coupled effects of pore geometries and vortices lead to large variation in the fluid velocity, which consequently leads to non-Fickian transport even though flow can still be described by a continuum-scale Darcy equation. We find that the permeability increases and vorticity decreases with decreasing angularity of the grains. The flow velocities in the stagnant zone increases linearly with higher Reynolds number flows, with the rate of increase largest among the angular grains. The mass transfer mechanism between main pores and stagnant zones is mainly molecular diffusion, but the concentration gradient between the main pore and the stagnant zone is significantly influenced by the mixing effect associated with vortices. The overall effect of an increase in vorticity manifests itself as an increase in the global dispersion of the solute, which results both in an early arrival and a prolonged tail of a solute’s break-through curve. We find that the related effects of grain shapes and vortices are important in understanding pore scale flow and transport processes and may have significant implication on the issues of contaminant transport in aquifers and the geological storage of

  6. VOF Modeling and Analysis of the Segmented Flow in Y-Shaped Microchannels for Microreactor Systems

    Directory of Open Access Journals (Sweden)

    Xian Wang

    2013-01-01

    Full Text Available Microscaled devices receive great attention in microreactor systems for producing high renewable energy due to higher surface-to-volume, higher transport rates (heat or/and mass transfer rates, and other advantages over conventional-size reactors. In this paper, the two-phase liquid-liquid flow in a microchannel with various Y-shaped junctions has been studied numerically. Two kinds of immiscible liquids were injected into a microchannel from the Y-shaped junctions to generate the segment flow mode. The segment length was studied. The volume of fluid (VOF method was used to track the liquid-liquid interface and the piecewise-liner interface construction (PLIC technique was adopted to get a sharp interface. The interfacial tension was simulated with continuum surface force (CSF model and the wall adhesion boundary condition was taken into consideration. The simulated flow pattern presents consistence with our experimental one. The numerical results show that a segmented flow mode appears in the main channel. Under the same inlet velocities of two liquids, the segment lengths of the two liquids are the same and depend on the inclined angles of two lateral channels. The effect of inlet velocity is studied in a typical T-shaped microchannel. It is found that the ratio between the lengths of two liquids is almost equal to the ratio between their inlet velocities.

  7. Psychiatric gene discoveries shape evidence on ADHD's biology

    Science.gov (United States)

    Thapar, A; Martin, J; Mick, E; Arias Vásquez, A; Langley, K; Scherer, S W; Schachar, R; Crosbie, J; Williams, N; Franke, B; Elia, J; Glessner, J; Hakonarson, H; Owen, M J; Faraone, S V; O'Donovan, M C; Holmans, P

    2016-01-01

    A strong motivation for undertaking psychiatric gene discovery studies is to provide novel insights into unknown biology. Although attention-deficit hyperactivity disorder (ADHD) is highly heritable, and large, rare copy number variants (CNVs) contribute to risk, little is known about its pathogenesis and it remains commonly misunderstood. We assembled and pooled five ADHD and control CNV data sets from the United Kingdom, Ireland, United States of America, Northern Europe and Canada. Our aim was to test for enrichment of neurodevelopmental gene sets, implicated by recent exome-sequencing studies of (a) schizophrenia and (b) autism as a means of testing the hypothesis that common pathogenic mechanisms underlie ADHD and these other neurodevelopmental disorders. We also undertook hypothesis-free testing of all biological pathways. We observed significant enrichment of individual genes previously found to harbour schizophrenia de novo non-synonymous single-nucleotide variants (SNVs; P=5.4 × 10−4) and targets of the Fragile X mental retardation protein (P=0.0018). No enrichment was observed for activity-regulated cytoskeleton-associated protein (P=0.23) or N-methyl-D-aspartate receptor (P=0.74) post-synaptic signalling gene sets previously implicated in schizophrenia. Enrichment of ADHD CNV hits for genes impacted by autism de novo SNVs (P=0.019 for non-synonymous SNV genes) did not survive Bonferroni correction. Hypothesis-free testing yielded several highly significantly enriched biological pathways, including ion channel pathways. Enrichment findings were robust to multiple testing corrections and to sensitivity analyses that excluded the most significant sample. The findings reveal that CNVs in ADHD converge on biologically meaningful gene clusters, including ones now established as conferring risk of other neurodevelopmental disorders. PMID:26573769

  8. Water behavior in a u-shaped flow channel of PEM fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Quan, P.; Zhou, B.; Sobiesiak, A. [Windsor Univ., ON (Canada). Dept. of Mechanical, Automotive and Materials Engineering; Liu, Z.S. [National Research Council of Canada, Vancouver, BC (Canada). Inst. for Fuel Cell Innovation

    2005-07-01

    A study was conducted to find a practical approach for predicting liquid water distribution in the U-shaped flow channels of a proton exchange membrane (PEM) fuel cell. Computational fluid dynamics modeling with the FLUENT software package was used to demonstrate the two-phase flow of the air-water transport process inside the channel. It was noted that no chemical reaction occurs inside the flow channels and the liquid water is formed either on the surfaces of the flow channels or inside the flow channels. The problem can therefore be simplified as a fluid mechanics problem with water sources inside its physical domain or on its boundaries. The volume-of-fluid (VOF) model was used to track dynamic air-water interactions. Three cases with a range of initial water phase distributions corresponding to different fuel cell operating conditions were simulated numerically to gain a better understanding of water behaviour inside the serpentine channel. It was concluded that the bend area in the serpentine flow field affects the fuel cell performance. This is because it influences the flow field which in turn influences the air-water flow and water liquid distribution inside the channel or along the inside channel surfaces. 15 refs., 1 tab., 11 figs.

  9. On the Symmetry of Molecular Flows Through the Pipe of an Arbitrary Shape (I) Diffusive Reflection

    Science.gov (United States)

    Kusumoto, Yoshiro

    Molecular gas flows through the pipe of an arbitrary shape is mathematically considered based on a diffusive reflection model. To avoid a perpetual motion, the magnitude of the molecular flow rate must remain invariant under the exchange of inlet and outlet pressures. For this flow symmetry, the cosine law reflection at the pipe wall was found to be sufficient and necessary, on the assumption that the molecular flux is conserved in a collision with the wall. It was also shown that a spontaneous flow occurs in a hemispherical apparatus, if the reflection obeys the n-th power of cosine law with n other than unity. This apparatus could work as a molecular pump with no moving parts.

  10. Pollen and gene flow in fragmented habitats

    NARCIS (Netherlands)

    Kwak, Manja M.; Velterop, Odilia; van Andel, Jelte

    1998-01-01

    . Habitat fragmentation affects both plants and pollinators. Habitat fragmentation leads to changes in species richness, population number and size, density, and shape, thus to changes in the spatial arrangement of flowers. These changes influence the amount of food for flower-visiting insects and t

  11. Pollen and gene flow in fragmented habitats

    NARCIS (Netherlands)

    Kwak, Manja M.; Velterop, Odilia; van Andel, Jelte

    1998-01-01

    . Habitat fragmentation affects both plants and pollinators. Habitat fragmentation leads to changes in species richness, population number and size, density, and shape, thus to changes in the spatial arrangement of flowers. These changes influence the amount of food for flower-visiting insects and t

  12. Viscous flow in simple curved gaps. I - An asymptotic theory. II - Viscous stress and shape function

    Science.gov (United States)

    Fan, D.-N.; Tong, W.

    1989-01-01

    The present asymptotic theory for generalized incompressible two-dimensional steady flow in curved channels has been constructed in the limit when gas thickness approaches zero with its lateral dimensions fixed; successive asymptotic solution terms are analytically generated by quadratures. In the second part of this work, the curvature of the gap treated is arbitrary. It is established that each term in the series solution of velocity and pressure is the product of a scale factor and a universal shape functions. Various interaction modes between the volume rate-of-flow, curvature, and its variations, are identified and quantitatively characterized.

  13. Psychiatric gene discoveries shape evidence on ADHD's biology

    NARCIS (Netherlands)

    Thapar, A.; Martin, J.; Mick, E.; Arias Vasquez, A.; Langley, K.; Scherer, S.W.; Schachar, R.; Crosbie, J.; Williams, N.; Franke, B.; Elia, J.; Glessner, J.; Hakonarson, H.; Owen, M.J.; Faraone, S.V; O'Donovan, M.C.; Holmans, P.

    2016-01-01

    A strong motivation for undertaking psychiatric gene discovery studies is to provide novel insights into unknown biology. Although attention-deficit hyperactivity disorder (ADHD) is highly heritable, and large, rare copy number variants (CNVs) contribute to risk, little is known about its pathogenes

  14. Shape optimization of multi-chamber cross-flow mufflers by SA optimization

    Science.gov (United States)

    Chiu, Min-Chie; Chang, Ying-Chun

    2008-05-01

    It is essential when searching for an efficient acoustical mechanism to have an optimally shaped muffler designed specially for the constrained space found in today's plants. Because the research work of optimally shaped straight silencers in conjunction with multi-chamber cross-flow perforated ducts is rarely addressed, this paper will not only analyze the sound transmission loss (STL) of three kinds of cross-flow perforated mufflers but also will analyze the optimal design shape within a limited space. In this paper, the four-pole system matrix used in evaluating acoustic performance is derived by using the decoupled numerical method. Moreover, a simulated annealing (SA) algorithm, a robust scheme in searching for the global optimum by imitating the softening process of metal, has been adopted during shape optimization. To reassure SA's correctness, the STL's maximization of three kinds of muffles with respect to one-tone and dual-tone noise is exemplified. Furthermore, the optimization of mufflers with respect to an octave-band fan noise by the simulated algorithm has been introduced and fully discussed. Before the SA operation can be carried out, an accuracy check of the mathematical model with respect to cross-flow perforated mufflers has to be performed by Munjal's analytical data and experimental data. The optimal result in eliminating broadband noise reveals that the cross-flow perforated muffler with more chambers is far superior at noise reduction than a muffler with fewer chambers. Consequently, the approach used for the optimal design of noise elimination proposed in this study is certainly easy and efficient.

  15. Numerical Investigation of Supersonic Oscillatory Flow with Strong Interference over a Capsule-shaped Abort System

    Science.gov (United States)

    Wang, Yunpeng; Ozawa, Hiroshi; Nakamura, Yoshiaki

    The flow past a capsule-shaped space transportation system (STS) is numerically analyzed using computational fluid dynamics (CFD) for different free stream Mach numbers ranging from 1.2 to 5.0, where a capsule is modeled by a cone, and a rocket by a circular cylinder. The objective of this research is to study Mach number effects on phenomena of the supersonic aerodynamic interference with periodic flow oscillations at supersonic regime. So far we have considered two models: model A (without disk) and model B (with disk). It was found from experimental and computational results that the flow around model A becomes steady, where aerodynamic interaction is not observed, while in model B, flow becomes unsteady with periodic oscillations. This flow oscillation is considered to be a potentially high risk in separation of the capsule and rocket. Therefore, the present study focuses on the unsteady case of model B. Numerical results at M=3.0 compared well with experimental ones, which validates the present CFD. Time-averaged results are employed to see the whole trajectories of shock waves and the variation in amplitude of flow oscillation during one cycle. Moreover, a fence is proposed as a device to suppress the flow oscillation.

  16. Microcapillary flow behavior of magnetic nanofluids in the presence of plate shaped bentonite particles

    Energy Technology Data Exchange (ETDEWEB)

    Parmar, Mayur; Virpura, Hiral [Department of Physics, Bhavnagar University, Bhavnagar 364001, GJ (India); Patel, Rajesh, E-mail: rjp@bhavuni.edu [Department of Physics, Bhavnagar University, Bhavnagar 364001, GJ (India); Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104 (United States)

    2013-04-15

    Plate shaped bentonite particles of size ∼600 nm and thickness ∼2 nm are dispersed in a magnetic nanofluid. Magnetic field dependent flow behavior of this composite suspension is studied using a horizontal microcapillary placed between the poles of an electromagnet. The plate shaped bentonite particle produces extra hindrance to the flow under the application of moderate magnetic field and produces an enhanced magnetoviscous effect. 75% volume concentration of bentonite produces eight times larger change in magnetic field dependent viscosity than does the pure magnetic nanofluid. Hindrance to the flow is due to the chain like structure of magnetic nanoparticles, tumbling and rotational motion of bentonite particles and interaction between magnetic and bentonite particles. The field-induced structures are also observed using an optical microscope. Results offer several advantages over the inverse MR effect as well as to study the motion of biological cells and tissues under the effect of magnetic field. -- Highlights: ► Dispersed plate shaped bentonite particles in magnetic fluids to study capillary viscosity. ► Increased viscosity is due to the hindrance to the rotation of the bentonite particles. ► Increase in viscosity is five times larger for bentonite particles than the pure magnetic fluids. ► This is a new kind of magnetoviscous effect, dispersing anisotropic particles in magnetic fluids.

  17. Effects of the shape of the hydrograph and unsteadiness on flow properties and hysteresis in open channel flow

    Science.gov (United States)

    Bagherimiyab, F.; Roy, A.; Lemmin, U.

    2013-12-01

    Flows in rivers and open channels become unsteady during flood events. This study examines experimentally the relationships between the shape of the hydrographs and the characteristics of the accelerating, stabilizing and decelerating phases and the hysteretic trajectories. Seven symmetrical hydrographs with different unsteadiness (20 s, 30 s, 45 s, 60 s, 90 s, 150 s and 210 s accelerating and decelerating phases) and 90 s peak steady range were investigated in open-channel flow over a loose gravel bed. Detailed, quasi-instantaneous velocity profiles were measured using a 3D Acoustic Doppler Velocity Profiler (ADVP). Even though discharge was varied linearly at a constant rate over the rising and falling limb of each hydrograph, the change in relative submergence was not linear during parts of these periods. Important variations were observed between the two limbs of the hydrographs, but also among the different unsteadiness conditions, resulting in considerable differences in the flow dynamics. The discrepancy between the variation of the discharge and the observed water level over time indicates that flow adjustment over the rough bed takes place along the channel. This adjustment differs for the accelerating and the decelerating phases. Different hysteretic loops are formed for each hydrograph. In each loop, water depth for the accelerating range is different from that of the decelerating range for the same discharge. The transition from the accelerating range to the peak flow range is gradual. It is particularly marked for the 20 s hydrograph, where steady state peak flow is only attained at the very end of the peak flow range. The hydrograph with the lowest unsteadiness (210 s) remains in steady state during the whole peak steady flow range. Compared to the other hydrographs, it is characterized by a higher water depth for the same discharge and at the end it reaches a lower water depth for the same discharge. During the accelerating range, both mean velocity

  18. Flow field simulation and establishment for mathematical models of flow area of spool valve with sloping U-shape notch machined by different methods

    Institute of Scientific and Technical Information of China (English)

    王兆强; 顾临怡; 冀宏; 陈家旺; 李林

    2014-01-01

    Precise function expression of the flow area for the sloping U-shape notch orifice versus the spool stroke was derived. The computational fluid dynamics was used to analyze the flow features of the sloping U-shape notch on the spool, such as mass flow rates, flow coefficients, efflux angles and steady state flow forces under different operating conditions. At last, the reliability of the mathematical model of the flow area for the sloping U-shape notch orifice on the spool was demonstrated by the comparison between the orifice area curve derived and the corresponding experimental data provided by the test. It is presented that the bottom arc of sloping U-shape notch (ABU) should not be omitted when it is required to accurately calculate the orifice area of ABU. Although the theoretical flow area of plain bottom sloping U-shape notch (PBU) is larger than that of ABU at the same opening, the simulated mass flow and experimental flow area of ABU are both larger than these of PBU at the same opening, while the simulated flow force of PBU is larger than that of ABU at the same opening. Therefore, it should be prior to adapt the ABU when designing the spool with proportional character.

  19. Modal Spectral Element Solutions to Incompressible Flows over Particles of Complex Shape

    Directory of Open Access Journals (Sweden)

    Don Liu

    2014-01-01

    Full Text Available This paper develops the virtual identity particles (VIP model to simulate two-phase flows involving complex-shaped particles. VIP assimilates the high efficiency of the Eulerian method and the convenience of the Lagrangian approach in tracking particles. It uses one fixed Eulerian mesh to compute the fluid field and the Lagrangian description to handle constitutive properties of particles. The interaction between the fluid and complex particles is characterized with source terms in the fluid momentum equations, while the same source terms are computed iteratively from the particulate Lagrangian equations. The advantage of VIP is its economy in modeling a two-phase flow problem almost at the cost of solving only the fluid phase with added source terms. This high efficiency in computational cost makes VIP viable for simulating particulate flows with numerous particles. Owing to the spectral convergence and high resolvability of the modal spectral element method, VIP provides acceptable resolution comparable to DNS but at much reduced computational cost. Simulation results indicate that VIP is promising for investigating flows with complex-shaped particles, especially abundant complex particles.

  20. Flow shear induced fluctuation suppression in finite aspect ratio shaped tokamak plasma

    Energy Technology Data Exchange (ETDEWEB)

    Hahm, T.S. [Princeton Univ., NJ (United States). Plasma Physics Lab.; Burrell, K.H. [General Atomics, San Diego, CA (United States)

    1995-01-01

    The suppression of turbulence by the E {times} B flow shear and parallel flow shear is studied in an arbitrary shape finite aspect ratio tokamak plasma using the two point nonlinear analysis previously utilized in a high aspect rat& tokamak plasma. The result shows that only the E {times} B flow shear is responsible for the suppression of flute-like fluctuations. This suppression occurs regardless of the plasma rotation direction and is therefore, relevant for the VH mode plasma core as well as for the H mode plasma edge. Experimentally observed in-out asymmetry of fluctuation reduction behavior can be addressed in the context of flux expansion and magnetic field pitch variation on a given flux surface. The adverse effect of neutral particles on confinement improvement is also discussed in the context of the charge exchange induced parallel momentum damping.

  1. Flow, heat transfer, and free surface shape during the optical fiber drawing process

    Science.gov (United States)

    Xiao, Zhihui

    1997-12-01

    A two-dimensional finite element model is introduced for analyzing glass and gas flows, heat transfer, and fiber formation during the optical fiber drawing process. This study consists of simulations in three different areas: the upper region, the tip region, and the whole furnace region. Conjugating the glass and gas flows and heat transfer, the shapes of an optical fiber as free surfaces in the upper neck-down and the tip regions are separately obtained by solving the coupled continuity, momentum, and energy equations. In the upper region simulation, a surface-to-surface radiation model is used for the enclosure which consists of the wall and the glass surface, and the Rosseland approximation radiation model is employed to account for the radiation effect in the glass region. In the tip region simulation, only the glass fiber region is considered and a convective heat transfer model on the fiber surface is employed to account for the energy exchange between the fiber surface and the purge gas. In the fiber, radiation in the axial direction is included. The whole furnace simulation uses a calculated fiber neck-down shape and an assumed fiber tip shape as a fixed interface and computes the convective heat transfer coefficient profile in the tip region which was used in the tip region simulation. The glass viscosity is temperature-dependent and significantly affects the fiber shape. The finite element code FIDAP is used in the study. The effects of various operating conditions such as draw speed, wall temperature distribution, and gas flow rate are studied.

  2. Design and application of a fish-shaped lateral line probe for flow measurement

    Science.gov (United States)

    Tuhtan, J. A.; Fuentes-Pérez, J. F.; Strokina, N.; Toming, G.; Musall, M.; Noack, M.; Kämäräinen, J. K.; Kruusmaa, M.

    2016-04-01

    We introduce the lateral line probe (LLP) as a measurement device for natural flows. Hydraulic surveys in rivers and hydraulic structures are currently based on time-averaged velocity measurements using propellers or acoustic Doppler devices. The long-term goal is thus to develop a sensor system, which includes spatial gradients of the flow field along a fish-shaped sensor body. Interpreting the biological relevance of a collection of point velocity measurements is complicated by the fact that fish and other aquatic vertebrates experience the flow field through highly dynamic fluid-body interactions. To collect body-centric flow data, a bioinspired fish-shaped probe is equipped with a lateral line pressure sensing array, which can be applied both in the laboratory and in the field. Our objective is to introduce a new type of measurement device for body-centric data and compare its output to estimates of conventional point-based technologies. We first provide the calibration workflow for laboratory investigations. We then provide a review of two velocity estimation workflows, independent of calibration. Such workflows are required as existing field investigations consist of measurements in environments where calibration is not feasible. The mean difference for uncalibrated LLP velocity estimates from 0 to 50 cm/s under in a closed flow tunnel and open channel flume was within 4 cm/s when compared to conventional measurement techniques. Finally, spatial flow maps in a scale vertical slot fishway are compared for the LLP, direct measurements, and 3D numerical models where it was found that the LLP provided a slight overestimation of the current velocity in the jet and underestimated the velocity in the recirculation zone.

  3. The Shape, Propagation and Mean-Flow Interaction of Large-Scale Weather Systems.

    Science.gov (United States)

    Hoskins, Brian J.; James, Ian N.; White, Glenn H.

    1983-07-01

    For a zonal average operator the Eliassen-Palm flux provides a diagnostic of both eddy behavior and the feedback of the eddies onto the mean flow. This paper addresses the diagnosis problem for other averaging operators and, in particular, for time averaging which has proved in recent years such a powerful means of viewing the three-dimensional tropospheric flow. The horizontal velocity correlation tensor gives a measure of the characteristic horizontal eddy shape at a point. It also implies the direction of the group velocity relative to the mean flow in cases where such a concept is valid. However the major emphasis here is on the mean-flow feedback of eddies. In this respect, the eddy vorticity flux is determined by derivatives of the components of the anisotropic part of the tensor. Making a reasonable approximation allows the eddy vorticity flux convergence to be written in terms of E = (v2 u2¯, uv¯). A simple interpretation of the mean flow feedback of eddies is then possible. A slightly more restrictive approximation allows the eddy shape and the sense of the relative group velocity to be determined also from E. The whole analysis may also be performed in the three-dimensional quasi-geostrophic case where it provides an approximate extension of the Eliassen-Palm flux concept.The theory and approximations are investigated for high-pass and low-pass transient eddies using data for single Northern and Southern Hemisphere winter seasons. The different signatures of the transient eddies in the two frequency bands are apparent and schematic pictures of the contrasting, dominant behavior in each band emerge. Data from one particular blocking event, when diagnosed using the theory developed here, give an indication of a positive feedback of the synoptic eddies onto the mean blocking flow.

  4. Compact disk (CD)-shaped device for single cell isolation and PCR of a specific gene in the isolated cell.

    Science.gov (United States)

    Furutani, Shunsuke; Nagai, Hidenori; Takamura, Yuzuru; Kubo, Izumi

    2010-12-01

    For immediate discrimination among isolated cells we propose a novel device and technique for isolation of cells and sequential detection of specific gene(s) within them by polymerase chain reaction (PCR). In this study, we isolated Salmonella enterica cells and detected the Salmonella-specific invA gene from isolated cells by PCR on a compact disk (CD)-shaped device. This device enabled liquid flow by centrifugal force without a micro pump, and was fabricated from silicon wafer and glass to avoid evaporation of a small amount of reagent. One device has 24 microchannels, and 313 microchambers integrated on each microchannel. One microliter of PCR mixture containing cells was separated into microchambers on the device at 5000 rpm for 30 s. Each microchamber contained approximately 1.5 nL PCR mixture. A Poisson distribution of S. enterica cells was observed for different densities of cell suspension. At 200 cells μL(-1) of S. enterica or less, isolated single cells could be determined on the device by amplification of DNA of the invA gene; at 400 cells μL(-1), chambers containing no, one, two, or three cells could be determined on the device. Selective detection of S. enterica was achieved by PCR from a mixture of S. enterica and Escherichia coli on the CD-shaped device.

  5. Shape effect of Cu-nanoparticles in unsteady flow through curved artery with catheterized stenosis

    Science.gov (United States)

    Ahmed, Ashfaq; Nadeem, Sohail

    In this study the arterial flow of Cu-nanofluid through catheterized arteries having a balloon angioplasty with time-varying overlapping stenosis is considered. The nanofluid comprises different shaped nanoparticles such as bricks, cylinders and platelets. In the arteries the nature of Cu-blood nanofluid is examined mathematically by considering it as a different shaped nanoparticles inclusion in viscous fluid in toroidal coordinate system. The problem is solved using a perturbation approximation in terms of a variant of curvature parameter (ɛ) to achieve the axial velocity, the stream function, the resistance impedance, and the wall shear stress distribution of nanofluid. Also, the results were obtained from explicit values of the physical parameters, such as the curvature parameter (ɛ), the balloon height (σ∗), the volume fraction (ϕ) and the shape factor of Cu-nanoparticles (m). The obtained results show that there is a notable difference between curvature and non-curvature annulus flows through catheterized stenosed arteries. The Platlets Cu-nanoparticle in the central portion of the tube are not sheared, and the slight velocity gradients are only found in the layers near the wall of artery than Bricks Cylinders Cu-nanoparticles.

  6. Speciation and gene flow between snails of opposite chirality.

    Directory of Open Access Journals (Sweden)

    Angus Davison

    2005-09-01

    Full Text Available Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent "single-gene speciation" or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be

  7. A D-Shaped Bileaflet Bioprosthesis which Replicates Physiological Left Ventricular Flow Patterns.

    Directory of Open Access Journals (Sweden)

    Sean Guo-Dong Tan

    Full Text Available Prior studies have shown that in a healthy heart, there exist a large asymmetric vortex structure that aids in establishing a steady flow field in the left ventricle. However, the implantation of existing artificial heart valves at the mitral position is found to have a negative effect on this physiological flow pattern. In light of this, a novel D-shaped bileaflet porcine bioprosthesis (GD valve has been designed based on the native geometry mitral valve, with the hypothesis that biomimicry in valve design can restore physiological left ventricle flow patterns after valve implantation. An in-vitro experiment using two dimensional particle velocimetry imaging was carried out to determine the hemodynamic performance of the new bileaflet design and then compared to that of the well-established St. Jude Epic valve which functioned as a control in the experiment. Although both valves were found to have similar Reynolds shear stress and Turbulent Kinetic Energy levels, the novel D-shape valve was found to have lower turbulence intensity and greater mean kinetic energy conservation.

  8. Effect of attack and cone angels on air flow characteristics for staggered wing shaped tubes bundle

    Science.gov (United States)

    Sayed Ahmed, Sayed E.; Ibrahiem, Emad Z.; Mesalhy, Osama M.; Abdelatief, Mohamed A.

    2014-12-01

    An experimental and numerical study has been conducted to clarify fluid flow characteristics and pressure drop distributions of a cross-flow heat exchanger employing staggered wing-shaped tubes at different angels of attack. The water-side Rew and the air-side Rea were at 5 × 102 and at from 1.8 × 103 to 9.7 × 103, respectively. Three cases of the tubes arrangements with various angles of attack, row angles of attack and 90° cone angles were employed at the considered Rea range. Correlation of pressure drop coefficient Pdc in terms of Rea, design parameters for the studied cases were presented. The flow pattern around the staggered wing-shaped tubes bundle were predicted using the commercial CFD FLUENT 6.3.26 software package. Results indicated that the values of Pdc increased with the angle of attack from 0° to 45°, while the opposite was true for angles of attack from 135° to 180°. The values of Pdc for the arrangements of (θ1,2,3 = 45°), (θ1 = 45°, θ2 = 0°, θ3 = 45°), and (θ1,2,3 = 0°) were lower than those for the arrangement of (ϕ1 = ϕ2 = ϕ3 = 90°) by about 33, 53, and 91 %, respectively. Comparisons between the experimental and numerical results of the present study and those obtained by similar previous studies showed good agreements.

  9. Effect of Marangoni Flows on the Shape of Thin Sessile Droplets Evaporating into Air

    Science.gov (United States)

    Tsoumpas, Yannis; Dehaeck, Sam; Rednikov, Alexey; Colinet, Pierre

    2015-11-01

    With the help of Mach-Zehnder interferometry, we study the (largely) axisymmetric shapes of freely receding evaporating sessile droplets of various HFE liquids. The droplets evaporate into ambient air and, although the liquids are perfectly wetting, possess small finite contact angles reckoned to be evaporation-induced. The experimentally determined droplet profiles are shown here to deviate, under some conditions, from the classical macroscopic static profile of a sessile droplet, as this is determined by gravity and capillarity. These deviations are attributed to a Marangoni flow, due to evaporation-induced thermal gradients along the liquid-air interface, and are mostly observed in conditions of high evaporation. Unlike the classical static shapes, the distorted experimental profiles exhibit an inflection point at the contact line area. When a poorly volatile liquid is considered, however, the temperature differences and the Marangoni stresses are weak, and the measurements are found to be in a good agreement with the classical static shape. Overall, the experimental findings are quantitatively confirmed by the predictions of a lubrication model accounting for the impact of the Marangoni effect on the droplet shape. Financial support of FP7 Marie Curie MULTIFLOW Network (PITNGA-2008-214919), ESA/BELSPO-PRODEX, BELSPO- μMAST (IAP 7/38) & FRS-FNRS is gratefully acknowledged.

  10. Imprints of fluctuating proton shapes on flow in proton-lead collisions at the LHC

    Science.gov (United States)

    Mäntysaari, Heikki; Schenke, Björn; Shen, Chun; Tribedy, Prithwish

    2017-09-01

    Results for particle production in √{ s} = 5.02TeV p + Pb collisions at the Large Hadron Collider within a combined classical Yang-Mills and relativistic viscous hydrodynamic calculation are presented. We emphasize the importance of sub-nucleon scale fluctuations in the proton projectile to describe the experimentally observed azimuthal harmonic coefficients vn, demonstrating their sensitivity to the proton shape. We stress that the proton shape and its fluctuations are not free parameters in our calculations. Instead, they have been constrained using experimental data from HERA on exclusive vector meson production. Including temperature dependent shear and bulk viscosities, as well as UrQMD for the low temperature regime, we present results for mean transverse momenta, harmonic flow coefficients for charged hadrons and identified particles, as well as Hanbury-Brown-Twiss radii.

  11. A fast algorithm for simulating multiphase flows through periodic geometries of arbitrary shape

    CERN Document Server

    Marple, Gary; Gillman, Adrianna; Veerapaneni, Shravan

    2015-01-01

    This paper presents a new boundary integral equation (BIE) method for simulating particulate and multiphase flows through periodic channels of arbitrary smooth shape in two dimensions. The authors consider a particular system---multiple vesicles suspended in a periodic channel of arbitrary shape---to describe the numerical method and test its performance. Rather than relying on the periodic Green's function as classical BIE methods do, the method combines the free-space Green's function with a small auxiliary basis, and imposes periodicity as an extra linear condition. As a result, we can exploit existing free-space solver libraries, quadratures, and fast algorithms, and handle a large number of vesicles in a geometrically complex channel. Spectral accuracy in space is achieved using the periodic trapezoid rule and product quadratures, while a first-order semi-implicit scheme evolves particles by treating the vesicle-channel interactions explicitly. New constraint-correction formulas are introduced that prese...

  12. River adjustments under varying flow and sediment sypply regimes. The role of hydrograh shape

    Science.gov (United States)

    Ferrer-Boix, C.; Elgueta, M. A.; Hassan, M. A.

    2016-12-01

    This research aims to explore how sediment supply conditions and hydrograph shape influence bed surface evolution, vertical and downstream sediment sorting, and sediment transport in gravel bed streams. While a significant body of research has been focused on channel evolution under constant flow regimes, few studies have focused on the impacts of flow variations in channel adjustments. Particularly, we are interested in examining the impact of the sediment supply regime and hydrograph magnitude and duration on channel adjustments and sediment transport rates. To this end, we conducted a set of experiments in a 0.8 m-wide, 5 m-long tilting flume. Flow discharge during the runs was increased and decreased at steps of certain duration allowing us to vary the steepness of rising and falling limbs of hydrographs. The influence of hydrograph shape (symmetrical and asymmetrical) on river morphodynamics was tested. Flow rates during the experiments ranged from 30 l/s to 70 l/s. Some of the experiments were conducted under no feed conditions while others were carried out with sediment supply, which ranged from 10 kg/h to 80 kg/h. The feed texture in these latter runs was identical to that of the original mixture (Dmin = 0.5 mm, Dmax = 64 mm, Dg = 5.65 mm and σg = 3.05). Initial bed slope and surface configuration were obtained after varying times of conditioning under constant flow and no feed. Finally, we conducted equilibrium experiments under constant flow and sediment supply that were used as reference. All these sets of experiments benefited from a very detailed and extensive data monitoring which allowed us to provide a unique description or river adjustments under varying flow conditions. Data acquisition included: 1) bed surface images covering the entire flume, 2) bed scans at 2 mm resolution of the whole flume and 3) real-time measurements of bedload transport (rate and texture) at the outlet of the flume. This set up allows us to obtain fractional particle

  13. Polyphyly and gene flow between non-sibling Heliconius species

    Directory of Open Access Journals (Sweden)

    Jiggins Chris D

    2006-04-01

    Full Text Available Abstract Background The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae, whose distributions overlap in Central and Northwestern South America. Results In these taxa, we sequenced 30–45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII, and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi, mannose-6-phosphate isomerase (Mpi and cubitus interruptus (Ci genes. A fifth gene, dopa decarboxylase (Ddc produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. Conclusion Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Müllerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

  14. Mushroom-Shaped Structures as Tracers of Buoyant Flow in the Galactic Disk

    CERN Document Server

    D'Avillez, M A; Avillez, Miguel A. de; Low, Mordecai-Mark Mac

    2001-01-01

    Recent HI emission observations of the Southern Galactic hemisphere have revealed a mushroom-like structure extending from z=-70 to -450 pc, composed of a stem and a cap. Similar structures occur in three-dimensional simulations of a dynamic galactic disk driven by isolated and clustered supernovae. Using these simulations, we show that hot gas in the Galactic disk that is not evacuated through chimneys expands into the cooler gas of the thick disk, forming mushroom-shaped structures. This new class of objects traces buoyant flow of hot gas into the thick disk.

  15. Sperm competition shapes gene expression and sequence evolution in the ocellated wrasse.

    Science.gov (United States)

    Dean, Rebecca; Wright, Alison E; Marsh-Rollo, Susan E; Nugent, Bridget M; Alonzo, Suzanne H; Mank, Judith E

    2017-01-01

    Gene expression differences between males and females often underlie sexually dimorphic phenotypes, and the expression levels of genes that are differentially expressed between the sexes are thought to respond to sexual selection. Most studies on the transcriptomic response to sexual selection treat sexual selection as a single force, but postmating sexual selection in particular is expected to specifically target gonadal tissue. The three male morphs of the ocellated wrasse (Symphodus ocellatus) make it possible to test the role of postmating sexual selection in shaping the gonadal transcriptome. Nesting males hold territories and have the highest reproductive success, yet we detected feminization of their gonadal gene expression compared to satellite males. Satellite males are less brightly coloured and experience more intense sperm competition than nesting males. In line with postmating sexual selection affecting gonadal gene expression, we detected a more masculinized expression profile in satellites. Sneakers are the lowest quality males and showed both de-masculinization and de-feminization of gene expression. We also detected higher rates of gene sequence evolution of male-biased genes compared to unbiased genes, which could at least in part be explained by positive selection. Together, these results reveal the potential for postmating sexual selection to drive higher rates of gene sequence evolution and shape the gonadal transcriptome profile.

  16. Flow field analysis of a pentagonal-shaped bridge deck by unsteady RANS

    Directory of Open Access Journals (Sweden)

    Md. Naimul Haque

    2016-01-01

    Full Text Available Long-span cable-stayed bridges are susceptible to dynamic wind effects due to their inherent flexibility. The fluid flow around the bridge deck should be well understood for the efficient design of an aerodynamically stable long-span bridge system. In this work, the aerodynamic features of a pentagonal-shaped bridge deck are explored numerically. The analytical results are compared with past experimental work to assess the capability of two-dimensional unsteady RANS simulation for predicting the aerodynamic features of this type of deck. The influence of the bottom plate slope on aerodynamic response and flow features was investigated. By varying the Reynolds number (2 × 104 to 20 × 104 the aerodynamic behavior at high wind speeds is clarified.

  17. On the similarity in shape between debris-flow channels and high-gradient flood channels: Initial insight from continuum models for granular and water flow

    Science.gov (United States)

    Kean, J. W.; McCoy, S. W.; Tucker, G. E.

    2011-12-01

    The cross-sectional shape of high-gradient bedrock channels carved by debris flows is often very similar to that of channels formed by fluvial erosion. Both tend to have narrow U-shapes with width-to-depth ratios much less than 10. Gullies and channels cut into colluvium by both water erosion and debris-flow erosion have similarly narrow geometries. Given that the physics governing debris flow and turbulent water flow are very different, why are channels eroded by these two processes so similar in shape? To begin to investigate this question, we conducted a series of numerical simulations using continuum models for the end-member cases of granular flow and water flow. Each model is used to evolve the steady-state channel shape formed by uniform flow of the respective material. The granular model is based on the constitutive equation for dense granular flow proposed by Jop et al. (Nature, 2006). They demonstrated that without any fitting parameters, a numerical model using this constitutive equation could reproduce the velocity and depth profiles observed in granular-flow laboratory experiments. The model for water flow uses a ray-isovel turbulence closure to calculate the boundary shear stress across the wetted perimeter of the channel. This fully predictive model has also been shown to be in good agreement with laboratory data. We start the calculations for the granular and water-flow cases by determining the velocity and boundary shear-stress fields in an initial V-shape cross section. We then erode both channels using a simple wear law scaled linearly by the bed-normal boundary shear stress. The calculation is repeated until the channel reaches an equilibrium shape. Initial comparisons of the granular and water-flow channels show that they have very similar width-to-depth ratios of about four, and only moderate differences in bottom geometries and boundary shear-stress distributions. The structure of the velocity field differs more substantially between the two

  18. Sensory flow shaped by active sensing: sensorimotor strategies in electric fish.

    Science.gov (United States)

    Hofmann, Volker; Sanguinetti-Scheck, Juan I; Künzel, Silke; Geurten, Bart; Gómez-Sena, Leonel; Engelmann, Jacob

    2013-07-01

    Goal-directed behavior in most cases is composed of a sequential order of elementary motor patterns shaped by sensorimotor contingencies. The sensory information acquired thus is structured in both space and time. Here we review the role of motion during the generation of sensory flow focusing on how animals actively shape information by behavioral strategies. We use the well-studied examples of vision in insects and echolocation in bats to describe commonalities of sensory-related behavioral strategies across sensory systems, and evaluate what is currently known about comparable active sensing strategies in electroreception of electric fish. In this sensory system the sensors are dispersed across the animal's body and the carrier source emitting energy used for sensing, the electric organ, is moved while the animal moves. Thus ego-motions strongly influence sensory dynamics. We present, for the first time, data of electric flow during natural probing behavior in Gnathonemus petersii (Mormyridae), which provide evidence for this influence. These data reveal a complex interdependency between the physical input to the receptors and the animal's movements, posture and objects in its environment. Although research on spatiotemporal dynamics in electrolocation is still in its infancy, the emerging field of dynamical sensory systems analysis in electric fish is a promising approach to the study of the link between movement and acquisition of sensory information.

  19. Urban land use limits regional bumble bee gene flow.

    Science.gov (United States)

    Jha, Shalene; Kremen, C

    2013-05-01

    Potential declines in native pollinator communities and increased reliance on pollinator-dependent crops have raised concerns about native pollinator conservation and dispersal across human-altered landscapes. Bumble bees are one of the most effective native pollinators and are often the first to be extirpated in human-altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic differentiation and fine-scale relatedness patterns of the yellow-faced bumble bee, Bombus vosnesenskii, to investigate how current and historic habitat composition impact gene flow. We conducted our study across a landscape mosaic of natural, agricultural and urban/suburban habitats, and we show that B. vosnesenskii exhibits low but significant levels of differentiation across the study system (F(ST) = 0.019, D(est) = 0.049). Most importantly, we reveal significant relationships between pairwise F(ST) and resistance models created from contemporary land use maps. Specifically, B. vosnesenskii gene flow is most limited by commercial, industrial and transportation-related impervious cover. Finally, our fine-scale analysis reveals significant but declining relatedness between individuals at the 1-9 km spatial scale, most likely due to local queen dispersal. Overall, our results indicate that B. vosnesenskii exhibits considerable local dispersal and that regional gene flow is significantly limited by impervious cover associated with urbanization.

  20. LONG DISTANCE POLLEN-MEDIATED GENE FLOW FROM CREEPING BENTGRASS

    Science.gov (United States)

    Researchers from USEPA WED have measured gene flow from experimental fields of Roundup? herbicide resistant genetically modified (GM) creeping bentgrass a grass used primarily on golf courses, to compatible non-crop relatives. Using a sampling design based on the estimated time ...

  1. Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

    KAUST Repository

    Bonnet-Lebrun, Anne-Sophie

    2017-03-17

    Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions. This article is protected by copyright. All rights reserved.

  2. Beekeeping practices and geographic distance, not land use, drive gene flow across tropical bees.

    Science.gov (United States)

    Jaffé, Rodolfo; Pope, Nathaniel; Acosta, André L; Alves, Denise A; Arias, Maria C; De la Rúa, Pilar; Francisco, Flávio O; Giannini, Tereza C; González-Chaves, Adrian; Imperatriz-Fonseca, Vera L; Tavares, Mara G; Jha, Shalene; Carvalheiro, Luísa G

    2016-11-01

    Across the globe, wild bees are threatened by ongoing natural habitat loss, risking the maintenance of plant biodiversity and agricultural production. Despite the ecological and economic importance of wild bees and the fact that several species are now managed for pollination services worldwide, little is known about how land use and beekeeping practices jointly influence gene flow. Using stingless bees as a model system, containing wild and managed species that are presumed to be particularly susceptible to habitat degradation, here we examine the main drivers of tropical bee gene flow. We employ a novel landscape genetic approach to analyse data from 135 populations of 17 stingless bee species distributed across diverse tropical biomes within the Americas. Our work has important methodological implications, as we illustrate how a maximum-likelihood approach can be applied in a meta-analysis framework to account for multiple factors, and weight estimates by sample size. In contrast to previously held beliefs, gene flow was not related to body size or deforestation, and isolation by geographic distance (IBD) was significantly affected by management, with managed species exhibiting a weaker IBD than wild ones. Our study thus reveals the critical importance of beekeeping practices in shaping the patterns of genetic differentiation across bee species. Additionally, our results show that many stingless bee species maintain high gene flow across heterogeneous landscapes. We suggest that future efforts to preserve wild tropical bees should focus on regulating beekeeping practices to maintain natural gene flow and enhancing pollinator-friendly habitats, prioritizing species showing a limited dispersal ability.

  3. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

    Directory of Open Access Journals (Sweden)

    Laurence D Hurst

    2015-12-01

    Full Text Available X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE and data from the Functional Annotation of the Mammalian Genome (FANTOM5 project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds, as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased

  4. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    Science.gov (United States)

    Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R. R.; Huminiecki, Lukasz

    2015-01-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression

  5. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

    Science.gov (United States)

    Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Huminiecki, Lukasz

    2015-12-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression

  6. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    KAUST Repository

    Hurst, Laurence D.

    2015-12-18

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression

  7. Analysis of natural convection flow characteristics in a square cavity with internal elliptic shape block

    Science.gov (United States)

    Mostafa, Golam; Munshi, M. Jahirul Haque; Hossain, Sumon; Ali, M.

    2017-06-01

    Analysis of hydro-magnetic natural convection flow in a square cavity with internal elliptic shape cold block at the centre with Prandtl number of 0.711 has been investigated numerically. The governing equations, mass, momentum, energy and induction equations are applied to the cavity. The governing differential equations are solved by using finite element method (Galerkin weighted residual method). The top wall, left wall, right wall and elliptic obstacle are kept at cold Tc. The bottom wall is kept at heated Th. The study is performed for different Rayleigh numbers(103 ≤ Ra ≥ 106) and Hartmann numbers(0 ≤ Ha ≥ 100). A cold elliptic block is located at the centre of the cavity. The object of this study is to describe the effects of MHD on the field of buoyancy-driven and flow in presence of such cold block by visualization of graph. The obtained results showed that temperature distribution and flow pattern inside the cavity depend on both strength of the magnetic field and Rayleigh number. For all cases, two or more counter rotating eddies were formed inside the cavity. The results are illustrated with the streamlines, isotherms, velocity and temperature fields. Numerical results show good accuracy and stability of the proposal strategy.

  8. Effect of Pin Tool Shape on Metal Flow During Friction Stir Welding

    Science.gov (United States)

    McClure, J. C.; Coronado, E.; Aloor, S.; Nowak, B.; Murr, L. M.; Nunes, Arthur C., Jr.; Munafo, Paul M. (Technical Monitor)

    2002-01-01

    It has been shown that metal moves behind the rotating Friction Stir Pin Tool in two separate currents or streams. One current, mostly on the advancing side, enters a zone of material that rotates with the pin tool for one or more revolutions and eventually is abandoned behind the pin tool in crescent-shaped pieces. The other current, largely on the retreating side of the pin tool is moved by a wiping process to the back of the pin tool and fills in between the pieces of the rotational zone that have been shed by the rotational zone. This process was studied by using a faying surface copper trace to clarify the metal flow. Welds were made with pin tools having various thread pitches. Decreasing the thread pitch causes the large scale top-to-bottorn flow to break up into multiple vortices along the pin and an unthreaded pin tool provides insufficient vertical motion for there to be a stable rotational zone and flow of material via the rotational zone is not possible leading to porosity on the advancing side of the weld.

  9. The connectivity of Mytilus galloprovincialis in northern Morocco: A gene flow crossroads between continents

    Science.gov (United States)

    Ouagajjou, Yassine; Presa, Pablo

    2015-01-01

    Previous population genetic studies on the Mediterranean mussel Mytilus galloprovincialis have shown the existence of two well differentiated sets of populations around Southern European coasts, one Atlantic and another Mediterranean. Those two population pools are kept apart by the Almería - Oran Oceanographic Front (AOOF), an oceanographic discontinuity acting either as a cause of such differentiation or simply as a means of maintaining two historically differentiated gene pools. The role of the Gibraltar Strait at shaping mussel larval flow entering the Alboran Sea has been much less addressed, especially regarding mussel swarms inhabiting the northern coast of Morocco. The present study applies seven microsatellite markers to describing the genetic status of northern Moroccan populations of M. galloprovincialis and their relationship with the two well-characterized mussel gene pools from southern Europe. We show that the Atlantic Iberia gene pool extending continuously from the Cantabrian Sea (NE Iberia) to the Alboran Sea (SE Iberia) up to the AOOF is well differentiated from the Atlantic Moroccan mussel. Either an oceanographic barrier or a limited larval dispersal or both, are required to explain this unexpected intercontinental differentiation regarding previous studies on this species. Populations from Atlantic Morocco conformed to a single gene pool (FST ± SD = 0.012 ± 0.007) as opposed to the reported latitudinal barrier to gene flow at Cape Ghir in western Morocco. Additionally, a significant restriction to gene flow was observed between Atlantic Morocco and Alboran Morocco (FST ± SD = 0.038 ± 0.010) in contrast to the reported mussel genetic continuity along the Iberian coast up to AOOF. Three major mussel gene pools appear to meet at this crossroads between continents and between seas, namely, a Mediterranean European subpopulation, an Atlantic Iberia subpopulation including the Alboran Sea, and an Atlantic Morocco subpopulation. Knowledge on

  10. A Numerical Methodology for Aerodynamic Shape Optimization in Turbulent Flow Enabling Large Geometric Variation

    Science.gov (United States)

    Osusky, Lana Maria

    The increase in the availability and power of computational resources over the last fifteen years has contributed to the development of many different types of numerical optimization methods and created a large area of research focussed on numerical aerodynamic shape optimization and, more recently, high-fidelity multidisciplinary optimization. Numerical optimization provides dramatic savings when designing new aerodynamic configurations, as it allows the designer to focus more on the development of a well-posed design problem rather than on performing an exhaustive search of the design space via the traditional cut-and-try approach, which is expensive and time-consuming. It also reduces the dependence on the designer's experience and intuition, which can potentially lead to more optimal designs. Numerical optimization methods are particularly attractive when designing novel, unconventional aircraft for which the designer has no pre-existing studies or experiences from which to draw; these methods have the potential to discover new designs that might never have been arrived at without optimization. This work presents an extension of an efficient gradient-based numerical aerodynamic shape optimization algorithm to enable optimization in turbulent flow. The algorithm includes an integrated geometry parameterization and mesh movement scheme, an efficient parallel Newton-Krylov-Schur algorithm for solving the Reynolds-Averaged Navier-Stokes (RANS) equations, which are fully coupled with the one-equation Spalart-Allmaras turbulence model, and a discrete-adjoint gradient evaluation. In order to develop an efficient methodology for optimization in turbulent flows, the viscous and turbulent terms in the ii governing equations were linearized by hand. Additionally, a set of mesh refinement tools was introduced in order to obtain both an acceptable control volume mesh and a sufficiently refined computational mesh from an initial coarse mesh. A series of drag minimization

  11. Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae

    Directory of Open Access Journals (Sweden)

    Jørgensen Marte H

    2011-11-01

    Full Text Available Abstract Background Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. Results Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid A. arenosa to tetraploid A. lyrata and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in A. arenosa and bidirectional in A. lyrata. Conclusions Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus Arabidopsis, we find very different evolutionary fates when it comes to introgression.

  12. CFD study of flow-diffusion process in Y-shape micromixer

    Institute of Scientific and Technical Information of China (English)

    陈卓; 张睿琦; 王晓娜

    2016-01-01

    A CFD simulation was carried out to investigate the mixing process in a Y-shape micromixer with the software Fluent 6.3. The definition of the “diffusion angle” is proposed to describe the molecular diffusion process associated with the flow at low Reynolds number. The linear relationship between the diffusion angle and the Peclet number (Pe) is determined by both theoretical analysis and numerical simulation. Moreover, the simulation results reveal that the diffusion angle is only related to the Peclet number whilst it is irrelevant to the changes ofRe (Reynolds number) andSc (Schmidt number). The range of Peclet number and Reynolds number for experimental measurement are also suggested asPe≤10000 andRe≤10.

  13. Characteristics of Traffic Flow at Nonsignalized T-Shaped Intersection with U-Turn Movements

    Directory of Open Access Journals (Sweden)

    Hong-Qiang Fan

    2013-01-01

    Full Text Available Most nonsignalized T-shaped intersections permit U-turn movements, which make the traffic conditions of intersection complex. In this paper, a new cellular automaton (CA model is proposed to characterize the traffic flow at the intersection of this type. In present CA model, new rules are designed to avoid the conflicts among different directional vehicles and eliminate the gridlock. Two kinds of performance measures (i.e., flux and average control delay for intersection are compared. The impacts of U-turn movements are analyzed under different initial conditions. Simulation results demonstrate that (i the average control delay is more practical than flux in measuring the performance of intersection, (ii U-turn movements increase the range and degree of high congestion, and (iii U-turn movements on the different direction of main road have asymmetrical influences on the traffic conditions of intersection.

  14. Characteristics of traffic flow at nonsignalized T-shaped intersection with U-turn movements.

    Science.gov (United States)

    Fan, Hong-Qiang; Jia, Bin; Li, Xin-Gang; Tian, Jun-Fang; Yan, Xue-Dong

    2013-01-01

    Most nonsignalized T-shaped intersections permit U-turn movements, which make the traffic conditions of intersection complex. In this paper, a new cellular automaton (CA) model is proposed to characterize the traffic flow at the intersection of this type. In present CA model, new rules are designed to avoid the conflicts among different directional vehicles and eliminate the gridlock. Two kinds of performance measures (i.e., flux and average control delay) for intersection are compared. The impacts of U-turn movements are analyzed under different initial conditions. Simulation results demonstrate that (i) the average control delay is more practical than flux in measuring the performance of intersection, (ii) U-turn movements increase the range and degree of high congestion, and (iii) U-turn movements on the different direction of main road have asymmetrical influences on the traffic conditions of intersection.

  15. Magnetic Resonance Flow Velocity and Temperature Mapping of a Shape Memory Polymer Foam Device

    Energy Technology Data Exchange (ETDEWEB)

    Small IV, W; Gjersing, E; Herberg, J L; Wilson, T S; Maitland, D J

    2008-10-29

    Interventional medical devices based on thermally responsive shape memory polymer (SMP) are under development to treat stroke victims. The goals of these catheter-delivered devices include re-establishing blood flow in occluded arteries and preventing aneurysm rupture. Because these devices alter the hemodynamics and dissipate thermal energy during the therapeutic procedure, a first step in the device development process is to investigate fluid velocity and temperature changes following device deployment. A laser-heated SMP foam device was deployed in a simplified in vitro vascular model. Magnetic resonance imaging (MRI) techniques were used to assess the fluid dynamics and thermal changes associated with device deployment. Spatial maps of the steady-state fluid velocity and temperature change inside and outside the laser-heated SMP foam device were acquired. Though non-physiological conditions were used in this initial study, the utility of MRI in the development of a thermally-activated SMP foam device has been demonstrated.

  16. Inverse design of a proper number, shapes, sizes, and locations of coolant flow passages

    Science.gov (United States)

    Dulikravich, George S.

    1992-01-01

    During the past several years we have developed an inverse method that allows a thermal cooling system designer to determine proper sizes, shapes, and locations of coolant passages (holes) in, say, an internally cooled turbine blade, a scram jet strut, a rocket chamber wall, etc. Using this method the designer can enforce a desired heat flux distribution on the hot outer surface of the object, while simultaneously enforcing desired temperature distributions on the same hot outer surface as well as on the cooled interior surfaces of each of the coolant passages. This constitutes an over-specified problem which is solved by allowing the number, sizes, locations and shapes of the holes to adjust iteratively until the final internally cooled configuration satisfies the over-specified surface thermal conditions and the governing equation for the steady temperature field. The problem is solved by minimizing an error function expressing the difference between the specified and the computed hot surface heat fluxes. The temperature field analysis was performed using our highly accurate boundary integral element code with linearly varying temperature along straight surface panels. Examples of the inverse design applied to internally cooled turbine blades and scram jet struts (coated and non-coated) having circular and non-circular coolant flow passages will be shown.

  17. Laboratory observations of saline and turbidity currents flowing in U-shaped flume

    Science.gov (United States)

    Stagnaro, M.; Bolla Pittaluga, M.

    2013-12-01

    Saline and turbidity currents belong to the large family of gravity currents. Due to the difficulties to predict and observe these kinds of phenomena, especially turbidity currents, we developed an experimental apparatus able to reproduce these currents in our Marchi Environmental Laboratory (Genova, Italy). The experiments were performed in a large U-shaped flume, 30 m long, characterized by a constant curvature bend (radius of 2.5 m) joining two straight reaches approximately 12 m long. The flume has a rectangular cross section 0.6 m wide and 0.5 m deep. Inside the flume we made a uniform concrete bottom slope (0.005), which proceeds from the inlet section along the first straight track and finishes 3 m after the bend exit. For each experiment we have been able to measure density distribution and velocity profiles along the vertical in different cross section. Density measurements were obtained using two ranks of siphons that sample the currents at different heights. Velocity was acquired with the DOP2000 ultrasound velocimeter; we measured longitudinal component in the straight reach of the flume, and both longitudinal and transversal velocity in the curved reach. We performed 30 experiments by changing the inlet conditions: primary defining the nature of the currents, saline or sediment laden, then varying two of the main parameters governing the currents: the density of the mixture and the flow discharge. The former covered a range between 1003 and 1023 kg/m^3 and the flow discharge ranged between 0.5 to 4.0 l/s. Both of these parameters influence the densimetric Froude Number, and allowed us to reproduce both subcritical and supercritical flow. In each experiment water entrainment from above was negligible hence the current was able to attain a quasi-uniform configuration in the first straight reach, whereby the longitudinal velocity and the thickness of the current were approximately constant. By varying the inlet conditions, it was possible to observe the

  18. Interspecific gene flow and maintenance of species integrity in oaks

    Directory of Open Access Journals (Sweden)

    Oliver Gailing

    2014-07-01

    Full Text Available Oak species show a wide variation in morphological and physiological characters, and species boundaries between closely related species are often not clear-cut. Still, despite frequent interspecific gene flow, oaks maintain distinct morphological and physiological adaptations. In sympatric stands, spatial distribution of species with different ecological requirements is not random but constrained by soil and other microenvironmental factors. Pre-zygotic isolation (e.g. cross incompatibilities, asynchrony in flowering, pollen competition and post-zygotic isolation (divergent selection contribute to the maintenance of species integrity in sympatric oak stands. The antagonistic effects of interspecific gene flow and divergent selection are reflected in the low genetic differentiation between hybridizing oak species at most genomic regions interspersed by regions with signatures of divergent selection (outlier regions. In the near future, the availability of high-density genetic linkage maps anchored to scaffolds of a sequenced Q. robur genome will allow to characterize the underlying genes in these outlier regions and their putative role in reproductive isolation between species. Reciprocal transplant experiments of seedlings between parental environments can be used to characterize selection on outlier genes. High transferability of gene-based markers will enable comparative outlier screens in different oak species.

  19. Interspecific gene flow and maintenance of species integrity in oaks

    Directory of Open Access Journals (Sweden)

    Oliver Gailing

    2014-07-01

    Full Text Available Oak species show a wide variation in morphological and physiological characters, and species boundaries between closely related species are often not clear-cut. Still, despite frequent interspecific gene flow, oaks maintain distinct morphological and physiological adaptations. In sympatric stands, spatial distribution of species with different ecological requirements is not random but constrained by soil and other microenvironmental factors. Pre-zygotic isolation (e.g. cross incompatibilities, asynchrony in flowering, pollen competition and post-zygotic isolation (divergent selection contribute to the maintenance of species integrity in sympatric oak stands. The antagonistic effects of interspecific gene flow and divergent selection are reflected in the low genetic differentiation between hybridizing oak species at most genomic regions interspersed by regions with signatures of divergent selection (outlier regions. In the near future, the availability of high-density genetic linkage maps anchored to scaffolds of a sequenced Q. robur genome will allow to characterize the underlying genes in these outlier regions and their putative role in reproductive isolation between species. Reciprocal transplant experiments of seedlings between parental environments can be used to characterize selection on outlier genes. High transferability of gene-based markers will enable comparative outlier screens in different oak species.

  20. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M.; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-01-01

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds. PMID:27966592

  1. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach.

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-12-14

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.

  2. Quasistatic analysis on configuration of two-phase flow in Y-shaped tubes

    KAUST Repository

    Zhong, Hua

    2014-12-01

    We investigate the two-phase flow in a horizontally placed Y-shaped tube with different Young\\'s angle and width in each branch. By using a quasistatic approach, we can determine the specific contact position and the equilibrium contact angle of fluid in each branch based on the minimization problem of the free energy of the system. The wettability condition and the width of the two branches play important roles in the distribution of fluid in each branch. We also consider the effect of gravity. Some fluid in the upper branch will be pulled down due to the competition of the surface energy and the gravitational energy. The result provides some insights on the theory of two-phase flow in porous media. In particular, it highlights that the inhomogeneous wettability distribution affects the direction of the fluid penetrating a given porous medium domain. It also sheds light on the current debate whether relative permeability may be considered as a full tensor rather than a scalar.

  3. A quasi-continuum hydrodynamic model for slit shaped nanochannel flow

    Science.gov (United States)

    Bhadauria, Ravi; Aluru, N. R.

    2013-08-01

    We propose a quasi-continuum hydrodynamic model for isothermal transport of Lennard-Jones fluid confined in slit shaped nanochannels. In this work, we compute slip and viscous contributions independently and superimpose them to obtain the total velocity profile. Layering of fluid near the interface plays an important role in viscous contribution to the flow, by apparent viscosity change along the confining dimension. This relationship necessitates computing density profiles, which is done using the recently proposed empirical-potential based quasi-continuum theory [A. V. Raghunathan, J. H. Park, and N. R. Aluru, J. Chem. Phys. 127, 174701 (2007)], 10.1063/1.2793070. Existing correlations for density dependent viscosity provided by Woodcock [AIChE J. 52, 438 (2006)], 10.1002/aic.10676 are used to compute viscosity profile in the nanopores. A Dirichlet type slip boundary condition based on a static Langevin friction model describing center-of-mass motion of fluid particles is used, the parameters of which are dependent on the fluctuations of total wall-fluid force from an equilibrium molecular dynamics simulation. Different types of corrugated surfaces are considered to study wall-fluid friction effects on boundary conditions. Proposed hydrodynamic model yields good agreement of velocity profiles obtained from non-equilibrium molecular dynamics simulations for gravity driven flow.

  4. Experimental simulation of a liquid-metal heat-transfer fluid flow in a T-shaped mixer

    Science.gov (United States)

    Kashinskii, O. N.; Lobanov, P. D.; Kurdyumov, A. S.; Pribaturin, N. A.

    2016-05-01

    The structure of the temperature field in a liquid-metal heat-transfer fluid flowing through a T-shaped mixer is studied experimentally. The experiments are carried out using Rose's alloy as a working fluid. To find the temperature distribution over the wall of a working section, IR thermography is applied. It is shown that the wall temperature distribution in the zone where fluid flows with different temperatures mix is heavily nonuniform. The temperature distribution substantially depends on the ratio between the hot and cold fluid flow rates. The results can be used to verify the thermal hydraulic computational codes for fluid metal flows.

  5. The population genomics of begomoviruses: global scale population structure and gene flow

    Directory of Open Access Journals (Sweden)

    Prasanna HC

    2010-09-01

    facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity.

  6. Co-option of the polarity gene network shapes filament morphology in angiosperms.

    Science.gov (United States)

    de Almeida, Ana Maria Rocha; Yockteng, Roxana; Schnable, James; Alvarez-Buylla, Elena R; Freeling, Michael; Specht, Chelsea D

    2014-08-29

    The molecular genetic mechanisms underlying abaxial-adaxial polarity in plants have been studied as a property of lateral and flattened organs, such as leaves. In leaves, laminar expansion occurs as a result of balanced abaxial-adaxial gene expression. Over- or under- expression of either abaxializing or adaxializing genes inhibits laminar growth, resulting in a mutant radialized phenotype. Here, we show that co-option of the abaxial-adaxial polarity gene network plays a role in the evolution of stamen filament morphology in angiosperms. RNA-Seq data from species bearing laminar (flattened) or radial (cylindrical) filaments demonstrates that species with laminar filaments exhibit balanced expression of abaxial-adaxial (ab-ad) genes, while overexpression of a YABBY gene is found in species with radial filaments. This result suggests that unbalanced expression of ab-ad genes results in inhibition of laminar outgrowth, leading to a radially symmetric structure as found in many angiosperm filaments. We anticipate that co-option of the polarity gene network is a fundamental mechanism shaping many aspects of plant morphology during angiosperm evolution.

  7. Identification and characterization of neutrophil extracellular trap shapes in flow cytometry

    Science.gov (United States)

    Ginley, Brandon; Emmons, Tiffany; Sasankan, Prabhu; Urban, Constantin; Segal, Brahm H.; Sarder, Pinaki

    2017-03-01

    Neutrophil extracellular trap (NET) formation is an alternate immunologic weapon used mainly by neutrophils. Chromatin backbones fused with proteins derived from granules are shot like projectiles onto foreign invaders. It is thought that this mechanism is highly anti-microbial, aids in preventing bacterial dissemination, is used to break down structures several sizes larger than neutrophils themselves, and may have several more uses yet unknown. NETs have been implied to be involved in a wide array of systemic host immune defenses, including sepsis, autoimmune diseases, and cancer. Existing methods used to visually quantify NETotic versus non-NETotic shapes are extremely time-consuming and subject to user bias. These limitations are obstacles to developing NETs as prognostic biomarkers and therapeutic targets. We propose an automated pipeline for quantitatively detecting neutrophil and NET shapes captured using a flow cytometry-imaging system. Our method uses contrast limited adaptive histogram equalization to improve signal intensity in dimly illuminated NETs. From the contrast improved image, fixed value thresholding is applied to convert the image to binary. Feature extraction is performed on the resulting binary image, by calculating region properties of the resulting foreground structures. Classification of the resulting features is performed using Support Vector Machine. Our method classifies NETs from neutrophils without traps at 0.97/0.96 sensitivity/specificity on n = 387 images, and is 1500X faster than manual classification, per sample. Our method can be extended to rapidly analyze whole-slide immunofluorescence tissue images for NET classification, and has potential to streamline the quantification of NETs for patients with diseases associated with cancer and autoimmunity.

  8. The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis

    NARCIS (Netherlands)

    Vroemen, C.W.; Mordhorst, A.P.; Albrecht, C.; Kwaaitaal, M.A.C.J.; Vries, de S.C.

    2003-01-01

    From an enhancer trap screen for genes expressed in Arabidopsis embryos, we identified a gene expressed from the octant stage onward in the boundary between the two presumptive cotyledons and in a variety of postembryonic organ and meristem boundaries. This gene, CUP-SHAPED COTYLEDON3 (CUC3),

  9. RNA interference-mediated simultaneous silencing of four genes using cross-shaped RNA.

    Science.gov (United States)

    Lee, Tae Yeon; Chang, Chan Il; Lee, Dooyoung; Hong, Sun Woo; Shin, Chanseok; Li, Chiang J; Kim, Soyoun; Haussecker, Dirk; Lee, Dong-Ki

    2013-04-01

    The structural flexibility of RNA interference (RNAi)-triggering nucleic acids suggests that the design of unconventional RNAi trigger structures with novel features is possible. Here, we report a cross-shaped RNA duplex structure, termed quadruple interfering RNA (qiRNA), with multiple target gene silencing activity. qiRNA triggers the simultaneous down-regulation of four cellular target genes via an RNAi mechanism. In addition, qiRNA shows enhanced intracellular delivery and target gene silencing over conventional siRNA when complexed with jetPEI, a linear polyethyleneimine (PEI). We also show that the long antisense strand of qiRNA is incorporated intact into an RNA-induced silencing complex (RISC). This novel RNA scaffold further expands the repertoire of RNAi-triggering molecular structures and could be used in the development of therapeutics for various diseases including viral infections and cancer.

  10. Measurement of bubble shape and size in bubbly flow structure for stagnant and pulsating liquid flow using an undivided electrochlorination cell and Telecentric Direct Image Method

    DEFF Research Database (Denmark)

    Andersen, Nikolaj; Stroe, Rodica-Elisabeta; Hedensted, Lau

    2016-01-01

    in MATLAB and NI Vision in LabVIEW to determine shape and diameter of the bubbles. Three bubble regions are observed; adherence, bubble diffusion and bulk region. For stagnant liquid flow the mean bubble diameter increases from 30 to 60 μm going from the adherence region to the bulk region, which...

  11. Effect of die shape on the metal flow pattern during direct extrusion process

    Energy Technology Data Exchange (ETDEWEB)

    Solomon, N.; Solomon, I.

    2010-07-01

    The geometric shape of the tools is the main factor by which an optimum technological process can be developed. In the case of extrusion process the strain distribution and other important variables that influence material structure, such as hydrostatic stress, are strongly dependent on the geometry of the die. Careful design of the extrusion die profile can therefore control the product structure and can be used to minimise the amount of inhomogeneity imparted into the product. A possibility to minimise the amount of product inhomogeneity is the using of a flat die with a fillet radius in front to the bearing surface with leads to a minimum dead zone and consequently to a minimum friction at billet-container interface. In the case of aluminium alloy type 2024, for an extrusion ratio of R=8.5, good results were obtained with a fillet radius of 3.0 mm. The experimental data have been used for the finite element numerical simulation of the extrusion process. The data obtained by numerical simulation with FORGE2 programme confirm the theoretical and experimental outcomes. The aim of this paper is to study the influence of such flat die on the material flow during direct extrusion process and consequently on extruded product microstructure and mechanical properties. (Author).

  12. Magnetic resonance flow velocity and temperature mapping of a shape memory polymer foam device

    Directory of Open Access Journals (Sweden)

    Wilson Thomas S

    2009-12-01

    Full Text Available Abstract Background Interventional medical devices based on thermally responsive shape memory polymer (SMP are under development to treat stroke victims. The goals of these catheter-delivered devices include re-establishing blood flow in occluded arteries and preventing aneurysm rupture. Because these devices alter the hemodynamics and dissipate thermal energy during the therapeutic procedure, a first step in the device development process is to investigate fluid velocity and temperature changes following device deployment. Methods A laser-heated SMP foam device was deployed in a simplified in vitro vascular model. Magnetic resonance imaging (MRI techniques were used to assess the fluid dynamics and thermal changes associated with device deployment. Results Spatial maps of the steady-state fluid velocity and temperature change inside and outside the laser-heated SMP foam device were acquired. Conclusions Though non-physiological conditions were used in this initial study, the utility of MRI in the development of a thermally-activated SMP foam device has been demonstrated.

  13. NUMERICAL ANALYSIS OF THE 3-D FLOW FIELD OF PRESSURE ATOMIZERS WITH V-SHAPED CUT AT ORIFICE

    Institute of Scientific and Technical Information of China (English)

    ZHOU Hua

    2011-01-01

    Axisymmetric liquid jets have been studied extensively for more than one century, while non-axisymmetric jets are also very common in engineering applications but attract less concern. Based on Eulerian fluid-fluid model in Fluent software, this article analysizes the 3-D flow fields of pressure atomizers with V-shaped cut at orifice, which will result in a non-axisymmetric liquid jet.Flow rate analysis and jet structure analysis are carried out, the results show that the flow rate can be formulated by adding a correction coefficient to the formula of inviscid axisymmetric jets in atomization regime, when the Weber number is low enough to make the flow fall out of atomization regime, and the jet structure together with the flow rate formula will change. Analysis shows that the evolution of the spray and therefore the structure of the liquid jet are affected much by relative velocity and the local volume fraction of liquid phase.

  14. Contemporary gene flow and mating system of Arabis alpina in a Central European alpine landscape

    OpenAIRE

    Buehler, D.; Graf, R; Holderegger, R; Gugerli, F.

    2017-01-01

    Background and Aims Gene flow is important in counteracting the divergence of populations but also in spreading genes among populations. However, contemporary gene flow is not well understood across alpine landscapes. The aim of this study was to estimate contemporary gene flow through pollen and to examine the realized mating system in the alpine perennial plant, Arabis alpina (Brassicaceae). Methods An entire sub-alpine to alpine landscape of 2 km2 was exhaustively sampled in the Swiss Alps...

  15. Migration and population genetics of the grain aphid Macrosiphum miscanti (Takahashi) in relation to the geographic distance and gene flow

    Institute of Scientific and Technical Information of China (English)

    GUO Wei; SHEN Zuorui; LI Zhihong; GAO Lingwang

    2005-01-01

    The population genetics of the grain aphid Macrosiphum miscanti (Takahashi) is analyzed by microsatellite markers.Samples collected from 15 locations in China have been examined at 5 polymorphic microsatellite loci. Overall, genetic diversity displays a relation between the migration and gene flow in the grain aphid: a free and frequent gene flow is found in the eastern populations, and gene isolation occurs in the two western populations, especially Datong population and Guiyang population. The natural barriers may present an insurmountable obstacle preventing gene flow and aphid migration. However, a spatial genetic differentiation between populations is correlated with their geographical separation, indicating the geographic differentiation may play an important role in shaping the genetic structure of M. miscanti populations. In addition, most populations of grain aphids are out of Hardy-Weinberg equilibrium and there is heterozygote deficit. Based on F statistics, the average genetic differentiation among different geographical populations is relatively low. It seems that the long distance migration of the grain aphid may enhance gene flow and decrease genetic differentiation among different populations.

  16. Sexual selection and magic traits in speciation with gene flow

    Institute of Scientific and Technical Information of China (English)

    Maria R.SERVEDIO; Michael KOPP

    2012-01-01

    The extent to which sexual selection is involved in speciation with gene flow remains an open question and the subject of much research.Here,we propose that some insight can be gained from considering the concept of magic traits (i.e.,traits involved in both reproductive isolation and ecological divergence).Both magic traits and other,“non-magic”,traits can contribute to speciation via a number of specific mechanisms.We argue that many of these mechanisms are likely to differ widely in the extent to which they involve sexual selection.Furthermore,in some cases where sexual selection is present,it may be prone to inhibit rather than drive speciation.Finally,there are a priori reasons to believe that certain categories of traits are much more effective than others in driving speciation.The combination of these points suggests a classification of traits that may shed light on the broader role of sexual selection in speciation with gene flow.In particular,we suggest that sexual selection can act as a driver of speciation in some scenarios,but may play a negligible role in potentially common categories of magic traits,and may be likely to inhibit speeiation in common categories of non-magic traits.

  17. Time to get moving: assisted gene flow of forest trees.

    Science.gov (United States)

    Aitken, Sally N; Bemmels, Jordan B

    2016-01-01

    Geographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a 'local is best' seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of clines. The maintenance of local adaptation despite high gene flow suggests selection for local adaptation to climate is strong. Concerns over maladaptation resulting from climate change have motivated many new genecological and population genomics studies; however, few jurisdictions have implemented assisted gene flow (AGF), the translocation of pre-adapted individuals to facilitate adaptation of planted forests to climate change. Here, we provide evidence that temperate tree species show clines along climatic gradients sufficiently similar for average patterns or climate models to guide AGF in the absence of species-specific knowledge. Composite provenancing of multiple seed sources can be used to increase diversity and buffer against future climate uncertainty. New knowledge will continue to refine and improve AGF as climates warm further.

  18. A study of optimum cowl shapes and flow port locations for minimum drag with effective engine cooling, volume 2

    Science.gov (United States)

    Fox, S. R.; Smetana, F. O.

    1980-01-01

    The listings, user's instructions, sample inputs, and sample outputs of two computer programs which are especially useful in obtaining an approximate solution of the viscous flow over an arbitrary nonlifting three dimensional body are provided. The first program performs a potential flow solution by a well known panel method and readjusts this initial solution to account for the effects of the boundary layer displacement thickness, a nonuniform but unidirectional onset flow field, and the presence of air intakes and exhausts. The second program is effectually a geometry package which allows the user to change or refine the shape of a body to satisfy particular needs without a significant amount of human intervention. An effort to reduce the cruise drag of light aircraft through an analytical study of the contributions to the drag arising from the engine cowl shape and the foward fuselage area and also that resulting from the cooling air mass flowing through intake and exhaust sites on the nacelle is presented. The programs may be effectively used to determine the appropriate body modifications or flow port locations to reduce the cruise drag as well as to provide sufficient air flow for cooling the engine.

  19. The Himalayas as a directional barrier to gene flow.

    Science.gov (United States)

    Gayden, Tenzin; Cadenas, Alicia M; Regueiro, Maria; Singh, Nanda B; Zhivotovsky, Lev A; Underhill, Peter A; Cavalli-Sforza, Luigi L; Herrera, Rene J

    2007-05-01

    High-resolution Y-chromosome haplogroup analyses coupled with Y-short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal--including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)--as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman-speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134-derived chromosomes, whose Y-STR-based age (+/-SE) was estimated at 8.1+/-2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives--namely, D1-M15 and D3-P47 in Tibet--involved two different demographic events (5.1+/-1.8 and 11.3+/-3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal

  20. Systematic deletion of homeobox genes in Podospora anserina uncovers their roles in shaping the fruiting body.

    Directory of Open Access Journals (Sweden)

    Evelyne Coppin

    Full Text Available Higher fungi, which comprise ascomycetes and basidiomycetes, play major roles in the biosphere. Their evolutionary success may be due to the extended dikaryotic stage of their life cycle, which is the basis for their scientific name: the Dikarya. Dikaryosis is maintained by similar structures, the clamp in basidiomycetes and the crozier in ascomycetes. Homeodomain transcription factors are required for clamp formation in all basidiomycetes studied. We identified all the homeobox genes in the filamentous ascomycete fungus Podospora anserina and constructed deletion mutants for each of these genes and for a number of gene combinations. Croziers developed normally in these mutants, including those with up to six deleted homeogenes. However, some mutants had defects in maturation of the fruiting body, an effect that could be rescued by providing wild-type maternal hyphae. Analysis of mutants deficient in multiple homeogenes revealed interactions between the genes, suggesting that they operate as a complex network. Similar to their role in animals and plants, homeodomain transcription factors in ascomycetes are involved in shaping multicellular structures.

  1. Systematic deletion of homeobox genes in Podospora anserina uncovers their roles in shaping the fruiting body.

    Science.gov (United States)

    Coppin, Evelyne; Berteaux-Lecellier, Véronique; Bidard, Frédérique; Brun, Sylvain; Ruprich-Robert, Gwenaël; Espagne, Eric; Aït-Benkhali, Jinane; Goarin, Anne; Nesseir, Audrey; Planamente, Sara; Debuchy, Robert; Silar, Philippe

    2012-01-01

    Higher fungi, which comprise ascomycetes and basidiomycetes, play major roles in the biosphere. Their evolutionary success may be due to the extended dikaryotic stage of their life cycle, which is the basis for their scientific name: the Dikarya. Dikaryosis is maintained by similar structures, the clamp in basidiomycetes and the crozier in ascomycetes. Homeodomain transcription factors are required for clamp formation in all basidiomycetes studied. We identified all the homeobox genes in the filamentous ascomycete fungus Podospora anserina and constructed deletion mutants for each of these genes and for a number of gene combinations. Croziers developed normally in these mutants, including those with up to six deleted homeogenes. However, some mutants had defects in maturation of the fruiting body, an effect that could be rescued by providing wild-type maternal hyphae. Analysis of mutants deficient in multiple homeogenes revealed interactions between the genes, suggesting that they operate as a complex network. Similar to their role in animals and plants, homeodomain transcription factors in ascomycetes are involved in shaping multicellular structures.

  2. Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes.

    Science.gov (United States)

    Gautam, Pramod; Chaurasia, Amit; Bhattacharya, Aniket; Grover, Ritika; Mukerji, Mitali; Natarajan, Vivek T

    2015-03-01

    Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.

  3. Inteins as Indicators of Gene Flow in the Halobacteria

    Directory of Open Access Journals (Sweden)

    Shannon Margaret Soucy

    2014-06-01

    Full Text Available This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed one hundred and eighteen genomes representing twenty-six genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified twenty-four proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein’s life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN; smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena, Bacteriodetes (Salinibacter, Betaproteobacteria (Delftia, Acidovorax, Firmicutes (Halanaerobium, Actinobacteria (Longispora, and Deinococcus-Thermus-group.

  4. Parentage versus two-generation analyses for estimating pollen-mediated gene flow in plant populations.

    Science.gov (United States)

    Burczyk, Jaroslaw; Koralewski, Tomasz E

    2005-07-01

    Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the NEIGHBORHOOD model--a representative of parentage analyses, and (ii) the recently developed TWOGENER analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (N(ep)) and the mean pollen dispersal distance (delta). We demonstrate that both methods provide very congruent estimates of N(ep) and delta, when the methods' assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the NEIGHBORHOOD model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of N(ep). The NEIGHBORHOOD model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the TWOGENER method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of TWOGENER it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied.

  5. Extensive gene flow over Europe and possible speciation

    Energy Technology Data Exchange (ETDEWEB)

    VINCENOT, Dr. LUCIE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; NARA, Dr. KAZUHIDE [Department of Natural Environmental Studies, The University of Tokyo, Japan; STHULTZ, CHRISTOPHER [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; Labbe, Jessy L [ORNL; DUBOIS, MARIE-PIERRE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; TEDERSOO, LEHO [University of Tartu, Estonia; Martin, Francis [INRA, Nancy, France; SELOSSE, Dr. MARC-ANDRE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France

    2012-01-01

    Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (104 km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average FST = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (FST = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.

  6. The Measurements of Water Flow Rate in the T-shape Microchannels Based on the Scanning Micro-PIV Technique

    Science.gov (United States)

    Han, W.; Wang, H. L.; Xu, M.

    2011-09-01

    In this study, the scanning microfluidic particle image velocimetry (scanning micro-PIV) technique is used to measure the water flow rate in a T-shape microchannel with the inlet and outlet width being 300 μm and 200 μm, respectively. The standard flow rates controlled by the syringe pump are ranging from 3.508 to 11.693 μL/min. The quasi-three-dimensional velocities at the branch point of the T-shape microchannel are constructed by measuring the two-dimensional velocities on 11 fluid layers from the bottom of microchannel to the top. Based on this, the flow rates are calculated by the discrete integration of velocity distributions on the cross-section of microchannel. The relative errors of the flow rates of the inlet and outlet are all within 3%, and we conclude that the main factors affecting the measurement precision of flow rate include the wall roughness of the microchannel, the spatial resolution of microscopic system and the algorithm of velocity evaluation.

  7. Control of Collection Efficiency for Axial Flow Cyclone Dust Collectors with Fixed Guide Vanes and with Funnel Shaped Exit Pipes

    Institute of Scientific and Technical Information of China (English)

    Akira Ogawa; Masaru Arakawa

    2006-01-01

    The experimental result of the collection efficiency of the axial flow cyclone with the fixed guide vanes is lower than that with the tangential inlet pipe to the cyclone body due to the weak angular momentum transfer given by flowing through the guide vanes. However, one of the interesting points is the control of the collection efficiency depended on the funnel shaped exit pipes. The collection efficiencies for these funnel shaped exit pipes are depended on the Froude number. Then, in this paper, the experimental results of the pressure drop and also the collection efficiency using the fly-ash particles and also the comparison of the calculated results of the collection efficiency with the experimental results are described in detail.

  8. Irregular response of nanofluid flow subject to chemical reaction and shape parameter in the presence of variable stream conditions

    Directory of Open Access Journals (Sweden)

    R. Kandasamy

    2016-09-01

    Full Text Available The problem of boundary layer of nanofluid flow which results from the stretching of a flat surface has been investigated numerically. The model includes the effects of Brownian motion, magnetic effect, non-linear velocity, variable thickness, thermophoresis, chemical reaction, porous medium, shape, thickness and heat source. The Partial differential equations are converted to ordinary deferential equations to solve analytically using shooting technique. The velocity, temperature and concentration profiles are discussed in detail for all parameters.

  9. Major role for mRNA stability in shaping the kinetics of gene induction

    Directory of Open Access Journals (Sweden)

    Zeller Karen I

    2010-04-01

    Full Text Available Abstract Background mRNA levels in cells are determined by the relative rates of RNA production and degradation. Yet, to date, most analyses of gene expression profiles were focused on mechanisms which regulate transcription, while the role of mRNA stability in modulating transcriptional networks was to a large extent overlooked. In particular, kinetic waves in transcriptional responses are usually interpreted as resulting from sequential activation of transcription factors. Results In this study, we examined on a global scale the role of mRNA stability in shaping the kinetics of gene response. Analyzing numerous expression datasets we revealed a striking global anti-correlation between rapidity of induction and mRNA stability, fitting the prediction of a kinetic mathematical model. In contrast, the relationship between kinetics and stability was less significant when gene suppression was analyzed. Frequently, mRNAs that are stable under standard conditions were very rapidly down-regulated following stimulation. Such effect cannot be explained even by a complete shut-off of transcription, and therefore indicates intense modulation of RNA stability. Conclusion Taken together, our results demonstrate the key role of mRNA stability in determining induction kinetics in mammalian transcriptional networks.

  10. Shaping skeletal growth by modular regulatory elements in the Bmp5 gene.

    Directory of Open Access Journals (Sweden)

    Catherine Guenther

    2008-12-01

    Full Text Available Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.

  11. Insights from ANA-grade angiosperms into the early evolution of CUP-SHAPED COTYLEDON genes.

    Science.gov (United States)

    Vialette-Guiraud, Aurélie C M; Adam, Hélène; Finet, Cédric; Jasinski, Sophie; Jouannic, Stefan; Scutt, Charles P

    2011-06-01

    The closely related NAC family genes NO APICAL MERISTEM (NAM) and CUP-SHAPED COTYLEDON3 (CUC3) regulate the formation of boundaries within and between plant organs. NAM is post-transcriptionally regulated by miR164, whereas CUC3 is not. To gain insight into the evolution of NAM and CUC3 in the angiosperms, we analysed orthologous genes in early-diverging ANA-grade angiosperms and gymnosperms. We obtained NAM- and CUC3-like sequences from diverse angiosperms and gymnosperms by a combination of reverse transcriptase PCR, cDNA library screening and database searching, and then investigated their phylogenetic relationships by performing maximum-likelihood reconstructions. We also studied the spatial expression patterns of NAM, CUC3 and MIR164 orthologues in female reproductive tissues of Amborella trichopoda, the probable sister to all other flowering plants. Separate NAM and CUC3 orthologues were found in early-diverging angiosperms, but not in gymnosperms, which contained putative orthologues of the entire NAM + CUC3 clade that possessed sites of regulation by miR164. Multiple paralogues of NAM or CUC3 genes were noted in certain taxa, including Brassicaceae. Expression of NAM, CUC3 and MIR164 orthologues from Am. trichopoda was found to co-localize in ovules at the developmental boundary between the chalaza and nucellus. The NAM and CUC3 lineages were generated by duplication, and CUC3 was subsequently lost regulation by miR164, prior to the last common ancestor of the extant angiosperms. However, the paralogous NAM clade genes CUC1 and CUC2 were generated by a more recent duplication, near the base of Brassicaceae. The function of NAM and CUC3 in defining a developmental boundary in the ovule appears to have been conserved since the last common ancestor of the flowering plants, as does the post-transcriptional regulation in ovule tissues of NAM by miR164.

  12. Individual Aesthetic Preferences for Faces Are Shaped Mostly by Environments, Not Genes.

    Science.gov (United States)

    Germine, Laura; Russell, Richard; Bronstad, P Matthew; Blokland, Gabriëlla A M; Smoller, Jordan W; Kwok, Holum; Anthony, Samuel E; Nakayama, Ken; Rhodes, Gillian; Wilmer, Jeremy B

    2015-10-19

    Although certain characteristics of human faces are broadly considered more attractive (e.g., symmetry, averageness), people also routinely disagree with each other on the relative attractiveness of faces. That is, to some significant degree, beauty is in the "eye of the beholder." Here, we investigate the origins of these individual differences in face preferences using a twin design, allowing us to estimate the relative contributions of genetic and environmental variation to individual face attractiveness judgments or face preferences. We first show that individual face preferences (IP) can be reliably measured and are readily dissociable from other types of attractiveness judgments (e.g., judgments of scenes, objects). Next, we show that individual face preferences result primarily from environments that are unique to each individual. This is in striking contrast to individual differences in face identity recognition, which result primarily from variations in genes [1]. We thus complete an etiological double dissociation between two core domains of social perception (judgments of identity versus attractiveness) within the same visual stimulus (the face). At the same time, we provide an example, rare in behavioral genetics, of a reliably and objectively measured behavioral characteristic where variations are shaped mostly by the environment. The large impact of experience on individual face preferences provides a novel window into the evolution and architecture of the social brain, while lending new empirical support to the long-standing claim that environments shape individual notions of what is attractive.

  13. A bow-shaped thermal structure traveling upstream of the zonal wind flow of Venus atmosphere

    Science.gov (United States)

    Taguchi, Makoto; Fukuhara, Tetsuya; Imamura, Takeshi; Kouyama, Toru; Nakamura, Masato; Sato, Takao M.; Ueno, Munetaka; Suzuki, Makoto; Iwagami, Naomoto; Sato, Mitsuteru; Hashimoto, George L.; Takagi, Seiko; Akatsuki Science Team

    2016-10-01

    The Longwave Infrared Camera (LIR) onboard the Japanese Venus orbiter Akatsuki acquires a snap shot of Venus in the middle infrared region, and provides a brightness temperature distribution at the cloud-top altitudes of about 65 km. Hundreds of images taken by LIR have been transferred to the ground since the successful Venus orbit insertion of Akatsuki on Dec. 7, 2015. Here we report that a bow shaped thermal structure extending from the northern high latitudes to the southern high latitudes was found in the brightness temperature map on Dec. 7, 2015, and that it lasted for four days at least surprisingly at almost same geographical position. The bow shape structure looks symmetrical with the equator, and consists of a high temperature region in east or upstream of the background strong westward wind or the super rotation of the Venus atmosphere followed by a low temperature region in west with an amplitude of 5 K. It appeared close to the evening terminator in the dayside, and seems not to have stayed in the same local time rather to have co-rotated with the slowly rotating ground where the western part of Aphrodite Continent was below the center of the bow shape. Meridionally aligned dark filaments similar to the bow shape structure in shape but in much smaller scale were also identified in the brightness temperature map on Dec. 7, and they propagated upstream of the zonal wind as well. The bow shape structure disappeared when LIR observed the same local time and longitude in the earliest opportunity on Jan. 16, 2016. Similar events, though their amplitudes were less than 1 K, were found on Apr. 15 and 26, 2016, but they appeared in different local times and longitudes. A simulation of a gravity wave generated in the lower atmosphere and propagating upward reproduces the observed bow shape structure. The bow shape structure could be a signature of transferring momentum from the ground to the upper atmosphere.

  14. Wind flow and wind loads on the surface of a tower- shaped building: Numerical simulations and wind tunnel experiment

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Flow structure and wind pressure distribution caused by obtuse obstacles are usually the focuses in Computational Wind Engineer researches (CWE). By solving the non- hydrostatical dynamic equations, PUMA model (Peking University Model of Atmospheric Environment) was developed and applied to simulating the flow structure and wind pressure distribution around a tower-shaped building. Evaluation about the wind environment and wind loads around the building was obtained through the analysis of the numerical simulation results and wind tunnel data. Comparisons between the simulation and wind tunnel study indicate that numerical simulation results agree well in the flow field and wind pressure distribution around the tower-shaped building. On the other hand, the horizontal grid interval of 2 m and the vertical grid of 3 m were still too crude to simulate the flow structure and wind pressure distribution on the building surface more exactly in detail; and the absence of suitable pressure perturbation parameterization scheme between the solid and the adjacent space also limits the accuracy of the numerical simulation. The numerical simulation model can be used to evaluate the wind environment and wind load around high buildings.

  15. Bi-Annual Report 2010-2011: Shaping pulse flows to meet environmental and energy objectives

    Energy Technology Data Exchange (ETDEWEB)

    Jager, Yetta [ORNL

    2010-10-01

    This report describes a bioenergetic model developed to allocate seasonal pulse flows to benefit salmon growth. The model links flow with floodplain inundation and production of invertebrate prey eaten by juvenile Chinook salmon. A unique quantile modeling approach is used to describe temporal variation among juvenile salmon spawned at different times. Preliminary model outputs are presented and future plans to optimize flows both to maximize salmon growth and hydropower production are outlined.

  16. Water behavior in a U-shaped flow channel of PEM fuel cells. Paper no. IGEC-1-036

    Energy Technology Data Exchange (ETDEWEB)

    Quan, P.; Zhou, B.; Sobiesiak, A. [Univ. of Windsor, Dept. of Mechanical, Automotive and Materials Engineering, Windsor, Ontario (Canada)]. E-mail: bzhou@uwindsor.ca; Liu, Z.-S. [National Research Council Canada, Inst. for Fuel Cell innovation, Vancouver, British Columbia (Canada)

    2005-07-01

    The behavior of liquid water inside a U-shaped channel for a Proton Exchange Membrane (PEM) fuel cell was investigated through CFD modeling with the FLUENT software package. The Volume-Of-Fluid (VOF) model was adopted to track dynamic air-water interfaces. Three cases with varying initial water phase distributions corresponding to different fuel cell operating conditions were numerically simulated to obtain a better understanding of water behavior inside the serpentine channel. The results show that the bend area in the serpentine flow channel has significant effects on the flow field, which in turn affects the air-water flow and water liquid distribution inside the channel or along the interior channel surfaces, thus affecting fuel cell performance. (author)

  17. POD analysis of flow over a backward-facing step forced by right-angle-shaped plasma actuator.

    Science.gov (United States)

    Wang, Bin; Li, Huaxing

    2016-01-01

    This study aims to present flow control over the backward-facing step with specially designed right-angle-shaped plasma actuator and analyzed the influence of various scales of flow structures on the Reynolds stress through snapshot proper orthogonal decomposition (POD). 2D particle image velocimetry measurements were conducted on region (x/h = 0-2.25) and reattachment zone in the x-y plane over the backward-facing step at a Reynolds number of Re h  = 27,766 (based on step height [Formula: see text] and free stream velocity [Formula: see text]. The separated shear layer was excited by specially designed right-angle-shaped plasma actuator under the normalized excitation frequency St h  ≈ 0.345 along the 45° direction. The spatial distribution of each Reynolds stress component was reconstructed using an increasing number of POD modes. The POD analysis indicated that the flow dynamic downstream of the step was dominated by large-scale flow structures, which contributed to streamwise Reynolds stress and Reynolds shear stress. The intense Reynolds stress localized to a narrow strip within the shear layer was mainly affected by small-scale flow structures, which were responsible for the recovery of the Reynolds stress peak. With plasma excitation, a significant increase was obtained in the vertical Reynolds stress peak. Under the dimensionless frequencies St h  ≈ 0.345 and [Formula: see text] which are based on the step height and momentum thickness, the effectiveness of the flow control forced by the plasma actuator along the 45° direction was ordinary. Only the vertical Reynolds stress was significantly affected.

  18. Four-way coupled simulations of small particles in turbulent channel flow: The effects of particle shape and Stokes number

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, F.; Wachem, B. G. M. van, E-mail: berend.van.wachem@gmail.com [Division of Thermofluids, Department of Mechanical Engineering, Imperial College, London SW7 2AZ (United Kingdom); George, W. K. [Department of Aeronautics, Imperial College, London SW7 2AZ (United Kingdom)

    2015-08-15

    This paper investigates the effects of particle shape and Stokes number on the behaviour of non-spherical particles in turbulent channel flow. Although there are a number of studies concerning spherical particles in turbulent flows, most important applications occurring in process, energy, and pharmaceutical industries deal with non-spherical particles. The computation employs a unique and novel four-way coupling with the Lagrangian point-particle approach. The fluid phase at low Reynolds number (Re{sub τ} = 150) is modelled by direct numerical simulation, while particles are tracked individually. Inter-particle and particle-wall collisions are also taken into account. To explore the effects of particles on the flow turbulence, the statistics of the fluid flow such as the fluid velocity, the terms in the turbulence kinetic energy equation, the slip velocity between the two phases and velocity correlations are analysed considering ellipsoidal particles with different inertia and aspect ratio. The results of the simulations show that the turbulence is considerably attenuated, even in the very dilute regime. The reduction of the turbulence intensity is predominant near the turbulence kinetic energy peak in the near wall region, where particles preferentially accumulate. Moreover, the elongated shape of ellipsoids strengthens the turbulence attenuation. In simulations with ellipsoidal particles, the fluid-particle interactions strongly depend on the orientation of the ellipsoids. In the near wall region, ellipsoids tend to align predominantly within the streamwise (x) and wall-normal (y) planes and perpendicular to the span-wise direction, whereas no preferential orientation in the central region of the channel is observed. Important conclusions from this work include the effective viscosity of the flow is not affected, the direct dissipation by the particles is negligible, and the primary mechanism by which the particles affect the flow is by altering the turbulence

  19. Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish.

    Science.gov (United States)

    Schneider, Ralf F; Li, Yuanhao; Meyer, Axel; Gunter, Helen M

    2014-09-01

    Phenotypic plasticity is the ability of organisms with a given genotype to develop different phenotypes according to environmental stimuli, resulting in individuals that are better adapted to local conditions. In spite of their ecological importance, the developmental regulatory networks underlying plastic phenotypes often remain uncharacterized. We examined the regulatory basis of diet-induced plasticity in the lower pharyngeal jaw (LPJ) of the cichlid fish Astatoreochromis alluaudi, a model species in the study of adaptive plasticity. Through raising juvenile A. alluaudi on either a hard or soft diet (hard-shelled or pulverized snails) for between 1 and 8 months, we gained insight into the temporal regulation of 19 previously identified candidate genes during the early stages of plasticity development. Plasticity in LPJ morphology was first detected between 3 and 5 months of diet treatment. The candidate genes, belonging to various functional categories, displayed dynamic expression patterns that consistently preceded the onset of morphological divergence and putatively contribute to the initiation of the plastic phenotypes. Within functional categories, we observed striking co-expression, and transcription factor binding site analysis was used to examine the prospective basis of their coregulation. We propose a regulatory network of LPJ plasticity in cichlids, presenting evidence for regulatory crosstalk between bone and muscle tissues, which putatively facilitates the development of this highly integrated trait. Through incorporating a developmental time-course into a phenotypic plasticity study, we have identified an interconnected, environmentally responsive regulatory network that shapes the development of plasticity in a key innovation of East African cichlids.

  20. Effect of die shape on the metal flow pattern during direct extrusion process

    Directory of Open Access Journals (Sweden)

    Solomon, N.

    2010-10-01

    Full Text Available The geometric shape of the tools is the main factor by which an optimum technological process can be developed. In the case of extrusion process the strain distribution and other important variables that influence material structure, such as hydrostatic stress, are strongly dependent on the geometry of the die. Careful design of the extrusion die profile can therefore control the product structure and can be used to minimise the amount of inhomogeneity imparted into the product. A possibility to minimise the amount of product inhomogeneity is the using of a flat die with a fillet radius in front to the bearing surface with leads to a minimum dead zone and consequently to a minimum friction at billet-container interface. In the case of aluminium alloy type 2024, for an extrusion ratio of R=8.5, good results were obtained with a fillet radius of 3.0 mm. The experimental data have been used for the finite element numerical simulation of the extrusion process. The data obtained by numerical simulation with FORGE2 programme confirm the theoretical and experimental outcomes. The aim of this paper is to study the influence of such flat die on the material flow during direct extrusion process and consequently on extruded product microstructure and mechanical properties.La forma geométrica de las herramientas es el principal factor a través del cual un proceso óptimo de deformación plástica puede ser mejor desarrollado. En el caso del proceso de extrusión, la distribución de la deformación y otras variables importantes, como la presión hidrostática, que pueden influir en la estructura del material, son fuertemente dependientes de la geometría del molde. Mediante un diseño apropiado del perfil del molde de extrusión se pueden controlar la estructura y las propiedades mecánicas del producto y, por lo tanto, se puede utilizar para minimizar la cantidad de la no homogeneidad del producto. Una posibilidad para reducir al mínimo la cantidad de

  1. Factors influencing the structure and shape of stenotic and regurgitant jets: an in vitro investigation using Doppler color flow mapping and optical flow visualization.

    Science.gov (United States)

    Krabill, K A; Sung, H W; Tamura, T; Chung, K J; Yoganathan, A P; Sahn, D J

    1989-06-01

    To evaluate factors influencing the structure and shape of stenotic and regurgitant jets, Doppler color flow mapping and optical flow visualization studies were performed with use of a syringe model with a constant rate of ejection to simulate jets of valvular regurgitation and a pulsatile flow model of the right heart chambers to simulate jets of mild, moderate and severe valvular pulmonary stenosis. Ink-(0 to 40%) glycerol-water jets (viscosity 1 to 3.5 centiPoise) were produced by injecting the fluid at a constant rate into a 10 gallon rectangular reservoir of the same still fluid through 1.4 and 3.4 mm needles. The Doppler color flow scanners imaged the laminar jet length within 3 mm of actual jet length (2 to 6 cm) and the jet width within 2 to 3 mm of the actual jet width. Jet flows with Reynolds numbers ranging from 230 to 1,200 injected into still fluid yielded jet length/width ratios that decreased with increasing Reynolds numbers and leveled off to a length/width ratio of 5-6:1 at a Reynolds number near 600. When the fluid reservoir was swirled to better mimic the effect of flow entering the same cardiac chamber from a second source, the jets showed diminution of the jet length/width ratio and a clearly defined zone of turbulence. Studies of the pulsatile flow model were performed at cardiac outputs of 1 to 6 liters/min for the normal and each stenotic valve. Mild stenosis had an orifice area of 2.8 cm2, moderate stenosis an area of 1.0 cm2 and severe stenosis an area of 0.5 cm2. Laminar jet length represented the length of the total jet, which had a symmetric width and was measured from the valve opening to a region where the jet exhibited a spray effect. Laminar jet lengths (0.2 to 1.1 cm) were imaged by Doppler color flow mapping and optical visualization only in the moderate and severely stenotic valves and only at flows less than or equal to 3 liters/min (mean Reynolds numbers less than or equal to 3,470). Beyond this flow rate the jets exhibited a

  2. Phenological mismatch and the effectiveness of assisted gene flow.

    Science.gov (United States)

    Wadgymar, Susana M; Weis, Arthur E

    2017-06-01

    The persistence of narrowly adapted species under climate change will depend on their ability to migrate apace with their historical climatic envelope or to adapt in place to maintain fitness. This second path to persistence can only occur if there is sufficient genetic variance for response to new selection regimes. Inadequate levels of genetic variation can be remedied through assisted gene flow (AGF), that is the intentional introduction of individuals genetically adapted to localities with historic climates similar to the current or future climate experienced by the resident population. However, the timing of reproduction is frequently adapted to local conditions. Phenological mismatch between residents and migrants can reduce resident × migrant mating frequencies, slowing the introgression of migrant alleles into the resident genetic background and impeding evolutionary rescue efforts. Focusing on plants, we devised a method to estimate the frequency of resident × migrant matings based on flowering schedules and applied it in an experiment that mimicked the first generation of an AGF program with Chamaecrista fasciculata, a prairie annual, under current and expected future temperature regimes. Phenological mismatch reduced the potential for resident × migrant matings by 40-90%, regardless of thermal treatment. The most successful migrant sires were the most resident like in their flowering time, further biasing the genetic admixture between resident and migrant populations. Other loci contributing to local adaptation-heat-tolerance genes, for instance-may be in linkage disequilibrium with phenology when residents and migrants are combined into a single mating pool. Thus, introgression of potentially adaptive migrant alleles into the resident genetic background is slowed when selection acts against migrant phenology. Successful AGF programs may require sustained high immigration rates or preliminary breeding programs when phenologically matched migrant

  3. A study of optimum cowl shapes and flow port locations for minimum drag with effective engine cooling, volume 1

    Science.gov (United States)

    Fox, S. R.; Smetana, F. O.

    1980-01-01

    The contributions to the cruise drag of light aircraft arising from the shape of the engine cowl and the forward fuselage area and also that resulting from the cooling air mass flow through intake and exhaust sites on the nacelle were analyzed. The methods employed for the calculation of the potential flow about an arbitrary three dimensional body are described with modifications to include the effects of boundary layer displacement thickness, a nonuniform onset flow field (such as that due to a rotating propeller), and the presence of air intakes and exhausts. A simple, reliable, largely automated scheme to better define or change the shape of a body is also presented. A technique was developed which can yield physically acceptable skin friction and pressure drag coefficients for isolated light aircraft bodies. For test cases on a blunt nose Cessna 182 fuselage, the technique predicted drag reductions as much as 28.5% by body recontouring and proper placements and sizing of the cooling air intakes and exhausts.

  4. NUMERICAL SIMULATION ANALYSIS OF EXTERNAL FLOW FIELD OF WAGON-SHAPED CAR AT THE MOMENT OF PASSING

    Institute of Scientific and Technical Information of China (English)

    GU Zhengqi; HE Yibin; ZHOU Wei; JIANG Bo

    2008-01-01

    In the course of studying on aerodynamic change and its effect on steering stability and controllability of an automobile in passing, because of multi interaction streams, it is difficult to use traditional methods, such as wind tunnel test and road test. If the passing process of an automobile is divided into many time segments, so as to avoid the use of moving mesh which takes large calculation resource and CPU processing time in calculating, the segments are simulated with computational fluid dynamics (CFD) method, then the approximate computational results about external flow field will be obtained. On the basis of the idea, the change of external flow field of wagon-shaped car at the moment of passing is simulated through solving three-dimensional, steady and uncompressible N-S equations with finite volume method. Numerical simulation analysis of side force coefficient, stream lines, body surface pressure distribution of wagon-shaped car are presented and a preliminary discussion of aerodynamic characteristics of correlative situations is obtained. Finally, the Cs -x/l curve of side force coefficient(Cs) of car following relative distance (x/l) between cars is obtained. By comparison, the curve is coincident well with the experimental data,which shows creditability of numerical simulation methods presented.Key words: External flow field Passing Numerical simulation Side force coefficient

  5. High rates of gene flow by pollen and seed in oak populations across Europe

    NARCIS (Netherlands)

    Gerber, S.; Chadoeuf, J.; Gugerli, F.; Lascoux, M.; Buiteveld, J.; Cottrell, J.; Dounavi, A.; Fineschi, S.; Forrest, L.; Fogelqvist, J.; Goicoechea, P.G.; Jensen, J.S.; Salvini, D.; Vendramin, G.G.; Kremer, A.

    2014-01-01

    Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult tree

  6. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    DEFF Research Database (Denmark)

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.

    2009-01-01

    and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...

  7. Euglossine bees mediate only limited long-distance gene flow in a tropical vine.

    Science.gov (United States)

    Opedal, Øystein H; Falahati-Anbaran, Mohsen; Albertsen, Elena; Armbruster, W Scott; Pérez-Barrales, Rocío; Stenøien, Hans K; Pélabon, Christophe

    2017-03-01

    Euglossine bees (Apidae: Euglossini) have long been hypothesized to act as long-distance pollinators of many low-density tropical plants. We tested this hypothesis by the analysis of gene flow and genetic structure within and among populations of the euglossine bee-pollinated vine Dalechampia scandens. Using microsatellite markers, we assessed historical gene flow by the quantification of regional-scale genetic structure and isolation by distance among 18 populations, and contemporary gene flow by the estimation of recent migration rates among populations. To assess bee-mediated pollen dispersal on a smaller scale, we conducted paternity analyses within a focal population, and quantified within-population spatial genetic structure in four populations. Gene flow was limited to certain nearby populations within continuous forest blocks, whereas drift appeared to dominate on larger scales. Limited long-distance gene flow was supported by within-population patterns; gene flow was biased towards nearby plants, and significant small-scale spatial genetic structure was detected within populations. These findings suggest that, although female euglossine bees might be effective at moving pollen within populations, and perhaps within forest blocks, their contribution to gene flow on the regional scale seems too limited to counteract genetic drift in patchily distributed tropical plants. Among-population gene flow might have been reduced following habitat fragmentation.

  8. Star-Shaped Fluid Flow Tool for Use in Making Differential Measurements

    Science.gov (United States)

    England, John Dwight (Inventor); Kelley, Anthony R. (Inventor); Cronise, Raymond J. (Inventor)

    2014-01-01

    A fluid flow tool's plate-like structure has a ring portion defining a flow hole, a support portion extending radially away from the ring portion and adapted to be coupled to conduit wall, and extensions extending radially away from the ring portion such that a periphery of the plate-like structure is defined by the extensions and trough regions between adjacent extensions. One or more ports formed in the ring portion are in fluid communication with the flow hole. A first manifold in the plate-like structure is in fluid communication with each port communicating with the flow hole. One or more ports are formed in the periphery of the plate-like structure. A second manifold in the plate-like structure is in fluid communication with each port formed in the periphery. The first and second manifolds extend through the plate-like structure to terminate and be accessible at the conduit wall.

  9. Observation of anisotropic event shapes and transverse flow in ultrarelativistic Au+Au collisions

    Energy Technology Data Exchange (ETDEWEB)

    Barrette, J.; Bellwied, R.; Bennett, S.; Braun-Munzinger, P.; Cleland, W.E.; Clemen, M.; Cole, J.; Cormier, T.M.; David, G.; Dee, J.; Dietzsch, O.; Drigert, M.; Gilbert, S.; Hall, J.R.; Hemmick, T.K.; Herrmann, N.; Hong, B.; Jiang, C.L.; Kwon, Y.; Lacasse, R.; Lukaszew, A.; Li, Q.; Ludlam, T.W.; McCorkle, S.; Mark, S.K.; Matheus, R.; O' Brien, E.; Panitkin, S.; Piazza, T.; Pruneau, C.; Rao, M.N.; Rosati, M.; daSilva, N.C.; Sedykh, S.; Sonnadara, U.; Stachel, J.; Takai, H.; Takagui, E.M.; Voloshin, S.; Wang, G.; Wessels, J.P.; Woody, C.L.; Xu, N.; Zhang, Y.; Zhang, Z.; Zou, C. (Brookhaven National Laboratory, Upton, New York 11973 (United States) Gesellschaft fuer Schwerionenforschung, Darmstadt (Germany) Idaho National Engineering Laboratory, Idaho Falls, Idaho 83402 (United States) McGill Univesity, Montreal, H3A 2T8 (Canada) University of Pittsburgh, Pittsburgh, Pennsylvania 15260 (United States) SUNY, Stony Brook, New York, 11794 (United States) University of Sao Paulo, Sao Paulo (B; (E877 Collaboration)

    1994-11-07

    Event shapes for Au + Au collisions at 11.4 GeV/[ital c] per nucleon were studied over nearly the full solid angle with the E877 apparatus. The analysis was performed by Fourier expansion of azimuthal distributions of the transverse energy ([ital E][sub [ital T

  10. Shape optimization of the stokes flow problem based on isogeometric analysis

    DEFF Research Database (Denmark)

    Park, Byong-Ug; Seo, Yu-Deok; Sigmund, Ole;

    2013-01-01

    Design-dependent loads related to boundary shape, such as pressure and convection loads, have been a challenging issue in optimization. Isogeometric analysis, where the analysis model has smooth boundaries described by spline functions can handle design-dependent loads with ease. In the present s...

  11. Numerical and Experimental Investigation of Turbulent Transport Control via Shaping of Radial Plasma Flow Profiles

    Energy Technology Data Exchange (ETDEWEB)

    Gilmore, Mark Allen [Univ. of New Mexico, Albuquerque, NM (United States)

    2017-02-05

    Turbulence, and turbulence-driven transport are ubiquitous in magnetically confined plasmas, where there is an intimate relationship between turbulence, transport, instability driving mechanisms (such as gradients), plasma flows, and flow shear. Though many of the detailed physics of the interrelationship between turbulence, transport, drive mechanisms, and flow remain unclear, there have been many demonstrations that transport and/or turbulence can be suppressed or reduced via manipulations of plasma flow profiles. This is well known in magnetic fusion plasmas [e.g., high confinement mode (H-mode) and internal transport barriers (ITB’s)], and has also been demonstrated in laboratory plasmas. However, it may be that the levels of particle transport obtained in such cases [e.g. H-mode, ITB’s] are actually lower than is desirable for a practical fusion device. Ideally, one would be able to actively feedback control the turbulent transport, via manipulation of the flow profiles. The purpose of this research was to investigate the feasibility of using both advanced model-based control algorithms, as well as non-model-based algorithms, to control cross-field turbulence-driven particle transport through appropriate manipulation of radial plasma flow profiles. The University of New Mexico was responsible for the experimental portion of the project, while our collaborators at the University of Montana provided plasma transport modeling, and collaborators at Lehigh University developed and explored control methods.

  12. Directional gene flow and ecological separation in Yersinia enterocolitica

    Science.gov (United States)

    Reuter, Sandra; Corander, Jukka; de Been, Mark; Harris, Simon; Cheng, Lu; Hall, Miquette; Thomson, Nicholas R.

    2015-01-01

    Yersinia enterocolitica is a common cause of food-borne gastroenteritis worldwide. Recent work defining the phylogeny of the genus Yersinia subdivided Y. enterocolitica into six distinct phylogroups. Here, we provide detailed analyses of the evolutionary processes leading to the emergence of these phylogroups. The dominant phylogroups isolated from human infections, PG3–5, show very little diversity at the sequence level, but do present marked patterns of gain and loss of functions, including those involved in pathogenicity and metabolism, including the acquisition of phylogroup-specific O-antigen loci. We tracked gene flow across the species in the core and accessory genome, and show that the non-pathogenic PG1 strains act as a reservoir for diversity, frequently acting as donors in recombination events. Analysis of the core and accessory genome also suggested that the different Y. enterocolitica phylogroups may be ecologically separated, in contrast to the long-held belief of common shared ecological niches across the Y. enterocolitica species.

  13. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    DEFF Research Database (Denmark)

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.;

    2009-01-01

    Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from...... and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...... landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North–South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin...

  14. Shape effects of nanoparticles on the squeezed flow between two Riga plates in the presence of thermal radiation

    Science.gov (United States)

    Ahmed, Naveed; Adnan; Khan, Umar; Tauseef Mohyud-Din, Syed; Waheed, Asif

    2017-07-01

    This paper aims to explore the flow of water saturated with copper nanoparticles of different shapes between parallel Riga plates. The plates are placed horizontally in the coordinate axis. Influence of the linear thermal radiation is also taken into account. The equations governing the flow have been transformed into a nondimensional form by employing a set of similarity transformations. The obtained system is solved analytically (variation-of-parameters method) and numerically (Runge-Kutta scheme). Under certain conditions, a special case of the model is also explored. Furthermore, influences of the physical quantities on velocity and thermal fields are discussed with the graphical aid over the domain of interest. The quantities of engineering and practical interest (skin friction coefficient and local rate of heat transfer) are also explored graphically.

  15. Spatiotemporal Pattern Formation in BioFluids I: Cell Shape Perturbants As Evidence of Spatially-Organised Membrane Flows

    CERN Document Server

    Lofthouse, J T

    2003-01-01

    I show the assumed Bilayer structure of cell membranes is Topologically falsified by known aminophospholipid dynamics in metabolically-active, Far from Equilibrium cells. The sensitivity of lipid and cytoplasmic flows to temperature, surfactants, viscosity and the gravity vector are used to suggest that rather than being random viscous fluids as currently assumed, both are actually spatially-organised by convective and shear driven mechanisms in vivo. I show how protein-lipid feedback provokes a Gestalt Shift in Cell Mechanics by demonstrating that the primary forces involved in shape changes are generated by bifurcations in fluid flow Topology, which induce affine deformations of the cytoskeletal lattice. The feedback model allows the transduction of Gravitational information into biological form, is universally applicable, and provides a rationale for Homeoviscous Adaptation, and the extensive lipid polymorphism observed in Nature.

  16. Shape optimization for viscous flows by reduced basis methods and free-form deformation

    OpenAIRE

    Manzoni, Andrea; Quarteroni, Alfio; Rozza, Gianluigi

    2011-01-01

    In this paper we further develop an approach previously introduced in [Lassila and Rozza, C.M.A.M.E 2010] for shape optimization that combines a suitable low-dimensional parametrization of the geometry (yielding a geometrical reduction) with reduced basis methods (yielding a reduction of computational complexity). More precisely, free-form deformation techniques are considered for the geometry description and its parametrization, while reduced basis methods are used upon a finite element dis...

  17. Analyzing the shape parameter effects on the performance of the mixed-flow fan using CFD and Factorial design

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Uk Hee; Kim, Joon Hyung; Kim, Sung; Kim, Jin Hyuk; Choi, Young Seok [Korea Institute of Industrial Technology, Cheonan (Korea, Republic of)

    2016-03-15

    Fans are representative turbo-machinery widely used for ventilation throughout the industrial world. Recently, as the importance of energy saving has been magnified with the fans, the demand for the fans with high efficiency and performance has been increasing. The representative method for enhancing the performance includes design optimization; in practice, fan performance can be improved by changing the shape parameters such as those of meridional plane, impeller, and diffuser. Before optimizing the efficient design, a process of screening to select important design parameters is essential. The present study aimed to analyze the effects of mixed-flow fans' shape parameters on fan performance (static pressure and fan static efficiency) and derive optimum models based on the results. In this study, the shape parameters considered in the impeller domain are as follows: tip clearance, number of blades, beta angle of Leading edge (LE) in the blade, and beta angle of Trailing edge (TE) in the blade. The shape parameters considered in the diffuser domain are as follows: meridional length of the Guide vane (GV), number of GV, beta angle of LE in the GV and beta angle of TE in the GV. The effects of individual shape parameters were analyzed using the CFD (Computational fluid dynamic) and DOE (Design of experiments) methods. The reliability of CFD was verified through the comparison between preliminary fan model's experiment results and CFD results, and screening processes were implemented through 24-1 fractional factorial design. From the analysis of DOE results, it could be seen that the tip clearance and the number of blades in the impeller domain greatly affected the fan performance, and the beta angle of TE at the GV in the diffuser domain greatly affected the fan performance. Finally, the optimum models with improved fan performance were created using linear regression equations derived from 24-1 fractional factorial design.

  18. Event-shape engineering for inclusive spectra and elliptic flow in Pb-Pb collisions at √sNN=2.76TeV

    NARCIS (Netherlands)

    Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahn, S. U.; Aimo, I.; Aiola, S.; Ajaz, M.; Akindinov, A.; Alam, S. N.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Anielski, J.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Armesto, N.; Arnaldi, R.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Bach, M.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Baldisseri, A.; Baltasar Dos Santos Pedrosa, F.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-moreno, E.; Belyaev, V.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blanco, F.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botta, E.; Böttger, S.; Braun-munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Cavicchioli, C.; Ceballos Sanchez, C.; Cepila, J.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Chochula, P.; Choi, K.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chunhui, Z.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa Del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danu, A.; Das, I.; Das, S.; Dash, A.; Dash, S.; De, S.; De Caro, A.; De Cataldo, G.; De Cuveland, J.; De Falco, A.; De Gruttola, D.; De Marco, N.; De Pasquale, S.; Deisting, A.; Deloff, A.; Dénes, E.; D'erasmo, G.; Di Bari, D.; Di Mauro, A.; Di Nezza, P.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrowolski, T.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Engel, H.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Eschweiler, D.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Felea, D.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-solis, E.; Gargiulo, C.; Gasik, P.; Germain, M.; Gheata, A.; Gheata, M.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; González-zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Grosse-oetringhaus, J. F.; Grossiord, J.-y.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gulkanyan, H.; Gunji, T.; Gupta, A.; Haake, R.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hansen, A.; Harris, J. W.; Hartmann, H.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Heide, M.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hilden, T. E.; Hillemanns, H.; Hippolyte, B.; Hosokawa, R.; Hristov, P.; Huang, M.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Ilkiv, I.; Inaba, M.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jadlovska, S.; Jahnke, C.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jung, H.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Khan, K. H.; Mohisin Khan, M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, B.; Kim, D. W.; Kim, D. J.; Kim, J. S.; Kim, M.; Kim, M.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein-bösing, C.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobayashi, T.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Koyithatta Meethaleveedu, G.; Kral, J.; Králik, I.; Kravčáková, A.; Kretz, M.; Krivda, M.; Krizek, F.; Kryshen, E.; Kubera, A. M.; Kučera, V.; Kugathasan, T.; Kuijer, P. G.; Kumar, J.; Kumar, L.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kushpil, S.; Kweon, M. J.; Kwon, Y.; La Rocca, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Legrand, I.; Lehas, F.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; Leoncino, M.; Lévai, P.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luz, P. H. F. N. D.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin Blanco, J.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Martynov, Y.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Massacrier, L.; Mastroserio, A.; Masui, H.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; Mcdonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Minervini, L. M.; Mischke, A.; Mishra, A. N.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Morando, M.; Moreira De Godoy, D. A.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Murray, S.; Musa, L.; Musinsky, J.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Nattrass, C.; Nayak, K.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira Da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, P.; Paić, G.; Pajares, C.; Pal, S. K.; Pan, J.; Pant, D.; Papcun, P.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Peitzmann, T.; Pereira Da Costa, H.; Pereira De Oliveira Filho, E.; Peresunko, D.; Pérez Lara, C. E.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Płoskoń, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poonsawat, W.; Pop, A.; Porteboeuf-houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Read, K. F.; Real, J. S.; Redlich, K.; Reed, R. J.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Rettig, F.; Revol, J.-p.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rivetti, A.; Rocco, E.; Rodríguez Cahuantzi, M.; Rodriguez Manso, A.; Røed, K.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Romita, R.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Russo, R.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Sadovsky, S.; Šafařík, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salgado, C. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Sanchez Castro, X.; Šándor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Scapparone, E.; Scarlassara, F.; Scharenberg, R. P.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schuster, T.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Seo, J.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shangaraev, A.; Sharma, M.; Sharma, M.; Sharma, N.; Shigaki, K.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Søgaard, C.; Soltz, R.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-stassinaki, M.; Srivastava, B. K.; Stachel, J.; Stan, I.; Stefanek, G.; Steinpreis, M.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Sultanov, R.; Šumbera, M.; Symons, T. J. M.; Szabo, A.; Szanto De Toledo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tangaro, M. A.; Tapia Takaki, J. D.; Tarantola Peloni, A.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thäder, J.; Tieulent, R.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vajzer, M.; Vala, M.; Valencia Palomo, L.; Vallero, S.; Van Der Maarel, J.; Van Hoorne, J. W.; Van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Venaruzzo, M.; Vercellin, E.; Vergara Limón, S.; Vernet, R.; Vickovic, L.; Viesti, G.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; Von Haller, B.; Vorobyev, I.; Vranic, D.; Vrláková, J.; Vulpescu, B.; Vyushin, A.; Wagner, B.; Wagner, J.; Wang, H.; Watanabe, D.; Watanabe, Y.; Westerhoff, U.; Wiechula, J.; Wikne, J.; Wilde, M.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yaldo, C. G.; Yang, H.; Yano, S.; Yokoyama, H.; Yoo, I.-k.; Yurchenko, V.; Yushmanov, I.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhao, C.; Zhigareva, N.; Zhou, Z.; Zhu, H.; Zhu, X.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.

    2016-01-01

    We report on results obtained with the event-shape engineering technique applied to Pb-Pb collisions at √sNN=2.76 TeV. By selecting events in the same centrality interval, but with very different average flow, different initial-state conditions can be studied. We find the effect of the event-shape

  19. DNA capture reveals transoceanic gene flow in endangered river sharks.

    Science.gov (United States)

    Li, Chenhong; Corrigan, Shannon; Yang, Lei; Straube, Nicolas; Harris, Mark; Hofreiter, Michael; White, William T; Naylor, Gavin J P

    2015-10-27

    For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.

  20. Multiple evidence for the role of an Ovate-like gene in determining fruit shape in pepper

    Directory of Open Access Journals (Sweden)

    Tsaftaris Athanasios S

    2011-03-01

    Full Text Available Abstract Background Grafting is a widely used technique contributing to sustainable and ecological production of many vegetables, but important fruit quality characters such as taste, aroma, texture and shape are known for years to be affected by grafting in important vegetables species including pepper. From all the characters affected, fruit shape is the most easily observed and measured. From research in tomato, fruit shape is known to be controlled by many QTLs but only few of them have larger effect on fruit shape variance. In this study we used pepper cultivars with different fruit shape to study the role of a pepper Ovate-like gene, CaOvate, which encodes a negative regulator protein that brings significant changes in tomato fruit shape. Results We successfully cloned and characterized Ovate-like genes (designated as CaOvate from two pepper cultivars of different fruit shape, cv. "Mytilini Round" and cv. "Piperaki Long", hereafter referred to as cv. "Round" and cv. "Long" after the shape of their mature fruits. The CaOvate consensus contains a 1008-bp ORF, encodes a 335 amino-acid polypeptide, shares 63% identity with the tomato OVATE protein and exhibits high similarity with OVATE sequences from other Solanaceae species, all placed in the same protein subfamily as outlined by expert sequence analysis. No significant structural differences were detected between the CaOvate genes obtained from the two cultivars. However, relative quantitative expression analysis showed that the expression of CaOvate followed a different developmental profile between the two cultivars, being higher in cv. "Round". Furthermore, down-regulation of CaOvate through VIGS in cv. "Round" changes its fruit to a more oblong form indicating that CaOvate is indeed involved in determining fruit shape in pepper, perhaps by negatively affecting the expression of its target gene, CaGA20ox1, also studied in this work. Conclusions Herein, we clone, characterize and study Ca

  1. From active shape model to active optical flow model: a shape-based approach to predicting voxel-level dose distributions in spine SBRT.

    Science.gov (United States)

    Liu, Jianfei; Wu, Q Jackie; Kirkpatrick, John P; Yin, Fang-Fang; Yuan, Lulin; Ge, Yaorong

    2015-03-07

    Prediction of achievable dose distribution in spine stereotactic body radiation therapy (SBRT) can help in designing high-quality treatment plans to maximally protect spinal cords and to effectively control tumours. Dose distributions at spinal cords are primarily affected by the shapes of adjacent planning target volume (PTV) contours. In this work, we estimate such contour effects and predict dose distributions by exploring active optical flow model (AOFM) and active shape model (ASM). We first collect a sequence of dose sub-images and PTV contours near spinal cords from fifteen SBRT plans in the training dataset. The data collection is then classified into five groups according to the PTV locations in relation to spinal cords. In each group, we randomly choose a dose sub-image as the reference and register all other sub-images to the reference using an optical flow method. AOFM is then constructed by importing optical flow vectors and dose values into the principal component analysis (PCA). Similarly, we build ASM by using PCA on PTV contour points. The correlation between ASM and AOFM is estimated via a stepwise multiple regression model. When predicting dose distribution of a new case, the group is first determined based on the PTV contour. The prediction model of the selected group is used to estimate dose distributions by mapping the PTV contours from the ASM space to the AOFM space. This method was validated on fifteen SBRT plans in the testing dataset. Analysis of dose-volume histograms revealed that the important D2%, D5%, D10% and D0.1cc dosimetric parameters of spinal cords between the prediction and the clinical plans were 11.7 ± 1.7 Gy versus 11.8 ± 1.7 Gy (p = 0.95), 10.9 ± 1.7 Gy versus 11.1 ± 1.9 Gy (p = 0.8295), 10.2 ± 1.6 Gy versus 10.1 ± 1.7 (p = 0.9036) and 11.2 ± 2.0 Gy versus 11.1 ± 2.2 Gy (p = 0.5208), respectively. Here, the ‘cord’ is the spinal cord proper (not the thecal sac) extended 5 mm inferior and superior to the involved

  2. Regulation of flow through a T-Shaped open cavity by temperature dependent P, PI, and PID controllers

    Science.gov (United States)

    Saha, Sourav; Mojumder, Satyajit; Saha, Sumon

    2016-07-01

    P (proportional), PI (proportional-integral), and PID (proportional-integral-derivative) controllers are popular means of controlling industrial processes. Due to superior response, accuracy, and stable performance, PID controllers are mostly used in control systems. This paper presents a mathematical model and subsequent response analysis regarding regulation of flow in mixed convection through a T-shaped open cavity by temperature dependent controllers. The T-shaped cavity has cold top and hot bottom walls, while air is flowing through the inlet at surrounding temperature. The inflow is regulated by a controlled gate which operates according to the signal received from the controller. Values of proportional gain (kp), integral gain (ki), and derivative gain (kd) are varied to obtain the desired system response and to ensure a stable system with fastest response. At first, only P controller is used and eventually PI and finally PID control scheme is applied for controller tuning. Tuning of different controllers (P, PI, and PID) are carried out systematically based on the reference temperature which is continuously monitored at a certain location inside the cavity. It is found that PID controller performs better than P or PI controller.

  3. Numerical Analysis of Effect of Boundary Layer Characteristics on the Flow Field in S-shaped Inlet

    Directory of Open Access Journals (Sweden)

    Ren Jia

    2015-01-01

    Full Text Available In order to explore the effect of boundary layer thickness and pressure gradient on the performance of the flow field in the inlet, we design a high offset rate S-shaped inlet based on a certain unmanned aerial vehicle (UAV, and its author has analyzed the effect of boundary layer characteristics on the inlet with numerical simulation method. The suction of boundary layer which leads to separation zone not only becomes longer in the inlet, but also moves to the center plane of symmetry, the separation point of boundary layer appears in advance as pressure gradient increases. Considering the influence of the boundary layer, various performance parameters all exceeds that of the uniform entrance inlet conditions, especially the circumferential total pressure distortion of outlet increased by 58.2% at most, obviously can’t meet the engine to work properly, so we must consider and pay attention to the effect of the boundary layer characteristics on the flow field in the S-shaped inlet.

  4. Examining the effect of pore size distribution and shape on flow through unsaturated peat using 3-D computed tomography

    Directory of Open Access Journals (Sweden)

    F. Rezanezhad

    2009-05-01

    Full Text Available The hydraulic conductivity of unsaturated peat soils is controlled by the peat structure which affects the air-filled porosity, pore size distribution and shape. This study investigates how the size and shape of pores affects the flow of water through peat soils. In this study we used X-ray Computed Tomography (CT, at 45 µm resolution under 5 specific soil-water pressure head levels to provide 3-D, high-resolution images that were used to detect the inner pore structure of peat samples under a changing water regime. Pore structure and configuration were found to be irregular, which affected the rate of water transmission through peat soils. The 3-D analysis suggested that pore distribution is dominated by a single large pore-space. At low pressure head, this single large air-filled pore imparted a more effective flowpath compared to smaller pores. Smaller pores were disconnected and the flowpath was more tortuous than in the single large air-filled pore, and their contribution to flow was negligible when the single large pore was active. We quantify the pore structure of peat soil that affects the hydraulic conductivity in the unsaturated condition, and demonstrate the validity of our estimation of peat unsaturated hydraulic conductivity by making a comparison with a standard permeameter-based method. Estimates of unsaturated hydraulic conductivities were made for the purpose of testing the sensitivity of pore shape and geometry parameters on the hydraulic properties of peats and how to evaluate the structure of the peat and its affects on parameterization. We also studied the ability to quantify these factors for different soil moisture contents in order to define how the factors controlling the shape coefficient vary with changes in soil water pressure head. The relation between measured and estimated unsaturated hydraulic conductivity at various heads shows that rapid initial drainage, that changes the air-filled pore properties, creates a

  5. Convective heat transfer of nanofluid flow through conduits with different cross-sectional shapes

    Energy Technology Data Exchange (ETDEWEB)

    Salimpour, Mohammad Reza; Dehshiri-Parizi, Amir [Isfahan University of Technology, Isfahan (Iran, Islamic Republic of)

    2015-02-15

    This study investigates the laminar forced convective heat transfer of TiO{sub 2}/water nanofluids through conduits with different cross sections, experimentally. The effects of different parameters, such as cross-sectional shape, Reynolds number, and concentration of nanoparticles, on the enhanced heat transfer are examined by designing and assembling an experimental apparatus. Results show that adding a small amount of nanoparticles to the base fluid improves heat transfer behavior in conduits. A conduit with a circular cross section performs better than conduits with square and triangular cross sections. However, conduits with square and triangular cross sections exhibit more relative enhancements than a conduit with a circular cross section.

  6. Hidden histories of gene flow in highland birds revealed with genomic markers.

    Science.gov (United States)

    Zarza, Eugenia; Faircloth, Brant C; Tsai, Whitney L E; Bryson, Robert W; Klicka, John; McCormack, John E

    2016-10-01

    Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation.

  7. Investigation of Unsteady Flow Physics around Blunt Shaped MAV using CFD

    Science.gov (United States)

    2010-09-24

    bus. Iaccarino and Durbin [32] performed unsteady three-dimensional RANS simulations with turbulence model to the solution of the flow around a...application. The eddy viscosity, which represents the effects of turbulence, is calculated from an algebraic expression which includes a model constant...32833. [32] G. Iaccarino and P. Durbin , Unsteady 3D RANS simulations using the model, Center for Turbulence Research, Anual Research Briefs 2000

  8. The Effects of Limiters on High Resolution Computations of Hypersonic Flows over Bodies with Complex Shapes

    Institute of Scientific and Technical Information of China (English)

    BoZHENG; Chun-HianLEE

    1998-01-01

    The effects of certain limiters used in TVD-type of schemes on the resolution of numerical computations in hypersonic flows are investigayted.An explicit TVD scheme of Harten-Yee type with velocity-dependent entropy correction function is employed in the computations,Numerical experiments for hypersonic invicid as well as viscous lfows over a double-ellipsoid show that the limiters will affect the numerical results substantially,and may even cause the solutions to diverge.

  9. Transient stability and control of renewable generators based on Hamiltonian surface shaping and power flow control. Part II, analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Robinett, Rush D., III; Wilson, David Gerald

    2010-11-01

    The swing equations for renewable generators connected to the grid are developed and a wind turbine is used as an example. The swing equations for the renewable generators are formulated as a natural Hamiltonian system with externally applied non-conservative forces. A two-step process referred to as Hamiltonian Surface Shaping and Power Flow Control (HSSPFC) is used to analyze and design feedback controllers for the renewable generators system. This formulation extends previous results on the analytical verification of the Potential Energy Boundary Surface (PEBS) method to nonlinear control analysis and design and justifies the decomposition of the system into conservative and non-conservative systems to enable a two-step, serial analysis and design procedure. The first step is to analyze the system as a conservative natural Hamiltonian system with no externally applied non-conservative forces. The Hamiltonian surface of the swing equations is related to the Equal-Area Criterion and the PEBS method to formulate the nonlinear transient stability problem. This formulation demonstrates the effectiveness of proportional feedback control to expand the stability region. The second step is to analyze the system as natural Hamiltonian system with externally applied non-conservative forces. The time derivative of the Hamiltonian produces the work/rate (power flow) equation which is used to ensure balanced power flows from the renewable generators to the loads. The Second Law of Thermodynamics is applied to the power flow equations to determine the stability boundaries (limit cycles) of the renewable generators system and enable design of feedback controllers that meet stability requirements while maximizing the power generation and flow to the load. Necessary and sufficient conditions for stability of renewable generators systems are determined based on the concepts of Hamiltonian systems, power flow, exergy (the maximum work that can be extracted from an energy flow) rate

  10. Final Technical Report: Numerical and Experimental Investigation of Turbulent Transport Control via Shaping of Radial Plasma Flow Profiles

    Energy Technology Data Exchange (ETDEWEB)

    Schuster, Eugenio

    2014-05-02

    The strong coupling between the different physical variables involved in the plasma transport phenomenon and the high complexity of its dynamics call for a model-based, multivariable approach to profile control where those predictive models could be exploited. The overall objective of this project has been to extend the existing body of work by investigating numerically and experimentally active control of unstable fluctuations, including fully developed turbulence and the associated cross-field particle transport, via manipulation of flow profiles in a magnetized laboratory plasma device. Fluctuations and particle transport can be monitored by an array of electrostatic probes, and Ex B flow profiles can be controlled via a set of biased concentric ring electrodes that terminate the plasma column. The goals of the proposed research have been threefold: i- to develop a predictive code to simulate plasma transport in the linear HELCAT (HELicon-CAThode) plasma device at the University of New Mexico (UNM), where the experimental component of the proposed research has been carried out; ii- to establish the feasibility of using advanced model-based control algorithms to control cross-field turbulence-driven particle transport through appropriate manipulation of radial plasma flow profiles, iii- to investigate the fundamental nonlinear dynamics of turbulence and transport physics. Lehigh University (LU), including Prof. Eugenio Schuster and one full-time graduate student, has been primarily responsible for control-oriented modeling and model-based control design. Undergraduate students have also participated in this project through the National Science Foundation Research Experience for Undergraduate (REU) program. The main goal of the LU Plasma Control Group has been to study the feasibility of controlling turbulence-driven transport by shaping the radial poloidal flow profile (i.e., by controlling flow shear) via biased concentric ring electrodes.

  11. Effect of trailing edge shape on the separated flow characteristics around an airfoil at low Reynolds number: A numerical study

    Science.gov (United States)

    Thomareis, Nikitas; Papadakis, George

    2017-01-01

    Direct numerical simulations of the flow field around a NACA 0012 airfoil at Reynolds number 50 000 and angle of attack 5° with 3 different trailing edge shapes (straight, blunt, and serrated) have been performed. Both time-averaged flow characteristics and the most dominant flow structures and their frequencies are investigated using the dynamic mode decomposition method. It is shown that for the straight trailing edge airfoil, this method can capture the fundamental as well as the subharmonic of the Kelvin-Helmholtz instability that develops naturally in the separating shear layer. The fundamental frequency matches well with relevant data in the literature. The blunt trailing edge results in periodic vortex shedding, with frequency close to the subharmonic of the natural shear layer frequency. The shedding, resulting from a global instability, has an upstream effect and forces the separating shear layer. Due to forcing, the shear layer frequency locks onto the shedding frequency while the natural frequency (and its subharmonic) is suppressed. The presence of serrations in the trailing edge creates a spanwise pressure gradient, which is responsible for the development of a secondary flow pattern in the spanwise direction. This pattern affects the mean flow in the near wake. It can explain an unexpected observation, namely, that the velocity deficit downstream of a trough is smaller than the deficit after a protrusion. Furthermore, the insertion of serrations attenuates the energy of vortex shedding by de-correlating the spanwise coherence of the vortices. This results in weaker forcing of the separating shear layer, and both the subharmonics of the natural frequency and the shedding frequency appear in the spectra.

  12. Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae

    Directory of Open Access Journals (Sweden)

    von der Heyden Sophie

    2008-12-01

    Full Text Available Abstract Background Oceanography and life-history characteristics are known to influence the genetic structure of marine species, however the relative role that these factors play in shaping phylogeographic patterns remains unresolved. The population genetic structure of the endemic, rocky shore dwelling Caffrogobius caffer was investigated across a known major oceanographic barrier, Cape Agulhas, which has previously been shown to strongly influence genetic structuring of South African rocky shore and intertidal marine organisms. Given the variable and dynamic oceanographical features of the region, we further sought to test how the pattern of gene flow between C. caffer populations is affected by the dominant Agulhas and Benguela current systems of the southern oceans. Results The variable 5' region of the mtDNA control region was amplified for 242 individuals from ten localities spanning the distributional range of C. caffer. Fifty-five haplotypes were recovered and in stark contrast to previous phylogeographic studies of South African marine species, C. caffer showed no significant population genetic structuring along 1300 km of coastline. The parsimony haplotype network, AMOVA and SAMOVA analyses revealed panmixia. Coalescent analyses reveal that gene flow in C. caffer is strongly asymmetrical and predominantly affected by the Agulhas Current. Notably, there was no gene flow between the east coast and all other populations, although all other analyses detect no significant population structure, suggesting a recent divergence. The mismatch distribution suggests that C. caffer underwent a population expansion at least 14 500 years ago. Conclusion We propose several possible life-history adaptations that could have enabled C. caffer to maintain gene flow across its distributional range, including a long pelagic larval stage. We have shown that life-history characteristics can be an important contributing factor to the phylogeography of marine

  13. Shape and Topology Optimization in Stokes Flow with a Phase Field Approach

    Energy Technology Data Exchange (ETDEWEB)

    Garcke, Harald, E-mail: harald.garcke@mathematik.uni-regensburg.de; Hecht, Claudia, E-mail: claudia.hecht@mathematik.uni-regensburg.de [Universität Regensburg, Fakultät für Mathematik (Germany)

    2016-02-15

    In this paper we introduce a new formulation for shape optimization problems in fluids in a diffuse interface setting that can in particular handle topological changes. By adding the Ginzburg–Landau energy as a regularization to the objective functional and relaxing the non-permeability outside the fluid region by introducing a porous medium approach we hence obtain a phase field problem where the existence of a minimizer can be guaranteed. This problem is additionally related to a sharp interface problem, where the permeability of the non-fluid region is zero. In both the sharp and the diffuse interface setting we can derive necessary optimality conditions using only the natural regularity of the minimizers. We also pass to the limit in the first order conditions.

  14. Genetic diversity and gene flow in the morphologically variable, rare endemics Begonia dregei and Begonia homonyma (Begoniaceae).

    Science.gov (United States)

    Matolweni, L O; Balkwill, K; McLellan, T

    2000-03-01

    Begonia dregei and B. homonyma (Begoniaceae), rare plants endemic to coastal forests of eastern South Africa, are two closely related species with high levels of variation among populations in the shape of leaves. Distribution of genetic variation and genetic relatedness were investigated in 12 populations of B. dregei and seven of B. homonyma using polyacrylamide gel electrophoresis. Twelve of the 15 enzyme loci examined were polymorphic, but only seven loci were polymorphic within at least one population. Genetic diversity measures indicated that the among-population gene differentiation represents >90% of the total genetic component in both species considered individually or combined. This indicated restricted gene flow, consistent with the limited dispersal abilities of Begonia generally and the ancient separation of isolated forest patches. Genetic distances among populations are much higher than usually found within species. Allozyme data provide no support for the recognition of B. dregei and B. homonyma as distinct species.

  15. Seepage flow behaviors of multi-stage fractured horizontal wells in arbitrary shaped shale gas reservoirs

    Science.gov (United States)

    Zhao, Yu-Long; Shan, Bao-Chao; Zhang, Lie-Hui; Liu, Qi-Guo

    2016-10-01

    The horizontal well incorporated with massive hydraulic fracturing has become a key and necessary technology to develop shale gas reservoirs efficiently, and transient pressure analysis is a practical method to evaluate the effectiveness of the fracturing. Until now, however, the related studies on the pressure of such wells have mainly focused on regular outer-boundaries, such as infinite, circular and rectangular boundary shapes, which do not always fulfill the practical conditions and, of course, could cause errors. By extending the boundary element method (BEM) into the application of multi-staged fractured horizontal wells, this paper presents a way of analyzing the transient pressure in arbitrary shaped shale gas reservoirs considering ad-/de-sorption and diffusion of the shale gas with the ‘tri-porosity’ mechanism model. The boundary integral equation can be obtained by coupling the fundamental solution of the Helmholtz equation with the dimensionless diffusivity equation. After discretizing the outer-boundaries and the fractures, the boundary integral equations are linearized and the coefficient matrix of the pressure on the boundaries is assembled, after which bottom-hole pressure can be calculated conveniently. Comparing the BEM solution with semi-analytical solution cases, the accuracy of the new solution can be validated. Then, the characteristic curves of the dimensionless pseudo pressure, as well as its derivative for a well in shale gas reservoirs, are drawn, based on which the parameters’ sensitivity analyses are also conducted. This paper not only enriches the well testing theory and method in shale gas reservoirs, but also provides an effective method to solve problems with complex inner- and outer-boundaries.

  16. A PLIC-VOF-Based Simulation of Water-Organic Slug Flow Characteristics in a T-Shaped Microchannel

    Directory of Open Access Journals (Sweden)

    Xian Wang

    2013-01-01

    Full Text Available A water-organic slug flow in a T-shaped microchannel was numerically studied due to its importance in the microreactor system. Various factors affecting the flow mode were studied, for example, channel width, fluid viscosity, interfacial tension, and inlet velocity. The volume of fluid (VOF method was used to track the liquid-liquid interface, and the piecewise-liner interface construction (PLIC technique was adopted to get a sharp interface. The interfacial tension was simulated with continuum surface force (CSF, model and the wall adhesion boundary condition was taken into consideration. The results show that strong vortexes appear in both phases at the meeting sites of main and lateral channels where an organic slug is producing. Inlet velocity influences the slug length and flow mode greatly. The ratio between the slug lengths of two phases in the main channel is almost equal to the ratio between their inlet velocities. If the slug is produced, the interfacial tension and organic viscosity have less effect on the slug length for 200 μm microchannel. The slug producing rate is much higher in a narrow channel than that in a wide channel.

  17. The role of ice dynamics in shaping vegetation in flowing waters.

    Science.gov (United States)

    Lind, Lovisa; Nilsson, Christer; Polvi, Lina E; Weber, Christine

    2014-11-01

    Ice dynamics is an important factor affecting vegetation in high-altitude and high-latitude streams and rivers. During the last few decades, knowledge about ice in streams and rivers has increased significantly and a respectable body of literature is now available. Here we review the literature on how ice dynamics influence riparian and aquatic vegetation. Traditionally, plant ecologists have focused their studies on the summer period, largely ignoring the fact that processes during winter also impact vegetation dynamics. For example, the freeze-up period in early winter may result in extensive formation of underwater ice that can restructure the channel, obstruct flow, and cause flooding and thus formation of more ice. In midwinter, slow-flowing reaches develop a surface-ice cover that accumulates snow, protecting habitats under the ice from formation of underwater ice but also reducing underwater light, thus suppressing photosynthesis. Towards the end of winter, ice breaks up and moves downstream. During this transport, ice floes can jam up and cause floods and major erosion. The magnitudes of the floods and their erosive power mainly depend on the size of the watercourse, also resulting in different degrees of disturbance to the vegetation. Vegetation responds both physically and physiologically to ice dynamics. Physical action involves the erosive force of moving ice and damage caused by ground frost, whereas physiological effects - mostly cell damage - happen as a result of plants freezing into the ice. On a community level, large magnitudes of ice dynamics seem to favour species richness, but can be detrimental for individual plants. Human impacts, such as flow regulation, channelisation, agriculturalisation and water pollution have modified ice dynamics; further changes are expected as a result of current and predicted future climate change. Human impacts and climate change can both favour and disfavour riverine vegetation dynamics. Restoration of streams

  18. Estimating exotic gene flow into native pine stands: zygotic vs. gametic components.

    Science.gov (United States)

    Unger, G M; Vendramin, G G; Robledo-Arnuncio, J J

    2014-11-01

    Monitoring contemporary gene flow from widespread exotic plantations is becoming an important problem in forest conservation genetics. In plants, where both seed and pollen disperse, three components of exotic gene flow with potentially unequal consequences should be, but have not been, explicitly distinguished: zygotic, male gametic and female gametic. Building on a previous model for estimating contemporary rates of zygotic and male gametic gene flow among plant populations, we present here an approach that additionally estimates the third (female gametic) gene flow component, based on a combination of uni- and biparentally inherited markers. Using this method and a combined set of chloroplast and nuclear microsatellites, we estimate gene flow rates from exotic plantations into two Iberian relict stands of maritime pine (Pinus pinaster) and Scots pine (Pinus sylvestris). Results show neither zygotic nor female gametic gene flow but moderate (6-8%) male gametic introgression for both species, implying significant dispersal of pollen, but not of seeds, from exotic plantations into native stands shortly after introduced trees reached reproductive maturity. Numerical simulation results suggest that the model yields reasonably accurate estimates for our empirical data sets, especially for larger samples. We discuss conservation management implications of observed levels of exposure to nonlocal genes and identify research needs to determine potentially associated hazards. Our approach should be useful for plant ecologists and ecosystem managers interested in the vectors of contemporary genetic connectivity among discrete plant populations.

  19. Examining the effect of pore size distribution and shape on flow through unsaturated peat using computed tomography

    Directory of Open Access Journals (Sweden)

    F. Rezanezhad

    2009-10-01

    Full Text Available The hydraulic conductivity of unsaturated peat soil is controlled by the air-filled porosity, pore size and geometric distribution as well as other physical properties of peat materials. This study investigates how the size and shape of pores affects the flow of water through peat soils. In this study we used X-ray Computed Tomography (CT, at 45 μm resolution under 5 specific soil-water pressure head levels to provide 3-D, high-resolution images that were used to detect the inner pore structure of peat samples under a changing water regime. Pore structure and configuration were found to be irregular, which affected the rate of water transmission through peat soils. The 3-D analysis suggested that pore distribution is dominated by a single large pore-space. At low pressure head, this single large air-filled pore imparted a more effective flowpath compared to smaller pores. Smaller pores were disconnected and the flowpath was more tortuous than in the single large air-filled pore, and their contribution to flow was negligible when the single large pore was active. We quantify the pore structure of peat soil that affects the hydraulic conductivity in the unsaturated condition, and demonstrate the validity of our estimation of peat unsaturated hydraulic conductivity by making a comparison with a standard permeameter-based method. Estimates of unsaturated hydraulic conductivities were made for the purpose of testing the sensitivity of pore shape and geometry parameters on the hydraulic properties of peats and how to evaluate the structure of the peat and its affects on parameterization. We also studied the ability to quantify these factors for different soil moisture contents in order to define how the factors controlling the shape coefficient vary with changes in soil water pressure head. The relation between measured and estimated unsaturated hydraulic conductivity at various heads shows that rapid initial drainage, that changes the air

  20. Distribution of coalescent histories under the coalescent model with gene flow.

    Science.gov (United States)

    Tian, Yuan; Kubatko, Laura S

    2016-12-01

    We propose a coalescent model for three species that allows gene flow between both pairs of sister populations. The model is designed for multilocus genomic sequence alignments, with one sequence sampled from each of the three species, and is formulated using a Markov chain representation that allows use of matrix exponentiation to compute analytical expressions for the probability density of coalescent histories. The coalescent history distribution as well as the gene tree topology distribution under this coalescent model with gene flow are then calculated via numerical integration. We analyze the model to compare the distributions of gene tree topologies and coalescent histories for species trees with differing effective population sizes and gene flow rates. Our results suggest conditions under which the species tree and associated parameters are not identifiable from the gene tree topology distribution when gene flow is present, but indicate that the coalescent history distribution may identify the species tree and associated parameters. Thus, the coalescent history distribution can be used to infer parameters such as the ancestral effective population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We conduct computer simulations to evaluate the performance of our method in estimating these parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 2015). Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Flow-less and shape-conformable CNT sheet nanogenerator for self-powered motion sensor.

    Science.gov (United States)

    Song, Hyelynn; Kim, Taewoo; Im, Hyeongwook; Ovalle-Robles, Raquel; Kang, Tae June; Kim, Yong Hyup

    2016-09-22

    A carbon nanotube (CNT) sheet nanogenerator that does not require any liquid or gas flow for power generation is developed on the basis of Coulombic interactions, making the device attractive as a building block for self-powered sensors. The working principle of the CNT nanogenerator is probed in terms of sweeping speed, distance between charged object and nanotube sheet, surface charge, and number of layers of nanotube sheet. The nature of the CNT sheet and its formation process is such that simply winding the CNT sheet stripe n times around a substrate leads to increasing the power n times. For a practical demonstration of the CNT nanogenerator, a self-powered sensor array screen is developed that can read finger movements, just as with a finger command on a smartphone screen.

  2. Measurement of radionuclides using ion chromatography and flow-cell scintillation counting with pulse shape discrimination

    Energy Technology Data Exchange (ETDEWEB)

    DeVol, T.A.; Fjeld, R.A. [Clemson Univ., Clemson, SC (United States)

    1995-10-01

    The use of ion chromatography (IC) for radiochemical separations is a well established technique. IC is commonly used in routine environmental monitoring applications as well as in specialized research applications. Typical usage involves the separation of a single radionuclide from the non-radioactive constituents. During the past decade, a limited amount of research has been conducted using automated IC systems in actinide separation applications (e.g.). More recently, separation procedures for common non-gamma emitting activation and fission products were developed utilizing a high performance liquid chromatography (HPLC) system. In addition, a separation procedure for six common actinides has been developed using a HPLC system. These latter systems used on-line flow-cell detectors for quantification of the radioactive constituents of the effluent stream.

  3. The Shape and Flow of Heavy Ion Collisions (490th Brookhaven Lecture)

    Energy Technology Data Exchange (ETDEWEB)

    Schenke, Bjoern [BNL Physics Department

    2014-12-18

    The sun can’t do it, but colossal machines like the Relativistic Heavy Ion Collider (RHIC) at Brookhaven Lab and Large Hadron Collider (LHC) in Europe sure can. Quarks and gluons make up protons and neutrons found in the nucleus of every atom in the universe. At heavy ion colliders like RHIC and the LHC, scientists can create matter more than 100,000 times hotter than the center of the sun—so hot that protons and neutrons melt into a plasma of quarks and gluons. The particle collisions and emerging quark-gluon plasma hold keys to understanding how these fundamental particles interact with each other, which helps explain how everything is held together—from atomic nuclei to human beings to the biggest stars—how all matter has mass, and what the universe looked like microseconds after the Big Bang. Dr. Schenke discusses theory that details the shape and structure of heavy ion collisions. He will also explain how this theory and data from experiments at RHIC and the LHC are being used to determine properties of the quark-gluon plasma.

  4. Self-recruitment and sweepstakes reproduction amid extensive gene flow in a coral-reef fish.

    Science.gov (United States)

    Christie, Mark R; Johnson, Darren W; Stallings, Christopher D; Hixon, Mark A

    2010-03-01

    Identifying patterns of larval dispersal within marine metapopulations is vital for effective fisheries management, appropriate marine reserve design, and conservation efforts. We employed genetic markers (microsatellites) to determine dispersal patterns in bicolour damselfish (Pomacentridae: Stegastes partitus). Tissue samples of 751 fish were collected in 2004 and 2005 from 11 sites encompassing the Exuma Sound, Bahamas. Bayesian parentage analysis identified two parent-offspring pairs, which is remarkable given the large population sizes and 28 day pelagic larval duration of bicolour damselfish. The two parent-offspring pairs directly documented self-recruitment at the two northern-most sites, one of which is a long-established marine reserve. Principal coordinates analyses of pair-wise relatedness values further indicated that self-recruitment was common in all sampled populations. Nevertheless, measures of genetic differentiation (F(ST)) and results from assignment methods suggested high levels of gene flow among populations. Comparisons of heterozygosity and relatedness among samples of adults and recruits indicated spatially and temporally independent sweepstakes events, whereby only a subset of adults successfully contribute to subsequent generations. These results indicate that self-recruitment and sweepstakes reproduction are the predominant, ecologically-relevant processes that shape patterns of larval dispersal in this system.

  5. Adaptation with gene flow across the landscape in a dune sunflower.

    Science.gov (United States)

    Andrew, Rose L; Ostevik, Katherine L; Ebert, Daniel P; Rieseberg, Loren H

    2012-05-01

    Isolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance (IBD) and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We have studied the divergence of Helianthus petiolaris ecotypes living in active sand dunes and adjacent non-dune habitat, using landscape genetics approaches, such as circuit theory and multiple regression of distance matrices, in addition to coalescent modelling. Divergence between habitats was significant, but not strong, and was shaped by IBD. We expected that increased resistance owing to patchy and unfavourable habitat in the dunes would contribute to divergence. Instead, we found that landscape resistance models with lower resistance in the dunes performed well as predictors of genetic distances among subpopulations. Nevertheless, habitat class remained a strong predictor of genetic distance when controlling for isolation by resistance and IBD. We also measured environmental variables at each site and confirmed that specific variables, especially soil nitrogen and vegetation cover, explained a greater proportion of variance in genetic distance than did landscape or the habitat classification alone. Asymmetry in effective population sizes and numbers of migrants per generation was detected using coalescent modelling with Bayesian inference, which is consistent with incipient ecological speciation being driven by the dune habitat.

  6. A Comparative Study of Fluid Flow and Mass Transfer in a Trumpet-Shaped Ladle Shroud Using Large Eddy Simulation

    Science.gov (United States)

    Zhang, Jiangshan; Li, Jingshe; Yan, Yi; Chen, Zhixin; Yang, Shufeng; Zhao, Jingwei; Jiang, Zhengyi

    2016-02-01

    The advantages of trumpet-shaped ladle shrouds (TLS) have been frequently demonstrated over conventional straight-bore ladle shrouds (CLS) with respect to production efficiency and molten steel quality in continuous casting practices. The present study is to shed some lights on why the TLS are better than the CLS design by examining the fluid dynamics and mass transfer using large eddy simulation. The obtained numerical results were validated with particle imaging velocimetry experiments. Flow velocity, deformation, turbulent energy dissipation, and mixing kinetics of tracer were discussed. The results showed that the entering jet of the CLS flowed straight down into the tundish with a relatively high speed (average at 0.710 to 0.815 m/s) and turbulent kinetic energy. However, the trumpet section of a TLS intensified velocity differences, strain rates, and vortices, and promoted an increase on turbulence dissipation rate in the interior of the ladle shroud. The average speed of the entering jet to the tundish was decreased to 0.270 to 0.410 m/s from the 0.708 m/s of the inlet speed. The entering jet from the TLS swung, twisted and well mixed with surrounding fluid in the tundish, and dissipated its kinetic energy. Consequently, the turbulence of the whole flow field as well as the mean skin friction coefficient of tundish wall and the velocity of free liquid surface were reduced. A tracer experiment was carried out to study mass transfer and flow mixing behavior, and the results demonstrated that the use of the TLS increased the plug volume and decreased the dead zone, thereby enhancing inclusion flotation.

  7. The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis

    DEFF Research Database (Denmark)

    Vroemen, Casper W; Mordhorst, Andreas P; Albrecht, Cathy

    2003-01-01

    From an enhancer trap screen for genes expressed in Arabidopsis embryos, we identified a gene expressed from the octant stage onward in the boundary between the two presumptive cotyledons and in a variety of postembryonic organ and meristem boundaries. This gene, CUP-SHAPED COTYLEDON3 (CUC3......), encodes a putative NAC-domain transcription factor that is homologous with CUC1 and CUC2. Analysis of a CUC3 hypomorph and a putative cuc3 null mutant indicates that CUC3 function is partially redundant with that of CUC1 and CUC2 in the establishment of the cotyledon boundary and the shoot meristem, thus...... revealing an even higher degree of redundancy in this class of genes than was thought previously. The CUC3 expression pattern, the cuc3 phenotypes, and CUC3 expression in a series of shoot meristem mutants and transgenes suggest a primary role for CUC3 in the establishment of boundaries that contain cells...

  8. Minimally destructive, Doppler measurement of a quantized flow in a ring-shaped Bose-Einstein condensate

    Science.gov (United States)

    Kumar, A.; Anderson, N.; Phillips, W. D.; Eckel, S.; Campbell, G. K.; Stringari, S.

    2016-02-01

    The Doppler effect, the shift in the frequency of sound due to motion, is present in both classical gases and quantum superfluids. Here, we perform an in situ, minimally destructive measurement, of the persistent current in a ring-shaped, superfluid Bose-Einstein condensate using the Doppler effect. Phonon modes generated in this condensate have their frequencies Doppler shifted by a persistent current. This frequency shift will cause a standing-wave phonon mode to be ‘dragged’ along with the persistent current. By measuring this precession, one can extract the background flow velocity. This technique will find utility in experiments where the winding number is important, such as in emerging ‘atomtronic’ devices.

  9. Silica nanowire conjugated with loop-shaped oligonucleotides: A new structure to silence cysteine proteinase gene in Leishmania tropica.

    Science.gov (United States)

    Bafghi, Ali Fatahi; Jebali, Ali; Daliri, Karim

    2015-12-01

    The main aim of this study was to evaluate the capability of silica nanowire conjugated with loop-shaped oligonucleotides (SNWCLSOs) to silence cysteine proteinase b (Cpb) gene in Leishmania (L) tropica. On the other hand, its toxicity on amastigotes and mouse peritoneal macrophages was evaluated by 5-diphenyl-tetrazolium bromide (MTT) assay. For control, two loop-shaped oligonucleotides (LSO) were considered. LSO1 and LSO2 were 5'-NH2-cccccaaaaaaaaaaaaaaaaaaaaaaaaaggggg-COOH-3' and LSO2: 5'-NH2-cccccttttttttttttttttttttttttttttttttttttttggggg-COOH-3', respectively. After 72 h incubation at 37 °C, AMSNW, LSO1, and LSO2 had no remarkable toxicity on L. tropica amastigote (2 × 10(5)/mL) and mouse peritoneal macrophages (2 × 10(5)/mL). In case of SNWCLSOs, they had high toxicity on L. tropica amastigote, but they had no effect on mouse peritoneal macrophages. At concentrations of 1, 10, and 25 μg/mL, AMSNW, LSO1 and LSO2 had no effect on the gene expression. But, at concentration of 50 and 100 μg/mL, decrease of gene expression was observed. In case of SNWCLSOs, they could dramatically decrease the gene expression. It could be concluded that since SNWCLSOs could silence Cpb gene with no remarkable toxicity, they are good choice for treat cutaneous leishmaniasis in future. As a new agent, it must be checked in vivo.

  10. Segmentation gene expression patterns in Bactrocera dorsalis and related insects: regulation and shape of blastoderm and larval cuticle.

    Science.gov (United States)

    Suksuwan, Worramin; Cai, Xiaoli; Ngernsiri, Lertluk; Baumgartner, Stefan

    2017-01-01

    The oriental fruit fly, Bactrocera dorsalis, is regarded as a severe pest of fruit production in Asia. Despite its economic importance, only limited information regarding the molecular and developmental biology of this insect is known to date. We provide a detailed analysis of B. dorsalis embryology, as well as the expression patterns of a number of segmentation genes known to act during patterning of Drosophila and compare these to the patterns of other insect families. An anterior shift of the expression of gap genes was detected when compared to Drosophila. This shift was largely restored during the step where the gap genes control expression of the pair-rule genes. We analyzed and compared the shapes of the embryos of insects of different families, B. dorsalis and the blow fly Lucilia sericata with that of the well-characterized Drosophila melanogaster. We found distinct shapes as well as differences in the ratios of the length of the anterior-posterior axis and the dorsal-ventral axis. These features were integrated into a profile of how the expression patterns of the gap gene Krüppel and the pair-rule gene even-skipped were observed along the A-P axis in three insects families. Since significant differences were observed, we discuss how Krüppel controls the even-skipped stripes. Furthermore, we discuss how the position and angles of the segmentation gene stripes differed from other insects. Finally, we analyzed the outcome of the expression patterns of the late acting segment polarity genes in relation to the anlagen of the naked-cuticle and denticle belt area of the B. dorsalis larva.

  11. Methane source strength and energy flow shape methanotrophic communities in oxygen-methane counter-gradients.

    Science.gov (United States)

    Krause, Sascha; Lüke, Claudia; Frenzel, Peter

    2012-04-01

    The role of microbial diversity for ecosystem functioning has become an important subject in microbial ecology. Recent work indicates that microbial communities and microbial processes can be very sensitive to anthropogenic disturbances. However, to what extent microbial communities may change upon, resist to, or overcome disturbances might differ depending on substrate availability. We used soil from an Italian rice field in gradient microcosms, and analysed the response of methanotrophic communities to an NH4 (+) pulse as a potential disturbance under two different CH4 source strengths. We found a significant influence of source strength, i.e. the energy flow through the methanotrophic community, while NH4 (+) had no effect. Our data suggest that historical contingencies, i.e. nitrogen fertilization, led to an ammonium-tolerant MOB community. Methanotrophs were able to oxidize virtually all CH4 diffusing into the oxic-anoxic boundary layer regardless of NH4 (+) addition. Total and active methanotrophic communities were assessed by a pmoA-specific microarray. From the reservoir of dormant methanotrophs, different species became active with Methylobacter and an environmental cluster affiliated with paddy soils being indicative for high CH4 source strength. Thus, a microbial seed bank is an important prerequisite to maintain functioning in a fluctuating environment.

  12. 3-D simulation of transient flow patterns in a corridor-shaped air-cushion surge chamber based on computational fluid dynamics

    Institute of Scientific and Technical Information of China (English)

    XIA Lin-sheng; CHENG Yong-guang; ZHOU Da-qing

    2013-01-01

    The 3-D characteristics of the water-air flow patterns in a corridor-shaped air-cushion surge chamber during hydraulic transients need to be considered in the shape optimization.To verify the reliability of the water-air two-phase model,namely,the volume of fluid model,the process of charging water into a closed air chamber is successfully simulated.Using the model,the 3-D flow characteristics under the load rejection and acceptance conditions within the air-cushion surge chamber of a specific hydropower station are studied.The flee surface waves,the flow patterns,and the pressure changes during the surge wave process are analyzed in detail.The longitudinal flow of water in the long corridor-shaped surge chamber is similar to the open channel flow with respect to the wave propagation,reflection and superposition characteristics.The lumped parameters of the 3-D numerical simulation agree with the results of a 1-D calculation of hydraulic transients in the whole water conveying system,which validates the 3-D method.The 3-D flow structures obtained can be applied to the shape optimization of the chamber.

  13. The strength of intron donor splice sites in human genes displays a bell-shaped pattern

    DEFF Research Database (Denmark)

    Wang, Kai; Wernersson, Rasmus; Brunak, Søren

    2011-01-01

    MOTIVATION: The gene concept has recently changed from the classical one protein notion into a much more diverse picture, where overlapping or fused transcripts, alternative transcription initiation, and genes within genes, add to the complexity generated by alternative splicing. Increased...... understanding of the mechanisms controlling pre-mRNA splicing is thus important for a wide range of aspects relating to gene expression. RESULTS: We have discovered a convex gene delineating pattern in the strength of 5' intron splice sites. When comparing the strengths of >18 000 intron containing Human genes......, we found that when analysing them separately according to the number of introns they contain, initial splice sites were always stronger on average than subsequent ones, and that a similar reversed trend exist towards the terminal gene part. The convex pattern is strongest for genes with up to 10...

  14. Gene Flow and the Measurement of Dispersal in Plant Populations.

    Science.gov (United States)

    Nicholls, Marc S.

    1986-01-01

    Reviews methods of estimating pollen and seed dispersals and discusses the extent and frequency of gene exchange within and between populations. Offers suggestions for designing exercises suitable for estimating dispersal distances in natural plant populations. (ML)

  15. Gene flow and herbicide resistance: Lessons learned from herbicide-resistant rice systems

    Science.gov (United States)

    Gene flow in plants is a process whereby genes are exchanged between members of the same or closely related species via pollen and become established in new populations. This natural process has long been an issue in breeding and the seed industry, but interest has increased since the deployment of ...

  16. Patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in the United States

    Science.gov (United States)

    Studies of gene flow between crops and their wild relatives have implications for both management practices for farming and breeding as well as understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene...

  17. Transient stability and control of wind turbine generation based on Hamiltonian surface shaping and power flow control

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, David G.; Robinett, Rush D. III [Sandia National Laboratories, Albuquerque, NM (United States). Energy, Resources and Systems Analysis Center

    2010-07-01

    The swing equations for renewable generators connected to the grid are developed and a simple wind turbine with UPFC is used as an example. The swing equations for renewable generator are formulated as a natural Hamiltonian system with externally applied non-conservative forces. A two-step process referred to as Hamiltonian Surface Shaping and Power Flow Control (HSSPFC) is used to analyze and design feedback controllers for the renewable generators system. This formulation extends previous results on the analytical verification of the Potential Energy Boundary Surface (PEBS) method to nonlinear control analysis and design and justifies the decomposition of the system into conservative and nonconservative systems to enable a two-step, serial analysis and design procedure. This paper presents the analysis and numerical simulation results for a nonlinear control design example that includes the One-Machine Infinite Bus (OMIB) system with a Unified Power Flow Control (UPEC) and applied to a simplified wind turbine generator. The needed power and energy storage/charging responses are also determined. (orig.)

  18. Y-linked variation for autosomal immune gene regulation has the potential to shape sexually dimorphic immunity.

    Science.gov (United States)

    Kutch, Ian C; Fedorka, Kenneth M

    2015-12-01

    Sexually dimorphic phenotypes arise from the differential expression of male and female shared genes throughout the genome. Unfortunately, the underlying molecular mechanisms by which dimorphic regulation manifests and evolves are unclear. Recent work suggests that Y-chromosomes may play an important role, given that Drosophila melanogaster Ys were shown to influence the regulation of hundreds of X and autosomal genes. For Y-linked regulatory variation (YRV) to facilitate sexually dimorphic evolution, however, it must exist within populations (where selection operates) and influence male fitness. These criteria have seldom been investigated, leaving the potential for dimorphic evolution via YRV unclear. Interestingly, male and female D. melanogaster differ in immune gene regulation. Furthermore, immune gene regulation appears to be influenced by the Y-chromosome, suggesting it may contribute to dimorphic immune evolution. We address this possibility by introgressing Y-chromosomes from a single wild population into an isogenic background (to create Y-lines) and assessing immune gene regulation and bacterial defence. We found that Y-line males differed in their immune gene regulation and their ability to defend against Serratia marcescens. Moreover, gene expression and bacterial defence were positively genetically correlated. These data indicate that the Y-chromosome has the potential to shape the evolution of sexually dimorphic immunity in this system.

  19. Large-eddy simulation of turbulent flow and structures in a square duct roughened with perpendicular and V-shaped ribs

    Science.gov (United States)

    Fang, Xingjun; Yang, Zixuan; Wang, Bing-Chen; Tachie, Mark F.; Bergstrom, Donald J.

    2017-06-01

    In this paper, highly disturbed turbulent flows confined within a square duct with uniformly spaced V-shaped ribs mounted on one wall are investigated using large-eddy simulation (LES). Two V-shaped (6 0° and 4 5°) rib cases are studied in comparison with the perpendicular (9 0°) rib case. The LES results are validated against a set of water-channel measurement data newly acquired by the authors. The effects of different shaped ribs on turbulent flow are systematically studied in terms of the mean velocity field, turbulence statistics, and coherent structures. The results show that strong secondary flows in the pattern of a pair of large symmetrical streamwise-elongated vortices exist in all three rib cases. The impacts of rib geometry on turbulent coherent structures are investigated using vortex identifiers, temporal autocorrections, spatial two-point autocorrelations, and velocity spectra.

  20. Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes.

    Science.gov (United States)

    Couturier, Etienne; Rocha, Eduardo P C

    2006-03-01

    The bidirectional replication of bacterial genomes leads to transient gene dosage effects. Here, we show that such effects shape the chromosome organisation of fast-growing bacteria and that they correlate strongly with maximal growth rate. Surprisingly the predicted maximal number of replication rounds shows little if any phylogenetic inertia, suggesting that it is a very labile trait. Yet, a combination of theoretical and statistical analyses predicts that dozens of replication forks may be simultaneously present in the cells of certain species. This suggests a strikingly efficient management of the replication apparatus, of replication fork arrests and of chromosome segregation in such cells. Gene dosage effects strongly constrain the position of genes involved in translation and transcription, but not other highly expressed genes. The relative proximity of the former genes to the origin of replication follows the regulatory dependencies observed under exponential growth, as the bias is stronger for RNA polymerase, then rDNA, then ribosomal proteins and tDNA. Within tDNAs we find that only the positions of the previously proposed 'ubiquitous' tRNA, which translate the most frequent codons in highly expressed genes, show strong signs of selection for gene dosage effects. Finally, we provide evidence for selection acting upon genome organisation to take advantage of gene dosage effects by identifying a positive correlation between genome stability and the number of simultaneous replication rounds. We also show that gene dosage effects can explain the over-representation of highly expressed genes in the largest replichore of genomes containing more than one chromosome. Together, these results demonstrate that replication-associated gene dosage is an important determinant of chromosome organisation and dynamics, especially among fast-growing bacteria.

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

    Science.gov (United States)

    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

    2014-12-01

    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 1.59 million 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 = 3.36 × 10(-9) to 1.20 × 10(-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.

  2. Long distance pollen-mediated flow of herbicide resistance genes in Lolium rigidum.

    Science.gov (United States)

    Busi, Roberto; Yu, Qin; Barrett-Lennard, Robert; Powles, Stephen

    2008-11-01

    Gene flow promotes genetic exchange among plant populations mediating evolutionary dynamics; yet, the importance of gene flow at distance via pollen movement is poorly understood. A field experiment at the landscape level was conducted with Lolium rigidum herbicide-susceptible individuals (population VLR1) placed into an otherwise Lolium-free bushland environment at increasing distances from adjacent large commercial crop fields infested with herbicide-resistant L. rigidum. Herbicide resistance was used as a marker to quantify the distance and the rate of pollen-mediated gene flow. About 21,245 seeds were produced on the isolated, susceptible mother plants of which 3,303 seedlings were tested for herbicide resistance and 664 seedlings were found to be resistant. Pollen-mediated gene flow occurred at 3,000 m (maximum tested distance). Both Mendelian and molecular analyses (sequencing and CAPS markers) confirmed the introgression of herbicide resistance genes. This is the first documented case of long-distance gene flow in L. rigidum. The results are important for future modeling simulations of herbicide resistance evolution and subsequent mobility. The adoption of integrated agronomic strategies, the control of potential receptor plants on fields' margins and conservative use of herbicides can be realistic options to minimize herbicide resistance spread.

  3. 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.

  4. Event shape engineering for inclusive spectra and elliptic flow in Pb-Pb collisions at $\\sqrt{s_\\rm{NN}}=2.76$ TeV

    OpenAIRE

    Adam, Jaroslav; Adamova, Dagmar; Ajaz, Muhammad; Bilandzic, Ante; Biswas, Rathijit; Biswas, Saikat; Bjelogrlic, Sandro; Blair, Justin Thomas; Blanco, Fernando; Blau, Dmitry; Blume, Christoph; Bock, Friederike; Bogdanov, Alexey; Akindinov, Alexander; Boggild, Hans

    2016-01-01

    We report on results obtained with the event-shape engineering technique applied to Pb-Pb collisions at sNN=2.76 TeV. By selecting events in the same centrality interval, but with very different average flow, different initial-state conditions can be studied. We find the effect of the event-shape selection on the elliptic flow coefficient v2 to be almost independent of transverse momentum pT, which is as expected if this effect is attributable to fluctuations in the initial geometry of the sy...

  5. Event shape engineering for inclusive spectra and elliptic flow in Pb-Pb collisions at $\\sqrt{s_\\rm{NN}}=2.76$ TeV

    OpenAIRE

    Adam; Adamová,, D.; Aggarwal,, M.M.; Aglieri, Rinella, G.; Dell'Agnello,; Agrawal; Ahammed,, Z.; Ahn; Aimo; Aiola,, S.; Ajaz,, M.; Akindinov,, A.; Alam, MR; Aleksandrov,, D.; Alessandro

    2015-01-01

    We report on results obtained with the Event Shape Engineering technique applied to Pb-Pb collisions at $\\sqrt{s_\\rm{NN}}=2.76$ TeV. By selecting events in the same centrality interval, but with very different average flow, different initial state conditions can be studied. We find the effect of the event-shape selection on the elliptic flow coefficient $v_2$ to be almost independent of transverse momentum $p_\\rm{T}$, as expected if this effect is due to fluctuations in the initial geometry o...

  6. Cell type-specific properties and environment shape tissue specificity of cancer genes.

    Science.gov (United States)

    Schaefer, Martin H; Serrano, Luis

    2016-02-09

    One of the biggest mysteries in cancer research remains why mutations in certain genes cause cancer only at specific sites in the human body. The poor correlation between the expression level of a cancer gene and the tissues in which it causes malignant transformations raises the question of which factors determine the tissue-specific effects of a mutation. Here, we explore why some cancer genes are associated only with few different cancer types (i.e., are specific), while others are found mutated in a large number of different types of cancer (i.e., are general). We do so by contrasting cellular functions of specific-cancer genes with those of general ones to identify properties that determine where in the body a gene mutation is causing malignant transformations. We identified different groups of cancer genes that did not behave as expected (i.e., DNA repair genes being tissue specific, immune response genes showing a bimodal specificity function or strong association of generally expressed genes to particular cancers). Analysis of these three groups demonstrates the importance of environmental impact for understanding why certain cancer genes are only involved in the development of some cancer types but are rarely found mutated in other types of cancer.

  7. Star-shaped copolymer grafted PEI and REDV as a gene carrier to improve migration of endothelial cells.

    Science.gov (United States)

    Lv, Juan; Hao, Xuefang; Li, Qian; Akpanyung, Mary; Nejjari, Abdelilah; Neve, Agnaldo Luis; Ren, Xiangkui; Feng, Yakai; Shi, Changcan; Zhang, Wencheng

    2017-01-17

    In this work, a biodegradable star-shaped copolymer poly(lactide-co-3(S)-methyl-morpholine-2,5-dione)6 (Star-(PLMD)6) was synthesized via ring-opening polymerization (ROP), and subsequently a gene carrier Star-PLMD-g-PEI-g-PEG-CREDVW was prepared by grafting polyethyleneimine (PEI), polyethylene glycol (PEG) and targeting peptide REDV onto Star-(PLMD)6. This gene carrier could form stable micelles to condense pEGFP-ZNF580 through electrostatic interaction. The resulting complexes were biocompatible and showed high efficiency in gene delivery. In addition, these complexes exhibited high selectivity for endothelial cells (ECs), high transfection efficiency and enhanced migration of ECs. The protein level of ZNF580 expression was significantly high (up to 85%), while the control group was only 51%. This combination of degradability, targeting ligand and star-structure strategy exhibits a significant advantage in transfection efficiency and migration of ECs.

  8. Experimental study on scour and flow field in a scour hole around a T-shape spur dike in a 90° bend

    Institute of Scientific and Technical Information of China (English)

    Masoud GHODSIAN; Mohammad VAGHEFI

    2009-01-01

    In this paper results of experimental study on scour and flow field around a T-shape spur dike in a 90 degree channel bend are presented. Experiments were conducted in a laboratory channel to measure the variations of bed topography under a clear water condition. The three dimensional flow field was measured by an Acoustic Doppler Velocimeter in a scour hole due to a T-shape spur dike. It was found that by increasing the Froude number and length of spur dike the amount of scour increases.Increasing the wing length of spur dike decreases the scour, The amount of scour at the upstream of spur dike is much more as compare to that at the downstream of spur dike. By increasing the wing length of spur dike the zone of flow separation expands. As a result the sizes of vortex increase.Details of flow field are also addressed in the paper.

  9. Event shape engineering for inclusive spectra and elliptic flow in Pb-Pb collisions at $\\sqrt{s_\\rm{NN}}=2.76$ TeV

    CERN Document Server

    Adam, Jaroslav; Aggarwal, Madan Mohan; Aglieri Rinella, Gianluca; Agnello, Michelangelo; Agrawal, Neelima; Ahammed, Zubayer; Ahn, Sang Un; Aimo, Ilaria; Aiola, Salvatore; Ajaz, Muhammad; Akindinov, Alexander; Alam, Sk Noor; Aleksandrov, Dmitry; Alessandro, Bruno; Alexandre, Didier; Alfaro Molina, Jose Ruben; Alici, Andrea; Alkin, Anton; Millan Almaraz, Jesus Roberto; Alme, Johan; Alt, Torsten; Altinpinar, Sedat; Altsybeev, Igor; Alves Garcia Prado, Caio; Andrei, Cristian; Andronic, Anton; Anguelov, Venelin; Anielski, Jonas; Anticic, Tome; Antinori, Federico; Antonioli, Pietro; Aphecetche, Laurent Bernard; Appelshaeuser, Harald; Arcelli, Silvia; Armesto Perez, Nestor; Arnaldi, Roberta; Arsene, Ionut Cristian; Arslandok, Mesut; Audurier, Benjamin; Augustinus, Andre; Averbeck, Ralf Peter; Azmi, Mohd Danish; Bach, Matthias Jakob; Badala, Angela; Baek, Yong Wook; Bagnasco, Stefano; Bailhache, Raphaelle Marie; Bala, Renu; Baldisseri, Alberto; Baltasar Dos Santos Pedrosa, Fernando; Baral, Rama Chandra; Barbano, Anastasia Maria; Barbera, Roberto; Barile, Francesco; Barnafoldi, Gergely Gabor; Barnby, Lee Stuart; Ramillien Barret, Valerie; Bartalini, Paolo; Barth, Klaus; Bartke, Jerzy Gustaw; Bartsch, Esther; Basile, Maurizio; Bastid, Nicole; Basu, Sumit; Bathen, Bastian; Batigne, Guillaume; Batista Camejo, Arianna; Batyunya, Boris; Batzing, Paul Christoph; Bearden, Ian Gardner; Beck, Hans; Bedda, Cristina; Behera, Nirbhay Kumar; Belikov, Iouri; Bellini, Francesca; Bello Martinez, Hector; Bellwied, Rene; Belmont Iii, Ronald John; Belmont Moreno, Ernesto; Belyaev, Vladimir; Bencedi, Gyula; Beole, Stefania; Berceanu, Ionela; Bercuci, Alexandru; Berdnikov, Yaroslav; Berenyi, Daniel; Bertens, Redmer Alexander; Berzano, Dario; Betev, Latchezar; Bhasin, Anju; Bhat, Inayat Rasool; Bhati, Ashok Kumar; Bhattacharjee, Buddhadeb; Bhom, Jihyun; Bianchi, Livio; Bianchi, Nicola; Bianchin, Chiara; Bielcik, Jaroslav; Bielcikova, Jana; Bilandzic, Ante; Biswas, Rathijit; Biswas, Saikat; Bjelogrlic, Sandro; Blair, Justin Thomas; Blanco, Fernando; Blau, Dmitry; Blume, Christoph; Bock, Friederike; Bogdanov, Alexey; Boggild, Hans; Boldizsar, Laszlo; Bombara, Marek; Book, Julian Heinz; Borel, Herve; Borissov, Alexander; Borri, Marcello; Bossu, Francesco; Botta, Elena; Boettger, Stefan; Braun-Munzinger, Peter; Bregant, Marco; Breitner, Timo Gunther; Broker, Theo Alexander; Browning, Tyler Allen; Broz, Michal; Brucken, Erik Jens; Bruna, Elena; Bruno, Giuseppe Eugenio; Budnikov, Dmitry; Buesching, Henner; Bufalino, Stefania; Buncic, Predrag; Busch, Oliver; Buthelezi, Edith Zinhle; Bashir Butt, Jamila; Buxton, Jesse Thomas; Caffarri, Davide; Cai, Xu; Caines, Helen Louise; Calero Diaz, Liliet; Caliva, Alberto; Calvo Villar, Ernesto; Camerini, Paolo; Carena, Francesco; Carena, Wisla; Carnesecchi, Francesca; Castillo Castellanos, Javier Ernesto; Castro, Andrew John; Casula, Ester Anna Rita; Cavicchioli, Costanza; Ceballos Sanchez, Cesar; Cepila, Jan; Cerello, Piergiorgio; Cerkala, Jakub; Chang, Beomsu; Chapeland, Sylvain; Chartier, Marielle; Charvet, Jean-Luc Fernand; Chattopadhyay, Subhasis; Chattopadhyay, Sukalyan; Chelnokov, Volodymyr; Cherney, Michael Gerard; Cheshkov, Cvetan Valeriev; Cheynis, Brigitte; Chibante Barroso, Vasco Miguel; Dobrigkeit Chinellato, David; Chochula, Peter; Choi, Kyungeon; Chojnacki, Marek; Choudhury, Subikash; Christakoglou, Panagiotis; Christensen, Christian Holm; Christiansen, Peter; Chujo, Tatsuya; Chung, Suh-Urk; Zhang, Chunhui; Cicalo, Corrado; Cifarelli, Luisa; Cindolo, Federico; Cleymans, Jean Willy Andre; Colamaria, Fabio Filippo; Colella, Domenico; Collu, Alberto; Colocci, Manuel; Conesa Balbastre, Gustavo; Conesa Del Valle, Zaida; Connors, Megan Elizabeth; Contreras Nuno, Jesus Guillermo; Cormier, Thomas Michael; Corrales Morales, Yasser; Cortes Maldonado, Ismael; Cortese, Pietro; Cosentino, Mauro Rogerio; Costa, Filippo; Crochet, Philippe; Cruz Albino, Rigoberto; Cuautle Flores, Eleazar; Cunqueiro Mendez, Leticia; Dahms, Torsten; Dainese, Andrea; Danu, Andrea; Das, Debasish; Das, Indranil; Das, Supriya; Dash, Ajay Kumar; Dash, Sadhana; De, Sudipan; De Caro, Annalisa; De Cataldo, Giacinto; De Cuveland, Jan; De Falco, Alessandro; De Gruttola, Daniele; De Marco, Nora; De Pasquale, Salvatore; Deisting, Alexander; Deloff, Andrzej; Denes, Ervin Sandor; D'Erasmo, Ginevra; Di Bari, Domenico; Di Mauro, Antonio; Di Nezza, Pasquale; Diaz Corchero, Miguel Angel; Dietel, Thomas; Dillenseger, Pascal; Divia, Roberto; Djuvsland, Oeystein; Dobrin, Alexandru Florin; Dobrowolski, Tadeusz Antoni; Domenicis Gimenez, Diogenes; Donigus, Benjamin; Dordic, Olja; Drozhzhova, Tatiana; Dubey, Anand Kumar; Dubla, Andrea; Ducroux, Laurent; Dupieux, Pascal; Ehlers Iii, Raymond James; Elia, Domenico; Engel, Heiko; Erazmus, Barbara Ewa; Erdemir, Irem; Erhardt, Filip; Eschweiler, Dominic; Espagnon, Bruno; Estienne, Magali Danielle; Esumi, Shinichi; Eum, Jongsik; Evans, David; Evdokimov, Sergey; Eyyubova, Gyulnara; Fabbietti, Laura; Fabris, Daniela; Faivre, Julien; Fantoni, Alessandra; Fasel, Markus; Feldkamp, Linus; Felea, Daniel; Feliciello, Alessandro; Feofilov, Grigorii; Ferencei, Jozef; Fernandez Tellez, Arturo; Gonzalez Ferreiro, Elena; Ferretti, Alessandro; Festanti, Andrea; Feuillard, Victor Jose Gaston; Figiel, Jan; Araujo Silva Figueredo, Marcel; Filchagin, Sergey; Finogeev, Dmitry; Fionda, Fiorella; Fiore, Enrichetta Maria; Fleck, Martin Gabriel; Floris, Michele; Foertsch, Siegfried Valentin; Foka, Panagiota; Fokin, Sergey; Fragiacomo, Enrico; Francescon, Andrea; Frankenfeld, Ulrich Michael; Fuchs, Ulrich; Furget, Christophe; Furs, Artur; Fusco Girard, Mario; Gaardhoeje, Jens Joergen; Gagliardi, Martino; Gago Medina, Alberto Martin; Gallio, Mauro; Gangadharan, Dhevan Raja; Ganoti, Paraskevi; Gao, Chaosong; Garabatos Cuadrado, Jose; Garcia-Solis, Edmundo Javier; Gargiulo, Corrado; Gasik, Piotr Jan; Germain, Marie; Gheata, Andrei George; Gheata, Mihaela; Ghosh, Premomoy; Ghosh, Sanjay Kumar; Gianotti, Paola; Giubellino, Paolo; Giubilato, Piero; Gladysz-Dziadus, Ewa; Glassel, Peter; Gomez Coral, Diego Mauricio; Gomez Ramirez, Andres; Gonzalez Zamora, Pedro; Gorbunov, Sergey; Gorlich, Lidia Maria; Gotovac, Sven; Grabski, Varlen; Graczykowski, Lukasz Kamil; Graham, Katie Leanne; Grelli, Alessandro; Grigoras, Alina Gabriela; Grigoras, Costin; Grigoryev, Vladislav; Grigoryan, Ara; Grigoryan, Smbat; Grynyov, Borys; Grion, Nevio; Grosse-Oetringhaus, Jan Fiete; Grossiord, Jean-Yves; Grosso, Raffaele; Guber, Fedor; Guernane, Rachid; Guerzoni, Barbara; Gulbrandsen, Kristjan Herlache; Gulkanyan, Hrant; Gunji, Taku; Gupta, Anik; Gupta, Ramni; Haake, Rudiger; Haaland, Oystein Senneset; Hadjidakis, Cynthia Marie; Haiduc, Maria; Hamagaki, Hideki; Hamar, Gergoe; Hansen, Alexander; Harris, John William; Hartmann, Helvi; Harton, Austin Vincent; Hatzifotiadou, Despina; Hayashi, Shinichi; Heckel, Stefan Thomas; Heide, Markus Ansgar; Helstrup, Haavard; Herghelegiu, Andrei Ionut; Herrera Corral, Gerardo Antonio; Hess, Benjamin Andreas; Hetland, Kristin Fanebust; Hilden, Timo Eero; Hillemanns, Hartmut; Hippolyte, Boris; Hosokawa, Ritsuya; Hristov, Peter Zahariev; Huang, Meidana; Humanic, Thomas; Hussain, Nur; Hussain, Tahir; Hutter, Dirk; Hwang, Dae Sung; Ilkaev, Radiy; Ilkiv, Iryna; Inaba, Motoi; Ippolitov, Mikhail; Irfan, Muhammad; Ivanov, Marian; Ivanov, Vladimir; Izucheev, Vladimir; Jacobs, Peter Martin; Jadlovska, Slavka; Jahnke, Cristiane; Jang, Haeng Jin; Janik, Malgorzata Anna; Pahula Hewage, Sandun; Jena, Chitrasen; Jena, Satyajit; Jimenez Bustamante, Raul Tonatiuh; Jones, Peter Graham; Jung, Hyungtaik; Jusko, Anton; Kalinak, Peter; Kalweit, Alexander Philipp; Kamin, Jason Adrian; Kang, Ju Hwan; Kaplin, Vladimir; Kar, Somnath; Karasu Uysal, Ayben; Karavichev, Oleg; Karavicheva, Tatiana; Karayan, Lilit; Karpechev, Evgeny; Kebschull, Udo Wolfgang; Keidel, Ralf; Keijdener, Darius Laurens; Keil, Markus; Khan, Kamal; Khan, Mohammed Mohisin; Khan, Palash; Khan, Shuaib Ahmad; Khanzadeev, Alexei; Kharlov, Yury; Kileng, Bjarte; Kim, Beomkyu; Kim, Do Won; Kim, Dong Jo; Kim, Hyeonjoong; Kim, Jinsook; Kim, Mimae; Kim, Minwoo; Kim, Se Yong; Kim, Taesoo; Kirsch, Stefan; Kisel, Ivan; Kiselev, Sergey; Kisiel, Adam Ryszard; Kiss, Gabor; Klay, Jennifer Lynn; Klein, Carsten; Klein, Jochen; Klein-Boesing, Christian; Kluge, Alexander; Knichel, Michael Linus; Knospe, Anders Garritt; Kobayashi, Taiyo; Kobdaj, Chinorat; Kofarago, Monika; Kollegger, Thorsten; Kolozhvari, Anatoly; Kondratev, Valerii; Kondratyeva, Natalia; Kondratyuk, Evgeny; Konevskikh, Artem; Kopcik, Michal; Kour, Mandeep; Kouzinopoulos, Charalampos; Kovalenko, Oleksandr; Kovalenko, Vladimir; Kowalski, Marek; Koyithatta Meethaleveedu, Greeshma; Kral, Jiri; Kralik, Ivan; Kravcakova, Adela; Kretz, Matthias; Krivda, Marian; Krizek, Filip; Kryshen, Evgeny; Krzewicki, Mikolaj; Kubera, Andrew Michael; Kucera, Vit; Kugathasan, Thanushan; Kuhn, Christian Claude; Kuijer, Paulus Gerardus; Kumar, Ajay; Kumar, Jitendra; Lokesh, Kumar; Kurashvili, Podist; Kurepin, Alexander; Kurepin, Alexey; Kuryakin, Alexey; Kushpil, Svetlana; Kweon, Min Jung; Kwon, Youngil; La Pointe, Sarah Louise; La Rocca, Paola; Lagana Fernandes, Caio; Lakomov, Igor; Langoy, Rune; Lara Martinez, Camilo Ernesto; Lardeux, Antoine Xavier; Lattuca, Alessandra; Laudi, Elisa; Lea, Ramona; Leardini, Lucia; Lee, Graham Richard; Lee, Seongjoo; Legrand, Iosif; Lehas, Fatiha; Lemmon, Roy Crawford; Lenti, Vito; Leogrande, Emilia; Leon Monzon, Ildefonso; Leoncino, Marco; Levai, Peter; Li, Shuang; Li, Xiaomei; Lien, Jorgen Andre; Lietava, Roman; Lindal, Svein; Lindenstruth, Volker; Lippmann, Christian; Lisa, Michael Annan; Ljunggren, Hans Martin; Lodato, Davide Francesco; Lonne, Per-Ivar; Loginov, Vitaly; Loizides, Constantinos; Lopez, Xavier Bernard; Lopez Torres, Ernesto; Lowe, Andrew John; Luettig, Philipp Johannes; Lunardon, Marcello; Luparello, Grazia; Ferreira Natal Da Luz, Pedro Hugo; Maevskaya, Alla; Mager, Magnus; Mahajan, Sanjay; Mahmood, Sohail Musa; Maire, Antonin; Majka, Richard Daniel; Malaev, Mikhail; Maldonado Cervantes, Ivonne Alicia; Malinina, Liudmila; Mal'Kevich, Dmitry; Malzacher, Peter; Mamonov, Alexander; Manko, Vladislav; Manso, Franck; Manzari, Vito; Marchisone, Massimiliano; Mares, Jiri; Margagliotti, Giacomo Vito; Margotti, Anselmo; Margutti, Jacopo; Marin, Ana Maria; Markert, Christina; Marquard, Marco; Martin, Nicole Alice; Martin Blanco, Javier; Martinengo, Paolo; Martinez Hernandez, Mario Ivan; Martinez-Garcia, Gines; Martinez Pedreira, Miguel; Martynov, Yevgen; Mas, Alexis Jean-Michel; Masciocchi, Silvia; Masera, Massimo; Masoni, Alberto; Massacrier, Laure Marie; Mastroserio, Annalisa; Masui, Hiroshi; Matyja, Adam Tomasz; Mayer, Christoph; Mazer, Joel Anthony; Mazzoni, Alessandra Maria; Mcdonald, Daniel; Meddi, Franco; Melikyan, Yuri; Menchaca-Rocha, Arturo Alejandro; Meninno, Elisa; Mercado-Perez, Jorge; Meres, Michal; Miake, Yasuo; Mieskolainen, Matti Mikael; Mikhaylov, Konstantin; Milano, Leonardo; Milosevic, Jovan; Minervini, Lazzaro Manlio; Mischke, Andre; Mishra, Aditya Nath; Miskowiec, Dariusz Czeslaw; Mitra, Jubin; Mitu, Ciprian Mihai; Mohammadi, Naghmeh; Mohanty, Bedangadas; Molnar, Levente; Montano Zetina, Luis Manuel; Montes Prado, Esther; Morando, Maurizio; Moreira De Godoy, Denise Aparecida; Moretto, Sandra; Morreale, Astrid; Morsch, Andreas; Muccifora, Valeria; Mudnic, Eugen; Muhlheim, Daniel Michael; Muhuri, Sanjib; Mukherjee, Maitreyee; Mulligan, James Declan; Gameiro Munhoz, Marcelo; Murray, Sean; Musa, Luciano; Musinsky, Jan; Nandi, Basanta Kumar; Nania, Rosario; Nappi, Eugenio; Naru, Muhammad Umair; Nattrass, Christine; Nayak, Kishora; Nayak, Tapan Kumar; Nazarenko, Sergey; Nedosekin, Alexander; Nellen, Lukas; Ng, Fabian; Nicassio, Maria; Niculescu, Mihai; Niedziela, Jeremi; Nielsen, Borge Svane; Nikolaev, Sergey; Nikulin, Sergey; Nikulin, Vladimir; Noferini, Francesco; Nomokonov, Petr; Nooren, Gerardus; Cabanillas Noris, Juan Carlos; Norman, Jaime; Nyanin, Alexander; Nystrand, Joakim Ingemar; Oeschler, Helmut Oskar; Oh, Saehanseul; Oh, Sun Kun; Ohlson, Alice Elisabeth; Okatan, Ali; Okubo, Tsubasa; Olah, Laszlo; Oleniacz, Janusz; Oliveira Da Silva, Antonio Carlos; Oliver, Michael Henry; Onderwaater, Jacobus; Oppedisano, Chiara; Orava, Risto; Ortiz Velasquez, Antonio; Oskarsson, Anders Nils Erik; Otwinowski, Jacek Tomasz; Oyama, Ken; Ozdemir, Mahmut; Pachmayer, Yvonne Chiara; Pagano, Paola; Paic, Guy; Pajares Vales, Carlos; Pal, Susanta Kumar; Pan, Jinjin; Pandey, Ashutosh Kumar; Pant, Divyash; Papcun, Peter; Papikyan, Vardanush; Pappalardo, Giuseppe; Pareek, Pooja; Park, Woojin; Parmar, Sonia; Passfeld, Annika; Paticchio, Vincenzo; Patra, Rajendra Nath; Paul, Biswarup; Peitzmann, Thomas; Pereira Da Costa, Hugo Denis Antonio; Pereira De Oliveira Filho, Elienos; Peresunko, Dmitry Yurevich; Perez Lara, Carlos Eugenio; Perez Lezama, Edgar; Peskov, Vladimir; Pestov, Yury; Petracek, Vojtech; Petrov, Viacheslav; Petrovici, Mihai; Petta, Catia; Piano, Stefano; Pikna, Miroslav; Pillot, Philippe; Pinazza, Ombretta; Pinsky, Lawrence; Piyarathna, Danthasinghe; Ploskon, Mateusz Andrzej; Planinic, Mirko; Pluta, Jan Marian; Pochybova, Sona; Podesta Lerma, Pedro Luis Manuel; Poghosyan, Martin; Polishchuk, Boris; Poljak, Nikola; Poonsawat, Wanchaloem; Pop, Amalia; Porteboeuf, Sarah Julie; Porter, R Jefferson; Pospisil, Jan; Prasad, Sidharth Kumar; Preghenella, Roberto; Prino, Francesco; Pruneau, Claude Andre; Pshenichnov, Igor; Puccio, Maximiliano; Puddu, Giovanna; Pujahari, Prabhat Ranjan; Punin, Valery; Putschke, Jorn Henning; Qvigstad, Henrik; Rachevski, Alexandre; Raha, Sibaji; Rajput, Sonia; Rak, Jan; Rakotozafindrabe, Andry Malala; Ramello, Luciano; Rami, Fouad; Raniwala, Rashmi; Raniwala, Sudhir; Rasanen, Sami Sakari; Rascanu, Bogdan Theodor; Rathee, Deepika; Read, Kenneth Francis; Real, Jean-Sebastien; Redlich, Krzysztof; Reed, Rosi Jan; Rehman, Attiq Ur; Reichelt, Patrick Simon; Reidt, Felix; Ren, Xiaowen; Renfordt, Rainer Arno Ernst; Reolon, Anna Rita; Reshetin, Andrey; Rettig, Felix Vincenz; Revol, Jean-Pierre; Reygers, Klaus Johannes; Riabov, Viktor; Ricci, Renato Angelo; Richert, Tuva Ora Herenui; Richter, Matthias Rudolph; Riedler, Petra; Riegler, Werner; Riggi, Francesco; Ristea, Catalin-Lucian; Rivetti, Angelo; Rocco, Elena; Rodriguez Cahuantzi, Mario; Rodriguez Manso, Alis; Roeed, Ketil; Rogochaya, Elena; Rohr, David Michael; Roehrich, Dieter; Romita, Rosa; Ronchetti, Federico; Ronflette, Lucile; Rosnet, Philippe; Rossi, Andrea; Roukoutakis, Filimon; Roy, Ankhi; Roy, Christelle Sophie; Roy, Pradip Kumar; Rubio Montero, Antonio Juan; Rui, Rinaldo; Russo, Riccardo; Ryabinkin, Evgeny; Ryabov, Yury; Rybicki, Andrzej; Sadovskiy, Sergey; Safarik, Karel; Sahlmuller, Baldo; Sahoo, Pragati; Sahoo, Raghunath; Sahoo, Sarita; Sahu, Pradip Kumar; Saini, Jogender; Sakai, Shingo; Saleh, Mohammad Ahmad; Salgado Lopez, Carlos Alberto; Salzwedel, Jai Samuel Nielsen; Sambyal, Sanjeev Singh; Samsonov, Vladimir; Sanchez Castro, Xitzel; Sandor, Ladislav; Sandoval, Andres; Sano, Masato; Sarkar, Debojit; Scapparone, Eugenio; Scarlassara, Fernando; Scharenberg, Rolf Paul; Schiaua, Claudiu Cornel; Schicker, Rainer Martin; Schmidt, Christian Joachim; Schmidt, Hans Rudolf; Schuchmann, Simone; Schukraft, Jurgen; Schulc, Martin; Schuster, Tim Robin; Schutz, Yves Roland; Schwarz, Kilian Eberhard; Schweda, Kai Oliver; Scioli, Gilda; Scomparin, Enrico; Scott, Rebecca Michelle; Seger, Janet Elizabeth; Sekiguchi, Yuko; Sekihata, Daiki; Selyuzhenkov, Ilya; Senosi, Kgotlaesele; Seo, Jeewon; Serradilla Rodriguez, Eulogio; Sevcenco, Adrian; Shabanov, Arseniy; Shabetai, Alexandre; Shadura, Oksana; Shahoyan, Ruben; Shangaraev, Artem; Sharma, Ankita; Sharma, Mona; Sharma, Monika; Sharma, Natasha; Shigaki, Kenta; Shtejer Diaz, Katherin; Sibiryak, Yury; Siddhanta, Sabyasachi; Sielewicz, Krzysztof Marek; Siemiarczuk, Teodor; Silvermyr, David Olle Rickard; Silvestre, Catherine Micaela; Simatovic, Goran; Simonetti, Giuseppe; Singaraju, Rama Narayana; Singh, Ranbir; Singha, Subhash; Singhal, Vikas; Sinha, Bikash; Sarkar - Sinha, Tinku; Sitar, Branislav; Sitta, Mario; Skaali, Bernhard; Slupecki, Maciej; Smirnov, Nikolai; Snellings, Raimond; Snellman, Tomas Wilhelm; Soegaard, Carsten; Soltz, Ron Ariel; Song, Jihye; Song, Myunggeun; Song, Zixuan; Soramel, Francesca; Sorensen, Soren Pontoppidan; Spacek, Michal; Spiriti, Eleuterio; Sputowska, Iwona Anna; Spyropoulou-Stassinaki, Martha; Srivastava, Brijesh Kumar; Stachel, Johanna; Stan, Ionel; Stefanek, Grzegorz; Steinpreis, Matthew Donald; Stenlund, Evert Anders; Steyn, Gideon Francois; Stiller, Johannes Hendrik; Stocco, Diego; Strmen, Peter; Alarcon Do Passo Suaide, Alexandre; Sugitate, Toru; Suire, Christophe Pierre; Suleymanov, Mais Kazim Oglu; Sultanov, Rishat; Sumbera, Michal; Symons, Timothy; Szabo, Alexander; Szanto De Toledo, Alejandro; Szarka, Imrich; Szczepankiewicz, Adam; Szymanski, Maciej Pawel; Tabassam, Uzma; Takahashi, Jun; Tambave, Ganesh Jagannath; Tanaka, Naoto; Tangaro, Marco-Antonio; Tapia Takaki, Daniel Jesus; Tarantola Peloni, Attilio; Tarhini, Mohamad; Tariq, Mohammad; Tarzila, Madalina-Gabriela; Tauro, Arturo; Tejeda Munoz, Guillermo; Telesca, Adriana; Terasaki, Kohei; Terrevoli, Cristina; Teyssier, Boris; Thaeder, Jochen Mathias; Thomas, Deepa; Tieulent, Raphael Noel; Timmins, Anthony Robert; Toia, Alberica; Trogolo, Stefano; Trubnikov, Victor; Trzaska, Wladyslaw Henryk; Tsuji, Tomoya; Tumkin, Alexandr; Turrisi, Rosario; Tveter, Trine Spedstad; Ullaland, Kjetil; Uras, Antonio; Usai, Gianluca; Utrobicic, Antonija; Vajzer, Michal; Vala, Martin; Valencia Palomo, Lizardo; Vallero, Sara; Van Der Maarel, Jasper; Van Hoorne, Jacobus Willem; Van Leeuwen, Marco; Vanat, Tomas; Vande Vyvre, Pierre; Varga, Dezso; Diozcora Vargas Trevino, Aurora; Vargyas, Marton; Varma, Raghava; Vasileiou, Maria; Vasiliev, Andrey; Vauthier, Astrid; Vechernin, Vladimir; Veen, Annelies Marianne; Veldhoen, Misha; Velure, Arild; Venaruzzo, Massimo; Vercellin, Ermanno; Vergara Limon, Sergio; Vernet, Renaud; Verweij, Marta; Vickovic, Linda; Viesti, Giuseppe; Viinikainen, Jussi Samuli; Vilakazi, Zabulon; Villalobos Baillie, Orlando; Vinogradov, Alexander; Vinogradov, Leonid; Vinogradov, Yury; Virgili, Tiziano; Vislavicius, Vytautas; Viyogi, Yogendra; Vodopyanov, Alexander; Volkl, Martin Andreas; Voloshin, Kirill; Voloshin, Sergey; Volpe, Giacomo; Von Haller, Barthelemy; Vorobyev, Ivan; Vranic, Danilo; Vrlakova, Janka; Vulpescu, Bogdan; Vyushin, Alexey; Wagner, Boris; Wagner, Jan; Wang, Hongkai; Wang, Mengliang; Wang, Yifei; Watanabe, Daisuke; Watanabe, Yosuke; Weber, Michael; Weber, Steffen Georg; Wessels, Johannes Peter; Westerhoff, Uwe; Wiechula, Jens; Wikne, Jon; Wilde, Martin Rudolf; Wilk, Grzegorz Andrzej; Wilkinson, Jeremy John; Williams, Crispin; Windelband, Bernd Stefan; Winn, Michael Andreas; Yaldo, Chris G; Yang, Hongyan; Yang, Ping; Yano, Satoshi; Yin, Zhongbao; Yokoyama, Hiroki; Yoo, In-Kwon; Yurchenko, Volodymyr; Yushmanov, Igor; Zaborowska, Anna; Zaccolo, Valentina; Zaman, Ali; Zampolli, Chiara; Correia Zanoli, Henrique Jose; Zaporozhets, Sergey; Zardoshti, Nima; Zarochentsev, Andrey; Zavada, Petr; Zavyalov, Nikolay; Zbroszczyk, Hanna Paulina; Zgura, Sorin Ion; Zhalov, Mikhail; Zhang, Haitao; Zhang, Xiaoming; Zhang, Yonghong; Zhao, Chengxin; Zhigareva, Natalia; Zhou, Daicui; Zhou, You; Zhou, Zhuo; Zhu, Hongsheng; Zhu, Jianhui; Zhu, Xiangrong; Zichichi, Antonino; Zimmermann, Alice; Zimmermann, Markus Bernhard; Zinovjev, Gennady; Zyzak, Maksym

    2016-03-31

    We report on results obtained with the Event Shape Engineering technique applied to Pb-Pb collisions at $\\sqrt{s_\\rm{NN}}=2.76$ TeV. By selecting events in the same centrality interval, but with very different average flow, different initial state conditions can be studied. We find the effect of the event-shape selection on the elliptic flow coefficient $v_2$ to be almost independent of transverse momentum $p_\\rm{T}$, as expected if this effect is due to fluctuations in the initial geometry of the system. Charged hadron, pion, kaon, and proton transverse momentum distributions are found to be harder in events with higher-than-average elliptic flow, indicating an interplay between radial and elliptic flow.

  10. Deregulation of the protocadherin gene FAT1 alters muscle shapes: implications for the pathogenesis of facioscapulohumeral dystrophy.

    Directory of Open Access Journals (Sweden)

    Nathalie Caruso

    2013-06-01

    Full Text Available Generation of skeletal muscles with forms adapted to their function is essential for normal movement. Muscle shape is patterned by the coordinated polarity of collectively migrating myoblasts. Constitutive inactivation of the protocadherin gene Fat1 uncoupled individual myoblast polarity within chains, altering the shape of selective groups of muscles in the shoulder and face. These shape abnormalities were followed by early onset regionalised muscle defects in adult Fat1-deficient mice. Tissue-specific ablation of Fat1 driven by Pax3-cre reproduced muscle shape defects in limb but not face muscles, indicating a cell-autonomous contribution of Fat1 in migrating muscle precursors. Strikingly, the topography of muscle abnormalities caused by Fat1 loss-of-function resembles that of human patients with facioscapulohumeral dystrophy (FSHD. FAT1 lies near the critical locus involved in causing FSHD, and Fat1 mutant mice also show retinal vasculopathy, mimicking another symptom of FSHD, and showed abnormal inner ear patterning, predictive of deafness, reminiscent of another burden of FSHD. Muscle-specific reduction of FAT1 expression and promoter silencing was observed in foetal FSHD1 cases. CGH array-based studies identified deletion polymorphisms within a putative regulatory enhancer of FAT1, predictive of tissue-specific depletion of FAT1 expression, which preferentially segregate with FSHD. Our study identifies FAT1 as a critical determinant of muscle form, misregulation of which associates with FSHD.

  11. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.

    Science.gov (United States)

    Poelstra, J W; Vijay, N; Bossu, C M; Lantz, H; Ryll, B; Müller, I; Baglione, V; Unneberg, P; Wikelski, M; Grabherr, M G; Wolf, J B W

    2014-06-20

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence. Copyright © 2014, American Association for the Advancement of Science.

  12. The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

    DEFF Research Database (Denmark)

    Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R R;

    2015-01-01

    abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed...

  13. Forest corridors maintain historical gene flow in a tiger metapopulation in the highlands of central India.

    Science.gov (United States)

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2013-09-22

    Understanding the patterns of gene flow of an endangered species metapopulation occupying a fragmented habitat is crucial for landscape-level conservation planning and devising effective conservation strategies. Tigers (Panthera tigris) are globally endangered and their populations are highly fragmented and exist in a few isolated metapopulations across their range. We used multi-locus genotypic data from 273 individual tigers (Panthera tigris tigris) from four tiger populations of the Satpura-Maikal landscape of central India to determine whether the corridors in this landscape are functional. This 45 000 km(2) landscape contains 17% of India's tiger population and 12% of its tiger habitat. We applied Bayesian and coalescent-based analyses to estimate contemporary and historical gene flow among these populations and to infer their evolutionary history. We found that the tiger metapopulation in central India has high rates of historical and contemporary gene flow. The tests for population history reveal that tigers populated central India about 10 000 years ago. Their population subdivision began about 1000 years ago and accelerated about 200 years ago owing to habitat fragmentation, leading to four spatially separated populations. These four populations have been in migration-drift equilibrium maintained by high gene flow. We found the highest rates of contemporary gene flow in populations that are connected by forest corridors. This information is highly relevant to conservation practitioners and policy makers, because deforestation, road widening and mining are imminent threats to these corridors.

  14. Considering spatial and temporal scale in landscape-genetic studies of gene flow.

    Science.gov (United States)

    Anderson, Corey Devin; Epperson, Bryan K; Fortin, Marie-Josée; Holderegger, Rolf; James, Patrick M A; Rosenberg, Michael S; Scribner, Kim T; Spear, Stephen

    2010-09-01

    Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.

  15. Studies on column size scale-up and flow profile in conical shape liquid chromatographic column of 10° by visualization method

    Institute of Scientific and Technical Information of China (English)

    Guan Wenna; Tan Feng; Guan Yafeng

    2006-01-01

    An improved visualization device made of polymethyl methacrylate (PMMA) was used to study the 3D flow profile inside conical columns of a 10° opening angle packed with C18 phase.The outside wall of the conical columns was rectangular in shape in order to improve the transparency property of the column wall and reduce the deformation of the image for better observation of the flow profiles of colored solutes inside the column.The influence of flow rate,particle size and shape on the flow profile of a colored band were studied on a 5-cm-long column and a scaled-up column of four fold in volume.It was found that the flow rates of the mobile phase had little influence on the flat flow profile of the iodine band while the properties of the stationary phase had a certain influence on them.We observed that the flow profiles of the scaled-up column were flat during the whole chromatographic process,and the efficiency and resolution of the column were also increased in accordance with theoretical prediction.The experimental results proved that the 10° conical columns can be proportionally scaled up while still keeping the flat flow profile,sample load per unit volume of packing material,and column efficiency,which are superior to the conventional column.

  16. Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of

  17. Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression.

    Directory of Open Access Journals (Sweden)

    Yichi Xu

    2016-05-01

    Full Text Available Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes in vivo. As genome-wide transcription is organized under the high-order chromosome structure, it is largely uncharted how circadian gene expression is influenced by chromosome architecture. We focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor in circadian rhythm. Using circular chromosome conformation capture sequencing, we systematically examined the interacting loci of a Bmal1-bound super-enhancer upstream of a clock gene Nr1d1 in mouse liver. These interactions are largely stable in the circadian cycle and cohesin binding sites are enriched in the interactome. Global analysis showed that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites are associated with high circadian rhythmicity of transcription. A model integrating the effects of cohesin and CTCF markedly improved the mechanistic understanding of circadian gene expression. Further experiments in cohesin knockout cells demonstrated that cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. This study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.

  18. The role of D4 receptor gene exon III polymorphisms in shaping human altruism and prosocial behavior

    Directory of Open Access Journals (Sweden)

    Yushi eJiang

    2013-05-01

    Full Text Available Human beings are an extraordinarily altruistic species often willing to help strangers at a considerable cost (sometimes life itself to themselves. But as Darwin noted …he who was ready to sacrifice his life, as many a savage has been, rather than betray his comrades, would often leave no offspring to inherit his noble nature. Hence, this is the paradox of altruism. Twin studies have shown that altruism and other prosocial behavior show considerable heritability and more recently a number of candidate genes have been identified with this phenotype. Among these first provisional findings are genes encoding elements of dopaminergic transmission. In this article we will review the evidence for the involvement of one of these, the dopamine D4 receptor (DRD4 gene, in shaping human prosocial behavior and consider the methodologies employed in measuring this trait, specific molecular genetic findings and finally, evidence from several Gene x Environment (GxE studies that imply differential susceptibility of this gene to environmental influences.

  19. Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests - the case of sympatric and parapatric Marantaceae species.

    Science.gov (United States)

    Ley, A C; Hardy, O J

    2014-08-01

    Gene flow within and between species is a fundamental process shaping the evolutionary history of taxa. However, the extent of hybridization and reinforcement is little documented in the tropics. Here we explore the pattern of gene flow between three sister species from the herbaceous genus Marantochloa (Marantaceae), sympatrically distributed in the understorey of the African rainforest, using data from the chloroplast and nuclear genomes (DNA sequences and AFLP). We found highly contrasting patterns: while there was no evidence of gene flow between M. congensis and M. monophylla, species identity between M. monophylla and M. incertifolia was maintained despite considerable gene flow. We hypothesize that M. incertifolia originated from an ancient hybridization event between M. congensis and M. monophylla, considering the current absence of hybridization between the two assumed parent species, the rare presence of shared haplotypes between all three species and the high percentage of haplotypes shared by M. incertifolia with each of the two parent species. This example is contrasted with two parapatrically distributed species from the same family in the genus Haumania forming a hybrid zone restricted to the area of overlap. This work illustrates the diversity of speciation/introgression patterns that can potentially occur in the flora of tropical Africa.

  20. Effect of Longitudinal-External-Fins on Fluid Flow Characteristics for Wing-Shaped Tubes Bundle in Crossflow

    Directory of Open Access Journals (Sweden)

    Sayed Ahmed E. Sayed Ahmed

    2015-01-01

    Full Text Available A numerical study is conducted to clarify fluid-flow characteristics, pressure drop coefficient (Pdc, and the average skin friction coefficient (Cf,m for wing-shaped-tubes bundle with longitudinal fins at downstream side of the tube using the commercial CFD FLUENT software package. The air-side Rea ranges from 1800 to 9700. The tubes are employed with various fin heights (hf and fin thicknesses (δ such as 2 mm ≤ hf ≤ 12 mm and 1.5 mm ≤ δ ≤ 3.5 mm at the considered Rea range. Results indicate that ΔPa increases with Rea for all hf. Pdc decreases with Rea for all hf values for 1800 ≤ Rea ≤ 4200 and then increases for 4200 ≤ Rea ≤ 10000. Lowest values of ΔPa, Pdc, and pumping power (PP occurred at hf = 6 mm. Values of Pdc for hf = 6 mm are lower than those of NOF and hf = 2 mm by about 73 % and 32 %, respectively, at Rea = 4000. Cf,m decreases with Rea. δ has negligible effect on Cf,m. ΔPa increases for 1.5 mm ≤ δ ≤ 2.5 mm while ΔPa decreases with 2.5 mm < δ ≤ 3.5 mm for the considered Rea range except for Rea = 1850.

  1. Applying gene flow science to environmental policy needs: a boundary work perspective.

    Science.gov (United States)

    Ridley, Caroline E; Alexander, Laurie C

    2016-08-01

    One application of gene flow science is the policy arena. In this article, we describe two examples in which the topic of gene flow has entered into the U.S. national environmental policymaking process: regulation of genetically engineered crops and clarification of the jurisdictional scope of the Clean Water Act. We summarize both current scientific understanding and the legal context within which gene flow science has relevance. We also discuss the process by which scientific knowledge has been synthesized and communicated to decision-makers in these two contexts utilizing the concept of 'boundary work'. Boundary organizations, the work they engage in to bridge the worlds of science, policy, and practice, and the boundary objects they produce to translate scientific knowledge existed in both examples. However, the specific activities and attributes of the objects produced varied based on the needs of the decision-makers. We close with suggestions for how scientists can contribute to or engage in boundary work with policymakers.

  2. A numerical study of channel-to-channel flow cross-over through the gas diffusion layer in a PEM-fuel-cell flow system using a serpentine channel with a trapezoidal cross-sectional shape

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Lan; Oosthuizen, Patrick H. [Department of Mechanical and Materials Engineering, McLaughlin Hall, Queen' s University, Kingston, ON, K7L 3N6 (Canada); McAuley, Kim B. [Department of Chemical Engineering, Dupuis Hall, Queen' s University, Kingston, ON, K7L 3N6 (Canada)

    2006-10-15

    A numerical study of pressure distribution and flow cross-over through the gas diffusion layer (GDL) in a PEMFC flow plate using a serpentine channel system has been undertaken for the case where the channel has a trapezoidal cross-sectional shape. The flow has been assumed to be 3-D, steady, incompressible and single-phase. The flow through the porous diffusion layer has been described using the Darcy model. The governing equations have been written in dimensionless form and solved by using the commercial CFD solver, FIDAP. The results obtained indicate that: (1) the size ratio, R, of trapezoidal cross-sectional shape has a significant effect on the flow cross-over. As R increases, the flow cross-over through GDL increases; (2) the ratio R also has a significant effect on the pressure variation in the flow field for both cross-over and no cross-over cases; (3) flow cross-over has a significant influence on the pressure variation through the channel, tending to decrease the pressure drop across the channel; (4) an increase in Re number can lead to a slight increase in the flow cross-over. (author)

  3. Gene flow among populations of two rare co-occurring fern species differing in ploidy level.

    Science.gov (United States)

    Bucharová, Anna; Münzbergová, Zuzana

    2012-01-01

    Differences in ploidy levels among different fern species have a vast influence on their mating system, their colonization ability and on the gene flow among populations. Differences in the colonization abilities of species with different ploidy levels are well known: tetraploids, in contrast to diploids, are able to undergo intra-gametophytic selfing. Because fertilization is a post-dispersal process in ferns, selfing results in better colonization abilities in tetraploids because of single spore colonization. Considerably less is known about the gene flow among populations of different ploidy levels. The present study examines two rare fern species that differ in ploidy. While it has already been confirmed that tetraploid species are better at colonizing, the present study focuses on the gene flow among existing populations. We analyzed the genetic structure of a set of populations in a 10×10 km study region using isoenzymes. Genetic variation in tetraploid species is distributed mainly among populations; the genetic distance between populations is correlated with the geographical distance, and larger populations host more genetic diversity than smaller populations. In the diploid species, most variability is partitioned within populations; the genetic distance is not related to geographic distance, and the genetic diversity of populations is not related to the population size. This suggests that in tetraploid species, which undergo selfing, gene flow is limited. In contrast, in the diploid species, which experience outcrossing, gene flow is extensive and the whole system behaves as one large population. Our results suggest that in ferns, the ability to colonize new habitats and the gene flow among existing populations are affected by the mating system.

  4. Assessment on alien herbicide-resistant gene flow among crucifers by sexual compatibility

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiangxiang; LU Weiping; QI Cunkou; PU Huiming; XIA Qiuxia; LU Dalei; LIU Geshan; WANG Youping

    2005-01-01

    Cross-pollination and high cross-compatibility are frequently found in many cruciferous plants, which implies that there might be potential risk of alien gene flow among crucifers. In this work, the alien glyphosate-resistant gene flow between GM (Genetically modified) rapeseed variety Q3 (Brassica napus) and 6 varieties from 5 cruciferous species was assessed by sexual compatibility through aniline blue fluorescence observation, manual cross, mentor pollination with the mixture pollen and DNA identification. The results indicated that the compatibility indices of two B. napus varieties, B. juncea var. multiceps Tsen et Lee and Chinese cabbage (B. chinensis) (as female) with Q3 (as male) were 16.15, 12.77, 2.345 and 0.85, respectively. F1 plants were examined by PCR and all of these samples were confirmed as positive. Crossing between Orychophragmus violaceus, Descurainia sophia (as female) and Q3 (as male) expressed high cross-incompatibility. Fluorescence microscope observation indicated that growing of pollen tube terminated at the upper 1/3 part of the style of O. violaceus and on the stigma surface of D. sophia. The mentor plants were further analyzed by PCR and all were shown to be negative. Under the neighboring growth and natural pollination conditions, the rates of gene flow to two B. napus varieties were 2.3278% and 2.1487%, respectively, B. juncea var. multiceps Tsen et Lee and Chinese cabbage were 1.0157% and 0.9236%, respectively. No gene flow was observed in O. violaceus and D. sophia. Frequency of gene flow was highly correlated with sexual compatibility. Due to possible alien gene flow among crucifers, special consideration and care should be taken to grow GM rapeseed.

  5. Gene flow between Atlantic and Pacific Ocean basins in three lineages of deep-sea clams (Bivalvia: Vesicomyidae: Pliocardiinae) and subsequent limited gene flow within the Atlantic

    Science.gov (United States)

    LaBella, Abigail Leavitt; Van Dover, Cindy L.; Jollivet, Didier; Cunningham, Clifford W.

    2017-03-01

    Pliocardiin (vesicomyid) clams rely on microbial symbionts for nutrition and are obligate inhabitants of deep-sea chemosynthetic ecosystems. Unlike many other invertebrate hosts of chemosynthetic microbes, pliocardiin clams are found in every ocean in a variety of reducing habitats, including hydrothermal vents, cold seeps, organic falls and deep-sea fans. The global distribution of pliocardiin clams suggests historical gene flow between ocean basins. We focus on 3 pliocardiin genera-'Pliocardia' I, Calyptogena and Abyssogena-each of which has a pair of sister clades in the Atlantic and Pacific. Our work tests the hypothesis that historical gene flow between the Atlantic and Pacific Oceans within these genera was interrupted by the closure of the Panamanian seaway and tests whether isolation between the ocean basins is the result of vicariance or past colonization. These questions are investigated in the context of fossil evidence, biogeography and phylogenetics. This study revealed a set of substitution rates consistent with other invertebrate studies (μ=0.8%/My/lineage), and a set consistent with much lower rates often attributed to deep-sea organisms (μ=0.3%/My/lineage). Among the Pacific/Atlantic sister pairs, 'Pliocardia' I COI divergence per lineage is intermediate (2.5%), Calyptogena is the highest (6.1%) and Abyssogena the lowest (0.8%). The substitution rates suggest that 'Pliocardia' I and Calyptogena have histories of at least 2.8 My in the Atlantic, with Calyptogena likely older. The slower rate, however, is inconsistent with both the maximum age of the family and several well studied fossils: leaving the faster rate preferred. With the faster rate, the Abyssogena southwardae clade diverged from its Pacific sister clade around 1 Mya, which likely post-dates the closure of the Isthmus of Panama and the opening of the Bering Strait. In light of this recent divergence, we test the previously proposed hypothesis that there is a high level of ongoing gene

  6. Comparing direct vs. indirect estimates of gene flow within a population of a scattered tree species.

    Science.gov (United States)

    Oddou-Muratorio, Sylvie; Klein, Etienne K

    2008-06-01

    The comparison between historical estimates of gene flow, using variance in allelic frequencies, and contemporary estimates of gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at six microsatellite loci was used to quantify genetic structure in the insect-pollinated, animal-dispersed, low-density tree Sorbus torminalis L. Crantz, and to derive historical estimates of gene flow. The neighbourhood size and root-mean-squared dispersal distance inferred from seedling genotypes (N(b) = 70 individuals, sigma(e) = 417 m) were similar to those inferred from adult genotypes (N(b) = 114 individuals, sigma(e) = 472 m). We also used parentage analyses and a neighbourhood model approach after an evaluation of the statistical properties of this method on simulated data. From our data, we estimated even contributions of seed- and pollen-mediated dispersal to the genetic composition of established seedlings, with both fat-tailed pollen and seed dispersal kernels, and slightly higher mean distance of pollen dispersal (248 m) as compared to seed dispersal (135 m). The resulting contemporary estimate of gene dispersal distance (sigma(c) = 211 m) was approximately twofold smaller than the historical estimates. Besides different assumptions and statistical nuances of both approaches, this discrepancy is likely to reflect a recent restriction in the scale of gene flow which requires manager's attention in a context of increasing forest fragmentation.

  7. A combination of independent transcriptional regulators shapes bacterial virulence gene expression during infection.

    Directory of Open Access Journals (Sweden)

    Samuel A Shelburne

    2010-03-01

    Full Text Available Transcriptional regulatory networks are fundamental to how microbes alter gene expression in response to environmental stimuli, thereby playing a critical role in bacterial pathogenesis. However, understanding how bacterial transcriptional regulatory networks function during host-pathogen interaction is limited. Recent studies in group A Streptococcus (GAS suggested that the transcriptional regulator catabolite control protein A (CcpA influences many of the same genes as the control of virulence (CovRS two-component gene regulatory system. To provide new information about the CcpA and CovRS networks, we compared the CcpA and CovR transcriptomes in a serotype M1 GAS strain. The transcript levels of several of the same genes encoding virulence factors and proteins involved in basic metabolic processes were affected in both DeltaccpA and DeltacovR isogenic mutant strains. Recombinant CcpA and CovR bound with high-affinity to the promoter regions of several co-regulated genes, including those encoding proteins involved in carbohydrate and amino acid metabolism. Compared to the wild-type parental strain, DeltaccpA and DeltacovRDeltaccpA isogenic mutant strains were significantly less virulent in a mouse myositis model. Inactivation of CcpA and CovR alone and in combination led to significant alterations in the transcript levels of several key GAS virulence factor encoding genes during infection. Importantly, the transcript level alterations in the DeltaccpA and DeltacovRDeltaccpA isogenic mutant strains observed during infection were distinct from those occurring during growth in laboratory medium. These data provide new knowledge regarding the molecular mechanisms by which pathogenic bacteria respond to environmental signals to regulate virulence factor production and basic metabolic processes during infection.

  8. An evolutionarily conserved gene, FUWA, plays a role in determining panicle architecture, grain shape and grain weight in rice.

    Science.gov (United States)

    Chen, Jun; Gao, He; Zheng, Xiao-Ming; Jin, Mingna; Weng, Jian-Feng; Ma, Jin; Ren, Yulong; Zhou, Kunneng; Wang, Qi; Wang, Jie; Wang, Jiu-Lin; Zhang, Xin; Cheng, Zhijun; Wu, Chuanyin; Wang, Haiyang; Wan, Jian-Min

    2015-08-01

    Plant breeding relies on creation of novel allelic combinations for desired traits. Identification and utilization of beneficial alleles, rare alleles and evolutionarily conserved genes in the germplasm (referred to as 'hidden' genes) provide an effective approach to achieve this goal. Here we show that a chemically induced null mutation in an evolutionarily conserved gene, FUWA, alters multiple important agronomic traits in rice, including panicle architecture, grain shape and grain weight. FUWA encodes an NHL domain-containing protein, with preferential expression in the root meristem, shoot apical meristem and inflorescences, where it restricts excessive cell division. Sequence analysis revealed that FUWA has undergone a bottleneck effect, and become fixed in landraces and modern cultivars during domestication and breeding. We further confirm a highly conserved role of FUWA homologs in determining panicle architecture and grain development in rice, maize and sorghum through genetic transformation. Strikingly, knockdown of the FUWA transcription level by RNA interference results in an erect panicle and increased grain size in both indica and japonica genetic backgrounds. This study illustrates an approach to create new germplasm with improved agronomic traits for crop breeding by tapping into evolutionary conserved genes.

  9. A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach.

    Science.gov (United States)

    López-Girona, Elena; Zhang, Yu; Eduardo, Iban; Mora, José Ramón Hernández; Alexiou, Konstantinos G; Arús, Pere; Aranzana, María José

    2017-07-27

    In peach, the flat phenotype is caused by a partially dominant allele in heterozygosis (Ss), fruits from homozygous trees (SS) abort a few weeks after fruit setting. Previous research has identified a SSR marker (UDP98-412) highly associated with the trait, found suitable for marker assisted selection (MAS). Here we report a ∼10 Kb deletion affecting the gene PRUPE.6G281100, 400 Kb upstream of UDP98-412, co-segregating with the trait. This gene is a leucine-rich repeat receptor-like kinase (LRR-RLK) orthologous to the Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) group. PCR markers suitable for MAS confirmed its strong association with the trait in a collection of 246 cultivars. They were used to evaluate the DNA from a round fruit derived from a somatic mutation of the flat variety 'UFO-4', revealing that the mutation affected the flat associated allele (S). Protein BLAST alignment identified significant hits with genes involved in different biological processes. Best protein hit occurred with AtRLP12, which may functionally complement CLAVATA2, a key regulator that controls the stem cell population size. RT-PCR analysis revealed the absence of transcription of the partially deleted allele. The data support PRUPE.6G281100 as a candidate gene for flat shape in peach.

  10. The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

    DEFF Research Database (Denmark)

    Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R R

    2015-01-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functional...

  11. Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms.

    Science.gov (United States)

    Bertelli, Claire; Greub, Gilbert

    2012-01-01

    Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).

  12. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    NARCIS (Netherlands)

    Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Clevers, JC; Huminiecki, Lukasz

    2015-01-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally

  13. Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms

    Directory of Open Access Journals (Sweden)

    Claire eBertelli

    2012-08-01

    Full Text Available Based on Darwin’s concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host’s factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms.

  14. On the quest for selective constraints shaping the expressivity of the genes casting retropseudogenes in human

    Directory of Open Access Journals (Sweden)

    Podder Soumita

    2011-08-01

    Full Text Available Abstract Background Pseudogenes, the nonfunctional homologues of functional genes are now coming to light as important resources regarding the study of human protein evolution. Processed pseudogenes arising by reverse transcription and reinsertion can provide molecular record on the dynamics and evolution of genomes. Researches on the progenitors of human processed pseudogenes delved out their highly expressed and evolutionarily conserved characters. They are reported to be short and GC-poor indicating their high efficiency for retrotransposition. In this article we focused on their high expressivity and explored the factors contributing for that and their relevance in the milieu of protein sequence evolution. Results We here, analyzed the high expressivity of these genes configuring processed or retropseudogenes by their immense connectivity in protein-protein interaction network, an inclination towards alternative splicing mechanism, a lower rate of mRNA disintegration and a slower evolutionary rate. While the unusual trend of the upraised disorder in contrast with the high expressivity of the proteins encoded by processed pseudogene ancestors is accredited by a predominance of hub-protein encoding genes, a high propensity of repeat sequence containing genes, elevated protein stability and the functional constraint to perform the transcription regulatory jobs. Linear regression analysis demonstrates mRNA decay rate and protein intrinsic disorder as the influential factors controlling the expressivity of these retropseudogene ancestors while the latter one is found to have the most significant regulatory power. Conclusions Our findings imply that, the affluence of disordered regions elevating the network attachment to be involved in important cellular assignments and the stability in transcriptional level are acting as the prevailing forces behind the high expressivity of the human genes configuring processed pseudogenes.

  15. A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data.

    Science.gov (United States)

    Flores, Kevin B

    2013-07-01

    We formulated a structured population model with distributed parameters to identify mechanisms that contribute to gene expression noise in time-dependent flow cytometry data. The model was validated using cell population-level gene expression data from two experiments with synthetically engineered eukaryotic cells. Our model captures the qualitative noise features of both experiments and accurately fit the data from the first experiment. Our results suggest that cellular switching between high and low expression states and transcriptional re-initiation are important factors needed to accurately describe gene expression noise with a structured population model.

  16. Experimental study on melting and flowing behavior of thermoplastics combustion based on a new setup with a T-shape trough.

    Science.gov (United States)

    Xie, Qiyuan; Zhang, Heping; Ye, Ruibo

    2009-07-30

    The objective of this work is to quantitatively study the burning characteristics of thermoplastics. A new experimental setup with a T-shape trough is designed. Based on this setup, the loop mechanism between the wall fire and pool fires induced by the melting and dripping of thermoplastic can be well simulated and studied. Additionally, the flowing characteristics of pool fires can also be quantitatively analyzed. Experiments are conducted for PP and PE sheets with different thicknesses. The maximum distances of the induced flowing pool flame in the T-shape trough are recorded and analyzed. The typical fire parameters, such as heat release rates (HRRs), CO concentrations are also monitored. The results show that the softening and clinging of the thermoplastic sheets plays a considerable role for their vertical wall burning. It is illustrated that the clinging of burning thermoplastic sheet may be mainly related with the softening temperatures and the ignition temperatures of the thermoplastics, as well as their viscosity coefficients. Through comparing the maximum distances of flowing flame of induced pool fires in the T-shape trough for thermoplastic sheets with different thicknesses, it is indicated that the pool fires induced by PE materials are easier to flow away than that of PP materials. Therefore, PE materials may be more dangerous for their faster pool fire spread on the floor. These experimental results preliminarily illustrate that this new experimental setup is helpful for quantitatively studying the special burning feature of thermoplastics although further modifications is needed for this setup in the future.

  17. Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

    Science.gov (United States)

    Lee, Justin S.; Ruell, Emily W.; Boydston, Erin E.; Lyren, Lisa M.; Alonso, Robert S.; Troyer, Jennifer L.; Crooks, Kevin R.; VandeWoude, Sue

    2012-01-01

    Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured--exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

  18. Gene flow from Sorghum bicolor to its weedy relatives and its ...

    African Journals Online (AJOL)

    computer user

    2015-04-29

    Apr 29, 2015 ... drummondii, has shown natural outcrossing ranging from. 0-100% on individual ... result of artificial and natural selection for more than one level of a particular ...... Possible effects of (trans) gene flow from crops on the genetic ...

  19. Gene flow from Sorghum bicolor to its weedy relatives and its ...

    African Journals Online (AJOL)

    computer user

    2015-02-18

    Feb 18, 2015 ... more quantitative and precise methods of analyzing target DNA ... laboratory located at the College of Agriculture and Veterinary .... emitted fluorescence exceeded the standardized ..... designing effective tools to measure gene flow. .... and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for.

  20. Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock.

    Science.gov (United States)

    Kwit, Charles; Stewart, C Neal

    2012-01-01

    There currently exists a large push for the use, improvement, and expansion via landscape modification of dedicated biofuel crops (feedstocks) in the United States and in many parts of the world. Ecological concerns have been voiced because many biofuel feedstocks exhibit characteristics associated with invasiveness, and due to potential negative consequences of agronomic genes in native wild populations. Seed purity concerns for biofuel feedstock cultivars whose seeds would be harvested in agronomic fields also exist from the agribusiness sector. The common thread underlying these concerns, which have regulatory implications, is gene flow; thus detailed knowledge of gene flow in biofuel crop plants is important in the formulation of environmental risk management plans. Here, we synthesize the current state of knowledge of gene flow in an exemplary biofuel crop, switchgrass (Panicum virgatum L.), which is native to eastern North America and is currently experiencing conventional and technological advances in biomass yields and ethanol production. Surprisingly little is known regarding aspects of switchgrass pollen flow and seed dispersal, and whether native populations of conspecific or congeneric relatives will readily cross with current agronomic switchgrass cultivars. We pose that filling these important gaps will be required to confront the sustainability challenges of widespread planting of biofuel feedstocks.

  1. Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient

    Science.gov (United States)

    Funk, W. C.; Murphy, M.A.; Hoke, K. L.; Muths, Erin L.; Amburgey, Staci M.; Lemmon, Emily M.; Lemmon, A. R.

    2016-01-01

    Evolutionary theory predicts that divergent selection pressures across elevational gradients could cause adaptive divergence and reproductive isolation in the process of ecological speciation. Although there is substantial evidence for adaptive divergence across elevation, there is less evidence that this restricts gene flow. Previous work in the boreal chorus frog (Pseudacris maculata) has demonstrated adaptive divergence in morphological, life history and physiological traits across an elevational gradient from approximately 1500–3000 m in the Colorado Front Range, USA. We tested whether this adaptive divergence is associated with restricted gene flow across elevation – as would be expected if incipient speciation were occurring – and, if so, whether behavioural isolation contributes to reproductive isolation. Our analysis of 12 microsatellite loci in 797 frogs from 53 populations revealed restricted gene flow across elevation, even after controlling for geographic distance and topography. Calls also varied significantly across elevation in dominant frequency, pulse number and pulse duration, which was partly, but not entirely, due to variation in body size and temperature across elevation. However, call variation did not result in strong behavioural isolation: in phonotaxis experiments, low-elevation females tended to prefer an average low-elevation call over a high-elevation call, and vice versa for high-elevation females, but this trend was not statistically significant. In summary, our results show that adaptive divergence across elevation restricts gene flow in P. maculata, but the mechanisms for this potential incipient speciation remain open.

  2. Pollen and seed mediated gene flow in commercial alfalfa seed production fields

    Science.gov (United States)

    The potential for gene flow has been widely recognized since alfalfa is pollinated by bees. The Western US is a major exporter of alfalfa seed and hay and the organic dairy industry is one of the fastest growing agricultural sectors. Because of this, many alfalfa producers are impacted by market sen...

  3. [Gene flow and its ecological risks of transgenic oilseed rape ( Brassica napus)].

    Science.gov (United States)

    Tang, Guixiang; Song, Wenjian; Zhou, Weijun

    2005-12-01

    Transgenic oilseed rape Brassica napus, one of the first genetically modified crops, has now been released to commercial use in Canada and Australia. As a cross-pollinating crop, its natural crossing rate is 30%, and it is liable to cross with other Brassica species. The ecological risk of transgenic oilseed rape has been concerned by the scientists all over the world. There are two ways for the pollens flow of transgenic oilseed rape, one takes place between transgenic oilseed rape and other related wild species, and the other occurs between transgenic and nontransgenic oilseed rape. The gene may flow to other related wild species, but it is unlikely to get hybrids in field. Because the gene can really flow to the conventional oilseed rape, it is necessary to have a sufficient isolation distance in cultivating transgenic oilseed rape.

  4. Local evolution of pyrethroid resistance offsets gene flow among Aedes aegypti collections in Yucatan State, Mexico.

    Science.gov (United States)

    Saavedra-Rodriguez, Karla; Beaty, Meaghan; Lozano-Fuentes, Saul; Denham, Steven; Garcia-Rejon, Julian; Reyes-Solis, Guadalupe; Machain-Williams, Carlos; Loroño-Pino, Maria Alba; Flores-Suarez, Adriana; Ponce-Garcia, Gustavo; Beaty, Barry; Eisen, Lars; Black, William C

    2015-01-01

    The mosquito Aedes aegypti is the major vector of the four serotypes of dengue virus (DENV1-4). Previous studies have shown that Ae. aegypti in Mexico have a high effective migration rate and that gene flow occurs among populations that are up to 150 km apart. Since 2000, pyrethroids have been widely used for suppression of Ae. aegypti in cities in Mexico. In Yucatan State in particular, pyrethroids have been applied in and around dengue case households creating an opportunity for local selection and evolution of resistance. Herein, we test for evidence of local adaptation by comparing patterns of variation among 27 Ae. aegypti collections at 13 single nucleotide polymorphisms (SNPs): two in the voltage-gated sodium channel gene para known to confer knockdown resistance, three in detoxification genes previously associated with pyrethroid resistance, and eight in putatively neutral loci. The SNPs in para varied greatly in frequency among collections, whereas SNPs at the remaining 11 loci showed little variation supporting previous evidence for extensive local gene flow. Among Ae. aegypti in Yucatan State, Mexico, local adaptation to pyrethroids appears to offset the homogenizing effects of gene flow.

  5. Local Evolution of Pyrethroid Resistance Offsets Gene Flow Among Aedes aegypti Collections in Yucatan State, Mexico

    Science.gov (United States)

    Saavedra-Rodriguez, Karla; Beaty, Meaghan; Lozano-Fuentes, Saul; Denham, Steven; Garcia-Rejon, Julian; Reyes-Solis, Guadalupe; Machain-Williams, Carlos; Loroño-Pino, Maria Alba; Flores-Suarez, Adriana; Ponce-Garcia, Gustavo; Beaty, Barry; Eisen, Lars; Black, William C.

    2015-01-01

    The mosquito Aedes aegypti is the major vector of the four serotypes of dengue virus (DENV1–4). Previous studies have shown that Ae. aegypti in Mexico have a high effective migration rate and that gene flow occurs among populations that are up to 150 km apart. Since 2000, pyrethroids have been widely used for suppression of Ae. aegypti in cities in Mexico. In Yucatan State in particular, pyrethroids have been applied in and around dengue case households creating an opportunity for local selection and evolution of resistance. Herein, we test for evidence of local adaptation by comparing patterns of variation among 27 Ae. aegypti collections at 13 single nucleotide polymorphisms (SNPs): two in the voltage-gated sodium channel gene para known to confer knockdown resistance, three in detoxification genes previously associated with pyrethroid resistance, and eight in putatively neutral loci. The SNPs in para varied greatly in frequency among collections, whereas SNPs at the remaining 11 loci showed little variation supporting previous evidence for extensive local gene flow. Among Ae. aegypti in Yucatan State, Mexico, local adaptation to pyrethroids appears to offset the homogenizing effects of gene flow. PMID:25371186

  6. Monitoring gene flow from transgenic sugar beet using cytoplasmic male-sterile bait plants.

    Science.gov (United States)

    Saeglitz, C; Pohl, M; Bartsch, D

    2000-12-01

    One of the most discussed environmental effects associated with the use of transgenic plants is the flow of genes to plants in the environment. The flow of genes may occur through pollen since it is the reproductive system that is designed for gene movement. Pollen-mediated gene escape is hard to control in mating plants. Pollen from a wind pollinator can move over distances of more than 1000 m. To investigate the efficiency of transgenic pollen movement under realistic environmental conditions, the use of bait plants might be an effective tool. In this study, cytoplasmic male-sterile (CMS) sugar beets were tested with regard to their potential for monitoring transgene flow. As the pollen source, transgenic sugar beets were used that express recombinant DNA encoding viral (beet necrotic yellow vein virus) resistance, and antibiotic (kanamycin) and herbicide (glufosinate) tolerance genes. In a field trial, the effectiveness of a hemp (Cannabis sativa) stripe containment strategy was tested by measuring the frequency of pollinated CMS bait plants placed at different distances and directions from a transgenic pollen source. The results demonstrated the ineffectiveness of the containment strategy. Physiological and molecular tests confirmed the escape and production of transgenic offspring more than 200 m behind the hemp containment. Since absolute containment is unlikely to be effective, the CMS-bait plant detection system is a useful tool for other monitoring purposes.

  7. Gene flow in Prunus species in the context of novel trait risk assessment.

    Science.gov (United States)

    Cici, S Zahra H; Van Acker, Rene C

    2010-01-01

    Prunus species are important commercial fruit (plums, apricot, peach and cherries), nut (almond) and ornamental trees cultivated broadly worldwide. This review compiles information from available literature on Prunus species in regard to gene flow and hybridization within this complex of species. The review serves as a resource for environmental risk assessment related to pollen mediated gene flow and the release of transgenic Prunus. It reveals that Prunus species, especially plums and cherries show high potential for transgene flow. A range of characteristics including; genetic diversity, genetic bridging capacity, inter- and intra-specific genetic compatibility, self sterility (in most species), high frequency of open pollination, insect assisted pollination, perennial nature, complex phenotypic architecture (canopy height, heterogeneous crown, number of flowers produced in an individual plant), tendency to escape from cultivation, and the existence of ornamental and road side Prunus species suggest that there is a tremendous and complicated ability for pollen mediated gene movement among Prunus species. Ploidy differences among Prunus species do not necessarily provide genetic segregation. The characteristics of Prunu s species highlight the complexity of maintaining coexistence between GM and non-GM Prunus if there were commercial production of GM Prunus species. The results of this review suggest that the commercialization of one GM Prunus species can create coexistence issues for commercial non-GM Prunus production. Despite advances in molecular markers and genetic analysis in agroecology, there remains limited information on the ecological diversity, metapopulation nature, population dynamics, and direct measures of gene flow among different subgenera represented in the Prunus genus. Robust environmental impact, biosafety and coexistence assessments for GM Prunus species will require better understanding of the mechanisms of gene flow and hybridization

  8. Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus).

    Science.gov (United States)

    Pérez-Espona, S; Pérez-Barbería, F J; McLeod, J E; Jiggins, C D; Gordon, I J; Pemberton, J M

    2008-02-01

    Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 x 87 km), significant population structure was found using F-statistics (F(ST) = 0.019) and the program structure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.

  9. Divergence and gene flow in the globally distributed blue-winged ducks

    Science.gov (United States)

    Nelson, Joel; Wilson, Robert E.; McCracken, Kevin G.; Cumming, Graeme; Joseph, Leo; Guay, Patrick-Jean; Peters, Jeffrey

    2016-01-01

    The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence-with-gene-flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue-winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub-lineages, the globally-distributed shoveler group and the New World blue-winged/cinnamon teal group. The blue-winged/cinnamon sub-lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler (A. clypeata) and the more sedentary, African Cape shoveler (A. smithii) into the Australasian shoveler (A. rhynchotis), although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue-winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.

  10. Interactions between the amnioserosa and the epidermis revealed by the function of the u-shaped gene

    Directory of Open Access Journals (Sweden)

    Karolina Lada

    2012-02-01

    Dorsal closure (DC is an essential step during Drosophila development whereby a hole is sealed in the dorsal epidermis and serves as a model for cell sheet morphogenesis and wound healing. It involves the orchestrated interplay of transcriptional networks and dynamic regulation of cell machinery to bring about shape changes, mechanical forces, and emergent properties. Here we provide insight into the regulation of dorsal closure by describing novel autonomous and non-autonomous roles for U-shaped (Ush in the amnioserosa, the epidermis, and in mediation of communication between the tissues. We identified Ush by gene expression microarray analysis of Dpp signaling targets and show that Ush mediates some DC functions of Dpp. By selectively restoring Ush function in either the AS or the epidermis in ush mutants, we show that the AS makes a greater (Ush-dependent contribution to closure than the epidermis. A signal from the AS induces epidermal cell elongation and JNK activation in the DME, while cable formation requires Ush on both sides of the leading edge, i.e. in both the AS and epidermis. Our study demonstrates that the amnioserosa and epidermis communicate at several steps during the process: sometimes the epidermis instructs the amnioserosa, other times the AS instructs the epidermis, and still other times they appear to collaborate.

  11. Negative control of cell division by mreB, a gene that functions in determining the rod shape of Escherichia coli cells.

    Science.gov (United States)

    Wachi, M; Matsuhashi, M

    1989-06-01

    Exponentially growing Escherichia coli cells containing additional copies of the shape-determining gene mreB were found to be elongated, whereas mreB mutant cells were spherical and overproduced penicillin-binding protein 3, a septum peptidoglycan synthetase. The effect of the mreB gene on expression of ftsI, the structural gene for penicillin-binding protein 3, was examined by using an ftsI-lacZ fusion gene on a plasmid. Formation of beta-galactosidase from the fusion gene was significantly increased in mreB129 mutant cells, and its overproduction was suppressed to a normal level by the presence of a plasmid containing the mreB gene. These results indicate a negative mechanism of control of cell division by this morphology gene and suggest that the gene functions in determining whether division or elongation of the cells occurs.

  12. Shaping the nervous system: role of the core planar cell polarity genes.

    Science.gov (United States)

    Tissir, Fadel; Goffinet, André M

    2013-08-01

    Planar cell polarity (PCP) is complementary to the intrinsic polarization of single cells and refers to the global coordination of cell behaviour in the plane of a tissue and, by extension, to the signalling pathways that control it. PCP is most evident in cell sheets, and research into PCP was for years confined to studies in Drosophila melanogaster. However, PCP has more recently emerged as an important phenomenon in vertebrates, in which it regulates various developmental processes and is associated with multiple disorders. In particular, core PCP genes are crucial for the development and function of the nervous system. They are involved in neural tube closure, ependymal polarity, neuronal migration, dendritic growth and axon guidance.

  13. Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior.

    Science.gov (United States)

    Kramer, Peter; Bressan, Paola

    2015-07-01

    Psychologists and psychiatrists tend to be little aware that (a) microbes in our brains and guts are capable of altering our behavior; (b) viral DNA that was incorporated into our DNA millions of years ago is implicated in mental disorders; (c) many of us carry the cells of another human in our brains; and (d) under the regulation of viruslike elements, the paternally inherited and maternally inherited copies of some genes compete for domination in the offspring, on whom they have opposite physical and behavioral effects. This article provides a broad overview, aimed at a wide readership, of the consequences of our coexistence with these selfish entities. The overarching message is that we are not unitary individuals but superorganisms, built out of both human and nonhuman elements; it is their interaction that determines who we are.

  14. 基于欧氏Ricci流的形状分析算法%Shape Analysis Algorithm Based on Euclidean Ricci Flow

    Institute of Scientific and Technical Information of China (English)

    董绍毅

    2014-01-01

    针对Ricci流强大的功能,提出了一种基于欧氏Ricci曲率流的形状分析算法,利用欧氏Ricci曲率流方法将双连通曲面映射为一个平面图像,通过测量平面图像内圆和外圆的半径,此曲面的共形模被给出,通过比较共形模的值,建立了曲面之间的形状分析算法。采用计算机模拟该算法,验证了在曲面的形状分析中有良好的性能。%The Ricci flow is a powerful curvature flow method. This paper presents a new shape analysis algorithm. A doublely connected surface maps a planar image by using Euclidean Ricci curvature flow method, via measuring the radius of inter circle and outer circle of the image, a conformal modules of the surface is given, by comparing the value of conformal modules, the shape analysis algorithm can be easily established between surfaces. Experiments comparison results show that it has a good performance for shape analysis of surface.

  15. The effect of channel shape, bed morphology, and shipwrecks on flow velocities in the Upper St. Clair River

    Science.gov (United States)

    Czuba, Jonathan A.; Oberg, Kevin; Best, Jim; Parsons, Daniel R.

    2009-01-01

    In the Great Lakes of North America, the St. Clair River is the major outlet of Lake Huron and conveys water to Lake St. Clair which then flows to Lake Erie. One major topic of interest is morphological change in the St. Clair River and its impact on water levels in the Upper Great Lakes and connecting channel flows. A combined multibeam echosounder (MBES) bathymetric survey and acoustic Doppler current profiler (ADCP) flow survey of the outlet of Lake Huron and the Upper St. Clair River was conducted July 21 – 25, 2008. This paper presents how channel morphology and shipwrecks affect the flow in the Upper St. Clair River. The river is most constricted at the Blue Water Bridge near Port Huron, Michigan, with water velocities over 2 ms-1 for a flow of 5,200 m3s-1. Downstream of this constriction, the river flows around a bend and expands creating a large recirculation zone along the left bank due to flow separation. This recirculation zone reduces the effective channel width, and thus increases flow velocities to over 2 ms-1 in this region. The surveys reveal several shipwrecks on the bed of the St. Clair River, which possess distinct wakes in their flow velocity downstream of the wrecks. The constriction and expansion of the channel, combined with forcing of the flow by bed topography, initiates channel-scale secondary flow, creating streamwise vortices that maintain coherence downstream over a distance of several channel widths.

  16. High rates of gene flow by pollen and seed in oak populations across Europe.

    Directory of Open Access Journals (Sweden)

    Sophie Gerber

    Full Text Available Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea distributed across Europe. Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423, mapped, and acorns were collected ([17,147], 51 from several mother trees ([3], [47], 23. Seedlings ([65,387], 178 were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5-8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale. On average, the percentage of the wind-borne pollen from outside the stand was 60%, with large variation among stands (21-88%. Mean seed immigration into the stand was 40%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20-66%. Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation. Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.

  17. Gene-splitting technology: a novel approach for the containment of transgene flow in Nicotiana tabacum.

    Directory of Open Access Journals (Sweden)

    Xu-Jing Wang

    Full Text Available The potential impact of transgene escape on the environment and food safety is a major concern to the scientists and public. This work aimed to assess the effect of intein-mediated gene splitting on containment of transgene flow. Two fusion genes, EPSPSn-In and Ic-EPSPSc, were constructed and integrated into N. tabacum, using Agrobacterium tumefaciens-mediated transformation. EPSPSn-In encodes the first 295 aa of the herbicide resistance gene 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS fused with the first 123 aa of the Ssp DnaE intein (In, whereas Ic-EPSPSc encodes the 36 C-terminal aa of the Ssp DnaE intein (Ic fused to the rest of EPSPS C terminus peptide sequences. Both EPSPSn-In and Ic-EPSPSc constructs were introduced into the same N. tabacum genome by genetic crossing. Hybrids displayed resistance to the herbicide N-(phosphonomethyl-glycine (glyphosate. Western blot analysis of protein extracts from hybrid plants identified full-length EPSPS. Furthermore, all hybrid seeds germinated and grew normally on glyphosate selective medium. The 6-8 leaf hybrid plants showed tolerance of 2000 ppm glyphosate in field spraying. These results indicated that functional EPSPS protein was reassembled in vivo by intein-mediated trans-splicing in 100% of plants. In order to evaluate the effect of the gene splitting technique for containment of transgene flow, backcrossing experiments were carried out between hybrids, in which the foreign genes EPSPSn-In and Ic-EPSPSc were inserted into different chromosomes, and non-transgenic plants NC89. Among the 2812 backcrossing progeny, about 25% (664 plantlets displayed glyphosate resistance. These data indicated that transgene flow could be reduced by 75%. Overall, our findings provide a new and highly effective approach for biological containment of transgene flow.

  18. Contrasting demographic history and gene flow patterns of two mangrove species on either side of the Central American Isthmus.

    Science.gov (United States)

    Cerón-Souza, Ivania; Gonzalez, Elena G; Schwarzbach, Andrea E; Salas-Leiva, Dayana E; Rivera-Ocasio, Elsie; Toro-Perea, Nelson; Bermingham, Eldredge; McMillan, W Owen

    2015-08-01

    Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed

  19. Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes.

    Science.gov (United States)

    Sutton, Jolene T; Nakagawa, Shinichi; Robertson, Bruce C; Jamieson, Ian G

    2011-11-01

    The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of different evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta-analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is ∼15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency-dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre-bottlenecked populations. © 2011 Blackwell Publishing Ltd.

  20. The role of genetic biases in shaping the correlations between languages and genes.

    Science.gov (United States)

    Dediu, Dan

    2008-09-21

    It has recently been proposed [Dediu, D., Ladd, D.R., 2007. Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin. Proc. Natl Acad. Sci. USA 104(26), 10944-10949] that genetically coded linguistic biases can influence the trajectory of language change. However, the nature of such biases and the conditions under which they can become manifest have remained vague. The present paper explores computationally two plausible types of linguistic acquisition biases in a population of agents implementing realistic genetic, linguistic and demographic processes. One type of bias represents an innate asymmetric initial state (initial expectation bias) while the other an innate asymmetric facility of acquisition (rate of learning bias). It was found that only the second type of bias produces detectable effects on language through cultural transmission across generations and that such effects are produced even by weak biases present at low frequencies in the population. This suggests that learning preference asymmetries, very small at the individual level and not very frequent at the population level, can bias the trajectory of language change through the process of cultural transmission.

  1. Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens.

    Science.gov (United States)

    Cooper, Brandon S; Burrus, Chad R; Ji, Chao; Hahn, Matthew W; Montooth, Kristi L

    2015-08-21

    Deleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (Ne) of the mitochondrial DNA and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes from Drosophila melanogaster and nuclear data available from the same samples, we reexamine the hypothesis that nonrecombining animal mitochondrial DNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction in Ne. Nevertheless, we find that the neutrality index, a measure of the excess of nonsynonymous polymorphism relative to the neutral expectation, is only weakly significantly different between mitochondrial and nuclear loci. This difference is likely the result of the larger proportion of beneficial mutations in X-linked relative to autosomal loci, and we find little to no difference between mitochondrial and autosomal neutrality indices. Reanalysis of published data from Homo sapiens reveals a similar lack of a difference between the two genomes, although previous studies have suggested a strong difference in both species. Thus, despite a smaller Ne, mitochondrial loci of both flies and humans appear to experience similar efficacies of purifying selection as do loci in the recombining nuclear genome.

  2. A functional NPSR1 gene variant and environment shape personality and impulsive action: a longitudinal study.

    Science.gov (United States)

    Laas, Kariina; Reif, Andreas; Kiive, Evelyn; Domschke, Katharina; Lesch, Klaus-Peter; Veidebaum, Toomas; Harro, Jaanus

    2014-03-01

    Neuropeptide S and its receptor NPSR1 are involved in the regulation of arousal, attention and anxiety. We examined whether the NPSR1 gene functional polymorphism Asn¹⁰⁷Ile (rs324981, A>T) influences personality, impulsivity, and attention-deficit/hyperactivity disorder (ADHD)-related symptoms in a population-representative sample, and whether any eventual associations depend on age, sex, family relations and stressful life events (SLE). We used self-reports or teachers' ratings for both the younger (n=593) and older (n=583) cohort of the longitudinal Estonian Children Personality, Behaviour and Health Study. Males with the TT genotype displayed more ADHD-related symptoms. Adaptive impulsivity and Extraversion increased the most from age 18 to 25. While highest increases were observed in AA men, TT women exhibited the largest decreases. For participants with the AA genotype, Warmth in family was inversely associated with Neuroticism, and positively associated with Extraversion and Adaptive impulsivity. High exposure to SLE increased impulsivity and ADHD scores in TT genotype subjects. We conclude that the NPSR1 A/T polymorphism is associated with impulsivity, ADHD symptoms and personality, mirroring the activity- and anxiety-mediating role of NPSR1. Heterozygous individuals were the least sensitive to environmental factors, whereas subjects with the AA genotype and TT genotype reacted to different types of environmental adversities.

  3. Wind flow and wind loads on the surface of a tower-shaped building:Numerical simulations and wind tunnel experiment

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Flow structure and wind pressure distribution caused by obtuse obstacles are usually the focuses in Computational Wind Engineer researches (CWE). By solving the non-hydrostatical dynamic equations, PUMA model (Peking University Model of Atmospheric Environment) was developed and applied to simulating the flow structure and wind pressure distribution around a tower-shaped building. Evaluation about the wind environment and wind loads around the building was obtained through the analysis of the numerical simulation results and wind tunnel data. Comparisons between the simulation and wind tunnel study indicate that numerical simulation results agree well in the flow field and wind pressure distribution around the tower-shaped building. On the other hand, the horizontal grid interval of 2 m and the vertical grid of 3 m were still too crude to simulate the flow structure and wind pressure distribution on the building surface more exactly in detail; and the absence of suitable pressure perturbation parameterization scheme between the solid and the adjacent space also limits the accuracy of the numerical simulation. The numerical simulation model can be used to evaluate the wind environment and wind load around high buildings.

  4. Minimally-Invasive Gene Transfection by Chemical and Physical Interaction of Atmospheric Pressure Plasma Flow

    Science.gov (United States)

    Kaneko, Toshiro

    2014-10-01

    Non-equilibrium atmospheric pressure plasma irradiated to the living-cell is investigated for medical applications such as gene transfection, which is expected to play an important role in molecular biology, gene therapy, and creation of induced pluripotent stem (iPS) cells. However, the conventional gene transfection using the plasma has some problems that the cell viability is low and the genes cannot be transferred into some specific lipid cells, which is attributed to the unknown mechanism of the gene transfection using the plasma. Therefore, the time-controlled atmospheric pressure plasma flow is generated and irradiated to the living-cell suspended solution for clarifying the transfection mechanism toward developing highly-efficient and minimally- invasive gene transfection system. In this experiment, fluorescent dye YOYO-1 is used as the simulated gene and LIVE/DEAD Stain is simultaneously used for cell viability assay. By the fluorescence image, the transfection efficiency is calculated as the ratio of the number of transferred and surviving cells to total cell count. It is clarified that the transfection efficiency is significantly increased by the short-time (cell viability (>90%). This result indicates that the physical effects such as the electric field caused by the charged particles arriving at the surface of the cell membrane, and chemical effects associated with plasma-activated products in solution act synergistically to enhance the cell-membrane transport with low-damage. This work was supported by JSPS KAKENHI Grant Number 24108004.

  5. In Situ Gene Expression Responsible for Sulfide Oxidation and CO2 Fixation of an Uncultured Large Sausage-Shaped Aquificae Bacterium in a Sulfidic Hot Spring.

    Science.gov (United States)

    Tamazawa, Satoshi; Yamamoto, Kyosuke; Takasaki, Kazuto; Mitani, Yasuo; Hanada, Satoshi; Kamagata, Yoichi; Tamaki, Hideyuki

    2016-06-25

    We investigated the in situ gene expression profile of sulfur-turf microbial mats dominated by an uncultured large sausage-shaped Aquificae bacterium, a key metabolic player in sulfur-turfs in sulfidic hot springs. A reverse transcription-PCR analysis revealed that the genes responsible for sulfide, sulfite, and thiosulfate oxidation and carbon fixation via the reductive TCA cycle were continuously expressed in sulfur-turf mats taken at different sampling points, seasons, and years. These results suggest that the uncultured large sausage-shaped bacterium has the ability to grow chemolithoautotrophically and plays key roles as a primary producer in the sulfidic hot spring ecosystem in situ.

  6. Involvement of calcitonin gene-related peptide in migraine: regional cerebral blood flow and blood flow velocity in migraine patients

    DEFF Research Database (Denmark)

    Lassen, L.H.; Jacobsen, V.B.; Haderslev, P.A.

    2008-01-01

    g/min) or placebo for 20 min was studied in 12 patients with migraine without aura outside attacks. Xenon-133 inhalation SPECT-determined regional cerebral blood flow (rCBF) and transcranial Doppler (TCD)-determined blood velocity (V-mean) in the middle cerebral artery (MCA), as well as the heart......Calcitonin gene-related peptide (CGRP)-containing nerves are closely associated with cranial blood vessels. CGRP is the most potent vasodilator known in isolated cerebral blood vessels. CGRP can induce migraine attacks, and two selective CGRP receptor antagonists are effective in the treatment...... of migraine attacks. It is therefore important to investigate its mechanism of action in patients with migraine. We here investigate the effects of intravenous human alpha-CGRP (h alpha CGRP) on intracranial hemodynamics. In a double-blind, cross-over study, the effect of intravenous infusion of haCGRP (2 mu...

  7. Evidence for gene flow between two sympatric mealybug species (Insecta; Coccoidea; Pseudococcidae).

    Science.gov (United States)

    Kol-Maimon, Hofit; Ghanim, Murad; Franco, José Carlos; Mendel, Zvi

    2014-01-01

    Occurrence of inter-species hybrids in natural populations might be evidence of gene flow between species. In the present study we found evidence of gene flow between two sympatric, genetically related scale insect species--the citrus mealybug Planococcus citri (Risso) and the vine mealybug Planococcus ficus (Signoret). These species can be distinguished by morphological, behavioral, and molecular traits. We employed the sex pheromones of the two respective species to study their different patterns of male attraction. We also used nuclear ITS2 (internal transcribed spacer 2) and mitochondrial COI (Cytochrome c oxidase sub unit 1) DNA sequences to characterize populations of the two species, in order to demonstrate the outcome of a possible gene flow between feral populations of the two species. Our results showed attraction to P. ficus pheromones of all tested populations of P. citri males but not vice versa. Furthermore, ITS2 sequences revealed the presence of 'hybrid females' among P. citri populations but not among those of P. ficus. 'hybrid females' from P. citri populations identified as P. citri females according to COI sequences. We offer two hypotheses for these results. 1) The occurrence of phenotypic and genotypic traits of P. ficus in P. citri populations may be attributed to both ancient and contemporary gene flow between their populations; and 2) we cannot rule out that an ancient sympatric speciation by which P. ficus emerged from P. citri might have led to the present situation of shared traits between these species. In light of these findings we also discuss the origin of the studied species and the importance of the pherotype phenomenon as a tool with which to study genetic relationships between congener scale insects.

  8. Evidence for gene flow between two sympatric mealybug species (Insecta; Coccoidea; Pseudococcidae.

    Directory of Open Access Journals (Sweden)

    Hofit Kol-Maimon

    Full Text Available Occurrence of inter-species hybrids in natural populations might be evidence of gene flow between species. In the present study we found evidence of gene flow between two sympatric, genetically related scale insect species--the citrus mealybug Planococcus citri (Risso and the vine mealybug Planococcus ficus (Signoret. These species can be distinguished by morphological, behavioral, and molecular traits. We employed the sex pheromones of the two respective species to study their different patterns of male attraction. We also used nuclear ITS2 (internal transcribed spacer 2 and mitochondrial COI (Cytochrome c oxidase sub unit 1 DNA sequences to characterize populations of the two species, in order to demonstrate the outcome of a possible gene flow between feral populations of the two species. Our results showed attraction to P. ficus pheromones of all tested populations of P. citri males but not vice versa. Furthermore, ITS2 sequences revealed the presence of 'hybrid females' among P. citri populations but not among those of P. ficus. 'hybrid females' from P. citri populations identified as P. citri females according to COI sequences. We offer two hypotheses for these results. 1 The occurrence of phenotypic and genotypic traits of P. ficus in P. citri populations may be attributed to both ancient and contemporary gene flow between their populations; and 2 we cannot rule out that an ancient sympatric speciation by which P. ficus emerged from P. citri might have led to the present situation of shared traits between these species. In light of these findings we also discuss the origin of the studied species and the importance of the pherotype phenomenon as a tool with which to study genetic relationships between congener scale insects.

  9. Historical divergence and gene flow: coalescent analyses of mitochondrial, autosomal and sex-linked loci in Passerina buntings.

    Science.gov (United States)

    Carling, Matthew D; Lovette, Irby J; Brumfield, Robb T

    2010-06-01

    Quantifying the role of gene flow during the divergence of closely related species is crucial to understanding the process of speciation. We collected DNA sequence data from 20 loci (one mitochondrial, 13 autosomal, and six sex-linked) for population samples of Lazuli Buntings (Passerina amoena) and Indigo Buntings (Passerina cyanea) (Aves: Cardinalidae) to test explicitly between a strict allopatric speciation model and a model in which divergence occurred despite postdivergence gene flow. Likelihood ratio tests of coalescent-based population genetic parameter estimates indicated a strong signal of postdivergence gene flow and a strict allopatric speciation model was rejected. Analyses of partitioned datasets (mitochondrial, autosomal, and sex-linked) suggest the overall gene flow patterns are driven primarily by autosomal gene flow, as there is no evidence of mitochondrial gene flow and we were unable to reject an allopatric speciation model for the sex-linked data. This pattern is consistent with either a parapatric divergence model or repeated periods of allopatry with gene flow occurring via secondary contact. These results are consistent with the low fitness of female avian hybrids under Haldane's rule and demonstrate that sex-linked loci likely are important in the initial generation of reproductive isolation, not just its maintenance.

  10. Gene flow from genetically modified herbicide-resistant rapeseed to cruciferous weeds

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiangxiang; XIA Qiuxia; LU Dalei; LU Weiping; QI Cunkou; PU Huiming; LIU Geshan; ZHAO Jian; WANG Youping

    2006-01-01

    The sexual compatibility between genetically modified (GM) glyphosate-resistant rapeseed variety Q3 (Brassica napus L. ) and 5 cruciferous weeds is studied through the observation of fluorescence microscopy and cross-fertility after manual pollination. The results indicated that Q3 (as male) was highly incompatible with Thlaspi arvense L., Capsella bursa-pastoris (L.) Medic, Cardamine hirsuta L. and Rorippa palustris (L.) Besser (as female). Fluorescence microscopic observation showed that growing of pollen tubes terminated on the stigma surface or at the upper 1/3 part of the style. However, B. juncea×Q3 was compatible, and the compatibility index was 1.65. Under the neighboring growth and natural pollination conditions, the rates of gene flow from Q3 to T. arvense, C.bursa-pastoris, C. hirsute and R. palustris were all 0, while it was 0.86 % for B. juncea. These results indicate that there is difference in the rate of gene flow between GM rapeseed and cruciferous wild weeds, and frequency of gene flow is highly correlated with sexual compatibility.

  11. Identification of landscape features influencing gene flow: How useful are habitat selection models?

    Science.gov (United States)

    Roffler, Gretchen H.; Schwartz, Michael K.; Pilgrim, Kristy L.; Talbot, Sandra; Sage, Kevin; Adams, Layne G.; Luikart, Gordon

    2016-01-01

    Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

  12. Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii).

    Science.gov (United States)

    Ujvari, Beata; Dowton, Mark; Madsen, Thomas

    2008-08-01

    By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

  13. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

    Science.gov (United States)

    Scorza, Ralph; Kriss, Alissa B; Callahan, Ann M; Webb, Kevin; Demuth, Mark; Gottwald, Tim

    2013-01-01

    Pollen flow from a 0.46 ha plot of genetically engineered (GE) Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera) were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree) to 0.033-0.017% at longer distances (384-998 m). Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  14. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

    Directory of Open Access Journals (Sweden)

    Ralph Scorza

    Full Text Available Pollen flow from a 0.46 ha plot of genetically engineered (GE Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree to 0.033-0.017% at longer distances (384-998 m. Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  15. Possible effects of (trans)gene flow from crops on the genetic diversity from landraces and wild relatives.

    Science.gov (United States)

    Gepts, Paul; Papa, Roberto

    2003-01-01

    Gene flow is a potential concern associated with the use of transgenic crops because it could affect genetic diversity of related landraces and wild relatives. This concern has taken on added importance with the looming introduction of transgenic crops in centers of crop domestication (Mexico, China) and those producing pharmaceutical compounds. For gene flow to take place among cultivars and their wild relatives, several steps have to be fulfilled, including the presence of cultivars or wild relatives within pollen or seed dispersal range, the ability to produce viable and fertile hybrids, at least partial overlap in flowering time, actual gene flow by pollen or seed, and the establishment of crop genes in the domesticated or wild recipient populations. In contrast with domestication genes, which often make crops less adapted to natural ecosystems, transgenes frequently represent gains of function, which might release wild relatives from constraints that limit their fitness. In most sexually reproducing organisms, the chromosomal region affected by selection of a single gene amounts to a small percentage of the total genome size. Because of gene flow, the level of genetic diversity present in the domesticated gene pool becomes a crucial factor affecting the genetic diversity of the wild gene pool. For some crops, such as cotton and maize, the introduction of transgenic technologies has led to a consolidation of the seed industry and a reduction in the diversity of the elite crop gene pool. Thus, diversity in improved varieties grown by farmers needs to be monitored. Several areas deserve further study, such as the actual magnitude of gene flow and its determinants in different agroecosystems, the long-term effects of gene flow on genetic diversity both across gene pools and within genomes, the expression of transgenes in new genetic backgrounds, and the effects of socio-economic factors on genetic diversity.

  16. Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Andres, Ryan J; Coneva, Viktoriya; Frank, Margaret H; Tuttle, John R; Samayoa, Luis Fernando; Han, Sang-Won; Kaur, Baljinder; Zhu, Linglong; Fang, Hui; Bowman, Daryl T; Rojas-Pierce, Marcela; Haigler, Candace H; Jones, Don C; Holland, James B; Chitwood, Daniel H; Kuraparthy, Vasu

    2017-01-03

    Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.

  17. Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow.

    Science.gov (United States)

    van Strien, Maarten J; Keller, Daniela; Holderegger, Rolf; Ghazoul, Jaboury; Kienast, Felix; Bolliger, Janine

    2014-03-01

    For conservation managers, it is important to know whether landscape changes lead to increasing or decreasing gene flow. Although the discipline of landscape genetics assesses the influence of landscape elements on gene flow, no studies have yet used landscape-genetic models to predict gene flow resulting from landscape change. A species that has already been severely affected by landscape change is the large marsh grasshopper (Stethophyma grossum), which inhabits moist areas in fragmented agricultural landscapes in Switzerland. From transects drawn between all population pairs within maximum dispersal distance (landscape planning.

  18. Measuring gene flow from two birdsfoot trefoil (Lotus corniculatus) field trials using transgenes as tracer markers.

    Science.gov (United States)

    De Marchis, F; Bellucci, M; Arcioni, S

    2003-06-01

    Genetic engineering is becoming a useful tool in the improvement of plants but concern has been expressed about the potential environmental risks of releasing genetically modified (GM) organisms into the environment. Attention has focused on pollen dispersal as a major issue in the risk assessment of transgenic crop plants. In this study, pollen-mediated dispersal of transgenes via cross-fertilization was examined. Plants of Lotus corniculatus L. transformed with either the Escherichia coli asparagine synthetase gene asnA or the beta-glucuronidase gene uidA, were used as the pollen donor. Nontransgenic plants belonging to the species L. corniculatus L., L. tenuis Waldst. and Kit. ex Willd, and L. pedunculatus Cav., were utilized as recipients. Two experimental fields were established in two areas of central Italy. Plants carrying the uidA gene were partially sterile, therefore only the asnA gene was used as a tracer marker. No transgene flow between L. corniculatus transformants and the nontransgenic L. tenuis and L. pedunculatus plants was detected. As regards nontransgenic L. corniculatus plants, in one location flow of asnA transgene was detected up to 18 m from the 1.8 m2 donor plot. In the other location, pollen dispersal occurred up to 120 m from the 14 m2 pollinating plot.

  19. Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae).

    Science.gov (United States)

    Li, Xiao-Wei; Wang, Ping; Fail, Jozsef; Shelton, Anthony M

    2015-01-01

    Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction) and thelytoky (asexual reproduction). Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene) allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction.

  20. Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae.

    Directory of Open Access Journals (Sweden)

    Xiao-Wei Li

    Full Text Available Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction and thelytoky (asexual reproduction. Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction.

  1. Dielectrophoresis based continuous-flow nano sorter: fast quality control of gene vaccines.

    Science.gov (United States)

    Viefhues, Martina; Wegener, Sonja; Rischmüller, Anja; Schleef, Martin; Anselmetti, Dario

    2013-08-01

    We present a prototype nanofluidic device, developed for the continuous-flow dielectrophoretic (DEP) fractionation, purification, and quality control of sample suspensions for gene vaccine production. The device consists of a cross injector, two operation regions, and separate outlets where the analytes are collected. In each DEP operation region, an inhomogeneous electric field is generated at a channel spanning insulating ridge. The samples are driven by ac and dc voltages that generate a dielectrophoretic potential at the ridge as well as (linear) electrokinetics. Since the DEP potential differs at the two ridges, probes of three and more species can be iteratively fully fractionated. We demonstrate the fast and efficient separation of parental plasmid, miniplasmid, and minicircle DNA, where the latter is applicable as a gene vaccine. Since the present technique is virtually label-free, it offers a fast purification and in-process quality control with low consumption, in parallel, for the production of gene vaccines.

  2. Shape and flow fluctuations in ultracentral Pb + Pb collisions at the energies available at the CERN Large Hadron Collider

    Science.gov (United States)

    Shen, Chun; Qiu, Zhi; Heinz, Ulrich

    2015-07-01

    In ultracentral heavy-ion collisions, anisotropic hydrodynamic flow is generated by density fluctuations in the initial state rather than by geometric overlap effects. For a given centrality class, the initial fluctuation spectrum is sensitive to the method chosen for binning the events into centrality classes. We show that sorting events by total initial entropy or by total final multiplicity yields event classes with equivalent statistical fluctuation properties, in spite of viscous entropy production during the fireball evolution. With this initial entropy-based centrality definition we generate several classes of ultracentral Pb + Pb collisions at Cern Large Hadron Collider energies and evolve the events using viscous hydrodynamics with nonzero shear but vanishing bulk viscosity. Comparing the predicted anisotropic flow coefficients for charged hadrons with CMS data we find that both the Monte Carlo Glauber (MC-Glb) and Monte Carlo Kharzeev-Levin-Nardi (MC-KLN) models produce initial fluctuation spectra that are incompatible with the measured final anisotropic flow power spectrum, for any choice of the specific shear viscosity. In spite of this failure, we show that the hydrodynamic model can qualitatively explain, in terms of event-by-event fluctuations of the anisotropic flow coefficients and flow angles, the breaking of flow factorization for elliptic, triangular, and quadrangular flow measured by the CMS experiment. For elliptic flow, this factorization breaking is large in ultracentral collisions. We conclude that the bulk of the experimentally observed flow factorization breaking effects are qualitatively explained by hydrodynamic evolution of initial-state fluctuations, but that their quantitative description requires a better understanding of the initial fluctuation spectrum.

  3. Pollination between maize and teosinte: an important determinant of gene flow in Mexico.

    Science.gov (United States)

    Baltazar, Baltazar M; de Jesús Sánchez-Gonzalez, José; de la Cruz-Larios, Lino; Schoper, John B

    2005-02-01

    Gene flow between maize [Zea mays (L.)] and its wild relatives does occur, but at very low frequencies. Experiments were undertaken in Tapachula, Nayarit, Mexico to investigate gene flow between a hybrid maize, landraces of maize and teosinte (Z. mays ssp. mexicana, races Chalco and Central Plateau). Hybridization, flowering synchrony, pollen size and longevity, silk elongation rates, silk and trichome lengths and tassel diameter and morphology were measured. Hybrid and open-pollinated maize ears produced a mean of 8 and 11 seeds per ear, respectively, when hand-pollinated with teosinte pollen, which is approximately 1-2% of the ovules normally produced on a hybrid maize ear. Teosinte ears produced a mean of 0.2-0.3 seeds per ear when pollinated with maize pollen, which is more than one-fold fewer seeds than produced on a maize ear pollinated with teosinte pollen. The pollination rate on a per plant basis was similar in the context of a maize plant with 400-500 seeds and a teosinte plant with 30-40 inflorescences and 9-12 fruitcases per inflorescence. A number of other factors also influenced gene-flow direction: (1) between 90% and 95% of the fruitcases produced on teosinte that was fertilized by maize pollen were sterile; (2) teosinte collections were made in an area where incompatibility systems that limit fertilization are present; (3) silk longevity was much shorter for teosinte than for maize (approx. 4 days vs. approx. 11 days); (4) teosinte produced more pollen on a per plant basis than the landraces and commercial hybrid maize; (5) teosinte frequently produced lateral branches with silks close to a terminal tassel producing pollen. Collectively these factors tend to favor crossing in the direction of teosinte to maize. Our results support the hypothesis that gene flow and the subsequent introgression of maize genes into teosinte populations most probably results from crosses where teosinte first pollinates maize. The resultant hybrids then backcross with

  4. High-beta analytic equilibria in circular, elliptical, and D-shaped large aspect ratio axisymmetric configurations with poloidal and toroidal flows

    Science.gov (United States)

    López, O. E.; Guazzotto, L.

    2017-03-01

    The Grad-Shafranov-Bernoulli system of equations is a single fluid magnetohydrodynamical description of axisymmetric equilibria with mass flows. Using a variational perturbative approach [E. Hameiri, Phys. Plasmas 20, 024504 (2013)], analytic approximations for high-beta equilibria in circular, elliptical, and D-shaped cross sections in the high aspect ratio approximation are found, which include finite toroidal and poloidal flows. Assuming a polynomial dependence of the free functions on the poloidal flux, the equilibrium problem is reduced to an inhomogeneous Helmholtz partial differential equation (PDE) subject to homogeneous Dirichlet conditions. An application of the Green's function method leads to a closed form for the circular solution and to a series solution in terms of Mathieu functions for the elliptical case, which is valid for arbitrary elongations. To extend the elliptical solution to a D-shaped domain, a boundary perturbation in terms of the triangularity is used. A comparison with the code FLOW [L. Guazzotto et al., Phys. Plasmas 11(2), 604-614 (2004)] is presented for relevant scenarios.

  5. Flow-dependent regulation of vascular function and gene expression in rat superior mesenteric artery

    Institute of Scientific and Technical Information of China (English)

    XIA Shang; DENG Chang-sheng

    2009-01-01

    Background Mesenteric artery thrombosis is prone to occur at specific arterial regions with different fluid flow patterns,yet mechanistic links between blood flow and vascular function remain unclear. This study aired to investigate the role of blood flow in regulation of vascular function and gene expression in rats.Methods Isometric tension was recorded in wire myograph to examine vascular function of specific regions (trunk parts and proximal parts from the origin) with different blood flow in superior mesenteric artery (SMA). Endothelial nitric oxide syntheses (eNOS), phosphorylated-eNOS (p-eNOS), serine-threonine kinase Akt and phosphorylated-Akt (p-Akt) protein expressions in SMA were examined by Western blotting. Significance was analyzed using a Student's ttest or analysis of variance (ANOVA) followed by a Dunnett's multiple-comparison post hoc test.Results Compared with trunks, proximal parts exhibited severely impaired relaxant responses to acetylcholine (Ach) (1 nmol/L to 10 pmol/L) (P 0.05).Conclusion Critical components that drive the vascular function and influence the localization of mesenteric artery thrombosis are flow-responsive elements within the vascular endothelium.

  6. STUDY OF GENE FLOW FROM GM COTTON (Gossypium hirsutum VARIETIES IN “EL ESPINAL” (TOLIMA, COLOMBIA.

    Directory of Open Access Journals (Sweden)

    Alejandro Chaparro Giraldo

    2013-10-01

    Full Text Available In 2009, 4088 hectares of genetically modified (GM cotton were planted in Tolima (Colombia, however there is some uncertainty about containment measures needed to prevent the flow of pollen and seed from regulated GM fields into adjacent fields. In this study, the gene flow from GM cotton varieties to conventional or feral cotton plants via seed and pollen was evaluated. ImmunostripTM, PCR and ELISA assays were used to detect gene flow. Fifty six refuges, 27 fields with conventional cotton and four feral individuals of the enterprise “Remolinos Inc.” located in El Espinal (Tolima were analyzed in the first half of 2010. The results indicated seeds mediated gene flow in 45 refuges (80,4 % and 26 fields with conventional cotton (96 %, besides a pollen mediated gene flow in one field with conventional cotton and nine refuges. All fields cultivated with conventional cotton showed gene flow from GM cotton. Two refuges and two feral individuals did not reveal gene flow from GM cotton. 

  7. On the Flow and Fluidization of Granular Materials: Applications to Large Lunar Craters, Cliff Collapses and Asteroid Shapes

    Science.gov (United States)

    Holsapple, K. A.

    2011-03-01

    About flows of granular materials and assumptions about fluidization mechanisms to explain large flat craters and landslide run outs. No such mechanisms are needed, the reasons and examples are given.

  8. Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene phylogeography.

    Science.gov (United States)

    Kotlík, Petr; Marková, Silvia; Choleva, Lukás; Bogutskaya, Nina G; Ekmekçi, F Guler; Ivanova, Petya P

    2008-02-01

    The Black and Caspian Seas have experienced alternating periods of isolation and interconnection over many Milankovitch climate oscillations and most recently became separated when the meltwater overflow from the Caspian Sea ceased at the end of the last glaciation. Climate-induced habitat changes have indisputably had profound impacts on distribution and demography of aquatic species, yet uncertainties remain about the relative roles of isolation and dispersal in the response of species shared between the Black and Caspian Sea basins. We examined these issues using phylogeographical analysis of an anadromous cyprinid fish Rutilus frisii. Bayesian coalescence analyses of sequence variation at two nuclear and one mitochondrial genes suggest that the Black and Caspian Seas supported separate populations of R. frisii during the last glaciation. Parameter estimates from the fitted isolation-with-migration model showed that their separation was not complete, however, and that the two populations continued to exchange genes in both directions. These analyses also suggested that majority of migrations occurred during the Pleistocene, showing that the variation shared between the Black and Caspian Seas is the result of ancient dispersal along the temporary natural connections between the basins, rather than of incomplete lineage sorting or recent human-mediated dispersal. Gene flow between the refugial populations was therefore an important source of genetic variation, and we suggest that it facilitated the evolutionary response of the populations to changing climate.

  9. Hexavalent chromium reduction with scrap iron in continuous-flow system. Part 2: Effect of scrap iron shape and size.

    Science.gov (United States)

    Gheju, M; Balcu, I

    2010-10-15

    Hexavalent chromium reduction with scrap iron has the advantage that two wastes are treated simultaneously. The reduction of hexavalent chromium by scrap iron was investigated in continuous system, using as reducing agent the following scrap iron shapes and sizes: (1) spiral fibers, (2) shavings, and (3) powder. The shape and size of scrap iron were found to have a significant influence on chromium and iron species concentration in column effluent, on column effluent pH and on Cr(VI) reduction mechanism. While for large scrap iron particles (spiral fibers) homogeneous reduction is the dominant Cr(VI) reduction process, for small scrap iron particles (powder) heterogeneous reduction appears to be the dominant reaction contributing to Cr(VI) reduction. All three shapes and sizes investigated in this work have both advantages and disadvantages. If found in sufficient quantities, scrap iron powder seem to be the optimum shape and size for the continuous reduction of Cr(VI), due to the following advantages: (1) the greatest reduction capacity, (2) the most important pH increase in column effluent (up to 6.3), (3) no chromium was detected in the column effluent during the first 60 h of the experiment, and (4) the lowest steady-state Cr(VI) concentration observed in column effluent (3.7 mg/L). But, despite of a lower reduction capacity in comparison with powder particles, spiral fibers and shavings have the advantage to result in large quantities from the mechanic processing of steel.

  10. Acoustic scaling of anisotropic flow in shape-engineered events: implications for extraction of the specific shear viscosity of the quark gluon plasma

    Science.gov (United States)

    Lacey, Roy A.; Reynolds, D.; Taranenko, A.; Ajitanand, N. N.; Alexander, J. M.; Liu, Fu-Hu; Gu, Yi; Mwai, A.

    2016-10-01

    It is shown that the acoustic scaling patterns of anisotropic flow for different event shapes at a fixed collision centrality (shape-engineered events), provide robust constraints for the event-by-event fluctuations in the initial-state density distribution from ultrarelativistic heavy ion collisions. The empirical scaling parameters also provide a dual-path method for extracting the specific shear viscosity {(η /s)}{QGP} of the quark-gluon plasma (QGP) produced in these collisions. A calibration of these scaling parameters via detailed viscous hydrodynamical model calculations, gives {(η /s)}{QGP} estimates for the plasma produced in collisions of Au + Au (\\sqrt{{s}{NN}}=0.2 {TeV}) and Pb + Pb (\\sqrt{{s}{NN}}=2.76 {TeV}). The estimates are insensitive to the initial-state geometry models considered.

  11. Performance of vertical up-flow constructed wetlands on swine wastewater containing tetracyclines and tet genes.

    Science.gov (United States)

    Huang, Xu; Liu, Chaoxiang; Li, Ke; Su, Jianqiang; Zhu, Gefu; Liu, Lin

    2015-03-01

    Antibiotics and antibiotic resistance genes (ARGs) pollution in animal feeding farms received more public attention recently. Livestock wastewater contains large quantities of antibiotics and ARGs even after traditional lagoon treatment. In this study, the performance of vertical up-flow constructed wetlands (VUF-CWs) on swine wastewater containing tetracycline compounds (TCs) and tet genes was evaluated based on three aspects, TCs and tet genes removal efficiencies, residual TCs and tet genes in soils and plants, and the effect of TCs accumulation on nutrients removal and tet genes development. High removal efficiencies (69.0-99.9%) were achieved for oxytetracycline (OTC), tetracycline (TC) and chlortetracycline (CTC) with or without OTC spiked in the influent additionally. TCs concentrations in surface soils increased at first two sampling periods and then decreased after plants were harvested. Satisfactory nutrients removal efficiencies were also obtained, but TN and NH4-N removal efficiencies were significantly negative correlated with total concentration of TCs (∑TCs) in the soils (p < 0.01). The absolute abundances of all the target genes (tetO, tetM, tetW, tetA, tetX and intI1) were greatly reduced with their log units ranging from 0.26 to 3.3. However, the relative abundances of tetO, tetM and tetX in some effluent samples were significantly higher than those in the influent (p < 0.05). The relative abundances of tet genes except for tetO were significantly correlated with ∑TCs in the soils (p < 0.05). In summary, the proposed VUF-CWs are effective alternative for the removal of TCs and tet genes. But it is of great importance to prevent large accumulation of TCs in the soils. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Gene flow between sympatric life history forms of Oncorhynchus mykiss located above and below migratory barriers.

    Directory of Open Access Journals (Sweden)

    Donald M Van Doornik

    Full Text Available Oncorhynchus mykiss have a diverse array of life history types, and understanding the relationship among types is important for management of the species. Patterns of gene flow between sympatric freshwater resident O. mykiss, commonly known as rainbow trout, and anadromous O. mykiss, commonly known as steelhead, populations are complex and poorly understood. In this study, we attempt to determine the occurrence and pathways of gene flow and the degree of genetic similarity between sympatric resident and anadromous O. mykiss in three river systems, and investigate whether resident O. mykiss are producing anadromous offspring in these rivers, two of which have complete barriers to upstream migration. We found that the population structure of the O. mykiss in these rivers appears to be influenced more by the presence of a barrier to upstream migration than by life history type. The sex ratio of resident O. mykiss located above a barrier, and smolts captured in screw traps was significantly skewed in favor of females, whereas the reverse was true below the barriers, suggesting that male resident O. mykiss readily migrate downstream over the barrier, and that precocious male maturation may be occurring in the anadromous populations. Through paternity analyses, we also provide direct confirmation that resident O. mykiss can produce offspring that become anadromous. Most (89% of the resident O. mykiss that produced anadromous offspring were males. Our results add to the growing body of evidence that shows that gene flow does readily occur between sympatric resident and anadromous O. mykiss life history types, and indicates that resident O. mykiss populations may be a potential repository of genes for the anadromous life history type.

  13. Style perception-oriented product family shape gene design%面向风格意象的产品族外形基因设计

    Institute of Scientific and Technical Information of China (English)

    傅业焘; 罗仕鉴

    2012-01-01

    为继承和传递工业设计中的产品族外形知识,保持特殊的产品族外形和风格,塑造差异化品牌形象,将生物界基因遗传与变异理论引入产品族外形设计中,提出一种面向风格意象的产品族外形基因设计方法。通过分析产品族风格意象,构建产品族外形基因体系,划分了基因层次,建立了产品族风格意象(心理的意象特征)和外形基因(物理的外形特征)之间的映射模型。以电话机产品为例,提取了风格意象和外形基因,计算了外形基因在各风格意象中的贡献率,基于映射模型构建了面向风格意象的产品族外形基因建模与设计系统,实现了产品族外形基因与风格意象之间的双向推理。该系统能提高电话机的开发设计效率,验证了面向风格意象的产品族外形基因理论体系。%To inherit and transform shape knowledge of product family in industrial design, keep the unique shape and design style of product family and build different brand image, a perception-oriented product family shape gene de- sign method was proposed by introducing the gene theory and variability theory of biology into product family shape design. Through analyzing the perception of product family, the construction system of product family shape gene was constructed, the gene representation level was divided and the mapping model between style perception(mental perception)and shape gene(physical appearance)was set up. The telephone product was taken as an example, the style perception and shape gene were extracted, and the contribution rate of shape gene was calculated in style per- ception. Based on the mapping model, a style perception-oriented gene rapid modeling and design system was built to support the bidirectional reasoning between product family shape gene and style perception. Through this system, the design performance of telephone shape could be improved, and the theory

  14. Water Tank Experiments on Stratified Flow over Double Mountain-Shaped Obstacles at High-Reynolds Number

    Directory of Open Access Journals (Sweden)

    Ivana Stiperski

    2017-01-01

    Full Text Available In this article, we present an overview of the HyIV-CNRS-SecORo (Hydralab IV-CNRS-Secondary Orography and Rotors Experiments laboratory experiments carried out in the CNRM (Centre National de Recherches Météorologiques large stratified water flume. The experiments were designed to systematically study the influence of double obstacles on stably stratified flow. The experimental set-up consists of a two-layer flow in the water tank, with a lower neutral and an upper stable layer separated by a sharp density discontinuity. This type of layering over terrain is known to be conducive to a variety of possible responses in the atmosphere, from hydraulic jumps to lee waves and highly turbulent rotors. In each experiment, obstacles were towed through the tank at a constant speed. The towing speed and the size of the tank allowed high Reynolds-number flow similar to the atmosphere. Here, we present the experimental design, together with an overview of laboratory experiments conducted and their results. We develop a regime diagram for flow over single and double obstacles and examine the parameter space where the secondary obstacle has the largest influence on the flow. Trapped lee waves, rotors, hydraulic jumps, lee-wave interference and flushing of the valley atmosphere are successfully reproduced in the stratified water tank. Obstacle height and ridge separation distance are shown to control lee-wave interference. Results, however, differ partially from previous findings on the flow over double ridges reported in the literature due to the presence of nonlinearities and possible differences in the boundary layer structure. The secondary obstacle also influences the transition between different flow regimes and makes trapped lee waves possible for higher Froude numbers than expected for an isolated obstacle.

  15. Solution strategies for finite elements and finite volumes methods applied to flow and heat transfer problem in U-shaped geothermal exchangers

    Science.gov (United States)

    Egidi, Nadaniela; Giacomini, Josephin; Maponi, Pierluigi

    2016-06-01

    Matter of this paper is the study of the flow and the corresponding heat transfer in a U-shaped heat exchanger. We propose a mathematical model that is formulated as a forced convection problem for incompressible and Newtonian fluids and results in the unsteady Navier-Stokes problem. In order to get a solution, we discretise the equations with both the Finite Elements Method and the Finite Volumes Method. These procedures give rise to a non-symmetric indefinite quadratic system of equations. Thus, three regularisation techniques are proposed to make approximations effective and ideas to compare their results are provided.

  16. Generalized event shape and energy flow studies in $e^+ e^-$ annihilation at $\\sqrt{s}$ = 91.2-208.0 GeV

    CERN Document Server

    Achard, P; Aguilar-Benitez, M; Alcaraz, J; Alemanni, G; Allaby, J; Aloisio, A; Alviggi, M G; Anderhub, H; Andreev, V P; Anselmo, F; Arefiev, A; Azemoon, T; Aziz, T; Bagnaia, P; Bajo, A; Baksay, G; Baksay, L; Baldew, S V; Banerjee, S; Banerjee, Sw; Barczyk, A; Barillere, R; Bartalini, P; Basile, M; Batalova, N; Battiston, R; Bay, A; Becker, U; Behner, F; Bellucci, L; Berbeco, R; Berdugo, J; Berges, P; Bertucci, B; Betev, B L; Biasini, M; Biglietti, M; Biland, A; Blaising, J J; Blyth, S C; Bobbink, G J; Bohm, A; Boldizsar, L; Borgia, B; Bottai, S; Bourilkov, D; Bourquin, M; Braccini, S; Branson, J G; Brochu, F; Burger, J D; Burger, W J; Cai, X D; Capell, M; Romeo, G Cara; Carlino, G; Cartacci, A; Casaus, J; Cavallari, F; Cavallo, N; Cecchi, C; Cerrada, M; Chamizo, M; Chang, Y H; Chemarin, M; Chen, A; Chen, G; Chen, G M; Chen, H F; Chen, H S; Chiefari, G; Cifarelli, L; Cindolo, F; Clare, I; Clare, R; Coignet, G; Colino, N; Costantini, S; Cruz, B; Cucciarelli, S; de Asmundis, R; Deglon, P; Debreczeni, J; Degre, A; Dehmelt, K; Deiters, K; Della Volpe, D; Delmeire, E; Denes, P; DeNotaristefani, F; De Salvo, A; Diemoz, M; Dierckxsens, M; Dionisi, C; Dittmar, M; Doria, A; Dova, M T; Duchesneau, D; Duda, M; Echenard, B; Eline, A; El Hage, A; Mamouni, H; Engler, A; Eppling, F J; Extermann, P; Falagan, M A; Falciano, S; Favara, A; Fay, J; Fedin, O; Felcini, M; Ferguson, T; Fesefeldt, H; Fiandrini, E; Field, J H; Filthaut, F; Fisher, P H; Fisher, W; Forconi, G; Freudenreich, K; Furetta, C; Galaktionov, Yu; Ganguli, S N; Garcia-Abia, P; Gataullin, M; Gentile, S; Giagu, S; Gong, Z F; Grenier, G; Grimm, O; Gruenewald, M W; Gupta, V K; Gurtu, A; Gutay, L J; Haas, D; Hatzifotiadou, D; Hebbeker, T; Herve, A; Hirschfelder, J; Hofer, H; Hohlmann, M; Holzner, G; Hou, S R; Jin, B N; Jindal, P; Jones, L W; de Jong, P; Josa-Mutuberria, I; Kaur, M; Kienzle-Focacci, M N; Kim, J K; Kirkby, J; Kittel, W; Klimentov, A; Konig, A C; Kopal, M; Koutsenko, V; Kraber, M; Kraemer, R W; Kruger, A; Kunin, A; Ladron de Guevara, P; Laktineh, I; Landi, G; Lebeau, M; Lebedev, A; Lebrun, P; Lecomte, P; Lecoq, P; Le Coultre, P; Le Goff, J M; Leiste, R; Levtchenko, M; Levtchenko, P; Li, C; Likhoded, S; Lin, C H; Lin, W T; Linde, F L; Lista, L; Liu, Z A; Lohmann, W; Longo, E; Lu, Y S; Luci, C; Luminari, L; Lustermann, W; Ma, W G; Malgeri, L; Malinin, A; Mana, C; Mans, J; Martin, J P; Marzano, F; Mazumdar, K; McNeil, R R; Mele, S; Merola, L; Meschini, M; Metzger, W J; Mihul, A; Milcent, H; Mirabelli, G; Mnich, J; Mohanty, G B; Muanza, G S; Muijs, A J M; Musy, M; Nagy, S; Natale, S; Napolitano, M; Nessi-Tedaldi, F; Newman, H; Nisati, A; Novak, T; Nowak, H; Ofierzynski, R; Organtini, G; Pal, I; Palomares, C; Paolucci, P; Paramatti, R; Passaleva, G; Patricelli, S; Paul, T; Pauluzzi, M; Paus, C; Pauss, F; Pedace, M; Pensotti, S; Perret-Gallix, D; Piccolo, D; Pierella, F; Pieri, M; Pioppi, M; Piroue, P A; Pistolesi, E; Plyaskin, V; Pohl, M; Pojidaev, V; Pothier, J; Prokofiev, D; Rahal-Callot, G; Rahaman, M A; Raics, P; Raja, N; Ramelli, R; Rancoita, P G; Ranieri, R; Raspereza, A; Razis, P; Rembeczki, S; Ren, D; Rescigno, M; Reucroft, S; Riemann, S; Riles, K; Roe, B P; Romero, L; Rosca, A; Rosemann, C; Rosenbleck, C; Rosier-Lees, S; Roth, S; Rubio, J A; Ruggiero, G; Rykaczewski, H; Sakharov, A; Saremi, S; Sarkar, S; Salicio, J; Sanchez, E; Schafer, C; Schegelsky, V; Schopper, H; Schotanus, D J; Sciacca, C; Servoli, L; Shevchenko, S; Shivarov, N; Shoutko, V; Shumilov, E; Shvorob, A; Son, D; Souga, C; Spillantini, P; Steuer, M; Stickland, D P; Stoyanov, B; Straessner, A; Sudhakar, K; Sultanov, G; Sun, L Z; Sushkov, S; Suter, H; Swain, J D; Szillasi, Z; Tang, X W; Tarjan, P; Tauscher, L; Taylor, L; Tellili, B; Teyssier, D; Timmermans, C; Ting, Samuel C C; Ting, S M; Tonwar, S C; Toth, J; Tully, C; Tung, K L; Ulbricht, J; Valente, E; Van de Walle, R T; Vasquez, R; Vesztergombi, G; Vetlitsky, I; Viertel, G; Vivargent, M; Vlachos, S; Vodopianov, I; Vogel, H; Vogt, H; Vorobiev, I; Vorobyov, A A; Wadhwa, M; Wang, Q; Wang, X L; Wang, Z M; Weber, M; Wynhoff, S; Xia, L; Xu, Z Z; Yamamoto, J; Yang, B Z; Yang, C G; Yang, H J; Yang, M; Yeh, S C; Zalite, An; Zalite, Yu; Zhang, Z P; Zhao, J; Zhu, G Y; Zhu, R Y; Zhuang, H L; Zichichi, A; Zimmermann, B; Zoller, M

    2011-01-01

    We present results from a study of hadronic event structure in high energy e(+)e(-') interactions using the L3 detector at LEP. A new class of event shape distributions are measured at and above the Z boson pole for light quark (u, d, s, c) flavours. Energy flow correlations are studied for all hadronic events. Next-to-leading-log QCD calculations and QCD models with improved leading-log approximations are compared to data and good agreement is found at the Z-pole whereas some discrepancies are observed at higher centre-of-mass energies.

  17. UNDERSTANDING THE POPULATION GENETIC STRUCTURE OF GLEDITSIA TRIACANTHOS L.: THE SCALE AND PATTERN OF POLLEN GENE FLOW.

    Science.gov (United States)

    Schnabel, Andrew; Hamrick, J L

    1995-10-01

    Spatial and temporal patterns of gene flow determine the extent to which populations can differentiate from one another as a result of natural selection or genetic drift. In this study, we investigated pollen-mediated gene flow in two eastern Kansas populations of the subdioecious tree species, Gleditsia triacanthos L. (Leguminosae), or honeylocust. In 2 yr at each site, we used paternity-exclusion analysis to estimate the proportion of seeds sired by immigrant pollen. We also used a single-parent and parent-pair exclusion analysis on naturally established seedlings and saplings to estimate gene flow into one site over a 12-yr period and into the second site over a 22-yr period. Results of both analyses showed high minimum estimates of pollen gene flow into each site (17%-30%). In each population, we found significantly less gene flow in years of high fruit production than in years of low fruit production, but in one population, we observed little variation in gene-flow rates among age classes of seedlings and saplings. The level of pollen gene flow showed weak negative dependence on the relative isolation distances of the maternal trees sampled (140-240 m at one site vs. 85-120 m at the second site), and gene-flow estimates from naturally established juveniles were very similar at the two sites. Within populations, a multiple regression model showed that maximum-likelihood estimates of male fertility were negatively associated with distances between mates and positively associated with male size as measured by stem diameter. In neither population, however, did the regression explain more than 16% of the total variation in male fertilities. © 1995 The Society for the Study of Evolution.

  18. Gene flow from transgenic oilseed rape (Brassica napus L.) to cruciferous weeds under mentor pollen inducement

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The alien gene flow between genetically modified glyphosate-resistant rapeseed variety Q3 ( Brassica napus L. ) and four cruciferous weeds was studied under mentor pollen inducement. The results showed that when Thlaspi arvense L., Capsella bursapastoris (L.) Medic, Cardamine hirsuta L. and Rorippa palustris (L.) Besser were pollinated with mentor pollen, the mixed Q3 and the weed, pollen grains aggregated largely and germinated quickly, and the numbers of pollen tubes penetrating into the style and the ovary were greatly increased as compared with corresponding self-pollination groups. Twenty four to forty eight hours after pollination, several pollen tubes were observed to penetrate into the ovule via micropyle in each mentor combination. However, when the mentor progenies were analyzed by PCR, all of them showed negative for the Q3 herbicide-resistant gene. Collectively, these results indicated that crossing between T. arvense, C. bursa-pastoris, C. hirsuta, R. palustris (as female) and Q3 (as male) was highly incompatible and the herbicide-resistant gene could not flow from Q3 to these four weeds.

  19. Is the Gibraltar strait a barrier to gene flow for the bat Myotis myotis (Chiroptera: Vespertilionidae)?

    Science.gov (United States)

    Castella, V; Ruedi, M; Excoffier, L; Ibáñez, C; Arlettaz, R; Hausser, J

    2000-11-01

    Because of their role in limiting gene flow, geographical barriers like mountains or seas often coincide with intraspecific genetic discontinuities. Although the Strait of Gibraltar represents such a potential barrier for both plants and animals, few studies have been conducted on its impact on gene flow. Here we test this effect on a bat species (Myotis myotis) which is apparently distributed on both sides of the strait. Six colonies of 20 Myotis myotis each were sampled in southern Spain and northern Morocco along a linear transect of 1350 km. Results based on six nuclear microsatellite loci reveal no significant population structure within regions, but a complete isolation between bats sampled on each side of the strait. Variability at 600 bp of a mitochondrial gene (cytochrome b) confirms the existence of two genetically distinct and perfectly segregating clades, which diverged several million years ago. Despite the narrowness of the Gibraltar Strait (14 km), these molecular data suggest that neither males, nor females from either region have ever reproduced on the opposite side of the strait. Comparisons of molecular divergence with bats from a closely related species (M. blythii) suggest that the North African clade is possibly a distinct taxon warranting full species rank. We provisionally refer to it as Myotis cf punicus Felten 1977, but a definitive systematic understanding of the whole Mouse-eared bat species complex awaits further genetic sampling, especially in the Eastern Mediterranean areas.

  20. Gene flow among different taxonomic units: evidence from nuclear and cytoplasmic markers in Cedrus plantation forests.

    Science.gov (United States)

    Fady, B; Lefèvre, F; Reynaud, M; Vendramin, G G; Bou Dagher-Kharrat, M; Anzidei, M; Pastorelli, R; Savouré, A; Bariteau, M

    2003-10-01

    Hybridization and introgression are important natural evolutionary processes that can be successfully investigated using molecular markers and open- and controlled-pollinated progeny. In this study, we collected open-pollinated seeds from Cedrus atlantica, Cedrus libani and C. libani x C. atlantica hybrids from three French-plantation forests. We also used pollen from C. libani and Cedrus brevifolia to pollinate C. atlantica trees. The progeny were analyzed using three different types of molecular markers: RAPDs, AFLPs and cpSSRs. Chloroplast DNA was found to be paternally inherited in Cedrus from the progeny of controlled-crosses. Heteroplasmy, although possible, could not be undoubtedly detected. There was no indication of strong reproductive isolating barriers among the three Mediterranean Cedrus taxa. Gene flow between C. atlantica and C. libani accounted for 67 to 81% of viable open-pollinated seedlings in two plantation forests. We propose that Mediterranean Cedrus taxa should be considered as units of a single collective species comprising two regional groups, North Africa and the Middle East. We recommend the use of cpSSRs for monitoring gene flow between taxa in plantation forests, especially in areas where garden specimens of one species are planted in the vicinity of selected seed-stands and gene-conservation reserves of another species.

  1. The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu.

    Science.gov (United States)

    Clegg, Sonya M; Phillimore, Albert B

    2010-04-12

    Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago.

  2. Gene flow and genetic diversity in cultivated and wild cacao (Theobroma cacao) in Bolivia.

    Science.gov (United States)

    Chumacero de Schawe, Claudia; Durka, Walter; Tscharntke, Teja; Hensen, Isabell; Kessler, Michael

    2013-11-01

    The role of pollen flow within and between cultivated and wild tropical crop species is little known. To study the pollen flow of cacao, we estimated the degree of self-pollination and pollen dispersal distances as well as gene flow between wild and cultivated cacao (Theobroma cacao L.). We studied pollen flow and genetic diversity of cultivated and wild cacao populations by genotyping 143 wild and 86 cultivated mature plants and 374 seedlings raised from 19 wild and 25 cultivated trees at nine microsatellite loci. A principal component analysis distinguished wild and cultivated cacao trees, supporting the notion that Bolivia harbors truly wild cacao populations. Cultivated cacao had a higher level of genetic diversity than wild cacao, presumably reflecting the varied origin of cultivated plants. Both cacao types had high outcrossing rates, but the paternity analysis revealed 7-14% self-pollination in wild and cultivated cacao. Despite the tiny size of the pollinators, pollen was transported distances up to 3 km; wild cacao showed longer distances (mean = 922 m) than cultivated cacao (826 m). Our data revealed that 16-20% of pollination events occurred between cultivated and wild populations. We found evidence of self-pollination in both wild and cultivated cacao. Pollination distances are larger than those typically reported in tropical understory tree species. The relatively high pollen exchange from cultivated to wild cacao compromises genetic identity of wild populations, calling for the protection of extensive natural forest tracts to protect wild cacao in Bolivia.

  3. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

    Directory of Open Access Journals (Sweden)

    Wall Jeffrey D

    2008-11-01

    Full Text Available Abstract Background Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions. Results Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000 than non-African populations (300–3,300. We estimate mean rates of bidirectional gene flow at 4.8 × 10-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10-3 than among African populations (2.7 × 10-4. Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4. Conclusion We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

  4. Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

    Science.gov (United States)

    Whittaker, Kerry A.; Rynearson, Tatiana A.

    2017-01-01

    The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations (FST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a. Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a, a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time. PMID:28209775

  5. Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis.

    Directory of Open Access Journals (Sweden)

    René M Malenfant

    Full Text Available Recently, an extensive study of 2,748 polar bears (Ursus maritimus from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago-an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study's main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1 highly unbalanced sample sizes and large amounts of systematically missing data; (2 incorrect calculation of FST and of significance levels; (3 misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and-importantly-we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada's expected last sea-ice refugium. Although polar bears' abundance, distribution, and population structure will certainly be negatively affected by ongoing-and increasingly rapid-loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.

  6. Contemporary human-altered landscapes and oceanic barriers reduce bumble bee gene flow.

    Science.gov (United States)

    Jha, S

    2015-03-01

    Much of the world's terrestrial landscapes are being altered by humans in the form of agriculture, urbanization and pastoral systems, with major implications for biodiversity. Bumble bees are one of the most effective pollinators in both natural and cultivated landscapes, but are often the first to be extirpated in human-altered habitats. Yet, little is known about the role of natural and human-altered habitats in promoting or limiting bumble bee gene flow. In this study, I closely examine the genetic structure of the yellow-faced bumble bee, Bombus vosnesenskii, across the southwestern US coast and find strong evidence that natural oceanic barriers, as well as contemporary human-altered habitats, limit bee gene flow. Heterozygosity and allelic richness were lower in island populations, while private allelic richness was higher in island populations compared to mainland populations. Genetic differentiation, measured for three indices across the 1000 km study region, was significantly greater than the null expectation (F(ST) = 0.041, F'(ST) = 0.044 and D(est) = 0.155) and correlated with geographic distance. Furthermore, genetic differentiation patterns were most strongly correlated with contemporary (2011) not past (2006, 2001) resistance maps calibrated for high dispersal limitation over oceans, impervious habitat and croplands. Despite the incorporation of dramatic elevation gradients, the analyses reveal that oceans and contemporary human land use, not mountains, are the primary dispersal barriers for B. vosnesenskii gene flow. These findings reinforce the importance of maintaining corridors of suitable habitat across the distribution range of native pollinators to promote their persistence and safeguard their ability to provide essential pollination services.

  7. Shape evolution of a single liquid-crystal droplet immersed in an isotropic matrix under transient and steady flow

    Science.gov (United States)

    Wu, Youjun; Yu, Wei; Zhou, Chixing; Xu, Yuanze

    2007-04-01

    The morphology evolution of immiscible polymer-liquid crystal systems is quite different from flexible polymer-polymer mixtures due to the anisotropic properties of liquid crystals. The deformation and retraction of a single low molar mass liquid crystal 4' -pentyl-4-biphenylcarbonitrile (5CB) droplet and 4' -octyl-4-biphenylcarbonitrile (8CB) dispersed in polydimethyl-siloxane under two-dimensional linear flow was investigated by a computer-controlled four-roll mill, which is equipped with an optical microscope and a digital camera. The deformation parameter and orientation angle during deformation versus capillary number was obtained and compared with calculations using the Maffettone-Minale (MM) model and the Yu-Zhou liquid-crystal (YZ-LC) model. The MM model can describe the behavior of a Newtonian droplet in another Newtonian matrix whereas the YZ-LC model can describe the behavior of a LC droplet in a Newtonian matrix. The results showed that the deformation and rotation of a LC droplet is more difficult than viscoelastic droplets, possibly because of the resistance of the nematic elastic energy induced by the nematic mesogens deformation and orientation under flow field. Furthermore, the different behavior between flow-aligning 5CB and flow-tumbling 8CB droplets and the influence of droplet size of LC on deformation and retraction were discussed by experiment and calculation; the results reveal that the different size LC droplets show different evolution curves.

  8. Biofluids, cell mechanics and epigenetics: Flow-induced epigenetic mechanisms of endothelial gene expression.

    Science.gov (United States)

    Davies, Peter F; Manduchi, Elisabetta; Jiménez, Juan M; Jiang, Yi-Zhou

    2017-01-04

    Epigenetics is the regulation of gene expression (transcription) in response to changes in the cell environment through genomic modifications that largely involve the non-coding fraction of the human genome and that cannot be attributed to modification of the primary DNA sequence. Epigenetics is dominant in establishing cell fate and positioning during programmed embryonic development. However the same pathways are used by mature postnatal and adult mammalian cells during normal physiology and are implicated in disease mechanisms. Recent research demonstrates that blood flow and pressure are cell environments that can influence transcription via epigenetic pathways. The principal epigenetic pathways are chemical modification of cytosine residues of DNA (DNA methylation) and of the amino tails of histone proteins associated with DNA in nucleosomes. They also encompass the post-transcriptional degradation of mRNA transcripts by non-coding RNAs (ncRNA). In vascular endothelium, epigenetic pathways respond to temporal and spatial variations of flow and pressure, particularly hemodynamic disturbed blood flow, with important consequences for gene expression. The biofluid environment is linked by mechanotransduction and solute transport to cardiovascular cell phenotypes via signaling pathways and epigenetic regulation for which there is an adequate interdisciplinary infrastructure with robust tools and methods available. Epigenetic mechanisms may be less familiar than acute genomic signaling to Investigators at the interface of biofluids, biomechanics and cardiovascular biology. Here we introduce a biofluids / cellular biomechanics readership to the principal epigenetic pathways and provide a contextual overview of endothelial epigenetic plasticity in the regulation of flow-responsive transcription. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Modelling Gene Flow between Fields of White Clover with Honeybees as Pollen Vectors

    DEFF Research Database (Denmark)

    Løjtnant, Christina; Boelt, Birte; Clausen, Sabine Karin

    2012-01-01

    % with an estimated 95% percentile of 70%. The results show that the European Union threshold limit of 0.9% GM admixture for food and feed will likely be exceeded at times and especially organic farmers that do not accept GM admixture and often have clover and clover–grass fields might face challenges with admixture.......7%, but subjected to large uncertainty. In a worst case scenario with adjacent fields—one with a genetically modified (GM) T. repens cultivar and the other with a conventional T. repens cultivar—and where all arriving bees were expected to transfer GM pollen, the median gene flow was modelled to be 7...

  10. Influence of the shape factor on the flow and heat transfer of a water-based nanofluid in a rotating system

    Science.gov (United States)

    Khan, Umar; Adnan; Ahmed, Naveed; Mohyud-Din, Syed Tauseef

    2017-04-01

    The flow of a nanofluid between two parallel plates (horizontally placed) has been investigated. Different shapes of nanoparticles (suspended in a base fluid) have been considered and the effect of the shape factor has been analyzed. The lower plate is being stretched in opposite directions with forces of the same magnitude. The plates and nanofluid rotate together with angular velocity Ω. The dimensionless form of the flow model, in the form of a system of ordinary differential equations, is obtained by employing some viable similarity transformations. A well-knows analytical method i.e. Variation of Parameters Method (VPM), has been used to solve the problem. Besides, the same system of equations has also been solved numerically by using the forth order Runge-Kutta method, combined with shooting technique. The graphs highlight the influence of ingrained dimensionless physical parameters on the skin friction coefficient, velocity and temperature profiles, and local rate of heat transfer. It is observed that the velocity increases by varying suction/injection parameter and the temperature seems to drop for higher values of the Reynolds number. A decrement in skin friction is observed for increasing nanoparticles volume fraction. On the other hand, the local rate of heat transfer increases for increasing suction/injection parameter, Reynolds number and nanoparticles volume fraction.

  11. Asymmetrical gene flow in a hybrid zone of Hawaiian Schiedea (Caryophyllaceae species with contrasting mating systems.

    Directory of Open Access Journals (Sweden)

    Lisa E Wallace

    Full Text Available Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1 putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2 gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3 in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s of S. menziesii.

  12. Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

    Science.gov (United States)

    Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

    2014-10-01

    Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.

  13. Prediction of Peak Shape and Characterization of Column Performance in Liquid Chromatography as a Function of Flow Rate

    Directory of Open Access Journals (Sweden)

    Juan José Baeza-Baeza

    2015-11-01

    Full Text Available Traditionally, column performance in liquid chromatography has been studied using information from the elution of probe compounds at different flow rates through van Deemter plots, which relate the column plate height to the linear mobile phase velocity. A more recent approach to characterize columns is the representation of the peak widths (or the right and left peak half-widths for a set of compounds versus their retention times, which, for isocratic elution, give rise to almost linear plots. In previous work, these plots have been shown to facilitate the prediction of peak profiles (width and asymmetry with optimization purposes. In this work, a detailed study on the dependence of the peak widths (or half-widths on the flow rate is reported. A new approach to quantify the deterioration of column performance for slow and fast flow rates and to characterize chromatographic columns is proposed. The approach makes use of the width (or half-widths for a set of compounds with similar interaction kinetics and does not require knowledge of the extra-column contributions to the total variance. The chromatographic data of two sets of compounds of different natures (sulfonamides and β-blockers, eluted from Spherisorb and Chromolith columns with acetonitrile-water mixtures, are used to illustrate the approach.

  14. Model-based calculating tool for pollen-mediated gene flow frequencies in plants.

    Science.gov (United States)

    Lei, Wang; Bao-Rong, Lu

    2016-12-30

    The potential social-economic and environmental impacts caused by transgene flow from genetically engineered (GE) crops have stimulated worldwide biosafety concerns. To determine transgene flow frequencies resulted from pollination is the first critical step for assessing such impacts, in addition to the determination of transgene expression and fitness in crop-wild hybrid descendants. Two methods are commonly used to estimate pollen-mediated gene flow (PMGF) frequencies: field experimenting and mathematical modeling. Field experiments can provide relatively accurate results but are time/resource consuming. Modeling offers an effective complement for PMGF experimental assessment. However, many published models describe PMGF by mathematical equations and are practically not easy to use. To increase the application of PMGF modeling for the estimation of transgene flow, we established a tool to calculate PMGF frequencies based on a quasi-mechanistic PMGF model for wind-pollination species. This tool includes a calculating program displayed by an easy-operating interface. PMGF frequencies of different plant species can be quickly calculated under different environmental conditions by including a number of biological and wind speed parameters that can be measured in the fields/laboratories or obtained from published data. The tool is freely available in the public domain (http://ecology.fudan.edu.cn/userfiles/cn/files/Tool_Manual.zip). Case studies including rice, wheat, and maize demonstrated similar results between the calculated frequencies based on this tool and those from published PMGF data. This PMGF calculating tool will provide useful information for assessing and monitoring social-economic and environmental impacts caused by transgene flow from GE crops. This tool can also be applied to determine the isolation distances between GE and non-GE crops in a coexistence agro-ecosystem, and to ensure the purity of certified seeds by setting proper isolation distances

  15. Pollen-mediated gene flow from glyphosate-resistant common waterhemp (Amaranthus rudis Sauer): consequences for the dispersal of resistance genes

    Science.gov (United States)

    Sarangi, Debalin; Tyre, Andrew J.; Patterson, Eric L.; Gaines, Todd A.; Irmak, Suat; Knezevic, Stevan Z.; Lindquist, John L.; Jhala, Amit J.

    2017-01-01

    Gene flow is an important component in evolutionary biology; however, the role of gene flow in dispersal of herbicide-resistant alleles among weed populations is poorly understood. Field experiments were conducted at the University of Nebraska-Lincoln to quantify pollen-mediated gene flow (PMGF) from glyphosate-resistant (GR) to -susceptible (GS) common waterhemp using a concentric donor-receptor design. More than 130,000 common waterhemp plants were screened and 26,199 plants were confirmed resistant to glyphosate. Frequency of gene flow from all distances, directions, and years was estimated with a double exponential decay model using Generalized Nonlinear Model (package gnm) in R. PMGF declined by 50% at pollen source, whereas 90% reduction was found at 88 m (maximum) depending on the direction of the pollen-receptor blocks. Amplification of the target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), was identified as the mechanism of glyphosate resistance in parent biotype. The EPSPS gene amplification was heritable in common waterhemp and can be transferred via PMGF, and also correlated with glyphosate resistance in pseudo-F2 progeny. This is the first report of PMGF in GR common waterhemp and the results are critical in explaining the rapid dispersal of GR common waterhemp in Midwestern United States. PMID:28327669

  16. Global magnetosphere-like 3D structure formation in kinetics by hot magnetized plasma flow characterized by shape of the particle distribution function

    Science.gov (United States)

    Gubchenko, Vladimir

    The task was to provide an analytical elementary magnetosphere-like model in kinetics for verification of the 3D EM PIC codes created for space/aerospace and HED plasmas applications. Kinetic approach versus cold MHD approach takes into account different behavior in the EM fields of resonant and non resonant particles in the velocity phase space, which appears via shape characteristics of the particle velocity distribution function (PVDF) and via the spatial dispersion effect forming the collisionless dissipation in the EM fields. The external flow is a hot collisionless plasma characterized by the particle velocity distribution function (PVDF) with different shapes: Maxwellian, kappa, etc. The flow is in a “hot regime”: it can be supersonic but its velocity remains less the thermal velocity of the electrons. The “internal” part of the magnetosphere formed by trapped particles is the prescribed 3D stationary magnetization considered as a spherical “quasiparticle” with internal magnetodipole and toroidal moments represented as a broadband EM driver. We obtain after the linearization of Vlasov/Maxwell equations a self-consistent 3D large scale kinetic solution of the classic problem. Namely, we: model the “outer” part of the magnetosphere formed by external hot plasma flow of the flyby particles. Solution of the Vlasov equation expressed via a tensor of dielectric permittivity of nonmagnetized and magnetized flowing plasma. Here, we obtain the direct kinetic dissipative effect of the magnetotail formation and the opposite diamagnetic effect of the magnetosphere “dipolization”. We get MHD wave cone in flow magnetized by external guiding magnetic (GM) field. Magnetosphere in our consideration is a 3D dissipative “wave” package structure of the skinned EM fields formed by the “waves” excited at frequency bands where we obtain negative values and singularities (resonances) of squared EM refractive index of the cold plasma. The hot regime

  17. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean.

    Science.gov (United States)

    Sá-Pinto, Alexandra; Branco, Madalena S; Alexandrino, Paulo B; Fontaine, Michaël C; Baird, Stuart J E

    2012-01-01

    Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.

  18. Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae.

    Science.gov (United States)

    Jenkins, Paul A; Song, Yun S; Brem, Rachel B

    2012-01-01

    Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.

  19. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean.

    Directory of Open Access Journals (Sweden)

    Alexandra Sá-Pinto

    Full Text Available Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.

  20. The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome.

    Science.gov (United States)

    Hu, Xin-Sheng; Filatov, Dmitry A

    2016-06-01

    The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7)  years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.

  1. Heat transfer characteristics and entropy generation for wing-shaped-tubes with longitudinal external fins in cross-flow

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Sayed Ahmed E. Sayed; Mesalhy, Osama M.; Abdelatief, Mohamed A. [Zagazig University, Zagazig (Egypt)

    2016-06-15

    A numerical study is conducted to clarify heat transfer characteristics, effectiveness and entropy generation for a bundle of wingshaped-tubes attached to Longitudinal fins (LF) at downstream side. The air-side Re{sub a} ranged from 1.8 x 10{sup 3} to 9.7 x 10{sup 3} . The fin height (h{sub f}) and fin thickness (δ) have been changed as: (2 mm <= hf <= 12 mm) and (1.5 mm <= δ <= 3.5 mm). The analysis of entropy generation is based on the principle of minimizing the rate of total entropy generation that includes the generation of entropy due to heat transfer and friction losses. The temperature field around the wing-shaped-tubes with (LF) is predicted using commercial CFD FLUENT 6.3.26 software package. Correlations of Nu{sub a}, St{sub a}, and Bejan number (Be), as well as the irreversibility distribution ratio (Φ) in terms of Re{sub a} and design parameters for the studied bundle are presented. Results indicated that, installing fins with heights from 2 to 12 mm results in an increase in Nu{sub a} from 11 to 36% comparing with that of wing-shaped tubes without fins (NOF). The highest and lowest values of effectiveness(ε) at every value of the considered Re{sub a} range are occurred at hf = 6 mm and (NOF), espectively. The wing-shaped-tubes heat exchanger with hf = 6 mm has the highest values of (ε), efficiency index (η) and area goodness factor (G{sub a}) and also the lowest values of Φ and hence the best performance comparing with other arrangements. The minimum values of Φ are occurred at hf = 6 mm. (Be) decreases with increasing Re{sub a} for all studied hf. The heat transfer irreversibility predominates for (1800 <= Re{sub a} <= 4200) while the opposite is true for (6950 < Re{sub a} <= 9700). δ has negligible effect on Nu{sub a} and heat transfer irreversibility. Comparisons between the experimental and numerical results of the present study and those, previously, obtained for similar available studies showed good agreements.

  2. Tocantins river as an effective barrier to gene flow in Saguinus niger populations

    Directory of Open Access Journals (Sweden)

    Marcelo Vallinoto

    2006-01-01

    Full Text Available The Saguinus represent the basal genus of the Callitrichinae subfamily. Traditionally this genus is divided into three groups: Hairy, Mottled and Bare-face, however, molecular data failed to validate these groups as monophyletic units, as well as raised some subspecies to the species status. This is the case of the former subspecies Saguinus midas midas and S. midas niger, which are now considered as different species. In the present study, we sequenced a portion of the D-loop mtDNA region in populations from the East bank of the Xingu and from both banks of the Tocantins river, in order to test the effectiveness of large rivers as barriers to the gene flow in Saguinus. According to our results, the populations from the East and West banks of the Tocantins river are more divergent than true species like S. mystax and S. imperator. The Tocantins river may be acting as a barrier to gene flow, and consequently these very divergent populations may represent distinct taxonomic entities (species?.

  3. Y-STR diversity and sex-biased gene flow among Caribbean populations.

    Science.gov (United States)

    Simms, Tanya M; Wright, Marisil R; Martinez, Emanuel; Regueiro, Maria; McCartney, Quinn; Herrera, Rene J

    2013-03-01

    In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Conservation, spillover and gene flow within a network of Northern European marine protected areas.

    Directory of Open Access Journals (Sweden)

    Mats Brockstedt Olsen Huserbråten

    Full Text Available To ensure that marine protected areas (MPAs benefit conservation and fisheries, the effectiveness of MPA designs has to be evaluated in field studies. Using an interdisciplinary approach, we empirically assessed the design of a network of northern MPAs where fishing for European lobster (Homarusgammarus is prohibited. First, we demonstrate a high level of residency and survival (50% for almost a year (363 days within MPAs, despite small MPA sizes (0.5-1 km(2. Second, we demonstrate limited export (4.7% of lobsters tagged within MPAs (N = 1810 to neighbouring fished areas, over a median distance of 1.6 km out to maximum 21 km away from MPA centres. In comparison, median movement distance of lobsters recaptured within MPAs was 164 m, and recapture rate was high (40%. Third, we demonstrate a high level of gene flow within the study region, with an estimated F ST of less than 0.0001 over a ≈ 400 km coastline. Thus, the restricted movement of older life stages, combined with a high level of gene flow suggests that connectivity is primarily driven by larval drift. Larval export from the MPAs can most likely affect areas far beyond their borders. Our findings are of high importance for the design of MPA networks for sedentary species with pelagic early life stages.

  5. Gene flow in a Yersinia pestis vector, Oropsylla hirsuta, during a plague epizootic

    Directory of Open Access Journals (Sweden)

    Philip H. Jones , Leigh R. Washburn & Hugh B. Britten

    2011-09-01

    Full Text Available Background & objectives: Appreciating how Yersinia pestis, the etiological agent of plague, spreads amongblack-tailed prairie dog (Cynomys ludovicianus colonies (BTPD, is vital to wildlife conservation programsin North American grasslands. A little-studied aspect of the system is the role of Y. pestis vectors, i.e. fleas,play in the spreading of plague in natural settings. We investigated the genetic structure and variability of acommon prairie dog flea (Oropsylla hirsuta in BTPD colonies in order to examine dispersal patterns. Giventhat this research took place during a widespread plague epizootic, there was the added advantage of gaininginformation on the dynamics of sylvatic plague.Methods & Results: Oropsylla hirsuta were collected from BTPD burrows in nine colonies from May 2005 toJuly 2005, and eight polymorphic microsatellite markers were used to generate genotypic data from them.Gene flow estimates revealed low genetic differentiation among fleas sampled from different colonies. NestedPCR plague assays confirmed the presence of Y. pestis with the average Y. pestis prevalence across all ninecolonies at 12%. No significant correlations were found between the genetic variability and gene flow of O.hirsuta and Y. pestis prevalence on a per-colony basis.Conclusion: Oropsylla hirsuta dispersal among BTPD colonies was high, potentially explaining the rapidspread of Y. pestis in our study area in 2005 and 2006.

  6. Gene flow in a Yersinia pestis vector, Oropsylla hirsuta, during a plague epizootic.

    Science.gov (United States)

    Jones, Philip H; Washburn, Leigh R; Britten, Hugh B

    2011-09-01

    Appreciating how Yersinia pestis, the etiological agent of plague, spreads among black - tailed prairie dog (Cynomys ludovicianus) colonies (BTPD), is vital to wildlife conservation programs in North American grasslands. A little - studied aspect of the system is the role of Y. pestis vectors, i.e. fleas, play in the spreading of plague in natural settings. We investigated the genetic structure and variability of a common prairie dog flea (Oropsylla hirsuta) in BTPD colonies in order to examine dispersal patterns. Given that this research took place during a widespread plague epizootic, there was the added advantage of gaining information on the dynamics of sylvatic plague. Oropsylla hirsuta were collected from BTPD burrows in nine colonies from May 2005 to July 2005, and eight polymorphic microsatellite markers were used to generate genotypic data from them. Gene flow estimates revealed low genetic differentiation among fleas sampled from different colonies. NestedPCR plague assays confirmed the presence of Y. pestis with the average Y. pestis prevalence across all nine colonies at 12%. No significant correlations were found between the genetic variability and gene flow of O. hirsuta and Y. pestis prevalence on a per -colony basis. Oropsylla hirsuta dispersal among BTPD colonies was high, potentially explaining the rapid spread of Y. pestis in our study area in 2005 and 2006.

  7. Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus).

    Science.gov (United States)

    Chavez, Andreas S; Maher, Sean P; Arbogast, Brian S; Kenagy, G J

    2014-04-01

    Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow. Sequence data have been archived in GenBank—accession numbers: KF882736–KF885216.

  8. Gene flow and mode of pollination in a dry-grassland species, Filipendula vulgaris (Rosaceae).

    Science.gov (United States)

    Weidema, I R; Magnussen, L S; Philipp, M

    2000-03-01

    Filipendula vulgaris is a characteristic species of dry nonacidic grasslands in Denmark. This habitat type occurs only on marginal areas not suitable for agriculture or urbanization and that are by their nature fragmented. The population genetic structure of F. vulgaris was investigated in 17 populations within two regions of Denmark, using isozyme electrophoresis. Small populations were found to have significantly fewer polymorphic loci than larger populations, but all populations maintained the same common allelic variants. The degree of isolation of individual populations did not affect the amount of genetic variation. Offspring arrays revealed a very high outcrossing rate (0.96). The field study demonstrated a very high level of gene flow between populations considering that small insects are thought to be the main pollinators of this species. An experiment to verify whether pollen transport by wind could explain the results from the field study demonstrated long-distance transport from isolated plants to bagged plants. Filipendula vulgaris pollen grains are very small and this explains why outcrossed progeny were found using pollination bags with small pore sizes. We conclude that wind pollination is indeed possible and together with insect pollination is causing the observed patterns of genetic variation. The substantial gene flow between populations may be reducing the effects of genetic drift in the small fragmented populations of F. vulgaris.

  9. Genome-wide data substantiate Holocene gene flow from India to Australia.

    Science.gov (United States)

    Pugach, Irina; Delfin, Frederick; Gunnarsdóttir, Ellen; Kayser, Manfred; Stoneking, Mark

    2013-01-29

    The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

  10. Flutter and Thermal Buckling Analysis for Composite Laminated Panel Embedded with Shape Memory Alloy Wires in Supersonic Flow

    Directory of Open Access Journals (Sweden)

    Chonghui Shao

    2016-01-01

    Full Text Available The flutter and thermal buckling behavior of laminated composite panels embedded with shape memory alloy (SMA wires are studied in this research. The classical plate theory and nonlinear von-Karman strain-displacement relation are employed to investigate the aeroelastic behavior of the smart laminated panel. The thermodynamic behaviors of SMA wires are simulated based on one-dimensional Brinson SMA model. The aerodynamic pressure on the panel is described by the nonlinear piston theory. Nonlinear governing partial differential equations of motion are derived for the panel via the Hamilton principle. The effects of ply angle of the composite panel, SMA layer location and orientation, SMA wires temperature, volume fraction and prestrain on the buckling, flutter boundary, and amplitude of limit cycle oscillation of the panel are analyzed in detail.

  11. T型微通道内弹状流流动特性%The Flow Characteristics of Slug Flow at T-shaped Micro-junction

    Institute of Scientific and Technical Information of China (English)

    周云龙; 刘博; 刘袖

    2013-01-01

    以空气为气相介质和不同表面张力的液体(纯水、0.01% SDS溶液、0.50% SDS溶液、乙醇)为液相介质,对矩形截面为l00μm×800μm的T型微通道内的气液弹状流进行了相分离可视化实验.实验结果表明:气相表现速度一定时,液相采出分率随着液体表观速度的增加而减小;液体表现速度一定时,气体表现速度变化对液相采出分率影响不大;两相的表观速度一定时,液相采出分率随着液体的表面张力降低而减小.另外,将所得的相分离实验数据与其他管径尺寸的数据进行比较,发现不同尺寸T型通道内弹状流相分离特性比较相似.%With both the air and the liquid of different surface tension (pure water,0.01% SDS solution,0.50% SDS solution,ethanol) as working fluid,a visualization experiment was carried out to study the split of slug flow through a T-junction with a rectangular cross section (100μm × 800μm).The experimental results show that the liquid extraction rate can decrease with the increase of superficial liquid velocity at a certain superficial gas velocity.When the superficial liquid velocity is certain,the effect of inlet gas flow rate on the liquid extraction rate is very little.The decrease in liquid surface tension makes the liquid extraction rate increase.Having the present data compared to those from other diameter junctions shows that the phase split characteristics of the slug flow are similar at different sized T-junction.

  12. Localizing F(ST) outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow.

    Science.gov (United States)

    Via, Sara; Conte, Gina; Mason-Foley, Casey; Mills, Kelly

    2012-11-01

    Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing F(ST) outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between-population recombination and gene exchange are reduced over large 'divergence hitchhiking' (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of F(ST) outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation-with-gene-flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence. © 2012 Blackwell Publishing Ltd.

  13. Removal of antibiotics and antibiotic resistance genes from domestic sewage by constructed wetlands: Effect of flow configuration and plant species.

    Science.gov (United States)

    Chen, Jun; Ying, Guang-Guo; Wei, Xiao-Dong; Liu, You-Sheng; Liu, Shuang-Shuang; Hu, Li-Xin; He, Liang-Ying; Chen, Zhi-Feng; Chen, Fan-Rong; Yang, Yong-Qiang

    2016-11-15

    This study aims to investigate the removal of antibiotics and antibiotic resistance genes (ARGs) in raw domestic wastewater by various mesocosm-scale constructed wetlands (CWs) with different flow configurations or plant species including the constructed wetland with or without plant. Six mesocosm-scale CWs with three flow types (surface flow, horizontal subsurface flow and vertical subsurface flow) and two plant species (Thaliadealbata Fraser and Iris tectorum Maxim) were set up in the outdoor. 8 antibiotics including erythromycin-H2O (ETM-H2O), monensin (MON), clarithromycin (CTM), leucomycin (LCM), sulfamethoxazole (SMX), trimethoprim (TMP), sulfamethazine (SMZ) and sulfapyridine (SPD) and 12 genes including three sulfonamide resistance genes (sul1, sul2 and sul3), four tetracycline resistance genes (tetG, tetM, tetO and tetX), two macrolide resistance genes (ermB and ermC), two chloramphenicol resistance genes (cmlA and floR) and 16S rRNA (bacteria) were determined in different matrices (water, particle, substrate and plant phases) from the mesocosm-scale systems. The aqueous removal efficiencies of total antibiotics ranged from 75.8 to 98.6%, while those of total ARGs varied between 63.9 and 84.0% by the mesocosm-scale CWs. The presence of plants was beneficial to the removal of pollutants, and the subsurface flow CWs had higher pollutant removal than the surface flow CWs, especially for antibiotics. According to the mass balance analysis, the masses of all detected antibiotics during the operation period were 247,000, 4920-10,600, 0.05-0.41 and 3500-60,000μg in influent, substrate, plant and effluent of the mesocosm-scale CWs. In the CWs, biodegradation, substrate adsorption and plant uptake all played certain roles in reducing the loadings of nutrients, antibiotics and ARGs, but biodegradation was the most important process in the removal of these pollutants.

  14. Understanding how gravity flows shape deep-water channels. The Rhone delta canyon (Lake Geneva, Switzerland/France)

    Science.gov (United States)

    Corella, Juan Pablo; Loizeau, Jean Luc; Hilbe, Michael; le Dantec, Nicolas; Sastre, Vincent; Girardclos, Stéphanie

    2014-05-01

    Deep-water marine channels are highly dynamic environments due to the erosive power of sediment-laden currents that are continuously reshaping the morphology of these major sediment conduits. Proximal levees are prone to scarp failures generating gravity flows that can be transported thousands of kilometres from the original landslide. Nevertheless, the evolution of these underflows is still poorly understood because of the spatial scale of the processes and their difficult monitoring. For this reason, the smaller size, well-known boundary conditions and detailed bathymetric data makes Lake Geneva's sub-aquatic canyon in the Rhone delta an excellent analogue to understand these types of sedimentary processes that usually occur in deep-water channels in the marine realm. A multidisciplinary research strategy including innovative coring via MIR submersibles, in-situ geotechnical tests, geophysical and sedimentological analyses, as well as acquisition of different multibeam bathymetric data sets, were applied to understand the triggering processes, transport mechanisms and deposit features of gravity flows throughout the Rhone delta active canyon. The difference between two bathymetric surveys in 1986 and 2000 revealed an inversion in the topography of the distal active canyon, as a former distal canyon was transformed into a mound-like structure. A 12 m-thick layer was deposited in the canyon and modified the sediment transfer conduit. Sediment cores from this deposit were retrieved in-situ in 2002 and 2011 via the "F.-A. Forel" and Russian MIR submersibles, respectively. These cores contained a homogeneous, sandy material. Its sediment texture, grain-size, high density and shear strength, and low water content suggests that it corresponds to a debris-flow deposit that possibly took place after the initiation of a mass movement due to a scarp failure in proximal areas of the canyon. In addition, in-situ geotechnical tests on the modern canyon floor have shown a soft

  15. Using seed purity data to estimate an average pollen mediated gene flow from crops to wild relatives.

    Science.gov (United States)

    Lavigne, C; Klein, E K; Couvet, D

    2002-01-01

    Gene flow from crops to wild related species has been recently under focus in risk-assessment studies of the ecological consequences of growing transgenic crops. However, experimental studies addressing this question are usually temporally or spatially limited. Indirect population-structure approaches can provide more global estimates of gene flow, but their assumptions appear inappropriate in an agricultural context. In an attempt to help the committees providing advice on the release of transgenic crops, we present a new method to estimate the quantity of genes migrating from crops to populations of related wild plants by way of pollen dispersal. This method provides an average estimate at a landscape level. Its originality is based on the measure of the inverse gene flow, i.e. gene flow from the wild plants to the crop. Such gene flow results in an observed level of impurities from wild plants in crop seeds. This level of impurity is usually known by the seed producers and, in any case, its measure is easier than a direct screen of wild populations because crop seeds are abundant and their genetic profile is known. By assuming that wild and cultivated plants have a similar individual pollen dispersal function, we infer the level of pollen-mediated gene flow from a crop to the surrounding wild populations from this observed level of impurity. We present an example for sugar beet data. Results suggest that under conditions of seed production in France (isolation distance of 1,000 m) wild beets produce high numbers of seeds fathered by cultivated plants.

  16. Effect of front guide nozzle shape on the flow characteristics in an augmentation channel of a direct drive turbine for wave power generation

    Institute of Scientific and Technical Information of China (English)

    Deepak; PRASAD; Mohammed; Asid; ZULLAH; Mohammed; Rafiuddin; AHMED; Young-Ho; LEE

    2010-01-01

    There is an increasing interest in cross flow turbines(also known as Banki turbines) for small and low head applications because of their simple structure as well as low capital and maintenance costs.The present work aims at implementing the direct drive turbine(DDT) of cross flow type for wave power generation.A numerical wave tank was used to simulate the waves and after obtaining the desired wave properties;the augmentation channel plus the front guide nozzle and rear chamber were integrated to the numerical wave tank.The waves in the numerical wave tank were generated by a piston type wave maker which was located at the wave tank inlet.The inlet which was modeled as a plate wall moved sinusoidally with the general function x = asinω t.The augmentation channel consisted of a front nozzle,rear nozzle and an internal fluid region which represented the turbine housing.The front and rear nozzles were geometrically the same.Three different front guide nozzle configurations were studied:a standard guide nozzle which was originally attached to the augmentation channel and two other front guide nozzles of different geometries.The purpose of this study is to observe how the front guide nozzle shape influences the flow downstream,mainly in the augmenta-tion channel,water power and the first stage energy conversion.The analysis was performed using a commercial CFD code ANSYS-CFX.The results of the flow in the augmentation channel for the three front guide nozzles are presented in this paper.

  17. An efficient, direct finite difference method for computing sound propagation in arbitrarily shaped two-dimensional and axisymmetric ducts without flow

    Science.gov (United States)

    Chakravarthy, S.

    1978-01-01

    An efficient, direct finite difference method is presented for computing sound propagation in non-stepped two-dimensional and axisymmetric ducts of arbitrarily varying cross section without mean flow. The method is not restricted by axial variation of acoustic impedance of the duct wall linings. The non-uniform two-dimensional or axisymmetric duct is conformally mapped numerically into a rectangular or cylindrical computational domain using a new procedure based on a method of fast direct solution of the Cauchy-Riemann equations. The resulting Helmholtz equation in the computational domain is separable. The solution to the governing equation and boundary conditions is expressed as a linear combination of fundamental solutions. The fundamental solutions are computed only once for each duct shape by means of the fast direct cyclic reduction method for the discrete solution of separable elliptic equations. Numerical results for several examples are presented to show the applicability and efficiency of the method.

  18. Population structure of barley landrace populations and gene-flow with modern varieties.

    Science.gov (United States)

    Bellucci, Elisa; Bitocchi, Elena; Rau, Domenico; Nanni, Laura; Ferradini, Nicoletta; Giardini, Alessandro; Rodriguez, Monica; Attene, Giovanna; Papa, Roberto

    2013-01-01

    Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.

  19. Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae).

    Science.gov (United States)

    Trénel, Philipp; Hansen, Michael M; Normand, Signe; Borchsenius, Finn

    2008-08-01

    Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape-Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron-Paute deflection. F-statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross-Andean dispersal in the AHZ. Along the cline, gene flow measured as F(ST) was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation (R(ST) > F(ST)) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution.

  20. Habitat availability and gene flow influence diverging local population trajectories under scenarios of climate change: a place-based approach.

    Science.gov (United States)

    Schwalm, Donelle; Epps, Clinton W; Rodhouse, Thomas J; Monahan, William B; Castillo, Jessica A; Ray, Chris; Jeffress, Mackenzie R

    2016-04-01

    Ecological niche theory holds that species distributions are shaped by a large and complex suite of interacting factors. Species distribution models (SDMs) are increasingly used to describe species' niches and predict the effects of future environmental change, including climate change. Currently, SDMs often fail to capture the complexity of species' niches, resulting in predictions that are generally limited to climate-occupancy interactions. Here, we explore the potential impact of climate change on the American pika using a replicated place-based approach that incorporates climate, gene flow, habitat configuration, and microhabitat complexity into SDMs. Using contemporary presence-absence data from occupancy surveys, genetic data to infer connectivity between habitat patches, and 21 environmental niche variables, we built separate SDMs for pika populations inhabiting eight US National Park Service units representing the habitat and climatic breadth of the species across the western United States. We then predicted occurrence probability under current (1981-2010) and three future time periods (out to 2100). Occurrence probabilities and the relative importance of predictor variables varied widely among study areas, revealing important local-scale differences in the realized niche of the American pika. This variation resulted in diverse and - in some cases - highly divergent future potential occupancy patterns for pikas, ranging from complete extirpation in some study areas to stable occupancy patterns in others. Habitat composition and connectivity, which are rarely incorporated in SDM projections, were influential in predicting pika occupancy in all study areas and frequently outranked climate variables. Our findings illustrate the importance of a place-based approach to species distribution modeling that includes fine-scale factors when assessing current and future climate impacts on species' distributions, especially when predictions are intended to manage and

  1. Estimating dispersal and gene flow in the neotropical freshwater turtle Hydromedusa maximiliani (Chelidae by combining ecological and genetic methods

    Directory of Open Access Journals (Sweden)

    Souza Franco L.

    2002-01-01

    Full Text Available Hydromedusa maximiliani is a vulnerable neotropical freshwater turtle endemic to mountainous regions of the Atlantic rainforest in southeastern Brazil. Random amplified polymorphic DNA (RAPD was used to estimate the gene flow and dispersal for individuals inhabiting rivers and streams within a drainage. Nine primers generated 27 scoreable bands, of which 9 (33% were polymorphic and produced 12 RAPD phenotypes. The gene flow estimates (Nm among turtles inhabiting different rivers and streams were variable, ranging from 0.09 to 3.00 (mean: 0.60. For some loci, the rates of gene flow could offset population differentiation (Nm > 1, whereas for others random genetic drift could result in population divergence (Nm < 1. Since the genetic variation of this turtle seems to be structured according to the natural hierarchical system of rivers and streams within drainages, management programs involving translocations between different regions across the geographical range of H. maximiliani should be viewed with caution.

  2. Gene flow between wheat and wild relatives: empirical evidence from Aegilops geniculata, Ae. neglecta and Ae. triuncialis.

    Science.gov (United States)

    Arrigo, Nils; Guadagnuolo, Roberto; Lappe, Sylvain; Pasche, Sophie; Parisod, Christian; Felber, François

    2011-09-01

    Gene flow between domesticated species and their wild relatives is receiving growing attention. This study addressed introgression between wheat and natural populations of its wild relatives (Aegilops species). The sampling included 472 individuals, collected from 32 Mediterranean populations of three widespread Aegilops species (Aegilops geniculata, Ae. neglecta and Ae. triuncialis) and compared wheat field borders to areas isolated from agriculture. Individuals were characterized with amplified fragment length polymorphism fingerprinting, analysed through two computational approaches (i.e. Bayesian estimations of admixture and fuzzy clustering), and sequences marking wheat-specific insertions of transposable elements. With this combined approach, we detected substantial gene flow between wheat and Aegilops species. Specifically, Ae. neglecta and Ae. triuncialis showed significantly more admixed individuals close to wheat fields than in locations isolated from agriculture. In contrast, little evidence of gene flow was found in Ae. geniculata. Our results indicated that reproductive barriers have been regularly bypassed during the long history of sympatry between wheat and Aegilops.

  3. Analysis of heat transfer and nanofluid fluid flow in microchannels with trapezoidal, rectangular and triangular shaped ribs

    Science.gov (United States)

    Behnampour, Ali; Akbari, Omid Ali; Safaei, Mohammad Reza; Ghavami, Mohammad; Marzban, Ali; Sheikh Shabani, Gholamreza Ahmadi; zarringhalam, Majid; Mashayekhi, Ramin

    2017-07-01

    In the present study, the effect of triangular, rectangular and trapezoidal ribs on the laminar heat transfer of water-Ag nanofluid in a ribbed triangular channel under a constant heat flux was numerically studied using finite volume method. Height and width of ribs have been assumed to be fixed in order to study the effect of different rib forms. Modeling were performed for laminar flow (Re=1, 50 and 100) and nanofluid volume fractions of 0, 2% and 4%. The results indicated that an increase in volume fraction of solid nanoparticle leads to convectional heat transfer coefficient enhancement of the cooling fluid, whereas increasing the Nusselt number results in a loss of friction coefficient and pressure. Also, along with the fluid velocity increment, there will be an optimal proportion between heat and hydrodynamic transfer behavior which optimizes performance evaluation criteria (PEC) behavior. Among all of the investigated rib forms, the rectangular one made the most changes in the streamlines and the triangular form has the best thermal performance evaluation criteria values. For all studied Reynold numbers, heat transfer values are least for rectangular rib from. Therefore, trapezoidal ribs are recommended in high Reynold numbers.

  4. Fine scale gene flow and individual movements among subpopulations of Centrolene prosoblepon (Anura: Centrolenidae

    Directory of Open Access Journals (Sweden)

    Jeanne M Robertson

    2008-03-01

    Full Text Available Dispersal capabilities determine and maintain local gene flow, and this has implications for population persistence and/or recolonization following environmental perturbations (natural or anthropogenic, disease outbreaks, or other demographic collapses. To predict recolonization and understand dispersal capacity in a stream-breeding frog, we examined individual movement patterns and gene flow among four subpopulations of the Neotropical glassfrog, Centrolene prosoblepon, at a mid-elevation cloud forest site at El Copé, Panama. We measured male movement directly during a two year mark-recapture study, and indirectly with gene flow estimates from mitochondrial DNA sequences (mtDNA. Individuals of this species showed strong site fidelity: over two years, male frogs in all four headwater streams moved very little (mean = 2.33 m; mode = 0 m. Nine individuals changed streams within one or two years, moving 675-1 108 m. For those males moving more than 10 m, movement was biased upstream (p ST = 0.007, p = 0.325 but gene flow was more limited across greater distances (CT = 0.322, p = 0.065, even within the same drainage network. Lowland populations of C. prosoblepon potentially act as an important source of colonists for upland populations in this watershed. Rev. Biol. Trop. 56 (1: 13-26. Epub 2008 March 31.La capacidad de dispersión determina y mantiene el flujo genético local, y esto tiene implicaciones para la persistencia poblacional y/o la recolonización que sigue a perturbaciones ambientales. Examinamos patrones individuales de movimiento y flujo genético entre subpoblaciones de Centrolene prosoblepon (Anura: Centrolenidae en un sitio de elevación media en El Copé, Panamá. Medimos directamente el movimiento de los machos durante un estudio de marcado-recaptura, e indirectamente con estimaciones de flujo genético a partir de secuencias de ADN mitocondrial (mtDNA. Los individuos mostraron fuerte fidelidad a su lugar: por más de dos a

  5. Glyphosate drift promotes changes in fitness and transgene gene flow in canola (Brassica napus) and hybrids

    Science.gov (United States)

    Londo, Jason P.; Bautista, Nonnatus S.; Sagers, Cynthia L.; Lee, E. Henry; Watrud, Lidia S.

    2010-01-01

    Background and Aims With the advent of transgenic crops, genetically modified, herbicide-resistant Brassica napus has become a model system for examining the risks and potential ecological consequences of escape of transgenes from cultivation into wild compatible species. Escaped transgenic feral B. napus and hybrids with compatible weedy species have been identified outside of agriculture and without the apparent selection for herbicide resistance. However, herbicide (glyphosate) exposure can extend beyond crop field boundaries, and a drift-level of herbicide could function as a selective agent contributing to increased persistence of transgenes in the environment. Methods The effects of a drift level (0·1 × the field application rate) of glyphosate herbicide and varied levels of plant competition were examined on plant fitness-associated traits and gene flow in a simulated field plot, common garden experiment. Plants included transgenic, glyphosate-resistant B. napus, its weedy ancestor B. rapa, and hybrid and advanced generations derived from them. Key Results The results of this experiment demonstrate reductions in reproductive fitness for non-transgenic genotypes and a contrasting increase in plant fitness for transgenic genotypes as a result of glyphosate-drift treatments. Results also suggest that a drift level of glyphosate spray may influence the movement of transgenes among transgenic crops and weeds and alter the processes of hybridization and introgression in non-agronomic habitats by impacting flowering phenology and pollen availability within the community. Conclusions The results of this study demonstrate the potential for persistence of glyphosate resistance transgenes in weedy plant communities due to the effect of glyphosate spray drift on plant fitness. Additionally, glyphosate drift has the potential to change the gene-flow dynamics between compatible transgenic crops and weeds, simultaneously reducing direct introgression into weedy species

  6. Geographic variation in advertisement calls in a tree frog species: gene flow and selection hypotheses.

    Directory of Open Access Journals (Sweden)

    Yikweon Jang

    Full Text Available BACKGROUND: In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation. METHODOLOGY: We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR, note duration (ND, and dominant frequency (DF, along with snout-to-vent length. RESULTS: The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters. CONCLUSIONS: Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japonica. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with

  7. Geographically weighted regression as a generalized Wombling to detect barriers to gene flow.

    Science.gov (United States)

    Diniz-Filho, José Alexandre Felizola; Soares, Thannya Nascimento; de Campos Telles, Mariana Pires

    2016-08-01

    Barriers to gene flow play an important role in structuring populations, especially in human-modified landscapes, and several methods have been proposed to detect such barriers. However, most applications of these methods require a relative large number of individuals or populations distributed in space, connected by vertices from Delaunay or Gabriel networks. Here we show, using both simulated and empirical data, a new application of geographically weighted regression (GWR) to detect such barriers, modeling the genetic variation as a "local" linear function of geographic coordinates (latitude and longitude). In the GWR, standard regression statistics, such as R(2) and slopes, are estimated for each sampling unit and thus are mapped. Peaks in these local statistics are then expected close to the barriers if genetic discontinuities exist, capturing a higher rate of population differentiation among neighboring populations. Isolation-by-Distance simulations on a longitudinally warped lattice revealed that higher local slopes from GWR coincide with the barrier detected with Monmonier algorithm. Even with a relatively small effect of the barrier, the power of local GWR in detecting the east-west barriers was higher than 95 %. We also analyzed empirical data of genetic differentiation among tree populations of Dipteryx alata and Eugenia dysenterica Brazilian Cerrado. GWR was applied to the principal coordinate of the pairwise FST matrix based on microsatellite loci. In both simulated and empirical data, the GWR results were consistent with discontinuities detected by Monmonier algorithm, as well as with previous explanations for the spatial patterns of genetic differentiation for the two species. Our analyses reveal how this new application of GWR can viewed as a generalized Wombling in a continuous space and be a useful approach to detect barriers and discontinuities to gene flow.

  8. Human-aided and natural dispersal drive gene flow across the range of an invasive mosquito.

    Science.gov (United States)

    Medley, Kim A; Jenkins, David G; Hoffman, Eric A

    2015-01-01

    Human-aided transport is responsible for many contemporary species introductions, yet the contribution of human-aided transport to dispersal within non-native regions is less clear. Understanding dispersal dynamics for invasive species can streamline mitigation efforts by targeting routes that contribute disproportionally to spread. Because of its limited natural dispersal ability, rapid spread of the Asian tiger mosquito (Aedes albopictus) has been attributed to human-aided transport, but until now, the relative roles of human-aided and natural movement have not been rigorously evaluated. Here, we use landscape genetics and information-theoretic model selection to evaluate 52 models representing 9240 pairwise dispersal paths among sites across the US range for Ae. albopictus and show that recent gene flow reflects a combination of natural and human-aided dispersal. Highways and water availability facilitate dispersal at a broad spatial scale, but gene flow is hindered by forests at the current distributional limit (range edge) and by agriculture among sites within the mosquito's native climatic niche (range core). Our results show that highways are important to genetic structure between range-edge and range-core pairs, suggesting a role for human-aided mosquito transport to the range edge. In contrast, natural dispersal is dominant at smaller spatial scales, reflecting a shifting dominance to natural movement two decades after introduction. These conclusions highlight the importance of (i) early intervention for species introductions, particularly those with readily dispersed dormant stages and short generation times, and (ii) strict monitoring of commercial shipments for transported immature stages of Ae. albopictus, particularly towards the northern edge of the US range.

  9. Geographic Variation in Advertisement Calls in a Tree Frog Species: Gene Flow and Selection Hypotheses

    Science.gov (United States)

    Jang, Yikweon; Hahm, Eun Hye; Lee, Hyun-Jung; Park, Soyeon; Won, Yong-Jin; Choe, Jae C.

    2011-01-01

    Background In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD) or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation. Methodology We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR), note duration (ND), and dominant frequency (DF), along with snout-to-vent length. Results The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters. Conclusions Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japoinca. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with restricted gene

  10. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus

    Directory of Open Access Journals (Sweden)

    Bradic Martina

    2012-01-01

    Full Text Available Abstract Background Cave animals converge evolutionarily on a suite of troglomorphic traits, the best known of which are eyelessness and depigmentation. We studied 11 cave and 10 surface populations of Astyanax mexicanus in order to better understand the evolutionary origins of the cave forms, the basic genetic structuring of both cave and surface populations, and the degree to which present day migration among them affects their genetic divergence. Results To assess the genetic structure within populations and the relationships among them we genotyped individuals at 26 microsatellite loci. We found that surface populations are similar to one another, despite their relatively large geographic separation, whereas the cave populations are better differentiated. The cave populations we studied span the full range of the cave forms in three separate geographic regions and have at least five separate evolutionary origins. Cave populations had lower genetic diversity than surface populations, correlated with their smaller effective population sizes, probably the result of food and space limitations. Some of the cave populations receive migrants from the surface and exchange migrants with one another, especially when geographically close. This admixture results in significant heterozygote deficiencies at numerous loci due to Wahlund effects. Cave populations receiving migrants from the surface contain small numbers of individuals that are intermediate in both phenotype and genotype, affirming at least limited gene flow from the surface. Conclusions Cave populations of this species are derived from two different surface stocks denoted "old" and "new." The old stock colonized caves at least three times independently while the new stock colonized caves at least twice independently. Thus, the similar cave phenotypes found in these caves are the result of repeated convergences. These phenotypic convergences have occurred in spite of gene flow from surface

  11. Population divergence and gene flow in an endangered and highly mobile seabird

    Science.gov (United States)

    Welch, A. J.; Fleischer, R. C.; James, H. F.; Wiley, A. E.; Ostrom, P. H.; Adams, J.; Duvall, F.; Holmes, N.; Hu, D.; Penniman, J.; Swindle, K. A.

    2012-01-01

    Seabirds are highly vagile and can disperse up to thousands of kilometers, making it difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given the great dispersal potential of these petrels, it remains unclear if populations are genetically distinct and which factors may contribute to isolation between them. We sampled petrels from across their range, including individuals from the presumably extirpated Molokai population. We sequenced 524 bp of mitochondrial DNA, 741 bp from three nuclear introns, and genotyped 18 microsatellite loci in order to examine the patterns of divergence in this species and to investigate the potential underlying mechanisms. Both mitochondrial and nuclear data sets indicated significant genetic differentiation among all modern populations, but no differentiation was found between historic samples from Molokai and modern birds from Lanai. Population-specific nonbreeding distribution and strong natal philopatry may reduce gene flow between populations. However, the lack of population structure between extirpated Molokai birds and modern birds on Lanai indicates that there was substantial gene flow between these populations and that petrels may be able to overcome barriers to dispersal prior to complete extirpation. Hawaiian petrel populations could be considered distinct management units, however, the dwindling population on Hawaii may require translocation to prevent extirpation in the near future.

  12. Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets.

    Science.gov (United States)

    Lange, Rebecca; Durka, Walter; Holzhauer, Stephanie I J; Wolters, Volkmar; Diekötter, Tim

    2010-11-01

    Effects of habitat fragmentation on genetic diversity vary among species. This may be attributed to the interacting effects of species traits and landscape structure. While widely distributed and abundant species are often considered less susceptible to fragmentation, this may be different if they are small sized and show limited dispersal. Under intensive land use, habitat fragmentation may reach thresholds at which gene flow among populations of small-sized and dispersal-limited species becomes disrupted. Here, we studied the genetic diversity of two abundant and widespread bush crickets along a gradient of habitat fragmentation in an agricultural landscape. We applied traditional (G(ST), θ) and recently developed (G'ST', D) estimators of genetic differentiation on microsatellite data from each of twelve populations of the grassland species Metrioptera roeselii and the forest-edge species Pholidoptera griseoaptera to identify thresholds of habitat fragmentation below which genetic population structure is affected. Whereas the grassland species exhibited a uniform genetic structuring (G(ST) = 0.020-0.033; D = 0.085-0.149) along the whole fragmentation gradient, the forest-edge species' genetic differentiation increased significantly from D habitat dropped below a threshold of 20% and its proximity decreased substantially at the landscape scale. The influence of fragmentation on genetic differentiation was qualitatively unaffected by the choice of estimators of genetic differentiation but quantitatively underestimated by the traditional estimators. These results indicate that even for widespread species in modern agricultural landscapes fragmentation thresholds exist at which gene flow among suitable habitat patches becomes restricted. © 2010 Blackwell Publishing Ltd.

  13. Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape.

    Directory of Open Access Journals (Sweden)

    Rachael V Adams

    Full Text Available Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus, along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart, but also within river systems by large treeless canyons (>100 km. Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic

  14. Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape

    Science.gov (United States)

    2015-01-01

    Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus), along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover) were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart), but also within river systems by large treeless canyons (>100 km). Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar) tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic variation. PMID

  15. Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade

    Directory of Open Access Journals (Sweden)

    Sarma Uddipan

    2012-07-01

    differentially shape the robustness and signal response behaviour of the MAPK cascade and phosphatase sequestration dramatically enhances the robustness to perturbations in each of the cascade. An implicit negative feedback loop was uncovered from our analysis and we found that strength of the negative feedback loop is reciprocally related to the strength of phosphatase sequestration. Duration of output phosphorylation in response to a transient signal was also found to be determined by the individual cascade’s kinase-phosphatase interaction design.

  16. Fat-tailed gene flow in the dioecious canopy tree species Fraxinus mandshurica var. japonica revealed by microsatellites.

    Science.gov (United States)

    Goto, S; Shimatani, K; Yoshimaru, H; Takahashi, Y

    2006-09-01

    Pollen flow, seed dispersal and individual reproductive success can be simultaneously estimated from the genotypes of adults and offspring using stochastic models. Using four polymorphic microsatellite loci, gene flow of the wind-pollinated and wind-seed-dispersed dioecious tree species, Fraxinus mandshurica var. japonica, was quantified in a riparian forest, in northern Japan. In a 10.5-ha plot, 74 female adults, 76 male adults and 292 current-year seedlings were mapped and genotyped, together with 200 seeds. To estimate dispersal kernels of pollen and seeds, we applied normal, exponential power, Weibull, bivariate t-distribution kernels, and two-component models consisting of two normal distribution functions, one with a small and one with a large variance. A two-component pollen flow model with a small contribution (26.1%) from short-distance dispersal (sigma = 7.2 m), and the rest from long-distance flow (sigma = 209.9 m), was chosen for the best-fitting model. The average distance that integrated pollen flows inside and outside the study plot was estimated to be 196.8 m. Tree size and flowering intensity affected reproduction, and there appeared to be critical values that distinguished reproductively successful and unsuccessful adults. In contrast, the gene flow model that estimated both pollen and seed dispersal from established seedlings resulted in extensive seed dispersal, and the expected spatial genetic structures did not satisfactorily fit with the observations, even for the selected model. Our results advanced small-scale individual-based parentage analysis for quantifying fat-tailed gene flow in wind-mediated species, but also clarified its limitations and suggested future possibilities for gene flow studies.

  17. Electrochemical reaction and performance of proton exchange membrane fuel cells with a novel cathode flow channel shape

    Energy Technology Data Exchange (ETDEWEB)

    Chiang, Mu-Sheng [Department of Mechanical Engineering, National Chiao Tung University, Hsin-Chu 30010 (Taiwan); Department of Mechanical Engineering, Nan Kai Institute of Technology, Nantou 54243 (Taiwan); Chu, Hsin-Sen [Department of Mechanical Engineering, National Chiao Tung University, Hsin-Chu 30010 (Taiwan); Chen, Cha' o-Kuang [Department of Mechanical Engineering, National Cheng Kung University, Tainan 70101 (Taiwan); Jian, Sheng-Rui [Department of Electrophysics, National Chiao Tung University, Hsin-Chu 30010 (Taiwan)

    2007-04-15

    This study focuses on the investigation of the electrochemical reaction along a novel cathode flow channel of PEM fuel cells with various shoulder/channel (S/C) ratios at the outlet port. A three-dimensional mathematical model, considering conservation principles of mass, momentum, species and electric current is employed. Local variations of important model variables such as reactant concentration and local current density are presented by contour plots to elucidate the effects of channel geometry on transport process, catalyst reaction and cell performance. The potential fields of solid and membrane phases are also resolved in the cell domain and the driving force of the electrochemical reactions - the catalyst activation overpotential - is harnessed in modeling. Numerical calculations reveal the influence of the cathode channel configuration on the local distributions of various model variables. The results also show the dependence between optimal channel configuration and cell operating condition. At a medium reaction rate, the reaction sites underneath the shoulder region generate more current than the channel region. Therefore, a convergent channel configuration with a larger S/C ratio at the outlet port develops more current because such a design facilitates the electron transport and enhances local activation overpotential. However, as the cell voltage decreases and the reaction rate increases, such configuration loses its merit gradually as the requirement for a higher reactant concentration is more important and the reaction sites underneath the channel region have a higher reaction rate. Consequently, the divergent channel configuration with a lower S/C ratio of 0.67 performs better at a cell voltage of 0.22 V. (author)

  18. Numerical simulation of nematic liquid crystalline flow in two-dimensional L-shaped channels; Nijigen L gata ryuro ni okeru nematic ekisho no nagare no suchi simulation

    Energy Technology Data Exchange (ETDEWEB)

    Chono, S.; Tsuji, T. [Fukui University, Fukui (Japan). Faculty of Engineering

    1995-05-25

    Finite difference solutions to the Leslie-Ericksen equations were obtained for flows in two-dimensional L-shaped channels with various contraction ratios of the upstream to downstream channel width. A streamline shift toward the outer wall occurs upstream of the reentrant corner. Such behavior is similar to that of viscoelastic fluids. With increasing contraction ratio, the streamline shift occurs further upstream. The effect of the wall anchoring angle for the director is remarkable; for example, when the anchoring angle along the downstream walls is set to be opposite to the main flow direction, a distortion of streamlines is produced in the corner region and the director moves to the downstream region upside down. At small Ericksen numbers, the orientation angle for the director is varied over a wide area so as to suppress its local deformation. In contrast, when the Ericksen number is large, the director profile in the upstream region is retained close to the corner region where the director turns rapidly to the downstream direction. 7 refs., 9 figs., 1 tab.

  19. Parallel evolution of local adaptation and reproductive isolation in the face of gene flow.

    Science.gov (United States)

    Butlin, Roger K; Saura, Maria; Charrier, Grégory; Jackson, Benjamin; André, Carl; Caballero, Armando; Coyne, Jerry A; Galindo, Juan; Grahame, John W; Hollander, Johan; Kemppainen, Petri; Martínez-Fernández, Mónica; Panova, Marina; Quesada, Humberto; Johannesson, Kerstin; Rolán-Alvarez, Emilio

    2014-04-01

    Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and amplified fragment length polymorphism markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonization of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically driven speciation.

  20. Independent domestication of Asian rice followed by gene flow from japonica to indica.

    Science.gov (United States)

    Yang, Ching-chia; Kawahara, Yoshihiro; Mizuno, Hiroshi; Wu, Jianzhong; Matsumoto, Takashi; Itoh, Takeshi

    2012-05-01

    Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.

  1. Afghan Hindu Kush: where Eurasian sub-continent gene flows converge.

    Directory of Open Access Journals (Sweden)

    Julie Di Cristofaro

    Full Text Available Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH. The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

  2. Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina

    Science.gov (United States)

    McCartney-Melstad, Evan; Waller, Tomás; Micucci, Patricio A.; Barros, Mariano; Draque, Juan; Amato, George; Mendez, Martin

    2012-01-01

    Yellow anacondas (Eunectes notaeus) are large, semiaquatic boid snakes found in wetland systems in South America. These snakes are commercially harvested under a sustainable management plan in Argentina, so information regarding population structuring can be helpful for determination of management units. We evaluated genetic structure and migration using partial sequences from the mitochondrial control region and mitochondrial genes cyt-b and ND4 for 183 samples collected within northern Argentina. A group of landscape features and environmental variables including several treatments of temperature and precipitation were explored as potential drivers of observed genetic patterns. We found significant population structure between most putative population comparisons and bidirectional but asymmetric migration in several cases. The configuration of rivers and wetlands was found to be significantly associated with yellow anaconda population structure (IBD), and important for gene flow, although genetic distances were not significantly correlated with the environmental variables used here. More in-depth analyses of environmental data may be needed to fully understand the importance of environmental conditions on population structure and migration. These analyses indicate that our putative populations are demographically distinct and should be treated as such in Argentina's management plan for the harvesting of yellow anacondas. PMID:22675425

  3. Continuous gene flow contributes to low global species abundance and distribution of a marine model diatom

    KAUST Repository

    Rastogi, Achal

    2017-08-15

    Unlike terrestrial ecosystems where geographical isolation often leads to a restricted gene flow between species, genetic admixing in aquatic micro-eukaryotes is likely to be frequent. Diatoms inhabit marine ecosystems since the Mesozoic period and presently constitute one of the major primary producers in the world ocean. They are a highly diversified group of eukaryotic phytoplankton with estimates of up to 200,000 species. Since decades, Phaeodactylum tricornutum is used as a model diatom species to characterize the functional pathways, physiology and evolution of diatoms in general. In the current study, using whole genome sequencing of ten P. tricornutum strains, sampled at broad geospatial and temporal scales, we show a continuous dispersal and genetic admixing between geographically isolated strains. We also describe a very high level of heterozygosity and propose it to be a consequence of frequent ancestral admixture. Our finding that P. tricornutum sequences are plausibly detectable at low but broadly distributed levels in the world ocean further suggests that high admixing between geographically isolated strains may create a significant bottleneck, thus influencing their global abundance and distribution in nature. Finally, in an attempt to understand the functional implications of genetic diversity between different P. tricornutum ecotypes, we show the effects of domestication in inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success.

  4. Investigation of the demographic and selective forces shaping the nucleotide diversity of genes involved in nod factor signaling in Medicago truncatula.

    Science.gov (United States)

    De Mita, Stéphane; Ronfort, Joëlle; McKhann, Heather I; Poncet, Charles; El Malki, Redouane; Bataillon, Thomas

    2007-12-01

    Symbiotic nitrogen-fixing rhizobia are able to trigger root deformation in their Fabaceae host plants, allowing their intracellular accommodation. They do so by delivering molecules called Nod factors. We analyzed the patterns of nucleotide polymorphism of five genes controlling early Nod factor perception and signaling in the Fabaceae Medicago truncatula to understand the selective forces shaping the evolution of these genes. We used 30 M. truncatula genotypes sampled in a genetically homogeneous region of the species distribution range. We first sequenced 24 independent loci and detected a genomewide departure from the hypothesis of neutrality and demographic equilibrium that suggests a population expansion. These data were used to estimate parameters of a simple demographic model incorporating population expansion. The selective neutrality of genes controlling Nod factor perception was then examined using a combination of two complementary neutrality tests, Tajima's D and Fay and Wu's standardized H. The joint distribution of D and H expected under neutrality was obtained under the fitted population expansion model. Only the gene DMI1, which is expected to regulate the downstream signal, shows a pattern consistent with a putative selective event. In contrast, the receptor-encoding genes NFP and NORK show no significant signatures of selection. Among the genes that we analyzed, only DMI1 should be viewed as a candidate for adaptation in the recent history of M. truncatula.

  5. A multilocus perspective on colonization accompanied by selection and gene flow.

    Science.gov (United States)

    Rosenblum, Erica Bree; Hickerson, Michael J; Moritz, Craig

    2007-12-01

    The colonization of novel habitats involves complex interactions between founder events, selection, and ongoing migration, and can lead to diverse evolutionary outcomes from local extinction to adaptation to speciation. Although there have been several studies of the demography of colonization of remote habitats, less is known about the demographic consequences of colonization of novel habitats within a continuous species range. Populations of the Eastern Fence Lizard, Sceloporus undulatus, are continuously distributed across two dramatic transitions in substrate color in southern New Mexico and have undergone rapid adaptation following colonization of these novel environments. Blanched forms inhabit the gypsum sand dunes of White Sands and melanic forms are found on the black basalt rocks of the Carrizozo lava flow. Each of these habitats formed within the last 10,000 years, allowing comparison of genetic signatures of population history for two independent colonizations from the same source population. We present evidence on phenotypic variation in lizard color, environmental variation in substrate color, and sequence variation for mitochondrial DNA and 19 independent nuclear loci. To confirm the influence of natural selection and gene flow in this system, we show that phenotypic variation is best explained by environmental variation and that neutral genetic variation is related to distance between populations, not partitioned by habitat. The historical demography of colonization was inferred using an Approximate Bayesian Computation (ABC) framework that incorporates known geological information and allows for ongoing migration with the source population. The inferences differed somewhat between mtDNA and nuclear markers, but overall provided strong evidence of historical size reductions in both white sand and black lava populations at the time of colonization. Populations in both novel habitats appear to have undergone partial but incomplete recovery from the

  6. Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

    Science.gov (United States)

    Cruse-Sanders, Jennifer M; Parker, Kathleen C; Friar, Elizabeth A; Huang, Daisie I; Mashayekhi, Saeideh; Prince, Linda M; Otero-Arnaiz, Adriana; Casas, Alejandro

    2013-01-01

    Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (HE = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear-cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species. PMID:23762520

  7. Selection shaped the evolution of mouse androgen-binding protein (ABP) function and promoted the duplication of Abp genes.

    Science.gov (United States)

    Karn, Robert C; Laukaitis, Christina M

    2014-08-01

    In the present article, we summarize two aspects of our work on mouse ABP (androgen-binding protein): (i) the sexual selection function producing incipient reinforcement on the European house mouse hybrid zone, and (ii) the mechanism behind the dramatic expansion of the Abp gene region in the mouse genome. Selection unifies these two components, although the ways in which selection has acted differ. At the functional level, strong positive selection has acted on key sites on the surface of one face of the ABP dimer, possibly to influence binding to a receptor. A different kind of selection has apparently driven the recent and rapid expansion of the gene region, probably by increasing the amount of Abp transcript, in one or both of two ways. We have shown previously that groups of Abp genes behave as LCRs (low-copy repeats), duplicating as relatively large blocks of genes by NAHR (non-allelic homologous recombination). The second type of selection involves the close link between the accumulation of L1 elements and the expansion of the Abp gene family by NAHR. It is probably predicated on an initial selection for increased transcription of existing Abp genes and/or an increase in Abp gene number providing more transcriptional sites. Either or both could increase initial transcript production, a quantitative change similar to increasing the volume of a radio transmission. In closing, we also provide a note on Abp gene nomenclature.

  8. ZO-1 knockout by TALEN-mediated gene targeting in MDCK cells: involvement of ZO-1 in the regulation of cytoskeleton and cell shape.

    Directory of Open Access Journals (Sweden)

    Shinsaku Tokuda

    Full Text Available ZO-1, ZO-2 and ZO-3 are tight junction-associated scaffold proteins that bind to transmembrane proteins of tight junctions and the underlying cytoskeleton. ZO-1 is involved in the regulation of cytoskeletal organization, but its detailed molecular mechanism is less well understood. Gene knockout is an ideal method to investigate the functions of proteins that might have redundant functions such as ZO proteins, when compared with methods such as RNA interference-mediated suppression of gene expression. In this study we applied transcription activator-like effector nucleases (TALENs, a recently developed genome editing method for gene knockout, and established ZO-1 knockout clones in Madin-Darby canine kidney (MDCK cells. ZO-1 knockout induced striking changes in myosin organization at cell-cell contacts and disrupted the localization of tight junction proteins; these findings were previously unseen in studies of ZO-1 knockdown by RNA interference. Rescue experiments revealed that trace ZO-1 expression reversed these changes while excessive ZO-1 expression induced an intensive zigzag shape of cell-cell junctions. These results suggest a role for ZO-1 in the regulation of cytoskeleton and shape of cell-cell junctions in MDCK cells and indicate the advantage of knockout analysis in cultured cells.

  9. Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication

    Science.gov (United States)

    Kiemnec-Tyburczy, K M; Richmond, J Q; Savage, A E; Lips, K R; Zamudio, K R

    2012-01-01

    Comparative studies of major histocompatibility complex (MHC) genes across vertebrate species can reveal the evolutionary processes that shape the structure and function of immune regulatory proteins. In this study, we characterized MHC class I sequences from six frog species representing three anuran families (Hylidae, Centrolenidae and Ranidae). Using cDNA from our focal species, we amplified a total of 79 unique sequences spanning exons 2–4 that encode the extracellular domains of the functional alpha chain protein. We compared intra- and interspecific nucleotide and amino-acid divergence, tested for recombination, and identified codon sites under selection by estimating the rate of non-synonymous to synonymous substitutions with multiple codon-based maximum likelihood methods. We determined that positive (diversifying) selection was acting on specific amino-acid sites located within the domains that bind pathogen-derived peptides. We also found significant signals of recombination across the physical distance of the genes. Finally, we determined that all the six species expressed two or three putative classical class I loci, in contrast to the single locus condition of Xenopus laevis. Our results suggest that MHC evolution in anurans is a dynamic process and that variation in numbers of loci and genetic diversity can exist among taxa. Thus, the accumulation of genetic data for more species will be useful in further characterizing the relative importance of processes such as selection, recombination and gene duplication in shaping MHC loci among amphibian lineages. PMID:22549517

  10. Hyperbolically Shaped Centrifugal Compressor

    Institute of Scientific and Technical Information of China (English)

    Romuald Puzyrewski; Pawel Flaszy(n)ski

    2003-01-01

    Starting from the classical centrifugal compressor, cone shaped in meridional cross section, two modifications are considered on the basis of results from 2D and 3D flow models. The first modification is the change of the meridional cross section to hyperbolically shaped channel. The second modification, proposed on the basis of 2D axisymmetric solution, concerns the shape of blading. On the strength of this solution the blades are formed as 3D shaped blades, coinciding with the recent tendency in 3D designs. Two aims were considered for the change of meridional compressor shape. The first was to remove the separation zone which appears as the flow tums from axial to radial direction. The second aim is to uniformize the flow at exit of impeller. These two goals were considered within the frame of 2D axisymmetric model. Replacing the cone shaped compressor by a hyperbolically shaped one, the separation at the corner was removed. The disc and shroud shape of the compressor was chosen in the way which satisfies the condition of most uniform flow at the compressor exit. The uniformity of exit flow from the rotor can be considered as the factor which influences the performance of the diffuser following the rotor. In the 2D model a family of stream surfaces of S1 type is given in order to find S2 surfaces which may be identified with the midblade surfaces of compressor blading. A computation of 3D type has been performed in order to establish the relations between 2D and 3D models in the calculation of flow parameters. In the presented example the 2D model appears as the inverse model which leads to 3D shape of blading whereas the 3D model has been used for the direct solution. In the presented example the confrontation of two models, 2D and 3D, leads to a better understanding of the application of these models to the design procedure.

  11. Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus.

    Science.gov (United States)

    Tremblay, Yannick D N; Deslandes, Vincent; Jacques, Mario

    2013-05-31

    Actinobacillus pleuropneumoniae is the Gram-negative bacterium responsible for porcine pleuropneumonia. This respiratory infection is highly contagious and characterized by high morbidity and mortality. The objectives of our study were to study the transcriptome of A. pleuropneumoniae biofilms at different stages and to develop a protocol to grow an A. pleuropneumoniae biofilm in a drip-flow apparatus. This biofilm reactor is a system with an air-liquid interface modeling lung-like environment. Bacteria attached to a surface (biofilm) and free floating bacteria (plankton) were harvested for RNA isolation. Labelled cDNA was hybridized to a microarray to compare the expression profiles of planktonic cells and biofilm cells. It was observed that 47 genes were differentially expressed (22 up, 25 down) in a 4 h-static growing/maturing biofilm and 117 genes were differentially expressed (49 up, 68 down) in a 6h-static dispersing biofilm. The transcriptomes of a 4 h biofilm and a 6 h biofilm were also compared and 456 genes (235 up, 221 down) were identified as differently expressed. Among the genes identified in the 4 h vs 6h biofilm experiment, several regulators of stress response were down-regulated and energy metabolism associated genes were up-regulated. Biofilm bacteria cultured using the drip-flow apparatus differentially expressed 161 genes (68 up, 93 down) compared to the effluent bacteria. Cross-referencing of differentially transcribed genes in the different assays revealed that drip-flow biofilms shared few differentially expressed genes with static biofilms (4 h or 6 h) but shared several differentially expressed genes with natural or experimental infections in pigs. The formation of a static biofilm by A. pleuropneumoniae strain S4074 is a rapid process and transcriptional analysis indicated that dispersal observed at 6 h is driven by nutritional stresses. Furthermore, A. pleuropneumoniae can form a biofilm under low-shear force in a drip-flow apparatus and

  12. 不同形状喷嘴内流场模拟分析%Simulation Analysis of Flow Field inside Different Shaped Nozzles

    Institute of Scientific and Technical Information of China (English)

    陈晓晨; 邓松圣; 郭联欢; 黄龙

    2015-01-01

    The mathematical model of solid⁃liquid two⁃phase flow was established to study the flow field of pre⁃mixed abrasive water jet nozzle. With the software Fluent, a numerical simulation was conducted on flow field inside the cylinder nozzle, cone noz⁃zle, streamline nozzle and cone⁃cylinder nozzle, the influences of nozzle inner surface shape on flow field and abrasive particle accel⁃eration performance were analyzed, and the reliability of the results was validated by the abrasive water jet cutting experiment. The results show that energy loss of the cylinder nozzle is large, abrasive particle acceleration performance of the cone nozzle is bad, the streamline nozzle has good performance but is not easy to be processed, and the cone⁃cylinder nozzle is suitable for pre⁃mixed abra⁃sive water jet.%建立了前混合磨料水射流喷嘴内固液两相流动的数学模型,运用Fluent软件对圆柱型、圆锥收敛型、流线型和圆锥带圆柱段收敛型喷嘴内流场进行了数值模拟,分析了喷嘴形状对喷嘴内流场和磨料颗粒加速性能的影响,并通过切割实验验证了仿真结果的可靠性。结果表明:圆柱型喷嘴能量损耗较大,圆锥收敛型喷嘴对磨料颗粒的加速性能差,流线型喷嘴性能良好但不易加工,只有圆锥带圆柱段收敛型喷嘴是用作前混合式磨料水射流喷嘴的最优选择。

  13. Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

    NARCIS (Netherlands)

    Piotti, A.; Leonardi, S.; Buiteveld, J.; Geburek, T.; Gerber, S.; Kramer, K.; Vettori, C.; Vendramin, G.G.

    2012-01-01

    The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of fac

  14. Dispersal and gene flow in the rare, parasitic Large Blue butterfly Maculinea arion

    DEFF Research Database (Denmark)

    Ugelvig, Line Vej; Andersen, Anne; Boomsma, Jacobus Jan

    2012-01-01

    decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark...

  15. Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape

    NARCIS (Netherlands)

    Mix, C.; Arens, P.F.P.; Rengelink, R.; Smulders, M.J.M.; Groenendael, van J.M.; Ouburg, J.

    2006-01-01

    Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in

  16. EVIDENCE FOR LANDSCAPE LEVEL, POLLEN-MEDIATED GENE FLOW FROM CREEPING BENTGRASS WITH CP4 EPSPS AS A MARKER

    Science.gov (United States)

    In a landscape level study, gene flow via pollen was tracked from multiple source fields of genetically modified (GM) herbicide resistant creeping bentgrass (Agrostis stolonifera L.) to 75 of 138 sentinel plants of A. stolonifera and to 29 of 69 resident populations of Agrostis s...

  17. Pollen-mediated gene flow and seed exchange in small-scale Zambian maize farming, implications for biosafety assessment

    Science.gov (United States)

    Bøhn, Thomas; Aheto, Denis W.; Mwangala, Felix S.; Fischer, Klara; Bones, Inger Louise; Simoloka, Christopher; Mbeule, Ireen; Schmidt, Gunther; Breckling, Broder

    2016-10-01

    Gene flow in agricultural crops is important for risk assessment of genetically modified (GM) crops, particularly in countries with a large informal agricultural sector of subsistence cultivation. We present a pollen flow model for maize (Zea mays), a major staple crop in Africa. We use spatial properties of fields (size, position) in three small-scale maize farming communities in Zambia and estimate rates of cross-fertilisation between fields sown with different maize varieties (e.g. conventional and transgene). As an additional factor contributing to gene flow, we present data on seed saving and sharing among farmers that live in the same communities. Our results show that: i) maize fields were small and located in immediate vicinity of neighboring fields; ii) a majority of farmers saved and shared seed; iii) modeled rates of pollen-mediated gene flow showed extensive mixing of germplasm between fields and farms and iv) as a result, segregation of GM and non-GM varieties is not likely to be an option in these systems. We conclude that the overall genetic composition of maize, in this and similar agricultural contexts, will be strongly influenced both by self-organised ecological factors (pollen flow), and by socially mediated intervention (seed recycling and sharing).

  18. Experience with needle-shaped conductivity sensors for determining parameters in two-phase flows; Erfahrungen mit nadelfoermigen Leitfaehigkeitssonden zur Bestimmung von Parametern in Zweiphasenstroemungen

    Energy Technology Data Exchange (ETDEWEB)

    Fleischer, S.; Hampel, R. [Hochschule fuer Technik, Wirtschaft und Sozialwesen Zittau/Goerlitz, Zittau (Germany). Inst. fuer Prozesstechnik, Prozessautomatisierung und Messtechnik e.V. (IPM)

    1997-12-01

    Two variants were developed. A wire grid sensor has two planes with 16 wires of 0.12 mm diameter each. The wires are arranged evenly over the diameter. The spacing between the two planes is 1.5 mm. The pipelines are covered in the corners of some measuring points. A second type was developed especially for the described pressure surge experiments. The `heavy` grid sensor with rod-shaped electrodes is made of stainless steel. The small rods have a lens-shaped crossection, in order to keep the hydraulic resistance and the effect on flow small. Sensors with 8 x 8 measuring points for NW50 and a sensor with 16 x 16 measuring points for NW100 were produced. They are designed for 7 MPa and a maximum of 150oC. The cavitation behind a fast-closing valve was visualised with the sensors, which is situated at the start of an approx. 200 m long pipeline. [Deutsch] Das Messverfahren mit nadelfoermigen Leitfaehigkeitssonden eignet sich zur lokalen Messung des Gasgehaltes, der Gasphasengeschwindigkeit, der Gasblasengroesse und deren statischen Verteilung. Die hohe zeitliche Aufloesung erlaubt die Messung von transienten Vorgaengen in Zweiphasenstroemungen. Mit dem Einsatz von mehreren Leitfaehigkeitssonden ist eine raeumliche Aufloesung moeglich. Als qualitative Groesse ist mit dem Messverfahren die Stroemungsform detektierbar. Auf Grund des invasiven Charakters des Messverfahren sind Einflussgroessen zu beachten bzw. zu beruecksichtigen. In den durchgefuehrten experimentellen Arbeiten wurde die Wirkung der Einflussgroessen auf das Messergebnis naeher untersucht und Verfahren zur Kalibrierung entwickelt. Die Arbeiten sind in den nachstehenden Literaturangaben dokumentiert. (orig.)

  19. Environmental implications of gene flow from sugar beet to wild beet--current status and future research needs.

    Science.gov (United States)

    Bartsch, Detlef; Cuguen, Joel; Biancardi, Enrico; Sweet, Jeremy

    2003-01-01

    Gene flow via seed or pollen is a basic biological process in plant evolution. The ecological and genetic consequences of gene flow depend on the amount and direction of gene flow as well as on the fitness of hybrids. The assessment of potential risks of transgenic plants should take into account the fact that conventional crops can often cross with wild plants. The precautionary approach in risk management of genetically modified plants (GMPs) may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Gene flow is hard to control in wind-pollinated plants like beet (Beta vulgaris). In addition, wild beet populations potentially can undergo evolutionary changes which might expand their geographical distribution. Unintended products of cultivated beets pollinated by wild beets are weed beets that bolt and flower during their first year of planting. Weed beets cause yield losses and can delay harvest. Wild beets are important plant genetic resources and the preservation of wild beet diversity in Europe has been considered in biosafety research. We present here the methodology and research approaches that can be used for monitoring the geographical distribution and diversity of Beta populations. It has recently been shown that a century of gene flow from Beta vulgaris ssp. vulgaris has not altered the genetic diversity of wild Beta vulgaris L. ssp. maritima (L.) Arcang. in the Italian sugar beet seed production area. Future research should focus on the potential evolution of transgenic wild beet populations in comparison to these baseline data. Two monitoring models are presented describing how endpoints can be measured: (1) "Pre-post" crop commercialization against today's baseline and (2) "Parallel" to crop commercialization against GMP free reference areas/ populations. Model 2 has the advantage of taking ongoing changes in genetic diversity and population dynamics into account. Model 1 is more applicable if

  20. Inferred vs realized patterns of gene flow: an analysis of population structure in the Andros Island Rock Iguana.

    Directory of Open Access Journals (Sweden)

    Giuliano Colosimo

    Full Text Available Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst =  0.117, p<<0.01. These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes.

  1. Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

    Directory of Open Access Journals (Sweden)

    Christine Dubreuil-Tranchant

    2011-01-01

    Full Text Available Miniature Inverted-repeat Transposable Elements (MITEs are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.

  2. Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

    Directory of Open Access Journals (Sweden)

    Victor Borges Rezende

    2016-10-01

    Full Text Available Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species’ reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index (D¯ of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c, among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.

  3. Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide.

    Science.gov (United States)

    Baker, C S; Slade, R W; Bannister, J L; Abernethy, R B; Weinrich, M T; Lien, J; Urban, J; Corkeron, P; Calmabokidis, J; Vasquez, O

    1994-08-01

    The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or 'stocks', world-wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world-wide genetic variation among oceanic populations, among subpopulations or 'stocks' within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south-eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or 'American' stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long-lived, mobile vertebrates in the marine ecosystem.

  4. Relating diseases by integrating gene associations and information flow through protein interaction network.

    Science.gov (United States)

    Hamaneh, Mehdi Bagheri; Yu, Yi-Kuo

    2014-01-01

    Identifying similar diseases could potentially provide deeper understanding of their underlying causes, and may even hint at possible treatments. For this purpose, it is necessary to have a similarity measure that reflects the underpinning molecular interactions and biological pathways. We have thus devised a network-based measure that can partially fulfill this goal. Our method assigns weights to all proteins (and consequently their encoding genes) by using information flow from a disease to the protein interaction network and back. Similarity between two diseases is then defined as the cosine of the angle between their corresponding weight vectors. The proposed method also provides a way to suggest disease-pathway associations by using the weights assigned to the genes to perform enrichment analysis for each disease. By calculating pairwise similarities between 2534 diseases, we show that our disease similarity measure is strongly correlated with the probability of finding the diseases in the same disease family and, more importantly, sharing biological pathways. We have also compared our results to those of MimMiner, a text-mining method that assigns pairwise similarity scores to diseases. We find the results of the two methods to be complementary. It is also shown that clustering diseases based on their similarities and performing enrichment analysis for the cluster centers significantly increases the term association rate, suggesting that the cluster centers are better representatives for biological pathways than the diseases themselves. This lends support to the view that our similarity measure is a good indicator of relatedness of biological processes involved in causing the diseases. Although not needed for understanding this paper, the raw results are available for download for further study at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/DiseaseRelations/.

  5. On Characterizing Particle Shape

    Science.gov (United States)

    Ennis, Bryan J.; Rickman, Douglas; Rollins, A. Brent; Ennis, Brandon

    2014-01-01

    It is well known that particle shape affects flow characteristics of granular materials, as well as a variety of other solids processing issues such as compaction, rheology, filtration and other two-phase flow problems. The impact of shape crosses many diverse and commercially important applications, including pharmaceuticals, civil engineering, metallurgy, health, and food processing. Two applications studied here include the dry solids flow of lunar simulants (e.g. JSC-1, NU-LHT-2M, OB-1), and the flow properties of wet concrete, including final compressive strength. A multi-dimensional generalized, engineering method to quantitatively characterize particle shapes has been developed, applicable to both single particle orientation and multi-particle assemblies. The two-dimension, three dimension inversion problem is also treated, and the application of these methods to DEM model particles will be discussed. In the case of lunar simulants, flow properties of six lunar simulants have been measured, and the impact of particle shape on flowability - as characterized by the shape method developed here -- is discussed, especially in the context of three simulants of similar size range. In the context of concrete processing, concrete construction is a major contributor to greenhouse gas production, of which the major contributor is cement binding loading. Any optimization in concrete rheology and packing that can reduce cement loading and improve strength loading can also reduce currently required construction safety factors. The characterization approach here is also demonstrated for the impact of rock aggregate shape on concrete slump rheology and dry compressive strength.

  6. Effects of Port Shape on Steady Flow Characteristics in an SI Engine with Semi-Wedge Combustion Chamber (2) - Velocity Distribution (2)

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Inkyoung; Ohm, Inyong [Seoul Nat’l Univ. of Science and Technology, Seoul (Korea, Republic of)

    2017-02-15

    This study is the second investigation on the steady flow characteristics of an SI engine with a semi-edge combustion chamber as a function of the port shape with varying evaluation positions. For this purpose, the planar velocity profiles were measured from 1.75B, 1.75 times of bore position apart from the bottom of head, to 6.00B positions using particle – image velocimetry. The flow patterns were examined with both a straight and a helical port. The velocity profiles, streamlines, and centers of swirl were almost the same at the same valve lift regardless of the measuring position, which is quite different from the case of the pent-roof combustion chamber. All the eccentricity values of the straight port were out of distortion criterion 0.15 through the lifts and the position. However, the values of the helical port exceeded the distortion criterion by up to 4 mm lift, but decreased rapidly above the 3.00B position and the 5 mm lift. There always existed a relative offset effect in the evaluation of the swirl coefficient using the PIV method due to the difference of the ideal impulse swirl meter velocity profile assumption, except for the cylinder-center-base estimation that was below 4 mm of the straight port. Finally, it was concluded that taking the center as an evaluation basis and the assumption about the axial velocity profile did not have any qualitative effect on swirl evaluation, but affected the value owing to the detailed profile.

  7. Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations

    NARCIS (Netherlands)

    Palsboll, PJ; Berube, M; Aguilar, A; Notarbartolo-Di-Sciara, G; Nielsen, R

    2004-01-01

    Genetic divergence among conspecific subpopulations can be due to either low recurrent gene flow or recent divergence and no gene flow. Here we present a modification of an earlier method developed by Nielsen and Wakeley (2001), which accommodates a finite-site mutation model, to assess which of the

  8. Investigating Pollen and Gene Flow of WYMV-Resistant Transgenic Wheat N12-1 Using a Dwarf Male-Sterile Line as the Pollen Receptor.

    Directory of Open Access Journals (Sweden)

    Shanshan Dong

    Full Text Available Pollen-mediated gene flow (PMGF is the main mode of transgene flow in flowering plants. The study of pollen and gene flow of transgenic wheat can help to establish the corresponding strategy for preventing transgene escape and contamination between compatible genotypes in wheat. To investigate the pollen dispersal and gene flow frequency in various directions and distances around the pollen source and detect the association between frequency of transgene flow and pollen density from transgenic wheat, a concentric circle design was adopted to conduct a field experiment using transgenic wheat with resistance to wheat yellow mosaic virus (WYMV as the pollen donor and dwarf male-sterile wheat as the pollen receptor. The results showed that the pollen and gene flow of transgenic wheat varied significantly among the different compass sectors. A higher pollen density and gene flow frequency was observed in the downwind SW and W sectors, with average frequencies of transgene flow of 26.37 and 23.69% respectively. The pollen and gene flow of transgenic wheat declined dramatically with increasing distance from its source. Most of the pollen grains concentrated within 5 m and only a few pollen grains were detected beyond 30 m. The percentage of transgene flow was the highest where adjacent to the pollen source, with an average of 48.24% for all eight compass directions at 0 m distance. Transgene flow was reduced to 50% and 95% between 1.61 to 3.15 m, and 10.71 to 20.93 m, respectively. Our results suggest that climate conditions, especially wind direction, may significantly affect pollen dispersal and gene flow of wheat. The isolation-by-distance model is one of the most effective methods for achieving stringent transgene confinement in wheat. The frequency of transgene flow is directly correlated with the relative density of GM pollen grains in air currents, and pollen competition may be a major factor influencing transgene flow.

  9. Gene flow and maintenance of genetic diversity in invasive mosquitofish (Gambusia holbrooki.

    Directory of Open Access Journals (Sweden)

    David Díez-del-Molino

    Full Text Available Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations.

  10. Spatial genetic structure and restricted gene flow in bed bugs (Cimex lectularius) populations in France.

    Science.gov (United States)

    Akhoundi, Mohammad; Kengne, Pierre; Cannet, Arnaud; Brengues, Cécile; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Simard, Frederic; Fontenille, Didier; Delaunay, Pascal

    2015-08-01

    Bed bugs (Cimex lectularius) are resurgent blood-sucking ectoparasites that are currently increasing at a rapid rate, particularly in industrialized countries, such as France. Despite the rapid spread of bed bugs, there is a lack of knowledge concerning the population structure and gene flow among C. lectularius populations in France. To fill this gap, a genetic study was conducted using 183 C. lectularius from 14 populations of bed bugs collected in a hotel and in individual apartments in the French Riviera and in the Saint Ouen suburb of Paris. The samples were genotyped using an isolated set of six polymorphic microsatellite loci, including five new loci which were newly isolated and chosen based on prior successful amplification, and one previously described loci (bb15b). The low genetic diversity observed in the samples (of one to five alleles) suggested that most of prospected populations were established by only a few individuals, possibly from a single mated female. The overall genetic differentiation was high and statistically significant (FST=0.556, plectularius populations in France; however, the available information should be expanded in further studies.

  11. Matching genetics with oceanography: directional gene flow in a Mediterranean fish species.

    Science.gov (United States)

    Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M

    2011-12-01

    Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. © 2011 Blackwell Publishing Ltd.

  12. Gene flow between insular, coastal and interior populations of brown bears in Alaska.

    Science.gov (United States)

    Paetkau, D; Shields, G F; Strobeck, C

    1998-10-01

    The brown bears of coastal Alaska have been recently regarded as comprising from one to three distinct genetic groups. We sampled brown bears from each of the regions for which hypotheses of genetic uniqueness have been made, including the bears of the Kodiak Archipelago and the bears of Admiralty, Baranof and Chichagof (ABC) Islands in southeast Alaska. These samples were analysed with a suite of nuclear microsatellite markers. The 'big brown bears' of coastal Alaska were found to be part of the continuous continental distribution of brown bears, and not genetically isolated from the physically smaller 'grizzly bears' of the interior. By contrast, Kodiak brown bears appear to have experienced little or no genetic exchange with continental populations in recent generations. The bears of the ABC Islands, which have previously been shown to undergo little or no female-mediated gene flow with mainland populations, were found not to be genetically isolated from mainland bears. The data from the four insular populations indicate that female and male dispersal can be reduced or eliminated by water barriers of 2-4 km and 7 km in width, respectively.

  13. Effect of vibrating electrode on temperature profiles, fluid flow, and pool shape in ESR system based on a comprehensive coupled model

    Institute of Scientific and Technical Information of China (English)

    Fang Wang; Yan-chun Lou; Rui Chen; Zhao-wei Song; Bao-kuan Li

    2015-01-01

    The vibrating electrode method was proposed in the electro-slag remelting (ESR) process in this paper, and the effect of vibrating electrode on the solidiifcation structure of ingot was studied. A transient three-dimensional (3D) coupled mathematical model was established to simulate the electromagnetic phenomenon, fluid flow as well as pool shape in the ESR process with the vibrating electrode. The finite element volume method is developed to solve the electromagnetic field using ANSYS mechanical APDL software. Moreover, the electromagnetic force and Joule heating are interpolated as the source term of the momentum and energy equations. The multi-physical fields have been investigated and compared between the traditional electrode and the vibrating electrode in the ESR process. The results show that the drop process of metal droplets with the traditional electrode is scattered randomly. However, the drop process of metal droplets with the vibrating electrode is periodic. The highest temperature of slag layer with the vibrating electrode is higher than that with the traditional electrode, which can increase the melting rate due to the enhanced heat transfer in the vicinity of the electrode tip. The results also show that when the amplitude and frequency of the vibrating electrode increase, the cycle of drop process of metal droplets decreases signiifcantly.

  14. Effect of vibrating electrode on temperature profiles, fluid flow, and pool shape in ESR system based on a comprehensive coupled model

    Directory of Open Access Journals (Sweden)

    Fang Wang

    2015-07-01

    Full Text Available The vibrating electrode method was proposed in the electro-slag remelting (ESR process in this paper, and the effect of vibrating electrode on the solidification structure of ingot was studied. A transient three-dimensional (3D coupled mathematical model was established to simulate the electromagnetic phenomenon, fluid flow as well as pool shape in the ESR process with the vibrating electrode. The finite element volume method is developed to solve the electromagnetic field using ANSYS mechanical APDL software. Moreover, the electromagnetic force and Joule heating are interpolated as the source term of the momentum and energy equations. The multi-physical fields have been investigated and compared between the traditional electrode and the vibrating electrode in the ESR process. The results show that the drop process of metal droplets with the traditional electrode is scattered randomly. However, the drop process of metal droplets with the vibrating electrode is periodic. The highest temperature of slag layer with the vibrating electrode is higher than that with the traditional electrode, which can increase the melting rate due to the enhanced heat transfer in the vicinity of the electrode tip. The results also show that when the amplitude and frequency of the vibrating electrode increase, the cycle of drop process of metal droplets decreases significantly.

  15. A numerical model for a soluble lead-acid flow battery comprising a three-dimensional honeycomb-shaped positive electrode

    Science.gov (United States)

    Oury, Alexandre; Kirchev, Angel; Bultel, Yann

    2014-01-01

    A novel reactor design is proposed for the soluble lead-acid flow battery (SLFB), in which a three-dimensional honeycomb-shaped positive PbO2-electrode is sandwiched between two planar negative electrodes. A two-dimensional stationary model is developed to predict the electrochemical behaviour of the cell, especially the current distribution over the positive structure and the cell voltage, as a function of the honeycomb dimensions and the electrolyte composition. The model includes several experimentally-based parameters measured over a wide range of electrolyte compositions. The results show that the positive current distribution is almost entirely determined by geometrical effects, with little influence from the hydrodynamic. It is also suggested that an increase in the electrolyte acidity diminishes the overvoltage during discharge but leads at the same time to a more heterogeneous reaction rate distribution on account of the faster kinetics of PbO2 dissolution. Finally, the cycling of experimental mono-cells is performed and the voltage response is in fairly good accordance with the model predictions.

  16. The vertebrate makorin ubiquitin ligase gene family has been shaped by large-scale duplication and retroposition from an ancestral gonad-specific, maternal-effect gene

    Directory of Open Access Journals (Sweden)

    Volff Jean-Nicolas

    2010-12-01

    Full Text Available Abstract Background Members of the makorin (mkrn gene family encode RING/C3H zinc finger proteins with U3 ubiquitin ligase activity. Although these proteins have been described in a variety of eukaryotes such as plants, fungi, invertebrates and vertebrates including human, almost nothing is known about their structural and functional evolution. Results Via partial sequencing of a testis cDNA library from the poeciliid fish Xiphophorus maculatus, we have identified a new member of the makorin gene family, that we called mkrn4. In addition to the already described mkrn1 and mkrn2, mkrn4 is the third example of a makorin gene present in both tetrapods and ray-finned fish. However, this gene was not detected in mouse and rat, suggesting its loss in the lineage leading to rodent murids. Mkrn2 and mkrn4 are located in large ancient duplicated regions in tetrapod and fish genomes, suggesting the possible involvement of ancestral vertebrate-specific genome duplication in the formation of these genes. Intriguingly, many mkrn1 and mkrn2 intronless retrocopies have been detected in mammals but not in other vertebrates, most of them corresponding to pseudogenes. The nature and number of zinc fingers were found to be conserved in Mkrn1 and Mkrn2 but much more variable in Mkrn4, with lineage-specific differences. RT-qPCR analysis demonstrated a highly gonad-biased expression pattern for makorin genes in medaka and zebrafish (ray-finned fishes and amphibians, but a strong relaxation of this specificity in birds and mammals. All three mkrn genes were maternally expressed before zygotic genome activation in both medaka and zebrafish early embryos. Conclusion Our analysis demonstrates that the makorin gene family has evolved through large-scale duplication and subsequent lineage-specific retroposition-mediated duplications in vertebrates. From the three major vertebrate mkrn genes, mkrn4 shows the highest evolutionary dynamics, with lineage-specific loss of zinc

  17. Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina

    Science.gov (United States)

    González-Wevar, Claudio A.; Rosenfeld, Sebastián; Segovia, Nicolás I.; Hüne, Mathias; Gérard, Karin; Ojeda, Jaime; Mansilla, Andrés; Brickle, Paul; Díaz, Angie; Poulin, Elie

    2016-01-01

    Glacial episodes of the Quaternary, and particularly the Last Glacial Maximum (LGM) drastically altered the distribution of the Southern-Hemisphere biota, principally at higher latitudes. The irregular coastline of Patagonia expanding for more than 84.000 km constitutes a remarkable area to evaluate the effect of Quaternary landscape and seascape shifts over the demography of near-shore marine benthic organisms. Few studies describing the biogeographic responses of marine species to the LGM have been conducted in Patagonia, but existing data from coastal marine species have demonstrated marked genetic signatures of post-LGM recolonization and expansion. The kelp-dweller limpet Nacella mytilina is broadly distributed along the southern tip of South America and at the Falkland/Malvinas Islands. Considering its distribution, abundance, and narrow bathymetry, N. mytilina represents an appropriate model to infer how historical and contemporary processes affected the distribution of intraspecific genetic diversity and structure along the southern tip of South America. At the same time, it will be possible to determine how life history traits and the ecology of the species are responsible for the current pattern of gene flow and connectivity across the study area. We conducted phylogeographic and demographic inference analyses in N. mytilina from 12 localities along Pacific Patagonia (PP) and one population from the Falkland/Malvinas Islands (FI). Analyses of the mitochondrial gene COI in 300 individuals of N. mytilina revealed low levels of genetic polymorphism and the absence of genetic differentiation along PP. In contrast, FI showed a strong and significant differentiation from Pacific Patagonian populations. Higher levels of genetic diversity were also recorded in the FI population, together with a more expanded genealogy supporting the hypothesis of glacial persistence of the species in these islands. Haplotype genealogy, and mismatch analyses in the FI population

  18. The impact of pollination syndrome and habitat on gene flow: a comparative study of two Streptocarpus (Gesneriaceae) species.

    Science.gov (United States)

    Hughes, Mark; Möller, Michael; Edwards, Trevor J; Bellstedt, Dirk U; Villiers, Margaret de

    2007-10-01

    Gene flow through pollen and seed dispersal is important in terms of population differentiation and eventually speciation. Seed and pollen flow are affected in turn by habitats and pollen vectors. We examined the effect of different pollinators and habitats on gene flow by comparing two species of Streptocarpus, using microsatellite and chloroplast RFLP markers. Populations of the forest-dwelling S. primulifolius were highly differentiated according to nuclear microsatellite data and had mutually exclusive chloroplast haplotypes. This result is congruent with infrequent seed dispersal and limited between-population foraging by the long-tongued fly pollinator Stenobasipteron wiedemanni. In contrast, populations of S. dunnii growing in exposed crags had lower levels of population differentiation according to both nuclear and chloroplast data, congruent with a hypothesis of more effective between population seed dispersal and greater pollen-mediated gene flow due to the sunbird pollinator Nectarinia famosa. The population genetic behavior of these species is reflected in their taxonomy and phylogenetic position; S. primulifolius belongs to a taxonomically complex clade in which recent speciation is evident, while the clade containing S. dunnii is characterized by taxonomically well-defined species on longer phylogenetic branches. Our study shows that pollinator movements and seed dispersal patterns are a major determinant of the evolutionary trajectories of these species.

  19. How developments in cryobiology, reproductive technologies and conservation genomics could shape gene banking strategies for (farm) animals

    NARCIS (Netherlands)

    Woelders, H.; Windig, J.J.; Hiemstra, S.J.

    2012-01-01

    Many local breeds are currently at risk because of replacement by a limited number of specialized commercial breeds. Concurrently, for many breeds, allelic diversity within breeds declines because of inbreeding. Gene banking of germplasm may serve to secure the breeds and the alleles for any future

  20. Migration between continents: geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota).

    Science.gov (United States)

    Buschbom, Jutta

    2007-05-01

    Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.

  1. The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.

    Science.gov (United States)

    Ferchaud, Anne-Laure; Hansen, Michael M

    2016-01-01

    Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three-spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the

  2. Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flow.

    Science.gov (United States)

    Martin, J; Guryev, V; Blinov, A

    2002-10-01

    Phylogenetic analysis of DNA sequences from mitochondrial (mt) genes (Cytochrome b and Cytochrome oxidase I) and one nuclear gene (globin 2b) was used for the investigation of Nearctic and Palearctic populations representing four Chironomus species of the subgenus Camptochironomus, namely C. biwaprimus, C. pallidivittatus, C. tentans sensu stricto and C. dilutus (the last two species constitute Holarctic C. tentans sensu lato). Phenograms constructed on the basis of mt sequences were not congruent with trees based on nuclear genes, or with morphological and cytological data. The mt tree divided the populations by continental region, rather than by the species groupings recognized by the other data sets. The incongruence is explained by mt gene flow resulting from hybridization between the sympatric species on each continent. Calculation of divergence times, based on the sequence data, suggest that C. tentans (s.l.) and C. pallidivittatus have both been in North America for about 2.5 My.

  3. Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes.

    OpenAIRE

    Kejnovský, E; Vrána, J; Matsunaga, S.; Soucek, P.; Siroký, J; Dolezel, J; Vyskot, B

    2001-01-01

    The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that ...

  4. 浸渍管形状对RH精炼中钢液流动和混合特性的影响%Influence of Snorkel Shape on Characteristics of Flow and Mixing of RH

    Institute of Scientific and Technical Information of China (English)

    贺庆; 刘浏; 李相臣; 薛利强

    2013-01-01

    通过水模拟试验,对采用椭圆形和圆形浸渍管的RH设备分别进行了混匀时间和循环流量的测定,比较后得知:在真空压力97709Pa,插深130mm的条件下,当驱动气体流量大于2.33 m3/h时,椭圆浸渍管的RH循环流量优势明显,大于2.7 m3/h时混匀时间明显减少.测出椭圆浸渍管RH设备在不同工艺参数下混匀时间和循环流量的变化规律,并进行了流场流线试验.分析得知,在相同的单位浸渍管截面积供气强度下,椭圆管RH的循环流量和混匀时间均优于普通RH,试验条件下循环流量可增大50%,最后回归出2种模型间循环流量的关系式.%The mixing time and circulation flow rate of RH with oval-shaped snorkel and round-shaped snorkel were investigated by water modeling.Compared with convention RH,under such conditions as 97709 Pa of vacuum pressure and 130mm of insertion depth,the RH with oval-shaped snorkel shows obvious superiority of the circulation flow rate when gas flow is higher than 2.33 m3/h.The mixing time is decreased obviously when gas flow is higher than 2.7 m3/h.Change law of mixing time and circulation flow rate of RH with oval-shaped snorkel were measured at different parameters,and stream line experiment were done.It is found after analysis that mixing time and circulation flow rate of RH with oval-shaped snorkel is better with same flow rate per unit snorkel area.The circulation flow rate of RH can increase by 50% in experimental condition.At last the relationship of circulation flow rate between 2 models was established.

  5. Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations

    Directory of Open Access Journals (Sweden)

    Chi C Vu

    2009-01-01

    between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens.

  6. Gene flow, subspecies composition, and dengue virus-2 susceptibility among Aedes aegypti collections in Senegal.

    Directory of Open Access Journals (Sweden)

    Massamba Sylla

    Full Text Available BACKGROUND: Aedes aegypti, the "yellow fever mosquito", is the primary vector to humans of the four serotypes of dengue viruses (DENV1-4 and yellow fever virus (YFV and is a known vector of Chikungunya virus. There are two recognized subspecies of Ae. aegypti sensu latu (s.l.: the presumed ancestral form, Ae. aegypti formosus (Aaf, a primarily sylvan mosquito in sub-Saharan Africa, and Ae. aegypti aegypti (Aaa, found globally in tropical and subtropical regions typically in association with humans. The designation of Ae. aegypti s.l. subspecies arose from observations made in East Africa in the late 1950s that the frequency of pale "forms" of Ae. aegypti was higher in populations in and around human dwellings than in those of the nearby bush. But few studies have been made of Ae. aegypti s.l. in West Africa. To address this deficiency we have been studying the population genetics, subspecies composition and vector competence for DENV-2 of Ae. aegypti s.l. in Senegal. METHODS AND FINDINGS: A population genetic analysis of gene flow was conducted among 1,040 Aedes aegypti s.l. from 19 collections distributed across the five phytogeographic regions of Senegal. Adults lacking pale scales on their first abdominal tergite were classified as Aedes aegypti formosus (Aaf following the original description of the subspecies and the remainder were classified as Aedes aegypti aegypti (Aaa. There was a clear northwest-southeast cline in the abundance of Aaa and Aaf. Collections from the northern Sahelian region contained only Aaa while southern Forest gallery collections contained only Aaf. The two subspecies occurred in sympatry in four collections north of the Gambia in the central Savannah region and Aaa was a minor component of two collections from the Forest gallery area. Mosquitoes from 11 collections were orally challenged with DENV-2 virus. In agreement with the early literature, Aaf had significantly lower vector competence than Aaa. Among pure Aaa

  7. Gene flow rise with habitat fragmentation in the bog fritillary butterfly (Lepidoptera: Nymphalidae

    Directory of Open Access Journals (Sweden)

    Descimon Henri

    2008-03-01

    Full Text Available Abstract Background The main components of the spatial genetic structure of the populations are neighbourhood size and isolation by distance. These may be inferred from the allele frequencies across a series of populations within a region. Here, the spatial population structure of Proclossiana eunomia was investigated in two mountainous areas of southern Europe (Asturias, Spain and Pyrenees, France and in two areas of intermediate elevation (Morvan, France and Ardennes, Belgium. Results A total of eight polymorphic loci were scored by allozyme electrophoresis, revealing a higher polymorphism in the populations of southern Europe than in those of central Europe. Isolation by distance effect was much stronger in the two mountain ranges (Pyrenees and Asturias than in the two areas of lower elevation (Ardennes and Morvan. By contrast, the neighbourhood size estimates were smaller in the Ardennes and in the Morvan than in the two high mountain areas, indicating more common movements between neighbouring patches in the mountains than in plains. Conclusion Short and long dispersal events are two phenomena with distinct consequences in the population genetics of natural populations. The differences in level of population differentiation within each the four regions may be explained by change in dispersal in lowland recently fragmented landscapes: on average, butterflies disperse to a shorter distance but the few ones which disperse long distance do so more efficiently. Habitat fragmentation has evolutionary consequences exceeding by far the selection of dispersal related traits: the balance between local specialisation and gene flow would be perturbed, which would modify the extent to which populations are adapted to heterogeneous environments.

  8. Differentiation and Gene Flow among European Populations of Leishmania infantum MON-1

    Science.gov (United States)

    Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A.; Schönian, Gabriele

    2008-01-01

    Background Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. Methodology/Principal Findings We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups—MON-1 and non-MON-1—could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands–Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. Conclusion In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological

  9. How much gene flow is needed to avoid inbreeding depression in wild tiger populations?

    Science.gov (United States)

    Kenney, John; Allendorf, Fred W; McDougal, Charles; Smith, James L D

    2014-08-22

    The number and size of tiger populations continue to decline owing to habitat loss, habitat fragmentation and poaching of tigers and their prey. As a result, tiger populations have become small and highly structured. Current populations have been isolated since the early 1970s or for approximately seven generations. The objective of this study is to explore how inbreeding may be affecting the persistence of remaining tiger populations and how dispersal, either natural or artificial, may reduce the potentially detrimental effect of inbreeding depression. We developed a tiger simulation model and used published levels of genetic load in mammals to simulate inbreeding depression. Following a 50 year period of population isolation, we introduced one to four dispersing male tigers per generation to explore how gene flow from nearby populations may reduce the negative impact of inbreeding depression. For the smallest populations, even four dispersing male tigers per generation did not increase population viability, and the likelihood of extinction is more than 90% within 30 years. Unless habitat connectivity is restored or animals are artificially introduced in the next 70 years, medium size wild populations are also likely to go extinct, with only four to five of the largest wild tiger populations likely to remain extant in this same period without intervention. To reduce the risk of local extinction, habitat connectivity must be pursued concurrently with efforts to increase population size (e.g. enhance habitat quality, increase habitat availability). It is critical that infrastructure development, dam construction and other similar projects are planned appropriately so that they do not erode the extent or quality of habitat for these populations so that they can truly serve as future source populations. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  10. Prezygotic barriers to gene flow between Taraxacum ceratophorum and the invasive Taraxacum officinale (Asteraceae).

    Science.gov (United States)

    Brock, Marcus T

    2009-08-01

    Prezygotic reproductive barriers limit interspecific gene flow between congeners. Here, I examine the strength of floral isolation and interspecific pollen-pistil barriers between an invasive apomictic, Taraxacum officinale, and the indigenous sexual alpine dandelion, Taraxacum ceratophorum. Experimental arrays of either native inflorescences or a mixture of native and exotic inflorescences were used to examine insect preference and to track movement of a pollen analog. Using hand-pollinations, conspecific and heterospecific pollen germination success on native stigmas was compared. To additionally test for interspecific pollen competition, T. ceratophorum plants received one of three possible hand-pollinations: control conspecific pollination, concomitant conspecific and heterospecific pollination (mixed), or conspecific pollen followed by heterospecific pollen 15 min later (staggered). Floral isolation was negligible as no insect preference was detected. On a presence/absence basis, florets on native inflorescences received slightly less pollen analog from heterospecific donors than from conspecific donors; however, the amount of dye particles transferred from either Taraxacum species to stigmas on recipient T. ceratophorum inflorescences was equivalent. In contrast to weak floral isolation, strong pollen germination and pollen competition barriers should reduce the potential for hybridization. Heterospecific T. officinale pollen exhibited reduced germination success on T. ceratophorum stigmas in comparison to conspecific pollen. Furthermore, a significant pollen-competition effect on the percentage of hybrid offspring was detected only when T. officinale preceded T. ceratophorum pollen by 15 min. This result indicates that conspecific pollen out-competes heterospecific pollen but further suggests that biotic and abiotic factors reducing pollen accrual rates may partially remove barriers to natural hybridization.

  11. Genetic differentiation and gene flow among six sheep breeds of Mongolian group in China

    Institute of Scientific and Technical Information of China (English)

    Yan GENG; Zhangping YANG; Hong CHANG; Yongjiang MAO; Wei SUN; Xiaoya GUO; Dongyan QU

    2008-01-01

    The level of genetic differentiation,gene flow and the relationship between geographical distance and genetic differentiation among six sheep populations of Mongolian group in China (Tong sheep,small-tailed Han sheep,Hu sheep,Tan sheep,Ujumuqin sheep and Bayinbuluk sheep) were analyzed using seven microsatellites.The trees were constructed from diversity coefficient (DC) distances among the six sheep populations.The overall heterozygote deficit across all the populations (Fit) was between 0.167 (OarAE101) and 0.044 (MAF33).The overall significant deficit of heterozygote,because of inbreeding within breeds,(Fis) was between 0.089 (OarFCB304) and 0.005 (MAF33).The coefficient of genetic differentiation (Fst) was between 0.100 (OarAE101) and 0.022 (Oar-FCB48).It indicated that 3.9% of the total genetic variation could be explained by breed differences and the remaining 96.1% by differences among individuals for each population.This illustrated that most variations existed within breeds and genetic differentiation level were very low among sheep breeds of the Mongolian Group in China.The average number of effective migrants exchanged per generation (Nem) ranged from 2.7369 (Tan sheep and Bayinbuluk sheep) to 44.3928 (Tong sheep and Hu sheep),and the mean value was 11.25213.Significantly positive relationships between the level of genetic differentiation and geographical distance and genetic distances were detected.It is concluded that genetic differentiation of sheep breeds of Mongolian group in China is mainly the result of natural selection (different living conditions).

  12. Divergence with gene flow across a speciation continuum of Heliconius butterflies.

    Science.gov (United States)

    Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

    2015-09-24

    A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

  13. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Science.gov (United States)

    Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A; Schönian, Gabriele

    2008-07-09

    Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands-Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological investigations.

  14. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Directory of Open Access Journals (Sweden)

    Katrin Kuhls

    Full Text Available BACKGROUND: Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. METHODOLOGY/PRINCIPAL FINDINGS: We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1 Greece; (2 Spain islands-Majorca/Ibiza; (3 mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. CONCLUSION: In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further

  15. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.

    Science.gov (United States)

    Frantz, Laurent A F; Schraiber, Joshua G; Madsen, Ole; Megens, Hendrik-Jan; Cagan, Alex; Bosse, Mirte; Paudel, Yogesh; Crooijmans, Richard P M A; Larson, Greger; Groenen, Martien A M

    2015-10-01

    Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

  16. Crossing the threshold: gene flow, dominance and the critical level of standing genetic variation required for adaptation to novel environments.

    Science.gov (United States)

    Nuismer, S L; MacPherson, A; Rosenblum, E B

    2012-12-01

    Genetic architecture plays an important role in the process of adaptation to novel environments. One example is the role of allelic dominance, where advantageous recessive mutations have a lower probability of fixation than advantageous dominant mutations. This classic observation, termed 'Haldane's sieve', has been well explored theoretically for single isolated populations adapting to new selective regimes. However, the role of dominance is less well understood for peripheral populations adapting to novel environments in the face of recurrent and maladaptive gene flow. Here, we use a combination of analytical approximations and individual-based simulations to explore how dominance influences the likelihood of adaptation to novel peripheral environments. We demonstrate that in the face of recurrent maladaptive gene flow, recessive alleles can fuel adaptation only when their frequency exceeds a critical threshold within the ancestral range.

  17. Gene flow among Anopheles albimanus populations in Central America, South America, and the Caribbean assessed by microsatellites and mitochondrial DNA.

    Science.gov (United States)

    Molina-Cruz, Alvaro; de Mérida, Ana María P; Mills, Katherine; Rodríguez, Fernando; Schoua, Carolina; Yurrita, María Marta; Molina, Eduviges; Palmieri, Margarita; Black, William C

    2004-09-01

    Gene flow was examined among Anopheles albimanus populations from Cuba, Mexico, Guatemala, El Salvador, Nicaragua, Costa Rica, Panama, Colombia, and Venezuela by examining variation at four microsatellite (MS) loci and a mitochondrial DNA (mtDNA) marker. There was little variation among Central American populations and weak isolation by distance was only observed with the MS loci. There was moderate to large variation between Central and South American populations, suggesting a barrier to gene flow between Central and South America. However, Panamanian and Pacific Costa Rican populations differed with respect to western Central America, suggesting that there may be another barrier within Central America. There was small to moderate variation among Caribbean and continental populations. Phylogenetic and diversity analyses of mtDNA indicate that more ancestral and diverse haplotypes were present in the Caribbean population, suggesting that current continental An. albimanus populations may have originated from the Caribbean.

  18. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

      FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute...... for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  19. Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds

    Science.gov (United States)

    Lam, T. T. -Y.; Ip, H. S.; Ghedin, E.; Wentworth, D. E.; Halpin, R. A.; Stockwell, T. B.; Spiro, D. J.; Dusek, R. J.; Bortner, J. B.; Hoskins, J.; Bales, B. D.; Yparraguirre, D. R.; Holmes, E. C.

    2012-01-01

    Despite the importance of migratory birds in the ecology and evolution of avian influenza virus (AIV), there is a lack of information on the patterns of AIV spread at the intra-continental scale. We applied a variety of statistical phylogeographic techniques to a plethora of viral genome sequence data to determine the strength, pattern and determinan